title: Broad ultrastructural and transcriptomic changes underlie the multinucleated giant hemocyte mediated innate immune response against parasitoids

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

institute: University of Zurich

summary: Multinucleated giant hemocytes (MGHs) represent a novel type of blood cell in insects that participate in a highly efficient immune response against parasitoid wasps involving isolation and killing of the parasite. Previously we showed that circulating MGHs have high motility and interaction with the parasitoid rapidly triggers encapsulation, structural and molecular mechanisms behind these processes remained elusive. Here, we use detailed ultrastructural analysis of MGHs and also live cell imaging to study encapsulation in Drosophila ananassae after parasitoid wasp infection. We found dynamic structural changes, mainly driven by the formation of diverse vesicular systems and a large variety of newly developed intracytoplasmic membrane organizations, moreover abundant generation of giant cell exosomes (GCE) in the MGHs. Moreover, we used RNA sequencing to study the transcriptomic profile of MGHs and the activated plasmatocytes 72 hours after infection, as well as the uninduced blood cells. This reveals that differentiation of MGHs is accompanied by broad changes in gene expression. Consistent with the observed structural changes, transcripts mainly related to vesicular function, cytoskeletal organization and adhesion were enriched in MGHs. In addition, transmembrane receptors were upregulated, which may be important for parasitoid recognition. Our results reveal coordinated molecular and structural changes in the course of MGH differentiation and parasitoid encapsulation, providing a mechanistic model for a powerful innate immune response.

overall_design: 5 samples from activated plasmatocytes, 5 samples from multinucleated giant hemocytes, 5 samples from uninduced blood cells.

first: Gyöngyi

last: Cinege

first: Lilla

last: Magyar

first: Attila

middle: L

last: Kovács

first: Zita

last: Lerner

first: Gábor

last: Juhász

first: David

last: Lukacsovich

first: Jochen

last: Winterer

first: Thomas

first: Zoltán

last: Hegedűs

first: Éva

last: Kurucz

first: Dan

last: Hultmark

first: István

last: Andó


title: Effects of magnetite nanoparticles and static magnetic field on neural differentiation of pluripotent stem cells

status: Public on Dec 17 2021

city: São Paulo

first: Lygia

last: da Veiga Pereira Carramaschi

state: São Paulo

address: Rua Ana Moreira dos Santos Mattos, 208

department: Depto. Genética e Biologia Evolutiva

country: Brazil

institute: Universidade de São Paulo

type: Expression profiling by high throughput sequencing

summary: Neural proliferation and differentiation fates of pluripotent stem cells are influenced by external natural forces. Despite the presence of biogenic magnetite nanoparticles in the central nervous system and constant exposure to Earth’s magnetic fields and other sources, there has been scant knowledge regarding the role of electromagnetic stimuli in neurogenesis. Moreover, the emerging application of electrical and magnetic stimulation to treat neurological disorders emphasizes the relevance of understanding the impact and mechanisms behind these stimuli. Here, the effects of magnetic nanoparticles (MNPs) contained in polymeric coatings and the static external magnetic field (EMF, 0.4 Tesla) were investigated on neural induction of murine embryonic stem cells (mESCs) and human induced pluripotent stem cells (hiPSCs) into induced dopaminergic neurons (iDA).

overall_design: In this study we investigate how external static magnetic field (EMF 0,4 Telsa) influences the neural dopaminergic differentiation of the Induced pluripotent stem cells (iPSCs) reprogrammed from three different human control samples (healthy individuals – above 59 years without neural diseases). Three iPSC samples (Tofoli et al., 2019a) were differentiated into midbrain dopaminergic neurons (or iDA = induced dopaminergic neurons) following Kriks et al., 2011 protocol (as described in Tofoli et al., 2019b) until 35 days. Same samples also were differentiated into iDA under EMF (0,4 Telsa) since day 0 of the dopaminergic differentiation. At day 35, iDA samples were collected into Trizol to RNA extraction. Functional assays (Reactive oxygen species production, Acid vesicles analyses, Membrane potential and free intracellular calcium concentration changes) also performed to compare dopaminergic differentiation with and without EMF stimulus.

last: da Veiga Pereira

first: Henning

last: Ulrich


title: Surface proteomics reveals CD72 as a target for in vitro-evolved nanobody-based CAR-T cells in refractory B-cell malignancies I

city: San Francisco

first: Matthew

last: Nix

state: CA

address: 185 Berry St

department: Laboratory Medicine

country: USA

institute: UCSF

summary: Alternate strategies are needed for B-cell malignancy patients relapsing after CD19-targeted immunotherapy. Here, integrated cell surface proteomics and epigenetic analysis initially revealed CD72 as an optimal target for poor-prognosis MLL-rearranged B-ALL, which we further found to be expressed widely across B-cell malignancies. Using a recently-described, fully-in vitro system we selected CD72-specific nanobodies, incorporated them into CARs, and demonstrated robust activity against B-cell malignancy models, including CD19 loss. “Antigen escape profiling” modeled membrane proteome changes in the context of CD72 loss while pharmacologic SHIP1 inhibition increased CD72 surface density. We establish CD72-nanobody CAR T’s as a promising therapy for refractory B-cell malignancies.

overall_design: Biological duplicates of B-ALL cell lines were profiled by RNA-seq using Illumina Sequencing.  We performed CRISPRi-mediated screening of the B-ALL cell line SEM, focused on the cell surfaceome, to identify cell surface receptors required for leukemia growth and survival.

middle: A

first: Arun

middle: P

last: Wiita


title: Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation [DNA-Seq]

status: Public on Dec 16 2021

city: Seattle

first: Sudarshan

last: Pinglay

state: WA

address: 3720 15th Ave NE

institute: University of Washington

summary: Precise Hox gene expression is crucial for embryonic patterning. Local transcription factor binding and distal enhancer elements have emerged as the major regulatory modes controlling the initiation and maintenance of Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce ‘synthetic regulatory reconstitution’, a novel conceptual framework for studying gene regulation and apply it to the mammalian HoxA cluster. To measure the HoxA intrinsic regulatory potential and distal enhancer contributions, we de novo synthesized and delivered variant rat HoxA clusters (130-170 kilobases each) to an ectopic location in the mouse genome. We find that a minimal HoxA cluster lacking distal enhancers induces the appropriate gene set and establishes distinct chromatin domains in response to patterning signals, while distal enhancers are required for full transcriptional output. These results suggest that the genomically compact Hox clusters contain all the information to decode patterning signals and maintain positional information

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: DNA-Seq was used to verify the identity of large synthetic constructs at all stages of the build and delivery pipeline from yeast to bacteria and mESCs

first: Milica

last: Bulajić

first: Dylan

last: Rahe

first: Emily

last: Huang

first: Ran

last: Brosh

first: Sergei

last: German

first: John

last: Cadley

first: Lila

last: Rieber

first: Nicole

last: Easo

first: Shaun

last: Mahony

middle: T

last: Maurano

first: Liam

middle: J

last: Holt

first: Esteban

middle: O

last: Mazzoni

first: Jef

middle: D

last: Boeke


title: N6- methyladenosine (m6A) detection in ammonium treated seedlings through RNA immunoprecipitation

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

type: Methylation profiling by high throughput sequencing

summary: Epitranscriptomics modifications constitute a gene expression checkpoint in all living organism including plants. Considering the relevance of nitrogen nutrition and metabolism for the correct plant growth and development, it can be hypothesized that epitranscriptome changes must regulate every biological process in plants including nitrogen nutrition. In the present work, the epritranscriptomics changes in maritime pine roots caused by ammonium nutrition have been monitored through RIP-seq. The main transcriptome responses to ammonium nutrition affected to transcripts involved in nitrogen and carbon metabolisms, defense response, hormone synthesis and signaling, and translation. The m6A deposition and its dynamics have been identified, which seems to be important regulators of translation when compared with the proteomic profiles of the same samples. The present study suggest that the epitranscriptome must modulate the responses to development and environmental changes, including ammonium nutrition, through buffering, filtering and focusing the final products of the gene expression.

overall_design: Ammonium nutrition was studied at short times (24 hours) in roots from one month-old seedlings of maritime pine. Control seedlings were irrigated with 80 mL of water (C) and the experimental seedlings with 80 mL of 3 mM NH4Cl. Root samples were collected at 24 hours post-irrigation and immediately frozen in liquid N. This experiment was carried out three independent times. The polyA-RNA was isolated, immunoprecipited (m6A) and sequenced with Illumina technology.

first: Francisco

last: Ortigosa

first: César

last: Lobato-Fernández

first: Juan

last: Pérez-Claros

middle: R

last: Cantón

first: Concepción

last: Ávila

middle: M

last: Cánovas


title: Postnatal SETD1B is essential for learning and the regulation of neuronal plasticity genes [WT scRNA-seq]

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Histone 3 lysine 4 methylation (H3K4me) is mediated by six different lysine methyltransferases. Amongst these enzymes SET domain containing 1b (SETD1B) has been linked to syndromic intellectual disability but its role in the postnatal brain has not been studied yet. Here we employ mice that lack Setd1b from excitatory neurons of the postnatal forebrain and combine neuron-specific ChIP-seq and RNA-seq approaches to elucidate its role in neuronal gene expression. We observe that SETD1B controls the expression of genes with a broad H3K4me3 peak at their promoters that represent neuronal enriched genes linked to learning and memory function. Comparative analysis to corresponding data from conditional Kmt2a and Kmt2b knockout mice suggests that this function is specific to SETD1B. Moreover, postnatal loss of Setd1b leads to severe learning impairment, suggesting that SETD1B-mediated regulation of H3K4me levels in postnatal neurons is critical for cognitive function.

overall_design: Single nuclei RNA sequencing from hippocampus of wildtype young mice.

first: M

middle: S

last: Sakib

first: Dennis

last: Krüger

first: Lalit

last: Kaurani


title: Epithelial membrane protein-2 promotes VEGF signaling to promote pathological neovascular growth in retinopathy of prematurity

city: LA

first: Madhuri

last: Wadehra

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

institute: UCLA

summary: Retinopathy of prematurity (ROP) is a leading cause of childhood blindness, and exclusively affects infants born prematurely. In this study, we test the hypothesis that EMP2 contributes to neovascularization in a mouse model of the disease.  We show that EMP2 promotes neuronal VEGF signaling and that its downregulation reduces severity of neovascularization.

overall_design: RNA-Seq was performed on RNA from frozen retinal tissues. Four replicates from the following conditions were profild: WT normoxia, EMP2 KO normoxia, WT hyperoxia, and EMP2 KO hyperoxia group at P17.

first: Michel

last: Sun

first: David

last: Casero

first: Brian

last: Aguirre

first: Lynn

last: Gordon

first: Alison

last: Chu


title: Evolution of antigen-specific follicular helper T cell transcriptional progams across effector function and through to memory

city: San Diego

first: Michael

last: McHeyzer-Williams

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

summary: We utilized single cell-indexed custom RNA-sequencing to interogate the transcriptomes of TFH cells at Day 7, Day 14, and Day 28 following NP-PCC immunization

overall_design: T  cells were isolated from draining lymph nodes of B10.Br mice following base of tail immunization with NP-PCC in MPL at Day 7, Day 14, and D28. Phenotypically defined T cell subsets sorted as: naïve CD4 T cells (CD4+, CD8- CD62L+, CD44-), Effector T helper cells (CD4+, CD8- CD44+ CD62L-, CXCR5-), T follicular cells (CD4+, CD8-, CD44+. CD62L-, CXCR5+). Cells were sorted into 384 well plates for library preparation. cDNA was amplied using a nested set of ~500 gene specific targeted primers.

first: Amanda

last: Robinson

first: Brett

middle: W

last: Higgins

first: Andrew

middle: G

last: Shuparski

first: Karen

middle: B

last: Miller

first: Louise


title: IRF3 binding regions in a basal-like breast cancer cell line, BT549 cells with Smad3 gene inactivation, transfected with polyI:C.

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The activation of RIG-I-like receptor (RLR) signaling in cancer cells is widely recognized as a critical cancer therapy method. The expected mechanism of RLR ligand-mediated cancer therapy involves the promotion of cancer cell death and strong induction of interferon (IFN)-β that affects the tumor microenvironment. We have recently shown that activation of RLR signaling in triple-negative breast cancer cells (TNBC) attenuates TGF-β signaling, which partly contributes to the promotion of cancer cell pyroptosis. However, the consequences of suppression of TGF-β signaling by RLR ligands with respect to IFN-β-mediated tumor suppression are not well characterized. This study showed that cytosolic induction of a typical RLR ligand polyI:C in cancer cells produces significant levels of IFN-β, which inhibits the growth of the surrounding cancer cells. In addition, IFN-β-induced cell cycle arrest in surrounding cancer cells was inhibited by the expression of constitutively active Smad3 (caSmad3). caSmad3 suppresses IFN-β expression through the alleviation of IRF3 binding to the canonical target genes, as suggested by ChIP-seq analysis. Based on these findings, a new facet of the pro-tumorigenic function of TGF-β that suppresses IFN-β expression is suggested when exploiting RLR-mediated cancer treatment in TNBC.

overall_design: IRF3 ChIP-seq analysis was performed in a basal-like breast cancer cell line, BT549 cells transfected with polyI:C. Smad3 gene was inactivated.

first: Yusuke

last: Tamura

first: Kohei

last: Miyazono


title: Differential regulation of gene expression in neurons by spontaneous or sensory-driven activity and its dysregulation with aging

city: Riverside

first: Christi Ann

last: Scott

address: 3401 Watkins Drive

department: Molecular, Cell, and Systems Biology

institute: University of California, Riverside

summary: We identify a network of genes that change immediately after odor and light exposure in peripheral and central nervous system tissues in the model Drosophila melanogaster. We demonstrate in the antenna, that this regulation is dependent on olfactory signaling. This study provides several intriguing candidate genes that have potential for involvement in synaptic plasticity and learning and memory. We find that regulation of these genes is disrupted in ageing flies that are memory compromised. This provides a framework to both characterize this important class of genes and understand how their regulation contributes to the molecular mechanisms behind declining memory. Furthermore, many of our strongest candidates could prove to be valuable tools for neuronal circuit tracing in this amenable genetic model system.

overall_design:
Drosophila antenna: RNA-Seq profiles were generated with the Illumina NextSeq500 platform with biological replicates. Odor and light-treated antennal samples (stim) were compared to control antennal samples from flies that remained sensory deprived (0min).
Drosophila brain time-series: RNA-Seq profiles were generated with the Illumina HiSeq2000 and NextSeq500 platforms with 3 biological replicates. Odor and light-stimulated brains were compared to samples from flies that remained sensory deprived (0min).
Drosophila brain aging: RNA-Seq profiles were generated with the Illumina HiSeq2000 and NextSeq500 platforms with biological replicates. Odor and light-stimulated brains (stim) were compared to  samples from flies that remained sensory deprived (0min) for 10- and 25-day old flies.
Drosophila HDAC6 mutant brains: RNA-Seq profiles were generated with the Illumina NextSeq500 platform with biological replicates. Odor and light-treated brain samples (stim) were compared to control samples form flies that remained sensory deprived.

first: Christi

first: Crystal

last: Pontrello

first: Timothy

last: Lo

first: Katherine

last: Kruckenberg

first: Anupama

last: Dahanukar

first: Anandasankar

last: Ray


title: Surface proteomics reveals CD72 as a target for in vitro-evolved nanobody-based CAR-T cells in refractory B-cell malignancies

first: Matthew

last: Nix

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

overall_design: Refer to individual Series


title: The Physcomitrium patens egg cell changes the epigenetic program and utilizes homologs of Arabidopsis male genes, including BONOBOs, for cell specification

city: Uppsala

first: Eva

last: Sundberg

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: We used single cell laser-assisted microdissection (LAM) to perform egg cell transcriptome analysis for comparison with available expression profiles of vegetative tissues and male reproductive organs. We observed an overlap in gene activity between bryophyte and angiosperm egg cells, but also clear differences. Strikingly, several processes that are male germline-specific in Arabidopsis are active in the P. patens egg cell. Among those were the moss PbBNB genes and using reporter lines and knock-out mutants we could show that they control proliferation and identity of both female and male germlines.

overall_design:
Single cell laser-assisted microdissection and RNA-seq of egg cells for comparative transcriptome analysis with available expression profiles of vegetative tissues and male reproductive organs.

The processed data includes re-analyzed samples from: https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=PhypatAtlaPlate2

first: Vera

middle: V

last: Sanchez

first: Katarina

last: Landberg

first: Mauricio

last: Lopez-Obando

first: Mattias

last: Thelander

first: Ulf

last: Lagercrantz

first: Rafael

last: Muñoz-Viana

first: Anja

last: Schmid

first: Ueli

last: Grossniklaus


title: RNAseq analysis of liver transcriptomes to understand the effect of humoral immunodeficiency on liver function

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: Objective: The objective of this study was to understand how humoral immuno-deficiency influences molecular crosstalk between the ileum and liver, and liver bile acid metabolism. RNAseq was performed to characterize liver transcriptomes pf WT and CD19-/- mice under steady-state conditions.

overall_design: examination of liver transcriptomes of WT and CD19-/- mice

first: Jason

last: Kubinak

first: Diego

last: Altomare

first: Hao

last: Ji

first: Michael

last: Shtutman


title: Regeneration of immunocompetent B lymphopoiesis from pluripotent stem cells guided by transcription factors

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

country: China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

summary: We identified that the coordinated expression of exogenous transcription factors(Lhx2, Hoxa9, and Runx1), efficiently guides PSC-derived hematopoietic progenitors (iHPC) preferentially towards B cell lineage commitment, which successfully regenerate B lymphopoiesis in B-cell deficient animals. Of note, the abundancy of in vivo lymphopoiesis includes pro/pre-B progenitors, immature B cells, and all subsets of mature B1a, B1b, FO B and MZ B reconstitution in vivo. We performed single-cell RNA-Seq using the sorted GFP+CD45+ Lin- cells from the bone marrow of recipients at day 7.5 after iHPC transplantation.

overall_design: At day 7.5 after iHPC transplantation, we sorted the GFP+CD45+ Lin- cells from the bone marrow of recipients for Droplet-based scRNA-seq.  Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics, PN120263) following manufacture’s instruction.

first: Qitong

last: Weng

first: Yunqing

last: Lin


title: Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation [Hi-C]

first: Sudarshan

last: Pinglay

overall_design: Hi-C was used to investigate topological organization in cells carrying synthetic Hox cluster variants during ESC-to-MN differentiation

first: Milica

last: Bulajić

first: Dylan

last: Rahe

first: Emily

last: Huang

first: Ran

last: Brosh

first: Sergei

last: German

first: John

last: Cadley

first: Lila

last: Rieber

first: Nicole

last: Easo

first: Shaun

last: Mahony

first: Matthew

last: Maurano

first: Liam

last: Holt

first: Esteban

last: Mazzoni

first: Jef

last: Boeke


title: Atrial Fibrillation Patient's Urine miRNA Microarray

city: Seoul

first: Hyewon

last: Park

address: Gangseo-gu

country: South Korea

institute: Ewha Womans University College of Medicine

summary: Analysis for early diagnosis of atrial fibrillation by finding changes in miRNA in the urine of patients with atrial fibrillation

overall_design: Eight urine samples were used in the study presented here. These samples were collected via catheterization prior to the procedure to eliminate the risk of contamination.

first: Jeonbeom

first: Hyewom


title: Microglia homeostasis mediated by epigenetic ARID1A to regulate neural progenitor cells response in brain development [RNA-seq]

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: Purpose:To gain a deeper insight into how microglia homeostasis regulates regulates neurogenesis through epigenetic ARID1A, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by  ARID1A  deletion in microglia at E14.
Methods: The microglia was extracted from E14 of Arid1acKO and Arid1afl/fl mice by fluorescence activated cell sorting.  Total RNA was immediately extracted by using the RNAeasy Mini kit (QIAGEN) following the manufacturer’s instructions. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics.
Results: Approximately approximately two thousands transcripts showed differential expression between the Arid1afl/fl and Arid1acKO brain cortex, with a fold change ≥2.0 and p value <0.05. Gene ontology (GO) analysis showed that the down-regulated genes were enriched in the terms related to neurogenesis, regulation of cell communication and chemokine-mediated signaling pathway. Up-regulated genes showed a significant enrichment of terms involved in negative regulation of forebrain neuron fate commitment and cell surface receptor signaling pathway involved in cell-cell signaling. These results reflected the importance of ARID1A regulates neurogenesis through remodeling microglia states.
Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how ARID1A regulates neurogenesis through remodeling microglia states brain cortical development.

overall_design: Total microglia RNA was extracted from E14 telencephalic tissue of  Arid1acKO and  Arid1afl/fl mice and generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Libo

last: Su


title: Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation [ChIP-Seq]

first: Sudarshan

last: Pinglay

overall_design: ChIP-Seq was used to investigate chromatin boundary formation in synthetic Hox cluster variants during ESC-to-MN differentiation

first: Milica

first: Dylan


title: Human prostate luminal epithelia adopt a club-like state in response to low androgen levels (spatial and single-cell transcriptomics)

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center


title: RNA-seq of lymph node CD4+ cells from WT mice and Pggt1bfl/flLys-Cre mice.

city: Gothenburg

first: Eric

last: Malmhäll-Bah

address: Bruna stråket 16

institute: University of Gothenburg

summary: Conditional knockout of protein geranylgeranyltransferase type I (GGTase-I) in macrophages (GLC) activates RHO-GTPases and causes arthritis in mice. Knocking out Rag1 in GLC mice alleviates arthritis which indicates that lymphocytes are required for arthritis development in those mice. To study GLC dependent changes in the adaptive immunity, we isolated CD4+ T cells from GLC mice (CD4+ GLCs). Spleen and joint draining lymph nodes (dLN) CD4+ GLCs exhibited high expression of Cdc42 and Rac1, which repressed the caudal HOXA proteins and activated the mechanosensory complex to facilitate migration. These Cdc42/Rac1 rich CD4+ GLCs presented a complete signature of GARP+NRP1+IKZF2+FOXp3+ thymic Tregs. Activation of the ß-catenin/Lef1 axis in CD4+ GLCs contributed to a pro-inflammatory Th1 phenotype of Tregs, which was strongly associated with arthritis severity. Knockout of Cdc42 in macrophages of GLC mice affected CD4+ cell biology and development enlarging population of non-thymic Tregs. Knockout of Rac1 and RhoA had no such effects on CD4+ cells although it alleviated arthritis in GLC mice. Disrupting macrophage and T cell interaction with CTLA4 fusion protein reduced the Th1-driven inflammation and enrichment of thymic Tregs into dLNs. Antigen challenge reinforced the CD4+ GLC phenotype in non-arthritic heterozygote GLC mice and increased accumulation of RHO protein–expressing thymic Tregs in dLNs. Our study demonstrates an unexpected role of macrophages in stimulating the development of pro-inflammatory thymic Tregs and reveal activation of RHO-proteins behind their arthritogenic phenotype.

overall_design: mRNA extracted from CD4+ Lymph node cells of  C57BL/6 WT mice  and C57BL/6 mice with a conditional deletion of the Pggt1b gene in macrophages (Pggt1bfl/flLys-Cre).

first: Karin

last: Andersson

first: Malin

middle: C

last: Erlandsson

first: Maria

middle: I

last: Bokarewa


title: Identification of the Potential Key circRNAs in Aged Mice With Postoperative Delirium

city: Yuzhong district

first: wei

last: ran

state: chongqing

address: No.1 Youyi Road

department: anesthesiology

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Postoperative delirium (POD) is a common postoperative complication in elderly patients. The exact mechanism of POD is still unclear. In order to reveal the effect of CircRNA on POD, We analyzed the differential expression profile of circRNAs by microarray technique in hippocampus of 12-month-old mice between tibial fracture and control group.

overall_design: Mice hioppcamus tissue were obtained 72 hours after surgery,6 hippocampal samples of 12-month-old mice were analyzed, 3 in the tibial fracture group and 3 in the control group.

first: Wei

last: Ran

first: Jin

last: Gao


title: Smad3 binding regions in human epidermal keratinocytes (HaCaT).

first: Daizo

last: Koinuma

summary: Smad proteins transduce signals downstream of transforming growth factor-b (TGF-b), and are one of the factors that regulate the expression of genes related to diseases affecting the skin. In the present study, we identified MAB21L4, also known as male abnormal 21 like 4 or C2orf54, as one of the most up-regulated targets of TGF-b and Smad3 in differentiated human progenitor epidermal keratinocytes using chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq). Smad2 and Smad3 bound to the regulatory regions of the MAB21L4 gene locus. We found that TGF-b induced expression of the barrier protein involucrin (encoded by the IVL gene). Transcriptional activity of the IVL promoter induced by TGF-b was inhibited by siRNAs for MAB21L4. Further analysis revealed that MAB21L4 siRNAs also down-regulated the expression of several target genes of TGF-b. MAB21L4 protein was located mainly in the cytosol, where it was physically bound to Smad3 and a transcriptional corepressor c-Ski. siRNAs for MAB21L4 did not inhibit the binding of Smad3 to their target genomic regions but down-regulated acetylation of histone H3 lys 27 (H3K27ac), an active enhancer mark, near the Smad3 binding regions. These findings suggest that TGF-b-induced MAB21L4 up-regulates the gene expression induced by TGF-b, possibly through physical interactions with a transcriptional corepressor c-Ski in the cytosol.

overall_design: Smad3 and Smad2 ChIP samples  were sequenced for analysis.

first: Tomohiro

last: Ogami

first: Yusuke

last: Tamura

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Keiji

last: Miyazawa

first: Kohei

last: Miyazono


title: RNAseq analysis of ileal transcriptomes to understand the effect of humoral immunodeficiency on small intestinal mucosal homeostasis

first: HAO

last: JI

summary: Objective: The objective of this study was to more fully chracterize an inflammatory small intestinal enteropathy observed in CD19-/- mice (a model of humoral immunodeficiency). RNAseq was performed to characterize ileal transcriptomes pf WT and CD19-/- mice under steady-state conditions.

overall_design: examination of ileal transcriptomes of WT (C57BL/6) and CD19-/- mice

first: Jason

middle: L

last: Kubinak

first: Diego

last: Altomare

first: Hao

last: Ji

first: Michael

last: Shtutman


first: Jinyong

last: Wang

summary: We identified that the coordinated expression of exogenous transcription factors efficiently guides PSC-derived hematopoietic progenitors (iHPC) preferentially towards B cell lineage commitment, which successfully regenerate B lymphopoiesis in B-cell deficient animals. Of note, the abundancy of in vivo lymphopoiesis includes pro/pre-B progenitors, immature B cells, and all subsets of mature B1a, B1b, FO B and MZ B reconstitution in vivo. We performed BCR deep sequencing using the sorted naive follicular B cells from the spleen of one recipient at week 4 after iHPC transplantation and one C57BL/6 mouse as control.

overall_design: Total RNA was extracted from the  iB cell using Trizol (Invitrogen). 5’ RACE was performed with SMARTer RACE cDNA Amplification Kit (Clontech). IgG /IgK/IgL NGS libraries were made by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Libraries were sequenced on the Illumina Miseq 2 × 300 platform.

first: Qitong

last: Weng


title: RNA-seq in human progenitor epidermal keratinocytes (HPEK) stimulated with TGF-beta.

summary: Smad family proteins transduce signals downstream of transforming growth factor-beta (TGF-beta) and are one of the factors that regulate target genes related to diseases affecting the skin. We here identified C2orf54, officially known as MAB21L4, as one of the most up-regulated targets of TGF-beta and Smad3 in a differentiated human progenitor epidermal keratinocyte, using chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq). Smad2 and Smad3 bind to the regulatory regions of the C2orf54 gene locus. We found that TGF-beta induced expression of a barrier protein involucrin (encoded by IVL gene), and transcriptional activity of the IVL promoter induced by TGF-beta was inhibited by siRNAs for C2orf54. Further analysis revealed that C2orf54 siRNAs also down-regulated the expression of several target genes of TGF-beta. C2orf54 protein located mainly in the cytosol, physically bound to Smad2 and Smad3, but did not inhibit the binding of Smad2 and Smad3 to the target genomic regions. These findings suggested that TGF-beta-induced C2orf54 up-regulates gene expression induced by Smads, possibly through its physical interaction with Smad proteins.

overall_design: Expression of mRNA in differentiated or undifferentiated HPEK cells, with or without TGF-beta stimulation.


title: Smad3 binding regions in differentiated human progenitor epidermal keratinocytes (HPEK).

overall_design: Smad3 ChIP sample and input genomic sample was sequenced for analysis.


title: IRF3 and Smad3 binding regions in a basal-like breast cancer cell line, BT549 transfected with polyI:C.

overall_design: IRF3 and Smad3 ChIP-seq analysis was performed in a basal-like breast cancer cell line, BT549 cells transfected with polyI:C. Constitutively active Smad3 was stably expressed to rescue the inhibitory effect of polyI:C.


title: ChIP-seq and RNA-seq of Human progenitor epidermal keratinocytes (HPEK) and HaCaT cells


title: Single cell RNA-sequencing of verumontanum region and peripheral zone of normal human prostate

first: Gervaise

last: Henry

summary: Dissected verumontanum region and peripheral zone region from a normal human prostate sample were digested into single-cell suspensions, cells were subject to single-cell RNA-sequencing using the 10x Genomics platform

overall_design: Fresh human prostate specimens were digested into single-cell suspensions, cells were subject to single-cell RNA-sequencing using the 10x Genomics platform.

first: Douglas

last: Strand

middle: H


title: Ribosome profiling and RNA sequencing reveal genome-wide cellular translation and transcription regulation under osmotic stress in Lactobacillus rhamnosus ATCC 53103

status: Public on Dec 15 2021

city: Harbin

first: Zhen

last: Feng

state: Heilongjiang

address: Changjiang road 600

institute: Northeast Agricultural University

summary: To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. DEGs involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phosphotransferase system pathways also were co-regulated at translation and transcription levels, while they showed opposite expression direction at two levels. Moreover, DEGs involved in the two-component system, amino acid metabolism, and pyruvate metabolism pathways were only regulated at the transcription level. And DEGs involved in fructose and mannose metabolism were only regulated at the translation level. The translation efficiency of DEGs involved in the biosynthesis of amino acids was downregulated while in quorum sensing and PTS pathways was upregulated. In addition, the ribosome footprints accumulated in open reading frame regions resulted in impaired translation initiation and elongation under osmotic stress. In summary, L. rhamnosus ATCC 53103 could respond to osmotic stress by translation regulation and control the balance between survival and growth of cells by transcription and translation.

overall_design: To systematically investigate the effect of osmotic stress on transcription and translation regulation, RNA-seq and ribosome profiling were analyzed in the same two sets of parallel populations of L. rhamnosus ATCC 53103 cells with two different concentrations of sodium lactate (control vs. 0.6 M). Each experiment was divided into control group (CG) and osmotic stress group (OS), respectively . The regulation of transcription and translation under osmotic stress were examined by deep sequencing of cellular total mRNAs and RPFs, respectively.

first: Xuejing

last: Fan


title: HIF2 regulates intestinal Wnt5a expression

city: Houston

first: Cullen

last: Taniguchi

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: Radiation therapy for abdominal tumors is challenging because the small intestine is exquisitely radiosensitive. Unfortunately, there are no FDA-approved therapies to prevent or mitigate GI radiotoxicity. The EGLN protein family are oxygen sensors that regulate cell survival and metabolism through the degradation of hypoxia-inducible factors (HIFs). Our group has previously shown that stabilization of HIF2 through genetic deletion or pharmacologic inhibition of the EGLNs mitigates and protects against GI radiotoxicity in mice by improving intestinal crypt stem cell survival. Here we aimed to elucidate the molecular mechanisms by which HIF2 confers GI radioprotection. We developed duodenal organoids from mice, transiently overexpressed non-degradable HIF2, and performed bulk RNA sequencing. Interestingly, HIF2 upregulated known radiation modulators and genes involved in GI homeostasis, including Wnt5a. Non-canonical Wnt5a signaling has been shown by other groups to improve intestinal crypt regeneration in response to injury. Here we show that HIF2 drives Wnt5a expression in multiple duodenal organoid models. Luciferase reporter assays performed in human cells showed that HIF2 directly activates the WNT5A promoter via a hypoxia response element. We then evaluated crypt regeneration using spheroid formation assays. Duodenal organoids that were pre-treated with recombinant Wnt5a had a higher cryptogenic capacity after irradiation, compared to vehicle-treated organoids. Conversely, we found that Wnt5a knockout decreased the cryptogenic potential of intestinal stem cells following irradiation. Treatment with recombinant Wnt5a prior to irradiation rescued the cryptogenic capacity of Wnt5a knockout organoids, indicating that Wnt5a is necessary and sufficient for duodenal radioprotection. Taken together, our results.txt suggest that HIF2 radioprotects the GI tract by inducing Wnt5a expression.

overall_design: Examination of differentially expressed genes in duodenal organoids infected with Ad-hHIF2, Ad-hHIF1 or Ad-GFP

first: F

middle: A

last: San Lucas


title: RNA Sequencing Analysis of Gene Expression Profiles in Cic-null B-1a and Follicular B (Fo B) cells

city: Pohang-Si

first: Hyebeen

last: Hong

address: Cheongam-Ro, 77

department: Department of Life Science

institute: POSTECH

summary:
Purpose: The goal of this study is to compare and examine the transcriptional profiles in control versus Cic-deficient B cells, specifically splenic B-1a and Fo B cells, by mRNA sequencing.
Methods: Splenic B-1a (IgM+, CD19+, CD5+, CD43+) and Fo B (B220+, CD93-, CD23+, CD21lo-mid) cells were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. The DNA library for mRNA sequencing was generated using SMART-seq v4 Ultra Input RNA Kit (Clontech, for B-1a cells) and TruSeq RNA Sample Prep Kit v2 (Illumina, for Fo B cells). DNA libraries were multiplexed and pooled for sequencing on the Illumina Hiseq 4000 platform.
Results: Trimmed reads were mapped to mouse reference genome (mm10 RefSeq) with HISAT2, a splice-aware aligner, and transcripts were assembled by StringTie with aligned reads, for known transcripts, novel transcripts, and alternatively spliced transcripts. A total of 712 genes were differentially expressed in Cic-null B-1a cells (325 upregulated and 387 downregulated), while 357 genes were differentially expressed in Cic-deficient Fo B cells (180 upregulated and 178 downregulated) when compared with their respective control cells (fold change >1.2 and P < 0.05). Several known CIC target genes, including Etv1, Etv4, Etv5, Spry4, Spred1, Spred2, Dusp4, Dusp6, and Per2, were included in the list of the upregulated differentially expressed genes (DEGs) in either Cic-null B-1a or Fo B cells or both, validating the reliability of RNA sequencing results.
Conclusions: Our study presents the first comparative gene expression analysis of B-1a and Fo B cells from control and B cell-specific Cic-deficient mice. We concluded that CIC deficiency promotes B-1a cell development through enhancing the BCR signaling pathway. The data reported here also provide references for the gene expression profiles of murine B-1a and Fo B cells.

overall_design: Splenic B-1a and Fo B cells from control and B cell-specific Cic-deficient mice. Two replicates each sample type.

first: Yoontae

last: Lee


title: RNAseq analysis of retinal microglia during early diabetes

city: Melbourne

first: Andrew

middle: Ian

last: Jobling

state: Victoria

address: Medical Building, Cnr Grattan St and Royal Pde

department: Anatomy & Physiology

country: Australia

institute: University of Melbourne

summary: We report the use of RNAseq to identify gene changes in isolated retinal microglia after 4 weeks of STZ-induced diabetes. At this early time point in diabetes induction, single retinal cell suspensions were sorted via FACS using a Cd11b-FITC conjugate. RNA was isolated and preamplified using the SMARTSeq v4 low RNA input kit. After library preparation a 50bp single end read was performed at a depth of 19-34 million reads per sample using the Illumina HiSeq. Constructs were mapped to the rat genome and differential expression calculated between the STZ-treated and control groups.

overall_design: Examination of 2 groups (control and diabetic) after 4 weeks of STZ induced diabetes

first: Erica

last: Fletcher


summary:
Purpose: B-1a cells have a distinct BCR repertoire compared with that of B-2 cells. To examine whether CIC loss affects the BCR repertoire in B-1a cells, we analyzed mRNA sequences of immunoglobulin heavy (Igh) and light (Igk and Igl) chain genes in B-1a cells from 12-week-old control and Cicf/f;Cd19-Cre mice.
Methods: Peritoneal cavity B-1a cells (IgM+, CD19+, CD5+, CD43+) were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. Long Read iR-Profile Reagent System (iRepertoire) was used to generate NGS libraries covering BCR chains including Igh, Igk, and Igl. Briefly, nested inside and outside primers selectively amplified all V- and C- regions and incorporated communal adaptors. Following clean up, only target amplicons, which contain 5’ and 3’ communal adaptors, were exponentially amplified. Amplified libraries were multiplexed for sequencing on the Illumina Miseq platform. Sequence reads were de-multiplexed according to the barcode sequences.
Results: Trimmed reads were mapped to germline V, D and J reference sequences downloaded from the IMGT database. IgH diversity and the usage of variable (V) segments in heavy (Ighv) chain and light (Igkv and Iglv) chain genes were comparable between control and Cic-null B-1a cells. Analysis of non-templated (N)-nucleotide addition at V(D)J junctions revealed that Cic-null B-1a cells have a higher proportion of zero to two N-nucleotides-containing-BCRs than control cells.
Conclusions: Our study presents the first comparative BCR repertoire analysis of wild-type and Cic-null B-1a cells. We concluded that CIC deficiency does not dramatically alter the BCR repertoire in B-1a cells.

overall_design: We analyzed mRNA sequences of immunoglobulin heavy (Igh) and light (Igk and Igl) chain genes in B-1a cells from 12-week-old control and Cicf/f;Cd19-Cre mice.


title: Treatment of noise-induced hearing loss by mesenchymal stromal cells: an RNAseq analysis of protective/repair pathways

city: Kansas City

first: Hinrich

last: Staecker

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas

summary: Mesenchymal stromal cells (MSCs) are an adult derived stem cell-like population that has been shown to mediate repair in a wide range of degenerative disorders. The protective effects of MSCs are mainly mediated by the release of growth factors and cytokines thereby modulating the diseased environment and the immune system. Within the inner ear, MSCs have been shown protective against tissue damage induced by sound and a variety of ototoxins. To better understand the mechanism of action of MSCs in the inner ear, mice were exposed to narrow band noise. After exposure, MSCs derived from human umbilical cord Wharton’s jelly were injected into the perilymph. RNAseq analysis of gene expression changes induced by MSCs was compared to sound trauma only treated animals.

overall_design: Mice were exposed to narrow band noise. After exposure, MSCs derived from human umbilical cord Wharton’s jelly were injected into the perilymph. Controls consisted of mice exposed to sound trauma only. Forty-eight hours post cell delivery, total RNA was extracted from the cochlea and RNAseq performed to evaluate the gene expression induced by the cell therapy.

first: Athanasia

last: Warnecke


title: Neutrophilic inflammation and epithelial barrier disruption in nasal polyps characterize NSAID-exacerbated respiratory disease

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: Chronic rhinosinusitis with nasal polyps (CRSwNP) is a debilitating inflammatory disease of the sinonasal cavities. Concomitant CRSwNP and asthma, together with hypersensitivity reactions to cyclooxygenase-1 (COX-1) inhibitors, is a particular phenotype known as NSAID-exacerbated respiratory disease (N-ERD), which is associated with greater disease severity. In this study, we attempted to characterize clinical, laboratory, and transcriptomic differences between CRSwNP patients with N-ERD (N-ERD; N=13) and CRSwNP patients without N-ERD (non-N-ERD, N=13).

overall_design: Genome-wide RNA sequencing of polyps patients

first: Anand

last: Kumar Andiappan

first: Duan

last: Kaibo


title: The analysis of gene expression profiles and BCR repertoire in control and Capicua (Cic)-deficient B cells

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

overall_design: Refer to individual Series


title: Col6a1+/CD201+ mesenchymal cells regulate intestinal morphogenesis and homeostasis

city: Vari

first: Vasiliki

last: Koliaraki

state: Attiki

address: 34 Fleming street

country: Greece

institute: BSRC "Alexander Fleming"

summary: This study shows that Col6a1cre+/CD201+  cells constitute a subpopulation of mesenchymal cells in the intestine that plays an important role in intestinal morphogenesis and homeostasis.

overall_design: 3' RNA-Seq (QuantSeq) profiling of 2 sorted mesenchymal cell subpopulations (Col6a1cre-GFP+, Col6a1cre-GFP-) and unsorted controls from the colon of normal and DSS-treated mice and 3 sorted mesenchymal cell subpopulations (Col6a1cre-GFPhi, Col6a1cre-GFPlo, Col6a1cre-GFP-) and unsorted controls from the small intestine of normal mice. 3 replicates per group.

first: Maria-Theodora

last: Melissari

first: Ana

last: Henriques

first: Christos

last: Tzaferis

first: Alejandro

last: Prados

first: Michalis

middle: E

last: Sarris

first: Niki

last: Chalkidi

first: Dimitra

last: Mavroeidi

first: Panagiotis

last: Chouvardas

first: Sofia

last: Grammenoudi

first: George

last: Kollias


title: Single nucleus RNA-seq of prefrontal cortex from methamphetamine-treated mice and control mice

city: Wuhan

first: Xuan

last: Yu

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology

summary: As one of the most commonly abused substances in the world, methamphetamine (METH) addiction and use disorders cause a huge burden for society. The prefrontal cortex (PFC) is a vital brain region associated with emotion and cognitive behaviors that is also intimately involved in the neurocircuitry of addiction syndrome. Bulk RNA-seq has revealed the effects of METH on disease-related genes alterations in the mouse PFC; however, the roles of different cell types are still unknown. We performed single nucleus RNA sequencing (snRNA-seq) to examine the transcriptomes of 20,698 nuclei isolated from the PFC of chronic METH-treated and control mice.

overall_design: Animals included in current study were all 2-month-old male C57BL/6 mice. All animals were socially housed on a 12-h light/dark cycle with water and food ad libitum. Mice were treated with 5 mg/kg METH or saline (intraperitoneal) for 14 days in the METH and control groups, respectively. Then all mice were deeply anesthetized with chloral hydrate and sacrificed, and the PFCs of three mice per group were rapidly removed and prepared for single nucleus isolation on ice. Then Iodixanol gradient centrifugation was used for single nucleus isolation. The library sequencing was performed in the Illumina Hiseq platform (Illumina, San Diego, CA, USA) under the 2 × 150-bp double-ended sequencing pattern to generate FastQ data.

first: Kuan

last: Zeng

first: Zhen

last: Wei

first: Xiaochuan

last: Wang


title: Transcriptome responses to sublethal concentration of abamectin in Tetranychus truncatus analyzed by deep-sequencing

city: nanjing

first: yang

last: niuzi

state: jiangsu

department: College of  Plant Protection

institute: jaas

summary: Purpose: In order to clarify the molecular response mechanism of Tetranychus truncatus to sublethal concentrations of abamectin. Methods: We sequenced the transcriptome of Tetranychus truncatus treated with sublethal concentration of abamectin and control. Results: we provide a comprehensive transcriptome resource for Tetranychus truncatus derived from treating with sublethal concentration abamectin and control. Conclusions: The new genomic resources and data that we present in this study for Tetranychus truncatus will substantially facilitate molecular studies of underlying mechanisms involved in abamectin resistance.

first: Lei

last: Yang

first: Tao

middle: J

last: Gao

first: Lu

middle: Y

last: Bai

first: Qin

last: Shang


title: Internal reference gene selection under salt, alkali, and drought stresses in ecological remediation plant giant reed

city: Guilin

first: deng

last: zhang

address: No. 85, Yanshan street, Yanshan District, Guilin, Guangxi

institute: Guangxi Institute of Botany

summary: Real-time quantitative PCR (RT–qPCR) is the favoured method for gene expression analysis in molecular biology due to its sensitivity, specificity, cost-effectiveness, and reproducibility. To obtain the accuracy and reliability of RT-qPCR, the use of reliable reference genes is inevitable. There were many reports about the physiological response of giant reed (Arundo donax L.) to abiotic stresses. However, there is little use in the validation of reference genes under different treatments. It still belongs to the blank that the research about selecting reference genes under salt and alkali. In this study, the expression stability of twenty-three candidate reference genes in leaves and roots were assessed under salt, drought, and alkali stresses using geNorm, NormFinder, BestKeeper, and Delta Ct algorithms. Our results showed that no one gene had an invariant expression under different conditions. For example, under drought stress, UPL3, UBC2, and APT1 were better reference genes in leaves, RPL5 and FPS2 were better in roots. Under alkali stress, GAPDH, APT1, and RPS5 were better reference genes in leaves; UPL3, ACT2, and SAMDC2 were better in roots. In addition, the expression of MSD1 was used to further confirm the validated reference genes under salt, drought, and alkali stresses. It was proved that the use of inappropriate reference genes in giant reed significantly altered the relative expression of target genes and even reversed the results. Consequently, our results provided guidelines for reference gene selection under salt, drought, and alkali stresses and a foundation for more accurate and widespread use of RT-qPCR in the giant reed.

overall_design: qPCR gene expression profiling.  tissues from three plants were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was pooled prior to gene expression analysis.

first: Deng

last: Zhang

first: Jianxiong

last: Liao


title: Comparison of cellular transcriptome between mouse cardiac microvascular cell types.

city: Portland

first: Jessica

last: Minnier

state: OR

address: 3181 SW Sam Jackson Park Rd, UHN62

institute: Oregon Health & Science University

summary: Aims: The microcirculation serves crucial functions in adult heart, distinct from those carried out by epicardial vessels. Microvessels are governed by unique regulatory mechanisms, impairment of which leads to microvessel-specific pathology. There are few treatment options for patients with microvascular heart disease, primarily due to limited understanding of underlying pathology. We developed an integrated process for simultaneous isolation and culture of the main cell types comprising the microcirculation in adult mouse heart: endothelial cells, pericytes and vascular smooth muscle cells, and here we characterize the transcriptional profile of each cell type.  Methods and Results: Confluent cultures of mouse cardiac endothelial cells, pericytes and vascular smooth muscle cells underwent transcriptional profiling using RNA sequencing. We define the top 50 transcripts expressed by each cell type.  Conclusions: We define microvascular cell transcriptional profiles, identify novel transcripts, and confirm established cell-specific markers. Our results allow identification of unique markers and regulatory transcripts that govern microvascular physiology and pathology.

overall_design: RNA was extracted from confluent primary mouse cultures of endothelial cells, pericytes and vascular smooth muscle cells.

first: Zhiping

last: Cao

first: Lijuan

last: Liu

first: Beth

last: Wilmot

first: Anthony

middle: P

last: Barnes

first: Catherine

last: Davis


title: Pan-Cancer Single Cell Landscape of Tumor-Infiltrating T Cells

first: Shishang

last: Qin

address: No.5 Yiheyuan Road, Haidian District

institute: Peking university

summary: T cells present diverse states in the tumor, playing a central role in cancer immunity and immunotherapies. However, their heterogeneity, dynamics and composition within tumors of various cancer types are not fully characterized. Integrating a pan-cancer single-cell RNA sequencing atlas of T cells cross multiple cancer types, we systematically characterized their diversity, identified the potentially tumor-reactive T cells, and revealed new cell types. Our findings provide new insights into T cell immunity and will facilitate immunotherapy development targeting T cells in human cancer.

overall_design:
We generated scRNA-seq data from cancer patients to investigate tumor-infiltrating T cells across multiple cancer types.

Please note that processed data files generated from multiple samples are available on Series record and are indicated in the associated sample description field.

****Raw sequence data were provided at China Genomic Sequence Archive (GSA). The accession number will be included once the paper is accepted.

first: Liangtao

last: Zheng

first: Wen

last: Si

first: Anqiang

first: Baocai

last: Xing

first: Ranran

first: Xianwen

last: Ren

first: Li

first: Xiaojiang

last: Wu

first: Ji

first: Ning

first: Hong

first: Hanqiang

last: Ouyang

first: Keyuan

last: Chen

first: Zhaode

last: Bu

first: Xueda

last: Hu

first: Jiafu

last: Ji

first: Zemin


title: Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration

city: Boston

first: Ryoji

last: Amamoto

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Cone photoreceptors in retina degeneration mouse models degenerate from the center to the periphery. However, the far peripheral cones survive long-term. We found that retinoic acid signaling is both necessary and sufficient for cone survival.

overall_design: Bulk RNA-seq of CAR+ cones and Muller glia was performed on P30 central and peripheral retinas. Briefly, the central one-third and peripheral one-third retinal tissues were dissected out from 3 mice. The tissue was dissociated into single cells and labeled with anti-CAR antibody. The CAR+ central and peripheral cells were FACS-isolated, and the RNA was extracted.

first: Constance

last: Cepko


title: Treatment of hepatocellular carcinoma with autologous platelets encapsulating sorafenib or lenvatinib: a novel therapy exploiting tumor-platelet interactions

city: Asahikawa

first: Hiroki

last: Tanaka

state: Hokkaido

address: Midorigaoka-higashi, 2-1-1-1

institute: Asahikawa Medical University

summary:
Hepatocellular carcinoma (HCC) activates platelets through the action of adjacent sinusoidal cells. Activated platelets bind to tumor-associated endothelial cells and release growth factors that promote tumor progression. We hypothesized that tumor inhibitors encapsulated in platelets would function as drug carriers for tumor therapy. We propose a therapeutic strategy for HCC using autologous platelets encapsulating multiple tyrosine kinase inhibitors in a rat chemically-induced HCC model. Sorafenib or lenvatinib was encapsulated in platelets isolated from tumor-bearing rats in vitro. The rats were divided into groups that received repeated intravenous injections (twice a week for 10 weeks) of the following materials: placebo, sorafenib (SOR), lenvatinib (LEN), autologous platelets, autologous platelets encapsulating sorafenib (SOR-PLT), and autologous platelets encapsulating lenvatinib (LEN-PLT). The therapeutic effect was then analyzed by ultrasonography (US) and histopathological analysis. Histopathological and US analysis demonstrated extensive tumor necrosis in the tumor tissue of SOR-PLT or LEN-PLT, but not in other experimental groups. By liquid chromatography-mass spectrometry, more abundant sorafenib was detected in tumor tissues after SOR-PLT administration than in surrounding normal tissues, but no such difference in sorafenib level was observed with SOR administration. Therefore, the use of autologous platelets encapsulating drugs might be a novel therapeutic strategy for HCC.
We investigated the effect of the drug encapsulation process on the degradation of resident mRNA inherited from megakaryocytes in platelets.

overall_design: Control platelets (PLT), sorafenib-encapsulated platelets (SOR-PLT), and lenvatinib-encapsulated platelets (LEN-PLT) were produced. In these three groups, the prepared platelet suspensions from five rats were pooled.

first: Kie

last: Horioka

first: Takumu

last: Hasebe

first: Koji

last: Sawada

first: Shunsuke

last: Nakajima

first: Hiroaki

last: Konishi

first: Shotaro

last: Isozaki

first: Masanori

last: Goto

first: Yumiko

last: Fujii

first: Yuki

last: Kamikokura

first: Katsuhiro

last: Ogawa

first: Yuji

last: Nishikawa


title: DNA methylation signature in monozygotic twins discordant for psoriatic disease [RNA-seq]

city: Pieve Emanuele

first: Elvezia

middle: Maria

last: Paraboschi

address: via Rita Levi Montalcini 4

department: Department of Biomedical Sciences

country: Italy

institute: Humanitas University

summary: Psoriatic disease is a multifactorial inflammatory condition spanning from skin and nail psoriasis (Pso) to spine and joint involvement characterizing psoriatic arthritis (PsA). Monozygotic twins provide a model to investigate genetic, early life environmental exposure and stochastic influences to complex diseases, mainly mediated by epigenetics. We performed a genome-wide DNA methylation and transcriptome study on whole blood of monozygotic twins from 7 pairs discordant for Pso/PsA. Transcriptomic profiling was performed by RNAseq.  We identified 2,564 differentially methylated positions between psoriatic disease and controls, corresponding to 1,703 genes, 59% within gene bodies. There were 19 regions with at least two DMPs within 1 kb of distance and significant within-pair Δβ-values (p<0.005), among them SNX25, BRG1 and SMAD3 genes, all involved in TGF-β signaling pathway, were identified. Co-expression analyses on transcriptome data identified IL-6/JAK/STAT3 and TNF-alpha pathways as important signaling axes involved in the disease, and they also suggested an altered glucose metabolism in patients’ immune cells, characteristic of pro-inflammatory T lymphocytes. The study suggests the presence of an epigenetic signature in affected individuals, pointing to genes involved in immunological and inflammatory responses. This result is also supported by transcriptome data, that altogether suggest a higher activation state of the immune system, that could promote the disease status.

overall_design: Transcriptome profiling of monozygotic twins discordant for psoriatic disease, using the Illumina Nextseq500 and a paired end strategy. Samples included 7 twin pairs.

first: Matteo

last: Vecellio

first: Angela

last: Ceribelli

first: Natasa

last: Isailovic

first: Francesca

last: Motta

first: Giulia

last: Cardamone

first: Michela

last: Robusto

first: Rosanna

last: Asselta

first: Sonia

last: Brescianini

first: Francesco

last: Sacrini

first: Antonio

last: Costanzo

first: Maria

last: De Santis

last: Stazi

first: Stefano

last: Duga

first: Carlo

last: Selmi


title: DNA methylation signature in monozygotic twins discordant for psoriatic disease [methylation array]

summary: Psoriatic disease is a multifactorial inflammatory condition spanning from skin and nail psoriasis (Pso) to spine and joint involvement characterizing psoriatic arthritis (PsA). Monozygotic twins provide a model to investigate genetic, early life environmental exposure and stochastic influences to complex diseases, mainly mediated by epigenetics. We performed a genome-wide DNA methylation study on whole blood of monozygotic twins from 7 pairs discordant for Pso/PsA using the Infinium Methylation EPIC array (Illumina). MeDiP – qPCR was used to confirm specific signals. Data were replicated in an independent cohort of 7 patients with Pso/PsA and 3 healthy controls.   We identified 2,564 differentially methylated positions between psoriatic disease and controls, corresponding to 1,703 genes, 59% within gene bodies. There were 19 regions with at least two DMPs within 1 kb of distance and significant within-pair Δβ-values (p<0.005), among them SNX25, BRG1 and SMAD3 genes, all involved in TGF-β signaling pathway, were identified. Co-expression analyses on transcriptome data identified IL-6/JAK/STAT3 and TNF-alpha pathways as important signaling axes involved in the disease, and they also suggested an altered glucose metabolism in patients’ immune cells, characteristic of pro-inflammatory T lymphocytes.  The study suggests the presence of an epigenetic signature in affected individuals, pointing to genes involved in immunological and inflammatory responses. This result is also supported by transcriptome data, that altogether suggest a higher activation state of the immune system, that could promote the disease status.

overall_design: Genome wide DNA methylation profiling of monozygotic twins discordant for psoriatic disease. The Illumina EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 800,000 CpGs in blood cell samples. Samples included 7 twin pairs.


title: Microglia homeostasis mediated by epigenetic ARID1A to regulate neural progenitor cells response in brain development

city: Beijing

first: Jianwei

last: Jiao

address: 1 Beichen West Road

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We report the genomic characterization of H3K9me3 occupancy in microglia at E14 brain.CUT&Tag experiment was performed with antibody against H3K9me3. We generated genome-wide characterization of H3K9me3 occupancy in microglia and find that H3K9me3 was prone to bind the promoters and the intergenic regions. The number and proximity of H3K9me3 occupancy to the transcription start sites determined the probability of transcriptional regulation on genes expression.The genomic localization of H3K9me3 might reveal the importance role of ARID1A in chromatin landscape of microglia homeostatic state during cortical development. Detailed investigation of the binding profiles show that the enrichments of H3K9me3 peaks in the regulatory regions of Prg3 gene. This study provides a framework for the epigenetic regulation of ARID1A in microglia homeostasis.

first: Libo

last: Su


title: The Renin-Angiotensin System, High Inherent Aerobic Capacity, and Low Breast Cancer Risk

city: Fort Collins

first: Henry

last: Thompson

state: CO

address: 1173 Campus Delivery

institute: Colorado State University

summary:
Purpose: Physical activity is associated with reduced breast cancer risk. Aerobic capacity, which is the ability to generate and use energy on a sustained basis, has been hypothesized as a mechanism linking physical activity and cancer. Using selectively bred rats with distinctly different inherent aerobic capacity (IAC) in concert with a well-characterized model of breast cancer, we have previously reported that high IAC is protective against chemically induced mammary carcinogenesis. The mechanism(s) by which differing IAC confers effects on cells that reside in the mammary gland is unknown.
Methods: To address this knowledge gap, RNA sequence analysis was performed on skeletal muscle, uninvolved mammary gland, and mammary carcinoma from rats of low or high IAC status.
Results: Investigation of effects on upstream regulators led to a focus on the role of the renin-angiotensin system (RAS) in mediating effects on downstream targets relevant to the development of breast cancer. Patterns of RAS gene expression in skeletal muscle and mammary gland of high versus low IAC were consistent with counter-regulatory RAS activity signaling promoting anti-cancer biological functions while an opposite expression pattern of these transcripts was observed in tumor tissue.
Conclusions: This study found a biologically plausible heritable relationship linking mechanisms associated with aerobic capacity and the development of breast cancer. Through RNA-seq analyses, we identified AGT as a biomarker pointing to differences in the regulation of RAS as a candidate mediator linking aerobic capacity and breast cancer.

first: Vanessa

middle: K

last: Fitzgerald

first: Angel

middle: M

last: Whiteman

first: John

middle: N

last: McGinley

first: David

last: King

first: Erin

last: Osborne Nishimura


title: RNAseq analysis on E14.5 cortical material from mouse, Nkx2.9  WT-vs-Het-vs-KO..

city: Amsterdam

first: Marten P.

middle: Piet

last: Smidt

address: Sciencepark 904

department: SILS

country: Netherlands

institute: UvA

summary: Nkx2.9 is involved in programming of mesodiencephalic dopaminergic neurons early in development.

overall_design: examination of 3 groups from Nkx2.9 genotypes, N=3 from all. RNA samples from E14.5 midbrain dissected material.

first: M

first: W

last: Kouwenhoven


title: Epigenome Association Study for DNA Methylation Biomarkers in Buccal and Monocyte Cells for Female Rheumatoid Arthritis

city: Pullman

first: Michael

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

summary: This study used buccal cells and purified blood monocytes from two different clinical cohorts involving Caucasian or African American female populations with or without arthritis. The differential DNA methylation regions (DMRs) between the control and RA populations were identified using MeDIP-seq. The DMRs (i.e., epimutations) identified in the buccal cells and monocytes were found to be distinct. The DMR associated genes were identified and many have previously been shown to be associated with arthritis. Observations indicate DMRs are cell type specific.

overall_design: Buccal and monocyte samples from females of similar age were collected for comparison of individuals with and without rheumatoid arthritis. White Caucasian non-Hispanic female samples were obtained by the Arthritis Northwest (ANW) Clinic in Spokane, Washington. The African American (AA) female samples were obtained by Dx Biosamples, LLC in San Diego, California, with sample collections in the Los Angeles California area. An MeDIP-seq procedure was used to detect methylation and differential DNA methylation sites between control and arthritis sample groups were identified. These DMRs were then compared and annotated. Four seperate comparisons were made. The Caucasian (CC) buccal cell control without RA (n=13) and with RA (n=13) were compared. The Caucasian monocyte cell control without RA (n=13) and with RA (n=13) were compared. The African American (AA) buccal cell control without RA (n=9) and with RA (n=13) were compared. A combination of Caucasian and African American samples without (n=23) and with RA (n=26) were compared.

first: Gary

last: Craig

first: Howard

last: Kenney

first: Eric

last: Nilsson

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck


title: Adropin transgenesis improves recognition memory in diet-induced obese LDLR-deficient C57BL/6J mice

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

summary: Obesity-related metabolic dysregulation causes mild cognitive impairment and increases risk for dementia. We used an LDLR-deficient C57BL/6J mouse model (LDLRKO) to investigate whether adropin, a neuropeptide linked to neurodegenerative disease, improves cognitive function in situations of metabolic dysregulation. Adropin transgenic mice (AdrTG) were crossed with LDLRKO; male and female progeny were fed a high fat diet for 3-months. Male chow-fed wild type (WT) mice were used as controls. Diet-induced obesity and LDLR-deficiency caused severe dyslipidemia, irrespective of sex. The AdrTG prevented reduced adropin protein levels in LDLRKO cortex. In males, metabolic dysregulation and AdrTG genotype significantly and bi-directionally affected performance in the novel object recognition (NOR) test, a declarative hippocampal memory task (discrimination index mean±SE for WT, 0.02±0.088; LDLRKO, -0.115±0.077; AdrTG;LDLRKO, 0.265±0.078; genotype effect, p=0.009; LDLRKO vs. AdrTG;LDLRKO, P<0.05). A 2-way ANOVA (fixed variables: sex, AdrTG genotype) indicated a highly significant effect of AdrTG (P=0.003). The impact of the diet-genotype interaction on the male mouse brain was investigated using RNA-seq. Gene-ontology analysis of transcripts showing fold-changes of >1.3 or <-1.3 (P<0.05) indicated metabolic dysregulation affected gene networks involved in intercellular/neuronal signaling, immune processes, angiogenesis, and extracellular matrix organization. The AdrTG selectively attenuated the impact of metabolic dysregulation on intercellular/neuronal signaling pathways. Intercellular/neuronal signaling pathways were also the predominant processes overrepresented when directly comparing AdrTG;LDLRKO with LDRKO. In summary, adropin over expression improves cognitive function in severe metabolic dysregulation through pathways related to cell-cell communication and neuronal processes, and independently of preventing inflammatory responses.

overall_design: We used an LDLR-deficient C57BL/6J mouse model (LDLRKO) to investigate whether adropin, a neuropeptide linked to neurodegenerative disease, improves cognitive function in situations of metabolic dysregulation. Adropin transgenic mice (AdrTG) were crossed with LDLRKO; male and female progeny were fed a high fat diet for 3-months. Male chow-fed wild type (WT) mice were used as controls. Brain tissue samples were collected and snap frozen using liquid nitrogen and subsequently used for RNA-Seq.

first: Sarbani

last: Ghoshal

first: Subhashis

last: Banerjee

first: Andrew

last: Butler


title: Gene expression analysis of the bone marrow microenvironment reveals distinct immunotypes in smoldering multiple myeloma associated to progression to symptomatic disease

city: Barcelona

first: Ester

last: Lozano

state: Barcelona

address: Rosselló, 153

department: Hemato-Oncology

institute: IDIBAPS

summary: Gene expression analysis of CD138-depleted bone marrow cells from patients with SMM, patients with monoclonal gammopathy of undetermined significance (MGUS) and patients with symptomatic MM was performed by using Nanostring Technology

overall_design: The aim of the study was to characterize the smoldering multiple myeloma (SMM) bone marrow microenvironment using the nanoString nCounter gene expression system, to better understand the role of immune surveillance in disease progression and to identify immune biomarkers associated with progression to symptomatic disease and potential therapeutic targets.

first: Carlos

last: Fernández de Larrea


title: Transcriptomics of rhinovirus persistence reveals sustained expression of RIG-I and interferon-stimulated genes

first: Nicholas

last: Ang

summary: The persistence of HRV RNA does not necessarily indicate an active infection during prolonged infection. The sustained expression of RIG-I, IFNs, chemokines, and ISGs in response to viral RNA persistence highlights the importance of assessing how immune-activating host factors change during an active HRV infection and the immune regulation that persists thereafter.

overall_design: Genome-wide RNA sequencing

first: Anand

last: Andiappan

first: Duan

last: Kaibo


title: DNA methylation signature in monozygotic twins discordant for psoriatic disease

first: Elvezia

last: Paraboschi

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


title: Engineering CAR-NK cells to secrete IL15 sustains their anti-AML functionality, but is associated with systemic toxicities

city: BALTIMORE

first: ILIAS

last: CHRISTODOULOU

state: MARYLAND

address: 1650 ORLEANS ST, CRB1

department: ONCOLOGY

institute: JOHNS HOPKINS UNIVERSITY

summary: Chronic stimulation with Acute Myeloid Leukemia can induce dysfunction in NK and CAR-NK cells. We evaluated transcriptomic differences on the day 10 of chronic antigen stimulation in NK cells secreting IL15 compared to non-secreting NK cells

overall_design:
Bulk RNAseq of  4 engineered NK cell conditions (2B4.ζ - 2B4.ζ.sIL15- sIL15-untransduced (UTD)) from 3 different donors

Contributor: SKCCC RNAseq core

first: Ilias

last: Christodoulou

last: Koldobskiy

first: Challice

last: Bonifant


title: Next Generation Sequncimg Facilitates Transcriptional Analysis of ∆mak-2, ∆mak-1 and Wild Type of Neurospora crassa

first: Xianyun

last: Sun

email: xysun3@163.com, sunxy@im.ac.cn

state: China

address: No.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: By analyzing genome-wide transcriptional responses to deletion of each of two MAP kinase coding genes mak-2 (PR-MAP kinase pathway) and mak-1 (CWI-MAP kinase pathway) in Neurospora crassa during protoperithecium formation, 430 genes co-regulated by MAK-1 and MAK-2 were found, functionally enriched at integral components of membrane and oxidoreductase.

overall_design: mRNA profiles of ∆mak-1, ∆mak-2 and wild type of Neurospora crassa at vegetative growth stage and the initial stage of protoperithecium formation.

last: Lan


title: Transcriptional profiling of a NAGA kinase (nag5) mutant in Yarrowia lipolyitica

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

summary: In the fungus Yarrowia lipolytica the transcription of the genes encoding the enzymes of the N-acetylgucosamine (NAGA) pathway (NAG genes) is regulated by the presence of NAGA in the culture medium. In a wild-type strain, those genes are expressed at a very low level during growth in glucose while their expression increases 20 to 40 fold in cultures grown in NAGA. However, a deletion of the gene YlNAG5, encoding the NAGA kinase, abolishes this regulation and renders the transcription of those genes independent of the presence of NAGA in the medium (Flores and Gancedo 2015). A possibility to explain this result is that the protein Nag5 is a moonlighting protein with two functions: one as a metabolic kinase, the other as a regulator implicated in the control of the expression of the genes of the NAGA catabolic pathway. An alternative explanation would be that the transcriptional deregulation of the NAG genes in the mutant is triggered by an intracellular NAGA accumulation derived from chitin turnover. Our objective in this work was to decide between these two possibilities. To this end we studied the regulation of the expression of the NAG genes in a double mutant Ylnag5 ngt1 that cannot internalize NAGA and in a Ylnag5 mutant expressing mutated versions of YlNag5 or heterologous NAGA kinases. Additionally, we performed RNA-seq experiments to monitor the effects of the Ylnag5 mutation on the expression of genes not related to the NAGA pathway.  Our results are consistent with the idea of NAGA kinase being a moonlighting protein with two roles, one as metabolic enzyme and other as regulatory protein in the transcription of some genes.

overall_design: Six samples are analyzed, corresponding to wild type (strain 660), a Ylnag5 deletant (strain 753) and the mutant strain carrying a plamid that harbors the YlNAG5 gene (886). Two biological replicas were made.

first: Joaquín

last: Ariño

first: Carmen-Lisset

last: Flores

last: Gancedo


title: Inflammatory molecular endotypes of nasal polyps derived from Caucasian and Japanese populations

city: Stanford

first: Tsuguhisa

last: Nakayama

state: CA

address: 801 Welch Road

department: Department of Otolaryngology-Head and Neck Surgery

institute: Stanford University

summary: Chronic rhinosinusitis with nasal polyps is a hallmaerk disease in the field of upper airway immunity and chronic inflammation. Diverse inflammatory patterns between nasal polyps have been described in patients that hail from disparate racial and geographic backgrounds. However, it remains unclear whether these immunologic differences in nasal polyps between racial groups are driven by unique molecular mechanisms. We interrogated the gene expression profiles of nasal polyp tissues from Western (United States) and East Asian (Japan) descent, compared to ethmoid sinus tissue controls.

overall_design: Examination of the key cell types that express critical molecular genes that differentiate between nasal polyp endtypes from 2 nasal polyp samples using droplet-based single-cell RNAseq.

first: Ivan

last: Lee

first: Sizun

last: Ziang

first: Jayakar

middle: V

last: Nayak


overall_design: Examination of the molecular differences between Caucasian (n=8), Asian CRSwNP (n=9), and contol (n=7) using whole-transcriptome RNA sequencing.


title: Methylation Array

city: Heidelberg

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

institute: German Cancer Research Center (DKFZ)

summary: Colorectal cancer tissues

overall_design: Tumor and corresponding normal tissue samples of colorectal cancer patients with different disease stages were compared alongside each other using the methylation 450K array

first: Nitin

last: Patil


title: Efffect of a high fructose diet on miRNA expression in vervet monkey livers

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: High-throughput profiling of miRNA expression in the livers of vervet monkeys fed a high fructose or chow diet. Analysis of differentially expressed miRNAs revealed miR-148a-3p, miR-181a-5p, miR-342-5p and miR-574-5p may have regulatory roles in coordinating changes in hepatic gene expression in response to a high fructose diet.

overall_design: miRNA profiles in the livers of 5 female vervet monkeys fed a high fructose diet and 5 female vervet monkeys fed a chow diet.

first: Laura

last: Cox


overall_design: Refer to individual Series


title: Blocking hyaluronan synthesis alleviates acute lung allograft rejection.

city: Syracuse

first: Auyon

last: Ghosh

address: 750 E Adams St

institute: SUNY Upstate Medical University

summary: Lung allograft rejection results in the accumulation of low molecular weight hyaluronic acid (LMW-HA), which further propagates inflammation and tissue injury. We have previously shown that therapeutic lymphangiogenesis in a murine model of lung allograft rejection reduced tissue LMW-HA and was associated with improved transplant outcomes.  Herein we investigated the use of 4-Methylumbelliferone (4-MU), a known inhibitor of HA synthesis, to alleviate acute allograft rejection in a murine model of lung transplantation. We found that treating mice with 4-MU from day 20-30 post-transplant was sufficient to significantly improve outcomes, characterized by a reduction in T-cell mediated lung inflammation, LMW-HA content and improved pathology scores. In vitro, 4-MU directly attenuated activation, proliferation, and differentiation of naïve CD4+ T-cells into Th1 cells. As 4-MU has already been demonstrated to be safe for human use, we believe examining 4-MU for the treatment of acute lung allograft rejection may be of clinical significance.

overall_design: Investigation of 4-methylumbelliferone use on murine naïve CD4+ T cell differentiation

first: Souheil

last: El-Chemaly

first: Jewel

last: Imani


title: Efffect of a high fructose diet on gene expression in vervet monkey livers.

summary: High-throughput profiling of gene expression in the livers of vervet monkeys fed a high fructose diet or chow diet. Analysis of differentially expressed genes revealed sirtuin signaling and a network of genes regulated by the peroxisome proliferator activated receptor alpha were significantly altered in response to the high fructose diet.

overall_design: Liver transcriptomes of 5 female vervet monkeys fed a high fructose diet and 5 female vervet monkeys fed a chow diet.


title: Gene expression profiles in mouse embryonic midbrain of Wnt1-lineage specific Gpr161 deletion.

city: Austin

first: Sung Eun

last: Kim

state: TX

address: 1400 Barbara Jordan Blvd

institute: The University of Texas at Austin

summary: To explore the differentially expressed genes in embryonic midbrain development in Wnt1-lineage specific Gpr161 deleted mouse embryos.

overall_design: Examination of mRNA profiles in embryonic midbrain tissues from E13.5 mouse embryos of each genotype (WT/Het/Homo)

first: Sung-Eun

first: Xuanye

last: Cao

first: Richard

last: Finnell


title: Conditionally Pathogenic Genetic Variants of a Hematopoietic Disease-Suppressing Enhancer

city: Madison

first: Emery

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

summary: Human genetic variants are classified based on potential pathogenicity to guide clinical decisions. However, mechanistic uncertainties often preclude definitive categorization. Germline coding and enhancer variants within the hematopoietic regulator GATA2 create a bone marrow failure and leukemia predisposition. The conserved murine enhancer promotes hematopoietic stem cell (HSC) genesis, and a single-nucleotide human variant in an Ets motif attenuates chemotherapy-induced hematopoietic regeneration. We describe “conditionally pathogenic” (CP) enhancer motif variants that differentially impact hematopoietic development and regeneration. The Ets motif variant functioned cell-autonomously in hematopoietic cells to disrupt hematopoiesis. Since an epigenetically-silenced normal allele can exacerbate phenotypes of a pathogenic heterozygous variant, we engineered a bone marrow failure model harboring the Ets motif variant and a severe enhancer mutation on the second allele. Despite normal developmental hematopoiesis, regeneration in response to chemotherapy, inflammation, and a therapeutic HSC mobilizer was compromised. The CP paradigm informs mechanisms underlying phenotypic plasticity and clinical genetics.

overall_design: 500-2000 LT-HSCs (Lin−Sca1+Kit+CD150+CD34-) were FACS isolated from total bone marrow from 8-16 week old WT and Gata2 CH animals.  CH animals contain a biallelic mutation of the Gata2 +9.5 enhancer.

first: Alexandra

last: Soukup

first: Peng

last: Liu


title: Single-cell Multi-omics Defines Tolerogenic Extrathymic Aire-Expressing Populations with Unique Homology to Thymic Epithelium

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Adaptive immunity requires multiple complementary mechanisms to maintain self-tolerance. Dedicated tolerogenic lymphoid populations and their key transcriptional regulators have been well characterized, but while recent evidence suggests some myeloid populations, particularly migratory dendritic cells (migDCs), may have similar functions, the identity of these populations and the transcriptional circuits regulating them remain obscure. The Autoimmune Regulator (Aire), well defined in medullary thymic epithelial cells (mTECs), is also expressed in extrathymic Aire-expressing cells (eTACs) in the secondary lymphoid organs. eTACs have been shown to have tolerogenic capabilities (ref), and recently work has shown them to be required for normal immune homeostasis in pregnancy (ref). But the precise identity and function of these cells remain unclear. Here using high-dimensional single-cell multiomics (scRNAseq/ASAPseq), we define the identity and biology of the principal extrathymic Aire-expressing populations at the transcriptional, genomic, and proteomic level, resulting in two related populations: CCR7+ Aire-regulated migratory dendritic cells (ArmDCs) and a novel population co-expressing RAR-related orphan receptor gamma-t (ROR-γt), with significant transcriptional and genomic homology to both migDCs and mTECs, which we termed Janus cells (JCs). We demonstrate these eTAC populations share a distinct transcriptional and genomic homology to medullary epithelium and, like mTECs, depend on RANK-RANK-ligand interactions to drive Aire expression. Lineage-tracing experiments suggest JCs are not a precursor population to the majority of ArmDCs. Further, self-antigen display by eTACs is sufficient to mediate negative selection of T cells that escape thymic selection. This remarkable central and peripheral homology suggests that a core Aire-associated transcriptional program may drive immune tolerance in both the thymus and periphery, and suggests a remarkable convergence of transcriptional programs in two disparate cell lineages in the thymus and periphery.

overall_design: A total of 3 WT and 6 Adig B6 mice were sacrificed. Lymph nodes were dissected and digested and pooled between the mice with the same genotype. Cells were then enriched via 1) magnetic depletion and 2) sorted as indicated for the GFP positive sample. For each pool of cells from the mice, both ASAP-seq and scRNA-seq were performed using the 10x Genomics chromium machine.

first: Jessica

last: Wang

first: Jay

last: Gardner


title: Modified forms of easyCLIP

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: The easyCLIP protocol describes a method for both normal CLIP library construction and the absolute quantification of RNA cross-linking rates, data which could be usefully combined to analyze RNA-protein interactions. Using these cross-linking metrics, significant interactions could be defined relative to a set of random non-RBPs. The original easyCLIP protocol did not use index reads, required custom sequencing primers, and did not have an easily reproducible analysis workflow. This short paper attempts to amend these deficiencies. It also includes some additional technical experiments and investigates the usage of alternative adapters. The results here are intended to allow more options to easily perform and analyze easyCLIP.

overall_design: Three replicates of HEK293T cells were UV cross-linked and endogenous RBFOX2 was purified with antibodies. easyCLIP libraries were created with a modified protocol. CLIP-seq sequencing was performed on a Novaseq, PE150, with ~35 M reads for each sample.

middle: F

first: Raghav

last: Garg

first: Weili

last: Miao

first: Robin

last: Meyers

first: Brian

last: Zarnegar

first: Luca

last: Ducoli

first: Paul

last: Khavari


title: Transcriptional dynamics of hepatic stellate cells during first hours of in vitro activation

city: Jette

first: Vincent

last: De Smet

state: Brussels

address: Laarbeeklaan, 103 D022

department: Liver Cell Biology Research Group

country: Belgium

institute: Vrije Universiteit Brussel

summary: Transcriptional alterations during the first hours of hepatic stellate cell activation were determined using RNA Sequencing. Cultured hepatic stellate cells were collected for RNA Sequencing at several timepoints during the first 24 hours. Illumina NovaSeq SP was used for sequencing.

overall_design:
Bulk RNA sequencing of cultured mouse hepatic stellate cells after following timepoints:
freshly isolated (n = 2)
3hours (n = 3)
6hours (n = 3)
12hours (n = 3)
18hours (n = 3)
24hours (n = 2)
96hours (n = 3)

first: V

first: S

last: Verhulst

first: L

last: van Grunsven


title: Single-cell RNA sequencing reveals dynamic process and novel markers in porcine spermatogenesis

city: Yangling

first: Lingkai

last: zhang

address: No. 3, Taicheng Road, Yangling District,  Xianyang 712100，Shaanxi Province，China.

institute: Northwest A&F University

summary: Purpose: To understand the overall transcriptional profile changes in porcine spermatogenesis.

overall_design: We firstly profiled single cell RNA-seq to shed light on transcriptional changes in spermatogenesis of porcine testis. The scRNA-seq analysis revealed spermatogonia, spermatocytes, spermatids and three somatic cell types in porcine testes. The functional enrichment analysis manifested these cell types played a diverse role in porcine spermatogenesis. The accuracy of the defined porcine germ cell types was further validated by comparing analysis of data from bulk RNA-seq and scRNA-seq. Four subsets of spermatogonia were revealed and two novel cell surface markers were identified, which would be helpful to characterize spermatogonial differentiation in pigs, probably also in the other farm animals.

first: Wenxian

last: Zeng

last: Zhang


title: Candidate genes and pathways involved in TTK-induced biological functions in ovarian carcinoma

city: jinan

first: Gonghua

last: Qi

state: State...

address: 107 wenhua xi road

department: Department of Obstetrics and Gynecology

institute: shandong university

summary: TTK has been shown to participate in the tumorigenesis of several cancer types but little is known about the function and molecular signalling in ovarian cancer cells. In this study we aim to identify the underlying mechanisms involved in TTK-induced biological functions in the human ovarian cancer cells.

overall_design: Next-generation sequencing (NGS) were performed on 6 samples of A2780 cells, including 3 samples transfected with negative control (NC) and 3 samples transfected with TTK specific siRNA (siTTK) for 48 h.

first: Hanlin

last: Ma

first: Yingwei

last: Li

first: Jiali

last: Peng

first: Jingying

last: Chen

first: Beihua

last: Kong


title: Transcriptional dynamics of hepatic stellate cells in experimental acute liver injury, liver fibrosis and liver fibrosis reversal.

summary: Transcriptional alterations during different stages of hepatic stellate cell activation were determined using RNA Sequencing. Models include acute liver injury (1 injection of CCl4) and chronic liver injury (8 injections of CCl4 over 4-week period) with different recovery timepoints. Illumina NextSeq 500 High was used for sequencing.

overall_design: Bulk RNA sequencing of isolated mouse hepatic stellate cells after following injury:  4wk CCl4 (8 injections) + 24h (n = 4)  4wk CCl4 (8 injections) + 72h (n = 4)  4wk CCl4 (8 injections) + 14days (n = 4)  1 injection CCl4 + 24h (n = 3)  1 injection CCl4 + 72h (n = 4)  1 injection CCl4 + 7days (n = 4)  healthy (non-injected) (n = 4)


title: Transcriptomic expression profiling of blood stages of Plasmodium berghei of wild-type and ΔHspJ62 line.

city: New Delhi

first: Agam

middle: Prasad

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

summary: The transmission of the malaria parasite between mosquitoes and mammals requires translational repression to ensure that only the proper proteins are expressed and correct folded at the right time, it will need for the next developmental stage.Due to their essential role for malaria transmission, gametocytes represent prime targets for transmission-blocking strategies intended to prevent spread of the deadly disease. In this study, we generate HspJ62 gene knockout line (ΔHspJ62) that is gametocyte non-producing lines. Transcriptional profiling of wild type Plasmodium berghei and genetic KO Hspj62 genes at single time points during erythrocytic parasite development.

overall_design: We performed Next Generation sequencing to compare transcriptome profiles of wild-type and ΔHspJ62 of blood stages of Plasmodium berghei

first: Mohammad

last: Kashif


title: A genetic program boosts mitochondrial function to power macrophage tissue invasion (RNA-seq/Polysome-seq, S2 cells)

city: Klosterneuburg

first: Daria

last: Siekhaus

address: Am Campus 1

department: Bertalanffy Building

country: Austria

institute: IST Austria

summary: Metabolic adaptation to changing demands underlies homeostasis. During inflammation or metastasis, cells leading migration into challenging environments require an energy boost, however what controls this capacity is unknown. We identify a previously unstudied nuclear protein, Atossa, as changing metabolism in Drosophila melanogaster immune cells to promote tissue invasion. Atossa's vertebrate orthologs, FAM214A-B can fully substitute for Atossa, indicating functional conservation from flies to mammals. Atossa increases mRNA levels of Porthos, an unstudied RNA helicase and two metabolic enzymes, LKR/SDH and GR/HPR. Porthos increases translation of a gene subset, including those affecting mitochondrial functions, the electron transport chain, and metabolism. Respiration measurements and metabolomics indicate that Atossa and Porthos power up mitochondrial oxidative phosphorylation to produce sufficient energy for pioneer macrophages to forge a path into tissues. As increasing oxidative phosphorylation enables many crucial physiological responses, this unique genetic program may modulate a wide range of cellular behaviors beyond migration.

overall_design: Input and Polysome mRNA content from Control, GFP dsRNA treated S2 cells and Porthos (CG9253) dsRNA

first: Shamsi

last: Emtenani

first: Elliot

middle: T

last: Martin

first: Attila

last: Gyoergy

first: Julia

last: Bicher

first: Jakob-Wendelin

last: Genger

first: Thomas

middle: R

last: Hurd

last: Köcher

first: Andreas

last: Bergthaler

first: Prashanth

last: Rangan


title: A genetic program boosts mitochondrial function to power macrophage tissue invasion (RNA-seq, sorted macrophages)

overall_design: mRNA profiling and differential expression analysis of FACS-sorted Wild Type and CG9005 mutant macrophages from Drosophila melanogaster embryos from stage 11.


title: Maternal benzophenone exposure impairs hippocampus development and cognitive function in mouse offspring

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

summary: To gain the new insights into the signaling pathways perturbed by 4-Hydroxybenzoic acid (4HBP) exposure in neural stem cells, we performed RNA-seq analysis in Hippocampus-derived primary NSCs. The NSCs were cultured under two conditions: proliferation and differentiation. In each condition, the cells were treated by 1μM 4HBP for 7 days as the treatment group and treated by EtOH (vehicle) as the control group.

overall_design: Gene expression profiles of 1) three replicates of NSC samples cultured in proliferation medium and treated by 1μM 4-Hydroxybenzoic acid for 7 days; 2) three replicates of NSC samples cultured in proliferation medium and treated by EtOH for 7 days; 3) three replicates of NSC samples cultured in differentiation medium and treated by 1μM 4-Hydroxybenzoic acid for 7 days; 2) two replicates of NSC samples cultured in differentiation medium and treated by EtOH for 7 days.

first: Xia

last: Sheng

first: Fengzhen

last: Cui