title: Impact of cigarette smoke on physical-chemical and molecular proprieties of human skin in an ex vivo model

status: Public on Sep 21 2020

city: LONGJUMEAU

first: Angela

last: PATATIAN

address: 1CHEMIN DE SAULXIER

department: ESSONNE

institute: GENEX

summary: This study deals with the skin aging exposome focusing on the effect of cigarette smoke, one of the main harmful components. To that purpose, human skin living explants, an ex vivo model, were exposed to cigarette smoke of two cigarettes for 2hours using a patented lab-made exposure chamber, the Pollubox®. The effect on the surface physico-chemistry and molecular properties of the skin were thus deepened and for the first time reported.  Basic Procedures: To evidence this effect, gene expression profile, MDA dosage and surface physiochemistry data (Surface free energy determination, Trans-Epidermal Water loss, skin pH and FTIR spectroscopy of the surface of the explants) were collected on non-treated and treated human skin explants  Main Findings: Results exhibit a decrease of the total surface free energy of the treated skin explants. This decrease reflects higher interactions with polar compounds from the environment and as a consequence a decrease of the hydrophobia of the surface. Additionally, an increase of the trans epidermal water loss and skin pH was measured after treatment.   The molecular analysis shows downregulation of specific genes combined with the increase of MDA in the cigarette smoke-treated skin explants.   Principal Conclusions: Cigarette smoke induced an oxidation of the lipids at the surface of the skin explants. This implies an alteration of the skin barrier function: interactions with polar products are enhanced and lipid chain packing at the surface is modified. As a consequence, skin permeation could increase. While as expectedly genes involved in the AHR pathway were induced in CS-exposed human skin explants, our molecular analysis suggested that mitochondrial functions were strongly impacted and oxidized lipids failed to be eliminated promoting skin barrier alteration.

overall_design: Neonatal human epidermal keratinocytes (HEKn) are primary cells derived from neonatal foreskins. They are supplied by the American Type Culture Collection (ATCC) in the form of 5 × 10 5 viable cells vials from different donors in order to have a constant homogeneity of cell populations. These cells were cultured in a specific medium (Epilife, Life Technologies) supplemented with a plant-derived supplement (HKSdaFREE and HKGE, AvantBio) that replaces the sera of animal origin more commonly used in cell culture. The cells were cultured at 37 ° C in an incubator (5% CO2 / 95% air). Total RNA was extracted from keratinocyte using RNeasy Mini Plus Kits (Qiagen). Total RNA were used for reverse transcription, amplification and Cy3 labeling, using the Low Input Labeling kit, one-color (Agilent Technologies). All cRNAs were hybridized to human whole genome oligo microarrays (Agilent Technologies v2 (AMADID 039494), which contains 60.000 probes, derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq. Microarray data were quantified (GeneExtraction Feature V11.0,1) and normalized with R tools (Bioconductor).

first: G

last: Percoco

first: A

last: Patatian

first: F

last: Eudier

first: M

last: Grisel

first: T

last: Bader

first: E

last: Lati

first: P

last: Benech

last: Savary

first: C

last: Picard


title: Endogenous Redox levels delineate functional heterogeneity and responsiveness of adult hippocampal stem cells in mice

status: Public on Sep 25 2020

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure adipocyte differentiation [RNA-seq]

status: Public on Sep 22 2020

city: Tokyo

first: Hironori

last: Waki

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

country: Japan

institute: The University of Tokyo

summary: The transcription factor nuclear factor I-A (NFIA) is a regulator of brown adipocyte differentiation. Here we show that the most C-terminal 17 amino acid residues of NFIA (which we named pro#3 domain) is required for transcriptional activity of NFIA. Full-length NFIA, but not deletion mutant lacking pro#3 domain rescued impaired Pparg expression and adipogenesis in NFIA-knockout cells. Mechanistically, the ability of NFIA to increase chromatin accessibility is mediated through pro#3 domain. However, the deletion mutant still binds to Myod1 enhancer to decrease chromatin accessibility and represses Myod1 as well as proximally transcribed non-coding RNA called DRReRNA, leading to suppression of myogenic gene program. Therefore, the negative effect of NFIA on myogenic gene program is, at least in part, independent from the positive effect on Pparg expression and its downstream adipogenic gene program. These results uncover multiple ways of action of NFIA to ensure optimal regulation of brown adipocyte differentiation.

overall_design: ChIP-seq , FAIRE-seq and RNA-seq analysis of control-, full-length NFIA and Δpro#3 mutant-expressing C2C12 myoblasts and RNA-seq analysis of NFIA-KO ingSVF cells

first: Yuta

last: Hiraike

first: Misato

last: Oguchi

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Toshimasa

last: Yamauchi

first: Takashi

last: Kadowaki


title: Prdm16 deficiency leads to age-dependent cardiac hypertrophy, adverse remodeling, mitochondrial dysfunction, and heart failure

city: Singapore

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS MEDICAL SCHOOL

summary: Hypertrophic cardiomyopathy (HCM) is one of the most frequent inherited heart condition and a well-established risk factor for cardiovascular mortality worldwide. Although hypertrophy is traditionally regarded as an adaptive response to increased workload caused by physiological or pathological stress, prolonged hypertrophy can lead to heart failure characterized by impaired systolic function, increased apoptosis, fibrosis, ventricular dilation, and impaired metabolic substrate flexibility. While the key regulators for cardiac hypertrophy are well studied, the role of Prdm16 in this process remains poorly understood. In the present study, we demonstrate that Prdm16 is dispensable for cardiac development. However, it is required in the adult heart to preserve mitochondrial function and inhibit hypertrophy with advanced age. Cardiac-specific deletion of Prdm16 results in cardiac hypertrophy, excessive ventricular fibrosis, mitochondrial dysfunction, and impaired metabolic flexibility, leading to heart failure. We demonstrate that Prdm16 and euchromatic histone-lysine N- methyltransferase factors (Ehmts) act together to reduce the expression of fetal genes reactivated in pathological hypertrophy by inhibiting the functions of pro- hypertrophic transcription factor Myc. Although young Prdm16 knockout mice show normal cardiac function, they are predisposed to develop heart failure in response to metabolic stress. Collectively, our results demonstrate that Prdm16 protects the heart against age-dependent cardiac hypertrophy, fibrosis, mitochondrial dysfunction, adverse metabolic remodeling, and heart failure.

overall_design: 6 samples are analyzed comprises of control (n = 3) and mutant (n = 3) for Prdm16 3 months. 4 samples were analysed which comprises of control (n = 2) and mutant (n = 2) for Prdm16 12 months.

first: Dasan

middle: M

last: Cibi

first: Kathleen

middle: W

last: Bi-Lin

first: Shamini

middle: G

last: Shekeran

first: Reddemma

last: Sandireddy

first: Nicole

last: Tee

first: Anamika

first: Yajun

last: Wu

first: Dinesh

middle: K

last: Srinivasan

first: Jean

middle: P

last: Kovalik

first: Sujoy

last: Ghosh

first: Patrick

last: Seale

first: Seshachalam

middle: V

last: Pratap


title: eIF2α pathway controls memory consolidation via excitatory and somatostatin inhibitory neurons

city: Montreal

first: Nahum

last: Sonenberg

state: Quebec

address: Goodman Cancer Research Centre 1160 Pine Avenue West, Room 614

department: Department of Biochemistry

country: Canada

institute: McGill University

summary: To study the impact of p-eIF2α reduction in excitatory neurons on translational landscape, we performed both excitatory neuron-specific translational profiling  and general proteomic analysis in the dorsal hippocampus of eIF2α cKICaMKIIα and control mice under basal conditions and following learning.

overall_design: Ribotag IP and RNA-Seq of mouse hippocampi  of eIF2α cKICaMKIIα and control mice

first: Vijendra

last: Sharma

first: Rapita

last: Sood

first: Abdessattar

last: Khlaifia

first: Mohammad

middle: J

last: Eslamizade

first: Tzu-Yu

last: Hung

first: Danning

last: Lou

first: Azam

last: Asgarihafshejani

first: Maya

last: Lalzar

first: Stephen

last: Kiniry

first: Matthew

last: Stokes

first: Noah

last: Cohen

first: Alissa

last: Nelson

first: Kathryn

last: Abell

first: Anthony

last: Possemato

first: Shunit

last: Gal-Ben-Ari

first: Vinh

middle: T

last: Truong

first: Peng

last: Wang

first: Adonis

last: Yiannakas

first: Fatemeh

last: Saffarzadeh

first: A

middle: C

last: Cuello

first: Karim

last: Nader

first: Randal

last: Kaufman

first: Mauro

last: Costa-Mattioli

first: Pavel

last: Baranov

first: Albert

last: Quintana

first: Elisenda

last: Sanz

first: Arkady

last: Khoutorsky

first: Jean-Claude

last: Lacaille

first: Kobi

last: Rosenblum


title: Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium

status: Public on Sep 23 2020

city: Philadelphia

first: Sarshan

middle: R.

last: Pather

state: PA

address: 415 Curie Boulevard

department: Department of Neuroscience

country: USA

institute: University of Pennsylvania

summary: Neurological complications are common in patients with COVID-19. While SARS-CoV-2, the causal pathogen of COVID-19, has been detected in some patient brains, its ability to infect brain cells and impact their function are not well understood, and experimental models using human brain cells are urgently needed. Here we investigated the susceptibility of human induced pluripotent stem cell (hiPSC)-derived monolayer brain cells and region-specific brain organoids to SARS-CoV-2 infection. We found modest numbers of infected neurons and astrocytes, but greater infection of choroid plexus epithelial cells. We optimized a protocol to generate choroid plexus organoids from hiPSCs, which revealed productive SARS-CoV-2 infection that leads to increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. Together, our results provide evidence for SARS-CoV-2 neurotropism and support use of hiPSC-derived brain organoids as a platform to investigate the cellular susceptibility, disease mechanisms, and treatment strategies for SARS-CoV-2 infection.

overall_design: Bulk RNA-seq of choroid plexus organoids (CPOs) was performed on mock 72 hours post-infection (hpi), SARS-CoV-2 24 hpi, and SARS-CoV-2 72 hpi samples. All conditions were profiled in triplicate.

middle: R


title: Comparative transcriptome analysis of dedifferentiation in mouse mature adipocytes

city: Fujisawa

first: Yoshinao

last: Oki

state: Kanagawa

address: 1866 Kameino

department: Department of Applied Biological Science

institute: Nihon University College of Bioresource Sciences

summary:
In mammals, terminally differentiated cells are generally incapable of reversing the differentiation process. We showed that adipocytes (AC), which is a terminally differentiated cell type, can dedifferentiate during culture in vitro and acquire multipotency.
We investigated the dedifferentiation mechanism of AC using global gene expression analyses.

overall_design: Using Affymetrix mouse genome array, we compared global gene expression profiles during dedifferentiation to search for particular biological functions in genes of which expression intensities were increased or decreased by AC dedifferentiation.

first: Koichiro

last: Kano


title: Thyroid hormone receptor a in skeletal muscle is essential for thyroid thermogenesis

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Thyroid hormones are important for homeostatic control of energy metabolism and body temperature. Although skeletal muscle is considered an important site for thyroid action, the contribution of thyroid hormone receptor signaling, in muscle, to whole-body energy metabolism and body temperature has not been resolved. Here, we show that thyroid hormone-induced increase in energy expenditure requires thyroid hormone receptor alpha 1 (TRa1) in skeletal muscle, but that thyroid hormone induced elevation in body temperature is independent of muscle-TRa1. In slow-twitch soleus muscle, ablation of TRa1 leads to an altered fiber type composition toward a more oxidative phenotype, which, however, does not influence running capacity or motivation to voluntary running. RNA-sequencing of soleus muscle from WT mice and TRaHSACre mice revealed differentiated transcriptional regulation of genes associated with muscle thermogenesis, such as sarcolipin and UCP3, thus providing molecular clues pertaining to the mechanistic underpinnings of TRa1-linked control of whole-body metabolic rate. Together, this work establishes a fundamental role for skeletal muscle in thyroid hormone-stimulated increase in whole-body energy expenditure.

overall_design: 22 samples from either wild-type (WT) or knockout (KO) mice either treated with T3 (treatment) or vehicle (vehicle).

first: Trine

middle: S

last: Nicolaisen

first: Anders

middle: B

last: Klein

first: Oksana

last: Dmytriyeva

first: Jens

last: Lund

first: Andreas

last: Fritzen

first: Christian

last: Strini

first: Annemarie

last: Lundsgaard

first: Mikkel

last: Frost

first: Tao

last: Ma

first: Peter

last: Schjerling

first: Zachary

last: Gerhart-Hines

first: Frederic

last: Flamant

first: Karine

last: Gauthier

first: Steen

last: Larsen

first: Erik

middle: A

last: Richter

first: Bente

last: Kiens

first: Christoffer

last: Clemmensen


title: Long-term expansion with germline potential of human primordial germ cell-like cells in vitro [RNA-seq]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Human germ cells perpetuate human genetic and epigenetic information. However, the underlying mechanism remains elusive, due to a lack of appropriate experimental systems. Here, we show that human primordial germ cell‐like cells (hPGCLCs) derived from human‐induced pluripotent stem cells (hiPSCs) can be propagated to at least ~10^6‐fold over a period of 4 months under a defined condition in vitro. During expansion, hPGCLCs maintain an early hPGC‐like transcriptome and preserve their genome‐wide DNA methylation profiles, most likely due to retention of maintenance DNA methyltransferase activity. These characteristics contrast starkly with those of mouse PGCLCs, which, under an analogous condition, show a limited propagation (up to ~50‐fold) and persist only around 1 week, yet undergo cell‐autonomous genome‐wide DNA demethylation. Importantly, upon aggregation culture with mouse embryonic ovarian somatic cells in xenogeneic‐reconstituted ovaries, expanded hPGCLCs initiate genome‐wide DNA demethylation and differentiate into oogonia/gonocyte‐like cells, demonstrating their germline potential. By creating a paradigm for hPGCLC expansion, our study uncovers critical divergences in expansion potential and the mechanism for epigenetic reprogramming between the human and mouse germ cell lineage.

overall_design: RNA-seq analysis of human iPSC, iMeLC, PGCLC, and expanded PGCLC.

first: Yusuke

last: Murase

first: Hiroshi

last: Ohta

first: Chika

last: Yamashiro

first: Tomonori

last: Nakamura

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Single cell lineage analysis reveals cell fate determination events during directed β-cell differentiation

status: Public on Sep 20 2020

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

summary: In vitro differentiation of human ES cells into insulin-producing β-like cells offers new opportunities for pancreatic development modeling and potential diabetes therapy. However, the precise molecular events associated with this multi-stage process remain unclear. Here, we generated 95,308 single cell transcriptome data encompassing the entire differentiation process, and reconstructed a tree delineating the fate choices of all major cell populations in both endocrine and non-endocrine lineages. Most detectable genes are dynamically regulated during differentiation, and stage-specific transcription factors create the time-dependent enhancer landscapes. Interestingly, we found that many diabetes/obesity risk genes are only transiently expressed during differentiation. One example is TCF7L2, which peaked during the pancreatic progenitor stages driven by an enhancer located within a diabetes GWAS locus. From the lineage analysis, we found that the NOTCH signaling-downstream gene HES1 is one of the “switch genes” associated with the choice of non-endocrine cell fate; this led to an improved differentiation protocol for better yield of endocrine cells by adjusting the timing of NOTCH inhibition. Additionally, we discovered that ROCKII inhibitor also promotes endocrine differentiation by suppressing non-endocrine lineage. Taken together, our comprehensive single cell lineage analyses provided a valuable resource for the study of pancreatic development and disease etiology.

overall_design: Single cell sequencing (Drop-seq) for  In vitro beta cell differentiation

first: Fulai

last: Jin

first: Jiajia

last: Xi

first: Haiyan

last: Li

first: Anniya

last: Gu

first: Konstantin

last: Leskov

first: Yan


title: Beclin1 Shapes Cardiomyocyte Cell Identity Independent of Its Autophagic Function during Cardiac Reprogramming

city: Chapel Hill

first: Li

last: Wang

state: NC

address: 111 Mason Farm Rd, Chapel Hill, NC 27599

department: UNC

institute: University of North Carolina at Chapel Hill

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This study aimed to compare the transcriptome profiling (RNA-seq) and chromatin accessibility landscape (ATACseq) of induced cardiomyocytes (iCMs) with Beclin1 (Becn1) knockdown and control iCMs (shNT). we generated ATAC-Seq data from day 3 shNT- and shBecn1-treated MGT or control LacZ transduced fibroblasts. We interrogated the enrichment of ATAC-seq reads at +1 and -1 Kb around TSS (Transcription starting site). Comparing MGT-iCMs with LacZ transduced cells, we found that MGT-iCMs gained numerous open chromatin regions compared to LacZ transduced cells. In total, 22,262 high-confidence open chromatin regions were identified when comparing MGT-shNT iCMs with LacZ-shNT cells, and 11,401 open regions were found in MGT-shBecn1 iCMs when comparing to LacZ-shBecn1 cells. However, MGT-shBecn1 iCMs exhibited minimal differences that did not reach statistical significance when compared with MGT-shNT cells. MGT-shBecn1 iCMs had same number of open chromatin regions as the MGT-shNT cells. In parallel, we performed RNA-seq to profile transcriptome changes among day 3 and day 5 shNT- or shBecn1-treated reprogramming and control cells. Next, we profiled the differentially expressed genes (DEGs) at each time point. Gene set enrichment analysis (GSEA) revealed that shBecn1 significantly up-regulated gene sets related to myogenesis, such as those involved in the formation of contractile fiber and myofibril assembly and down-regulated gene sets related to cell proliferation and inflammation. Interestingly, GSEA analysis demonstrated additional enrichment plots of Wnt/β-Catenin signaling in shBecn1 iCMs.

overall_design: mRNA profile and chromatin accessibility profile of neonatal cardiac fibroblasts that were transduced with MGT or control LacZ retroviras plus shBecn1 or shNT treatment.

first: Hong

last: Ma

first: Yuchen

last: Yang

last: Qian


title: CPL4 is a suppressor of de novo shoot organogenesis from roots of Arabidopsis thaliana

status: Public on Sep 19 2020

city: College Station

first: Akihito

last: Fukudome

state: Texas

address: Dept. Horticultural Sciences MS2133 Texas A&M Univ.

institute: Texas A&M University

summary: De novo shoot organogenesis (DNSO) is a commonly used pathway for plant biotechnology, and is a hormonally regulated process, where auxin and cytokinin coordinates suites of genes encoding transcription factors, general transcription factors, and RNA metabolism machinery genes. Here we report that silencing Arabidopsis thaliana CTD phosphatase-like 4 (CPL4RNAi), which increases phosphorylation level of RNA polymerase II (pol II) CTD, altered lateral root development and DNSO efficiency of the host plants, suggesting an importance of precise control of pol II activities during DNSO. Under standard condition, roots of CPL4RNAi lines produced no or few lateral roots. When induced by high concentration of auxin, CPL4RNAi lines failed to produce focused auxin maxima at the meristem of lateral root primordia, and produced fasciated lateral roots. By contrast, root explants of CPL4RNAi lines were highly competent for DNSO. Efficient DNSO of CPL4RNAi lines were observed even under 10 times less cytokinin required for wild type explants. Transcriptome analysis showed CPL4RNAi but not wild type explants expressed high levels of shoot meristem related genes during priming by high auxin/cytokinin ratio, and subsequent shoot induction with cytokinin. These results indicate that CPL4 functions as a repressor of the early stage of DNSO, during acquisition of competency by high auxin/cytokinin ratio, perhaps via regulation of pol II activities.

overall_design: Examination of two genotypes (wild-type and CPL4 knockdown) and two conditions (roots on shoot-induction media with or without cytokinin) in biological triplicate.

first: Hisashi

last: Koiwa


title: Single-cell functional pharmacogenomics reveal cell decision information within gene expression noise

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Single HeLa cells were treated with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL, 25ng/ml, 50min) to determine their response profiles (“high” or “low”) by live-cell microscopy using a FRET sensor of capase-8 dynamics, a predictor of “cell death” or “cell survival”, respectively. Based on their response profile, cells were isolated by laser-capture microdissection and analyzed by single-cell RNA sequencing to determine the gene expression signature associated with their drug response profile.

overall_design: Evaluation of two different drug response profiles in HeLa cells treated with TRAIL: “high” and “low” response profiles.

first: Jeremie

last: Roux

first: Marie-Jeanne

last: Arguel

first: Agnes

last: Paquet

first: Pascal

last: Barbry


title: Anergic CD8+ T cells with lower levels of IL-7 receptor α (Agilent)

city: Seoul

first: Hang-Rae

last: Kim

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University College of Medicine

summary: We investigated the entity of IL-7Rα low effector memory (EM) CD8+ T cells in healthy individuals and finally uncovered that they were unable to proliferate and produce IL-2 in response to TCR stimulation

overall_design: Total RNA obtained from both resting and activated human IL-7Rα high and low effector memory (EM) CD8+ T cells upon TCR stimulation with anti-CD3/CD28 Abs for 18 hr.


title: P0, mouse, RNA-seq, epithelial vs neuronal, mesenchymal and vascular endothelial cells in the auditory and vestibular systems

city: Baltimore

first: Seth

last: Ament

state: MD

address: 670 W Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: Inner ears from newborn ICR mice were dissociated, stained antibodies for CD326, CD49f and CD34, and sorted to the aforementioned cell types, followed by RNA-seq

overall_design: This dataset includes samples from epithelial vs neuronal vs mesenchymal vs vascular endothlial cells in the auditory and vestibular systems (8 cell types total).

first: Ronna

last: Hertzano


title: Immunogenic chemotherapy enhances recruitment of CAR-T cells to solid tumors and improves anti-tumor efficacy when combined with checkpoint blockade [RNA-Seq]

status: Public on Sep 18 2020

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

summary: CAR-T cell therapy is effective in hematologic malignancies but not in solid tumors. In breast and lung cancer patients, CAR-T cells targeting ROR1 infiltrated tumors poorly and became dysfunctional. To test strategies for enhancing efficacy, we induced ROR1+ lung tumors in KrasLSL-G12D/+;p53fl/f mice. Murine ROR1 CAR-T cells transferred after lymphodepletion with cyclophosphamide (Cy) transiently controlled tumor growth but infiltrated tumors poorly and lost function, as observed in patients. Adding oxaliplatin (Ox) to the lymphodepletion regimen activated tumor macrophages to express T cell-recruiting chemokines, resulting in improved CAR-T cell infiltration, remodeling of the tumor microenvironment, and increased tumor sensitivity to anti-PD-L1. Combination therapy with Ox/Cy and anti-PD-L1 synergistically improved CAR-T mediated tumor control and survival, providing a strategy to improve CAR-T cell efficacy in the clinic.

overall_design: 9 samples of bulk RNA sequencing from murine lung tumors treated in vivo +/- chemotherapy

first: Scott

last: Furlan

first: Shivani

last: Srivastava

first: Stanley

last: Riddell


title: Multiplexed and ultralow-input ChIP-seq enabled by tagmentation-based indexing and facile microfluidics

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Epigenome constitutes an important layer that regulates gene expression and dynamics during development and diseases. Extensive efforts have been made to develop epigenome profiling methods using a low number of cells and with high throughput. Chromatin immunoprecipitation (ChIP) is the most important approach for profiling genome-wide epigenetic changes such as histone modifications. In this report, we demonstrate microfluidic ChIPmentation (mu-CM), a microfluidic technology that enables profiling cell samples that individually do not generate enough ChIP DNA for sequencing library preparation. We used a simple microfluidic device to allow 8 samples to be processed simultaneously. The samples were indexed differently using a tagmentation-based approach (ChIPmentation) and then merged for library preparation. Histone modification profile for each individual sample was obtained by demultiplexing the sequencing reads based on the indexes. Our technology allowed profiling 20 cells and is well suited for cell-type-specific studies using low-abundance tissues.

overall_design: We profiled H3K4me3 of GM12878 cell line starting with 100 cells down to as few as 20 cells per assay. We also examined H3K4me1 with 1,000 GM cells. We developed a tagmentation-based microfluidic method, which performed 8 replicate experiments in parallel. The file name contains information on the histone modification type, the number of cells per unit, and the number of the unit. For example, "H3K4me3-100-1" refers to the data set on H3K4me3 using 100 cells per assay/unit produced by unit 1 of the 8-unit microfluidic device.

first: Chengyu

last: Deng


title: TbRAP1's dsDNA binding activity plays an important role in subtelomeric gene expression regulation

city: CLEVELAND

first: Bibo

last: Li

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease

institute: CLEVELAND STATE University

summary: We examine the function of the TbRAP1 DB domain in gene expression regulation in Trypanosoma brucei that causes human African trypanosomiasis. TbRAP1 is required for normal VSG monoallelic expression, a key aspect of antigenic variation that is used by T. brucei to evade the host immune response.

overall_design: High-throughput paired-end RNA sequencing on the Illumina platform was performed. Mutant T. brucei strain has one WT TbRAP1 allele flanked by  loxP repeats (floxed) and a FLAG-HA-HA and an SV40 NLS- tagged TbRAP1-5A, TbRAP1-2SD, or a deleted allele. Control T. brucei strain has one floxed and a WT TbRAP1 allele. Both mutant and control cells were induced for Cre induction for 30 hrs (to remove the floxed TbRAP1 allele) before total RNA was isolated. Three independent induction were performed for both cells. RNA samples were sent to Novogene for subsequent experiments. Poly(A) RNA was purified for generating cDNA library and paired-end sequencing was done using Illumina. Gene expression profiles were compared between the mutant and control cells by differential gene expression analysis.

first: Marjia

last: Afrin

first: Amit

last: Gaurav

first: Xian

last: Yang

first: Xuehua

last: Pan

first: Yanxiang

last: Zhao


title: NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure adipocyte differentiation [chromatin]

first: Hironori

last: Waki

summary: The transcription factor nuclear factor I-A (NFIA) is a regulator of brown adipocyte differentiation. Here we show that the C-terminal 17 amino acid residues of NFIA (which we named pro#3 domain) is required for transcriptional activity of NFIA. Full-length NFIA, but not deletion mutant lacking pro#3 domain rescued impaired Pparg expression and adipogenesis in NFIA-knockout cells. Mechanistically, the ability of NFIA to increase chromatin accessibility is mediated through pro#3 domain. However, the deletion mutant still binds to Myod1 enhancer to decrease chromatin accessibility and represses Myod1 as well as proximally transcribed non-coding RNA called DRReRNA, leading to suppression of myogenic gene program. Therefore, the negative effect of NFIA on myogenic gene program is, at least in part, independent from the positive effect on Pparg expression and its downstream adipogenic gene program. These results uncover multiple ways of action of NFIA to ensure optimal regulation of brown adipocyte differentiation.

overall_design:
ChIP-seq , FAIRE-seq and RNA-seq analysis of control-, full-length NFIA and Δpro#3 mutant-expressing C2C12 myoblasts and RNA-seq analysis of NFIA-KO ingSVF cells

ChIP target is Flag-tagged wildtype or delta pro#3 mutant NFIA.

first: Yuta

last: Hiraike

first: Misato

last: Oguchi

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Toshimasa

last: Yamauchi

first: Takashi

last: Kadowaki


title: CD19 expression in human brain mural cells as a target of immunotherapy-associated neurotoxicity

city: Stanford

first: Ansuman

last: Satpathy

state: CA

address: BMI1 4600, 240 Pasteur Drive

institute: Stanford University

summary: Single-cell RNA-sequencing data generated from mouse brain, enriched for neurovascular and CD19+ cells.

overall_design: Brains from four mice were dissected.  Enzymatic digestion was performed using STEMxyme I, followed by the removal of myelin debris using a sucrose gradient. Cells were blocked and stained, then sort-enriched for CD19+, CD13+, and CD31+ events.  The resulting cells were captured using the 10x Genomics 5' scRNA sequencing kit.

first: Kevin

last: Parker

first: Howard

middle: Y

last: Chang

first: Denis

last: Migliorini

first: Avery

middle: D

last: Posey


title: Directly induced oocyte-like Cells (DIOLs)

city: Fukuoka

first: Nobuhiko

last: Hamazaki

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku,

department: Department of Developmental Stem Cell Biology

institute: Kyushu University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Chimeric Antigen Receptors with a MyD88 and CD40 costimulatory endodomain endow T cells with superior antitumor activity

city: Memphis

first: Patrick

middle: Allen

last: Schreiner

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Children's Research Hospital

summary: CAR T-cell therapy for solid tumors has shown limited efficacy in early phase clinical studies. The majority of CARs encode CD28 and/or 41BB costimulatory endodomains and we explored here if MyD88 and CD40 (MC) costimulatory endodomains in CARs improve their antitumor activity. We generated CD28-, 41BB-, and MC-CAR T-cells and demonstrate that MC-CAR T-cells have greater proliferative capacity and antitumor activity in repeat stimulation assays and in tumor models in vivo. Transcriptomic analysis revealed that MC-CAR T-cells expressed higher levels of MYB and FOXM1, key cell cycle regulators, and are activated at base line. After stimulation, MC-CAR T-cells remain in a less differentiated state than CD28- and 41BB-CAR T-cells as judged by low levels of TBET and BLIMP1 expression, and lower cytolytic activity in comparison to CD28- and 41BB-CAR T-cells. Thus, including MyD88 and CD40 signaling domains in CARs may improve current CAR T-cell therapy approaches for solid tumors.

overall_design: Examination of CD4+ and CD8+ unstimulated and stimulated 4H5D-, CD28-, 41BB- and MC-CAR T cell costimulatory endodomains

first: Brooke

last: Prinzing

first: Matthew

last: Bell

first: Yiping

last: Fan

first: Giedre

last: Krenciute

first: Stephen

last: Gottschalk


title: Pancreatic cancer cells require the transcription factor MYRF (Myelin Regulatory Factor) to maintain ER homeostasis (ChIP-Seq).

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: Many tumors of endodermal origin are composed of highly secretory cancer cells that must adapt endoplasmic reticulum (ER) activity to enable proper folding of secretory proteins, prevent ER stress and thus maintain their viability. In pancreatic ductal adenocarcinoma (PDAC), well-differentiated and secretory cancer cells coexist with poorly differentiated cells with quasi-mesenchymal features. We found that the differentiated PDAC cells, but not the undifferentiated ones, expressed an ER membrane-associated transcription factor (TF), Myelin Regulatory Factor (MYRF), that is released by self-cleavage and translocates to the nucleus. MYRF expression was directly controlled by HNF1B, a TF maintaining epithelial identity in PDAC, and it acted to fine-tune the expression of genes encoding highly glycosylated and cysteine-rich secretory proteins, thus preventing ER overload. MYRF-deficient PDAC cells showed anatomical and biochemical signs of ER stress, impaired proliferation and inability to form spheroids in vitro, while in vivo they generated highly secretory but poorly proliferating and hypo-cellular tumors. These data indicate a role of MYRF in the control of homeostasis and proliferation of cancer cells with high secretory activity

overall_design: Chromatin from human pancreatic ductal adenocarcinoma cell lines was immunoprecipitated with various transcription factors and histone modification targeting antibodies and subjected to multiparallel sequencing. Experiments were carried out in unmodified and genome edited clonal CFPAC1 cells.


title: Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes

city: Stockholm

first: Urban

last: Lendahl

state: State...

address: SE-171 77 Stockholm

department: CMB

country: Sweden

institute: Karolinska Insitute

summary: In this study, we express an activated form of Notch1 in the mouse mammary luminal lineage and analyse the consequences for tumour formation and the transcriptomic landscape in the luminal lineage. Simultaneous conditional activation of a Notch1 intracellular domain (Notch1 ICD) and EGFP in the luminal lineage was achieved by removal of a stop cassette by CRE-recombinase expression from the whey acidic protein (WAP) promoter. Gene expression differences were analysed by single cell RNA-sequencing.

overall_design:
Mammary gland single cell RNA profiles of after a 3-4 months lactation  of WAP-CRE; R26-N1ICD and WAP-CRE; R26-tdTomato mice were generated by single cell RNA sequencing, using HiSeq2500 sequencer.
Each sample (GSM) represents a single cell.

first: Yee

last: Phoon

first: Indira

last: Chivukula

first: Yat

middle: L

last: Tsoi

first: Shigeaki

last: Kanatani

first: Per

last: Uhlén

first: Raoul

last: Kuiper


title: Myf6/MRF4 Mediated Myokine Signaling is Required for the Maintenance of the Adult Skeletal Muscle Stem Cell Pool

city: Ottawa

first: Theodore

last: Perkins

state: Ontario

address: 501 Smyth Rd.

department: Regenerative Medicine Program

institute: Ottawa Hospital Research Institute

summary: In metazoans, skeletal muscle evolved to contract and to produce force. Recent experimental evidence suggests, however, that skeletal muscle has also acquired endocrine functions and produces a vast array of myokines, but how myokine production is regulated and how they affect the resident stem cell population of the skeletal muscle is unknown. Here, we show that in adult skeletal muscle, Myf6/MRF4 is a major regulator of myokine expression. Genetic deletion of Myf6 in skeletal muscles leads to exhaustion of the muscle stem cell (MuSCs) pool in adult mice in a myokine-dependent manner but, surprisingly, does not disrupt muscle differentiation. Using ChIP-Seq and gene expression analyses of myogenic factors, we show that Myf6/MRF4 is essential for the transcriptional activation of many myokines and muscle-secreted proteins, including ligands for canonical signaling pathways such as EGFR, VEGFR and STAT3.  Consequently, MuSCs from Myf6 knockout animals show impaired activation of those signaling pathways and exhibit impaired quiescence, defective self-renewal, but nevertheless undergo differentiation. Lastly, we show that induction of myokine expression during aerobic and anaerobic exercise closely correlates with Myf6 expression. Together, these findings indicate that control of myokine signaling by Myf6 is critical to maintain muscle stem cell pool in adult skeletal muscle.

overall_design: ChIP-seq for Myf6 in adult mouse muscle satellite cells, and RNA-seq in WT and Myf6 KO conditions, with or without injury.

first: Vahab

last: Soleimani


title: RNA deep sequencing data of the whole transcriptomes of the wild-type and crp1 (MSMEG_6189) mutant strains of Mycobacterium smegmatis MC2 155

city: Pusan

first: Eon-Min

last: Ko

address: pusandaehak-ro

institute: Pusan national university

summary: Our comparative RNA sequencing analysis of the wild-type strain of M. smegmatis and its isogenic crp1 (MSMEG_6189) mutant strain lacking the cAMP receptor protein 1 revealed Crp1 regulon in the M. smegmatis

overall_design: Comparison of gene expression between the wild-type and crp1 (MSMEG_6189) mutant strains of Mycobacterium smegmatis that are aerobically grown.

first: Jeong-Il

last: Oh


title: Temporal control of species-specific motor neuron differentiation [Hs]

city: London

first: Teresa

last: Rayon

address: Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: How species-specific developmental timing is controlled is largely unknown. By following human embryonic stem cell (hESC) and mouse stem cell (mESC) differentiation to motor neurons through detailed RNA-sequencing time courses, we wish to find if there is a global scaling factor between species

overall_design: RNA samples from mouse and human in vitro differentiations. Human and mouse stem cells monolayer differentiations towards motor neurons upon addition of Retinoic Acid and a Sonic Hedgehog agonist. Mouse samples were collected every 12h for the first three days and daily up to day 7 in triplicates. Human samples are collected daily in triplicates up to day 15.


title: Genetic compensation rather than genetic assimilation drives the evolution of plasticity in response to mild warming across latitudes in a damselfly

city: Leuven

first: Janne

last: Swaegers

address: Charles Deberiotstraat 32

country: Belgium

institute: KU Leuven

summary: Global warming is causing plastic and evolutionary changes in the phenotypes of ectotherms. Yet, we have limited knowledge on how the interplay between plasticity and evolution shapes thermal responses and underlying gene expression patterns. We assessed thermal reaction norm patterns across the transcriptome and identified associated molecular pathways in northern and southern populations of the damselfly Ischnura elegans. Larvae were reared in a common garden experiment at the mean summer water temperatures experienced at the northern (20 °C) and southern (24 °C) latitudes. This allowed a space-for-time substitution where the current gene expression levels at 24 °C in southern larvae are a proxy for the expected responses of northern larvae under gradual thermal evolution to the predicted 4 °C warming. Most differentially expressed genes showed fixed differences across temperatures between latitudes, suggesting that thermal genetic adaptation will mainly evolve through changes in constitutive gene expression. Northern populations also frequently showed plastic responses in gene expression to mild warming, while southern populations were much less responsive to temperature. Thermal responsive genes in northern populations showed to a large extent a pattern of genetic compensation, i.e. gene expression that was induced at 24 °C in northern populations remained at a lower constant level in southern populations, and were associated with metabolic and translation pathways. There was instead little evidence for genetic assimilation of an initial plastic response to mild warming. Our data therefore suggest that genetic compensation rather than genetic assimilation may drive the evolution of plasticity in response to mild warming in this damselfly species.

overall_design: RNA was extracted from six larvae per combination of temperature and population. The RNA of three larvae per combination of temperature and population was pooled. This resulted in a total of 24 pooled RNA samples (2 rearing temperatures x 2 latitudes x 3 populations x 2 replicates).

first: Katina

middle: I

last: Spanier

first: Robby

last: Stoks


title: Physiologic RNA Targets and Refined Sequence Specificity of Coronavirus EndoU

city: Aurora

first: Jay

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: Coronavirus EndoU inhibits double-stranded RNA (dsRNA)-activated antiviral responses; however, it is unclear how this occurs because the physiologic RNA substrates of EndoU are unknown. In this study, we used Mouse Hepatitis Virus (MHV)-infected bone-marrow-derived macrophage (BMM) and cyclic phosphate cDNA sequencing to identify the RNA targets of EndoU

overall_design: cyclic phosphate and RNA seqeuncing libraries generated from MHV infected bone marrow macrophages.

first: Rachel

last: Ancar


title: Temporal control of species-specific motor neuron differentiation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Genes regulated by nuclear Lipin in the fed and fasting state

city: Fayetteville

first: Michael

last: Lehmann

state: AR

address: SCEN 601

department: Biological Sciences

institute: University of Arkansas

summary: Lipins are eukaryotic proteins with functions in lipid synthesis and the homeostatic control of energy balance. They execute these functions by acting as phosphatidate phosphatase enzymes in the cytoplasm and by changing gene expression after translocation into the cell nucleus, in particular under fasting conditions. Here, we asked how gene expression changes, under both fed and fasting conditions, when nuclear translocation of Lipin is impaired. To address this question, we created a Drosophila mutant expressing Lipin lacking a nuclear localization signal (LipinDNLS). Notably, adult LipinDNLS flies were not only viable but also exhibited improved life expectancy. In contrast, they were highly susceptible to starvation. To examine how these phenotypes correlate with changes in gene expression, we carried out an RNA-seq analysis with mRNA from female and male LipinDNLS and control flies that had been kept under fed or fasting conditions. We found that genes involved in metabolism, feeding behavior, and the immune response were mis-regulated in LipinDNLS flies. The changed expression of these genes supports hypotheses explaining improved life expectancy under fed and decreased life expectancy under fasting conditions. For instance, metabolic rate measurements confirmed the prediction based on the RNA-seq data that energy production by oxidative phosphorylation is reduced in fed LipinDNLS flies.

overall_design: Wild-type and mutant fruit flies were normally fed or subjected to starvation. mRNA-seq libraries of males and females of the 4 treatment groups were sequenced in two separate runs (191105_A00639_0138_BHG2HNDRXX-NovaRS-06-FC1-ML-RS24 and 191108_A00639_0140_BHFYTTDRXX-NovaRS-06-FC2-ML-RS24).


title: DNA methylome analysis of directly induced oocyte-like cells (DIOLs)

first: Nobuhiko

last: Hamazaki

summary: During female germline development oocytes become a highly specialized cell type, and form a maternal cytoplasmic store of crucial factors during oocyte growth. Oocyte growth is triggered at the primordial-primary follicle transition accompanied with dynamic changes in gene expression, yet the gene regulatory network underpinning oocyte growth remains elusive. Here we identified a set of transcription factors sufficient to trigger oocyte growth. By dissection of the change in gene expression and functional screening using an in vitro oocyte development system, we identified 8 transcription factors, each of which was essential for the primordial-primary follicle transition. Surprisingly, enforced expression of these transcription factors swiftly converted pluripotent stem cells to oocyte-like cells that were competent for fertilization and subsequent cleavage. These transcription factor-induced oocyte-like cells were formed without PGC specification, epigenetic reprogramming or meiosis, establishing that oocyte growth and lineage-specific de novo DNA methylation is separable from the preceding epigenetic reprogramming in PGCs. This study identifies a core set of transcription factors for orchestrating oocyte growth, and also provides an alternative source of ooplasm, which is a unique material for reproductive biology and medicine.

overall_design: paired-end PBAT sequence for whole genome methylome of directly induced oocyte-like cells (DIOLs)

first: Katsuhiko

last: Hayashi

first: Nobuhuko


title: Pancreatic cancer cells require the transcription factor MYRF (Myelin Regulatory Factor) to maintain ER homeostasis (RNA-Seq).

first: Chiara

last: Balestrieri

overall_design: Total RNA from human pancreatic ductal adenocarcinoma cell lines was processed for multiparallel sequencing. Experiments were carried out in genome edited clonal CFPAC1 cells (3 MYRF-deleted CRISPR-Cas9 clones and 3 wt clones).


title: RNA-seq of knocked-out oocytes and directly induced oocyte-like cells (DIOLs)

overall_design: polyA+RNA was harvested from mouse oocytes and directly induced oocyte-like cells (DIOLs). Extracted polyA+RNA were used for the directional (strand-specific) RNA-seq library construction.


title: Temporal control of species-specific motor neuron differentiation [Mm]


title: LCM-Seq analysis of microscopically defined human embryo HSC microenvironment

status: Public on Sep 17 2020

city: Edinburgh

first: Edie

last: Crosse

address: 5 Little France Road

department: Centre for Regenerative Medicine

institute: University of Edinburgh

summary: This dataset contains RNA-Seq data for cells within spatially defined subdomains of the human embryo dorsal aorta, subdissected from tissue sections using laser capture microdissection. This dataset explores dorsal-ventral polarisation across the dorsal aorta, the site of hematopoietic stem cell emergence.

overall_design: In total 30 samples (subdomains) from 6 human embryos are analysed. This includes 6 subdomains (V_Inner, D_Inner, V_Mid, D_Mid, V_Outer, D_Outer) from 3 CS16 embryos and 4 subdomains ([V], [VL], [DL], [D]) from 3 CS17 embryos.

first: Alexander

last: Medvinsky


title: RNA-Seq analysis of sorted hematoendothelial populations from the human embryo dorsal aorta

summary: This dataset contains RNA-Seq data for sorted hematoendothelial subpopulations from the ventral (AoV) and dorsal (AoV) portions of the CS15-16 human embryo dorsal aorta. This includes endothelial (VC+CD45-), Hematopoietic Stem/Progenitor Cells (VC+CD45+) and more mature hematopoietic cells (VC-CD45+) from both the AoV and AoD.

overall_design: 3 populations: endothelial (VC+CD45-), Hematopoietic Stem/Progenitor Cells (VC+CD45+) and hematopoietic cells (VC-CD45+) were sorted from the AoV and AoD from 2 embryos (Carnegie stages 15-16).

first: Stanislav

last: Rybtsov

first: Fiona

last: Rossi


title: Immunogenic chemotherapy enhances recruitment of CAR-T cells to solid tumors and improves anti-tumor efficacy when combined with checkpoint blockade  [scRNA-Seq]

first: Warren

last: Shlomchik

summary: CAR-T cell therapy is effective in hematologic malignancies but not in solid tumors. In breast and lung cancer patients, CAR-T cells targeting ROR1 infiltrated tumors poorly and became dysfunctional. To test strategies for enhancing efficacy, we induced ROR1+ lung tumors in KrasLSL-G12D/+;p53fl/f mice. Murine ROR1 CAR-T cells transferred after lymphodepletion with cyclophosphamide (Cy) transiently controlled tumor growth but infiltrated tumors poorly and lost function, as observed in patients. Adding oxaliplatin (Ox) to the lymphodepletion regimen activated tumor macrophages to express T cell-recruiting chemokines, resulting in improved CAR-T cell infiltration, remodeling of the tumor microenvironment, and increased tumor sensitivity to anti-PD-L1. Combination therapy with Ox/Cy and anti-PD-L1 synergistically improved CAR-T mediated tumor control and survival, providing a strategy to improve CAR-T cell efficacy in the clinic.

overall_design: 5 samples of single cell RNA sequencing from CAR-T cell infusion product and murine lung tumors treated in vivo +/- chemotherapy and +/- CAR T cells

first: Scott

last: Furlan

first: Shivani

last: Srivastava

first: Stanley

last: Riddell


title: Transcriptional profiling by RNA-seq of an evolved hyper-ethanol surviving yeast strain and a wild-type yeast strain at various stress time points

city: New York

first: Jamie

last: Yang

state: NY

address: 1150 St. Nicholas Avenue

institute: Columbia University

summary: Our evolved hyper-ethanol surviving strain showed more than a 10-fold survival under lethal ethanol stress. To determine the strategies the yeast cells employed to achieve this superior survival, we performed transcriptional profiling by RNA-seq to compare the gene expression states between these two strains. Our study found that the evolved strain reprogrammed its gene expression such that its pre-stress state was shifted towards that of the wild-type strain at 15 minutes post-stress.

overall_design: A wild-type and an evolved hyper-ethanol surviving strain were each exposed to 2 minutes of lethal ethanol stress and slowly recovered, with samples taken for sequencing at the following time points: growth in rich media, immediately pre-stress, recovery at 15 min, 30 min, 60 min, 4 hrs.


title: IFI16 functions as an antiviral factor during influenza virus infection by binding viral RNA and enhancing the RIG-I signaling

city: Bei jing

first: zhimin

last: jiang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

department: college of Veterinary medicine

country: China

institute: China agriculture university

sample_organism:
Homo sapiens
Influenza A virus

platform_organism:
Homo sapiens
Influenza A virus

overall_design: Refer to individual Series


title: Dyspigmented hypertrophic scars: Beyond skin color

city: Silver Spring

first: Aarti

last: Gautam

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Although pigment synthesis is well understood, relevant mechanisms of psychologically debilitating dyspigmentation in nascent tissue after cutaneous injuries are still unknown. Here, differences in genomic transcription of hyper- and hypopigmented tissue relative to uninjured skin were investigated using a red Duroc swine scar model. Transcription profiles differed based on pigmentation phenotypes with a trend of more upregulation or downregulation in hyper- or hypopigmented scars, respectively. Ingenuity Pathway Analysis of significantly modulated genes in both pigmentation phenotypes showed pathways related to redox, metabolic, and inflammatory responses were more present in hypopigmented samples, while those related to stem cell development differentiation were found mainly in hyperpigmented samples. Cell-cell and cell-extracellular matrix interactions and inflammation responses were predicted (z-score) active in hyperpigmented and inactive in hypopigmented. The proinflammatory high-mobility group box 1 pathway showed the opposite trend. Analysis of differentially regulated mutually exclusive genes showed an extensive presence of metabolic, proinflammatory, and oxidative stress pathways in hypopigmented scars, while melanin synthesis, glycosaminoglycans biosynthesis, and cell differentiation pathways were predominant in hyperpigmented scar. Several potential therapeutic gene targets have been identified.

overall_design: The red Duroc swine wound model was selected because of many similarities its skin shares with that of human, which made this animal models the prime choice for human wound healing and burn studies. Juvenile castrated male Duroc swine were used to minimize potential interference from the estrogen cycle and to reduce animal aggressiveness. A total of 28 biopsies were collected from two red Duroc pigs, and the transcriptome changes in these biopsies were evaluated during the course of wound healing and scar formation in the context of dyspigmentation.

first: Abdulnaser

last: Alkhalil

first: Bonnie

last: Carney

first: Taryn

middle: E

last: Travis

first: Seid

last: Muhie

first: Stacy

last: Miller

first: Jessica

last: Ramella-Roman

first: Pejhman

last: Ghassemi

first: Rasha

last: Hammamieh

first: Marti

last: Jett

first: Lauren

last: Moffatt

first: Jeffrey

middle: W

last: Shupp


title: Fitness profiling using the yeast deletion library to determine contribution of all non-essential genes to survival under acute exposure to lethal ethanol stress

type: Genome variation profiling by high throughput sequencing

summary: To determine the contribution of yeast genes to acute lethal ethanol stress, we performed fitness profiling of a pooled haploid yeast deletion library. This deletion library contains 4,500 deletions of most non-essential yeast genes. Comparing the abundance of post-stress gene deletions to pre-stress gene deletions allows for the quantification of the effects of each gene deletion on survival

overall_design: The yeast deletion library was exposed to 2 minutes of 24.5% ethanol. A pre-stress sample was saved for comparison to a post-stress sample, which was subjected to an outgrowth period until early log phase. All experiments were performed in triplicates.


title: IFI16 functions as an antiviral factor during influenza virus infection by binding viral RNA and enhancing the RIG-I signaling (RIP-seq)

summary: RIG-I is thought to be the most important sensor of influenza virus infection and plays critical roles in the recognition of cytoplasmic dsRNA and activation of type I IFNs and initiates the innate antiviral immune responses. How the binding of viral RNA to and activation of RIG-I are regulated remains enigmatic. Here, by an affinity proteomics approach with viral RNA as the bait, we found that IFI16, previously identified as a DNA sensor, was significantly induced both in vitro and in vivo during influenza virus infection. Using an IFI16 knockout cells and p204-deficient mice model, we demonstrated that IFI16 enhanced RIG-I-mediated production of type I IFNs and thereby inhibited viral replication during influenza virus infection. Furthermore, we showed that IFI16 regulated the RIG-I signaling by enhancing its transcriptional expression through recruitment of RNA Pol II to the RIG-I promoter. We also verified that IFI16 directly interacted with both viral RNA by HINa domain and associated with RIG-I through its PYRIN domain as well as promoted influenza virus-induced K63-linked polyubiquitination of RIG-I. In addition, we found that IFI16 lost its ability to inhibit viral replication in the absence of RIG-I in virus-infected cells. These results indicate that IFI16 is a key regulator of the RIG-I signaling during antiviral innate immune responses, which highlights a novel mechanism of IFI16 in IAV and other RNA viruses infection, expands our knowledge in antiviral innate immunity, and suggests its possible use as a new strategies to manipulate antiviral responses.

overall_design: To test if IFI16 bound IAV RNA, we eluted RNA co-precipitating with FLAG-tagged IFI16 from IAV-infected RIG-I knockout cells and examined eluates for the presence of IAV RNA. In parallel, we evaluated RNA co-precipitating with FLAG-RIG-I, a known sensor of IAV RNA, as a positive control. And the Flag empty vector as the negative control. We readily detected IAV-specific vRNA mapping to all eight IAV gene segments in IFI16 or RIG-I immunoprecipitates.

first: Jiang

last: Zhimin

first: Wei

last: Fanhua


title: Multivalent proteins rapidly and reversibly phase-separate upon osmotic cell volume  change

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Processing bodies (PBs) and stress granules (SGs) are prominent examples of subcellular,  membrane-less compartments that are observed under physiological and  stress conditions, respectively. We observe that the trimeric PB protein DCP1A rapidly  (within ~10 s) phase-separates in mammalian cells during hyperosmotic stress and  dissolves upon isosmotic rescue (over ~100 s) with minimal impact on cell viability  even after multiple cycles of osmotic perturbation. Strikingly, this rapid intracellular  hyperosmotic phase separation (HOPS) correlates with the degree of cell volume  compression, distinct from SG assembly, and is exhibited broadly by homo-multimeric  (valency ≥ 2) proteins across several cell types. Notably, HOPS sequesters pre-mRNA  cleavage factor components from actively transcribing genomic loci, providing a  mechanism for hyperosmolarity-induced global impairment of transcription termination.  Together, our data suggest that the multimeric proteome rapidly responds to changes  in hydration and molecular crowding, revealing an unexpected mode of globally  programmed phase separation and sequestration that adapts the cell to volume  change.

overall_design: Bru-seq of U2OS cells stably overexpressing GFP-DCP1a were performed under isotonic (150 mM Na+) or hypertonic (300 mM Na+) conditions to assess nascent transcripts

first: Ameya

middle: P

last: Jalihal

first: Sethuramasundaram

last: Pitchiaya

first: Lanbo

last: Xiao

first: Pushpinder

last: Bawa

first: Xia

last: Jiang

first: Karan

last: Bedi

first: Abhijit

last: Parolia

first: Marcin

last: Cieslik

first: Arul

middle: M

last: Chinnaiyan

first: Nils

middle: G

last: Walter


title: Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome

city: Oxford

first: Christoph

last: Treiber

address: Mansfield Rd

department: Centre for Neural Circuits and Behaviour

institute: University of Oxford

summary: Bulk mRNA sequencing reads, mapped to masked Drosophila reference genome

overall_design: Detection of chimeric mRNA transcripts

first: Scott

last: Waddell


title: Polyunsaturated Fatty Acids from Astrocytes Activates PPAR Gamma Signaling in Cancer Cells to Promote Brain Metastasis

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Brain metastasis, the most ominous form of melanoma and carcinoma, is the consequence of favorable interactions between the invaded cancer cells and the brain cells. Peroxisome proliferator-activated receptor gamma (PPARɣ) has ambiguous functions in cancer development and its relevance in advanced brain metastasis remains unclear. Here, we demonstrate that astrocytes, the unique brain glia cells, activate PPARɣ in brain metastatic cancer cells. PPARɣ activation enhances cell proliferation and metastatic outgrowth in the brain. Mechanistically, astrocytes have a high content of polyunsaturated fatty acids that acts as ‘donors’ of PPARɣ activators to the invaded cancer cells. In clinical samples, PPARɣ signaling is significantly higher in brain metastatic lesions. Notably, systemic administration of PPARɣ antagonist significantly reduces brain metastatic burden in vivo. Our study clarifies a prometastatic role for PPARɣ signaling in cancer metastasis in the lipid rich brain microenvironment and argues for the use of PPARɣ blockade to treat brain metastasis.

overall_design: RNA-seq analysis of high and low brain metastatic cell lines cultured alone or with presence of astrocytes.

first: Yongkang

last: Zou

first: Qing

last: Chen


title: Structure-function analysis of microRNA 3′-end trimming by Nibbler

city: Vienna

first: Ivica

last: Sowemimo

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

type: Non-coding RNA profiling by high throughput sequencing

summary: Nibbler (Nbr) is a 3′-to-5′exoribonuclease whose catalytic 3′-end trimming activity impacts miRNA and piRNA biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr’s N-terminal (NTD) and exonucleolytic (EXO) domains in miRNA 3′-end trimming. We have solved the crystal structures of the NTD-core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Aedes aegypti Nbr adopts a HEAT-like repeat scaffold, with basic patches constituting an RNA-binding surface exhibiting a preference for binding dsRNA over ssRNA. Structure-guided functional assays in DrosophilaS2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, that depends on basic surface patches.Gain-of-function experiments revealed a potential role of the NTD in recruitingNbr to Argonaute-bound small RNA substrates.The EXO domain of Aedes aegypti and Drosophila melanogaster Nbr adopt a mixed a/b scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr’sEXO domain exhibits Mn2+-dependent ssRNA-specific 3′-to-5′exoribonuclease activity. Modeling of a 3′ terminal Uridine in to the catalytic pocket of Nbr EXO indicates that 2′-O-methylation of the 3′-U would result in a steric clash with a Tryptophanside chain, suggesting that 2′-O-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease domain.

overall_design: 4 small RNA libraries from Drosophila melanogaster S2 cells.

first: Wei

last: Xie

first: Rippei

last: Hayashi

first: Juncheng

last: Wang

first: Julius

last: Brennecke

first: Stefan

last: Ameres

first: Dinshaw

last: Patel


title: Meta-transcriptomic Analyses Reveal Improved Gamma-amino butyric acid Production Machinery in Levilactobacillus brevis NPS-QW 145 Co-cultured with Streptococcus thermophilus ASCC1275 during Milk Fermentation

status: Public on Sep 16 2020

city: Hong Kong

first: Tingting

last: Xiao

address: Kadoorie Building, Pokfulam Road, Hong kong Island

institute: University of Hong Kong

summary: Purpose: High γ-aminobutyric acid (GABA)-producing Levilactobacillus brevis strain NPS-QW 145 along with Streptococcus thermophilus (one of the two starter bacteria used to make yogurt for its proteolytic activity) to enhance GABA production in milk. But a mechanistic understanding on how Levilactobacillus brevis cooperated with S. thermophilus to stimulate GABA production has been lacking. Method: Metatranscriptomic analyses combined with peptidomics were carried out to unravel the casein and lactose utilization patterns during milk fermentation with the co-culture. Results: We found particular peptides hydrolyzed by S. thermophilus 1275 were transported and biodegraded with peptidase in Lb. brevis 145 to meet the growth needs of the latter. In addition, amino acid synthesis and metabolism in Lb. brevis 145 were also activated to further support its growth. Glucose, as a result of lactose hydrolysis by S. thermophilus 1275, but not available lactose in milk, was outcompeted by Lb. brevis 145 as a main carbon source for glycolysis to produce ATP.In the stationary phase, under the acidic condition due to accumulation of lactic acid produced by S. thermophilus 1275, genes expression involved in pyridoxal phosphate (coenzyme of glutamic acid decarboxylase) metabolism and glutamic acid decarboxylase (Gad) in Lb. brevis 145 were induced for GABA production.

sample_organism:
Levilactobacillus brevis
Streptococcus thermophilus ASCC 1275

overall_design: 6 samples; triplicates; Control group (S): mRNA profiles of 18-h fermented milk inoculated with Streptococcus thermophilus; Experimental group (SL): mRNA profiles of 18-h fermented milk inoculated with Streptococcus thermophilus and Levilactobacillus brevis strain NPS-QW 145

first: Nagendra

last: Shah


title: Novel cancer-selective and disease subtype-independent mechanistic targets of withaferin A in human breast cancer cells

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: We report differential gene expression changes by withaferin A in breast cancer cells versus a normal mammary epithelial cell line.

overall_design: Examination of withaferin A-regulated transcriptome in a normal mammary epithelial cell line (MCF-10A) and human breast cancer cells belonging to different subtypes including MCF-7 (luminal type), SK-BR-3 (HER2 enriched type), and MDA-MB-231 (basal type).


title: Peripheral Sensory Neuron EC-tagging experiments

city: Merced

first: Michael

last: Cleary

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

summary: Larvae expressing CD:UPRT under control of 109(2)80-Gal4 were fed 5EC at early L3 stage, prior to carcass dissection and RNA extraction.  Reference RNA was prepared from carcasses of stage-matched larvae fed EUd and mock RNA was prepared from carcasses of

overall_design: Multidendritic senory neuron transcriptome profiles

first: Mike


title: Transcriptome-wide maps of STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

city: Birmingham

first: Pran

middle: K

last: Datta

state: AL

address: 1824 6th Ave South, WTI 520C

department: Medicine

institute: University of Alabama at Birmingham

summary: We report the application of enhanced cross-linking immunoprecipitation (eCLIP) sequencing technology for high-throughput profiling of STRAP-RNA interactions in mouse embryos (E9.5) or embryoid body (EB) cells. Based on the eCLIP-seq data, we computationally identified a transcriptome-wide set of high-confidence peaks (over ten thousands) and most of STRAP-peaks distributed in the murine genome by defining certain exons and introns as well as their intersection. STRAP eCLIP signals in embryos were dramatically enriched at exon/intron and intron/exon borders. Numerous STRAP peaks are significantly enriched on the genes with critical roles in early organ development. Finally, we show two examples of STRAP-RNA binding that link to its regulated genes at the alternative splicing level.   Together, we uncover the position- and context- dependent effects of STRAP on splicing regulation during mouse embryonic stem cells lineage commitment. Our studies provide a very useful platform to decipher STRAP’s role in the many steps in RNA biogenesis for future studies.

overall_design: Examination of STRAP-RNA interactions in mouse embryos and embryoid body cells.

first: Lin

last: Jin


title: Time course analysis of the effect of embedded metal on skeletal muscle gene expression [Array]

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary: As a consequence of military operations, many veterans suffer from penetrating wounds and long-term retention of military grade heavy metal fragments. Fragments vary in size and location, and complete surgical removal may not be feasible or beneficial in all cases. Increasing evidence suggests retention of heavy metal fragments may have serious biological implications, including increased risks for malignant transformation. Previous studies assessed the tumorigenic effects of metal alloys in rats, demonstrating combinations of metals are sufficient to induce tumor formation after prolonged retention in skeletal muscle tissue. In this study, we analyzed transcriptional changes in skeletal muscle tissue in response to eight different military-relevant pure metals over 12 months. We found that most transcriptional changes occur at 1 and 3 months after metal pellets are embedded in skeletal muscle and these effects resolve at 6 and 12 months. We also report significant immunogenic effects of nickel and cobalt and suppressive effects of lead and depleted uranium on gene expression. Overall, skeletal muscle exhibits a remarkable capacity to adapt to and recover from internalized metal fragments; however, the cellular response to chronic exposure may be restricted to the metal-tissue interface. This data suggests that unless affected regions are specifically captured by biopsy, it would be difficult to reliably detect changes in muscle gene expression that would be indicative of long-term adverse health outcomes.

overall_design: We investigated the effects of eight militarily relevant metals: tungsten (W), nickel (Ni), cobalt (Co), iron (Fe), copper (Cu), aluminum (Al), lead (Pb), and depleted uranium (DU). The control group followed all the same procedures utilizing the metal tantalum (Ta) to serve as the surgery sham, which would control for changes such as inflammatory response to surgery and embedded foreign material. Rats were randomly assigned to one of the nine metal implant groups (n=8/group) with each metal group conducted in 4 cohorts – 1, 3, 6, or 12 months post-implant surgery. A total of 288 rats (n=8 x 9 metal groups x 4 timed cohorts) were used in this study. All metal “pellets” were cylinders 1 mm in diameter x 2 mm in length.

first: John

last: McCarthy

first: Charlotte

last: Peterson


title: STRAP-dependent alternative splicing events; STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

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


title: Time course analysis of the effect of embedded metal on skeletal muscle gene expression


title: Next generation sequencing facilitates quantitative analysis of STRAP-dependent alternative splicing events

summary: We report the application of next generation sequencing for evaluating alternative splicing (AS) events on lineage-committed WT and Strap-KO embryoid body (EB) cells. We also analyzed AS during mouse embryo development using RNA-seq data. Of all STRAP-regulated AS, exon-skipping events were the most frequent ones with significant changes in 49% (240 out of 489) cases. Retained introns were also overrepresented (20%, 97 out of 489) as compared to other types of AS STRAP appears to function in promoting both exon inclusion and skipping at different exons. GO function revealed STRAP-regulated AS events involve in protein catabolism, molecular binding and cell motility.  More specifically, they included neuronal migration and development. Together, these analyses uncovered the previous unknown role of STRAP involved in the substantial transcriptional diversity at the exon level in certain development stage.  Our study also represents the first detailed analysis of AS events in the mouse early organogenesis with biologic replicates, generated by RNA-seq technology.

overall_design: Examination of STRAP- and development-regulated AS events, respectively.


title: Time course analysis of the effect of embedded metal on skeletal muscle gene expression [RNA-seq]

overall_design: We investigated the effects of eight militarily relevant metals: tungsten (W), nickel (Ni), cobalt (Co), iron (Fe), copper (Cu), aluminum (Al), lead (Pb), and depleted uranium (DU). The control group followed all the same procedures utilizing the metal tantalum (Ta) to serve as the surgery sham, which would control for changes such as inflammatory response to surgery and embedded foreign material. Rats were randomly assigned to one of the nine metal implant groups (n=8/group) with each metal group conducted in 4 cohorts – 1, 3, 6, or 12 months post-implant surgery. A total of 288 rats (n=8 x 9 metal groups x 4 timed cohorts) were used in this study. All metal “pellets” were cylinders 1 mm in diameter x 2 mm in length. We performed RNA sequencing on a subset of muscle samples embedded with Ni, Co, Pb, DU, and Ta.


title: A bisulfite‐free approach for base‐resolution analysis of genomic 5-carboxylcytosine

status: Public on Sep 15 2020

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

summary: Due to an extreme rarity of 5-carboxylcytosine (5caC) in mammalian genome, investigation of its role brings a considerable challenge. Methods based on bisulfite sequencing have been proposed for genome-wide 5caC analysis. However, bisulfite-based sequencing of scarcely abundant 5caC demands significant experimental/computational resources increasing sequencing cost. Here, we present a bisulfite-free approach, caCLEAR, for high resolution mapping of 5caCGs. The method employs an atypical activity of the methyltransferase eM.SssI to remove a carboxyl group from 5caC generating unmodified CGs which are localized by uTOP-seq sequencing. Validation of caCLEAR on model DNA systems and mouse ESCs supported the suitability of caCLEAR for analysis of 5caCGs. The 5caCG profiles of naive and primed pluripotent ESCs reflected their distinct demethylation dynamics and demonstrated an association of 5caC with gene expression. Generally, we demonstrated that caCLEAR is a robust economical approach that could help provide deeper insights into biological roles of 5caC.

overall_design: 5-carboxylcytosine analysis in mouse embryonic stem cells. DNA modifications were analysed in the naive and primed pluripotency states - two techinal replicates for each input. Serum triple Tet knockout DNA was used as a negative control and prepared identically with other samples.

first: Janina

last: Ličytė

first: Povilas

last: Gibas

first: Kotryna

last: Skardžiūtė

first: Vaidotas

last: Stankevičius

first: Audronė

last: Rukšėnaitė

first: Edita

last: Kriukienė


title: Maternal Oxycodone Treatment Causes Pathophysiological Changes in the Mouse Placenta

status: Public on Sep 14 2020

city: Columbia

first: Cheryl

middle: S

last: Rosenfeld

state: MO

address: 1201 Rollins Street

department: BIOMEDICAL SCIENCES

institute: University of Missouri.edu

summary:
Purpose: The goals of this study are to examine how maternal exposure to oxycodone affects the global transcriptome and histological structure of the mouse placenta at 12.5 dpc of pregnancy.retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: A high throughput RNA sequencing method was used to examine the global transcriptomic changes affected by oxycodone in male and female conceptuses. Histomorphometrics were used to assess the various regions of the placenta, namely the labyrinth, spongiotrophoblast, and parietal trophoblast giant cell (pTGC) region. The open-sourced software, weighted correlation network analysis (WGCNA) was used to link gene expression changes and histological (phenotypic) changes.
Results: Using an optimized data analysis workflow, we mapped over 40 million sequence reads per sample to the mouse genome (build grcm38). An average of 95.6% of reads (38.7 million) was mapped with HISAT2 workflow. We identified 12,138 transcripts in the placenta of saline control and oxycodone mice with featureCounts workflow. One hundred eighty-eight transcripts showed differential expression between the OXY male vs. CTL male placenta, with a log2Foldchange ≥1 and p value <0.05. Fifty-eight transcripts showed differential expression between the OXY female vs. CTL female placenta, with a log2Foldchange ≥1 and p value <0.05. Hierarchical clustering of differentially expressed genes uncovered several genes that may contribute to placenta function.
Conclusions: Our study represents the first detailed analysis of placental transcriptomes in oxycodone-exposed mice, with biologic replicates, generated by RNA-seq technology. The data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that oxycodone exposure changed transcriptome characterization and these changes were associated with placenta histological features.

overall_design: Placental RNA profiles at 12.5 embryo day old in Control and Oxcodone exposed mice

first: Madison

middle: T

last: Green

first: Rachel

last: Martin

first: Jessica

last: Kinkade

first: Robert

middle: R

last: Schmidt

first: Nathan

last: Bivens

first: Geetu

last: Tuteja

first: Jiude

last: Mao


title: Brown adipose expansion and remission of glycemic dysfunction in obese SM/J mice

city: St Louis

first: Caryn

last: Carson

state: Missouri

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St Louis

summary: The purpose of the study was to identify differential expression in the interscapular brown adipose tissue of high fat-fed SM/J mice between 20 and 30 weeks of age. Low fat-fed mice at the same ages were used as an intra-strain control, LG/J mice on the same diets and at the same ages were used as an inter-strain control, and reproductive white adipose tissue from the same mice was used as an inter-tissue control.

overall_design: 128 samples were analyzed, with 4 biological replicates in each strain x diet x age x sex x tissue cohort.

first: Juan

middle: F

last: Macias-Velasco

first: Celine

last: St. Pierre

last: Wayhart

first: Heather

middle: A

last: Lawson


title: An endothelial subtype-specific communication network orchestrates capillarization in liver tumorigenesis via the Hgf/c-Met pathway

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

overall_design: Refer to individual Series


title: Gene profiles regulated and targeted by PRC2 in oligodendrocyte lineage cells

city: Buffalo

first: Soo-Kyung

last: Lee

address: 109 Cooke Hall

department: Department of Biological Sciences

institute: University at Buffalo, The State University of New York

summary: The PRC2 complex creates a repressive mark histone-H3-Lys27-trimethylation. Although PRC2 is involved in various biological processes, its role in glial development remains ambiguous. We find PRC2 complex is required for oligodendrocyte (OL) differentiation and myelination,  but not for OL precursor formation. Furthermore, most PRC2-null OL lineage cells (cKO) acquire astrocyte features. RNA profiles from RNAseq assay reveal that many transcription factors involved in oligodendrocyte and astrocyte development are regulated by PRC2. Moreover, PRC2-null OL lineage cells aberrantly induce Notch-NFIA and Wnt pathway genes. The chromatin immunoprecipitation-sequencing (ChIPseq) assay further reveals that PRC2 is recruited to many of Notch-NFIA and Wnt pathway genes. The datasets demonstrate the molecular program underlying the  specific action of PRC2 and suggest PRC2 as a gatekeeper that determines the timing of OL lineage progression and myelination.

overall_design: Examination of RNAseq profiles in the culture of OL lineage cells in proliferative and differentiating conditions from control and PRC2-cKO brain, and ChIPseq profiles in P3 spinal cords when and where OL precursors and differentiating OLs reside.

first: Wenxian

last: Wang

first: Hyeyoung

last: Cho

first: Younjung

last: Park

first: Su

last: Lim

first: Soung

last: Youn

first: Sangsoo

last: Kim

first: Jae

first: Ben

last: Emery

first: Seunghee


title: Identification of human cytotoxic ILC3s

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

summary: Human ILCs are classically categorized into five subsets; cytotoxic CD127-CD94+ NK cells and non-cytotoxic CD127+CD94-, ILC1s, ILC2s, ILC3s and LTi cells. Here, we identify a novel subset within the CD127+ ILC population, characterized by the expression of the cytotoxic marker CD94. These CD94+ ILCs strongly resemble conventional ILC3s in terms of phenotype, transcriptome and cytokine production, but are highly cytotoxic. IL-15 was unable to induce differentiation of CD94+ ILCs towards mature NK cells. Instead, CD94+ ILCs retained RORγt, CD127 and CD200R expression and produced IL-22 in response to IL-15. Culturing non-cytotoxic CD127+ ILC1s or ILC3s with IL-12 induced upregulation of CD94 and cytotoxic activity, effects that were not observed with IL-15 stimulation. Thus, human helper ILCs can acquire a cytotoxic program without differentiating into NK cells.

overall_design: 9 samples of 3 celltype, 1 conditions with 3 replicates

first: Lisette

last: Krabbendam

first: Chantal

last: Kradolfer

first: Hergen

last: Spits

first: Jochem

middle: H

last: Bernink


title: Engineered IL-10 variants elicit potent immuno-modulatory activities at therapeutic low ligand doses

city: Dundee

first: Ignacio

last: Moraga

address: Dow Street

institute: University of Dundee

summary: Interleukin-10 is a dimeric cytokine with potent anti-inflammatory and anti-cancer activities. Despite its immune-regulatory potential, IL-10-based therapies have shown only marginal benefits in the clinic. Here we have explored whether the stability of the IL-10-receptor complex contributes to IL-10 immuno-modulatory potency. For that, we have generated an IL-10 mutant with greatly enhanced affinity for its IL-10Rβ receptor via yeast surface display. The affinity enhanced IL-10 variants formed surface active complexes more efficiently than the wild-type cytokine and triggered more potent STAT1 and STAT3 activation in human monocytes and CD8 T cells. This in turn led to more robust induction of IL-10-mediated gene expression programs at a wide range of ligand concentrations in both human cell subsets. IL-10 regulated genes involved in monocyte energy homeostasis, migration and trafficking, and genes involved in CD8 T cell exhaustion. Interestingly, at non-saturating doses, IL-10 lost key components of its gene-expression program, which may explain its lack of efficacy in a clinical set up. Remarkably, our engineered IL-10 variant exhibited a more robust bioactivity profile than IL-10 wt at all the doses tested in monocytes and CD8 T cells. Our study provides unique insights into how IL-10-receptor complex stability contributes to fine-tune IL-10 biology, and open new opportunities to revitalize failed IL-10 therapies.

overall_design: Human monocytes and CD8 T cells were stimulated under 7 conditions each; control (unstimualted), WTD50 nM, WTD 0.1 nM, R5A11D  50 nM, R5A11D 0.1 nM, WTM 50 nM, R5A11M 50 nM. Each condition has three biolocial replicates (human donors)

first: Claire

last: Gorby

first: Junel

last: Sotolongo-Bellon

first: Stephan

last: Wilmes

first: Elizabeth

last: Pohler

first: Paul

last: Fyfe

first: Suman

last: Mitra

first: Jacob

last: Piehler


title: RNA-seq transcriptional analysis of mouse lung tissue with and without Coccidioides immitis lung infection

city: La Jolla

first: Aaron

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

summary: Our previous data suggested that CXC ELR+ chemokines might be involved in neutrophil recruitment to the lungs during Coccidioides infection. To test that hypothesis, we infected IL-8R2 (Cxcr2) KO mice on a BALB/c background. IL-8R2 KO mice had fewer neutrophils in infected lungs than BALB/c controls, but unexpectedly the IL-8R2 KO mice also had 10-fold fewer organisms in their lungs than did control mice. To better understand the differences in IL-8R2 KO mouse lungs during Coccidioides infection we performed RNA-seq on lung tissue from uninfected and Coccidioides immitis infected mouse lungs in control and IL-8R2 (Cxcr2) KO mice. IL-8R2 KO mouse lungs had higher expression of genes associated with lymphocyte activation, including Th1 and Th17-related genes Ifnγ and Il17a and transcription factors Stat1 and Rorc. Bronchial alveolar lavage (BAL) fluid from infected IL-8R2 KO mice similarly contained more IL-17A and IFNγ.

overall_design: RNA-seq of lung tissue from BALB/c DBA/2 Nramp1 congenic (Potter M et al. (1983) PMID: 6343242) (wild-type or WT) and Balb/c CXCR2tm (IL-8R2) knockout (IL-8R2 KO) mice with or without Coccidioides immitis infection on day 14 after infection.

first: Joshua

last: Fierer


title: RNA-seq of ATF-3 overexpressing and Neomycin control melanoma cell lines

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: The present study demonstrates that ATF-3 plays a tumor suppressing function in melanoma. Overexpression of ATF-3 in metastatic melanoma cell lines significantly inhibited their growth, migration and invasion in vitro as well as inhibited tumor growth in human melanoma xenograft mouse model in vivo.

overall_design: We performed RNA-seq of the melanoma cell lines A2058 and C8161 overexpressing ATF-3 by retroviral transduction and their corresponding neomycin controls.

first: Catherine

last: Lee

middle: Y


title: High spatial resolution multi-omics atlas sequencing of mouse embryos

city: New Haven

first: Mingyu

last: Yang

state: CT

address: 55 Prospect St., Room 103

department: Biomedical Engineering

institute: Yale

summary: Microfluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high throughput sequencing enables the construction of high-spatial-resolution multi-omics atlas at the genome scale. Applying it to mouse embryo tissues revealed major tissue (sub)types in early-stage organogenesis, brain micro-vasculatures, and the fine structure of an optical vesicle at the single-cell-layer resolution.

overall_design: Applying new approach – microfluidic Deterministic Barcoding in Tissue for spatial omics sequencing to mouse embryo tissues in different resolution (10μm, 25μm, 50μm).

first: Rong

last: Fan

first: Yang

last: Liu

first: Yanxiang

last: Deng


title: Functional Compensation Precedes Recovery of Tissue Mass Following Acute Liver Injury

city: Cambridge

first: Alex

last: Shalek

address: 77 Massachusetts Avenue

department: Chemistry

institute: MIT

summary: We identify a new phase of functional compensation following acute liver injury that occurs prior to cellular proliferation. By coupling single-cell RNA-seq with in situ transcriptional analyses in two independent murine liver injury models, we discover adaptive reprogramming to ensure expression of both injury response and core liver function genes dependent on macrophage-derived WNT/b-catenin signaling. Interestingly, transcriptional compensation is most prominent in non-proliferating cells, clearly delineating two separate phases of liver recovery. Overall, our work describes a new mechanism by which the liver maintains essential physiological functions prior to cellular reconstitution and characterizes macrophage-derived WNT signals required for this compensation.

overall_design: Examination by single-cell RNA-Seq of hepatocyte response to acute liver injury at multiple time points in an acetaminophen toxicity and a partial hepatectomy injury model. Untreated controls are also included.

first: Kellie

last: Kolb


title: Transcriptomic analysis of WT, 35S:ERF13:MYC and erf3-3.

city: Qingdao

first: bingsheng

last: lv

state: shan dong

address: Jimo Binhai Lu 72

institute: shandong university

summary: The goal of this study is to clarify the function of ERF13 in the pathway of auxin inducing lateral root development. We isolated total RNA from the roots of 9-day-old WT, 35S:ERF13:MYC and erf3-3 seedlings. New genes act downstream of ERF13 during the lateral root formation are discovered.

first: Bingsheng

last: Lv

first: ZhaoJun

last: Ding


title: Transcriptomic analysis of amp1-13 and cyp78a5,7 Arabidopsis seedlings

city: Freising

first: Tobias

last: Sieberer

address: Liesel-Beckmann-Strasse 1

department: Plant Sciences

institute: Technical University of Munich

summary: ALTERED MERISTEM PROGRAM1 (AMP1) is a member of the M28 family of carboxypeptidases with a pivotal role in cell fate maintenance in the embryo and shoot meristem. A defect in AMP1 function results in suspensor to embryo conversion and a hypertrophic shoot meristem forming ectopic stem cell pools. However, so far the role of AMP1 in shoot development could not be assigned to a specific molecular pathway nor is its biochemical function resolved. Double mutants in CYP78A5 and CYP78A7 develop a similar set of cell fate defects. To further assess whether this phenotypic overlap is also depicted in a congruency at the global gene expression level, we analyzed the transcriptomic responses of both genotypes

overall_design: Seedlings of indicated genotypes were germinated and grown for 10 d in liquid medium. For each genotype three biological replicates were used for RNA extraction and subsequent hybridization on Affymetrix microarrays.

first: Olena

last: Poretska


title: Kidney Cancer PDOX Models

status: Public on Sep 12 2020

city: L'HOSPITALET DE LLOBREGAT

first: ORIOL

last: CASANOVAS

address: AV. GRAN VIA, 199. 3 PL.

department: ProCURE, OncoBell

country: Spain

institute: CATALAN INSTITUTE OF ONCOLOGY - IDIBELL

summary: RNA seq of two independent kidney cancer orthotopic patient-derived xenograft models (RenPDOX-13 & RenPDOX-50) that show differential proinvasive response to antiangiogenics

overall_design: RNA sequencing of bulk tumor tissue of RenPDOX-13 & RenPDOX-50 models in triplicate and quadruplicate tumors, respectively.

first: Lidia

last: Moserle

first: Susana

last: Aguilar

first: Jordi

last: Senserrich

first: Oriol

last: Casanovas


title: Metabolic determinants of cellular fitness dependent on mitochondrial reactive oxygen species

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

summary: Mitochondria-derived reactive oxygen species (mROS) are required for the survival, proliferation, and metastasis of cancer cells. The mechanism by which mitochondrial metabolism regulates mROS levels to support cancer cells is not fully understood. To address this, we conducted a metabolism-focused CRISPR/Cas9 genetic screen and uncovered that loss of genes encoding subunits of mitochondrial complex I were deleterious in the presence of the mitochondria-targeted antioxidant Mito-Vitamin E (MVE). Genetic or pharmacologic inhibition of mitochondrial complex I in combination with the mitochondria-targeted antioxidants, MVE or MitoTEMPO, induced a robust integrated stress response (ISR) and markedly diminished cell survival and proliferation in vitro. Notably, this was not observed following inhibition of mitochondrial complex III.  Administration of MitoTEMPO in combination with the mitochondrial complex I inhibitor phenformin decreased the leukemic burden in a mouse model of T-cell acute lymphoblastic leukemia. Thus, mitochondrial complex I is a dominant metabolic determinant of mROS-dependent cellular fitness.

overall_design: RNA sequencing of Jurkat cell lines , 48 total samples, 1 hour and 24 hours of treatment with vehicle control, mitoTEMPO, Piericidin, Antimycin, Piericidin+mitoTEMPO, or Antimycin+mitoTEMPO

first: Hyewon

last: Kong

first: Colleen

last: Reczek

first: Gregory

last: Mcelroy

first: Elizabeth

last: Steinert

first: Tim

last: Wang

first: David

last: Sabatini


title: Impact of Gm15441 knockdown on gene expression profile of mouse liver in response to activation of PPARA by WY-14643.

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Gene expression in livers of wild type adult male mice and in Gm15441 knockdown adult male mouse liver (Gm15441-LSL mice) was assayed by RNA-seq, as part of a study of liver transcriptomic changes in response to activation of PPARA by WY-14643.

overall_design: Twelve independent pools, comprised of RNA isolated from n=2-3 individual 12 wk old male livers per pool, were prepared and used for RNA-seq. Three pools were untreated, intact male mice livers; three pools were treated (WY-14,643), intact male mice livers; three pools were untreated, Gm15441-LSL mouse livers and three pools were treated, Gm15441-LSL mouse livers. Wy-14,643 treatment was via the diet, at 0.1% for 24 hr.

first: Chad

middle: N

last: Brocker

first: Kritika

last: Karri

first: Frank

last: Gonzalez


title: A safe inhalational treatment prevents SARS–CoV-2 viral replication in human airway epithelial cells.

city: Indianapolis

first: Michael

middle: Denning

last: Davis

state: Indiana

address: 1044 West Walnut Street R4-472

department: Pediatrics

institute: Indiana University

summary: Because epithelial surface pH affects airway inflammation and host defense, we study the benefit of an inhaled buffer in patients with asthma.  Inhaled Optate is designed safely to raise airway surface pH and is well-tolerated in humans. Epithelial infection with SARS-CoV2 is attenuated by raising intracellular pH.  Here, we show that Optate raises intracellular pH in primary normal human airway epithelial (NHAE) cells without affecting cell viability. Moreover, doses of Optate used in our human trials inhibit SARS-CoV-2 replication in NHAE cells.  Specifically, Optate almost completely ablates viral plaque formation and nucleocapsid protein expression, decreasing expression of critical processing proteins.  Optate could be a candidate to evaluate for treating COVID-19 patients.

overall_design: Six samples of extracted and purified RNA from one line of primary human airway epithelial cells were processed for RNAseq analysis. This included three samples that were exposed to Optate for 48 hours and three control samples.

middle: D

first: Benjamin

last: Gaston


title: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (RNA-Seq 1)

status: Public on Sep 13 2020

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

summary: Cis Regulatory Elements (CREs) regulate the expression of the genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of its target genes in the cellular native environment. In this study, we performed a Features Oriented CRISPR Utilized Systematic (FOCUS) screen of Oct4-bound CREs using CRISPR/Cas9 to identify functional CREs important for pluripotency maintenance in mouse ES cells.

overall_design: RNA profiling of shLrrc31 mESCs(2 shRNAs) and shEV mESCs(2 EVs), RNA-seq was performed in biology replicates

first: H

first: T

last: Warrier

first: C

last: Li

first: Y

last: Loh


title: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (ChIP-Seq)

overall_design: Genomic binding profile of Stat3 in WT E14 mES and in treated E14 mES depeleted of either Stat3 or Lrrc31.


title: Gene expression profiles in SATB2-knockdown and control human glioblastoma stem cells

city: Cleveland

first: weiwei

last: tao

state: OH

address: 9500 Euclid Avenue, NE30

department: Lerner Research Institute

institute: Cleveland Clinic

summary: Effects of SATB2 knockdown on gene expression were evaluated by microarray analysis in human glioblastoma stem cells

overall_design: Human glioblastoma stem cells were transduced with lentiviral-mediated non-targeting shRNA or SATB2 shRNA. Total RNA was prepared and gene expression profiles were obtained by micriarray analysis.

first: Weiwei

last: Tao

first: Shideng

last: Bao