CD45 (PTPRC) as a candidate gene in multiple sclerosis

Analysis of multiple databases identifies crucial genes correlated with prognosis of hepatocellular carcinoma

Despite advancements made in the therapeutic strategies on hepatocellular carcinoma (HCC), the survival rate of HCC patient is not satisfactory enough. Therefore, there is an urgent need for the valuable prognostic biomarkers in HCC therapy. In this study, we aimed to screen hub genes correlated with prognosis of HCC via multiple databases. 117 HCC-related genes were obtained from the intersection of the four databases. We subsequently identify 10 hub genes (JUN, IL10, CD34, MTOR, PTGS2, PTPRC, SELE, CSF1, APOB, MUC1) from PPI network by Cytoscape software analysis. Significant differential expression of hub genes between HCC tissues and adjacent tissues were observed in UALCAN, HCCDB and HPA databases. These hub genes were significantly associated with immune cell infiltrations and immune checkpoints. The hub genes were correlated with clinical parameters and survival probability of HCC patients. 147 potential targeted therapeutic drugs for HCC were identified through the DGIdb database. These hub genes could be used as novel prognostic biomarkers for HCC therapy.

Concentrations of plasma-borne extracellular particles differ between multiple sclerosis disease courses and compared to healthy controls

BACKGROUND

Multiple sclerosis is a neurodegenerative, autoimmune disease of the central nervous system. Both peripheral blood and central nervous system facets play a role in the pathophysiology. Extracellular vesicles are small membrane-bound vesicles that are released by most cells in response to stress, activation, or pathology. As extracellular vesicles can cross the blood-brain barrier, they have the ability to link peripheral blood inflammation to central nervous system pathology in multiple sclerosis. The aim of this study was to obtain a comprehensive picture of the cellular origins of plasma-borne extracellular particles in multiple sclerosis.

METHODS

Platelet-free plasma was obtained from 39 multiple sclerosis patients and 27 healthy controls via a series of centrifugation steps and assessed by flow cytometry. Plasma samples were stained with antibodies against CD4, CD8, CD14, CD20, CD41b, CD45, CD146, and CD235a. Gates were set using size-reference beads and extracellular particles were enumerated using commercial counting beads at known concentrations.

RESULTS

In relapsing patients (n = 13) erythrocyte-derived (CD235a) extracellular particles were increased, while platelet-derived (CD41b), leukocyte-derived (CD45), and CD4⁺T cell-derived (CD4) extracellular particles were decreased compared to both healthy controls (n = 27) (p<0.05) and secondary progressive multiple sclerosis patients (n = 9) (p < 0.05). Endothelium-derived extracellular particles (CD146) were increased in stable relapsing-remitting multiple sclerosis patients (n = 17) compared to healthy controls (p < 0.05). Extracellular particles from several different cells of origin correlated with each other and clinical parameters (e.g. disease duration, number of relapses, EDSS), though clinical correlations did not withstand corrections for multiple comparisons.

CONCLUSIONS

Concentrations of erythrocyte-, leukocyte-, and platelet-derived extracellular particles were altered in relapsing multiple sclerosis patients and endothelium-derived extracellular particles were increased in stable relapsing-remitting patients compared to healthy controls. Extracellular particles may provide insights into altered the crosstalk between peripheral blood cells in multiple sclerosis, which may lead to the discovery of novel therapeutic targets.

Metabolic Pathways Associated with Kimchi, a Traditional Korean Food, Based on In Silico Modeling of Published Data

Kimchi is a traditional Korean food prepared by fermenting vegetables, such as Chinese cabbage and radishes, which are seasoned with various ingredients, including red pepper powder, garlic, ginger, green onion, fermented seafood (Jeotgal), and salt. The various unique microorganisms and bioactive components in kimchi show antioxidant activity and have been associated with an enhanced immune response, as well as anti-cancer and anti-diabetic effects. Red pepper inhibits decay due to microorganisms and prevents food from spoiling. The vast amount of biological information generated by academic and industrial research groups is reflected in a rapidly growing body of scientific literature and expanding data resources. However, the genome, biological pathway, and related disease data are insufficient to explain the health benefits of kimchi because of the varied and heterogeneous data types. Therefore, we have constructed an appropriate semantic data model based on an integrated food knowledge database and analyzed the functional and biological processes associated with kimchi in silico. This complex semantic network of several entities and connections was generalized to answer complex questions, and we demonstrated how specific disease pathways are related to kimchi consumption.

Splicing Regulation of Pro-Inflammatory Cytokines and Chemokines: At the Interface of the Neuroendocrine and Immune Systems

Alternative splicing plays a key role in posttranscriptional regulation of gene expression, allowing a single gene to encode multiple protein isoforms. As such, alternative splicing amplifies the coding capacity of the genome enormously, generates protein diversity, and alters protein function. More than 90% of human genes undergo alternative splicing, and alternative splicing is especially prevalent in the nervous and immune systems, tissues where cells need to react swiftly and adapt to changes in the environment through carefully regulated mechanisms of cell differentiation, migration, targeting, and activation. Given its prevalence and complexity, this highly regulated mode of gene expression is prone to be affected by disease. In the following review, we look at how alternative splicing of signaling molecules—cytokines and their receptors—changes in different pathological conditions, from chronic inflammation to neurologic disorders, providing means of functional interaction between the immune and neuroendocrine systems. Switches in alternative splicing patterns can be very dynamic and can produce signaling molecules with distinct or antagonistic functions and localization to different subcellular compartments. This newly discovered link expands our understanding of the biology of immune and neuroendocrine cells, and has the potential to open new windows of opportunity for treatment of neurodegenerative disorders.

Protein tyrosine phosphatases as potential therapeutic targets

Protein tyrosine phosphorylation is a key regulatory process in virtually all aspects of cellular functions. Dysregulation of protein tyrosine phosphorylation is a major cause of human diseases, such as cancers, diabetes, autoimmune disorders, and neurological diseases. Indeed, protein tyrosine phosphorylation-mediated signaling events offer ample therapeutic targets, and drug discovery efforts to date have brought over two dozen kinase inhibitors to the clinic. Accordingly, protein tyrosine phosphatases (PTPs) are considered next-generation drug targets. For instance, PTP1B is a well-known targets of type 2 diabetes and obesity, and recent studies indicate that it is also a promising target for breast cancer. SHP2 is a bona-fide oncoprotein, mutations of which cause juvenile myelomonocytic leukemia, acute myeloid leukemia, and solid tumors. In addition, LYP is strongly associated with type 1 diabetes and many other autoimmune diseases. This review summarizes recent findings on several highly recognized PTP family drug targets, including PTP1B, Src homology phosphotyrosyl phosphatase 2(SHP2), lymphoid-specific tyrosine phosphatase (LYP), CD45, Fas associated phosphatase-1 (FAP-1), striatal enriched tyrosine phosphatases (STEP), mitogen-activated protein kinase/dual-specificity phosphatase 1 (MKP-1), phosphatases of regenerating liver-1 (PRL), low molecular weight PTPs (LMWPTP), and CDC25. Given that there are over 100 family members, we hope this review will serve as a road map for innovative drug discovery targeting PTPs.

The CD45 77C/G allele is not associated with myasthenia gravis - a reassessment of the potential role of CD45 in autoimmunity

Background

The G allele of the CD45 77C/G SNP (rs17612648), which has previously been suggested to be associated with autoimmune disorders, was genotyped in 446 Swedish myasthenia gravis (MG) patients and 2303 matched controls.

Results

There was no association between the polymorphism and patient group as a whole (p = 0.199), nor with clinical subgroups. Our results add to a growing number of studies unable to find association between the 77C/G polymorphism and autoimmune disorders. One control sample, from an adult blood donor, was homozygous for the G allele, yet negative for a panel of auto-antibodies, representing the first homozygous individual studied in this respect.

Conclusions

The 77C/G mutation does not predispose to MG, and its role in autoimmunity may have to be re-evaluated.

Is multiple sclerosis a mitochondrial disease?

Multiple sclerosis (MS) is a relatively common and etiologically unknown disease with no cure. It is the leading cause of neurological disability in young adults, affecting over two million people worldwide. Traditionally, MS has been considered a chronic, inflammatory disorder of the central white matter in which ensuing demyelination results in physical disability. Recently, MS has become increasingly viewed as a neurodegenerative disorder in which axonal injury, neuronal loss, and atrophy of the central nervous system leads to permanent neurological and clinical disability. In this article, we discuss the latest developments on MS research, including etiology, pathology, genetic association, EAE animal models, mechanisms of neuronal injury and axonal transport, and therapeutics. In this article, we also focus on the mechanisms of mitochondrial dysfunction that are involved in MS, including mitochondrial DNA defects, and mitochondrial structural/functional changes.

Unusual case presentations associated with the CD45 C77G polymorphism

CD45, the leucocyte common antigen, is a haematopoietic cell specific tyrosine phosphatase. Human polymorphic CD45 variants are associated with autoimmune and infectious diseases and alter the phenotype and function of lymphocytes, establishing CD45 as an important regulator of immune function. Here we report four patients with diverse diseases with unusual clinical features. All four have the C77G polymorphism of CD45 exon 4, which alters the splicing and CD45RA/CD45R0 phenotype of lymphocytes. We suggest that C77G may be a contributing factor in these unusual cases.

Immunogenetic factors determining the evolution of T-cell large granular lymphocyte leukaemia and associated cytopenias

T-cell large granular lymphocyte leukaemia (T-LGL) is a chronic clonal proliferation of cytotoxic T lymphocytes (CTL). T-LGL presents with cytopenias, often accompanied by autoimmune diseases, suggesting clonal transformation arising from an initially polyclonal immune response. Various immunogenetic predisposition factors, previously described for both immune-mediated bone marrow failure and autoimmune conditions, may promote T-LGL evolution and/or development of cytopenias. The association of T-LGL was analysed with a number of immunogenetic factors in 66 patients, including human leucocyte antigen (HLA) and killer-cell immunoglobulin-like receptor (KIR) genotype, KIR/KIR-L mismatch, CTLA-4 (+49 A/G),CD16-158V/F, CD45 polymorphisms, cytokine single nucleotide polymorphisms including: TNF-alpha (-308G/A), TGF-beta1 (codons 10 C/T, 25 G/C), IL-10 (-1082 G/A), IL-6 (-174 C/G), and IFN-gamma(+874 T/A). A statistically significant increase in A/A genotype for TNF-alpha-308, IL-10-1082, andCTLA-4 +49 was observed in T-LGL patients compared with control, suggesting that the G allele serves a protective role in each case. No association was found between specific KIR/HLA profile and disease. KIR/KIR-L analysis revealed significant mismatches between KIR3DL2 and KIR2DS1 and their ligands HLA-A3/11 and HLA-C group 2 (P = 0.03 and 0.01 respectively); the biological relevance of this finding is questionable. The significance of additional genetic polymorphisms and their clinical correlation to evolution of T-LGL requires future analysis.

Combinations of CD45 isoforms are crucial for immune function and disease

Expression of the CD45 Ag in hemopoietic cells is essential for normal development and function of lymphocytes, and both mice and humans lacking expression exhibit SCID. Human genetic variants of CD45, the exon 4 C77G and exon 6 A138G alleles, which alter the pattern of CD45 isoform expression, are associated with autoimmune and infectious diseases. We constructed transgenic mice expressing either an altered level or combination of CD45 isoforms. We show that the total level of CD45 expressed is crucial for normal TCR signaling, lymphocyte proliferation, and cytokine production. Most importantly, transgenic lines with a normal level, but altered combinations of CD45 isoforms, CD45(RABC/+) and CD45(RO/+) mice, which mimic variant CD45 expression in C77G and A138G humans, show more rapid onset and increased severity of experimental autoimmune encephalomyelitis. CD45(RO/+) cells produce more TNF-alpha and IFN-gamma. Thus, for the first time, we have shown experimentally that it is the combination of CD45 isoforms that affects immune function and disease.

CD45: all is not yet crystal clear

CD45 has been recognized as an important player in regulating signalling in lymphocytes. However, compared with tyrosine kinases, phosphatases are still poorly understood in terms of the details of their specificity and regulation. Here, the recent progress in understanding the biology of the first recognized receptor tyrosine phosphatase, CD45, is reviewed.

Geographical distribution and disease associations of the CD45 exon 6 138G variant

CD45 is crucial for normal lymphocyte signalling, and altered CD45 expression has major effects on immune function. Both mice and humans lacking CD45 expression are severely immunodeficient, and single-nucleotide polymorphisms in the CD45 gene that cause altered splicing have been associated with autoimmune and infectious diseases. Recently, we identified an exon 6 A138G polymorphism resulting in an increased proportion of activated CD45RO T cells and altered immune function. Here we report a significantly reduced frequency of the 138G allele in hepatitis C Japanese patients and a possibly reduced frequency in type I diabetes. The allele is widely distributed in the Far East and India, indicating that it may have a significant effect on disease burden in a large part of the human population.

The 77C->G mutation in the human CD45 (PTPRC) gene leads to increased intensity of TCR signaling in T cell lines from healthy individuals and patients with multiple sclerosis

The 77C-->G mutation in exon A of the human CD45 gene occurs with low frequency in healthy individuals. An enhanced frequency of 77C-->G individuals has been reported in cohorts of patients suffering from multiple sclerosis, systemic sclerosis, autoimmune hepatitis, and HIV-1. To investigate the mechanisms by which the variant allele may contribute to disease susceptibility, we compared T cell reactivity in heterozygous carriers of the mutation (healthy individuals and multiple sclerosis patients) and wild-type controls. In vitro-generated T cell lines and freshly isolated CD4+CD45R0+ primed/memory T cells from 77C-->G individuals aberrantly expressed CD45RA isoforms and showed enhanced proliferation and IL-2 production when stimulated with anti-TCR/CD3 mAb or Ag. Mutant T cell lines contained a more active pool of p56lck tyrosine kinase and responded with increased phosphorylation of Zap70 and TCR-zeta and an enhanced Ca2+ flux to TCR/CD3 stimulation. These data suggest that 77C-->G may act as a risk factor for certain diseases by increasing the intensity of TCR signaling.

Altered CD45 expression and disease

CD45, the leucocyte common antigen, is a haemopoietic cell-specific tyrosine phosphatase. Many isoforms are generated by alternative splicing, but their function remains obscure. The extracellular domain of CD45 is highly polymorphic in all vertebrates. Importantly, human polymorphic variants that alter CD45 isoform expression are associated with autoimmune and infectious diseases, establishing CD45 as an important immunomodulator with a significant influence on disease burden. Here, we discuss the new opportunities provided by the human variants for investigating and understanding how CD45 regulates antigen receptor signalling, cytokine responses and apoptosis.

Genomics, proteomics, metabolomics: what is in a word for multiple sclerosis?

PURPOSE OF REVIEW

Multiple sclerosis (MS) is the most common chronic inflammatory neurological disease. Despite major advances the aetiology of this disease it is still not completely understood. In the post-genome era, advances in global screening technologies offer an opportunity to accelerate the search of new pathological pathways and to identify new therapeutic targets. Some recent publications using novel global screening methods at the genome, transcriptome, proteome and metabolome levels are discussed.

RECENT FINDINGS

The genetic association of susceptibility to MS with loci outside the MHC has been reconfirmed. Evidence of parent-of-origin and seasonal effects on disease susceptibility add further complexity to the genetics of MS. The search for MS susceptibility genes continues using the candidate-gene approach as well as large-scale single-nucleotide-polymorphism association studies and novel cross-species synteny analysis. Genome-wide expression profiling using microarrays produced numerous therapeutic targets and is progressing towards profiling of rare cells. Advances in classical proteomics methods paved the way to new initiatives aiming at determining the proteome of the nervous system in normal and diseased states. Although progress is still slow, array-based methods are making an impact on the MS field.

SUMMARY

The complexity of MS is clearly reflected in the latest findings using global profiling methods. Nevertheless, these new technologies are confirming some of the basic aspects of the disease pathophysiology, i.e. its polygenicity, the central role of neuroinflammation and the emerging neurodegenerative processes. These data are primarily the results of genomic approaches, yet promising attempts are also made using proteomics and metabolomics.