title: Fate mapping of single NK cells identifies a type 1 innate lymphoid-like lineage that bridges innate and adaptive recognition of viral infection [scRNAseq_Ly49H+_NK_retrogenic_spleen]

status: Public on Aug 25 2021

city: München

first: Sophie

last: Flommersfeld

address: Trogerstr. 30

department: Institute for Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technical University of Munich

summary: Upon viral infection, NK cells expressing certain germline-encoded receptors are selected, expanded and maintained in an adaptive-like manner. Currently, these are thought to differentiate along a common pathway. However, by fate mapping of single NK cells upon murine cytomegalovirus (MCMV) infection, we identified two distinct NK cell lineages that contributed to adaptive-like responses. One was equivalent to conventional NK (cNK) cells while the other was transcriptionally similar to type 1 innate lymphoid cells (ILC1s). ILC1-like NK cells showed splenic-residency and strong cytokine production but also recognized and killed MCMV-infected cells, guided by activating receptor Ly49H. Moreover, they induced clustering of conventional type 1 dendritic cells and facilitated antigen-specific T cell priming early during MCMV infection, which depended on Ly49H and the NK cell-intrinsic expression of transcription factor Batf3. Thereby, ILC1-like NK cells bridge innate and adaptive viral recognition and unite critical features of cNK cells and ILC1s.

overall_design: One mRNA profile of total Ly49H+ NK cells from retrogenic spleen.

first: Jan

last: Böttcher

first: Jonatan

last: Ersching

first: Michael

last: Flossdorf

first: Philippa

last: Meiser

first: Ludwig

middle: O

last: Pachmayr

first: Justin

last: Leube

first: Inge

last: Hensel

first: Sebastian

last: Jarosch

first: Qin

last: Zhang

first: M

middle: Z

last: Chaudhry

first: Immanuel

last: Andrä

first: Mattias

last: Schiemann

first: Dirk

last: Busch

first: Luka

last: Cicin-Sain

first: Joseph

last: Sun

first: Georg

last: Gasteiger

first: Gabriel

middle: D

last: Victora

first: Thomas

last: Höfer

first: Veit

last: Buchholz

first: Simon

last: Grassmann


title: Fate mapping of single NK cells identifies a type 1 innate lymphoid-like lineage that bridges innate and adaptive recognition of viral infection [scRNAseq_spleen_LN_total_NK]

first: Sophie

last: Flommersfeld

type: Expression profiling by high throughput sequencing

overall_design: One mRNA profile of total NK cells from uninfected spleen and one from lymph nodes.

first: Jan

middle: P

last: Böttcher

first: Jonatan

last: Ersching

first: Michael

last: Flossdorf

first: Philippa

last: Meiser

middle: H

middle: C

middle: R


title: Fate mapping of single NK cells identifies a type 1 innate lymphoid-like lineage that bridges innate and adaptive recognition of viral infection

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

overall_design: Refer to individual Series


title: Fate mapping of single NK cells identifies a type 1 innate lymphoid-like lineage that bridges innate and adaptive recognition of viral infection [scRNAseq_spleen_Ly49H+_steady-state]

overall_design: One mRNA profile of total Ly49H+ NK cells from uninfected spleen.

first: Ludwig

last: Pachmayr

first: Justin

last: Leube

first: Inge

last: Hensel

first: Sebastian

last: Jarosch

first: Qin

last: Zhang


title: Genome-wide synthetic lethal screen unveils novel CAIX – NFS1/xCT axis as a targetable vulnerability in hypoxic solid tumors.

status: Public on Aug 28 2021

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

summary: Hypoxia is an important clinicopathological feature of solid tumours that limits response to therapy.  Carbonic Anhydrase IX (CAIX) is a hypoxia-induced, pH regulator that has emerged as a viable therapeutic target.  Targeting CAIX has demonstrated promise in difficult to treat preclinical models of breast pancreatic, melanoma and brain cancers when combined with chemotherapy and immunotherapy, however resistance ultimately develops and this mechanism is unclear.  Here we used an unbiased genome-wide synthetic lethal CRISPR knock-out screen in basal breast cancer cells to identify co-vulnerabilities and mechanisms of compensation for CA9 loss.  We identified a redox homeostasis network containing thioredoxin and the iron-sulfur cluster enzyme, cysteine desulfurase, NFS1, indicative of the critical importance of CAIX in this role.

overall_design: Genome-wide CRISPR knock-out screen for synthetic lethal interactions of Carbonic anhydrase IX in hypoxic SUM159PT triple negative breast cancer cells. There are 4 samples done in duplicates.

first: Shawn

last: Chafe

first: Shoukat

last: Dedhar


title: Fate mapping of single NK cells identifies a type 1 innate lymphoid-like lineage that bridges innate and adaptive recognition of viral infection [bulk_RNAseq_steady_state]

overall_design: 4 distinct Ly49H+ NK cell subsets defined by differential expression of CD27 and CD62L as well as ILC1s were sorted from spleen of uninfected C57BL/6 mice. 2x 500 cells were sorted from each population and bulk RNA-Seq was performed of all samples.

first: M

last: Chaudhry

first: Immanuel

last: Andrä

first: Mattias

last: Schiemann

first: Dirk

last: Busch

first: Luka

last: Cicin-Sain

first: Joseph

last: Sun

first: Georg

last: Gasteiger

first: Gabriel

last: Victora


title: Vitis vinifera embryogenic callus epigenomics

status: Public on Aug 27 2021

city: Blenheim

first: Darrell

middle: Karl

last: Lizamore

state: Marlborough

address: 85 Budge St

country: New Zealand

institute: Bragato Research Institute

type: Non-coding RNA profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue.


title: Profiling of microRNA expression of mouse cardiac neural crest cells and non neural crest cells

city: Guangzhou

first: Youchen

last: Yan

state: Guangdong

address: No.58 Zhongshan Road II

country: China

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

summary: In this study, we investigate the miRNA expression profile of cardiac neural crest cells (NCCs) and non-NCCs. Rosa-mT-mG reporter mice, which possess loxP sites on either side of a membrane-targeted tdTomato (mT) cassette and express strong red fluorescence in all tissues and cell types, were applied in this study. The presence of Wnt1-Cre leads to the deletion of the mT cassette and the expression of the membrane-targeted EGFP (mG) cassette located just downstream in NCCs. E10.5 Rosa-mT-mG/Wnt1-Cre EGFP positive embryos were collected. The 3rd, 4th and 6th pharyngeal arches and outflow tract were dissected out, digested and sorted for both EGFP+ cranial NCCs and EGFP- control cells by FACS sorting. Total RNAs were prepared for microRNA microarray from cardiac NCCs and non-NCCs.

overall_design: Examine the expression of global microRNAs in cardiac NCCs and non-NCCs

first: Jinghai

last: Chen

first: Zhan-Peng

last: Huang


title: Immune subtype of ovarian clear cell carcinoma

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary:
Background: Recent data demonstrated efficacy of immune checkpoint inhibitors in advanced OCCC, but little is known about the immune microenvironment of these tumours and its impact on outcomes. We studied the expression of a panel of immune response genes in OCCC to identify the presence and prognostic relevance of irGES in these tumours.
Methods: Immune response gene profiling was performed on 96 FFPE OCCC tumour samples with matched clinical outcomes, collected from the National University Hospital, Singapore between 2003 – 2016, using the nanoString nCounter PanCancer Immune Profiling Panel. Unsupervised hierarchical clustering analysis was performed to stratify OCCCs to derive the irGES profiles. Upregulation of specific genes of interest at the protein level and the status of mismatch repair (MMR) and ARID1A were validated using immunohistochemistry (IHC).
Results: Total of 74/84 samples were successfully profiled. Median age at diagnosis was 53 yrs. 41 (55.4%) were stage 1, 7 (9.5%) stage 2, 24 (32.4%) Stage3, 2 (2.7%) stage 4. 64/74 (86.5%) of patients received adjuvant chemotherapy post debulking surgery with 38% recurrence rate (median PFS 27 months). Median follow up was 36 months. Based on irGES, 4 distinct molecular subgroups of OCCCs were identified. G1 was hallmarked by NK cell markers and PD-1 expression (PD-1 high), G2 by increased CTLA-4 expression, G3 by upregulation of genes associated with immunogenicity and antigen presentation, and G4 by increased levels of pro - angiogenic genes. The PD-1 high group was observed to have significantly poorer PFS (median PFS 20 months vs 68 months, p= 0.011) and a trend towards poorer OS when compared with G2/3/4 (median OS 38.8 months vs undefined, p = 0.0501). The pro - angiogenic (G4) carried the best prognosis (median PFS 108 months vs 26 months, p= 0.0515; median OS undefined, p= 0.0726). This difference in OS and PFS was consistently observed between stage 1 and non-stage 1 pts (hazard ratio 5.856 and 5.659, p < 0.0001, respectively). Significant correlation was observed between gene and protein expression of tumour PD-1, tumour and stromal PD-L1, and tumour IL-6 using IHC (p < 0.0001 for all comparisons). 6 (8.1%) pts were MMR deficient and there was no significant association between ARID1A and MMR expression across each irGES groups.
Conclusion: OCCCs are heterogeneous and can be classified into 4 molecular subgroups based on their irGES profiles representing distinct clinicopathological characteristics and prognostic outcomes. If validated in larger datasets, these signatures may serve to guide clinical trial design and personalized treatment for OCCC pts.

overall_design: FFPE of ovarian clear cell carcinoma were profiled using NanoString Pan-cancer immune panel.

first: Valerie

last: Heong

first: Ye

last: Jieru

first: Huang

middle: Y

last: Ruby

first: Tuan


title: Fate mapping of single NK cells identifies a type 1 innate lymphoid-like lineage that bridges innate and adaptive recognition of viral infection [bulk_RNAseq_d8pi]

first: Sophie

last: Flommersfeld

overall_design: CD27+ CD62L- and CD27- CD62L+ Ly49H+ NK cells were sorted and adoptively transferred into Rag2-/- Il2rg-/- mice infected with MCMV. At day 8 p.i., CD27+ CD62L- and CD27- CD62L- cells were sorted from progenies of CD27+ CD62L- cells and CD27- CD62L+ and CD27- CD62L- were sorted from progenies of CD27- CD62L+ cells in spleen. 2x 500 cells were sorted from each population and bulk RNA-Seq was performed of all samples.

first: Jan

last: Böttcher

first: Jonatan

last: Ersching

first: Michael

last: Flossdorf

first: Philippa

last: Meiser

first: Ludwig

last: Pachmayr

first: Justin

last: Leube

first: Inge

last: Hensel

first: Sebastian

last: Jarosch

first: Qin

last: Zhang

first: M

first: Thomas

last: Höfer

first: Veit

last: Buchholz

first: Simon

last: Grassmann


title: A time-resolved transcriptome landscape of the developing mouse ovary

status: Public on Aug 24 2021

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: The ovarian structure is complex and diverse, including egg cells, granulosa cells and other cell types. Its organ function depends heavily on normal development. Numerous studies have focused on certain gene function changes during ovarian development, but systematic analyses of its molecular changes are extremely rare. Here, we present a comprehensive transcriptional profile of the mouse ovary from 11 time points across multiple developmental stages, which enables us to explore the dynamics of ovarian development. By performing coexpression analysis, we identified gene modules with similar expression trends and determined 159 functional gene interaction networks based on machine learning. Most of these gene interaction networks are related to biological processes involved in the development of the ovary, which provides functional predictions for some genes with unknown functions and a reference for subsequent functional research. In general, our study provides a resource for understanding ovarian development.

overall_design: Purpose: To asses the gene expression profile of the developing mose ovary,we performed bulk RNA-seq for the whole mouse ovary at 11 time points ranging from the embryo to the adulthood.  Methords:Total RNA was isolated and sequenced using an illumina high-seq 2500. Raw data was analyzed using TopHat.

first: Xiaodan


title: Ablation of SOX10 impaired the differentiation and migration potential of neural crest derived from human pluripotent stem cells

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

summary: Here, control human pluripotent stem cells (hiPSCs) and SOX10 knockout (SOX10 KO) hiPSCs were induced to differentiate to neural crest stem cells (NCSCs). We sequenced mRNA samples of differentiated cells at day 7 during NCSC differentiation to generate the gene expression profiles of these cells.

overall_design: 6 samples from differentiated cells at day 7, including control hiPSC-derived cells (WT1-1, WT1-2), SOX10 KO1 hiPSC-derived cells (KO1-1, KO1-2), and SOX10 KO2 hiPSC-derived cells (KO2-1, KO2-2) were analyzed.

first: Xingqiang

last: Lai

first: Zhengwei

last: Zou

first: Jia

first: Andy

last: Xiang


title: the role of hsa_circ_0000073 in Osteosarcoma

city: Gui Yang

first: Xiaobin

last: Tian

state: State...

address: Zhongshan East Road 83

institute: Guizhou Provincial People's Hospital

summary:
Osteosarcoma (OS) is one of the leading causes of cancer mortality in children and teenagers. Patients with OS have been shown to have a poor prognosis and may suffer from potential distant metastasis. Emerging evidence has revealed that circular RNAs (circRNAs) are involved in OS progression. In this paper, we aim to explore the function of hsa_circ_0000073 in the progression of OS.
OS cells transfected with sh‐NC or sh-circ_0000073 were enrolled in this study.We used microarray analysis to identify the mRNA expression in the cells.

overall_design: MG-63-and Saos-2 cells transfected with sh‐NC or sh-circ_0000073 were subjected to total RNA isolation using TRIzol reagent. Then, a microarray analysis was taken to analyze the differentially expressed mRNAs.

first: Zhen

last: Yang


title: Transcriptome analysis of blood Vγ9 Vδ2 gdT cells upon TCR and Notch signalling

city: Greater Noida

first: Sanjeev

last: Galande

state: Uttar Pradesh

address: Center of Excellence in Epigenetics  Department of Life Sciences  School of Natural Sciences  Shiv Nadar Institute of Eminence  NH91, Tehsil Dadri

department: Biology

country: India

institute: Shiv Nadar University

summary: We utilized RNA-seq to identify differential gene expression in Vγ9 Vδ2 gdT cells isolated from human PBMCs upon TCR stimulation. We find that ~30% genes are commonly up- and down-regulated between different phosphoantigen treatments (p<0.05). Inhibition of Notch signaling alongside TCR activation results in downregulation of many effector genes in Vγ9 Vδ2 T cells.

overall_design: PBMCs from healthy donors were subjected to MACS based gdT cell isolation. The isolated cells (~1 million each) were either untreated, treated with rIL2 only, or a combination of rIL2+IPP, rIL2+HDMAPP and rIL2+anti-CD3 for T cell activation. Notch signaling inhibitor treatment was done using GSI-X along with TCR activation. Three replicates were sequenced for all the 8 treatment samples.

first: Shubhada

middle: V

last: Chiplunkar


title: Single cell transcriptomic profiling of day 114 patient-specific pluripotent stem cell-derived alveolar epithelial type 2 cells expressing the SFTPCI73T mutation and their gene-edited corrected counterparts [D114]

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

country: USA

institute: Center for Regenerative Medicine at Boston University

summary: We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using our previously described distal lung directed differentiation protocol to generate alveolar epithelial type 2 cells (iAEC2s). We used the SPC2 human iPSC line and specifically the SPC2-ST-B2 (SFTPCtdT/WT) and SPC2-ST-C11 (SFTPCI73T/tdT) clones containing a SFTPCtdTomato knock-in reporter. SFTPCtdTomato+ cells were sorted on day 51 of differentiation and maintained without further sorting in self-renewing 3D alveolosphere cultures passaged approximately every 2 weeks through day 114. On day 114, all live cells were sorted and encapsulated for scRNA-seq using the 10X Chromium System. We find that mutant (SFTPCI73T/tdT) iAEC2s display a less proliferative and more mature AEC2 phenotype compared to their corrected (SFTPCtdT/WT) counterparts with a concomitant upregulation of lysosomal and autophagy related pathways in mutant cells.

overall_design: Global transcriptomic profiling of day 114 patient-specific induced pluripotent stem cell (iPSC)-derived alveolar epithelial type 2 cells (iAEC2s) expressing the SFTPCI73T mutation and their gene-edited corrected counterparts by scRNA-seq

first: Konstantinos-Dionysios

last: Alysandratos

first: Darrell

middle: N

last: Kotton


title: Single cell transcriptomic profiling of day 113 patient-specific pluripotent stem cell-derived alveolar epithelial type 2 cells expressing the SFTPCI73T mutation and their gene-edited corrected counterparts [D113]

summary: We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using our previously described distal lung directed differentiation protocol to generate alveolar epithelial type 2 cells (iAEC2s). We used the SPC2 human iPSC line and specifically the SPC2-ST-B2 (SFTPCtdT/WT) and SPC2-ST-C11 (SFTPCI73T/tdT) clones containing a SFTPCtdTomato knock-in reporter. SFTPCtdTomato+ cells were sorted on day 41 and again on day 79 of differentiation. iAEC2s were single-cell passaged in self-renewing 3D alveolosphere cultures approximately every 2 weeks through day 113. Live SFTPCtdTomato+ iAEC2s were sorted on day 113 and encapsulated for scRNA-seq using the 10X Chromium System. We find that mutant (SFTPCI73T/tdT) iAEC2s display a less proliferative and more mature AEC2 phenotype compared to their corrected (SFTPCtdT/WT) counterparts with a concomitant upregulation of lysosomal and autophagy related pathways in mutant cells.

overall_design: Global transcriptomic profiling of day 113 patient-specific induced pluripotent stem cell (iPSC)-derived alveolar epithelial type 2 cells (iAEC2s) expressing the SFTPCI73T mutation and their gene-edited corrected counterparts by scRNA-seq


title: Differential contribution to gene expression prediction of histone modifications at enhancers or promoters

city: Barcelona

first: Mar

last: Gonzalez-Ramirez

address: C/ Dr Aiguader 88

country: Spain

institute: Center for Genomic Regulation (CRG)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Whereas the ChIP-seq signal of histone modifications at promoters is reported to be a good predictor of gene expression in different cellular contexts, this question has been poorly addressed for enhancers. Embryonic stem cells (ESCs) ―where the full spectrum of active and repressed (poised) enhancers can be identified― are the appropriate model system to tackle this problem. Since many poised enhancers in ESCs switch towards an active state during differentiation, predictive models can be learnt from poised enhancers throughout differentiation. Modelling gene expression from histone modifications at enhancers will allow us to study the different contribution of promoters and enhancers to gene expression. We have obtained quantitative models to characterize the relationship of gene expression with histone modifications at enhancers or promoters. Remarkably, we have determined that histone modifications at enhancers, as well as promoters, are predictive of gene expression in ESCs and throughout differentiation. The contribution of histone modifications to the predictive models varies depending on their location in enhancers or promoters. We have designed a novel approach based on local regression (LOESS) to normalize sequencing data from different sources, which allowed us to apply predictive models learnt in a specific cellular context to a different one. Therefore, this allowed us to conclude that the relationship between gene expression and histone modifications at enhancers is universal.

overall_design: ChIP-seq experiments of mESC

last: González-Ramírez

first: Luciano

last: Di Croce


title: Single-cell transcriptomic profiling of patient-specific pluripotent stem cell-derived alveolar epithelial type 2 cells expressing the SFTPCI73T mutation and their gene-edited corrected counterparts


title: Single cell transcriptomic profiling of day 30 patient-specific pluripotent stem cell-derived alveolar epithelial type 2 cells expressing the SFTPCI73T mutation and their gene-edited corrected counterparts [D30]

summary: We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using our previously described distal lung directed differentiation protocol to generate alveolar epithelial type 2 cells (iAEC2s). We used the SPC2 human iPSC line and specifically the SPC2-ST-B2 (SFTPCtdT/WT) and SPC2-ST-C11 (SFTPCI73T/tdT) clones containing a SFTPCtdTomato knock-in reporter. Live SFTPCtdTomato+ iAEC2s were sorted on day 30 and encapsulated for scRNA-seq using the 10X Chromium System. We find that mutant (SFTPCI73T/tdT) and corrected (SFTPCtdT/WT) iAEC2s have similar transcriptomes with only 403 genes being differentially expressed at this early time point after the initial onset of SFTPC expression.

overall_design: Global transcriptomic profiling of day 30 patient-specific induced pluripotent stem cell (iPSC)-derived alveolar epithelial type 2 cells (iAEC2s) expressing the SFTPCI73T mutation and their gene-edited corrected counterparts by scRNA-seq


title: Rheumatoid arthritis synovium response to abatacept

status: Public on Aug 23 2021

city: Brussels

first: Clement

last: Triaille

address: avenue Hippocrate, 10

department: IREC (Institut de Recherche Expérimentale et Clinique)

country: Belgium

institute: UCLouvain

summary: Our goal was to assess for the histological and transcriptomic effects of Abatacept on RA synovia, and to compare them with previously published data from four other DMARDs: Tocilizumab, Rituximab, Methotrexate and Adalimumab.

overall_design: Paired analysis (before vs. after treatment) of transcriptomic data from ten patients with active RA treated with Abatacept. All patients met the ACR/EULAR 2010 RA classification criteria. For each patient, synovial biopsies (3-5 fragments pooled) were obtained from the same affected joint before (W0) and 16 weeks after (W16) starting treatment with Abatacept 125mg per week subcutaneously. Total RNA was extracted and hybridized on HGU133 Plus 2.0 arrays.

first: Clément

first: Patrick

last: Durez

first: Bernard

last: Lauwerys

first: Nisha

last: Limaye


title: Cannabinoid receptor 2 is necessary to induce toll-like receptor-mediated microglial activation.

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: The tight regulation of microglia activity is key for precise responses to potential threats, while uncontrolled and exacerbated microglial activity is neurotoxic. Microglial toll-like receptors (TLRs) are indispensable for sensing different types of assaults and triggering an innate immune response. Cannabinoid receptor 2 (CB2) signaling is a key pathway to control microglial homeostasis and activation, and its activation is connected to changes in microglial activity. We aimed to investigate how CB2 signaling impacts TLR-mediated microglial activation. Here, we demonstrate that deletion of CB2 causes a dampened transcriptional response to prototypic TLR ligands in microglia. Loss of CB2 results in distinct microglial gene expression profiles, morphology, and activation. We show that the CB2-mediated attenuation of TLR-induced microglial activation is p38 MAPK-dependent. Taken together, we demonstrate that CB2 expression and signaling are necessary to fine-tune TLR-induced activation programs in microglia.

overall_design: Primary neonatal microglia derived from WT and CB2-/- mice were stimulated for 16h in vitro with LPS/IFN-γ, PolyI:C or CpG to activate TLR4, TLR3 and TLR9, respectively. Subsequently, bulk RNA-sequencing was performed from these samples.

first: Nico

last: Reusch

first: Kishore

middle: A

last: Ravichandran

first: Bolanle

middle: F

last: Olabiyi

first: Joanna

last: Komorowska-Müller

first: Jan

last: Hansen

first: Thomas

last: Ulas

first: Marc

last: Beyer

first: Andreas

last: Zimmer

first: Anne-Caroline

last: Schmöle


title: Transcriptional Network Analysis Reveals the Role of miR-223-5p During Diabetic Corneal Epithelial Regeneration [RNA-seq]

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

summary: Diabetes mellitus (DM) is a complex metabolic disorder. Long-term hyperglycemia may induce diabetic keratopathy (DK), which is mainly characterized by delayed corneal epithelial regeneration. MicroRNAs (miRNAs) have been reported to play regulatory roles during tissue regeneration. However, the molecular mechanism by which miRNAs influence epithelial regeneration in DK is largely unknown. In this study, we performed miRNA and mRNA sequencing of regenerative corneal epithelium tissue from streptozotocin-induced type 1 diabetic (T1DM) and wild-type mice to screen for differentially expressed miRNAs and mRNAs. Based on regulatory network analysis, miR-223-5p was selected for subsequent experiments and Hpgds was then identified as a direct target gene. MiR-223-5p downregulation significantly promoted diabetic corneal epithelial wound healing and nerve regeneration. However, the beneficial effects of miR-223-5p inhibition were abolished by an Hpgds inhibitor. Furthermore, mechanistic studies demonstrated that miR-223-5p suppression ameliorated inflammation and enhanced cell proliferation signaling in DK. Taken together, our findings revealed that the regulatory role of miR-223-5p in diabetic corneal epithelial and nerve regeneration by mediating inflammatory processes and cell proliferation signaling. And silencing miR-223-5p may contribute to the development of potential therapeutic strategies for DK.

overall_design: Regenerative corneal epithelium tissue mRNA profiles of streptozotocin-induced type 1 diabetic (T1DM) and counterparts

first: Yuan

first: Qun

last: Wang

first: Lixin

last: Xie


title: A mechanism of cooling hot tumors: lactate attenuates inflammation in dendritic cells

city: Kumamoto

first: Hisashi

last: Kanemaru

state: Kumamoto

address: 1-1-1 Honjo Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

summary: The epigenetic status of H3K27Ac was comparable between Egr1 deficient and WT bone marrow-derived dendritic cells (BMDCs). We identified a region that suggested the interaction of EGR1 in the Cd80 promoter.

overall_design: We analysed the status of H3K27Ac and EGR1 in LPS and lactic acid (LA)-stimulated WT or Egr1 deficient BMDCs using ChIP-sequencing.


title: RNA-seq of BON-1 cells

first: Shenglin

last: Huang

address: 270 Dongan

summary: BON-1 cells were co-cultured with different amounts of CAFs. BON-1 cells were then isolated from the co-culture system by flow cytometry. RNA-seq analyses were performed to examine the expression profile.

overall_design: BON-1 cells were isolated from the co-culture system by flow cytometry. Then total RNAs were subjected to RNA isolation and RNA-seq analyses were generated by deep sequencing using Illumina NovaSeq 6000.

first: Zeng

last: Ye


title: Transcriptional Network Analysis Reveals the Role of miR-223-5p During Diabetic Corneal Epithelial Regeneration [miRNA-seq]

overall_design: Regenerative corneal epithelium tissue miRNA profiles of streptozotocin-induced type 1 diabetic (T1DM) and counterparts


title: A novel oral arginase 1/2 inhibitor enhances the antitumor effect of PD-1 inhibition in murine experimental gliomas by altering the immunosuppressive environment.

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

summary: Malignant gliomas are common and aggressive primary brain tumors which are incurable by conventional therapies. Immunotherapy with the immune checkpoint inhibitors is not effective due to the highly immunosuppressive tumor microenvironment (TME). Clinical and experimental data show upregulation of Arginase1 (ARG1) expression in rodent and human malignant gliomas. The elevated ARG1 activity leads to depletion of L-arginine required for proliferation of T lymphocytes and natural killer cells. Inhibition of ARG1 in TME may unblock T cell proliferation and activate effective antitumor responses. To explore an antitumor potential of ARG1 inhibition, first we analyzed bulk and single cell RNA sequencing (scRNA-seq) data from human and murine gliomas, and found upregulation of ARG1 expression in malignant gliomas, both in tumor cells and in tumor infiltrating microglia, monocytes/macrophages. We employed the novel, selective arginase inhibitor - OAT-1746 to interfere with microglia-induced glioma invasion in microglia-glioma co-cultures. We determined its antitumor efficacy as a monotherapy and in combination with immunotherapy. In a Matrigel invasion assay OAT-1746 blocked microglia-dependent invasion of U87-MG and LN18 glioma cells better than reference compounds, without affecting cell viability. OAT-1746 effectively crossed the BBB and increased arginine levels in brains of GL261 glioma bearing mice. The compound reduced glioma growth and increased antitumor effects of the anti-PD-1 antibody. Treatment with OAT-1746 modified TME as demonstrated by profound transcriptomic changes visualized by RNA sequencing. Our findings provide the evidence that inhibition of ARG1 in tumor cells and myeloid cells in TME abolishes the immunosuppressive reprograming of myeloid cells and improves the efficacy of immunotherapy.

overall_design: RNA libraries for sequencing were prepared using a KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, MA, USA) Poly-A mRNAs were purified from 100ng of total RNA using poly-T-oligo-magnetic beads. First-strand cDNA was synthesized using reverse transcriptase and random hexamers. Second cDNA synthesis was performed by removing RNA templates and synthesizing replacement strands, incorporating dUTP in place of dTTP to generate double-stranded (ds) cDNA. Libraries were loaded at a concentration of 8,5 pM onto a rapid run flow cell and were paired-end sequenced on an Illumina HiSeq 1500. Illumina-specific adapters, short reads and low quality 5' and 3' bases were filtered out in the FASTQ format files using Trimmomatic tool. Resulting RNA sequencing reads were aligned to a reference mouse genome sequence. differential expression analysis was performed to identify transcriptomic differences across groups. Gene Ontology Biological Processes (GO: BP) was employed to better understand the mechanistic insights of enriched gene lists. The variance stabilizing transformation (vst function) was used for visualization purposes. A pathway enrichment analysis was performing by selecting statistically significantly genes (adjusted p-values < 0.05) and type I errors in multiple testing was corrected using the Bonferroni-Hochberg (BH) method.

first: Paulina

last: Pilanc

first: Kamil

last: Wojnicki

first: Adria

first: Salwador

last: Cyranowski

first: Aleksandra

last: Ellert-Miklaszewska

first: Natalia

last: Ochocka

first: Barłomiej

last: Gielniewski

first: Marcin

middle: M

last: Grzybowski

first: Roman

last: Błaszczyk

middle: S

last: Stańczak

first: Paweł

last: Dobrzański

first: Bozena

last: Kaminska


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

overall_design: Refer to individual Series


title: Brg1-dependent enhancer-promoter interactions support B cell activation and germinal center formation

status: Public on Aug 21 2021

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Activation and differentiation of B cells depend on extensive rewiring of gene expression networks through changes in chromatin structure and accessibility. The chromatin remodeling complex BAF with its catalytic subunit Brg1 was previously identified as an essential regulator of early B cell development, however, how Brg1 orchestrates gene expression during mature B cell activation is less clear. Here, we find that Brg1 is required for B cell proliferation and germinal center formation through selective interactions with enhancers. Brg1 recruitment to enhancers was associated with increased chromatin accessibility and transcriptional activation of their coupled promoters following B cell activation and expression of cell cycle-associated genes. Accordingly, Brg1-deficient B cells were unable to mount germinal center reactions and support the formation of class-switch plasma cells. Our findings show that changes in B cell transcriptomes that support cell proliferation and GC formation depend on enhancer activation by Brg1. Thus, the BAF complex plays a critical role during the onset of the humoral immune response.

overall_design: RNA-seq and ATAC-seq of activated B cells, harvested after 96 hours activation using LPS and IL-4.

first: Dominik

last: Schmiedel

first: Hadas

last: Hezroni

first: Amit

last: Hamburg


title: Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization

status: Public on Aug 22 2021

city: Hong Kong

first: Zhongyang

last: LIN

address: 4S17 Kadoorie Biological Sciences Building, Pokfulam Road

institute: the University of Hong Kong

summary: To investigate how exogenous DNA concatemerizes to form episomal artificial chromosomes (ACs), acquire equal segregation ability and maintain stable holocentromeres, we injected DNA sequences with different features, including sequences that are repetitive or complex, and sequences with different AT-contents, into the gonad of Caenorhabditis elegans to form ACs in embryos, and monitored AC mitotic segregation. We demonstrated that AT-poor sequences (26% AT-content) delayed the acquisition of segregation competency of newly formed ACs. We also co-injected fragmented Saccharomyces cerevisiae genomic DNA, differentially expressed fluorescent markers and ubiquitously expressed selectable marker to construct a less repetitive, more complex AC. We sequenced the whole genome of a strain which propagates this AC through multiple generations, and de novo assembled the AC sequences. We discovered CENP-AHCP-3 domains/peaks are distributed along the AC, as in endogenous chromosomes, suggesting a holocentric architecture. We found that CENP-AHCP-3 binds to the unexpressed marker genes and many fragmented yeast sequences, but is excluded in the yeast extremely high-AT-content centromeric and mitochondrial DNA (> 83% AT-content) on the AC. We identified A-rich motifs in CENP-AHCP-3 domains/peaks on the AC and on endogenous chromosomes, which have some similarity with each other and similarity to some non-germline transcription factor binding sites.

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: WYY35; Developmental Stage: Early Embryos; Genotype: wild type; Sex: Hermaphrodite; NUMBER OF REPLICATES: 2;  temp (temperature) 22 degree celsius; Antibody: SDQ0804 (Rabbit anti-HCP-3)

last: Lin

first: Karen W.Y.

last: Yuen


title: Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease Mechanisms [RNA-Seq]

status: Public on Aug 20 2021

city: New York

first: Robert

last: Sebra

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Our work illustrates how high-resolution molecular and spatial profiling of COVID-19 patient tissues collected during rapid autopsies can serve as a hypothesisgenerating tool to identify key mediators driving the pathophysiology of COVID-19 for diagnostic and therapeutic target testing. Here we employ bulk RNA sequencing to identify key regulators of COVID-19 and list specific mediators for further study as potential diagnostic and therapeutic targets. We use single-nuclei RNA sequencing to highlight the diversity and heterogeneity of coronavirus receptors within the brain, suggesting that it will be critical to expand the focus from ACE2 to include other receptors, such as BSG and ANPEP, and we perform digital spatial profiling of lung and lymph node tissue to compare two patients with different clinical courses and symptomatology.

overall_design: Two technical replicates across ten tissues (Patient 1) with two technical replicates of a pool of brain RNA from multiple donors as control (no SARS-CoV-2 infection).

first: Carlos

last: Cordon-Cardo


title: HIV infection drives interferon signaling within intestinal SARS-CoV-2 susceptible target cells

status: Public on Aug 18 2021

city: Copenhagen N

first: Rabiah

last: Fardoos

address: Blegdamsvej 3B

department: Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

summary: SARS-CoV-2 infects epithelial cells of the human gastrointestinal (GI) tract and causes related symptoms. HIV infection impairs gut homeostasis and is associated with an increased risk of COVID-19 fatality. To investigate the potential link between these observations, we analyzed single-cell transcriptional profiles and SARS-CoV-2 entry receptor expression across lymphoid and mucosal human tissue from chronically HIV-infected individuals and uninfected controls. Absorptive gut enterocytes displayed the highest coexpression of SARS-CoV-2 receptors ACE2, TMPRSS2, and TMPRSS4, of which ACE2 expression was associated with canonical interferon response and antiviral genes. Chronic treated HIV infection was associated with a clear antiviral response in gut enterocytes and, unexpectedly, with a substantial reduction of ACE2 and TMPRSS2 target cells. Gut tissue from SARS-CoV-2–infected individuals, however, showed abundant SARS-CoV-2 nucleocapsid protein in both the large and small intestine, including an HIV-coinfected individual. Thus, upregulation of antiviral response genes and downregulation of ACE2 and TMPRSS2 in the GI tract of HIV-infected individuals does not prevent SARS-CoV-2 infection in this compartment. The impact of these HIV-associated intestinal mucosal changes on SARS-CoV-2 infection dynamics, disease severity, and vaccine responses remains unclear and requires further investigation.

overall_design: We have used unique tissue samples from HIV infected individuals and performed a comprehensive global single cell transcriptional profiling of putative SARS-CoV-2 target cells

first: Osaretin

middle: E

last: Asowata

first: Nicholas

last: Herbert

first: Sarah

middle: K

last: Nyquist

first: Yenzekile

last: Zungu

first: Alveera

last: Singh

first: Abigail

last: Ngoepe

first: Ian

last: Mbano

first: Ntombifuthi

last: Mthabela

first: Dirhona

last: Ramjit

first: Farina

last: Karim

first: Warren

last: Kuhn

first: Fusi

middle: G

last: Madela

first: Vukani

middle: T

last: Manzini

first: Frank

last: Anderson

first: Bonnie

last: Berger

first: Tune

last: Pers

first: Alex

last: Shalek

first: Alasdair

last: Leslie

first: Henrik

last: Kløverpris


title: Transcriptome data of WT and Ddb1-KO activated CD4+ T cells

status: Public on Aug 19 2021

city: xiamen fujian

first: Nengming

last: Xiao

address: xiangan south road

institute: School of Life Sciences, Xiamen University

summary: The goals of this study are to compare the transcriptome profiling (RNA-seq) of wild type and Ddb1-knock out activated CD4+ T cells

overall_design: We sorted Ddb1-KO and WT SMARTA cells in adoptive transfer experiments at day 5 after LCMV Armstrong infection, and performed RNA-sequencing (RNA-seq) analysis of these cells.

first: Lingtao

last: Yang


title: Multi-omics analysis of neuroblastoma cells reveals a diversity of  malignant transformations

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

summary: Neuroblastoma (NB) is a pediatric cancer of the developing sympathetic nervous system that exhibits significant variation in the stage of differentiation and cell composition of tumours. Global loss of DNA methylation and genomic 5-hydroxymethylcytosine (5hmC) is a hallmark of human cancers. Here, we used our recently developed single base resolution approaches, hmTOP-seq and uTOP-seq, for construction of 5hmC maps and identification of large hypomethylated domains (PMDs) in different NB cell subpopulations. The 5hmC profiles revealed distinct signatures characteristic of different cell lineages and stages of malignant transformation of NB cells in a conventional and oxygen depleted environment, which often occurs in tumours. The analysis of the cell type-specific PMD distribution highlighted differences in global genome organization among NB cells that were ascribed to the same lineage identity by transcriptome assays. Collectively, we demonstrated a high informativeness of the integrative epigenomic and transcriptomic research in relation to large scale genome structure in investigating the mechanisms that regulate cell identities and developmental stages of NB cells. Such multi-omics analysis, as compared to mutational studies, open new ways for identification of novel disease-associated features which bring prognostic and therapeutic value in treating this aggressive pediatric disease.

overall_design: 5-hydroxymethylcytosine, unmodified CG sites and RNA expression analysis in neuroblastoma cell lines and their clonal subpopulations cultivated in hypoxic and normoxic conditions.

first: Milda

last: Narmontė

first: Povilas

last: Gibas

first: Kristina

last: Daniūnaitė

first: Juozas

last: Gordevičius

first: Edita

last: Kriukienė


title: Genome-wide transcriptome profiling of human organoids, colon intestine-chip and human alveolus-chips using RNA-seq

first: S. Jordan

last: Kerns

address: 27 Drydock Ave

institute: Emulate

summary: The goal of this study was to compare RNA expression of the A) CEA gene obtained from i) colon intestine organoids cultured in conventional plastic-adherent Matrigel drop overlaid with growth medium; ii) Colon Intestine-Chips derived from organoids in the presence of constant flow and stretch; iii) human colon intestine tissue and to verify whether Colon Intestine-Chip faithfully recapitulates human duodenum tissue and to better understand how much it differs from the organoids from which it’s derived, and B) FLOR1 gene obtained from i) human alveolar epithelial cells in T-25 Flasks, ii) human Alveolus Lung-Chip on day 5 and day 10 of the culture.

overall_design: Global RNA expression profiles of colon intestine organoids (Organoids; n=3); Colon Intestine-Chips derived from organoids (Colon Intestine-Chip; n=3); Alveolus epithelial-cells Day 0 (n=3); Alveolus Lung-Chip Day 5 (n=3); Alveolus Lung-Chip Day 10 (n=3) were generated by deep sequencing using Illumina HiSeq 4000.

first: S

first: Dimitris

last: Manatakis


title: A mechanism of cooling hot tumors: lactate attenuates inflammation in dendritic cells [BMDCs]

first: Hisashi

last: Kanemaru

summary:
Lactic acid (LA) accumulation in the tumour environment occurs as a result of the accelerated glucose metabolism in tumour cells, the so-called Warburg effect.
Because TLR4 agonists are one of the damage-associated molecular patterns, which are important stimulators of dendritic cells in the tumour microenvironment, we assessed the effects of LA on the response to LPS, the TLR4 ligand.

overall_design: We performed microarray analyses using bone marrow-derived dendritic cells (BMDCs) from WT mice that had been stimulated with LPS, LA, or LPS together with LA.


title: Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells [Affymetrix]

status: Public on Aug 17 2021

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

summary: Stromal-derived follicular dendritic cells (FDCs) are essential for germinal centers (GCs), the site where B cells maturate their antibodies. FDCs present native antigen to B cells and maintain a CXCL13 gradient to form the B cell follicle. Yet despite their essential role, the transcriptome of human FDCs remains undefined. Using single-cell RNA sequencing and microarray, we provided the transcriptome of these enigmatic cells as a comprehensive resource. Key genes were validated by flow cytometry and microscopy. Surprisingly, marginal reticular cells (MRCs) rather than FDCs expressed B cell activating factor (BAFF). Furthermore, we found that human FDCs expressed TLR4 and can alter antigen availability in response to pathogen-associated molecular patterns (PAMPs). High expression of PD-L1 and PD-L2 on FDCs activated PD1 on T cells. In addition, we found expression of genes related to T cell regulation, such as HLA-DR, CD40, and others. These data suggest intimate contact between human FDCs and T cells.

overall_design: 12 samples of 4 celltype, 1 conditions with 3 replicates

first: Kyah

last: van Megesen

first: Ilhan

last: Tomris

first: Robert

middle: P

last: de Vries

first: Giuliana

last: Magri

first: Hergen

last: Spits


title: Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells [scRNA-seq]

overall_design: Single cell sequencing of human Follicular Dendritic Cells (FDC) from Tonsil


title: A mechanism of cooling hot tumors: lactate attenuates inflammation in dendritic cells [EGR1-KO]

summary: We assessed the role of early growth response protein 1 (EGR1) in dendritic cells.

overall_design: We performed microarray analyses using bone marrow-derived dendritic cells (BMDCs) from WT and EGR1-deficient mice.


title: Limited access to antigen drives the generation of early B cell memory while restraining the plasmablast response

city: Solna

first: Taras

last: Kreslavsky

address: Nks Bioclinicum, J7:30, Visionsgatan 4

department: Department of Medicine, Solna (MedS)

country: Sweden

institute: Karolinska Institutet

summary: The cell fate decisions between plasmablasts (PBs), germinal center B cells (GCBCs) and non-GC-derived memory B cells (MBCs) during early B cell activation determine the outcome of the immune responses to pathogens and vaccines. In this study, we dissected these poorly characterized lineage choices by single-cell RNA-sequencing. Early after immunization, a homogenous population of activated precursors (APs) gave rise to a transient wave of PBs, followed a day later by the emergence of the first GCBCs, with the transcriptomes of both rapidly diverging from that of APs. The majority of APs started to withdraw from the cell cycle very early on and gave rise to GC-independent MBCs, a developmental transition that involved limited transcriptional changes. These events were controlled by antigen availability, and provision of antigen excess interfered with cell cycle exit and induced a new wave of PBs. Fate mapping experiments revealed a prominent contribution of GC-independent memory to the overall MBC pool. Quiescent cells with an MBC phenotype also dominated the early response to immunization in primates, indicating evolutionary conservation. Thus, excess APs, kept in reserve as early MBCs, can be rapidly re-recruited if failure to contain a threat is manifested by increased antigen availability, thus providing a feedback mechanism for rapid readjustment of the immune response.

overall_design: 16 bulk RNA-seq samples

first: Vassilis

last: Glaros

first: René

last: Rauschmeier

first: Artem

last: Artemov

first: Annika

last: Reinhardt

first: Sebastian

last: Ols

first: Aikaterini

last: Emmanouilidi

first: Charlotte

last: Gustafsson

first: Yuanyuan

last: You

first: Claudio

last: Mirabello

first: Åsa

last: Björklund

first: Laurent

last: Perez

first: Neil

last: King

last: Månsson

first: Davide

last: Angeletti

first: Karin

last: Loré

first: Igor

last: Adameyko

first: Meinrad

last: Busslinger


title: The bulges control in pri-miRNA processing in the position and strand-dependent manner

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: The microRNA (miRNA) biogenesis is responsible for the production of miRNAs that play critical roles in gene expression and numerous human diseases. The adequate biogenesis of miRNAs is largely determined by the efficiency and fidelity of primary microRNA (pri-miRNA) processing by Microprocessor. Here, we investigated the roles of a secondary RNA element, an RNA bulge, in pri-miRNA processing. We discovered that the 3p-strand bulges in positions 7-9 from the Microprocessor cleavage sites (midB_7-9) contributes to determining the cleavage sites of Microprocessor, the 5p- and 3p-strand bugles in positions 10-12 (midB_10-12) blocked the unproductive cleavage, and the 3p-strand bulges in positions 6-7 (seedB) inhibited the productive cleavage of Microprocessor. The 5p-strand midB_10-12 was found enriched and conserved in many pri-miRNAs of humans and other organisms. In addition, by analyzing the published Microprocessor-RNA structure and doing mutagenesis, we identified several amino acid residues of Microprocessor that explains a structure basis for the processing inhibition caused by seedB. The revealed functions of bulges in our study improves our understanding of the pri-miRNA processing by Microprocessor and implies their roles in regulating miRNA expression.

overall_design: HCT116 cells were transfected with pcDNA3.0 plasmids encoding pri-mir-342 or its variants. Small RNA sequencing libraries of the transfected cells were generated. The experiment was repeated three times.

first: Tuan

first: Thi

last: Le

first: Shaohua

last: Li

first: Trung

middle: D


title: Transcriptional profiling of Cdh1-associated genes in mouse melanoma.

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

institute: National Center for Geriatrics and Gerontology

summary: To analyze the effects of Cdh1 signaling on melanoma properties, we performed microarray analysis to identify genes induced by soluble Cdh1 in mouse melanoma cell line B16-F10.

overall_design: B16-F10 cells were stimulated with recombinant Cdh1 for 24 hours and gene expression was analyzed in control and stimulated B16-F10 cells. Two independent sets  (-/+ Cdh1)  were analyzed.

first: Koichiro

last: Kawaguchi

first: Kaori

last: Komoda


title: Transcriptional Network Analysis Reveals the Role of miR-223-5p During Diabetic Corneal Epithelial Regeneration

first: Bin

last: Zhang


title: Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease Mechanisms [scRNA-Seq]

first: Robert

last: Sebra

overall_design: Three technical replicates for olfactory bulb and prefontal cortex tissues from Patient 1.

first: Carlos

last: Cordon-Cardo


title: YAP regulates NFI/KLF5 transcriptional and epigenetic networks directing alveolar epithelial cell differentiation

status: Public on Aug 16 2021

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: Aberrant Yap expression alters AT2 cell differentiation via chromatin remodeling, NFIB and  KLF5 resulting in  abnormal AT1 differentiation, multi linage AT2 cells and doublet AT2 cells.

overall_design: Yap activation or deletion in PND3 mouse AT2 cells sacrificed and analyzed at PND14

first: Jason

middle: J

last: Gokey

first: Anusha

last: Sridharan

first: Parvathi

last: Sudha

first: Joseph

last: Kitzmiller

last: Sridhara

first: Yan

last: Xu

first: Jeffrey

last: Whitsett


title: Reconstructing aspects of human embryogenesis with pluripotent stem cells

status: Public on Aug 13 2021

city: Pasadena

first: Victoria

last: Jorgensen

state: CA

address: 1200 E California Blvd.

department: Biology and Bioengineering

institute: California Institute of Technology

summary: We have established an in vitro model that reconstructs aspects of human embryogensis using human expanded potential pluripotent stem cells (hEPSCs). We performed single-cell RNA sequencing (scRNA-seq) on hEPSCs grown in 2D (prior to aggregation), hEP-structures at day 5, hEP-structures grown in IVC for 24h, and natural human blastocysts at day 5/6.

overall_design: Single cell transcriptome analysis of hEPSCs grown in 2D (2 replicates), hEP-structures at Day 5 (3 replicates), hEP-structures at Day 6 (3 replicates), and D5/D6 natural human embryos (6 embryos).

first: Berna

last: Sozen

first: Sisi

last: Chen


title: Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease Mechanisms

overall_design: Refer to individual Series


title: The Rac1/Cdc42 regulator CdGAP promotes prostate cancer metastasis by regulating epithelial-to-mesenchymal transition, cell cycle progression, and apoptosis

status: Public on Aug 12 2021

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

summary: The high mortality of prostate cancer (PCa) patients is primarily due to metastasis, which can be associated with castration-resistant PCa. Therefore, understanding the mechanisms controlling metastatic processes remains essential to improve the success of targeted therapies. The Rac1/Cdc42 regulator CdGAP (Cdc42 GTPase-activating protein) has been implicated in fundamental cellular processes involved during cancer progression. Here, we demonstrate that elevated CdGAP expression is associated with early biochemical relapse (BCR) and bone metastasis in PCa patients. Furthermore, gene expression analysis of CdGAP in PCa data sets revealed a positive association between high CdGAP expression and early BCR. CdGAP protein and mRNA levels were elevated in PC-3 cells with high metastatic potential compared to low levels of CdGAP in the androgen receptor positive LNCaP cell line. Knockdown of CdGAP in PC-3 cells reduced cell motility, invasion, proliferation and colony-formation ability while inducing an increase in cell apoptosis. Conversely, overexpression of CdGAP in DU-145 cells increased cell migration and invasion. Using global gene expression approaches we found that CdGAP regulates the expression of genes involved in EMT, apoptosis and cell cycle progression. Subcutaneous injection of CdGAP-depleted PC-3 cells into mice showed a delayed tumor initiation and attenuated tumor growth. Orthotopic prostate injection of CdGAP-depleted PC-3 cells reduced cancer metastasis to kidneys, bones, and testis. Collectively, these findings support a pro-oncogenic role of CdGAP in prostate tumorigenesis and unveil CdGAP as a novel biomarker and potential target for prostate cancer treatments.

overall_design: Differential gene expression profile between control shRNA (shCon) PC-3 cells and shCdGAP PC-3 cells.

first: Jean-François

last: Côté

first: Nathalie

last: Lamarche

first: David

last: Labbé


title: Mechano-Hypoxia Conditioning of Engineered Human Meniscus

city: Edmonton

first: Adetola

middle: B

last: Adesida

state: Alberta

address: 3.002E Li Ka Shing Centre for Health Research Innovation

department: Surgery

institute: University of Alberta

summary: Meniscus fibrochondrocytes (MFCs) experience simultaneous hypoxia and mechanical loading in the knee, conditions that have promising applications in human meniscus tissue engineering. We hypothesized that “mechano-hypoxia conditioning,” using mechanical loading such as dynamic compression (DC) and cyclic hydrostatic pressure (CHP), would enhance development of human meniscus fibrocartilage extracellular matrix in vitro. MFCs from inner human meniscus surgical discards were pre-cultured on porous type I collagen scaffolds with TGF-β3 supplementation to form baseline tissues with newly-formed matrix. They were then treated with DC or CHP under hypoxia (HYP, 3% O2) for 5 days. DC was the more effective load regime, and combined HYP/DC enhanced gene expression of fibrocartilage precursors. The individual treatments of DC and HYP regulated thousands of genes and combined in an overwhelmingly additive rather than synergistic manner. Baseline tissues were then treated with a short course of DC (5 vs 60 minutes, 10-20% vs 30-40% strain) with different pre-culture durations (3 vs 6 weeks). Longer courses of loading had diminishing returns in terms of gene regulation. There was a dose-effect for higher DC strains, whereas outcomes were mixed for different MFC donors in pre-culture durations. Finally, baseline tissues were conditioned for 3 weeks with mechano-hypoxia conditioning to assess mechanical and protein-level outcomes. There were 1.8 to 5.1-fold gains in the dynamic modulus relative to baseline in HYP/DC, but matrix outcomes were equal or inferior to static controls. Long-term mechano-hypoxia conditioning was effective in suppressing hypertrophic markers (e.g., COL10A1 10-fold suppression vs static/normoxia). Applied appropriately, mechano-hypoxia conditioning can support meniscus fibrocartilage development in vitro and may be useful as a strategy for developing non-hypertrophic articular cartilage using mesenchymal stem cells.

overall_design: Examination completed using 12 sequenced samples. These came from 3 meniscus donors (4 samples per donor). Each donor had 2 samples treated in hypoxia and 2 in normoxia. In each oxygen tension, the treatments were Dynamic Compression (DC) or Static Vehicle Control (Stat). Each individual sample came from pooled equal masses of RNA from 4 biological replicates in the same condition from the same donor.

first: Alexander

middle: R

last: Szojka

middle: X

last: Li

first: Malou

last: Sopcak

first: Zhiyao

last: Ma

first: Melanie

last: Kunze

first: Aillette

last: Mulet-Sierra

first: Samer

last: Adeeb

first: Lindsey

last: Westover

first: Nadr

last: Jomha


title: Defining a methylation signature associated with operational tolerance in renal transplant

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: Operational tolerance after solid organ transplantation is defined as stable graft acceptance without immunosuppression while maintaining normal immunocompetence against immunological insults. However, it is not clear yet which cellular and molecular pathways are driving tolerance in these patients and how this state can be induced in order to improve graft survival. Several transcriptomic analysis have shown that transcription signatures in blood can reflect the immunological state associated with operational tolerance in kidney transplant. Nonetheless, epigenetic dynamics orchestrating these transcription signatures have not yet been studied. Here, we performed genome-wide analysis of DNA methylation of kidney transplant recipients with chronic rejection and operational tolerance. Our data showed that chronic rejection and operational tolerance recipients have differential DNA methylation in 2737 genes, indicating that each patient group has a specific epigenetic signature associated with transplant outcome. In addition, we observed that operational tolerance is associated with DNA demethylation in genes involved in immune function, including B cell activation (e.g. ST6GAL1, MS4A1 and MEF2C) and the Th17 differentiation program (e.g. LY9 and BATF), while in CR patients is mostly associated intracellular signaling and ubiquitination pathways. Finally, we used weighted gene co-expression network analysis (WGCNA) to select the more defining epigenetic changes associated with operational tolerance. By this method, we select 12 genomic regions specifically hypomethylated (HIVEP2, HOMER1, UTRN, PTPRO, SP100 and JAZF1) or hypermethylated (EMZ8, EZR-AS, WDR20, NADSYN1, TBCD and MED17) in  tolerant patients. Analysis of these genes in stable transplant recipients with immunosuppression showed that these patients have a similar methylation signature to operational tolerance recipients. Overall, these results demonstrate that DNA methylation in blood can mirror the immune status associated with kidney transplant outcome and provides a starting point for understanding the epigenetic mechanisms associated with operational tolerance.

overall_design: 22 samples in total (7 healthy volunteers, 6 chronic rejection patients, 9 operational tolerance patients)

first: Ramon

last: Rodriguez

first: Viviana

last: Corte-Iglesias

first: Juan

last: Lozano

last: Cortazar

first: Maria

last: Hernandez-Fuentes

first: Carlos

last: Lopez-Larrea

first: Beatriz

last: Suarez-Alvarez


title: Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast [SNP array]

status: Public on Aug 11 2021

city: La Jolla

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: During pregnancy, normal extravillous trophoblast (EVT) invade the endomyometrium of the maternal uterus and remodel the spiral arteries to control blood supply and nutrient transfer. Recent reports have described first trimester EVT as polyploid and senescent. Here we extend these earlier reports by performing comprehensive profiling of the genomic organization and transcriptome of first trimester EVT and term EVT. We define pathways and gene regulatory networks involved in both initial differentiation and maturation of this important trophoblast lineage at the maternal-fetal interface. Our results suggest that like first trimester EVT, term EVT undergo senescence and endoreduplication, are primarily tetraploid, and lack high rates of copy number variations. Additionally, we have highlighted senescence and polyploidy-related genes, pathways, networks, and transcription factors that appeared to be important in normal EVT differentiation and maturation and have validated a critical role for the unfolded protein response in EVT differentiation.

overall_design: A total of 13 samples were analyzed (two first trimester EVT, two first trimester CTB, three term EVT, three term CTB, and three umbilical cord MSC). The samples were isolated from a total of five placentas (two first trimester placentas and three term placentas). Matched EVT and CTB were isolated from all five placentas and MSCs were isolated from the three term placentas as controls. One of the CTB samples (1391) was removed from analysis due to poor call rates.

first: Mana

last: Parast


title: CARM1 determines endoplasmic reticulum stress response by controlling XBP1 in ovarian cancer

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

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


title: Why some rainbow trout genotypes grow better with a complete plant-based diet? A transcriptomic and physiological analyses on three isogenic lines

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

country: France

institute: INRA

summary: We have investigated the mechanisms behind the response to a plant based diet over a long term period by comparing the transcriptome of 3 isogenic lines (R23h, AB1h, A22h) of rainbow trout. These families represent an interesting genetic materiel to work on as they have similar responses when fed marine based-diet (M diet) but highly different responses when fed a plant-based diet (V diet). Fish were fed since 1st feeding with either a plant-based diet, or a marine diet (ad libitum (M diet) or restricted (MR)). We  showed that differences in the ability to grow with the V diet observed amongst genotypes was not due to higher feed intake, but to higher feed efficiencies. The comparison of transcriptome profiles revealed 575, 1770 and 2973 probes differentially expressed amongst the three genotypes when fed the V diet. Interestingly, genotypes which were the less affected by the V diet had exhibited the highest growth. These results demonstrated that those fish were able to maintain energy production and protein synthesis. Moreover, those genotypes were also able to activate pathways linked to lipid and cholesterol metabolism, such as the biosynthesis of omega 3 LC-PUFA. Finally, as it has already been demonstrated, immunity seems also to play an important role in the ability of fish to use the V diet, and further investigations are needed to understand by which ways immunity interacts with growth.

overall_design: Transcriptomic response were studied in the liver of 3 isogenic lines (R23h, AB1h, A22h). Fish were fed since the 1st feeding with either a plant-based diet completly devoid of fish oil and fish meal (V diet) or a marine resources based diet (ad libitum: M diet or restricted: MR diet). Sampling took place after 6 months of feeding (n=6/condition).

first: Mathilde

last: Dupont-Nivet

first: Françoise

last: Médale


title: Polη-ChIP-seq

first: Jan

middle: Eric

last: Grosser

address: Solnavägen 9

institute: Karolinska institutet

summary: Polη-ChIP-seq analysis to investigate genome-wide distribution of Polη in budding yeast.

overall_design: Strains of interest were arrested in G2/M, followed by a site specific double strand breaks (PGAL-HO) induction for one hour. Cells were harvested before and after DSB-induction and proceed to immunoprecipitation. Polη was immunoprecipitated by the C-terminal Myc tag. Untagged strain was included as control.

first: Lena

last: Ström

first: Pei-Shang

last: Wu

first: Donald

last: Cameron

first: Laura

last: Baranello


title: RNA sequence of the subcutaneous microenvironment surrounding the rabbit's engineered cartilage

city: Shanghai

first: Tianji

last: Ji

state: Shanghai

address: 1678 Dongfang Road

department: Department of Pediatric Cardiology

institute: Shanghai Children's Medical Center

summary:
Purpose: To identify how axitinib stabilized the rabbit's engineered cartilage through the niche
Methods: Rabbit's engineered cartilage was encapsulated in the PCL/collagen nanofibrous membrane containing no axitinib (0%-Axitinib group) or 3% axitinib (3%-Axitinib group) and implanted into nude mice. After 12 weeks of implantation,  samples from the 0%-Axitinib group and 3%-Axitinib group were harvested, with the murine tissues entangled. Transcriptional profiles were generated by deep sequencing, in triplicate, using an Illumina HiSeqTM2000 machine, and filtered using Fastp software. The trimmed reads were mapped to the mouse genome (mm10, genome.UCSC.edu) using the STAR software to identify the transcriptional information in the niche of engineered cartilage. Then, the DESeq2 “counts” function of the R package was used to normalize gene expression levels based on the number of total reads of each sample. Differentially expressed genes between the 0%-Axitinib group and 3%-Axitinib group were identified as meeting the criteria of fold change ≥ 1.5 and P-value＜0.05. Lastly, we used Metascape (http://metascape.org) for gene ontology analysis.
Results: Using an optimized data analysis workflow, we mapped about 20 to 30 million sequence reads per sample to the mouse genome (build mm10) and identified 20318 transcripts in the 0%-Axitinib and 3%-Axitinib groups. 837 genes were differentially expressed by more than 1.5-fold, p-value <0.05, with 313 genes downregulated and 524 genes upregulated in the 3%-Axitinib group. Gene ontology (GO) analysis revealed that the genes downregulated in the 3%-Axitinib group were mainly enriched in endothelial development, angiogenesis, and immune response. Genes upregulated in the 3%-Axitinib group were mainly enriched in response to hypoxia, Hif-1 signaling pathway, cartilage differentiation and development, and muscle structure development.  Altered expression of 15 genes was further illustrated by heatmap, demonstrating the inhibited angiogenesis and improved chondrogenesis. Especially, Timp1, as a response to hypoxia, was remarkably upregulated, which also in turn inhibited the activity of matrix metalloproteinases (MMPs) and played an important role in preventing ossification.
Conclusion: In this study, we proposed the first detailed transcriptional analysis of the effects of the sustainable and localized release of axitinib on the subcutaneous niche of engineered cartilage. The sustainable and localized release of axitinib created a relatively avascular, hypoxia, and low immune response niche in the 3%-Axitinib group. In this niche, Timp1 was remarkably upregulated, which inhibited the activity of MMPs and prevented endochondral ossification.

overall_design: mRNA profiles of murine tissues surrounding the rabbit's engineered cartilage in  0%-Axitinib  and 3%-Axitinib groups after 12-week subcutaneous implantation

first: Tian-Ji

first: Fen

last: Li

first: Min

last: Zhang


title: Transcriptomic analysis of short/branched-chain acyl-coenzyme A dehydrogenase knocked out bMECs revealed its regulatory effect on lipid metabolism

status: Public on Aug 10 2021

city: Zhanjiang

first: Ping

last: Jiang

address: Mazhang district haida street

department: College of Coastal Agricultural Sciences, Guangdong Ocean University

summary: The 21st century is an era of molecular breeding, leading to fundamental dairy market and production system changes. Milk fat is the main economic trait in dairy cattle production. Our previous study revealed that the ACADSB gene has a crucial regulatory role in lipid metabolism, which can alter the contents of TGs, CHOL and fatty acids by regulating some related gene which involve in lipid metabolism. As usual, when we explored the function of interest genes, we often design interference and overexpression vectors to regulate the expression level of related gene, and transiently transfect vectors into cells, however, it is limited by transfection efficiency. therefore, we committed to finding a stable mode of gene expression. Knocking out of the ACADSB gene in bovine mammalian epithelial cells (bMECs), which represents a promising and effective means of further research on the effects of ACADSB in vivo lipid metabolism of dairy cattle. At the same time, the knock-out ACADSB gene's bMECs could also be useful genetic material and tools for future research into gene functions related to lipid and fatty acid metabolism, which also can directly use for further exploring the gene molecular mechanism or related pathway.

overall_design: RNA  sequence between three ACADSB knock out bovine mammalian epithelial cells (bMECs) cell line and BMECs

first: Zhihui

last: Zhao


title: CARM1 determines endoplasmic reticulum stress response by controlling XBP1 in ovarian cancer [RNA-seq]

summary: Cancer cells exploit adaptive responses such as endoplasmic reticulum (ER) stress to support their survival.  ER stress response is mediated in part by the ER-localized transmembrane sensor IRE1α endoribonuclease and its substrate XBP1 to regulate XBP1 target gene expression.  However, the mechanism that controls the IRE1α/XBP1 pathway remains poorly understood. CARM1 is an oncogene that is often overexpressed in a number of cancer types including ovarian cancer. Here we report that CARM1 determines ER stress response by controlling the IRE1α/XBP1 pathway. Genome-wide profiling revealed that CARM1 regulates XBP1 target gene expression during ER stress response. CARM1 directly interacts with XBP1.  Inhibition of the IRE1α/XBP1 pathway was effective in ovarian cancer in a CARM1-dependent manner both in vitro and in vivo in orthotopic and patient-derived xenograft models.  In addition, IRE1α inhibitor B-I09 synergizes with immune checkpoint blockade anti-PD1 antibody in an immunocompetent CARM1-expressing ovarian cancer model.

overall_design: RNA-seq and Cut&Run in control cells and cells treated with tunicamycin (TM)

first: Rugang

first: Jianhuang

last: Lin


title: Expression data from CD115+ preosteoclasts stimulated by conditioned medium from CT-26 cells

status: Public on Aug 14 2021

city: Chongqing

first: Ziming

last: Wang

address: #10, Changjiang Branch road

institute: Army Medical Center, Army Medical University

summary:
In osteolytic tumor, bone resportion can be occured after bone metastasis. Bone metastasis of colorectal cancer can induce obvious bone destruction. Aberrant activation of osteoclasts and the precursors is responsible for tumor-induced osteolysis.  The biological process of osteoclast precursors could be modified by different tumor microenvironment.
Microarrays were used to detail the differentially expressed genes or non-coding RNAs between normal osteoclast precursors and osteoclast precursors treated by secreta from CT-26 cells.

overall_design: We sorted out primary osteoclast precursors labelled with CD115. CD115+ osteoclast precursors were treated by conditioned medium from colorectal cancer cell line, CT-26 or normal culture medium.

first: Zi-ming


title: Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast [RNA-seq]

first: Robert

last: Morey

overall_design: Paited-end mRNA-seq was performed on 36 placental samples (10 first trimester CTB, 10 first trimester EVT, 10 term CTB, and 6 term EVT). First trimester placentae were between 10 and 16 weeks and term placentae were between 37 and 40 weeks.

first: Mana

middle: M

last: Parast


title: Activation of STING pathway contributed to cisplatin-induced cardiac dysfunction via promoting the activation of TNF-α-AP-1 signal pathway

city: Nanjing

first: Lintao

state: Jiangsu

address: Long Mian Da Dao

institute: China Pharmaceutical University

summary: In this study, cisplatin activated cGAS-STING signal pathway and deficiency of STING attenuated cisplatin-induced cardiotoxicity in vivo and in vitro. Mechanistically, STING-TNF-α-AP-1 axis contributed to cisplatin-induced cardiotoxicity by triggering cardiomyocyte apoptosis.

overall_design: Mice were randomly divided into four groups: saline group (Saline, n=6), cisplatin group (CDDP, n=6), STING-/- group (STING-/-, n=6), STING-/-+cisplatin group (STING-/-+CDDP, n=6). Cisplatin (6 mg/kg) in 0.9% normal saline was administered by intraperitoneal injection on 1th day, 8th day and 15th day as previously reported

first: Suya

first: Jibo

last: Han

first: Xiaoyan

last: Nie


title: A novel processing-free method for RNAseq analysis of spontaneous sputum in chronic obstructive pulmonary disease

city: Parma

first: Mirco

last: Govoni

address: Largo Francesco Belloli 11/A

country: Italy

institute: Chiesi Farmaceutici

summary:
Background: Assessments of airways inflammation in patients with chronic obstructive pulmonary diseases (COPD) require semi-invasive procedures and specialized sample processing know-how. In this study we aimed to set up and validate a novel non-invasive processing-free method for RNA sequencing (RNAseq) of spontaneous sputum samples collected from COPD patients.
Methods: Spontaneous sputum samples were collected and stabilized, with or without selection of plugs and with or without the use of a stabilizer specifically formulated for downstream diagnostic testing (PrimeStore® Molecular Transport Medium). After 8-day storage at ambient temperature RNA was isolated according to an optimized RNAzol® method. An average percentage of fragments longer than 200 nucleotides (DV200) >30% and an individual yield >50ng were required for progression of samples to sequencing. Finally, to assess if the transcriptome generated would reflect a true endotype of COPD inflammation, the outcome of single-sample gene-set enrichment analysis (ssGSEA) was validated using an independent set of processed induced sputum samples
Results: RNA extracted from spontaneous sputum using a stabilizer showed an average DV200 higher than 30%. 70% of the samples had a yield >50ng and were submitted to downstream analysis. There was a straightforward correlation in terms of gene expression between samples handled with or without separation of plugs. This was also confirmed by principal component analysis and ssGSEA. The top ten enriched pathways resulting from spontaneous sputum ssGSEA were associated to features of COPD, namely, inflammation, immune responses and oxidative stress; up to 70% of these were in common within the top ten enriched pathways resulting from induced sputum ssGSEA.
Conclusion: This analysis confirmed that the typical COPD endotype was represented within spontaneous sputum and supported the current method as a non-invasive processing-free procedure to assess the level of sputum cell inflammation in COPD patients by RNAseq analysis.

overall_design: A bulk-RNA sequencing of spontaneous sputum was performed, samples from 7 subjects were collected and stabilized with or without selection of plugs

first: Francesca

last: Ricci

first: Michele

last: Bassi

first: Cathy

last: McGeough

first: Gera

middle: L

last: Jellema


title: Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

institute: INRAE - Aix Marseille University

summary:
Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers.

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE156163
SuperSeries of: GSE156164
SuperSeries of: GSE156166
SuperSeries of: GSE156899

sample_organism:
Irpex lacteus
Trametes elegans
Cubamyces sp. BRFM 1775
Pilatotrama ljubarskyi


title: The Spleen as a Target to Characterize Immunomodulatory Effects of Down-Stream Processed Cyberlindnera jadinii Yeasts in Atlantic Salmon Exposed to a Dietary Soybean Meal Challenge

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

summary: In this experiment, we used four diets, one based on FM, a challenging diet with 40% soybean meal (SBM), and two diets containing 40% SBM with 5% of Cyberlindnera jadinii yeast exposed to different down-stream processing conditions (heat-inactivated or autolysation). The immunomodulatory effects of the diets were analyzed in the spleen of Atlantic salmon after 37 days of feeding. The results showed that the inclusion of autolysed C. jadinii (ACJ) was able to modulate the response of Atlantic salmon compared to fish fed the SBM-diet, through the activation of biological pathways related to endocytosis, PPRs-signal transduction and transporter activity. Finally, we suggest that the spleen is a good candidate to characterize the immunomodulatory effects of functional ingredients in Atlantic salmon.

overall_design:
Spleen mRNA profiles from Atlantic salmon after 37 days fed different functional diets.

Grants:
.Foods of Norway a Centre for Research-based Innovation (237841/030), Research Council of Norway
.Trained immunity and nutritional programming for resilient salmon (RCN 294821), Research Council of Norway

first: Margareth

last: Øverland


title: H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

city: Uppsala

first: Shujing

last: Liu

state: Uppsala

address: Torgny Segerstedts Alle 20

department: Plant Biology

institute: Swedish University of Agricultural Sciences

summary: Polycomb repressive complex 1 (PRC1) and PRC2 are chromatin regulators maintaining transcriptional repression by depositing H2A mono-ubiquitination (H2Aub) or H3 lysine 27 tri-methylation (H3K27me3), respectively. While PRC1 is known to be required for transcriptional repression, the contribution of H2Aub in the Polycomb repressive system remains unclear in plants. Here, we directly test the requirement of H2Aub for gene repression in Marchantia polymorpha by generating point mutants in H2A that fail to be ubiquitinated by PRC1. These mutants show reduced H3K27me3 levels on the same target sites as mutants in PRC1 subunits MpBMI1 and the homolog MpBMI1L, revealing that  PRC1-catalyzed H2Aub is essential for Polycomb system function. Furthermore, we demonstrate that H2Aub contributes to the PRC1-mediated silencing of genes and transposable elements. Together, our data provide evidence that H2Aub plays indispensable roles in the PRC1-initiated repressive system in Marchantia.

overall_design: ChIP-seq and RNA-seq

first: Minerva

middle: S

last: Trejo-Arellano

first: Yichun

last: Qiu

first: D

last: Eklund

first: Claudia

last: Köhler

first: Lars

last: Hennig


title: Next generation sequencing and de novo transcriptome analysis of Papilio clytia and Atrophaneura mencius larvae upon lipopolysaccharide challenge

city: Beijing

first: Xianda

last: Hu

address: 218 Anwaixiaoguanbeili St

country: China

institute: Beijing Tibetan Hospital, CTRC

summary: Gene expression profiling was performed by next generation sequencing strategy to explore the transcriptional changes of Papilio clytia and Atrophaneura mencius larvae in response to LPS challenge

sample_organism:
Papilio clytia
Byasa mencius

platform_organism:
Papilio clytia
Byasa mencius

overall_design: The fatbody tissues of Papilio clytia and Atrophaneura mencius larvae were collected for RNA isolation and high-throughput sequencing


title: Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast

first: Robert

middle: E

last: Morey

overall_design: Refer to individual Series


title: Inhibition of CK1e potentiates the therapeutic efficacy of CDK4/6 inhibitor in breast cancer

first: Chen

last: Chu

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

summary: In this study, we found that combination treatment of breast cells with CK1 inihbitor (D 4476) and CDK4/6 inhibitor (Ribociclib) exhibited greatly enhanced therapeutic efficacy than CDK4/6 inhiitor single treatment

overall_design: RNA-seq study of human triple negative breast cancer cell line MDA-MB-231 with DMSO, CDK4/6 inihbitor (Ribociclib) single treatment, Ribociclib and CK1 inhibitor (D 4476) combination treatment for 48 hours

first: Fabin

last: Dang

first: Li

last: Nie

first: Wenyi

last: Wei


title: Transcription is dysregulated in Polη-deficient cells

city: Solna

first: Pei-Shang

last: Wu

address: Tomtebodavägen 16

institute: Karolinska Institutet

summary: This RNA-seq analysis was performed to address transcriptional response of Polη-deficient cells (rad30Δ) before and after DSB-induction. We found that transcriptional response is dysregulated in the rad30Δ mutant regardless of DSBs, with decreased chromatin association of RNAPII on active genes. Based on these results, we further investigated formation of damage-induced cohesion in relation to active transcription.

overall_design: RNA-sequencing to compare gene expression between WT and Polη-deficient cells, before and after DSB-induction in G2/M phase.

first: Donald

last: Cameron

first: Jan

last: Grosser

first: Laura

last: Baranello

first: Lena

last: Ström


title: Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [ATAC-seq]

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

summary: Here, we describe CRISPRpath, a CRISPR screening strategy for simultaneously characterizing CREs in multiple genomic loci by leveraging converging phenotypes resulted from transcriptional defects in genes linked to the same biological pathway.

overall_design: Examination of chromatin accessibility (ATAC-seq) in WTC11 human iPSCs.

first: Xingjie

last: Ren


title: Microarray expression data of A375 eIF4B-knockout (KO; KO/LacZ) and eIF4B-rescued (KO/eIF4B) cells with or without vemurafenib treatment

city: Koto-ku

first: Hitomi

last: Shirahama

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

summary: Activating Transcription Factor 4 (ATF4) is a key transcription factor of the integrated stress response, which assists cells to survive in response to tumor microenvironmental and therapeutic stresses. BRAF inhibitors, such as vemurafenib, are also known to induce ATF4 in BRAF-mutated melanoma cells, but the mechanisms of ATF4 induction are not fully elucidated. Here, we show that ATF4 expression can be upregulated by eIF4B (eukaryotic initiation factor 4B) in BRAF-mutated A375 cells. In fact, knockout (KO) of eIF4B hindered ATF4 induction as well as ATF4 translation mechanism under vemurafenib treatment, which were effectively recovered by rescue of eIF4B. Transcriptome analysis revealed that eIF4B KO selectively affected ATF4-target gene expression among gene expression altered by vemurafenib. Our results indicate that eIF4B can contribute to cellular stress adaptation by regulating ATF4 expression.

overall_design: A375 eIF4B-knockout (KO) cells were established by CRISPR technology. Then, willdtype eIF4B gene or LacZ gene as a negative control was transduced by lentiviral system. The established stable cell lines (KO/eIF4B and KO/LacZ) were treated with 10 µM vemurafenib for 6 or 18 hours. Vehicle (DMSO) control samples were also preapred.

first: Yukie

last: Iwao

first: Yuka

last: Okamoto

first: Satomi

last: Tsukahara

first: Akihiro

last: Tomida


title: CARM1 determines endoplasmic reticulum stress response by controlling XBP1 in ovarian cancer [CUT&RUN]

first: Priyankara

last: Wickramasinghe

first: Rugang

last: Zhang

first: Jianhuang

last: Lin


title: Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath

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


title: Codon usage and protein length-dependent feedback from translation elongation to translation initiation and kinetics

city: Dallas

first: xueliang

last: lyu

state: Texas

address: 6001 Forest Park Road

department: Physiology

institute: UT Southwestern Medical Center

summary: In yeast and mammals, activated GCN2 can phosphorylate its substrate eIF2α, which is a part of the eIF2-GTP-Met-tRNAiMet ternary complex. The eIF2α phosphorylation blocks the ternary complex formation and therefore inhibits translation initiation. Meanwhile, GCN2 activation associates with ribosomes and some translation elongation factors such as eEF1A. In Neurospora crassa, the homolog of GCN2 is CPC-3. Ribosome profiling and accompanying RNA-seq experiments in this project were used to explore the effects of CPC-3 on translation kinetics. Here we show that poor codon usage of mRNAs with long CDS preferentially causes CPC-3 activation, which in turn suppresses the translation initiation and elongation in both codon usage and CDS length dependent manner.

overall_design: The ribosome protected fragment (RPF) profiles and transcription profiles of Δcpc-3 and wild-type strains of Neurospora crassa were generated by high-throughput sequencing

first: Xueliang

last: Lyu

first: Yi

last: Liu


title: Interferon Signaling After TBI in Aged Mice

city: Washington DC

first: Susan

last: Knoblach

state: District of Columbia

address: 111 Michigan Ave NW

department: Research Ctr for Genetic Medicine

institute: CNH

summary: Type I Interferons (IFN-I) contribute to the neuropathology of traumatic brain injury (TBI) and age-related neurodegenerative disease, where Cyclic GMP-AMP Synthase (cGAS) and the Stimulator of Interferon Genes (STING) pathway are implicated as key inducers of IFN-I responses. This study evaluated cGAS/STING activation, IFN-I signaling and neuroinflammation in the cortex and hippocampus of young and aged C57Bl/6 male mice, 24 hrs after controlled cortical impact injury. TBI increased expression of transcripts related to IFN-I signaling and activation of cGAS in the injured cortex of aged mice compared to younger mice.  These observations were confirmed by RT-PCR, western blotting and phosphorylation/activation of STAT1, a downstream IFN-I effector molecule

overall_design: Young (3 month-old) and aged (22 month-old) adult male C57Bl/6 mice (National Institute of Aging colony, Charles River Laboratories) were housed under a 12 hour light-dark cycle, with ad libitum access to food and water.  Under an approved Institutional Animal Care and Use Committee protocol, mice were anesthetized and subjected to mild controlled cortical impact, or identical preparation with no injury (sham).  Twenty-four hours later, mice were re-anesthetized, perfused with 0.9% saline (100 ml), and ipsilateral cortical and hippocampal tissues were removed and frozen in liquid nitrogen for RNA or protein extraction. Study groups (n=6, for each) were: young sham, young TBI, aged sham, and aged TBI.  One sample from the 3 month injured group was not included in the dataset/study as it did not meet NanoString quality control metrics.

first: James

last: Barrett

first: David

last: Loane


title: Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [Cut&Tag]

overall_design: Examination of histone modification (H3K4me3) and transcription factor binding (CTCF) in WTC11 human iPSCs.


title: Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [RNA-seq]

overall_design: Examination of gene expression with RNA-seq in WTC11 human iPSCs.


title: Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [ChIP-seq]

overall_design: Examination of histone modification (H3K27ac) in WTC11 human iPSCs.


title: Revealing the angiopathy of lacrimal gland lesion in type 2 diabetes

status: Public on Aug 08 2021

city: Qingdao

first: Bin

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

summary:
Purpose: The goals of this study are to compare type 2 diabetes lacrimal gland transcriptome profiling (RNA-seq) with the counterparts.
Methods: Lacrimal gland mRNA profiles of 24 weeks T2DM mice (C57 mice with high fat diet + STZ intraperitoneal injection) and counterparts were enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and the produced RNA was used for construction library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The prepared RNA-seq libraries were qualified using Agilent 2100 Bioanalyzer and quantified by qPCR absolute quantification method. The sequencing was then performed using Illumina NovaSeq 6000. After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered <=16 bp reads with cutadapt software. The trimmed reads were aligned to a reference genome with Hisat2 software. The transcript abundance for each sample was estimated with StringTie (v1.2.3), and the FPKM values for gene level were calculated with R package Ballgown (v2.6.0). The differentially expressed genes (DEGs) analysis was also performed with Ballgown. Fold change (cutoff 1.5), p-value (cutoff 0.05) and FPKM (≥0.5 mean in one group) were used for filtering differentially expressed genes and transcripts.
Conclusions: Our study represents the first detailed analysis of T2DM lacrimal gland transcriptomes, 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 showed that the vascular related genes were altered in the T2DM.

overall_design: Lacrimal gland mRNA profiles of 24 weeks T2DM mice (C57 mice with high fat diet + STZ intraperitoneal injection) and counterparts.

first: Junfa

last: Xue

first: Qingjun

last: Zhou


title: Astrocyte alterations that accompany neuroinflammation induced anhedonia

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: The Khakh laboratory sequenced RNA from both whole and astrocyte specific RNAs from mouse prefrontal cortex and visual cortex by using Aldh1l1-CreERT2 - RiboTag mice. RNA  was purified from controls and LPS injected mice, 1, 2 and 14 days after the injection.

overall_design: Mice were injected i.p. with PBS or LPS (5 mg/kg). 1, 2 and 14 days after the injection PFC and VCX were homogenized and RNA was purified from (i) cleared lysate as the input, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag. LPS samples were compared to PBS samples. PFC samples were compared to VCX samples.

first: Blanca

last: Diaz-Castro

first: Alexander

last: Bernstein

first: Michael

middle: V

last: Sofroniew

first: Baljit

last: Khakh


title: Translational Autoregulation of the S. cerevisiae High-affinity Polyamine Transporter Hol1

status: Public on Aug 09 2021

city: Bethesda

first: Thomas

last: Dever

state: MD

address: BG 6 RM 228 6 CENTER DR

department: NICHD

institute: National Institutes of Health

summary: Study is aimed to understand translation regulation of mRNA in low and high polyamines in S. cerevisiae. mRNA seq and Ribosome profiling were performed in yeast cells, in duplicates, under low (0 spermidine) and high (10 µM) spermidine. Translation efficiency was calculated (low vs high SPD) and GO analysis reveals 23 transporters as the only class undergo TE downregulation in high SPD condition. Further, we investigated role of these 23 transporters in polyamine transport and identified HOL1 as the high affinity polyamine transporter. This study further show that HOL1 is under polyamine control of translation regulation through conserved fungal uORF MLLLPS*.

overall_design: To understand mRNA translation regulation in low and high polyamines, ribosome profiling and total RNAseq were performed in duplicates under two conditions. In total, 8 datasets are generated, 4 of Riboseq and 4 of RNAseq.

first: Arya

last: Vindu

first: Byung

last: Sik-Shin