Gene Expression Profiling in Fibromyalgia Indicates an Autoimmune Origin of the Disease and Opens New Avenues for Targeted Therapy
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patients
2.2. PBMCs Isolation
2.3. Microarray Analysis
2.4. Protein-Protein Interaction (PPI) Network Construction and Network Clustering
2.5. Gene Functional Classification and Enrichment Analysis
2.6. Real-Time RT-PCR
2.7. FACS Analysis
2.8. Detection of Soluble Mediators in Sera of FM Patients and Healthy Controls
2.9. Sjögren’s Autoantibodies Detection in FM patients’ Sera
2.10. Statistical Analysis
3. Results
3.1. High-Throughput Gene Expression Profiling in Peripheral Blood Mononuclear Cells of FM Patients
3.2. PPI Network and Modular Analysis of Genes Modulated in FM
3.3. High-Throughput Long Non-Coding RNA Expression Profiling in Peripheral Blood Mononuclear Cells of Patients with FM
3.4. Frequency of IL-17 Positive CD4+ T Cells in PBMCs from Patients with FM
3.5. Detection of Soluble Mediators in FM Sera
3.6. Autoantibodies Detection in FM Patients’ Sera
4. Discussion and Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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ID | p-Value | Gene Symbol | Description |
---|---|---|---|
Th-17 Related Genes | |||
TC0100010686.hg.1 | 0.005 | CACYBP | calcyclin binding protein |
TC0200010980.hg.1 | <0.001 | CCL20 | chemokine (C-C motif) ligand 20 |
TC1700007558.hg.1 | 0.005 | CCL7 | chemokine (C-C motif) ligand 7 |
TC0 × 00008540.hg.1 | 0.004 | CD40LG | CD40 ligand |
TC2000007682.hg.1 | 0.001 | CEBPB | CCAAT/enhancer binding protein (C/EBP). beta |
TC1200011177.hg.1 | 0.008 | IFNG | interferon. Gamma |
TC0100017107.hg.1 | 0.001 | IL10 | interleukin 10 |
TC0200013916.hg.1 | 0.001 | IL1B | interleukin 1 beta |
TC0700006890.hg.1 | <0.001 | IL6 | interleukin 6 |
TC2000007514.hg.1 | 0.002 | MMP9 | matrix metallopeptidase 9 |
TC0400008271.hg.1 | 0.002 | NFKB1 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 |
TC0100009241.hg.1 | 0.005 | S1PR1 | sphingosine-1-phosphate receptor 1 |
TC1600009395.hg.1 | 0.006 | SOCS1 | suppressor of cytokine signaling 1 |
TC0600007596.hg.1 | <0.001 | TNF | tumor necrosis factor |
Type I Interferon Related Genes | |||
TC0600007495.hg.1 | 0.003 | HLA-A | major histocompatibility complex. class I. A |
TC0200014772.hg.1 | 0.008 | IFIH1 | interferon induced. with helicase C domain 1 |
TC0100017107.hg.1 | 0.001 | IL10 | interleukin 10 |
TC0700006890.hg.1 | <0.001 | IL6 | interleukin 6 |
TC0400012606.hg.1 | 0.002 | IRF2 | interferon regulatory factor 2 |
TC1400010584.hg.1 | 0.005 | IRF9 | interferon regulatory factor 9 |
TC0700008875.hg.1 | <0.001 | MET | MET proto-oncogene. receptor tyrosine kinase |
TC1500007833.hg.1 | <0.001 | PML | promyelocytic leukemia |
TC0900012231.hg.1 | 0.0004 | SHB | Src homology 2 domain containing adaptor protein B |
TC1600009395.hg.1 | 0.006 | SOCS1 | suppressor of cytokine signaling 1 |
TC0 × 00007149.hg.1 | 0.006 | TIMP1 | TIMP metallopeptidase inhibitor 1 |
TC0 × 00006625.hg.1 | <0.001 | TLR7 | toll-like receptor 7 |
TC1400008362.hg.1 | 0.008 | TRAF3 | TNF receptor-associated factor 3 |
TC1900009627.hg.1 | 0.005 | TYK2 | tyrosine kinase 2 |
TC0600008109.hg.1 | 0.003 | VEGFA | vascular endothelial growth factor A |
LncRNAs | FC | Targeted miRNAs | Targeted FM-DEGs | Targeted Module-Associated FM-DEGs | Targeted Modules |
---|---|---|---|---|---|
CTD-2651B20.6 | 5.23 | 2 | 12 | 4 | M3 M5 M6 |
RP1-151F17.1 | 4.65 | 15 | 75 | 16 | M2 M3 M4 M5 M6 |
AC009299.3 | −4.52 | 29 | 183 | 38 | M1 M2 M3 M4 M5 M6 |
RP11-283I3.6 | −5.05 | 1 | none | none | none |
RP11-747H7.3 | −9 | 8 | 57 | 12 | M1 M2 M3 M4 M5 M6 |
Module Associated Gene | Module | Diseases (GeneCards) |
---|---|---|
SOCS1 | 1 | coronary heart disease 1, myeloproliferative neoplasm, b-cell lymphoma, placental insufficiency, multiple sclerosis |
ASB6 | 1 | None |
LMO7 | 1 | cardiomyopathy, dilated, 1dd |
UBE2H | 1 | pontocerebellar hypoplasia, Type 7 |
TNFSF11 | 2 | bone disease, depersonalization disorder, psoriatic arthritis |
TNFRSF1B | 2 | juvenile rheumatoid arthritis, psoriatic arthritis, Guillain-Barre syndrome |
CCL3 | 2 | aseptic meningitis, bone disease, rheumatoid arthritis, arthritis, demyelinating disease, immune deficiency disease |
GNG5 | 2 | echolalia |
S1PR1 | 2 | autoimmune disease of central nervous system, multiple sclerosis |
IL10 | 3 | rheumatoid arthritis, arthritis, ulcerative colitis, rheumatic heart disease, chronic fatigue syndrome |
THBS1 | 3 | thrombotic thrombocytopenic purpura, thrombocytopenia |
TRAF3 | 3 | encephalitis, lymphoma, Hodgkin, classic, myeloma, multiple |
KIF2A | 3 | cortical dysplasia, complex, with other brain malformations 3, Walker-Warburg syndrome |
CCL7 | 3 | nephrogenic systemic fibrosis, demyelinating disease, inflammatory bowel disease, multiple sclerosis |
RCC2 | 3 | spermatogenic failure 5, renal cell carcinoma, nonpapillary |
BORA | 3 | branchiootic syndrome |
CEP97 | 3 | spinocerebellar ataxia 11, nephronophthisis, bardet-biedl syndrome |
NHLRC2 | 3 | fibrosis, neurodegeneration, and cerebral angiomatosis |
HSPA5 | 4 | rheumatoid arthritis, wolfram syndrome 1 |
CDKN1A | 4 | Tumors |
BCL2L11 | 4 | autoimmune lymphoproliferative syndrome, leukemia |
PPP2R2A | 4 | syndromic intellectual disability |
GRIA1 | 4 | depression |
ZEB1 | 4 | congenital hypothyroidism, corneal endothelial dystrophy |
BET1 | 4 | leukodystrophy, hypomyelinating |
CWC22 | 4 | bruxism |
CLP1 | 4 | pontocerebellar hypoplasia |
SEC23IP | 4 | Warrensburg’s syndrome |
CSTF1 | 4 | None |
PPIL1 | 4 | None |
TFRC | 5 | immunodeficiency 46, iron deficiency anemia |
EXOSC10 | 5 | systemic scleroderma, collagen disease |
FAS | 5 | lymphoproliferative syndrome, Sjogren syndrome |
CCNH | 5 | capillary malformation-arteriovenous malformation 1, weber syndrome, xeroderma pigmentosum |
WASL | 5 | Wiskott–Aldrich syndrome, x-linked recessive disease |
CTSB | 5 | acute pancreatitis |
GNA13 | 5 | Burkitt lymphoma, retinitis pigmentosa 14 |
SURF4 | 5 | spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2, macular degeneration, age-related |
HBEGF | 5 | perinatal necrotizing enterocolitis, interstitial cystitis, bladder disease, urinary tract obstruction |
MEIS1 | 5 | myeloid leukemia, restless legs syndrome |
SDC2 | 5 | autism, rheumatic disease, fibrodysplasia ossificans progressiva |
RPS3 | 6 | Warrensburg syndrome |
CEBPB | 6 | alk-positive anaplastic large cell lymphoma, myxoid liposarcoma, retinoblastoma, acute promyelocytic leukemia, |
DDIT3 | 6 | liposarcoma, fatty liver disease, lipomatosis, multiple |
CTPS1 | 6 | nemaline myopathy, immunodeficiency, sleeping sickness |
CRY2 | 6 | major depressive disorder, advanced sleep phase syndrome, nephronophthisis, delayed sleep phase disorder |
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Dolcino, M.; Tinazzi, E.; Puccetti, A.; Lunardi, C. Gene Expression Profiling in Fibromyalgia Indicates an Autoimmune Origin of the Disease and Opens New Avenues for Targeted Therapy. J. Clin. Med. 2020, 9, 1814. https://doi.org/10.3390/jcm9061814
Dolcino M, Tinazzi E, Puccetti A, Lunardi C. Gene Expression Profiling in Fibromyalgia Indicates an Autoimmune Origin of the Disease and Opens New Avenues for Targeted Therapy. Journal of Clinical Medicine. 2020; 9(6):1814. https://doi.org/10.3390/jcm9061814
Chicago/Turabian StyleDolcino, Marzia, Elisa Tinazzi, Antonio Puccetti, and Claudio Lunardi. 2020. "Gene Expression Profiling in Fibromyalgia Indicates an Autoimmune Origin of the Disease and Opens New Avenues for Targeted Therapy" Journal of Clinical Medicine 9, no. 6: 1814. https://doi.org/10.3390/jcm9061814
APA StyleDolcino, M., Tinazzi, E., Puccetti, A., & Lunardi, C. (2020). Gene Expression Profiling in Fibromyalgia Indicates an Autoimmune Origin of the Disease and Opens New Avenues for Targeted Therapy. Journal of Clinical Medicine, 9(6), 1814. https://doi.org/10.3390/jcm9061814