title: Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection [RNA-Seq]

city: New York

first: Elodie

last: Ghedin

state: New York

address: 12 Waverly Place

department: Biology

institute: NYU

summary: Antibiotic resistance genes expressed in the upper respiratory tract of patients infected with influenza viruses were associated with the microbial community and microbial activities. Interactions between the host systemic responses to influenza infection and ARG expression highlight the importance of antibiotic resistance in viral-bacterial co-infection.

overall_design: The microbial gene expression were profiled from the 35 respiratory samples taken from influenza infected individuals

first: Lingdi

last: Zhang


title: Systemic approaches reveal anti-adipogenic signals at the onset of obesity–related inflammation in white adipose tissue [RNA-seq]

status: Public on Mar 19 2020

city: Lausanne

first: Richard

last: Coward

address: Dorothy Hodgkin Building, Whitson Street, Bristol

department: Bristol Medical School

country: United Kingdom

institute: Bristol Royal hospital for Sick Children & University of Bristol

type: Expression profiling by high throughput sequencing

summary: HFD feeding induces a rapid adipocyte progenitors (APs) proliferation in visceral adipose tissue (vWAT), followed by a block of differentiation. In contrast, subcutaneous adipose tissue (scWAT), in obesity, undergoes trans-differentiation of beige adipocytes to white and, consequently, a hyperplastic growth at later stages. We performed RNA-seq to investigate the global transcriptomic changes induced by HFD feeding

overall_design: We had 6 experimental conditions in C67Bl/6 mice: 1) mice fed with CTR diet for 1 week, 2) mice fed with HFD diet for 1 week, 3) mice fed with CTR diet for 8 weeks, 4) mice fed with HFD diet for 1 week, 5) mice fed with CTR diet for 20 weeks, 6) mice fed with HFD diet for 20 weeks. For all the experimental group we analyzed both vWAT and scWAT with 2 biological replicate per condition.

first: Tiziana

last: Caputo

first: Van

middle: D

last: Tran

first: Nasim

last: Bararpour

first: Federica

last: Gilardi

first: Béatrice

last: Desvergne


title: AT-hook transcription factors repress petiole growth by antagonizing PIF4 [ChIP-seq]

city: Yokohama

first: David

middle: Seth

last: Favero

state: International

address: 1-7-22 Suehirocho, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

type: Genome binding/occupancy profiling by high throughput sequencing

summary: As sessile organisms, plants rely heavily on growth and developmental plasticity to respond to external challenges threatening their survival. Strict regulation of growth in organs such as hypocotyls and petioles enables plants to respond optimally to varying environmental conditions, such as changes in light and temperature, while also ensuring that resources are not needlessly wasted on unnecessary growth. Studies performed in Arabidopsis thaliana have established the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factor family as key positive regulators of growth, particularly in hypocotyls and petioles. In this study, we identify members of the AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) family, including SUPPRESSOR OF PHYTOCHROME B4-#3 (SOB3), as repressors of PIF4-mediated petiole elongation. Specifically, we found that high levels of SOB3 lead to a short-petiole phenotype similar to that conferred by removal of PIF4. Conversely, the dominant-negative sob3-6 mutant has long petioles, a phenotype which is dependent on PIF4. Additionally, we show that AHLs repress the expression of many PIF-activated genes, including a number involved in hormone-mediated promotion of growth and a subset of which are directly bound by both SOB3 and PIFs. Taken together these results suggest that AHLs repress petiole growth by antagonizing PIF-mediated transcriptional activation of growth-promoting genes, including ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 2 (ATHB2), BRASSINOSTEROID INSENSITIVE 1 (BRI1), INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19), PIN-FORMED 3 (PIN3), SMALL AUXIN UP RNA 24 (SAUR24), and YUCCA8 (YUC8). Elucidating a mechanism by which positive and negative growth factors influence growth in petioles achieves a critical first step towards understanding the gene regulatory networks which modulate leaf growth in response to the environment.

overall_design: Genome-wide identification of SOB3 binding sites in juvenile rosettes of Arabidopsis

first: D

middle: S

first: K

last: Sugimoto


title: AT-hook transcription factors repress petiole growth by antagonizing PIF4 [RNA-seq]

overall_design: Identification of AHL and PIF regulated genes in juvenile rosettes of Arabidopsis. RNA-seq was performed in triplicate for WT Col-0, sob3-6, SOB3-D, and pif4 pif5 pif7. Processed data available for download are parts per million mapped tags (ppm) for each transcript.


title: Regulatory Sharing Between Estrogen Receptor α Bound Enhancers [ChIP-seq]

status: Public on Mar 18 2020

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

country: USA

institute: University of Utah

summary: The human genome encodes an order of magnitude more gene expression enhancers than promoters, suggesting that most genes are regulated by the combined action of multiple enhancers. We have previously shown that neighboring estrogen-responsive enhancers, which are approximately 5,000 basepairs apart, exhibit complex synergistic contributions to the production of an estrogenic transcriptional response. Here we sought to determine the molecular underpinnings of the observed enhancer cooperativity. We generated genetic deletions of individual estrogen receptor  (ER) bound enhancers and found that enhancers containing full estrogen response element (ERE) motifs control ER binding at neighboring sites, while enhancers with pre-existing histone acetylation/accessibility confer a permissible chromatin environment to the neighboring enhancers. Genome engineering revealed that a cluster of two enhancers with half EREs could not compensate for the lack of a full ERE site within the cluster. In contrast, two enhancers with full EREs produced a transcriptional response greater than the wild-type locus. By swapping genomic sequences between enhancers, we found that the genomic location in which a full ERE resides strongly influences enhancer activity. Our results lead to a model in which a full ERE is required for ER recruitment, but the presence of pre-existing histone acetylation within an enhancer cluster is also needed in order for estrogen-driven gene regulation to occur.

overall_design:
ChIP-seq is used to study DNA binding proteins at deleted estrogen receptor alpha-bound cis-regulatory regions
deletion coordinates:
CISH-1_deletion: chr3:50642561-50642781
CISH-2_deletion: chr3:50638578-50638723
MMP17-1_deletion: chr12:132284767-132284881
MMP17-2_deletion: chr12:132288584-132288687

first: Julia

middle: B

last: Carleton

first: Matthew

last: Ginley-Hidinger


title: Regulatory Sharing Between Estrogen Receptor α Bound Enhancers

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

overall_design: Refer to individual Series


title: Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection [16s rRNA gene V4 region]

overall_design: The microbial 16s rRNA gene V4 region was amplified and sequenced from the respiratory samples


title: GDE2-dependent activation of canonical Wnt signaling in neurons regulates oligodendrocyte maturation

city: Daejun

first: Bo-Ran

last: Choi

address: E22 3F 291 Daehak-ro, Yuseong-gu

department: Center for Vascular Research

country: South Korea

institute: Institute of Basic Science

summary: Neurons and oligodendrocytes communicate to regulate oligodendrocyte development and ensure appropriate axonal myelination. Here, we show that Glycerophosphodiester phosphodiesterase 2 (GDE2) encodes a neuronal pathway that promotes oligodendrocyte maturation through the release of soluble neuronally-derived factors. Mice lacking global or neuronal GDE2 expression have reduced mature oligodendrocytes and myelin proteins but retain normal numbers of oligodendrocyte precursor cells (OPCs). WT OPCs cultured in conditioned medium (CM) from Gde2 null (Gde2KO) neurons exhibit delayed maturation, recapitulating in vivo phenotypes. Gde2KO neurons show robust reduction in canonical Wnt signaling and genetic activation of Wnt signaling in Gde2KO neurons rescues in vivo and in vitro oligodendrocyte maturation. Phosphacan, a known stimulant of oligodendrocyte maturation, is reduced in CM from Gde2KO neurons but is restored when Wnt signaling is activated. These studies identify GDE2 control of Wnt signaling as a neuronal pathway that signals to oligodendroglia to promote oligodendrocyte maturation.

overall_design: Ventral half of the lumbar spinal cords from 5 week WT and Gde2KO mices were dissected.

first: Shanthini

last: Sockanathan


title: Sterol-response pathways mediate alkaline survival in diverse fungi.

city: Durham

first: J

middle: Andrew

last: Alspaugh

state: NC

address: 337 Sands Research Building, 303 Research Drive, DUMC 102359

department: Molecular Genetics and Microbiology

institute: Duke University

summary: To determine how the fungal sterol homeostasis pathway contributes to the fungal pH response. To do so, we compared the transcriptomes of the sre1∆ mutant strain to that of the WT H99 strain in acidic (pH 4) and alkaline (pH 8) conditions.

overall_design: Comparing the transcriptome of two different strains of C. neoformans (H99 and sre1∆) in pH4 and pH8 conditions. A total of 6 replicates were performed for each strain in each condition, for a total of 24 samples.

first: Hannah

middle: E

last: Brown

first: Calla

middle: L

last: Telzrow

first: Joseph

middle: W

last: Saelens

middle: A


title: AT-hook transcription factors repress petiole growth by antagonizing PIF4


title: Regulatory Sharing Between Estrogen Receptor α Bound Enhancers [ATAC-seq]

overall_design:
ATAC-seq is used to study chromatin accessibility at deleted estrogen receptor alpha-bound cis-regulatory regions
deletion coordinates:
CISH-1_deletion: chr3:50642561-50642781
CISH-2_deletion: chr3:50638578-50638723
MMP17-1_deletion: chr12:132284767-132284881
MMP17-2_deletion: chr12:132288584-132288687


title: Metabolic regulation of the epigenome drives lethal infantile ependymoma [Cut&Run]

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

summary: PFA (posterior fossa group A) ependymomas are a lethal glial malignancy of the hindbrain found in infants and toddlers. Lacking any highly recurrent somatic mutations, PFAs have been proposed as a largely epigenetically driven tumor type. An almost complete lack of model systems has inhibited discovery of novel PFA therapies. Both in vitro and in vivo, the PFA hypoxic microenvironment controls the availability of specific metabolites to diminish histone methylation, and to increase both histone demethylation and acetylation at H3K27. PFA ependymoma initiates from a cell lineage in the first trimester of human development where there is a known hypoxic microenvironment. Unique to PFA cells, transient exposure to ambient oxygen results in irreversible cellular toxicity. PFA tumors exhibit a low basal level of H3K27me3, and paradoxically inhibition of H3K27 methylation shows significant and specific activity against PFA. Targeting metabolism and/or the epigenome presents a unique opportunity for rational therapy for infants with PFA ependymoma.

overall_design: Cut&Run (H3KMe3) was performed using cells cells grown in hypoxia and normaxia.

first: Ahmad

last: Malik

first: Ricky

last: Tsai

first: Sachin

last: Kumar

first: Michael

last: Taylor


title: RNA-seq study of HUVEC/MSC cell growth on micropatterned Si-TiB2 substrates

city: Houston

first: Fatima

last: Merchant

state: TX

address: Technology Building, Room 304 4300 Calhoun Road

department: Engineering Technology

institute: University of Houston

summary: Analysis of transcriptome changes in human umbilical vein cells (HUVEC) and mesenchymal stem cells (MCS) grown on deposited films of TiB2 micropatterns compared to conventional tissue culture flasks

overall_design: Total RNA was obtained from HUVEC/MCS cells growing on micropatterned Si-TiB2 substrates and conventional tissue culture flasks. TiB2 samples were compared to Plastic samples.

first: Marcos

last: Quintela


title: Profiling of the immune microenvironment in FL [PanCancer Immune Profiling]

city: Munich

first: Oliver

last: Weigert

address: Max-Lebsche-Platz 30

country: Germany

institute: Experimental Leukemia and Lymphoma Research

summary:
Tumor cells orchestrate their microenvironment. Here, we provide biochemical, structural, functional and clinical evidence that Cathepsin S (CTSS) alterations induce a tumor-promoting immune microenvironment in follicular lymphoma (FL). We found CTSS mutations at Y132 in 6% of FL (19/305). Another 13% (37/286) had CTSS amplification, which was associated with higher CTSS expression. CTSS Y132 mutations lead to accelerated autocatalytic conversion from pro-CTSS to active CTSS and increase substrate cleavage, including CD74 which regulates MHC-II-restricted antigen presentation. Lymphoma cells with hyperactive CTSS more efficiently activated antigen-specific CD4+ T-cells in vitro. Tumors with hyperactive CTSS showed increased CD4+ T-cell infiltration and proinflammatory cytokine perturbation in a mouse model and in human FLs. In mice, this CTSS-induced immune microenvironment promoted tumor growth. Clinically, patients with CTSS-hyperactive FL had better treatment outcomes with standard immunochemotherapies, indicating that these immunosuppressive regimens target both the lymphoma cells and the tumor-promoting immune microenvironment.
Digital multiplexed gene expression profiling of formalin-fixed and paraffin-embedded biopsy specimens of the GLSG2000 cohort was performed as previously described (Hellmuth et al., Blood 2018)

overall_design: 54 fully assigned follicular lymphoma patient samples were analysed with the PanCancer 730 immune gene panel from NanoString.

first: Johannes

last: Hildebrand


title: FASN-dependent metabolism links neurogenic stem/progenitor cell activity to intellectual disability

city: Zürich

first: Baptiste

middle: N

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

summary: Failure of neural stem/progenitor cell (NSPC) activity and subsequently neurogenesis during brain development has been linked to cognitive impairment and intellectual disability. However, it remains unclear if changes in metabolism, recently discovered as a key regulator of somatic stem cell activity, contribute to altered neurogenesis and cognitive deficits in humans. To investigate a link between NSPC-associated lipid metabolism and brain development, we generated mice and human embryonic stem cells (hESCs) mimicking a variant in fatty acid synthase (FASN; R1819W), a metabolic regulator of rodent NSPC activity recently identified in humans with intellectual disability. Mice homozygous for the FASN R1812W variant have impaired hippocampal NSPC activity associated with cognitive impairment due to presumed toxic accumulation of lipids in NSPCs and subsequent lipogenic ER stress. Human NSPCs homozygous for the FASN R1819W variant show reduced rates of proliferation in embryonic 2D cultures and 3D forebrain regionalized organoids, revealing that the functional significance of lipid metabolism for neurogenic proliferation of progenitors is conserved between rodents and humans. By taking a disease modeling approach, using mouse and human tissue genome engineering, our data provide genetic evidence for a link between altered lipid metabolism, NSPC activity and brain function.

overall_design: Examination of i) 764 single-nuclei from NeuN+ hippocampal neurons isolated from 8.5-month-old WT (382 nuclei) and Fasn-R1812W mice (382 nuclei), ii) 764 single-nuclei from EdU+ hippocampal cells isolated from 8.5-month-old WT (382 nuclei) and Fasn-R1812W mice (382 nuclei), iii) 190 single-nuclei from embryonic cortices isolated from E14.5 WT (89 nuclei) and Fasn-R1812W mice (101 nuclei).

first: Megan

last: Bowers

first: Tong

last: Liang

last: Gonzalez-Bohorquez

first: Sara

last: Zocher

first: Werner

middle: J

last: Kovacs

first: Clemens

last: Röhrl

first: Kaitlyn

last: Cramb

first: Jochen

last: Winterer

first: Merit

last: Kruse

first: Slavica

last: Dimitrieva

first: Rupert

last: Overall

first: Thomas

last: Wegleiter

first: Hossein

last: Najmabadi

first: Clay

middle: F

last: Semenkovich

first: Gerd

last: Kempermann

first: Csaba

last: Földy

first: Sebastian

last: Jessberger


title: Profiling of the immune microenvironment in FL

status: Public on Mar 17 2020

first: Oliver

last: Weigert

summary:
Tumor cells orchestrate their microenvironment. Here, we provide biochemical, structural, functional and clinical evidence that Cathepsin S (CTSS) alterations induce a tumor-promoting immune microenvironment in follicular lymphoma (FL). We found CTSS mutations at Y132 in 6% of FL (19/305). Another 13% (37/286) had CTSS amplification, which was associated with higher CTSS expression. CTSS Y132 mutations lead to accelerated autocatalytic conversion from pro-CTSS to active CTSS and increase substrate cleavage, including CD74 which regulates MHC-II-restricted antigen presentation. Lymphoma cells with hyperactive CTSS more efficiently activated antigen-specific CD4+ T-cells in vitro. Tumors with hyperactive CTSS showed increased CD4+ T-cell infiltration and proinflammatory cytokine perturbation in a mouse model and in human FLs. In mice, this CTSS-induced immune microenvironment promoted tumor growth. Clinically, patients with CTSS-hyperactive FL had better treatment outcomes with standard immunochemotherapies, indicating that these immunosuppressive regimens target both the lymphoma cells and the tumor-promoting immune microenvironment.
Digital multiplexed gene expression profiling of formalin-fixed and paraffin-embedded biopsy specimens of the validation cohort was performed as previously described (Hellmuth et al., Blood 2018)

overall_design: 104 follicular lymphoma patient samples were analysed with a 12 gene nCounter® Elements™ XT Reagents gene kit from NanoString.

first: Johannes

last: Hildebrand


title: Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell Acute Lymphoblastic Leukemia

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

summary: Prolonged or enhanced expression of the proto-oncogene Lmo2 is associated with a severe form of T-cell Acute Lymphoblastic Leukemia (T-ALL), designated Early T-progenitor ALL (ETP-ALL), that is characterized by the aberrant self-renewal and subsequent oncogenic transformation of immature thymocytes. Recent data suggest that Lmo2 may exert these effects by functioning as component of a multi-subunit transcription complex that includes the ubiquitous adapter Ldb1 along with b-HLH and/or GATA family transcription factors. In this study, we investigated the importance of Ldb1 for Lmo2-induced T-ALL by conditional deletion of Ldb1 in thymocytes in a Lmo2 transgenic mouse model of T-ALL. Our results identify a critical requirement for Ldb1 in the induction of thymocyte self-renewal, thymocyte radio-resistance and transition to T-ALL in Lmo2 transgenic mice. Ldb1 was also required for acquisition of the pre-leukemic ETP gene expression signature in immature Lmo2 transgenic thymocytes. Together, these results support a model where Lmo2-induced T-ALL results from failure to down-regulate Ldb/Lmo2 nucleated transcription complexes that normally function to enforce self-renewal in bone marrow hematopoietic progenitors

overall_design: 2 cell types (DN2/3 and DN4), 3 genotypes: C57BL/6 (wild type) – 4 replicates, Lmo2tg – 5 replicates, Lmo2tg; Ldb1-KO – 4 replicates. Total = 28 samples.

first: LiQi

last: Li

first: Bin

last: Zhao

first: Seeyoung

last: Choi

first: Jan

middle: Y

last: Lee

first: Daniel

last: Stamos

first: Claude

last: Warzecha

first: Karl

last: Pfeifer

first: Joyce

last: Hardwick

first: Utpal

middle: P

last: Dave

first: Paul

last: Love


title: The P2Y14/UDP-Glucose pathway is a therapeutic target for ischemic AKI

city: Boston

first: Maria

middle: Agustina

last: Battistone

state: Massachusetts

department: Program in Membrane Biology, Center for Systems Biology and Nephrology Division, Department of Medicine

institute: Massachusetts General Hospital. Harvard Medical Scholl

summary: Ischemic acute kidney injury (AKI), a complication that frequently occurs in hospital settings, is often associated with hemodynamic compromise, sepsis, cardiac surgery or exposure to nephrotoxicants. AKI is associated with immune cell infiltration into the kidney stroma, which causes acute tubular injury.  Here, using a murine renal ischemic-reperfusion injury (IRI) model we show that intercalated cells (ICs) rapidly adopt a pro-inflammatory phenotype post IRI.  During the early phase of AKI, we demonstrate that either blocking the pro-inflammatory P2Y14 receptor located on the apical membrane of ICs, or ablation of the gene encoding the P2Y14 receptor in ICs: 1) inhibits IRI-induced chemokine expression increase in ICs; 2) reduces neutrophil and monocyte renal infiltration; 3) reduces the extent of kidney dysfunction; and 4) attenuates proximal tubule (PT) damage. These observations indicate that the P2Y14 receptor participates in the very first inflammatory steps associated with ischemic AKI. In addition, we show that the concentration of the P2Y14 receptor ligand, uridine diphosphate-glucose (UDP-Glc), is higher in urine samples from intensive care unit patients who developed AKI when compared with urine from patients without AKI. In particular, we observed a strong correlation between UDP-Glc concentration and the development of AKI in cardiac surgery patients. Our study identifies the UDP-Glc/P2Y14 receptor axis as a potential target for the prevention and/or attenuation of ischemic-AKI.

overall_design: EGFP+ intercalated cells were isolated by double cell sorting from the renal medullary region from B1 VATPase EGFP mice, 2 hours after renal ischemia reperfusion injury or sham surgery. The B1 VATPase EGFP transgenic mice specifically express EGFP in intercalated cells.

first: Alexandra

middle: C

last: Mendelsohn

first: Raul

middle: G

last: Spallanzani

first: Andrew

last: Allegretti

first: Rachel

last: Liberman

first: Juliana

last: Sesma

first: Sahir

last: Kalim

first: Susan

middle: M

last: Wall

first: Joseph

middle: V

last: Bonventre

first: Eduardo

middle: R

last: Lazarowski

first: Dennis

last: Brown

first: Sylvie

last: Breton


title: Uncoupling histone H3K4 trimethylation from developmental gene expression via an epigenetic equilibrium of Polycomb, COMPASS and DNA methylation

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

type: Methylation profiling by high throughput sequencing

summary: The COMPASS family catalyzes histone H3 lysine 4 (H3K4) methylation and its members are essential for regulating developmental gene expression. MLL2/COMPASS methylates H3K4 on many genes but only a subset lose expression upon MLL2 loss. To understand MLL2 -dependent transcriptional regulation, we performed a CRISPR screen in mouse embryonic stem cells (mESCs) and found that MLL2 protects developmental genes from repression by repelling PRC2 and DNA methylation machineries from these loci.  Repression in the absence of MLL2 is relieved by inhibition of PRC2 and DNA methyltransferases, demonstrating that prevention of active repression and not H3K4me3 underlies their transcriptional state. DNA demethylation on such loci leads to reactivation of MLL2-dependent genes not only by removing DNA methylation but also by opening up previously CpG methylated regions for PRC2 recruitment, diluting PRC2 at Polycomb-repressed genes. These findings reveal how the context and function of these three epigenetic modifiers can orchestrate transcriptional decisions.

overall_design: CRISPR screen for regulators of MagohB expression followed ChIP-seq, RNAseq, PRO-seq and bisulfite sequencing analyses of selected candidates and their regulators

first: Delphine

last: Douillet

first: Elizabeth

last: Bartom


title: Gene expression profiling of Tsp1 deficient rat aortic smooth muscle cells with mechanical stretch

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

summary: The extracellular matrix (ECM) initiates mechanical cues and transduces intracellular signaling through matrix-cell interactions. The nature of cues and how they coordinate with a mechanical microenvironment are not fully understood. We identified the matricellular protein, thrombospondin-1 (Tsp1, also called Thbs1), as a mediator of matrix mechanotransduction that acts via integrin αvβ1 to establish focal adhesions and promotes nuclear shuttling of Yes-associated protein (YAP) in response to cyclic stretch. Thbs1-mediated YAP activation depends on the small GTPase Rap2 and Hippo pathway, and is not influenced by altered actin fibers. Hence, to gain insight into the molecular mechanisms underlying the Tsp1-mediated matrix mechanotransduction, we performed a comprehensive analysis of gene expression changes in Tsp1deficiant SMCs with mechanical stretch using RNA sequencing (RNA-Seq).

overall_design: mRNA profiles of rat aortic smooth muscle cells were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Yoshito

last: Yamashiro


title: mRNA sequencing  of WT, ∆CDK19 and ∆CYC9 cells in starvation and costimulation (S, co) of Tetrahymena thermophila

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

country: China

institute: Institute of hydrobiology, CAS

summary: The goals of this study is to investigate the function of CDK19 and CYC9 of Tetrahymena thermophila.

overall_design: Compare the expression of genes amnong WT, ∆CDK19 and ∆CYC9 cells in starvation and costimulation.


title: POSH2 Promotes Breast Cancer Stem-Like Properties through JNK Activation and PTX3 Upregulation [MCF10AT_POSH2_OE]

status: Public on Mar 16 2020

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary: We conduct transcriptome comparison of control and POSH2-overexpressed MCF10AT cells to gain genomic insights on the biological processes that POSH2 is involved in breast cancer cells.

overall_design: In the study presented here, POSH2 was overexpressed in the MCF10AT breast cancer cells. RNA sequencing profiling of mRNA levels was performed in the control and overexpression cells.

first: Peiyuan

last: Zhang


title: POSH2 Promotes Breast Cancer Stem-Like Properties through JNK Activation and PTX3 Upregulation [PTX3_OE]

summary: We conduct transcriptome comparison of control and PTX3-overexpressed HMLER cells to gain genomic insights on the biological processes that PTX3 is involved in breast cancer cells.

overall_design: In the study presented here, PTX3 was overexpressed in the HMLER breast cancer cells. RNA sequencing profiling of mRNA levels was performed in the control and overexpression cells.


title: RNA sequencing of infected and uninfected WT and HIF-1ɑ-/- peritoneal macrophages

status: Public on Mar 15 2020

city: Montréal

first: Tarik

last: Moroy

state: Québec

address: 110 Avenue des Pins

institute: Institut de recherches cliniques de Montréal (IRCM)

summary: The goal of this study is to perform transcriptome profiling of both infected and uninfected WT and HIF-1ɑ-/- peritoneal macrophages using RNA sequencing techniques. For that, WT and HIF-1ɑ-/- peritoneal macrophages were infeced for 6 hours with L. donovani promastigotes (or left uninfected as a control) and RNA samples were stored in TRI reagent (Sigma), for further analysis.

overall_design: Samples from 5 WT and 5 HIF-1ɑ-/- mice were analyzed

first: R

last: Silvestre

first: M

last: Mesquita


title: Genome-wide identification of estrogen receptor binding sites reveals novel estrogen-responsive pathways in adult male germ cells

city: Mumbai

first: Nafisa

last: Balasinor

state: Maharashtra

address: Jehangir Merwanji Street

department: Neuroendocrinology

country: India

institute: ICMR-National Institute for Research in Reproductive Health (NIRRH-ICMR)

summary: Spermatogenesis occurs in the seminiferous epithelium that shows presence of estrogen receptors alpha (ERα) and beta (ERβ), both of which regulate gene transcription by binding to the DNA. Hormone responsive phases of spermatogenesis are well documented; yet, the genes regulated remain inexplicit. To study the regulation of genes by estrogen in male germ cells, we performed chromatin immunoprecipitation (ChIP) sequencing for ERα and ERβ under normal physiological conditions. We observed a total of 27,221 peaks in ERα and 20,926 peaks in ERβ. Majority of the peaks were present in the intronic regions and located 20kb upstream or downstream from the transcription start site (TSS). Upon pathway analysis, the genes enriched showed involvement in several biological pathways. Genes involved in pathways whose role in spermatogenesis is unexplored were validated; these included prolactin, GnRH and oxytocin signalling. All the genes showed presence of estrogen response elements (EREs) and majority of them showed significant enrichment by ChIP-qPCR. Functional validation using seminiferous tubule culture after treatment with receptor specific agonist and antagonist confirmed the regulation of these genes by estrogen through its receptors. This study provides new insights about the estrogen regulated genes during spermatogenesis.

overall_design: Examination of 2 different nuclear receptors (estrogen receptor alpha and beta) in germ cells of adult rat testes

first: Sanketa

middle: S

last: Raut

first: Anita

last: Kumar

first: Kushaan

middle: K

last: Khambata

first: Sharvari

last: Deshpande

middle: H


title: Activation of a nerve injury transcriptional signature in airway-innervating sensory neurons after lipopolysaccharide induced lung inflammation III

first: Melanie

middle: Maya

last: Kaelberer

address: 203 Research Drive

summary: While the inflammatory immune response of the lung to allergens and pathogens has been extensively studied, little is known about how sensory nerves change in response to an inflammatory insult within the organ they innervate. In our  study we describe the collection of vagal sensory neurons innervating the mouse lung, labelled with a retrograde fluorescent tracer instilled into the airways, and the analysis of their transcriptomes by RNAseq. We also determined transcriptomes of the complete sensory ganglia (vagal, trigeminal, DRG) for comparison. We identified transcripts of genes exclusively expressed in vagal nerves, and not in any other sensory nerve type or any other organ. These include unique ion channels, G-protein coupled receptors and several transcripts of unknown function.

overall_design: Examination of airway innervating vagal vagal neurons with and without lung inflammation

first: Ana

middle: I

last: Caceres

first: Sven-Eric

last: Jordt


title: Transcriptomic analysis from ciprofloxacin treated human triple negative breast cancer cells

city: Seoul

first: Jong Seung

address: Anan-ro 145

department: Department of Chemistry

institute: Korea University

summary:
A DNA microarray study was conducted to determine the impact of Mt-CFX on mRNA expression and pathway activation in human triple negative breast cancer cells.
We used microarrays to detail the global program of gene expression underlying cellularisation and identified distinct classes of up- and down-regulated genes during this process.

overall_design: MDA-MB-231 cells were treated with Mt-CFX, CFX, or 1% DMSO as a control for 72 h.

first: Kyong

last: Sunwoo

first: Miae

last: Won

first: Peter

last: Verwilst


title: LOX inhibition (BAPN treatment) attenuates satellite cell differentiation

city: Haifa

first: Peleg

last: Hasson

address: 1 Efron Street

department: Department of Genetics and Developmental Biology

country: Israel

institute: Technion

summary: Integration of extracellular matrix (ECM)-derived cues into transcriptional programs is essential primarily in rapidly morphing environments such as regenerating tissues. Here we demonstrate that Lysyl oxidase (Lox), known for its ECM modifying activities, primarily collagen crosslinking and fibronectin matrix assembly, also directly regulates transcription factor (TF) localization. Using genetic and pharmacological strategies, we highlight a novel intracellular role for Lox in myogenic progenitors essential for muscle regeneration. We show that Lox interacts with, and directly oxidizes, Vestigial-Like 3 (Vgll3), a transcriptional co-activator acting with Mef2 and TEF TFs. This enzymatic activity is required for Vgll3 cytoplasmic to nuclear translocation in regulation of myogenic differentiation. Our work highlights a novel mechanism for TF sub-cellular localization and suggests a mechanism for integrating ECM organization with transcriptional output during myogenic differentiation. Modulating this integration mechanism could affect the balance between ECM organization and cell differentiation and serve as a basis for novel therapeutic strategies targeting fibrotic pathologies.

overall_design: satellite cells were isolated from C57Bl/6 8 week old mice and grown on matrigel in Bioamf-2 media. Following transfer to differentiation media (DMEM +4% Horse serum), cells were either treated with or without 0.25% BAPN for 24 hrs. Each of the three replicates designates an indepdent biological control.

first: Ravit

last: Gabay Yehezkely

first: Shelly

last: Zaffryar-Eilot

first: Anna

last: Kaganovsky

first: Nurit

last: Fainshtain Malka

first: Rohtem

last: Aviram

first: Ido

last: Livne


title: Activation of a nerve injury transcriptional signature in airway-innervating sensory neurons after lipopolysaccharide induced lung inflammation I

overall_design: Examination of whole vagal ganglia with and without lung inflammation


title: Cytotoxic therapy-induced effects on both hematopoietic and marrow stromal cells promotes therapy-related myeloid neoplasms

first: Angela

last: Stoddart

address: 900 E. 57th Street, Lab 5220A

department: Pathology

institute: University of Chicago

summary: Therapy-related myeloid neoplasms (t-MNs) comprise therapy-related acute myeloid leukemia (t-AML)  and myelodysplastic syndrome (t-MDS), and are a late complication of cytotoxic therapy — chemotherapy and/or radiation therapy — used in the treatment of both malignant and non-malignant diseases. The genetic profile of t-MN is markedly skewed towards high-risk cytogenetic and molecular abnormalities, and complex karyotypes with a del(5q), and TP53 mutation/loss are profoundly over-represented in t-MN as compared with de novo counterparts. To model this genetic subset, we showed that concurrent haploinsufficient expression of the del(5q) tumor suppressor genes, early growth response 1 (EGR1) and adenomatous polyposis coli (APC), cooperate with TP53 (p53) loss to induce myeloid leukemia in mice. The frequency of disease increased upon exposure to the alkylating agent, N-ethyl-N-nitrosurea (ENU) .  In the context of alkylating agent therapy, cell intrinsic loss of the  Egr1 and Apc del(5q) genes was sufficient to promote the development of MDS, but concurrent loss of Trp53 (p53) was required to drive AML development.  We examined RNA expression in 1) LSK (Lin-, Sca1+, Kit+) hematopoietic stem and progenitor cells isolated from mice with Trp53 knockdown or without, prior to myeloid disease development, 2)  bone marrow cells isolated from mice with MDS (no Trp53 knockdown) or AML (Trp53 knockdown), and 3) early passage mesenchymal stromal cells isolated from mice injected i.p. with  10% ethanol (mock) or ENU (100 mg/kg).

overall_design: RNA was isolated from LSK (Lin-, Sca1+, Kit+) bone marrow cells prior to myeloid disease development; from total bone marrow of mice that had developed MDS (Egr1, Apc haploinsufficiency without Trp53 knockdown) or AML (Egr1, Apc haploinsufficiency with Trp53 knockdown); and from early passage mesenchymal stromal cells isolated from mice injected i.p. with  10% ethanol (mock) or ENU (100 mg/kg).

first: Michelle

last: LeBeau


title: RNA-Seq Analysis of Murine Chondrocytes Reveals Pathways Associated with Cartilage Regeneration and Degeneration

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary:
Objectives: Understanding the molecular mechanisms underlying cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). We report transcripts and pathways differentially expressed in chondrocytes obtained from genotypically and phenotypically distinct mouse strains.

Methods: We performed RNA-sequencing and computational analysis on chondrocytes derived from LG/J (large, healer, n=16) and SM/J (small, non-healer, n=16) mouse strains. We validated the expression of candidate genes using real-time PCR and immunostaining.

Results: Of those nearly 6,000 differentially expressed genes between LG/J and SM/J, 138 genes (99 protein-coding) were up-regulated and 145 (103 protein-coding) were down-regulated with log2 fold changes of 2 or more. Interestingly, we found the top up-regulated gene ontology biological pathways in the chondrocytes from the LG/J mice were related to chondrocyte development, cartilage condensation, and regulation of chondrocyte differentiation. In contrast, the top upregulated pathways in the SM/J mice were mostly inflammation related. Real-time PCR confirmed the expression pattern of a number of differentially expressed genes. Immunostaining of two candidate genes revealed that Tnfrsf23 and Car2 were respectively increased in LG/J and SM/J strains.

Conclusions: The enrichment of genes and pathways related chondrocyte differentiation, cartilage development and cartilage condensation in LG/J appear to be responsible for their superior healing potential. The enrichment of pathways related to cytokine production, immune cell activation and inflammation in SM/J suggests a compromised chondrocyte proliferation and/or survival ability and a higher sensitivity to inflammation and OA. Tnfrsf23 and Car2 warrant further investigation to discern their specific role(s) in chondrocyte function and OA.

overall_design:
chondrocyte mRNA profiles of 21-day old LG/j and SM/j mice were generated by RNA-sequencing and validated by real-time PCR and immunohistochemistry.

Please see PubMed ID 16688532 for information on strain origins.

first: Xin

last: Duan

first: Eric

last: Tycksen

first: Muhammad


title: Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy [Pre&Post-Tx]

status: Public on Mar 14 2020

city: Cambridge

first: Martin

middle: Lee

last: Miller

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

summary:
In metastatic cancer, the degree of heterogeneity of the tumor-immune microenvironment and its molecular underpinnings remain largely unstudied. To characterize the tumor-immune interface at baseline and during neoadjuvant chemotherapy in high-grade serous ovarian cancer (HGSOC), we performed immunogenomics analysis of treatment-naive and paired pre/post-chemotherapy treated samples. In treatment-naive HGSOC, we find that immune cell-excluded and inflammatory microenvironments co-exist within the same individuals and within the same tumor sites, indicating ubiquitous variability in immune cell infiltration. Analysis of tumor microenvironment cell composition, DNA copy number, mutations and gene expression showed that immune cell exclusion was associated with amplification of Myc target genes and increased expression of canonical Wnt signaling in treatment-naive HGSOC. Following neoadjuvant chemotherapy, increased natural killer cell infiltration and oligoclonal expansion of T cells were detected. We demonstrate that the tumor-immune microenvironment of advanced HGSOC is intrinsically heterogeneous and that chemotherapy induces local immune activation, suggesting that chemotherapy can potentiate the immunogenicity of immune-excluded HGSOC tumors.
The goal of this particular experiment was quantify RNA expression using microarray technology, and then evaluate differences in the trasncirptomic landscape of treatment naïve metastatic high grade serous ovarian cancer.

overall_design: Samples analyzed: Described in figure 5a. 9 patients with 18 matched pre/post treatment tumor samples and 19 patients with 38 unmatched pre/post treatment tumor samples. Affymetrix mRNA microarrays were collected and analyzed for these samples.

first: Alejandro

last: Jimenez-Sanchez

first: Katherine

middle: L

last: Magner

first: Alexandra

last: Snyder

first: Britta

last: Weigelt

first: Evis

last: Sala


title: RNA-Seq analysis of Tcf7-deficient and -sufficient lung CD8+ TRM cells after influenza infection

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

institute: German cancer research center (DKFZ)

summary: T cell factor 1 (Tcf1, encoded by Tcf7) promotes the central memory CD8+ T cell (TCM) differentiation and homeostatic proliferation in lymphoid tissues. It remains unclear if and how Tcf1 regulates the CD103high tissue-resident memory CD8+ T cell (TRM) formation in non-lymphoid tissues. Using an influenza A infection mouse model, we collected Tcf7-deficient and -sufficient lung CD8+ TRM cells for RNA sequencing analysis.

overall_design: To understand the global gene expression profiles in Tcf7-deficient and -sufficient lung CD8+ TRM cells, we infected mice receiving Tcf7-deficient and -sufficient TCR transgenic P14 CD8+ T cells with influenza A virus X31 expressing LCMV epitope GP33-41 (X31-33). Eight days after infection, the mice were injected with PE-conjugated anti-CD8beta to intravascularly label circulating CD8+ T cells. Lung-infiltrating T cells were stained with CD8a and CD103. CD103high Tcf7-deficient and -sufficient P14 CD8+ T cells were FACS-sorted on day 8 after X31 infection for RNA extraction and RNA sequencing (RNA-seq) analysis.

first: Jingxia

last: Wu


title: Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy

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

overall_design: Refer to individual Series


title: Genome-wide maps of SMXL6 binding sites in Arabidopsis seedlings [pSMXL6:SMXL6-HA]

city: Beijing

first: Jiayang

last: Li

address: West Beichen Road

institute: Institute of Genetics and Developmental Biology, CAS

summary:
Purpose: SMXL6 is a key repressor in strigolactone signaling. The goal of this study is to identify the targeted genes of SMXL6 in the model plant Arabidopsis thaliana.
Methods: The stable pSMXL6:SMXL6-HA transgenic line in the smxl6/7/8 background and the smxl6/7/8 mutant were grown for two weeks in 0.5 x MS medium and collected for extraction of the protein-DNA complexes. After ChIP analyses, DNA profiles were generated by deep sequencing, in double replicate, using Illumina system Novaseq 6000. The sequence reads were analyzed using BWA software and SAMtools. ChIP-qPCR validation was performed using Bio-Rad CFX 96 real-time PCR detection system.
Results: We identified 1665 and 1401 peaks in replicate experiment 1 and 2.

overall_design: Investigating the binding sites of SMXL6 in the smxl6/7/8 pSMXL6:SMXL6-HA transgenic plants, using the smxl6/7/8 mutant as a control.

first: Bing

last: Wang


title: Chromatin binding protein PHF6 regulates activity-dependent transcription networks to promote hunger response [RNA-Seq]

first: Qian

address: 280 South Chongqing Road, Building No.5, Room 408

department: Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

summary: We revealed that PHF6 bound to the promoters of a subset of neuronal immediate-early genes (IEGs) and regulate their expression levels.  hunger state.

overall_design: Examination of differentially expressed genes under fed and fasted conditions in wild type and PHF6 conditional knockout mice.

first: Ju

last: Huang


title: Chronic peripheral inflammation causes a region-specific myeloid response in the central nervous system

city: La Jolla

first: Johannes

middle: Carolus Magnus

last: Schlachetzki

state: CA

address: 9500 Gilman Drive  #0651

department: Cellular and Molecular Medicine

institute: UCSD

summary:
Systemic immune dysregulation contributes to the development of neuropsychiatric and neurodegenerative diseases. The precise effect of chronic peripheral immune stimulation on myeloid cells across anatomical brain regions is unclear.
We used the human TNF-α transgenic mouse model of RA (TNFtg mice, strain Tg197) (Keffer et al., 1991), which shows increased levels of peripheral cytokines and severe joint pathology at young age and leads to severe disability within 3-4 months after birth (Keffer et al., 1991; Suss et al., 2015) to assess the effect of chronic peripheral inflammation on myeloid cells in the cortex.
To examine the response of brain myeloid cells to systemic chronic inflammation, we performed single cell RNA-seq on isolated CD11b+CD45+ cells from the cortex of wt and TNFtg mice.

overall_design: Single cell RNA-seq of cortical myeloid (CD45+) cells from C57Bl6/J wild type and TNF transgenic mice

first: Patrick

last: Süß

first: Alana

last: Hoffmann

first: Tobias

last: Rothe

first: Zhengyu

last: Ouyang

first: Wolfgang

last: Baum

first: Ori

last: Staszewski

first: Georg

last: Schett

first: Marco

last: Prinz

first: Gerhard

last: Krönke

first: Christopher

last: Glass

first: Jürgen

last: Winkler


title: Expression data from FACS-isolated lung endothelial cells

city: Mannheim

first: Mahak

last: Singhal

address: Ludolf-Krehl-Straße 13-17

institute: European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University

summary:
To investigate the role of a TIE1-function blocking antibody on gene expression of lung endothelial cells.
Lung endothelial cells were FACS-isolated from primary tumor-bearing mice. Mice were treated either with IgG or TIE1-blocking antibody during primary tumor growth. Total RNA were used for microarray analysis using Clariom S mouse assays (Applied Biosystems).

overall_design: LLC primary tumors were treated with IgG or TIE1-blocking antibody. Lung EC were FACS-isolated. Total RNA was isolated with Arcturus PicoPure RNA isolation kit. cDNA libraries were prepared and analyzed by the DKFZ Genomics core facility, according to the standard operating protocols.

first: Singhal

last: Mahak

first: Augustin

last: Hellmut


title: Chromatin binding protein PHF6 regulates activity-dependent transcription networks to promote hunger response [ChIP-Seq]

first: Qian

last: Li

summary: We revealed that PHF6 was bound to the promoters of a subset of neuronal immediate-early genes (IEGs), and this chromatin binding was dynamically regulated by  hunger state.

overall_design: Examination of genome-wide PHF6 binding pattern in fed and fasted conditions.


title: Chromatin binding protein PHF6 regulates activity-dependent transcription networks to promote hunger response


title: Evolutionary selection of pestivirus variants with altered or no miRNA dependency

status: Public on Mar 13 2020

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

summary: Host microRNA (miRNA) dependency is a hallmark of the human pathogen hepatitis C virus (HCV) and was recently also described for the related pestiviruses, which are important livestock pathogens. HCV critically depends on the liver-specific miR-122, whereas the broadly expressed let-7 and miR-17 families bind two sites (S1 and S2) in the pestiviral 3’ untranslated region (UTR). Here, we elucidated the miRNA dependency of bovine viral diarrhea virus (BVDV) and confirmed its critical dependence on miR-17 and Argonaute 2 (AGO2). Let-7 binding to S1 had only minor effect on virus production but was required for full translational efficiency. Evolutionary selection experiments using seed site randomized genomes revealed that tropism could be re-directed to different miRNAs. AGO cross-linking and immunoprecipitation (AGO-CLIP) and miRNA antagonism demonstrated that these alternative variants bound and depended on the corresponding miRNAs. Furthermore, we identified variants with miRNA independent replication through acquisition of compensatory mutations near the genomic 3’ terminus. Rescue experiments using miRNA mimics demonstrated that miRNA binding and 3’ mutagenesis contribute to replication through mutually exclusive mechanisms. Our findings illustrate that pestiviruses, although capable of miRNA independent replication, took advantage of miRNAs as essential host factors, suggesting a favorable path during evolutionary adaptation.

overall_design: To study miRNA interactions with bovine viral diarrhea virus (BVDV), cross-linking immunoprecipitation (CLIP) was performed on the Argonatue (AGO) protein. To unambiguously identify interactions with specific miRNAs, we used the CLEAR-CLIP (Moore 2015 Nat Comm) iteration to enrich for miRNA-target chimeras. Prior to cross-linking, bovine Madin-Darby Bovine Kidney (MDBK) cells were infected with wild-type or mutant virus as indicated. Processed reads were aligned to the host (BosTau7) and the viral genome (BVDV). Alignment statistics of CLIP reads are given in the processed data file “Table S1”. A complete table of standard AGO-CLIP reads aligning to BVDV is given in “Table S2”. miRNA-target chimeras were identified in MDBK cells from CLEAR-CLIP experiments as indicated. A complete list of individual miRNA-target chimeras on BVDV is given in “Table S3”.

first: Konstantinos

last: Kokkonos

first: Nicolas

last: Fossat

first: Louise

last: Nielsen

first: Christina

last: Holm

first: Wytske

last: Hepkema

first: Jens

last: Bukh


title: POSH2 Promotes Breast Cancer Stem-Like Properties through JNK Activation and PTX3 Upregulation

first: Guohong

last: Hu


title: Next Generation Sequencing of Arabidopsis seedlings upon Mock or GR244DO Transcriptomes

first: Jiayang

address: Beichen West Road

summary:
Purpose: Strigolactones (SLs), a class of carotenoid-derived plant hormones, have fundamental effects on plant development. But only a few SL-responsive genes have been identified. The goal of this study is to identify SL early responsive genes in the model system Arabidopsis thaliana.
Methods: The 10-day-old wild-type seedlings were treated with GR244DO or solvent for 2 h or 4 h. The mRNA profiles were generated by deep sequencing, in triplicate, using Illumina system Hiseq2000. The sequence reads were analyzed using STAR and R package DESeq. To limit interference of circadian clock and environmental factors, GR244DO treatment at 2 h was compared to solvent treatment control at 2 h as well as the start point of treatment, and genes upregulated at both conditions were considered as up-regulated SL responsive genes at 2 h. The same comparison criteria were applied to identify down-regulated responsive genes at 4 h. qRT-PCR validation was performed using CFX 96 real-time PCR detection system.
Results: We identified 99 upregulated and 57 downregulated genes at 2 h treatment, as well as 147 upregulated and 150 downregulated genes at 4 h treatment in Arabidopsis thaliana using the cutoff of fold-change more than 1.5 and P-value less than 0.05.

overall_design: The mRNA profiles of 10-day-old wild-type seedlings under GR244DO or solvent treatment were generated by deep sequencing, in triplicate, using Illumina Hiseq2000.

first: Bing

last: Wang


title: POSH2 Promotes Breast Cancer Stem-Like Properties through JNK Activation and PTX3 Upregulation [HMLER_sublines]

summary: We conduct transcriptome comparison of HMLER-derived CD44H,CD44LS and CD44L subpopulation cells to gain transcriptomic insights on the differences between breast cancer stem cells and non-breast cancer stem cells.

overall_design: In the study presented here,CD44+CD24-(CD44H) cells and CD44-CD24+(CD44L) cells were sorted from HMLER cells by flow cytometry. CD44L cells were cultured in low adhesion plate with tumorsphere medium for several generations and we got the new subpopulation,CD44LS. RNA sequencing profiling of mRNA levels was performed in these three subpopulation cells.

first: Peiyuan

last: Zhang


title: Convergence of Cockayne Syndrome Group A and B Proteins at rRNA Transcription through Nucleolin Regulation

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Cockayne Syndrome (CS) is a rare neurodegenerative disease characterized by short stature, cachexia, sun-sensitivity, accelerated aging, and short lifespan. Mutations in two human genes, ERCC8/CSA and ERCC6/CSB, are causative for CS and the protein products of these genes, CSA and CSB, while structurally unrelated, play roles in DNA repair and other aspects of DNA metabolism in human cells. Many clinical and molecular features of CS remain poorly understood, and it has been suggested that CSA and CSB regulate transcription of rDNA genes and ribosome biogenesis. The goal of this study was to investigate the dysregulation of rRNA synthesis in CS. Here, we report that Nucleolin (Ncl), a nucleolar protein that regulates rRNA synthesis and ribosome biogenesis, interacts specifically with CSA and CSB. In addition, CSA induces ubiquitination of Ncl, enhances binding of CSB to Ncl, and CSA and CSB both stimulate binding of Ncl to rDNA and subsequent rRNA synthesis. These findings suggest that CSA and CSB are positive regulators of rRNA synthesis via Ncl regulation. A majority of CS patients carry mutations in CSA and CSB and present with similar clinical features, thus our findings may provide novel insights into disease mechanism and the neuropathological features of CS.

overall_design: Examination of CSB UBD mutation expression compared to WT CSB in CS1AN cells

first: Mustafa

middle: N

last: Okur

first: Osmani

last: Wasif

first: Jong

last: Lee

first: Tyler

last: Demarest

first: Deborah

last: Croteau

first: Vilhelm

middle: A

last: Bohr


title: Activation of a nerve injury transcriptional signature in airway-innervating sensory neurons after lipopolysaccharide induced lung inflammation

city: Durham

first: Melanie

last: Kaelberer

institute: Duke University


title: Activation of a nerve injury transcriptional signature in airway-innervating sensory neurons after lipopolysaccharide induced lung inflammation II

summary: While the inflammatory immune response of the lung to allergens and pathogens has been extensively studied, little is known about how sensory nerves change in response to an inflammatory insult within the organ they innervate. In our  study we describe the collection of vagal sensory neurons innervating the mouse lung, labelled with a retrograde fluorescent tracer instilled into the airways, and the analysis of their transcriptomes by RNAseq. We also determined transcriptomes of the complete sensory ganglia (vagal, trigeminal, DRG) for comparison. We identified transcripts of genes exclusively expressed in vagal nerves, and not in any other sensory nerve type or any other organ. These include unique ion channels, G-protein coupled receptors and several transcripts of unknown function.

overall_design: Comparison between sensory ganglia: trigeminal (tg), dorsal root (drg), and jugular nodose/vagal (jnc) ganglia

first: Ana

last: Caceres

first: Sven-Eric

last: Jordt


title: Molecular signature of pruriceptive MrgprA3+ neurons

city: Atlanta, Georgia, USA

first: Liang

last: Han

state: GA

address: 950 Atlantic Dr.

department: Biological Sciences

institute: Georgia Institute of Technology

summary: We performed RNA sequencing of genetically labeled MrgprA3+ neurons under both naïve and allergic contact dermatitis conditions. Our results revealed the unique molecular signature of itch-sensing neurons and the distinct transcriptional profile changes that result in response to dermatitis. We found enrichment of nine Mrgpr family members and two histamine receptors in MrgprA3+ neurons, suggesting that MrgprA3+ neurons are a direct neuronal target for histamine and Mrgprs agonists. In addition, Ptpn6 and Pcdh12 were identified as novel and highly selective markers of MrgprA3+ neurons. We also discovered that MrgprA3+ neurons respond to skin dermatitis in a way that is unique from other sensory neurons by regulating a combination of transcriptional factors, ion channels, and key molecules involved in synaptic transmission. These results significantly increase our knowledge of itch transmission and uncover potentially novel targets for combating itch.

overall_design:
RNA sequencing data were generated for genetically labeled MrgprA3+ (GFP) and MrgprA3- (N) neurons of mice, under both Control and allergic contact dermatitis (ACD) conditions.

***Please note that the raw data files have been lost and thus were not provided.

first: Jingjing

last: Yang


title: DNA methylation of chronic lymphocytic leukemia with differential response to chemotherapy

city: Ulm

first: Deyan

middle: Yordanov

last: Yosifov

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University Hospital Ulm

type: Methylation profiling by genome tiling array

summary: Acquired resistance of chronic lymphocytic leukemia (CLL) to chemotherapy is an important clinical problem and is often caused by cytogenetic aberrations or gene mutations affecting the ATM-p53 DNA damage response pathway or other pathways. However, there are also a lot of resistant cases without detectable mutations and we decided to check whether there are specific epigenetic changes at the level of DNA methylation that might underlie resistance development in CLL. We used Illumina Infinium HumanMethylation450 BeadChips to obtain DNA methylation profiles of 71 CLL patients with different responses to chemotherapy. Fifty-one patients were subjects of the CLL2O clinical trial and 36 of them were categorized as relapsed/refractory after treatment with fludarabine- or bendamustine-containing regimens, whereas the other 15 patients as well as 20 additional patients not on the trial were untreated at the time of sampling. Although we could not correlate chemoresistance with epigenetic changes, we believe that the dataset is valuable and can be used by researchers to test other hypotheses, especially as the patients are well characterized regarding different prognostic and molecular markers (IGHV mutation status, chromosome aberrations, TP53 mutation status, etc.).

overall_design: 72 samples of CLL patients were analyzed by Illumina Infinium HumanMethylation450 BeadChips. Two consecutive samples (40 months apart) from one patient were used to confirm reproducibility of the assay, as well as stability of DNA methylation profiles over time. Fifty-one of the patients were subjects of the multi-centre CLL2O clinical trial (clinicaltrials.gov: NCT01392079) and we have subdivided them here in 4 subgroups depending on their del(17p)/TP53mut and treatment/response statuses as follows: groups A (N = 15), B (N = 10) and C (N = 11) consisted of patients with del(17p) and/or TP53 mutation and group E (N = 15) consisted of patients without del(17p) or TP53 mutation. Patients in group A were not treated previously but required treatment, patients in group B had relapsed after treatment with fludarabine- or bendamustine-containing regimens and patients in groups C and E were refractory to fludarabine or bendamustine. Samples from patients in all these groups were taken prior to the start of the CLL2O clinical trial. Additional 20 cases (group D) were patients of the University Hospital in Ulm who did not have del(17p) or TP53 mutation and who were not previously treated.

middle: Y

first: Johannes

last: Bloehdorn

first: Hartmut

last: Döhner

first: Peter

last: Lichter

first: Stephan

last: Stilgenbauer

first: Daniel

last: Mertens


title: Epigenetic profiling of EMT in pancreatic cancer cells (ATAC-seq)

city: Philadelphia

first: Salina

last: Yuan

state: PA

address: 421 Curie Blvd

department: Medicine

institute: University of Pennsylvania

summary: Epithelial plasticity – reversible modulation of a cell’s epithelial and mesenchymal features – is associated with cancer metastasis and chemoresistance. This process is classically driven by a small cohort of transcription factors, several of which have been reported to functionally interact with epigenetic modifiers at the promoters of key epithelial and mesenchymal genes. However, the extent to which epigenetic changes underlie epithelial plasticity at the genomic level remains largely unknown. Here we show that genome-wide regulation of a single histone mark, H3K36me2, is critical for establishing stable epithelial-mesenchymal states in various genetic, chemical, and cellular contexts. Through targeted CRISPR-Cas9 screening, we discovered two histone-modifying enzymes involved in the writing and erasing of H3K36me2 that act reciprocally to regulate epithelial-mesenchymal identity, tumor differentiation, and metastasis. Using genetic approaches to inhibit H3K36me2, we found that modulation of the mark itself is a conserved mechanism underlying the mesenchymal state. Although H3K36me2 is distributed broadly throughout the genome, it is associated with altered enhancer activity affecting a relatively small number of genes, including those associated with master epithelial-mesenchymal regulatory factors. Our results thus outline an epigenome-scale mechanism by which a specific histone modification regulates cellular plasticity in cancer.

overall_design: 6 samples were sequenced. Samples include Ecad+ and Ecad- sorted cells from 3 cell lines.

first: Ben

middle: Z

last: Stanger


title: The jasmonate-response genome regulatory program is defined by the direct targets of transcription factors MYC2 and MYC3, chromatin modification and gene expression changes

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: The hormone jasmonic acid (JA) controls a plethora of crucially important processes in plants through a signaling pathway orchestrated by the transcription factor MYC2 and its closest relatives. Understanding the systems-level actions of transcription factors provides insight into how the genome is reprogrammed in response to environmental stimuli. However, deeper biological insight can be obtained if transcription factor activity is set in the broader regulatory context of the cell and the downstream organismal phenotypes the transcription factors control. Here, we have investigated the MYC2-governed genome regulatory network that controls JA responses in Arabidopsis thaliana etiolated seedlings. We have generated an integrated framework of the response to JA that spans from the activity of master and secondary-regulatory transcription factors, through gene expression outputs and alternative splicing to protein abundance changes, protein phosphorylation and chromatin remodeling. We have integrated time series transcriptome analysis with (phospho)proteomic data using gene regulatory network models. These enable us to predict previously unknown points of crosstalk from JA to other signaling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant studies. The result is a comprehensive understanding of how a plant hormone remodels cellular function and plant behavior, the general principles of which provide a framework for analysis of cross-regulation between other hormone and stress signaling pathways.

overall_design: ChIP-seq, DAP-seq and RNA-seq was applied to comprehensively profile the chromatin landscape in Col-0 and myc2 mutants.

first: Mark

last: Zander

first: Mathew

middle: G

last: Lewsey

first: Natalie

last: Clark

first: Lingling

last: Yin

first: Anna

last: Bartlett

first: Jessica

middle: P

last: Saldierna Guzmán

first: Elizabeth

last: Hann

first: Amber

middle: E

last: Langford

last: Nery

first: Huaming

last: Chen

first: Justin

middle: W

last: Walley


title: Antitumor Activity of Z-endoxifen in Aromatase Inhibitor-Sensitive and Resistant Estrogen Receptor-Positive Breast Cancer

city: ROCHESTER

first: Swaathi

last: Jayaraman

state: Minnesota

address: 200 1st St SW

department: Oncology

institute: Mayo Clinic

summary:
The overarching goal of this study was to explore the antitumor activity of Z-endoxifen, a tamoxifen metabolite, with first-line endocrine therapies tamoxifen and letrozole in the letrozole-sensitive MCF7 aromatase expressing model (MCF7AC1), and with second-line endocrine therapies including tamoxifen, fulvestrant, exemestane, and exemestane plus everolimus, in letrozole-resistant MCF7 model (MCF7LR) in vivo.
We used microarray to identify genes that are commonly and differently reguated by Z-endoxifen and tamoxifen treatments in the letrozole-resistant MCF7LR tumors.

overall_design: In the first study MCF7AC1 tumors-bearing mice were randomized to control (no drug), letrozole (10μg/day), tamoxifen (500 µg/day) or Z-endoxifen (25 and 75 mg/kg) and the efficacy of Z-endoxifen compared to first-line endocrine therapies were studied.  Treatment in the letrozole arm was continued for an extended period of time until resistance developed in vivo.  Owing to mouse body weight loss observed with the 75 mg/kg dose of Z-endoxifen, the MCF7LR tumor-bearing mice were randomized to 50 mg/kg dose of Z-endoxifen or tamoxifen for four weeks and Z-endoxifen efficacy was compared to tamoxifen in the resistant setting. At the end of four weeks, tumors were harvested for microarray and immunohistochemistry analysis. In the second in vivo study, the efficacy of Z-endoxifen in the second-line setting was compared with FDA approved endocrine therapies (exemestane, exemestane+everolimus and fulvestrant) for the treatment of AI-resistant breast tumors.

first: Xiaonan

last: Hou

first: Mary

middle: J

last: Kuffel

first: Vera

last: Suman

first: Tanya

last: Hoskin

first: Kathryn

last: Reinicke

first: David

last: Monroe

first: Krishna

middle: R

last: Kalari

first: Xiaojia

last: Tang

first: Megan

last: Zeldenrust

first: Jingfei

last: Cheng

middle: S

last: Bruinsma

first: Sarah

last: Buhrow

first: Renee

middle: M

last: McGovern

first: Stephanie

last: Safgren

first: Chad

last: Walden

first: Jodi

last: Carter

first: Joel

last: Reid

first: James

last: Ingle

first: Matthew

last: Ames

first: John

last: Hawse

last: Goetz


title: Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

status: Public on Mar 12 2020

city: Seattle

first: Anneke

middle: Dixie

last: Kakebeen

state: WA

address: 5611 9th Ave NW

department: Biochemistry

institute: University of Washington

summary: Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.

overall_design: Investigation of chromatin accessiblity dynamics in neural progenitor cells over the course of tadpole tail regeneration

first: Kakebeen

last: Anneke

first: Chitsazan

last: Alex


title: Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy [naïve]

first: Martin

middle: Lee

last: Miller

summary:
In metastatic cancer, the degree of heterogeneity of the tumor-immune microenvironment and its molecular underpinnings remain largely unstudied. To characterize the tumor-immune interface at baseline and during neoadjuvant chemotherapy in high-grade serous ovarian cancer (HGSOC), we performed immunogenomics analysis of treatment-naive and paired pre/post-chemotherapy treated samples. In treatment-naive HGSOC, we find that immune cell-excluded and inflammatory microenvironments co-exist within the same individuals and within the same tumor sites, indicating ubiquitous variability in immune cell infiltration. Analysis of tumor microenvironment cell composition, DNA copy number, mutations and gene expression showed that immune cell exclusion was associated with amplification of Myc target genes and increased expression of canonical Wnt signaling in treatment-naive HGSOC. Following neoadjuvant chemotherapy, increased natural killer cell infiltration and oligoclonal expansion of T cells were detected. We demonstrate that the tumor-immune microenvironment of advanced HGSOC is intrinsically heterogeneous and that chemotherapy induces local immune activation, suggesting that chemotherapy can potentiate the immunogenicity of immune-excluded HGSOC tumors.
The goal of this particular experiment was quantify RNA expression using microarray technology, and then evaluate differences in the trasncirptomic landscape of treatment naïve metastatic high grade serous ovarian cancer.

overall_design: Samples analyzed: Described in figure 1a. Ten patients with 38 Affymetrix mRNA microarrays (I.e Multiple samples per patient).

first: Alejandro

last: Jimenez-Sanchez

first: Paulina

last: Cybulska

first: Alexandra

last: Snyder

first: Britta

last: Weigelt

first: Evis

last: Sala

middle: L


title: Comparative transcriptomic analyses of developing melanocortin neurons reveal new regulators for the anorexigenic neuron identity

city: Dallas

first: Li

last: Li

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

summary: Despite their opposing actions on food intake, POMC and NPY/AgRP neurons in the arcuate nucleus of the hypothalamus (ARH) are derived from the same progenitors that give rise to ARH neurons. However, the mechanism whereby common neuronal precursors subsequently adopt either the anorexigenic (POMC) or the orexigenic (NPY/AgRP) identity remains elusive.We hypothesize that POMC and NPY/AgRP cell fates are specified and maintained by distinct intrinsic factors. In search of them, we profiled the transcriptomes of developing POMC and NPY/AgRP neurons in E15.5 mice embryos. Moreover, cell-type-specific transcriptomic analyses revealed transcription regulators that are selectively enriched in either population, but whose developmental functions are unknown in these neurons.Among them, we found the expression of the PR domain-containing factor 12 (Prdm12) was enriched in POMC neurons but absent in NPY/AgRP neurons. To study the role of Prdm12 in vivo, we developed and characterized a floxed Prdm12 allele. Selective ablation of Prdm12 in embryonic POMC neurons led to significantly reduced Pomc expression as well as early-onset obesity in mice of either sex that recapitulates symptoms of human POMC deficiency. Interestingly, however, specific deletion of Prdm12 in adult POMC neurons showed that it is no longer required for Pomc expression nor energy balance. Collectively, these findings establish a critical role for Prdm12 in the anorexigenic neuron identity and suggest that it acts developmentally to program body weight homeostasis. Finally, the combination of cell-type-specific genomic and genetic analyses provides a means to dissect cellular and functional diversity in the hypothalamus whose neurodevelopment remains poorly studied.

overall_design: Transcriptomic profiling of  purified (Fluorescence activated cell sorting) hypothalamic E15.5 Pomc and NPY neurons using an Illumina HiSeq 2500.

first: X

last: Chen

first: S

middle: C

last: Wyler

first: L

first: A

last: Arnold

first: R

last: Wan

last: Jia

first: M

last: Landry

last: Lai

last: Xu

first: C

last: Liu


title: AP-1 Imprints a Reversible Transcriptional Programme of Senescent Cells

city: Paris Cedex 15

first: Oliver

last: Bischof

address: 28 rue du Docteur Roux

department: Cell Biology & Infection

country: France

institute: Institut Pasteur

summary: Senescent cells affect many physiological and pathophysiological processes. While select genetic and epigenetic elements for senescence induction have been identified, the dynamics, epigenetic mechanisms and regulatory networks defining senescence competence, induction and maintenance remain poorly understood, precluding the deliberate therapeutic targeting of senescence for health benefits. Here, we examined the possibility that the epigenetic state of enhancers determines senescent cell fate. We explored this by generating time-resolved transcriptomes and epigenome profiles during oncogenic RAS-induced senescence and validating central findings in different cell biology and disease models of senescence. Through integrative analysis and functional validation, we reveal links between enhancer chromatin, transcription factor recruitment and senescence competence. We demonstrate that activator protein 1 (AP-1) 'pioneers' the senescence enhancer landscape and defines the organizational principles of the transcription factor network that drives the transcriptional programme of senescent cells. Together, our findings enabled us to manipulate the senescence phenotype with potential therapeutic implications.

overall_design: We performed time-series experiments on doxycycline-inducible RAF WI-38 fibroblasts treated with with 100ng/ml doxycycline, or on WI38 experiencing proliferative exhaustion under 21% O2. Total RNA was collected at 6 time points for RAF OIS (0, 12, 24, 48, 72 and 96 h, 2 biological replicates) and 9 time point for replicative senescence (0, 144, 264, 792, 1008, 1368 and 2112 h) , and global gene expression levels were determined using Affymetrix HTA2.0 microarrays.

first: Ricardo

last: Martínez Zamudio

first: Pierre-François

last: Roux

first: Gregory

last: Doré


title: Identification of transcriptional targets of PHF20L1 by RNA sequencing [RNA-seq]

city: tianjin

first: Yongqiang

last: Hou

address: No. 22 Qixiangtai Road, Heping District, Tianjin

institute: Tianjin Medical University

summary: To gain insights into global gene expression regulated by PHF20L1, RNA sequencing (RNA-Seq) experiments were performed in MDA-MB-231 cells using siRNA against PHF20L1 and control.

overall_design: mRNA profiles of MDA-MB-231 cells under different treaments were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Yongqang

first: Yan

last: Wang


title: RNA-seq expression analysis of control and Myb mutant wing discs

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry and Molecular Biology

institute: University of Iowa

summary: Study of genome-wide differential gene expression of Drosophila Melanogaster Myb mutant wing discs of 3rd instar larvae compared to control animals.

overall_design: RNA-seq was performed from total RNA was isolated from yw67 control (3 biological replicates) and Myb mutant (5 biological replicates) 3rd instar mesothoracic wing discs

first: Juan

middle: F

last: Santana

first: Mrutyunjaya

last: Parida

first: John

last: Manak


title: Genome-wide maps of chromatin state in MDA-MB-231 cells [ChIP-seq]

summary: We report a series of ChIP-Seq results in MDA-MB-231 cells. Briefly, we performed ChIP-Seq experiments with antibodies specific for PHF20L1, MTA1, EZH2, H3K27me2, H3K27me3 and H3K27ac in normal or knockdown of PHF20L1 MDA-MB-231 cells . We found that knockdown of PHF20L1 reduced the enrichment of MTA1, EZH2, H3K27me2, and H3K27me3 on the PHF20L1 target gene, and the enrichment of H3K27ac increased. This study gave us a new understanding of the role of PHF20L1 in chromatin status and gene transcription.

overall_design: Examination of PHF20L1, MTA1, EZH2, H3K27me2, H3K27me3 and H3K27ac  target genes in MDA-MB-231 cell line


title: EP4-Tg aortic VSMCs: Control vs PGE2

status: Public on Mar 11 2020

city: Tokyo

first: Taro

last: Hiromi

state: Not required for this country

address: 6-1-1, shinjyuku, shinjyuku-ku

institute: Tokyo Medical University

summary: Microarray data of EP4-Tg VSMCs with or without 24 h of PGE2 (1 µmol/L)

overall_design: EP4-Tg aortic VSMCs, Biological replicates: 2 control groups, 2 PGE2 treated groups.

first: Utako

last: Yokoyama


title: Nasal Allergen Challenge and Environmental Exposure Chamber Challenge: A Comparison of Clinical and Biological Responses to Cat Allergen

city: Bethesda

first: Tielin

last: Qin

state: MD

address: 7500 Old Georgetown Road, Suite 800

institute: Immune Tolerance Network

summary: A direct comparison of NAC and EEC allergen challenges revealed differences in the kinetics and magnitude of clinical responses, but comparable immunological responses indicating similarity in the biological pathways elicited by both challenge methodologies

overall_design: Nasal brushing samples collected from ITN cat allergic individuals at baseline (prior to allergen exposure), 8 hours after nasal allergen challenge (NAC) exposure, and 8 hours after environmental exposure challenge (EEC). Cross over study design

last: Larson

first: Piyush

last: Patel

first: Anne-Marie

last: Salapatek

first: Peter

last: Couroux

first: Don

last: Whitehouse

first: Adela

last: Pina

first: Jacqueline

last: Johnson

first: Michelle

last: Sever

first: Srinath

last: Sanda

first: Julian

last: Poyser

first: Theresa

last: Allio

first: Guy

last: Scadding

first: Mohamed

last: Shamji

first: William

last: Kwok

first: Eddie

middle: A

last: James

first: Deanna

last: French

first: Alina

last: Lelic

first: Mark

last: Larché

first: Matthew

last: Altman

first: Alkis

last: Togias

first: Stephen

last: Durham


title: scRNA-sequencing of dorsal root ganglia neurons from vitamin E deficient mice

city: Davis

first: Carrie

middle: Jacqueline

last: Finno

address: Room 4206 Vet Med 3A

department: Vet Med: PHR

institute: UC Davis

summary: We report the effects of vitamin E deficiency using the Ttpa-null mouse model on transcriptome profiles of dorsal root ganglia neurons

overall_design: scRNA-seq of n=2 mice in 3 experimental groups (wild-type, Ttpa-/- on a vitamin E deficient diet and Ttpa-/- on a vitE supplemented diet)


title: Transcriptome analysis in buds of peach trees treated with hydrogen cyanamide that advanced bud break

city: Lake Alfred

first: Lisa

last: Tang

state: FL

address: 700 Experiment Station Rd.

department: Citrus Research and Education Center

institute: University of Florida

summary: To determine how dormancy breaking agent, hydrogen cyanamide (HC) advances bud break in peach (Prunus persica), this research compared the transcriptome of buds of low-chill ‘TropicBeauty’ peach trees treated with 1% (v/v) HC and that of non-treated trees at 3 and 7 days after treatment (DAT), respectively, using RNA sequencing analysis. The peak of total bud break occurred 6 weeks earlier in the HC treated trees (at 32 DAT) than the non-treated trees (at 74 DAT). There were 1312 and 1095 differentially expressed genes (DEGs) at 3 and 7 DAT, respectively. At 3 DAT, DEGs related to oxidative stress, including response to hypoxia, lipid oxidation, and reactive oxygen species (ROS) metabolic process, were up regulated in HC-treated buds. Additionally, DEGs encoding enzymes for ROS scavenging and pentose phosphate pathway were up regulated at 3 DAT but were not differently expressed at 7 DAT, indicating a temporary demand for defense mechanisms against HC-triggered oxidative stress. Up regulation of DEGs for cell division and development at 7 DAT, which were down regulated at 3 DAT, suggests cell activity was initially suppressed but enhanced within 7 days following the treatment. At 7 DAT, DEGs related to cell wall degradation and modification were up-regulated, possibly responsible for the burst of buds. The results of this study strongly suggest that HC induces transient oxidative stress shortly after application leading to the release of bud dormancy and, subsequently, causes an increase in cell activity and cell wall loosening, thereby accelerating bud break in peach.

overall_design: Samples (bud tissue) of 'TropicBeauty' peach trees treated with 1% (v/v) hydrgen cyanamide (HC) and non-treated control trees at 3 and 7 day after treatment; each sample was analyzed in four biological replicates.

first: Shweta

last: Chhajed

first: Trjipti

last: Vashisth

first: Mercy

last: Olmstead

first: James

first: Thomas

last: Colquhoun


title: Understanding the roles of dksA and greA in inorganic polyphosphate accumulation in Escherichia coli

city: Birmingham

first: Michael

middle: Jeffrey

last: Gray

state: AL

department: Microbiology

institute: University of Alabama at Birmingham

summary: Inorganic polyphosphate (polyP) is synthesized by bacteria in response to various stresses, but the mechanism of its regulation is unknown. Mutants of Escherichia coli lacking the RNA polymerase-binding transcription factor dksA are defective in polyP synthesis after a nutrient limitation stress, and this defect is reversed in a dksA greA mutant. In this work, we used RNA sequencing to compare transcription in wild-type, dksA, and dksA greA strains of E. coli before and after nutrient limitation, to identify genes whose expression pattern correlates with ability to synthesize polyP.


title: Microarray analysis of Dorsal root ganglion (DRG) sensory neurons from the liver kinase B1 (LKB1) knockout

city: Rehovot

first: Avraham

last: Yaron

address: Herzl st. 234

institute: Weizmann Institute of Science

summary: The goal of this study is to uncover the changes in the transcriptome of sensory neurons of the liver kinase B1 (LKB1) knockout

overall_design: Methods:  mRNA profiles of Dorsal root ganglion (DRG) sensory neurons directly isolated from E13.5 embryos were generated. 5 independent replicates of RNA purification of each genotype were prepared, each replica is of DRGs from 2 embryos

first: Valeria

last: Ulisse

first: Adi

last: Minis


title: Physical interactions between Gsx2 and Ascl1 balance progenitor expansion versus neurogenesis in the mouse lateral ganglionic eminence

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: These findings suggest that physical interactions between Gsx2 and Ascl1 limit Ascl1:Ascl1 and Ascl1:Tcf3 interactions, and thereby inhibit Ascl1-dependennt neurogenesis and allow for progenitor expansion within the LGE.

overall_design: E12.5 mouse LGE cells were analyzed using 10X single-cell rna-seq

first: Kenneth

last: Campbell


title: Stringent-controlled stress adaption of Pseudomonas aeruginosa

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

summary:
Surfing motility is a complex adaptation that is different from swarming motility and requires the stringent stress response in Pseudomonas aeruginosa LESB58
Cystic fibrosis (CF) is a genetic disease that affects mucin-producing body organs such as the lungs. Characteristic of CF is the production of thick and sticky mucus that can lead to progressive airway obstruction. The glycoprotein mucin is the major macromolecular component of mucus. Recently, we identified that the presence of mucin induced a rapid surface adaptation termed surfing motility in motile bacteria. P. aeruginosa, the main colonizing pathogen in CF employs several stress coping mechanisms to survive the highly viscous environment of the CF lung. Here, RNA-Seq was used to study the stringent stress response in the hypervirulent CF isolate LESB58 (Liverpool Epidemic Strain) via transcriptional profiling. As the stringent response is regulated by relA and spoT, we created a double knockout of these genes in LESB58 to study the impact of these stress regulators on surfing motility using RNA-Seq.

overall_design: Three replicates each of wild type and mutant P. aeruginosa LESB58 were analyzed via RNASeq to determine effects of stringent response on surfing motility

first: Daniel

last: Pletzer

first: Evelyn

last: Sun

first: Caleb

middle: T

last: Ritchie

first: Lauren

last: Wilkinson

first: Leo

last: Liu

last: Trimble

first: Heidi

last: Wolfmeier

first: Robert

last: Hancock


title: Epigenetic profiling of EMT in pancreatic cancer cells

first: Salina

last: Yuan

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

overall_design: Refer to individual Series


title: Stabilizing heterochromatin by ZKSCAN3 safeguards hMSCs from senescence

city: Beijing

first: ji

middle: qian

last: zhao

address: 15 Datun Road Chaoyang District

institute: institute of zoology ,CAS

summary: Zinc finger protein with KRAB and SCAN domain 3 (ZKSCAN3), a transcriptional repressor, involves in multiple cellular functions. However, the functions of ZKSCAN3 in the homeostatic maintenance of human stem cells remains elusive. Here, we demonstrated that ZKSCAN3 was crucial for preventing human mesenchymal stem cells (hMSCs) from senescence in an autophagy-independent manner. Downregulation of ZKSCAN3 was observed in senescent hMSCs, and depletion of ZKSCAN3 led to premature aging in hMSCs. Further study uncovered that ZKSCAN3 maintained heterochromatin (HC) stability by interacting with heterochromatin associated proteins KAP1 and HP1 as well as nuclear envelope proteins Lamin B1, LBR and Emerin. Deficiency of ZKSCAN3 resulted in detachment of Lamina-associated domains (LADs) from the lamina, loss of heterochromatin and more accessible chromatin status within the heterochromatin and aberrant expression of repetitive sequences. Overexpression of ZKSCAN3, KAP1 or HP1 respectively rescued the senescent phenotypes in ZKSCAN3-/- hMSCs. Notably, reintroduction of ZKSCAN3 protein also retarded the cellular senescence in the replicative senescent hMSCs, as well as the pathological or physiological aging hMSCs. Together, our study reveals a novel, autophagy-independent role of ZKSCAN3 in the maintenance of heterochromatin stability and attenuation of hMSC senescence. Thus, ZKSCAN3 may be a candidate for alleviating human aging-related disorders.

overall_design: Multi-omics sequencing of ZKSCAN3+/+ and  ZKSCAN3-/-  hMSCs.

first: Guanghui


title: Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development [RNA-Seq]

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: Copenhagen University

summary: Aim: Innate circadian rhythms are critical for optimal tissue-specific functions, including skeletal muscle, a major insulin-sensitive tissue responsible for glucose homeostasis. We determined whether transcriptional oscillations are associated with CpG methylation changes in skeletal muscle. Materials & methods: We performed rhythmicity analysis on the transcriptome and CpG methylome of circadian synchronized myotubes. Results: We identified several transcripts and CpG-sites displaying oscillatory behavior, which were enriched with GO terms related to metabolism and development. Oscillating CpG methylation was associated with rhythmic expression of 31 transcripts. Conclusion: Although circadian oscillations may be regulated by rhythmic DNA methylation, strong rhythmic associations between transcriptome and CpG methylation were not identified. This resource constitutes a transcriptomic/epigenomic atlas of skeletal muscle and regulation of circadian rhythms.

overall_design: Time course in triplicate of C2C12 cells in 6h time intervals from 12h til 60h after synchronization by serum shock.

last: Altıntaş

first: Rhianna

last: Laker

first: Christian

last: Garde

first: Romain

last: Barrès

first: Juleen

last: Zierath


title: Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2/3 islands located in genomic euchromatin

city: Montpellier

first: Giacomo

last: Cavalli

address: IGH - CNRS, 141, rue de la Cardonille

institute: CNRS

summary: We aim to investigate the spatial contacts between heterochromatin domain and the euchromatic genome. We found that euchromatic transposable elements, which are usually associated with H3K9me2 enrichment, are in 3D contacts with the main heterochromatin domain

overall_design: genomic DNA sequencing of Drosophila melanogaster Oregon-R w1118

first: Yuh

last: Lee

first: Yuki

last: Ogiyama

first: Nuno

last: Martins

first: Brian

last: Beliveau

first: David

last: Acevedo

first: C-ting

last: Wu

first: Gary

last: Karpen


title: Epigenetic profiling of EMT in pancreatic cancer cells (ChIP-seq)

city: Philadelphia

address: 421 Curie Blvd

institute: University of Pennsylvania

summary: Epithelial plasticity – reversible modulation of a cell’s epithelial and mesenchymal features – is associated with cancer metastasis and chemoresistance. This process is classically driven by a small cohort of transcription factors, several of which have been reported to functionally interact with epigenetic modifiers at the promoters of key epithelial and mesenchymal genes. However, the extent to which epigenetic changes underlie epithelial plasticity at the genomic level remains largely unknown. Here we show that genome-wide regulation of a single histone mark, H3K36me2, is critical for establishing stable epithelial-mesenchymal states in various genetic, chemical, and cellular contexts. Through targeted CRISPR-Cas9 screening, we discovered two histone-modifying enzymes involved in the writing and erasing of H3K36me2 that act reciprocally to regulate epithelial-mesenchymal identity, tumor differentiation, and metastasis. Using genetic approaches to inhibit H3K36me2, we found that modulation of the mark itself is a conserved mechanism underlying the mesenchymal state. Although H3K36me2 is distributed broadly throughout the genome, it is associated with altered enhancer activity affecting a relatively small number of genes, including those associated with master epithelial-mesenchymal regulatory factors. Our results thus outline an epigenome-scale mechanism by which a specific histone modification regulates cellular plasticity in cancer.

overall_design: 18 samples were sequenced for 4 histone marks (H3K36me2, H3K27ac, H3K4me1, H3K27me3) in duplicate and inputs. Comparison groups include WT and sgNsd2 mouse pancreatic cancer cells from the Panc02 cell line. Sonicated Drosophila melanogaster DNA was spiked into each sample at 1-2.5% of mouse chromatin.

first: Ben

middle: Z

last: Stanger


title: Epigenetic profiling of EMT in pancreatic cancer cells (RNA-seq)

first: Salina

last: Yuan

overall_design: 28 samples were sequenced with duplicates. Samples include wild type, sgNsd2, sgKdm2a, and Tgf-b treatment.


title: Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties

status: Public on Mar 10 2020

city: New York

first: Joseph

last: Devlin

state: NY

address: 430 East 29th Street

institute: New York University Langone Health


title: Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties [scRNA-seq]

summary: Tissue-resident macrophages are a diverse population of cells that perform specialized functions including sustaining tissue homeostasis and tissue surveillance. Here we report an interstitial subset of CD169+ lung-resident macrophages that are transcriptionally and developmentally distinct from alveolar macrophages (AMs). They are primarily localized around the airways and are found in close proximity to the sympathetic nerves located in the bronchovascular bundle. These nerve- and airway-associated macrophages (NAMs) are tissue-resident, yolk sac-derived, self-renewing, and do not require CCR2+ monocytes for development or maintenance. Unlike AMs, the development of NAMs requires CSF1, but not GM-CSF. Bulk population and single cell transcriptome analysis indicated that NAMs are distinct from other lung resident macrophage subsets and highly express immunoregulatory genes under steady state and inflammatory conditions. NAMs proliferated robustly following influenza infection and activation with the TLR ligand poly I:C, and in their absence, the inflammatory response was augmented resulting in excessive production of inflammatory cytokines and innate immune cell infiltration. Overall, our study provides insights into a distinct subset of airway-associated pulmonary macrophages that function to maintain immune and tissue homeostasis.

overall_design: Diverse population of lung resident macrophages characterization in naïve mice by scRNA-seq

first: Basak

middle: B

last: Ural

first: Stephen

last: Yeung

first: Kamal

last: Khanna


title: yongqianghou_data

first: Yongqiang

last: Hou


title: Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties [bulk-seq]

overall_design: Diverse population of lung resident macrophages characterization in naïve mice by bulk RNA-seq


title: RNA Sequencing Facilitates Quantitative Analysis of Wild Type and FAK-/- Wnt1 driven mammary tumor cell transcriptomes

first: Jun

middle: lin

last: Guan

address: 3125 Eden Ave

department: Cancer Biology

institute: University of Cincinnati

summary: We examined FAK deletion induced changes in various cellular processes and signalling pathways in an unbiased manner by transcriptomic analysis

overall_design: Tumor cells were isolated from MMTV-Wnt1 Fak flox/flox mice. Tumor cells were then transduced with Cre-ERT and deletion of FAK was induced by treating with 100 nM OHT for 3days. RNA was isolated from untreated cells serving as controls and treated cells with FAK deletion and subjected to RNA sequencing.

first: Paul

last: Ritama

first: Jun-lin

first: Yeo

last: Kok


title: Single cell RNA sequencing of P7 cortex from Top1 knockout mice

city: Chapel Hill

first: Jesse

last: Niehaus

state: NC

address: 116 Manning Drive, 7008B Mary Ellen Jones Building

department: Neuroscience Center

institute: University of North Carolina at Chapel Hill

summary: Topoisomerase 1 (TOP1) relieves torsional stress in DNA during transcription and facilitates the expression of long (>100 kb) genes, many of which are important for neuronal functions. To evaluate how loss of Top1 affected neurons in vivo, we conditionally deleted (cKO) Top1 in postmitotic excitatory neurons in the mouse cerebral cortex and hippocampus. We found that Top1 cKO neurons developed properly but then showed biased transcriptional downregulation of long genes, signs of DNA damage, neuroinflammation, increased poly(ADP-ribose) polymerase-1 (PARP1) activity, single-cell somatic mutations, and ultimately degenerated. We used single-cell RNA-seq to verify cell-type decreases in long-gene expression as well as investigate how TOP1 loss may lead to premature neuronal death.

overall_design: Topoisomerase I(Top1) f/f mice were crossed with Top1 f/+; NEX-cre mice to generate Top1 f/f; NEX-cre animals where Top1 is conditionally knocked out of cortical and hippocampal excitatory neurons. Cortical tissue was dissociated into single-cell suspensions from Top1 f/f;NEX-cre mice (n=2) and littermate controls (NEX-cre negative; n=2)  at postnatal day 7. Single-cell transcriptomes were generated using the microfluidic approach known as Dropseq.

first: Giulia

last: Fragola

middle: K

first: Mark

middle: J

last: Zylka


title: Canonical Wnt/β-catenin activity and differential epigenetic marks direct sexually dimorphic regulation of Irx3 and Irx5 in developing mouse gonads

city: Durham

first: Sara

middle: A.

last: Garcia-Moreno

state: North Carolina

address: Nanaline Bldg. Research Drive

institute: Duke University

summary:
Irx3 and Irx5 are important for oocyte and
follicle survival within the developing ovary, but their regulation had not been elucidated.
Methods: XX and XY supporting cells of the gonad were FACS-purified at E13.5, and submitted to ChIP-seq for H3K27me3 and H3 as a means to normalize across cell populations.
Results: We identified TCF/LEF-binding sequences within two distal enhancers of the IrxB locus that promote β-catenin responsive ovary expression. Meanwhile, Irx3 and Irx5 transcription is suppressed
within the developing testis by the presence of H3K27me3 on these
same sites.

overall_design: ChIP-seq for H3 and H3K27me3 was performed in duplicate on FACS-sorted  XX and XY gonadal supporting cells from E13.5 mouse embryonic gonads.

first: Megan

last: Koth