title: Paired-end RNA Sequencing on human dermal microvascular endothelial cells (HMEC-1) infected or not with Borrelia burgdorferi (MOI= 200 bacteria/cell) examined at different times post-infection (namely 4, 24 or 48 h post-infection)

city: Seattle

first: Effie

middle: Efthimia

last: Bastounis

state: WA

address: UW Biology Life Sciences Bldg, Room 565, 4000 15th Ave NE

department: Biology

institute: University of Washington

summary:
Purpose: When we infect human dermal microvascular endothelial cells (HMEC-1) infected or not with Borrelia burgdorferi (MOI= 200 bacteria/cell) and examine the host cell kinematics and dynamics over the course of 3 days post-infection we observe a change in those at early times post-infection, but at late times (> 20 h post-infection) cells from infected or not wells behave similarly. To get a sense of the biochemical signals that might be driving the changes in host cell mechanics, we performed RNA-Sequencing and gene expression profiling for uninfected HMEC-1 cells or cells infected for 4, 24 or 48 h with Borrelia burgdorferi at an MOI of 200 bacteria/cell.
Methods and Results: By analyzing the differentially expressed genes between all conditions we find a significant number of up- or down-regulated genes infected and uninfected cells just at 4 h post-infection. Through pathway enrichemnet analysis we find that compared to cells not exposed to infection infected cells showed significant upregulation to genes related IL-17 and NF-kB and TNF related signaling pathways. Interestingly these changes are not present at 24 or 48 h post-infection where cells from infected wells are more similar gene expression-wise to uninfected cells.
Conclusions: The changes in kinematics and dynamics of HMEC-1 cells exposed to Borrelia burgdorferi (MOI= 200 bacteria/cell) at early times post-infection are associated with changes in innate immune signaing of the host cells. At later times post-infection were these changes in gene expression are not present anymore, host cell kinematics and dynamics are identical between infected and uninfected cells. Thus it is possible that innate immune singaling might be underlying the changes that host cells undergo in their motion and traction forces at early infection.

overall_design:
Endothelial HMEC-1 cell mRNA profiles of cells previously residing in confluency on glass substrates coated with 0.25 mg/mL collagen I and being (1) uninfected; or (2) infected with Borrelia burgdorferi (MOI=200) for different amounts of time (4, 24 or 48 h)  were generated in quadruplicate, using Illumina NovaSeq 6000 using the NovaSeq 6000 S4 Reagent Kit (300 cycles). Equipment: Illumina with 2x150 read length and 40 million reads per sample.
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Reasearch funded by Lyme disease association (LDA) research grant award, for the research proposal "Biomechanical alterations of endothelial cells infected with Borrelia burgdorferi".

middle: E


title: New prognostic factor identification by screening changes in differentially expressed genes during oral squamous cell carcinoma progression

status: Public on May 18 2021

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

type: Expression profiling by high throughput sequencing

summary: Identification of differentially expressed genes in human oral squamous cell carcinoma cell line UPCI-SCC-040 after TGF-ß1 treatment compared to untreated controls

overall_design: Differentely expressed genes after treatment

first: Boris

last: Schminke

first: Orr

last: Shomroni

last: Salinas-Riester

first: Felix

last: Bremmer

first: Philipp

last: Kauffmann

first: Henning

last: Schliephake

first: Michal

middle: A

last: Rahat

first: Phillipp

last: Brockmeyer


title: Proximal tubular transcriptional response to aristolochic acid

city: Stony Brook

first: Sandeep

last: Mallipattu

state: NY

address: 101 Nicolls Road

department: Department of Medicine

country: USA

institute: Stony Brook University

summary: The proximal tubule is particularly susceptible to acute kidney injury caused by ischemic or toxic insults, due to its high oxygen demand, and role in excreting drugs such as DNA-damaging chemotherapeutics. AKI triggers PT cell de-differentiation, expression or pro-inflammatory and pro-fibrotic signaling molecules, and a dramatic shift in PT cell metabolism with severe suppression of fatty acid oxidation. The aim of this study was to investigate the transcriptional changes that occur in the S2 and S3 segments of the PT in response to the DNA damaging agent aristolochic acid I (AAI).

overall_design: mRNA profiles were generated from combined S2/S3 kidney proximal tubules segments in control mice harvested 24 hours after injecting a single 3mg/kg dose of DMSO or AAI, using RNA-sequencing.

first: Sian

last: Piret

middle: K


title: Loss of proximal tubular Kruppel-like factor 6 (KLF6) is protective against AKI and CKD

summary: Altered cellular metabolism in kidney proximal tubule (PT) cells plays a critical role in the development and progression of acute kidney injury (AKI). The transcription factor Krüppel-like factor 6 (KLF6) is rapidly and robustly induced in the PT after AKI, suggesting an early-inducible injury response gene. PT-specific Klf6 knockdown (Klf6PTKO) are protected from AKI and resulting fibrosis in mice. Combined RNA-sequencing and ChIP-sequencing demonstrated preserved expression of genes encoding branched chain amino acid (BCAA) catabolic enzymes in Klf6PTKO mice, with several of the genes also having KLF6 binding sites close to their transcription start sites. Conversely, inducible KLF6 overexpression suppressed expression of BCAA genes and exacerbated kidney injury and fibrosis in mice. Injured kidney cells could not respond to the BCAA catabolic activator BT2, and injured cells overexpressing KLF6 were less able to utilize BCAA. Thus, targeting KLF6-mediated suppression of BCAA catabolism may serve as key therapeutic target in AKI and kidney fibrosis.

overall_design: Kidney cortex mRNA profiles were generated in Klf6fl/fl and Klf6PTKO mice treated with DMSO or AAI for 3 weeks or AAI for 3 weeks followed by 3 weeks remodeling time, using RNA-sequencing.


title: Single cell RNA sequencing of mouse donor T cells after graft-versus-host disease (GVHD) model

city: Tsukuba

first: Akira

last: Shibuya

state: Ibaraki

address: 1-1-1 Tennodai

department: Immunology

country: Japan

institute: University of Tsukuba

summary: Lethally irradiated mice were transferred with bone marrow cells together with allogeneic Treg cells isolated from CD226+/+ TIGIT+/+, CD226-/- TIGIT+/+, CD226+/+ TIGIT-/-, or CD226-/- TIGIT-/- mice, followed by allogeneic wild-type Tconv cells two days later to induce acute GVHD. We performed scRNA sequencing of donor T cells isolated from the spleen of recipient mice eight days after GVHD induction.

overall_design: Mice on the BALB/c background were transferred after lethal irradiation with T cell-depleted bone marrow cells derived from wild-type C57BL/6 mice together with Treg cells (CD4+ Foxp3-GFP+ CD25hi) isolated from the spleen of CD226+/+ TIGIT+/+, CD226-/- TIGIT+/+, CD226+/+ TIGIT-/-, or CD226-/- TIGIT-/- mice on the C57BL/6 background, followed by Treg cell-depleted Tconv cells derived from wild-type C57BL/6 mice two days later to induce acute GVHD. PI- H-2Kb+ TCRb+ donor T cells isolated from the spleen of recipient mice eight days after GVHD induction. Three donor T cells were pooled per each sample. To distinguish between Tconv and Treg cells, the sorted donor T cells were re-stained with barcode sequence-conjugated anti-mouse CD45.1 and CD45.2 antibodies. The viability of all samples were more than 85%. Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics, PN-1000092), the Chromium Single Cell B Chip Kit (10X Genomics, PN-1000074), and the TotalSeq™-A Antibodies with 10x Single Cell 3' Reagent Kit v3 (BioLegend) as per the manufacturer’s protocol. The sequencing of libraries was performed at Macrogen Japan (Kyoto, Japan) using an Illumina HiSeq X. Processed files were generated from Cell Ranger (10X Genomics) pipeline.

first: Kazumasa

last: Kanemaru

first: Kazuki

last: Sato

first: Fumie

last: Abe

first: Kazuko


title: Aire+ Cell Depletioin Results in Expansion of Activated T Cells in Pregnant Mice

city: San Francisco

first: Tippi

last: MacKenzie

state: California

address: 550 16th Street

department: Surgery, Pediatrics, Center for Maternal-Fetal Precision Medicine

institute: University of California, San Francisco

summary: We explored the role of the autoimmune regulator (Aire) gene in supporting fetal tolerance during pregnancy with transgenic diphtheria toxin receptor (Aire-DTR) mice, in which Aire-expressing populations can be deleted by injection of diptheria toxins (DT).  Aire-expressing cell depletion was found to cause intruterine growth restriction (IUGR) in both allogenic and syngeneic pregnancies. This phenotype is immune-mediated, as IUGR is rescued in Rag1-deficient mice, and involves a memory response, as demonstrated by severe IUGR in second pregnancies. We further explored this phenotype through single-cell RNA sequencing of leukocytes obtained from the secondary lymphoid organs (uterine and non-uterine-draining lymph nodes) of wild-type (WT) and Aire-DTR pregnant dams during allogeneic pregnancy. Transciptomic data reveals a shift in population distributions from naïve to effector CD4+ and CD8+ T cells in Aire-DTR mice. Within the effector CD4+ compartment, there was a significant shift away from Tregs and toward mature T effectors, most notably T follicular helper (Tfh) and Th17 cells. These findings support the idea that Aire is essential in maintaining immune homeostasis.

overall_design: Seven Aire-DTR or WT dams were bred to BALB/c males and given DT for the first 9 days of pregnancy. Uteruses, uterine-draining lymph nodes (udLN) and brachial lymph nodes (brLN) from each mouse were harvested at E9.5 and subjected to Percoll gradient. Isolated cells from these tissues were stained for CD45, and CD3, and sorted to keep live, single CD45+ cells. Cells from multiple mice and tissues were multiplexed into single sequencing runs by hash-tagging cells with totalseq-C anti-mouse hashtags. Three cell pools were created: (i) Pool 1 (ii) Pool 2, and (iii) Pool LN. Pool 1 and Pool 2 consisted of cells isolated from uterus, udLN and brLN tissues from one Aire-DTR and one WT mouse each. In each pool, 160,000 cells were split into two wells for sequencing.. Pool LN consisted of cells isolated from udLN and brLN tissues from two Aire-DTR mice and one WT mouse. 13,200 cells from Pool LN were split into two wells for sequencing. Gene expression profiles from all batches were analyzed together after demultiplexing.

first: Eva-Gillis

last: Buck

first: Haleigh

last: Miller

first: Vasilis

last: Ntranos


title: Astrocytes and neurons share brain region-specific transcriptional signatures

city: San Juan de Alicante

first: Guillermina

last: López-Bendito

state: Alicante

address: Av Ramon y Cajal s/n, Campus de San Juan

department: Instituto Neurociencias CSIC-UMH

country: Spain

institute: Universidad Miguel Hernández (UMH)

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

overall_design: Refer to individual Series


title: Astrocytes and neurons share brain region-specific transcriptional signatures (RNAseq: NeuronsP0)

summary: Neuronal cell diversity is essential to endow distinct brain regions with specific functions. During development, progenitors within these regions are characterised by specific gene expression programs, contributing to the generation of diversity in postmitotic neurons and glia. While the region-specific molecular diversity of neurons and astrocytes is increasingly understood, whether these cells share region-specific programs remains unknown. Here, we show that in the neocortex and thalamus, neurons and astrocytes express shared region-specific transcriptional and epigenetic signatures. These signatures not only distinguish cells across brain regions but are also detected across substructures within regions, such as distinct thalamic nuclei, where clonal analysis reveals the existence of common nucleus-specific progenitors for neurons and glia. Consistent with their shared molecular signature, regional specificity is maintained following astrocyte-to-neuron reprogramming. A detailed understanding of these regional-specific signatures may thus inform strategies for future cell-based brain repair.

overall_design: Thalamic neurons were isolated by FACS based on fluorescence intensity of dual genetic labelling by Gbx2CreER-IRES-EGFP/+::R26lsl-tdTomato/+. Transcriptomic analysis was made on total RNA from 3 different populations of Thalamic nuclei (dorsolateral Geniculate Nucleus (dLGN), Medial Geniculate Nucleus, ventral division (MGv) and Ventral Posteriomedial Nucleus(VPM) at Post-natal day 0 (P0). In overall, 11 samples replicates were analyzed from thalamic primary sensory nuclei (4 from dLGN, 3 from MGV and 4 from VPM).

first: Lorenzo

last: Puche-Aroca

first: Álvaro

last: Herrero-Navarro

first: Jose

middle: P

last: López-Atalaya


title: Astrocytes and neurons share brain region-specific transcriptional signatures (RNAseq: Astrocytes)

overall_design:
Astrocytes from 2 different tissues (Cortex and Thalamus) were isolated by FACS based on fluorescence intensity of genetic labelling Gfap::Gfp.
Transcriptomic analysis was made on total RNA from 3 different populations of thalamic primary sensory nuclei (dorsolateral Geniculate Nucleus (dLG), Medial Geniculate Nucleus, ventral division (MGv) and Ventral Posteriomedial Nucleus(VPM)) and somatosensory cortex (S1) at Post-natal day 7 (P7). In overall, 4 samples replicates were analyzed from S1 and 13 samples from thalamic nuclei (5 from dLGN, 4 from MGV and 4 from VPM).


title: Genome-wide analysis of long noncoding RNAs and mRNAs associated with contrast-induced acute kidney injury

city: Fuzhou

first: Zhiqing

last: Wang

state: Fujian

address: NO. 156, North Xierhuan Road

department: Department of Cardiology

country: China

institute: 900 Hospital of the Joint Logistics Team

summary:
Purpose:little is known about the roles of lncRNA in the pathogenesis of contrast-induced acute kidney injury (CI-AKI). Here, we compared the expression profiles of lncRNAs and mRNAs in kidney tissue between CI-AKI rats and controls.
Methods:Based on a reliable CI-AKI rat model, we sought to investigate the roles of lncRNA in the kidney injury following intra-arterial contrast exposure by RNA sequencing.
Results: We identified 88 differentially expressed known and novel lncRNAs at 12 hours following intra-arterial iodinated contrast medium injection. Functional enrichment analysis implied that these lncRNAs were potentially associated with oxidative stress and DNA damage response.
Conclusions:These prefound findings provide the first evidence of lncRNA in the development of CI-AKI.

overall_design: Three-month-old male Sprague-Dawley rats were used in this study. Kidney lncRNA profiles of CI-AKI rats and controls were generated by deep sequencing.

first: Mingfang

last: Huang

first: Weiwei

last: Bao


title: Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

country: United Kingdom

institute: University of Bath

summary: The identification of high-resolution chromatin interactions with the Paupar and Pax6 promoters and the comparison of these profiles between different mouse cell types.

overall_design: Examination of three viewpoints (Paupar, Pax6P0 and Pax6P1 promoter) in 4 different mouse cell types (N2a cell line, mouse embryonic stem cells, neuronal stem cells, differentiated cortical neurons)

first: Ioanna

last: Pavlaki

first: Michael

last: Shapiro

first: Robert

middle: J

last: Williams

first: Silvia

last: Muñoz Descalzo

first: Jim

middle: R

last: Hughes

first: Jelena

last: Telenius

first: Giuseppina

last: Pisignano

middle: W


title: Modulation of medaka transcriptome by trametinib and cisplatin

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary: We employed a transgenic strain of a small aquarium fish medaka (Oryzias latipes) that overexpresses a malignant melanoma driver gene. In this model, melanoma develops with 100 % penetrance. Using the medaka malignant melanoma model, we tested whether cisplatin and trametinib are able to suppress the transcriptomic changes induced by the transgene.

overall_design: Wild type, or transgenic medaka (3-4 weeks old, 10±1mm long) were treated with 70uM Cisplatin, 20nM Trametinib, Saline,  DMSO, or not treated. Five days after drug or solvent treatment, total RNA was isolated from whole fish. RNA-Seq was performed on sequencing libraries constructed from poly-A RNA.

first: Barbara

last: Klotz

first: Susanne

last: Kneitz

first: William

last: Boswell

first: Manfred

last: Schartl

first: Ronald

last: Walter

first: Wesley

last: Warren

first: John

last: Postlethwait


title: Single cells from adipose and liver

status: Public on May 17 2021

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main St

institute: The Broad Institute of MIT and Harvard

summary: We isolated single cells (using either liberase or collagenase A  dissociation) from subcutaneous adipose tissue collected from abdominoplasty surgery, and healthy liver tissue adjacent to tumor from liver resection and ran 10X v2 3' scRNA Seq. We ran 3 channels for adipose (IRB   2007P002165/1(ORSP-3877)) and 4 channels for liver (IRB 02-240; ORSP 1702 and ORSP-2630 under ORSP-2169). Channels were merged and uploaded here.  *Raw data files absent*

overall_design:
We isolated nuclei from autopsy derived tissue () and ran 5 10X v2 3' channels for adpipose tissue and 4 channels for nuclei from liver tissue.
*Raw data files absent*


title: CREBBP/EP300 bromodomain inhibition affects the proliferation of AR positive breast cancer cell lines

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

institute: ISCIII

summary: Changes in gene expression caused by CREBBP/EP300 bromodomain inhibitors  in breast cancer cell lines

overall_design: MDA-MB-231, SKBR3 and MDA-MB-453 cells were treated with JQ1 and CBP30 and changes in gene expression evaluated by RNA-seq

first: Veronica

last: Garcia-Carpizo


title: Gene and miRNA expression in radioiodine refractory and avid papillary thyroid carcinomas (miRNA expresseion dataset)

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: We performed gene and miRNA expression profiling in a series of 39 papillary thyroid carcinomas (PTCs) and 13 matched non-neoplastic thyroids derived from PTC patients with metastatic disease and submitted to radioiodine (RAI) treatment.

overall_design: Gene and miRNA expression profiles were established by microarray analysis in a retrospective series of 52 snap-frozen thyroid samples including 35 tissues collected before RAI treatment (17 primary PTC tumors, 5 synchronous lymph node metastases (LNMs), and 13 matched non-neoplastic thyroids included as control) and 17 RAI-refractory LNMs collected as successive surgery following RAI treatment. Patients were stratified based on RAI uptake at the metastatic site and on RAI response in either avid or refractory, displaying disease remission or persistance, respectively, after RAI treatment. Gene profiles were established by Thermo Fisher Human Clariom S Assay, and the corresponding miRNA profiles were established by Agilent SurePrint Human miRNA microarrays. Tumor samples were also characterized for the most common driving mutations and gene fusions typical of PTC by a PTC-Mass Array platform (PTC-MA).

first: C

last: Colombo

first: L

last: Fugazzola

first: E

last: Minna

first: M

middle: G

last: Borrello

last: De Cecco


title: Oocyte piRNAs mediate intergenerational transmission of an acquired metabolic disorder (small RNA sequencing)

city: Shanghai

first: Yanchang Wei

last: Wei

address: #845 Lingshan Rd., Pudong New District, Shanghai 200135, China

institute: Shanghai Jiao Tong University

type: Non-coding RNA profiling by high throughput sequencing

summary: Traditional research has focused on DNA as the molecule that carries heritable information from the parent to the offspring. However, increasing evidence suggests that information beyond the DNA sequence, termed epigenetic information, can also transmit certain information from one generation to the next. Whereas paternal epigenetic germline inheritance has been well elucidated, as the father contributes little more than a sperm cell to the offspring, maternal epigenetic inheritance via gametes remains largely unclear. Here, using an in vitro fertilization system and a micromanipulation strategy, we demonstrate that oocyte piRNAs mediate intergenerational transmission of an acquired metabolic disorder. Changes in the expression profiles of many oocyte piRNAs are observed in a maternal chronic high-fat diet (HFD) mouse model. Injection of the oocyte piRNAs from HFD females into normal zygotes resulted in impaired glucose tolerance and decreased insulin sensitivity in the F1 offspring. A series of genes involved in glucose metabolism and the insulin signaling pathway were differentially expressed in the pancreatic islets of the F1 offspring. Bisulfite genome sequencing of the islets of the F1 offspring revealed changes in cytosine methylation that correlated with the observed gene expression patterns. These data identified oocyte piRNAs as novel carriers of epigenetic information and highlight the importance of long-term maternal health before conception.

overall_design: Examination of the effect of maternal high-fat diet on the oocyte small-RNA expression profiles.

first: Yanchang


title: RNA-seq analysis of HeLa METTL5-KO cells compared to WT HeLa cells

city: New Haven

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

summary: To identify transcripts upregulated and downregulated upon METTL5 knockout in HeLa cells.

overall_design: Comparing RNA isolated from input samples to RNA isolated from a FLAG immunoprecipitation of FLAG-METTL5 overexpressed in HeLa cells.

first: Caraline

last: Sepich-Poore

first: Chuan

last: He


title: Cooperative JAK-STAT/MAP-kinase/MYC deregulation in Plasmablastic Lymphoma

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

institute: IDIBAPS

summary: Plasmablastic lymphoma is an aggressive B-cell lymphoma with an immunoblastic/large cell morphology anda plasmacytic differentiation. The differential diagnosis with Burkitt lymphoma, plasma cell myeloma and some variants of diffuse large B-cell lymphoma may be challenging due to the overlapping morphological, genetic and immunophenotypic features. Furthermore, the profile of chromosomal alterations is not well known.

overall_design: The aim of this study was to perform a complete genetic characterization of PBL. Thirty-four cases were analyzed byFISH, copy number array and targeted next-generation sequencing of 94 B-cell lymphoma related genes.

last: Ramis-Zaldivar

first: Itziar

last: Salaverria

first: Elias

last: Campo


title: Comparison of transcriptomic profiles of Pseudomonas protegens H78 and its hfq mutant (H78Δhfq)

first: Xianqing

last: Huang

address: DongChuan RD, Minhang District

department: School of Life Sciences and Biotechnology

summary: Transcriptomic profiles of  Pseudomonas protegens H78 and its hfq mutant, which were grown to the late exponential phase (OD600 = 5.0 to 6.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on Illumina HiSeq 2500.

overall_design: Two bacterial strains, Pseudomonas protegens H78 wild type strain and its hfq mutant strain, each was replicated three times.


title: The microRNA landscape of MYCN-amplified neuroblastoma

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

summary: Neuroblastoma is a common childhood cancer with almost a third of those affected still dying, thus new therapeutic strategies need to be explored. Current experimental therapies focus mostly on inhibiting oncogenic transcription factor signalling. Dysregulation of miRNAs has oncogenic or suppressive tumor functions in a variety of cancer, also including neuroblastoma. Therefore, we investigated the miRNA landscape in 97 neuroblastoma samples from different INSS stages, including MYCN-amplified (MNA) tumor samples.

overall_design: Small RNA-sequencing (miRNA) of neuroblastoma samples.

first: Sven

last: Hagemann

first: Jessica

middle: L

last: Bell

first: Bianca

last: Busch

first: Marcell

middle: I

last: Lederer

first: Nadine

last: Bley

first: Johannes

middle: H

last: Schulte

first: Stefan

last: Hüttelmaier


title: IFNg Signature in Plasma Proteome Distinguishes Pediatric Hemophagocytic Lymphohistiocytosis from Sepsis and SIRS

status: Public on May 16 2021

city: Houston

first: Carl

last: Allen

state: Texas

address: 1102 Bates Street, Suite 750

institute: Texas Children's Hospital

summary:
Expression data from CD8+ T cells and CD68+ monocytes from patients with hemophagocytic lymphohistiocytosis, sepsis, and persistent systemic inflammatory response syndrome
Hemophagocytic lymphohistiocytosis (HLH) is a syndrome characterized by pathologic immune activation in which prompt recognition and initiation of immune suppression is essential for survival. Children with HLH have many overlapping clinical features with critically ill children with sepsis and persistent systemic inflammatory response syndrome (SIRS) in whom alternative therapies are indicated. To determine if plasma biomarkers could differentiate HLH from other inflammatory conditions and to better define a ‘core inflammatory signature’ of HLH, concentrations of inflammatory plasma proteins were compared in 40 patients with HLH to 47 pediatric patients with severe sepsis or SIRS.  Seventeen of 135 analytes were significantly different in HLH plasma compared to SIRS/sepsis, including increased interferon-gamma (IFNg)-regulated chemokines CXCL9, CXCL10 and CXCL11. Further, a 5-analyte plasma protein classifier including these chemokines was able to differentiate HLH from SIRS/sepsis. Gene expression in CD8+ T cells and CD68+ monocytes from blood were also enriched for IFNg pathway signatures in peripheral blood cells from patients with HLH compared to SIRS/sepsis. This study identifies differential expression of inflammatory proteins as a diagnostic strategy to identify critically ill children with HLH. Further, comprehensive unbiased analysis of inflammatory plasma proteins and global gene expression demonstrates that IFNg signaling is uniquely elevated in HLH.  In addition to demonstrating the ability of diagnostic criteria for HLH, sepsis and SIRS to identify groups with distinct inflammatory patterns, results from this study support the potential for prospective evaluation of inflammatory biomarkers to aid in diagnosis of and optimizing therapeutic strategies for children with distinctive hyperinflammatory syndromes.

overall_design: 42 samples: CD8+ T cell subpopulation cohort consisting of 12 samples with HLH and 10 with severe sepsis. CD68+ monocyte subpopulation cohort consisting of 12 samples with HLH and 8 with severe sepsis.

first: Howard

last: Lin

first: Brooks

last: Scull

first: Trung

last: Nguyen

first: Tsz-Kwong

last: Man


title: snRNA-seq of Beiging Inguinal Adipose Tissue from UCP1-KO and WT mice under cold-stress and mice treated with Beta-Blocker and mild cold exposure.

city: Bronx

first: Kosaku

last: Shinoda

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Atlas of UCP1-KO Beiging inguinal adipose tissue and tissue in which beta adrenergic signaling is blocked provides further insight into UCP1-independent mechanisms of beiging.

overall_design: Ucp1-KO mice and WT littermate controls: 1 wk cold exposure. Beta-Blocker and Saline mice: 5 days RT follwed by 5 day mild cold exposure, injections each day.

first: Gabrielle

last: Benitez


title: Transcript profiling in peritoneal macrophages from wildtype, Fra-1ΔMxCre or Fra-2ΔLysMCre mice

city: Erlangen

first: Aline

last: Bozec

address: Ulmenweg 18

institute: Universitätsklinikum Erlangen, Department of Internal Medicine 3 – Rheumatology and Immunology

summary: The polarization and activation of macrophages are controlled synergistically by transcription factors such as NF-κB and AP-1 transcription factor members. Surprisingly, little is known about the role of the Fra proteins, both members of the AP-1 transcription factor family, in macrophage activity. To determine the full profile of Fra network, microarray RNA expression analysis using Agilent Technologies platform was performed in wild-type, Fra-1ΔMxCre or Fra-2ΔLysMCre macrophages.

overall_design: For microarray analyses, peritoneal macrophages were collected by peritoneal lavage of 8 week old wild-type (n=4), Fra-1ΔMxCre (n=2) or Fra-2ΔLysMCre (n=2) mice. Peritoneal cells were plated over night. The next day, suspension cells were removed and only adherent cells were used for RNA isolation.

first: Nicole

last: Hannemann

first: Stephen

last: Reid

first: Sophia

last: Sonnewald


title: scATAC-seq of Inguinal Adipose Tissue of UCP1-KO and WT mice.

status: Public on May 15 2021

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Single cell level analysis of transcriptional circuits regulating UCP1-indepednent theremogensis through Lgr6 in inguinal Adipose tissue.  We previously identified an increase in Lgr6 gene expression in the beige adipocyte population of UCP1-KO mice and hypothesized its involvement in UCP1-independent thermogensis.   Consistent with our previous data the scATAC-seq  data reveals that chromatin accessibility at the Lgr6 loci is significantly higher in Ucp1- KO beige adipocytes as compared to WT and the promter is also more accessible in Ucp1- KO beige  adipocytes. Other DNA-binding motifs involved in UCP-1 indepedent thermogensis were also analyzed and found to be upregulated in the KO model.

overall_design: Comaparison of  UCP1-KO and WT mice under cold exposure.

first: Li

last: Liu


title: Comparison of transcriptomic profiles of Pseudomonas protegens H78 and its crc-deleted mutant (H78Δcrc)

first: Xianqing

last: Huang

summary: Transcriptomic profiles of  Pseudomonas protegens H78 and its crc-deleted mutant (H78Δcrc), which were grown to the late exponential phase (OD600 = 5.0 to 6.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on Illumina HiSeq 2500.

overall_design: Two bacterial strains, Pseudomonas protegens H78 wild type strain and its crc-deleted mutant strain (H78Δcrc), each was replicated three times.


title: A cascade for zinc mediated transcriptional activation by the zinc-sensing nuclear receptor HIZR-1 on the regulator of lysosome biogenesis HLH-30 to achieve homeostasis

city: Saint Louis

first: Ciro

last: Cubillas Ramirez

state: Missouri

address: 4577 McKinley, Campus Box 8103, 3607 Cancer Research Building

department: Developmental Biology

institute: Washington University in St Louis, School of Medicine

summary: Zinc is an essential element for animals and stored in de novo synthesized lysosome related organelles called bilobed granules in Caenorhabditis elegans. Defining how zinc regulated transcription drives the observed lysosome remodeling is key to understand zinc homeostasis processes. Here we describe a positively regulated zinc network controlled by HIZR-1 and HLH-30, the zinc sensor and the master regulator of the autophagy-lysosomal pathway in Caenorhabditis elegans, respectively; essential for connecting zinc homeostasis to lysosome biogenesis. Our studies indicate that either hizr-1 and hlh-30 are necessary and sufficient to activate transcription of lysosome-genes under high dietary zinc conditions. Consistent with the hizr-1 and hlh-30 dependency for high zinc response, we found DNA enhancer elements corresponding to the high zinc activation element consistently adjacent to E-boxes in the promoter regions of lysosome-genes. We defined a regulatory network based on the contribution of each transcription factor. Since zinc cannot be degraded, the autophagy-lysosomal pathway could play a key role in removing zinc excess

overall_design: Two Caenorhabditis elegans strains, wild type and a hizr-1 loss-of-function mutant were independtly exposed to high dietary zinc conditions and compared to a non-supplemented zinc condition. Two biological samples each strain and each condition were used.

last: Cubillas

first: Adelita

middle: D

last: Mendoza

first: Daniel

last: Schneider

first: John

last: Murphy

last: Herrera

last: Edwards

first: Clifford

last: Luke

last: Pak

first: Gary

last: Silverman

first: Abhinav

last: Diwan

first: Kerry

last: Kornfeld


title: Expanding highly homogenous population of human primordial germ cell like cells in long-term and feeder-free culture condition [RNA-Seq]

city: Charlestown

first: Mutsumi

last: Kobayashi

state: Massachusetts

address: Building 147, 13th street, Rm# 7103

institute: MGH, center for cancer reserch

summary: The culture methods for human primordial germ cell like cells (hPGCLCs) has not been established. Here we report the culture method to expand long-term culture hPGCLCs (LTC-hPGCLCs) representing migrating morphology and early hPGC transcriptome and methylome. Key components of the culture media are stem cell factor, STO-conditioned media and absence of fetal calf serum. In this condition, these LTC-hPGCLCs were highly homogenous population without feeder cells and expanded at least 150 days. They did not express senescent phenotype such as β-galactosidase activity and shortening of telomere length at the 150-day culture, indicating that the cell might be a perpetual cell line. LTC-hPGCLCs still have potent pluripotency indicating the phenotype that the cells become human embryonic germ cells which were distinguishable from human iPS cells in strong DLK1 expression and H19 biallelic expression. In summary this simple culture method and highly homogenous LTC-hPGCLCs would be a useful resource that supports investigations on human germline cells.

overall_design: Transcriptomal profiles of human iPS cells, human embryonic germ cells, freshly isolated human PGC-like cells, and long-term culture hPGCLCs.

first: Toshi

last: Shioda


title: Testudinidosis: A New Mechanism of Resistance to Immune Attack

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: Antibody dependent cell-mediated cytotoxicity (ADCC) provides a model for uncovering immune resistance mechanisms. We continuously exposed epidermal growth factor receptor (EGFR)+ A431 cells to KIR-deficient NK92-CD16V effector cells and the anti-EGFR mAb cetuximab. Persistent ADCC exposure yielded ADCC-resistant cells (ADCCR1) that, compared with control ADCC-sensitive cells (ADCCS1), exhibited reduced EGFR expression, overexpression of histone- and interferon-related genes and failure to activate NK cells, without evidence of epithelial: mesenchymal transition. These properties gradually reversed following withdrawal of ADCC selection pressure. A second A431-derived ADCC-resistant cell line maintained EGFR expression. Remarkably, ADCCR1 cells possessed lower expression of multiple cell surface molecules that contribute to cell: cell interactions and immune synapse formation. Classic immune checkpoints did not modulate ADCC in this unique model system of immune resistance. Just as giant tortoises (Testudinidae) can hide in their shells to avoid predation, this novel immune evasion mechanism, termed testudinidosis, can protect cells against immune attack.

overall_design: Time course Illumina microarray data for continuously exposed epidermal growth factor receptor (EGFR)+ A431 cells to KIR-deficient NK92-CD16V effector cells and the anti-EGFR mAb cetuximab and control sensitive cells.

first: Louis

middle: M

last: Weiner


title: Mouse totipotent stem cells captured and maintained through spliceosomal repression

city: Beijing

first: Min

last: Yang

state: Beijing

address: No. 5, yiheyuan road, haidian district,

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary: Since the establishment of the first embryonic stem cells (ESCs), in vitro culture of totipotent cells functionally and molecularly comparable to in vivo blastomeres with embryonic and extraembryonic developmental potency is unviable. Spliceosomes are responsible for mRNA splicing and maturation. Here, we report that spliceosomal repression in mouse ESCs drives pluripotent-to-totipotent state transition. Using the splicing inhibitor Pladienolide B, we realize in vitro culturing of totipotent ESCs comparable to 2- and 4-cell blastomeres at molecular levels for long-time passages, which are therefore termed as totipotent blastomere-like cells (TBLCs). Mouse chimeric assays combined with single-cell RNA-seq technology demonstrate that TBLCs own a robust bidirectional development capability to generate multiple embryonic and extraembryonic cell lineages. Mechanically, spliceosomal repression causes widespread splicing inhibition of pluripotent genes, whereas the totipotent genes featured with few short introns are efficiently spliced and transcriptionally activated. Our study provides a principle for capturing and maintenance of totipotent stem cells.

overall_design:
Poly(A) RNA-seq were performed from mESCs with siRNAs against different splicing factors cultured in Serum/LIF medium, TBLCs cultured in SLP medium and mESCs/H1299 upon high concentration treatment.
TBLCs cultured in SLP medium and extracted the RNA and DNA for highthrough sequencing.

first: Hui

last: Shen

first: Shiyu

last: Li

first: Peng

last: Du


title: NPTX2, Homeostatic Scaling, and Schizophrenia

first: Meifang

last: Xiao

address: 725 N Wolfe Street, PCTB904

department: Neuroscience

institute: JHMI

summary: Schizophrenia is a complex genetic and developmental disorder. We present a model of disease resulting from disruption of a specific stage of homeostatic scaling (HS). HS modifies synapses and circuits in response to changes in neuronal activity and underlies cortical development and memory consolidation. Neuronal pentraxin 2 (NPTX2) plays a critical role in HS and its homeostatic action requires exocytosis at excitatory synapses on parvalbumin interneurons (PV) whereupon a portion is later shed into the CSF. CSF NPTX2 is reduced in two independent cohorts of patients with schizophrenia. To understand the relationship of this biomarker to disease we confirmed that in normal volunteers CSF NPTX2 increases rapidly with sleep deprivation consistent with behavior-linked exocytosis/shedding. In mouse neocortex NPTX2 exocytosis/shedding are activity-dependent and coupled to circadian behavioral. By contrast, in mouse genetic models that interrupt early events in HS NPTX2 exocytosis/shedding are erratic and not linked to behavior. The vital contribution of NPTX2 to homeostasis is revealed in Nptx2-/- mice, which exhibit sensitivity to social isolation stress and multiple schizophrenia-domain phenotypes. NPTX2 is not implicated by human genome studies; rather we propose that diverse mutations linked to schizophrenia disrupt activity-dependent mechanisms required for NPTX2 function. The ability to monitor NPTX2 in human subjects provides an opportunity to translate fundamental neuroscience to human neuropsychiatric disease.

overall_design: Parvalbumin interneuron-specific ribosome-associated mRNA profiles of wild-type and Nptx2 KO mice were generated by RiboTag pulldown and deep sequencing.Three biological replicates were analyzed for each of 4 conditions (two genotypes; two treatments per genotype)

first: Mei-Fang

first: Paul

middle: F

last: Worley


title: Eliciting plant defenses by exposition to HIPV’s: a new sustainable approach to manage agricultural pests

city: Moncada

first: Alberto

last: Urbaneja

state: Valencia

address: Carretera CV-315  Km 10,7

institute: Instituto Valenciano de Investigaciones Agrarias

summary: Plants communicate with each other using specific volatiles to warn of attacks and thus are able to activate defense mechanisms that make them more robust against external aggressions. In this research, we have activated defense responses of tomato plants by exposing them to two synthetic Herbivore Induced Plant Volatiles (HIPVs): (Z)-3-hexenyl propanoate (HP) [(Z)-3-HP] and methyl salicylate (MeSA). Tomato plants induced by both volatiles turned out to be less attractive to key tomato pests such as Bemisia tabaci and Tuta absoluta and more attractive to natural enemies. Under semi-field conditions the (Z)-3-HP-mediated activation reduced the subsequent attack of Tetranychus urticae and T. absoluta to less than half. With this knowledge, dispensers to release (Z)-3-HP under field conditions were designed and calibrated. The use of these selected dispensers in commercial tomato greenhouses maintained defensively activated plants and reduced the impact of T. absoluta by almost 60%. Metabolomics analysis indicated increased production of fatty acid-derived compounds in treated leaves, consistent with the activation of the lipoxygenase pathway. Plants elicited with (Z)-3-HP and MeSA also accumulated specific defense compounds like glykoalkaloids and phenylpropanoids. Transcriptomic profiling confirmed the activation of transcripts involve in defense (ie. proteinase inhibitors) and specialized defense metabolism. Our work demonstrates for the first time under real field conditions how the use of HIPVs as elicitors of plant defenses can be successfully integrated as a new biorational and sustainable tool within pest management programs.

overall_design: Examine the different gene expression profiles of tomato plants exposed to two volatiles during 24h, (Z)-3-hexenyl propanoate and methyl salicylate, and in non-exposed plants.

first: Meritxell

last: Perez-Hedo

first: Miquel

last: Alonso-Valiente

first: Sandra

last: Vacas

first: Carolina

last: Gallego

first: Clara

last: Pons

first: Vicente

last: Arbona

first: José

last: Rambla

last: Navarro

first: Antonio

last: Granell


title: Expanding highly homogenous population of human primordial germ cell like cells in long-term and feeder-free culture condition [WGBS]

first: Mutsumi

last: Kobayashi

overall_design: Methylome of human iPS cells, human embryonic germ cells, freshly isolated human PGC-like cells, and long-term culture hPGCLCs.

first: Toshi

last: Shioda


title: Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production

city: Medellin

first: Adriana

middle: Gallego

last: Rua

state: Antioquia

address: Carrera 53 No. 61-30

department: Antioquia

country: Colombia

institute: Universidad de Antioquia

summary: We performed RNA-Seq technology for quantification of differential expression of cacao cell suspensions under light/dark conditions. By obtaining over 15 millions of reads per sample, we cuantified the differential gene expression in structural, regulatory and light signaling genes associated with flavonoid biosynthesis. Our results indicated that light treatments can effectively regulate flavonoid profiles, shifting catechin - epicatechin ratios, in particular as a response to switching from white to blue light. The results demonstrated that HY5, MYB12, ANR and LAR were differentially regulated under light/dark conditions and could be targeted by overexpression aiming to improve catechin synthesis in cell cultures. Additionally, co-expression analyses of late flavonoid biosynthetic genes ANS, ANR and LAR showed a larger number of shared partners in the dark compared to selective partners in white-blue treatment. In conclusion, our RNA-Seq analysis of cacao cells cultured under different light conditions provides a platform to dissect key aspects into the genetic regulatory network of flavonoids. These light-responsive candidate genes can be used further to modulate the flavonoid production in in vitro systems with value-added characteristics.

overall_design: we used cacao cell suspension cultures exposed to white followed by blue light treatment and compared them to cultures grown in the dark over a time course of 14 days. Cell samples were collected at 0, 1, 7, 8, and 14 days after treatment initiation and RNA-Seq was applied to evaluate differential gene expression.

first: Andrew

middle: S

last: Fister


title: A Hightroughput Approach for Screening Potential Green Plasticizers Using A Human Prostate Cell Line [set1]

city: Montreal

first: Claudia

last: Lalancette

state: QC

address: 3655 Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary: The prostate is one of the main accessory glands of the male reproductive system, responsible of up to 30% of the secretions constituting seminal plasma, and is essential for male fertility (Burden et al. 2006 and references therein). Animal studies have shown that phthalates can trigger cellular events associated with the onset of prostatic diseases. There is increasing interest in developing safe alternative plasticizers to phthalates. Many potential candidates were recently reported, and their mechanisms of action on prostatic cells warrant investigation. The goal of this study was to evaluate the toxicity of four families of chemicals that are candidate plasticizer using a non-cancerous human prostate cell line, PNT1A. These candidate plasticizers were compared to diethylhexyl phthalate (DEHP), its main bioactive metabolite monohexylethyl phthalate (MEHP), and a current “green” plasticizer that is being used increasingly, 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH), using a combination of classical (MTT) and high throughput techniques (HCS, microarray). High content screening provided additional information about cell counts and range of parameters related to cell function. The incorporation of gene expression studies revealed that several of the compounds tested in this study had an effect on cellular functions, even those that had not shown any effect with the other assays. While DINCH was found to have wide ranging effects, we show that candidate plasticizers of the dibenzoate family have no effects on metabolic activity, cellular morphology, cellular proliferation or gene expression in PNT1A cells. Candidate plasticizers of the succinate family had an effect only at the gene expression level.

overall_design: Ten treatments are compared to the 0.4% DMSO control: Five compounds (DHS, DINCH, DOM, DOS, MEHP) at two different concentrations (mid = 10E-6M, low = 10E-8M). MEHP_low was analyzed in triplicate, whereas the other treatments were analyzed in quadriplicate

first: Bernard

last: Robaire


title: A Hightroughput Approach for Screening Potential Green Plasticizers Using A Human Prostate Cell Line [set2]

summary: The prostate is one of the main accessory glands of the male reproductive system, responsible of up to 30% of the secretions constituting seminal plasma, and is essential for male fertility. Animal studies have shown that phthalates can trigger cellular events associated with the onset of prostatic diseases. There is increasing interest in developing safe alternative plasticizers to phthalates. Many potential candidates were recently reported, and their mechanisms of action on prostatic cells warrant investigation. The goal of this study was to evaluate the toxicity of four families of chemicals that are candidate plasticizer using a non-cancerous human prostate cell line, PNT1A. These candidate plasticizers were compared to diethylhexyl phthalate (DEHP), its main bioactive metabolite monohexylethyl phthalate (MEHP), and a current “green” plasticizer that is being used increasingly, 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH), using a combination of classical (MTT) and high throughput techniques (HCS, microarray). High content screening provided additional information about cell counts and range of parameters related to cell function. The incorporation of gene expression studies revealed that several of the compounds tested in this study had an effect on cellular functions, even those that had not shown any effect with the other assays. While DINCH was found to have wide ranging effects, we show that candidate plasticizers of the dibenzoate family have no effects on metabolic activity, cellular morphology, cellular proliferation or gene expression in PNT1A cells. Candidate plasticizers of the succinate family had an effect only at the gene expression level.

overall_design: Three treatments are compared to the 1% DMSO control: 3 compounds (MEHP, BDB, DOS) at 10E-4M (high). Each treatment was analyzed in quadruplicate.


title: A Hightroughput Approach for Screening Potential Green Plasticizers Using A Human Prostate Cell Line [set3]

overall_design: Four treatments are compared to the 0.4% DMSO control: 2 compounds (BDB, HDB) at two different concentrations (MID = 10E-6M, LOW = 10E-8M). Each treatment was analyzed in quadruplicate.


title: A Hightroughput Approach for Screening Potential Green Plasticizers Using A Human Prostate Cell Line

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

overall_design: Refer to individual Series


title: Identifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation

status: Public on May 14 2021

first: Sigrid

last: Nachtergaele

summary: To identify the substrates of METTL5, we used crosslinking-assisted immunoprecipitation of overexpressed, FLAG-METTL5 followed by high throughput sequencing.

overall_design: Comparing RNA isolated from input samples to RNA isolated from a FLAG immunoprecipitation of FLAG-METTL5 overexpressed in HeLa cells.

first: Caraline

last: Sepich-Poore

first: Chuan

last: He


title: Sexual dimorphism in early osteoclasts demonstrates enhanced inflammatory pathway activation in female cells

city: New York

first: Kyung-Hyun

last: Park-Min

email: ParkminK@HSS.EDU, parkmink@gmail.com

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

summary: Sexual dimorphism of the skeleton is well documented. At maturity, the male skeleton is typically larger and has a higher bone density than the female skeleton. However, the underlying mechanisms for these differences are not completely understood. In this study, we examined sexual dimorphism in the formation of osteoclasts between cells from female and male mice. We found that the number of osteoclasts in bones was greater in females. Similarly, in vitro osteoclast differentiation was accelerated in female osteoclast precursor (OCP) cells. To further characterize sex differences between female and male osteoclasts, we performed gene expression profiling of cultured, highly purified, murine bone marrow OCPs that had been treated for 3 days with M-CSF and RANKL. We found that 125 genes were differentially regulated in a sex-dependent manner. In addition to genes that are contained on sex chromosomes, transcriptional sexual dimorphism was found to be mediated by genes involved in innate immune and inflammatory response pathways. Furthermore, the NFκB-NFATc1 axis was activated earlier in female early osteoclasts, which partially explains the differences in transcriptomic sexual-dimorphism in these cells. Collectively, these findings identify a sex-dependent intrinsic difference in early osteoclasts, which results from an altered response to osteoclastogenic stimulation. In humans these differences could contribute to the lower peak bone mass and increased risk of osteoporosis that females demonstrate relative to males.

overall_design: Osteoclast precursaor cells (OCP) from male and female RUNX1/+ mice (PMID: 15784726, Growney et al., Blood . 2005 Jul 15;106(2):494-504) were isolated from murine bone marrow by first flushing the marrow and then using fluorescent activcated cell soring to isolate CD3-, CD45R-, CD11b-/lo, CD115+ cells (PMID: 23165930, Jacome-Galarza et al.  J Bone Miner Res  2013 May;28(5):1203-13). Cells were then cultured with MCSF and RANKL for 3 days to strimulate osteoclastogenesis before being extracted for RNA sequencing.

first: Joseph

last: Lorenzo


title: Transcriptome deep sequencing (RNA-seq) analysis on 9 DPA fibers from wild type and GhWRKY16-RNAi

city: Wuhan

first: Yang

last: Li

address: NO.152 Luoyu Road

department: School of Life Science

institute: central china normal university

summary: To explore the regulation mechanism of GhWRKY16 in fiber development, we performed a transcriptome deep sequencing (RNA-seq) analysis on 9 DPA fibers from wild type and GhWRKY16-RNAi seeds. We identified 2,186 differentially expressed genes (DEGs), consisting of 1,088 upregulated genes and 1,098 downregulated genes Gene ontology (GO) cluster analysis showed that the DEGs regulated by GhWRKY16 are classified in diverse molecular functions, cellular components and biological processes.

overall_design: 9DPA fiber mRNA profiles of wild type and GhWRKY16 RNAi cotton

first: Nana

last: Wang

first: Xuebao


title: The analysis of gene expression in hematopietic stem/progenitor cells (HSPCs; LSK cells, Lineage-, c-kit+, Sca-1+) from diabetic/nondiabetic mice.

city: Otsu

first: Miwako

last: Katagi

address: seta tukinowa-cho

institute: Shiga university of medical science

summary: To evaluate gene expression of STZ-induced diabetic mice and nondiabetic control mice

overall_design: To evaluate the difference of gene expression between STZ-induced diabetic mice and nondiabetic mice.

first: Tomoya

last: Terashima

first: Natsuko

last: Ohashi

first: Yuki

last: Nakae

first: Akane

last: Yamada

first: Takahiko

last: Nakagawa

first: Itsuko

last: Miyazawa

first: Hiroshi

last: Maegawa

first: Junko

last: Okano

first: Yoshihisa

last: Suzuki

first: Kazunori

last: Fujino

first: Yutaka

last: Eguchi

first: Hideto

last: Kojima


title: Toxoplasma gondii RH strain tachyzoites Transcriptome or Gene expression

city: Guangzhou

first: Kexing

last: Huang

state: Guangdong

address: Southern Medical University, Sha Tai North Road, Baiyun District

department: Department of Pathogen Biology

institute: School of Public Health, Southern Medical University

summary: Toxoplasma gondii is a globally distributed obligate intracellular parasite which can cause zoonotic toxoplasmosis with great harms. The average death time of mice that infected with Toxoplasma gondii RH strain tachyzoites recovered from the liquid nitrogen was shortened after multiple generations. It has been reported that the parasite is in a state of static virulence during cryopreservation and the virulence of the protozoan parasite can be enhanced after continuous passages in hosts under laboratory conditions. However, no research has been conducted to elucidate its biological mechanism. Herein, we sequenced the T. gondii transcriptome using RNA-Seq technology and performed de novo assembly to investigated the virulence factors expression changes by comparing gene expression profiles between incipiently recovered and completely resuscitated tachyzoites. Transcriptome analysis identified 1,951 differentially expressed transcripts in infected liver, of which 1,752 were significantly downregulated and 199 upregulated. We identified many differentially expressed proteins and genes, including serine/threonine kinase, calnexin, myosin and microtubule-associated protein which have previously been reported to be either involved in cell adhesion, parasite gliding or participate in cell invasion. The great majority of the virulence factors including microneme proteins, rhoptry proteins and dense granule proteins were upregulated in fully recovered tachyzoites. The enhanced virulence of recovered Toxoplasma gondii RH strain from the liquid nitrogen is associated with the up-regulated expression of MICs, ROPs and GRAs. Our data will facilitate future genomic research and in-depth annotation of Toxoplasma gondii RH strain genomes. This study provides a profile of the candidate genes that are suspected to be involved with virulence enhancement of recovered Toxoplasma gondii RH strain tachyzoites. Many further studies should be carried out to confirm the function of the candidate genes. Moreover, the preliminary identification of genes and pathways exhibiting differential expression in complete resuscitation stage may further our general understanding of virulence enhancement in this parasite.

overall_design: R1A represent control group that recovered incipiently from liquid nitrogen and were collected from peritoneal fluid of the 1st generation infected mice; R5A is completely recorved tachyzoites that were collected from peritoneal fluid of the 5th generation infected mice.

first: Kun

last: Wu


title: microRNAs Restrain Proliferation in BRAFV600E Melanocytic Nevi [miRNA-Seq]

status: Public on May 13 2021

city: Salt Lake City

first: Robert

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

summary: We conducted small RNA sequencing on low passage human melanocytes derived from melanocytic nevi and normal skin.

overall_design: 8 normal skin derived melanocyte cultures and 6 nevus derived melanocyte cultures were sequenced.

first: Andrew

last: McNeal


title: Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations

city: BOSTON

first: Rajat

last: Gupta

address: 77 Avenue Louis Pasteur

institute: THE BROAD INSTITUTE INC

summary: The cells that form the arterial wall contribute to multiple vascular diseases. The extent of cellular heterogeneity within these populations has not been fully characterized. Recent advances in single-cell RNA-sequencing make it possible to identify and characterize cellular subpopulations. Clustering analysis of gene expression from aortic cells identified 10 populations of cells representing each of the main arterial cell types: fibroblasts, vascular smooth muscle cells, endothelial cells (ECs), and immune cells, including monocytes, macrophages, and lymphocytes. The most significant cellular heterogeneity was seen in the 3 distinct EC populations. Gene set enrichment analysis of these EC subpopulations identified a lymphatic EC cluster and 2 other populations more specialized in lipoprotein handling, angiogenesis, and extracellular matrix production. These subpopulations persist and exhibit similar changes in gene expression in response to a Western diet. Immunofluorescence for Vcam1 and Cd36 demonstrates regional heterogeneity in EC populations throughout the aorta. We present a comprehensive single-cell atlas of all cells in the aorta. By integrating expression from >1900 genes per cell, we are better able to characterize cellular heterogeneity compared with conventional approaches. Gene expression signatures identify cell subpopulations with vascular disease-relevant functions.

overall_design: We validate a method for generating a droplet-based single-cell atlas of gene expression in a normal blood vessel. Enzymatic dissociation of 4 whole mouse aortas was followed by single-cell sequencing.

first: Aditya

last: Kalluri

first: Shamsudheen

middle: K

last: Vellarikkal

first: Elazer

last: Edelman

first: Lan

last: Nguyen

first: Ayshwarya

last: Subramanian

first: Patrick

middle: T

last: Ellinor

first: Aviv

last: Regev

first: Sekar

last: Kathiresan


title: microRNAs Restrain Proliferation in BRAFV600E Melanocytic Nevi [RNA-Seq]


title: Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [primer extension]

city: Bethesda

first: Daniel

last: Larson

address: 41 Medlar Dr.

institute: NIH

summary: The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. We find that all observed genes show transcriptional bursting. We also observe large kinetic variation in intron removal for single introns in single cells which is inconsistent with deterministic splice site selection. Transcriptome-wide footprinting of the U2AF complex further reveals widespread splice site selection within introns. We propose and validate a unified theoretical model for transcription and splicing based on pervasive stochastic recursive splicing.

overall_design: splicing intermediates detection by primer extension sequencing

first: Yihan

last: Wan

first: Dimitrios

last: Anastasakis

first: Markus

last: Hafner


title: Next-generation interaction screening to discover protein-protein interactions regulating barley powdery mildew disease immunity and susceptibility.

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

summary: The goals of this study were to identify novel proteins involved in barley immune responses. Yeast-two-hybrid (Y2H) screening was coupled with next-generation sequencing to identify and quantify interacting proteins. Y2H baits consisted of Blumeria graminis effector proteins and different domains of the barley MLA6 powdery mildew resistance protein. These baits were mated to a cDNA prey library derived from a 0-48 hour time course of infected leaf tissue. Screens were performed in batch liquid culture to enrich yeast populations for cells expressing positive interactions. After two rounds of enrichment under selective (Histidine absent) and non-selective (Histidine present) conditions, yeast cells were collected. Y2H plasmids were extracted and prey cDNA amplicons were generated via low-cycle PCR. Fragmented amplicons were used as input to generate sequencing libraries and processed on the HiSeq 3000 platform. Reads were mapped to the barley and Blumeria graminis genomes and read counts were analyzed using a custom data processing and scoring pipeline. Putative interactors were cloned and binary Y2H was used to confirm interactions. We demonstrate a high rate of confirmations for top-ranked candidates. Altogether, this study establishes a high-throughput method for protein-protein interaction discovery in non-model organisms where ORF libraries are not available.

sample_organism:
Hordeum vulgare
Blumeria hordei

platform_organism:
Hordeum vulgare
Blumeria hordei

overall_design: Y2H screening of a cDNA library was coupled to next-generation sequencing to identify and rank positive protein-protein interactions. For each bait, screens were conducted in triplicate with yeast cells grown in selective and non-selective conditions. NuGEN's AnyDeplete technology was used to deplete HORVU3Hr1G072260 (zinc finger protein) from the samples. Two constructs of luciferase were used as bait negative controls. Samples were run on three lanes of Illumina's HiSeq 3000.

first: Sagnik

last: Banerjee

first: Valeria

last: Velasquez-Zapata

first: James

last: Elmore

first: Gregory

last: Fuerst

middle: P


title: The effects of SGLT-2 inhibitors canagliflozin on hepatic transcription

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

summary: We assessed the change in hepatic transciptional pattern after treatment with SGLT-2 inhibitors canagliflozin in a mice model of diet-induced obesity.

overall_design: Diet induced obesity C57Bl/6J were treated with canagliflozin (30mg/kg) for 4 weeks and the effects on hepatic transcription were compared with HFD control and weight-matched control by caloric restriction.

first: Soravis

last: Osataphan

first: Chiara

last: Macchi

first: Vicencia

last: Sales

first: Chisayo

last: Kozuka

first: Mary-Elizabeth

last: Patti


title: High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica

city: Wageningen

first: Christian

last: Südfeld

state: Gelderland

address: Droevendaalsesteeg 1

department: Bioprocess Engineering

country: Netherlands

institute: Wageningen University & Research

summary: Oleaginous microalgae are considered a promising platform for the sustainable production of high-value lipids and biofuel feedstocks. However, current lipid yields are too low to allow for an economically feasible production process. Lipid yields could be enhanced by improving microalgal strains through genetic engineering. Strain improvement strategies for the industrially relevant genus Nannochloropsis have met limited success because most genes of this genus lack a functional annotation, hindering our understanding of lipid metabolism and its regulation. To gain fundamental insights and to provide targets for genetic engineering of lipid metabolism, the aim of this study was to discover novel genes that are associated with higher neutral lipid (NL) content in Nannochloropsis oceanica. Therefore, we constructed a random gene knockout (KO) insertional mutagenesis library of N. oceanica, and we screened it by five rounds of fluorescence-activated cell sorting to select high lipid mutant (HLM) strains. Several strains showed increased NL contents compared to the wild type under favorable growth conditions. By using an adapted cassette PCR strategy involving the type IIS restriction endonuclease MmeI, we traced the responsible genetic KO of the five most promising mutant strains. One particularly promising mutant strain (HLM23) was disrupted in gene NO06G03670, which encodes a putative APETALA2-like transcription factor. HLM23 was not affected in growth rate, had increase d photosynthetic performance and a NL content of 30% dry cell weight^(-1), a 40% increase compared to the wild type. RNA sequencing revealed a transcriptional upregulation of genes related to plastidial fatty acid biosynthesis, glycolysis and the Calvin–Benson–Bassham cycle in this mutant.

overall_design: Transcriptome of an insertional loss-of-function mutant for gene NO06G03670 (strain HLM23) compared to the wild type, cultivated under favorable growth conditions.

first: Michal

last: Hubáček

last: Figueiredo

first: Mihris

last: Naduthodi

first: John

last: van der Oost

first: René

last: Wijffels

first: Maria

middle: J

last: Barbosa

first: Sarah

last: D’Adamo


title: Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [PARCLIP]

first: Daniel

middle: R

last: Larson

overall_design: PARCLIP of U2AF complex in HEK293 cells

first: Yihan

last: Wan

first: Dimitrios

last: Anastasakis

first: Markus

last: Hafner


title: RNA-CASing

status: Public on May 12 2021

city: Marburg

first: Lennart

last: Randau

state: Hessen

address: Karl-von-Frisch-Str. 4

department: Biology

institute: Phillips-Universität Marburg

summary: The specificity of the RNA-CASing  process was analysed by Next-Generation Sequencing. Therfor small RNAs were isolated from purified proteins of Escherichia coli and subjected to Illumina sequencing or nanopore sequencing.

overall_design: cDNA libraries were created with the NEBNext® Multiplex Small RNA Library Pret Set for Illumunia according to the manufacturer’s instructions. 100 ng of input RNA was used and amplified cDNA libraries were separated by native PAGE for size selection of 120-250 bp. E. coli small RNA isolates were then subjected to Illumina. Extracted RNA was treated with E. coli Poly(A) Polymerase (NEB) for 30 min 37°C to add a poly(A) tail and then processed for Nanopore sequencing with the Direct RNA Sequencing Kit according to the protocol provided by Oxford Nanopore Technologies.


title: Single-cell RNA-sequencing reveals the landscape of cervical cancer heterogeneity

city: Shanghai

first: Chunbo

last: Li

address: 419 FangXie Road, Shanghai

department: Department of Obstetrics and Gynecology

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: Cervical cancer (CC) is the forth leading cause of deaths in gynecological tumor. Although the etiology of CC has been extensively investigated, the exact pathogenesis of CC remains incomplete. Therefore, we applied single-cell RNA sequencing on cancer tissue and normal adjacent tissue from a patient with CC. Together, we identified four tumor cell subpopulations in tumor cells, which had specific signature genes with different biological functions and presented different prognosis. Among them, we identified a subset of cancer stem cell (CSCs), which was related to the developmental hierarchy of tumor progression. These data facilitate the understanding of the CC landscape and provides deeper insights into the development of prognostic biomarkers and therapeutic targets in the CC.

overall_design: In this study, we performed single cell RNA sequencing on cervical tumor tissue and normal adjacent tissue from cervical patients in an aim to discover the heterogeneity of tumor cells in cervical cancer and their interactions with other cells.

first: Keqin

last: Hua


title: Inducible meiotic cDNA libraries for genome-wide studies of gene isoforms

city: Berkeley

first: Tina

middle: Lynn

last: Sing

state: California

address: Barker Hall, Rm 616, University of California, Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary:
We report the construction of 5 yeast meiotic cDNA libraries and perform proof-of-principle screens to show that these yeast cDNA libraries can be used to identify genes and gene isoforms that are important for competitive fitness.
Samples 1-25 are from different stages of cDNA library construction and deep sequencing was used to characterize gene representation in each yeast cDNA library.
Samples 26-175 are from proof-of-principle competitive fitness screens.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae

overall_design: Synchronous meiotic timecourses were performed to obtain stage-specific mRNA, mRNA was converted to cDNA using TGIRT reverse transcriptase, Gateway cloning was used to insert cDNA libraries into galactose-inducible vectors, and plasmid libraries were transformed into yeast using electroporation. Competitive screens were performed in the indicated liquid media over 5 days.

first: Elçin

last: Ünal


title: RNA  microarray analysis of Human Umbilical Vein Endothelial Cells in normal pregnancy and preeclampsia

first: xingyu

last: yang

address: 910 Hengshan Road

institute: IPMCH

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

summary:
To investigate the differentially expressed lncRNAs,CircRNAs and mRNAs in Human Umbilical Vein Endothelial Cells between normal pregnancy and preeclampsia,
we performed the human lncRNA,cirRNA and mRNA microarray analysis of 8 samples from clinical patients.

overall_design: Ten preeclampsia patients (mean age 33.1 ± 1.84 years) and ten control patients (mean age 30.4 ± 1.36 years) who received a caesarean section were included in this study. Preeclampsia was clinically diagnosed before caesarean. The main criteria for PE diagnosis were: SBP ≥ 140 or DBP ≥ 90 on two occasions at least 4 h apart; and proteinuria >0.3 g/24h. The control pregnancy was defined as: no medical complications and proteinuria, maternal blood pressure < 140/90 mm Hg. Of the ten pairs of placenta samples, four pairs were randomly selected for lncRNA, circRNA and mRNA microarray analysis, and the other samples were used for the following verification.

first: C

last: Sha

first: Y

last: Xingyu


title: Staphylococcus aureus modulate cellular metabolism to survive in epithelial cells

city: Beijing

first: Mengrui

last: Wang

address: No. 2, Yuanmingyuan West Road

institute: China Agricultural University

summary: This work aimed to investigate the metabolic changes of epithelial cell metabolism during S. aureus infection. We revealed that persistent S. aureus survived in epithelial cells by modulating the cellular pathways of one carbon pool by folate. These results highlight the persistence mechanisms of S. aureus survived in epithelial cells by regulation of cellular metabolism, shedding light on the development of intervention strategies to combat S. aureus associated infections.

overall_design: ATAC-seq of rat intestinal epithelial cells infected and uninfected with Staphylococcus aureus


title: KLF1 knock-down for HbF high-expression discovered by RNA-Seq profiles under human erythropoiesis

city: Augusta

first: Biaoru

state: GA

department: Pediatrics

institute: MCG

summary: Krueppel-like factor 1 (KLF1) is a major transcription factor, which regulates the γ-globin to β-globin gene switch during erythropoiesis. The goal of this study was to investigate genome-wide transcriptome expression pattern in the presence of KLF1 knockdown to discover targets of KLF1 regulation involved in γ-globin silencing. To achieve KLF1 gene silencing, we stably transfected human primary erythroid cells generated from CD34+ cells, with a short hairpin lentiviral vector carrying a shKLF1 (short hairpin RNA for KLF1 loop) and a puromycin resistance gene. A set of three shKLF1 were designed uusing siDesign Center (Dharmacon) with the designations: 1) shKLF1-1, located in zinc finger at 3'-terminal; 1) shKLF1-2 located in Transcription Factor II H, and 3) shKLF1-3 located in 5’-terminal without a function region. After lentiviral packaging and transduction into CD34+ cells, each expression virus with encoding GFP, puromycin resistance fragment, and a loop consists of the KLF1 knock-down domain. The three shKLF1 vectors (shKLF1-1, shKLF1-2, shKLF1-3), along with scrambled control (shScr) was used to transduce human adult CD34+ stem cells isolated from peripheral blood of healthy adults. The cells were grown in one-phase liquid culture system as previously published by our group (Li B et al. Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation. BMC Genomics. 2012; 13:153). At day-15 in the 28-day culture period, by real-time PCR and Western blot analysis we found KLF1 gene silencing mainly for shKLF-1 and shKLF-2; however, we isolated total RNA from the three stable lines for RNA-seq analysis.

overall_design: Twelve RNA samples including shKLF1-1, shKLF1-2, shKLF1-3 and shScr control, each in triple repeats, were harvested on day-15 with KLF1 gene silencing occurs and we previously confirmed highest γ-globin and lower β-globin expression. Total RNA was extracted with Trizol solution according to the manufacturer’s instructions. After dissolving in 30 μl of RNase free water, the RNA concentration (A260 nm) and purity (A260/280 and A260/230 ratios) were assessed with a ND-1000 spectrophotometer (Thermo Scientific, Wilmington DE); quality measurement was assayed by the Georgia Cancer Center Genomics Core facility. Total RNA was used to construct sequencing libraries using 1µg of RNA; analysis was performed by Agilent TapeStation 2200 High-Seq 2500 technology, in triple for each stable line.

first: Betty

last: Pace

first: Chang

last: Chang-Sheng

first: Eiko

last: Kitamura

first: Baolin

last: Kang

first: Mayuko

last: Takezaki


title: Androgen receptor, although not a specific marker for, is a novel target to suppress glioma stem cells as a therapeutic strategy for glioblastoma

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: Targeting androgen receptor (AR) has been shown to be promising in treating glioblastoma (GBM) in cell culture and flank implant models but the mechanisms remain unclear. AR antagonists including enzalutamide are available for treating prostate cancer patients in clinic and can pass the blood–brain barrier, thus are potentially good candidates for GBM treatment but have not been tested in GBM orthotopically. Our current studies confirmed that in patients, a majority of GBM tumors overexpress AR in both genders. Enzalutamide inhibited the proliferation of GBM cells both in vitro and in vivo. Although confocal microscopy demonstrated that AR is expressed but not specifically in glioma cancer stem cells (CSCs) (CD133+), enzalutamide treatment significantly decreased CSC population in cultured monolayer cells and spheroids, suppressed tumor sphere-forming capacity of GBM cells, and downregulated CSC gene expression at mRNA and protein levels in a dose- and time-dependent manner. We have, for the first time, demonstrated that enzalutamide treatment decreased the density of CSCs in vivo and improved survival in an orthotopic GBM mouse model. We conclude that AR antagonists potently target on glioma CSCs in addition to suppressing the overall proliferation of GBM cells as a mechanism supporting their repurposing for clinical applications treating GBM.

overall_design: To check the response of the genes of U87MG cell line after the treatment of enzalutamide.

last: Zhao


title: Transcriptome Analysis of Gene Expression Regulation Mechanisms in the Spleen of Rainbow Trout (Oncorhynchus mykiss) Against Infectious Hematopoietic Necrosis Virus

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

summary: Here, RNA-seq technology was used for comparative transcriptome analysis of spleens of rainbow trout 48 hours after IHNV infection. A total of 9144 significantly differentially expressed genes (FDR<0.05 and |log2FC|>1) were obtained, of which 3274 genes were up-regulated and 5870 genes were down-regulated. Gene set enrichment analysis revealed the existence of pathways directly related to the innate immune response, such as Toll-like receptor signaling pathway, Cytokine-cytokine receptor interaction, NOD-like receptor signaling pathway, and RIG-I-like receptor signaling pathway. Responses to the virus were observed to activate pathogen recognition receptor-related genes containing TLR2, TLR3, TLR5S, NOD2, LGP2, JAKS, and trigger downstream interferon (IFN) responses, and IFNA was significantly up-regulated. Also, the host response to this virus is largely driven by the interferon regulatory factor IRF (IRF3/7). In this data, JNK, SOS, was also found to be strongly down-regulated with IHNV at 48 hpi. The differential expression of these transcripts may be related to host resistance to pathogen invasion as well as viral replication. The results of this study improve our understanding of innate immune responses and host-pathogen interactions in rainbow trout infected with IHNV to further investigate the detailed antiviral mechanisms.

overall_design: mRNA expression profiles in spleens of rainbow trout (Oncorhynchus mykiss) infected and uninfected with IHNV at 48 h

first: Jin-Qiang

last: Huang

first: Yu-Cai

last: Pan


title: Transcriptomic analysis of cspC deficient Acinetobacter baumannii

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

summary: This study examined the response of A. baumannii to cspC disruption via transposon mutagenesis. The goal was to gain insight into how a cold shock protein highly expressed within A. baumannii biofilms, CspC, functioned and identify pathways in which it may be involved.

overall_design: A. baumannii RNA was extracted to compare global gene expression of two samples: AB5075 wild type and AB5075 cspC transposon mutant. AB5075 wild type serves as the parental control strain. Each sample was generated by pooling three independent biological replicate RNA preps.

first: Brooke

last: Tomlinson


title: Transcriptomic analysis of Acinetobacter baumannii biofilm

summary: Differential expression of A. baumannii strain AB5075 biofilm compared to planktonic counterparts after 24 h of growth.

overall_design: A. baumannii biofilms were formed in LB using 96-well plates. Biofilm samples and their planktonic counterparts were collected in biological triplicate after 24 h of growth. Each sample was generated by pooling three independent biological replicate RNA preps.


title: Homeostatic regulation of T follicular helper and antibody response to particle antigens by IL-1Ra of medullary sinus macrophage origin

first: Hong

last: Tang

state: Shanghai

address: Life Science Research Building 320 Yueyang Road, Xuhui District, 200031

institute: Institut Pasteur of Shanghai, Chinese Academy of Sciences

summary: HBV vaccine is composed of surface antigen (HBsAg) that spontaneously assembles into subvirus particles. Factors that impede its humoral immunity in 5-10% of vaccinees remain elusive. Herein we showed that the low-level interleukin-1 receptor antagonist (IL-1Ra) can predict antibody protection both in mice and humans. Mechanistically, murine IL-1Ra inhibited Tfh cell expansion and subsequent GC dependent humoral immunity, resulting in significantly weakened protection against HBV challenge. Compared to soluble antigens, HBsAg particle antigen displayed a unique capture/uptake and innate immune activation, including IL-1Ra expression, preferably of medullary sinus macrophages (MSM). In humans, a unique polymorphism in RelA/p65 binding site of IL-1Ra enhancer associated IL-1Ra levels with ethnicity dependent vaccination outcome. Therefore, the differential IL-1Ra response to particle antigens probably creates a suppressive milieu for Tfh/GC development, and neutralization of IL-1Ra would resurrect antibody response in HBV vaccine non-responders.

overall_design: mRNA profiles of wt mouse lymph node and spleen derived CD169+ macrophages 2h after HBsAg and ova immunization

first: Xinwen

last: Lin

first: Trix

last: Twelkmeyer


title: Circular RNA expression profiles in the plasma of patients with infantile hemangioma determined using microarray analysis

city: Jinan

first: Zhiyu

last: Li

address: Jingwu Road

department: Department of Plastic and Aesthetic Surgery

institute: Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University

summary:
This study compared the circRNA expression levels in plasma samples from patients with IH and control individuals. The circRNA expression profiles were determined using microarray in three pairs of plasma samples from patients with proliferative IH and healthy control individuals. Expression of the identified circRNAs was verified using quantitative reverse transcription polymerase chain reaction (RT-qPCR), and bioinformatic analysis was performed to predict the microRNAs targeted by the validated circRNAs. In the circRNA expression profiles in the plasma of patients with IHs, we found 128 differentially expressed circRNAs, of which 72 were upregulated and 56 were downregulated. The downregulated expression of three circRNAs (hsa_circRNA_101566, hsa_circRNA_103546, and hsa_circRNA_103573) was verified using RT-qPCR.
Circular RNAs (circRNAs) are noncoding RNAs that play important roles in tumor progression. Few studies have examined the circRNAs involved in infantile hemangioma (IH) progression. This study compared the circRNA expression levels in plasma samples from patients with IH and control individuals. The circRNA expression profiles were determined using microarray in three pairs of plasma samples from patients with proliferative IH and healthy control individuals. Expression of the identified circRNAs was verified using quantitative reverse transcription polymerase chain reaction (RT-qPCR), and bioinformatic analysis was performed to predict the microRNAs targeted by the validated circRNAs. In the circRNA expression profiles in the plasma of patients with IHs, we found 128 differentially expressed circRNAs, of which 72 were upregulated and 56 were downregulated. The downregulated expression of three circRNAs (hsa_circRNA_101566, hsa_circRNA_103546, and hsa_circRNA_103573) was verified using RT-qPCR. Gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that all identified networks participated in angiogenesis and tumor formation and progression. We found that hsa_circRNA_101566, which can regulate the mammalian target of rapamycin signaling pathway, may be an important regulatory molecule in IH development and that targeting of hsa_miR_520c can indirectly regulate the vascular endothelial growth factor signaling pathway. Further studies are needed to clarify these effects and the underlying mechanisms.

overall_design: The circRNA expression profiles were determined using microarray in three pairs of plasma samples from patients with proliferative IH and healthy control individuals. Expression of the identified circRNAs was verified using quantitative reverse transcription polymerase chain reaction (RT-qPCR) in 17 pairs of plasma samples.

first: Yimeng

last: Chai

first: Zifu

last: Zhou

first: Xueqing

first: Jianhai

last: Bi

first: Ran

last: Huo


title: Meloxicam and Filgrastim for Mobilization of Autologous Peripheral Blood Stem Cells in Patients with Multiple Myeloma

city: Indianapolis

first: Andrea

middle: Marie

last: Patterson

state: IN

address: 980 W. Walnut St.

department: Medicine

institute: Indiana University School of Medicine

summary: The purpose of this RNA sequencing dataset was to analyze transcriptional changes in human stem cells when Meloxicam is added to the standard Filgrastim mobilization regimen in patients with Multiple Myeloma.

overall_design: RNA sequencing was performed on stem cells isolated from apheresis products from patients mobilized with either Filgrastim alone (n=10), or Meloxicam + Filgrastim (n=22).

first: Louis

last: Pelus


title: Comparative transcriptomic analysis between wild-type (WT) and Cables2-null embryos.

city: Tsukuba

first: Tra

middle: Thi Huong

last: Dinh

state: Ibaraki

address: 1-1-1 Tennodai

department: Faculty of Medicine

institute: University of Tsukuba

summary: We found that conventional targeted disruption of the entire Cables2 locus caused post-gastrulation embryonic lethality in mouse. To examine global gene changes during gastrulation, we performed the RNA-seq experiment using WT- and Cables2-null embryos at embryonic day 6.5 and 7.5.

overall_design: mRNA profiles of WT- and Cables2-null mouse embryos at E6.5 and E7.5

first: Dinh

last: TH Tra

first: Muratani

last: Masafumi

first: Sugiyama

last: Fumihiro


title: Calibration of cell-intrinsic Interleukin-2 response thresholds guides design of a regulatory T cell biased agonist

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Interleukin-2 (IL-2) is a pleotropic cytokine that mediates both pro- and anti-inflammatory functions. Immune cells natural differ in their sensitivity to IL-2 due to cell-type and activation-state dependent expression of receptors and signaling pathway components. To probe differences in IL-2 signaling across cell types, we created through structure-based design, and then profiled, a series of IL-2 variants with the capacity to titrate signal strength in fine increments. One of these partial agonists, IL-2-REH, specifically expanded FoxP3+ regulatory T cells (Tregs) with reduced activity on CD8+ T cells due to cell-type intrinsic differences in IL-2 signaling. IL-2-REH elicited cell-type dependent differences in gene expression and provided therapeutic benefit in an in vivo model of mouse Colitis. Our findings show that cytokine partial agonists can be used to calibrate intrinsic differences in response thresholds across responding cell types to narrow pleiotropic actions, which may be generalizable to other cytokine and growth factor systems.

overall_design: RNA-Seq analyses using CD8+ T cells and Tregs that were treated with either no cytokine, or with IL-2 or IL-2-REH.

first: Caleb

last: Glassman

first: Leon

last: Su

first: Sonia

last: Majri-Morrison

first: Hauke

last: Winkelmann

first: Fei

last: Mo

first: Magdiel

last: Pérez-Cruz

first: Peggy

last: Ho

first: Levgen

last: Koliesnik

first: Nadine

last: Nagy

first: Tereza

last: Hnizdilova

first: Lora

last: Picton

first: Marek

last: Kovář

first: Paul

last: Bollyky

first: Lawrence

last: Steinman

first: Everett

last: Meyer

first: Jacob

last: Piehler

first: Warren

last: Leonard

first: K

middle: C

last: Garica


title: Single cell RNA-seq reveals the urothelium and stroma cell heterogeneity in acute and chronic injured urinary bladder by single-cell analysis

first: Jia

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

summary: Some studies have demonstrated the heterogeneity of bladder epithelium and fibroblasts, as well as their crosstalk during bladder development and regeneration. However, due to the limitations of techniques, a comprehensive understanding of cellular heterogeneity and crosstalk during bladder regeneration is still lacking. Here, we used droplet-based scRNA-seq to recover the heterogeneity of urothelial cells, cell cycle characteristic of proliferative cell population and proliferative niches after acute and chronic injury induced by cyclophosphamide.

overall_design: Bladder mucosal layer single cell mRNA profiles of 8-weeks old C57BL/6 mice, 8-weeks old C57BL/6 mice treated with CPP for 48 hours and 8-weeks old C57BL/6 mice treated with 4 round CPP for 11 days were generated by 10X Genomics plartform, with 2 biological replications, and sequenced by NovaSeq 6000 (Illumina).

first: Wei-Qiang

last: Gao


title: Zbtb16 regulates social cognitive behaviors and neocortical development

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Recent genomic studies suggest that a single gene is involved in multiple diseases, however it is unclear what mechanism destined for different diseases by a single gene. Mutations of ZBTB16 are associated with autism spectrum disorder (ASD) and schizophrenia (SCZ), but how ZBTB16 fates ASD or SCZ are unknown. Here we show the deletion of Zbtb16 in mice leads to both ASD- and SCZ-like behaviors such as social impairment, repetitive behaviors, risk-taking behaviors, and cognitive impairment. To elucidate the mechanism underlying the behavioral phenotypes, we carried out histological studies and observed impairments in thinning of neocortical layer 6 (L6) and a reduction of TBR1+ neurons in the prefrontal cortex (PFC) of Zbtb16 KO mice. Furthermore, we found increased dendritic spines and microglia as well as developmental defects in oligodendrocytes and neocortical myelination in the PFC of Zbtb16 KO mice. Using a genomics approach, we identified the Zbtb16-transcriptome that includes genes involved in both ASD and SCZ pathophysiology and neocortical maturation such as neurogenesis and myelination. Co-expression networks further identified Zbtb16-correlated modules that are unique to ASD or SCZ respectively. Our study provides insight into the differential role of the single gene ZBTB16 in ASD and SCZ.

overall_design: Zbtb16 KO and wild-type mice at 7 weeks age were used. Each group contains 5 mice. RNA-seq were conducted using RNAs extracted from prefrontal cortex of these mice.

first: Noriyoshi

last: Usui

first: Stefano

last: Berto

first: Ami

last: Konishi

first: Makoto

last: Kondo

first: Hideo

last: Matsuzaki

first: Shoichi

last: Shimada


title: HSPB3 promotes myogenic differentiation by targeting the lamin B receptor.

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: HSPB3 is a member of the HSPB family that is absent in cycling cells. HSPB3 expression is induced by the myogenic specific transcription factor MyoD in muscle cells, where HSPB3 localizes to the nucleus. Yet, whether HSPB3 participates to muscle cell differentiation is unknown. One of the early events of cell differentiation consists in the switch between the lamin B receptor (LBR) and the lamin A/C (LMNA) tethers, which modulates chromatin remodeling and transcription. Here, we identified LBR as a specialized substrate regulated by HSPB3. HSPB3 affected the expression and nuclear distribution of LBR mimicking the changes that occur during differentiation. HSPB3 upregulation promoted the differentiation of two human muscle cell types: LHCNM2 cells, derived from satellite cells and fusion-negative rhabdomyosarcoma cells, which fail to commit to terminal differentiation. Conversely, HSPB3 depletion stabilized the LBR tether and affected the myogenic transcriptional program.  Four mutations in the HSPB3 gene are linked to distal hereditary motor neuropathy and congenital myopathy with unknown mechanisms. We focused on R116P-HSPB3, which was discovered in a myopathy patient with chromatin alterations and muscle fiber disorganization. Upon overexpression in cells R116-HSPB3 formed nuclear aggregates that immobilized LBR-GFP. In LHCNM2 cells R116-HSPB3 deregulated the transcriptional program required for cytoskeleton and ECM remodeling, while activating the unfolded protein response. We propose that HSPB3 is a highly specialized chaperone that participates to muscle cell differentiation by targeting LBR. Our findings pave the way for a better understanding of HSPB3 implication in the physiology and pathology of the neuromuscular system.

overall_design: Examination of transcriptional changes upon HSPB3 overexpression /  knock-down

first: Tatiana

last: Tiago

first: Ritwick

last: Sawarkar

first: Serena

last: Carra


title: Transcriptome analysis of T-cell subsets before and under lenalidomide treatment sorted from the blood of 6 first-line follicular lymphoma (FL) patients

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

summary:
Purpose: the goal of this study is to analyze the effect of lenalidomide on CD4pos PD-1pos, CD4pos PD-1neg, CD8pos PD-1neg and CD8pos PD-1pos subsets
Methods: genome-wide mRNA profiles of 6 first-line follicular lymphoma patients (GALEN protocol) were generated using deep sequencing before and after one-week lenalidomide, using Illumina HiSEq4000.   All paired-end sequence reads passed quality filters.and were analyzed at the gene level with STAR followed by Featurecount.
Results: Important differences in functional biological pathways related to proliferation, immune system, metabolism and immune synapse in PD-1pos T-cells triggered by lenalidomide were highlighted by the experiment.

overall_design: RNAseq was performed on paired samples collected at Day 0 and Day 7 (after one-week lenalidomide) from 6 FL patients. For each sample, T-cell subsets were FACSorted for CD3pos/CD4pos/PD-1neg, CD3pos/CD4pos/PD-1pos, CD3pos/CD8pos/PD-1neg, and CD3pos/CD8pos/PD-1pos populations. Day 0 populations were used as pairwise control.

first: Cédric

last: Ménard


title: Morchella importuna SI transcriptome raw sequence

first: CH

last: Dong

address: NO.3 Park 1, Beichen West Road, Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

summary: Sclerotial formation is one of the most important phases during the morel life cycle, and previous reports indicated that reactive oxygen species (ROS) play an important role in sclerotial formation. However, the mechanisms of ROS response in sclerotial initiation (SI) stage are poorly understood.

overall_design: Comparative transcriptome analyses were performed with the cells of sclerotial and hyphal at different areas in a same plate at SI stage, named as SII and SIO, respectively.

first: C

middle: H

first: Q

middle: Z

last: Liu


title: OAS1/RNase L executes 5’-triphosphate RNA-dependent tumor cell apoptosis

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Cytoplasmic double-stranded RNA is sensed by RIG-I-like receptors (RLR) leading to induction of type-I interferons (IFN-I), proinflammatory cytokines and apoptosis in tumor cells. Here, we elucidate the differential signaling mechanisms leading to cytokine secretion and/or cell death induction upon stimulation with the bona fide RIG-I ligand 5’-triphosphate RNA (3p-RNA). We show that both outcomes are mediated by distinct dsRNA-receptor families with RLR being essential for cytokine production and IFN-mediating priming of effector pathways, but not apoptosis itself. Affinity purification followed by mass spectrometry revealed 3p-RNA-specific binding and activation of oligoadenylate synthetase 1/RNase L. RNase L-deficient cells were profoundly impaired in their ability to undergo apoptosis. Mechanistically, the concerted action of translational arrest triggered by RNase L and upregulation of NOXA was needed to deplete anti-apoptotic MCL-1 causing intrinsic apoptosis. Thus, 3p-RNA-induced apoptosis is a two-step process consisting of a RIG-I-dependent priming and a RNase L-dependent effector phase.

overall_design: mRNA sequencing of 1205Lu WT and RIG-I KO cells stimulated with 3p-RNA in presence or absence of IFN-⍺2a.

first: Daniel

last: Boehmer

first: Simone

last: Formisano

first: Stephan

middle: A

last: Mueller

first: Michael

last: Kluge

first: Philipp

last: Metzger

first: Meino

last: Rohlfs

first: Christine

last: Hörth

first: Lorenz

last: Kocheise

first: Stefan

last: Lichtenthaler

last: Endres

first: Simon

last: Rothenfusser

first: Peter

last: Duewell

first: Max

last: Schnurr

first: Lars

middle: M

last: Koenig