Draft:CAGE-1

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Cancer Antigen 1 (CAGE-1) is a protein which, in Homo Sapiens (humans), is encoded by the CAGE-1 gene, with a structure containing of mostly alpha helices. CAGE-1 seems to be involved in cancer, when it has a higher expression in the tissue, but is expressed in the testis in healthy tissue . It also has been identified that it does not have any extracellular functions and is localized in the cell nucleus and cytoplasm.

In the human genome, CAGE-1 is located on the minus strand of Chromosome 6 at gene locus p24.3. Figure Cytogenetic Locus of CAGE-1, shows the exact location of where CAGE-1 is located according to NCBI Gene.^[1] There are 14 exons (Transcript Variant 1) in the sequence of CAGE-1 and approximately 120,000 base pairs (bp),^[2] with the coding sequence only spanning about 3,300 bp.

Aliases: Cancer/Testis Antigen 3 (CT3); Cancer/Testis Antigen 95 (CT95)

In Homo Sapiens, CAGE-1 is moderately, ubiquitously expressed across tissues with a higher expression at Universal Human Reference RNA and the testis in healthy tissue^[3]. Since CAGE-1 is ubiquitously expressed across tissues, this leads to it being relatively more abundant than other proteins.^[4] Higher expression can lead to different types of cancers, such as lung or cervical cancer.

CAGE-1 is known to have three transcript variants, each with unique distinctions, which are described in Table 1.^[5] A 5' Untranslated Region (UTR) and a 3' UTR were both identified in the nucleotide sequence with neither of them having excessive length.

In Homo Sapiens, the Cancer Antigen 1 protein is encoded by the CAGE-1 gene. The predicted average molecular weight of CAGE-1 (isoform 1) in Homo Sapiens is 90 kDa and the isoelectric point (pI) is 5.2^[6]. Since the pI is 5.2, this means that the pH is also 5.2 leading CAGE-1 to being more of an acidic protein. CAGE-1 thus contains more acidic residues like glutamic and aspartic acid, as demonstrated in a Compositional Analysis done by SAPS.^[7] These results were also consistent among orthologs of the protein, including Mus musculus (mouse) and Gallus gallus (chicken).

CAGE-1 human protein has three different isoforms, as shown in Table 2.^[8]

CAGE-1 in Homo Sapiens has four sequence motifs, according to Genome Net-Motif Search.^[10] The first motif is called CAGE-1 and has two sections that overlap. It is classified as a Cancer-associated gene protein 1 family. The second motif is DUF2209 and is classified as an uncharacterized domain-containing protein conserved in archaea. The third motif is PDZ_4 and is a protein domain that helps regulate cell function and mediates protein-protein interactions. Finally, the fourth motif is DUF1327, which is a domain-containing protein of unknown function. The four motifs and their positions on the CAGE-1 protein can be seen in Figure Four CAGE-1 Protein Motifs Identified.

While four motifs were identified, no transmembrane domains are located in CAGE-1, but one intrinsically disordered region has been identified.^[11] There are other disordered regions that are predicted, but one has been confidently shown.

The secondary structure^[12] of CAGE-1 consists of Alpha Helices with multiple side chains as seen in Figure CAGE-1 Secondary Structure^[13].

Phyre2^[14] was used to predict the tertiary structure of CAGE-1 with the long chains at the end of the structure showing the disordered regions.

CAGE-1 protein in Homo Sapiens has a subcellular localization in the cell nucleus and cytoplasm, which means it functions and resides there.^[15] It also contains coiled coil domains and a nuclear localization signal, which directs the protein from the cytoplasm to the cell’s nucleus. The nuclear presence of CAGE-1 in cancer cells implies it is involved in regulating the nuclear events associated with tumor progression.

Depicted on the right is a thumbnail for the conceptual translation of the Homo Sapiens CAGE-1 with annotations to the right-hand side. Things included in the conceptual translation are the 5' Untranslated Region (UTR), the coding sequence, and the 3' UTR. Annotations include Post-Translation Modifications, Start and Stop Codons, Common Variants in CAGE-1, Amino Acids that are conserved, Polyadenylation Sites/Signals and Exon borders

Many proteins have been found to interact with CAGE-1 using methods such as STRING Consortium. ^[21] Ten proteins were identified to be interacting with CAGE-1 in Homo Sapiens, but only four were of importance and most related to CAGE-1, as seen in Table 4.

Protein CAGE-1, which is associated with the Cancer Antigen gene family, first appeared approximately 352 million years ago, which was when amphibians first came around.^[22] CAGE-1 was not found in fish, invertebrates, fungi, and plants, and its earliest ancestor is primates.

There are no known paralogs of CAGE-1.

CAGE-1 is highly conserved in Homo Sapiens. It can also be found in mammals, reptiles, birds, and amphibians. Table 5 below identifies eighteen orthologs, including humans, to demonstrate how CAGE-1's protein sequence has changed overtime compared to humans.

CAGE-1 in Homo Sapiens is a quickly evolving protein as seen in the Figure CAGE-1 Corrected sequence divergence vs. Median Date of Divergence. It evolves around the same rate as Fibrinogen Alpha Chain, which is known to evolve at a very fast pace.

CAGE-1 has been researched to show that it is involved in the progression of tumorigenesis, which is the process of normal cells turning into cancer cells.^[23] This has been identified by cancer tissues being compared to surrounding mucosa tissues and CAGE-1 having a higher expression in tissues that have cancer. ^[24] The cancers that are known to consistently have a higher expression of CAGE-1 are cervical, lung, gastric, lung, hepatic, and melanoma. Other cancers have shown CAGE-1 expression, but not as consistently.^[25] CAGE-1 continues to show signs of being involved in the progression of cancer, while also being expressed in healthy tissue of the testis.