Gene Expression Profiles Of Fibroblasts Research Articles

Characterization of early psychosis patients carrying a genetic vulnerability to redox dysregulation: a computational analysis of mechanism-based gene expression profile in fibroblasts

In view of its heterogeneity, schizophrenia needs new diagnostic tools based on mechanistic biomarkers that would allow early detection. Complex interaction between genetic and environmental risk factors may lead to NMDAR hypofunction, inflammation and redox dysregulation, all converging on oxidative stress. Using computational analysis, the expression of 76 genes linked to these systems, known to be abnormally regulated in schizophrenia, was studied in skin-fibroblasts from early psychosis patients and age-matched controls (N = 30), under additional pro-oxidant challenge to mimic environmental stress. To evaluate the contribution of a genetic risk related to redox dysregulation, we investigated the GAG trinucleotide polymorphism in the key glutathione (GSH) synthesizing enzyme, glutamate-cysteine-ligase-catalytic-subunit (gclc) gene, known to be associated with the disease. Patients and controls showed different gene expression profiles that were modulated by GAG-gclc genotypes in combination with oxidative challenge. In GAG-gclc low-risk genotype patients, a global gene expression dysregulation was observed, especially in the antioxidant system, potentially induced by other risks. Both controls and patients with GAG-gclc high-risk genotype (gclcGAG-HR) showed similar gene expression profiles. However, under oxidative challenge, a boosting of other antioxidant defense, including the master regulator Nrf2 and TRX systems was observed only in gclcGAG-HR controls, suggesting a protective compensation against the genetic GSH dysregulation. Moreover, RAGE (redox/inflammation interaction) and AGMAT (arginine pathway) were increased in the gclcGAG-HR patients, suggesting some additional risk factors interacting with this genotype. Finally, the use of a machine-learning approach allowed discriminating patients and controls with an accuracy up to 100%, paving the way towards early detection of schizophrenia.

Adult skin fibroblast state change in murine wound healing

Wound healing is a well-organized dynamic process involving coordinated consecutive phases: homeostasis, inflammation, proliferation and resolution. Fibroblasts play major roles in skin wound healing such as in wound contraction and release of growth factors which are of importance in angiogenesis and tissue remodeling. Abnormal fibroblast phenotypes have been identified in patients with chronic wounds. In this work, we analyzed scRNA-seq datasets of normal and wounded skin from mice at day 4 post-wound to investigate fibroblast heterogeneity during the proliferative phase of wound healing. Compositional analysis revealed a specific subset of fibroblast (cluster 3) that primarily increased in wounded skin (14%) compared to normal skin (3.9%). This subset was characterized by a gene signature marked by the plasma membrane proteins Sfrp2 + Sfrp4 + Sfrp1 + and the transcription factors Ebf1 + Prrx1 + Maged1 + . Differential gene expression and enrichment analysis identified epithelial to mesenchymal transition (EMT) and angiogenesis to be upregulated in the emerging subset of fibroblasts of the wounded skin. Using two other datasets for murine wounded skin confirmed the increase in cluster 3-like fibroblasts at days 2, 7 and 14 post-wounding with a peak at day 7. By performing a similarity check between the differential gene expression profile between wounded and normal skin for this emerging fibroblast subset with drug signature from the ConnectivityMap database, we identified drugs capable of mimicking the observed gene expression change in fibroblasts during wound healing. TTNPB, verteprofin and nicotinic acid were identified as candidate drugs capable of inducing fibroblast gene expression profile necessary for wound healing. On the other hand, methocarbamol, ifosfamide and penbutolol were recognized to antagonize the identified fibroblast differential expression profile during wound healing which might cause delay in wound healing. Taken together, analysis of murine transcriptomic skin wound healing datasets suggested a subset of fibroblasts capable of inducing EMT and further inferred drugs that might be tested as potential candidates to induce wound closure.

Combined - whole blood and skin fibroblasts- transcriptomic analysis in Psoriatic Arthritis reveals molecular signatures of activity, resistance and early response to treatment.

BackgroundAn interplay between immune cells and resident skin and joint stromal cells is implicated in psoriatic arthritis (PsA), yet the mechanisms remain elusive with a paucity of molecular biomarkers for activity and response. Combined transcriptomic and immunophenotypic analysis of whole blood and skin fibroblasts could provide further insights.MethodsWhole blood RNA-seq was performed longitudinally in 30 subjects with PsA at the beginning, one and six months after treatment, with response defined at six months. As control groups, 10 healthy individuals and 10 subjects with rheumatoid arthritis (RA) were recruited combined with public datasets from patients with psoriasis (PsO) and systemic lupus erythematous (SLE). Differential expression analysis and weighted gene co-expression network analysis were performed to identify gene expression signatures, while deconvolution and flow cytometry to characterize the peripheral blood immune cell profile. In a subset of affected and healthy individuals, RNA-seq of skin fibroblasts was performed and subjected to CellChat analysis to identify the blood-skin fibroblast interaction network.ResultsPsA demonstrated a distinct “activity” gene signature in the peripheral blood dominated by TNF- and IFN-driven inflammation, deregulated cholesterol and fatty acid metabolism and expansion of pro-inflammatory non-classical monocytes. Comparison with the blood transcriptome of RA, PsO, and SLE revealed a “PsA-specific signature” enriched in extracellular matrix remodeling. This was further supported by the skin fibroblast gene expression profile, displaying an activated, proliferating phenotype, and by skin-blood interactome analysis revealing interactions with circulating immune cells through WNT, PDGF and immune-related semaphorins. Of note, resistance to treatment was associated with upregulation of genes involved in TGFβ signaling and angiogenesis and persistent increase of non-classical monocytes. Differentially expressed genes related to platelet activation and hippo signaling discriminated responders and non-responders as early as one month after treatment initiation.ConclusionTranscriptome analysis of peripheral blood and skin fibroblasts in PsA reveals a distinct disease activity signature and supports the involvement of skin fibroblasts through their activation and interaction with circulating immune cells. Aberrant TGFβ signaling and persistently increased non-classical monocytes characterize treatment-resistant PsA, with pro-inflammatory pathways related to platelet activation and Hippo signaling predicting early response to treatment.

Fibroblast morphology, growth rate and gene expression in facial melasma

BackgroundIn addition to melanocytic hyperfunction, changes are observed in the upper dermis of melasma, and fibroblasts play a central role in collagen synthesis and pigmentation induction. ObjectiveTo explore the morphology, growth rate, and gene expression profile of fibroblasts from the skin with melasma in comparison to fibroblasts from the adjacent healthy skin. MethodsTen women with facial melasma were biopsied (lesion and adjacent healthy skin), and the fragments were processed for fibroblast culture. Samples from five participants were seeded to evaluate growth (days 2, 5 and 8) and senescence (SA-β-gal) curves. The samples from the other participants were submitted to real-time PCR to comparatively evaluation of the expression of 39 genes. ResultsCultured fibroblasts from melasma skin were morphologically less fusiform in appearance and on average a 34% (95% CI 4%‒63%) greater proportion of cells labeled with SA-β-gal than the fibroblasts from the adjacent skin. The cell growth rate was lower for the melasma samples after eight days (p < 0.01). TheWNT3A, EDN3, ESR2, PTG2, MMP1, and SOD2 genes were up-regulated, whereas the COL4A1, CSF2, DKK3, COL7A1, TIMP4, CCL2, and CDH11 genes were down-regulated in melasma skin fibroblasts when compared to the ones from adjacent healthy skin. Study limitationsSmall sample size; absence of functional tests. ConclusionsFibroblasts from the skin with melasma showed a lower growth rate, less fusiform morphology and greater accumulation of SA-β-gal than those from adjacent photo exposed skin. Moreover, their gene expression profile comprised factors that may contribute to upper dermis damage and sustained melanogenesis.

NSD1 Mutations in Sotos Syndrome Induce Differential Expression of Long Noncoding RNAs, miR646 and Genes Controlling the G2/M Checkpoint.

An increasing amount of evidence indicates the critical role of the NSD1 gene in Sotos syndrome (SoS), a rare genetic disease, and in tumors. Molecular mechanisms affected by NSD1 mutations are largely uncharacterized. In order to assess the impact of NSD1 haploinsufficiency in the pathogenesis of SoS, we analyzed the gene expression profile of fibroblasts isolated from the skin samples of 15 SoS patients and of 5 healthy parents. We identified seven differentially expressed genes and five differentially expressed noncoding RNAs. The most upregulated mRNA was stratifin (SFN) (fold change, 3.9, Benjamini–Hochberg corrected p < 0.05), and the most downregulated mRNA was goosecoid homeobox (GSC) (fold change, 3.9, Benjamini–Hochberg corrected p < 0.05). The most upregulated lncRNA was lnc-C2orf84-1 (fold change, 4.28, Benjamini–Hochberg corrected p < 0.001), and the most downregulated lncRNA was Inc-C15orf57 (fold change, −0.7, Benjamini–Hochberg corrected p < 0.05). A gene set enrichment analysis reported the enrichment of genes involved in the KRAS and E2F signaling pathways, splicing regulation and cell cycle G2/M checkpoints. Our results suggest that NSD1 is involved in cell cycle regulation and that its mutation can induce the down-expression of genes involved in tumoral and neoplastic differentiation. The results contribute to defining the role of NSD1 in fibroblasts for the prevention, diagnosis and control of SoS.

Effects of Immunoglobulins G From Systemic Sclerosis Patients in Normal Dermal Fibroblasts: A Multi-Omics Study.

Autoantibodies (Aabs) are frequent in systemic sclerosis (SSc). Although recognized as potent biomarkers, their pathogenic role is debated. This study explored the effect of purified immunoglobulin G (IgG) from SSc patients on protein and mRNA expression of dermal fibroblasts (FBs) using an innovative multi-omics approach. Dermal FBs were cultured in the presence of sera or purified IgG from patients with diffuse cutaneous SSc (dcSSc), limited cutaneous SSc or healthy controls (HCs). The FB proteome and transcriptome were explored using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and microarray assays, respectively. Proteomic analysis identified 3,310 proteins. SSc sera and purified IgG induced singular protein profile patterns. These FB proteome changes depended on the Aab serotype, with a singular effect observed with purified IgG from anti-topoisomerase-I autoantibody (ATA) positive patients compared to HC or other SSc serotypes. IgG from ATA positive SSc patients induced enrichment in proteins involved in focal adhesion, cadherin binding, cytosolic part, or lytic vacuole. Multi-omics analysis was performed in two ways: first by restricting the analysis of the transcriptomic data to differentially expressed proteins; and secondly, by performing a global statistical analysis integrating proteomics and transcriptomics. Transcriptomic analysis distinguished 764 differentially expressed genes and revealed that IgG from dcSSc can induce extracellular matrix (ECM) remodeling changes in gene expression profiles in FB. Global statistical analysis integrating proteomics and transcriptomics confirmed that IgG from SSc can induce ECM remodeling and activate FB profiles. This effect depended on the serotype of the patient, suggesting that SSc Aab might play a pathogenic role in some SSc subsets.

Single-Cell Transcriptomics Identifies Heterogeneity of Mouse Mammary Gland Fibroblasts With Distinct Functions, Estrogen Responses, Differentiation Processes, and Crosstalks With Epithelium.

Fibroblasts have been shown to be one of the essential players for mammary gland organization. Here, we identify two major types of mouse mammary gland fibroblasts through single-cell RNA sequencing analysis: Dpp4 + fibroblasts and Dpp4 - fibroblasts. Each population exhibits unique functional characteristics as well as discrete localization in normal mouse mammary glands. Remarkably, estrogen, a crucial mediator of mammary gland organization, alters the gene expression profiles of fibroblasts in a population-specific manner, without distinct activation of estrogen receptor signaling. Further integrative analysis with the inclusion of five other publicly available datasets reveals a directional differentiation among the mammary gland fibroblast populations. Moreover, the combination with the mouse mammary epithelium atlas allows us to infer multiple potential interactions between epithelial cells and fibroblasts in mammary glands. This study provides a comprehensive view of mouse mammary gland fibroblasts at the single-cell level.

Expression signature of the Leigh syndrome French-Canadian type

As a result of a founder effect, a Leigh syndrome variant called Leigh syndrome, French-Canadian type (LSFC, MIM / 220,111) is more frequent in Saguenay–Lac-Saint-Jean (SLSJ), a geographically isolated region on northeastern Quebec, Canada. LSFC is a rare autosomal recessive mitochondrial neurodegenerative disorder due to damage in mitochondrial energy production. LSFC is caused by pathogenic variants in the nuclear gene leucine-rich pentatricopeptide repeat-containing (LRPPRC). Despite progress understanding the molecular mode of action of LRPPRC gene, there is no treatment for this disease.The present study aims to identify the biological pathways altered in the LSFC disorder through microarray-based transcriptomic profile analysis of twelve LSFC cell lines compared to twelve healthy ones, followed by gene ontology (GO) and pathway analyses.A set of 84 significantly differentially expressed genes were obtained (p ≥ 0.05; Fold change (Flc) ≥ 1.5). 45 genes were more expressed (53.57%) in LSFC cell lines compared to controls and 39 (46.43%) had lower expression levels. Gene ontology analysis highlighted altered expression of genes involved in the mitochondrial respiratory chain and energy production, glucose and lipids metabolism, oncogenesis, inflammation and immune response, cell growth and apoptosis, transcription, and signal transduction. Considering the metabolic nature of LSFC disease, genes included in the mitochondrial respiratory chain and energy production cluster stood out as the most important ones to be involved in LSFC mitochondrial disorder. In addition, the protein-protein interaction network indicated a strong interaction between the genes included in this cluster. The mitochondrial gene NDUFA4L2 (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex, 4-like 2), with higher expression in LSFC cells, represents a target for functional studies to explain the role of this gene in LSFC disease.This work provides, for the first time, the LSFC gene expression profile in fibroblasts isolated from affected individuals. This represents a valuable resource to understand the pathogenic basis and consequences of LRPPRC dysfunction.

Bioinformatics study on different gene expression profiles of fibroblasts and vascular endothelial cells in keloids.

Keloid is a benign fibroproliferative skin tumor. The respective functions of fibroblasts and vascular endothelial cells in keloid have not been fully studied. The purpose of this study is to identify the respective roles and key genes of fibroblasts and vascular endothelial cells in keloids, which can be used as new targets for diagnosis or treatment.The microarray datasets of keloid fibroblasts and vascular endothelial cells were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened out. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for functional enrichment analysis. The search tool for retrieval of interacting genes and Cytoscape were used to construct protein-protein interaction (PPI) networks and analyze gene modules. The hub genes were screened out, and the relevant interaction networks and biological process analysis were carried out.In fibroblasts, the DEGs were significantly enriched in collagen fibril organization, extracellular matrix organization and ECM-receptor interaction. The PPI network was constructed, and the most significant module was selected, which is mainly enriched in ECM-receptor interaction. In vascular endothelial cells, the DEGs were significantly enriched in cytokine activity, growth factor activity and transforming growth factor-β (TGF-β) signaling pathway. Module analysis was mainly enriched in TGF-β signaling pathway. Hub genes were screened out separately.In summary, the DEGs and hub genes discovered in this study may help us understand the molecular mechanisms of keloid, and provide potential targets for diagnosis and treatment.

Analysis of fibroblast genes selected by NMF to reveal the potential crosstalk between ulcerative colitis and colorectal cancer

Patients with ulcerative colitis (UC) have an increased risk of developing colorectal cancer (CRC). The CRC risk extent raises with increasing age, duration of symptoms, severity of inflammation and dysplasia. CRC is a complex multi-stage process and associated with UC represents 2% of all colon cancers. With the aim of clarifying some aspects of the evolution of UC towards CRC, we characterized the phenotype of fibroblasts present in the mucosa of subjects affected by UC to verify whether they can contribute to the genesis of a microenvironment favorable to tumor transformation. The fibroblast phenotype was obtained with the help of transcriptome analysis adopting a novel framework based on Nonnegative Matrix Factorization (NMF) which automatically extracts a limited number of genes from fibroblast gene expression profiles of patients with UC and CRC. These genes may be considered possible candidates in generating a permissive microenvironment for the evolution of disease under study.

Fibroblasts upregulate expression of adhesion molecules and promote lymphocyte retention in 3D fibroin/gelatin scaffolds

Bioengineered scaffolds are crucial components in artificial tissue construction. In general, these scaffolds provide inert three-dimensional (3D) surfaces supporting cell growth. However, some scaffolds can affect the phenotype of cultured cells, especially, adherent stromal cells, such as fibroblasts. Here we report on unique properties of 3D fibroin/gelatin materials, which may rapidly induce expression of adhesion molecules, such as ICAM-1 and VCAM-1, in cultured primary murine embryonic fibroblasts (MEFs). In contrast, two-dimensional (2D) fibroin/gelatin films did not show significant effects on gene expression profiles in fibroblasts as compared to 3D culture conditions. Interestingly, TNF expression was induced in MEFs cultured in 3D fibroin/gelatin scaffolds, while genetic or pharmacological TNF ablation resulted in diminished ICAM-1 and VCAM-1 expression by these cells. Using selective MAPK inhibitors, we uncovered critical contribution of JNK to 3D-induced upregulation of these adhesion molecules. Moreover, we observed ICAM-1/VCAM-1-dependent adhesion of lymphocytes to fibroblasts cultured in 3D fibroin/gelatin scaffolds, but not on 2D fibroin/gelatin films, suggesting functional reprogramming in stromal cells, when exposed to 3D environment. Finally, we observed significant infiltration of lymphocytes into 3D fibroin/gelatin, but not into collagen scaffolds in vivo upon subcapsular kidney implantation in mice. Together our data highlight the important features of fibroin/gelatin scaffolds, when they are produced as 3D sponges rather than 2D films, which should be considered when using these materials for tissue engineering.

Gene expression profiles of oral soft tissue-derived fibroblast from healing wounds: correlation with clinical outcome, autophagy activation and fibrotic markers expression.

Our aim was to evaluate gene expression profiling of fibroblasts from human alveolar mucosa (M), buccal attached gingiva (G) and palatal (P) tissues during early wound healing, correlating it with clinical response. M, G and P biopsies were harvested from six patients at baseline and 24hr after surgery. Clinical response was evaluated through Early wound Healing Score (EHS). Fibrotic markers expression and autophagy were assessed on fibroblasts isolated from those tissues by Western blot and qRT-PCR. Fibroblasts from two patients were subjected to RT2 profiler array, followed by network analysis of the differentially expressed genes. The expression of key genes was validated with qRT-PCR on all patients. At 24hr after surgery, EHS was higher in P and G than in M. In line with our clinical results, no autophagy and myofibroblast differentiation were observed in G and P. We observed significant variations in mRNA expression of key genes: RAC1, SERPINE1 and TIMP1, involved in scar formation; CDH1, ITGA4 and ITGB5, contributing to myofibroblast differentiation; and IL6 and CXCL1, involved in inflammation. We identified some genes involved in periodontal soft tissue clinical outcome, providing novel insights into the molecular mechanisms of oral repair (ClinicalTrial.gov-NCT04202822).

EXTH-11. PATIENT DERIVED INDUCED NEURAL STEM CELLS FOR TREATMENT OF GLIOBLASTOMA

Abstract Induced neural stem-cells (iNSCs) represent a new opportunity in the emerging field of cellular immunotherapy. Patient-derived iNSCs modified to produce anti-tumoral compounds could lead to less rejection and safer outcomes than an off-the-shelf therapy. In this study, we established fibroblast lines (PFs) from skin-biopsies of patients being treated for glioblastoma (GBM) and transdifferentiated those fibroblasts into iNSC lines that produce anti-tumor compounds. We designed a combination of genomic and functional testing to assess iNSC line efficacy. Functional testing revealed differences in rate of transdifferentiation, therapeutic agent production, and tumor-homing amongst cell lines all of which varied among patients. RNAseq profiles of individual cells lines revealed biomarker signatures that differed in tumor-homing-pathways. There was no observed neuronal differentiation in the iNSCs from the transcriptomic profiles, indicating stability after transdifferentiation amongst PFs. Anti-tumor activity of patient-derived iNSCs was measured in vivo by surgical-resection mouse models with invasive CD133+ GBM cells. Patient-derived iNSCs showed variable tumoricidal effectiveness; more highly effective iNSC cells lines reduced tumor burden and increased survival post-resection from 28 to 45 days, whereas less effective cells lines could increase post-resection survival with increased iNSC dosage. PF origination and transcriptomic profile accounted for the differences amongst the iNSC lines. Identification of differentially expressed genes could indicate the cellular pathways that are most important for guaranteeing high, anti-tumoral activity. Further, the cellular profile of the patient-derived fibroblast influences the resulting cellular profile of the iNSC; potentially, correlation of fibroblast gene expression profile could predict tumoricidal efficacy of derived iNSCs.

Drug-Induced Gingival Overgrowth: A Pilot Study on the Effect of Diphenylhydantoin and Gabapentin on Human Gingival Fibroblasts.

Introduction. The administration of several classes of drugs can lead to the onset of gingival overgrowth: anticonvulsants, immunosuppressants, and calcium channel blockers. Among the anticonvulsants, the main drug associated with gingival overgrowth is diphenylhydantoin. Materials and Methods. In this study, we compared the effects of diphenylhydantoin and gabapentin on 57 genes belonging to the “Extracellular Matrix and Adhesion Molecule” pathway, present in human fibroblasts of healthy volunteers. Results. Both molecules induce the same gene expression profile in fibroblasts as well as a significant upregulation of genes involved in extracellular matrix deposition like COL4A1, ITGA7, and LAMB3. The two treatments also induced a significant downregulation of genes involved in the expression of extracellular matrix metalloproteases like MMP11, MMP15, MMP16, MMP24, and transmembrane receptor ITGB4. Conclusions. Data recorded in our study confirmed the hypothesis of a direct action of these drugs at the periodontium level, inducing an increase in matrix production, a reduction in its degradation, and consequently resulting in gingival hyperplasia.

Gene Expression Profiles of Fibroblasts Irradiated with Two Protocols in vitro

Irradiation of exponentially growing fibroblasts induces premature differentiation to postmitotic functional cells depositing increased amounts of extracellular matrix (ECM) proteins. On the other hand, a predictive test for patients’ risk of developing fibrosis was based on a gene expression signature after fractionated irradiation of confluent cultures (Alsner et al., Radiother. Oncol. 83:261-6, 2007). The purpose was to characterize the radiation-induced gene expression profiles for the two protocols. Established skin fibroblast cultures were irradiated with 6 MV X-rays in vitro. Fibroblast differentiation was determined by cytomorphological scoring in clonal culture. Gene expression was determined using Affymetrix HgU133+ microarrays. After batch normalization, differentially expressed genes were identified by ANOVA using JMP Genomics software. The expression of selected genes was validated by real-time PCR. Pathway analysis was performed by Gene Set Enrichment Analysis using the R-package ReactomePA, filtering pathways with normalized enrichment scores (NES) >1.5 or < -1.5 and adjusted p-values <0.05. On day 5 after irradiation with 4 Gy, exponentially growing cultures showed the terminally differentiated phenotype. Microarray analysis showed >4-fold upregulation of 157 genes, including several collagen genes and >4-fold downregulation of 244 genes, including many cell cycle-related genes. Irradiation of confluent cultures with 3×4 Gy yielded 91 up- and 195 down-regulated genes (> 4-fold). Differential gene expression for the two protocols correlated better for down- than for up-regulated genes but GDF15 was strongly upregulated in both. Pathway analysis showed 37 common pathways, 51% of which were related to ECM or glycosaminoglycans (GAG), 14% to inflammation, and 11% to cholesterol and bile acid/salts. 37 pathways were more specific for 1×4 Gy (exponential cultures) with 41% related to GAG or cell-cell/cell-matrix interactions, and 16% to inflammation. 27 pathways were more specific to 3×4 Gy (confluent cultures) with 22% related to cholesterol and bile acid/salts, 15% to each of translation and metabolism, and 11% to inflammation. The expression profile of exponentially growing cells reflected premature terminal differentiation to a postmitotic phenotype. However, both protocols upregulated ECM and, notably, inflammatory pathways. Additional upregulated pathways represented GAG and cell-cell/cell-matrix interactions relating to differentiation after 1×4 Gy (exponential cultures). By contrast, upregulated cholesterol and bile acid/salts, translation, and metabolism, pathways after 3×4 Gy (confluent cultures) might indicate a role of lipid metabolism. Thus, different aspects of the fibrogenic process appear to be detected with the two protocols which may complement each other as model systems for mechanistic studies of radiation-induced fibrosis.

Gene expression profiling of fibroblasts in a family with LMNA-related cardiomyopathy reveals molecular pathways implicated in disease pathogenesis

BackgroundIntermediate filament proteins that construct the nuclear lamina of a cell include the Lamin A/C proteins encoded by the LMNA gene, and are implicated in fundamental processes such as nuclear structure, gene expression, and signal transduction. LMNA mutations predominantly affect mesoderm-derived cell lineages in diseases collectively termed as laminopathies that include dilated cardiomyopathy with conduction defects, different forms of muscular dystrophies, and premature aging syndromes as Hutchinson-Gilford Progeria Syndrome. At present, our understanding of the molecular mechanisms regulating tissue-specific manifestations of laminopathies are still limited.MethodsTo gain deeper insight into the molecular mechanism of a novel LMNA splice-site mutation (c.357-2A > G) in an affected family with cardiac disease, we conducted deep RNA sequencing and pathway analysis for nine fibroblast samples obtained from three patients with cardiomyopathy, three unaffected family members, and three unrelated, unaffected individuals. We validated our findings by quantitative PCR and protein studies.ResultsWe identified eight significantly differentially expressed genes between the mutant and non-mutant fibroblasts, that included downregulated insulin growth factor binding factor protein 5 (IGFBP5) in patient samples. Pathway analysis showed involvement of the ERK/MAPK signaling pathway consistent with previous studies. We found no significant differences in gene expression for Lamin A/C and B-type lamins between the groups. In mutant fibroblasts, RNA-seq confirmed that only the LMNA wild type allele predominately was expressed, and Western Blot showed normal Lamin A/C protein levels.ConclusionsIGFBP5 may contribute in maintaining signaling pathway homeostasis, which may lead to the absence of notable molecular and structural abnormalities in unaffected tissues such as fibroblasts. Compensatory mechanisms from other nuclear membrane proteins were not found. Our results also demonstrate that only one copy of the wild type allele is sufficient for normal levels of Lamin A/C protein to maintain physiological function in an unaffected cell type. This suggests that affected cell types such as cardiac tissues may be more sensitive to haploinsufficiency of Lamin A/C. These results provide insight into the molecular mechanism of disease with a possible explanation for the tissue specificity of LMNA-related dilated cardiomyopathy.

The Effects of Epigallocatechin Gallate (EGCG) on Pulmonary Fibroblasts of Idiopathic Pulmonary Fibrosis (IPF)-A Next-Generation Sequencing and Bioinformatic Approach.

Idiopathic pulmonary fibrosis (IPF) is a disabling and lethal chronic progressive pulmonary disease. Epigallocatechin gallate (EGCG) is a polyphenol, which is the major biological component of green tea. The anti-oxidative, anti-inflammatory, and anti-fibrotic effects of EGCG have been shown in some studies, whereas its effects in altering gene expression in pulmonary fibroblasts have not been systematically investigated. This study aimed to explore the effect of EGCG on gene expression profiles in fibroblasts of IPF. The pulmonary fibroblasts from an IPF patient were treated with either EGCG or water, and the expression profiles of mRNAs and microRNAs were determined by next-generation sequencing (NGS) and analyzed with the bioinformatics approach. A total of 61 differentially expressed genes and 56 differentially expressed microRNAs were found in EGCG-treated IPF fibroblasts. Gene ontology analyses revealed that the differentially expressed genes were mainly involved in the biosynthetic and metabolic processes of cholesterol. In addition, five potential altered microRNA–mRNA interactions were found, including hsa-miR-939-5p–PLXNA4, hsa-miR-3918–CTIF, hsa-miR-4768-5p–PDE5A, hsa-miR-1273g-3p–VPS53, and hsa-miR-1972–PCSK9. In summary, differentially expressed genes and microRNAs in response to EGCG treatment in IPF fibroblasts were identified in the current study. Our findings provide a scientific basis to evaluate the potential benefits of EGCG in IPF treatment, and warrant future studies to understand the role of molecular pathways underlying cholesterol homeostasis in the pathogenesis of IPF.

Abstract 5090: Exportin-1 enables pro-tumorigenic metabolic reprogramming of lung fibroblasts through relocalization of p53 and p62/SQSTM1

Abstract Bi-directional interactions between cancer cells and the surrounding microenvironment actively contribute to cancer development and progression. Cancer-associated fibroblasts (CAFs) are one of the most prevalent cellular components in the tumor microenvironment and their metabolic reprogramming towards an activated phenotype reminiscent of fibroblasts found at sites of wound healing is involved in the acquisition of pro-tumorigenic properties. Specific determinants of tumor-promoting function of fibroblasts in lung cancer are however not well characterized. Here we used microarray gene expression profiling of fibroblasts isolated from lung cancer patients and functional in vitro and in vivo assays to identify enablers of fibroblasts pro-tumorigenic activity. Gene expression profiles of CAFs and normal fibroblasts (n=60) identified increased levels of the nuclear transporter Exportin 1 (XPO1/CRM1) in patient-derived fibroblasts endowed with an in vivo pro-tumorigenic phenotype in co-injection experiments with lung cancer cells. Elevated levels of XPO1, which controls cellular localization of numerous proteins including oncosuppressors, have been observed in cancer cells but the role of XPO1-related signaling in stromal cells has not been investigated. Pharmacological inhibition of XPO1 in fibroblasts resulted in anti-proliferative effects with a G2/M cell cycle arrest linked to p53 accumulation, increased CDKN1a transcription, induction of senescence (2-4 fold increase of β-galactosidase positive cells) and accumulation of γ-H2AX foci. Interestingly these effects were persistent only in activated fibroblasts compared to control fibroblasts suggesting a central role for XPO1 in mediating and sustaining permanent reprogramming of pro-tumorigenic fibroblasts. Additionally XPO1 inhibition was associated with cellular relocalization of p62/SQSTM1, a master regulator of energy metabolism in tumor stroma. Low levels of nuclear p62 were observed in activated fibroblasts and could be restored to normal levels through XPO1-activity inhibition. p62 nuclear accumulation inhibited DNA-damage repair and reduced extracellular acidification, indicating potential modification of metabolic properties of activated fibroblasts. Consistently, in heterotypic co-cultures experiments, we found that XPO1 inhibition prevented the ability of activated fibroblasts to stimulate migration of lung cancer cell lines and to increase the frequency of CD133+ cancer stem cells thereby reducing their pro-tumorigenic activity in vivo. Overall these evidences suggest that XPO1 is a potent enabler of the tumor promoting functions of fibroblasts and that XPO1-driven metabolic reprogramming in stromal cells could be targeted to affect cancer progression. Citation Format: Antonina Bruccoleri, Francesca Andriani, Federica Facchinetti, Ugo Pastorino, Gabriella Sozzi, Luca Roz. Exportin-1 enables pro-tumorigenic metabolic reprogramming of lung fibroblasts through relocalization of p53 and p62/SQSTM1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5090.

Regulating the transcriptomes that mediate the conversion of fibroblasts to various nervous system neural cell types.

Our understanding of the mechanism of cell fate transition during the direct reprogramming of fibroblasts into various central nervous system (CNS) neural cell types has been limited by the lack of a comprehensive analysis on generated cells, independently and in comparison with other CNS neural cell types. Here, we applied an integrative approach on 18 independent high throughput expression data sets to gain insight into the regulation of the transcriptome during the conversion of fibroblasts into induced neural stem cells, induced neurons (iNs), induced astrocytes, and induced oligodendrocyte progenitor cells (iOPCs). We found common down-regulated genes to be mostly related to fibroblast-specific functions, and suggest their potential as markers for screening of the silencing of the fibroblast-specific program. For example, Tagln was significantly down-regulated across all considered data sets. In addition, we identified specific profiles of up-regulated genes for each CNS neural cell types, which could be potential markers for maturation and efficiency screenings. Furthermore, we identified the main TFs involved in the regulation of the gene expression program during direct reprogramming. For example, in the generation of iNs from fibroblasts, the Rest TF was the main regulator of this reprogramming. In summary, our computational approach for meta-analyzing independent expression data sets provides significant details regarding the molecular mechanisms underlying the regulation of the gene expression program, and also suggests potentially useful candidate genes for screening down-regulation of fibroblast gene expression profile, maturation, and efficiency, as well as candidate TFs for increasing the efficiency of the reprogramming process.

Understanding Xeroderma Pigmentosum Complementation Groups Using Gene Expression Profiling after UV-Light Exposure.

Children with the recessive genetic disorder Xeroderma Pigmentosum (XP) have extreme sensitivity to UV-light, a 10,000-fold increase in skin cancers from age 2 and rarely live beyond 30 years. There are seven genetic subgroups of XP, which are all resultant of pathogenic mutations in genes in the nucleotide excision repair (NER) pathway and a XP variant resultant of a mutation in translesion synthesis, POLH. The clinical symptoms and severity of the disease is varied across the subgroups, which does not correlate with the functional position of the affected protein in the NER pathway. The aim of this study was to further understand the biology of XP subgroups, particularly those that manifest with neurological symptoms. Whole genome gene expression profiling of fibroblasts from each XP complementation group was assessed before and after UV-light exposure. The biological pathways with altered gene expression after UV-light exposure were distinct for each subtype and contained oncogenic related functions such as perturbation of cell cycle, apoptosis, proliferation and differentiation. Patients from the subgroups XP-B and XP-F were the only subgroups to have transcripts associated with neuronal activity altered after UV-light exposure. This study will assist in furthering our understanding of the different subtypes of XP which will lead to better diagnosis, treatment and management of the disease.