title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [AmpliSeq]

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

summary:
Background: High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades since the first mRNA profiling microarrays. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability and to what extent gene expression data from different platforms can be compared or integrated.
Purpose: In this study, we describe our experiences using nine new and established mRNA profiling techniques including Lexogen QuantSeq, Qiagen QiaSeq, BioSpyder TempO-Seq, Ion AmpliSeq, Nanostring, Affymetrix Clariom S or U133A, Illumina BeadChip and Ion Total RNA-seq of formalin-fixed paraffin embedded (FFPE) and fresh frozen (FF) sequential patient-matched breast tumour samples.
Results: The number of genes represented and reliability were found to vary between the platforms, but overall all methods provided data which were largely comparable. Crucially we found that it is possible to integrate data for combined analyses across FFPE/FF and platforms using established batch correction methods as required to increase cohort sizes. However, some platforms appear to be better suited to FFPE samples, particularly archival material. Overall, we illustrate that technology selection is a balance between required resolution, sample quality, availability and cost.

overall_design: Sequencing of patient-matched sets of human breast cancer biopsy samples using 9 different mRNA profiling platforms. We assess the feasibility of integrating data from FFPE or FF tissue sequenced using different platforms and compare these different technoolgies.

first: Arran

middle: K

last: Turnbull

first: Cigdem

last: Selli

first: Andrew

last: Sims


title: Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissue-of-origin

status: Public on May 07 2019

city: Chicagp

first: Yaping

last: Liu

state: IL

address: 303 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

summary: Three-dimensional chromatin organization varies across different cell types and is essential for gene regulation. However, current technologies are unable to assess in vivo genome-wide chromatin organization non-invasively. Here, we showed that long-range correlations in the fragment length of cell-free DNA (cfDNA) estimated from whole-genome sequencing recapitulate three-dimensional chromatin organization. The inferred organization is highly concordant with that measured by Hi-C in white blood cells from healthy donors, and is not explained by technical bias or sequence composition. Furthermore, the inferred organization reflects the differing genome organizations in the various cell types contributing to cfDNA, allowing quantification of cfDNA tissue-of-origin that is concordant with previous methods, but at much lower required DNA input. Our results, demonstrated in cfDNA from healthy individuals and cancer patients, may enable noninvasive monitoring of in vivo genome organization and accurate quantification of cell death in different clinical conditions.

overall_design: Compare two-dimensional fragmentation pattern in cell free DNA with Hi-C at white blood cell and then deconvolute the signals to reference cell types


title: PIPKIγ promotes tumor growth by facilitating Warburg effect in colorectal cancer

city: Shanghai

first: Junli

last: Xue

address: 1800 Yuntai Road, Pudong District

department: Department of Oncology

country: China

institute: Shanghai East Hospital, Tongji University School of Medicine

summary: Analysis of gene alterations in SW480 cells upon PIPKIγ knockdown. Our findings reveal a new regulatory role of PIPKIγ in Warburg effect and provide a key contributor in colorectal cancer metabolism with potential therapeutic potentials.

overall_design: sh-Ctrl SW480 cells versus sh-PIPKIγ SW480 cells.

first: Wei

last: Peng


title: RNA-seq data for Arabidopsis cbfs-1

city: Beijing

first: Yuxin

last: Jia

address: No. 2 Yuanmingyuan west road, Haidian district

department: Biology

institute: China Agricultural University

type: Expression profiling by high throughput sequencing

summary: In Arabidopsis, CBFs transcription factors (CBF1, CBF2 and CBF3) play fundamental roles in plant cold tolerance, especially in cold-acclimation. By employing CRISPR/Cas9, we knocked out CBF1 and CBF2 simultaneously in cbf3 background and generated cbfs triple mutant. This mutant facilitated the discovery of CBF-regulated genes. In this study, Arabidopsis 14-d-old Col-0 and cbfs mutant were treated with cold stress (4 degree centigrade) for 0, 3 and 24 hours. The seedlings were harvested for total RNA extraction and sequencing.

overall_design: 14-day-old Col and cbfs-1 seedlings were treated under 4 degree for 0, 3 and 24 h. The RNA were extracted for RNA-sequencing.

first: Shuhua

last: Yang


title: Engineering epigenetic memory requires co-targeting of histone methylatransferases and DNA methylatransferases [Methylation]

city: Los Angeles

first: Suhn

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve using targeted systems. Here, we report that robust and persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). DNMT3A-dCas9 was dependent on full-length DNMT3L for maximal activity. Co-targeting with Ezh2-dCas9, DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days and maintained a heterochromatic environment. Interestingly, substitution of Ezh2-dCas9 for KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the loci tested. Conversely, robust hypermethylation was observed at HER2. These data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci in the same cell, or the same locus in different cells.

overall_design: Genome-wide nethylation analysis of cells after treatment with Ezh2-dCas9 or KRAB-dCas9 cocktail with DNMT3A/DNMT3L or with dCas9 control using the Infinium Human MethylationEPIC BeadChip (Illumina)

first: Henriette

last: O'Geen

first: Peggy

middle: J

last: Farnham

first: David

last: Segal


title: Pollution Effects on Sensitive and Resistant Embryos: Integrating Structure and Function with Gene Expression

city: San Diego

first: Goran

last: Bozinovic

address: 3370 Dale Street

institute: Boz Institute

summary: To explore how gene expression translates to developmental phenotype in both sensitive and resistant Fundulus embryos upon POP exposure, we exposed Fundulus embryos from the Elizabeth River Superfund population and the Magotha Bay, VA clean population to Elizabeth River polluted sediment extracts and measured chemical uptake, gene expression, and altered embryo anatomy, morphology and cardiac physiology during four critical developmental stages: somitogenesis, heart beat initiation, late organogenesis, and pre-hatching.

overall_design:
A loop design was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores (PMID: 11355567;  12933549) modified as per Altman (PMID: 17371610).  The loop consisted of Cy3 and Cy5 labeled embryo aRNAs from 4 biological pools for four developmental stages (S: S21, S25, S31, and S35) and four different treatments (MM, ME, EM, and EE where the first letter denotes the family, sensitive (M = Magothas Bay) or resistant (E = Elizabeth River) and the second letter denotes the exposure, clean (M) or polluted (E) sediment extract.  In total, 64 biological pools were hybridized to 32 microarrays.  Each array had different combinations of biological pools, so that the most direct comparisons (i.e. EE vs MM stage 31 samples) are hybridized to the same array.  The loop formed was S21EE -- S21MM --S21EM--S21ME--S25EE--S25MM--S25EM--S25ME-- S31EE-- S31MM--S31EM--S31ME-- S35EE-- S35MM-- S35EM-- S35ME, where each dash represents a separate hybridization (array) with the biological pool at the left of the dash labeled with Cy3 and the biological pool at the right of the dash labeled with Cy5.
S21 = somitogenesis; S35 = heart beat initiation; S31 = late organogenesis; S35 = pre=hatching

first: Marjorie

middle: F

last: Oleksiak


title: RNA-seq analysis of hair cell regeneration in the mammalian vestibular system and its potentiation by Atoh1

city: Houston

first: Hsin-i

last: Jen

state: TX

address: One baylor plaza

department: Developmental biology

institute: Baylor college of medicine

summary: We used RNA-seq to probe the transcriptional and epigenetic responses of utricle supporting cells to damage and Atoh1 transduction.

overall_design: mRNA profiles of 4-6 weeks old mice utricle endogenous hair cell, supporting cells, supporting cell cultured for 10 days and supporting cells with overexpression of Atoh1 cultured for 10 days were generated by deep sequencing, in duplicate or triplicate, using Illumina Nextseq500 instrument

last: Groves


title: Engineering epigenetic memory requires co-targeting of histone methylatransferases and DNA methylatransferases

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The Hippo Pathway Blocks Mammalian Retinal Müller Glial Cell Reprogramming

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Müller glial cells (MGs) of the zebrafish retina exhibit the remarkable ability to reprogram to proliferative, retinal progenitor-like cells that can regenerate lost photoreceptors and restore vision. Unfortunately, mammalian MGs are not regenerative and this is at least in part due to the inability of MGs to undergo sustained cell cycle re-entry in response to retinal damage. Here, we identify the Hippo pathway as the core regulatory mechanism that normally prevents mammalian MG reprogramming to a proliferative, progenitor-like state. Specifically, in adult MGs within the damaged retina, Hippo signaling represses the activity of the transcription cofactor YAP, which would otherwise promote sustained MG cell cycle re-entry. MG-specific deletion of Hippo pathway components Lats1 and Lats2 resulted in Cyclin D1 upregulation and spontaneous MG proliferation. These data suggest that sustained YAP activity in reactive MGs induces MG proliferation and reprogramming, but this response is normally repressed by the Hippo pathway. Generation of MGs that express a variant of YAP (YAP5SA) that is non-responsive to Hippo signaling, resulted in cellular reprogramming whereby MG identity was lost and the cells acquired a highly proliferative, progenitor-like state.  Together, our results reveal that MGs may have latent regenerative capacity that can be “reawakened” by blocking Hippo signaling.

overall_design: Adult Glast-CreERT2+/tg; Yap5SA+/tg; R26R-tdTomato+/tg mice were induced with tamoxifen followed by NMDA injection.  After 2 days, tdTomato+ cells were isolated by fluorescence-activated cell sorting (FACS) followed by scRNA-seq using the 10X Genomics platform.

first: Ross

middle: A

last: Poche


title: Contrasting roles of transcription factors spineless and EcR in the highly dynamic chromatin landscape of butterfly wing metamorphosis

city: Ithaca

first: Karin

middle: Revka Loek

last: van der Burg

state: NY

address: 215 Tower Road, Corson Hall

department: EEB

institute: Cornell University

summary:
Background: We studied the chromatin accessibility landscsape in wings during butterfly metamorphosis, and investigate which transcription factors might be driving changes in accessibility
Methods: We sequencing the Junonia coenia genome, and we studied chromatin accessibility using ATAC seq in multiple stages of wing development in both forewings and hindwings. For sites showing a large change in accessibility, we investigate which motifs are enriched, and correlate this with changes in gene expression of associated transcription factors. We confirm promising candidates with ChIP-seq
Results: We find a highly dynamic landscape, with multiple peaks showing a double increase in accessibility throughout development. We show that transcription factor spineless, but not ecdysone receptor, is highly predictive of opening sites
Conclusions: This work provides a characterization of the chromatin dynamics of insect wing metamorphosis, identifies novel candidate chromatin remodeling factors in insects, and provides the first genome assembly of the model butterfly Junonia coenia, with gene and cis-regulatory element annotations

overall_design: ChIP-seq from left and right hindwings at three developmental stages.

middle: R

first: James

last: Lewis

first: Arnaud

last: Martin

first: H

last: Nijhout

first: Charles

middle: G

last: Danko

first: Robert

middle: D

last: Reed


title: Engineering epigenetic memory requires co-targeting of histone methylatransferases and DNA methylatransferases [ChIP-seq]

overall_design: ChIP-seq using cells 24 days after treatment with dCas9 cocktail (Ezh2 plus DNMT3A/DNMT3L) or with dCas9 control to determine genome-wide effect on H3K27ac


title: Time course of nitrogen-responsive transcriptomes in Nostoc sp. PCC7120

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

summary: In order to analyze the responses of a heterocystous cyanobacterium to combined-nitrogen depletion/addition, we have used customized microarrays to identify genes potentially involved in heterocysts differentiation by comparing the responses in the control strain and a hetR mutant unable to differentiate heterocysts. RNA samples were isolated from cells growing in the presence of combined nitrogen (ammonium) or after 6, 8, 12 or 24 h of nitrogen deprivation. Additionally, RNA was isolated from cells growing in the absence of combined nitrogen or 8 h after addition of ammonium

overall_design: Nitrogen deprivation-induced expression in Nostoc sp. PCC 7120 was measured in cells subjected to nitrogen deprivation for 0, 6, 8, 12 and 24 hours. Two different experiments were performed for each time-point, except for time 0 (three experiments), and time 8 (one experiment). Additionally, samples were isolated from cells growing without combined nitrogen (one experiment) and 8 h after ammonium addition (one experiment).

first: Manuel

last: Brenes-Álvarez

first: Jan

last: Mitschke

first: Wolfgang

last: Hess

first: Agustín

last: Vioque

first: Alicia

middle: M

last: Muro-Pastor


title: In vivo analysis of Influenza A mRNA secondary structures identifies critical regulatory motifs

status: Public on May 05 2019

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: The Influenza A virus (IAV) is a continuous health threat to humans as well as animals due to its high mutational rate and recurring epidemics and pandemics. The IAV genome is segmented and the eight negative-sense viral RNAs (vRNAs) are transcribed into positive sense RNAs (cRNAs) and viral messenger RNAs (vmRNAs) inside infected host cells. A role for the secondary structure of vmRNAs has been hypothesized and debated for many years, but knowledge on the structure vmRNAs adopt in vivo is currently missing. Here we solve, for the first time, the in vivo secondary structure of vmRNAs in living infected cells. We demonstrate that, compared to the in vitro refolded structure, in vivo vmRNAs are more unstructured but exhibit specific locally stable elements. Moreover, we show that the targeted disruption of these high-confidence structured domains results in an extraordinary attenuation of IAV replicative capacity. Collectively, our data provide the first comprehensive map of the in vivo structural landscape of IAV vmRNAs, hence providing the means for the development of new RNA-targeted antivirals.

sample_organism:
Escherichia coli
Influenza A virus

platform_organism:
Escherichia coli
Influenza A virus

overall_design: RNA structure probing

first: Lisa

last: Simon

first: Edoardo

last: Morandi

first: Anna

last: Luganini

first: Giorgio

last: Gribaudo

first: Luis

last: Martinez-Sobrido

first: Douglas

middle: H

last: Turner

first: Salvatore

last: Oliviero


title: The white adipose tissue transcriptional response to withdrawal of vitamin B3

status: Public on May 06 2019

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Distinct markers for early, mild vitamin B3 deficiency are lacking. To identify these, we examined the molecular responses of white adipose tissue to vitamin B3 withdrawal. We performed a dietary intervention in male C57Bl/6JRcc mice. A diet with a low but adequate level of tryptophan without nicotinamide riboside (NR) was compared to the same diet with NR at the recommended vitamin B3 (30 mg NR per kg diet). Physiological and circulating parameters were determined and global transcriptomics, qRT-PCR and histology of epididymal white adipose tissue (eWAT) were done. We observed a decreased insulin sensitivity and a shift from carbohydrate to fatty acid oxidation. This was consistent with molecular changes in eWAT, where we observed an altered MEK/ERK signalling, a lowering of glucose utilization markers and an increase in makers of fatty acid catabolism, which may be related to the consistent reduction of mitochondrial OXPHOS Complex I (mRNAs and protein). The synthesis pathway of tetrahydropteridine (BH4), an essential cofactor for neurotransmitter synthesis, was found to be increased. Based on our results, we propose the technically validated downregulation of Anp32a, Tnk2 and the upregulation of Mapk1, Map2k1, Mthfs, Mthfsl and Qdpr as a WAT transcriptional signature marker for mild vitamin B3 deficiency.

overall_design: The C57BL/6JRcc male mice (8 or 9 weeks old) were individually housed (12h light–dark cycle, 23±1°C, 55±15% humidity), with ad libitum access to feed and water. A semi-synthetic diet (40% energy from fat, 19% energy from protein, 41% energy from carbohydrates) was designed to contain a low, but sufficient amount of tryptophan (calculated 0.115% L-tryptophan) and either 0 or 30 mg nicotinamide riboside (NR) per kg diet as vitamin B3 (referred to as No NR and Ctrl NR, respectively). Mice were accustomed to this diet (Ctrl NR) for two weeks. Subsequently, mice were stratified into 2 experimental groups on mean body weight (n=12/group) and received the Ctrl NR or No NR diet for 18 weeks. Mice were provided with a limited amount of diet (with 0.8 gram of fresh experimental diet) at start of dark phase to have them fasted at end of dark phase; they were subsequently refed at start of light phase with 1.8 gram of diet for four hours and then sacrificed by decapitation.

first: Wenbiao

last: Shi

first: Vincent

last: de Boer

first: Inge

last: van der Stelt

first: Jaap

last: Keijer


title: Gene expression profiling identifies potential biomarkers for colorectal cancer using NanoString nCounter assay

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

institute: Shanghai Jiaotong University

summary:
The purpose of this study was to identify the differentially expressed genes and new potential predictive and prognostic molecular biomarkers for CRC.
We identified 101 genes that were upregulated and 76 genes that were downregulated in metastatic tumors. After validation, a reduced set of 27 genes revealed evident correlation with CRC in the tumor tissue. Several genes in the pan-cancer panel showed significant differential expression, which were more universal than others in the CRC tissue. Since some of them have not been reported as being directly related to CRC yet, future mechanism studies can be designed based on this study.Our study demonstrated NanoString nCounter assay could serve as an alternative approach for gene expression analysis and identified several unreported differently expressed genes in CRC patients, which may provide some important clues for more in-depth study of CRC and may serve as potential predictive molecular biomarkers for clinical diagnosis application as well.

overall_design: In this study, CRC and matched normal tissues acquired from the same patient were used to extract total RNA. The NanoString nCounter assay was applied to determine the differentially expressed genes. The results were then validated using the TCGA data.

first: Zhanrui

last: Mao

first: Xiaochen

last: Yang

first: Wei

last: Xu

first: Xiaoqian

last: Wu

first: Hua

last: Li

first: Xiaoyan

last: Wang

first: Yani


title: Characterization of the ALK7 signaling pathway in PanNET, using cell lines that either express dominant negative ALK7 (ALK7-DN), or subjected to ALK7 knock-down (shALK7), treated with activin B

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Herein we report that the TGFß superfamily receptor ALK7 is a suppressor of tumorigenesis and metastasis, as revealed by functional studies in mouse models of pancreatic neuroendocrine and luminal breast cancer, complemented by experimental metastasis assays. Activation in neoplastic cells of the ALK7 signaling pathway by its principal ligand activin B induces apoptosis. During tumorigenesis, cancer cells use two different approaches to evade this barrier, either downregulating activin B and/or ALK7. Suppressing ALK7 expression additionally contributes to the capability for metastatic seeding. ALK7 is associated with shorter relapse-free survival of various human cancers and distant-metastasis-free survival of breast cancer patients. This study introduces a new mechanistic insight into primary and metastatic tumor development, in the form of a protective barrier that triggers apoptosis in cells that are not ‘authorized’ to proliferate within a particular tissue, by virtue of those cells expressing ALK7 in a tissue microenvironment bathed in its ligand.

overall_design: We performed RNA-seq after treatment with activin B of control ßTC3 cells,  ßTC3 cells with DOX-inducible expression of either wild type ALK7 or ALK7-DN, and ßTC3 cells with DOX-inducible ALK7 knock-down.

first: Iacovos

last: Michael

last: Zangger

last: Hanahan


title: A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [RNA-seq]

status: Public on May 04 2019

first: Guoliang

address: 320 Yueyang Road

institute: Shanghai institute of biochemistry and cell biology

summary: Methylation of cytosine to 5-methylcytosine (5mC) is a prevalent DNA modification found in many organisms. Sequential oxidation of 5mC by TET dioxygenases results in a cascade of additional epigenetic marks and promotes DNA demethylation in mammals. However, the enzymatic activity and the function of TET homologs present in lower eukaryotes remains largely unexplored. In our study of TET homologs in the green alga Chlamydomonas reinhardtii (C. reinhardtii), we have found a 5mC-modifying enzyme (CMD1) that catalyzes conjugation of a glyceryl moiety onto the methyl group of 5mC through a carbon-carbon bond, resulting in two novel stereoisomeric nucleotide products. The catalytic activity of CMD1 requires Fe(II) and the integrity of its His-x-Asp (HxD) binding motif, which is conserved in Fe-dependent oxygenases. However, unlike all previous described TET enzymes which utilize 2-oxoglutarate (2-OG) as a co-substrate, CMD1 utilizes L-ascorbic acid (vitamin C, VC) as an essential co-substrate. VC itself is the source of the glyceryl moiety that modifies 5mC, with concurrent formation of glyoxylic acid and CO2. The VC-derived DNA modification is present in the genome of C. reinhardtii and its level decreases significantly in a CMD1 mutant strain. The fitness of CMD1 mutant cells to high light exposure is reduced, mainly due to deficient expression of the critical non-photochemical quenching (NPQ) effector gene LHCSR3, which is hypermethylated in the mutant cells. Our study thus reveals a new eukaryotic DNA base modification, and its involvement in a functionally conserved but mechanistically divergent DNA demethylation pathway for the epigenetic regulation of photosynthesis.

overall_design: Test the change of gene expression in CMD1 mutant cells

first: Jianhuang

last: Xue

last: Feng

first: Han

last: Yan

first: Changpeng

last: Xin


title: Reduction in Pax5 activity drives ionizing radiation-mediated B-cell acute lymphoblastic leukemia development by modulating DNA-damage response

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary: We used microarrays to investigate gene expression changes in tumor-bearing Pax5+/- IR and WT-IR mice. We also analyze gene expression changes in preleukemic Pax5+/- IR and WT-IR mice

overall_design: Tumor-bearing bone marrows of ten Pax5+/- IR and four WT-IR mice compared with preleukemic pro/pre-B bone marrow cells after three weeks of irradiation from seven Pax5+/- IR and three WT-IR mice respectively

first: Guillermo

last: Rodríguez-Hernández

first: Franziska

last: Auer

first: Idoia

last: García-Ramírez

first: Ute

last: Fisher

first: Inés

last: González-Herrero

first: Ana

last: Casado-García

first: Javier

last: Raboso-Gallego

first: Adrián

last: Blanco-Gómez

first: Alberto

last: Orfao

first: Oscar

last: Blanco

first: Diego

last: Alonso-López

last: De Las Rivas

first: Sara

last: de Tena-Dávila

first: Francisco

last: García Criado

first: María

middle: B

last: García Cenador

first: Jesús

last: Pérez-Losada

first: Julia

last: Hauer

first: Carolina

last: Vicente-Dueñas

last: Sanchez-Garcia

first: Arndt

last: Borkhardt


title: H3K4me3 profiling in SWD2-like Arabidopsis mutant seedlings

city: Paris

first: Lorenzo

last: Concia

email: colore@gmail.com, concia@bio.ens.psl.eu

address: 46 Rue d'Ulm

department: Institut de Biologie

country: France

institute: École Normale Supérieure

summary: The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution in defining gene expression programs are poorly defined in plant systems. Differently from S. cerevisiae in which a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with SET1), this activity involves multiple histone methyltransferases (HMTs) in Arabidopsis thaliana, among which the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. Here we report that SDG2 co-regulates hundreds genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of the evolutionarily conserved COMPASS complex. Accordingly, S2Lb associates with the AtCOMPASS core subunit WDR5a within a high-molecular weight complex and is required for proper H3K4me3 enrichment over genes highly occupied by RNA Polymerase II. S2Lb knock-out plants display little transcriptomic defects, suggesting that H3K4me3 deposition is important for optimal gene induction rather than for determining on/off transcriptional states. We further report that S2Lb and H3K4me3 are accurately targeted over most genes in hub1 mutant plants lacking histone H2B monoubiquitination. Collectively, our study indicates that a plant-specific COMPASS-like complex acting mainly through an H2Bub-independent mechanism is a major determinant of H3K4me3 deposition in Arabidopsis.

overall_design: 16 ChIP-seq libraries were sequenced

first: Fredy

last: Barneche

first: Moussa

last: Benhamed

first: Martin

last: Rougée

first: Clara

last: Bourbousse


title: ChIP-seq profiling in SWD2-like Arabidopsis mutant seedlings

overall_design: 6 ChIP-seq libraries were sequenced


title: Immune Resistance Emerges from Tumor-Initiating Stem Cells

city: New York

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

summary: Tumors are initiated and maintained by a stem cell-like population. However, our bodies have a powerful immune surveillance system to clear out cancerous cells as they emerge. Whether tumor-initiating stem cells (tSCs) are programmed to resist anti-tumor immunity and/or how they overcome the barrier of immune surveillance remains poorly understood. To address these questions, we designed a murine skin tumor model that can be effectively challenged by adoptive cell transfer (ACT)-based immunotherapy. By lineage tracing the tumor cells that survive targeted T cell treatment, we discovered that a subset of TGFβ-responding tSCs are refractory and responsible for tumor relapse. Single cell RNA-sequencing revealed that during malignant transformation, these tSCs selectively acquire CD80.  Thought to be an immune cell ligand, stem cell CD80 (scCD80) engagement with CTLA4 on activated cytotoxic T cells attenuates their attack. Moreover, without CD80 or in the face of CTLA4 blocking antibodies, tSCs become vulnerable to ACT immunotherapy. Our findings place the tumor-initiating stem cell at the crux of how immune checkpoint pathways are activated, and add a new mechanism to the fray.

overall_design: Mouse skin squamous cell carcinoma cells including tumor initiating cells before and after adoptive cell transfer (ACT)-based immunotherapy were FACS-purified and analyzed by single cell RNA-seq.

first: Yuxuan

last: Miao

first: Elaine

last: Fuchs


title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [Nanostring]

status: Public on May 03 2019

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

country: United Kingdom

institute: The University of Edinburgh

summary:
Background: High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades since the first mRNA profiling microarrays. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability and to what extent gene expression data from different platforms can be compared or integrated.
Purpose: In this study, we describe our experiences using nine new and established mRNA profiling techniques including Lexogen QuantSeq, Qiagen QiaSeq, BioSpyder TempO-Seq, Ion AmpliSeq, Nanostring, Affymetrix Clariom S or U133A, Illumina BeadChip and Ion Total RNA-seq of formalin-fixed paraffin embedded (FFPE) and fresh frozen (FF) sequential patient-matched breast tumour samples.
Results: The number of genes represented and reliability were found to vary between the platforms, but overall all methods provided data which were largely comparable. Crucially we found that it is possible to integrate data for combined analyses across FFPE/FF and platforms using established batch correction methods as required to increase cohort sizes. However, some platforms appear to be better suited to FFPE samples, particularly archival material. Overall, we illustrate that technology selection is a balance between required resolution, sample quality, availability and cost.

overall_design: Sequencing of patient-matched sets of human breast cancer biopsy samples using 9 different mRNA profiling platforms. We assess the feasibility of integrating data from FFPE or FF tissue sequenced using different platforms and compare these different technoolgies.


title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [BioSpyder_TempoSeq]

first: Arran

last: Turnbull

first: Cigdem

last: Selli

first: Andrew

last: Sims


title: PR attentuation of interferon signaling

city: San Antonio

first: Tianbao

last: Li

state: Texas

address: 7703 Floyd Curl

department: Molecular Medicine

institute: University of Texas Health Science Center at San Anotnio

summary: Why some tumors remain indolent and others progress to clinical relevance remains a major unanswered question in cancer biology. Interferon signaling in nascent tumors, mediated by STAT1, is a critical step through which the surveilling immune system can recognize and destroy developing tumors. Herein, we have identified an interaction between the progesterone receptor (PR) and STAT1 in breast cancer cells. This interaction inhibited efficient interferon-induced STAT1 phosphorylation, as we observed a decrease in phospho-STAT1 in response to interferon treatment in PR-positive breast cancer cell lines. This phenotype was further potentiated in the presence of PR ligand. In human breast cancer samples, PR-positive tumors exhibited lower levels of phospho-STAT1 as compared to their PR-negative counterparts, indicating that this phenotype translates to human tumors. Breast cancer cells lacking PR exhibited higher levels of interferon-stimulated gene (ISG) RNA, the transcriptional endpoint of interferon activation, indicating that unliganded PR alone could decrease transcription of ISGs. Moreover, the absence of PR led to increased recruitment of STAT1, STAT2 and IRF9 (key transcription factors necessary for ISG transcription) to ISG promoters. These data indicate that PR, both in the presence and absence of ligand, attenuates interferon-induced STAT1 signaling, culminating in significantly abrogated activation of genes transcribed in response to interferons. PR-positive tumors may use downregulation of STAT1-mediated interferon signaling to escape immune surveillance, leading to the development of clinically relevant tumors. Selective immune evasion of PR-positive tumors may be one explanation as to why over 65% of breast cancers are PR-positive at the time of diagnosis.

overall_design: 2 different cell lines (T47D-Y [PR null] and T47D-co [PR-positive]) were treated +/- interferon and R5020 (PR ligand), in biologic triplicate. There are a total of 8 groups, 3 replicates each, making for 24 samples total

first: Christy

last: Hagan


title: Brain transcriptome profiling in wildtype mice and mice with Igf2 enhancer deletion (Igf2enh-/-) [RNA-seq]

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

summary: Impaired neuronal processes, including dopamine imbalance, are central to the pathogenesis of major psychosis, but the molecular origins are unclear. We report the first multi-omics study of neurons isolated from the prefrontal cortex of individuals with schizophrenia and bipolar disorder, including genome-wide neuronal DNA methylation using Illumina EPIC microarrays, transcriptomes and SNP genotypes (n=55 cases and 27 controls). Epigenetic, transcriptomic, and genetic-epigenetic interactions in disease converged on pathways of neurodevelopment, synaptic activity, and immune functions. Notably, we discovered prominent hypomethylation of an enhancer within the insulin-like growth factor 2 (IGF2) gene in neurons of major psychosis patients. Chromatin conformation analysis revealed that this enhancer targets the nearby tyrosine hydroxylase (TH) gene, which is responsible for dopamine synthesis. IGF2 enhancer hypomethylation was associated with increased TH protein levels in the human brain. The Igf2 enhancer was deleted in mice to explore the transcriptomic and proteomic consequences of this genomic locus in the frontal cortex and striatum. In mice, Igf2 enhancer deletion disrupted levels of TH protein and striatal dopamine, as well as induced transcriptional and proteomic abnormalities affecting development and synaptic function. Epigenetic control of the IGF2 enhancer may regulate dopamine levels and contribute to psychosis risk.

overall_design: We profiled transcriptomes froom the frontal cortex and striatum of wild-type (N=14) and Igf2enh-/- (N=13) mice

middle: S

first: Viviane

last: Labrie


title: Gene expression profiling in SWD2-like Arabidopsis mutant seedlings

overall_design: 4 RNA-seq libraries were sequenced


title: Plant microRNA profiling of amiRNAs transgenic lettuce

city: Nanjing

last: Zhang

state: Jiangsu

address: 163 Xianlin Road

department: Life of Science

institute: Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: We conducted two amiRNA (amiR417 and amiR519) transgenic lettuce lines. In order to confirm that the target artificial miRNAs (amiR417 and amiR519) were correctly transcribed and analysis the cleavage sites of the 3’ and 5’ ends of amiR471, small RNA fragments were extracted from ten independent positive T2 generations and examined using Solexa deep sequencing.

overall_design: Total RNA from 10 regular or T3 generation expressing amiR471 or amiR519 lettuce plants were extractedfor Solexa deep sequencing

first: Shuo

first: Xiaolin

last: Sang


title: A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [Bisulfite-seq]

city: Shanghai

first: Guoliang

last: Xu

type: Methylation profiling by high throughput sequencing

summary: Methylation of cytosine to 5-methylcytosine (5mC) is a prevalent DNA modification found in many organisms. Sequential oxidation of 5mC by TET dioxygenases results in a cascade of additional epigenetic marks and promotes DNA demethylation in mammals1,2. However, the enzymatic activity and the function of TET homologs present in lower eukaryotes remains largely unexplored. In our study of TET homologs in the green alga Chlamydomonas reinhardtii (C. reinhardtii), we have found a 5mC-modifying enzyme (CMD1) that catalyzes conjugation of a glyceryl moiety onto the methyl group of 5mC through a carbon-carbon bond, resulting in two novel stereoisomeric nucleotide products. The catalytic activity of CMD1 requires Fe(II) and the integrity of its His-x-Asp (HxD) binding motif, which is conserved in Fe-dependent oxygenases3. However, unlike all previous described TET enzymes which utilize 2-oxoglutarate (2-OG) as a co-substrate4, CMD1 utilizes L-ascorbic acid (vitamin C, VC) as an essential co-substrate. VC itself is the source of the glyceryl moiety that modifies 5mC, with concurrent formation of glyoxylic acid and CO2. The VC-derived DNA modification is present in the genome of C. reinhardtii and its level decreases significantly in a CMD1 mutant strain. The fitness of CMD1 mutant cells to high light exposure is reduced, mainly due to deficient expression of the critical non-photochemical quenching (NPQ) effector gene LHCSR3, which is hypermethylated in the mutant cells. Our study thus reveals a new eukaryotic DNA base modification, and its involvement in a functionally conserved but mechanistically divergent DNA demethylation pathway for the epigenetic regulation of photosynthesis.

overall_design: Test the change of cytosine methylation  level in CMD1 mutant cells

first: Jianhuang

last: Xue

first: Zhaoyuan

last: Fang

first: Han

last: Yan

first: Changpeng

last: Xin


title: Deficiency of Socs3 Leads to Brain-targeted EAE via Enhanced Neutrophil Activation and Production of Reactive Oxygen Species

city: Birmingham

first: Etty

last: Benveniste

state: AL

address: 510 20th Street South, 1220 Faculty Office Tower

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

summary: Dysregulation of the JAK/STAT signaling pathway is associated with Multiple Sclerosis (MS) and its mouse model, Experimental Autoimmune Encephalomyelitis (EAE). Suppressors Of Cytokine Signaling (SOCS) negatively regulate the JAK/STAT pathway. We previously reported a severe, brain-targeted, atypical form of EAE in mice lacking Socs3 in myeloid cells (Socs3ΔLysM), which is associated with cerebellar neutrophil infiltration. There is emerging evidence that neutrophils are detrimental in the pathology of MS/EAE, however, their exact function is unclear. Here we demonstrate that neutrophils from the cerebellum of Socs3ΔLysM mice show a hyper-activated phenotype with excessive production of reactive oxygen species (ROS) at the peak of EAE. Neutralization of ROS in vivo delayed the onset and reduced severity of atypical EAE. Mechanistically, Socs3-deficient neutrophils exhibit enhanced STAT3 activation, a hyper-activated phenotype in response to G-CSF, and upon G-CSF priming, increased ROS production. Neutralization of G-CSF in vivo significantly reduced the incidence and severity of the atypical EAE phenotype. Overall, our work elucidates that hypersensitivity of G-CSF/STAT3 signaling in Socs3ΔLysM mice leads to atypical EAE by enhanced neutrophil activation and increased oxidative stress, which may explain the detrimental role of G-CSF in MS patients.

overall_design: Bone marrow cells were isolated from the femurs of Socs3fl/fl or Socs3ΔLysM mice. Red blood cells were lysed by incubation in ACK lysis buffer for 1 min.  CD45+CD11b+Ly6G+ neutrophils were flow sorted and stimulated with or without G-CSF (10 ng/ml) for 8 hours. Total RNA was purified from cells using Trizol reagent extraction, and 500 ng–2 μg of RNA was sent to GENEWIZ (South Plainfield, NJ) for RNA-seq and bioinformatics analysis.

first: Zhaoqi

first: Wei

last: Yang

first: Luke

last: Parkitny

first: Sara

last: Gibson

first: Kevin

last: Lee

first: Forrest

last: Collins

first: Jessy

last: Deshane

first: Wayne

last: Cheng

first: Amy

last: Weinmann

first: Hairong

last: Wei

first: Hongwei

last: Qin

middle: N


title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [QiaSeq]

first: Carlos

last: Martinez-Perez

first: Arran

last: Turnbull

first: Cigdem

last: Selli

first: Andrew

last: Sims


title: Transcriptional response of Ostreococcus tauri to Cu challenge

city: Santiago

first: Rodrigo

last: De la Iglesia

address: Portugal 49

country: Chile

institute: Pontificia Universidad Católica de Chile

summary: We test the transcriptional response of O. tauri RCC745 cells to two different copper concentration (0,4 and 2 µM), after 1, 4 and 12 h of copper amendments.

overall_design: RNAseq libraries were constructed using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) by the NGS Service FASTERIS (Switzerland). Libraries were multiplexed in one channel of 1 x 50 bp run on a MiSeq run for titration and quality control. Finally, the libraries were sequenced using an Illumina HiSeq 2000 sequencer. All sequences were searched for homologies against the KEGG database and against the most recent O. tauri genome annotation.

first: François-Yves

last: Bouget


title: DNA methylation in neurons from post-mortem brains in schizophrenia and bipolar disorder (Bisulfite-Seq)

first: Shraddha

last: Pai

summary: We fine-mapped DNA methylation in neuronal nuclei (NeuN+) isolated by flow cytometry from post-mortem frontal cortex of the brain of individuals diagnosed with schizophrenia, bipolar disorder, and controls (n=29, 26, and 27 individuals).

overall_design: Targeted bisulfite sequencing was performed on genomic DNA using the captured using the SeqCap Epi Enrichment System (Roche).

first: Viviane

last: Labrie


title: Transcriptome analysis in Jurkat cell with sufficient and deficient ZBTB24 expressions

city: Suzhou

first: Jun

last: Wang

address: 199 Ren-Ai Rd, Suzhou University,, Suzhou Industrial Park,

institute: Soochow University

summary: We knocked down ZBTB24 expressions in Jurkat cells by lentiviral infections. Four-five days later, virus infected cells (GFP+) were FACS purified for RNA extraction with the Total RNA Kit II (OMEGA). Library construction and sequencing was performed on a BGISEQ-500 by Beijing Genomics Institution (BGI) in Wuhan, China.

overall_design: RNA-seq of 6 samples.

first: Xiao-Yuan

first: Ge

last: Chen

first: Jing

last: Feng

first: Xun-Wu

last: Dou

first: Qiao

last: Zhong

first: Fang-Yuan

last: Gong

first: Ying

last: Zhao

first: Xiao-Ming

last: Gao


title: H3K4me3 profiling in HUB1 Arabidopsis mutant seedlings

first: Lorenzo

last: Concia

overall_design: 8 ChIP-seq libraries were sequenced. Two biological replicates each consisting of one Input and one IP for each genotype (WT and hub1-3 mutant)

first: Fredy

last: Barneche

first: Moussa

last: Benhamed

first: Martin

last: Rougée

first: Clara

last: Bourbousse


title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [Lexogen_QuantSeq]

first: Carlos

last: Martinez-Perez

first: Arran

last: Turnbull

first: Cigdem

last: Selli

first: Andrew

last: Sims


title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [Affy_ClariomS]


title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [Illumina]


title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [Affy_U133A]


title: Targeting mitochondrial structure sensitizes AML to Venetoclax

city: new york

first: Xufeng

address: 550 First Avenue, Smilow 1307

institute: NYU Langone Medical Center

summary: The BCL-2 family plays important roles in acute myeloid leukemia (AML) and Venetoclax, a selective BCL-2 inhibitor, has received FDA approval for treatment of AML. However, drug resistance ensues after prolonged treatment, highlighting the need for a greater understanding of the underlying mechanisms.  Using a genome-wide CRISPR/Cas9 screen in human AML, we identified genes whose inactivation sensitizes AML blasts to Venetoclax. Genes involved in mitochondrial organization and function were significantly depleted throughout our screen, including the mitochondrial chaperonin CLPB. We demonstrated that CLPB is upregulated in human AML, it is further induced upon acquisition of Venetoclax resistance and its ablation sensitizes AML cells to Venetoclax. Mechanistically, CLPB maintains the mitochondrial cristae structure via its interaction with the cristae-shaping protein OPA1, whereas its loss promotes apoptosis by inducing cristae remodeling and mitochondrial stress responses. Overall, our data suggest that targeting mitochondrial architecture may provide a promising approach to circumvent Venetoclax resistance.

overall_design: RNA-sequencing (RNA-Seq) was performed to 1) explore the molecular mechanisms underpinning the Venetoclax resistance and 2) underlying mechanisms of CLPB function in AML cells.

first: Christina

last: Glytsou

first: Iannis

last: Aifantis


title: Transcriptome analysis of nascent hematopoietic cells

city: Kumamoto

first: Tomomasa

last: Yokomizo

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary:
During ontogeny, hematopoietic stem cells (HSCs) and erythroid-myeloid progenitors (EMPs) are generated from distinct hemogenic endothelium. Nascent HSCs and EMPs are distinguished by the expression of Hlf.
To obtain mechanistic insight into HSC specification, we compared the gene expression profiles between Hlf+ and Hlf- nascent hematopoietic cells.

overall_design: Hlf+ and Hlf- nascent hematopoietic cells (c-Kit+CD45-) were isolated from embryonic day (E)10.5 caudal half and E9.5 yolk sac, respectively, and were subjected to RNA-seq analysis.

first: T

last: Umemoto

last: Suda

first: M

last: Osato


title: Role of fatty acid synthase in oligodendrocyte myelination

city: Zürich

first: Laura

last: Montani

state: ZH

address: Otto Stern Weg 7

institute: IMHS - ETH Zürich

summary: In the central nervous system, oligodendrocytes encase axons with myelin, a highly organized multilayered membrane structure. Myelin allows the rapid propagation of action potentials along the axons, while also supporting their mantainance metabolically. Fatty acids are basic building blocks for both glyco- and phospholipids, key constituents of cell membranes. Moreover, fatty acids can modify proteins via palmitoylation and activate transcriptional networks, e.g. through the PPARs transcription factors. Due to the high demand of membrane oligodendrocytes face to produce myelin, we hypothesized that they strongly rely upon fatty acid synthesis rather than mostly on their intake from the dietary pool. We tested this hypothesis by deleting the enzyme Fatty Acid Synthase specifically from neonatal oligodendrocyte progenitor cells, in vivo in C57Bl/6 olig2Cre FASN floxed mice. We addressed the consequences of this depletion on oligodendrocytes differentation and myelination potential in the central nervous system. In particular, we analyzed by RNA-seq how lack of FASN affected the transcriptome of optic nerves dissected from P14 mutant (olig2Cre FASN lox/lox) versus control (FASN lox/lox) mice.

overall_design:
Mice (Mus musculus) homozygous for the fatty acid synthase (Fasn) floxed allele (Strain of origin: 129X1/SvJ, subsequently crossed with 129X1/SvJ * C57BL/6 * DBA) were crossed with mice expressing Cre recombinase under the control of the Olig2 promoter (Strain of origin: C57Bl/6), to obtain Cre+ Fasn lox/lox mutant mice, and Cre- Fasn lox/lox control mice. Fasn floxed mice were backcrossed for at least 3 generations into C57Bl/6 background and Olig2Cre mice were kept on a C57Bl/6 background.

n = 3 mice for mutants (olig2cre FASN lox/lox) and n = 4 mice for controls (FASN lox/lox) were compared. For both P14 mice were used and both optic nerves dissected from each mouse.

first: Ueli

last: Suter


title: Exon Level Expression Profiling of Focal Segmental glomerulosclerosis (FSGS)

first: Jingsong

last: Shi

state: China

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

institute: Jinling Hospital, Nanjing University School of Medicine

summary:
Transcriptome comparison of glomeruli from kidneys with FSGS and glomeruli from the unaffected portion of tumor nephrectomies.
This study aims to investigate the pathogenesis and the mechanism of FSGS

overall_design: We applied high-throughput transciptomics method and tested the gene expression profile of microdissected glomeruli from FSGS patients. RNA was processed using the Affymetrix® microarray platform (Human Transcriptome Array 2.0, HTA 2.0). Array data was processed by Affymetrix Expression Console software. No techinical replicates were performed.

first: Zhihong

last: Liu

first: Hao

last: Bao

first: Song

last: Jiang

first: Qing

last: Hou

first: Weibo

last: Le

first: Yinhui

last: Lu


title: Genotypes of case-control samples in major psychosis

first: Shraddha

last: Pai

summary: We fine-mapped DNA methylation in neuronal nuclei (NeuN+) isolated by flow cytometry from post-mortem frontal cortex of the brain of individuals diagnosed with schizophrenia, bipolar disorder, and controls (n=29, 26, and 28 individuals). These genotype arrays were generated in the same samples to identify genetic-epigenetic interactions.

overall_design: Post-mortem brain samples were obtained through the NIH NeuroBioBank at the University of Pittsburgh; the Harvard Brain Tissue Resource Center; the Human Brain and Spinal Fluid Resource Center at Sepulveda; and the University of Miami Brain Endowment Bank. Genotypes were mapped in 103 samples (84 biological replicates: 28 control; 29 schizophrenia; 27 bipolar disorder), using genomic DNA extracted from brain tissue. 8 samples were assayed in triplicate, and the rest had no technical replicates. SNPs in each sample (n=104) were determined using the Infinium PsychArray-24 processed by The Centre for Applied Genomics (Toronto, Canada). Samples were randomized across SNP arrays. GenomeStudio was used to extract genotype data for each sample.

first: Viviane

last: Labrie


title: DNA methylation in neurons from post-mortem brains in schizophrenia and bipolar disorder (RNA-Seq)

summary: We fine-mapped DNA methylation in neuronal nuclei (NeuN+) isolated by flow cytometry from post-mortem frontal cortex of the brain of individuals diagnosed with schizophrenia, bipolar disorder, and controls (n=29, 26, and 28 individuals).

overall_design: Brain tissue samples (n=34 human samples, 17 case and 17 control) were lysed using QIAzol Lysis Reagent (Qiagen) and homogenized with a TissueLyser (Qiagen). Total RNA from each sample was isolated using the RNeasy Plus Universal Mini kit (Qiagen) according to manufacturer’s instructions and included an enzymatic DNase (Qiagen) digestion step. RNA quality was measured on a 2100 Bioanalyzer (Agilent) and quantity was determined with a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific). Only RNA samples with a RIN quality score >7 proceeded to RNA-seq library preparation (RIN between 7.1 to 9.4 for all samples). Libraries were prepared by the Van Andel Genomics Core from 300 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bioo Scientific). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp.), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).  Individually indexed libraries were pooled, and 75 bp paired-end sequencing was performed on an Illumina NextSeq 500 sequencer, with all libraries run across 3 flowcells.  Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.    Trimgalore (v0.11.5) was used for adapter removal prior to genome alignment. STAR33 (v2.3.5a) index was generated using Ensemble GRCh38 p10 primary assembly genome and the Gencode v26 primary assembly annotation. Read alignment was performed using a STAR two-pass mode. Gene counts matrix was imported into R (3.4.1) and low expressed genes (counts per million (CPM) < 1 in all samples) were removed prior to differential expression in EdgeR. Gene counts were normalized using the trimmed mean of M-values, fitted in a generalized linear model and differentially tested using a likelihood ratio test. The generalized linear model contained covariates age, sex, post mortem interval and neuronal cell composition. Cell-type compositions for each sample was accessed using CIBERSORT34 on normalized sample counts against cell-type specific markers, identifying the proportion of neurons in each samples. Benjamini Hochberg correction was used to adjust for multiple testing.


title: RPL12/uL11 phosphorylation regulates translation during mitosis [RIP-seq]

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

summary: Emerging evidence indicates that heterogeneity in ribosome composition can give rise to specialized functions. Until now, research mainly focused on differences in core ribosomal proteins and associated factors. The impact of posttranslational modifications has not yet been studied systematically. Analyzing ribosome heterogeneity is challenging since individual proteins can be part of different subcomplexes (40S, 60S, 80S and polysomes). Here, we develop polysome proteome profiling to obtain unbiased proteomic maps across ribosomal subcomplexes. Our method combines extensive fractionation by sucrose gradient centrifugation with quantitative mass spectrometry. The high resolution of the profiles allows us to assign proteins to specific subcomplexes. Phosphoproteomics on the fractions reveals that phosphorylation of serine 38 in RPL12/uL11 -- a known mitotic CDK1 substrate -- is strongly depleted in polysomes. Follow-up experiments confirm that RPL12/uL11 phosphorylation regulates translation of specific subsets of mRNAs during mitosis. Together, our results show that posttranslational modification of ribosomal proteins can regulate translation.

overall_design: Gene expression profiling of immunoprecipitated RPL12 protein-RNA complexes

first: Koshi

last: Imami

first: Miha

last: Milek

first: Boris

last: Bogdanow

first: Nicolai

last: Kastelic

first: Tomoharu

last: Yasuda

first: Matthias

last: Selbach


title: RPL12/uL11 phosphorylation regulates translation during mitosis [Ribosome profiling]

overall_design: Ribosome profiling of B cells with different mutant RPL12 backgrounds


title: RPL12/uL11 phosphorylation regulates translation during mitosis

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RPL12/uL11 phosphorylation regulates translation during mitosis [RNA-seq]

overall_design: 3'mRNAseq of B cells with different mutant RPL12 backgrounds


title: DNA methylation in neurons from post-mortem brains in schizophrenia and bipolar disorder (Methylation)

overall_design: Whole-genome DNA methylation profiling for each sample was done with Illumina MethylationEPIC BeadChip microarrays at the The Centre for Applied Genomics (Toronto, Canada). Bisulfite converted DNA samples (n=104) were randomized across arrays (8 samples/array). Data generated from the microarrays were preprocessed with Minfi v1.19.12. Normalization was performed with noob, followed by quantile normalization. All samples had sex matching that predicted from the methylome.  Probes that overlapped SNPs (MAF > 5%) on the CpG or single-base extension were excluded (11,812 probes), as were probes known to be cross-reactive (42,558 probes; PMID: 27330998) and those that failed detectability (P>0.01) in >20% samples (1,170 probes). After processing, 812,663 probes were left. Based on principal component analysis (PCA) co-clustering, one sample, despite being labeled NeuN+, clustered with NeuN- samples and was excluded from downstream analyses. Surrogate variable analysis identified no such variables; for this the null model used age and sex as covariates, while the full model included diagnosis.


title: DNA methylation in neurons from post-mortem brains in schizophrenia and bipolar disorder


title: Gene expression profiling in two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells

status: Public on May 02 2019

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

summary: A549 and MDA-MB-231 cells were cultured in 2D and Matrigel based 3D culture for 4 days. Total RNA was extracted using Trizol. RNA-SEQ was carried out to profile the gene expression in both culture conditions.

overall_design: The goal of this experiment was to profie the genes that are regulated by extracellular matrix in cancer cells. Gene expression was probed globally using RNA-SEQ.

first: Simon

last: Alsager


title: Cytosine methylation profiling in two dimensional and extracellular matrix based three-dimensional cultures of breast cancer cells

summary: MDA-MB-231 cells were cultured in 2D and Matrigel based 3D culture for 4 days. Total DNA was extracted. Bisulfite treatment and BS-SEQ were carried out to profile global cytosine methylation in both culture conditions.


title: Two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells


title: MCMV-experienced ILC1 acquire an m12-dependent memory response

city: New Haven

first: Orrel

last: Weizman

state: CT

address: 333 Ceder Street

department: Immunology

institute: Yale

summary: Innate and adaptive immune cells can acquire “memory” of encounters with a diverse  range of activating signals to tune their response to secondary stimuli. Group 1 innate  lymphoid cells (ILC1) are recently discovered tissue-resident sentinels that are essential  for early host protection from intracellular pathogens at initial sites of infection.  However, whether ILC1 function as short-lived effectors or persist and refine their  responsiveness following pathogen challenge is not well understood. Furthermore,  whether pathogen-derived antigens directly modulate tissue-resident ILC responses  remains unclear. Here, we found that liver-resident ILC1 expand locally and persist  following the resolution of mouse cytomegalovirus (MCMV) infection. MCMVexperienced  ILC1 acquired stable transcriptional, epigenetic, and phenotypic changes,  with an enhanced protective effector response to secondary MCMV challenge. Protective  memory ILC1 responses were dependent on the MCMV-encoded glycoprotein m12, but  not formed during bystander cytokine activation following heterologous infection. Thus,  liver ILC1 acquire adaptive features in a MCMV-specific manner.

overall_design: RNA and ATAC sequencing analysis of sorted liver ILC1 from naïve and MCMV experienced WT mice. PRJNA528997 SRP189404

first: Orr-El

first: Timothy

last: O'Sullivan


title: Affymetrix SNP array data for Dwarf and Rhode Island Red chicken samples

city: Beijing

first: Changsheng

last: Nie

address: Yuanmingyuan road 2#

department: Animal Genetics and Breeding

institute: China Agricultural University

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

summary: The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. We found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples.

first: Liang

last: Qu

first: Zhihua

last: Jiang

first: Kehua

last: Wang

first: Lujiang

first: Zhonghua

last: Ning


title: Overexpression of poly(rC) binding protein 2 by alternative cleavage and polyadenylation promotes breast cancer progression via regulating UFD1 and NT5E

city: Hefei

first: Hao

state: Anhui

address: 81 Meishan Road

institute: Anhui Medical University

summary: Alternative cleavage and polyadenylation (APA) is an important post-transcriptional regulatory mechanism, which could lead many diseases. PCBP2 plays critical roles in mRNA stabilization, translational enhancement and contributes to human cancer development and progression even though the molecular mechanism is not completely understood. Herein, we report that increased expression of PCBP2 is observed in human breast cancer tissues compared to benign or normal breast tissues, and high expression of PCBP2 is significantly associated with disease progression and poor outcome in patients with breast cancer. Knockdown of PCBP2 expression significantly decreased breast cancer cell proliferation, migration and invasion in vitro and in vivo. Molecularly, UFD1 and NT5E were identified as the downstream genes of PCBP2, which were scanned and verified based on RNA sequencing. Moreover, PCBP2 promotes oncogenic behaviors of breast cancer cells via upregulating the expression of UFD1 and NT5E by directly binding to their 3' untranslated regions (UTRs). Furthermore, we determine that the APA process is involved in regulating the overexpression PCBP2 in breast cancer cells. Therefore, our findings reveal that APA of PCBP2 3' UTR contributes to its overexpression and then promotes breast cancer progression by regulating the expression of UFD1 and NT5E.

overall_design: The expression of PCBP2 in human benign breast disease tissues and breast cancer tissues was evaluated by immunohistochemistry and western blot. Second, the association of PCBP2 expression with clinicopathological parameters and survival of breast cancer patients were analyzed. Third, the role of PCBP2 in breast cancer cell proliferation, migration and invasion was determined in vitro and in vivo. In the following stage, the downstream genes of PCBP2 was scanned by RNA sequencing and verified by western blotting, immunohistochemistry as well as qRT-PCR. Meanwhile, Biotin pull-down assay was carried out to examine the binding site of PCBP2 protein in UFD1 or NT5E mRNA. Finally, 3'RACE was performed to detect the APA status of PCBP2 mRNA.

first: Sheng

last: Tan

first: Zhengsheng

last: Wu


title: Identification and validation of miRNAs in colorectal cancer (CRC) in early age diagnosed patients without MMR defect

city: Madrid

first: ELISA

last: CONDE MORENO

address: Carretera de Colmenar KM9.100

department: Pathology

institute: Instituto Ramón y Cajal de Investigación Sanitaria, IRYCIS

summary: transcriptional profiling (miRNAs) of human biopsies of colorectal cancer tumors (Lynch Sindrome, Sporadic old, Sporadic young and normal mucosa)

overall_design: Four experimental groups: Normal mucosa, Lynch sindrome, Sporadic CRC diagnosed under 45 years, Sporadic CRC diagnosed over 45 years. Biological replicates:1 non-tumour colonic mucosae as control, 2 sporadic CRC patients diagnosed under 45 years without Lynch syndrome, 3 CRC patients with Lynch syndrome, 2 sporadic CRC patients diagnosed over 45 years without Lynch syndrome. One replicate per array.

first: Laura

last: García Bermejo

first: Elisa

last: Conde Moreno


title: MAFB controls the transcriptional profile of human anti-inflammatory macrophages

first: Ángel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu, 9

department: Molecular Microbiology and Infection Biology

institute: Consejo Superior de Investigaciones Científicas


title: Genetic characterization of bronchoalveolar lavage fluid cells from patients with IPF and sarcoidosis

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary:
Background: Sarcoidosis and idiopathic pulmonary fibrosis (IPF) are two most frequent forms of interstitial lung diseases (ILDs). Cellular and biochemical composition of bronchoalveolar lavage fluid (BALf) was shown to reflect the proliferative and fibrotic changes in the local environment in the lung. However, the usefulness of BALf cellular profile evaluation in the diagnosis of ILDs is limited. The aim of the study was a multivariate, molecular, comparative analysis of BALf cells from IPF and sarcoidosis patients.

Methods: Transcriptomic measurements were carried out using Affymetrix Human Gene 2.1 ST ArrayStrip in 21 samples: 9 IPF and 12 sarcoidosis. The mRNA expression for the most significantly differentiating genes was evaluated by real time PCR in 32 samples (11 IPF and 21 sarcoidosis).

Results: The number of genes differentially expressed between IPF and sarcoidosis groups were 4832 (13359 probesets). Our cluster analysis indicated that sarcoidosis BALf cells are characterized by increased mRNA expression of genes associated with ribosome biogenesis, transcription machinery. Clusters formed by genes with changed mRNA expression in IPF samples were implicated in the processes of cell adhesion and migration, metalloproteinase expression and negative regulation of cell proliferation. PCR verification showed higher expression of ANK3 in the sarcoidosis compared to the IPF group, and higher expression of MMP7 and PPBP in patients with IPF. The GO analysis indicated that predominant biological processes associated with the differential mRNA gene expression of BALf cells were upregulation of neutrophils in IPF and lymphocytes in sarcoidosis.

Conclusions: Analysis of BALf from sarcoidosis and IPF showed highly different mRNA profile of cells present in bronchoalveolar compartment and provided new data on the pathobiology of these ILDs. The changes of most important biological processes observed at the molecular level in BALf cells were associated with ribosome biogenesis and proteasome apparatus in sarcoidosis and neutrophilic dysfunction in IPF.

overall_design: The microarray experiments were performed using 21 samples: 9 IPF and 12 sarcoidosis.

first: Magdalena

last: Paplinska-Goryca

first: Paulina

last: Misiukiewicz-Stępień

first: Patrycja

last: Nejman-Gryz

first: Małgorzata

last: Proboszcz

first: Katarzyna

last: Górska

first: Marta

last: Maskey-Warzęchowska

first: Rafał

last: Krenke


title: ChIP-seq and RNA-seq in HUB1 and SWD2 Arabidopsis mutant seedlings

city: Paris

first: Lorenzo

last: Concia

address: 46 Rue d'Ulm

institute: École Normale Supérieure


title: MAFB controls the acquisition of the anti-inflammatory transcriptional profile of M-MØ.

summary: Macrophage phenotypic and functional heterogeneity derives from tissue-specific transcriptional signatures shaped by the local microenvironment. Most studies addressing the molecular basis for macrophage heterogeneity have focused on murine cells, while the factors controlling the functional specialization of human macrophages are less known. M-CSF drives the generation of human monocyte-derived macrophages with a potent anti-inflammatory activity upon stimulation. We now report that knock-down of MAFB impairs the acquisition of the anti-inflammatory profile of human macrophages, identify the MAFB-dependent gene signature in human macrophages and illustrate the co-expression of MAFB and MAFB-target genes in CD163+ tissue-resident and tumor associated macrophages. The contribution of MAFB to the homeostatic/anti-inflammatory macrophage profile is further supported by the skewed polarization of monocyte-derived macrophages from Multicentric Carpo Tarsal Osteolysis (OMIM#166300), a pathology caused by mutations in the MAFB gene. Our results demonstrate that MAFB critically determines the acquisition of the anti-inflammatory transcriptional and functional profiles of human macrophages.

overall_design: Macrophages were differentiated from peripheral blood monocytes from 3 healthy donors with M-CSF (M-MØ) to generate anti-inflammatory M-MØ. Macrophages were transfected with either Control or MAFB-specific siRNA for 24h and global gene expression was analysed.

first: Víctor

last: Cuevas

first: Miguel

last: Vega


title: Genome-wide maps of Set1 and H3K4me3 in budding yeast

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: We report the application of ChIP-sequencing technology for high-throughput profiling of histone modifications in budding yeast. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide maps of Set1 and H3K4me3 in yeast cells. We find that Set1 and H3 lysine 4 trimethylation locate primarily in open reading frame of genes. In addition, we focus on the distribution of Set1 and H3K4me3 in histone gene clusters and found strong similar binding of Set1 and H3K4me3 on all histone genes.

overall_design: Examination of Set1-FLAG, H3 and H3K4me3 in yeast cells. Untagged Set1 was used as control.

first: Shanshan

last: Li


title: Mutations in MAFB that cause Multicentric Carpo Tarsal Osteolysis (MCTO) affect the transcriptome of M-MØ

overall_design: Macrophages were differentiated with M-CSF from peripheral blood monocytes from 1 patient with MCTO and 2 healthy donors. Two RNA samples from macrophages derived from the MCTO patient were analysed in parallel.


title: Transcriptome response study of arabidopsis wild type (Col6-3), gun1-9 mutant and MORF2 overexpression lines to norflurazon treatment in retrograde signaling

city: La Jolla

first: Joanne

last: Chory

state: CA

address: 10010 N Torrey Pines Rd

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

summary: Analysis of transcriptome response of norflurazon treated or untreated 5-day old whole seedlings with genotypes: Col6-3 (wild type), gun1-9 and MORF2 overexpression lines.  GUN1 and MORF2 are involved in chloroplast-to-nucleus retrograde signaling. Results provide insight into the nuclear genes expression profile under control of GUN1 retrograde pathways and the regulation similarity between gun1-9 and MORF2 overexpression lines.

overall_design: Total RNA samples were isolated from 5-day old whole seedlings with genotypes Col6-3 (wild type), gun1-9 and MORF2 overexpression lines grew under 24 h light condition with 100 µmol.m-2.s-1 light intensity at 22 °C with or without 5 μM norflurazon treatment. MORF2OX and MORF2OX(w) are both overexpression lines of MORF2 but they have different strengths of the phenotype. mRNA expression profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.

first: Xiaobo

last: Zhao

first: Jianyan

last: Huang


title: Fasting and the side effects of irinotecan

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary: We investigated the transcriptional responses of fasting against side effects of irinotecan chemotherapy in both tumor and healthy liver tissue

overall_design: 41 samples, each from individual mice

first: Franny

last: Jongbloed


title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in chronic lymphocytic leukemia

city: New York

first: Omar

last: Abdel-Wahab

address: 1275 York Ave

department: HOPP

institute: MSKCC

summary: Cancer evolution is fueled by genetic and epigenetic diversity, and intra-tumoral heterogeneity in DNA methylation has been shown to co-operate with genetic heterogeneity to empower evolutionary capacity of cancers such as chronic lymphocytic leukemia. Here, we show that epigenetic diversification leads to decreased coordination across layers of epigenetic information, likely reflecting an admixture of cells with diverging epigenetic identities. This manifests in incomplete gene silencing by the Polycomb complex, unexpected co-occurrence of typically mutually exclusive activating and repressing histone modifications, and greater cell-to-cell transcriptional heterogeneity.

overall_design: Given the importance of histone modifications to lineage plasticity in cancer15-17, intra-leukemic epigenetic heterogeneity may extend to histone modifications, likely promoting lineage plasticity by enabling permissive chromatin states. To address this question, we complemented DNAme analysis with a chromatin immunoprecipitation sequencing (ChIP-seq) compendium of histone post-translational modifications (H3K4me3, H3K27ac, H3K4me1, H3K27me3, H3K9me3 and H3K36me3) and transcriptome sequencing (RNA-seq) in a cohort of primary CLL and healthy B lymphocytes samples (CLL IGHV unmutated, n = 12; CLL IGHV mutated, n = 10; peripheral blood NBCs [CD23+CD19+CD27−IgD+], peripheral blood memory B cells [GCBs; CD23+CD19+CD27+IgD-], peripheral blood CD20+ cells.

first: Alessandro

last: Pastore

first: Federico

last: Gaiti

first: Sydney

middle: X

last: Lu

first: Ryan

last: Brand

first: Scott

last: Kulm

first: Kevin

middle: Y

first: Hongcang

last: Gu

first: Elena

last: Stamenova

first: Ronan

last: Chaligne

first: Wendy

last: Béguelin

first: Yanwen

last: Jiang

first: Rafael

last: Schulman

first: Kyu-Tae

last: Kim

first: Alicia

last: Alonso

first: John

last: Allan

first: Richard

last: Furman

first: Catherine

last: Wu

first: Ari

last: Melnick

first: Andreas

last: Gnirke

first: Alexander

last: Meissner

first: Bradley

middle: E

last: Bernstein

first: Dan

last: Landau


title: Next generation sequencing transcriptomic analysis of bone marrow derived macrophages within control, Cbl-/-, Cbl-b -/- and DKO genotypes

status: Public on May 01 2019

city: Brookings

first: Adam

middle: David

last: Hoppe

state: SD

address: Avera Health and Sciences Building RM 131, Box 2202

department: Chemistry and Biochemistry

institute: South Dakota State University

summary: The goal of the transcriptomic profiling is to understand what genes or pathway Cbl and Cbl-b regulate for CSF-1R dependent growth signaling

overall_design: Comparision of the transcriptome of Bone marrow derived macrophages within control, Cbl-/-, Cbl-b -/- and DKO, each genotype has 3 replicates

first: Lu

last: Huang

first: Natalie

last: Thiex

first: Jason

last: Kerkvliet


title: The effect of carbon fiber after 1 month instillation on mouse

city: Gifu

first: Akihiro

last: Moriyama

address: 1-1, Yanagido

institute: Gifu University

summary: Gifu Prefecture and Gifu University are developing technologies for recycling used carbon fiber because the waste disposal process is highly cost and energy intensive. However, generation of carbon fiber dust during the recycling process is a serious issue, especially in the occupational environment. Recycling requires carbonization by partial firing treatment at 500℃ followed by firing treatment at 440℃: these processes produce dust as a by-product. In this study, three types of carbon fibers; before recycling, after carbonization, and after firing were evaluated for their toxic effects on mice. It is important to study the influence of carbon fibers on human health at a gene expression level.

overall_design: Stress induced gene expression in mouse lung was measured at 1 month after exposure to doses of 200 µg/ mouse carbon fiber by intratracheal administeration.  Series contains at least three hybridization results from independent biological samples respectively in four injection conditions (Condition 1. carbon fiber before recycled (VCF), 2. carbon fiber after carbonization (CCF), 3. carbon fiber after firing (RCF), 4.  PBS vehicle control).

first: Hitoshi

last: Iwahashi


title: Next Generation Sequencing Analysis of Beta-actin knockout (KO) Mouse Embryonic Fibroblast (MEFs) Transcriptomes Stimulated by Viral Mimics

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: mRNA profiles of beta-actin knockout (KO) MEFs stimulated by viral mimics to study how global transcriptome changes after innate viral immunity activation

overall_design: The goals of this study are to use NGS to perform transcriptome profiling (RNA-seq) to find the changes of the global gene expression programs after viral mimic stimulation in beta-actin knockout (KO) Mouse Embryonic Fibroblasts (MEFs). MEFs were stimulated by 10 ug/ml Poly(dA:dT) or Poly(I:C) using Lipofectamine 2000 (Invitrogen) as transfection reagent in Opti-MEM medium for 6 hours. Mock groups were treated only with transfection reagent. Total RNA was extracted and submitted to RNA-seq

first: Xin

last: Xie

first: Nizar

last: Drou

first: Raza

last: Mahmood


title: Apple fruit superficial scald resistance mediated by ethylene inhibition is associated with diverse metabolic processes

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

summary: Fruits stored at low temperature for long time can undergo to different type of chilling injuries. In apple, superficial scald represents one of the most serious physiopathy. The typical symptoms of this disorder are represented by the development of important discoloration and black patches on the fruit exocarp. Although this phenomenon has been historically related to α-farnesene, its etiology and physiology are not yet fully disclosed. In the attempt to elucidate the regulating mechanism of its development and prevention, a multidisciplinary survey was performed, integrating different level of metabolite screening (volatiles, polyphenols and lipids) with a large-scale transcriptomic analysis. The comparison between scalded and non-scalded apples (treated with an ethylene competitor) revealed that the prevention of superficial scald is associated with the triggering of cold acclimation-related processes. The interference at the ethylene receptor level stimulates the production of antioxidant compounds to scavenge reactive oxygen species (ROS), the synthesis of unsaturated fatty acids to stabilize plastid and vacuole membranes against cold temperature and the accumulation of sugar alcohols with important cryoprotectant roles, such as sorbitol. The accumulation pattern of this polyalcohol was also consistent with the expression profile of MdS6PDH. Moreover, the overexpression of this gene in transgenic line of Arabidopsis thaliana plants provided functional validation of its involvement in the biosynthetic pathway of sorbitol and elucidated its role in the cold acclimation and freezing tolerance process.

overall_design: RNA-Seq analysis of 5 samples of apple exocarp. T0 (control), T2_CTRL (2 months of cold storage in control condition), T2+7_CTRL (7 days of shelf-life after 2 months of cold storage in control condition), T2_MCP (2 months of cold storage treated with 1-MCP), T2+7_MCP (7 days of shelf-life after 2 months of cold storage treated with 1-MCP). Each sample was replicated three times.

first: Nicola

last: Busatto

first: Brian

last: Farneti

first: Mauro

last: Commisso

first: Martino

last: Bianconi

first: Barbara

last: Idarola

first: Elisa

last: Zago

first: Benedetto

last: Ruperti

first: Francesco

last: Spinelli

first: Angelo

last: Zanella

first: Riccardo

last: Velasco

first: Alberto

last: Ferrarini

first: Giulia

last: Chitarrini

first: Massimo

last: Delledonne

first: Urska

last: Vrhovsek

first: Flavia

last: Guzzo

first: Guglielmo


title: The effect of carbon fiber after 6 month instillation on mouse

first: Akihiro

last: Moriyama

overall_design: Stress induced gene expression in mouse lung was measured at 6 month after exposure to doses of 200 µg/ mouse carbon fiber by intratracheal administeration.  Series contains at least three hybridization results from independent biological samples respectively in four injection conditions (Condition 1. carbon fiber before recycled (VCF), 2. carbon fiber after carbonization (CCF), 3. carbon fiber after firing (RCF), 4.  PBS vehicle control).

first: Hitoshi

last: Iwahashi


title: The effect of carbon fiber after 1 or 6 months instillation on mouse

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

overall_design: Refer to individual Series


title: RNAseq of E. coli Sakai O157:H7 in the presence of the flexicate compound Λ-5b

city: Coventry

first: Alexia

last: Hapeshi

address: Gibbet Hill

institute: University of Warwick

summary: The synthetic flexicate compound Λ-5b shows potent antimicrobial activity against E. coli. In this study we investigated the transcriptomic response of a clinically relevant E. coli, EHEC O157:H7, to a sublethal concentration of the compound.

overall_design: E. coli Sakai O157:H7 stx- grown to mid-exponential was treated with either methanol (control) or 0.5 µg/ml of Λ-5b (dissolved in methanol). Samples undergoing the two treatments were paired ie they originated from the same culture. Following a 40 min incubation samples were harvested and RNA was extracted.

first: Dan

last: Simpson

first: Guy

middle: J

last: Clarkson

first: Joseph

last: Healey

first: Gemma

last: Kay

first: Viktor

last: Brabec

first: Andrew

last: King

last: Millard

first: David

last: Roper

first: Nicholas

last: Waterfield

first: Peter

last: Scott

first: Jaroslav

last: Malina

first: Ondrej

last: Hrabina

last: Fox

first: Hualong

last: Song

first: John

last: Moat


title: Comparison of endogenous gene expression of HCT116 colorectal cancer cells and HCT116-derived DAPK1 knockout (ko) clones.

city: Erlangen

first: Regine

last: Schneider-Stock

state: Bavaria

address: Universitaetsstrasse 22

department: Department of Pathology

institute: University Hospital Erlangen

type:
Expression profiling by array
Other

summary:
Data were obtained via Nanostring nCounter Gene Expression Assay (PanCancer Progression Panel, XT_PGX_HuV1_CancerProg_CSO XT-CSO-PROG1-12, Cat. no. 115000152, Nanostring Technologies, Hamburg, Germany)
We aimed to reveal Death-associated protein kinase 1 (DAPK1)-dependent gene expression in the context of tumor progression covering genes involved in extracellular matrix, epithelial-mesenchymal transition, metastasis and angiogenesis comparing  HCT116 DAPK1 wt cells and three different monoclonal DAPK1 ko clones named clone 7/6, clone 10/8 and clone 21/9. DAPK1 ko clones were generated by CRISPR/Cas9-mediated genomic editing.

overall_design: In this study, untreated biological replicates of HCT116 wt (n =3) and DAPK1 ko clones (clone 7/6: n = 2; clone 10/8: n = 3; clone 21/9: n = 1) were screened for gene expression of cancer progression related genes (770 genes including 30 housekeeping genes). Tumor cells were cultured in a 100 mm cell culture dish in RPMI 1640 medium supplemented with 1% penicillin/streptomycin and 10% FBS until 80% confluency and harvested via scraping off the plate. RNA was isolated from snap-frozen cell pellets. Gene expression analysis was performed using the human nCounter® PanCancer Progression Panel (NanoString Technologies). Total RNA was isolated from frozen cell pellets by QIAzol-chloroform extraction followed by RNeasy Mini Kit (Qiagen, Hilden, Germany) preparation. Isolated RNA (100 ng) was processed through the NanoString nCounter Prep Station. Briefly, the hybridization reaction (3 µl Reporter CodeSet, 5 µl hybridization buffer, 2 µl Capture ProbeSet and 5 µl total RNA) containing 100 ng RNA (HCT116: n = 3; clone 7/6: n = 2; clone 10/8: n = 3; clone 21/9: n = 1) was conducted for 16 h at 65 °C. Subsequently, samples were processed according to the manufacturer’s instructions and signals of reporter probes were counted and tabulated using the nCounter Digital Analyzer (NanoString Technologies). Finally, housekeeping gene (geometric mean of 30 genes) normalization for quantitating gene expression levels, positive control normalization for background noise correction and data analysis was performed using nSolver™ Analysis Software 3.0 (NanoString Technologies, Hamburg, Germany) and standard settings. The fold-change of counts was determined by averaging results per DAPK1 ko cell line and comparing them to average counts of HCT116 cells.

first: Sara

last: Steinmann

first: Philipp

last: Kunze

first: Markus

last: Eckstein

first: Jesper

last: Bertram Bramsen

first: Julienne

last: Muenzner

first: Birgitta

last: Carlé

first: Benardina

last: Ndreshkjana

first: Pierluigi

last: Gasparini

first: Oliver

last: Friedrich

first: Claus

last: Andersen

first: Shengbao

last: Wang

first: Ilker

last: Eyuepoglu

first: Tobias

last: Bäuerle

first: Arndt

last: Hartmann


title: RNA-seq of erythroid cells from 24 hours post fertilization sf3b1 mutant and sibling zebrafish

city: Bronx

first: Teresa

last: Bowman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development.

overall_design: mRNA profiling of gata1-positive erythroid cells isolated from 24 hours post fertilization sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.

middle: V


title: Conjugation, genetic reprogamming and horizontal transfer of pathogenicity between Roseobacters

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Horizontal transfer of plasmids is one of the main drivers of bacterial adaptation, resulting e.g. in the spread of antibiotic resistance. We investigated the marine Roseobacter group and studied how conjugation affects the gene expression and biology of the new host. We showed that the two syntenic 126 kb and 191 kb plasmids of Dinoroseobacter shibae can be conjugated into representatives of all major lineages of Rhodobacteraceae. In the model organism Phaeobacter inhibens their acquisition resulted in differential expression of genes related to motility, transport and the synthesis of vitamins. Moreover, the decrease of the potent antibiotic tropodithietic acid reduced the energetic burden of Phaeobacter and resulted in an enhanced growth. While the T4SS systems of both plasmids were silenced in the new host, the ability to kill the dinoflagellate was exclusively transferred via the 191 kb plasmid from D. shibae to P. inhibens. Our findings showed drastic consequences of plasmid conjugation; genetic reprogramming of the novel host resulted in considerable fitness changes leading to the prediction that horizontal gene transfer triggers bacterial speciation.

sample_organism:
Dinoroseobacter shibae
Phaeobacter inhibens

overall_design: 2 to 3 independent biological replicates for each of the strains were collected. Replicons present in all strains were taken into account for each comparison.

first: Victoria

last: Ringel

first: Hui

first: Pascal

last: Bartling

first: John

last: Vollmers

first: Michael

last: Jarek

first: Irene

last: Wagner-Döbler

first: Jörn

last: Petersen


title: DNA methylation analysis of NNMT overexpression and knockdown in stromal cells

city: Chicago

first: Mark

middle: Adam

last: Eckert

state: IL

address: 929 East 57th St, W107

department: OB/GYN

institute: University of Chicago

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA  methylation profiling in response to overexpression or knockdown of NNMT in stromal cells. The Illumina MethylationEPIC array was used to profiled genome-wide methylation of normal fibroblasts expressing a control construct or NNMT overexpression construt and cancer-associated fibroblasts (CAFs) expressing an shCtrl or shNNMT construct. Two biological replicates of each experimental group were profiled following growth in 10 micromolar methionine growth media for 21 days.

overall_design: Bisulphite converted DNA from the 8 samples (4 experimental groups with two biological replicates per group) were hybridised to the Illumina InfiniumMethylationEPIC array.

middle: A

first: Ernst

last: Lengyel


title: Mice modeling human CNVs associated with psychiatric disorders

city: Los Angeles

first: Aaron

last: Gordon

address: Gonda Building, 695 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: 139 samples from cortex and hipocampus of the mice modeling human CNVs associatted with schizophrenia: Df(h15q13)/+, Df(h15q13)/-, Df(h22q11)/+, and Df(h1q21)/+

first: Annika

last: Grønborg-Forsingdal

first: Ib

last: Klewe

first: Jacob

last: Nielsen

last: Didriksen

first: Thomas

last: Werge

first: Daniel

last: Geschwind


title: Effect of Salmeterol and Roflumilast N-oxide (RNO) alone and in combination on gene expression changes in BEAS-2B human airway epithelial cell line

city: Calgary

first: Radhika

last: Joshi

state: Alberta

address: 2500 UNIVERSITY DR NW

department: Physiology and Pharmacology

institute: University of Calgary

summary: RNA-sequencing was performed to study the effect of phosphodiesterase 4 inhibition by Roflumilast N-oxide (RNO) on gene expression changes produced by sub-maximal concentrations of the long acting β2-adrenoceptor agonist, Salmeterol. Our results indicate that RNO enhanced the expression of all salmeterol-regulated genes, but the degree of enhancement varied between genes due to the difference in their sensitivities to salmeterol.

overall_design: Confluent BEAS-2B cells were treated for two hours with vehicle, RNO (1 µM), a maximal concentration of Salmeterol (100 nM), two sub-maximal concentrations of Salmeterol (0.3 nM and 0.5 nM), and their combination with RNO (Salm0.3 + RNO, Salm0.5 + RNO). Total RNA was extracted, quantified, processed into mRNA libraries, and sequenced across two high-throughput sequencing kits on a NextSeq 500 instrument (Illumina).

last: Giembycz


title: endogenous mRNA decay in 293t, hela, RPE cell line

first: Shiyuan

middle: (Cynthia)

last: Chen

department: Computational Biology

institute: Stowers Institute for Medical Research

summary:
mRNA endogenous decay profiles approach in 293T, HeLa and RPE cells.
mRNA translation decodes nucleotide into amino acid sequences. However, translation has also been shown to affect mRNA stability depending on codon composition in model organisms, although universality of this mechanism remains unclear. Here, using three independent approaches to measure exogenous and endogenous mRNA decay, we define which codons are associated with stable or unstable mRNAs in human cells. We demonstrate that the regulatory information affecting mRNA stability is encoded in codons and not in nucleotides. Stabilizing codons tend to be associated with higher tRNA levels and higher charged/total tRNA ratios. While mRNAs enriched in destabilizing codons tend to possess shorter poly(A)-tails, the poly(A)-tail is not required for the codon-mediated mRNA stability. This mechanism depends on translation; however, the number of ribosome loads into a mRNA modulates the codon-mediated effects on gene expression. This work provides definitive evidence that translation strongly affects mRNA stability in a codon-dependent manner in human cells.

overall_design: 3 different cells with different timepoint,  Cells were sub-cultured in 24 well plate overnight, so the cells were at around 80% coverage before treatment. Actinomycin D was added into the well, with final concentration of (5ug/ml), in 0.1% DMSO. Cells were directly collected with Trizol, at desired time-point for RNA extract. RNA-seq with ribo depletion  was done for each sample, to calculate mRNA decay based on time-course mRNA-seq. For 293t, it is also treated with Cycloheximide. It was added at 2ug/ml, in H2O.  "ad" in sample name means actinomycin D treatment, "chx" in the name means Cycloheximide.

first: Qiushuang

last: Wu

first: Ariel

last: Bazzini


title: Genome-wide analysis of uterine natural killer cell gene expression from control diet-fed and high fat diet-fed female mice in early pregnancy

city: Vancouver

first: Alexander

middle: G

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

institute: The University of British Columbia

summary: Analysis of gene expression in uterine natural killer cells purified from control, diet-induced obese and diet-induced obese resistant female mice. The aim of the study is to identify differentially expressed genes and pathways in uterine natural killer cells  affected by maternal diet and obesity in pregnancy.

overall_design: Total RNA isolated from FACS-sorted uterine natural killer cells from Gd10.5 pregnancies in 10 control, 6 diet-induced obese and 4 diet-induced obese resistant mice.

first: Jennet

last: Baltayeva


title: BDE-47 CpG Methylomic Alterations in Human Embryonic Stem Cell-derived Neural Precursor Cells

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

summary: Methylomic characterization of BDE-47 exposures in human neural precursor cells

overall_design:
Methylome of human neural precursor cells exposed to BDE-47 (10 or 1μM) or vehicle for 24h.
Sample processing and hybridization was performed by the UCSF Gladstone Institute

first: H

middle: C

first: Y

last: Kim

first: J