title: Single-cell characterization of transcriptomic heterogeneity in lymphoblastoid cell lines

status: Public on Feb 15 2021

city: Durham

first: Elliott

middle: Daniel

last: SoRelle

state: NC

address: 130 Research Drive (CARL Building)

department: Molecular Genetics & Microbiology

country: USA

institute: Duke University

summary: We report single-cell RNA sequencing datasets for three lymphoblastoid cell lines (LCLs) prepared by infection of primary B cells with Epstein-Barr Virus (EBV). Inter- and intra-sample transcriptional variance is observed with respect to immunoglobulin heavy chain class; host gene sets involved in survival, proliferation and differentiation; and viral replication state. We propose that the observed heterogeneity arises from the dynamic nature of host-pathogen interactions, donor-specific compositions of primary B cells, and other experimental factors such as stochastic clonal evolution in cell culture conditions.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: Characterization of three different lymphoblastoid cell lines. Two samples (LCL_777_B958 and LCL_777_M81) were derived from the same donor and infected with different EBV strains (B95-8 and M81). A third sample (LCL_461_B958) was derived from a different donor and infected with B95-8.

first: Joanne

last: Dai

first: Jeffrey

last: Zhou

first: Stephanie

last: Giamberardino

last: Bailey

first: Simon

middle: G

last: Gregory

first: Cliburn

last: Chan

first: Micah

last: Luftig


title: Expression data from paired human primary HCC tissues and adjacent non-cancerous liver tissues.

status: Public on Feb 12 2021

city: Beijing

first: chen

middle: wen

last: jia

address: Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences

country: China

institute: institute

summary:
Hepatic cirrhosis or advanced fibrosis caused by chronic hepatitis may be the main risk factor contributing to the occurrence of HCC. Growing clinical evidence show that patients with hepatic cirrhosis or advanced fibrosis may have a 7-fold higher incidence rate of HCC than those without, suggesting a crucial role of inflammation-carcinogenesis malignant transformation in HCC development and progression.
We used microarrays to detail the global programme of gene expression underlying inflammation-carcinogenesis malignant transformation in HCC and identified distinct classes of up-regulated and down-regulated genes during this process

overall_design: Three paired human primary HCC tissues and adjacent non-cancerous liver tissues were collected according to proper tumor stage (T2) and tumor grade (G2).

first: Yanqiong

last: Zhang

last: Lin


title: Single-cell profiling of normal and tumor intestinal tissue

status: Public on Feb 11 2021

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

type: Expression profiling by high throughput sequencing

summary: Normal and adjacent tumor tissue of CRC patents was profiled using scRNA-seq.

overall_design:
Tissue of 12 patients was collected from tumor areas and adjacent normal tissue after surgical removal of the tumor. Tissue was dissociated into single cell suspensions. Single cells were loaded into a comercial drop-seq device (Chromium controller, 10x genomics) and scRNA-seq libraries were generated using single cell 3' v 2 kits from 10x genomics
----------------------------------------------------
Authors state "Unfortunately, we can currently not supply raw data files (sequencing) as these are patient sequences for which the current data access policies in our institution only allow submission of count data. "

first: Florian

last: Uhlitz

first: Philip

last: Bischoff

first: Anja

last: Sieber

first: Alexandra

last: Trinks

first: Markus

last: Morkel

first: Christine

last: Sers

first: Carsten

last: Kamphues

first: Benedikt

last: Obermayer


title: Crosstalk between gut microbiota and mitochondria during endurance: a new example of holobiont in mammals

status: Public on Feb 09 2021

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

country: France

institute: INRA

summary: Endurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the microbiota-mitochondria inter-talk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of the Lachnospiraceae family, especially Eubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted on PPARδ, the FRX-CREB axis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis appears therefore as a potential strategy to enhance athletic performance.

overall_design: Twenty horses were studied before (T0) and after (TF) an endurance race. All the analyses were carried out by comparing TF to T0.

first: Nuria

last: Mach

first: Eric

last: Barrey


title: Identification of genes are regulated by DROSHA at mRNA level [microarray]

status: Public on Jan 28 2021

city: Dalian

first: jinxin

last: lu

state: Liaoning

address: lvshunkou district lvshun south goad west sector No.9

institute: Dalian Medical University

summary: Purpose: DROSHA plays an important role in breast cancer progression. Exploring the gene expression profiles regulated by DROSHA will facilitate to understand the mechanism which is responsible for DROSHA-induced breast cancer development. Results: We found that 105 genes were significantly up-regulated during DROSHA silencing in MDA-MB-231 cells, 200 genes were significantly down-regulated during DROSHA silencing in MDA-MB-231 cells. Conclusions: Our study indicated that DROSHA-mediated 305 differentially expressed genes might be invovled in  breast cancer development.

overall_design: Differential expression analysis of DROSHA KD versus mock-transfected MDA-MB-231 cells, in 2 biological replicates

first: Quentin

last: Liu


title: Reconstitution of miR-550a-3p in diffuse malignant peritoneal mesothelioma cell line

status: Public on Jan 23 2021

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

country: Italy

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

summary: We aimed at analyzing the transcriptome changes associated with the reconstitution of miR-550a-3p in STO cells.

overall_design: Trascriptome of STO cells 24 h after the reconstitution of mimic pre-miR-550a-3p compared to negative controls. Experiments were conducted in triplicate.

first: Valentina

last: Zuco


title: MCF7 cells treated with hypoxia for 0, 5, 10, 16 hours

status: Public on Feb 05 2021

first: Lihua

last: Ding

address: 27th Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

summary: To investigate the hypoxia-regulated gene, we treated MCF7 cells with hypoxia for 0, 5, 10, 16 hours.


title: Next Generation Sequencing of MDA-MB-231 cells with variable subcellular localization of Aurora-A Kinase (Wild-type (WT), no localization signal sequence, Cytoplasmic (NES) or Nuclear (NLS)) .

status: Public on Jan 31 2021

city: Morgantown

first: Elena

last: Pugacheva

state: WV

address: 44 Medical Center Drive

department: Biochemistry

institute: West Virginia University

summary:
Purpose: The goal of this study was to determine a specific gene expression profile of Nuclear Aurora-A Kinase expressing cells. It has been previously shown that AURKA localizes to the nucleus in patient biopsies in multiple aggressive malignancies including breast cancer but functional significance of this localization in cancer progression is still undetermined. To define the role nuclear AURKA plays in metastatic dissemination and colonization of distant organs, we created TNBC (triple negative breast cancer) cell lines with CRISPR/Cas9 based deletion of endogenous AURKA and rescue with exogenous AURKA specifically targeted to the nucleus, cytoplasm or both. The TNBC cells expressing nuclear AURKA show significant increase in dissemination and colonization of multiple organs when compared to controls. The RNA sequencing analysis of nuclear AURKA expressing cell lines shows significant changes in gene expression profile associated with hypoxia, migration/invasion and survival/death pathways supporting the metastatic phenotype observed in vivo.
Methods: The total RNA was isolated using Quagen RNeasy kit, the library was build using KAPA mRNA Hyper Prep Kit with TruSeq adapters for the build, RNA profiles of WT-AURKA, NES-AURKA, NLS-AURKA and Empty (including no-localization tag-Empty, NLS-empty, NES-empty) vector controls expressing  MDA-MB-231 cells were generated by deep sequencing of 2 biological clones of each cell line in triplicate, using Illumina HiSeq2500, 2 x 50 paired-end reads in the High Output Mode. The sequence reads that passed quality filters were analyzed with Hisat2 followed by Samtools. Genes whose expression is changed between the control samples and WT, NES, NLS-AURKA samples were identified using Partek Genomic Suite and functions associated with that set of genes mapped using Ingenuity Pathway Analysis. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: Using an optimized data analysis workflow, we identified 33,563 transcripts after mapping reads to the human genome. Approximately 3,000 of the transcripts showed differential expression between the Empty control and NLS-AURKA  and NES-AURKA, with a fold change ≥1.5 and p value <0.05. Altered expression of 96 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several well characterized genes that contribute to hypoxia, migration/invasion and survival/death pathways. Data analysis revealed a significant changes in transcriptome profiling upon introduction of AURKA in the nucleus supporting its active role on regulation of transcription.
Conclusions: Our study represents the first detailed analysis of transcriptome changes upon manipulation of AURKA localization in triple negative breast cancer cells, with multiple biologic and technical replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles in patient samples in future studies. Our results show that AURKA expression in nucleus might be a key event triggering metastatic dissemination and offers a comprehensive and qualitative evaluation of mRNA content. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions of nuclear AURKA.

overall_design: The mRNA profiles of MDA-MB-231 cells with variable subcellular localization of Aurora-A Kinase in Cytoplasm or Nucleus or both were generated by deep sequencing, in triplicate, using Illumina HiSeq and correlated with metstatic potenital of these cell in vivo xenograft studes.

first: Kristina

middle: M

last: Whately


title: ChIP-seq of Runx2-FLAG in primary chondrocytes.

status: Public on Jan 21 2021

city: Bunkyo-ku

first: Kosei

last: Nagata

state: Tokyo

department: Graduate School of Medicine

country: Japan

institute: the University of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Purpose: To demonstrate the role of Transcription factor Runx2 in primary chondrocytes with or without IL-1beta.  Method: Fragmented DNA samples were collected from primary chondrocytes of 5-day-old Runx2-Biotin-FLAG-tag  mice, cultured with or without IL-1beta.  Results: More than 20,000 and 10,000 peaks were gained from chondrocytes without and with IL-1beta, resepectively.  Conclusions: Runx2 are associated cellular process and extracellular matrics transcription in primary chondrocytes.

overall_design: DNA fragment gathered by Anti-Flag antibody or Anti-IgG antibody from primary chondrocytes of 5-day old Runx2-Biotin-FLAG-tag mice.

first: Taku

last: Saito


title: RNA-seq of Runx2 cKO primary chondrocytes.

summary: Purpose: To demonstrate Runx2's association with organizing the extracellular matrix in primary chondrocytes.  Method: RNA samples were collected from primary chondrocytes of 5-day-old Col2a1-CreERT2;Runx2fl/fl and Runx2fl/fl mice, cultured with or without IL-1beta.  Results: Thirty-three genes cultured without IL-1beta and 45 genes with IL-1beta were up- or down-regulated by more than 2-fold in the Runx2 knockout in primary chondrocytes.  Conclusions: Genes including collagen fibers were down-regulated in Runx2 cKO primary chondrocytes.

overall_design: Primary chondrocytes mRNA profiles of 5-day old Cntl and Runx2 cKO mice.


title: The alx3 gene functions to regulate skeletal cell differentiation timing during zebrafish neurocranium development.

status: Public on Mar 23 2021

city: Aurora

first: James

middle: T

last: Nichols

state: Colorado

address: 12700 East 19th Avenue

department: Craniofacial Biology

institute: University of Colorado - Anschutz Medical Campus

summary: During craniofacial development, different populations of cartilage and bone forming cells develop in precise locations in the head. Most of these cells are derived from pluripotent cranial neural crest cells. The mechanisms that divide neural crest cells into distinct populations are not fully understood. Here we use single-cell RNA sequencing to transcriptomically define different populations of cranial neural crest cells. We discovered that the transcription factor encoding alx gene family is restricted to the frontonasal population of neural crest cells. Furthermore, genetic mutant analyses indicate that alx3 functions to subdivide the frontonasal population into medial versus lateral subpopulations. Our results support a mechanism in which the alx gene family functions as an identity code, subdividing frontonasal neural crest cells into distinct subpopulations. This study furthers our understanding of how different skeletal cell fates are established during craniofacial development and how these mechanisms can go awry in genetic diseases.

overall_design: neural crest cell profiling of 24 hpf WT D. rerio

first: Jennyfer

last: Mitchell

first: Juliana

last: Sucharov

first: Anthony

last: Pulvino

first: Elliot

middle: P

last: Brooks

first: Austin

middle: E

last: Gillen


title: Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A.

status: Public on Jan 19 2021

city: Stellenbosch

first: Hugh

last: Patterton

state: Western Cape

address: Merriman Avenue

country: South Africa

institute: Stellenbosch University

summary: Trypanosomes diverged from the main eukaryotic lineage about 600 million years ago, and display some unusual genomic and epigenetic properties that provide valuable insight into the early processes employed by eukaryotic ancestors to regulate chromatin-mediated functions. We sequenced Trypanosoma brucei core histones by high mass accuracy middle-down mass spectrometry to map core histone post-translational modifications (PTMs) and elucidate cis‑histone combinatorial PTMs (cPTMs). T. brucei histones are heavily modified and display intricate cPTMs patterns, with numerous hypermodified cPTMs that could contribute to the formation of non‑repressive euchromatic states. The T. brucei H2A C‑terminal tail is hyperacetylated, containing up to 5 acetylated lysine residues. MNase-ChIP-seq revealed a striking enrichment of hyperacetylated H2A at Pol II transcription start regions, and showed that H2A histones that are hyperacetylated in different combinations localised to different genomic regions, suggesting distinct epigenetic functions. Our genomics and proteomics data provide insight into the complex epigenetic mechanisms used by this parasite to regulate a genome that lacks the transcriptional control mechanisms found in higher eukaryotes. The findings further demonstrate the complexity of epigenetic mechanisms that were probably shared with the last eukaryotic common ancestor.

overall_design: MNase-ChIP-seq to identify genomic distribution of hyperacetylated histone H2A in two different life-cycle stages of T. brucei: BF (bloodstream form) and PF (procyclic form). We provide 1 sample for H3, 2 samples for H2AK125ac, and one sample for H2AK115ac BF isolates and PF isolates.

first: Johannes

last: Maree

first: Andrey

last: Tvardovskiy

first: Ole

middle: N

last: Jensen

first: Gloria

last: Rudenko

first: Hugh-G


title: m6A alterations through FTO in breast cancer [m6ARIP-seq]

status: Public on Jan 11 2021

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Our understanding of posttranscriptional modifications that decorate RNA, a regulatory layer positioned between DNA and proteins, is in its infancy. N6-methyladenosine (m6A) is the most prevalent internal modification in messenger RNAs that is installed and erased by m6A methyltransferases and demethylases. The importance of these enzymes in cancer is rapidly emerging, yet information of their specific mode of actions during disease progression remain largely unknown. In the present study, we report that the m6A RNA demethylase FTO controls EMT and invasion in cancer through regulation of the Wnt pathway. We find that loss of FTO, in contrast to acute myeloid leukemia, is frequent in many cancer types, including breast and prostate cancers. Knockdown of FTO promotes tumor progression – specifically migration and invasion – in breast and prostate cancer cells. Furthermore, implantation of these cells accelerates tumor progression in recipient mice in vivo. In these tumors, FTO depletion leads to m6A-dependent activation of Wnt signaling, which drives an enhanced EMT program and invasion, thus leading to poor clinical outcome. However, loss of FTO also sensitizes cancers cells to Wnt inhibition, offering a rationale for the therapeutic targeting of Wnt for cancer patients with low FTO levels. Together, our work reveals FTO as a novel regulator of EMT and an unexpected mechanism by which Wnt signals are dysregulated in tumors, providing a rationale to stratify cancer patients treated with Wnt inhibitor. These data uncover a previously unrecognized relationship between RNA modification and EMT in cancer.

overall_design: Identification of m6A RNA marks in breast cancer biopsies (3 samples), SK-BR-3 cell line FTO-depleted through RNAi (2 samples) or RNAi control (2 samples) and PC-3 cell line FTO-depleted through RNAi (1 sample) or RNAi control (1 sample) using m6A RNA immunoprecipitation and Input controls

first: Jana

last: Jeschke

first: Evelyne

last: Collignon

first: Clémence

last: Al Wardi

first: Mohammad

last: Krayem

first: Yan

last: Jia

first: Emilie

last: Calonne

first: Bouchra

last: Hassabi

first: Zena

last: Wimana

first: Renato

last: Morandini

first: Rachel

last: Deplus

first: Pascale

last: Putmans

first: Gaurav

last: Dube

first: Nitesh

last: Singh

first: Alexander

last: Koch

first: Kateryna

last: Shostak

first: Lara

last: Rizzotto

first: Robert

middle: L

last: Ross

first: Soizic

last: Garaud

first: Christine

last: Desmedt

first: Yaccine

last: Bareche

first: Françoise

last: Rothe

first: Jacqueline

last: Lehmann-Che

first: Martine

last: Duterque-Coquillaud

first: Xavier

last: Leroy

first: Gerben

last: Menschaert

first: Luis

last: Teixeira

first: Mingzhou

last: Guo

first: Patrick

middle: A

last: Limbach

first: Pierre

last: Close

first: Alain

last: Chariot

first: Eleonora

last: Leucci

first: Ghanem

last: Ghanem

first: Bi-Feng

last: Yuan

first: Christos

last: Sotiriou

first: Jean-Christophe

last: Marine

first: François

last: Fuks


title: m6A alterations through FTO in breast cancer

first: Martin

last: Bizet

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

overall_design: Refer to individual Series


title: Ethanol induction of the yeast-to-mycelium dimorphic transition in the Basidiomycota fungus Ustilago maydis

status: Public on Jan 18 2021

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

summary: The sexual cycle of Ustilago maydis includes the succession of a saprophytic haploid yeast stage to a virulent hyphal dikaryotic stage, product of the mating of sexually compatible yeast cells. This dimorphic transition may be replicated in vitro by different means. Recently, it was shown that ethanol induced filamentous growth on solid medium, and we observed that this process also occurred in liquid media. Since the utilization of a six- or a two-carbon source involves different metabolic pathways, we considered that the morphogenetic process might be associated with this alteration. Accordingly, we analyzed the transcriptome of U. maydis grown in glucose or in ethanol using the Illumina RNA Seq. Around 18 million reads were obtained from each treatment. From the 6788 U. maydis genes, 542 were differentially expressed (158 upregulated and 384 downregulated) during incubation with ethanol compared to glucose-grown cells, revealing a noticeable alteration in the metabolism of the fungus through their adaptation to either carbon source. The present phenomenon is a further example of how an alteration in a two-dimensional mechanism (metabolism) can affect a three-dimensional process (cell morphogenesis).

overall_design:
Glucose vs. Ethanol
Three biological replicates were made per treatment and they were pooled for sequencing.

first: José

last: Sánchez-Arreguín

first: Claudia

last: León-Ramírez

first: Mayela

middle: F

last: Salazar-Chávez

first: Lino

last: Sánchez-Segura

first: Roberto

last: Ruiz-Medrano

last: Ruiz-Herrera


title: Tuberculosis in Malnourished Individuals

status: Public on Jan 01 2021

city: Boston

first: William

middle: Evan

last: Johnson

state: MA

address: 72 E Concord St E609

department: Division of Computational Biomedicine

institute: Boston University

summary: Whole blood gene expression profiling from well and malnourished Indian individuals with TB and severely malnourished household contacts with latent TB infection (LTBI). Severe malnutrition was defined as body mass index (BMI) <16. kg/m2 in adults and based on weight-for-height Z scores in children <18 years. Gene expression was measured using RNA-sequencing.


title: H3K27Ac modification and gene expression in psoriasis

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

summary: Applying ChIP-seq with anti-acetylation of lysine 27 on Histone 3 (H3K27Ac), we report high-throughput profiling of H3K27Ac in human skin biopsies taken from psoriasis patients, both from the lesion and from adjacent non-lesion skin, and from skin biopsies from healthy match volunteers, in term of age, gender, and the biopsies place in the body. From each group we had 4 samples.   On three samples of each group we performed mRNA array.  There is a clearly different H3K27 acetylation patterns in psoriatic skin compared to uninvolved or healthy volunteer skin. in many of the most over express genes in psoriasis lesion, there is enrichment of H3K27Ac. However, loss of acetylation on H3K27 is not part of the biochemical mechanism by which gene expression is decreased in psoriatic skin.  Finally, we show Many of the over express genes in psoriasis lesion, that also were enriched with H3K27Ac harbor a putative GRHL transcription factor binding site.

overall_design: mRNA array was applied on skin biopsies from psoriasis patients, both from the lesion and from adjacent non-lesion skin. in parallel to skin biopsies from healthy match volunteers.

first: Dror

last: Avni

first: Moamen

last: Masalha


title: Transient cell-in-cell formation underlies tumor relapse and resistance to immunotherapy

status: Public on Dec 31 2020

city: Tel Aviv

first: Amit

last: Gutwillig

address: 35 klachkin st.

department: Pathology

institute: Tel Aviv University


title: Quantifying RNA-Protein Interactions Characterizes Recurrent Mutationsin RNA Binding Proteins in Cancer

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: Quantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP target RNAs. Here, we develop an ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing method, easyCLIP. easyCLIP provides absolute cross-link rates, as well as increased simplicity, efficiency, and capacity to visualize RNA libraries. Measurement of >200 independent cross-link experiments across >35 proteins identifies an RNA cross-link rate threshold that distinguishes RBPs from non-RBPs and defines target RNAs as those with a complex frequency unlikely for a random protein. We apply easyCLIP to the 33 most recurrent cancer mutations across 28 RBPs, finding increased RNA binding per RBP molecule for PCBP1 L100P/Q cancer mutations. Quantitating RBP-RNA interactions can thus nominate proteins as RBPs and define the impact of specific disease-associated RBP mutations on RNA association.

overall_design: RNA-binding landscapes of 13 proteins and 7 mutants, with 2-4 replicates. Some proteins are not RBPs and have low complexity libraries.

first: Weili

last: Miao

first: Xue

last: Yang

first: Grant

last: Goda

first: Andrew

last: Ji

first: Laura

middle: K

last: Donohue

first: Maria

last: Aleman

first: Daniel

last: Dominguez

first: Paul

last: Khavari


title: Umbilical Mesenchymal Stem Cell-derived Exosomes Facilitate Spinal Cord Functional Recovery Through miR-199a-3p/145-5p mediated NGF/TrkA Signaling Pathway in Rats

status: Public on Dec 08 2020

city: Guangzhou

first: Yang

last: Wang

state: Guangdong

address: number 600, Tianhe road

institute: Third affiliated hospital of sun yat-sen unversity

type: Non-coding RNA profiling by high throughput sequencing

summary: Background:  Though exosomes, as the by-products of human umbilical cord mesenchymal stem cells (hUC-MSCs), have been demonstrated to be an effective therapy for traumatic spinal cord injury (SCI), it remains unclear through which manner exosomes act.  Aim:    In order to figure out whether exosomes attenuate lesion size of SCI by the amelioration of neuronal injury triggered by secondary inflammatory storm and induction of inner motivation of neurite outgrowth, we designed and performed this experiment.   Methods:   We determined absolute contents of all exosomal miRNAs and investigated the potential mechanisms of miR-199a-3p/145-5p in inducing neurite outgrowth in vivo and vitro.  Results:  miR-199a-3p/145-5p, which were relatively top-ranking miRNAs in exosomes, promoted PC12 cells differentiation suppressed by lipopolysaccharide (LPS) in vitro through the modulation of NGF/TrkA pathway. We also demonstrated that Cblb was the direct target of miR-199a-3p and Cbl was the direct target of miR-145-5p. Cblb and Cbl genes knock down revealed that TrkA ubiquitylation level significantly decreased, subsequently, activating the NGF/TrkA downstream pathways Akt and Erk. In return, overexpression of Cblb and Cbl suggested that TrkA ubiquitylation level significantly increased, subsequently, inactivating the NGF/TrkA downstream pathways Akt and Erk. Western blot and co-immunoprecipitation confirmed the direct interaction between TrkA and Cblb, TrkA and Cbl. In vivo experiment, exosomal miR-199a-3p/145-5p were found to up-regulate TrkA expression in the lesion site and promote locomotor function of SCI rats as well.  Conclusion:  In summary, our study suggested that hUC-MSCs derived exosomes may treat SCI by transferring miR-199a-3p/145-5p to neurons, and modulating TrkA ubiquitylation, and strengthening the NGF/TrkA signaling pathway in SCI rats.

overall_design: Three samples from exosomes derived from non-treated human umbilical cord mesenchymal stem cells

first: Xunwei

last: Lai

first: Depeng

last: Wu


title: Transient cell-in-cell formation underlies tumor relapse and resistance to immunotherapy [B16F10]

summary: Despite the remarkable successes of cancer immunotherapies, the majority of patients do not exhibit durable responses. While treatment resistance has frequently been attributed to clonal selection and immunoediting, currently, little evidence directly demonstrates this process in epithelial cancers. Here, we demonstrate in both mouse models and human cells, that tumor cells evade immunotherapy by generating transient cell-in-cell structures, which are impenetrable to immune-derived cytotoxic compounds and to chemotherapies. This formation is mediated predominantly by DLL4/DLL1 which are elevated on activated T cells and along with IFNg induces STAT3 phosphorylation in tumors cells. In contrast to previous reports on cell-in-cell formations, here both cells remain alive and disseminate into single tumor cells once T cells are no longer present. Overall, this work highlights a previously unknown resistance mechanism which enable tumor cells to survive immune pressure and provides a new theoretical framework to cancer immunotherapies.

overall_design: comparison of gene expression profile of B16F10 cells following different treatments.

first: Nadine

last: Santana-Magal

first: Leen

last: Farhat-Younis

first: Diana

last: Rasoulouniriana

first: Asaf

last: Madi

first: Chen

last: Luxenburg

first: Jonathan

last: Cohen

first: Krishnanand

last: Padmanabhan

first: Noam

last: Shomron

first: Guy

last: Shapira

first: Meora

last: Feinmesser

first: Oran

last: Zlotnik

first: Reno

last: Debets

first: Nathan

last: Reticker-Flynn

first: Peleg

last: Rider

first: Yaron

last: Carmi


title: Single-cell B receptor VDJ sequencing from HGSOC isolated B cells

status: Public on Nov 24 2020

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Purpose: Evaluation of the BCR profile of HGSOC associated/infiltrated B cells

overall_design: Method: We isolated B cells from 2 HGSOC disscociated tumors and performed 10X single-cell B receptor VDJ sequencing

first: Subir

last: Biswas

first: Xiaoqing

last: Yu

first: Jose

middle: R

last: Conejo-Garcia


title: Transient cell-in-cell formation underlies tumor relapse and resistance to immunotherapy [T cells]

first: Amit

last: Gutwillig

overall_design: comparison of gene expression profile of T cells following different activations.

first: Nadine

last: Santana-Magal

first: Leen

last: Farhat-Younis

first: Diana

last: Rasoulouniriana


title: IgA transcytosis and tumor antigen recognition govern anti-tumor immunity in ovarian cancer


title: Quantifying RNA-Protein Interactions Characterizes Recurrent Mutations in RNA Binding Proteins in Cancer

status: Public on Dec 01 2020

first: Douglas

last: Porter

summary: Quantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP “target” RNAs. To address this, an ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing method, easyCLIP, was developed. easyCLIP, provides absolute cross-link rates, as well as increased simplicity, efficiency, and capacity to visualize unamplified libraries. 213 cross-link measurements were performed and found that RBPs could be distinguished from non-RBPs by RNA cross-link rates and that target RNAs could be defined as those with a complex frequency unlikely for a random protein. easyCLIP was used to study the 33 most recurrent cancer mutations across 28 RBPs. This demonstrated increased RNA binding per RBP molecule for KHDRBS2 and A1CF cancer mutants, and showed that the PCBP1L100P/Q cancer mutation also dramatically increased RNA binding. Quantitating RBP-RNA interactions can thus categorize proteins as RBPs or not and define the impact of specific disease-associated RBP mutations on RNA binding.

overall_design: RNA-seq libraries for the expression of wild-type or mutant forms of three RBPs recurrently mutated in cancer at different expression levels, with 2 replicates.

first: Weili

last: Miao

first: Xue

last: Yang

first: Andrew

last: Ji

first: Laura

last: Donohue

first: Paul

last: Khavari


summary: Methodology: We have treated OVCAR3 cells in vitro and RNA was extracted. Nex Gen RNA seq has been performed.

overall_design: Transcriptional changes in in vitro treated OVCAR3 cells with non-specific IgG and IgA and Specific IgA antibodies by RNA-seq


title: Single Nucleus ATAC-Seq Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection [scATAC-Seq]

status: Public on Nov 23 2020

city: Cincinnati

first: LungMAPP

last: DCC

state: OH

address: 3333 Burnet Ave

institute: LungMAP DCC

summary: Respiratory failure is the leading cause of COVID-19 death and disproportionately impacts adults more than children. Here, we present a large-scale snATAC-seq dataset (90,980 nuclei) of the human lung, generated in parallel with snRNA-seq (46,500 nuclei), from healthy donors of ~30 weeks, ~3 years and ~30 years of age. Focusing on genes implicated in SARS-CoV-2 cell entry, we observed an increase in the proportion of alveolar epithelial cells expressing ACE2 and TMPRSS2 in adult compared to young lungs. Consistent with expression dynamics, 10 chromatin peaks linked to TMPRSS2 exhibited significantly increased activity with age and harbored IRF and STAT binding sites. Furthermore, we identified 14 common sequence variants in age-increasing peaks with predicted regulatory function, including several associated with respiratory traits and TMPRSS2 expression. Our findings reveal a plausible contributor to why children are more resistant to COVID-19 and provide an epigenomic basis for transferring this resistance to older populations.

overall_design:
snATAC-seq of human non-diseased lungs from donors of three age groups: ~30 week old gestational age (GA, prematurely born, 30wkGA), ~3 year old (3yo), and ~30 year old (30yo). Three lungs were sampled for each age group, with both males and females represented. Of the 9 donors, 5 were Caucasian, 1 was African American and 3 were of unknown ancestry. For all samples, flash frozen biopsies from equivalent small airway regions of the lung were used. Nuclei were isolated from individual biopsies and split into two pools, one for snRNA-seq and one for snATAC-seq. We generated technical replicates for one of the 3yo donors (D032). Donor lung samples were provided through the federal United Network of Organ Sharing via National Disease Research Interchange (NDRI) and International Institute for Advancement of Medicine (IIAM) and entered into the NHLBI LungMAP Biorepository for Investigations of Diseases of the Lung (BRINDL) at the University of Rochester Medical Center overseen by the IRB as RSRB00047606, as previously described (Ardini-Poleske et al., 2017; Bandyopadhyay et al., 2018). Portions (0.25-1.0 cm3) of small airway region of right middle lobe (RML) lung tissue were frozen in cryovials over liquid nitrogen and placed at −80°C for storage.

The raw sequencing data is available through dbGaP (controlled access) due to patient privacy concerns. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1

first: Allen

last: Wang

first: Joshua

last: Chiou

first: Olivier

middle: B

last: Poirion

first: Justin

last: Buchanan

first: Michael

middle: J

last: Valdez

first: Jamie

last: Verheyden

first: Xiaomeng

last: Hou

first: Minzhe

last: Guo

first: Jacklyn

last: Newsome

first: Parul

last: Kudtarkar

first: Dina

last: Faddah

first: Kai

last: Zhang

first: Randee

last: Young

first: Justinn

last: Barr

first: Ravi

last: Misra

first: Heidie

last: Huyck

first: Lisa

last: Rogers

first: Cory

last: Poole

first: Jeffery

last: Whitsett

first: Gloria

last: Pryhuber

first: Yan

last: Xu

first: Kyle

last: Gaulton

first: Sebastian

last: Preissl

first: Xin

last: Sun


title: Single Nucleus RNA-Seq Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection [scRNA-Seq]

first: LungMAPP

last: DCC

overall_design:
snRNA-seq of human non-diseased lungs from donors of three age groups: ~30 week old gestational age (GA, prematurely born, 30wkGA), ~3 year old (3yo), and ~30 year old (30yo). Three lungs were sampled for each age group, with both males and females represented. Of the 9 donors, 5 were Caucasian, 1 was African American and 3 were of unknown ancestry. For all samples, flash frozen biopsies from equivalent small airway regions of the lung were used. Nuclei were isolated from individual biopsies and split into two pools, one for snRNA-seq and one for snATAC-seq. We generated technical replicates for one of the 3yo donors (D032). Donor lung samples were provided through the federal United Network of Organ Sharing via National Disease Research Interchange (NDRI) and International Institute for Advancement of Medicine (IIAM) and entered into the NHLBI LungMAP Biorepository for Investigations of Diseases of the Lung (BRINDL) at the University of Rochester Medical Center overseen by the IRB as RSRB00047606, as previously described (Ardini-Poleske et al., 2017; Bandyopadhyay et al., 2018). Portions (0.25-1.0 cm3) of small airway region of right middle lobe (RML) lung tissue were frozen in cryovials over liquid nitrogen and placed at −80°C for storage.

The raw sequencing data is available through dbGaP (controlled access) due to patient privacy concerns. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1

first: Allen

last: Wang

first: Joshua

last: Chiou

first: Olivier

last: Poirion

first: Justin

last: Buchanan

first: Michael

last: Valdez

first: Jamie

last: Verheyden

first: Xiaomeng

last: Hou

first: Minzhe

last: Guo


title: Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection

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

The raw sequencing data is available through dbGaP (controlled access) due to patient privacy concerns. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1


title: Quantifying the effect of experimental perturbations in single-cell3RNA-sequencing data using graph signal processing

status: Public on Nov 14 2020

city: Somerville

first: Daniel

last: Burkhardt

address: 101 South Street, 6th Floor

institute: Cellarity

summary: Current methods for quantification of differences between scRNA-seq datasets collected in multiple conditions focus on discrete regions of the transcriptional state space such as clusters of cells. Here, we describe a continuous measure of the effect of a perturbation across the transcriptomic space with single cell resolution. We describe the cellular state space as manifold, use a heat filter to estimate the density of each sample over the manifold, and normalize these densities to obtain the relative likelihood of observing each cell in each of the observed conditions. We develop vertex frequency clustering to identify populations of affected cells at the appropriate level of granularity. Using these selected populations we can derive gene signatures of affected populations of cells. We demonstrate both algorithms using a combination of biological and synthetic datasets.

overall_design: Nondiabetic human islets obtained from Prodo Laboratories were allowed to rest for 1 day and were treated or were not treated with 25ng/ml IFNg for 24 hrs

first: Jay

middle: S

last: Stanley III

first: Alexander

last: Tong

first: Ana

last: Perdigoto

first: Scott

last: Gigante

first: Kevan

middle: C

last: Herold

first: Guy

last: Wolf

first: Antonio

last: Giraldez

first: David

last: van Dijk

first: Smita

last: Krishnaswamy


title: Expression profiling by RNA-seq of LNCaP cells expressing wild-type androgen receptor (AR-WT), AR-V7 splice variant or mutant AR-Q641X

status: Public on Nov 01 2020

city: Illkirch

first: Jocelyn

last: CERALINE

address: 1, rue Laurent Fries

department: IGBMC

institute: University of Strasbourg

summary: The androgen receptor (AR) signaling remains the key therapeutic target in metastatic prostate cancer (PCa). However, development of castration resistant PCa is frequently observed and can be in part attributed to the expression of mutant AR variants, which lack the ligand binding domain and are thus constitutively active. These constitutive AR variants have been associated with castration resistance but also with tumor progression. However, little data is available regarding their transcriptional activities. In this study, we depicted the transcriptional landscapes of the two constitutive AR variants AR-Q641X and AR-V7 by whole transcriptome sequencing and Gene Set Enrichment Analysis.

overall_design: Inducible expression of eGFP-AR-WT, eGFP-AR-Q641X, eGFP-AR-V7 or eGFP alone as a control was obtained from stable lentivirally transduced LNCaP cells. After 48 hours of growth /culture in hormone-depleted medium, cells were treated for 24 hours with 20ng/ml of doxycycline and 10nM of DHT or ethanol (EtOH) as vehicle. Total RNA was isolated and proceeded for RNA-seq.

first: Éva

last: Erdmann

first: Pauline

middle: O

last: Madi Berthélémy

first: Bruno

last: Kieffer

last: Céraline


title: PERICYTE-LIKE CELLS UNDERGO TRANSCRIPTIONAL REPROGRAMMING AND DISTINCT FUNCTIONAL ADAPTATIONS IN ACUTE LUNG INJURY

status: Public on Oct 31 2020

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

summary: Background: We previously reported on the role of pericyte-like cells as functional sentinel immune cells in lung injury. However, much about the biology of pericytes in lung injury remains unknown. Lung pericyte-like cells are well-positioned to sense disruption to the epithelial barrier and coordinate local inflammatory responses due to their anatomic niche within the alveoli. In this report, we characterized transcriptional responses and functional changes in pericyte-like cells following activation by alveolar components from injured and uninjured lungs. Methods: We purified pericyte-like cells from lung digests using PDGFR_ as a selection marker and expanded them in culture as previously described (1). We induced sterile acute lung injury in mice with recombinant human Fas ligand (rhFasL) instillation followed by mechanical ventilation (1). We then collected bronchoalveolar lavage fluid (BALF) from injured and uninjured mice. Purified pericyte-like cells in culture were exposed to growth media only (control), BALF from uninjured mice, and BALF from injured mice for 6 and 24 h. RNA collected from pericyte-like cells for each of these treatment conditions underwent genome-wide sequencing using RNA-seq. Targets of interest identified by bioinformatics analysis of RNA-seq data were validated using in vitro and in vivo assays. Results: We observed robust global transcriptional changes in pericyte-like cells following treatment with uninjured and injured BALF at 6 h, but this response persisted for 24 h only after exposure to injured BALF. Functional enrichment analysis of pericytes treated with injured BALF revealed activation of immuno-inflammatory, cell migration and angiogenesis-related pathways, whereas processes associated with tissue development and remodeling were down-regulated. We validated select targets in the inflammatory, angiogenesis-related, and cell migratory pathways using functional assays in vitro and in vivo. Conclusion: Lung pericyte-like cells are highly responsive to alveolar compartment content from both uninjured and injured lungs, but injured BALF elicits a more sustained response. The inflammatory, angiogenic, and migratory changes exhibited by activated pericyte-like cells underscore the phenotypic plasticity of these specialized stromal cells in the setting of acute lung injury.

overall_design: Mouse lung pericyte-like cell mRNA profiles from culutre after exposure to injured BALF (6h, 24h; n = 6 per time point), uninjured BALF (6h, 24h; n = 6 per time point) or media only (6h, 24h; n = 6 per time point)  were generated by deep sequencing using Illumina HiSeq.


title: Cells in healthy periodontal ligament

status: Public on Oct 29 2020

city: london

first: Paul

last: Sharpe

address: Craniofacial Development & Stem cell bio, Guy's Tower Floor 27

country: United Kingdom

institute: King's college London

summary: Loss of tissue attachment as a consequence of bacterial infection and inflammation represents the main therapeutic target for the treatment of periodontitis. Cementoblasts, the cells that produce the mineralized tissue, cementum, that is responsible for connecting the soft periodontal tissue to the tooth, are a key cell type for maintaining/restoring tissue attachment following disease. Here, we identify two distinct stem cell populations that contribute to cementoblast differentiation at different times by lineage tracing and single cell RNA sequencing. During postnatal development, cementoblasts are formed from perivascular‐derived cells expressing CD90 and perivascular‐associated cells that express Axin2. During adult homeostasis, only Wnt‐responsive Axin2+ cells form cementoblasts but following experimental induction of periodontal disease, CD90+ cells become the main source of cementoblasts. We thus show that different populations of resident stem cells are mobilized at different times and during disease to generate precursors for cementoblast differentiation and thus provide an insight into the targeting cells resident cells for novel therapeutic approaches.

overall_design: Mouse PDL mRNA profiles during adult homeostasis.

first: Jing

last: Zhao

first: Louis

last: Faure

first: Igor

last: Adameyko


title: Genome-wide study of human methylation profile of J-Lat cells upon EGCG-treatment and UHRF1 knockdown

status: Public on Oct 24 2020

first: Martin

last: Bizet

type: Methylation profiling by genome tiling array

summary: HIV-1 latent reservoirs constitute a major barrier to viral eradication. The various potencies of latency-reversing agents reflect the multiplicity of the silencing mechanisms underlying latency, and the dynamic and heterogeneous nature of the HIV-1 latent reservoirs. Here, we investigated the mechanisms of the DNA methylation inhibitor 5-aza-2’-deoxycytidine (5-AzadC) potency in HIV-1 latency reversal. We report that this potency was directly linked to 5-AzadC-induced demethylation of the HIV-1 promoter, which occurred at non-random CpG dinucleotides. Specifically, the methylation status of one of those CpGs allowed the recruitment of the epigenetic integrator UHRF1 to the HIV-1 promoter. 5-AzadC-induced viral reactivation led to a decreased in vivo recruitment of UHRF1. RNA interference-mediated knockdown of UHRF1 demonstrated its role in DNA methylation-mediated silencing of the latent HIV-1 promoter. Pharmacological downregulation of UHRF1 in ex vivo HIV+ patient cell cultures resulted in potent reactivation of latent HIV-1, further highlighting that UHRF1 could constitute a new molecular target to devise innovative HIV-1 curative strategies.

overall_design: Total genomic DNA from J-Lat cells. EGCG-treated cells, UHRF1 knock down and their respectives controls were analysed.


title: Integrative single-cell chromatin and transcriptome profiling uncovers cell-type specific regulatory interactions

status: Public on Oct 23 2020

city: New York

first: Sai

last: Ma

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Simultaneous measurement of different molecular aspects of gene regulation can help infer functional relationships between genome regulation and gene expression, and understand their distinct and contribution to cell phenotype. Here, we present SHARE-seq, a highly scalable, sensitive, and cost-effective approach for joint measurement of chromatin accessibility and gene expression from the same single cells. Applying SHARE-seq to adult mouse tissues (skin, brain, lung) we show a direct congruence in cell type definition by either chromatin accessibility or RNA expression and create cell-type specific regulatory maps. We leverage naturally occurring cell-cell variation to infer chromatin-expression regulatory relationships and develop a broadly applicable computational strategy to define cis- ad trans- regulatory programs. The cis-regulatory programs, which largely overlap with super-enhancers, are found at key lineage-specifying genes. We demonstrate dynamic chromatin evidence of both gene expression lineage-priming and lineage-memory. The combined scalability and depth of SHARE-seq provide an extensible platform to study the regulatory relationships governing chromatin and gene expression changes across diverse cells within tissues.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: SHARE-seq to profile chromatin accessibility and gene expression in the same cell from cell lines (GM12878, 3T3, K562, Raw 267.4), mouse skin, brain, and lung.

first: Jason

last: Buenrostro


title: Lamin A/C promotes DNA base excision repair (human arrays)

status: Public on Sep 30 2020

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The A-type lamins (lamin A/C), encoded by the Lmna gene, are important structural components of the nuclear lamina. Lmna mutations lead to degenerative disorders, including the premature aging disease Hutchinson-Gilford progeria syndrome (HGPS). In addition, altered lamin A/C expression is found in various cancers. Reports indicate that lamin A/C plays a role in DNA double strand break repair, but a role in DNA base excision repair (BER) has not been described. We provide evidence for reduced BER efficiency in lamin A/C-depleted cells. The mechanism involves impairment of the APE1 and POLβ enzyme activities in BER. Also, Lmna null mouse fibroblasts displayed reduced expression of several core BER enzymes (PARP1, LIG3, and POLβ). Moreover, the robustness of APE1 and POLβ activities and the rate of BER were enhanced by lamin A/C-augmented poly(ADP-ribose) polymer formation (PARylation). Finally, we report that HGPS fibroblasts are defective in BER. Collectively, our results provide novel insights into the functional interplay between the nuclear lamina and cellular defenses against oxidative DNA damage, with implications for human cancer and aging.

overall_design: Microarray analysis of cell lines from Hutchinson-Gilford progeria syndrome (HGPS)-affected individuals and a clinically unaffected parent (three patient-parent pairs, three replicates per condition) for a total of eighteen microarray samples.

first: Scott

last: Maynard

first: Guido

last: Keijzers

first: Mansour

last: Akbari

first: Marya

last: Morevati

first: Morten

last: Scheibye-Knudsen

first: Susana

last: Gonzalo

first: Jiri

last: Bartek

first: Vilhelm

last: Bohr


title: Epigenome analysis of Control and PLX4032 Resistant Clones with EPIC array.

status: Public on Sep 20 2020

first: Ze-yan

last: Zhang

state: NY

address: 522 First Ave

department: Radiation Oncology

institute: NYU Langone Health

summary: Genome wide DNA methylation profiling of control and PLX4032 resistant clones to identify resistance-associated methylome alternations, and to integrate with transcriptome analysis. Results provide insight into clonal epigentic adaption of PLX4032 resistance in BRAF V600E melanoma.

overall_design: Bisulphite converted DNA from 2 controls (parental and parallel) and 15 PLX4032 resistant clones were hybridised to the Illumina Infinium MethylationEPIC BeadChip.

first: Yingwen

last: Ding

first: Erik

last: Sulman


title: Transcriptomic Analysis of Control and PLX4032 Resistant Clones with RNA Sequencing

summary: NGS-derived transcriptome profiling (RNA-seq) of control and PLX4032 resistant clones to identify resistance-associated gene-expression changes and pathway enrichments, and to integrate with exome and methylome analysis. Results provide insight into PLX4032 resistance in BRAF V600E melanoma.

overall_design: RNA sequencing of 2 controls (parental and parallel) and 15 PLX4032 resistant clones using Illumina HiSeq 4000.


title: Keratin5-cytoskeleton-BMP4 network regulates cell phenotype conversions during cardiac regeneration

status: Public on Sep 18 2020

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

summary: The reconstruction of a blood supply system and myocardial recovery from inflamamtory reactions in the infract zone remains a challenge in cardiac regeneration after myocardial infarction. Here, we observed that the local myocardial cells and the clotted blood cells undergo cellular remodeling via cytoplasmic exocytosis and nuclear reorganization in zebrafish hearts after resection of the ventricular apex. The subsequent tissue regeneration processes were visualized by detection of the spatiotemporal expression of three tissue specific genes (α-SMA which marks for vasculature/fibrogenesis, Flk1for angiogenesis/hematopoiesis, and Pax3a for remusculogensis), and two histone modification markers (H3K9Ac and H3K9Me3 for chromatin remodeling). By analyzing the composition of the blastema tissue fractions we found that Krt5 peptide could promote F-actin assembly, BMP4-pSmad2/5/8 signaling activity, and H3K9Me3-mediated chromatin accessibility at the blastema representative genes in the cultured zebrafish embryonic fibroblasts. Further in vivo tests demonstrated that Krt5 interacted with beta actin, and promoted Gata3 expression and Flk1-GFP marked blastema angiogenesis. These results proposed a new Krt5-cytoskeleton-BMP4 mechanotransduction mechanism in the epithelial-dependent and cell phenotype conversion-based tissue regeneration.

overall_design: Examination of H3K9ac and H3K9me3 modifications and differential expression genes during zebrafish heart regeneration.

first: Huiping

last: Guo

first: Jizhou

last: Yan


title: Comparative transcriptomic study of skeletal muscles response to muscular dystrophy with myositis

status: Public on Sep 22 2020

city: Lowell

first: Matthew

last: Gage

address: One University Avenue

institute: University of Massachusetts Lowell

summary: Muscular dystrophy with myositis (mdm) is a severe degenerative muscle disease arising from a spontaneous mutaton at the N2A-PEVK junction of titin protein. The affected mice show a complex disease phenotype, and more organism-wide spread response compared to other myopathies. The project objectives forcus on undertanding the response pattetern of different skelelal muscles to mdm.

overall_design: Examin the transcriptomic resposne of mdm afected skeletal muscle compared to wildype in the B6C3Fe a/a-Ttnmdm/J +/+ mice

first: Pabodha

last: Hettige


title: ChIP-seq of Runx3 in SFZ chondrocytes.

status: Public on Sep 03 2020

city: Bunkyo-ku

first: Kosei

last: Nagata

institute: the University of Tokyo

summary: Purpose: To demonstrate Runx3's association with organizing the extracellular matrix in SFZ chondrocytes.  Method: Fragment DNA samples were collected  by using Anti-FLAG or IgG, from SFZ chondrocytes treated with lipofection of RUNX3-FLAG  Results: 21,730 raw peaks met the peak calling criterion.   Conclusions: By GO analysis, the extracellular structure organization and collagen fibril organization terms were the most significantly enriched.

overall_design: Examination of Runx3 target in SFZ chondrocyte cells.

first: Taku

last: Saito


title: RNA-seq of select neural tissue in SHIV infected and control rhesus macaques

status: Public on Sep 09 2020

city: Davis

first: Smita

last: Iyer

address: county rd 98 & hutchison, ccm room 2075

department: Center for Immunology and Infectious Disease

institute: University of California-Davis

summary: HIV+ patients are at an alarmingly higher risk of developing HIV associated neurocognitive disorders (HAND). HAND is a spectrum of neurocognitive deficits linked to impairments in the prefrontal cortex (PFC) and hippocampus, areas controlling higher cognitive processes. Studies in HIV+ patients implicate acute viremia and inflammation in driving central nervous system (CNS) impairment. However, the timing and implications of viral dissemination to the CNS, particularly the PFC and hippocampus, remain undefined. We tested the hypothesis that HIV-1 is rapidly and actively established within areas of the CNS responsible for controlling cognition.

overall_design: Comparison of transcriptome profiles across select neural tissues in SHIV model.


title: Profiling the immune cell gene signature of in vivo model of IBD

status: Public on Aug 12 2020

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

country: Hungary

institute: Seqomics Ltd.

summary: Identification of genes differentially expressed in inflamed and intact colon samples of TNBS treated in vivo rat model of Inflammatory Bowel Disease

overall_design: To investigate the transcriptional changes between inflamed and phenotypically normal or uninflamed tissue regions along the colons, male Wistar rats were randomly divided into two groups: first group served as control (n=2; vehicle-treated hence non-colitis induced) and the second group was induced by 2,4,6-trinitrobenzene sulphonic acid (TNBS) (n=6; colitis-induced). TNBS was intracolonically administered in a volume of 0.25 ml, via an 8 cm long plastic catheter under transient ether anaesthesia. 72 hours after the treatment all animals were sacrificed, ~8cm of distal colons were removed, opened longitudinally and gently cleaned of fecal content using ice-cold physiological saline. In the case of the control group, since non-inflamed, samples were taken from random colon sections. In case of colitis-induced animals, samples were taken from inflamed colon region as well as from non-adjacent uninflamed region.

first: Éva

last: Boros

first: Bence

last: Prontvai

first: Zoltán

last: Kellermayer

first: Péter

last: Balogh

first: Patrícia

last: Sarlós

first: Áron

last: Vincze

first: Csaba

last: Varga

last: Maróti

first: Balázs

last: Bálint

first: István

last: Nagy


title: Differentially expressed genes after miRNA transfection in human cancer cell lines

status: Public on Aug 05 2020

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: To identify differentially expressed genes by miRNAs transfection in human cancer, several cell lines (colon cancer and pancreatic cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (HCT116 and PANC-1) were treated with miRNAs (miR-139-5p, miR-139-3p, miR-143-5p, miR-143-3p, miR-30c-5p, miR-30c-2-3p, miR-30a-5p, and miR-30a-3p).

first: Reona

last: Okada


title: CRISPR/Cas9 targeted deletions in frataxin rescue Friedreich’s ataxia pathology in a human stem cell-based peripheral sensory neural circuitry

status: Public on Jul 27 2020

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: Friedreich's ataxia (FRDA) is an autosomal-recessive neurodegenerative and cardiac disorder which occurs when transcription of the FXN gene is silenced due to an excessive expansion of GAA repeats into its first intron. Herein, we generate dorsal root ganglia organoids (DRGOs) by in vitro differentiation of human iPSCs. Bulk and single-cell RNA sequencing show that DRGOs present a close transcriptional signature with native DRGs and display the main peripheral sensory neuronal and glial cell subtypes. Furthermore, when co-cultured with human intrafusal muscle fibers, DRGO sensory neurons contact their peripheral targets and reconstitute the muscle spindle proprioceptive receptors. FRDA DRGOs recapitulate key molecular and cellular deficits of the disease that are extensively rescued only when the entire FXN intron 1 is removed and not with the excision of merely the expanded GAA tract. These results strongly suggest that removal of the repressed chromatin flanking the GAA tract might be necessary to obtain a complete rescue of FXN expression and fully revert the pathological hallmarks of FRDA DRG neurons.

overall_design: 2x Ctrl DRGO, 1x CRISPR-treated FRDA DRGO

first: Vania

last: Broccoli

first: Pietro

middle: G

last: Mazzzara


title: In vitro restoration of Friedreich's Ataxia defect with novel Cas9-edited hiPSC-derived Dorsal Root Ganglion-like Organoids (DRGOs) and Microfluidic System

summary: Friedreich's ataxia (FRDA) is an autosomal-recessive neurodegenerative and cardiac disorder which occurs when transcription of the frataxin (FXN) gene is silenced due to the expansion of GAA·TTC repeats in intron 1 of the same gene, leading loss of the essential mitochondrial protein frataxin with several impairment in iron metabolism and respiration, primarily affects the sensory DRG neurons. A major limitation in the study of FRDA is the lack of robust animal and cellular models. To fill this gap, this study presents a novel 3D protocol to generate dorsal root ganglia-like organoids (DRGOs) from human iPSCs in which to model Friedreich's ataxia. DRGOs show a robust expression pattern of peripheral markers, are electro-physiologically active and out-perform peripheral sensory neurons generated with a traditional 2D protocol. Furthermore, when co-cultured with human stretch receptor intrafusal muscle fibers, DRGOs contact their peripheral target and form an in vitro muscle spindle. DRGOs generated from FRDA patient-derived iPSCs recapitulate several aspects of FRDA pathology including reduced expression of FXN and TCA-cycle components and mitochondrial fragmentation. We present also the recovery of this pathological signs, achieved by a new CRISPR-Cas9 mediated deletion of the GAA·TTC tract along with the majority of the affected intron. FRDA patient edited DRGOs with the long deletion boast normalized markers of oxidative stress, as well as recovered mitochondrial defect, particularly in the axonal compartment.

overall_design: 3x Dorsal Root Ganglia Organoids

last: Mazzara


title: C9orf72 in myeloid cells suppresses STING-induced inflammation

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: In this study we report that loss of C9orf72 expression in myeloid cells drives STING/type I interferon mediated autoimmunity and enhanced tumor immunity in mice.  Additionally, we show that the immunophenotypic signature identified in C9orf72-/- mice is present in blood derived macrophages, whole blood and autopsy brain tissue from C9orf72 repeat expansion ALS/FTD patients.

overall_design: DCs:  4 WT & 4 C9orf72 KO; Bcells, CD4, CD8 & CD11B:  4 WT, 4 Cx3Cr1-CRE conditional C9orf72 KO, 3 C9orf72 KO & 4 C9orf72 KO x Golden Ticket (Tmem173 KO); hMDMs:  5 Normal Controls, 5 with C9ORF72 expansion & 5 Sporadic ALS; hMDMs_H151:  2 C9ORF72 expansion samples treated with H151 & the same 2 C9ORF72 expansion samples treated with DMSO

first: Madelyn

last: McCauley

first: Jacqueline

last: O’Rourke

first: Alberto

last: Yáñez

first: Janet

last: Markman

first: Ritchie

last: Ho

first: Xinchen

last: Wang

first: Mengyao

last: Jin

first: A

last: Muhammad

first: Jesse

last: Landeros

first: Viviana

last: Valencia

first: Matthew

last: Harms

first: Moshe

last: Arditi

first: Caroline

last: Jefferies

first: Robert

middle: H

last: Baloh


title: RNA-seq of Runx3 cKO SFZ/DZ chondrocytes.

status: Public on Sep 04 2020

first: Kosei

last: Nagata

summary:
Purpose: To demonstrate Runx3's association with organizing the extracellular matrix in SFZ/DZ chondrocytes.
Method: RNA samples were collected from SFZ/DZ chondrocytes of 5-day-old Col2a1-Cre;Runx3fl/fl and Runx3fl/fl mice.
Results: 18 genes were up- or down-regulated by more than 2-fold in the Runx3 knockout in SFZ.
Conclusions: However, genes organizing the extracellular matrix were down-regulated in Runx3 cKO DZ chondrocytes.

overall_design: SFZ chondrocytes mRNA profiles of 5-day old Cntl and Runx3 cKO mice.

first: Taku

last: Saito


title: Immunophenotyping of COVID-19 and Influenza Underscores the Association of Type I IFN Response in Severe COVID-19

status: Public on Jul 06 2020

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

summary: Although most SARS-CoV-2-infected individuals experience mild COVID-19, some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly upregulation of the TNF/IL-1beta-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1beta-driven inflammation, and this was not seen in patients with milder COVID-19 infection. Based on this, we propose that the type I IFN response exacerbates inflammation in patients with severe COVID-19 infection.

overall_design:
Single-cell RNA sequencing performed with PBMC of 5 flu, 11 COVID-19 patients and 4 healthy controls.

The suffix of each barcode sequence represents patient information.
'-1' - 'Sample1' - 'nCoV 1 scRNA-seq'
'-2' - 'Sample2' - 'nCoV 2 scRNA-seq'
'-3' - 'Sample3' - 'Flu 1 scRNA-seq'
'-4' - 'Sample4' - 'Flu 2 scRNA-seq'
'-5' - 'Sample5' - 'Normal 1 scRNA-seq'
'-6' - 'Sample6' - 'Flu 3 scRNA-seq'
'-7' - 'Sample7' - 'Flu 4 scRNA-seq'
'-8' - 'Sample8' - 'Flu 5 scRNA-seq'
'-9' - 'Sample9' - 'nCoV 3 scRNA-seq'
'-10' - 'Sample10' - 'nCoV 4 scRNA-seq'
'-11' - 'Sample11' - 'nCoV 5 scRNA-seq'
'-12' - 'Sample12' - 'nCoV 6 scRNA-seq'
'-13' - 'Sample13' - 'Normal 2 scRNA-seq'
'-14' - 'Sample14' - 'Normal 3 scRNA-seq'
'-15' - 'Sample15' - 'nCoV 7 scRNA-seq'
'-16' - 'Sample16' - 'nCoV 8 scRNA-seq'
'-17' - 'Sample17' - 'nCoV 9 scRNA-seq'
'-18' - 'Sample18' - 'nCoV 10 scRNA-seq'
'-19' - 'Sample19' - 'Normal 4 scRNA-seq'
'-20' - 'Sample20' - 'nCoV 11 scRNA-seq'

first: S

last: Park

first: J

last: Lee

first: I

first: E

last: Shin


title: CFTR modulator therapy enhances peripheral blood monocyte contributions to immune responses in people with cystic fibrosis

status: Public on Jul 31 2020

first: Sina

last: Gharib

summary:
Background: CFTR modulators will decrease some etiologies of inflammation in the CF airway; however, current data indicate that non-resolving airway infection and inflammation will persist in individuals with CF and chronic bacterial infections. Thus, identification of therapies that diminish CF airway inflammation without allowing unrestrained bacterial growth remains a critical research goal. Novel strategies for combatting deleterious airway inflammation require a better understanding of the cellular contributions to chronic CF airway disease, and how cells change after initiation of CFTR modulator therapy. Peripheral blood monocytes, which traffic to the CF airway, can develop both pro-inflammatory and inflammation-resolving phenotypes, and represent intriguing targets for focused therapies to dampen CF airway inflammation.
Material and Methods: In order to characterize the inflammatory phenotype of CF blood monocytes, and how these cells change after initiation of CFTR modulator therapy, we studied adults (n=10) with CF, chronic airway infections, and the CFTR-R117H mutations before and 7 days after initiation of ivacaftor. Transcriptomes of freshly isolated blood monocytes were interrogated by RNA-sequencing (RNA-seq).  Plasma concentrations of cytokines and chemokines were evaluated by multiplex ELISA.
Results: RNAseq identified approximately 50 monocyte genes for which basal expression was significantly changed in all 10 subjects after 7 days of ivacaftor.  Of these, the majority were increased in expression post ivacaftor, including many genes traditionally associated with enhanced inflammation and immune responses. Pathway analyses confirmed that transcriptional pathways were overwhelmingly up-regulated in monocytes after 7 days of ivacaftor, including transcriptional modules associated with immunity, cell cycle, oxidative phosphorylation, and the unfolded protein response. Ivacaftor increased plasma concentrations of CXCL2, a neutrophil chemokine secreted by monocytes and macrophages, and CCL2, a monocyte chemokine. These results demonstrate that ivacaftor causes acute changes in blood monocytes and plasma chemokines, and suggest that increased monocyte inflammatory signals and potentially improved trafficking to the lung contribute to changes in airway inflammation in people taking CFTR modulators.  To our knowledge, this is the first report investigating the transcriptomic response of isolated blood monocytes in CF subjects.

overall_design:
Human monocyte mRNA profiles from 10 CF subjects before treatment with ivacaftor (Day 0) and after 7 days of therapy (Day 7) were generated by deep sequencing.

-------------------------------------------------------------------------------
Submitter states that raw data are not availble for open access due to patient privacy concerns, and that the sequence data can be shared on a case by case basis with personal contact.
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title: Genetic studies of MYC in prostate cancer cell lines

status: Public on Jun 30 2020

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: In order to dissect the contribution of MYC to prostate cancer development, we overexpressed MYC in RWPE-1 cells and knocked down MYC in LNCaP cells. We performed RNA-seq on those cells. In the LNCaP cells only, we also performed ChIP-seq against MYC, H3K27ac, H3K27me3, and RNAP2.

overall_design: 5 RWPE-1 cell lines (two empty vector and 3 MYC overexpression) and 5 LNCaP cell lines (wild-type, scrambled control, and 3 knockdown constructs) were used for RNA-seq. RWPE-1 RNA-seq was performed in duplicate. LNCaP RNA-seq was performed twice with scrambled control and constructs 627 and 637, and three times with wild-type, scrambled control, and the 512, 627 and 637 constructs along with ERCC spike-ins. ChIP-seq was performed on LNCaP wild-type, scrambled control, and MYC knockdown 512, 627 and 637 constructs in duplicate for MYC, H3K27ac and RNAP2, and once for H3K27me3.

first: Nichelle

last: Whitlock

first: Brian

last: Capaldo


title: mRNA-seq analysis of oral squamous cell carcinoma (OSCC) cell line OC3 and TW2.6 derived xenografts (CDXs)

status: Public on Jul 07 2020

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

country: Taiwan

institute: National Health Research Institutes, Taiwan

summary: In many solid tumors, tissue of mesenchymal subtype is frequently associated with epithelial-mesenchymal transition (EMT) state, strong stromal infiltration, and poor prognosis. Emerging evidence from tumor ecosystem studies indicate that the stromal components, including cancer associated fibroblast (CAFs), actively participate in cancer growth and progression. Transcriptomic analysis of xenograft tissues provides a unique advantage in dissecting hallmark genes of tumor (human) or stromal (murine) origins.

overall_design: For each mouse, a half millions of mycoplasma-free TW2.6 or OC3 cells mixed with equal volume of Corning® Matrigel® matrix (Corning, NY, USA) was subcutaneously implanted into the flank of 10-16 (Exp1) or 11 (Exp2) week-old NOG (National Institute of Infectious Diseases and Vaccinology, Taiwan). We measured the tumor size and mouse weight twice a week. For Exp1, all tumors were collected at day 68. For Exp2, to obtain tumor with ~500 mm3 in size, tumors of TW2.6-NOG were collected at day 32; tumors of OC3-NOG were collected at day 81.

first: Sheng-Yao

last: Su

first: Chung-Yen


title: RNAseq analysis of EC109 cells transfected by lncRPL34-AS1 plasmid and scramble pcDNA

status: Public on Jul 16 2020

city: nanjing

first: Hu

last: Zhang

address: gulou street

institute: southeast university

summary: We constructed EC109 cells transfected by lncRPL34-AS1 plasmid and scramble pcDNA to select differentially expressed genes and transcripts

overall_design:
EC109 cells transfected by lncRPL34-AS1 plasmid and scramble pcDNA were used for RNA-seq.
RNA quantification and quality assurance were evaluated by NanoDrop ND-1000, and RNA integrity and gDNA contamination tested by standard denaturing agarose gel electrophoresis.
After oligo dT enrichment (rRNA removal) of 1~2ug selected total RNA, the sequencing libraries were constructed using KAPA Stranded RNA-Seq Library Prep Kit (Illumina).
The mixed different sample libraries were sequenced by IlluminaNovaSeq6000 sequencer, raw sequencing data performs sequencing quality control (QC) to evaluate sequencing data analysis.
The Solexa pipeline version1.8 (Off-Line Base Caller software, version1.8) software was used for image processing and base recognition.
FastQC software evaluates the sequencing quality of unconnected reads (using cutadapt to remove 3 'and 5' connectors).
The reference genome was compared by Hisat2 software. The transcriptional abundance was estimated by using StringTie software with reference to the annotated information of the official database.
The R software Ballgown was used to calculate the FPKM at gene level and transcript level, and the differences of expression at gene level and transcript level were calculated respectively.
Based on the PCA analysis and correlation analysis of gene and transcript expression level, the differentially expressed genes were analyzed by scatter plot, volcano diagram, cluster diagram, GO function and KEGG pathway significant enrichment


title: Gene expression within the periaqueductal gray in Pink1 knockout rats

status: Public on May 21 2020

city: Madison

first: Cynthia

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

summary:
Background: Parkinson’s disease (PD) is a progressive, degenerative disease with early-stage pathology hypothesized to manifest in brainstem regions. Vocal deficits, including soft monotone speech, result in significant clinical and quality of life issues and are present in 90% of PD patients; yet, the underlying pathology mediating these significant voice deficits is unknown. The Pink1-/- rat is a valid model of early-onset PD that presents with analogous vocal communication deficits (e.g. reduced loudness). Previous work shows abnormal α-synuclein protein aggregation in the periaqueductal gray (PAG), a brain region critical and necessary to the modulation of mammalian vocal behavior. In this study, we used high-throughput RNA sequencing to examine gene expression within the PAG of both male and female Pink1-/- rats as compared to age-matched wildtype controls. We used a bioinformatic approach to (1) test the hypothesis that loss of Pink1 in the PAG will influence expression of genes that interact with Pink1, (2) highlight other key genes that relate to Mendelian PD, and (3) catalog molecular targets important for the production of rat vocalizations.
Results: Knockout of the Pink1 gene resulted in differentially expressed genes for both male and female rats. Pathway analysis highlighted several significant metabolic pathways. Weighted gene co-expression network analysis (WGCNA) was used to identify gene nodes and their interactions in (A) males, (B) females, and (C) combined-sexes datasets. For each analysis, within the module containing the Pink1 gene, Pink1 itself was the central node with the highest number of interactions with other genes including solute carriers, glutamate metabotropic receptors, and genes associated with protein localization. Strong connections between Pink1 and Krt2 and Hfe were found in both males and female datasets. In females a number of modules were significantly correlated with vocalization traits. Of interest, gene enrichment of the key vocal Cyan module in females showed a significant number of neuromodulatory genes including Nts, Slc6a4, Slc10a4, Ndnf, and Gpr160, that may be responsible for the modulation of rat vocalizations. The top biological pathways within the female Cyan vocal module included the regulation of membrane depolarization, indolalkylamine metabolic process, and monoamine transport.
Conclusions: Overall, this work supports the premise that gene expression changes in the PAG may contribute to the vocal behavioral and deficits observed in this PD rat model. Additionally, this dataset identifies genes that represent new therapeutic targets for PD voice disorders.

overall_design: Eight month old Long Evans rats; 8 male (n=4 Pink1-/-, n=4 WT) and 8 female (n=4 Pink1-/-, n=4 WT).

first: Stephen

last: Gammie


title: Dysregulation of MITF in the context of defective MC1R and RB1/p16/CDK4 leads to melanocyte transformation [microarray]

status: Public on Jul 02 2020

city: Oslo

first: Alfonso

last: Urbanucci

state: Oslo

address: Trondheimsveien 8

country: Norway

institute: Oslo University Hospital

summary: Expression analysis of immortalized melanocytes Hermes 3c and Hermes 4c derivative cell lines following lentiviral transduction of a HA-tagged MITF-M construct (pLX3xHAvar4mCherry) or control construct (pLVX IRES mCherry).

overall_design: Total RNA obtained from control transduced 3C and 4C cells compared to 3C-HA-MITF and 4C-HA-MITF


title: Dysregulation of MITF in the context of defective MC1R and RB1/p16/CDK4 leads to melanocyte transformation [ChIP-Seq]

summary: Chip-seq analysis of  immortalized melanocytes Hermes 3c and Hermes 4c derivative cell lines following lentiviral transduction of a HA-tagged MITF-M construct (pLX3xHAvar4mCherry)

overall_design: ChIP-seq study using one antibody against human influenza hemagglutinin (HA)-tag in immortalized melanocytes Hermes 3c and Hermes 4c derivative cell lines following lentiviral transduction of a HA-tagged MITF-M construct (pLX3xHAvar4mCherry)


title: Dysregulation of MITF in the context of defective MC1R and RB1/p16/CDK4 leads to melanocyte transformation

first: Eivind

last: Hovig

address: PO Box 4950 Nydalen

department: Tumor biology

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

overall_design: Refer to individual Series


title: RNF12 E3 ligase activity-dependent transcriptional profile in mouse embryonic stem cells

status: Public on Apr 29 2020

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

summary: RNF12 is a developmental E3 ligase mutated in Tonne-Kalscheuer Syndrome patients. To identify the gene expression programme controlled by RNF12 activity  in mouse embryonic stem cells we employ RNA-Sequencing.

overall_design: RNF12 knockout embryonic stem cells transfected with: 1) empty vector, 2) RNF12 wild type, and 3) RNF12 W576Y catalytic mutant. Total RNA was extracted, libraries generated and subjected to RNA-sequencing in an Illumina NextSeq 500 instrument. FastQ files were generated using the BaseSpace inbuilt BCL to FastQ workflow.

first: Francisco

last: Bustos

first: Anna

last: Segarra-Fas

first: Andrew

last: Cassidy

first: Martin

last: Montecino

first: Greg

middle: M

last: Findlay


title: Comparison of single cell and single nucleus RNASeq approaches in mouse lung

status: Public on Jun 23 2020

city: Saint Louis

first: Jeffrey

last: Koenitzer

state: MO

address: 660 Euclid Ave.

institute: Washington University in St. Louis

summary: 16,110 single nucleus and 11,934 single cell transcriptomes from control C57Bl/6J mice were analyzed. We noted similar gene detection rates by both techniques when using intronic and exonic reads for mapping. snRNASeq improves dissociation bias and enhances epithelial cell detection compared with scRNASeq, and eliminates artifactual gene expression.

overall_design: 10X Chromium (3’v3 kits) was used to profile isolated lung cells and nuclei

first: Benjamin

middle: D

last: Humphreys


title: Genome-wide DNA methylation analysis of peripheral blood samples of moderate-to-severe psoriasis patients treated with anti-TNF drugs

status: Public on May 28 2020

city: MADRID

first: María

last: Ovejero-Benito

state: MADRID

address: C DIEGO DE LEÓN 62

country: Spain

institute: Instituto de Investigación Sanitaria la Princesa (IIS-IP)

summary: Genome wide DNA methylation profiling of peripheral blood samples of moderate-to-severe psoriasis patients treated with anti-TNF drugs. Patients were distributed on Excellent Responders (ER) if they achieved PASI90 (a 90% reduction with respect to baseline PASI) at 3 and 6 months of treatment with anti-TNF drugs and Partial responders if they did not achieve a PASI75 (a 75% reduction with respect to baseline PASI) at 3 and 6 months of treatment. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,000 CpGs in 49 ER and 21 PR which were obtained from peripheral blood samples of anti-TNF drug treated patients. We have searched for pharmaoepigenetic biomarkers of anti-TNF response in moderate-to-severe psoriasis patients.

overall_design: Bisulphite converted DNA from the 70 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Ancor

last: Sanz-García

first: Mar

last: Llamas-Velasco

first: Alejandra

last: Reolid

first: Esteban

last: Daudén

last: Abad-Santos


title: Gene expression in cutaneous T cell lymphoma (CTCL), dermatitis (D), and healthy subjects (HS)

status: Public on Jun 16 2020

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

summary:
FFPE skin biopsy samples from patients with CTCL, dermatitis, or healthy controls were profiled by NanoString gene expression analysis
A classifier was constructed that was able to identify mycosis fungoides (MF) samples from dermatitis and healthy controls.

overall_design: A discovery set  of 43 early-stage MF biopsies, 29 dermatitis biopsies, and biopsies from 12 healthy controls were profiled by an 800 gene NanoString panel. An independent validation cohort of 27 MF and 17 dermatitis samples was applied.

first: Pia

last: Nielsen

first: Jens

last: Eriksen


title: Loss of Snord116 impacts lateral hypothalamus, sleep, and food-related behaviors

status: Public on May 25 2020

first: Alfonso

last: Urbanucci

summary: Imprinted genes are highly expressed in the hypothalamus, however whether specific imprinted genes affect hypothalamic neuromodulators and their functions is unknown. It has been suggested that Prader-Willi syndrome (PWS), a neurodevelopmental disorder caused by lack of paternal expression at the chromosome 15q11-q13, characterised with a hypothalamic insufficiency. Here we investigate the role of paternally expressed Snord116 gene within the context of sleep and metabolic abnormalities of PWS, and we report a novel role of this imprinted gene in the function and organisation of the two main neuromodulatory systems of the lateral hypothalamus (LH), namely the orexin (OX) and the melanin concentrating hormone (MCH). We observe that the dynamic between neuronal discharge in the LH and sleep-wake states of mice carrying the paternal deletion of the Snord116 (PWScrm+/p-) is compromised. This abnormal state-dependent neuronal activity is paralleled by a significant reduction of OX neurons in LH of mutants. Therefore, we propose that unbalance between OX- and MCH- expressing neurons in the LH of mutants reflects in a series of deficits manifested in the PWS, such as dysregulation of rapid eye movement (REM) sleep, food intake and temperature control.

overall_design: Investigation of the effect of loss of Snord116 and Sleep Deprivation (SD) on the hypothalamus transcriptome  in both normal and PWScrm+/p− mutant mice (paternal Snord116 loss) by performing RNA-sequencing (RNA-seq).  The mice (3-5 per condition) were investigated at the beginning of the light period ZT0 (group 1, G1), six hours later at ZT6 (group 2, G2) and at same ZT6 but following 6-hrs of SD (group 3, G3).

first: Marta

last: Pace

first: Matteo

last: Falappa

first: Andrea

last: Freschi

first: Edoardo

last: Balzani

first: Chiara

last: Berteotti

first: Viviana

last: Lo Martire

first: Fatemeh

last: Kaveh

first: Eivind

last: Hovig

first: Givanna

last: Zoccoli

last: Cerri

first: Roberto

last: Amici

first: Valter

last: Tucci


title: Overexpression of OsbHLH044 transcription factor controls a negative regulatory module associated with plant cell death and stress inhibition in rice crown root development

status: Public on Mar 20 2020

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

institute: Université Montpellier 2

summary:
Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by genetics and functional genomics approaches. The CROWN ROOTLESS1 (CRL1) transcription factor is necessary for crown root initiation in rice. The basic helix-loop-helix 044 (OsbHLH044) transcription factor was identified as a CRL1-regulated gene. In this study, we aimed to determine OsbHLH044-regulated genes, with transcriptome analysis of OsbHLH44 overexpressing plants in crl1 mutant background. We analysed the transcriptional profile of overexpressing lines stem bases in comparison with corresponding null segregant sister control lines.
Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ .

overall_design: Stem bases of six days old plantlets were used. The experiment was repeated independently three times with 2 pC5300.OE-OsbHLH044 overexpression lines and with their coresponding null segregant sister lines. For each biological replicate, ten to fifteen stem bases were collected and immediately frozen in liquid nitrogen. After grounding stem bases in liquid nitrogen, RNA were extracted and quantified at 260 nm with a ND-1000 spectrophotometer (Thermo-Fisher, Waltham, MA, USA).

first: Mathieu

last: Gonin

first: Jeremy

last: Lavarenne


title: Genome-wide maps of liver in high-fat fed mice treated with kaempferol

status: Public on May 01 2020

city: shanghai

first: Lu

last: Yifei

address: Pudong New area

country: China

institute: Shanghai University of traditional Chinese Medicine

summary:
Purpose: The goals of this study were to compare the liver transcriptome (RNA-seq) of mice induced by high fat diet and treated with kaempferol, and to reveal the effective treatment and biomarkers of kaempferol.
Methods: mRNA profiles of six-week-old C57/BL6 which were fed with a control diet, high fat diet and treated with kaempferol were generated by sequencing, using Illumina HiSeq 4000 sequencer. The sequence reads that passed quality filters were controlled by Q30, using cutadapt software (v1.9.3). The high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Result: RNA-seq data confirmed stable expression of 277 common regulated differential genes among three groups with p-value <0.05, |Fold change| >1.5 and FPKM>1 in at least one group and the most five obvious differentially expressed genes were Cyp2b9, Cyp4a12b, Mup7, Mup17 and Mup16 while the metabolic pathways were involved in fatty acid degradation, ribosome, glyoxylic acid and dicarboxylic acid metabolism.
Conclusion: Our study represents the first detailed analysis of hepatic transcriptomes, with high-fed diet induced treated with kaempferol, generated by RNA-seq technology. Our results show that kaempferol improved high fat diet induced NASH through change the expression of specific genes and RNA-seq based transcriptome may be a promising tool in exploring the anti-NASH effects of kaempferol and provided a better understanding of the mechanisms.

first: Yifei

last: Lu

first: Mingmei

last: Shao

first: Hongjiao

last: Xiang

first: Tao

last: Wu


title: Thyroarytenoid muscle gene expression in Pink1 knockout rats

status: Public on May 27 2020

first: Cynthia

last: Kelm-Nelson

country: USA

summary: Loss of function in the PTEN-induced kinase 1 gene (Pink1) causes an early-onset, autosomal recessive form of PD. The translational Pink1-/- rat shows cranial sensorimotor deficits including: declines in ultrasonic vocalization, negative impacts on social vocal function, and alterations to thyroarytenoid muscle structure. The aim of this study was to identify differentially expressed genes using RNA-sequencing and bioinformatic analysis of the thyroarytenoid muscle of male Pink1-/- rats compared to wildtype controls. To construct gene co-expression networks and gene modules, a WGCNA was used to identify biological networks of interest including where Pink1 was a central node with interconnecting genes. Data are congruent with previous findings demonstrating changes to thyroarytenoid muscle structure. These data are consistent with the hypothesis that differences in peripheral biology may influence the early pathogenesis of vocalizations at the level of the thyroarytenoid muscle.

overall_design: Eight month old Long Evans rats; 8 male (n=4 Pink1-/-, n=4 WT).

first: Stephen

last: Gammie


title: Dysregulation of MITF in the context of defective MC1R and RB1/p16/CDK4 leads to melanocyte transformation [RNA-Seq]

first: Alfonso

last: Urbanucci

summary: RNAseq Expression analysis of immortalized melanocytes Hermes 3c (3C) and Hermes 4c (4C) cell lines following siRNA transfection with a control scrambled siRNA or an RNA targeting MITF

overall_design: Total RNA obtained from control transfected 3C and 4C cells compared to 3C 4C transfected with siRNA targteting MITF


title: Targeting the mevalonate pathway to overcome acquired anti-HER2 treatment resistance in breast cancer [RNA-seq]

status: Public on Apr 04 2020

city: Houston

first: Xiaoyong

last: Fu

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Despite effective strategies, therapy resistance in HER2+ breast cancer remains a challenge. While the Mevalonate pathway (MVA) is suggested to promote cell growth and survival, including in HER2+ models, its potential role in resistance to HER2-targeted therapy is unknown. Using HER2+ breast cancer parental (P) cell models (AU565, SKBR3, and UACC812), we have established anti-HER2-resistant derivatives made resistant to lapatinib (LR) or lapatinib plus trastuzumab (LTR). We performed RNA-seq on these resistant models and the P cells treated with lapatinib or lapatinib plus trastuzumaba for 24 h. We found that the average expression of the key genes in the MVA pathway, as a surrogate for pathway activity, was dramatically reduced in P cells with short-term treatment. In contrast, expression was restored or further upregulated relative to P cells in all three resistant (LR/LTR) models. Specific blockade of this pathway with lipophilic but not hydrophilic statins and with the n-bisphosphonate zoledronic acid led to apoptosis and substantial growth inhibition of resistant cells. Inhibition was rescued by mevalonate or the intermediate metabolites farnesyl pyrophosphate (FPP) or geranylgeranyl pyrophosphate (GGPP), but not by cholesterol. Activated YAP/TAZ and mTORC1 signaling and their downstream target gene product Survivin were inhibited by MVA blockade especially in the LR/LTR models. Overexpression of constitutively active YAP rescued Survivin and phosphorylated S6 levels despite blockade of the MVA. The MVA may provide alternative signaling leading to cell survival and resistance when HER2 is blocked by activating YAP/TAZ-mTORC1-Survivin signaling suggesting novel therapeutic targets. MVA inhibitors including lipophilic statins and N-bisphosphonates may circumvent resistance to anti-HER2 therapy and warrant further clinical investigation.

overall_design: RNA-seq of three HER2+ breast cancer anti-HER2-resistant cell models, including parental (P) cells treated with short-term anti-HER2 therapy and their derivatives made resistant to lapatinib (LR) or lapatinib plus trastuzumab (LTR), using Illumina HiSeq with paired-end 100 bp reads.

first: Obi

last: Griffith

first: Laura

last: Heiser

first: Rachel

last: Schiff


title: CYP2J2 Modulates Diverse Transcriptional Programs in Adult Human Cardiomyocytes

status: Public on Mar 07 2020

city: Seattle

first: Sina

last: Gharib

address: 850 Republican St.

institute: University of Washington

summary: CYP2J2, a member of the Cytochrome P450 family of enzymes, is the most abundant epoxygenase in the heart and has multifunctional properties including bioactivation of epoxyeicosatrienoic acids, which, in turn, have been implicated in mediating several cardiovascular conditions. In order to elucidate the complex role played by CYP2J2 in cardiac tissue, we performed targeted silencing of CYP2J2 expression in human adult cardiomyoctes and interrogated whole genome transcriptional responses. We found that knockdown of CYP2J2 elicits widespread alterations in gene expression of ventricular cardiomyocytes and leads to the activation of a diverse repertoire of programs, including those involved in ion channel signaling, development, extracellular matrix, and metabolism. Several members of the differentially up-regulated ion channel module have well-known pathogenetic roles in cardiac dysrhythmias. By leveraging causal network and upstream regulator analysis, we identified several candidate drivers of the observed transcriptional response to CYP2J2 silencing; these master regulators have been implicated in aberrant cardiac remodeling, heart failure, and myocyte injury and repair. Collectively, our study demonstrates that CYP2J2 plays a central and multifaceted role in cardiomyocyte homeostasis, and provides a framework for identifying critical regulators and pathways influenced by this gene.

overall_design: Adult human cardiomyocte mRNA profiles from culutre after treatmente with CYP2J2 siRNA (n = 3) or scramble siRNA (n = 3  were generated by deep sequencing, using Illumina HiSeq.


title: Gene expression in human endometrium cells (ATCC 4003) after Sox4 was abolished by siRNA

status: Public on Mar 04 2020

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

summary: To detect the gene profiles in decidualized stromal cells affected by SOX4, cultured stromal cells were transfected with siSOX4 and subjected to RNA-Seq. After aligned to mouse mm10 by HISAT2, RPKM value was calculated by Edger. Our results show that SOX4 was remarkable dimished after siSOX4 transfection. Meanwhile, some decidual marker genes were also changed significantly after SOX4 knockdow. The expression of SOX4 and other downstream genes were further confirmed by qPCR and westerblot. This RNA-Seq data provides fundamental information for our further physiological study of SOX4 during human stromal cells decidualization and fertility.

overall_design: Total RNAs from decidualized stromal cells (ATCC 4003) were extracted by TRIzol and purified by ploy-A before subjected to RNA-Seq by HiSeq2500. The expression of level of each gene is normalized to RPKM.


title: Sphere-derived multipotent progenitor cells obtained from human oral tissue neural crest-derived cells

status: Public on Nov 01 2021

city: Itabashi-ku, Tokyo

first: Shigehiro

last: Abe

address: 30-1 Oyaguchikami-cho

department: Oral Surgery

institute: Nihon University

summary: The purpose of this study was to isolate neural crest stem cells from apical papilla, periodontal ligament and oral mucosa.

overall_design: Total RNA from human sphere-forming apical papilla, periodontal ligament and oral mucosa derived cells were collected and compared at their gene expression level. Each sample form 3 patients were analyzed (patient-matched).