title: Multi-omics approaches reveal TNF-mediated inhibition of tissue reparative macrophages is via a gene-selective transcriptional mechanism (bulk RNA-Seq)

overall_design:
Methods: BMDMs mRNA profiles of 8 weeks old wild-type (WT) mice were generated, prestimulated with DMSO or JNK-inhibitors and stimulated with IL4/IL13, IL4/IL13+ TNF or TNF, deep sequenced, in triplicate, using Illumina NovaSeq 6000 platform.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9).
Conclusions: Our study represents the first detailed analysis of IL4/IL13 or IL4/IL13+TNF stimulated BMDMs in the presence of JNK-inhibitors, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
mRNA profiles of wild-type BMDMs prestimulated with DMSO, JNK-IN-8 or SP600125 for 1 hour and stimulated with IL4/IL13, IL4/IL13 + TNF or TNF for 6 hours


title: Epigenomic and Transcriptional Basis of Human Insulin Resistance

status: Public on Jan 11 2022

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

country: USA

institute: Beth Israel Deaconess Medical Center

type: Expression profiling by high throughput sequencing

summary: Development of insulin resistance is a key pathogenic component underlying metabolic syndrome and Type 2 diabetes (T2DM). Despite its importance, the molecular mechanisms underlying insulin resistance are poorly understood. Genome-wide association studies for T2DM and other metabolic traits have led to the identification of many candidate SNPs, but the majority of these SNPs are noncoding and determination of associated causal genes and/or specific tissue sites of action have been difficult. Adipocytes are critical regulators of mammalian metabolic homeostasis, with important effects on appetite, satiety, glucose and lipid homeostasis, energy expenditure, blood pressure, and immune function. Although insulin resistance (IR) in skeletal muscle, the major source of glucose disposal, is responsible for the bulk of the hyperglycemia observed in T2DM, muscle IR KO mice are generally healthy, IR also occurs in adipocytes, and inflammation within adipose tissue has been proposed as a primary mediator of IR, resulting in excess release of free fatty acids as well as alterations in adipokine release. Absence of adipose tissue, as observed in various lipodystrophies, or adipocyte-specific knockout of genes such as GLUT4 or insulin receptor, also alter systemic IR and T2DM risk. Transcriptional changes in adipocytes associated with metabolic disease. Despite the importance of adipocytes to metabolic disease, we have a poor understanding of how the adipocyte transcriptome changes in the disease state. Studies investigating transcriptional changes in whole adipose tissue have shown decreases in genes involved in adipogenesis, as well as alterations in inflammation, mitochondrial metabolism, lipid metabolism, detoxification, and insulin signaling. However, the vast majority of these studies use total adipose tissue samples, which does not allow for the exclusive evaluation of gene expression in mature adipocytes due to the substantial number of nonadipocyte cells (immune cells, fibroblasts, endothelial cells, pre-adipocytes, and mesenchymal cells) that also reside in adipose tissue. This is particularly relevant when studying metabolic disorders related to obesity-associated insulin resistance because these conditions are characterized by an increased influx of inflammatory cells into the adipose tissue.

overall_design: We performed RNA-seq on purified adipocytes collected from subcutaneous panniculus samples of 43 individuals in the first and 4th quartiles for HOMA-IR from a population of plastic surgery patients at our institution.  Adipocytes were isolated via modified Rodbell protocol form 300g-2kg of starting material.  400ul of floated adipocyte material was used for RNA isolation.  Total RNA from ~400 μl of thawed floated adipocytes was isolated in TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. For RNA-seq library construction, mRNA was purified from 100 ng of total RNA by using a Ribo-Zero rRNA removal kit (Epicentre) to deplete ribosomal RNA and convert into double-stranded complementary DNA by using an NEBNext mRNA Second Strand Synthesis Module (E6111L). cDNA was subsequently tagmented and amplified for 12 cycles by using a Nextera XT DNA Library Preparation Kit (Illumina FC-131). Sequencing libraries were analyzed with Qubit and Agilent Bioanalyzer, pooled at a final loading concentration of 1.8 pM and sequenced on a NextSeq500. No technical or biological replicates were performed.

first: Linus

last: Tsai

first: Evan

last: Rosen


title: Sex differences in embryonic gonad transcriptomes and benzo[a]pyrene metabolite levels after transplacental exposure

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: Polycyclic aromatic hydrocarbons like benzo[a]pyrene (BaP) are generated during incomplete combustion of organic materials. Prior research has demonstrated that BaP is a prenatal ovarian toxicant and carcinogen. However, the metabolic pathways active in the embryo and its developing gonads and the mechanisms by which prenatal exposure to BaP predisposes to ovarian tumors later in life remain to be fully elucidated. To address these data gaps, we orally dosed pregnant female mice with BaP from E6.5-11.5 (0, 0.2 or 2 mg/kg-day) for metabolite measurement or E9.5-11.5 (0 or 3.33 mg/kg-day) for embryonic gonad RNA-sequencing. Embryos were harvested at E13.5 for both experiments. The sum of BaP metabolite concentrations increased significantly with dose in the embryos and placentas, and concentrations were significantly higher in female than male embryos and in embryos than placentas. RNA sequencing revealed that enzymes involved in metabolic activation of BaP are expressed at moderate to high levels in embryonic gonads and that greater transcriptomic changes occurred in the ovaries in response to BaP than in the testes. We identified 490 differentially expressed genes (DEGs) with FDR p-values <0.05 when comparing BaP-exposed to control ovaries, but no statistically significant DEGs between BaP-exposed and control testes. Genes related to monocyte/macrophage recruitment and activity, prolactin family genes, and several keratin genes were among the most upregulated genes in the BaP-exposed ovaries. Results show that developing ovaries are more sensitive than testes to prenatal BaP exposure, which may be related to higher concentrations of BaP metabolites in female embryos.

overall_design: Pregnant mice were exposed to benzo[a]pyrene, and gonads were collected from E13.5 embryos for RNA-seq.

first: Toshi

first: Junhwan

last: Lim

first: Ulrike

last: Luderer

first: Aramandla

last: Ramesh

first: Kathleen

last: Leon


title: Tumor-derived lactic acid modulates activation and metabolic status of draining lymph node stroma

city: Würzburg

first: Angela

last: Riedel

state: Bavaria

address: Josef-Schneider-Straße 2

department: Mildred-Scheel-Nachwuchszentrum (MSNZ) für Krebsforschung

country: Germany

institute: University Hospital Würzburg

summary: Communication between tumors and the stroma of tumor draining lymph nodes (TDLNs) exists before metastasis arises, altering structure and function of the TDLN niche. Transcriptional profiling of fibroblastic reticular cells (FRCs), the dominant stromal population of the LN, revealed reprogramming of these cells in immune related pathways, but also in fibroblast activation and mitochondrial function. However, tumor derived factors driving the changes in FRCs remained to be identified. Taking an unbiased approach, we show that lactic acid (LA), a metabolite released by cancer cells, is not only secreted by B16.F10 and 4T1 tumors in high amounts, but that it is also enriched in TDLNs. LA supports an upregulation of Pdpn and Thy1 and downregulation of Il7 in FRCs of TDLNs, making them akin to activated fibroblasts found at the primary tumor site. Furthermore, we show that tumor-derived LA alters mitochondrial function of FRCs of TDLNs. Thus, our results demonstrate a novel mechanism by which a tumor-derived metabolite connected with a low pH environment modulate the function of fibroblasts in TDLNs.

overall_design: RNA sequencing

first: Moutaz

last: Helal

first: Luisa

last: Pedro

first: Jonathan

last: Swietlik

first: David

last: Shorthouse

first: Werner

last: Schmitz

first: Lisa

last: Haas

first: Tim

last: Young

first: Ana

middle: H

last: Costa

first: Sarah

last: Davidson

first: Pranjali

last: Bhandare

first: Elmar

last: Wolf

first: Benjamin

middle: A

last: Hall

first: Christian

last: Frezza

first: Thordur

last: Oskarsson

first: Jacqueline

last: Shields


title: Characterization of the stromal vascular fraction (SVF) of human subcutaneous adipose tissue (SAT)

first: NORC

last: Boston

summary: We report single-cell RNA-seq (Drop-seq) data from the stromal vascular fraction (SVF) of human subcutaneous adipose tissue (SAT).

overall_design:
Potential subjects were recruited in a consecutive fashion, as scheduling permitted, from the plastic surgery operating room rosters at Beth Israel Deaconess Medical Center. Female subjects over the age of 18 undergoing elective plastic surgery procedures and free of other acute medical conditions were included and provided written informed consent preoperatively. Excess adipose tissue from the surgical site was collected at the discretion of the surgeon during the normal course of the procedure. Subjects with a diagnosis of diabetes, or taking insulin-sensitizing medications such as thiazolidinediones or metformin, chromatin-modifying enzymes such as valproic acid, anti-retroviral medications, or drugs known to induce insulin resistance such as mTOR inhibitors or systemic steroid medications, were excluded.
>>> Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns. <<<

first: Evan

middle: D

last: Rosen

first: Linus

middle: T

last: Tsai


title: Analysis of HeLa cell transcriptome changes induced by IDO1-metabolism

city: Martinsried

first: Assa

last: Yeroslaviz

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary: We analyzed the mRNA changes iduced by treatment with IFNγ in the presence of the IDO1 inhibitors (indoximod, epacadostat and BMS986205) in wt and IDO1 ko HeLa cells.

overall_design: mRNA sequencing of wt  and IDO1 ko HeLa cells treated for with 10 ng/ml of IFNγ, 100µM indoximod, 1µM epacadostat and 1µM BMS986205.

first: Allessandra

last: Fiore

first: Rin Ho

last: Kim

first: Peter

middle: J

last: Murray


title: Development, Cryo-EM structure and function of potent monospecific and bispecific monoclonal antibodies that neutralize SARS-CoV-2 and variant B.1.351

city: West Haven

first: Ryan

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

summary: The COVID-19 pandemic prompted an unprecedented effort to develop effective countermeasures against SARS-CoV-2. While efficacious vaccines and certain therapeutic monoclonal antibodies are available, here, we report the development, cryo-EM structures and functional analyses of distinct potent monoclonal antibodies (mAbs) that neutralize SARS-CoV-2 and its variant B.1.351. We established a platform for rapid identification of highly potent and specific SARS-CoV-2-neutralizing antibodies by high-throughput B cell receptor single cell sequencing of spike receptor binding domain immunized animals. We identified two highly potent and specific SARS-CoV-2 neutralizing mAb clones that have single-digit nanomolar affinity and low-picomolar avidity. We also generated a bispecific antibody of these two lead clones. The lead monospecific and bispecific antibodies showed strong neutralization ability against prototypical SARS-CoV-2 and the highly contagious South African variant B.1.351 that post a further risk of reducing the efficacy of currently available therapeutic antibodies and vaccines. The lead mAbs showed potent in vivo efficacy against authentic SARS-CoV-2 in both prophylactic and therapeutic settings. We solved five cryo-EM structures at ~3 resolution of these neutralizing antibodies in complex with the ectodomain of the prefusion spike trimer, and revealed the molecular epitopes, binding patterns and conformations between the antibodies and spike RBD, which are distinct from existing antibodies. Our recently developed antibodies expand the repertoire of the toolbox of COVID-19 countermeasures against the SARS-CoV-2 pathogen and its emerging variants.

overall_design: 10x 5' single-cell VDJ sequencing of CD138+ B cells from mice (C57BL/6 and BALBc) immunized with SARS-CoV-2 RBD. From C57BL/6 mice: 1 sample from spleen+LN, 1 sample from bone marrow. From Balbc mice: 2 samples (pooled spleen+LN+bone marrow).

first: Lei

last: Peng

first: Yingxia

last: Hu

first: Madeleine

middle: C

last: Mankowski

first: Jin

last: Wei

first: Min

last: Zhao

first: Ping

last: Ren

first: Tongqing

last: Li

first: Therese

last: Tripler

first: Lupeng

last: Ye

first: Chunxiang

last: Wu

first: Matthew

middle: B

last: Dong

last: Cook

first: Guilin

last: Wang

first: Paul

last: Clark

first: Bryce

last: Nelson

first: Daryl

last: Klein

first: Richard

last: Sutton

first: Craig

last: Wilen

first: Yong

last: Xiong

first: Sidi

last: Chen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Bat3-/- BMDC Transcriptomes

city: Cambridge

first: Ayshwarya

last: Subramanian

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Bat3-/- BMDC Transcriptomes I

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived WT or Bat3 KO BMDC transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Methods: BMDC mRNA profiles of wild-type (WT) and Bat3 KO mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Conner

last: Lambden


title: A single cell atlas of human adipose tissue

first: NORC

last: Boston

summary: White adipose tissue (WAT), once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic, heterogenous, and involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, blood pressure control, and host defense.  High fat feeding and other metabolic stressors cause dramatic changes in adipose morphology, physiology, and cellular composition, and alterations in adiposity are associated with insulin resistance, dyslipidemia, and Type 2 diabetes (T2D). Here we provide detailed cellular atlases of human and murine subcutaneous and visceral white fat at single cell resolution across a range of body weight.  We identify subpopulations of adipocytes, adipose stem and progenitor cells (ASPCs), vascular, and immune cells and demonstrate commonalities and differences across species and dietary conditions.  We link specific cell types to increased risk of metabolic disease, and we provide an initial blueprint for a comprehensive set of interactions between individual cell types in the adipose niche in leanness and obesity.  These data comprise an extensive resource for the exploration of genes, traits, and cell types in the function of WAT across species, depots, and nutritional conditions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Human samples: at BIDMC, potential subjects were recruited in a consecutive fashion, as scheduling permitted, from the gynecological, vascular, and general surgery rosters. Male and female subjects over the age of 18 undergoing elective plastic surgery procedures and free of other acute medical conditions were included and provided written informed consent preoperatively. Excess adipose tissue from the surgical site was collected at the discretion of the surgeon during the normal course of the procedure. The exclusion criteria were any subjects taking thiazolidinediones, chromatin-modifying enzymes such as valproic acid, anti-retroviral medications, and drugs known to induce insulin resistance such as mTOR inhibitors or systemic steroid medications. At UPMC, inclusion criteria were patients receiving bariatric surgery or lean controls ages 21-60, exclusion criteria were diagnosis of diabetes (type 1 or type 2), pregnancy, alcohol or drug addiction, bleeding or clotting abnormality, or inflammatory abdominal disease. All patients provided written informed consent preoperatively. Excess adipose tissue from the surgical site was collected at the discretion of the surgeon during the normal course of the procedure. 200-500 mg samples were flash frozen immediately after collection for downstream processing.  Mouse samples: Male and female C57Bl/6J 16-week old high fat diet fed (JAX 380050) and chow fed (JAX 380056) mice were obtained from The Jackson Laboratory and maintained on 60% high fat diet (Research Diets, D12492) or chow diet (8664 Harlan Teklad, 6.4% wt/wt fat), respectively, for three weeks before sacrifice. Mice were maintained under a 12 hr light/12hr dark cycle at constant temperature (23ºC) with free access to food and water.

>>> Submitter declares that the human samples' raw data will be deposited in dbGaP due to patient privacy concerns. <<<

first: Evan

last: Rosen

first: Linus

last: Tsai

first: Margo

middle: P

last: Emont


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Bat3-/- BMDC Transcriptomes II

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: BMDC mRNA profiles of wild type (WT) and Bat3-/- mice


title: Early changes in the immune microenvironment during oral tumorigenesis reveal an unexpected protective role of M2 macrophages in oral potentially malignant disorders

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

summary: Understanding the dynamics of the immune microenvironment is critical to the development of immuno-prevention strategies for the prevention of oral potentially malignant disorders transformation to oral squamous cell carcinoma (OSCC). We generated gene expression profiles of the microdissected epithelial and stromal compartments normal mucosa, hyperplasia, dysplasia and invasive tumors in the 4-nitroquinolein (4-NQO) murine model of oral carcinogenesis. Most gene expression changes were observed in the stromal compartment and related to immune biological processes. Immune cell deconvolution identified infiltration by the macrophage population as the most important quantitatively especially at the stage of dysplasia. In 86 patients with oral leukoplakia, three M2 macrophages signatures were independently associated and highly predictive of improved oral cancer-free survival.

overall_design: We generated gene expression profiles of the microdissected epithelial and stromal compartments normal mucosa, hyperplasia, dysplasia and invasive tumors in the 4-nitroquinolein (4-NQO) murine model of oral carcinogenesis. Genes differentially expressed at each step of transformation were defined. Immune cell deconvolution and enrichment scores various biological processes including immune-related ones were computed. Immunohistochemistry was performed to characterize the immune infiltrates by T-cells (T-cells CD3+, helper CD4+, cytotoxic CD8+, regulatory FoxP3+), B-cells (B220+) and macrophages (macrophages F4/80+, M1 iNOS+, M2 CD163+) at each histological step. Enrichment of three independent M2 macrophages signatures were computed in 86 oral leukoplakia with available clinical outcome.

first: Jebrane

last: Bouaoud

first: Antonin

last: Tortereau

first: Sandra

last: Boyault

first: Lucas

last: Michon

first: Pierre

last: Saintigny


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Bat3-/- BMDC Transcriptomes III


title: Physical interaction with antigen presenting cells primes a T helper tumor lineage

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Cellular interactions in the tumor microenvironment (TME) drive T cell effector function, or dysfunction, and define a primary mechanism to target anti-tumor T cell immunity. Currently, the interactions that shape T cell function in the TME remain poorly understood. Here, we mapped the molecular programs of T and antigen-presenting cell interactions in human early non-small cell lung carcinoma lesions by physically interacting cell (PIC) sequencing. PIC-seq and imaging identified that in the TME, but not normal lung, PICs are enriched in clonally expanded CD4+PD-1+CXCL13+ T cells, expressing a unique combination of checkpoint molecules, transcription-factors, and cytokines, defining a novel T helper tumor-specific (Tht) program, conserved across cancer types. In vitro and in vivo genetic models of antigen specificity confirmed that the Tht prevalence in TME PICs is driven by tumor-antigen presentation of dendritic cells. Our study highlights CD4+ T-dendritic cell physical interaction as a key factor regulating the TME.

overall_design: Transcriptional profiling of thousands of single cells and doublets (PIC) of interacting T and dendritic cells from both human tumors and mouse tumor models

first: Miriam

last: Merad

first: Amos

last: Tanay

first: Merav

last: Cohen

first: Amir

last: Giladi

first: Pauline

last: Hamon

first: Baoguo

last: Li

first: Oren

last: Barboy

first: Mor

last: Zada


title: Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [RNA-Seq]

city: Barcelona

first: Fatima

last: Gebauer

address: C/Dr. Aiguader, 88

department: Gene Regulation, Stem cells and Cancer Programme

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: We show that the RNA-binding protein CSDE1/UNR promotes oncogene-induced senescence (OIS) in primary mouse keratynocytes challenged by over-expression of H-RASv12. Depletion of CSDE1 leads to senescence bypass, cell immortalization and tumor formation. Combining individual nucleotide cross-linking and immunoprecipitation (iCLIP), RNA-seq and polysome profiling followed by functional studies, we identify targets regulated by CSDE1 and uncover the downstream molecular mechanisms.

overall_design: RNA-seq from iCLIP samples extracts.

first: Rosario

last: Avolio

first: Sarah

last: Bonnin


title: Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [RNA-Seq-sh]

overall_design: RNA-seq from H-Ras infected PMK upon CSDE1 depletion was performed to identify the CSDE1 targets regulated at the steady state level during OIS.


title: Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [i-CLIP]

overall_design: iCLIP combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of CSDE1 in primary mouse keratinocytes in resting conditions or upon oncogene-induced senescence.


title: Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [polysome profiling]

overall_design: Polysome Profiling-seq from H-Ras infected PMK upon CSDE1 depletion was performed to identify the CSDE1 targets regulated at the level of translation during OIS.


title: Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence


title: Single cell RNA sequencing of ascending aorta in smooth muscle-targeted elastin deletion

status: Public on Jan 10 2022

city: Saint Louis

first: Chien-Jung

last: Lin

state: MO

address: 660 Euclid Ave CB 8228

department: Cell Biology and Physiology

institute: Washington University School of Medicine in St. Louis

summary: We performed single cell RNA sequencing (scRNA-seq) on ascending aortae from P8 TaglnCre;Elnf/f mice or controls.

overall_design: Ascending aortae from mixed background P8 TaglnCre;Elnf/f mice (pooled 4 aortae, mixed sex) and littermate controls (pooled 3 aortae from 1 Elnf/f and 2 Elnf/+, mixed sex) were dissected out. Single cell suspension was prepared by enzymatic digestion and fluorescence-activated cell sorting, and subjected to 10X Chromium 3' v3 library preparation. Sequencing was performed with a Illumina NovaSeq sequencer.

first: Bridget

middle: M

last: Hunkins

first: Robyn

last: Roth

first: Chieh-Yu

first: Jessica

middle: E

last: Wagenseil

first: Robert

last: Mecham


title: RNA sequencing of chronic graft versus host disease skin lesions defines shared and unique inflammatory pathways characterizing lichen planus and morphea

city: Paris

first: Jean-David

last: Bouaziz

address: Hôpital Saint-Louis 1, avenue Claude Vellefaux

department: Skin Research Center Service de Dermatologie

institute: INSERM U976

summary: Providing new insights into the mechanisms of each skin cGVHD subtype to discover new potentially efficient drugs.

overall_design: Skin mRNAseq analysis of recipients and controls included in cutaneous cGHVD study.Were considered lichen planus cGVHD (n=8), morphea cGVHD and healthy skin (referred as controls) (n=6).

first: Habib

last: Zouali


title: A Bacillus anthracis RNA binding protein post-transcriptionally regulates two component signaling through RNA turnover [RIP-Seq]

city: Nashville

first: Hualiang

last: Pi

state: TN

address: 1161 21st Avenue South

institute: VUMC

summary: Formaldehyde cross-linking RNA immunoprecipitation coupled with illumina sequencing (fRIP-seq) was performed to pinpoint the direct RNA targets of KrrA using a FLAG-tagged KrrA construct that is driven by a constitutive promoter Plgt (pOS1.PlgtkrrA-FLAG).

overall_design: Two different growth conditions were implemented: LB and LB supplemented with ‘205. Two controls were included to ensure specificity: (i) a WT strain that does not harbor the FLAG-tagged KrrA construct as a nonspecific background control, and (ii) RNA extracted from WT cells harvested before immunoprecipitation, serving as an input RNA control.

first: Eric

last: Skaar


title: A Bacillus anthracis RNA binding protein post-transcriptionally regulates two component signaling through RNA turnover [RNA-Seq]

summary: To uncover the effects of KrrA regulation on gene transcription and define the bacterial response imposed by this regulation, a transcriptomic study was carried out in which Bacillus anthracis krrA was compared to WT in two growth conditions: LB in the presence or absence of ‘205.

overall_design: Two strains of Bacillus anthracis (WT and krrA deletion mutant) in the presence or absence of 50 µM ‘205 were compared. RNA was isolated from each of the strains and conditions in triplicte and RNA sequencing performed. Transcriptomes and changes in expression patters were compared across each samples using CLC genomics workbench.


title: A Bacillus anthracis RNA binding protein post-transcriptionally regulates two component signaling through RNA turnover


title: Next generation sequencing contributes to the quantitative analysis of AGEs stimulated HK-2 cell transcriptome

city: guangzhou

first: Ming

last: WANG

state: Guangdong

address: 1838 Guangzhou Avenue North, Baiyun District

country: China

institute: School of Traditional Chinese Medicine, Southern Medical University

summary: We sequenced the HK-2 gene expression profile stimulated by ages by high-throughput RNA analysis. Select Ctrl group and ages group, Differentially expressed genes (DEGs) were analyzed. Under the screening condition of fold change greater than or equal to 2, P < 0.05. We obtained 284 up-regulated genes and 193 down-regulated genes. It can be seen that there are obvious gene differences between Ctrl group and ages group (Fig. 3a). Gene ontology analysis (go) was completed. Through goseq software, the biological process of quantitative distribution of rich differential genes was intuitively reflected (BP), molecular function (MF) and cell composition (CC). In addition, in order to explore the impact of ages on cell pathways, we used the Kyoto Encyclopedia of biology to analyze the significantly rich metabolic pathways. There are 221 differentially expressed genes in Ctrl group and ages group. A total of 276 pathways have been established, of which 46 pathways have p < 0.05, and the first 20 pathways are shown in Figure 2C.

overall_design: shCtrl-Normal group，shCtrl-AGEs group，shJMJD1A-AGE group

last: Wang

first: Shaoting


title: Single-cell RNA sequencing of human iPSC-derived lacrimal gland-like organoids

city: Osaka

first: Ryuhei

last: Hayashi

state: US and Canada only

address: 2-2 Yamadaoka, Suita

department: Graduate School of Medicine

country: Japan

institute: Osaka University

summary: Gene expression profile of human iPSC-derived lacrimal gland-like organoids.

overall_design: TenX Genomics Chromium and Illumina NovaSeq 6000 were used for preparing and sequencing the cDNA libraries of human iPSC-derived lacrimal gland-like organoids in three time points (day 0, day10, and day20).

first: Yuki

last: Ishikawa

first: Toru

last: Okubo

first: Yuji

last: Kudo

first: Sung-Joon

last: Park


title: RNAseq data of differentiated vs undifferentiated tonsil-derived mesenchymal stem cells into parathyroid-like cells seeded at 100% confluency

city: Seoul

first: Sung-Chul

last: Jung

address: 25, Magokdong-ro 2-gil, Gangseo-gu

department: Department of Biochemistry

country: South Korea

institute: Ewha Womans University

summary: High-cell density/confluency leads to contact inhibition of proliferation, as seen in the majority of epithelial cells, and is associated with the initiation of differentiation. To determine potential effect of  In this regard, we analyzed transcriptomes using RNAseq, then performed a large-scale expression profiling of T-MSCs and performed a comparison between un-differentiated T-MSCs and T-MSC-PTHCs. Genes with a mean fold change of > 1.5 (T-MSCs vs. T-MSC-PTHCs) with p < 0.05 were analyzed using gene ontology enrichment analysis.RNAseq analysis showed that total of 228 genes were found to be significantly changed. Of them, the genes involved in the proliferation contributed 28% (total count of 63 genes) was the largest of the altered gene population followed by the genes involved in neurogenesis (30 counts; 13%) and extracellular matrix (16 counts; 7%). Among the genes in differentiation, WNT2 showed the highest fold-increase (2.8-fold) in the T-MSC-PTHCs compared to un-differentiated T-MSCs. When KEGG pathway analyses were performed, we found WNT signaling and stem cell pluripotency-regulating pathways as the pathways, where the WNT2 was involved in. This indicates that the differentiation of the T-MSCs could have induced through both of these pathways.

overall_design: Examinations of the genes involved in the differentiation of the TMSCs into parathyroid-like cells

first: Kim

last: Ji Yeon

first: Park

last: Saeyoung

first: Oh

last: Se-Young

first: Jung

last: Sung-Chul


title: bHLH cascade regulate 24-nt phasiRNA biogenesis in maize anther

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Anthers are the male reproductive floral organs, but loss of the 24-nt class of phased small-interfering RNAs (phasiRNAs) may confer temperature-sensitive male sterility in maize. 24-nt phasiRNAs from 176 loci are abundant coordinately in fertile maize anthers after the last periclinal divisions are complete,  all four wall layers are formed, and meiosis has initiated in the pollen mother cells. In this study, we found male sterile maize ms23, ms32, and bhlh122 mutants with various degrees of tapetal defects lack 24-PHAS mRNA precursors and 24-nt phasiRNAs, which were not affected in another male sterile mutant, bhlh51. Transcription from  most of 24-PHAS loci depends on bHLH122 while  bHLH122 and Dcl5 transcription depends on both Ms23 and Ms32. Multiple lines of evidence suggest that 24-nt phasiRNAs biogenesis is primarily controlled at multiple layers by MS23 and MS32, with distinctive action on 24-PHAS transcription by bHLH122, creating a transcription factor cascade in maize tapetal cells.

overall_design: Transcriptome and small RNA profiling of maize bhlh male sterile anthers by RNA- and sRNA-seq, comparing to fertile anthers

first: Virginia

last: Walbot

first: Guo-Ling

first: Chong

last: Teng


title: Hypoxic culture maintains cell growth of the primary human valve interstitial cells with stemness

city: Toon

first: Tomohisa

last: Sakaue

state: Ehime

address: Shitsukawa

department: Proteo-Science center

institute: Ehime University

summary: Characterization of aortic valve interstitial cells (VICs) maintained in an optimized culture is es-sential for understanding the molecular mechanism underlying aortic valve stenosis. Here, we propose 2% hypoxia as an optimum VIC culture condition. Harvested leaflets from patients with aortic valve regurgitation were digested using collagenase and VICs were cultured under the 2% hypoxic condition. Significant elevation in VIC growth was observed in the 2% hypoxia group (hypo-VICs), compared to the normoxia group (normo-VICs). RNA-sequencing revealed that downregulation of oxidative stress-marker genes (such as superoxide dismutase) and upregula-tion of cell cycle accelerators (such as cyclins) were detected in hypo-VICs.

overall_design: To characterize VICs cultured in hypoxic condition (hypo-VICs), we examined the gene expression profiles of hypo-VICs using RNA-sequencing and evaluated their ability to differentiation into osteoblasts.

first: Kaho

last: Kanno

first: Hironoti

last: Izutani


title: The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2

city: Bangkok

first: Praewa

last: Suthapot

address: 272 Rama VI Road

department: Department of Biochemistry, Faculty of Science

country: Thailand

institute: Mahidol University, Thailand

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Unique angiogenesis from cardiac arterioles during pericardial adhesion formation

department: Cardiovascular and Thoracic Surgery

summary: The molecular mechanisms underlying postoperative pericardial adhesions are poorly understood. We aimed to unveil the temporal molecular and cellular mechanisms underlying tissue dynamics during adhesion formation, including inflammation, angiogenesis, and fibrosis. Using a previously established murine model, we successfully visualized the cell-based tissue dynamics during pericardial adhesion and discovered a unique angiogenic process for the induction of fibrosis. Masson’s trichrome staining revealed that collagen production was promoted from the fourth day after cardiac injury inflicted by talc injection into the pericardial cavity. A high degree of adhesion formation was observed during the stages in which collagen production was promoted. Histological analysis demonstrated that arterioles excessively sprouted from pericardial tissues in mice as well as in humans. The combination of RNA-seq and histological analyses revealed that hyperproliferative endothelial cells and myofibroblasts appeared in cytokine-exposed sprouting vessels and adhesion tissues, but not in quiescent vessels in the heart. Additionally, vascular smooth muscle cells were dedifferentiated from the contractile to the synthetic phenotype in heart tissue, and matrix metalloproteinase-dependent tissue remodeling in the pre-angiogenic stage potentially contributed to neovascularization and fibrosis in the pericardial cavity. Our findings will assist in developing prevention strategies for pericardial adhesions by targeting the recruitment of vascular cells from heart tissues.

overall_design: To elucidate the molecular mechanism underlying pericardial adhesion, RNA sequencing using Illumina Miseq was performed on samples obtained from heart and adhesion tissues.

first: Kenji

last: Namiguchi


title: Identification of DDX5 and DDX17 target genes in human ECCs and their neural derivartives

summary: Neural cell fate specification is a highly regulated process in which stem cells sequentially possess the transcriptional profile changed and give raise to particular cell lineages such as neuron and glial cells. The NTERA2 cell line is one of the well-characterized hEC cells that can be used as a model system for identifying the regulatory network during human pluripotent stem cells differentiated toward the neural lineage. It has been demonstrated that DDX5 and DDX17, as transcriptional co-regulator, can play a role in various cellular mechanisms depending on their interaction with the different types of transcription factors. Here, we performed ChIP-seq for DDX5 and DDX17 to identify their preferential binding targets during stage transition from pluripotent to neural cell lineage.

overall_design: Chromatin immunoprecipitation and sequencing (ChIP-seq) of the RNA helicases DDX5 and DDX17 were prepared in triplicates from hPSC NTERA2 cultures (-RA) and retinoic acid-induced neural cultures differentiated for 14 days (+RA). ChIP-seq of DDX5 in the undifferentiated culture was previously submitted to the GEO database under the accession number GSE58641.

first: Patompon

last: Wongtrakoongate

first: Gary

last: Felsenfeld


title: Single cell RNAseq of mouse colon stroma during chronic DSS and homeostatic condition

first: Alok

last: Jaiswal

state: MASSACHUSETTS

institute: The Broad Institute of MIT and Harvard

summary: We implemented a murine model of intestinal inflammation based on oral administration of multiple cycles of low dose dextran sulfate sodium (DSS) to induce epithelial injury and ECM deposition. Mice were subjected to 3 repetitive cycles of DSS displayed progressive accumulation of immune cell infiltrates associated with excessive deposition of collagen fibers. Lamina propria cells from water-fed and DSS-fed mice were isolated using enzymatic digestion,  and enriched for stromal cells by FACS using antibodies excluding hematopoietic cells (CD45), epithelial cells (EpCAM), and erythrocytes. Prepared single cell suspensions were then profiled using the 10x Chromium V2 droplet-based single cell RNA sequencing platform. Tissues were collected from proximal and distal colon.

overall_design: A total of 3 female mice (12 weeks old) were processed for each treatment group and analyzed by single-cell RNA-seq. Female mice were utilized because they were able to withstand 3 cycles of DSS, whereas males exhibited morbidity.

first: Guadalupe

last: Jasso

first: Daniel

last: Graham

first: Ramnik

last: Xavier


title: Transcriptional impact of EGFR-AT1R-crosstalk  (Transient transfection of AT1R in HEK293 cells)

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

summary: The impact of AT1R and EGFR on SRF transcriptional activity, signaling pathways and transcriptome regulation were investigated in HEK293, HK-2 and vascular smooth muscle cells, applying reporter gene, protein and mRNA expression techniques as well as RNAseq followed by bioinfor-matic analysis.

overall_design:
RNASequencing of HEK293 cells *transiently* tranfected with human angiotensin II receptor type 1 (AT1R) and stimulated for 6 and 24h with either EGF, angiotenin II or EGF+angiotensin II.
Raw RNASequencing data were treated successively with HISAT2 (mapping) and featureCounts (counting).

first: Michael

last: Gekle

first: Stefanie

last: Hübschmann

first: Sigrid

last: Mildenberger

first: Sindy

last: Rabe

first: Barbara

last: Schreier


title: The homeotherm-conserved protein CGGBP1 connects heat stress to chromosomal fusions

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

type: Methylation profiling by high throughput sequencing

summary: We report that heat stress induces chromosomal fusion events in cell culture. We describe the findings first using normal primary fibroblasts [Coriell Cell Repository GM02639] and subsequently apply it to a system of HEK293T stable lines called CT and KD [described in PMID 31547883]. The stable line CT stands for Control shRNA and KD stands for a knockdown of human CGGBP1 using specific shRNA [Origene Lentiviral system TL313955V]. Our results suggest that as measured by the frequency of chromosomal fusions, the CGGBP1 knockdown in KD, when compared to CT, imitates the effects of heat stress. Further, ChIP-sequencing for TP53BP1 show genome-wide misdirected repairs at repeat flanks in KD as compared to CT. We show that CGGBP1 depletion and heat give rise to chromosomal fusions due to overlapping mechanisms that involve misdirected repair in the flanks of repeats genome-wide.

overall_design: Genomic DNA was isolated and MeDIP-seq was perforrmed for GM01391-CT and -KD as described elsewhere (PMID: 32727353 and GSE145300) on IonTorrent platform. For genotype identification, parental DNA from fibroblasts (GM01392 and GM01393 from Coriell Repository) were also sequenced on the same platform. The analysis parameters for read QC, alignment, variant calling were as described in PMID: 32727353.

first: Subhamoy

last: Datta

first: Manthan

last: Patel

first: Divyesh

first: Sukesh

last: Kashyap


title: Transcriptional impact of EGFR-AT1R-crosstalk

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


title: PHLPP1 promotes lipid accumulation through AMPK/ChREBP dependent lipid uptake and fatty acid synthesis pathway

status: Public on Jan 09 2022

city: Hyderabad

first: Kishore

last: Parsa

state: TELANGANA

address: University of Hyderabad Campus, Gachibowli

department: CIMPS

institute: Dr. Reddy's Institute of Life Sciences

summary:
Methods: We performed mRNA sequence analysis by deep sequencing, in triplicate, using Illumina HiSeq to assess the impact of PHLPP1 knockdown in regulating gene expression in RAW 264.7 cells treated with/without OxLDL. The transcriptome libraries were constructed using the NEB adapters and were sequenced on at 150 nucleotide read length using the paired-end chemistry. The raw reads were subjected to Adapter and low-quality reads removal by Trimmomatic -0.36v. The raw reads were subjected to contamination [structural RNA / low complexity sequences] removal by mapping with bowtie 2-2.2.1. The decontaminated data set was mapped to the mouse genome. Reads mapping to gene list were counted using feature count module of sub reads package. The read counts were normalized in DESeq2-3.5, and subject to differential expression analysis. Differentially expressed genes were selected based on log2-ratio change with p-value <0.05 (Student’s t-test, unpaired). Hierarchical clustering was performed with the programs Cluster (uncentered correlation; average linkage clustering) and Treeview.
Results: To gain a deeper understanding of the role of PHLPP1 in lipid metabolism in macrophages, we performed mRNA Seq analysis to assess the gene expression changes in a mouse macrophage cell line. The experiment has been carried out in triplicates. Alignment of the reads showed 97% alignment to the reference mouse genome. Identification of the differentially expressed genes were then carried out by DESeq2 version 1.2.10 with stringent criteria (FDR <0.05% with 2 fold up and down regulation) which reveals in control treated vs. control (121-down, 396-Up), Test vs. Control - (326-down, 569 Up) and Test treated vs. control treated (1314-down, 1328 up) of DEG to be altered in expression respectively.
Inference: RNA-seq analysis revealed that PHLPP1 knockdown parallel with OxLDL treatment resulted in diminished expression profile of cholesterol biosynthesis and lipid metabolism genes.

overall_design:
Effect of PHLPP1 knockdown on OxLDL treated and untreated RAW 264.7 macrophage cell transcriptome.

**Submitter declares that the raw data files have been lost.**

middle: V

first: B

last: Keerthana

first: Madhumohan

middle: R

last: Katika


title: Comparison of RNA sequencing profiles in domed and flat colonies of ocular surface epithelial stem cells induced from human pluripotent stem cell

city: Kizugawa

first: Toru

last: Okubo

state: Kyoto

address: 6-5-4 Kunimidai

department: Basic Research Development Division

institute: Rohto Pharmaceutical

summary: RNA-seq analysis revealed that genes associated with lacrimal gland development, such as BARX2, SIX1, SIX2, SOX9, and KRT15, were upregulated in domed colonies compared to flat colonies. In flat colonies, mucosal epithelial keratin, KRT13 and the corneal epithelial progenitor cell markers, CDH2 and NGFR were up-regulated, along with YAP1 and its downstream genes, CTGF and CYR61, which are involved in epithelial development.

overall_design: RNA sequencing profiles of domed and flat colonies of ocular surface epithelial stem cells

first: Ryuhei

last: Hayashi


title: Partial monosomy 21 mirrors gene expression of trisomy 21 in a patient-derived neuroepithelial stem cells model

city: Stockholm

first: Jakob

last: Schuy

address: Akademiska stråket 1

country: Sweden

institute: Karolinska Institutet

summary: Induced pluripotent stem cells (iPSCs) from patients are an attractive disease model to study tissues with poor accessibility such as the brain. Using this approach, we and others have shown that trisomy 21 results in genome-wide transcriptional dysregulations. The effects of loss of genes on chromosome 21 is much less characterized. Here, we use patient-derived neural cells from an individual with neurodevelopmental delay and a ring chromosome 21 with two deletions spanning 3.8 Mb at the terminal end of 21q22.3, containing 60 protein-coding genes. To investigate the molecular perturbations of the partial monosomy on neural cells, we established patient-derived iPSCs from fibroblasts retaining the ring chromosome 21, and we then induced iPSCs into neuroepithelial stem cells (NESCs). RNA-Seq analysis of NESCs with the ring chromosome revealed downregulation of 18 genes within the deleted region together with global transcriptomic dysregulations when compared to euploid NESCs. Since the deletions on chromosome 21 represent a genetic “contrary” to trisomy of the corresponding region, we further compared the dysregulated transcriptomic profile in with that of two NESC lines with trisomy 21. The analysis revealed opposed expression changes for 23 genes on chromosome 21 as well as 149 non-chromosome 21 genes. Taken together, our results bring insights into the effects on the global and chromosome 21 specific gene expression from a partial monosomy of chromosome 21qter during early neuronal differentiation.

overall_design: RNA-Seq on NESCs, 6 samples (3x controls, 2x Down Syndrome, 1x RD_P26) in triplicates

first: Jesper

last: Eisfeldt

first: Maria

last: Pettersson

first: Niloofar

last: Shahrokhshahi

first: Mohsen

last: Moslem

first: Daniel

last: Nilsson

first: Niklas

last: Dahl

first: Mansoureh

last: Shahsavani

first: Anna

last: Falk

last: Lindstrand


title: Transcriptional impact of EGFR-AT1R-crosstalk (Stable transfection of AT1R  in HEK293 cells)

first: Virginie

last: Dubourg

overall_design:
RNASequencing of HEK293 cells *stably* tranfected with human angiotensin II receptor type 1 (AT1R) and stimulated for 6 and 24h with either EGF, angiotenin II or EGF+angiotensin II.
Raw RNASequencing data were treated successively with HISAT2 (mapping) and featureCounts (counting).

first: Michael

last: Gekle

first: Stefanie

last: Hübschmann

first: Sigrid

last: Mildenberger

first: Sindy

last: Rabe

first: Barbara

last: Schreier


title: Transcriptomic and functional analysis of Ab1-42 oligomer-stimulated human monocyte-derived microglia-like cells

city: Amsterdam

first: Vanessa

last: Donega

address: Boelelaan 1108

department: Anatomy and Neuroscience

country: Netherlands

institute: Amsterdam UMC

summary: Dysregulation of microglial function contributes to Alzheimer’s disease (AD) pathogenesis. Several genetic and transcriptome studies have revealed microglia specific genetic risk factors, and changes in microglia expression profiles in AD pathogenesis, viz. the human-Alzheimer’s microglia/myeloid (HAM) profile in AD patients and the disease-associated microglia profile (DAM) in AD mouse models. The transcriptional changes involve genes in immune and inflammatory pathways, and in pathways associated with Aβ clearance. Aβ oligomers have been suggested to be the initial trigger of microglia activation in AD. To study the direct response to Aβ oligomers exposure, we assessed changes in gene expression in an in vitro model for microglia, the human monocyte-derived microglial-like (MDMi) cells. We confirmed the initiation of an inflammatory profile following LPS stimulation, based on increased expression of IL1B, IL6, and TNFα. In contrast, the Ab1-42 oligomers did not induce an inflammatory profile or a classical HAM or DAM profile. Interestingly, we observed a specific increase in the expression of metallothioneins in the Aβ1-42 oligomer treated MDMi cells. Metallothioneins are involved in metal ion regulation, protection against reactive oxygen species, and have anti-inflammatory properties. In conclusion, our data suggests that Aβ1-42 oligomers may trigger a protective response both in vitro and in vivo.

overall_design: Bulk RNAseq analysis on MDMi cells stimulated with AB1-42 oligomers, LPS, PBS and vehicle.  Libraries were de-multiplexed and raw reads were aligned to the hg19 human RefSeq transcriptome with Burrows-Wheeler Aligner (BWA) (Li and Durbin, 2010). Duplicate reads and reads that mapped equally well to multiple locations were discarded. The quality control, normalization, and identification of differentially expressed genes were done with DESeq2, an R (version 3.6.3) based package (Love MI et al 2014).

first: Tamar

last: Smit

first: Paul

last: Ormel

first: Jacqueline

last: Sluijs

first: Lianne

last: Hulshof

first: Jinte

last: Middeldorp

first: Lot

last: de Witte

first: Elly

last: Hol


title: Transcriptome profiles of liver biopsy tissues before and after cenicriviroc treatment in patients with non-alcoholic steatohepatitis

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Non-alcoholic steatohepatitis (NASH) is a sharpy emerging cause of liver fibrosis and cancer that leads to poor prognosis of the patients. A dual CCR2/CCR5 inhibitor, cenicriviroc, was tested in a phase IIb CENTAUR trial for its efficacy to reduce fibrosis.

overall_design: Liver biopsy tissues were obtained before and after 1-year treatment with cenicriviroc 150mg once daily from fibrotic NASH patients who showed improvement (n=10) or no improvement (n=9) of fibrosis after the therapy, and genome-wide transcriptome profiles were generated by RNA-Seq.

first: Shijia

last: Zhu

first: Tongqi

last: Qian

first: Naoto

last: Fujiwara


title: Pharmacologic IRE1/XBP1s Activation Promotes Systemic Adaptive Remodeling in Obesity

status: Public on Jan 08 2022

city: La Jolla

first: R. Luke

last: Wiseman

state: CA

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

summary: RNA was isolated from livers of DIO mice treated with IXA4 or vehicle (n=4 per condition) using the Zymo Research Quick-RNA Miniprep Kit according to the manufacturer’s instructions. RNA sequencing was performed by BGI Americas on the BGI proprietary platform (DNBseq), providing single-end 50 bp reads at 20 million reads per sample. Alignment of the sequencing data to the Mus musculus MGSCv37 NCBI build 37.2 was performed using DNAstar Lasergene SeqManPro. Assembled data were then imported into ArrayStar 12.2 with QSeq (DNAStar Inc) to quantify gene expression and normalized reads per kilobase million (RPKM). Differential expression analysis and statistical significance calculations between conditions were assessed using DESeq in R using a standard negative binomial fit for the aligned counts data and are described relative to the indicated control

overall_design: Comparisons of the transcriptomes of livers from DIO mice treated with or without IRE1 activator, IXA4.

first: Aparajita

last: Madhavan

first: Bernard

last: Kok

first: Julia

last: Grandjean

first: Evan

last: Powers

first: Enrique

last: Saez

first: R

middle: L


title: Prevalence of inflammatory pathways over immuno-tolerance in peripheral blood mononuclear cells of recent-onset type 1 diabetes

city: Marseille

first: Pauline

last: Brochet

address: 13288 MARSEILLE cedex 09

summary: Background Changes in innate and adaptive immunity occurring in/around pancreatic islets had been observed in peripheral blood mononuclear cells (PBMC) of Caucasian T1D patients by some, but not all researchers. The aim of our study was to investigate whether gene expression patterns of PBMC of the highly admixed Brazilian population could add knowledge about T1D pathogenic mechanisms.  METHODS: We assessed global gene expression in PBMC from two groups matched for age, sex and BMI: 20 patients with recent-onset T1D (≤ 6 months from diagnosis, in a time when the autoimmune process is still highly active), testing positive for one or more islet autoantibodies and 20 islet autoantibody-negative healthy controls.  RESULTS: We identified 474 differentially expressed genes between groups. The most expressed genes in T1D group favored host defense, inflammatory and anti-bacterial/antiviral effects (LFT, DEFA4, DEFA1, CTSG, KCNMA1) and cell cycle progression. Several of the downregulated genes in T1D target cellular repair, control of inflammation and immune tolerance. They were related to T helper 2 pathway, induction of FOXP3 expression (AREG) and immune tolerance (SMAD6). SMAD6 expression correlated negatively with islet ZnT8 antibody. The expression of PDE12, that offers resistance to viral pathogens was decreased and negatively related to ZnT8A and GADA levels. The increased expression of long non coding RNAs MALAT1 and NEAT1, related to inflammatory mediators, autoimmune diseases and innate immune response against viral infections reinforced these data  CONCLUSIONS: Our analysis suggested the activation of cell development, anti-infectious and inflammatory pathways, indicating immune activation, whereas immune-regulatory pathways were downregulated in PBMC from recent-onset non-Caucasian T1D patients with a different genetic profile.

overall_design: RNA Extraction was done on PBMC. Whole genome expression analysis was conducted on 40 patients : 20 healthy controls and 20 with recent-onset T1D.

first: Aritania

middle: S

last: Santos

first: Edecio

last: Cunha-Neto

first: Nelson

last: Gonfinetti

first: Fernanda

last: Bertonha

first: Aurelie

last: Bergon

first: Carlos

last: Moreira-Filho

first: Christophe

last: Chevillard

first: Maria

last: Silva


title: RNA-Seq analysis of HL-60 AML cells resistant to daunorubicin or cytarabine

city: Montpellier

first: Guillaume

last: Bossis

address: 1919 Route de Mende

department: IGMM

institute: CNRS

summary: The Acute Myeloid Leukemia cell line HL-60 was rendered resistant to daunorubicin (DNR) or cytarabine (Ara-C) by continuous exposure to the drug up to concentrations of 30nM for DNR and 100nM for Ara-C. Transcriptomic analysis were then performed by RNA-Seq to compare the cell lines

overall_design: 3 biological replicates were performed for parental HL-60, Ara-C resistant (HRA) and DNR-resistant (HRD)

first: Mathias

last: Boulanger

first: Paolillo

last: Rosa


title: Gene expression differences between control and overexpressing U3 snoRNA in HPF

city: shanghai

first: Xin

last: Zhang

state: Shanghai

address: 450 tengyue road

department: Ophthalmology

institute: Yangpu Hospital, School of Medicine, Tongji University

summary: Comparison of endogenous gene expression differences between control and overexpressing U3 snoRNA in HPF.

overall_design: RNA was obtained from the two groups of HPFs overexpressing U3 snoRNA and their control cells for assessment of gene expression differences.

first: Yaping

last: Jiang

first: Yihui

last: Chen


title: Conventional NK cells and ILC1s do not influence pathogenesis of experimental glomerulonephritis

status: Public on Jan 07 2022

city: Hamburg

first: Jan-Eric

last: Turner

state: Hamburg

address: Martinistraße 52

department: III. Department of Medicine

institute: University Medical Center Hamburg-Eppendorf

summary: Innate lymphoid cells (ILCs) that express NK cell receptors (NCRs) and the transcription factor T-bet populate non-lymphoid tissues and are crucial in immune responses against viral infections and malignancies. Recent studies highlighted the heterogeneity of this ILC population and extended their functional spectrum to include important roles in tissue homeostasis and autoimmunity. Here, we provide detailed profiling of NCR+T-bet+ ILC populations in the murine kidney, identifying conventional NK (cNK) cells and type 1 ILCs (ILC1s) as the two major subsets. Induction of renal inflammation in a mouse model of glomerulonephritis did not substantially influence abundance or phenotype of cNK cells or ILC1s in the kidney. For functional analyses in this model, widely used depletion strategies for total NCR+ ILCs (αNK1.1 antibody application) and cNK cells (α-asGM1 serum application) were unreliable tools, since they were accompanied by significant off-target depletion of kidney NKT cells and CD8+ T cells, respectively. However, neither depletion of cNK cells and ILC1s in NKT cell-deficient mice, nor specific genetic deletion of cNK cells in Ncr1Cre/wt x Eomesfl/fl mice altered the clinical course of experimental glomerulonephritis. In summary, we show here that cNK cells and ILC1s are dispensable for initiation and progression of immune-mediated glomerular disease and advise caution in the use of standard antibody depletion methods to study NCR+ ILC function in mouse models.

overall_design: Three replicates of cNK cells and ILC1s were FACS sorted from total leukocytes isolated from the kidneys of naive B6 WT animals.

first: Constantin

last: Rickassel

first: Ann-Christin

last: Gnirck

first: Nikhat

last: Shaikh

first: Virginia

last: Adamiak

first: Alex

last: Waterhölter

first: Yakup

last: Tanriver

first: Katrin

last: Neumann

first: Tobias

last: Huber

first: Georg

last: Gasteiger

first: Ulf

last: Panzer


title: Three tissue resident macrophage subsets co-exist across organs with conserved origins and lifecycles

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

summary: Resident macrophages orchestrate homeostatic, inflammatory, and reparative activities. It is appreciated that different tissues instruct specialized macrophage functions. However, individual tissues contain heterogeneous subpopulations, and how these subpopulations are related is unclear. We asked whether common transcriptional and functional elements could reveal an underlying framework across tissues. Using single-cell RNA sequencing and random forest modeling, we observed that four genes could predict three macrophage subsets that were present in murine heart, liver, lung, kidney, and brain. Parabiotic and genetic fate mapping studies revealed that these core markers predicted three unique life cycles across 17 tissues. TLF+ (expressing TIMD4 and/or LYVE1 and/or FOLR2) macrophages were maintained through self-renewal with limited monocyte input; CCR2+ (TIMD4−LYVE1−FOLR2−) macrophages were almost entirely replaced by monocytes, and MHC-IIhi macrophages (TIMD4−LYVE1−FOLR2−CCR2−), while receiving modest monocyte contribution, were not continually replaced. Rather, monocyte-derived macrophages contributed to the resident macrophage population until they reached a defined upper limit after which they did not outcompete pre-existing resident populations. TLF+ macrophages were first to emerge in the yolk sac and early fetal organs. Fate mapping studies in the mouse and human single-cell RNA sequencing indicated that TLF+ macrophages originated from both yolk sac and fetal monocyte precursors. Furthermore, TLF+ macrophages were the most transcriptionally conserved subset across mouse tissues and between mice and humans, despite organ- and species-specific transcriptional differences. Here, we define the existence of three murine macrophage subpopulations based on common life cycle properties and core gene signatures, and suggest a common starting point to understand tissue macrophage heterogeneity.

overall_design: Single cell RNA sequencing of tissue macrophages in 5 tissues in mice.

first: Homaira

last: Hamidzada


title: Single-nucleus RNA sequencing of  gastrocnemius and plantaris muscles.

city: Kumamoto

first: Shin

last: Fujimaki

address: Honjo 2-2-1

department: IMEG

institute: Kumamoto University

summary: Skeletal muscle is composed of multinucleated myofibers, in which nuclei share the cytoplasm, and other cell types. Here, we performed single-nucleus RNA sequencing (snRNA-Seq) to determine the gene expressions in each nucleus in gastrocnemius and plantaris muscles collected from 12-week-old C57BL/6 wild-type mice. Our datasets also provided a basis for comparing gene expressions between myofibers and other cell types and discovering the novel cell populations in muscle tissues.

overall_design: Single-nucleus RNA sequensing of gastrocnemius and plantaris muscles of 12-week-old C57BL/6 wild-type mice.

first: Hiroshi

last: Nagahisa

first: Shingo

last: Usuki

first: Keiichiro

last: Yasunaga

first: Yusuke

last: Ono


title: The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes [sgRNA-seq]

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: In pluripotent cells, a delicate activation-repression balance maintains pro-differentiation genes ready for rapid transcription. The identity of transcription factors (TFs) that specifically repress pro-differentiation genes remains obscure. By targeting ~1,700 TFs with CRISPR loss-of-function perturbations, we found that ZBTB11 and ZFP131 are required to maintain pluripotency in mouse embryonic stem cells (ESCs). ZBTB11 and ZFP131 bind to pro-differentiation genes along with RNA Polymerase II and pausing factor NELF, but without Polycomb repression. Loss of ZBTB11 or ZFP131 leads to a decrease in NELF binding, an increase in H3K4me3, transcriptional upregulation of genes associated with three germ layers, and concomitant ESC differentiation. Together, our results suggest ZBTB11 and ZFP131 maintain pluripotency by pausing pro-differentiation genes transcription and present a generalizable framework to maintain cellular potency.

overall_design: Bulk RNA-seq was used to characterize gene expression in Wildtype, Zbtb10Δ, Zbtb11Δ, and Zfp131Δ cells grown in the presence of +2i+LIF or -2i+LIF.

first: Görkem

last: Garipler

first: Congyi

last: Lu

first: Alexis

last: Morrisey

first: Lorena

last: Lopez-Zepeda

first: Simon

last: Vidal

first: Begüm

last: Aydin

first: Matthias

last: Stadtfeld

first: Uwe

last: Ohler

first: Neville

last: Sanjana

first: Esteban

middle: O

last: Mazzoni


title: T-cell receptor repertoire in metastatic colorectal cancer during chemotherapy

city: Tao-Yuan

first: Ian Yi-Feng

last: Chang

state: Type below ...

address: 259 Wen-Hwa 1st Road, Kwei-Shan

department: Molecular Medicine Research Center

country: Taiwan

institute: CHANG GUNG UNIVERSITY

summary: In this study, we aimed to determine the characteristics and clinical significance of the TCR repertoire in patients with unresectable metastatic colorectal cancer (mCRC).

overall_design: Analysis of TCR sequences from 103 unresectable metastatic colorectal cancer (mCRC) patient blood samples.

first: Chia-Yu

last: Yang


title: POLIE suppresses telomerase-mediated telomere G-strand extension and helps ensure proper telomere C-strand synthesis in trypanosomes

city: CLEVELAND

first: Bibo

last: Li

state: OH

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease

institute: CLEVELAND STATE University

summary: T. brucei regularly switches its major surface antigen, VSG, to evade the mammalian host immune response. VSGs are expressed from subtelomeric loci in a strictly monoallelic manner. We identify POLIE as an intrinsic component of the T. brucei telomere complex and examined the effect of POLIE depletion on VSG expression regulation by RNAseq.

overall_design: Tet-inducible POLIE RNAi strains were established. Total RNA was isolated from POLIE RNAi cells before or 30 hr after the induction of POLIE RNAi. Two biological replicates were included. RNA samples were sent to Novogene for subsequent experiments. Poly(A) RNA was purified for generating cDNA library and paired-end sequencing was done using Illumina. Gene expression profiles were compared between the induced and uninduced cells by differential gene expression analysis.

first: M

last: Rabbani

first: Maiko

last: Tonini

first: Marjia

last: Afrin


title: The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes [scRNA-Seq]

first: Shaun

last: Mahony

overall_design: Single-cell RNA-seq was used to characterize gene expression in mixed populations of mES cells containing H2B::GFP expressing wildtype cells and Zbtb11 or Zfp131 knockout cells.


title: Notch2 deficiency prevents muscle atrophy induced by mechanical unloading and diabetes.

first: Shin

last: Fujimaki

summary: Notch signaling plays essential roles in maintenance of muscle stem cell pool. We found that Notch2, but not Notch1 and Notch3, is expressed in fully differentiated myofibers. To study the specific role of Notch2 in adult myofibers, we generated muscle-specific Notch2-knockout mice. Here, we showed that muscle-specific Notch2 deficiency prevented muscle atrophy induced by hindlimb unloading and diabetes millitus. RNA sequencing analysis revealed that the loss of Notch2 gene in myofibers inhibited gene responses to unloading and diabetes. Especially, several FoxO-target genes and atrogenes were upregulated in wildtype muscles but not in Notch2-deficient muscles by unloading and diabetes. Thus, our characterization of muscle-specific Notch2-knockout mice indicates that Notch2 acts as a regulatory factor of skeletal muscle plasticity and could be a therapeutic target of muscle atrophy.

overall_design: mRNA profiles of gastrocnemius muscle tissues obtained from WT and Notch2-mKO mice under unloading, diabetic, or control condition.

first: Yusuke

last: Ono


title: The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes

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

overall_design: Refer to individual Series


title: Organelle dysfunction upon asrij depletion causes aging-like changes in mouse hematopoietic stem cells

status: Public on Jan 06 2022

city: Bangalore

first: Maneesha

last: Inamdar

state: Karnataka

address: JNCASR, Jakkur, Bangalore.

department: Molecular Biology and Genetics Unit (MBGU)

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

summary: Asrij deletion in mice causes loss of HSC quiescence, myeloid skewing, reduced p53 and increased DNA damage, features attributed to aged hematopoietic stem cells (HSCs). To identify the pathways and processes driving the observed HSC aging-like phenotypes upon asrij depletion and to compare the asrij KO transcriptome with aged wild type HSCs, we performed RNA-seq gene expression profiling of Lin- Sca-1+ c-Kit+ CD150+ CD48- stem cells isolated from asrij KO or asrij floxed (control) mouse bone marrow. Our results identify Asrij as a potential driver of aging-like alterations in HSCs and the RNA-seq based transcriptome could help identify additional aging biomarkers and develop strategies to rejuvenate aged HSCs or prevent premature HSC aging.

overall_design: This dataset contains RNA-seq experiments for four replicates of long-term HSCs isolated from asrij floxed or asrij KO mice.

first: Saloni

last: Sinha


title: Mitochondrial respiration maintains autophagy to support stress resistance in quiescent cells

city: Vestec by Prague

first: Jakub

last: Rohlena

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, CAS, v.v.i.

summary: Mitochondrial oxidative phosphorylation (OXPHOS) generates ATP and is required for pyrimidine nucleotide synthesis during proliferation. In contrast, the role of OXPHOS in post-mitotic cells, beyond its contribution to ATP production, is less understood. Here, we show that in non-proliferating cells, OXPHOS ensures protection against oxidative stress by sustaining autophagy. Autophagy is suppressed and oxidative stress resistance is compromised in OXPHOS-deficient non-proliferating cells in vitro and in TFAM knockout mice in vivo, while attenuation of autophagy in OXPHOS-functional cells phenocopies the effects of OXPHOS deficiency. Mechanistically, the regulation of the autophagy / stress response by OXPHOS does not require changes in gene expression, AMPK/mTOR1/ULK1 signaling or NADH levels. Instead, OXPHOS maintains ROS levels to prevent activation of ATG4, a ROS-activated inhibitor of autophagy. We propose that protection against oxidative stress via the ROS-ATG4 axis is a novel function of mitochondrial respiration in non-proliferating cells that may have consequences for cancer therapy and beyond.

overall_design: Cultured Ea.hy926 cells, parental (Eahy) and OXPHOS-deficient (Rho0), were grown to confluence and 4 biological replicates were collected for bulk RNA-seq analysis.

first: Silvia

last: Novais

first: Pavel

last: Abaffy

first: Shawez

last: Khan


title: Next Generation Sequencing Facilitates Quantitative Analysis of CAFR and CAFS Transcriptomes in pancreatic cancer

city: Guangzhou

first: xiang

last: zhang

state: Guangzhou

address: 58 Zhongshan Second Road, Yuexiu District

department: Department of General Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: We extracted primary CAFs from the tumor tissue of chemoresistant and chemosensitive pancreatic cancer patients (namely CAFR and CAFS). The Goal of this study is to compare the transcriptomes difference between CAFR and CAFS. And we come to a conclusion that CAFR is possessed of a iCAF phenotype.

overall_design: mRNA profiles of CAFR and CAFS.

first: Xiang

last: Zhang

first: Chonghui

last: Hu

first: Shangyou

last: Zheng


title: Glucose Starvation Induces a Switch in the Histone Acetylome for Activation of Gluconeogenic and Fat Metabolism Genes

first: Wen-Chuan

last: Hsieh

state: Texas

department: Biochemistry

institute: UTSouthwestern Medical Center


title: Integrative molecular roadmap for reprogramming mouse fibroblasts into induced myogenic stem and progenitor cells [ATAC-Seq]

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Direct lineage reprogramming provides a unique system to study cell fate transitions and unearth molecular mechanisms that safeguard cellular identity. We previously reported on direct conversion of mouse fibroblasts into induced myogenic progenitor cells (iMPCs) by means of transient MyoD overexpression in concert with small molecules treatment. Here we employed integrative multi-omic assays to delineate the molecular landscape of fibroblast reprogramming into iMPCs in comparison to transdifferentiation into myogenic cells solely by MyoD overexpression. Utilizing bulk RNA-sequencing and mass spectrometry we characterized molecular regulators and pathways that endow a myogenic stem cell identity on fibroblasts only in the presence of small molecule treatment. We further demonstrate that iMPC reprogramming is a stepwise process, commencing with the appearance of myofibers and committed myogenic progenitors prior to the formation of satellite cell-like myogenic progenitors that express a suite of stem cell markers including Pax7, Dek, Myf5, Sox8, and Dmrt2. To directly compare iMPCs to satellite cell-derived primary myoblasts, we employed a fluorescent Pax7-GFP reporter to purify Pax7+ cells from the heterogenous iMPC cultures and assess their equivalency to FACS-purified Pax7-GFP+ myoblasts. We demonstrate that Pax7+ iMPCs share molecular attributes with myoblasts, however also express genes and signaling pathways that are indicative of activated satellite cells including Carm1, Dlk1, Lgr5, Fos, Dek, Calcr and Pitx3. We further establish that iMPC formation and maintenance is dependent on the Notch pathway, as small molecule inhibition of Notch abrogates iMPC formation and derails stable iMPC cultures via depletion of Pax7 expressing cells. Lastly, using single cell RNA-sequencing we determine the cell populations that comprise iMPCs in addition to reconstructing the differentiation trajectory present in these heterogenous cultures. We demonstrate that a highly proliferative activated satellite cell-like population differentiates into committed myoblasts and myocytes that further give rise to myofibers that express mature muscle markers, thus capturing a dynamic differentiation program in vitro. Collectively, this study charts a molecular blueprint for reprogramming fibroblasts into myogenic stem and progenitor cells and further establishes the fidelity of stable iMPC cultures in capturing skeletal muscle regeneration in vitro for disease modeling and basic research applications.

overall_design: We established a dox-inducible overexpression system with the muscle transcription factor MyoD in transgenic MEFs carrying a Pax7-nGFP reporter. We reprogrammed these MEFs into multinucleated myotubes by Dox (MyoD) treatment or into induced myogenic progenitor cells (iMPCs) by Dox+F/R/C (MyoD+F/R/C) treatment. Utilizing this system, we conducted bulk RNA-seq transcriptome profiling of MEFs subjected to MyoD overexpression alone or with small molecules (F/R/C) every two days. In addition, we performed RNA-Seq analysis of FACS-purified Pax-nGFP+ iMPCs and Pax-nGFP+ myoblasts. Lastly, we also analyzed via RNA-Seq bulk myoblasts and established dox-independent iMPC clones.

first: Inseon

last: Kim

first: Adhideb

last: Ghosh


title: Molecular hallmarks of heterochronic parabiosis at single cell resolution

city: Stanford

first: Robert

last: Palovics

address: 290 Jane Stanford Way

department: Neurology

institute: Stanford University

summary: Single-cell RNA sequencing data of Mus Musculus heterochronic parabionts

overall_design:
This dataset contains single-cell transcriptomic information from Mus musculus heterochronic parabionts across 20 organs: bladder, brain, brown adipose tissue (BAT, interscapular depot), diaphragm, gonadal adipose tissue (GAT, inguinal depot), heart, kidney, large intestine, limb muscle, liver, lung, marrow, mesenteric adipose tissue (MAT), pancreas, skin (epidermis), spleen, subcutaneous adipose tissue (SCAT, posterior depot), thymus, tongue, and trachea.
Raw sequencing data is available via the following public AWS S3 bucket: https://registry.opendata.aws/tabula-muris-senis/

first: Nicholas

last: Schaum

first: Angela

last: Pisco

first: Stephen

last: Quake

first: Tony

last: Wyss-Coray


title: Glucose Starvation Induces a Switch in the Histone Acetylome for Activation of Gluconeogenic and Fat Metabolism Genes [ChIP-seq]

summary: Acetyl-CoA is a key intermediate in metabolism situated at the intersection of many metabolic pathways. The reliance of histone acetylation on acetyl-CoA enables gene expression to be coordinated with metabolic state. Previous studies have linked abundant histone acetylation to activation of genes involved in cell growth or tumorigenesis. However, under glucose starvation, the extent to which histone acetylation is important for gene expression remains poorly understood.  Here, we use a yeast starvation model to unravel a dramatic alteration in global occupancy of histone acetylation following carbon starvation. We observe a shift in the location of histone acetylation marks from growth-promoting genes to genes required for gluconeogenesis and fat metabolism. This switch is mediated by both the histone deacetylase Rpd3 and the Gcn5p/SAGA acetyltransferase. Our findings reveal a striking specificity for histone acetylation in promoting pathways that generate acetyl-CoA for oxidation when intracellular acetyl-CoA is limiting .

overall_design: H3K9ac ChIP-seq to compare between two different conditions and three different strains. HA ChIP-seq is performed to compare two conditions in WT cells.

first: Benjamin

last: Tu


title: RNA sequencing of lung tissue of GRdim/dim and wildtype mice after hemorrhagic shock in mouse intensive care unit

status: Public on Jan 05 2022

city: Ulm

first: Sabine

last: Vettorazzi

address: Helmholtzstr. 8/1

institute: University Ulm

summary: We performed bulk RNA sequencing of lung tissue from mice with impaired GR (GRdim/dim) and wildytype mice after resuscitated hemorrhagic shock

overall_design: Three lung tissue samples of each genotype were used for bulk RNA sequencing

first: Jonathan

last: Preuss

first: Martin

last: Wepler

first: Jan

last: Tuckermann

first: Ute

last: Burret

first: Sandra

last: Kress

first: Michael

last: Gröger

first: Angelika

last: Scheuerle

first: Peter

last: Möller


title: Integrative molecular roadmap for reprogramming mouse fibroblasts into induced myogenic stem and progenitor cells [single-cell RNA-seq]

first: Ori

last: Bar-Nur

overall_design: Identification of cell types in iMPCs and examination of myogenic differentiation trajectories present in a stable iMPC clone

first: Inseon

last: Kim


title: Regulation of gene expression in human ECCs and their neural derivatives by DDX5 and DDX17

city: Bangkok

first: Praewa

last: Suthapot

address: 272 Rama VI Road

department: Department of Biochemistry, Faculty of Science

institute: Mahidol University, Thailand

summary: The fate of NSCs is strictly controlled by dynamic programs related to time. This process requires an interconnection between intrinsic and extrinsic factors to modulate the gene expression programs and precisely control the action of various downstream signaling. Several studies have been identified the uncovered functions of DDX5 and DDX17 involved in multiple aspects of gene regulatory networks and some of those have been suggested their potential roles regarding neural differentiation. In this study, we sought to distinguish the mode of action of DDX5 and DDX17 underlying the neurogenesis between two distinct cell stages including pluripotent and neural stem cell pools. We employ the ability of RNA interference to investigate the functional involvement of these two RNA helicases during embryonic and adult neurogenesis.

overall_design: The hPSCs NTERA2 (-RA) and retinoic acid-induced neural cultures differentiated for 14 days (+RA) were transfected with individual siRNA targeting DDX5 or DDX17 or using co-treatment. The samples were prepared in triplicates and submitted to RNA-seq using Illumina HiSeq2500. The non-targeting siRNA was used as a control.

first: Patompon

last: Wongtrakoongate

first: Gary

last: Felsenfeld


title: Glucose Starvation Induces a Switch in the Histone Acetylome for Activation of Gluconeogenic and Fat Metabolism Genes [RNA-seq]

city: Dallas

first: Wen-Chuan

last: Hsieh

address: 5323 Harry Hines Blvd

overall_design: RNA-seq to compare between two different conditions and three different strains.


title: Expression data of cultured organoids derived from human colorectal cancer.

city: Tokyo

first: Kohta

last: Toshimitsu

address: 35, Shinanomachi, Shinjuku-ku

institute: Keio University

summary: We analyzed gene expression of 3 lines of patient-derived colorectal cancer organoids.

overall_design: mRNA from 3 cultured organoids were extracted and hybridized to GeneChip PrimeView Human Gene Expression Array, and scanned using GeneChip Scanner 3000 7G.

first: Masayuki

last: Fujii


title: A pathogenic Th17/CD38+ macrophage feedback loop drives inflammatory arthritis through TNFa

city: San Diego

first: David

last: Muench

address: 10290 Campus Point Drive

institute: Eli Lilly and Company

summary: The pathobiology of rheumatoid inflammatory diseases, including rheumatoid arthritis (RA) and psoriatic arthritis (PsA), involves the interplay between innate and adaptive immune components and resident synoviocytes. Single-cell analyses of patient samples and relevant mouse models have characterized many cellular subsets in RA. However, the impact of interactions between cell types is not fully understood. Here, we temporally profiled murine arthritic synovial isolates at the single-cell level to identify perturbations like those found in human RA. Notably, murine macrophage subtypes like those in RA patients were expanded in arthritis and linked to promoting the function of Th17 cells in the joint. In vitro experiments identified a capacity for murine macrophages to maintain the functionality and expansion of Th17 cells. Reciprocally, murine Th17 cell-derived TNFa induced CD38+ macrophages that enhanced Th17 functionality. Murine synovial CD38+ macrophages were expanded during arthritis and their depletion or blockade via TNFa-neutralization alleviated disease while reducing IL-17A-producing cells. These findings identify a cellular feedback loop that promotes Th17 cell pathogenicity through TNFa to drive inflammatory arthritis.

overall_design: scRNA-Seq analysis of FACS-sorted live synovial cells isolated from naïve mice (two replicates) or from mice at day 6, 14, or 25 of GPI-induced arthritis (one replicate per time point).

first: Zhe

last: Sun


title: YAP1 and PRDM14 converge to promote cell survival and tumorigenesis

city: Boston

first: Miju

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The transcriptional co-activator YAP1 oncogene is the downstream effector of the Hippo pathway, which regulates tissue homeostasis, organ size, regeneration and tumorigenesis. Multiple cancers are dependent on sustained expression of YAP1 for cell proliferation, survival and tumorigenesis, but the molecular basis of this oncogene dependency is not well understood. To identify genes that can functionally substitute for YAP1, we performed a genome-scale genetic rescue screen in YAP1-dependent colon cancer cells expressing an inducible YAP1-specific shRNA. We found that the transcription factor PRDM14 rescued cell proliferation and tumorigenesis upon YAP1 suppression in YAP1-dependent cells, xenografts, and colon cancer organoids. YAP1 and PRDM14 individually activated the transcription of calmodulin 2 (CALM2) and a glucose transporter SLC2A1 upon YAP1 suppression; and CALM2 or SLC2A1 expression was required for the rescue of YAP1 suppression. Together, these findings implicate PRDM14-mediated transcriptional upregulation of CALM2 and SLC2A1 as key components of oncogenic YAP1 signaling and dependency.

overall_design: To perform RNA-sequencing or ChIP-sequencing in HT29, SKCO1 and SW48 shYAP1 cells expressing either GFP, YAP1 or PRDM14 upon suppression of YAP1

first: Yingtian

last: Xie

first: Henry

middle: W

last: Long

first: William

last: Hahn


title: Integrative molecular roadmap for reprogramming mouse fibroblasts into induced myogenic stem and progenitor cells


title: The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes [RNA-Seq]

first: Shaun

last: Mahony

overall_design: Bulk RNA-seq was used to characterize gene expression in Wildtype, Zbtb10KO, Zbtb11KO, and Zfp131KO cells grown in the presence of +2i+LIF or -2i+LIF.

first: Görkem

last: Garipler

first: Congyi

last: Lu

first: Alexis

last: Morrisey

first: Lorena

last: Lopez-Zepeda

first: Simon

last: Vidal

first: Begüm

last: Aydin

first: Matthias

last: Stadtfeld

first: Uwe

last: Ohler

first: Neville

last: Sanjana

first: Esteban

last: Mazzoni


title: Yes tyrosine kinase signaling promotes liver cancer development [DSP294_SNU449]

city: Montreal

first: Sylvain

last: Meloche

state: Quebec

address: 2950, Chemin de Polytechnique

institute: Institute of Research in Immunology and Cancer

summary: Hepatocellular carcinoma (HCC) is a disease with high unmet medical need. Most patients are diagnosed at late stage with few therapeutic options and a dismal prognosis. While molecular genomic studies have been helpful in improving the understanding and treatment of many types of cancer, their impact on HCC has been negligible so far. This is largely due to a poor understanding of the underlying mechanisms of this cancer and the lack of dominant oncogene that can be targeted pharmacologically. Here we report the identification of a novel Yes oncogenic signaling pathway in HCC that has escaped large-scale molecular genetic studies. Using a combination of genetic and pharmacological interventions in cellular and mouse models of HCC, we show that Yes activity is necessary for HCC cell proliferation. Transgenic expression of activated Yes in mouse hepatocytes is sufficient to induce liver tumorigenesis. Mechanistically, we found that Yes directly phosphorylates YAP and TAZ, promoting their nuclear accumulation and transcriptional activity in HCC cells and liver tumors, and that YAP/TAZ are effectors of Yes oncogenic transformation. Src-family kinase activation correlates with YAP tyrosine phosphorylation and nuclear localization in human HCC, and is associated with increased tumor burden. Specifically, high Yes activity predicts significantly shorter overall survival in HCC patients. Our findings identify Yes as a potential therapeutic target in HCC.

overall_design: We compared the transcriptomes of SNU-449 HCC cells expressing YES wild type (n=3) or YES T348I gatekeeper mutant (n=3) and treated with Dasatinib.


title: Yes tyrosine kinase signaling promotes liver cancer development


title: Yes tyrosine kinase signaling promotes liver cancer development [DSP244_262_PLC]

overall_design: We compared the transcriptomes of PLC/PRF/5 HCC cells expressing YES wild type (n=4) or YES T348I gatekeeper mutant (n=5) and treated with Dasatinib.


title: Integrative molecular roadmap for reprogramming mouse fibroblasts into induced myogenic stem and progenitor cells [bulk RNA-seq]

first: Ori

last: Bar-Nur

first: Inseon

last: Kim

first: Adhideb

last: Ghosh


title: Yes tyrosine kinase signaling promotes liver cancer development [DSP244_262_SNU387]

overall_design: We compared the transcriptomes of SNU-387 HCC cells expressing YES wild type (n=5) or YES T348I gatekeeper mutant (n=5) and treated with Dasatinib.


title: The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes [ChIP-Seq]

summary: In pluripotent cells, a delicate activation-repression balance maintains pro-differentiation genes ready for rapid transcription. The identity of transcription factors (TFs) that specifically repress pro-differentiation genes remains obscure. By targeting ~1,700 TFs with CRISPR loss-of-function perturbations, we found that ZBTB11 and ZFP131 are required to maintain pluripotency in mouse embryonic stem cells (ESCs). ZBTB11 and ZFP131 bind to pro-differentiation genes along with RNA Polymerase II and pausing factor NELF, but without Polycomb repression. Loss of ZBTB11 or ZFP131 leads to a decrease in NELF association, an increase in H3K4me3, transcriptional upregulation of genes associated with three germ layers, and concomitant ESC differentiation. Together, our results suggest ZBTB11 and ZFP131 maintain pluripotency by pausing pro-differentiation genes transcription and present a generalizable framework to maintain cellular potency.


title: Transcriptomic measurements of Nannochloropsis oceanica CCMP1779 after pulses of blue or red light

city: East Lansing

first: Eva

last: Farre

state: MI

address: 612 Wilson Road, Plant Biology, Room 166

department: Plant Biology

institute: Michigan State University

summary: We investigated light dependent gene expression changes in the marine ochrophyte Nannochloropsis oceanica CCMP1779. These algae have several putative blue light photoreceptors but appear to lack red light photoreceptors. To study early light signaling in N. oceanica and avoid as much as possible secondary downstream events, we quantified gene expression changes in dark-adapted cells after a short blue or red light pulse. More genes were differentially expressed under blue than under red light. In addition, fold change in expression was smaller for the red light-treated samples. For example, the median fold change of induced genes was 3 for blue light and 2.5 for red light. Moreover, hierarchical cluster analysis showed that gene expression after red light treatment was more similar to the dark control than after blue light treatment.

overall_design: Nannochloropsis oceanica were pulsed with blue light or red light, or kept in the dark. Two replicates each.

first: Eric

last: Poliner

first: Linsey

last: Newton

first: Young

middle: U

first: Byeong-ryool

last: Jeong


title: Reduced RXRa signaling increases dry eye disease inducing gdT17 cells in the conjunctiva [Nanostring]

status: Public on Jan 04 2022

city: Houston

first: JEHAN

last: ALAM

state: TEXAS

address: Baylor One Plaza

institute: Baylor College of Medicine

summary: Purpose: To investigate the mechanism for developing dry eye disease in the Pinkie mouse strain with a loss of function RXR mutation.   Methods: Measures of dry eye disease were assessed in the cornea and conjunctiva. Expression profiling by single-cell RNA sequencing (scRNA-seq)was performed to compare gene expression in conjunctival immune cells. Conjunctival immune cells were immunophenotyped by flow cytometry and confocal microscopy. Activity of RXR ligand 9-cis retinoic acid (RA) was evaluated in cultured monocytes and  T cells.   Results: Compared to wild type (WT) C57BL/6, Pinkie has increased signs of dry eye disease, including corneal barrier disruption, conjunctival cornification and goblet cell loss, and corneal vascularization, opacification, and ulceration with aging. scRNA-seq of conjunctival immune cells identified  T cells as the predominant IL-17 expressing population in both strains and there is a 4-fold increased percentage of  T cells in Pinkie. Compared to WT, significantly increased expression of IL-17a and IL-17f in conventional T cells and IL-17f in  T cells was found in Pinkie. Flow cytometry and immunostaining revealed an increased number of IL-17+  T cells in Pinkie. Tear concentration of the IL-17 inducer IL-23 is significantly higher in Pinkie. 9-cis RA treatment suppresses stimulated IL-17 production by  T and stimulatory activity of monocyte supernatant on  T cell IL-17 production. Compared to WT bone marrow chimeras, Pinkie chimeras have increased IL-17+  T cells in the conjunctiva after desiccating stress and anti-IL-17 treatment suppresses dry eye induced corneal MMP-9 production/activity and conjunctival goblet cell loss.   Conclusion: These findings indicate that RXR suppresses generation of dry eye disease inducing  T17 cells in the conjunctiva and identifies RXR as a potential therapeutic target in dry eye.

overall_design:
There are two experiments for which we performed Nano string RNA analysis:
Experiment#1 : We compare the cornea from C57B6 control mice with Pinkie mice strain have a normal cornea or Pinkie mice with ulcerated cornea.
Experiment#2 : In this experiment we compared the control monocytes with monocytes either treated with LPS alone or both LPS and 9CisRA.

first: Jehan

last: Alam

first: Ghasem

last: Yazdanpanah

first: Rinki

last: Ratnapriya

first: Nicholas

last: Borcherding

first: Cintia

last: de Paiva

first: DeQuan

last: Li

first: Rodrigo

middle: G

last: de Souza

first: Zhiyuan

last: Yu


title: TIRAP drives myelosuppression through an Ifnγ-Hmgb1 axis that disrupts the endothelial niche.

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

address: 675 West 10th Avenue

institute: BC Cancer

summary:
Purpose: The goals of this study are to compare the transcriptome profile of mouse hematopoietic stem/progenitor cells (HSPC) from the bone marrow overexpressing the innate immune adaptor protein TIRAP to control vector expressing HSPC using RNA-Seq.
Methods: mRNA profiles of wild-type (WT) mice bone marrow overexpressing TIRAP or control vectors were generated by deep sequencing, in triplicate, using the Illumina platform. RNA-Seq data were aligned using JAGuaR (v2.0.3), using the mm10 reference. Expression quantification was performed with Sailfish (v0.6.2), using RefSeq gene models. The differential expression analysis between TIRAP expressing bone marrow and control was performed using DESeq2 (v1.10.1).
Results: Using an optimized data analysis workflow, we mapped approximately 92% sequenced reads on average per sample to the mouse genome (build mm10).

overall_design: Bone marrow mRNA profiles of wild type (WT) mice overexpressing either TIRAP or control (MIG) vectors.


title: Transcripts identified by microarray analysis that were deregulated in P4 Tbx18(cre/+);Rbpj(fx/fx) (Rbpj-cKO) ureters

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of transcriptional changes in the P4 ureters upon loss of Rbpj in the urereteric mesenchyme.

overall_design: Total RNA was extracted from dissected P4 ureters of Rbpj-cKO and control mice and analyzed by microarray analysis.

first: Jennifer

last: Kurz


title: The BNT162b2 vaccine elicits robust lymph node T follicular helper cell responses

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

summary: COVID-19 mRNA vaccines generate high concentrations of circulating anti-Spike antibodies and Spike-specific CD4+ T cells following prime-boost vaccination. It is not yet clear if vaccine-induced CD4+ T cell responses in the draining lymph node contribute to this outstanding immunogenicity. Using fine needle aspiration of draining axillary lymph nodes from individuals who received the BNT162b2 mRNA vaccine, we found large populations of Spike-specific CD4+ T follicular helper cells in the draining lymph node. A broadly immunodominant HLA-DPB1*04-restricted response to Spike166-180 composes one of the largest populations of T follicular helper cells in individuals with this allele, which is itself among the most common HLA alleles in the human population. Spike-specific T follicular helper cells are present in the lymph node 30 days after vaccine boost and persist in some individuals more than 170 days. Collectively, our results underscore the key role that robust T follicular helper cell responses play in the establishment of long-term immunity in this very efficacious human vaccine.

overall_design:
Bulk T cell receptor (TCR) sequences were obtained from the lymph nodes of four donors, each at two distinct time points after vaccination.
The metadata.txt (representing 16 samples) contains each sample information and additional details required for demultiplexing.

first: Anastasia

middle: A

last: Minervina

first: Mikhail

last: Pogorelyy

first: Paul

last: Thomas