title: Dual recognition of H3K4me3 and H3K27me3 by bivalent histone reader SHL regulates plant flowering

status: Public on May 31 2019

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

country: USA

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SHL genome-wide binding sites were investigated by ChIP sequencing,

overall_design: Arabidopsis wild-type Col (containing no FLAG-tagged transgene) and SHL-FLAG (containing FLAG-tagged transgenic SHL), plants were subject to ChIP-sequecing analysis using the FLAG beads.

first: Ray

last: Scheid


title: Function of l-Pipecolic acid as a compatible solute in Corynebacterium glutamicum as the basis for its production under hyperosmolar conditions

city: Bielefeld

first: Fernando

last: Pérez-García

address: Universitaetsstr. 25

country: Germany

institute: University of Bielefeld

type: Expression profiling by high throughput sequencing

summary: Pipecolic acid or L-PA is a cyclic amino acid derived from L-lysine which has gained interest in the recent years within the pharmaceutical and chemical industries. L-PA can be produced efficiently using recombinant Corynebacterium glutamicum strains by expanding the natural L-lysine biosynthetic pathway. We show that de novo synthesized or externally added L-PA partially is beneficial for growth under hyper-osmotic stress conditions. C. glutamicum cells accumulated L-PA under elevated osmotic pressure and released it after an osmotic down shock. The proline permease ProP was identified as a candidate L-PA uptake system since RNAseq analysis revealed increased proP RNA levels upon L-PA production

overall_design: mRNA profiles of a C. glutamicum pipecolic acid producer compared with the mRNA profiles of a C. glutamicum proline producer. Samples were generated in triplicated and pooled

first: Luciana

last: Fernandes de Brito

first: Volker

last: Wendisch


title: Adipose tissue RNAseq in T-cell-specific IFNAR-deficient mice.

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: We sequenced whole adipose tissue from control and LCMV infected mice 6dpi, in control vs T cell-specific IFNAR knockoutmice to understand the transcriptional changes in adipose tissue upon loss of type I IFN-T cell singaling axis, and how it contributes to cachexia.

overall_design: inguinal fat pad (after removing iLN) was used for sequencing in control and infected mice (LCMV clone13 2x10^6PFU), this was done in two genotypes (IFNARfl/fl) as controls, vs (IFNARfl/fl-CD4cre/+) as T-cell specific IFNAR knockouts.

first: Hatoon

last: Baazim

first: Alexandra

last: Popa


title: Gene expression alternations in the offspring adipose from chromium restriction diet dams

status: Public on May 30 2019

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

summary: Maternal chromium restriction may disturb susceptibility in offspring. Adipose from maternal chromium diet has 85 up- and 109 down- regulated genes, compared to control. Especially, PPAR signaling pathway was affected.

overall_design: We performed microarray analyses of offspring adipose from chromium restriction dams and control diet dams at 32 week (n=3 per group).

first: Xiaofang

last: Sun

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Zhixin

last: Wang

first: Cuijuan

last: Qi

first: Tong

first: Xiaojing


title: MiRNA expression alternations in the offspring liver from chromium restriction diet dams

summary: Maternal chromium restriction may disturb susceptibility in offspring. Liver from maternal chromium diet has 8 up- and 6 down- regulated miRNAs, compared to control.

overall_design: We performed miRNA array analyses of offspring adipose from chromium restriction dams and control diet dams at 16 week (n=3 per group).


title: MiRNA expression alternations in the offspring adipose from chromium restriction diet dams

summary: Maternal chromium restriction may disturb susceptibility in offspring. Adipose from maternal chromium diet has 6 up- and 8 down- regulated miRNAs, compared to control.


title: Reduction of Protein Kinase A-mediated Phosphorylation of ATXN1-S776 in Purkinje Cells Delays Onset of Ataxia in a SCA1 Mouse Model.

city: Minneapolis

first: Harry

middle: T

last: Orr

state: MN

address: 2101 6th Strreet SE

department: Laboratory Medicine and Pathology

institute: University of Minnesota

summary: Spinocerebellar ataxia type 1 (SCA1) is a polyglutamine (polyQ) repeat neurodegenerative disease in which a primary site of pathogenesis are cerebellar Purkinje cells. In addition to polyQ expansion of ataxin-1 protein (ATXN1), phosphorylation of ATXN1 at the serine 776 residue (ATXN1-pS776) plays a significant role in protein toxicity. Utilizing a biochemical approach, pharmacological agents and cell-based assays, including SCA1 patient iPSC-derived neurons, we examine the role of Protein Kinase A (PKA) as an effector of ATXN1-S776 phosphorylation. We further examine the implications of PKA-mediated phosphorylation at ATXN1-S776 on SCA1 through genetic manipulation of the PKA catalytic subunit Cα in Pcp2-ATXN1[82Q] mice. Here we show that pharmacologic inhibition of S776 phosphorylation in transfected cells and SCA1 patient iPSC-derived neuronal cells lead to a decrease in ATXN1. In vivo, reduction of PKA-mediated ATXN1-pS776 results in enhanced degradation of ATXN1 and improved cerebellar-dependent motor performance. These results provide evidence that PKA is a biologically important kinase for ATXN1-pS776 in cerebellar Purkinje cells.

overall_design: Cerebellar mRNA profiles of 8-9 week old wild type (WT), Atxn1[82Q] knockin and Atxn1[82Q]CαLoxM120A mice were generated by deep sequencing, 5 replicates per treatment, using Illumina HiSeq2500.

first: Christine

last: Henzler

first: Sarita

last: Lagalwar


title: Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation

status: Public on May 29 2019

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

type: Methylation profiling by high throughput sequencing

summary: Transposable elements (TEs) are largely inactive. Interestingly, a subset of TEs are naturally expressed in the vegetative cell (VC) of the male gametophyte, pollen in Arabidopsis. However, the extent and mechanism of such TE activation were unknown. Through RNA-seq, we identified pollen-activated TEs and annotated the transcriptional start sites (TSSs) and transcriptional termination sites (TTSs) using a program called Mikado. We have previously shown that H1 is expressed in sperm but not in VC, which prompted us to ectopically express H1 in VC for studying TE regulation through RNA-seq and bisulfite-seq. Our RNA-seq data shows that H1 expression in VC represses some of pollen-activated TEs. Furthermore, bisulfite-seq data from the pollen nuclei isolated via fluorescence-activated cell sorting (FACS) shows that H1 expression in VC increases DNA methylation of some of H1-repressed TEs around their TSSs, while leaving other H1-repressed TEs unchanged in DNA methylation. Our results indicate that H1 represses TE expression through both DNA methylation-dependent and -independent mechanisms and that natural depletion of H1 in VC allows TEs to be activated.

overall_design: To identify pollen-activated TEs, we did RNA-seq using pollen grains from WT and four replicates were included. To find out if H1 expression in VC can repress TE expression, we performed RNA-seq using pollen grains from WT or pVC::H1 with three replicates being done for each genotype. Bisulfite-seq was performed using sperm nuclei (SN) and vegetative nuclei (VN) from WT as well as VN from pVC::H1. By comparing WT SN with WT VN, we want to show if pollen-activated TEs are regulated by DEMETER-mediated DNA demethylation and if H1 represses TE expression through DNA methylation regulation.

first: Shengbo

last: He

first: Martin

last: Vickers

first: Jingyi


title: Gene expression variation in grape transgenic calli lines

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

institute: University of Chinese Academy of Sciences

summary: RNA-seq was used to assess gene expression variation in transgenic calli lines expressing Vitis vinifera chardonnay VvSWEET10 gene.

overall_design: three controls and three grape transgenic calli lines

first: Zhan

first: Zhenchang

last: Liang


title: Transcriptome analysis of erythroblastic island macrophages

city: zhengzhou

first: huizhi

last: zhao

address: No.100 Science Avenue

institute: zhengzhou university

summary: The erythroblastic island (EBI), composed of a central macrophage and surrounding erythroid cells, was the first hematopoietic niche discovered. The identity of EBI macrophages has thus far remained elusive. Gene expression profiles of BM F4/80+Epor-eGFP+ macrophages suggest a specialized function in supporting erythropoiesis.

overall_design: Examination of 2 different macrophage types from mouse bone marrow

first: An

last: Xiuli


title: Acetic Acid Treatment Enhances the Drought Avoidance in Cassava (Manihot esculenta Crantz)

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

summary: External application of acetic acid has been recently reported to enhance the survival to drought in plants such as Arabidopsis, rapeseed, maize, rice and wheat, but the effects of acetic acid application on increased drought tolerance in woody plants such as a tropical crop “cassava” remain elusive. A molecular understanding of acetic acid-induced drought avoidance in cassava will contribute to the development of technology that can be used to enhance drought tolerance without resorting to transgenic technology or advancements in cassava cultivation. In the present study, morphological, physiological and molecular responses to drought were analyzed in cassava after the treatment with acetic acid. Results indicated that the acetic acid-treated cassava plants had a higher level of drought avoidance than water-treated, control plants.  Specifically, higher leaf relative water content, and chlorophyll and carotenoid levels were observed as soils dried out during the drought treatment. Leaf temperatures in acetic acid-treated cassava plants were higher relative to leaves on plants pretreated with water and the increase of ABA content was observed in leaves of acetic acid-treated plants, suggesting that stomatal conductance and the transpiration rate in leaves of acetic acid-treated plants decreased to maintain relative water contents and avoid drought. Transcriptome analysis revealed that the acetic acid treatment increased the expression of ABA signaling-related genes, such as OPEN STOMATA 1　(OST1) and protein phosphatase 2C; as well as drought response and tolerance-related genes, such as outer membrane tryptophan-rich sensory protein (TSPO), and heat shock proteins. Collectively, the external application of acetic acid enhances drought avoidance in cassava through the upregulation of ABA signaling pathway genes and several stress response- and tolerance-related genes. These data support the idea that adjustments of the acetic acid application to plants is useful to enhance drought tolerance in order to minimize the growth inhibition in the agricultural field.

overall_design: After reaching an approximate stem length of approximately 15 cm from soil surface, the plants were transferred to a plastic pot (7.9 diameter x 6 height cm) with vermiculite. After transfer, they were incubated at 28 degree in a greenhouse for 2 weeks and used as experimental samples. The plants of approximately 20 cm stem were treated with 10 mM acetic acid or water (control) for 7 days, and exposed to drought treatments for 14 days. Total RNA was prepared from the first to third leaves from top of three plants and used for the microarray hybridization. One replicative hybridization experiment was performed using the independent biological samples.

first: Yoshinori

last: Utsumi

first: Chikako

first: Maho

last: Tanaka

first: Chien

middle: V

last: Ha

first: Satoshi

last: Takahashi

first: Akihiro

last: Matsui

first: Tomoko

middle: M

last: Matsunaga

first: Sachihiro

first: Yuri

last: Kanno

first: Mitsunori

last: Seo

first: Yoshie

last: Okamoto

first: Erika

last: Moriya

first: Motoaki

last: Seki


title: Ribonucleotide excision repair is essential to prevent skin cancer [CD45+ CD49f- epidermal cells]

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: Heidelberg University Hospital

summary: Large numbers of ribonucleotides are incorporated into the eukaryotic nuclear genome during S-phase due to imperfect discrimination against ribonucleoside triphosphates by the replicative DNA polymerases. Ribonucleotides, by far the most common DNA lesion in replicating cells, destabilize the DNA, and an evolutionarily conserved DNA repair machinery, ribonucleotide excision repair (RER), ensures ribonucleotide removal. Complete lack of RER is embryonically lethal. Partial loss-of-function mutations in the genes encoding subunits of RNase H2, the enzyme essential for initiation of RER, cause the SLE-related type I interferonopathy Aicardi-Goutières syndrome. Here we establish that selective inactivation of RER in mouse epidermis results in spontaneous DNA damage, epidermal hyperproliferation associated with loss of hair follicle stem cells and hair follicle function. The animals develop keratinocyte intraepithelial neoplasia and invasive squamous cell carcinoma with complete penetrance, despite potent type I interferon production and skin inflammation. Compromised RER-mediated genome maintenance might represent an important tumor-promoting principle in human cancer.

overall_design: CD45+ CD49f- cells were were isolated from skin cell suspensions by FACS. Total RNA was isolated using the RNeasy Micro Kit+ (Qiagen). mRNA libraries were prepared using a SMART protocol and subjected to deep sequencing on an Illumina®HiSeq 2500.

first: Rayk

last: Behrendt


title: Ribonucleotide excision repair is essential to prevent skin cancer [CD49f+ epidermal cells]

overall_design: Keratinocytes (CD49f+) cells were isolated from skin cell suspensions by FACS. Total RNA was isolated using the RNeasy Mini Kit+ (Qiagen). mRNA libraries were prepared and subjected to deep sequencing on an Illumina®HiSeq.


title: DNA methylation alternations in the offspring liver from chromium restriction diet dams

first: Qian

last: Zhang

type: Methylation profiling by genome tiling array

summary: Maternal chromium restriction may disturb susceptibility in offspring. Adipose from maternal chromium diet has 935 genes that exhibit differential DNA methylationregulated compared to control.

overall_design: We performed DNA methylation array analyses of offspring liver from chromium restriction dams and control diet dams at 32 week (n=3 per group).

first: Xiaofang

last: Sun

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Zhixin

last: Wang

first: Cuijuan

last: Qi

first: Tong

first: Xiaojing


title: Human gut derived-organoids as model to study gluten response and effects of microbiota bioproducts in celiac disease

city: Boston

first: Stefania

last: Senger

state: MA

address: 114, 16th st. Charlestown, Navy Yard

department: Pediatrics

institute: Massachusetts General Hospital

summary: Celiac disease (CeD) is an intestinal immune-mediated disorder caused by gluten ingestion in genetically predisposed subjects. CeD is characterized by villous atrophy, altered intestinal permeability, crypt hyperplasia and innate and adaptive immune response. This study aimed to develop and validate the use of intestinal organoids from celiac patients to study CeD. A repository of organoids from duodenum of non-celiac and celiac patients was generated and characterized accordingly to standard procedures. RNA-seq analysis was employed to study the global gene expression program of CeD (n=3) and non-CeD (n=3) organoids sets. While the three celiac derived organoids shared similar transcriptional signatures the NC samples set appeared more heterogeneous. We found 486 genes differentially expressed between the two groups. Of them, 299 genes were downregulated (FC<2; FDR<0.05) and 187 were upregulated in CeD (FC >2; FDR<0.05). We observed CeD organoids had significantly altered expression of genes associated with barrier function, innate immunity, and stem cell function.

overall_design: mRNA profiles of 3 non-celiac healthy controls and 3 celiac organoids derived from duodenal biopsies.

first: Rachel

last: Freire

first: Gloria

last: Serena

first: Laura

last: Ingano

first: Ruslan

last: Sadreyev

first: Anna

last: Sapone

first: Dennis

last: Kasper

first: Alessio

last: Fasano


title: Quantitative profiling of the UGT transcriptome in human drug metabolizing tissues [Total RNA]

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

country: Canada

institute: Laval University

summary:
Purpose: Maintenance of cellular homeostasis and xenobiotics detoxification relies on the glucuronidation pathway mediated by 19 human UDP-glucuronosyltransferase enzymes (UGTs) encoded by 10 highly homologous genes. Recent evidence suggests that alternative splicing largely expands the human UGT transcriptome.
Results: we establish the quantitative portrait of the UGT transcriptome in major metabolic organs. RNA sequencing uncovered that AS significantly shapes the UGT transcriptome, with variants quantitatively representing up to 35% and 60% UGT transcripts in normal and tumoral tissues respectively. Novel distinctive in-frame sequences were present in 20% alternative transcripts, which potentially encode UGT isoforms with distinct structural and functional features.
Conclusions: This work exposes the important quantitative and biological significance of alternative UGT expression likely creating unparalleled protein diversity evolving from enzymes to regulators of cell metabolism.

overall_design: Total RNA was extracted from liver, kidney, intestine and colon from multiple human donors. RNA-sequencing was conducted with a Illumina HiSeq 2500 system

first: Alan

last: Tourancheau

first: Michèle

last: Rouleau

first: Arnaud

last: Droit


title: Modulation of Macrophage Subpopulation Response in Radiation-Treated Gliomas Circumvents Tumor Recurrence

city: Philadelphia

first: Robert

middle: L

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

summary: Thorough examination of tumor associated macrophage/microglia have shed light into their pro-tumorigenic functions in glioblastoma multiforme (GBM) development and progression. However, the dynamic evolution of these two ontogenically distinct macrophage subpopulation in the course of therapeutic response and recurrence is unknown. We employed multiple mouse models of GBM to show that infiltrating bone marrow derived macrophages (BMDM) and brain resident microglia (MG) content and phenotype are altered post radiotherapy. We identified IR specific and stage-dependent shared and distinct BMDM and MG signatures, and demonstrated that only dual targeting of these populations using CSF-1R inhibition combined with IR led to a sustained overall survival. Our findings establish that plasticity underlie macrophage evolution in the irradiated tumor microenvironment, and reveals the therapeutic potential of their targeting to enhance the efficacy of standard of care treatment in GBM.

overall_design: Paired Microglia (MG) and bone marrow-derived macrophages (BMDM) were isolated from Vehicle (n=4) mice or mice treated with the following condiitons:  5-days BLZ945 (n=4), 5-days BLZ945+IR (n=3), 5-days IR (n=2), recurrent BLZ945 (n=2), recurrent IR (n=4), and recurrent IR+BLZ945 (n=4).  RNA was isolated and RNA-sequencing was performed to assess how BMDM and MG respond to different types of therapy in both regressing and progressing tumors,

first: Leila

last: Akkari

first: Johanna

last: Joyce


title: Distinct requirements of CHD4 during B cell development and antibody response

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Immunoglobulin heavy chain (Igh) class switch recombination (CSR) requires B cell proliferation, germline transcription, AID-instigated generation of DNA double strand breaks and DNA end-joining. How these various DNA-protein interactions and DNA transactions at Igh occur within the context of the chromatin landscape are largely unknown. Histone post-translational modifications can modulate chromatin accessibility and one such epigenetic mark, H3K9me3 is present at activated Igh switch sequences that serve as recombination targets during CSR. The chromatin remodeling protein CHD4 binds H3K9me3 and shapes chromatin accessibility and gene expression in various cell types, but its role in B cell biology is yet to be elucidated. Here, we conditionally ablated CHD4 expression in different stages of B cell development. We find that while CHD4 is essential for early B cell development, it is dispensable for homeostatic maintenance of mature naïve B cells and differentiation into antigen-specific early memory B cells and plasmablasts. However, loss of CHD4 in activated B cells leads to a severe defect in CSR, accompanied by markedly impaired cellular proliferation. Conditional deletion of p53 rescued the proliferation defect but failed to restore CSR due to a failure of AID to be efficiently recruited to Igh. This work unmasks a context-dependent role of CHD4 in B cell development and identifies CHD4 as a novel effector of CSR that influences B cell proliferation and recruitment of AID to Igh.

overall_design: RNA-seq was performed on purified splenic B cells unstimulated (0hr) or stimulated ex vivo with LPS (10μg/ml) plus mouse IL4 (25ng/ml) for 48 hrs.

first: Jayanta

last: Chaudhuri


title: Ultrasound-directed emergence of pluripotent-like spheroids from human fibroblasts

city: Incheon Metropolitan City

first: Yong Seung

last: Lee

address: SimGokro 100gil 25

department: College of Medicine

country: South Korea

institute: Catholic Kwandong University

summary: We have developed a gene- and chemical-free method of generating pluripotency from HDF cell, we called pluripotent-like spheroids yielded by ultrasonic stimulus (Physics).  Physics were very similar to embryoid bodies (EB) in terms of cluster formation, pluripotency with three germ layer markers, and multi-lineage differentiation potential.

overall_design: To microarrys assay, cells were cultured period to 6 or 40 days with hESC medium after ultrasound stimulus.

first: Yong

middle: S

first: Hyejung

last: Heo

first: Jonghwan

first: Ki-Sung

last: Hong

first: Hyeok

last: Jang

first: Sung

middle: U

last: Moon

first: Hana

last: Gu

first: Woon

middle: Y

last: Jung

first: Seung-Hun

last: Oh

first: Soonhag

last: Kim


title: Identification of monocyte-like precursors of granulocytes as a mechanism for accumulation of PMN-MDSC in cancer

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) inhibit immune responses in cancer, limit the effects of therapies and promote tumor cell metastasis. Here, we have identified a new precursor that differentiates into granulocytes in vitro and in vivo yet belong to the monocytic lineage. We have termed these cells monocyte-like precursors of granulocytes (MLPG). Under steady state conditions MLPG were absent in the spleen and barely detectable in the bone marrow (BM). In contrast, these cells significantly expanded in tumor-bearing mice. Selective depletion of monocytic cells had no effect on the number of granulocytes present in naïve mice but decreased the population of PMN-MDSC in tumor-bearing mice by 50%. The expansion of MLPG was found to be controlled by the down-regulation of the protein Rb1 and not the IRF8 transcription factor that is known to regulate the expansion of PMN-MDSC from classical granulocytes precursors. In cancer patients, putative MLPG were found within the population of CD15 CD14+HLA-DR-/lo M-MDSC. CXCR1+CD15 CD14+HLA-DR-/lo cells lacked immune suppressive activity but had potential to differentiate to neutrophils in contrast to monocytes and CXCR1- suppressive M-MDSC. These findings describe a mechanism of abnormal myelopoiesis in cancer and suggest potential new approaches for selective targeting of MDSC.

overall_design: RNA-seq gene expression of monocytes and M-MDSC cells in tumor burden patients

first: Jerome

last: Mastio

first: Dmitry

middle: I

last: Gabrilovich


title: Comparison of gene expression in the long-lived hsb-1 mutant and hsf-1 overexpression C. elegans strains

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary:
Purpose: We used RNA-Seq to compare the gene expression profiles in two long-lived C. elegans strains: (1) animals with a loss-of-function mutation in the hsb-1 gene, and (2) animals overexpressing hsf-1 under its endogenous promoter. Previous studies indicated that life span extension in both these strains is hsf-1-dependent.
Methods: mRNA-Seq profiles for three biological replicates each of day 1 adult wild-type (N2 strain), hsb-1 mutant and hsf-1 overexpression strains were generated using 50 bp single-end sequencing on an Illumina HiSeq 2500 platform. The sequencing reads that passed quality control were aligned to the C. elegans reference transcriptome (WS220 release) using Bowtie 2 and splicing junctions were mapped using TopHat. Cufflinks was used to calculate FPKM values and CuffDiff 2 was used to identify differentially expressed genes based on the following two criteria: false discovery rate (FDR)-adjusted p value < 0.05 and fold-change ≥ 1.5.
Results: Using our mRNA-Seq workflow, we mapped at least 14 million reads per sample to the C. elegans transcriptome at greater than 96 percent alignment rate for the raw reads. Expression of 7,478 genes was found to be significantly altered in the hsf-1 overexpression strain relative to wild-type worms, while only 1,855 genes had singnificantly different expression in the hsb-1 mutant strain relative to wild-type. Using our criterion of ≥ 1.5-fold change in gene expression, we found 1,820 and 662 genes to be differentially expressed relative to wild-type in hsf-1 overexpression and hsb-1 mutant strains, respectively. The 247 genes that were differentially expressed in both hsf-1 overexpression and hsb-1 mutant strains showed a strongly correlated expression pattern in the two strains.
Conclusions: hsf-1 overexpression induces global transcriptional suppression in C. elegans. Genetic ablation of hsb-1 produces similar life span extension in worms as hsf-1 overexpression, but alters expression of a much smaller subset of the C. elegans transcriptome. Hence, HSB-1 is a specific regulator of the transactivation potential of HSF-1 that selectively modulates gene expression relevant to longevity determination in worms.

overall_design: Whole animal mRNA profiles of day 1 adult wild-type (N2 strain), hsb-1 mutant and hsf-1 overexpression strains were generated, in triplicates, using 50 bp single-end sequencing on an Illumina HiSeq 2500 platform.

first: Sural

last: Surojit

first: Ao-Lin

last: Hsu


title: Von Hippel-Lindau Acts as a Metabolic Switch Controlling Nephron Progenitor Differentiation

city: Pittsburgh

first: Andrew

middle: Scott

last: Clugston

address: 872 Mirror Street

department: Integrative Systems Biology

institute: University of Pittsburgh

summary: RNA sequencing was performed on VHLNP+/- and VHLNP-/- E17.5 isolated nephron progenitors. E17.5 kidneys were dissected and screened using the GFP expression. Dissected kidneys that expressed GFP were dissociated into single cell suspensions and FACS sorted; each sample consisted of approximately 150,000 pooled nephron progenitor cells. RNA was extracted using the RNeasy Micro Kit (Qiagen). The Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh performed library construction and RNA sequencing (single-end reads, 75bp). Bioinformatics quality control was performed using FastQC (version 0.11.5), and adapters were trimmed using BBDuk from the BBMap software package (version 37.41). Reads were aligned to transcripts assembled from the mm10 genome (GRCm38, GENCODE M17 ) using the Spliced Transcripts Alignments to a Reference software package (STAR, version 2.5.3a). Reads aligned to known transcripts were counted using the Bioconductor GenomicAlignments R package (version 1.10.1), and differential expression between VHLNP+/- and VHLNP-/- kidney samples was calculated using DESeq2 (version 1.18.1). Expression levels of 245 genes were identified as significantly altered between VHLNP+/- and VHLNP-/- samples (padj <= 0.05, fc > 2).

overall_design: Measurement of mRNA expression in isolated a cell type with a homozygous gene knockout versus a heterozygous control.

first: Kasey

last: Cargill

first: Anjana

last: Murali

first: Elina

last: Mukherjee

first: Daniel

last: Bushnell

first: Jiao

last: Liu

first: Zubaida

last: Saifudeen

first: Jacqueline

last: Ho

first: Dennis

last: Kostka

first: Carlton

last: Bates

first: Eric

last: Goetzman

first: Sunder

last: Sims-Lucas


title: Toxic C9orf72 poly(PR) binds heterochromatin, disrupts HP1α and causes dsRNA accumulation

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

summary: How G4C2 repeat expansions in C9orf72 cause frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is not understood. Here, we report the first mouse model to express poly(PR), a dipeptide repeat protein synthesized from expanded G4C2 repeats. Expression of GFP-(PR)50 throughout the mouse brain yielded progressive brain atrophy, neuron5 loss, loss of poly(PR)-positive cells and gliosis, culminating in motor and memory impairments. We found that poly(PR) bound DNA, localized to heterochromatin, and caused abnormal histone methylation, lamin invaginations, decreases in HP1α expression, and disruptions of HP1α liquid phases. These aberrations of histone methylation, lamins and HP1α, which regulate heterochromatin structure and gene expression, were accompanied by repetitive element10 expression and double-stranded RNA accumulation. Thus, we uncover new mechanisms by which poly(PR) contributes to c9FTD/ALS pathogenesis.

overall_design: Examination of  transcriptome profiles using RNA-seq on 3 month old mice expressing PR and GR polypetides with an AAV expression vector. The Poly(PR) analysis consisted of 7 mice expressing AAV-GFP-(PR)50 and 4 AAV-GFP harvest-matched controls. The Poly(GR) analysis consisted of 4 mice expressing AAV-GFP-(GR)100 and 4 AAV-GFP harvest-matched controls.

first: Yong-Jie

last: Zhang

first: Lin

last: Guo

first: Patrick

middle: K

last: Gonzales

middle: D

first: James

last: Shorter

first: Leonard

last: Petrucelli


title: Ribonucleotide excision repair is essential to prevent skin cancer

first: Axel

last: Roers

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

overall_design: Refer to individual Series


title: Gene expression of Cholangiocarcinoma patients derived organoids and matching biopsy

city: Glasgow

first: Chiara

last: Braconi

address: Switchback road

department: Wolfson Wohl Cancer Research Centre

institute: University of Glasgow

summary: Gene expression was compared between PDO and matching FFPE tissue

overall_design: Patients Derived Organoids (PDO) were established from a biopsy core of a patient with intrahepatic chemotherapy refractory cholangiocarcinoma, while a matching core was processed through formalin fixation and paraffin embedding. PDOs were cultured and expanded; RNA was extracted from PDOs and matching FFPE tissue and subjected to nanostring analysis for gene expression.


title: Distinct modes of cell competition shape mammalian tissue morphogenesis

city: New York

first: Nicholas

last: Gomez

address: 1230 York Ave

department: Laboratory of Mammalian Cell Biology and Development

institute: Rockefeller Univeristy

summary: Cell competition (CC)—the sensing and elimination of less fit “loser” cells by neighbouring “winner” cells—was first described in Drosophila. Although proposed as a selection mechanism to optimize tissue and organ development, its evolutionary generality remains unclear. Here, by employing live-imaging, lineage-tracing, single cell transcriptomics and genetics, we unearth two intriguing CC mechanisms that sequentially shape and maintain stratified tissue architecture during mouse skin development. Early in embryonic epidermis, winner progenitors within the single-layered epithelium kill and clear neighbouring losers by engulfment. Upon stratification and skin barrier formation, the basal layer instead expels losers through a homeostatic upward flux of differentiating progeny. This CC switch is physiologically relevant, as when it is perturbed, so too is barrier formation. Our findings establish CC as a selective force to optimize function of a vertebrate tissue, but also illuminate how a tissue dynamically adjusts its CC strategies to preserve fitness as it encounters increased architectural complexity during morphogenesis.

overall_design: Single cell RNA sequencing experiments were performed on wildtype and/or Mycn+/- primary murine epidermal cells isolated from two embryonic time points (E12.5 and E17.5).

first: Stephanie

last: Ellis

first: Aaron

middle: F

last: Mertz

first: Yejing

last: Ge

first: John

last: Levorse

first: Elaine

last: Fuchs


title: The WT1-like transcription factor Klumpfuss maintains lineage commitment in the intestine

city: Novato

first: Tal

last: Ronnen Oron

state: CA

address: 8001 Redwood blvd.

department: Bioinformatics Core

institute: Buck Institute for Research on Aging

summary: DamID-Seq experiment with Kllu-Dam

overall_design: DamID on Klu-Dam samples compared to control (Dam only) in triplicate from esg-positive stem-progenitors from Drosophila midgut

first: Jerome

last: Korzelius

middle: R

last: Oron


title: Chromatin accessiblity in mouse thymic epithelial cells to determine active regulatory elements.

city: Bethesda

first: Yongge

last: Zhao

state: MD

address: 9000 Rockville Pike

institute: NCI

summary: The thymus is the site of T cell development. Although much is known about the development and differentiation of the T lymphocyte compartment, less is known about the thymic epithelial cell (TEC). Foxn1 is critical for the development and function of the thymus. Here, we used ATAC-Seq to identify regions of accessible chromatin in TEC and keratinocytes of the skin to identify candidate active regulatory elements critical for tissue specific expression of Foxn1.

overall_design: ATAC-Seq was performed on sorted thymic epithelial cells and sorted keratinocytes of the skin

first: Brian

last: Larsen

first: Ben

last: Voisin

first: Keisuke

last: Nagao

first: Avinash

last: Bhandoola


title: Effect of foliar GSH treatment on gene expression profile in the root of Brassica napus

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Glutathione is a tripeptide involved in diverse aspects of plant metabolism. We investigated how the reduced form of glutathione, GSH, applied site-specifically to plants, affects zinc (Zn) distribution and behavior in oilseed rape plants (Brassica napus) cultured hydroponically. Foliar-applied GSH significantly increased the Zn content in shoots and the root-to-shoot Zn translocation ratio; furthermore, this treatment raised the Zn concentration in the cytosol of root cells and substantially enhanced Zn xylem loading. Notably, microarray analysis revealed that the gene encoding pectin methylesterase was upregulated in roots following foliar GSH treatment. We conclude that certain physiological signals triggered in response to foliar-applied GSH were transported via sieve tubes and functioned in root cells, which, in turn, increased Zn availability in roots by releasing Zn from their cell wall. Consequently, root-to-shoot translocation of Zn was activated and Zn accumulation in the shoot was markedly increased.

overall_design: Seeds of oilseed rape (Brassica napus L. cv. Nourin No.16, Kaneko Seed Co. Ltd., Gumma, Japan) were germinated in vermiculite by using bottom irrigation. Modified Hoagland solution (nutrient solution), described previously [Soil Sci. Plant Nutr. 54 (2008) 118–127.], was used as the irrigation solution. At 10 days after germination, young seedlings were transferred to 1.5-L containers (4 seedlings/container) containing 1.2 L of the nutrient solution, and the containers were maintained in a growth chamber for a 16-h photoperiod (~200μmol m-2s-1) at 24 °C, and at 16°C at night. Nutrient solutions were aerated continuously and renewed twice weekly. Each tested plant was grown for 4 weeks before being harvested.  Plants were exposed to glutathione for 4 days. GSH (glutathione, reduced form) was applied to source leaves (fully expanded leaves). In the leaf GSH treatment, 50 µL of 100 mM GSH in a foliar-application solution (10 mM MES-KOH, pH6.1, 0.01% [w/v] Triton X-100) was applied to each leaf with a painting brush; GSH was applied to 3 expanded leaves per plant daily before harvest.

first: Shin-ichi

last: Nakamura

first: Arunee

last: Wongkaew

first: Hiroki

last: Rai

first: Naoko

last: Ohkama-Ohtsu


title: Sex-biased expression of small RNA by microarray in critically endangered Amur sturgeon

city: Guangzhou

first: Linmiao

last: Li

address: Xin-Gang-Xi-Lu 105

institute: Guangdong Institute of Applied Biological Resources

summary: In this study, we utilized the microfluidics chip technology on the gonads of Amur sturgeon to identifiy gender-specific sRNAs. The probes of all miRNAs about 2751 published in fish and our novel miRNAs from sturgeon were chosed in the microarray experiment.

overall_design: Above 6µg total RNA from one female and one male separativley were performed the sRNA microarray assays.Each probe was repeated three times on the chip to ensure reproducibility of microarray.

first: Lihong

last: Yuan

first: Jinping

last: Chen


title: Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Liver cancer is a common cause of cancer death, with a male-predominant incidence due, in part, to increased estrogen levels in cirrhotic patients. It is unknown, however, how estrogen is sensed to influence this process. Here, we show that estrogen activates the G protein-coupled estrogen receptor 1 (GPER1), expressed in hepatocytes, to enhancing hepatocyte size, cell cycle progression and cell proliferation, thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling, and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis, specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender-specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth, mTOR activation, and can serve as a therapeutic target for liver cancer treatment.

overall_design: RNA-Seq analysis of control DMSO-treated livers and β-Estradiol exposed livers were examined.

first: Wolfram

last: Goessling

first: Saireudee

last: Chaturantabut

first: Song

last: Yang


title: Transcriptomic analysis of effect of oncolytic measles virus (MV) on transformed and non-transformed bone marrow-derived mesenchymal stem cells (MSCs)

city: London

first: Sarah

last: Aref

address: 72 Huntley St, Fitzrovia,

department: Haematology department

institute: UCL Cancer Institute

summary:
The mechanisms by which oncolytic vaccine strains of measles virus exert their tumor selectivity are not well elucidated.
The goal of this study is to compare the gene expression profiles of MV-resistant MSC cell line (hTERT) and MV-susceptible MSC cell line (5H) before and after infection with MV (24 hours post infection)
Through RNA-seq we were able to identify genes that are potentially contribute to the resistant phenotype of hTERT cells compared to their malignant counterparts, 5H cells.

overall_design:
hTERT cells and 5H cells were either mock-infected or infected with MV at the muliplicity  (MOI of 1.0). 24hours post infection, RNA was extracted by the TriZol method according to manufacturer's instructions. The experiment was done three independent times (n=3).
[contributor] UCL Genomics

first: Adele

last: Fielding


title: The Wnt/β-catenin and RAS-ERK Pathways were Activated  in Tissues of Chemotherapy-Resistant Gastric Cancer PDX Tumor

status: Public on May 26 2019

city: Seoul

first: Won-Ji

last: Ryu

address: 262 Seonsanno, Seodaemun-Gu

institute: Yonsei University

summary: Chemotherapy resistance and disease recurrence remains major causes of gastric cancer patient mortality. We describe possible relationship between Wnt/b-catenin and RAS/ERK pathways in GC patients and acquired-resistant GC PDX tumors against FOLFOX, 5-fluorouracil-based chemotherapy. RNA sequencing analysis also demonstrates that Wnt/b-catenin pathway is an actionable target pathway for overcoming the chemotherapy resistance. These provide that an approach targeting both Wnt/b-catenin and RAS/ERK pathways could be novel therapeutic strategy in GC resistant to standard chemotherapy.

overall_design: Examination of vehicle- and FOLFOX-treated gastric cancer PDX tumors

first: Jae

middle: E

last: Lee

first: Gunho

first: Jae-Ho

last: Cheong

first: Kang-Yell

last: Choi


title: Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery

status: Public on May 27 2019

city: Gainesville

first: Scott

last: Tibbetts

state: Florida

address: 1200 Newell Drive

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Gammaherpesviruses, including the human pathogens Epstein-Barr virus and Kaposi’s sarcoma-associated herpesvirus, establish lifelong latent infection in B cells and are associated with a variety of tumors. In addition to protein coding genes, these viruses encode numerous microRNAs (miRNAs) within their genomes. While putative host targets of EBV and KSHV miRNAs have been previously identified, the specific functions of these miRNAs during in vivo infection are largely unknown. Murine gammaherpesvirus 68 is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV elements such as miRNAs in the context of infection and disease. However, MHV68 the specific targets of miRNAs remain unknown. Using a technique known as quick CLASH (crosslinking, ligation, and sequencing of hybrids), we have now identified specific, Ago-associated mRNA targets of MHV68 miRNAs during lytic infection, latent infection and reactivation from latency.

overall_design: MHV68 infected cells were harvested from three biological conditions: latency (murine B cell line latently infected with MHV68), reactivation (reactivation of MHV68 from latently infected murine B cells), and lytic infection (MHV68 infected murine fibroblast cells. Cells were lysed, UV crosslinked and argonaute complexes were immunoprecipitated. Argonaute associated RNAs were ligated to one another, isolated, and sequenced.

first: Whitney

last: Bullard

first: Mehmet

last: Kara

first: Lauren

last: Gay

first: Sunantha

last: Sethuraman

first: Shreya

last: Nirmalan

first: Alim

last: Esemenli

first: April

last: Feswick

first: Rolf

last: Renne


title: Expression data of human CD19pos B lymphocytes (B) and CD19negCD22neg non-B cells (ENV) from non tumoral reactive lymph nodes (RLN), tonsils (TONS) or follicular lymphoma (FL)

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

summary: GEP on Affymetrix U133+2.0 microarrays was performed on ex vivo CD19+ B lymphocytes or CD19-CD22- fractions from reactive or FL lymph nodes or normal tonsils.

overall_design: GEP was performed on B fractions of 15 RLN and 23 FL lymph nodes, and on ENV fractions of 6 RLN and 10 FL (mostly paired to B fractions as identifiable by same sample number) and 5 TONS

first: Karin

last: Tarte

first: Thierry

last: Fest


title: mRNA m6A regulates porcine intramuscular fat deposition via YTHDF1-dependent enhancement of MTCH2 translation

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: We performed m6A sequencing to compare N6 transcriptome methylation profiles of the longissimus dorsi muscles (LDMs) between Landrace pigs (a Danish pig breed) and Jinhua (a Chinese pig breed with higher levels of intramuscular fat). The results show m6A is widely spread and highly conserved in pig mRNA. m6A occurs in the conserved sequence motif of GGACU and exhibits a unique topology in pig.Transcriptome-wide m6A profiling revealed that about 20% of transcribed genes were modified by m6A, with the consensus sequence GGACU appearing highly in m6A-modified genes. Functional enrichment analysis showed that genes differentially methylated in LDMs of the two porcine breeds were related to gene regulation and muscle development and differentiation,suggesting that the m6A modification is tissue-specific and influences mRNA stability or translation.

overall_design: m6A-seq from Landrace and Jinhua pig to reveal m6A function in intramuscular fat deposition.

first: Qin

last: Jiang

first: Baofa

first: Yizhen

last: Wang

first: Xinxia


title: Gene amplification driven-long noncoding RNA SNHG17 regulates cell proliferation and migration in human non-small cell lung cancer

city: nanjing

first: zhaoxia

last: wang

address: jiangjiayuan road 121

department: Cancer Medical Center

institute: The Second Affiliated Hospital of Nanjing Medical University

summary: Our findings indicated gene amplification driven-long noncoding RNA SNHG17 promotes cell proliferation and migration in NSCLC, suggesting its potential value as biomarker in NSCLC.

overall_design: RNA-seq analysis of SNHG17 knockdown in one cell type

first: Zhaoxia

first: Erbao

last: Zhang


title: Small RNA Profiles of Serum Exosomes Derived from Individuals with Latent and Active Tuberculosis

status: Public on May 28 2019

first: Fei

last: Chen

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed small RNA sequencing to explore small RNA profiles of serum exosomes derived from LTBI and TB patients and healthy controls (HC). Our results revealed distinct miRNA profile of the exosomes from the three samples. We identified many differentially expressed miRNAs, including some specifically expressed miRNAs in the three samples. Besides the specially expressed miRNAs, we demonstrated distinct expression panels of the serum exosomal miRNAs from LTBI and TB samples, and six expression patterns among the three samples. These specifically expressed miRNAs and differentially expressed miRNAs in different panels and patterns provide potential biomarkers for detection/diagnosis of latent and active TB using exosomal miRNAs. Additionally, we also discovered plenty of small RNAs derived from genomic repetitive sequences (e.g., SINEs, LINEs and LTR), which might play roles in host immune responses along with Mtb infection progresses. Overall, our findings provide important reference and improved understanding about miRNAs and repetitive region-derived small RNAs in exosome during Mtb infectious process, and facilitate the development of potential molecular targets for detection/diagnosis of latent and active tuberculosis.

overall_design: Examined three samples


title: Tracking of Individual Cell Populations by 19F MRI using a "Cargo Internalization Receptor (CIR)" System

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary: Magnetic resonance imaging (MRI) is an important key for non-invasive visualization of immigrating cells in in vivo studies. We use Perflourcarbons (PFC) coupled to green fluorescent protein (GFP) for a 1H and 19F MRI detection. To this end, we engineered synthetic cell surface receptors, “Cargo Internalization Receptors” (CIR), which contain a GFP-nanobody and specifically bind GFP, followed by a rapid internalization of the GFP-PFC particles, but without inducing any signaling in the targeted cells. In order to explore the suitability of different uptake mechanisms we constructed three different CIRs, which contain different cytoplasmic domains that have different internalizations motifs and properties to enable the specific uptake of the GFP-PFC cargo in CIR-transfected cells. We show that the CIR approach is working in vitro, and has the potential to specifically track CIR containing cells by 1H and 19F MRI.

overall_design: We used microarrays to detail the overall influence of the constructs to confirm background free action of the CIR  receptor constructs.

first: Paul

last: Baran

first: Sebastian

last: Temme

first: Jürgen

last: Scheller


title: Identification of two novel candidate genes for insulin secretion by comparative genomics of multiple backcross populations

summary: To identify novel disease genes for type 2 diabetes (T2D) we generated two backcross populations of obese and diabetes-susceptible New Zealand Obese (NZO) with the two lean mouse strains 129P2 and C3H/FeJ. Subsequent whole-genome linkage scan revealed 36 novel quantitative trait loci (QTL) for T2D-associated traits. The strongest association with blood glucose (12 cM, LOD 13.3) and plasma insulin (17 cM, LOD 4.8) was detected on proximal chromosome 7 (designated Cdp7prox) exclusively in the NZOxC3H crossbreeding, suggesting that the causal gene is unique for the C3H genome. Introgression of the critical C3H fragment into the genetic NZO background by generating recombinant congenic strains (RCS) and metabolic phenotyping validated the phenotype. For the detection of candidate genes in the critical region (30-46 Mb) we used a combined approach of haplotype- and gene expression analysis to search for C3H-specific gene variants in the pancreatic islets, which appeared as the most likely target tissue for the QTL. Only the two genes Potassium-transporting ATPase alpha chain 1 (Atp4a) and Ribonuclease P protein subunit p29 (Pop4) fulfilled the criteria from our candidate gene approaches. The knockdown of both genes in MIN6 cells led to a decreased glucose-stimulated insulin secretion (GSIS), indicating a stimulating role of both genes in insulin secretion, thereby likely contributing to the phenotype linked to Cdp7prox. In conclusion, our combined- and comparative-cross analysis approach has successfully led to the identification of two novel diabetes susceptibility genes and thus has proven to be a powerful tool for the discovery of novel disease genes.

overall_design: We used microarrays to enable the detection of candidate genes in the critical region (30-46 Mb) in a combined approach of haplotype- and gene expression analysis to search for C3H-specific gene variants in the pancreatic islets.

first: Tanja

last: Schallschmidt

first: Sandra

last: Lebek

first: Hadi

last: Al-Hasani


title: Modulatory role of skin microbiome against UV

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

institute: Medical University Graz

summary: The role of the skin microbiome in UV-induced immune suppression has been overlooked. We addressed the question of microbial involvement in UV-induced immune suppression by using the standard model of contact hypersensitivity in the presence or absence of the microbiome (in germ-free [GF] and disinfected mice) and found that the microbiome inhibits UV-induced immune suppression. Furthermore, our transcriptome analysis (24 hours after irradiation) showed differential regulation of many genes in the presence or absence of the microbiome, including a predominance of pro-inflammatory cytokines versus immunosuppressive cytokines

overall_design: 3 mice per experimental group

first: V

last: Patra

first: P

last: Wolf


title: Liquid profiling in plants: identification and analysis of extracellular miRNAs in of Ginkgo biloba

city: Yangzhou

first: Li

address: Wenhui east road no. 48

institute: Yangzhou University

summary: We sequenced sRNA from the ovular secretions of G. biloba to identify the presence of miRNAs, which provide the first evidence of the extracellular miRNAs function in ovular secretions of gymnosperms .

overall_design: sRNA sequencing in ovular secretions of G. biloba

first: Zhaogeng

last: Lu


title: Reverse Phase Protein Array (RPPA) profiling of cell signaling events in 468 cells induced by PTEN overexpression or PTEN-Long overexpression

status: Public on May 25 2019

first: Ramon

last: Parsons

address: 1425 Madison Ave, L1-15C

department: Oncological Sciences

institute: Icahn school of medicine at Mount Sinai

summary: To investigate the novel functions of PTEN-L, we performed a Reverse Phase of Protein Array (RPPA) profiling on 468.Ctrl, 468.PTEN, and 468.PTEN-L sublines to compare cell signaling events between PTEN expression

overall_design: To study the molecular mechanism underlying the tumor suppression function of PTEN-L, we established a pair of PTEN-L and PTEN overexpression stable cell lines in PTEN-/- breast cancer cell lines-MDA-MB-468 cells through Lentivirus infection. Cell lysates were extracted from 468.Ctrl, 468.PTEN, 468.PTEN-L cells and subjected to RPPA analysis.

first: Jia

last: Xu


title: RNA sequencing of single cells from the midline posterior extremity in planarian Schmidtea mediterranea

city: Cambridge

first: Peter

middle: W

last: Reddien

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: RNA sequencing of single cells from the midline posterior tip of the tail and posterior blastema in planarian Schmidtea mediterranea identified new posterior-pole enriched genes

overall_design: RNA sequencing was performed on wnt1+ and wnt- single muscle cells (collagen+) from the midline tail tips in uninjured animals and the midline posterior blastemas in regenerating animals 72-hours after transverse amputation, and gene expression of posterior pole cells (wnt1+; collagen+) was compared with that of non-posterior pole muscle cells (wnt1-; collagen+) to identify genes differentially expressed in the posterior pole.

first: Dayan

last: Li

first: Conor

last: McMann


title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders [lnc-Nr2f1 overexpression]

city: Stanford

first: Cheen Euong

last: Ang

address: 265 Campus Drive, G3145

institute: Stanford University

summary: The goal is to examine the global transcriptomic changes upon lnc-Nr2f1 overexpression in human neuroblastoma cells

overall_design: Examination of global transcriptional changes and genome wide binding events of lnc-Nr2f1

first: Qing

last: Ma

first: Cheen


title: TET1 contributes to allergic airway inflammation and regulates interferon and aryl hydrocarbon receptor signaling pathways in bronchial epithelial cells

city: Davis

first: Hong

last: Ji

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

summary: RNA-seq analysis to understand the regulation of genes by TET1 in mouse lungs and human bronchial epithelial cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: An allergic airway inflammation model was established in Tet1+/+ mice and Tet1-/- mice using house dust mite allergen with appropriate controls. Lung RNA were extracted and compared using RNA-seq. In addition, endogenous TET1 expression was activated in human bronchial epithelial cells by dCasCRISPR for 24 hrs. RNA was extracted and compared between control and TET1 activated cells.


title: Next generation sequencing on knockdown of AC093323.3 in lung cancer cells

first: Danish

last: Memon

address: Robinson Way

institute: CRUK Cambridge Institute, University of Cambridge

summary: In this study we predict functionally important long intergenic non-coding RNAs (lincRNAs) with a role in core essential processes in human. One of the candidate lincRNA, AC093323.3, was experimentally verified to affect cell viability. We performed RNASeq on knockdown of AC093323.3 to further investigate the functional role of this lincRNA.

overall_design: RNA profiles of NCI-H460 lung cancer cells after treatment with scrambled siRNAs and AC093323.3-siRNA.

first: Jing

last: Bi

first: Crispin

last: Miller


title: Bacterial RNase III cleaves long dsRNA at preferred sites

city: Frederick

first: Shuo

last: Gu

address: 1050 Boyles Str. Building 560 Room 11-6B

institute: National Cancer Institute

summary: Members of the ribonuclease (RNase) III family regulate gene expression by processing double-stranded (ds) RNA. The founding member of the family, Escherichia coli (Ec) RNase III, is the most comprehensively studied and its E38A mutant (EcE38A) is an economical reagent for the preparation of small interfering (si) RNA cocktails. Previously, it was shown that EcRNase III recognizes dsRNA with little specificity and that EcE38A mainly produces 23-nucleotide (nt) siRNAs. To characterize substrate specificity and product size, we performed in vitro cleavage of dsRNAs by bacterial RNase IIIs and delineated the cleavage products by next generation sequencing. Surprisingly, we found that RNase III cleaves dsRNA at preferred sites and most siRNAs produced by EcE38A are 22 nt long. We eliminated the sequence specificity of EcE38A through the introduction of additional mutations, thereby creating a reagent that is ideally suited for producing heterogeneous siRNA cocktails to be used in gene silencing studies.

sample_organism:
Escherichia coli
Aquifex aeolicus

platform_organism:
Escherichia coli
Aquifex aeolicus

overall_design: In vitro cleavages of FF-Luc and MBP dsRNAs by variious bacterial Rnases III and their mutants were deep sequened and analyzed to investigate the cleavage preference of those Rnase III enzymes

first: Lan

last: Jin

first: Xinhua


title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders [human ChiRP]

summary: The goal is to examine the global binding of lnc-Nr2f1


title: Serum miRNA-based risk prediction for stroke

city: Kamakura

first: Ichikawa

last: Makiko

institute: Toray Industries, Inc.

summary: The serum miRNAs were correlated with predicted the incidence of stroke.

overall_design: Serum microRNA profiles of 1785 samples, which consist of 173 of CVD patients, 1612 of non-CVD control.

first: Takumi

last: Sonoda

first: Juntaro

last: Matsuzaki

first: Yusuke

last: Yamamoto

first: Yoshiaki

last: Aoki

first: Satoko

last: Takizawa

first: Shumpei

last: Niida

first: Takahiro

last: Ochiya


title: Intestinal stem cell differentiation is associated with dynamic changes in the chromatin landscape [atac-seq]

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: Genome-wide chromatin accessbilility data in 4 populations of intestinal epithelial cells defined by different levels of Sox9 expression.

overall_design: Chromatin accessibility data from 4 populations of intestinal epithelial cells

first: Adam

last: Gracz


title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders [RNA-seq]

first: Cheen Euong

last: Ang

summary: The goal is to examine the global transcriptomic changes upon lnc-Nr2f1 overexpression in both Control and lnc-Nr2f1 KO ES cells.

first: Cheen

first: Qing

last: Ma


title: Gene silenced-based, individualized cancer progression outcome prediction for shATMIN stable transfectants

city: Taipei

first: Chen

middle: Shih

last: Wen

address: Changde St.

department: Graduate Institute of Oral Biology

country: Taiwan

institute: National Taiwan University

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling in stable transfectants

overall_design: To investigate whether knock-down ATMIN protein affect cancer progression

first: Yue-Ju

last: Li

first: Cheng-Chi

last: Chang

first: Mark

last: Kuo

first: Been-Ren

last: Lin


title: RNA sequencing of the head and tail of planarian Schmidtea mediterranea during nr4A inhibition

first: Peter

last: Reddien

summary: RNA sequencing identified various nr4A-regulated genes in the head and tail, including a large number of muscle-enriched genes and many positional control genes, most of which were down-regulated by nr4A inhibition.

overall_design: RNA sequencing was performed on transversely resected heads and tails of animals after 2, 3, 4, or 5 weeks of control or nr4A RNAi. Gene expression in the heads and tails of nr4A RNAi animals was compared with gene expression in the heads and tails, respectively, of control RNAi animals to identify nr4A-dependent genes.

first: Dayan

first: Conor

last: McMann


title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders

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

overall_design: Refer to individual Series


title: RNA sequencing studies in planarian Schmidtea mediterranea


title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders [ChiRP]


title: RNA sequencing of pole-containing anterior tip regions in planarian Schmidtea mediterranea

summary: RNA sequencing identified new anterior-pole enriched genes encoding transcription factors, a secreted protein, and a transmembrane protein, including NR4A, a nuclear receptor gene that is important in patterning the planarian head and tail.

overall_design: RNA sequencing was performed on pole-containing anterior tip regions and their flanking regions in uninjured animals and regenerating animals 72-hours after transverse amputation, and gene expression of pole-containing regions was compared against that of flanking regions to identify genes differentially expressed in pole regions.


title: Expression data from young and senescence ovarian cancer cells from patients with or without chemotherapy

status: Public on May 24 2019

city: Poznan

first: Anna

last: Witucka

state: Greater Poland

address: Dluga 1/2

department: Department and Clinic of Hypertensiology, Angiology and Internal Medicine

country: Poland

institute: Poznan University of Medical Sciences

summary: There is a paradigm that cancer cells are immortal, which indicates that they have an ability to bypass cellular senescence. This is often linked with an expression of telomerase which restores the telomeric DNA. Cellular senescence may be induced in cancer cells by their exposure to clinically relevant doses of ionizing radiation (radiotherapy) and chemotherapy. It means that even though cancer cells avoided senescence in the course of their immortalization, they preserved intact molecular effectory pathways leading to senescence under some therapy-related conditions. Interestingly, it has repeatedly been described that tumors from patients who had no received any form of therapy also contain a fraction of cells bearing morphological and biochemical signature of senescence. Taking this into account, the goal of our project was to examine the presence of spontaneously senescent ovarian cancer cells in vivo and in vitro, and to describe molecular mechanisms underlying this phenomenon.

overall_design: There were three experimental groups with three controls and three experimental samples in each.

first: Karol

last: Jopek

first: Marcin

last: Rucinski

first: Krzysztof

last: Książek


title: Intestinal stem cell differentiation is associated with dynamic changes in the chromatin landscape

first: Jesse


title: bHLH-PAS protein RITMO1 regulates diel biological rhythms in the marine diatom Phaeodactylum tricornutum

city: Paris

first: Angela

last: Falciatore

address: 15 rue de l'ecole de Medicine

department: UMR 7238, LCQB

institute: CNRS

summary: Periodic light–dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved.  Although prominent marine phytoplanktonic organisms such as diatoms show robust diel rhythms, the mechanisms regulating these processes are still obscure. By characterizing a Phaeodactylum tricornutum bHLH-PAS nuclear protein, hereby named RITMO1, we shed light on the regulation of the daily life of diatoms. Alteration of RITMO1 expression levels and timing by ectopic overexpression results in lines with deregulated diurnal gene expression profiles compared with the wild-type cells. Reduced gene expression oscillations are also observed in these lines in continuous darkness, showing that the regulation of rhythmicity by RITMO1 is not directly dependent on light inputs. We also describe strong diurnal rhythms of cellular fluorescence in wild-type cells, which persist in continuous light conditions, indicating the existence of an endogenous circadian clock in diatoms. The altered rhythmicity observed in RITMO1 overexpression lines in continuous light supports the involvement of this protein in circadian rhythm regulation. Phylogenetic analysis reveals a wide distribution of RITMO1-like proteins in the genomes of diatoms as well as in other marine algae, which may indicate a common function in these phototrophs. This study adds elements to our understanding of diatom biology and offers perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but under-investigated, branch of the tree of life.

overall_design: Phaeodactylum tricornutum wild type (Wt) and bHLH1a overexpressing line (OE-1) cultures were entrained to 16 hours of light and 8 hours of dark (16L:8D) for 2 weeks. The preadapted Wt and OE-1 lines were transferred to DD and sampled every 3 hours for a period of 24 hours, starting one hour after the beginning of the presumptive light period (time point 1). Three biological replicates were sampled for each condition. The expression of 15 selected genes, identified by their expression profiles in a previous screening in LD and DD conditions, was analyzed over the time series in both the Wt and OE-1 lines.

first: Rossella

last: Annunziata

first: Antonio Emidio

last: Fortunato


title: Salt-deficient diet exacerbates cystogenesis in ARPKD via epithelial sodium channel (ENaC)

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

summary: We report the changes in miRNA expression in the renal cortex od the PCK rats fed diets with different sodium content

overall_design: 6 week old PCK (PCK/CrljCrlPkhd1pck/CRL) rats were fed a 0.01%, 0.4% or 4% NaCl diet from Dyets, Inc ad libitum for 8 weeks. Renal tissue was isolated at the end of the protocol after kidney flush, cortex was snap-frozen and subjected to miRNA analysis.

first: Daria

middle: V

last: Ilatovskaya

first: Vladislav

last: Levchenko

first: Tengis

last: Pavlov

first: Elena

last: Isaeva

first: Christine

middle: A

last: Klemens

first: Jessica

last: Johnson

first: Pengyuan

last: Liu

first: Alexander

last: Staruschenko


title: ApoE determines the metabolic fate of apoC-III

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Hypertriglyceridemia results from accumulation of triglyceride (TG)-rich lipoproteins (TRLs) in the circulation and is associated with increased cardiovascular disease risk. ApoC-III is an apolipoprotein on TRLs and a prominent negative regulator of TG catabolism. We recently established that in vivo apoC-III predominantly inhibits LDLR and LRP1 mediated hepatic TRL clearance and that apoC-III enriched TRLs are preferentially cleared by syndecan-1 (SDC1). In this study, we determined the impact of apoE, a common ligand for all three receptors, on apoC-III metabolism using apoC-III antisense oligonucleotide (ASO) treatment in mice lacking apoE and functional SDC1 (Apoe(-/-) Ndst1(f/f) Alb-Cre+). ApoC-III ASO treatment significantly reduced plasma TG levels in Apoe(-/-) Ndst1(f/f) Alb-Cre+ mice without reducing hepatic VLDL production or improving hepatic TRL clearance. Further analysis revealed that apoC-III ASO treatment lowered plasma TGs in Apoe(-/-) Ndst1(f/f) Alb-Cre+ mice, which was associated with increased LPL activity in white adipose tissue (WAT) in the fed state. Finally, clinical data confirm that ASO-mediated lowering of apoC-III via volanesorsen can reduce plasma TG levels independent of the apoE isoform genotype. Our data indicate that apoE determines the metabolic impact of apoC-III as we establish that apoE is essential to mediate inhibition of TRL clearance by apoC-III and that in the absence of functional apoE apoC-III inhibits tissue LPL activity.

overall_design: Comparison of five mice with apoC-III antisense oligonucleotide against four control mice

first: Bastian

last: Ramms

first: Philip

middle: L

last: Gordts


title: Intestinal stem cell differentiation is associated with dynamic changes in the chromatin landscape [rna-seq]

last: Raab

summary: Gene expression data in 4 populations of intestinal epithelial cells defined by different levels of Sox9 expression.

overall_design: Gene expression data from 4 populations of intestinal epithelial cells generated by RNA-seq following FACS purification of cell populations.

first: Adam

last: Gracz


title: RNA-sequencing of Control and TLE3-deficient Beige Adipocytes

status: Public on May 23 2019

city: Salt Lake City

first: Stephanie

last: Pearson

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

summary: Prolonged cold exposure stimulates the recruitment of beige adipocytes within white adipose tissue. Beige adipocytes depend on mitochondrial oxidative phosphorylation to drive thermogenesis. The transcriptional coregulator TLE3 inhibits mitochondrial and metabolic gene expression in beige adipocytes.

overall_design: mRNA profiles of iWAT immortalized preadipocytes, differentiated in culture, and knocking out TLE3 after differentiation, were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Claudio

last: Villanueva


title: Gene expression profile (RNAseq) of wild-type and Zeb1 (+/-) peritoneal mouse macrophages

city: Barcelona

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

country: Spain

institute: IDIBAPS/ICREA

summary:
Purpose: Characterize the gene expression profile of wild-type and Zeb1 (+/-) peritoneal mouse macrophages through RNA sequencing
Methods: RNA sequencing of RNA from peritoneal macrophages isolated by peritoneal lavage and FACS sorting (F4/80+ CD11b+) from  wild-type and Zeb1 (+/-) mice (2 mice pooled for each sample/set)
Results:  Wild-type and Zeb1 (+/-) peritoneal mouse macrophages display differential gene expression. Zeb1 (+/-) peritoneal macrophages express lower levels of SPM (F4/80low)-associated genes
Conclusions: Wild-type and Zeb1 (+/-) peritoneal mouse macrophages display differential gene expression. Zeb1 (+/-) peritoneal macrophages express lower levels of SPM (F4/80low)-associated genes

overall_design: RNA sequencing of RNA from peritoneal macrophages isolated by peritoneal lavage and FACS sorting (F4/80+ CD11b+) from  wild-type and Zeb1 (+/-) mice (2 mice pooled for each sample)

first: Marlies

last: Cortes

first: Anna

last: Esteve-Codina


title: The repressive role of H2A.Z variant in transcriptional regulation depends on AtBMI1 activity in Arabidopsis

city: Sevilla

first: Myriam

last: Calonje

address: Americo Vespucio 49

institute: Institute for Plant Biochemistry and Photosynthesis (CSIC -  University of Sevilla)

summary: H2A.Z variant has emerged as a critical player in regulating plant responses to environment; however, the mechanism by which H2A.Z mediates this regulation remains unclear. In Arabidopsis, H2A.Z has been proposed to have opposite effects on transcription depending on its localization within the gene. These opposite roles have been assigned by correlating gene expression and H2A.Z enrichment analyses but without considering the impact of possible H2A.Z posttranslational modifications. Here we show that H2A.Z can be monoubiquitinated by the PRC1 components AtBMI1A/B/C. The incorporation of this modification is required for H2A.Z-mediated transcriptional repression through a mechanism that does not require PRC2 activity. Our data suggest that the dual role of H2A.Z in regulating gene expression depends on the modification that it carries, while the levels of H2A.Z within genes depend on the transcriptional activity.

overall_design: mRNA profiles of 7DAG Arabidopsis seedlings Col-0; doble mutant hta9hta11 ; hta9hta11_FLAG-HTA9_N, hta9hta11_FLAG-HTA9_RR and weak double mutant atbmi1ab_weak


first: Angela

last: Falciatore


overall_design: Phaeodactylum tricornutum wild type (Wt) cultures were entrained to 16 hours of light and 8 hours of dark (16L:8D) for 2 weeks. The preadapted cultures were split and put in parallel in normal 16L:8D cycles or in continuous darkness (DD) conditions. Sampling was performed every 4 hours for 32 hours in total, starting from the beginning of the dark period (time point -8). Three biological replicates were sampled for each condition. The expression of 104 transcripts belonging the transcription factor, cell cycle and metabolism-related gene categories, was followed over the time series in both LD and DD conditions to identify genes whose expression was not light-regulated.

first: Rossella

last: Annunziata

first: Antonio Emidio

last: Fortunato


title: Intestinal stem cell differentiation is associated with dynamic changes in the chromatin landscape [5hmc-seal-seq]

first: Jesse

summary: The global localization of 5-hydroxymethylcytosine (5hmc) were measured by 5hmc-seal-seq in four populations of intestinal epithelium defined by their levels of a GFP reporter transgene that is driven by the regulatory elements of the Sox9 gene.

overall_design: Genome-wide 5hmc localization in sox9 expression defined populations of the mouse intestinal epithelium.


title: Profiling of differential allelic expression in mouse placental tissues from two reciprocal crosses at embryonic day 13.5 and 17.5.

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

summary: Mammals achieve parity in expression of X linked genes in somatic tissue of males and females through the mechanism of X inactivation. Not all X-linked genes are silenced on the inactivated X, and genes that escape X-inactivation provide key insights about the mechanism of X inactivation. In humans, 15% of X-linked genes escape random X inactivation whereas in mouse 3% of X-linked genes escape inactivation. In marsupials and mouse, extraembryonic tissues (which give rise to the placenta) display another form of dosage compensation called imprinted X inactivation. Imprinted X inactivation is not random, as it is always the paternal X that is inactivated. There are as yet no reports in the literature of genes that might escape imprinted X inactivation. Here, we performed a deep RNA-seq study in mouse placenta samples from reciprocal crosses and discovered that 7.4% (21/282) of X-linked genes escape imprinted X inactivation. Strikingly, there is zero overlap between the set of imprinted X inactivation escapers and random X inactivation escapers. Imprinted X inactivation escapers are stable and show >35% paternal expression compared to >10% expression from the inactive X for random X inactivation escapers. Imprinted X inactivation escapers are all of clear functional importance to the placenta, and they are strongly clustered on the X. GO analysis reveals that glycoproteins and transmembrane proteins are significantly enriched among imprinted X inactivation escapers. The X-added region (XAR) of the eutherian mammal X is autosomal in marsupials and these genes were added to the X in eutherian mammals since the time of common ancestry. Fully 70% of the genes in the XAR escape random X inactivation, as though they have yet to acquire normal dosage compensation. But fewer than 10% of the genes in the X-added region (XAR) escape imprinted X inactivation, consistent with a imprinted X inactivation being a default state, and escape occurs only for genes requiring biallelic expression. The deep interspecific conservation of X inactivation escaper status that we find across mammals (including marsupials) despite the radical variation in mechanism provides strong evidence that there is a functional basis for escaper genes to retain their biallelic expression. Discussion of the specific genes that are escapers of imprinted X inactivation will suggest reasons for this functional conservation.

overall_design: Examine allelic expression in E17.5 and E13.5 placenta tissues from two reciprocal crosses, AKR-PWD and B6-CAST.

first: Xu

last: Wang


title: Cell resilience to folate deprivation boosts aberration tolerance

city: Madrid

first: Inmaculada

last: Rapado

address: Avenida Cordoba s/n

institute: Hospital Universitario 12 de Octubre

type: Genome variation profiling by genome tiling array

overall_design:
Refer to individual Series

***There is an error in the PMID 29291002 quoting the GSE54920 accession number [Erratum PMID 30112119]***


title: Gene expression from WT and Id2-deficient Tregs from adipose tissue and spleen

status: Public on May 22 2019

city: Pittsburgh

first: Louise

last: D'Cruz

state: Pennsylvania

address: E1053 Biomedical Science Tower, 200 Lothrop Street

department: Immunolgy

institute: University of Pittsburgh

summary: We report the gene expreesion changes that occur in regulatory T cells (Tregs) isolated from the spleen and visceral adipose tissue of mice that were either WT orI d2-deficient

overall_design: Examination of mRNA expression in sorted cells from mice

first: Adolfo

last: Frias


title: Uropathogenic E. coli mediated ACLY dependent acetyl-CoA change control IL 8 expression

city: Giessen

first: Melanie

last: Markmann

state: Hessen

address: Rudolf-Buchheim-Str. 7

department: Anaesthesiology

institute: University of Giessen

summary:
The virulence factor HlyA of Uropathogenic Escherichia coli (UPEC) could modulate host cell metabolism and inhibits NF-κB signaling pathway. However, whether there is a link between these two processes remains elusive. Here, we demonstrated UPEC could suppress metabolic enzyme ATP citrate lyase (ACLY) that resulted into histone deacetylation by decreasing the levels of acetyl-CoA. The level of histone acetylation was rescued supplementation of acetate.
Furthermore, using H3 Lysine9 acetylation (H3K9ac) immunoprecipitation coupled next generation sequencing (ChIP-seq), we found that UPEC cause site specific regulation of H3K9ac which correlates with the expression of pro-inflammatory cytokines and chemokines. To be more specific, the expression of pro-inflammatory cytokines and chemokines like IL 8, CXCL2, and IL-1α are suppressed by UPEC mediated decreasing of H3K9ac at TSS-promoter region. Thus, this study established that UPEC manipulate host cell metabolism to impact histone acetylation at specific loci, correlating with cytokines and chemokines expression, as a means to inhibit NF-κB signaling.

overall_design: 15 samples: 3 replicates CTRL, 3 replicates HDM 2h, 3 replicates HDM 4h, replicates UPEC 2h, 3 replicates UPEC 4h

first: Zhengguo

last: Zhang

first: Ming

first: Hamid

last: Hossain

first: Andreas

last: Meinhardt

first: Sudhanshu

last: Bhushan


title: A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

summary: Many human cancers are resistant to immunotherapy, for reasons that are poorly understood. We used a genome-scale CRISPR-Cas9 screen to identify mechanisms of tumor cell resistance to killing by cytotoxic T cells, the central effectors of antitumor immunity. Inactivation of >100 genes—including Pbrm1, Arid2, and Brd7, which encode components of the PBAF form of the SWI/SNF chromatin remodeling complex—sensitized mouse B16F10 melanoma cells to killing by T cells. Loss of PBAF function increased tumor cell sensitivity to interferon-γ, resulting in enhanced secretion of chemokines that recruit effector T cells. Treatment-resistant tumors became responsive to immunotherapy when Pbrm1 was inactivated. In many human cancers, expression of PBRM1 and ARID2 inversely correlated with expression of T cell cytotoxicity genes, and Pbrm1-deficient murine melanomas were more strongly infiltrated by cytotoxic T cells.

overall_design: Contro and Pbrm1 deficient B16F10 cells were either left untreated or treated with IFNg for 24 hours.

first: Deng

last: Pan

first: Kai

last: Wucherpfennig


title: Expression study of the Hodgkin’s lymphoma cell line L-1236 upon CRISPR Cas9-mediated knockout of lymphotoxin alpha (LTA) compared to control

city: Berlin

first: Marina

last: Kolesnichenko

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Center

summary: Persistent NF-κB activation is a hallmark of the malignant Hodgkin/Reed-Sternberg (HRS) cells in classical Hodgkin lymphoma (cHL). Analysis of the cHL cell-secreted key factors for NF-κB activation by chromatography and subsequent mass spectrometry revealed lymphotoxin-α (LTA) as the causative factor for autocrine and paracrine activation of canonical and noncanonical NF-κB in cHL cell lines. Upon CRISPR/Cas9-mediated gene knockout of LTA in the cell line L-1236, we performed expression analysis of LTA knockout versus control cells by using the Affymetrix array, Clariom S human, profiling tool.

overall_design: L-1236 cells were purchased from the DSMZ (Braunschweig, Germany) and cultured in RPMI (Gibco) with 10% heat-inactivated fetal calf serum (FCS; Gibco). Cells were transducted with the lentiCRIPSPR v2 vector containing gRNAs which target the second (g2) and the fourth exon (g3) of LTA. Following single cell clonal selection, L-1236 control cells (v2) and two LTA knockout (KO) clones g2_1 and g3_4 were cultured in normal culture medium for 72 h. The RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer’s instructions. Preparation of cDNA, fragmentation and labeling was performed with the GeneChIPTM WT PLUS reagent kit (ThermoFisher Scientific). Samples were analyzed using the human Clariom™ S Assay (ThermoFisher Scientific).

first: Eva

last: Kärgel

first: Linda

last: von Hoff

first: Claus

last: Scheidereit


title: Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

summary: Using machine learning to identify biological targets for natural products with anticancer properties and unknown modes of action is gaining momentum. Herein, we employ machine intelligence to deconvolute the phenotypic effects of the natural product Piperlongumine (PL) and establish an unprecedented link to allosteric modulation of the human transient receptor potential vanilloid 2 (hTRPV2) channel. Using cryo-electron microscopy (cryo-EM), we determined the structure of the PL-bound full-length rat TRPV2 channel at an overall resolution of 3.4 Å. We disclose binding of PL to a novel allosteric pocket which is responsible for a new mode of anticancer activity by PL, in particular against the aggressive glioblastoma (GBM), where TRPV2 is overexpressed. By creating CRISPRi TRPV2 knockdown GBM cells we found that the down-regulation of TRPV2 reduces sensitivity to PL and decreases ROS production. By analyzing GBM patients’ samples, we associated TRPV2 overexpression with tumor grade, disease progression and poor prognosis. Finally, formulating PL for sustained local therapy, we obtained tumor remission in a murine model of orthotopic GBM. Altogether, our strategy for target identification counter cycles established methods is broadly applicable and leverages data-motivated research hypotheses for the swift discovery of new biology and therapeutics.

overall_design: 12 Samples, wild type and TRPV2 CRISPRi KD and 2 treatments

first: Daniel

last: Picard

first: Gonçalo

last: Bernardes


title: Mechanical stretch differentially regulates the expression of specific miRNA in the extracellular vesicles released from lung epithelial cells

city: Providence

first: Tanbir

last: Najrana

address: 200 Chestnut street

institute: Brown University

summary:
Mechanical force is critical for lung development. In this study we identified specific  EV-miRNAs released from the mouse epithelial cell line in response to mechanical stretch involve in lung development.
In utero fetal lung experiences significant continuous transpulmonary pressure as a result of epithelial secretion in to the airway lumen, and periodic fetal breathing movement that move the fluid along the developing airway. Mechanical force is important factors for fetal lung development. However, the effect of mechanical force on the functions of lung cells is not known precisely. Extracellular vesicles –microRNAs (EV-miRNA)   are increasingly recognized as a new mode of cell-to-cell communication.  miRNA is well known as a regulator of physio-pathological process. In this study, we used oligonucleotide microarray technology to investigate miRNA expression in EV-released from mouse lung epithelial cell MLE12 after exposed to 10% cyclic or 5% continuous stretch. Analysis of microarray data identified 9 and 33 miRNAs significantly differentially expressed by the cyclic and continuous stretch respectively. Several differentially expressed miRNAs were reported dynamically expressed in mouse developing lung.  miRNAs associated with important transcription factors for cell function and key signaling pathways for fetal lung development also identified in this study. We conclude that mechanical signals differentially regulate the expression of specific EV/miRNAs in MLE12 are important for intercellular communication during lung fetal development.

overall_design: MLE12 cell line was obtained from Americal Type Culture Collection (Manassas, Virginia) expresses features of type II lung epithelial cells. Cells were culture in bioflex multiwall plates precoated with collagen-1 for 24 h, after fresh medium was replaced, plates were mounted in Flexcell FX-4000 Stretch Unit to expose 10% cyclic or 5% continuous stretch for 24 h. Parallel, cells grown on non-stretched membrane were used as control. Cell culture media (250 ml) from 175 x 106 cells  were used to isolate EVs for a single experiment. The Flexcell Strain Unit has capacity to culture approximately 35 x 106 cells for experiment, a combination of 5 independent experiments were combined to take single experiment.

first: T

first: A

last: Mahadeo

first: E

last: Kreienberg

first: V

last: Schulte

last: Uzun

first: R

last: Abu-Eid

first: C

last: Schorl

first: L

last: Goldberg

first: P

last: Quesenberry

first: J

last: Sanchez-Esteban


title: AIBP-mediated Cholesterol Efflux Instructs  Hematopoietic Stem and Progenitor Cell Fate

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

summary: Hypercholesterolemia, the driving force of atherosclerosis, accelerates the expansion and mobilization of hematopoietic stem and progenitor cells (HSPCs). The molecular determinants connecting hypercholesterolemia with hematopoiesis are underexplored. Here we report that a novel somite-derived pro-hematopoietic cue, AIBP, orchestrates HSPC emergence from the hemogenic endothelium, a type of specialized endothelium manifesting hematopoietic potential. Mechanistically, AIBP-mediated cholesterol efflux activates endothelial Srebp2, the master transcription factor for cholesterol biosynthesis, which transactivates Notch and promotes HSPC emergence. Srebp2 inhibition impairs hypercholesterolemia-induced HSPC expansion. Srebp2 activation and Notch upregulation are associated with HSPC expansion in hypercholesterolemic human subjects. Genome-wide ChIP-seq, RNA-seq, and ATAC-seq indicate that Srebp2 trans-regulates Notch pathway genes required for hematopoiesis. Our studies outline a novel AIBP-regulated Srebp2-dependent paradigm for HSPC emergence in development and HPSC expansion in atherosclerotic cardiovascular disease.

overall_design:
The ATAC-Seq was performed using 50,000 c-Kit+CD144+ CD45.2- cells isolated from AGM region of E11.5 wild-type B6 mouse embryos. The Tn5 transposome was purified and assembled following a published protocol (46).  The permeabilization was performed with 50 µl cold ATAC-RSB buffer (0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and the transposition was performed with 50 µl transposition mix (10µl 5× HEPES DMF Buffer, 3 µl 5 µM Tn5 transposome, 37 µl PBS, 0.5 µl 10% Tween-20, and 0.5 µl 1% digitonin) and incubated at 37° for 30 min. After transposition, the cleaned-up DNA fragments were pre-amplified for 5 cycles using NEB Q5 master mix. Each reaction contains 2.5 µl of 25 µM i5 primer, 2.5 µl of 25 µM i7 primer, 25 µl 2× NEB Q5 master mix, and 20 µl cleaned up samples.  PCR settings were 5 min at 72°C, 30 sec at 98°C, and followed by additional 5 cycles (98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min). After pre-amplification, 1 µl of the pre-amplified mixture was used to run a 10 µl qPCR test to determine the optimal amplification cycle. The final amplified DNA library was purified using Qiagen DNA purification kit and sequenced on NextSeq 500 with SE75 strategy.
This submission represents the ATA-Seq component of study.

first: Jie


title: Cell resilience to folate deprivation boosts aberration tolerance [Agilent]

first: Inmaculada

last: Rapado

summary: We detected numerous copy number aberrations in SNP arrays from follicular lymphoma patients. Additionally, we found an outstanding homozygous state involving folic acid-related genes. To study a hypothetical association between both traits, we cultured folate-depleted cell lines. After restoring normal medium to the cultures, we performed CGH arrays to examine the induced copy number aberrations.

overall_design: To study genome lesions in newly diagnosed follicular lymphoma patients, we performed 55 SNP arrays using DNA extracted from whole peripheral blood or bone marrow. 19 additional SNP arrays of DNA collected from patients during the follow-up were included in the homozygosity analysis. To evaluate the effects of folic acid depletion, we cultured five replicates of IM9 and DOHH2 cell lines during 15 days with 0 or 0.01 µM folate. Two culture replicates of cell lines with normal media (1  µM folate) were used as controls. After a 15-day folate deprivation, we restored normal media and cultured the cells for up to 1 month. CGH arrays were performed using DNA extracted from two IM9 samples and two DOHH2 samples. DNA pools of normal media culture replicates were used as reference samples.

first: Santiago

last: Barrio

first: Ana

last: Rivero

first: Florinda

last: Gilsanz

first: Joaquin

last: Martinez-Lopez


title: Gingolic acid, a sumoylation inhibitor, promotes pre-adipogenesis but suppresses adipocyte maturation

city: Grand Rapids

first: Tao

last: Yang

state: MI

address: 333 Bostwick Ave NE

department: Cancer and Cell Biology

institute: Van Andel Research Institute

summary: To understand the effect of ginkgolic acid in Bone marrow stromal cells (BMSCs) differentiation, we compared the transcriptomic profiles of primary BMSCs treated with Ginkgolic acid and Dexamethasone vs. DMSO and Dexamethasone.

overall_design: Total RNA were extracted from ginkgolic acid/ Dexamethasone or DMSO/Dexamethasone treated primary BMSCs (n=2), and used for RNAseq service provided by Novogene.


title: Lin28-mediated promotion of protein synthesis is critical for neural progenitor cell maintenance and brain development in mice

city: Los Angeles

first: WEI

last: ZHANG

state: California

address: 2250 Alcazar St

department: CCMB

institute: University of Southern California

summary: Neural progenitor cells (NPCs) undergo rapid proliferation during neurulation in early development. This rapid growth generates a high demand for mRNA translation in a timing-dependent manner, but its underlying mechanism and functional importance remain poorly understood. Lin28 is an RNA-binding protein with two paralogs, Lin28a and Lin28b, in mammals. Lin28b deletion exhibited no developmental defects in mice, while we previously reported that Lin28a deletion led to microcephaly. Here we found that Lin28a/b double knockout (dKO) mice displayed neural tube defects (NTDs) coupled with reduced proliferation and precocious differentiation of NPCs. We used ribosomal protein 24 hypomorphic mice (Rpl24Bst/+) as a genetic tool to dampen global protein synthesis. In support of the importance of Lin28-mediated translation promotion, Lin28a-/-;Rpl24Bst/+ compound mutants exhibited NTDs resembling those seen in Lin28a/b dKO mice. Furthermore, increased NPC numbers and brain sizes in Lin28a-overexpressing mice were rescued by Rpl24Bst/+ heterozygosity. Mechanistically, RNA-sequencing of polysome sucrose gradient fractions revealed a reduced translation of genes involved in the regulation of cell cycle, ribosome biogenesis, and translation in mutants. Lin28a localizes in the nucleoli of NPCs, and ribosome biogenesis was reduced in dKO and increased in Lin28a-overexpressing NPCs. Together, these results suggest that Lin28-mediated promotion of protein synthesis is essential for NPC maintenance and early brain development.

overall_design: Examination of  3 groups of transcriptomes and polysome profilings in mouse brain

first: Jian-Fu

last: Chen

first: Li-Wei

last: Xie


title: Cell resilience to folate deprivation boosts aberration tolerance [Illumina]

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array


title: Trans-maternal exposure to Helicobacter pylori induces stable and highly suppressive regulatory T-cells and protects against allergic airway inflammation

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

summary:
Purpose: The gastric microbe Helicobacter pylori represents an ancestral constituent of the human microbiota that causes gastric disorders on the one hand, and is inversely associated with allergies and chronic inflammatory conditions on the other. This study aims to investigate the consequences of trans-maternal exposure to H. pylori extract in utero and during lactation on the regulatory T-cell transcriptome profile.
Experiment type: Expression profiling by high throughput sequencing

overall_design: Transcriptome profling (RNA-seq) of lung regulatory T-cells in mice after perinatal PBS and H. pylori extract exposure. One factorial design with 2 levels (with and without H. pylori exposure) including 2-3 biological replicates per experimental group. A biological replicate represents pools from 3-4 animals.

first: Angela

last: Falleger

first: Hubert

last: Rehrauer

first: Anne

last: Müller