Genomics and Proteomics Engineering in Medicine and Biology - Metin Akay

264 TUMOUR AND TUMOUR SUPPRESSOR PROTEINS

TABLE 10.2 Characteristic RRM Frequencies for Protein Groups and DNA Requlatory Sequences

(IL-2), and viral and tumor suppressor proteins that can elucidate why melatonin and IL-2 might play a critical role as supplements in treatment of cancer diseases.

10.3. RESULTS AND DISCUSSIONS

10.3.1. Interactions Between Viral and Tumor Suppressor Proteins

The human neurotropic polyoma virus (JCV), produces a regulatory protein T-antigen, which is a key component in the completion of the viral life cycle. T-antigen has the ability to transform neural cells in vitro and its expression has been detected in several human neural-origin tumors. The JC virus most likely infects humans through the upper respiratory tract and remains in most people throughout their lives and, in some cases, causes minor subclinical problems. However, in people whose immune systems are depressed, either through chemotherapy given to organ transplant recipients or an illness such as AIDS, JCV can become active and may contribute to cancer in the brain [2]. Experimental findings revealed that interactions of viral oncoprotein T-antigen with tumor suppressor proteins could lead to induction of cancer [1–4].

In this study 8 JC viral T-antigen protein sequences, 13 p53 protein sequences, and 9 pRb protein sequences were investigated concerning the understanding of the structure–function relationship within these proteins. A multiple cross-spectral analysis was performed for each selected protein group as well as for their mutual combination using the EIIP values (Figs. 10.3a to 10.3f ). As a result, characteristic frequencies of analyzed protein groups were obtained and are shown in Table 10.3. The RRM analysis was applied to a group of 8 T-antigen proteins, and the common feature in terms of characteristic frequency was identified at f ¼ 0.2061 + 0.125, S/N ¼ 129.58. This frequency component is common to all analyzed sequences and therefore can be considered as the consensus characteristic of their common biological activity for all protein sequences in this functional group.

The p53 tumor suppressor gene has proven to be one of the genes most often mutated in human cancers. It involves mainly point mutations leading to amino acid substitutions in the central region of the protein and thus causes its abnormal functions. Because p53 and pRb proteins are the key players in defending our body against cancer, it is of great importance to determine the characteristic frequencies of these proteins that correspond to their biological functionality. Thus, the RRM procedure was repeated with p53 and pRb tumor suppressor proteins and their cross-spectral functions obtained are shown in Figures 10.3b and 10.3c. The prominent characteristic frequencies of p53 and pRb tumor suppressor proteins were identified at f ¼ 0.4326 + 0.077, S/N ¼ 159.97 and at f ¼ 0.4316 + 0.111, S/N ¼ 164.28, respectively. As was mentioned above each specific biological function of the protein is characterized by a single frequency. The similarity of characteristic frequencies of p53 and pRb proteins (Table 10.3) is expected as both p53 and pRb proteins are tumor suppressors sharing the same biological function. Thus, the frequency f ¼ 0.4326 identified within the RRM analysis is

FIGURE 10.3. Multiple cross-spectral functions of protein groups: (a) JC viral T-antigen proteins, (b) p53 proteins, (c) pRb proteins, (d) JC viral T-antigen and p53 proteins, (e) JC viral T-antigen and pRb proteins, and ( f ) T-antigen, p53 and pRb proteins. The prominent peak(s) denote common frequency components. The abscissa represents RRM frequencies, and the ordinate is the normalised intensity. The prominent peaks were found for T-antigen at f1 ¼ 0.2061 and for p53 (pRb) proteins at f2 ¼ 0.4326.

268 TUMOUR AND TUMOUR SUPPRESSOR PROTEINS

TABLE 10.3 Peak Frequency and Signal-to-Noise Ratio of Protein Groups

considered as a characteristic feature of the specific biological activity of p53 and pRb proteins—ability to stop the formation of tumors. After careful examining of the corresponding consensus spectrums of p53 and pRb proteins (Figs. 10.3b and 10.3c), we observe more than one less significant peak corresponding to other biological functions determined within the RRM analysis.

It is known that the human polyomavirus (JCV) also contains an open reading frame within the late region of the viral genome that encodes a 71-aminoacid protein, the agnoprotein. Following accumulating evidence in support of an association between JCV infection and human brain tumors, the expression of agnoprotein in a series of 20 well-characterized medulloblastomas was assessed [24]. Importantly, some medulloblastoma samples that expressed agnoprotein had no sign of T-antigen expression. The p53 protein was detected in only 6 of the 11 tumors in which agnoprotein was expressed. None of the 20 samples showed expression of the viral late capsid proteins, ruling out productive infection of the tumor cells with JCV. These data provide evidence that the JCV late gene encoding the auxiliary agnoprotein is expressed in tumor cells. The finding of agnoprotein expression in the absence of T-antigen expression suggests a potential role for agnoprotein in pathways involved in the development of JCV-associated medulloblastomas [24]. Despite all of this, the role of agnoprotein in the development of brain tumors is still unknown. Recent studies suggest, however, that the interaction of T-antigen with agnoprotein may affect T-antigen ability to control cell growth. The communication between these two viral proteins may impact the ability of the virus to induce brain tumors [24]. The researchers also found agnoprotein and T-antigen in about 50% of the samples, with some samples containing only agnoprotein. They postulated “the finding of agnoprotein expression in the absence of T-antigen expression suggests a potential role for agnoprotein in pathways that control the development of JCV-associated medulloblastomas [24].” Obviously further study is needed to prove that the virus plays a significant role in formation of medulloblastomas [24].

272 TUMOUR AND TUMOUR SUPPRESSOR PROTEINS

of melatonin and its effects on cancer have been conducted. Some suggest that melatonin extends survival and improves the quality of life for patients with certain types of untreatable cancers. Melatonin combined with IL-2 has been studied as an anticancer treatment [25–28]. In one study of 80 cancer patients, use of melatonin in conjunction with IL-2 led to more tumor regression and better survival rates than treatment with IL-2 alone. However, it was also reported that the results of 32 clinical studies designed to measure the effects of melatonin on cancer were mixed and inconclusive [28]. A study of melatonin’s ability to ease the side effects of chemotherapy drugs found that high doses of the hormone had little effect. It was summarized that the antitumor activity of IL-2 is augmented by melatonin, resulting in a decrease in the number of IL-2 doses needed to exert an anticancer response. Moreover, melatonin may increase the antitumor activity of IL-2 by inhibiting tumor growth factor production. A pilot study was done using low-dose IL-2 plus melatonin in 14 patients with untreatable endocrine tumors. The results suggest that lowdose IL-2 and melatonin may be a well-tolerated therapy for advanced endocrine tumors. Also the results of the study show the objective tumor regression was noted in 3 of the 14 patients (lung, kidney, and liver tumors) [28].

Taking into account the existing documented evidence of the possible influence of melatonin on the biological performance of IL-2, a computational analysis of mutual interactions between melatonin, IL-2, and oncogene proteins using the RRM approach was performed. The values of characteristic frequencies and signal-to noise ratios of each protein group analyzed are shown in Table 10.4. Multiple cross-spectral functions of analyzed protein groups are shown in Figures 10.5a to 10.5g. In addition, the RRM was used to determine the characteristic frequencies of melatonin protein and its interactions with viral and tumor suppressor proteins. The peak frequencies of these selected proteins are shown in Table 10.5. The resulting cross-spectral functions of the analyzed proteins can be observed from Figures 10.6a to 10.6l.

It is proposed that the RRM characteristic frequencies present the common feature of the interacting sequences and thus a common interaction. In our previous work it was also proposed that this characteristic frequency could represent the oscillations of a physical field, which are responsible for information transfer between the interacting biomolecules [9]. As a consequence, it is postulated that

TABLE 10.4 Peak Frequency and Signal-to-Noise Ratio of Protein Groups

FIGURE 10.5. Multiple cross-spectral functions of protein groups analysed: (a) Oncogene, (b) Inerleukin-2, (c) Melatonin, (d) Interleukin-2 and Melatonin, (e) Interleukin-2 and Oncogene, ( f ) Interleukin-2, Melatonin and Oncogene, and (g) Melatonin and Oncogene proteins. Prominent peaks were identified for Oncogenes at fx ¼ 0.0317, Melatonin at fy ¼ 0.0205, Melatonin and Oncogene at fz ¼ 0.3379.