SARS-CoV-2 ORF8 and SARS-CoV ORF8ab: Genomic Divergence and Functional Convergence

The COVID-19 pandemic, in the first seven months, has led to more than 15 million confirmed infected cases and 600,000 deaths. SARS-CoV-2, the causative agent for COVID-19, has proved to be a great challenge for its ability to spread in asymptomatic stages and the diverse disease spectrum it has generated. This has created a challenge of unimaginable magnitude, not only affecting human health and life but also potentially generating a long-lasting socioeconomic impact. Both medical sciences and biomedical research have also been challenged, consequently leading to a large number of clinical trials and vaccine initiatives. While known proteins of pathobiological importance are targets for these therapeutic approaches, it is imperative to explore other factors of viral significance. Accessory proteins are one such trait that have diverse roles in coronavirus pathobiology. Here, we analyze certain genomic characteristics of SARS-CoV-2 accessory protein ORF8 and predict its protein features. We have further reviewed current available literature regarding its function and comparatively evaluated these and other features of ORF8 and ORF8ab, its homolog from SARS-CoV. Because coronaviruses have been infecting humans repeatedly and might continue to do so, we therefore expect this study to aid in the development of holistic understanding of these proteins. Despite low nucleotide and protein identity and differentiating genome level characteristics, there appears to be significant structural integrity and functional proximity between these proteins pointing towards their high significance. There is further need for comprehensive genomics and structural-functional studies to lead towards definitive conclusions regarding their criticality and that can eventually define their relevance to therapeutics development.

c-Jun N-terminal kinase is activated in non-small-cell lung cancer and promotes neoplastic transformation in human bronchial epithelial cells

c-Jun N-terminal kinase (JNK) has been reported to either potentiate or inhibit oncogenesis, depending upon the cellular context, but its role in lung neoplasia is unclear. Here we sought to define the role of JNK in lung neoplasia by examining evidence of JNK phosphorylation in non-small-cell lung cancer (NSCLC) biopsy samples and by using genetic and pharmacologic approaches to modulate JNK expression and activity in cultured cells. Immunohistochemical staining for JNK phosphorylation was detected in 114 (45%) of 252 NSCLC biopsy samples and was predominantly nuclear, providing evidence of JNK activation in a subset of NSCLC cases. Introduction of a doxycycline-inducible, constitutively active, mutant mitogen-activated protein kinase kinase 4 (MKK4) into the human bronchial epithelial cell lines BEAS-2B and HB56B increased the cells' proliferation, migration, invasion and clonogenicity. Depletion of JNK in MKK4 mutant-transformed BEAS-2B cells by introduction of JNK1/2 short hairpin RNA reversed the transformed phenotype, indicating that JNK activation is oncogenic and MKK4 confers neoplastic properties in these cells. The proliferation of NSCLC cell lines HCC827 and H2009, in which JNK and its substrate c-Jun are constitutively phosphorylated, was inhibited by SP600125, a JNK kinase inhibitor. We conclude that JNK is activated in a subset of NSCLC biopsy samples and promotes oncogenesis in the bronchial epithelium, suggesting that strategies to inhibit the JNK pathway should be considered for the prevention and treatment of NSCLC.

Identification of feline MAGE-1 gene product by monoclonal antibodies

Melanoma antigens (MAGE) are thought to induce a tumor-specific immune response and to be potential therapeutical targets for cancer immunotherapy. We have earlier identified the cDNA of feline melanoma antigen 1 (fMAGE-1), but its product was not characterized in detail. We have expressed the recombinant fMAGE-1 protein and have generated monoclonal antibodies (mAbs) against it, to identify the native fMAGE-1 protein in feline lymphoma cell lines and tumor tissues. The fMAGE-1 protein was found to be approximately 39 kDa in molecular mass on sodium dodecyl-sulphate-polycrylamide gel electrophoresis (SDS-PAGE), and it was found to be located in the cytoplasm of the cells by immunofluorescence. Immunoblotting analysis detected the fMAGE-1 gene product in the fMAGE-1-mRNA-positive cells, but not in the fMAGE-1-mRNA-negative cells. An interesting finding of the present study was the distribution of the fMAGE-1 protein, which was found to have a spindle-like distribution, with filaments twining around the nucleus, suggesting that the fMAGE-1 protein may be associated with or form some cytoplasmic filaments. This type of finding is so far the first report of its kind, and to the best of our knowledge it has not been reported in either human or mouse MAGE proteins until now. It most probably implies the major diversity of the MAGE family genes.

Molecular cloning and sequencing of feline melanoma antigen 2 (fMAGE-2) obtained from a lymphoma cell line

Melanoma antigens (MAGE), thought to induce tumor-specific immune responses, are used as potential therapeutical targets for cancer immunotherapy. We hereby report the cloning and sequencing of MAGE cDNA clone, called feline MAGE-2 (fMAGE-2), obtained from a lymphoma cell line. fMAGE-2 cDNA is 1535 base pairs (bp) in length and contains an open reading frame (ORF) of 1131 bp encoding a protein of 376 amino acids. The predicted amino acid sequence shows 45%, 32-42%, 44-47%, and 33% homology with feline MAGE-1, human MAGE-A, human MAGE-B, and human MAGE-C proteins, respectively. mRNA transcripts of fMAGE-2 were detected by RT-PCR in some feline tumors, as well as in testis of adult cat, but not in other normal tissues, indicating that the expression pattern of fMAGE-2 is similar to that of the human MAGE family genes in tumors and normal tissues.

Molecular cloning and expression analysis of feline melanoma antigen (MAGE) obtained from a lymphoma cell line

Melanoma antigens (MAGE) are regarded as inducing tumor-specific immune response and thought to be potential therapeutical agents for cancer immunotherapy. We hereby report the cloning of feline MAGE cDNA obtained from a lymphoma cell line derived from cat malignant lymphoma, and its expression pattern in tumor and normal tissues. The cDNA encoding the MAGE is 1668 base pairs (bp) in length, and contains an open reading frame (ORF) of 936 bp encoding a protein of 311 amino acids. The predicted amino acid sequence has 29-46% of homology with other MAGE proteins from human and mouse. mRNA transcripts for the feline MAGE were detected in certain tumors, but not in adult cat normal tissues except in testis, by reverse transcription polymerase chain reaction (RT-PCR) analysis. This indicates that the expression pattern of feline MAGE mRNA is similar to those of other MAGE family genes in tumors and normal tissues.

Characterization of monoclonal antibodies specific for feline serum amyloid (SAA) protein

Serum amyloid A (SAA) has been characterized as an inflammatory marker in many species. In this study, we have developed and characterized monoclonal antibodies (MAbs) against feline SAA (fSAA) derived from culture hybridomas. These hybridomas were produced from the fusion of Balb/c-derived myeloma s/p20-Ag14 and splenocytes from mice immunized with purified recombinant feline SAA (rfSAA). Six hybridomas secreting MAbs, M2, M5, M7, M8, M13, and M15, were selected and subcloned on the basis of their specificity to rfSAA by enzyme-linked immunoabsorbent assay (ELISA), and confirmed based on their specificity to rf-SAA by immunoblot analysis. Out of six clones, two clones (M5 and M7) showed higher reactivity with rf-SAA, and were selected for further analysis of ELISA additivity and Western blot cross-reactivity tests. As a result, M5 and M7 clones recognized the same or excessively near epitopes on rfSAA and reacted with rfSAA, fSAA and equine recombinant SAA, but showed no reaction with human recombinant SAA. Because of their specificity, these MAbs may be usefully applied in studying the measurement of SAA concentration in cat serum.

Molecular cloning and sequencing of canine T-cell costimulatory molecule (CD28)

T-cells express CD28 and CTLA-4, and through binding to their shared ligands (CD80/CD86) on antigen presenting cells, provide a potent co-stimulatory signal for T-cell activation and proliferation. To investigate the role of CD28 in canine immune system, we hereby report the molecular cloning and sequencing of the full-length complementary DNA (cDNA) coding for canine CD28, from pokeweed mitogen stimulated canine peripheral blood lymphocytes. The cloned cDNA contains an open reading frame of 663 nucleotides, encoding for a polypeptide of 221 amino acids. The amino acid sequence of the canine CD28 showed 91.9, 80, and 79.6% similarities with those of the cat, cattle, and human counterparts, respectively. Five sequence motifs of TATT or ATTTA involved in the regulation of gene expression by influencing mRNA stability are found in the 3' untranslated region. The hexapeptide motif (MYPPPY), five cysteine residues, a potential N-glycosylation site and a cytoplasmic phosphatidylinositol 3-kinase binding site in canine CD28 molecule are completely conserved in canine CTLA-4. The availability of full length canine CD28 will provide a useful molecule for studying its role in dog immune system.

Molecular cloning and sequencing of equine cDNA encoding serum amyloid A (SAA)

The serum amyloid A (SAA) protein is a characteristic and sensitive acute phase reactant in all vertebrates investigated. We molecularly cloned the equine cDNA encoding SAA from the liver of a healthy horse by polymerase chain reaction (PCR). The cloned cDNA is 480 bases in length, and contains an open reading frame (ORF) of 387 nucleotides encoding a precursor SAA protein of 128 amino acids. The precursor of horse SAA seems to have an 18-residue signal peptide and differs from the reported amino acid sequences of the horse SAA by substitution of valine at residue 81. It shows high homology with SAA amino acid sequence of other species such as dog (80.6%), mink (77.5%), human (76.9%) and duck (71.9%). An insertion of eight amino acids at residues between 85 and 92, as compared to human SAA, has also been found in horse SAA. The availability of the equine SAA cDNA will provide a useful reagent for studying its role in diseased horses.

Cloning of canine cDNA encoding tektin

Tektins are a group of proteins that form filamentous polymers in the walls of ciliary microtubules. The cloning of canine cDNA encoding tektin, was carried out and identified from the testis of beagle dog. Canine tektin cDNA is 1,523 bp in length, has an open reading frame of 1,281 bp nucleotides encoding a protein of 426 deduced amino acids. The predicted amino acid sequence has 77% and 33-50% of homology with the murine tektin and the sea urchin tektins. The amino acid sequence RPNVELCRD and four cysteine residues were conserved in the dog, mouse and sea urchin, suggesting the functional significance of this protein domain and the amino acid residues in the tektin proteins.

Cloning and sequencing of canine MAGE cDNA

Melanoma antigens (MAGE) are regarded to induce tumour-specific immune response and thought to be potential therapeutical agents for cancer immunotherapy. We hereby report the canine MAGE cDNA cloned from the testis of a beagle dog. Canine MAGE cDNA is 1,455 base pair (bp) nucleotides in length, and contains an open reading frame (ORF) of 1,137 bp nucleotides encoding a protein of 378 amino acids. The predicted amino acid sequence has 22-49% of homology with other MAGE proteins. mRNA transcripts of canine MAGE were detected only in the melanoma and testis and not in other normal tissues of adult dog by reverse transcriptase-polymerase chain reaction (RT-PCR), indicating that the expression pattern of canine MAGE mRNA is similar to that of the MAGE family genes in tumor and normal tissues.

Cloning of feline cDNA encoding the cytotoxic T lymphocyte-associated antigen 4 (CTLA-4)

Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) is a CD28 homologue which down-modulate T cell responses rather than augment them. To investigate its biological role in feline immune system, we cloned and sequenced full-length feline CTLA-4 (fCTLA-4) cDNA by RT-PCR from pokeweed mitogen stimulated peripheral blood lymphocytes. The fCTLA-4 contains an open reading frame of 669 nucleotides, coding for a polypeptide of 223 amino acids. The predicted fCTLA-4 amino acids sequence shows the homology of 86.6%, 87.0%, and 76.2% with human, bovine, and murine molecules respectively. The hexapeptide motif (MYPPPY) within the extra-cellular domain of CTLA-4 molecule, which is believed to be responsible for interaction with the B7 family members, is completely conserved in all the species.

Cloning of a full length cDNA encoding canine Interleukin-4

Primer designed on the basis of the conserved transcription start point (tsp) region of human and bovine gene transcripts, encoding the Interleukin-4 (IL-4), and subsequently the gene specific primer and an adaptor primer pair, was successfully used, to generate the full-length complementary DNA (cDNA) sequence coding for canine IL-4 (cIL-4), from pokeweed mitogen stimulated canine peripheral blood lymphocytes. The full-length cIL-4 contains an open reading frame of 399 nucleotides (nt), with a 5' ends of 66 base pairs (bp) and 3' ends of 125 bp. The nucleotide sequence contains six possible Asn-X-Thr or Asn-X-Ser linked glycosylation sites. Five sequence motifs of TATT or ATTTA, responsible for the regulation of gene expression, are found in the 3' untranslated region.