title: Aegilops tauschii reference genome sequence Aet v5.0 including annotation of small RNAs and reannotation of protein-coding genes

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research.   Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research.   Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research.

overall_design: 6 Small RNA libraries from 4 different tissues were sequenced and analyzed based on improved genome reference. No replicates were included in this work.

last: Baldrich

first: Blake

last: Meyers

first: Le

last: Wang

first: Jan

last: Dvorak


title: SMAD4 Controls Morphogenetic SHH Signaling via Direct Transcriptional Regulation of Cholesterol Biosynthesis in Early Mouse Limb Buds [ATAC-seq]

status: Public on Jul 29 2021

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This study describes the functions of SMAD4 during early mouse limb bud development by identifying the direct transcriptional targets

overall_design: ATAC-seq of either e9.5 or e10.5 limb buds

first: J

last: Gamart

first: F

last: Laurent

first: I

first: A

last: Visel

first: L

last: Ramos Martins

first: R

last: Zeller

last: Zuniga


title: SMAD4 Controls Morphogenetic SHH Signaling via Direct Transcriptional Regulation of Cholesterol Biosynthesis in Early Mouse Limb Buds

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: SMAD4 Controls Morphogenetic SHH Signaling via Direct Transcriptional Regulation of Cholesterol Biosynthesis in Early Mouse Limb Buds [RNA-seq]

overall_design: Total mRNAs from either e10.0 or e10.5 forelimb buds, from wild-type or Smad4∆/∆c mice


title: Profiling of sorted cell populations in mouse bleomycin induced lung fibrosis

status: Public on Aug 06 2021

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

country: USA

institute: Genentech

summary: To understand the cellular composition and transcriptional phenotype of different cell populations in the mouse bleomycin induced fibrosis model, we performed RNAseq analysis on leukocyte, endothelial, epithelial and stroma (other) cell populations isolated from mouse lung samples.

overall_design: Mice recieved intratracheal injection of either saline or bleomycin. We selected time point day 14, which was the peak of gene expression of most pro-fibrotic genes in this model. We isolated four different cell types from C57/B6 mouse lungs by FACS sorting: epithelial (EpCAM+), leukocytes (CD45+), endothelial (CD31+), and others (triple negative; EPCAM-CD45-CD31-). RNA was harvested via RNeasy kit (Qiagen). There were two groups, G1:C57/B6, male mice I.T. with Saline (n=5) ; and G2: C57/B6, male mice I.T. with Bleomycin (n=8).

first: Tianhe

last: Sun

middle: A

first: Joseph

middle: R

last: Arron

first: Claire

middle: L

last: Emson

first: Alexander

last: Abbas

first: Zhiyu

last: Huang


title: Metformin affects transcriptomic pathways involved in cell survival, metabolism and angiogenesis in ovarian cancer cells

status: Public on Aug 17 2021

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

summary: The objectives of the present study are to determine the effect of metformin on sphere formation, extracellular matrix invasion, and transcriptome profile of ovarian cancer (COVCAR) cells isolated from ascites of chickens that naturally developed ovarian cancer.  Our results suggest that metformin treatment significantly decreased sphere formation and invasiveness of COVCAR cells.  Pairwise statistical analysis of transcriptomic data using Deseq2 software revealed 0, 4, 365 genes that were differentially expressed (DEGs) in cells treated with 0.5, 1, 2 mM metformin-treated cells compared to controls, respectively.

overall_design: COVCAR cells were subjected to metformin treatment at 0, 0.5, 1, 2-mM concentration. We performed RNAseq analysis using the Illumina® software platform on RNA samples extracted from metformin-treated COVCAR cells.  Four replicates were sequenced for each condition. On average, 50 million 75 base pair single-end reads were sequenced for each replicate. Statistical analysis was performed for pairwise comparison between treatment and control group.

first: Lalitha

last: Gopalan

first: Ramesh

last: Ramachandran

first: Istvan

last: Albert

first: Craig

last: Praul


title: NTRK1 fusions for the therapeutic intervention of Korean patients with colon cancer

status: Public on Jul 31 2021

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

country: South Korea

institute: Seoul National University

summary: The identification and clinical validation of cancer driver genes are essential to accelerate the translational transition of cancer genomics, as well as to find clinically confident targets for the therapeutic intervention of cancers. Here we identified recurrent LMNA-NTRK1 and TPM3-NTRK1 fusions in Korean patients with colon cancer (3 out of 147, 2%) through next-generation RNA sequencing (RNA-seq). NTRK1 fusions were mutually exclusive oncogenic drivers of colon cancer that were accompanied with in vitro potential of colony formation and in vivo tumorigenicity comparable to KM12, a human colon cancer cell line harboring TPM3-NTRK1 fusion. NTRK1-encoded TrkA protein was prevalent in 11 out of 216 Korean (5.1%) and 28 out of 472 Chinese patients (5.9%) from independent cohorts, respectively. The expression level of TrkA was significantly correlated with NTRK1 fusion (p = 0.0192), which was verified by a fluorescence in situ hybridization (FISH). Korean patients with TrkA-positive colon cancer had a marginal but significant shorter overall survival time than TrkA-negative colon cancer [hazard ratio (HR) = 0.5346, 95% confidential interval (CI) = 0.2548-0.9722, p = 0.0411]. In addition, KM12 cell line was sensitive to selective TrkA inhibitors. These results demonstrate that NTRK1 fusion is granted as a clinically relevant target for therapeutic intervention of colon cancer.

overall_design: Fresh frozen tissues resected between 2008 and 2012 from patients with primary colon cancer and matched normal controls were used in this study. Informed consent was obtained from all patients. Tumor tissues were selected according to the tumor sample inclusion criteria of the International Cancer Genome Consortium (ICGC). Briefly, tumor tissues composed of more than 60% of tumor cells and less than 20% of necrotic cells or normal cells on histological assessment were included. Tumor tissues from patients who had a family history of colon cancer were excluded. In total, 150 tumor and 50 matched normal tissues were analyzed.

first: Do

middle: Y

first: Chan

last: Choi

first: Jong-Il

last: Kim


title: Extracellular vesicles mediate molecular signalling during Hydra regeneration

status: Public on Jul 30 2021

city: Pozzuoli

first: Claudia

last: Tortiglione

address: Via Campi Flegrei, 34

department: Istituto di Scienze Applicate e Sistemi Intelligenti "E.caianiello"

country: Italy

institute: National Research Council of Italy

summary: Recent body of evidence demonstrates that extracellular vesicles (EVs) represent the first language of cell-cell communication emerged during evolution. In aquatic environments, transferring signals between cells by EVs offer protection against degradation, allowing delivering of chemical information in high local concentrations to the target cells. The packaging of multiple signals, including those of hydrophobic nature, ensures target cells to receive the same EV-conveyed messages, and the coordination of a variety of physiological processes across cells of a single organisms, or at the population level, i.e. mediating the population´s response to changing environmental conditions. Here, we purified EVs from the medium of the freshwater invertebrate Hydra vulgaris, and the molecular profiling by proteomic and transcriptomic analyses revealed multiple markers of the exosome EV subtype. Moreover, positive and negative regulators of the Wnt/β-catenin signaling pathway, the major developmental pathway acting in body axial patterning, were identified. Functional analysis on amputated polyps revealed EV ability to interfere with both head and foot regeneration, suggesting an active role in setting up tissue gradients and oro-aboral polarity through delivery of short and long-distance signals. Our results open the path to unravel EV biogenesis and function in all cnidarian species, tracing back the origin of the cell-cell, cross-species or cross-kingdom communication in aquatic ecosystems

overall_design: Morphological and molecular characherization of Extracellular Vescicles (Evs) isolated from Hydra Vulgaris specimens

first: Maria

last: Moros

first: Eugenio

last: Fergola

first: Valentina

last: Marchesano

first: Margherita

last: Mutarelli

first: Giuseppina

last: Tommasini

first: Beata

last: Miedziak

first: Giuliana

last: Palumbo

first: Alfredo

last: Ambrosone

first: Angela

last: Tino


title: A quantitative map of human primary microRNA processing sites [2]

status: Public on Jul 27 2021

city: Gwanak

last: Baek

state: Seoul

address: Gwank 1

type: Non-coding RNA profiling by high throughput sequencing

summary: Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). Over 1,800 miRNA loci are annotated in humans, but it remains largely unknown if and at which sites the pri-miRNAs are cleaved by DROSHA. Here we performed in vitro processing on a full set of human pri-miRNAs (miRBase v21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs based on DROSHA-dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing as well as unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.

overall_design: In vitro processing of human pri-miRNAs with the purified Microprocessor

first: Kijun

first: S

middle: C

first: Young-Yoon

last: Lee

first: Carolien

last: Bastiaanssen

first: Jeesoo

first: Headong

first: V

middle: N


title: Analysis of long and short enhancers in melanoma cell states

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

summary: Understanding how enhancers drive cell type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assay (MPRA) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state specific H3K27 acetylation close to differentially expressed genes. A more in-depth evaluation of those regions was then pursued by investigating the activity of ATAC-seq peaks found therein along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions and we were able to precisely locate the active regions within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity, while SOX and MITF both influence MEL enhancer activity with SOX being required to achieve high levels of activity. Overall, our MPRA assays shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity as reporters across melanoma cell states.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Eight MPRA libraries are used in this study, including 7 CHEQ-seq libraries and 1 STARR-seq library. For each CHEQ-seq library an enhancer - barcode assignment is done by sequencing of the plasmid library with PacBio or Illumina sequencing. Libraries CHEQ-seq 5' H3K27ac, CHEQ-seq Intron H3K27ac, CHEQ-seq ATAC and STARR-seq ATAC are transfected in seven cell lines. Libraries CHEQ-seq enhancer tiling A and B are transfected in 5 cell lines. Library CHEQ-seq SOX10-KD is transfected in one cell line. Library CHEQ-seq SOX-MITF combinations is transfected in 3 cell lines.

first: David

last: Mauduit

first: Liesbeth

last: Minnoye

first: Ibrahim

middle: I

last: Taskiran

first: Maxime

last: de Waegeneer

first: Valerie

last: Christiaens

first: Jonas

last: Demeulemeester

first: Jasper

last: Wouters

first: Stein

last: Aerts


title: A quantitative map of human primary microRNA processing sites [1]

last: Kim


title: Genome-wide association studies reveal susceptibility loci for noninfectious claw lesions in Holstein dairy cattle

status: Public on Jul 23 2021

first: Anita

last: Oberbauer

address: One Shields Ave.

department: Animal Science Department

institute: University of California, Davis

summary: Sole ulcers (SU) and white line disease (WLD) are noninfectious claw lesions that arise due to compromised horn production and are common causes of lameness in dairy cattle, imposing welfare and profitability concerns. The low to moderate heritability estimates of SU and WLD susceptibility indicate that genetic selection could reduce their prevalence. To identify loci associated with SU and WLD susceptibility, generalized linear mixed model (GLMM) regression and random forest (RF) genome-wide association studies (GWAS) were performed. Cows from five commercial dairies in California were classified as sound controls having no instances of lameness and above six years of age (n = 102) or cases having SU (n = 152), WLD (n = 117), SU and/or WLD (SU+WLD, n = 198), or any type of noninfectious claw lesion (n = 217). Top SNPs were defined as those passing Bonferroni-corrected suggestive and significance thresholds in the GLMM analysis or those that a validated RF model considered important. Effects of top SNPs were quantified using Bayesian estimation. Linkage disequilibrium (LD) blocks defined by top SNPs were explored for candidate genes and previously identified, functionally relevant quantitative trait loci. The GLMM GWAS revealed regions of association on BTA8 for SU and BTA13 common to WLD, SU+WLD, and noninfectious claw lesions. Bayesian estimation of effect sizes indicated that these SNPs had effects significantly different from zero, indicating their small but notable contribution to susceptibility. Promising candidate genes identified in these regions were involved in wound healing, skin lesions, bone growth and mineralization, adipose tissue, and keratinization. The LD block defined by the most significant SNP on BTA8 for SU included a SNP previously reported to be associated with SU. The RF models were overfitted, indicating that SNP effects were very small and thereby preventing meaningful interpretation of SNPs with the highest importance values and downstream analyses. These findings suggested that variants associated with a variety of physiological systems may contribute to susceptibility for noninfectious claw lesions, demonstrating the complexity of genetic predisposition.

overall_design: Whole blood was collected from 326 cows (cases with any noninfectious claw lesion n = 222, controls n = 104) from the coccygeal vein in the tail. Blood samples were centrifuged, and genomic DNA was extracted from the resulting buffy coat layer using the QIAGEN QIAamp DNA Blood Mini Kit . DNA samples were genotyped on the Illumina BovineHD BeadChip, and Illumina’s GenCall algorithm was used to call genotypes. Of the 326 samples, seven were removed during quality filtering (cases n = 5, controls n = 2), leaving 319 cows for analysis (cases n = 217, controls n = 102).

first: Ellen

last: Lai

first: Alexa

last: Danner

first: Thomas

last: Famula

middle: M


title: Transcriptome analysis of mRNA and long non-coding RNA during subsequent embryo development of porcine cloned zygotes after vitrification

status: Public on Jul 22 2021

city: Kunming

first: Decai

last: Xiang

address: Qinglongshan

country: China

institute: Yunnan Animal Science and Veterinary Institute

summary: this study was designed to acquire mRNA and long non-coding RNA (lncRNA) profiles of 2-cells, 4-cells and blastocysts derived from vitrified porcine cloned zygotes using transcriptome sequencing. We identified 167 differentially expressed (DE) mRNAs and 516 DE lncRNAs in 2-cell stage, 469 DE mRNAs and 565 lncRNAs in 4-cell stage, and 389 DE mRNAs and 816 DE lncRNAs in blastocyst stage. Functional enrichment analysis revealed that DE mRNAs during embryo development were involved in many regulatory mechanisms related to cell cycle, cell proliferation, apoptosis, metabolism and others. Moreover, the target genes of DE lncRNAs in the three embryonic stages were also enriched in many key GO terms or pathways such as ‘defense response’, ‘linoleic acid metabolic process’, ‘embryonic axis specification’, ‘negative regulation of protein neddylation’, etc. In conclusion, the present study provided comprehensive transcriptomic data about mRNA and lncRNA for the vitrified porcine cloned zygotes during different developmental stages, which contributed to further understand the potential cryodamage mechanisms responsible for impaired embryo development.

first: Guoquan

last: Wu


title: Gilteritinib-induced upregulation of S100A9 is mediated through BCL6 in Acute Myeloid Leukemia (RNA-Seq II)

city: WEST HOLLYWOOD

first: Moray

last: Campbell

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

summary:
Purpose: Compare transcriptional changes between drug treated (gilteritinib, TP-0903) and vehicle in acute myeloid leukemia xenografts.
Methods: FLT3-ITD+ MOLM13-Luc+ AML cells were xenografted into NSG mice. Mice were randomized according to bioluminescence imaging, and treatment of FLT3 tyrosine kinase inhibitors (TP-0903, 60 mg/kg, once daily for 5 days/week; gilteritinib, 30 mg/kg, once daily for 5 days/week) was started on day 7 post-tail vein injection. At study end point, mice were humanely euthanized and bone marrow was collected. AML cells (human CD45+) were isolated, and RNA-seq was performed on total RNA. Sequencing reads were aligned and analyzed for differential gene expression of treatment vs vehicle cohorts.
Results: The analysis revealed the transcriptional changes induced by TP-0903 or gilteritinib in MOLM13 AML xenograft model.

overall_design: RNA-seq and ATAC-seq analyses were generated in FLT3-ITD+ AML cell lines from xenograft models treated with FLT3 tyrosine kinase inhibitors vs vehicle.

first: M

middle: E

last: Zavorka Thomas

first: J

last: Jeon

first: D

last: Buelow

middle: J

first: S

middle: D

last: Baker


title: Gilteritinib-induced upregulation of S100A9 is mediated through BCL6 in Acute Myeloid Leukemia (RNA-Seq I)

summary:
Purpose: Compare transcriptional changes between drug treated (gilteritinib, TP-0903) and vehicle in acute myeloid leukemia xenografts.
Methods: FLT3-ITD+ MOLM13-RES-Luc+ (MOLM13 cells with a D835Y mutation generating a resistant phenotype) AML cells were xenografted into NSG mice. Mice were randomized according to bioluminescence imaging, and treatment of FLT3 tyrosine kinase inhibitors (TP-0903, 60 mg/kg, once daily for 5 days/week; gilteritinib, 30 mg/kg, once daily for 5 days/week) was started on day 13 post-tail vein injection. At study end point, mice were humanely euthanized and bone marrow was collected. AML cells (human CD45+) were isolated, and RNA-seq was performed on total RNA. Sequencing reads were aligned and analyzed for differential gene expression of treatment vs vehicle cohorts.
Results: The analysis revealed the transcriptional changes induced by TP-0903 or gilteritinib in MOLM13-RES AML xenograft model.


title: Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations [CUT&RUN]

status: Public on Jul 20 2021

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

summary: Some human families display severe shortening and bending of the radius and ulna, a condition referred to as mesomelic dysplasia. Many of these families contain chromosomal rearrangements at 2q31, where the human HOXD locus maps. In mice, the dominant X-ray-induced Ulnaless inversion of the HoxD gene cluster produces a similar phenotype suggesting that the same pathological mechanism is at work in humans and mice. A tentative hypothesis was proposed where the various alterations to the genomic structure of HOXD could translocate Hoxd13 near to proximal limb enhancers, leading to its deleterious gain-of-expression in the embryonic forelimb. We evaluated this hypothesis by engineering a ca. 1Mb large inversion including the HoxD gene cluster, in order to position Hoxd13 within a chromatin domain rich in proximal limb enhancers. We show that these enhancers contact and activate Hoxd13 in proximal cells, concomitant to the formation of a mesomelic dysplasia phenotype. A secondary mutation in the coding frame of the HOXD13 protein in-cis with the inversion completely rescued the limb alterations, demonstrating that ectopic HOXD13 is indeed the unique cause of this bone anomaly. Single cell expression analysis and evaluation of HOXD13 binding sites in cells from this ectopic expression domain suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.

overall_design: wild type and mutant (inv2) tissue samples were collected from E12.5 mouse embryos. Proximal limbs, distal limbs, and forebrain were collected and processed according to the CUT&RUN protocol described in Skene et al. Nature Protocols, 2018

first: Christopher

last: Bolt

first: Bénédicte

last: Mascrez

first: Denis

last: Duboule


title: Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations


title: Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations [cHi-C]

overall_design: wild type and mutant (inv2) tissue samples were collected from E12.5 mouse embryos. Proximal limb domain, and distal limb domains were collected and processed as described in Buenrostro 2013.


title: Actionable genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma

status: Public on Jul 16 2021

city: Berlin

first: Matthias

last: Wirth

address: Hindenburgdamm 30

country: Germany

institute: Charité Berlin

summary: SUMOylation is a post-translational modification of proteins that regulates these proteins’ localization, turnover or function. Aberrant SUMOylation is frequently found in cancers but its origin remains elusive. Using a genome-wide transposon mutagenesis screen in a MYC-driven B-cell lymphoma model, we identified the SUMO isopeptidase (or deconjugase) SENP6 as a tumor suppressor that links unrestricted SUMOylation to tumor development and progression. Notably, SENP6 is recurrently deleted in human lymphomas and SENP6 deficiency results in unrestricted SUMOylation.  Mechanistically, SENP6 loss triggers release of DNA repair- and genome maintenance-associated protein complexes from chromatin thereby impairing DNA repair in response to DNA damages and ultimately promoting genomic instability. In line with this hypothesis, SENP6 deficiency drives synthetic lethality to PARP inhibition. Together, our results link SENP6 loss to defective genome maintenance and reveal the potential therapeutic application of PARP inhibitors in B-cell lymphoma.

overall_design: OCI-Ly1 cells with SENP6 knockdown versus parental cell line; three biological replicates, each.

first: Markus

last: Schick

first: Stefan

last: Müller

first: Ulrich

last: Keller


title: Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations [ATAC-Seq]


title: SARS-CoV-2 infects the brain vasculature in COVID-19 patients and a hiPSC-derived model of the blood-brain barrier

status: Public on Jul 14 2021

city: Hamburg

first: Ole

last: Pless

state: Hamburg

address: Schnackenburgallee 114

institute: Frauenhofer ITMP

summary: We report the transcriptional changes of an hipsc-derived model of the blood-brain barrier to infection with SARS-CoV-2. Furthermore, the neurovascular niche was isolated from human brain biopsies to compare the transcriptional signatures of hipsc-derived endothelial cells and human neurovascular niche.

overall_design: hipsc-derived endothelial cells were either mock infected of exposed to SARS-CoV-2.

first: Susanne

last: Krasemann

first: Marcel

middle: S

last: Woo


title: nCounter NanoString Human Immunology V2 panel

status: Public on Aug 02 2021

city: Lund

first: Juan

middle: José

last: Nieto-Fontarigo

address: Sölvegatan 17

department: Experimental Medical Science

country: Sweden

institute: Lund University

summary: mRNA expression in human bronchial epithelial cells unstimulated was compared with mRNA expression of cells stimulated with poly (I:C) (viral mimic) and poly (I:C) in combination with imiquimod (TLR7 agonist; Treatment). The aim was to assess the effect of imiquimod treatment on poly (I:C)-dependent changes in bronchial epithelium from asthmatics.

overall_design: Nanostring Human Immunology v2 panel was performed on  whole RNA from in vitro cultured human bronchial epithelial cells unstimulated (Control cells) or stimulated with poly (I:C) (viral mimic) or poly (I:C) in combination with imiquimod (TLR7 agonist; treatment) for 24h on asthma patients (N=3).

first: Lena

last: Uller


title: The interaction of mircroRNA171f with SCARECROW-LIKE6-I and II enhances drought stress tolerance through regulation of flavonoid biosynthesis genes in rice

status: Public on Jul 18 2021

city: Chuncheon

first: Taeyoung

last: Um

address: 1, Kangwondaehak-gil

institute: kangwon national university

summary: Plants have evolved a sophisticated defense system to survive under natural drought conditions. MicroRNAs (miRNA) are small noncoding RNAs that act as a post-transcriptional regulator in the environmental stress response and developmental process. Although many studies have reported the involvement of the miRNAs in drought response, molecular mechanisms by which miRNAs confer drought tolerance remain elusive. Here, we show that MIR171f, a member of MIR171 gene family, is mainly expressed in response to drought stress and regulate transcript levels of SCARECROW-LIKE6-I (SCL6-I) and SCL6-II. The SCL6 genes are known to be involved in shoot branching and flag leaf morphology. The MIR171f-overexpressing (MIR171f-OE) transgenic plants showed reduced drought symptoms as compared with non-transgenic (NT) control plants under both field drought and PEG-mediated dehydration stress conditions. Transcriptome analysis using the MIR171f-OE and mir171f-K/O mutants revealed that MIR171f regulates the expression of flavonoid biosynthesis genes, consequently leading to drought tolerance. Flavonoid biosynthesis genes were up-regulated in MIR171f-OE plants as compared with NT control plants under both normal and drought conditions. Together, our findings demonstrated that MIR171f plays an important role in plant drought-tolerance mechanism by regulating transcript levels of SCL6-I and SCL6-II.

overall_design: RNA-Seq on leaves of nontransgenic control (wild type, WT), MIR171f-overexpressing transgenic plants and mir171f-knockout (Ko) mutants

first: Ju-Kon

last: Kim


title: Gene expression profiles of PD-L1 SP142 expression in triple-negative breast cancer

city: Daejeon

first: Seon-Kyu

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The SP142 PD-L1 assay is a companion diagnostic for atezolizumab in metastatic triple-negative breast cancer (TNBC). The VENTANA SP142 assay was used to identify PD-L1 expression from TMA slides where PD-L1-positivity for an individual sample was defined as ≥1% of tumor-infiltrating immune cells as having PD-L1 expression. The PD-L1-positive gene signature consisted of 94 immune-related genes. The PD-L1-positive signature was predictive of pathologic complete response and survival outcome in multiple TNBC cohorts. In other malignancies treated with ICIs, the PD-L1-positive signature was associated with response and improved survival.

overall_design: We prospectively collected tumor tissues from specimens of surgically resected breast cancer at the Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea, between July 1997 and December 2007. A total of 82 patients with triple negative breast cancer were enrolled for gene expression profiling.

first: SungGwe

last: Ahn

first: Joon

last: Jeong

first: Charles

last: Perou


title: A mechanism of coupling leading and lagging strand DNA synthesis under replication stress in budding yeast

city: New York

first: Xu

last: Hua

state: New York

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

summary: Here we show that the asymmetric DNA synthesis is also observed in mec1-100 and mrc1-AQ cells defective in replication checkpoint, but surprisingly, not in mrc1∆ cells in which both DNA replication and checkpoint functions of Mrc1 are missing. Furthermore, depletion of Mrc1 or its partner in DNA replication, Tof1, suppresses the asymmetric DNA synthesis in rad53-1 mutant cells.

overall_design: ChIP-Seq was performed for Rfa1; BrdU was performed for yeast cells under different conditions.

first: Albert

last: Serra-Cardona

first: Chuanhe

last: Yu

first: Xinmin

last: Zhang

first: Haiyun

last: Gan

first: Zhiguo


title: Dual roles for piRNAs in promoting and preventing transgenerational gene silencing in C. elegans

status: Public on Jul 10 2021

city: Fort Collins

first: Taiowa

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

summary: To explore the roles of piRNAs in regulating 22G-RNA production and transgenerational gene silencing, we used RNA-seq to assess changes in small RNA and mRNA levels in piwi/prg-1 and mutator mutants at an early generation and again at a late generation. We identified that in the absence of piRNAs, many genes gain 22G-RNAs which in turn guide transgenerational gene silencing.

overall_design: Small RNA and mRNA high-throughput sequencing was done using RNA isolated from adult wild type and prg-1 and mutator mutant whole animals. Differential expression analysis was done to identify changes in gene expression in mutants relative to wild type animals.


title: A probabilistic framework for cellular lineage reconstruction using integrated single-cell 5-hydroxymethylcytosine and genomic DNA sequencing

status: Public on Jul 08 2021

city: Santa Barbara

first: Siddharth

last: Dey

address: 3357 Engrg II UCSB

department: Chemical Engineering

institute: UCSB

type: Methylation profiling by high throughput sequencing

summary: Lineage reconstruction is central to understanding tissue development and maintenance. While powerful tools to infer cellular relationships have been developed, these methods typically have a clonal resolution and require a transgene. Here, we report scPECLR, a probabilistic algorithm to endogenously infer lineage trees at a single cell-division resolution using 5-hydroxymethylcytosine (5hmC). When applied to 8-cell mouse embryos, scPECLR predicts the full lineage tree with greater than 95% accuracy, with the ability to infer larger lineage trees depending on the distribution of 5hmC patterns. Finally, we show that scPECLR can also be used to test the "immportal strand" hypothesis in stem cell biology. Thus, scPECLR provides a generalized method to endogenously reconstruct lineage trees at an individual cell-division resolution.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study, strand-specific 5-hydroxymethylcytosine (5hmC) was detected on a genome-wide scale in single cells from 8-cell mouse embryos. The distribution of 5hmC in single cells was used to reconstruct cellular lineages using a new probabilistic framework called scPECLR. Moreover, scH&G that can detect 5hmC and gDNA from the same single cell was developed to increase the reconstruction power of scPECLR.

first: Chatarin

last: Wangsanuwat

first: Alex

last: Chialastri

first: Javier

middle: F

last: Aldeguer

first: Nicolas

last: Rivron


title: SMAD4 Controls Morphogenetic SHH Signaling via Direct Transcriptional Regulation of Cholesterol Biosynthesis in Early Mouse Limb Buds [ChIP-seq]

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

summary: This study describes the functions of SMAD4 during early mouse limb bud development by identifying the direct transcriptional targets

overall_design: Chromatin-immunoprecipitation of Smad4 from either e9.5 or e10.5 limb buds

first: J

last: Gamart

first: F

last: Laurent

first: I

first: A

last: Visel

first: L

last: Ramos Martins

first: R

last: Zeller

last: Zuniga


title: Retinoblastoma genome methylation data

status: Public on Jul 06 2021

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

type: Methylation profiling by genome tiling array

summary: Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic profiling of primary retinoblastoma samples. Most of the patients whose tumors were studied had received no treatment prior to surgical enucleation.

overall_design:
Immediately following enucleation, a needle was inserted through the eye's anterior chamber to extract a tumor sample by aspiration; the tumor specimen was then snap frozen. For these arrays, DNA was extracted from these snap frozen samples.
We used Illumina HumanMethylation450 BeadChip arrays to study the genome methylation patterns of 67 primary retinoblastoma tumors and 3 foetal retina samples.

first: François

last: Radvanyi

first: Meriem

last: Sefta

first: Daniela

last: Ottaviani

first: Celine

last: Desbrousses

first: Jing

last: Liu

last: Chapeaublanc


title: Transcriptomic analysis of tendon progenitors of Drosophila leg

status: Public on Jul 01 2021

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

summary: The  progenitors of Drosophila leg tendon are specified among leg disc epithelium during third larval instar. At the end of larval stages and beiginning of pupae formation, tendon cells invaginate and then collectively migrate to form a tube-shaped structure.

overall_design: Drosophila leg discs were dissected from  0h after pupae formation  (Stripe-gal4>UAS-GFP). Leg disc cells were dissociated in collagenase and papain solution and cell-sorted using. RNA from GFP positive cells and from control cells (whole leg disc cells)  were extracted for analysis by deep sequencing, in triplicate, using Illumina NextSeq sequencing platform.

first: Cedric

last: Soler

first: Yoan

last: Renaud


title: A novel NGS-based method can improve the efficiency and sensitivity of Y2H screening with cDNA library

status: Public on Jul 09 2021

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

summary: The NGS-based Y2H screening methods have been adopted to increase the efficiency and sensitivity, while reducing the labor and experimental cost of the canonical Y2H screening. However, most of NGS-based Y2H screening methods are suitable for well-constructed ORFeomes but not cDNA libraries. Thus, we developed a novel NGS-based Y2H screening method to accomplish a precise Y2H screening with cDNA libraries. With newly designed primers, we can distinguish and filter out those non-in-frame reads from all mapped reads, which facilitates the estimation of the interaction intensity between baits and preys.

overall_design: The prey inserts were PCR-amplified from selected yeast colonies (>3000 colonies per sample). After fragmentation, the DNA fragment of prey inserts were ligated to standard Illumina adaptor. Then, the second round PCR amplification was performed to enrich the DNA fragments with 29 bp vector sequence and simultaneously the standard Illumina DNA library for paired-end sequencing was obtained.

first: Yan

last: Guo

first: Yinghui

last: Gu


title: Neuronal Nsun2 deficiency is associated with codon-specific epitranscriptomic dysregulation of Gly-tRNAs and corresponding proteomic shift impacting synaptic signaling and behavior

first: Jennifer

last: Blaze

address: 1470 Madison Ave 9-202

institute: Icahn School of Medicine at Mount Sinai

summary: Epitranscriptomic mechanisms linking the brain proteome to cognition and complex behaviors essentially remain unexplored. Here, we describe bi-directional changes in depression-related behaviors after genetic disruption of neuronal tRNA cytosine methylation, including conditional ablation and transgene-derived overexpression of NOL1/NOP2/SUN domain 2 (Nsun2) in the prefrontal cortex (PFC). Neuronal Nsun2-deficiency was associated with a sharp drop in tRNA m5C levels, resulting in significant deficits in expression of 70% (7/10) of tRNAGlyGCC, GlyCCC GlyTCC isodecoders, while expression changes in non-glycinergic tRNAs were minimal (4/152). Altogether, 1488/5820 proteins were sensitive to neuronal Nsun2-deficiency, in conjunction with GCC and CCC codon-specific defects in translational efficiencies and loss of Gly-rich proteins critical for glutamatergic neurotransmission, resulting in impaired synaptic signaling at PFC pyramidal neurons and impairments in contextual fear memory. These distortions in the neuronal translatome were associated with an adaptive, 2.46-fold up-regulation in PFC glycine levels with increased expression of multiple enzymes in the glycine biosynthetic pathway. These findings highlight the methylation sensitivity of glycinergic tRNAs in the adult PFC and link synaptic plasticity and complex behaviors to epitranscriptomic regulation of cognate tRNAs and the proteomic homeostasis associated with specific amino acids.

overall_design: mRNA and small RNA profiles of adult Nsun2 KO and WT cortex

first: Schahram

last: Akbarian


title: Transcriptome data of APP infected and healthy pig PBMCs

city: Changchun

first: Zhu

last: Rining

address: Xi'an Road No.5333

institute: Jilin University

summary: Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of pigs at different time points (0, 24 and 120 h) post infection and their transcriptome determined by Illumina HiSeq 4000 high-throughput sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs revealed the close relationship between the peripheral blood and inflammatory response from the perspective of molecular function, cell composition, biological processes and signalling pathways.

overall_design:
Examination of 3 different PBMCs samples
***Please note that the raw data has been lost and thus is not provided for the records****

first: Lei

last: LIancheng


title: A quantitative map of human primary microRNA processing sites

city: Gwanak

last: Baek

address: Gwank 1

institute: Seoul National University

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

overall_design: Refer to individual Series


title: Genome-wide identification of microRNA targets during mouse liver development using Ago HITS-CLIP

city: Guangzhou

first: Zhang

last: Yin

address: Xin Gang West 135

institute: Sun Yat-sen University

summary: By using Ago HITS-CLIP, we report genome-wide identification of microRNA-target interactions from e12.5, e15.5, e18.5, P7(postnatal day 7) and adult liver,

overall_design: Ago binding RNAs tags from different developmental stages of  mouse liver

first: Yin

last: Zhang

first: Hui

last: Xu

first: Shu-juan

last: Xie

first: Ye-ya

last: Tan

first: Jian-hua

last: Yang

first: Liang-hu

last: Qu


title: Xenogeneic Skin Transplantation Promotes Angiogenesis and Tissue Regeneration

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

summary: 1) We analyzed the impact of vitamind D3 (cholecalciferol) treatment on transcriptional signatures of bone marrow derived macrophages 2) Moreover, we analyzed cell populations infiltrating human split-thickness skin grafts (STSG) that had been subcutaneously implanted into wild-type mice (C57BL6/J).

overall_design: scRNA-seq was performed on:  1) cultured murine bone marrow derived macrophages with or without treatment with vitamind D3 for 24 h and 2) human split-thickness skin grafts that had been subcutaneously implanted into wild-type (C57BL6/J) mice for 14 days, n=5 mice

first: Dominic

last: Henn

first: Geoffrey

last: Gurtner


title: Integrated transcriptomic and translatomic exploration of the effect of betaine on lipid metabolic dysregulation induced by a high-fat diet

city: chengdu

first: Tengda

last: Huang

state: Sichuan

address: gaopeng road

department: West China Hospital

institute: Sichuan University

summary: An excessive high-fat/energy diet is a major cause of obesity and associated complications, such as non-alcoholic fatty liver disease (NAFLD). Betaine has been shown to effectively improve hepatic lipid metabolism. However, the mechanistic basis for this improvement is largely unknown. Herein, integration of transcriptomics sequencing (RNA-seq) and ribosome footprints profiling (Ribo-seq) was used to investigate the means by which betaine alleviates hepatic lipid metabolic disorders induced by a high-fat diet. For the transcriptome, gene set enrichment analysis demonstrated betaine to reduce liver steatosis by up-regulation of fatty acid beta oxidation, lipid oxidation, and fatty acid catabolic processes. For the translatome, 574 differentially expressed genes were identified, 17 of which were associated with the NAFLD pathway. By combined analysis of RNA-seq and Ribo-seq, we found that betaine had the greatest effect on NAFLD at the translational level. Further, betaine decreased translational efficiency (TE) for IDI1, CYP5A1, TM7SF2, and APOA4, which are related to lipid biosynthesis. In summary, this study demonstrates betaine to alleviate lipid metabolic dysfunction at the translational level. The powerful multi-omics data integration approach used herein provides for a new understanding of the means by which to treat NAFLD.

overall_design: High-throughput sequencing of liver tissue from high-fat and betaine treated high-fat mice.

first: Lin

last: Yu

first: Hongyuan

last: Pan

first: Zeqiang

last: Ma

first: Tian

last: Wu

first: Lifang

first: Kang

last: Liu

first: Qi

last: Qi

first: Weiwei

last: Miao

first: Ziyi

last: Song

first: Haojie

last: Zhou

first: Yixing

last: Li


title: Transcriptome analysis of wild type and sweet1 seeds upon treatments during germination

status: Public on Jun 30 2021

city: Urbana

first: Xueyi

last: Xue

state: Illinois

address: 1201 W. Gregory Dr.

department: Department of Plant Biology

institute: University of Illinois at Urbana-Champaign

summary:
Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination.
Methods: After 3-day imbibition, WT and sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads.
Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. There are 6230 candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function.
Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.

overall_design: Seed transcript profiles in WT and sweet1 under glucose, ABA and ABA+glucose treatments in 30 hours after imbibition.

first: Li-Qing


title: Cues from mRNA splicing prevent default Argonaute silencing in C. elegans

status: Public on Jun 28 2021

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: UMass Med School/HHMI

summary: In animals Argonaute small-RNA pathways scan germline transcripts to silence self-replicating genetic elements. Little is known however about how endogenous gene expression is recognized and licensed. Here we show that the presence of introns and by inference the process of mRNA splicing prevents default Argonaute-mediated silencing in the C. elegans germline. Silencing of intronless genes is initiated independently of the piRNA pathway but nevertheless engages multiple components of the downstream amplification and maintenance mechanisms that mediate transgenerational silencing including both nuclear and cytoplasmic members of the worm-specific Argonaute gene family (WAGOs). Small RNAs amplified from intronless mRNAs can trans-silence cognate intron-containing genes. Interestingly, a second small RNA-independent cis-acting mode of silencing also acts on intronless mRNAs. Our findings suggest that cues put in place during mRNA splicing license germline gene expression and provide evidence for a splicing-dependent and dsRNA- and piRNA-independent mechanism that can program Argonaute silencing.

overall_design: Total small RNAs from strains carrying intronless reporters and controls, in wild-type and mutant C. elegans backgrounds, were cloned and sequenced.

first: Yekaterina

middle: V

last: Makeyeva

first: Masaki

last: Shirayama


title: Chronic IL-15 stimulation and impaired mTOR signaling and metabolism in natural killer cells during acute myeloid leukemia

city: Marseille

first: Ghislain

last: BIDAUT

address: 27 Bd Leï Roure

department: Bioinformatics

institute: Centre de Recherche en Cancérologie de Marseille

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: Examination of 2 different histone modifications in Neural progenitor cells.

first: Berna

last: Bou-Tayeh

first: Vladimir

last: Laletin

first: Nassim

last: Salem

first: Sylvaine

last: Just-Landi

first: Joanna

last: Fares

first: Raphael

last: Leblanc

first: Marielle

last: Balzano

first: Yann

last: Kerdiles

last: Bidaut

first: Olivier

last: Hérault

first: Daniel

last: Olive

first: Michel

last: Aurrand-Lions

first: Thierry

last: Walzer

first: Jacques

last: Nunès

first: Cyril

last: Fauriat


title: 1,25(OH)2D3 upregulated lncRNA

status: Public on Jun 29 2021

city: Iwaki

first: Yoshiaki

last: Kanemoto

state: Fukushima

address: kaminodai 57, jyobankamiyunagaya-town

country: Japan

institute: Jyoban Hospital

summary: Purpose: The goals of this study are to compare lncRNA between Wild Type and VDR KO in HaCat cell line using NET-CAGE.

overall_design: Examination of 2 different method in 2 cell types.

first: Koichi

last: Nishimura

first: Rei

last: Amano

first: Takahiro

last: Sawada

first: Jinichi

last: Mori

first: Shigeaki

last: Kato


title: RNA Sequencing of PGE2 or MEHP treated human THP-1 derived macrophages transcriptomes

city: Chengdu

first: Miao

last: Xu

address: 37#,Guoxue alley, Wuhou district

department: Clinical Nutrition

institute: West China hospital of Sichuan university

summary: THP-1 cells were treated with phorbol 12-myristate 13-acetate (PMA) at 25μg/ml for 48h.Then remove PMA and rest for 24h to obtain M0 macropahges. Further applied LPS and IFNγ or IL-4 and IL-13 for 24h to obtain M1, M2 macrophages, respectively. During polarization, cells were treated with prostaglandin E2 or MEHP.Then M1,M2 cells were collected and applied to RNA-sequencing. We found that PGE2 and MEHP significantly impacted metabolic signature of macrophages.

overall_design: mRNA profiles of PGE2 or MEHP treated  M1 and M2 macrophages were examined by Illumina Hiseq.

first: Hui

last: Yang


title: Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Liver)

status: Public on Jun 24 2021

city: Melbourne

first: Luke

last: Gandolfo

state: Victoria

address: 1G Royal Parade Parkville

country: Australia

institute: WEHI

summary: Tissue-resident memory T cells (TRM) are non-recirculating cells that exist throughout the body. While TRM in various organs rely on common transcriptional networks to establish tissue residency, location-specific factors adapt these cells to their tissue of lodgment. Here, we chart TRM heterogeneity between organs and find that the different environments in which these cells differentiate dictate TRM function, durability and malleability. We find that unequal responsiveness to TGF-β is a major driver of this diversity. Strikingly, dampened TGF-b signaling engendered CD103- TRM with increased proliferative potential, enhanced function, and reduced longevity compared to their TGF-β-responsive CD103+ TRM counterparts. Further, while CD103- TRM readily modified their phenotype upon relocation, CD103+ TRM were comparatively resistant to trans-differentiation. Thus, despite common requirements for TRM development, adaptation of these cells to their tissue of residence confers discrete functional properties such that TRM exist along a spectrum of differentiation potential that is governed by their local microenvironment.

overall_design: Effector CD8+ OT-I Tcells or OT-I cells deficient in the TGFbRII were injected into LmOVA infected mice 2 days post-infection and CD69+ cells were sorted at day 14 post-infection from the liver. Alternatively, the OT-I cells were infected into HSV mice infected 2 days prior and then sorted from the epidermin skin on day 14 post-infection. Cells were subject to RNA sequencing for transcriptional analysis.

first: Susan

last: Christo

first: Laura

middle: K

last: Mackay


title: Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Salivary Gland)

overall_design: Naive OT-I cells were injected into LmOVA infected and CD69+CD103-/+ cells were sorted at day 30 post-infection from the salivary gland. Cells were subject to RNA sequencing for transcriptional analysis.


title: Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity


title: Maternal background alters the penetrance of growth phenotypes and sex-specific placental adaptation of offspring sired by alcohol-exposed males

status: Public on Jul 15 2021

city: College Station

first: Michael

last: Golding

state: Texas

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

summary: Here, we describe the use of high-throughput sequencing to examine the developmental basis of placental growth defects observed in the male offspring of alcohol-exposed fathers. We exposed C57BL/6J male mice to 10% ethanol for ten weeks, then bred them to naïve CD-1 dams. The male offspring of ethanol-exposed sires exhibited placental growth defects. We isolated total RNA from four F1 male placentae from each control and ethanol preconception treatment and conducted deep-sequencing analysis of the transcriptome. These studies identified programmed increases in the genetic pathways controlling oxidative phosphorylation, mitochondrial function, and Sirtuin signaling. This study furthers our understanding of growth and metabolic phenotypes induced by preconception paternal exposures.

overall_design: Examination of maternal strain influence on gene expression in placentae.

first: Kara

last: Thomas

first: Katherine

last: Zimmel

first: Alexis

last: Roach

first: Alison

last: Basel

first: Nicole

last: Mehta

first: Yudishtar

last: Bedi


title: DNA Methylation Profiling of Human Colonoid Monolayers Under Repeated Submergence Injury

status: Public on Jun 23 2021

city: Vancouver

first: Theodore

last: Steiner

state: BC

address: Rm. C328 HP East, VGH

department: Medicine/Infectious Diseases

country: Canada

institute: University of British Columbia

summary:
Acute damage to the intestinal epithelium can be repaired via de-differentiation of mature intestinal epithelial cells to a stem cell state, but there is a lack of knowledge on how these stem cells function after chronic injury, such as in inflammatory bowel disease (IBD). We developed a chronic injury model in human colonoid monolayers by repeated rounds of air-liquid interface and submerged growth. We used this model to understand how chronic intestinal damage affects the ability of IECs to respond to microbial stimulation, using the TLR5 agonist FliC; and to regenerate and protect the epithelium from further damage.
Here, we profiled the effect of repeated rounds of damage on global DNA methylation levels of these human colonid monolayers. We observed a trend towards global demethylation with repeated damage, including in loci associated with genes implicated in DNA repair (NHEJ1) and colon hemostatsis and inflammation regulation (FAM3D).

overall_design: Genome-wide DNA methylation was assessed from 12 cultured human colonoid samples (including 2 replicates) using the Illumina Infinium Human MethylationEPIC BeadChip array. The samples were derived from the same donor but tested over two distinct passages, cultured in air-liquid interface(ALI) for seven days following full confluency, and harvested at 7 days-post culture (differentiated), or after post-submergence injury after differentiation with or without flagellin (at 1 round and 5 rounds of damages).

first: W

last: Rees

first: T

first: N

last: Zachos


title: RNA sequencing of chronically damage human colon organoids via Air-liquid interface submergence

summary: We report that repeated rounds of media submergence damage of human colon organoids led to the inability of cells to regrow and respond appropriately to TLR stimulation. We also identified mRNA expression and DNA methylation changes in genes associated with IBD and colon cancer.

overall_design: Analysis of two separate human colon organoids from ascending, and transverse colon that have been grown for 10 days, undergone differentiation via air-liquid interface, one round of submergence damage with or without bacterial flagellin stimulation, and five rounds of submergence damage with or without bactieral flagellin stimulation.

first: William

first: Nicholas


title: Single cell transcriptomics defines keratinocyte differentiation in avian scutate scales

city: Vienna

first: Julia

last: Lachner

address: Waehringer Guertel 18-20

institute: Medical University of Vienna

summary: Epidermal keratinocytes form cornified skin appendages such as scutate scales on the legs of birds. Here, we investigated the molecular pathways of keratinocyte differentiation in chicken scutate scales by single cell transcriptomics. We identified two distinct populations of differentiated keratinocytes. The first type of differentiated keratinocytes is characterized by mRNAs encoding scale-type corneous beta-proteins (CBPs), also known as beta-keratins and cysteine-rich keratins, indicating that these cells form hard scales. The second type of differentiated keratinocytes contains mRNAs encoding keratinocyte-type CBPs and cysteine-poor keratins, indicating that these cells form the soft interscale epidermis. Immunostaining with a newly raised antibody confirmed that keratin 9-like cysteine-rich 2 (KRT9LC2) or Hard Acid Sauropsid-specific 2 (HAS2) keratin, which is a marker of the first type of keratinocytes, is expressed in the suprabasal epidermal layers of scutate scales but not in interscale epidermis. Furthermore, mRNA of CTNN1B, previously implicated in scale placode formation, was enriched in differentiated scale keratinocytes, whereas genes involved in lipid metabolism, such as ELOVL4 and FADS1 were enriched in keratinocytes of the interscale epidermis. In conclusion, this study defines the gene expression programs that build the scutate scales and interscale epidermis of birds.

overall_design: Comparision of gene expression in various keratinocyte differentiation stages

first: Leopold

last: Eckhart


title: A population of CD4+CD8+ double-positive T cells associated with risk of plasma leakage in dengue viral infection

status: Public on Jun 16 2021

city: San Diego

first: Hao

last: Wang

address: 9452 Medical Center Dr

institute: University of California, San Diego

summary: According to the WHO 2009 classification, dengue with warning signs (D+W) is at the risk of developing severe form of dengue disease. One of the most important warning signs is plasma leakage, which is a serious complication associated with higher morbidity and mortality. We report that the frequency of CD4+CD8+ double-positive (DP) T cells is significantly increased in patients at risk of developing plasma leakage. Transcriptomic analysis demonstrated that CD4+CD8+ DP cells were distinct from CD4+ Single Positive (SP) T cells, but co-clustered with CD8+ SP cells indicating a largely similar transcriptional profile. 20 significant differentially expressed (DE) genes were identified between CD4+CD8+ DP and CD8+ SP cells. These genes encode OX40 and CCR4 (TNFRSF4 and CCR4), as well as other molecules associated with cell signaling on the cell surface (NT5E, MXRA8, PTPRK). While 5 significant DE genes were identified, the profile of gene expression in CD4+CD8+ DP cells was mostly similar between patients with and without warning signs of plasma leakage, implying a role of CD4+CD8+ DP cells in plasma leakage through a quantitative increase rather than functional alteration. The differentially expressed genes identified could have diagnostic utility, perhaps as PCR-based diagnostic markers.

overall_design: RNA-sequencing of sorted T cells from 55 dengue patients with warning signs of plasma leakage (D+W), and 33 dengue patients without warning signs of plasma leakage (D-W)

first: Esther

last: Yu

first: Yuan

last: Tian

first: April

last: Frazier

first: Alba

last: Grifoni

first: Daniela

last: Weiskopf

first: Ricardo

last: da Silva Antunes

first: Alessandro

last: Sette


title: Transcriptome profiling of the cytarabine response in U2OS cells overexpressing DNMT3A R882C isoform (compared to DNMT3A wt and empty vector control)

status: Public on Jun 02 2021

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary:
Purpose:  The goal of this study was to investigate the effect of the cytarabine treatment on the transcriptional profiles of U2OS cells retrovirally expressing DNMT3A R882C isoform, compared to DNMT3A WT and empty vector controls
Methods: U2OS DNMT3A WT, R882C, and empty vector cells were treated with 10uM cytarabine or vehicle control for 24 hours. Biological triplicates were generated, ie each replicate was performed on different day using a new batch of cells. Total RNA was collected and QC'd; mRNA was enriched using Poly-T oligo attached to magnetic beads and Illumina libraries were prepared and sequenced on Novaseq6000 (PE 150). Library construction and sequencing were performed by Novogene Corporation, Inc according to standard workflow.
Results: Using a custom built pipeline in PartekFlow, the reads were aligned to human (build hg38) genome with the STAR aligner 2.6.1d and low quality alignments were filtered. About 25 million sequence reads per sample were mapped to the human genome. We identified 5714 transcripts/sample and low expression genes with counts less than 10 were filtered and the raw read counts were normalized using TMM model with an offset of 1 to avoid zero counts. Unsupervised hierarchical clustering was performed on the top 2000 genes with highest variance
Conclusions: The study identifies gene networks involved in cytarabine response that are deregulated by presence of mutant DNMT3A.

overall_design: RNA profiles of U2OS overexpression cell lines (DNMT3A WT, DNMT3A R882C, and MigR1 empty vector control), treated with 10uM cytarabine for 24 hours, or vehicle control

first: Kartika

last: Venugopal

first: Santhi

last: Pondugula

first: Olga

last: Guryanova


title: Expression of immune response genes in human corneal epithelial cells interacting with Asperrgillus flavus conidia

status: Public on Jun 01 2021

city: Madurai

first: Divya

last: Arunachalam

state: Tamil Nadu

address: No 1 Anna Nagar

department: Proteomics

country: India

institute: Aravind Medical Research Foundation

summary:
Human corneal epithelial cells internalize Aspergillus flavus conidia. But the biochemical response of corneal epithelial cells in response to A.flavus is not clear. In this study, NanoString analysis was used to study the immune genes expression in primary corneal epithelial cells and cell line infected with A. flavus conidia.
The study revealed the differential expression of immune genes associated with TNF, Th17, NF-kB signaling and B cell receptor signaling in corneal epithelial cells. There is also difference in the response between cell line and primary cells to A. flavus implies the use of both cells to understand the host-pathogen interaction.

overall_design: Primary corneal epithelial cells and corneal epithelial cell line were infected with clinical isolates of A .flavus CI1698 and CI1123 for 6h. The experiment was done in duplicates. Un infected cells were taken as control. After infection, total RNA was isolated and after quantity and quality check it was subjected to NanoString. Total samples-12 (6-cell line; 6-primary HCE)

first: Athul

last: Menon

first: Lekshmi

last: Madhav

first: Gopalakrishna

last: Ramaswamy

first: Venkatesh

last: Prajna Nampermalsamy

first: Lalitha

last: Prajna

first: Dharmalingam

last: Kuppamuthu


title: The diarrheal pathogen Cryptosporidium parvum exports proteins into the cytoplasm of the infected host cell

status: Public on Jun 04 2021

city: Philadelphia

first: Boris

last: Striepen

state: Pennsylvania

address: 380 S University Ave, Room H344

department: Pathobiology

institute: University of Pennsylvania

summary: We found members of the polymorphic C. parvum MEDLE protein family to be targeted into the cytoplasm of infected cells. Direct expression of MEDLE2 in mammalian cells triggers an ER stress response that is also observed during infection.

overall_design: Three biological replicates were analyzed for each of 4 conditions (transfected or untransfected based on green fluorescence assessed by flow cytometry  from the MEDLE2-GFP or GFP control)

first: Jennifer

last: Dumaine


title: Simultaneous sequencing of coding and non-coding RNA from patients with Alzheimer's disease

city: Dunedin

first: Joanna

last: Williams

address: Great King St

department: Anatomy

country: New Zealand

institute: University of Otago

summary: Human post-mortem brain samples (middle temporal gyrus) from Alzheimer's disease (AD) and control individuals were processed for simultaneous coding and non-coding RNA-Seq analysis using a novel RNA-Seq protocol. These data were then analyzed for differential expression.

overall_design: Total RNA was extracted from human post-mortem brain samples (Middle temporal gyrus; 3 AD, 4 healthy control), and a modified RNA-Seq protocol used to simultaneously examine coding and non-coding RNA.

first: Nikita

last: Potemkin

first: Diane

last: Guévremont

first: Catriona

last: McLean

first: Jackson

last: Treece

first: Christy

last: Rand

first: Jo-Ann

last: Stanton


title: Nuclear NAD+-biosynthetic enzyme NMNAT1 facilitates survival of developing retinal neurons

status: Public on Jun 17 2021

city: Morgantown

first: Saravanan

last: Kolandaivelu

state: WV

address: 1 Medical Center Dr.

department: Ophthalmology, Biochemistry

institute: West Virginia University Eye Institute

summary: Despite mounting evidence that the mammalian retina is exceptionally reliant on proper NAD+ homeostasis for health and function, the specific roles of subcellular NAD+ pools in retinal development, maintenance, and disease remain obscure. Here, we show that deletion of the nuclear-localized NAD+ synthase nicotinamide mononucleotide adenylyltransferase-1 (NMNAT1) in the developing murine retina causes early and severe degeneration of photoreceptors and select inner retinal neurons via multiple distinct cell death pathways. This severe phenotype is associated with disruptions to retinal central carbon metabolism, purine nucleotide synthesis, and amino acid pathways. Furthermore, large-scale transcriptomics reveals dysregulation of a collection of photoreceptor and synapse-specific genes in NMNAT1 knockout retinas prior to detectable morphological or metabolic alterations. Collectively, our study reveals previously unrecognized complexity in NMNAT1-associated retinal degeneration and suggests a yet-undescribed role for NMNAT1 in gene regulation during photoreceptor terminal differentiation.

overall_design: mRNA profiles of Nmnat1-/- and wild-type control (Nmnat1 fl/fl) murine retinas at two ages: embryonic day 18.5 (E18.5) and postnatal day 4 (P4)

first: David

last: Sokolov


title: An Integrated Epigenomic and Genomic View on Phyllodes and Phyllodes-like Breast Tumors

status: Public on Jul 07 2021

city: Basel

first: Juergen

last: Hench

state: BS

address: Schoenbeinstr. 40

department: Pathology

institute: University Hospital Basel

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

summary:
Phyllodes tumor of the breast (human) as well as a set of related tumors
Phyllodes tumor, Fibroadenoma, Breast Cancer

overall_design: DNA extracted from native and FFPE tumor tissue samples with high tumor cell content

first: Tatjana

last: Vlajnic

first: Savas

last: Deniz Soysal

first: Ellen

last: Obermann

first: Stephan

last: Frank

first: Simone

last: Muenst


title: Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

status: Public on May 31 2021

city: New York

first: Federico

last: Gaiti

state: NY

address: 413 East 69th St.

institute: Weill Cornell Medicine

summary: Single cell RNA-sequencing revealed extensive transcriptional cell state diversity in cancer, often observed independently from genetic heterogeneity, raising the central question of how malignant cell states are encoded epigenetically. To address this, we performed multi-omics single-cell profiling – integrating DNA methylation, transcriptome, and genotyping within the same cells – of diffuse gliomas, tumors characterized by defined transcriptional cell state diversity. Direct comparison of the epigenetic profiles of distinct cell states revealed key switches for state transitions recapitulating neurodevelopmental trajectories, and highlighted dysregulated epigenetic mechanisms underlying gliomagenesis. We further developed a quantitative framework to measure cell state heritability and transition dynamics based on high resolution lineage trees directly in human samples. We demonstrated heritability of malignant cell states, with key differences in hierarchal vs. plastic cell state architectures in IDH-mutant glioma vs. IDH-wildtype glioblastoma, respectively. This work provides a framework anchoring transcriptional cancer cell states in their epigenetic encoding, inheritance and transition dynamics.

overall_design:
We profiled CD45- enriched, viable cells from GBM (n = 7) and IDH-MUT (n = 7) primary samples with multi-modality single-cell sequencing of scDNAme (by reduced representation bisulfite sequencing [RRBS]) and scRNAseq (Smart-seq2).
*** Raw data access can be requested through the Data Use Oversight System (DUOS) Dataset Catalog with dataset ID DUOS-000133 as well as the European Genome phenome Archive (EGA) with dataset ID EGAS00001005472. ***

first: Ronan

last: Chaligne

first: Dana

last: Silverbush

first: Joshua

last: Schiffman

first: Mario

last: Suvà

first: Dan

last: Landau


title: Pharmacologic modulation of RNA splicing enhances anti-tumor immunity.

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

summary: Although mutations in DNA are the best-studied source of neoantigens that determine response to immune checkpoint blockade, alterations in RNA splicing within cancer cells could similarly result in neoepitope production. However, the endogenous antigenicity and clinical potential of such splicing-derived epitopes have not been tested. Here, we demonstrate that pharmacologic modulation of splicing via specific drug classes generates bona fide neoantigens and elicits anti-tumor immunity, augmenting checkpoint immunotherapy. Splicing modulation inhibited tumor growth and enhanced checkpoint blockade in a manner dependent on host T cells and peptides presented on tumor MHC class I. Splicing modulation induced stereotyped splicing changes across tumor types, altering the MHC I-bound immunopeptidome to yield splicing-derived neoepitopes that trigger an anti-tumor T cell response in vivo. These data definitively identify splicing modulation as an untapped source of immunogenic peptides and provide a means to enhance response to checkpoint blockade that is readily translatable to the clinic.

overall_design: Mouse and human cell lines treated with 1 µM indisualm, 1 µM MS-023, or control (DMSO) treatment

first: Sydney

middle: X

last: Lu

first: Emma

last: De Neef

first: Robert

last: Bradley

first: Omar

last: Abdel-Wahab


title: Gene expression analysis of chronic myeloid leukemic stem cells and progenitor cells from untreated and imatinib-treated CML-like mice

status: Public on May 23 2021

city: Minato

first: Yosuke

last: Tanaka

state: Tokyo

address: Shirokanedai

institute: IMS, The University of Tokyo

summary: To understand gene expression signatures of CML stem cells underlying imatinib-resistance, we compared transcriptomes of CML stem and progenitor cells from vehicle and imatinib-treated CML mice, respectively.

overall_design: Transcriptomes of CML stem cells and progenitor cells from vehicle and imatinib treated CML mice were generated by deep sequencing, in 3 replecates, using Next-Seq system.

first: Terumasa

last: Umemoto

first: Hitoshi

last: Takizawa


title: Single-cell analysis identifies a key role for Hhip in murine coronal suture development

status: Public on Jun 26 2021

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: Craniofacial development depends on formation and maintenance of sutures between bones of the skull. In sutures, growth occurs at osteogenic fronts along the edge of each bone and suture mesenchyme separates adjacent bones. We performed single-cell RNA-seq analysis of the embryonic, murine coronal suture. Seven populations at E16.5 and nine at E18.5 comprised the suture mesenchyme, osteogenic cells, and associated populations. Expression of Hhip, an inhibitor of hedgehog (HH) signaling, marked a mesenchymal population distinct from other neurocranial sutures. At E18.5, Hhip-/- coronal osteogenic fronts were closely apposed and HH signaling was increased throughout the depleted suture mesenchyme compared to WT, demonstrating that Hhip is required for normal coronal suture development. Tracing of the neonatal Hhip-expressing population showed that descendant cells persisted in the coronal suture and contributed to calvarial bone growth. Our transcriptomic approach provides a rich resource for insight into normal and abnormal development.

overall_design: Laser capture microdissection (LCM) was performed on fresh frozen sections of the coronal (C), lambdoid (L), sagittal (S), and frontal (IF) sutures of C57BL/6J mice at embryonic stages E16.5 and E18.5. Five biological replicates of the suture mesenchyme (SM) and osteogenic front regions were obtained from each suture. RNA was isolated from each LCM sample, converted to RNA-Seq libraries, and sequenced on the Illumina HiSeq 2500 platform. For each suture and time point, pairwise comparisons were then performed for each osteogenic front region compared to suture mesenchyme to identify differentially expressed genes between front and mesenchymal regions.

first: Greg

last: Holmes

first: Ana

last: Gonzalez-Reiche

first: Madrikha

last: Saturne

first: Susan

last: Motch Perrine

first: Xianxiao

last: Zhou

last: Borges

first: Bhavana

last: Shewale

first: Joan

middle: T

last: Richtsmeier

first: Bin

last: Zhang

last: van Bakel

first: Ethylin

last: Wang Jabs


title: A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary

status: Public on May 19 2021

first: Mostafa

last: ElMaghraby

address: Fasangasse 39-41/1/24

institute: IMBA

summary: Argonaute proteins of the PIWI-clade, complexed with PIWI-interacting RNAs (piRNAs), protect the animal germline genome by silencing transposable elements. One of the leading experimental systems for studying piRNA biology is the Drosophila melanogaster ovary. In addition to classical mutagenesis, transgenic RNA interference (RNAi), which enables tissue-specific silencing of gene expression, plays a central role in piRNA research. Here, we establish a versatile toolkit focused on piRNA biology that integrates transgenic RNAi in the germline, GFP-marker lines for key proteins of the piRNA pathway, and reporter transgenes to establish genetic hierarchies. We compare constitutive, pan-germline RNAi with an equally potent transgenic RNAi system that is activated only upon germ cell cyst formation. Stage specific RNAi allows investigating the role of genes essential for cell survival (e.g. nuclear RNA export or the SUMOylation pathways) in piRNA-dependent and independent transposon silencing. Our work forms the basis for an expandable genetic toolkit available from the Vienna Drosophila Resource Center.

first: Laszlo

last: Tirian

first: Kirsten

middle: A

last: Senti

first: Katharina

last: Meixner

first: Julius

last: Brennecke


title: Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Skin)

first: Luke

middle: C

last: Gandolfo

summary: Tissue-resident memory T cells (TRM) are non-recirculating cells that exist throughout the body. While TRM in various organs rely on common transcriptional networks to establish tissue residency, location-specific factors adapt these cells to their tissue of lodgment. Here, we chart TRM heterogeneity between organs and find that the different environments in which these cells differentiate dictate TRM function, durability and malleability. We find that unequal responsiveness to TGF-β is a major driver of this diversity. Strikingly, dampened TGF-b signaling engendered CD103- TRM with increased proliferative potential, enhanced function, and reduced longevity compared to their TGF-β-responsive CD103+ TRM counterparts. Further, while CD103- TRM readily modified their phenotype upon relocation, CD103+ TRM were comparatively resistant to trans-differentiation. Thus, despite common requirements for TRM development, adaptation of these cells to their tissue of residence confers discrete functional properties such that TRM exist along a spectrum of differentiation potential that is governed by their local microenvironment.

overall_design: Effector CD8+ OT-I Tcells or OT-I cells deficient in the TGFbRII were injected into HSV-OVA infected mice 2 days post-infection and sorted at day 14 post-infection from the epidermal skin. Cells were subject to RNA sequencing for transcriptional analysis.

last: Christo

first: Laura

last: Mackay


title: Single cell RNA sequencing of femur bone marrow cells from the NZBWF1 systemic lupus erythematosus mouse model and its progenitors.

status: Public on May 20 2021

city: Jackson

first: Kurt

last: Showmaker

state: MS

address: 2500 North State St.

department: Pharmacology and Toxicology

institute: UMMC

summary: Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by failure of self-tolerance mechanisms and the resultant production of autoreactive antibodies. The NZBWF1 mouse spontaneously develops a lupus-like syndrome and is used as model of SLE. The NZBWF1 model represents the F1 generation of a cross between New Zealand Black (NZB) and New Zealand White (NZW) mice. In this study we investigated the model and its progenitors (NZB, NZW) gene expression with single cell RNA sequencing on cells isolated from bone marrow and processed with the 10X Chromium.

overall_design: Cells isolated from femur bone marrow from female 9 - 10 weeks old mice (n=3) for each strain (n=3; NZBWF1, NZB, NZW) was prepared on the 10x Genomics Chromium Single Cell controller using the 10x Chromium Single Cell 3’ v3.1 Reagent Kit (10x Genomics Product Code 1000268).

first: Subhi

last: Younes

first: Ashley

last: Johnson

first: Michael

middle: R

last: Garrett

last: Ryan


title: Unraveling the molecular mechanism of hyperlipidemia using integrated lncRNA and mRNA microarray data

status: Public on May 18 2021

city: Zhengzhou

first: Bianling

last: Xu

address: 91 Ruhe Road, Zhongyuan District, Zhengzhou City, Henan Province, China

institute: Zhengzhou Hospital of Traditional Chinese Medicine

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Long non-coding RNAs (lncRNAs) play key roles in various diseases; however, their functions in hyperlipidemia (HLP) are unclear. In the present study, microarray technology was utilized to analyze the differential expression of lncRNAs and mRNAs in liver tissues of HLP ApoE-/- mice and control mice. We identified 104 and 96 differentially expressed lncRNAs and mRNAs, respectively. Differentially expressed genes were significantly enriched in biological processes such as nitric oxide biosynthesis, innate immune response, and inflammatory response. Two pairs of target genes and 38 transcription factors with regulatory functions in HLP were predicted based on the lncRNA and mRNA co-expression network. The lncRNA expression profile changes significantly in liver tissues of HLP mice model, and can provide new targets for research and treatment.

overall_design: A total of 10 samples were analyzed,including 5 control samples and 5 model samples.

last: Wang

first: Xuegong

first: Yongmin

last: Cai


title: Alteration of ribosome function upon 5-fluorouracil treatment favours cancer cell drug-tolerance

status: Public on Jun 25 2021

city: MONTPELLIER

first: Julie

last: Ripoll

state: OCCITANIE

address: 860 rue de St Priest

department: Informatics

institute: LIRMM

summary: Partial response to chemotherapy leads to disease resurgence. Upon treatment, a subpopulation of cancer cells, called drug-tolerant persistent cells, displays a transitory drug tolerance that lead to treatment resistance. Though drug-tolerance mechanisms remain poorly known, they have been linked to non-genomic processes, including epigenetics, stemness and dormancy. 5-fluorouracil (5-FU), the most widely used chemotherapy in cancer treatment, is associated with resistance. While prescribed as an inhibitor of DNA replication, 5-FU alters all RNA pathways. Here, we show that 5-FU treatment leads to the unexpected production of fluorinated ribosomes, exhibiting altered mRNA translation. 5-FU is incorporated into ribosomal RNAs of mature ribosomes in cancer cell lines, colorectal xenografts, and human tumors. Fluorinated ribosomes appear to be functional, yet, they display a selective translational activity towards mRNAs according to the nature of their 5'-untranslated region. As a result, we found that sustained translation of IGF-1R mRNA, which codes for one of the most potent cell survival effectors, promoted the survival of 5-FU-treated colorectal cancer cells. Altogether, our results demonstrate that "man-made" fluorinated ribosomes favour the drug-tolerant cellular phenotype by promoting translation of survival genes. This could be exploited for developing novel combined therapies. By unraveling translation regulation as a novel gene expression mechanism helping cells to survive a drug-challenge, our study extends the spectrum of molecular mechanisms driving drug-tolerance.

overall_design: Treated colorectal cancer HCT116 cells with clinically relevant concentrations of 5-FU (10-50 µM) compared to control cells (translatome study)

first: Gabriel

last: Therizols

first: Zeina

last: Bash-Imam

first: Baptiste

last: Panthu

first: Christelle

last: Machon

first: Anne

last: Vincent

first: Sophie

last: Nait-Slimane

first: Mounira

last: Chalabi-Dchar

first: Angéline

last: Gaucherot

first: Maxime

last: Garcia

first: Florian

last: Lafôrets

first: Virginie

last: Marcel

first: Jihane

last: Boubaker-Vitre

first: Marie-Ambre

last: Monet

first: Céline

last: Bouclier

first: Christophe

last: Vanbelle

first: Guillaume

last: Souahlia

first: Elise

last: Berthel

first: Marie-Alexandra

last: Albaret

first: Hichem

last: Mertani

first: Michel

last: Prudhomme

first: Martin

last: Bertrand

first: Alexandre

last: David

first: Jean-Christophe

last: Saurin

first: Philippe

last: Bouvet

first: Eric

last: Rivals

first: Théophile

last: Ohlmann

first: Jérôme

last: Guitton

first: Nicole

last: Dalla-Venezia

last: Pannequin

first: Frédéric

last: Catez

first: Jean-Jacques

last: Diaz


title: CCND3 knockdown modulates gene expression outside of the CDK4/6 complex

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

summary: We compared gene expression profiles of B-ALL cell lines of different genotypes after CCND3 knockdown or inhibition of its associated kinases CDK4/6 by palbociclib and found that a distinct subset of genes is exclusively regulated after CCND3 knockdown, likely responsible for induction of apoptosis after CCND3 knockdown but not treatment with palbociclib.

overall_design: B-ALL cell lines NALM-6, RS4;11 and BV-173 were either transduced with shCCND3 or  scrambled control in the pRSI12-U6-shUbiC-TagRFP lentiviral vector (BioCat, Heidelberg, Germany) or treated with 1 µM palbociclib or equivalent amounts of DMSO for 3 days. Transduced cells were isolated on day 4 post transduction, palbociclib treated cells were collected after three days. RNA was isolated with the RNeasy mini kit (QIAGEN). RNA-sequencing and data processing was done by BGI (Hong-Kong). RNA libraries were prepared for sequencing using standard BGI protocols. SOAPnuke was used for data filtering and Bowtie2 was used to map clean reads to reference. RSEM was used to calculate gene expression levels and DEseq2 was used to detect DEGs. hg38 was used as reference genome.

first: Franz

last: Ketzer

first: Thomas

last: Wirth


title: Transcriptome analysis of the host immune responses to Sarcoptes scabiei

status: Public on Jun 22 2021

city: Rawalpindi

first: Huma

last: Shehwana

address: Pak Emirates Military Hospital, The Mall, Abid Majeed Rd

country: Pakistan

institute: National University of Medical Sciences

summary: Scabies is a human skin disease due to the burrowing ectoparasite Sarcoptes scabiei resulting in intense itching and inflammation and manifesting as skin allergy. Little is known about the specific scabies molecules and genes involved in the host inflammatory and immunologic responses. We interrogated the transcriptome profiles of skin biopsies using next generation sequencing and a combined clustering and pathway mapping approach which will enable us in the identification of key signaling events in the host immune and inflammatory responses to S. scabiei infestation.  With the comprehensive analysis of RNA-seq results, it has been found that the immune response of host inhibits S. scabiei immune pathway, proliferation and metabolism signaling pathways, out of which the signaling pathway seems to be the main pathway in innate immune response of S. scabiei. The analysis of immune pathway, hydrolase and allergen will contribute to the research of S. scabiei pathogenesis, diagnosis and development of vaccines.

overall_design: The skin biopsies were collected from two groups of 08 participating individuals: Ordinary scabies (OS) subjects (“OS” n = 05) and subjects naïve to scabies and allergy with no known exposure to scabies or allergy (“naive” n = 03).

first: Shumaila

last: Naz


title: RNA sequencing analysis of MCF7 cells treated with several combinations of steroids

status: Public on May 17 2021

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

institute: University of Liège

summary: We report the transcriptomic profile induced on MCF7 cells by several combinations of steroids (estetrol, estradiol, progesterone, R5020).

overall_design: Routinely cultured MCF7 cells were treated in red phenol-free DMEM medium, supplemented with 2% heat-inactivated and dextran-coated charcoal- treated FBS with estradiol (10-9M), estetrol (10-7M or 10-10M) or vehicle (DMSO 0.001%) for 20h, then progesterone (10-7M) or R5020 (10-8M) were added in some conditions for 4 additional hours. After 24h total treatment, RNA was extracted, quantified and submitted to RNAseq analysis.

first: Anne

last: Gallez

first: Erika

last: Konradowski

first: Erik

last: Maquoi

first: Marc

last: Joiret

first: Christel

last: Pequeux


title: The VIL gene CRAWLING ELEPHANT controls plant maturation and differentiation in tomato via polycomb silencing

status: Public on May 14 2021

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

summary: VERNALIZATION INSENSITIVE 3-LIKE (VIL) proteins are PHD-finger proteins that recruit the repressor complex Polycomb Repressive Complex 2 (PRC2) to the promoters of flowering repressors to promote flowering. Here, we show that the tomato VIL gene CRAWLING ELEPHANT (CREL) promotes differentiation throughout plant development and affects the trimethylation of Histone H3 on lysine 27 (H3K27me3) at a subset of PRC2 targets across the genome. We identified the crel mutant in a screen for suppressors of the simple-leaf phenotype of entire (e), a mutant in the AUX/IAA gene ENTIRE/SlIAA9, which is involved in compound-leaf development in tomato. crel mutants have increased leaf complexity, and suppress the ectopic blade growth of e mutants. In addition, crel mutants are late flowering, and have delayed and aberrant stem, root and flower development. Consistent with a role for CREL in recruiting PRC2, the H3K27me3 modification is altered at a subset of PRC2 targets throughout the genome in crel mutants. Our results uncover a wide role for CREL in plant and organ differentiation in tomato and suggest that CREL is required for targeting PRC2 activity, and thus silencing, to a specific subset of polycomb targets.

overall_design: ChIP-seq analysis of H3K27me3 and RNA-seq analysis in wild-type and the crel mutant of tomato (Solanum lycopersicum)

first: Naomi

last: Ori


title: RNA Sequencing Analysis of Gene Expression Profiles in WT and CIC-deficient DP Thymocytes

status: Public on May 06 2021

city: Pohang

first: Soeun

last: Kim

address: 77, Cheongam-ro

institute: POSTECH

summary:
Purpose : The goal of this study is to compare the gene expression profiles between wild-type (WT) and CIC-deficient DP thymocytes to understand the molecular mechanisms of CIC regulation of T cell development, especially in DP thymocytes.
Methods : DP thymocytes (lin-CD4+CD8+TCRlo (Lineage : CD11b, CD11c, CD19, NK1.1, Gr-1, γδTCR, and TER119)) from thymus were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using RiboEX (GeneAll) according to the manufacturer's instructions. The library for mRNA sequencing was generated using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequencing was performed with NovaSeq 6000 (Illumina).
Results : Trimmed reads were mapped to the mouse reference genome (mm10 RefSeq) with HISAT2, and the transcripts were assembled using StringTie. A total of 482 differentially expressed genes (DEGs; fold change > 2 and P-value < 0.05) were generated using edgeR. The 263 upregulated genes included known CIC target genes such as Etv1, Etv4, Etv5, Spry4, Spred1, Dusp4, and Dusp6.
Conclusions : Our study represents the first comparative analysis of DP thymocytes from WT and hematopoietic lineage cell-specific Cic deficient mice. We concluded that CIC deficiency leads to impaired positive and negative selection, and TCR signaling in DP cells. The attenuation of TCR signaling is caused by derepression of CIC target genes involved in dephosphorylation of ERK.

overall_design: mRNA profiles of CD4+CD8+ DP thymocytes from 7-week-old wild type (WT, Cicf/f) and Cicf/f;Vav1-Cre mice. Two replicates for each genotypes were anaylzed.

first: Yoontae

last: Lee


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis

status: Public on May 21 2021

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

institute: Karolinska Institutet

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

overall_design: Refer to individual Series