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HCV is a small 50nm, enveloped, single-stranded, positive sense RNAvirus in the family Flaviviridae.
HCV has a high rate of replication with approximately one trillion particles produced each day in an infected individual. Due to lack of proofreading by the HCV RNA polymerase, the HCV has an exceptionally high mutation rate, a factor that may help it elude the host's immune response. Hepatitis C virus is classified into six genotypes(1-6) with several subtypes within each genotype. The preponderance and distribution of HCV genotypes varies globally. Genotype is clinically important in determining potential response to interferon-based therapy and the required duration of such therapy. Genotypes 1 and 4 are less responsive to interferon-based treatment than are the other genotypes (2, 3, 5 and 6).

PAX9 (Paired box protein Pax-9) belongs to the paired box (PAX) family of transcription factors. Members of PAX9 family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. In addition, PAX9 is vital for the development of different organs and skeletal elements.

VPS29 is a member of a group of genes coding for vacuolar protein sorting (VPS) proteins which, when functionally damaged, lessens the efficient transfer of vacuolar hydrolases. VPS29 is a late Golgi transmembrane protein that operates as the sorting receptor for soluble vacuolar hydrolases, from the prevacuolar endosome back to the Golgi. Moreover, VPS29 takes part in the creation of the inner shell of the retromer coat for retrograde vesicles parting the prevacuolar compartment.

Serine/threonine/tyrosine-interacting protein (STYX) is a member of the protein-tyrosine phosphatase family. STYX contains a Gly residue instead of a conserved Cys residue in the dsPTPase catalytic loop which makes it catalytically inactive as a phosphatase. On the other hand, the binding pocket is adequately preserved to bind phosphorylated substrates, and may protect them from phosphatases. STYX may have a role in spermiogenesis. STYX is a possible pseudophosphatase.

Chemokine (C-C motif) ligand 11 (CCL11) is a small cytokine belonging to the CC chemokine family that is also known as eotaxin. CCL11 selectively recruits eosinophils by inducing their chemotaxis, and therefore, is implicated in allergic responses. The effects of CCL11 are mediated by its binding to a G-protein-linked receptor known as a chemokine receptor. Chemokine receptors for which CCL11 is a ligand include CCR2, CCR3 and CCR5. The gene for human CCL11 (scya11) is encoded on three exons and is located on chromosome 17.

Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit and have about 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Mitochondrial Ribosomal Protein S2 (MRPS2) is a 28S subunit protein which is a part of the ribosomal protein S2 family and comprises a 12S rRNA and about 30 distinct proteins.

SDF-1 (stromal cell-derived factor-1) is small cytokine belonging to the chemokine family that is officially designated Chemokine (C-X-C motif) ligand 12 (CXCL12). It is produced in two forms, SDF-1?/CXCL12a and SDF-1?/CXCL12b, by alternate splicing of the same gene. Chemokines are characterized by the presence of four conserved cysteines, which form two disulfide bonds. The CXCL12 proteins belong to the group of CXC chemokines, whose initial pair of cysteines are separated by one intervening amino acid. CXCL12 is strongly chemotactic for lymphocytes and has been implicated as an important cell co-ordinator during development. During embryogenesis it directs the migration of hematopoietic cells from foetal liver to bone marrow. Mice which were knocked-out for CXCL12 gene were lethal before the birth or within just 1 hour of life. As another role, CXCL12a alters also the electrophysiology of neurons. CXCL12 was shown to be expressend in many tissues in mice (including brain, thymus, heart, lung, liver, kidney, spleen and bone marrow).
The receptor for this chemokine is CXCR4, which was previously called fusin. This CXCL12-CXCR4 interaction used to be considered exclusive (unlike for other chemokines and their receptors), but recently it was suggested that CXCL12 is also bound by CXCR7 receptor.
The gene for CXCL12 is located on human chromosome 10. In human and mouse both CXCL12 and CXCR4 show high identity of sequence: 99% and 90%, respectively.

N-acetylneuraminate lyase (NanA) is a member of a family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. NanA catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetyl-D-mannosamine. NanA is inhibited by reduction with NaBH4 in the presence of the substrate, which indicates that it belongs to the Schiff-base-forming Class I aldolases. NanA is strongly inhibited by Cu2+ ions, p-chloromercuribenzoate and N-bromosuccinimide, it is also inhibited competitively by the reaction product, pyruvate, and its structurally related compounds, dihydroxyacetone and DL-glyceraldehyde.

HTATIP2 is part of the short-chain dehydrogenases/reductases (SDR) family which acts as a tumor suppressor in metabolic suppression, inhibition of angiogenesis and induces the expression of apoptosis related genes Bad and Siva. HTATIP2 cooperates with the activation domain of HIV-1 TAT and enhances its transcription by phosphorylating RNA polymerase II (Pol II). Defects in HTATIP2 are related with hepatocellular carcinomas and apoptotic resistant tumor cells, implicating a probable use for HTATIP2 in antitumor therapy.

Survivin is part of the of the inhibitor of apoptosis (IAP) family, which encodes negative regulatory proteins that prevent apoptotic cell death. Members of the IAP family include multiple baculovirus IAP repeat (BIR) domains, but Survivin has only a single BIR domain.
Survivin is an inhibitor of caspase activation therefore leading to negative regulation of apoptosis. BIRC5 is expressed in Merkel cell carcinoma.
BIRC5 polymorphism causes survivin expression, thus contributing to the genetic susceptibility to lung cancer. BIRC5 expression in large cell lung cancer is substantially higher than in normal tissue cells. Survivin mRNA is up-regulated in tumors. Apoptotic response of infected intestinal epithelial cells is suppressed by C. parvum via upregulation of BIRC5, favoring parasite infection. Up-regulation of of Survivin is associated with breast carcinomas.
BIRC5 increases the activity of an oncolytic adenovirus in the presence of low-dose radiotherapy. ER- breast cancer cells become dependent on Notch-survivin signaling for their maintenance, in vivo. Survivin mRNA positive cases are related with bladder tumour recurrence elevated expression of survivin might play an important role of development in nasal polyps.

Serine/threonine-protein kinase 16 (STK16) is a membrane-associated protein kinase which phosphorylates on serine and threonine residues. STK16 is involved in secretory vesicle trafficking or intracellular signaling. Furthermore, the STK16 protein may have a role in regulating stromal-epithelial interactions which occur during ductal morphogenesis in the mammary gland. STK16 can autophosphorylate on Tyr residue; it is however unclear whether STK16 has tyrosine-protein kinase toward other proteins. STK16 may also be involved in TGF-beta signaling.

CCL28 is part of the subfamily of small cytokine CC genes. CCL28 shows chemotactic activity for resting CD4 or CD8 T cells and eosinophils. CCL28 binds to chemokine receptors CCR3 and CCR10. CCL28 is involved in the physiology of extracutaneous epithelial tissues, including diverse mucosal organs. CCL28 mediates mucosal immunity in HIV exposure and infection. CCL28 is involved in the pathogenesis of inflammatory skin diseases.
Human CCL28 cDNA encodes a 127 amino acid residue precursor protein with a putative 22 amino acid residue signal peptide that is cleaved to produce the 105 amino acid residue mature protein. Human and mouse CCL28 are highly conserved, sharing 83% amino acid identity in their mature regions. CCL28 shares the most homology with CCL27/CTACK. Human and mouse CCL28 RNA expression was found to be highest in normal and pathologic colon with the protein being expressed by epithelial cells. Human CCL28 RNA was also present in normal and asthmatic lung tissues.

Chemokine (C-X-C motif) ligand 5 (CXCL5) is a small cytokine belonging to the CXC chemokine family that is also known as epithelial-derived neutrophil-activating peptide 78 (ENA-78). It is produced following stimulation of cells with the inflammatory cytokines interleukin-1 or tumor necrosis factor-alpha. Expression of CXCL5 has also been observed in eosinophils, and can be inhibited with the type II IFN. This chemokine stimulates the chemotaxis of neutrophils possesses angiogenic properties. It elicits these effects by interacting with the cell surface chemokine receptor CXCR2. The gene for CXCL5 is encoded on four exons and is located on human chromosome 4 amongst several other CXC chemokine genes. CXCL5 has been implicated in connective tissue remodelling.

Chemokine (C-C motif) ligand 7 (CCL7) is a small cytokine known as a chemokine that was previously called monocyte-specific chemokine 3 (MCP3). Due to CCL7 possessing two adjacent N-terminal cysteine residues in its mature protein, it is classified among the subfamily of chemokines known as CC chemokines. CCL7 specifically attracts monocytes, and regulates macrophage function. It is produced by certain tumor cell lines and by macrophages. This chemokine is located on chromosome 17 in humans, in a large cluster containing many other CC chemokines and is most closely related to CCL2(previously called MCP1).

Interleukin-4 is a pleiotropic cytokine produced primarily by activated T lymphocytes, basophils and mast cells. Multiple immune response-modulating functions are performed by IL-4 on a variety of cell types and it has an important role in the regulator of isotype switching, induction of IgE production in B lymphocytes and differentiation of precursor T helper cells. IL-4 binds to both membrane-bound and secreted soluble IL-4 receptors.

Synovial Sarcoma, X Breakpoint 2 (SSX2) is a part of the family of highly homologous synovial sarcoma X breakpoint proteins which play a role as transcriptional repressors. Homologous synovial sarcoma X breakpoint proteins are also able to bring out spontaneous humoral and cellular immune responses in cancer patients, and are effective targets in cancer vaccine-based immunotherapy.

Actin is one of the most highly-conserved proteins, differing by no more than 20% in species as diverse as algae and humans .Actin or ACTA is aprotein localized in the I band of the myofibrils in the muscle, Acting together with myosin.Actin takes part in the contraction and relaxation of muscle. Actin exists as a monomer in low salt concentrations, but filaments form rapidly as salt concentration rises, with the consequent hydrolysis of ATP.Each actin protomer binds one molecule of ATP and has one high affinity site for either calcium or magnesium ions, as well as several low affinity sites. It occurs in globular (G-actin) and fibrous (F-actin) forms. Actin is found in all eukaryotic cells (except for nematode sperm). Its other activitiessuch as cell motility, cell division and cytokinesis, vesicle and organelle movement, cell signaling, and the establishment and maintenance of cell junctions and cell shape.

α-Synuclein (amino acids 1-140), an acidic neuronal protein of 140 amino acids, is extremely heat-resistant and is natively unfolded with an extended structure primarily composed of random coils. α-synuclein has been suggested to be implicated in the pathogenesis of Parkinson’s disease and related neurodegenerative disorders, and more recently, to be an important regulatory component of vesicular transport in neuronal cells. Moreover, recent studies have shown that α-synuclein has chaperone activity and that this activity is lost upon removing its C-terminal acidic tail (amino acids 96-140).

Cytochrome C Oxidase Subunit Va (COX5A) is a member of the cytochrome c oxidase subunit 5A family. COX (Cytochrome C Oxidase), which is the terminal component of the mitochondrial respiratory chain, catalyzes the electron transfer from reduced Cytochrome C to oxygen. The COX component is a heteromeric complex comprised of three catalytic subunits encoded by mitochondrial genes and multiple structural subunits encoded by nuclear genes. The mitochondrially-encoded subunits serve in electron transfer, and the nuclear-encoded subunits act in the regulation and assembly of the complex. COX5A is the heme A-containing chain of Cytochrome C Oxidase,which is the terminal oxidase in mitochondrial electron transport.

Chromosome 7 Open Reading Frame 49 (C7ORF49) is affiliated with the lncRNA class. C7ORF49 characterizes the hamster ortholog and suggests that it may modulate the ability of the proteasome to degrade retroviral cores upon cellular infection.

Endoglin is a type I membrane glycoprotein located on cell surfaces and is part of the TGF beta receptor complex.
The protein consists of a homodimer of 180 kDA with disulfide links. It has been found on endothelial cells, activated macrophages, fibroblasts, and smooth muscle cells. Endoglin has been found to be part of the TGF-beta1 receptor complex. It thus may be involved in the binding of TGF-beta1, TGF-beta3, activin-A, BMP-2, and BMP-7. Beside TGF-beta signaling endoglin may have other functions. It has been postulated that endoglin is involved in the cytoskeletal organization affecting cell morphology and migration. Endoglin has a role in the development of the cardiovascular system and in vascular remodeling. Its expression is regulated during heart development . Experimental mice without the endoglin gene die due to cardiovascular abnormalities.

TNFAIP3-interacting protein 1 (TNIP1) interacts with zinc finger protein A20/TNFAIP3 and inhibits TNF-induced NF-kappa-B-dependent gene expression by interfering with a RIP- or TRAF2-mediated transactivation signal. Furthermore, TNIP1 interacts with HIV-1 matrix protein and is packaged into virions and its overexpression can inhibit viral replication. TNIP1 can regulate matrix nuclear localization, both nuclear import of Preintegration complex (PIC) and export of GAG polyprotein and viral genomic RNA during virion production.

The 14-3-3 family of proteins plays a key regulatory role in signal transduction, checkpoint control, apoptotic and nutrient-sensing pathways. 14-3-3 proteins are highly conserved and ubiquitously expressed. There are at least seven isoforms that have been identified in mammals. The 14-3-3gamma, a subtype of the 14-3-3 family of proteins, was thought to be brain and neuron-specific. It has been shown to interact with RAF1 and protein kinase C, proteins involved in various signal transduction pathways.