title: Large-scale analysis of human and mouse RNA-seq datasets to identify undiscovered male reproductive tract-specific genes (human)

city: Houston

first: Thomas

last: Garcia

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: The development of a safe and effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades, yet none have reached clinical trials. To advance progress, further identification of novel reproductive tract-specific, potentially druggable protein targets is imperative. In this study, we expand on previous single tissue, single species studies by integrating analysis of a vast number of publicly available human and mouse RNA-seq datasets whose initial published purpose was not focused on identifying male reproductive tract-specific targets. We also incorporate analysis of additional newly acquired human and mouse testis and epididymis samples to increase the number of targets identified. Enclosed in this accession is the RNA-seq data for the 12 new human testis and epididymis segment samples we processed for analysis.

overall_design: The de novo isolated human testes and epididymides included in this study were obtained from three donors through a local organ transplant program in Quebec, Canada called Transplant Quebec. All procedures were approved by the local ethics committee and written consent was obtained from each respective donor’s family. The donors were of 40, 52, and 65 years of age with no preexisting medical condition that could affect reproductive function. Donor testes and epididymides were removed under artificial circulation to preserve other organs that were assigned for transplantation. Each testis and epididymis were dissected in the laboratory of Dr. Robert Sullivan at Université Laval. Each epididymis was dissected into three segments corresponding to the caput, corpus and cauda regions and minced into small tissue pieces. Testes and epididymides tissue fragments were immediately snap frozen in liquid nitrogen, stored at −80°C, and shipped frozen to the laboratory of Dr. Thomas Garcia at Baylor College of Medicine for further processing.

first: Cristian

last: Coarfa


title: IGF2BP1 is the first positive marker for anaplastic thyroid carcinoma diagnosis [RNA-Seq]

status: Public on Jul 07 2020

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

type: Expression profiling by high throughput sequencing

summary: Anaplastic thyroid carcinomas (ATC) are rare, but represent the most lethal malignancy of the thyroid. Selective molecular markers and drivers distinguishing ATC from other thyroid carcinomas of follicular origin remain largely unknown, limiting advances in diagnosis and treatment. In a retrospective study, we analyzed gene expression in 36 ATC, 18 poorly-differentiated, 132 papillary and 55 follicular thyroid carcinoma, as well as 124 paired and un-paired normal thyroid tissues in three independent cohorts by RNA-sequencing and immunohistochemistry. RNA-sequencing data in the test cohort suggested selective ATC protein biomarkers. Evaluation of these revealed that ATCs are characterized by the de novo expression of various testis antigens, including melanoma-associated antigen A3 (MAGEA3), but most importantly the oncofetal IGF2 mRNA binding protein 1 (IGF2BP1). Shallow whole genome-sequencing essentially excluded, that IGF2BP1 upregulation results from gene copy number alterations. Immunohistochemical analyses in all three tumor cohorts confirmed selective de novo expression of IGF2BP1 protein in ATC. In sum, 75 % (27/36) of all tested ATC and 0.5 % (1/204) of poorly and well-differentiated thyroid carcinoma tissue samples were positive for IGF2BP1 protein. This indicates that IGF2BP1 protein expression identifies ATC with a diagnostic odds ratio of 612 (95 % CI: 74.6 to 5021). In addition, we found that MAGEA3 is exclusively, although less consistently upregulated in ATC, presenting with an odds ratio of 411 (95 % CI: 23.8 to 7098.7). Importantly, we provide confirmatory evidence that IGF2BP1 and MAGEA3 expression distinguishes ATC from partially differentiated thyroid carcinomas (PDTCs). IGF2BP1 furthermore identified ATC foci within low-grade follicular thyroid carcinoma. In conclusion, IGF2BP1 represents the most promising single-gene marker available for ATC, followed by MAGEA3, improving on current techniques. Robust markers are essential to help distinguish this high-grade malignancy from other thyroid carcinomas, to guide surgical decision making, therapy and post-resection/therapy monitoring strategies.

overall_design: Total RNA-sequencing of ATC samples.

first: Jacob

last: Haase

first: Nikolaos

last: Pazaitis

first: Marcus

last: Bauer

first: Juliane

last: Braun

first: Rebecca

last: Pötschke

first: Alexander

last: Mensch

first: Jessica

middle: L

last: Bell

first: Henning

last: Dralle

first: Udo

last: Siebolts

first: Claudia

last: Wickenhauser

first: Kerstin

last: Lorenz

first: Stefan

last: Hüttelmaier


title: Heat-killed Fusarium-elicited W22-stem time_course

status: Public on Jul 08 2020

city: La Jolla

first: Alisa

last: Huffaker

state: CA

address: 9500 Gilman Drive #0116

department: Cell & Developmental Biology

country: USA

institute: UC San Diego

summary: We aim to examine dynamic defense transcript changes in maize stems following elicitation with heat-killed Fusarium hyphae.

overall_design: We look at defense transcript changes in W22 maize stems at time 0, 2h, 4h, 8h, 12h, 24h, 48h, 72h, 96h, and 120h after heat-killed Fusarium hyphae.

first: Yezhang

last: Ding

first: Eric

last: Schmelz


title: Transcriptome profiling of Blimp-1-deficient B cells from distinct divisions during plasma cell differentiation

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To examine the cell division that Blimp-1 functioned during B cell differentiation we adoptively transferred CellTrace Violet labeled Blimp-1-deficient or control B cells into congenically disparate uMT hosts.  Following transfer, mice were innoculated with LPS to induce B cell differentiation and 72 hours later cells from distinct divisions were FACS sorted for RNA-seq

overall_design: RNA-seq on cohorts of Blimp-1-deficient or control B cells from distinct divisions during in vivo B cell differentiation

first: C

middle: D

first: J

middle: M

last: Boss


title: Heat-killed Fusarium-elicited B73 and Mo17 stems for 36 h

summary: We aim to examine defense transcript changes in maize stems following elicitation with heat-killed Fusarium hyphae in B73 and Mo17.

overall_design: We compared defense transcript changes in B73 and Mo17 at 36 h after heat-killed Fusarium hyphae (elicted) vs damage controls.


title: Gene regulatory markers in pregnant, term non-labouring, labouring, and postpartum myometrium.

status: Public on Jul 10 2020

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We have generated genome-wide binding and expression datasets in uterine smooth muscle (myometrium) from murine models of pregnancy and labour. ChIP-seq and total RNA-seq experiments were conducted to evaluate changes in the genomic and transcriptomic landscape of the myometrium prior to, during, and after labour onset.

overall_design: Examination of total RNA and POL2 enrichment in pregnant and labouring myometrium; examination of euchromatin-associated histone marks (H3K27ac, H3K4me3) in pregnant, term non-labouring, labouring, and postpartum myometrium

first: Virlana

last: Shchuka

middle: A


title: High-throughput error corrected Nanopore single cell transcriptome sequencing

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: E18 mouse brain single cell profiling using the 10x Genomics Chromium instrument workflow with either Illumina short read sequencing for the standard gene profiling and Nanopore PromethION long read sequencing for isoform profiling.

overall_design: E18 mouse brain single cell Chromium emulsion was split into two aliquots targeting 190 and 951 cells and processed in parallel for gene and isoform profiling with Illumina and Nanopore sequencing.

first: Rainer

last: Waldmann


title: Lack of TREM2 differentially affects the phenotype and transcriptome of mice expressing human APOE3 and APOE4

status: Public on Jul 09 2020

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

summary: We aim to investigate the interaction between two of the major genetic risk factors for AD: inheritance of APOEε4 and deficiency of Triggering Receptor Expressed on Myeloid cells 2 (TREM2). Trem2 deletion worsened memory in AD model mice but not in their WT littermates. Interestingly, the lack Trem2 resulted in a significantly less microglia around amyloid plaques in APP mice expressing both APOE isoforms but had no impact on amyloid load. Gene expression analysis identified as Trem2 signature a cluster of highly connected immune response genes, commonly downregulated as a result of Trem2 deletion in all experimental groups, such as Clec7a, Itgax, Cts7, Mpeg1, Csf1r, Cx3cr1, Pik3cg and Spi1/PU.1. In vitro experiments with primary microglia demonstrated a decrease of Aβ phagocytosis in APOE4 versus APOE3 microglia a difference that was augmented by the absence of Trem2. Our data demonstrate that the lack of Trem2 differentially impact the phenotype and brain transcriptome of APP mice expressing human APOE isoforms probably reflecting the difference between APOE isoforms to transport lipids that can affect APOE receptor-binding properties.

overall_design: We crossed 6.5 month old male and female Trem2ko mice with APP/PSEN1dE9 mice expressing human APOE3 or APOE4 isoforms and assessed amyloid pathology, glial response, and whole-brain transcriptome.

first: Nicholas

middle: F

last: Fitz

first: Cody

last: Wolfe

first: Brittany

middle: E

last: Playso

first: Richard

middle: J

last: Biedrzycki

first: Yi

last: Lu

first: Kyong

middle: N

last: Nam

first: Radosveta

last: Koldamov


title: Sexually dimorphic effects of forkhead box a2 (FOXA2) and uterine glands on decidualization and fetoplacental development

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: Glands of the uterus are essential for the establishment of pregnancy in mice, sheep and likely humans. Forkhead box a2 (FOXA2) is expressed specifically in the glands of the uterus and a critical regulator of glandular epithelium (GE) differentiation, development and function. Mice with a conditional deletion of FOXA2 in the adult uterus, created using the lactotransferrin iCre (Ltf-iCre) model, have a morphologically normal uterus with glands, but lack a considerable number of FOXA2-dependent GE-expressed genes. Adult FOXA2 conditional knockout (cKO; Ltf-iCre:Foxa2 flox) mice are infertile due to defective embryo implantation arising from a lack of leukemia inhibitory factor (LIF), a critical implantation factor of uterine gland origin. Intraperitoneal injections of LIF can initiate embryo implantation in the uterus of adult FOXA2 cKO mice with pregnancies maintained to term. Here, we tested the hypothesis that FOXA2-regulated genes in the uterine glands impact development of the decidua, placenta and fetus. On gestational day (GD) 8.5, the anti-mesometrial and mesometrial decidua transcriptome was noticeably altered in FOXA2 cKO mice. Viable fetuses were reduced in FOXA2 cKO mice on GDs 12.5 and 17.5. Sex-dependent differences in fetal weight, placenta histoarchitecture, and the placenta and metrial gland transcriptome were observed between control and FOXA2 cKO mice. The transcriptome of the placenta with a female fetus was considerably more altered than the placenta with a male fetus in FOXA2 cKO dams. These studies reveal previously unrecognized sexually dimorphic effects of FOXA2 and uterine glands on fetoplacental development with potential impacts on offspring health into adulthood.

overall_design: The overall design employed studies of littermate control and conditional Foxa2 deleted dams on various days of gestation.

first: Pramod

last: Dhakal

first: Andrew

last: Kelleher

first: Susanta

middle: K

last: Behura


title: RNA Sequencing  Analysis of macrophages from Wild Type and Gsdmd-/- colitis mice

status: Public on Jul 06 2020

city: Nanjing

first: Chunmei

last: Ma

address: 101 Longmian road,Nanjing

country: China

institute: Nanjing medical university

summary: We identified that GSDMD protected against DDS-induced colitis, and GSDMD deficiency in macrophages promoted the development of DSS-induced colitis.The purpose of this experiment was to identify how GSDMD protected against DSS-induced colitis.

overall_design: Macrophages mRNA profiles of wild type (WT) and Gsdmd-/- mice with colitis were generated by deep sequencing, in triplicate, using BGISEQ-500

first: Shuo

last: Yang

first: Dongxue


title: RNAseq analysis of the effects of inorganic long-chain polyphosphates on murine macrophages

city: Boston

first: Markus

last: Bosmann

state: MA

address: 72 East Concord Street

department: Pulmonary Center, Department of Medicine

institute: Boston University School of Medicine

summary:
We used unbiased RNAseq analysis from bone marrow-derived macrophages of five individually treated sets of cells from C57BL/6J mice. Cells were treated for 12h with LPS, LPS+L-polyP, L-polyP, or remained untreated.
We found several hundred genes to be regulated by the addition of L-polyP. In the combinated treatment with LPS as compared to LPS alone, we found especially interferon-regulated genes to be differentially expressed.

overall_design: Five individual sets of bone marrow-derived macrophages were stimulated with LPS/LPS+L-polyP/L-polyP or remained untreated (20 samples in total of 4 conditions)

first: Julian

last: Roewe

first: Federico

last: Marini


title: Large-scale analysis of human and mouse RNA-seq datasets to identify undiscovered male reproductive tract-specific genes

last: Garcia

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Genome-wide transcriptional regulation of the long non-coding RNA steroid receptor RNA activator in human erythroblasts

status: Public on Jul 04 2020

city: Bangkok

first: Waritta

last: Sawaengdee

address: 272 Rama VI Road

department: Department of Biochemistry, Faculty of Science

country: Thailand

institute: Mahidol University, Thailand

summary: We report a novel function of the lncRNA SRA in regulation of global gene expression through direct chromatin binding in human erythroleukemia cell line K562 and in primary human proerythroblasts derived from HSCs. We demonstrate that SRA, together with CTCF, H3K4me3, and H3K27me3, occupies various genomic regions. Further, SRA facilitates transcriptome-wide expression of erythroid program and expression of erythroid markers in K562 and in primary human proerythroblasts. Hence, a possible function of the lncRNA SRA during erythroid development is to promote transcription of erythroid genes and therefore erythropoiesis.

overall_design: RNA-seq analysis of both K562 and CD36-positive proerythroblasts was performed upon depletion of SRA using an Illumina HiSeq platform. Differentially expressed genes with at least two fold-change were subsequently identified by using DEseq. Three individual shRNA knockdown samples, which contain different siRNA targets, were used as biological replicates for the analysis.

first: Keji

last: Zhao

first: Patompon

last: Wongtrakoongate


title: Triacylglycerol synthesis enhances macrophage inflammatory function

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Macrophages stimulated with lipopolysaccharide (LPS) plus interferon-g (IFNg) accumulate TGs in LDs, and long-chain acylcarnitines. Inhibition of TG synthesis results in diminished LD development, and increased long chain acylcarnitine levels, suggesting that FA fate is balanced between TG and acylcarnitine synthesis. Nevertheless, TG-synthesis is required for inflammatory macrophage function, since its inhibition negatively affects production of proinflammatory IL-1b, IL-6 and PGE2, and phagocytic capacity, and protects against LPS-induced sock in vivo.

overall_design: RNA-Seq was performed on resting or activated Macrophages treated with or without the DGAT1 inhibitor T863

first: Angela

last: Castoldi

first: Lauar

middle: B

last: Monteiro

first: Nikki

last: van Teijlingen Bakker

first: David

last: Sanin

first: Nisha

last: Rana

first: Mauro

last: Corrado

first: Alanna

last: Cameron

first: Fabian

last: Hässler

first: Mai

last: Matsushita

first: George

last: Caputa

first: Ramon

middle: I

last: Klein Geltink

first: Jrg

last: Büscher

first: Joy

last: Edwards-Hicks

first: Erika

last: Pearce

first: Edward


title: Comparative Analysis of the Development of Acquired Radioresistance in Canine and Human Mammary Cancer Cell Lines

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

summary:
Background: Research using in vitro canine mammary carcinoma cell lines and studies involving naturally occurring canine mammary tumours are not only fundamental models used to advance the understanding of cancer in veterinary patients but are also regarded as excellent translational models for human breast cancer. In human medicine, following disease classification and staging breast cancer is typically treated with multimodal therapies including radiotherapy. The response of a breast tumour to radiation depends not only on its innate radiosensitivity but also on tumour repopulation by cells that have developed radioresistance. Comparative canine and human studies investigating the molecular mechanisms of radioresistance may lead to the development of effective cancer treatments that benefit both species.
Methods: Human (MDA-MB-231, MCF-7 and ZR-751) and canine (REM-134) radioresistant cell lines were established by exposing parental cells to increasing weekly doses of radiation. The development of radioresistance was evaluated through proliferation and colony formation assays. Phenotypic characterisation included migration and invasion assays and immunohistochemistry. Intrinsic differences between parental and radioresistant cells were investigated by whole-transcriptome gene expression analysis. Gene enrichment and pathway-focused analyses identified signalling networks differentially activated in radioresistant cells.
Results: Colony formation assays identified a range of intrinsic radiosensitivities in the human and canine parental cell lines with the REM-134 cell line showing significantly greater radioresistance compared to the human cell lines. Colony formation and proliferation assays confirmed radioresistance in all developed radioresistant cell lines. Radioresistant cells exhibited enhanced migration and invasion, with evidence of epithelial-to-mesenchymal-transition. Gene analysis identified that following the acquisition of radioresistance in MCF-7 and ZR-751 cell lines the cell lines changed subtype classification from their parental luminal A to HER2-overexpressing (MCF-7 RR) and normal-like (ZR-751 RR) subtypes, indicating the extent of phenotypic changes and cellular plasticity involved in this process. MDA-MB-231 and MDA-MB-231 RR cell lines both classified as basal, whereas the REM-134 and REM-134 RR cell lines with enriched for HER2 overexpression. Whole-transcriptome gene expression analysis identified down-regulation of ER signalling genes and up-regulation of genes associated with PI3K, MAPK and WNT pathway activity in radioresistant cell lines derived from ER+ cells; this was confirmed by western blot, which showed increased p-AKT and p-ERK expression following radiation.
Conclusions: To our knowledge, our study is the first to develop a canine radioresistant cell line and provide a comparative genetic and phenotypic analysis of the mechanisms of acquired radioresistance between canine and human cell lines. The cellular process that occur with the development of acquired radioresistance are similar between the human and canine cell lines; this suggests that not only is the canine model an appropriate model to study human disease but that treatment strategies used in human medicine may also be applicable to veterinary patients.

sample_organism:
Homo sapiens
Canis lupus familiaris

overall_design: Comparative whole-transcriptome gene expression analysis of 3 breast cancer cell lines (MCF-7, ZR-751 and MDA-MB-231) and 1 canine breast cancer cell line (REM-134) and the radio-resistant models derived from these (MCF-7-RR, ZR-751-RR, MDA-MB-231-RR and REM-134-RR, respectively), using Lexogen QuantSeq technology. The study included both radiosensitive and radioresistant models exposed to different levels of radiation therapy (untreated or 2 Gray), with samples collected at different timepoints post-treatment.

first: Mark

last: Gray

first: Arran

last: Turnbull


title: scRNA-seq of T cell Independent B cell responses

first: Chris

last: Scharer

summary: To fine map the continuum of molecular changes that occur as B cells differentiate to antibody secreting plasma cells in response to the T cell independent antigens LPS and NP-Ficoll we performed scRNA-seq.  WT or IRF4-deficient B cells were CTV labeled and adoptively transferred into congenically disparate uMT hosts.  One day later, the mice were innoculated with LPS and all transferred cells isolated at 72 hours and profiled on the 10x Genomimcs 5' Library Kit.  In addition, we adoptively transferred WT B cells into congenically disparate WT hosts and innoculated the animals with either LPS or NP-Ficoll, and 72 hours later performed scRNA-seq on all responding B cells.

overall_design: scRNA-seq on two independent biological replicates of wild-type or IRF4-deficient B cells responding to LPS in uMT mice and wild-type B cells responding to LPS or NP-Ficoll in wild-type hosts.

first: C

first: J

last: Boss


title: Cross-talk between GLI transcription factors and FOXC1 promotes T-cell acute lymphoblastic leukemia dissemination

status: Public on Jul 03 2020

city: Padua

first: Erich

last: Piovan

address: via Gattamelata 64

department: Dep. Surgery, Oncology and Gastroenterology

institute: University of Padua


title: Single cell transcriptomic analyses of the developing meninges reveal   meningeal fibroblast diversity and function

city: AURORA

first: Julie

last: Siegenthaler

state: CO

department: Pediatrics

institute: UNIVERSITY OF COLORADO, ANSCHUTZ MEDICAL CAMPUS

summary: The meninges are a multilayered structure composed of fibroblasts, blood and lymphatic vessels, and immune cells. Meningeal fibroblasts secrete a variety of factors that control CNS development, yet strikingly little is known about their heterogeneity or development. Using single cell sequencing, we report distinct transcriptional signatures for fibroblasts in the embryonic dura, arachnoid and pial. We define new markers for meningeal layers and show conservation in human meninges. We find that embryonic meningeal fibroblasts are transcriptionally distinct between brain regions and identify a regionally localized pial sub-population marked by expression of µ-Crystallin. Developmental analysis reveals a progressive, ventral to dorsal maturation of telencephalic meninges. Our studies present an unprecedented view of meningeal fibroblasts, providing a molecular profile of embryonic meningeal fibroblasts by layer that yield insights into mechanisms of meninges development and function.

overall_design: Examination of gene transcripts of Collagen1-GFP (Col1a1-GFP) cells isolated from E14 forebrain mouse meninges using single cell RNA-sequencing

first: Rebecca

last: O'Rourke


title: T-cell acute lymphobalstic leukemia xenografts in NOD/SCID mouse

summary: Gene expression analysis of twenty patient-derived T-ALL xenografts was performed to determine if a GLI activation signature was enriched in GANT-61 sensitive cells.

overall_design: Gene expression analysis of twenty patient-derived T-ALL xenografts using cells obtained from the spleens of diseased mice. Cells obtained from independent mice were evaluated in vitro for their sensitivity to the GLI inhibitor, GANT-61.

first: Gloria

last: Milani

first: Pieter

last: van Vlierberghe

first: Sonia

last: Minuzzo

first: Stefano

last: Indraccolo


title: RNA sequencing of primary bronchial airway epithelial cells from young children with and without CF, including those with and without rhinovirus infection in vitro

city: Perth

first: Kak Ming

last: Ling

state: WA

address: 15 Hospital Avenue (North Entrance)

country: Australia

institute: Telethon Kids Institute

summary: Early life viral infections are responsible for pulmonary exacerbations that can contribute to disease progression in young children with CF. The most common respiratory viruses detected in the CF airway are human rhinoviruses (RV) and susceptibility to infection has been attributed to dysregulated airway epithelial responses, although evidence has been conflicting. Here, we exposed airway epithelial cells from children with and without CF to RV in vitro. Using RNA-Seq, we profiled the transcriptomic differences of CF and non-CF airway epithelial cells at baseline and in response to RV. There were only modest differences between CF and non-CF cells at baseline. In response to RV there were 1442 and 896 differentially expressed genes in CF and non-CF airway epithelial cells respectively. The core antiviral responses in CF and non-CF airway epithelial cells were mediated through interferon signaling although type 1 and 3 interferon proteins were reduced in CF airway epithelial cells following viral challenge consistent with previous reports. The transcriptional responses in CF airway epithelial cells were more complex than in non-CF airway epithelial cells with more over-represented biological pathways ranging from cytokine signaling to metabolic and biosynthetic pathways. Network analysis highlighted that the differentially expressed genes of CF airway epithelial cells transcriptional responses were highly interconnected and formed a more complex network than observed in non-CF airway epithelial cells. These data provide novel insights to the CF airway epithelial cells responses to RV infection and highlight potential pathways that could be targeted to improve antiviral and anti-inflammatory responses in CF.

overall_design: Two participant groups; non-CF and CF - paired control and rhinovirus-infected samples for all participants.

first: Kak-Ming

first: Luke

middle: W

last: Garratt

first: Erin

last: Gill

first: Amy

middle: H

last: Lee

first: Patricia

last: Agudelo-Romero

last: Sutanto

first: Thomas

last: Iosifidis

first: Stuart

last: Turvey

first: Timo

last: Lassmann

first: Robert

last: Hancock

first: Anthony

last: Kicic

first: Stephen

last: Stick


title: Large-scale analysis of human and mouse RNA-seq datasets to identify undiscovered male reproductive tract-specific genes (mouse)

last: Garcia

summary: The development of a safe and effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades, yet none have reached clinical trials. To advance progress, further identification of novel reproductive tract-specific, potentially druggable protein targets is imperative. In this study, we expand on previous single tissue, single species studies by integrating analysis of a vast number of publicly available human and mouse RNA- seq datasets whose initial published purpose was not focused on identifying male reproductive tract-specific targets. We also incorporate analysis of additional newly acquired human and mouse testis and epididymis samples to increase the number of targets identified. Enclosed in this accession is the RNA-seq sequence data for the 9 new mouse epididymis segment samples we processed for analysis.

overall_design: The de novo isolated mouse epididymis segments (caput, corpus, and cauda) included in this study were obtained from dissection of 3 month old B6/129 mice.

first: Cristian

last: Coarfa


title: The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos

status: Public on Jul 02 2020

city: Beijing

first: Feifei

last: Li

address: Chaoyang West Road, No.1

institute: Beijing Institute of Genomics


title: The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [Hi-C]

summary: Pigs are important animals for agricultural and biomedical research, and its assisted reproductive technologies are urgently needed to be improved. Determining the underlying mechanism of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis (PA) and androgenesis (AG), will not only contribute to assisted reproduction technologies of pigs but also will shed light into early human development. We generated 3D chromatin profiles for pig somatic cells, IVF, PA and AG preimplantation embryos. We found that the chromosomes in the pig preimplantation embryos are enriched for superdomains, i.e., the larger than 10M compartment domains, which are much rarer in mice. Wheras, p(s) curves, compartments and TADs, are largely conserved in somatic cells, and are gradually establishing during preimplantation embryogenesis. In the uniparental pig embryos, the establishment of chromatin architecture was highly asynchronized at all levels from IVF embryos, and a remarkably strong decompartmentalization was observed during zygotic genome activation (ZGA). Finally, chromosomes originating from oocytes always establish TADs faster than chromosomes originating from sperm, both before and during ZGA.

overall_design: We generated 3D chromatin profiles for pig embryonic fibroblasts (PEFs), IVF, PA and AG preimplantation embryos.

first: Danyang

last: Wang

first: Ruigao

last: Song

first: Chunwei

last: Cao

first: Zhihua

last: Zhang

first: Yu

first: Xiaoli

first: Jiaojiao

last: Huang

first: Qiang

last: Liu

first: Naipeng

last: Hou

first: Bingxiang

last: Xu

first: Xiao

first: Xiaomeng

last: Gao

first: Yan

last: Jia

first: Jianguo

last: Zhao

first: Yanfang


title: The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [ChIP-seq]

overall_design: We generated two histone modifications and CTCF binding profiles for pig embryonic fibroblasts (PEFs).


title: Reversal of pre-existing NGFR-driven tumor and immune therapy resistance

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

summary: In spite of the remarkable clinical benefit from immune checkpoint blockade in melanoma, both intrinsic and acquired resistance prevent durable clinical responses in many patients. Whereas melanomas are known to acquire MART-1 T cell resistance by reversible phenotype switching to an NGFRhi state, less is known about mechanisms of intrinsic immune resistance. To mimic recurrent T cell attack, we chronically exposed a panel of (patient-derived) melanoma cell lines to clinically relevant MART-1 differentiation antigen-specific cytotoxic T cells. This led to strong enrichment of a pre-existing cell population that exhibited immune resistance in vitro and in mice. These fractions showed high expression of NGFR, were maintained stably, and were found to be present in patients’ melanomas prior to treatment. Remarkably, these NGFRhi melanoma cells also displayed resistance also to T cells recognizing antigens that are unrelated to melanoma differentiation. Furthermore, these cells exhibited multidrug-resistance to other therapies including BRAF + MEK inhibition, suggesting that they exist in a stable and distinct cellular state. Clinically corroborating these findings, a tumor-intrinsic NGFR signature predicted aPD-1 therapy resistance, while NGFRhi melanoma fractions in patients were associated with immune exclusion. Lastly, genetic or pharmacologic NGFR inhibition restored tumor sensitivity to T cell attack in vitro and in melanoma xenografts. These findings demonstrate the existence of a stable and pre-existing NGFRhi multitherapy-refractory melanoma subpopulation, which ought to be eliminated to revert intrinsic resistance to immunotherapeutic intervention.

overall_design: RNA sequence data of three sets of cell lines, either the parental cell line (parental) or the cell lines resistant to Tcell killing (TR).

first: Julia

last: Boshuizen

first: Daniel

middle: S

last: Peeper


title: RNA-Sequencing of  PEG-stressed Sesame roots in drought sensitive and tolerant genotypes

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

summary: Purpose: The goals of this study are to understand transcriptional changes in the roots of drought-tolerant and sensitive sesame genotypes using PEG (Polyethylene glycol) induced osmotic stress.

overall_design: Methods:The removal of sequence adapters, mapping to reference genome, and normalization of gene expression was performed using CLC Genomics Workbench (V4.5, CLC Bio.). The RNAseq reads were first assessed for quality with FastQC; adapters were removed with Cutadapt (Martin 2011) and trimmed the low-quality bases (q < 20) with FastX-toolkit (Gordon and Hannon 2010). Quality-filtered reads were then mapped to the reference Sinbase database (Wang et al. 2014) using TopHat2 (Kim et al. 2013) with default parameters. Novel transcripts were assembled by Cufflink (Trapnell et al. 2010), then combined with available gene annotation using CuffMerge. Normalized expression levels of genes were expressed in FPKM values as generated by Cuffquant and Cuffnorm running with the option “–frag-bias-correct” and “–multi-read-correct” (Trapnell et al. 2012). The differential expressed genes (DEGs) of pooled samples from each condition was determined using Cuffdiff, using the FPKM values.


title: Altered 3D chromatin structure permits inversional recombination at the IgH locus (Capture Hi-C)

status: Public on Jul 01 2020

first: Xiang

last: Qiu

address: 251 Bayview Blvd.

institute: National Institutes of Health

summary: We reoprt that in the absence of intergenic control region 1 (IGCR1), a regulatory sequence that specifies the RAG scanning domain on WT IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA.

overall_design: We performed capture Hi-C to explore chromatin struture in pro-B cells at the WT or IGCR1 deficient IgH alleles.

first: Fei

last: Ma

first: Mingming

first: Yaqiang

first: Lily

last: Shipp

first: Angela

first: Arun

last: Dutta

first: Amit

last: Singh

first: Fatima

middle: Z

last: Braikia

first: Supriyo

last: De

first: William

last: Wood

first: Kevin

middle: G

last: Becker

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji

first: Keji

first: Michael

last: Atchison

first: Ranjan

last: Sen


title: Efflux pump activity potentiates the evolution of antibiotic resistance across S. aureus

status: Public on Jul 05 2020

city: Oxford

first: Craig

last: MacLean

address: 11a Mansfield Road

institute: University of Oxford

summary: The rise of antibiotic resistance in many bacterial pathogens has been driven by the spread of a few successful strains, suggesting that some bacteria are genetically pre-disposed to evolving resistance. We tested this hypothesis by challenging a diverse set of 222 strains of Staphylococcus aureus with the antibiotic ciprofloxacin in a large-scale evolution experiment. Surprisingly, we found that a single efflux pump, norA, causes widespread variation in evolvability across the diversity of S. aureus. In most lineages of S. aureus, elevated norA expression potentiated evolution by increasing the fitness benefit provided by resistance mutations in DNA topoisomerase under ciprofloxacin treatment. Amplification of norA provided a further mechanism of rapid evolution, but this was restricted to strains from CC398. Crucially, chemically inhibiting NorA effectively prevented the evolution of resistance across the diversity of S. aureus. Our study shows that the underlying genetic diversity of pathogenic bacteria plays a key role in shaping resistance evolution. Understanding this link makes it possible to predict which strains are likely to evolve resistance and to optimize inhibitor use to prevent this outcome.

overall_design: 14 pairs of high and low evolvability Staphylococcus aureus strains after 1 hour exposure to 1mg/l ciprofloxacin

first: Jessica

last: Hedge

first: Andrei

last: Papkou


title: Transcriptional Profiling of Normal, Stenotic, and Regurgitant Human Aortic Valves

city: Palo Alto

middle: James

last: Jaatinen

address: 870 Quarry Rd Ext

department: Cardiothoracic Surgery

institute: Stanford University

summary:
Purpose: The goal of this study is to characterize the gene expression profiles and identify genes of interest (GOI) in stenotic (AS) and regurgitant (AI) human aortic valves using RNA sequencing technology.
Methods: Aortic valve leaflets were collected from non-matched transplant donor hearts (NC) and from aortic valve replacement operations (AS or AI).  Leaflets were washed in cold PBS, snap frozen, and stored at -80°C until RNA extraction.  For each sample, total RNA was extracted, a cDNA library was generated, and an Illumina HiSeq 2500 was used to sequence each sample.  150-bp paired-ends reads were generated with approximately 30 million reads per sample.  Sequencing was performed in duplicate for each sample.  Paired-end clean reads were aligned to the reference genome using STAR.  HTSeq v0.6.1 was used to count the read numbers mapped to each gene.  Fragments per kilobases per million (FPKM) were calculated to estimate the level of gene expression.  Differential gene expression analysis was performed using the DESeq2 R package. A model based on the negative binomial distribution was used to determine differential gene expression (log 2 [fold change]). P-values were adjusted using the Benjamini-Hochberg approach for controlling false discovery rate. Genes with adjusted P-values <0.05 found by DESeq2 were assigned as differentially-expressed genes (DEGs).
Results: RNA sequencing analysis identified 8,621 DEGs among the AS, AI, and NC valves. Specifically, 6,438 genes were found to be differentially expressed between the AS and NC groups; 4,994 genes were found to be differentially expressed between the AI and NC groups; and 2,771 genes were found to be differentially expressed between the AS and AI groups. Of these, 1,979 (31%) genes were expressed at statistically different levels between the AS and NC groups, and 1,428 (29%) genes were expressed at statistically different levels between the AI and NC groups
Conclusions: Overall, we have sequenced aortic leaflets from non-matched transplant donor hearts , thereby establishing a new standard for normal aortic valve transcriptional profiling. We have also sequenced human aortic valves with AI and demonstrated that valves with AI and AS possess unique gene expression patterns. The plethora of DEGs identified and our novel PPI networks for AS and AI have revealed new pathways missed by previous aortic valve studies. Our data lays the foundation for future gene editing studies and may guide researchers in developing novel therapeutic interventions for AS and AI.

overall_design: Discovery of differentially expressed genes when comparing Normal, Stenotic, and Regurgitant Human Aortic Valves using RNA-seq technology.

first: Christina

last: Greene

first: Hanjay

last: Wang

first: Tiffany

last: Koyano

first: Mary

last: Bilbao

first: Y

last: Woo


title: Genome-wide map of long non-coding RNA steroid receptor RNA activator (SRA) in human erythroleukemic K562 cell line

first: Waritta

last: Sawaengdee

summary: We performed Chromatin Isolation by RNA Purification (ChIRP) of SRA by high-throughput sequencing in K562 cell line. We find that SRA occupied genome-wide including alpha- and beta-globin loci.

overall_design: SRA and LacZ ChIRP of triplicate samples in K562 cell line

first: Gary

last: Felsenfeld

first: Patompon

last: Wongtrakoongate


title: Next Generation Sequencing (RNA sequencing) of Wild Type and GLI1 knock-out CUTLL1 childhood T lymphoblastic lymphoma cell line

first: Erich

last: Piovan

summary: T-cell acute lymphoblastic leukemia (T-ALL) is a highly malignant pediatric leukemia, where few therapeutic options are available for patients which relapse. The evolutionarily conserved Hedgehog (Hh) pathway plays a crucial role in patterning and organogenesis during early development, in adult tissue maintenance and repairing functions. Once Hh ligands bind to PTCH1/2 on target cells, the inhibition of Patched proteins for Smo is relieved. Smo translocates to the primary cilium and leads to the breakdown of a protein complex formed by Suppressor of Fused (SUFU) and GLI proteins. GLI transcription factors (GLI1-3) are released and translocate to the nucleus, initiating transcription of Hh target genes. GLI2 and GLI3 have transcriptional activation and repression properties, while GLI1 is a strong positive regulator of Hh transcriptional targets. In T-ALL rare hedgehog pathway mutations have been observed and  approximately 20% of T-ALL cases present with ectopic expression of Hh pathway ligands and GLI1. However, the function of Hh signaling and in particular GLI transcription factors in T-ALL initiation and/or tumor progression is not well-known. RNA sequencing was performed in the CUTLL1 T-ALL cell line after knocking out GLI1 gene using CRISPR/Cas9 system.

overall_design: mRNA profiles of wild type (WT) and  GLI1 CRISPR knock out in CUTLL1 cells


title: GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

summary: Ribosome-associated Quality Control (RQC) pathways protect cells from toxicity caused by incomplete protein products resulting from translation of damaged or problematic mRNAs. Extensive work in yeast has identified highly conserved mechanisms that lead to the degradation of the faulty mRNA and partially synthesized polypeptide. Here, we used CRISPR-Cas9-based screening to search for additional RQC strategies in mammals. We found that failed translation leads to specific inhibition of translation initiation on that message. This negative feedback loop is mediated by two translation inhibitors, GIGYF2 and 4EHP. Both model substrates and growth-based assays established that inhibition of additional rounds of translation acts in concert with known RQC pathways to prevent buildup of toxic proteins. Inability to block translation of faulty mRNAs, and subsequent accumulation of partially synthesized polypeptides, could explain the neurodevelopmental and neuropsychiatric disorders observed in mice and humans with compromised GIGYF2 function.

overall_design: This datasets consists of paired ribosome profiling and RNA-seq datasets collected in replicate after the CRISPRi-mediated knockdown of NEMF, ZNF598, EIF4E2, GIGYF2, and non-targeting negative controls.

first: Kelsey

last: Hickey

first: Jonathan

last: Weissman

first: Kamena

last: Kostova


title: Altered 3D chromatin structure permits inversional recombination at the IgH locus

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: We report that in the absence of intergenic control region 1 (IGCR1), a regulatory sequence that specifies the RAG scanning domain on WT IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA.

overall_design:
Analysis of VH and DH utilization in different Pro-B cell lines.
Immunoglobulin heavy chain (IgH) locus comprises variable (V), diversity (D) and joining (J) gene segments. Both DQ52 and DSP2 belong to D gene segments. Our main purpose was to identify deletional (and inversional) recombination at the WT or IGCR1 deficient IgH locus. Therefore, we used deep sequencing method to test our hypothesis with DQ52 as bait and DSP as bait. DQ52 as bait refers to DQ52-J or DQ52-VH81X (the first functional proximal VH gene segment) recombination. DSP as bait refers to DSP-J or DSP-VH81X recombination.

first: Xiang

last: Qiu

first: Mingming

last: Zhao

first: Lily

last: Shipp

first: Angela

last: Liu

first: Arun

last: Dutta

first: William

last: Wood III

first: Kevin

last: Becker

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji

first: Michael

middle: L

last: Atchison

first: Ranjan

last: Sen


title: Expression Of Amyloidogenic Transthyretin Drives Hepatic Proteostasis Remodeling In An Induced Pluripotent Stem Cell Model Of Systemic Amyloid Disease

first: George

last: Murphy

address: 670 Albany Street

institute: Center for Regenerative Medicine of Boston University and Boston Medical Center

summary: The systemic amyloidoses are diverse disorders in which misfolded proteins are secreted by effector organs and deposited as proteotoxic aggregates at downstream tissues. Although well-described clinically, the contribution of synthesizing organs to amyloid disease pathogenesis is unknown. Here, we utilize hereditary transthyretin amyloidosis (ATTR amyloidosis) induced pluripotent stem cells (iPSCs) to define the contribution of HLCs to the proteotoxicity of secreted TTR. To this end, we generated isogenic, patient-specific iPSCs expressing either amyloidogenic or wild-type TTR. We subsequently differentiated these lines into HLCs and performed single cell RNA sequencing (scRNAseq) via the Fluidigm C1 platform in an effort to identify a destabilized TTR-derived disease signature. Upon doing so, we identified a number of hepatic proteostasis factors (e.g. the unfolded protein response, UPR, as well as known and novel chaperone genes) whose expression correlates with the production destabilized TTR production.

overall_design: Single cell transcriptomic profiling of day 16 ATTR amyloidosis patient-specific iPSC-derived HLCs compared to syngeneic, isogenic control HLCs. Generation of isogenic "corrected" line was achieved via insertion of TTR-WT cDNA cassette at ATG-site of endogenous, mutant TTR allele via TALEN-mediated gene editing.

first: Richard

last: Giadone

first: Taylor

last: Matte


title: Diploid genome architecture revealed by multi-omic data of hybrid mice

city: Shenzhen

first: Zhijun

last: Han

state: Guangdong

address: No 1088,xueyuan Rd., Nanshan District

institute: Southern University of Science and Technology

summary: While mammalian genomes are diploid, previous studies extensively investigated the average chromatin architectures without considering the differences between homologous chromosomes. Here we generated Hi-C, ChIP-seq and RNA-seq datasets from CD4 T cells of B6, Cast and hybrid mice, to investigate the diploid chromatin organization and epigenetic regulation. Our data indicate that inter-chromosomal interaction patterns between homologous chromosomes are similar and the similarity is highly correlated with their allelic co-expression levels. Reconstruction of 3D nucleus revealed that distances of the homologous chromosomes to the center of nucleus are almost the same. The inter-chromosomal interactions at centromere-ends are significantly weaker than those at telomere-ends, suggesting that they are located in different regions within the chromosome territories. The majority of A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments due to cis-effect. About 95% of the trans-effected B6/Cast divergent compartments converge to the same compartment status potentially due to a shared cellular environment. We showed the differentially expressed genes between the two haploids in hybrid were associated with either genetic or epigenetic effects. In summary, our multi-omics data from the hybrid mice provided haploid-specific information on the 3D nuclear architecture and a rich resource for further understanding the epigenetic regulation of haploid-specific gene expression.

overall_design: Two Hi-C replicates for hybrid mouse, four Hi-C replicates for male B6 and two Hi-C replicates for female Cast. Three RNA-seq replicates for hybrid, B6 and Cast. H3K4me2, H3K4me3, H3K27me3, CTCF and PolII ChIP-seq samples for hybrid mouse.

first: Kairong

last: Cui

first: Katarzyna

last: Placek

first: Ni

last: Hong

first: Wei

last: Chen

first: Keji

first: Wenfei

last: Jin


title: DUX4-expressing immortalised FSHD lymphoblastoid cells express genes elevated in FSHD muscle biopsies, correlating with the early stages of inflammation

status: Public on Jun 30 2020

city: London

first: Christopher

middle: Raja Socrates

last: Banerji

address: New Hunts House

department: Randall Division of Cell and Molecular Biophysics

institute: King's College London

summary: RNAseq of FSHD and control LCLs and primary myoblasts with corresponding in vitro differentiated myotubes

overall_design: Lymphoblastoid FSHD cell lines GSM16283, GSM16414, GSM16278 and respective matched control lines GSM16281, GSM16320, GSM16412, were analysed by RNA-seq in triplicate; FSHD primary myoblasts and 3 day in vitro differentated myotubes (FSHD3, FSHD6 and FSHD9), alongslide matched control samples (CTRL3, CTRL6 and CTRL 9) were analysed by RNA-seq in singlet

first: Peter

last: Zammit


title: Using next-generation sequencing to measure the histone protein H2B and monoubiquitinated H2B (H2Bub) in single yeast cells

city: Pasadena

first: Yandong

last: Zhang

state: California

address: 1200 E. California Blvd

institute: California Institute of Technology

summary: we report a novel strategy to detect targeted protein and its PTM isoforms in single cells. We barcode the proteins from single cells by tagging them with oligonucleotides, pool barcoded cells together, run bulk gel electrophoresis to separate protein and its PTM isoform and quantify their abundances by sequencing the oligonucleotides associated with each protein species. We used this strategy to measure histone protein H2B and its monoubiquitination isoform, H2Bub, in single yeast cells. Our results revealed the heterogeneities of H2B ubiquitination levels in single cells from different cell-cycle stages, which is obscured in ensemble measurements.

overall_design: Measure the copy number of H2B and H2Bub in single cells in two different yeast strain: wild-type (wt) and double knockout (dub8&dub10) strain (DKO)

first: Changho

last: Sohn

first: Seoyeon

last: Lee

first: Long

last: Cai


title: Global Gene Expression Characterization of Circulating Tumor Cells in Metastatic Castration-Resistant Prostate Cancer Patients

city: SANTIAGO DE COMPOSTELA

first: Laura

middle: Muinelo

last: Romay

state: A Coruña

address: Rua Magdalena 11, 3J

department: Liquid Biopsy Analysis Unit

country: Spain

institute: IDIS

summary: Background: Current therapeutic options in the course of metastatic castration-resistant prostate cancers (mCRPC) reinforce the need for reliable tools to characterize the tumor in a dynamic way. Circulating tumor cells (CTCs) have emerged as a viable solution to the problem, whereby patients with a variety of solid tumors, including PC, often do not have recent tumor tissue available for analysis. The biomarker characterization in CTCs could provide insights into the current state of the disease and an overall picture of the intra-tumor heterogeneity. Methods: in the present study, we applied a global gene expression characterization of the CTC population from mCRPC (n = 9), with the goal to better understand the biology of these cells and identify the relevant molecules favoring this tumor progression. Results: This analysis allowed the identification of 50 genes specifically expressed in CTCs from patients. Six of these markers (HOXB13, QKI, MAOA, MOSPD1, SDK1, and FGD4), were validated in a cohort of 28 mCRPC, showing clinical interest for the management of these patients. Of note, the activity of this CTC signature was related to the regulation of MYC, a gene strongly implicated in the biology of mCRPC. Conclusions: Overall, our results represent new evidence on the great value of CTCs as a non-invasive biopsy to characterize PC.

overall_design: Briefly, the CTCs were immunoisolated from 7.5 mL of peripheral blood from mCRPC patients (n = 9) at baseline. For that, we used magnetic beads coated with a monoclonal antibody towards the human Epithelial Cell Adhesion Molecule (EpCAM). RNA from isolated CTCs was purified using a kit specifically designed for samples with low cellularity. In parallel, the same protocol was applied to blood samples from healthy donors (n = 6) to establish the baseline of background from unspecific non-CTC immunoisolation.  A total RNA extraction, complete Whole Transcriptome Amplification, and gene expression array were performed on samples from the 9 patients and controls.

first: Luis

last: León-Mateos

first: Alicia

last: Abalo

first: Helena

last: Casas

first: Urbano

last: Anido

first: Óscar

last: Rapado-González

first: María

last: Vieito

first: Mercedes

last: Suárez-Cunqueiro

first: Antonio

last: Gómez-Tato

first: Miguel

last: Abal

first: Rafael

last: López-López

last: Muinelo-Romay


title: Metabolic Maturation Media Improves Physiological Function of Human iPSC-derived Cardiomyocytes

first: Mark

last: Mercola

address: 1651 Page Mill Road

department: Department of Medicine

institute: Stanford University School of Medicine

summary: iPSC-derived cardiomyocytes (iPSC-CMs) have enormous potential for the study of human cardiac disorders. However, their physiological immaturity severely limits their utility as a model system and their adoption for drug discovery. In this study, we describe a maturation media (MM) designed to provide oxidative substrates adapted to the metabolic needs of hiPSC-CMs as compared to standard RPMI/B27 media. RNA sequencing was performed to gain insight into the underlying molecular basis for the changes. Compared to baseline (day 21) conditions, three weeks subsequent exposure to MM (day 41) caused a significant differential expression in genes. GO analysis of the MM-differentially upregulated genes were informative, mapping to mitochondrial metabolism. Additionally, multiple Ca2+ cycling/sarcoplasmic reticulum (SR), sarcomeric, and ion channel genes were differentially expressed.  These gene expression changes indicated that supplementation with oxidative substrates and subsequent metabolic changes might affect cardiomyocyte electrophysiology, Ca2+ cycling and contractility.

overall_design: examination of gene expression changes after 3 weeks (day 41) of culture in either RPMI or MM media (compared to baseline, day 20 iPSC-CMs)

first: Mercola

last: Mark


title: Decidual glycodelin-A polarizes human monocytes into a decidual macrophage-like phenotype through Siglec-7

city: Hong Kong

first: Jian

last: Wu

state: Hong Kong

address: 5 Sassoon Road, Pokfulam

country: Hong Kong

institute: HKU

summary: GdA induces the differentiation of human monocytes into dM-like phenotypes in terms of transcriptome

overall_design: Peripheral blood monocytes were induced to differentiate into  macrophages in the presence or absence of MCSF, GdA, IL-10 or both

first: Philip

middle: C

last: Chiu


title: DNA Methylation in PBMC of chronically HIV infected individuals

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Genome wide DNA Methylation in PBMC of untreated HIV-chronic individuals with different HIV control. For a total of 70 PBMC samples we determined DNA Methylation levels of more than 450,000 CpG sites with the platform Infinium HumanMethylation450 BeadChip (450K, Illumina). Finally, we compared DNA methylation between HIV-High (>50,000 HIV RNA copies/ml, n=29) and HIV-Low (<10,000 HIV RNA copies/ml, n=41) individuals and identified 2,649 gene-annotated CpG positions that were differentially methylated between the two groups.

overall_design: Bisulphite converted DNA from the 70 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip (450K array).

first: M

last: Ruiz-Riol

first: C

last: Brander


title: Structural cells are key regulators of organ-specific immune response

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

summary: The mammalian immune system implements a remarkably effective set of mechanisms for fighting pathogens. Its main actors are hematopoietic immune cells, including myeloid cells with their focus on innate immunity and lymphoid cells as enablers of adaptive immunity. Nevertheless, immune functions are not unique to hematopoietic cells, and basic mechanisms of pathogen defense are present in many other cell types. To advance our understanding of immunology outside of the hematopoietic system, we systematically investigated immune gene regulation in the three major types of structural cells: Epithelium, endothelium, and fibroblasts. We characterized these cell types across 12 organs in mice, using cellular phenotyping, transcriptome sequencing, chromatin accessibility profiling, and epigenome mapping. This comprehensive dataset uncovered a striking complexity of immune gene activity and regulation in structural cells. The observed patterns were highly organ-specific and appear to modulate interactions between structural cells and hematopoietic immune cells. Moreover, we identified an epigenetically encoded immune potential in structural cells under tissue homeostasis, which was triggered in response to systemic viral infection. This study highlights an underappreciated complexity of organ-specific immune gene regulation beyond hematopoietic cells, and it provides a high-resolution, multi-omics atlas of the epigenomic and transcription-regulatory circuitry of structural cells in the mouse.

overall_design: 230 RNA-seq (SMART-seq2) samples of 3 types of structural cells (endothelium, epithelium, fibroblasts) sort-purified from 4 organs and treated with 6 stimuli in mice.

first: Thomas

last: Krausgruber

first: Nikolaus

last: Fortelny

first: Victoria

last: Gernedl

first: Linda

last: Schuster

first: Amelie

last: Nemc

first: Christian

last: Schmidl

first: André

middle: F

last: Rendeiro

first: Alexander

last: Lercher

first: Andreas

last: Bergthaler


title: Microarray analysis of the synovial membrane of rheumatoid arthritis patients undergoing anti-TNF therapy

city: Barcelona

first: Antonio

last: Julià

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

institute: Vall d'Hebron Hospital Research Institute

summary: Synovial biopsies of Rheumatoid Arthritis patients were obtained at week 20 of anti-TNF therapy. The clinical response to therapy was determined comparing the DAS28 at this time point with the baseline DAS28, using the EULAR response criteria. Gene expression profiles of patients responding to anti-TNF therapy were compared to non-responders and different genes, pathways and deconvoluted cell types were found to be differential between both groups of rheumatoid arthritis patients.

overall_design: Synovial samples were obtained by guided arthroscopy using a 2.7 mm arthroscope from 11 Rheumatoid Arthritis patients starting anti-TNF therapy. Samples were immediately preserved in RNALater at -80ºC until extraction. After total RNA extraction, gene expression profiles for 21,000 genes were obtained using WG6 Illumina Sentrix whole genome Beadchips .

first: Sara

last: Marsal

first: Juan

middle: D

last: Cañete


overall_design: 208 RNA-seq (SMART-seq2) samples of 3 types of structural cells (endothelium, epithelium, fibroblasts) sort-purified from 12 organs in mice.


title: m6A directs the demethylation of histone H3K9me2 co-transcriptionall

city: wuhan

first: linjian

last: xia

address: wuhan

institute: wuhan University

summary: Here we show the repressive H3K9me2 mark is specifically removed by the induction of m6A-modified transcripts. We demonstrate that the methyltransferase METTL3/METTL14 regulates H3K9me2 modification. We observed a genome-wide correlation between m6A and occupancy by the H3K9me2 demethylase KDM3B, and we found m6A reader YTHDC1 physically interacts and recruits KDM3B to m6A-associated chromatin regions, promoting H3K9me2 demethylation and gene expression. This study establishes a direct link between m6A and dynamic chromatin modification and provides mechanistic insight into the co-transcriptional interplay between RNA modification and histone modifications.

overall_design: Examination of m6A methylation and H3K9me2 histone modification

first: Laxin

last: Xia

first: Shan

last: Xiao


title: A MULTIPLEX HUMAN PLURIPOTENT STEM CELL PLATFORM DEFINES MOLECULAR AND FUNCTIONAL SUBTYPES OF AUTISM

city: New York

first: Lorenz

last: Studer

state: NY

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We report a multiplex human pluripotent stem cell platform to investigate autism associated genetic variation during the development of the prefrontal cortex. This dataset represents the biological replicate datasets of our hPSC-derived prefrontal (PFC) and occipital (OCC) differentiation compared with neural stem cells (NSCs). We find that the top genes associated with PFC identity correlate well with in vivo PFC using the Allen Developmental Transcriptome data.

overall_design:
Directed differentiation of hPSCs in quadruplicates to PFC or OCC identity

Please note that GSM3430882-GSM3430884 NSC* samples (in GSE104232) were re-analyzed in the current study. The duplicated sample records (GSM4405478-GSM4405480) have been created for the convenient retrieval of the complete raw data from SRA.

first: Gustav

last: Cederquist


title: RNAseq on Dengue specific mice immunoglobulin repertoires

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: This study aims to understand the characteristics and diversification of Dengue specific immunoglobulin repertoires after different immunization strategies in mouse. We propose two different immunization strategies in dengue vaccine development. One is tetravalent strategy, which pre-mixed four serotype dengue DNA vaccine and administrated four times. The other one is sequential strategy, which sequentially administrated four time, each serotype vaccine for each dose as sequences of Den1, Den2, Den3 and Den4.

overall_design: C57BL/6J (B6) mice were injected Dengue Envelope DNA vaccine with either tetravalent or sequential strategy. The Dengue specific B cells were fished out from immunized mice splenocytes by Dengue Env protein probes. After cDNA and Ig specific amplification, the RNA-seq libraries were prepared and subjected to MiSeq V3 2 × 301 bp sequencing.

first: Jianzhu

last: Chen

first: Jue

last: Hou


title: RNA-Seq analysis of prostate cancer cell line PC-3 treated with siRNA control (siCont) and siELL2

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: To identify the genes associated with the knockdown of ELL2. PC-3 mRNA profiles of cells treated with RNA interference ELL2 compared to non-targeted control siRNA were tested using RNA seq.  RNA isolation was performed using RNeasy Plus Mini kit. In this study, we identified 1939 differentially expressed genes associated with ELL2 deletion. Of these transcripts,1579 genes involve in cancer, while 695 genes are asscoicated with cell death and survival. Bioinformatics analysis indicated that ELL2 knockdown activates the IFNγ-STAT1-IRF1 signaling pathway, which is known to play important roles in prostate cancer.

overall_design: PC-3  cells were seeded in a 6-well plate at density of 3x10^5 per well. Cells were treated with 25nM siELL2 or siControl for 72 hour in standard culture condition and then were harvested for RNA extraction.

first: Zhi

last: Wang

middle: R

first: Srilakshmi

last: Chaparala

first: Anish

last: Chakka


title: Integrative tissue analysis of men with prostate cancer II

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Prostate cancer is a multi-focal disease and understanding the relationship between primary disease and relapse has remained a challenge.

overall_design:
To identify the genetic events that drive tumor aggressivity, we performed whole transcriptome sequencing and gene expression analysis of multiple foci of prostate cancer from men who underwent radical prostatectomy as definitive therapy.
---------------------------------------------
Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

first: Shana

middle: Y

last: Trostel

first: Nichelle

last: Whitlock

first: Huihui

last: Ye

first: Brian

middle: J

last: Capaldo


title: MicroRNA microarray of CD8+ T cells

status: Public on Jun 29 2020

city: Boston

first: Caroline

last: Wasen

state: Massachusetts

address: 60 Fenwood road

department: Ann Romney Center for Neurological Disease

institute: Brigham and Women's Hospital

summary: ABSTRACT: OBJECTIVE. Smoking suppresses PD-1 expression in patients with rheumatoid arthritis (RA). In this study, we assess if smoking changed the epigenetic control over CD8+ T cell memory formation through a microRNA (miR) dependent mechanism. METHODS. Phenotypes of CD8+ T cells from smokers and non-smokers, RA and healthy, were analyzed by flow cytometry. A microarray analysis was used to screen for differences in miR expression. Sorted CD8+ cells were in vitro stimulated with nicotine and analyzed for transcription of miRs and genes related to memory programming by qPCR. RESULTS. CD27+CD107a–CD8+ T cells, defining a naïve-memory population, had low expression of PD-1. Additionally, the CD27+ population was more frequent in smokers (p=0.0089). Smokers were recognized by differential expression of 8 miRs. Let-7c-5p, let-7d-5p and let-7e-5p, miR-92a-3p, miR-150-5p and miR-181-5p were up regulated, while miR-3196 and miR-4723-5p were down regulated. These miRs were predicted to target proteins within the FOXO-signaling pathway involved in CD8+ memory programming. Furthermore, miR-92a-3p was differentially expressed in CD8+ cells with naïve-memory predominance. Nicotine exposure of CD8+ cells induced the expression of miR-150-5p and miR-181a-5p in the naïve-memory cells in vitro. Additionally, nicotine exposure inverted the ratio between mRNAs of proteins in the FOXO pathway and their targeting miRs. CONCLUSIONS. Smokers have a high prevalence of CD8+ T cells with a naïve-memory phenotype. These cells express a miR profile that interacts with the memory programming conducted through the FOXO pathway.

overall_design: 16 samples pooled from 1-3 individuals were analyzed. Each sample consisted of RNA from sorted CD8+ T cells isolated from human peripheral blood monocytes (PBMC). The study subjects were healthy controls (HC) and patients with rheumatoid arthritis (RA) with known smoking status (S=smoker, NS=non-smoker).

last: Wasén

first: Maria

last: Bokarewa


title: Cysteine and methionine biosynthetic enzymes have distinct effects on seed nutritional quality and on molecular phenotypes associated with accumulation of a methionine-rich seed storage protein in rice.

city: Madison

first: Sarah

last: Whitcomb

state: WI

address: 502 Walnut St

department: Cereal Crops Research Unit

institute: USDA-ARS

summary: Staple crops in human and livestock diets suffer from deficiencies in certain “essential” amino acids including methionine. With the goal of increasing methionine in rice seed, we generated a pair of “PushxPull” double transgenic lines, each containing a methionine-dense seed storage protein (2S albumin from sunflower, HaSSA) and an exogenous enzyme for either methionine (feedback desensitized cystathionine gamma synthase from Arabidopsis, AtD-CGS) or cysteine (serine acetyltransferase from E. coli, EcSAT) biosynthesis. In both double transgenic lines, the total seed methionine content was approximately 50% higher than in their untransformed parental line, Oryza sativa ssp. japonica cv. Taipei 309. HaSSA-containing rice seeds were reported to display an altered seed protein profile, speculatively due to insufficient sulfur amino acid content. However, here we present data suggesting that this may result from an overloaded protein folding machinery in the endoplasmic reticulum rather than primarily from redistribution of limited methionine from endogenous seed proteins to HaSSA. We hypothesize that HaSSA-associated endoplasmic reticulum stress results in redox perturbations that negatively impact sulfate reduction to cysteine, and we speculate that this is mitigated by EcSAT-associated increased sulfur import into the seed, which facilitates additional synthesis of cysteine and glutathione. The data presented here reveal challenges associated with increasing the methionine content in rice seed, including what may be relatively low protein folding capacity in the endoplasmic reticulum and an insufficient pool of sulfate available for additional cysteine and methionine synthesis. We propose that future approaches to further improve the methionine content in rice should focus on increasing seed sulfur loading and avoiding the accumulation of unfolded proteins in the endoplasmic reticulum.

overall_design: 22 milkripe (10 DAF) seed samples in total; Taipei is the reference/parental line for all 5 transgenic lines; biological replicates n = 3 to 5, depending on the line

first: Apidet

last: Rakpenthai

first: Franziska

last: Brückner

first: Axel

last: Fischer

first: Saroj

last: Parmar

first: Alexander

last: Erban

first: Joachim

last: Kopka

first: Malcolm

last: Hawkesford

first: Rainer

last: Hoefgen


title: Measuring the dependence of the yeast heat shock response on intracellular pH and translation during stress

city: Chicago

first: Catherine

middle: Genevieve

last: Triandafillou

state: IL

address: 929 E 57th St

institute: University of Chicago

summary: S. cerevisiae cells acidify when they experience stressful temperatures. In addition, newly-translated proteins are thought to misfold, triggering the heat shock response. To determine whether heat-shock associated acidification and translation state are important for the cellular response, we manipulated intracellular pH, blocked translation, heat shocked cells, and sequenced the transcriptome.

overall_design: Diploid yeast cells (BY4743 expressing 1 copy of SSA4 tagged genomically with mCherry and expressing pHluorin from the leu locus) were heat shocked (42C for 20 minutes) or mock treated (RT for 20 minutes) in media where acidification was allowed or blocked, with translation ongoing or blocked; samples were collected just after treatment.

first: Aaron

last: Dinner

first: D

middle: A

last: Drummond


title: Copy number data from Patient-Derived tumor models (PDX) establish from bone metastases of breast cancer.

city: Paris

first: Elisabetta

last: Marangoni

address: 26 rue d'Ulm

institute: Institut Curie

summary:
A significant proportion of patients with oestrogen receptor (ER) positive breast cancers (BC) develop resistance to endocrine treatments (ET) and relapse with metastatic disease. Bone is the most common metastatic site in ER+ patients, however bone metastases are technically challenging to biopsy and analyse. Difficulties concern both tumour tissue acquisition and techniques for analysis and RNA extractions. Patient-derived xenografts (PDX) of BC bone metastases have not been reported yet. For the first time we established PDX models from bone metastatic biopsies of patients progressing on ET and treated by vertebroplasty. PDX models were analysed at genomic level to identify new therapeutic targets associated with endocrine resistance in the metastatic setting.
Identification of chromosomic alterations in bone metastasis derived PDX.

overall_design: CytoScan of 3 PDX established from bone metastasis samples. No replicate.

first: E

last: Montaudon

first: Z

last: Tariq


title: HuD interacting circular RNAs in the mouse striatum

status: Public on Jun 28 2020

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

summary:
This study explores whether HuD could bind to and regulate the expression circRNAs from genes associated with neuronal development and synaptic plasticity
circRNAs bound to HuD were isolated from the striatum of HuD-OE mice by RNA immunoprecipitation (RIP) as described in Bolognani et al, 2010 (https://doi.org/10.1093/nar/gkp863) using Dynabeads® (Thermo Fisher Scientific) coated with mouse monoclonal anti-myc tag antibody (9B11; Cell Signalling Technology Inc.) specifically recognizing myc-tagged HuD transgenic protein expressed in HuD-OE as described before (Bolognani et al., 2010; Zimmerman et al., 2020). Controls for RIP assays were performed using either non-immune IgG and HuD-OE tissue or the myc-tag antibody and wild type (WT) tissue.

overall_design: RIP assay were run in triplicates using 3 HuD transgenic and 3 wildtype mice

first: Michela

last: Dell'Orco


title: circRNAs in the mouse striatum of HuD ovreexpressing OE mice and wildtype mice

status: Public on Jun 27 2020

summary: This study explores the expression circRNAs in the striatum

overall_design: 3 HuD OE mice vs. 3 WT mice

first: Rob

last: Oliver


title: JMJD5 couples with CDK9 to release the paused RNA polymerase II

city: Aurora

first: Srinivas

last: Ramachandran

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: More than 30% of genes in higher eukaryotes are regulated by RNA Polymerase II (Pol II) promoter proximal pausing. Pausing is released by the positive transcription elongation factor complex (P-TEFb). However, the exact mechanism by which this occurs and whether phosphorylation of the carboxyl-terminal domain of Pol II is involved in the process remains unknown. We previously reported that JMJD5 could generate tailless nucleosomes at position +1 from transcription start sites (TSS) thus perhaps enable progression of Pol II. Here we find that knockout of JMJD5 leads to accumulation of nucleosomes at position +1. Absence of JMJD5 also results in loss of or lowered transcription of a large number of genes. Interestingly, we found that phosphorylation, by CDK9, of Ser2 within two neighboring heptad repeats in the carboxy-terminal domain of Pol II together with phosphorylation of Ser5 within the second repeat, HR-Ser2p(1,2)-Ser5p(2) for short, allows Pol II to bind JMJD5 via engagement of the N-terminal domain of JMJD5. We suggest that these events bring JMJD5 near the nucleosome at position +1, thus allowing JMJD5 to clip histones on this nucleosome, a phenomenon that may contribute to release of Pol II pausing.

overall_design: Promoter accessibility in JMJD5 KO compared to WT

first: Haolin

last: Liu

first: Sonia

last: Leach

first: Gongyi

last: Zhang


title: Measuring the dependence of the yeast heat shock response on intracellular pH during stress

summary: S. cerevisiae cells acidify when they experience stressful temperatures. To determine whether this heat-shock associated acidification is important for the cellular response, we manipulated intracellular pH, heat shocked cells, and sequenced the transcriptome.

overall_design: Diploid yeast cells (BY4743 expressing 1 copy of SSA4 tagged genomically with mCherry and expressing pHluorin from the leu locus) were heat shocked (42C for 20 minutes) with and without ionophore treatment at 2 pH values; samples were collected just after treatment. Ionophore treatment at 6.8 mimicks normal cellular acidification; treatment at 7.4 prevents pH change during heat shock.

first: Allan


title: circRNAs in the mouse nucleus accumbens (ventral striatum) after cocaine conditioned place preference (CPP)

summary: This study explores how CPP regulates the expression circRNAs in the nucleus accumbens (NAc)

overall_design: 3 cocaine CPP trained mice vs. 3 saline control mice


title: Unique molecular signatures of microRNAs in ocular fluids and plasma in diabetic retinopathy

city: Davis

first: Zeljka

last: Smit-McBride

state: CA

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

institute: University of California, Davis Eye Center

summary:
PURPOSE: To investigate the circulatory microRNA (miRNA) profiles of aqueous, vitreous, and plasma in order to identify biomarkers in aqueous humor or plasma that are reflecting changes in vitreous of patients with diabetes.
METHODS:  Aqueous, vitreous and plasma samples were collected from a total of 27 patients - 11 controls (macular pucker or macular hole patients) and 16 patients with diabetes mellitus (DM) undergoing vitreoretinal surgery:  DM-Type I with proliferative diabetic retinopathy (PDR) (DMI-PDR), DM Type II with PDR (DMII-PDR) and DM Type II with nonproliferative DR (DMII-NPDR).   MiRNAs were isolated using Qiagen microRNeasy kit, quantified on BioAnalyzer, labeled with FlashTag kit, and profiled on Affymetrix GeneChip miRNA 3.0 microarrays.  Data analysis was done using Expression Console (EC), Transcriptome Analysis Console (TAC), and Ingenuity Pathway Analysis (IPA) software.
RESULTS: Our comparison of circulatory miRNA population of aqueous and vitreous  humor and plasma showed that out of total of  847 human miRNA probes on the Affymetrix GeneChip miRNA 3.0 we found common miRNAs for both  aqueous and vitreous samples, as well as larger number of unique miRNA, dependent on the DM type and presence of retinopathy.  Most of the dysregulated miRNAs in aqueous and vitreous of DM patients were upregulated, while in plasma, most of the DM-specific miRNAs were downregulated. Dysregulation of miRNAs in aqueous generally do not appear to be a good representative of the miRNA abundance in vitreous, or plasma, although we did identify a few candidates for common biomarkers: let-7b, miR-320b, miR-762 and miR-4488.  Additionally, each of the DR subtypes showed a set of miRNA that is uniquely dysregulated in each fluid, for example in aqueous samples for DMII-NPDR it was miR-455-3p, for DMII-PDR was miR-296, and for DMI-PDR it was miR-3202.  Pathway analysis identified TGF-beta and VEGF pathways as the common targets for miRNAs dysregulated in DR aqueous and vitreous.
CONCLUSIONS: The comparative profiling of circulatory miRNAs in aqueous, vitreous, and plasma showed that a small number of circulatory miRNAs displayed differential presence in controls vs. diabetic retinopathy. A pattern is emerging of sets of miRNA that are common or uniquely dysregulated in the blood plasma or ocular fluids of DR subtypes, offering promise for the use of ocular fluids and plasma for identifying diagnostic and therapeutic targets.


first: Christoph

last: Bock

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

overall_design: Refer to individual Series


title: Sustained fetal hematopoiesis causes juvenile death from leukemia: evidence from a dual-age-specific mouse model

status: Public on Jun 25 2020

city: Stanford

first: Y. Lucy

address: 240 Pasteur Drive, BMI Suite 2550

department: Pediatrics

institute: Stanford Medical School

summary: It is not clear whether disrupted age-specific hematopoiesis contributes to the complex manifestations in leukemia patients who carry identical mutations, particularly in pediatric and adult patients with similar clinical characteristics. By studying a dual-age-specific mouse model, we demonstrate: 1) loss of Pten during the fetal-to-adult hematopoiesis switch (HSC switch) causes sustained fetal hematopoiesis, resulting in death in juvenile leukemia; 2) myeloid-biased hematopoiesis in juvenile mice is associated with the sustained fetal properties of hematopoietic stem cells (HSCs); 3) the age specificity of juvenile myelomonocytic leukemia (JMML) depends on the dosage of Pten and Nf1; 4) single-allelic Pten deletion during the HSC switch causes constitutive activation of mitogen-activated protein kinase (MAPK) in juvenile mice with Nf1 loss of heterozygosity (LOH); and 5) Nf1 LOH causes monocytosis in juvenile mice with Pten haploinsufficiency but does not cause lethality until adulthood. Our data suggest that one copy of Pten is sufficient to maintain an intact negative feedback loop of the Akt pathway and HSC function in reconstitution, despite MAPK being constitutively activated in juvenile mice with Pten+/DNf1LOH. However, two copies of Pten are required to maintain the integrity of the MAPK pathway in juvenile mice with Nf1 haploinsufficiency. Our data indicate that previous investigations of Pten function in wild type mice may not reflect the impact of Pten loss in mice with Nf1 mutations or other genetic defects. We provide a proof-of-concept that disassociated age-specific hematopoiesis contributes to leukemogenesis and pediatric demise.

overall_design: Case (JMML) vs. control (WT) experiment. 3 replicates in each group.

first: Nitza

last: Vara

first: Yuqing

first: Yan

last: Yan

first: Shelly

last: Lensing

first: Natalia

last: Colorado

first: Delli

last: Robinson

first: Jingliao

first: Xin

first: Erich

last: Peterson

first: Nicholas

last: Baltz

first: Daohong

last: Zhou

first: Alice

last: Bertaina

first: Donald

last: Johann Jr

first: Peter

last: Emanuel

first: Y


title: GMM-Demux: sample demultiplexing, multiplet detection, experiment planning and novel cell type verification in single cell sequencing.

status: Public on Jun 24 2020

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

summary: Identifying and removing multiplets is essential to improving the scalability and the reliability of single cell RNA sequencing (scRNA-seq). Multiplets create artificial cell types in the dataset. We propose a Gaussian-mixture-model-based multiplet identification method, GMM-Demux. GMM-Demux accurately identifies and removes multiplets through sample barcoding, including cell hashing and MULTI-seq. GMM-Demux uses a droplet formation model to authenticate putative cell types discovered from a scRNA-seq dataset. We generated two in-house cell hashing datasets and compared GMM-Demux against three state-of-the-art sample barcoding classifiers. We show that GMM-Demux is stable, highly accurate and recognized 9 multiplet-induced fake cell types in a PBMC dataset.

overall_design: Peripheral blood mononuclear cells were profiled by CITE-seq using a panel of 10 antibodies and cell hashing using 4 HTOs. CD4+ Memory T cells enriched from peripheral blood were profiled by scRNA-seq and cell hashing using 5 HTOs. Each HTO  is constructed with a combination of CD298 and B2M antibodies, labeled with different barcodes.


title: Tissue restricted antigen expression by medullary thymic epithelial cell subsets induces distinct autoreactive T cell fates

status: Public on Jun 26 2020

city: Montreal

first: Marie

last: Coutelier

address: 845 Rue Sherbrooke Ouest

institute: McGill University

summary: Cellular interactions in the thymus play an essential role in ensuring the development of a self-tolerant T cell repertoire. Medullary thymic epithelial cells (mTECs) contribute to tolerance by expressing and presenting tissue-restricted antigens (TRA) so that developing T cells can assess the self-reactivity of their antigen receptors prior to leaving the thymus. This has largely been studied in the context of autoimmune regulator (Aire) dependent TRA expression in mature mTECs. Yet, mTECs are a heterogeneous population of cells that differentially express unique pools of TRA, and whether mTEC subsets induce distinct autoreactive T cell fates remains unclear. Here we attribute unique roles for mTEC subsets in directing distinct mechanisms of T cell tolerance that significantly impact infection and tumor control. These results have important implications in the design of effective therapeutic approaches that aim to modulate the function of self-reactive T cells.

overall_design: Thymic epithelial cells were sorted from CRPhi, CRPlo and INShi transgenic mice

first: Marie-Ève

last: Lebel

first: Heather

last: Melichar

first: Claudia

last: Kleinman


title: Transcriptomics analysis of heterozygous mutant and wild-type flies for presynaptic homeostatic plasticity

city: Seoul

first: Joon Yong

last: An

address: 145 Anam-ro, Anam-dong, Seongbuk-gu

country: South Korea

institute: Korea University

summary: We identify a set of common phenotypic modifiers that interact with five independent autism gene orthologs (RIMS1, CHD8, CHD2, WDFY3, ASH1L) causing a common failure of presynaptic homeostatic plasticity (PHP). Heterozygous null mutations in each autism gene are demonstrated to have normal baseline neurotransmission and PHP. However, we find that PHP is sensitized and rendered prone to failure. A subsequent electrophysiology-based genetic screen identifies the first known heterozygous mutations that commonly genetically interact with multiple ASD gene orthologs, causing PHP to fail. Two phenotypic modifiers identified in the screen, PDPK1 and PPP2R5D, are characterized. Finally, transcriptomic, ultrastructural and electrophysiological analyses define one mechanism by which PHP fails; an unexpected, maladaptive up-regulation of CREG, a conserved, neuronally expressed, stress response gene and a novel repressor of PHP. Thus, we define a novel genetic landscape by which diverse, unrelated autism risk genes may converge to commonly affect the robustness of synaptic transmission.

overall_design:
RNA-seq analysis of heterozygous mutant files of ASD risk genes, compared to wild-type flies

**Please note that each 'table.raw_counts.*.xlsx' processed data file contains raw counts data for all replicates and is linked to the corresponding *rep1 sample records.

first: Ozgur

last: Genc

first: Joon


title: Polyploidy in the adult Drosophila melanogaster brain

city: Ann Arbor

first: Laura

last: Buttitta

state: MI

address: 1105 N.University Ave

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

summary: To understand gene expression changes in different regions of the Drosophila brain with age, we performed RNAseq different regions of the adult drosophila CNS at different ages.

overall_design: 10 brains per sample from Canton-S females and males raised at 25°C on Cornmeal/Dextrose food under normal 12h L/D cycles at ZT = 2, were dissected into optic lobes, VNC and Central brain per sample. Time points are day of eclosion(day0), day 2, day 7 and day 21.

first: Shyama

last: Nandakumar


title: Structural cells are key regulators of organ-specific immune response

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

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

summary: The mammalian immune system implements a remarkably effective set of mechanisms for fighting pathogens. Its main actors are hematopoietic immune cells, including myeloid cells with their focus on innate immunity and lymphoid cells as enablers of adaptive immunity. Nevertheless, immune functions are not unique to hematopoietic cells, and basic mechanisms of pathogen defense are present in many other cell types. To advance our understanding of immunology outside of the hematopoietic system, we systematically investigated immune gene regulation in the three major types of structural cells: Epithelium, endothelium, and fibroblasts. We characterized these cell types across 12 organs in mice, using cellular phenotyping, transcriptome sequencing, chromatin accessibility profiling, and epigenome mapping. This comprehensive dataset uncovered a striking complexity of immune gene activity and regulation in structural cells. The observed patterns were highly organ-specific and appear to modulate interactions between structural cells and hematopoietic immune cells. Moreover, we identified an epigenetically encoded immune potential in structural cells under tissue homeostasis, which was triggered in response to systemic viral infection. This study highlights an underappreciated complexity of organ-specific immune gene regulation beyond hematopoietic cells, and it provides a high-resolution, multi-omics atlas of the epigenomic and transcription-regulatory circuitry of structural cells in the mouse.

overall_design: 71 ChIPseq (ChIPmentation) samples with antibodies for H3K4me2 in 3 types of structural cells (endothelium, epithelium, fibroblasts) sort-purified from 12 organs in mice.

first: Thomas

last: Krausgruber

first: Nikolaus

last: Fortelny

first: Victoria

last: Gernedl

first: Linda

last: Schuster

first: Amelie

last: Nemc

first: Christian

last: Schmidl

first: André

last: Rendeiro

first: Alexander

last: Lercher

first: Andreas

last: Bergthaler


title: Symmetric neural progenitor divisions require chromatin-mediated homologous recombination DNA repair by Ino80 [RNA-seq]

first: Kenneth

last: Kwan

address: 109 Zina Pitcher Pl

department: MBNI & Human Genetics

summary: Chromatin regulates spatiotemporal gene expression during neurodevelopment, but it also mediates DNA damage repair crucial to proliferating neural progenitor cells (NPCs). Here, we uncover molecularly dissociable roles for nucleosome remodeler INO80 in chromatin-mediated transcriptome and genome maintenance in corticogenesis. We find that conditional Ino80 deletion from cortical NPCs impairs DNA double-strand break repair, triggering p53 activation, robust apoptosis, and microcephaly, whereas co-deletion of Trp53 with Ino80 leads to remarkable reversal of these phenotypes. Using an in vivo DNA repair assay, we find that Ino80 is selectively required for homologous recombination (HR) DNA repair, which is mechanistically distinct from INO80 function in YY1-associated transcription. Unexpectedly, sensitivity to loss of INO80-mediated HR is dependent on the mode of NPC division: Ino80 deletion causes extensive DNA damage and apoptosis in symmetric NPC-NPC divisions, but not in asymmetric neurogenic divisions. Thus, distinct modes of NPC division have divergent requirements for Ino80-dependent HR DNA repair.

overall_design: We analyzed a total of 19 samples of rRNA-depleted RNA from E13.5 mouse cortex using UMI RNA-seq. Libraries were generated using Click-seq. 7 samples were controls, 5 samples were Emx1-Cre Ino80 conditional mutants, and 7 samples were Emx1-Cre Ino80/Trp53 conditional double mutants.

first: Jason

middle: M

last: Keil

first: Adel

last: Qalieh

first: Mandy

last: Lam

first: Daniel

last: Doyle

first: Yaman

first: Lei

last: Shi

first: Nitesh

last: Mohan


first: Christoph

last: Bock

overall_design: 70 ATAC-seq samples of 3 types of structural cells (endothelium, epithelium, fibroblasts) sort-purified from 12 organs in mice.

first: Thomas


title: RNA sequencing of control versus tauR406W transgenic Drosophila heads at day 10 of adulthood

city: Providence

first: Bess

last: Frost

state: RI

address: 185 Meeting St

institute: Center for Alzheimer’s Disease Research, Brown University

summary: Paired-end RNA sequencing was performed on heads of control and human tauR406W transgenic Drosophila aged to day 10 of adulthood. TauR406W is one of many mutations in the Microtubule-Associated Protein Tau (MAPT) gene that cause an autosomal dominant neurological disorder termed Frontotemporal Lobar Degeneration (FTLD)-tau with MAPT mutation. The tauR406W Drosophila model was developed by Dr. Mel Feany, and has been used widely to study tau biology due to its mild toxicity at day 10 of adulthood, which is convenient for genetic analyses and precedes exponential decline in survival. Using control and tauR406W Drosophila RNA-seq datasets, we found that CREB-regulated genes are overrepresented among differentially expressed genes in tauR406W transgenic Drosophila.

overall_design: Control (Elav-Gal4/+) and tauR406W transgenic (Elav-Gal4/+;UAS-tauR406W/+) Drosophila were aged to day 10 of adulthood. RNA was extracted from heads using Trizol. Each biological replicate consisted of 15-30 ng of total RNA from 18 pooled male and female Drosophila heads per genotype. RNA-sequencing was performed on six biologically independent replicates per genotype. The Ovation RNA-Seq System for Drosophila (#0350, NuGen) was used for library preparation according to the User Guide, including depletion of Drosophila rRNAs. After quantification by Qubit and bioanalysis, barcoded libraries were pooled, purified by magnetic bead extraction and sequenced on the Illumina HiSeq 3000 platform with 100 base pair paired-end sequencing.

first: Paulino

last: Ramirez

first: Elizabeth

last: Ochoa Thomas


title: Regenerative reprogramming of the intestinal stem cell state via Hippo signaling suppresses metastatic colorectal cancer [LATS_scRNAseq]

first: Priscilla

last: Cheung

state: MA

address: 1 Blackfan Circle

department: Stem Cell Program

institute: Boston Children's Hospital

summary: Although the Hippo transcriptional coactivator YAP is considered oncogenic in many tissues, its roles in intestinal homeostasis and colorectal cancer (CRC) remain controversial. Here, we demonstrate that the Hippo kinases LATS1/2 and MST1/2, which inhibit YAP activity, are required for maintaining Wnt signaling and canonical stem cell function. Hippo inhibition induces a distinct epithelial cell state marked by low Wnt signaling, a wound-healing response, and transcription factor Klf6 expression. Notably, loss of LATS1/2 or overexpression of YAP is sufficient to reprogram Lgr5+ cancer stem cells to this state and thereby suppress tumor growth in organoids, patient-derived xenografts, and mouse models of primary and metastatic CRC. Finally, we demonstrate that genetic deletion of YAP and its paralog TAZ promotes the growth of these tumors. Collectively, our results establish the role of YAP as a tumor suppressor in the adult colon and implicate Hippo kinases as therapeutic vulnerabilities in colorectal malignancies.

overall_design: Single-cell mRNA profiles of intestinal epithelial cells isolated from Lats1fl/fl Lats2fl/fl and Lrig1-CreERT2 Lats1fl/fl Lats2fl/fl mice 7 days post tamoxifen injection.

first: Jordi

last: Xiol

first: Raffaele

last: Calogero

first: Fernando

last: Camargo


title: Genetic deletion of microRNA-22 blunts the inflammatory transcriptional response to status epilepticus and exacerbates epilepsy in mice

city: Dublin 2

first: David

last: Henshall

address: 123 Saint Stephen Green

country: Ireland

institute: FutureNeuro centre, Royal College of Surgeons in Ireland

summary: Mice lacking miR-22 displayed normal behavior and brain structure and developed similar status epilepticus after intraamygdala kainic acid compared to wildtype animals. Subsequent continuous EEG monitoring revealed an accelerated and exacerbated epileptogenesis whereby spontaneous seizures began sooner, occurred more frequently and were of longer duration in miR-22-deficient mice. RNA sequencing analysis of the hippocampus of mice during the period of epileptogenesis revealed a widespread suppression of inflammatory signalling in the hippocampus of miR-22-deficient mice. Taken together, these findings indicate a role for miR-22 in establishing early inflammatory responses to status epilepticus. Inflammatory signalling may serve anti-epileptogenic functions and cautions the timing of anti-inflammatory treatments for the treatment of status epilepticus.

overall_design: two groups: Wildtype and miR-22-/- mice (n = 4 each) were subjected to status epilepticus. Twenty-four hours later, mice were euthanized and the ipsilateral hippocampus was obtained. Total RNA was extracted and library preparation was performed using an Illumina TruSeq Stranded mRNA Sample Prep Kit (poly-A enrichment)

first: Luiz

last: Silva

first: Cristina

last: Reschke

first: Ngoc

middle: T

last: Nguyen

first: Elena

last: Langa

first: Amaya

middle: S

last: Rodriguez

first: Ronan

last: Conroy

first: Gary

middle: P

last: Brennan

first: Tobias

last: Engel


title: Regenerative reprogramming of the intestinal stem cell state via Hippo signaling suppresses metastatic colorectal cancer [Organoid_RNAseq]

overall_design: mRNA profiles of Apc knockout and Apc-/- KrasG12D p53-/- (AKP) colon organoids upon YAP activation.