title: ALK–transformed mature T lymphocytes restores early thymus progenitor features

city: Toulouse

first: Fabienne

last: MEGGETTO

address: adresse pro

institute: CTCT INSRM 1037

summary: Anaplastic large cell lymphoma (ALCL) is a mature T cell neoplasm that often expresses the CD4+ T cell surface marker. (It usually harbors the t(2;5) (p23;q35) translocation, leading to the ectopic expression of NPM-ALK, a chimeric tyrosine kinase. We demonstrated that in vitro transduction of normal human CD4+ T lymphocytes with NPM-ALK results in their immortalization and malignant transformation. The tumor cells displayed morphological and immunophenotypical characteristics of primary patient–derived anaplastic large cell lymphomas. Cell growth, proliferation, and survival were strictly dependent on NPM-ALK activity and include activation of the key factors STAT3 and DNMT1 and expression of CD30 (the hallmark of anaplastic large-cell lymphoma). Implantation of NPM-ALK–transformed CD4+ T lymphocytes into immunodeficient mice resulted in the formation of tumors indistinguishable from patients’ anaplastic large cell lymphomas. Integration of “Omic” data revealed that NPM-ALK–transformed CD4+ T lymphocytes and primary NPM-ALK+ ALCL biopsies share similarities with early T cell precursors. Of note, these NPM-ALK+ lymphoma cells overexpress stem cell regulators (OCT4, SOX2, and NANOG) and HIF2A, which is known to affect hematopoietic precursor differentiation and NPM-ALK+ cell growth. Altogether, for the first time our findings suggest that NPM-ALK could restore progenitor-like features in mature CD30+ peripheral CD4+ T cells, in keeping with a thymic progenitor-like pattern.

overall_design: examination of origin of ALCL

first: F

last: Meggetto


title: TUT4 affected genes and lncRNA  in human  esophageal carcinoma cell and cervical cancer cell

status: Public on Dec 07 2020

city: Jiangyin

first: Pengfei

last: Liu

state: Jiangsu province

address: NO. 163 Shoushan Road

country: China

institute: Jiangsu Jiangyin People's Hospital

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aims to evaluate the effect of TUT4  knockdown on the function and global gene expression and know and novel lncRNAs respectively  in human esophageal carcinoma cell (TE-1) and cervical cancer cell (Hela). Cells with TUT4  silencing were compared with control cells by LncRNA-Seq.

overall_design: RNA-seq of shNC and shTUT4 TE-1 and HeLa cells.

first: J

middle: D

last: Luo


title: Expression profiles of circRNAs in peripherial blood mononuclear cells  from cryptococcal meningitis and healthy individuals.

city: Shanghai

first: Weihua

last: Pan

address: 415 Fengyang Road

department: Department of Dermatology

institute: Shanghai Changzheng Hospital

summary: CircRNAs are a recently well-known regulator that mediates a variety of biological processes. Cryptococcus neoformans is an environmental fungal pathogen that can cause fatal cryptococcal meningitis in immunocompromised individuals. However, the involvement of circRNA in cryptococcal infection remains unclear. In this study, high‐throughput microarray was performed to identify the circRNA expression profile in cryptococcal meningitis patients.

overall_design: Three cryptococcal meningitis (CN) patientsand healthy individuals (HC) were included and PBMCs were isolated by Ficoll-10771 (Sigma Aldrich, USA) according to the manufacturer’s manual. All samples were stored at -80°C before experiments.

first: Lei

last: Zhang


title: Role of SRRM4 in regulating microexons in Circular RNAs in brain tissue

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: Studying the role of splicing factor SRRM4 on circular RNAs in human cells

overall_design: Total RNA was harvested from brain tissue (healthy and glioma tumour), RNAse R treated to enrich for circular RNAs

first: Vanessa

first: Shashikanth

last: Marri

first: Marta

last: Gabryelska


title: Transciption profiling of leptin receptor-expressing neurons in the Nucleus of the Solitary Tract

city: Chicago

first: Marco

last: Martina

state: IL

address: 300 E Superior

department: Physiology

country: USA

institute: Northwestern University

summary: This study aims to identify and compare unique transcription profiles of neurons in the NTS that express the leptin receptor. We conducted single-cell patch RNA-sequencing experiments to classify neurons first by their unique firing properties and, second, transciptional profiles. We found two unique cellular populations: type1 and type2 distinguishable by firing patterns and transciption profile.

overall_design: cytoplasmic and nuclear RNA were harvested from single-neurons of transgenic mice with yellow flourescent protein expressed in leptin receptor-expressin neurons (LepRb-Cre; Halo-eYFP)

first: Jeehaeh

last: Do


title: Macrophage-derived thrombospondin1 promotes obesity-associated non-alcoholic fatty liver disease

city: lexington

first: Shuxia

last: Wang

state: KY

address: 900 S. Limestone street, Wethington Bldg. Room 583

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

summary: Thrombospondin 1 (TSP1) is a multifunctional matricellular protein. Previously we have shown that TSP1 plays an important role in obesity-associated metabolic complications including inflammation, insulin resistance, cardiovascular and renal disease. However, its contribution to obesity-associated non-alcoholic fatty liver disease (NAFLD) or non-alcoholic steatohepatitis (NASH) remains largely unknown and is determined in this study. High fat diet or AMLN diet-induced obese and insulin resistant NAFLD/NASH mouse models were utilized. In addition, tissue specific TSP1 knockout mice were utilized to determine the contribution of different cellular sources of obesity-induced TSP1 to NAFLD/NASH development. The data demonstrated that liver TSP1 levels were increased in experimental obese and insulin resistant NAFLD/NASH mouse models as well as in human obese NASH patients. Moreover, TSP1 deletion in hepatocyte or adipocytes did not protect mice from diet-induced NAFLD/NASH. However, myeloid/macrophage-specific TSP1 deletion protected mice against obesity-associated liver injury, accompanied by reduced liver inflammation and fibrosis. Importantly, this protection is independent of the levels of obesity and hepatic steatosis.  Mechanistically, through an autocrine effect, macrophage-derived TSP1 suppressed SMPDL3B expression in liver, which amplified liver pro-inflammatory signaling (TLR4 signal pathway) and promoted NAFLD progression. Together, out data suggest that macrophage-derived TSP1 is a significant contributor to obesity-associated NAFLD/NASH development and progression and may serve as a therapeutic target for this disease.

overall_design: TSP1 floxed mice and macrophage specific TSP1 knockout mice were fed with LF or HF diet for 8 months. Then mie were sacrficed and livers were harvested for further analysis.

first: Taesik

last: Gawg

first: Raja

middle: G

last: Mooli

first: Dong

last: Li

first: Eun

middle: Y

last: Lee


title: Area postrema cell types that mediate nausea-associated behaviors

city: Boston

first: Judith

last: Kaye

state: Massachusetts

address: 240 Longwood Ave, LHRRB 6th floor

department: Cell Biology

institute: Harvard University

summary: Nausea, the unpleasant sensation of visceral malaise, remains a mysterious process. The area postrema is implicated in some nausea responses, and contains poorly understood brain-resident sensory neurons that are anatomically privileged to detect bloodborne signals. To investigate nausea mechanisms, we built an area postrema cell atlas through single-nucleus RNA sequencing, revealing a few neuron types. Using mouse genetic tools for cell-specific manipulation, we discovered excitatory neurons that induce nausea-related behaviors, with one neuron type mediating aversion imposed by multiple poisons. Nausea-associated responses were observed to agonists of identified area postrema receptors, and suppressed by targeted cell ablation and/or gene knockout. Anatomical mapping revealed a distributed network of long-range excitatory but not inhibitory projections with subtype-specific patterning. These studies reveal the basic organization of area postrema nausea circuitry, and provide a framework towards understanding and therapeutically controlling nausea.

overall_design: Single-nuclei sequencing of murine area postrema.

first: Steve

last: Liberles

first: Chuchu

middle: A

first: Zerong

last: Cai

first: Yandan

first: Sara

middle: L

last: Prescott


title: RNA-seq profiling of C. elegans O2-sensing neurons at different age and activity states

city: Edinburgh

first: Karl

middle: Emanuel

last: Busch

address: Hugh Robson Building, George Square

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

summary: We report that the transcriptome of the C. elegans URX, AQR and PQR O2-sensing neurons changes with age and is affected by neuronal activity states

overall_design: total RNA profiles of O2-sensing neurons or whole worms from 1-day or 7-day adult worms cultured at 7% O2 or 21% O2

first: Qiaochu


title: Dysregulation of transcription factor activity during formation of cancer associated fibroblasts.

city: Krakow

first: Paweł

last: Wołkow

address: Kopernika 7c

department: Centre for Medical Genomics - OMICRON

country: Poland

institute: Jagiellonian University Medical College

summary:
Introduction: The reciprocal interactions between cancer cells and the CAFs serve an important role in cancer progression. Those feedback loops depend on tumor developmental stage and the tissue microenvironment and may promote different CAFs subpopulations in different types of malignancy. Here, we investigated the activation of transcription factors (TFs) in cocultures of fibroblasts with normal prostate or tumorous cells with mRNA sequencing.
Materials and Methods: Coculture of WPMY-1 (normal prostate fibroblasts) with RWPE-1 (normal prostate epithelial cells) or RWPE-2 (cancer prostate epithelial cells) were done using transwell inserts. As a control, we used WPMY-1 culture alone. After 6h and 24h of coculture, we performed mRNA-sequencing., We used SEPIRA (Systems EPigenomics Inference of Regulatory Activity) package and mRNA-seq data of 483 cultured fibroblasts from GTEx to calculate the TFs activity score from mRNA-seq expression in our samples.
Results: We determined changes in TFs activity between time points in each group. We found 5 TFs (RUFY3, SCMH1, NFIX, ZBTB25, NFE2L1), that increase activity between 6h and 24h in each condition (control, coculture with RWPE1 and coculture with RWPE2). Only one TF (RNF4) increased activity in RWPE-1 coculture, while dysregulation of 45 TFs (7 decreased activity and 38 increased activity) was observed in coculture with RWPE-2. Pathway analysis showed that these 45 dysregulated TFs in fibroblasts after coculture with RWPE2 cells may be associated with RUNX1 and PTEN pathways.
Conclusion: Our results demonstrate that CAFs transformation can be orchestrated by dysregulation of multiple TFs, therefore may suggest multiple signaling pathways that participate in CAFs transformation. Moreover, we show potential pathways, that could be involved in feedback loop between fibroblast and epithelial cells in tumors.

overall_design: mRNA profiles of WPMY-1 cocultured with RWPE-1 or RWPE-2 after 6 and 24 hours of incubation

first: Przemysław

last: Kapusta

first: Justyna

last: Totoń-Żurańska

first: Michał

middle: T

last: Seweryn

middle: P


title: Whole blood transcriptome analysis during immunization and mammary challenge with E. coli

city: TOULOUSE

first: gilles

last: FOUCRAS

state: State/Province/Region

address: 23 Chemin des Capelles

country: France

institute: ENVT INRA

summary:
Methods: During the last trimester of the gestation, 12 heifers were immunized using intramuscular injection with heat-killed E. coli P4 emulsified in Montanide ISA 61VG® oil adjuvant (SEPPIC), as recommended by the manufacturer. Two months later, half of the heifers (IM group, n=6) got a second injection as a booster. Others received 50 µg of protein concentrate prepared from E. coli P4 supernate in two quarters (IMM group, n=6). Cows of the control group (CONT, n=6) were injected intramuscularly with adjuvant only at the same dates. Cows were then challenged on average at 49 days in milk in one healthy quarter by infusion of a E. coli P4 bacterial suspension (10e3 bacteria). Blood was collected before experiment, and seven days after the first and the second injection (immunization phase), and then at 0, 12 and 40 hours after infection (challenge phase).
Results : Whole blood transcriptome through RNA-seq identifies the main biological functions altered during an E. coli mastitis. Systemic and mammary routes of E. coli immunization elicit different gene expression profiles that correlated with the levels of protection
Conclusions: Intramuscular immunization is correlated with a high systemic Th1 response that is not as protective as the local route of immunization.
During the last trimester of the gestation, 12 heifers were immunized using intramuscular injection with heat-killed E. coli P4 emulsified in Montanide ISA 61VG® oil adjuvant (SEPPIC), as recommended by the manufacturer. Two months later, half of the heifers (IM group, n=6) got a second injection as a booster. Others received 50 µg of protein concentrate prepared from E. coli P4 supernate in two quarters (IMM group, n=6). Cows of the control group (CONT, n=6) were injected intramuscularly with adjuvant only at the same dates. Cows were then challenged on average at 49 days in milk in one healthy quarter by infusion of a E. coli P4 bacterial suspension (10e3 bacteria). Blood was collected before experiment, and seven days after the first and the second injection (immunization phase), and then at 0, 12 and 40 hours after infection (challenge phase).

overall_design: Gilles,Foucras

first: Nathan

last: CEBRON

first: Sarah

last: MAMAN

first: Pascal

last: RAINARD


title: Transcriptome analysis of mammary CD45+ CD4+ lymphocytes after immunization against E. coli P4 strain and homologous challenge

summary:
Methods: During the last trimester of the gestation, three heifers were immunized using intramuscular injections of heat-killed E. coli P4 emulsified in Montanide ISA 61VG® adjuvant (SEPPIC). Two months later, they received a mammary ductal injection of 50 µg protein from concentrated E. coli supernate as a booster. Control cows were injected intramuscularly with adjuvant only at the same dates. Cows were then challenged on average at 140 days in milk in one healthy quarter by infusion of a E. coli P4 bacterial suspension (10e3 bacteria in total). Cows were then euthanized 16 hours after inoculation for mammary tissue collection. After collagenase and DNase treatment and Percoll-gradient separation, CD45+ CD4+ mononuclear cells were sorted by flow cytometry. RNA was extracted and sequenced using Illumina protocol.
Results : Mammary Th17-polarized CD4 T cells predominate in the mammary tissue of cows immunized through the local route, and are activated after challenge with E. coli.
Conclusions: Local immunization promotes the development of TH17 immunity that correlated with protection.

first: Gilles


title: Cigarette smoke but not novel tobacco vapor product cause epigenetic disruption and cell apoptosis.

city: Nagasaki

first: Naoko

last: Hattori

address: Sakamoto 1-12-4

country: Japan

institute: Nagasaki university

summary: Novel tobacco vapor product, generating vapor without combusting tobacco leaves, has been developed expecting the number and quantity of chemicals in the vapor of these products to be reduced compared to conventional combustible cigarettes. However, if the lower chemical levels correlate with lower toxicity remained to be clarified.    Here we examined the difference of conventional cigarette smoke (CS) and novel tobacco vapor product (NTV) using cultured cancer cell line A549 and normal bronchial epithelium cell line BEAS-2B. 0.5% of 3R4F which is conventional CS markedly decreased cell proliferation of both A549 and BEAS-2B, however Ploom TECH or Ploom TECH+ which are commercially available NTV did not affect cell growth. To clarify the cause of decreased cell proliferation, Tunnel assay was performed and clarified that apoptosis was observed in both A549 and BEAS-2B after 24hours after exposure to 3R4F. To further explore the effect of CS to epigenetics, we performed western blotting Histone H2A phosphorylation which is known to correlate transcriptional regulation. Only 3R4F decreased histone H2A phosphorylation of both A549 and BEAS-2B. Then we examined alterations of gene expression after 3R4F treatment of A549 cell. 339, 107, 103 genes which were upregulated more than 2fold were observed in 3R4F, Ploom TECH or Ploom TECH+ treated A549 cell, respectively. Among 339 genes which was upregulated 3R4F, we focused EGR1, FOS, and FOSB gene since they were upregulated more than100 fold. We confirmed this upregulation using RTqPCR. These data suggest that Cigarette smoke but not novel tobacco vapor product cause epigenetic disruption and cell apoptosis possibly by elevating genes such as EGR1.

overall_design: A549 cell mRNA profile of adding DMSO control, cigarette smoke (3R4F) and novel tobacco vapor product (Ploom TECH, and Ploom TECH plus) were generated by deep sequencing in duplicate, using Illumina MiSeq.

first: Takeya

last: Nakagawa

first: Mitsuhiro

last: Yoneda

first: Hiromi

last: Hayashida

first: Kaori

first: Takashi

last: Ito


title: IGF2R-initiated Proton Rechanneling Dictates an Anti-inflammatory Property in Macrophages

first: Xuefeng

last: Wang

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Metabolic trait in macrophages can be rewired by insulin like growth factor 2 (IGF2), however, how IGF2 modulates the cellular dynamics and functionality remains unclear. We demonstrate here that IGF2 exhibits dual and opposing roles in controlling inflammatory phenotypes in macrophages via regulating glucose metabolism. Such difference relies on the dominant activation of IGF2R by low dose IGF2 and IGF1R by high dose IGF2. IGF2R activation leads to proton rechanneling to the mitochondrial intermembrane space, and enables sustained oxidative phosphorylation. Mechanistically,low dose IGF2 induces nucleus translocation of IGF2R that promotes Dnmt3a-mediated DNA methylation via activating GSK3β, and subsequently impairs the expression ofvacuolar-type H+-ATPase (v-ATPase).This sequestrated assembly of v-ATPase inhibits the channeling of protons to lysosomes and leads to their rechanneling to mitochondria. An IGF2R-specific IGF2 mutant only induces anti-inflammatory response and inhibits colitis progression. Altogether, our findings highlight a novel role of IGF2R activation in dictating anti-inflammatory macrophages.

overall_design: Three samples of IGF2-preprogrammed peritoneal macrophages were analyzed by genome-wide methylation sequencing

first: Yufang

last: Shi

first: Ying


title: Protein synthesis inhibitors stimulate MondoA transcriptional activity by driving accumulation of glucose 6-phosphate

city: Salt Lake City

first: Donald

middle: E

last: Ayer

state: UT

address: 2000 Circle of Hope

institute: University of Utah

summary: BACKGROUND: Protein synthesis is regulated by the availability of amino acids, the engagement of growth factor signaling pathways and ATP levels sufficient to support translation. Crosstalk between these inputs is extensive, yet other regulatory mechanisms remain to be characterized. For example, the translation initiation inhibitor Rocaglamide A (RocA) induces Thioredoxin Interacting Protein (TXNIP). TXNIP is a negative regulator of glucose uptake, thus its induction by RocA links translation to the availability of glucose. MondoA is the principal regulator of glucose-induced transcription and its activity is triggered by the glycolytic intermediate, glucose 6-phosphate (G6P). MondoA responds to G6P generated by cytoplasmic glucose and mitochondrial ATP (mtATP), suggesting a critical role in the cellular response to these energy sources. TXNIP expression is entirely dependent on MondoA, therefore, we investigated how protein synthesis inhibitors impact its transcriptional activity. METHODS: We investigated how translation regulates MondoA activity using cell line models and loss-of-function approaches. We examined how protein synthesis inhibitors effect gene expression and metabolism using RNA-sequencing and metabolomics, respectively. The biological impact of RocA was evaluated using both cell line models and Patient-Derived Xenograft Organoid models. RESULTS: We discovered that multiple protein synthesis inhibitors, including RocA, increase TXNIP expression in a manner that depends on MondoA, a functional electron transport chain and mtATP synthesis. Furthermore, RocA increases mtATP and G6P levels and TXNIP induction depends on interactions between the Voltage-Dependent Anion Channel (VDAC) and hexokinase, which generates G6P. RocA treatment impacts the regulation of ~1200 genes and ~250 of those genes are MondoA-dependent. RocA treatment is cytotoxic to Triple Negative Breast Cancer cell lines and shows preferential cytotoxicity against ER- patient-derived breast cancer models. Finally, RocA-driven cytotoxicity is partially-dependent on MondoA or TXNIP. CONCLUSION: Our data suggest that protein synthesis inhibitors rewire metabolism, resulting in an increase in mtATP and G6P, the latter driving MondoA-dependent transcriptional activity. Further, MondoA is a critical component of the cellular transcriptional response to RocA. Our functional assays suggest that RocA or similar translation inhibitors may show efficacy against ER- tumors and that the levels of MondoA and TXNIP should be considered when exploring these potential treatment options.

overall_design: mRNA sequencing of HeLa and HeLa:MondoA-KO cells treated with DMSO or 100nM Rocaglamide A (RocA) for 4 hours

first: Blake

middle: R

last: Wilde

first: Mohan

last: Kaadige

first: Katrin

last: Guillen

first: Andrew

last: Butterfield

first: Bryan

last: Welm


title: Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

summary: Anterior mesoderm (AM) and definitive endoderm (DE) progenitors represent the earliest embryonic cell types that are specified during germ layer formation at the primitive streak (PS) of the mouse embryo. Genetic experiments indicate that both lineages segregate from Eomes expressing progenitors in response to different NODAL signaling levels. However, the precise spatiotemporal pattern of the emergence of these cell types and molecular details of lineage segregation remain unexplored. We combined genetic fate labeling and imaging approaches with single cell RNA sequencing (scRNA-seq) to follow the transcriptional identities and define lineage trajectories of Eomes dependent cell types. Accordingly, all cells moving through the PS during the first day of gastrulation express Eomes AM and DE specification occurs before cells leave the PS from Eomes positive progenitors in a distinct spatiotemporal pattern. ScRNA-seq analysis further suggest the immediate and complete separation of AM and DE lineages from Eomes expressing cells as last common bipotential progenitor.

overall_design: Single cell RNA sequencing was performed on 576 hand-picked mouse embryonic cells at embryonic day 6.75 and 1172 FACS sorted cells from mouse embryos at embryonic day 7.5. Single-cell RNA sequencing was performed using the CEL-Seq2 protocol for hand-picked cells and mCEL-Seq2 protocol, an automated and miniaturized version of CEL-Seq2 for FACS-sorted cells (Hashimshony et al., 2016; Herman et al., 2018).

first: Simone

last: Probst

last: Sagar

first: Dominic

last: Gruen

first: Sebastian

middle: J

last: Arnold


title: Defining a critical Nanog enhancer using chromatin-focused approaches identifies RNAPII recruitment as required for expression [ATAC-Seq]

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid reporter assays, rather than within native chromatin. We employed a combination of approaches to investigate the Nanog locus in mouse embryonic stem cells (ESCs) and an associated cis regulatory element (CRE) which may operate as a super-enhancer (SE) or alternative promoter. We establish the element is a SE within chromatin using distance- and orientation-independence as criteria.  We next demonstrate this SE regulates Nanog by recruiting and/or initiating RNA Polymerase II. Our work highlights that enhancers likely operate through a diverse set of mechanisms.

overall_design: ATAC-Seq of 2 conditions, 3 replicates of each

first: Puja

last: Agrawal


title: Alleviating FGF19’s tumorigenic risk by suppressing its FGF Receptor dimerization ability

city: Wenzhou

first: Jianlou

last: Niu

state: Zhejiang

address: Chashan Town

institute: Wenzhou Medical University

summary: Administration of FGF19 - a physiological regulator of bile acid homeostasis - to diabetic and diet-induced-obese mice can suppress plasma glucose concentration and improve insulin sensitivity.  Repurposing FGF19 as a therapeutic agent for treating type 2 diabetes and cholestatic liver disease is therefore of significant interest.  However, the tumorigenic risk associated with prolonged FGF19 administration is a major hurdle in realizing its full clinical potential.  Here we show that non-mitogenic FGF19 variants that retain full beneficial glucose-lowering activity of wild-type FGF19 (FGF19WT) can be engineered by diminishing FGF19’s ability to induce dimerization of its cognate FGF receptors (FGFR).  As proof-of-principle, we generated three such mutants, each with a partial defect in binding affinity to FGFR (FGF19ΔFGFR), and its co-receptors klotho (FGF19ΔKLB) or heparan sulfate (FGF19ΔHBS).  Pharmacological assays in healthy and db/db mice confirmed that these variants incur a dramatic loss in mitogenic activity, yet are indistinguishable from FGF19WT in eliciting glycemic control.  Our approach provides a simple framework for the development of safer and efficacious FGF19 analogs.

overall_design: Lver tissues of db/db mice treated with PBS, FGF19WT, or FGF19ΔKLB for 12 weeks were collected.  Total RNA was extracted using the TRIzol reagent (Invitrogen) and analyzed using a Bio-analyzer 2100 and an RNA 6000 Nano Lab Chip Kit

first: Zhifeng

last: Huang


title: Post-transcriptional tuning of FGF signaling mediates neural crest induction

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

summary: Ectodermal patterning is required for the establishment of multiple components of the vertebrate body plan. Previous studies have demonstrated that precise combinations of extracellular signals determine the induction of neural or neural crest progenitors. Yet, we still have a limited understanding of how the response to inductive signals is optimized to generate the proper transcriptional output in target cells. Here we show that post-transcriptional attenuation of signaling gradients is essential for the formation of the neural crest. We found that neural crest cells display enhanced expression of Dicer, which promotes the maturation of a set of cell-type-specific miRNAs. These miRNAs target multiple components of the FGF signaling pathway, a central player in the process of neural induction in avian embryos. Loss of neural crest miRNAs prevented the attenuation of this neuralizing signal, leading to the expansion of the neural plate at the expense of neural crest cells. Thus, the post-transcriptional attenuation of FGF signaling is pre-requisite for neural crest specification. These findings demonstrate how post-transcriptional repression may reshape signaling gradients to set the boundaries between distinct spatial domains of progenitor cells.

overall_design: Small RNA-sequencing data for FACS sorted chicken neural plate and neural crest cells at one developmental timepoint (HH8).

first: Jacqueline

last: Copeland


title: Transcriptomic differences between mouse tumor-infiltrating and splenic regulatory T cells with or without Treg-specific loss of CD177

city: Gainesville

first: Ryan

last: Kolb

state: FL

address: 1275 Center Drive, M656

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

summary:
The goal of this study was to identify transcriptomic differences between splenic regulatory T cells and tumor-infiltrating regualtory T cells with or without Treg-specific loss of CD177.
Methods: MC38 tumors from CD177flox/flox/FOXP3-CreYFP and CD177flox/flox  C57Bl/6 mice were ezymatically dissocaited and a single cell suspension was obtained. Spleens from the same mice were collected and single cell suspension was obtained by mechanical dissociation. Regulatory T cells, identified as CD45+ CD4+ CD25hi GITR+, were isolated by flourenscence activated cell sorting. RNA from the regualtory T cell populations were isolated and libraries were generated using the NextSeq500 system. Samples were aligned using Kallisto pseudoalignment protocol and the mm19 mouse genome. Counts were processed and aggregated by gene symbol using the sleuth R package.
Results: The pro-survival gene Bcl2l1 is selectivley upregulated in tumor-infiltratign regulatory T cells compared to splenic T cells

overall_design: Analyze differentially regulated genes in tumor-infiltrating regualtory T cells compared to splenic regulatory T cells in wild-type or Treg-specific CD177 knockout mice

first: Weizhou

last: Zhang

first: Daohong

last: Zhou


title: Combined miRNA-mRNA transcriptional profiling in the human skin [mRNA_PSOR]

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary: mRNA and miRNA transcription changes during epidermal differentiation and between lesional psoriatic skin and normal skin were analysed

overall_design: 3 skin biopsies of lesional psoriatic skin and 3 healthy control skin samles were used for miRNA analysis.

first: Michael

last: Mildner

first: Lucian

last: Beer


title: Role of SRRM4 in regulating microexons in Circular RNAs

first: Simon

last: Conn

summary: Stduying the role of splicing factor SRRM4 on circular RNAs in human cells

overall_design: Biological triplicates of each sample type were sequenced to identify circular RNAs in Rnase R-treated RNA

first: Conn

last: Vanessa

first: Gabryelska

last: Marta

first: Marri

last: Shashikanth

last: Simon


title: Combined miRNA-mRNA transcriptional profiling in the human skin [miRNA_PSOR]

summary: mRNA and miRNA transcription changes during epidermal differentiation and between lesional psoriatic skin and normal skin were analyzed

overall_design: 4 skin biopsies of lesional psoriatic skin and 4 healthy control skin samples were used for miRNA analysis.


title: Combined miRNA-mRNA transcriptional profiling in the human skin

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Combined miRNA-mRNA transcriptional profiling in the human skin [mRNA_Kera]

summary: mRNA and miRNA transcription changes during epidermal differentiation were analysed using proliferating keratinoctes (pKC), differentiated keratinocytes (dKC) and skin equivalents (SE)

overall_design: from each condition (pKC, dKC, SE) one samples from an individual healy participan was analysed


title: Combined miRNA-mRNA transcriptional profiling in the human skin [Kera]


title: MeRIP-sequencing data from H1975 cells with NC or METTL3-sh

first: Lifang

last: Ma

state: China

address: No.241 West Huaihai Road, Xuhui District, Shanghai, P.R. China

institute: Shanghai Chest Hospital, Shanghai Jiao Tong University

summary: We use MeRIP-sequencing to evaluate the effect of METTL3 knockdown on the gene changes in H1975 cells.

overall_design: Examining three replicates of each group.

first: Jiayi

last: Wang


title: Combined miRNA-mRNA transcriptional profiling in the human skin [miRNA_Kera]


title: Defining a critical Nanog enhancer using chromatin-focused approaches identifies RNAPII recruitment as required for expression [-5delRNASeq]

first: Sridhar

last: Rao

summary: Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid reporters rather than native chromatin. We employed a combination of approaches to investigate the Nanog locus in mouse embryonic stem cells (ESCs) and an associated cis regulatory element (CRE) which may operate as either a super-enhancer (SE) or alternative promoter. We establish this element is a SE within chromatin using distance- and orientation-independence as criteria, and that it regulates Nanog by recruiting and/or initiating RNA Polymerase II. Our work highlights that enhancers can regulate gene expression through a diverse set of mechanisms.

overall_design: RNA-seq of 2 conditions, 3 replicates of each

first: Puja

last: Agrawal


title: miRNA information of Yiqi-Bushen-Tiaozhi Recipe against NASH

city: Hangzhou

first: Chen

last: Zhiyun

address: No. 9, Street 9, Xiasha economic development zone, Jianggan district

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

summary: MicroRNAs (miRNAs) have emerged as potential therapeutic targets for non-alcoholic fatty liver disease/non-alcoholic steatohepatitis (NAFLD/NASH). Traditional Chineses Medicine (TCM) plays an important role in the prevention or treatment of NAFLD/NASH. However, miRNA targets of TCM against NASH still remain largely unknown. Here, we showed that Yiqi-Bushen-Tiaozhi (YBT) recipe effectively attenuated diet-induced NASH in C57BL/6 mice. To identify the miRNA targets of YBT and understand the potential underlying mechanisms, we performed network pharmacology using miRNA and mRNA deep sequencing data combined with Ingenuity Pathway Analysis (IPA). Mmu-let-7a-5p, mmu-let-7b-5p, mmu-let-7g-3p and mmu-miR-106b-3p were screened as the main targets of YBT. Our results suggested that YBT might alleviate NASH by regulating the expression of these miRNAs that potentially modulate inflammation/immunity and oxidative stress. This study provides useful information for guiding future studies on the mechanism of YBT against NASH by regulating miRNAs.

overall_design: Nine samples were analyzed. The samples included 3 groups, each group including three replicates. ND group, normal diet for 16 weeks; WD group, Western diet for 16 weeks; YBT (Yiqi-Bushen-Tiaozhi recipe) group, Western diet for 16 weeks combined with YBT treatment for 12 weeks.

first: Wei

last: Hong

first: Songsong

last: Li

first: Yueqin

last: Cai

first: Tingting

first: Qingrou

last: Yang

first: Beihui

last: He

first: Jianshun

last: Yu

first: Zhiyun

last: Chen


title: DLBCL-reminiscent MyD88- or CARD11-mutant aggressive B-cell lymphomas exhibit strong pro-senescent and immune-evasive phenotypes [part2]

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

summary: Aberrant B-cell receptor (BCR)/NF-kB signaling activity is a prominent feature of diffuse large B-cell lymphoma (DLBCL), particularly of, but not restricted to the activated B-cell (ABC) subtype. Recurrent mutations in this cascade, e.g. in CD79B, CARD11, A20/TNFAIP3 or NFKBIZ, but also in the Toll-like receptor (TLR) pathway transducer MyD88, all converge at NF-kB deregulation, but their differential impact on lymphoma development and biology remains to be dissected. Recapitulating oncogenic myc rearrangements as another common feature of DLBCL, we functionally investigate here primary mouse lymphomas that formed after propagation of Eµ-myc transgenic hematopoietic stem cells (HSC), stably transduced with naturally occurring DLBCL-derived NF-kB mutants, in recipient mice. While most mutants tested supported Myc-driven lymphoma formation through repressed apoptosis, selectively deregulated CARD11- or MyD88-mutant lymphoma cells presented with a macrophage-activating secretion profile, which, in turn, enforced TGF-b-mediated feedback senescence in the lymphoma cell compartment. Moreover, MyD88- or CARD11-mutant Eµ-myc lymphomas – mirrored by matching signatures in their mutant DLBCL counterparts – exhibited high-level expression of the immune checkpoint mediator PD-L1, thus preventing their efficient clearance by adaptive host cell immunity. Conversely, these mutant-specific dependencies were therapeutically exploitable by anti-PD1 immune checkpoint blockade, leading to the direct T-cell-mediated lysis of predominantly but not exclusively senescent lymphoma cells. Our functional, cross-species interrogation of a syngeneic and fully immune-competent, BCR/NF-kB-deregulated and DLBCL-reminiscent in vivo-model platform unveils common principles and therapeutic vulnerabilities related to human DLBCL subsets that will inform future personalized treatment strategies.  Specifically, for the shown FLC transplantation experiments, 8-12 week-old female C57BL/6N recipient mice (Charles River Laboratories) received a single, myelo-ablative dose of 9 Gy total-body gamma-irradiation. After in vitro-transduction of FLC, 10% GFP-positive Sca1+; c-Kit+; lin- cells with the indictaed transgenic and/or knock out genotypes were transplanted via tail vein injection into irradiated mice, which were subsequently monitored until a well-palpable lymphadenopathy had formed. Retroviral vectors used in this experiment were the MSCV 2.2 derived constructs

overall_design: mRNA profiles of manifest Eµ-myc mouse lymphoma cells (mouse strain C57BL/6N ) transduced either with retroviral MSCV vector co-expressing green fluorescent protein (GFP) for control group, or retroviral MSCV-GFP vector with following mutants: CARD11-L251P or CD79B-Y195H or MYD88-L265P; or retroviral MSCV-GFP vector with NFKBIZ or PD-L1 for overexpression. SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) and Nextera XT Kit (Illumina) followed by sequencing with 50 bp single-end reads on HiSeq 2000.

first: Clemens

last: Schmitt

first: Jens

last: Schrezenmeier

first: Maurice

last: Reimann


title: DLBCL-reminiscent MyD88- or CARD11-mutant aggressive B-cell lymphomas exhibit strong pro-senescent and immune-evasive phenotypes [part1]

summary: Aberrant B-cell receptor (BCR)/NF-kB signaling activity is a prominent feature of diffuse large B-cell lymphoma (DLBCL), particularly of, but not restricted to the activated B-cell (ABC) subtype. Recurrent mutations in this cascade, e.g. in CD79B, CARD11, A20/TNFAIP3 or NFKBIZ, but also in the Toll-like receptor (TLR) pathway transducer MyD88, all converge at NF-kB deregulation, but their differential impact on lymphoma development and biology remains to be dissected. Recapitulating oncogenic myc rearrangements as another common feature of DLBCL, we functionally investigate here primary mouse lymphomas that formed after propagation of Eµ-myc transgenic hematopoietic stem cells (HSC), stably transduced with naturally occurring DLBCL-derived NF-kB mutants, in recipient mice. While most mutants tested supported Myc-driven lymphoma formation through repressed apoptosis, selectively deregulated CARD11- or MyD88-mutant lymphoma cells presented with a macrophage-activating secretion profile, which, in turn, enforced TGF-b-mediated feedback senescence in the lymphoma cell compartment. Moreover, MyD88- or CARD11-mutant Eµ-myc lymphomas – mirrored by matching signatures in their mutant DLBCL counterparts – exhibited high-level expression of the immune checkpoint mediator PD-L1, thus preventing their efficient clearance by adaptive host cell immunity. Conversely, these mutant-specific dependencies were therapeutically exploitable by anti-PD1 immune checkpoint blockade, leading to the direct T-cell-mediated lysis of predominantly but not exclusively senescent lymphoma cells. Our functional, cross-species interrogation of a syngeneic and fully immune-competent, BCR/NF-kB-deregulated and DLBCL-reminiscent in vivo-model platform unveils common principles and therapeutic vulnerabilities related to human DLBCL subsets that will inform future personalized treatment strategies.

overall_design: mRNA profiles of Eµ-myc mouse lymphoma cells isolated from lethally irradiated C57BL/6N mice transplanted with Eµ-myc HSC (hematopoetic stem cells) retrovirally transduced with either MYD88-L265P;sh-scrambled MSCV-GFP or MyD88-L265P;sh-PDL1 MSCV-GFP. SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) and Nextera XT Kit (Illumina) followed by sequencing with 50 bp single-end reads on HiSeq 2000.


title: Immediate early transcriptional responses of airway epithelial cells

city: Miami

first: Hitendra

middle: S

last: Chand

department: Dept of Immunology & Nano-Medicin

institute: Florida International University Herbert Wertheim College of Medicine

summary: Airway epithelial cells are crucial for mucosal and adaptive immunity as they produce mucins that trap and clear inhaled particulates by mucociliary activity, and also secrete diverse inflammatory mediators. But whether these cells respond in a memory-dependent manner to a secondary exposure is poorly studied. Our recent studies have highlighted the role of 'memory-based' or ‘trained’ immune responses. In this proposal we would like to probe for the molecular basis underlying the memory-based response in AECs. We will first establish an in-vitro model of memory-based responses using differentiated AECs. Here we will delineate the kinetics of memory-based response in AECs using a microbial ligand, LPS or endotoxin. The cells will be grown in air-liquid interface to study the effect of memory response on mucous phenotype. The RNAseq analyses will be performed on AECs exposed to endotoxin and compared to that of non-exposed AECs to determine the changes in coding and noncoding RNA regions.

overall_design: Air-liquid interface cultured 3D airway epithelial cells were treated with LPS (100 ng/ml) and cells analyzed at 2 h post treatment and compared to non-treated cells. The primary human airway epithelial cells (HAECs) were differentiated at the air-liquid interface for 14 days and were treated with LPS (100 ng/ml) for 2 h. Total RNA was isolated from cells treated with and without LPS using RNeasy isolation kit (Qiagen Inc.). RNA seq analysis was performed by HudsonAlpha Institute for Biotechnology, Huntsville, Alabama. Briefly, Illumina TruSeq Stranded Total RNAseq libraries with ribosomal depletion were prepared per manufacturer’s instructions (Illumina, Inc, San Diego, CA).

first: Raymond

last: Langley

first: Grant

last: Daly

first: Glen

last: Borchert


title: Effect of dietary n-3 PUFA supplementation and post-insemination plane of nutrition on global gene expression patterns in bovine uterine endometrial tissue

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: The objectives of this study were to examine the effect of (i) dietary supplementation with  n-3 PUFA and (ii) post-insemination plane of nutrition on the global transcriptome of uterine endometrial tissue, with particular focus on key genes and pathways that may affect pregnancy outcome. A total of 60 estrous-synchronised continental crossbred heifers were offered a concentrate-based diet supplemented (n-3 PUFA; n=32) or not (Control; n=28) with an n-3 PUFA-enriched product for 30 days prior to insemination. Following insemination, animals were allocated, within treatment, to one of two post insemination diets, either remaining on their existing high plane of nutrition (Control + High (n = 14); n-3 PUFA + High (n = 15)), or fed a low plane of nutrition diet (Control + Low (n = 14); n-3 PUFA + Low (n = 17)). Uterine endometrial tissue was collected, RNA isolated and gene expression analysis conducted using RNAseq. Comparison of transcript abundance across groups, highlighted a significant effect of diet on the endometrial transcriptome. The mTOR signalling pathway as well as pathways involved in early pregnancy/fertility was significantly enriched as a consequence of diet.

overall_design: A total of 60 estrous-synchronised continental crossbred heifers were offered a concentrate-based diet supplemented (n-3 PUFA; n=32) or not (Control; n=28) with an n-3 PUFA-enriched product for 30 days prior to insemination. Following insemination, animals were allocated, within treatment, to one of two post insemination diets, either remaining on their existing high plane of nutrition (Control + High (n = 14); n-3 PUFA + High (n = 15)), or fed a low plane of nutrition diet (Control + Low (n = 14); n-3 PUFA + Low (n = 17)). Uterine endometrial tissue samples were collected from all heifers following 16 days of differential feeding during the post-insemination phase.

first: Carla

last: Surlis

first: Paul

last: Cormican

first: Sinead

last: Waters

first: Patrick

last: Lonergan

first: David

last: Doyle

last: Kenny


title: DLBCL-reminiscent MyD88- or CARD11-mutant aggressive B-cell lymphomas exhibit strong pro-senescent and immune-evasive phenotypes


title: Reduced Physical Activity Alters the Leucine-Stimulated Translatome in Aged Skeletal Muscle

status: Public on Dec 06 2020

first: Michael

last: Howard

department: Human Genetics

summary: Background: Periods of inactivity experienced by older adults induce nutrient anabolic resistance creating a cascade of skeletal muscle transcriptional and translational aberrations contributing to muscle dysfunction. Objective: To identify how inactivity alters leucine-stimulated translation of molecules and pathways within the skeletal muscle of older adults.

overall_design: Design: We performed ribosomal profiling alongside RNA sequencing from skeletal muscle biopsies taken from older adults (n=8; ~72y; 6F/2M) in response to a leucine bolus before (Healthy) and after (Inactive) 2-weeks of reduced physical activity. At both visits, muscle biopsies were taken at baseline, 60min (early response), and 180min (late response) after leucine ingestion.

first: Micah

last: Drummond


title: Distinguishing smoking related lung disease phenotypes via imaging and molecular features

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Using unsupervised machine learning applied to computed tomography-based imaging characteristics we have found three distinct phenotypes of lung disease in two large cohorts of ever-smokers and have identified their molecular correlates.

overall_design: Using K-means clustering, we clustered participants from the COPDGene study (n=5273) based on computed tomography (CT) imaging characteristics and then evaluated their clinical phenotypes.  These clusters were replicated in the Detection of Early Lung Cancer Among Military Personnel (DECAMP) cohort (n=360), and were further characterized using bronchial epithelial gene expression, including differential gene expression analysis, over-representation analysis, gene set enrichment analysis and gene set variation analysis.

first: Ke

last: Xu

first: Ehab

last: Billatos


title: The Epigenetic dysregulation of lncRNA on gene expression in Colorectal tumor

city: GuangZhou

first: Zhu

last: Hao

address: Shatai Road

institute: Southern Medical University


title: The Epigenetic dysregulation of lncRNA on gene expression in Colorectal tumor [RNA-seq]

summary: Our data analysis unveils that differentially expressed long noncoding RNAs and some wrongly transcribed noncoding transcripts have potential DNA binding sites at promoters of differentially expressed or wrongly transcribed coding transcripts, gains and losses of differentially methylated DNA regions also occur at relevant sites, but less specifically. Moreover, both differentially expressed or wrongly transcribed transcripts and gains and losses of differentially methylated DNA regions show significant case-to-case variation.

overall_design: we applied RNA-seq and MeDIP-seq to 12 colorectal cancer cases with varied differetiation stages and 3 normal colon tissue cases

first: Hao

last: Zhu


title: Single-cell RNA-sequencing of migratory breast cancer cells: discovering genes associated with cancer metastasis

city: Ann Arbor

first: Yu-Chih

last: Chen

state: MI

address: 1301 Beal Ave.

institute: University of Michigan

summary: We isolated fast moving migratory breast cancer cells and would like to see the differences as compared to WT cancer cells

overall_design: We compared the wild-type (WT) and migratory breast cancer cell lines


title: The Epigenetic dysregulation of lncRNA on gene expression in Colorectal tumor [MeDIP-seq]


title: Comparative transcriptomic analysis of THP‑1 derived macrophages infected with Mycobacterium tuberculosis H37Rv, H37Ra and BCG

city: Nanjing

first: Chen

last: Zhao

state: Jiangsu

address: 22nd Hankou Road

institute: Nanjing University

summary: In this study, RNA sequencing (Transcriptome sequencing) was employed to investigate the global transcriptome changes in the macrophages during the different strains of M.tb infection. THP-1 cells derived macrophages were exposed to the virulent M.tb strain H37Rv (Rv) or the avirulent M.tb strain H37Ra (Ra), and the M.tb BCG vaccine strain was used as a control. The cDNA libraries were prepared from M.tb infected macrophages and then sequenced.

overall_design: The experiments were divided into four groups include; control, H37Rv, H37Ra, and BCG infected groups respectively. There are three samples in each group and 12 samples in total

first: Wenyuan

last: Pu

first: Hongwei

last: Wang


title: Analysis of CD8 T cells in aged mice

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Aging is associated with systemic chronic inflammation (inflammaging) that leads to impaired physiological functions and vulnerability to several diseases. However, underlying alterations in aged immune system resulting in gradual loss of immune fitness remain unclear. Using a combination of bulk and single-cell RNA sequencing, we characterized the age-associated alterations in CD8 T cells. We defined organ-specific and common changes in immune cell populations and identified a distinct subpopulation of granzyme K (GZMK)-expressing clonal CD8+ T cells that accumulate with age in multiple tissues. These cells have a distinct epigenetic signature, express markers of exhaustion but, paradoxically, show an increased capacity to produce mediators of inflammation that increase secretion of inflammatory cytokines from non-immune cells. Our findings suggest that accumulation of GZMK+ CD8+ T cells is a conserved hallmark of inflammaging.

overall_design: Viable CD3e+CD8a+CD44-PD1-,  CD3e+CD8a+CD44+PD1- and CD3e+CD8a+PD1+ cells were sorted from spleen of 4 57BL/6J 18 months old female mice and total RNA was immediately isolated.

first: Denis

last: Mogilenko

first: Oleg

last: Shpyno

first: Prabhakar

last: Andhey

first: Laura

last: Arthur

first: Amanda

last: Swain

first: Ekaterina

last: Esaulova

first: Simone

last: Brioschi

first: Irina

last: Shchukina

first: Martina

last: Kerndl

first: Zhangting

last: Yao

first: Anwesha

last: Laha

first: Konstantin

last: Zaitsev

first: Samantha

last: Burdess

first: Susan

last: Gillfilan

first: Sheila

last: Stewart

first: Marco

last: Colonna

middle: N


title: Identification of microRNAs in response to low potassium stress in the shoots of Tibetan wild barley and cultivated barley [degradome]

city: hangzhou

first: zhilan

last: ye

state: zhejiang

address: yuhangtang road

institute: zhejiang university

summary: Soil potassium deficiency has become a global problem in agricultural production, seriously restricting crops productions and agricultural sustainable development. Identification of the microRNAs and understanding their functions in response to low K stress will be helpful for developing crop varieties with low K tolerance. Our previous study identified a low K tolerant accession XZ153 from Tibetan wild barley. In this study, small RNA and degradome analysis were performed on two barley genotypes differing in low K tolerance (XZ153, tolerant; ZD9, sensitive) to identify the miRNAs and their targets responding to low K stress. A total of 1108 miRNAs were detected in shoots of XZ153, and ZD9 at 2 d and 7 d after low K stress, and their targets were identified through bioinformatics prediction and degradome analysis. We identified 65 differentially expressed miRNAs responding to low K stress. The results also showed that miR164c, miR169h and miR395a modules could mediate TCA cycle, glycolysis pathway and pentose phosphate pathway responding to low K stress. The osa-miR166g-3p and ghr-miR482b may act as the regulators in Ca2+ signaling pathway in response to low K stress. The methionine salvage cycle involved in ethylene biosynthesis process mediated by miR396c-3p and osa-miR171e-5p might be also involved in responding to low K stress. Some miRNAs, including miR160a, miR396c and miR169h modules, which participated in photosynthesis regulation under low K stress, differed between the two barley genotypes. In conclusion, these exclusively expressed miRNAs and their targets play the crucial roles in low K tolerance.

overall_design: Degradome-seq for two samples: ZD9 and XZ153

first: Zhilan

last: Ye

first: Jianbin

last: Zeng

first: Lizhi

last: Long

first: Lingzhen

first: Guoping

last: Zhang


title: Identification of microRNAs in response to low potassium stress in the shoots of Tibetan wild barley and cultivated barley [miRNA-seq]

overall_design: A total of 24 shoot samples (two genotypes × two potassium conditions × two time periods × three replications) were harvested for further RNA isolation and library construction.


title: Expression data of lentivirus sponge Protein Arginine Methyltransferase 5 downregulated NCI-H929 cell line compared with control lentivirus sponge

first: Tian

last: Xia

summary:
Multiple myeloma is characterized by frequent chromosomal alterations. Protein Arginine Methyltransferase 5 (PRMT5) catalyzes symmetric dimethylation of arginine, a post-translational modification involved in cancer and embryonic development.
We sought to functionally validate the role of PRMT5 and delineate their downstream target genes in MM. Using “sponge” lentiviral vectors to knock down PRMT5 in vitro and in vivo, we have documented enhanced apoptosis and descend proliferation of MM cells compared with control lentivirus sponge . Expression profiling analysis of PRMT5-deficient cells identified a large number of downstream target genes, which provides a valuable tool to investigate their function in MM pathogenesis and their potential use as therapeutic targets.

overall_design: MM cell line NCI-H929 was stably tranduced and sorted with lentiviruses expressing PRMT5 downregulating sponges or control sponges, and analyzed for GEP to asses possible PRMT5 target genes. Cells were lysed and the RNA extraction and hybridization was peformed on Affymetrix microarrays. We sought to obtain homogeneous populations of cells and therefore collected all at the same timepoint.

first: Peipei

last: Xu


title: Shear Stresses Associated with Cardiopulmonary Bypass Activate Expression Inflammatory Cytokines and Induce Necroptosis in Monocytes Via Calcium Dependent Signaling

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Cardiopulmonary bypass (CPB), the mechanical support required during the majority of cardiac surgeries, causes significant systemic inflammation and multi-organ dysfunction that is especially severe in neonatal patients. Currently, the limited understanding of the molecular mechanisms that underlie CPB-associated inflammation presents a significant barrier to the development of therapeutic interventions. To address this knowledge gap, we performed mRNA sequencing of total circulating leukocytes from neonatal patients undergoing CPB. The transcriptional signatures across 7 time points ranging from pre-CPB, during CPB, to 24 hours post-CPB were found to be dominated by myeloid cells, particularly monocytes. INTERLEUKIN-8 (IL8) and TUMOR NECROSIS FACTOR-α (TNFα) were two inflammatory cytokines specifically and robustly upregulated in the leukocytes from both CPB patients and piglets exposed to CPB. To delineate the mechanism how CPB activates cytokine production, we exposed THP-1 cells, a human monocyte cell line, in vitro to CPB-like conditions including artificial surfaces, high shear stress and cooling/rewarming. The in vitro CPB data recapitulated the in vivo CPB condition in that IL8 and TNFα were strongly upregulated. Shear stress was the major driver of cytokine expression as compared to the temperature or plastic exposure. Extracellular calcium influx was found essential for the shear-stress mediated upregulation of cytokines via the MEK/ERK/AP-1 and Calcineurin/NFAT pathways. After being exposed to CPB conditions, a subpopulation of THP-1 cells died by apoptosis and TNFα-mediated necroptosis, the latter form of which potentially contribute to the post-CPB tissue injuries. Together, our study is the first to elucidate the shear-stress modulated molecular mechanisms leading to systemic inflammation in pediatric CPB and the link between inflammation and organ damage. Calcium signaling pathways and TNFα signaling are novel targets for therapeutic development to improve clinical outcomes. To our knowledge, these are also the first data to implicate necroptosis in CPB and show that shear stress can activate necroptosis.

overall_design: Gene expression profiling of circulating leukocytes from neonatal patients undergoing cardiopulmonary bypass (5 patients, 7 time points each)

first: Lan

last: Tu

first: Vishal

last: Nigam


title: Comparison of gene expression in CD8 T cells treated with the agonist of PPAR isoforms

city: kyoto

first: partha sarathi

last: chowdhury

address: Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan

institute: kyoto university

summary:
We performed gene expresion analysis of T cell treated with agonist of three isoform of PPAR. This analysis allowed us to explain why the activation of PPAR g is the best in boosting PD-1 blockade efficacy compared with other isoform activation.
We demonstrated that activation of the PPAR-γ isoform specifically enhanced PD-1 blockade greater than activation of the other two PPAR isoforms (a and b) in mouse tumor model. Using the microarray assay we found genes that were most differentially regulated by PPAR agonist treatment were with a well-documented role in T cell biology, such as Ddx3y, Ifng, Il17c, Ccr3, Acrv1, Btk and metabolic process such as Pygl, P2rx1, Tph2, Kynu, and Ugt2b37. Therefore, microarray data has been useful to establish that activation of PPAR-g in T cell uniquely modulate genes, which include metabolic as well genes related to immune function.

overall_design: We used in vitro system to obtain gene expression data. In vitro stimulated naive CD8+ T cells were treated with each PPAR isoforms agonist separately for 48 hours.

first: Partha

last: Chowdhury

first: Alok

last: Kumar

first: Kenji

last: Chamoto

first: Tasuku

last: Honjo


title: Cell type specificity of intralocus interactions reveals oligodendrocyte intrinsic mechanisms for multiple sclerosis

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

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

overall_design: Refer to individual Series


title: Identification of microRNAs in response to low potassium stress in the shoots of Tibetan wild barley and cultivated barley

first: zhilan


title: Analysis of the contribution of CsrA, CsrB/C, and CsrD to gene expression in E. coli

first: Anastasia

middle: Haley

last: Potts

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

overall_design: Epistatis differential expression analysis of 3 biological replicates from wild type, csrA, csrBC, and csrD mutant and complimented strains during stationary phase

middle: H

first: Tony

last: Romeo


title: scRNA-seq studies

first: Maxim

last: Artyomov


title: Cell type specificity of intralocus interactions reveals oligodendrocyte intrinsic mechanisms for multiple sclerosis [ChIP-Seq]

summary: Multiple sclerosis (MS) is an autoimmune disease characterized by attack on oligodendrocytes within the central nervous system (CNS). Despite widespread use of immunomodulatory therapies, patients face progressive disability due to failure of myelin regeneration and loss of neurons, suggesting additional cellular pathologies. Here, we describe a general approach for identifying specific cell types in which a disease allele exerts a pathogenic effect.  Applying this approach to MS risk loci, we pinpoint likely pathogenic cell types for 70%. In addition to T cell loci, we unexpectedly identified myeloid and CNS-specific risk loci, including two sites that dysregulate transcriptional pause release in oligodendrocytes. Functional studies demonstrated inhibition of transcriptional elongation is a dominant pathway blocking oligodendrocyte maturation. Furthermore, pause release factors are frequently dysregulated in MS brain tissue and are associated with white matter microstructure. These data implicate cell-intrinsic aberrations outside of the immune system and suggest new avenues for therapeutic development.

overall_design: ChIPseq profiles comparing RNApolII distribution during oligodendrocyte maturation in the presence of the inactive (R-) or active (S-) enantiomers of JQ1

first: Daniel

last: Factor

first: Olivia

last: Corradin


title: scRNA-seq analysis of mouse splenic CD8 T cells 1 month post transfer of CD8 T cells from 3 months old donor into 24 months old recipient

summary: Aging is associated with systemic chronic inflammation (inflammaging) that leads to impaired physiological functions and vulnerability to several diseases. However, underlying alterations in aged immune system resulting in gradual loss of immune fitness remain unclear. Using a combination of CD8 T cell transfer from young to old and from old to young mice and single-cell RNA sequencing, we characterized the age-associated alterations in CD8 T cells. We transferred 2 millions of purified CD8+ T cells pooled from 3 CD45.1 C57BL/6J 3 months old female mice (donor) by i.v. injection into CD45.2 C57BL/6J 24 months old female mouse (recipient) and sorted CD45.1+CD3e+CD8a+ and CD45.2+CD3e+CD8a+ T cells from the spleen 1 month post transfer to perform scRNA/TCR-seq.

overall_design:
Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by isolating mouse CD45.1+ CD3e+CD8a+ (3 months old donor) and CD45.2+CD3e+CD8a+ (24 months old recipient) cells sorted by FACS from the spleen and 5'GEX and TCR libraries were prepared using Chromium Single Cell 5′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using NovaSeq S4 sequencers.
Mouse CD45.1+CD3e+CD8a+ (young donor) and CD45.2+CD3e+CD8a+ (old recipient) T cells from the spleen 1 month post transfer sorted, processed and sequensed

first: Denis

last: Mogilenko

first: Oleg

last: Shpyno

first: Prabhakar

last: Andhey

first: Laura

last: Arthur

first: Amanda

last: Swain

first: Ekaterina

last: Esaulova

first: Simone

last: Brioschi

first: Irina

last: Shchukina

first: Martina

last: Kerndl

first: Zhangting

last: Yao

first: Anwesha

last: Laha

first: Konstantin

last: Zaitsev

first: Samantha

last: Burdess

first: Susan

last: Gillfilan

first: Sheila

last: Stewart

first: Marco

last: Colonna


title: Identification and Comparative Analysis of Differentially Expressed Chemosensory Genes in the Male and Female Galleria mellonella (Linnaeus) Wax Moth

city: Mengzi

first: shuang

last: yang

address: Caoba street

institute: Institute of Sericulture and Apiculture, Yunnan Academy of Agriculture

summary: To better understand the olfactory mechanisms in G. mellonella, we established six transcriptomes from the antennae of male and female adults. A total of 226 chemosensory gene transcripts were identified, which included 36 chemosensory proteins, 52 odorant-binding proteins, 2 sensory neuron membrane proteins, 80 olfactory receptors, and 56 ionotropic receptors. The expression patterns of these genes were calculated from the estimated fragments per kilobase of transcript sequence per million fragments mapped, and the differentially expressed genes (DEGs) related to olfaction were validated by qRT-PCR. Among the 114 DEGs identified, 66 were exclusively or primarily expressed in the female antenna, whereas the rest were specifically expressed in the male antenna. These antenna-specific genes may provide useful subjects for advanced studies of their biological functions; this may provide a theoretical basis for the control of G. mellonella and the prevention of damage caused by this species using the male pheromone as a bait.

overall_design: Analysis of Chemosensory Genes in antenna of the Male and Female Galleria mellonella (Linnaeus) Wax Moth

first: Shuang

last: Yang

first: Yusuo

last: Jiang


title: scRNA-seq analysis of aged immune system in mice

first: Maxim

last: Artyomov

summary: Aging is associated with systemic chronic inflammation (inflammaging) that leads to impaired physiological functions and vulnerability to several diseases. However, underlying alterations in aged immune system resulting in gradual loss of immune fitness4 remain unclear. Using a combination of single-cell RNA/TCR/BCR-sequencing and extensive FACS/CyTOF-based validation, we comprehensively characterize age-associated alterations in immune cells in 4 mouse organs and human blood. We identified both organ-specific and common changes in immune cell populations and their transcriptional programs and found age-associated subpopulation of CD8+ T cells marked with expression of GZMK.

overall_design:
Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by isolating mouse CD45+ cells sorted by FACS from the spleen, peritoneal cavity, the lungs and the liver and libraries (5'GEX, TCR, and BCR enrichment libraries) were prepared using Chromium Single Cell 5′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using NovaSeq S4 sequencers.
3 biologically independent mice per age were pooled, processed and sequenced.

first: Denis

last: Mogilenko

first: Oleg

last: Shpyno

first: Prabhakar

last: Andhey


title: Cell type specificity of intralocus interactions reveals oligodendrocyte intrinsic mechanisms for multiple sclerosis [RNA-Seq]

first: Paul

last: Tesar

overall_design: RNAseq profiles comparing oligodendrocyte maturation in the presence and absence of JQ1

first: Daniel

last: Factor

first: Olivia

last: Corradin


title: Neural Stem Cells Direct Axon Guidance via their Radial Fiber Scaffold

status: Public on Dec 05 2020

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

institute: Yale University School of Medicine

summary:
To determine the genes regulated by Fezf2 during neocortical development, we performed RNA-seq on Fezf2 +/+; Emx1-cre (Fezf2 wildtype) and Fezf2 fl/+; Emx1-Cre (Fezf2 Knockout) neocortices isolated from the P0 mice.  After RNA isolation from the dissected tissue the samples were processed for library preperation using Illumina Poly-A RNA kit.
Fezf2 can reprogram the upper layer neocortical neurons to form corticospinal tract. To understand the key transcriptomic changes driven by Fezf2 that drive this reprogramming, we performed in RNA-seq on the cells over-expressing Fezf2 and Gfp or Gfp.  At E15.5, in utero electroporations targeting cortical plate, were performed in pregnant mice with Fezf2 and Gfp plasmids or with Gfp plasmid alone, which was used as control. At P3, the Gfp positive cells were FAC sorted from Fezf2 and Gfp, or Gfp cortices and processed for library preparations using NUGEN Ovation® V2 system. Libraries were sequenced using Illumina 2000 platform to generate 75bp single reads. At least 10 million uniquely mapped reads were obtained for each sample.
To determine the genes directly regulated by FEZF2, we performed the ChIP-Seq on N2A cells that were transfected to over express FEZF2 using pCAG- Fezf2-V5 and pCAG-V5. After 48 hr, of transfection, cells were fixed and processed for ChIP seq. Libraries were prepared using Illumina TruSeq ChIP Libary Preparation Kit.

overall_design:
Determining the unique genes regulated by Fezf2 during the neocortex development by RNA-seq and ChIP-seq
ChIP antibody information: V5 Tag Monoclonal Antibody (ThermoFisher Scientific, Cat# R960-25, RRID:AB_2556564)

first: Wenqi

last: Han

first: Navjot

last: Kaur

first: Mingfeng

last: Li


title: MYCN drives chemoresistance in small cell lung cancer while USP7 inhibition can restore chemosensitivity [tumor]

city: Seattle

first: David

last: MacPherson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: This study assessed gene expression in mouse SCLC with inducible MYCN overexpression in tumors

overall_design: Identification of differentially expressed genes regulated by MYCN in SCLC tumors grown in presence or of doxycycline (MYCN ON Condition), or in tumors with doxyxline removed from feed for 7 days


title: 35S-SUC2 WT and antisilencing mutants

city: Shanghai

first: Huang

last: Huan

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress  Biology

institute: Chinese Academy of Sciences


title: H2A.Z ChIP-seq of WT, ros1-14, idm1-9, arp6-4 and pie1-6

summary: Using ChIP-seq to study the deposition of H2A.Z in different anti-silencing mutants

overall_design: Examination of H2A.Z deposition using ChIP-Seq

first: Wenfeng

last: Nie

first: Mingguang

last: Lei

first: Huan

last: Huang

first: Cui-jun

last: Zhang

first: Daisuke

last: Miki

first: Jian-Kang

last: Zhu


title: The SWR1 Complex Regulates Active DNA Demethylation in Arabidopsis

summary: Using BS-Seq to provide single-base resolution of DNA methylation status in 35S-SUC2 WT and antisilencing mutants (arp6, pie1, h2a.z, idm1, and ros1)

overall_design: BS-Seq: WT and antisilencing mutants (arp6, pie1, h2a.z, idm1, and ros1)


title: Genomic analysis of ketoconazole resistance in the dandruff-associated cutaneous yeast Malassezia restricta.

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: To understand ketoconazole resistance mechanism in M. restricta, we investigated differentially expressed genes in the azole resistant isolates using transcriptome profile. Transcriptomes of ketoconazole susceptible and resistant M. restricta cells in the absence and precence of ketoconazole were compared and analyzed by RNA sequencing.

overall_design: Transcriptome of ketoconazole susceptible M. restricta vs. transcriptome of ketoconazole resistant M. restricta

first: Minji

last: Park

first: Won

last: Jung


title: Temporal Splicing Switches in Elements of the TNF-Pathway Identified by Computational Analysis of Transcriptome Data for Human Cell Lines

status: Public on Dec 04 2020

first: Nikolai

last: Genov

state: Berlin

address: Invalidenstraße 110

institute: Humboldt University Berlin/Charite Medical University Berlin

summary: Alternative splicing plays an important role in numerous cellular processes and aberrant splice decisions are associated with cancer. Although some studies point to a regulation of alternative splicing and its effector mechanisms in a time-dependent manner, the extent and consequences of such a regulation remains poorly understood. In the present work, we investigated the time-dependent production of isoforms in two Hodgkin lymphoma cell lines of different progression stages (HD-MY-Z, stage IIIb and L-1236, stage IV) compared to a B lymphoblastoid cell line (LCL-HO) with a focus on tumour necrosis factor (TNF) pathway-related elements. For this, we used newly generated time-course RNA-sequencing data from the mentioned cell lines and applied a computational pipeline to identify genes with isoform-switching behaviour in time. We analysed the temporal profiles of the identified events and evaluated in detail the potential functional implications of alterations in isoform expression for the selected top-switching genes. Our data indicate that elements within the TNF pathway undergo a time-dependent variation in isoform production with a putative impact on cell migration, proliferation and apoptosis. These include the genes TRAF1, TNFRSF12A and NFKB2. Our results point to a role of temporal alternative splicing in isoform production, which may alter the outcome of the TNF pathway and impact on tumorigenesis.

overall_design: A 30-h time-course RNA-seq study was performed to analyse the different circadian phenotypes of  and L- cell lines. Samples were taken every 3 h for a period of 30 h resulting in 11 time-points for each cell line.

first: Alireza

last: Basti

first: Monica

last: Abreu

first: Angela

last: Relogio


title: MYCN drives chemoresistance in small cell lung cancer while USP7 inhibition can restore chemosensitivity [cells]

summary: This study assessed gene expression in mouse SCLC with inducible MYCN overexpression

overall_design: Identification of differentially expressed genes regulated by MYCN in SCLC cell lines derived from mouse SCLC tumors grown in presence of doxycycline (MYCN-ON condition) or absence of doxycycline for 4 days (MYCN-OFF condition)


title: Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes [Control+DON]

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

summary:
Purpose: DON inhibits the activation of gamadelta T cells. The goals of this study are to identify genes and pathways invovled in the regulation.
Methods: Mouse splenic gamadelta T cells were stimulated with IL-23 and IL1β, together with or without DON for 3 days. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/), the enrichr database (https://maayanlab.cloud/Enrichr/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Results: Genes in the IL-23/STAT3 pathway were inhibited by taurine. As a result, the production of IL-17A decreased upon DON treatment.

overall_design: MRNA profiles of IL-23+IL1β stimulated and IL-23+IL-1β plus DON treated gamadelta T cells were generated by deep sequencing, in triplicate, using illumina HiSeq ⅹ10 system


title: MYCN drives chemoresistance in small cell lung cancer while USP7 inhibition can restore chemosensitivity


title: Reactive oligodendrocyte progenitor cells (re-)myelinate the regenerating zebrafish spinal cord

city: Dresden

first: Vasiliki

last: Tsata

state: Saxony

address: Fetscherstrasse 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

institute: TU Dresden


title: Reactive oligodendrocyte progenitor cells (re-)myelinate the regenerating zebrafish spinal cord [Single cell]

summary: Spinal cord injury (SCI) results in loss of neurons, oligodendrocytes and myelin sheaths, all of which are not efficiently restored. The scarcity of oligodendrocytes in the lesion site impairs remyelination of spared fibres, which leaves axons denuded, impedes signal transduction and contributes to permanent functional deficits. In contrast to mammals, zebrafish can functionally regenerate the spinal cord. Yet, little is known about oligodendroglial lineage biology and remyelination capacity after SCI in a regeneration-permissive context. Here, we report that in adult zebrafish, SCI results in axonal, oligodendrocyte and myelin sheath loss. We find that OPCs, the oligodendorocyte progenitor cells, survive the injury, enter a reactive state, proliferate and differentiate into oligodendrocytes. Concomitantly, the oligodendrocyte population is re-established to pre-injury levels within two weeks.Transcriptional profiling revealed that reactive OPCs upregulate the expression of several myelination-related genes. Interestingly, global reduction of axonal tracts and partial re-myelination, relative to pre-injury levels, persist at later stages of regeneration, yet suffices for functional recovery. Taken together, these findings imply that in the zebrafish spinal cord, OPCs replace lost oligodendrocytes and, thus, re-establish myelination during regeneration.

overall_design: Single cell transcriptome of reactive olig2:eGFP+ OPCs from the zebrafish spinal cord at 7 days post lesion (dpl) and sham controls.

first: Volker

last: Kroehne

first: Michael

last: Brand


title: Loss of SWI/SNF Chromatin Remodeling Alters NRF2 Signaling in Non-Small Cell Lung Carcinoma

city: Chapel Hill

first: Vinh

last: Nguyen

state: NC

address: 450 West Drive

department: Toxicology

institute: UNC- Chapel Hill

summary: Purpose: RNA-seq of CRISPR Knockout of SMARCA4 and SMARCA2 in H358 focused on examining the effects of the knockouts on NRF2 signaling

overall_design: CRISPR Knockout of SMARCA4 and SMARCA2 in H358. RNAseq was performed


title: RNA-seq analysis of bone marrow stromal and hematopoietic TNCs

city: Bronx

first: Paul

last: Frenette

state: NY

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: Bone marrow stromal cells are commonly defined by CD45–Ter119–CD31– (Triple-negative cells or TNCs). In this study, we show that most TNCs are not labeled by mesenchymal cell genetic labeling models but are derived from hematopoietic stem and progenitor cells. RNA-Seq analysis of TNCs reveals erythroid and lymphoid progenitor signatures among CD51– TNCs which was confirmed by in vitro culture studies with primary bone marrow stromal cells and by in vivo transplantation experiments. We also show that CD44+CD51– TNCs expands during phenylhydrazine-induced hemolytic anemia and in a mouse model of sickle cell disease. These results uncover new classes of stromal-associated hematopoietic progenitors.

overall_design: mRNA profiles of sorted CD44+CD51- and CD51+ bone marrow TNCs were generated by illumina HiSeq2500.

first: Philip

last: Boulais


title: Transcriptome Analysis Reveals High Similarities between Adult Human Cardiac Stem Cells and Neural Crest-Derived Stem Cells

city: Bielefeld

first: Christian

last: Kaltschmidt

address: Universitätstraße 25

department: Department of Cell Biology

institute: University of Bielefeld

summary: Global transcriptome analysis via RNAseq shows a high silimarity between the expression profiles of adult human cardiac stem cells and adult human inferior turbinate stem cells

overall_design: RNAseq data of two adult human neural crest-derived stem cell populations with 4 biological replicates each

first: Anna

last: Höving

first: Katharina

last: Sielemann

first: Johannes

last: Greiner

first: Barbara

first: Cornelius

last: Knabbe


title: Strand asymmetry in MPRA Signal

city: Huntsville

first: Brian

middle: Scott

last: Roberts

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: We analyzed data from sequencing-based massively parallel reporter assays (MPRAs) retaining the strand orientation of the alignments. These analyses showed pervasive asymmetry in reporter signal from test element strand orientation.  Present in elements derived from all regions of the human genome, we found test elements derived from gene bodies display concordant strand asymmetry with the sense orientation of the gene body.  Furthermore, we observe that test elements form Alu sequence also present concordant strand asymmetry with Alu retrotransposon features.  We establish sequence features that drive some of this asymmetry.

overall_design: In one set of experiments, we created a STARR-seq library from several BACs encompassing a region near the HTT gene.  We transfected these into four cell types: A549, BE(2)-C, HepG2, and K562 cells. We harvested both RNA and DNA and created sequencing libraries.  We sequenced the sequencing libraries using an Illumina Next-seq.  In another set of experiments, a STARR-seq library was created using BACs near the SORT1 gene.  We transfected these into HepG2 cells.  Again, we harvested RNA and DNA and created sequencing libraries. We sequenced these libraries on an Illumina Next-Seq

first: Vikram

last: Agarwal

first: Gregory

middle: M

last: Cooper

first: Jay

last: Shendure

first: Richard

last: Myers


title: Reactive oligodendrocyte progenitor cells (re-)myelinate the regenerating zebrafish spinal cord [transcriptome]

first: Vasiliki

overall_design: Transcriptome of reactive olig2:eGFP+ OPCs from the zebrafish spinal cord at 7 days post lesion (dpl) and sham controls.


title: Capture of mouse and human stem cells with features of formative pluripotency [ChIP-seq]

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary:
Pluripotent cells emerge as a naïve founder population in the blastocyst, acquire capacity for germline and soma formation, and then undergo lineage priming. Mouse embryonic stem (ES) cells and epiblast stem cells (EpiSCs) respectively represent the initial naïve and final primed phases of pluripotency. Here we investigated the intermediate formative stage. Using minimal exposure to specification cues, we derived stem cells from formative mouse epiblast. Unlike ES cells or EpiSCs, formative stem (FS) cells responded directly to germ cell induction. They colonised somatic tissues and germline in chimaeras. Whole transcriptome analyses showed similarity to pre-gastrulation formative epiblast. Signal responsiveness and chromatin accessibility features reflect lineage capacitation. Furthermore, FS cells showed distinct transcription factor dependencies, relying critically on Otx2. Finally, FS cell culture conditions applied to human naïve cells or embryos supported expansion of similar stem cells, consistent with a conserved staging post on the trajectory of mammalian pluripotency.

This submission is ChIP-seq.

overall_design: Chromatin immuno-precipitation analysis of four different histone markes across different pluripotency phases

first: Masaki

last: Kinoshita

first: Giuliano

middle: G

last: Stirparo

first: Arash

last: Shahsavari

first: Austin

last: Smith


title: Capture of mouse and human stem cells with features of formative pluripotency [scRNA-seq]

summary:
Pluripotent cells emerge as a naïve founder population in the blastocyst, acquire capacity for germline and soma formation, and then undergo lineage priming. Mouse embryonic stem (ES) cells and epiblast stem cells (EpiSCs) respectively represent the initial naïve and final primed phases of pluripotency. Here we investigated the intermediate formative stage. Using minimal exposure to specification cues, we derived stem cells from formative mouse epiblast. Unlike ES cells or EpiSCs, formative stem (FS) cells responded directly to germ cell induction. They colonised somatic tissues and germline in chimaeras. Whole transcriptome analyses showed similarity to pre-gastrulation formative epiblast. Signal responsiveness and chromatin accessibility features reflect lineage capacitation. Furthermore, FS cells showed distinct transcription factor dependencies, relying critically on Otx2. Finally, FS cell culture conditions applied to human naïve cells or embryos supported expansion of similar stem cells, consistent with a conserved staging post on the trajectory of mammalian pluripotency.

This submission is scRNA-seq.

overall_design: Single-cell RNA sequencing to identify homogeneity of FS cells in culture.


title: Combined epigenetic and metabolic treatments overcome differentiation blockade in acute myeloid leukemia [RNA-Seq]

city: Boston

first: Barry

last: Zee

address: 61 Binney Street

department: Newborn Medicine

institute: Boston Children's Hospital

summary: A hallmark of acute myeloid leukemia (AML) is the inability of self-renewing malignant cells to mature into a non-dividing terminally differentiated state. To better understand how chromatin factors such as LSD1 interact with metabolic pathways to support the differentiation blockade, we screened a small molecule library to identify druggable substrates that promote myeloid maturation. We found that differentiation caused by LSD1 inhibition is enhanced by combinatorial perturbation of purine nucleotide salvage and de novo lipogenesis pathways. We used RNA-seq to determine whether the drug combination induces gene expression changes consistent with myeloid differentiation.

overall_design: Gene expression analysis of non-treated cells at beginning of experiment and of vehicle or drug treated cells after 3 days, with 2 biological replicates per condition.


title: Identification of genes contributing to a long circadian period in Drosophila melanogaster

city: Bethesda

first: Susan

last: Harbison

state: MD

address: 10 Center Drive, Bldg. 10, Rm. 7D13

department: Center for Systems Biology

institute: National Heart Lung and Blood Institute

summary: Our objective was to identify candidate genes that contribute to the long 31-hour circadian period previously observed in DGRP_892. We performed transcriptional profiling of whole fly heads from two genotypes: DGRP_892, and Canton-S B, a line with a normal 24-hour circadian period. We collected fly heads every two hours over a 24-hour period. We quantified differential expression among genotype, time, and sex.

overall_design: We sequenced RNA from a Drosophila Genetic Reference Panel (DGRP) line with a long circadian period (DGRP_892) and a line with a 24-hour circadian period (Canton-S B). We collected 150 virgin male heads and 150 virgin female heads from each genotype every two hours over a 24-hour period to produce RNA sequence profiles. We reared fly cultures in two incubators on standard Drosophila food (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/bloomfood.htm) at 25°C, 60% humidity, and a 12:12-hour light:dark cycle. One incubator was set to a 6:00 am "lights on": 6:00 pm "lights off" schedule, while the second incubator was set on the reciprocal light:dark cycle of 6:00 pm "lights on": 6:00 am "lights off". Adult flies were entrained to their respective light:dark cycles for three days. Both groups of flies were transferred to a common incubator and then subjected to constant darkness for three days. Flies were flash frozen on dry ice every 2 hours and frozen at -80 deg. C until processed. Flies were decapitated on dry ice, and total RNA was extracted. This process was repeated three times to produce 144 samples (three biological replicates per genotype/timepoint/sex). Prior to library preparation, ERCC Spike-in Control Mix I was added to each sample as a control. PolyA RNA stranded libraries were prepared using Illumina TruSeq Stranded mRNA Sample Prep kits. Unique bar code adapters were applied to each library, and dual indices were used. We performed sequencing on an Illumina HiSeq4000 using version 4 chemistry to achieve a minimum of 20-25 million 125-bp read pairs. Reads were mapped to FlyBase release 6 version 01 of the Drosophila melanogaster genome and the ERCC sequences. Mapped reads were counted at the gene level.

first: Shailesh

last: Kumar

first: Ilker

last: Tunc

first: Terry

last: Tansey

first: Mehdi

last: Pirooznia


title: Capture of mouse and human stem cells with features of formative pluripotency

summary:
Pluripotent cells emerge as a naïve founder population in the blastocyst, acquire capacity for germline and soma formation, and then undergo lineage priming. Mouse embryonic stem (ES) cells and epiblast stem cells (EpiSCs) respectively represent the initial naïve and final primed phases of pluripotency. Here we investigated the intermediate formative stage. Using minimal exposure to specification cues, we derived stem cells from formative mouse epiblast. Unlike ES cells or EpiSCs, formative stem (FS) cells responded directly to germ cell induction. They colonised somatic tissues and germline in chimaeras. Whole transcriptome analyses showed similarity to pre-gastrulation formative epiblast. Signal responsiveness and chromatin accessibility features reflect lineage capacitation. Furthermore, FS cells showed distinct transcription factor dependencies, relying critically on Otx2. Finally, FS cell culture conditions applied to human naïve cells or embryos supported expansion of similar stem cells, consistent with a conserved staging post on the trajectory of mammalian pluripotency.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Combined epigenetic and metabolic treatments overcome differentiation blockade in acute myeloid leukemia [ATAC-Seq]

summary: A hallmark of acute myeloid leukemia (AML) is the inability of self-renewing malignant cells to mature into a non-dividing terminally differentiated state. To better understand how chromatin factors such as LSD1 interact with metabolic pathways to support the differentiation blockade, we screened a small molecule library to identify druggable substrates that promote myeloid maturation. We found that differentiation caused by LSD1 inhibition is enhanced by combinatorial perturbation of purine nucleotide salvage and de novo lipogenesis pathways. We used ATAC-seq to determine whether the drug combination induces chromatin  changes.

overall_design: ATAC-seq analysis of non-treated cells at beginning of experiment and of vehicle or drug treated cells after 2 days, with 2 biological replicates per condition.


title: The RNA Polymerase II subunit RPB-9 directs transcriptional elongation at piRNA loci in C. elegans

city: cambridge

first: Eric

last: Miska

address: tennis court road

department: The Gurdon Institute

summary: PIWI-interacting RNAs (piRNAs) are genomically-encoded small RNAs that regulate germ cell development and guarantee germline integrity. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. To date, piRNA biogenesis mechanisms are still unclear. Here, we show that the RNA Polymerase II subunit RPB-9 is required to promote transcription elongation at piRNA loci. Through genetic and biochemical experiments, we demonstrate that rpb-9-mediated piRNA production is needed to repress two DNA transposon families and a subset of somatic genes in the C. elegans germline.

overall_design: 3 replicates for ChIP-seq, RNA-seq, smallRNA-seq, and 2 replicates for capped RNA-Seq

middle: A

first: Ahmet

last: Berkyurek

first: Giulia

last: Furlan

first: Lisa

last: Lampersberger

first: Peter

last: Sarkies

first: Toni

last: Beltran


title: Total RNA seq transcriptome profiling of thymocytes

city: South San Francisco

first: Juliette

last: Roels

state: CA

address: 1 DNA Way

institute: Genentech

summary: Circular RNAs (circRNAs) are stable RNA molecules whose deregulation can drive disease and cancer mechanisms by impacting on their interactions with microRNAs and proteins and on expression of the encoded peptides. This study describes the landscape of circRNA expressed in T-cell Acute Lymphoblastic Leukemia (T-ALL). Analysis by CirComPara of RNA-seq data of 25 T-ALL patients of five genetic T-ALL subtypes and human thymocyte populations from healthy donors detected over 68,500 circRNAs. Further study of 3 447 highly expressed circRNAs derived mostly from exonic regions of 1,966 loci informed prominent differences in circRNA expression between normal and malignant T-cells, with 944 circRNAs differentially expressed in T-ALL, mostly upregulated. Next, circRNA expression signatures of different molecular genetic subgroups were defined. Examination of circRNA expression variation during thymocyte maturation and comparison with putative-cell of origin of each T-ALL subtype identified ectopic group-specific circRNAs, whose expression and backsplice sequence were confirmed in T-ALL cell lines. Our findings on circRNAs significantly extend previous data on expression of linear transcripts in subtypes of human T-ALL, opening functional investigation of deregulated circRNAs so far uncharacterized in human T-ALL, including a few for which oncogenic roles or molecular functions have been already proven in different settings.

overall_design: Profiling of the total RNA transcriptome of different CD34+ and DP stages of T cell development isolated from human postnatal thymus, for two or three donors.

first: Alessia

last: Buratin

first: Matthias

last: De Decker

first: Pieter

last: Van Vlierberghe

first: Stefania

last: Bortoluzzi

first: Tom

last: Taghon


title: Profiling Kupffer cells with different origins in NASH

city: Paris

first: Sebastien

last: Dussaud

address: 91 bd de l'hopital

institute: UPMC

summary: Kupffer cells (KCs) self-renew by local proliferation in the adult independently from monocytes (Mos). However, how they maintain during chronic metabolic disorders such as non-alcoholic steatohepatitis (NASH) remains ill-defined. We characterized KCs during NASH and observed diversity in the KC pool, with a significant fraction of monocyte-derived KCs (MoKCs). Here, we aim to uncover the transcriptional landscapes of KCs subsets found in a mouse model of methionine and choline deficient (MCD)-diet induced non-alcoholic steatohepatitis (NASH).

overall_design: Wild-type mice were fed a MCD diet for 4 weeks and Kupffer cell subsets were sorted by flow cytometry. EmKCs were CLEC2+ TIMD4+ while MoKCs were CLEC2+ TIMD4-.

first: Sébastien

first: Emmanuel

last: Gautier


title: Defining the Transcriptional Targets of Leptin Reveals a Role for Atf3 in Leptin Action

status: Public on Dec 03 2020

city: Ann Arbor

first: Martin

last: Myers Jr

address: 1000 Wall St

institute: University of Michigan

summary: We employed translating ribosome affinity purification followed by RNA sequencing to isolate and analyze mRNA from the hypothalamic LepRb neurons of wild-type or leptin-deficient (Lepob/ob) mice treated with vehicle or exogenous leptin. Although the expression of most of the genes encoding the neuropeptides commonly considered to represent the main targets of leptin action were altered only following chronic leptin deprivation, our analysis revealed other transcripts that were coordinately regulated by leptin under multiple treatment conditions. Among these, acute leptin treatment increased expression of the transcription factor Atf3 in LepRb neurons.

overall_design: 28 samples, 14 Bead and 14 Supernatant

first: Alan

last: Rupp

first: Margaret

middle: B

last: Allison


title: Anti-fibrosis effects of dihydroartemisinin on primary skin fibroblast from healthy people

first: Rui

last: Li

address: Huangpu area

department: Rheumatology

institute: Shanghai Jiao Tong university, School of Medicine, affiliated Renji hospital

summary: The objective of this study was to determine whether Dihydroartemisinin (DHA), a drug highly effective in treating malaria infection with good safety, could be repurposed for the treatment of skin fibrosis in systemic sclerosis (SSc). mRNA-seq of primary human fibroblast cultures from healthy donors treated with DHA or vehicle were performed. By KEGG and Reactome analysis, we identified autophagy was one of the most significantly enriched terms.

overall_design: Transcriptomes from primary human skin fibroblast of 3 DMSO-treated and 3 Dihydroartemisinin (DHA) treated cultures.

first: Hanlin

last: Yin

first: Juan

last: Wang

first: Qingran

last: Yan

first: Liangjing

last: Lu


title: Molecular mechanism of EPC1-PHF1 fusion protein

city: Quebec City

first: Deepthi

last: Sudarshan

state: Quebec

address: 9 Rue Mc Mahon

country: Canada

institute: Université Laval

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