Alteration of p16 (CDKN2) gene is associated with interleukin-2-induced tumor cell growth in adult T-cell leukemia

Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics

Pediatric cancer multi-omics is a uniquely rewarding and challenging domain of biomedical research. Public generosity bestows an abundance of resources for the study of extremely rare diseases; this unique dynamic creates a research environment in which problems with high-dimension and low sample size are commonplace. Here, we present a few statistical methods that we have developed for our research setting and believe will prove valuable in other biomedical research settings as well. The genomic random interval (GRIN) method evaluates the loci and frequency of genomic abnormalities in the DNA of tumors to identify genes that may drive the development of malignancies. The association of lesions with expression (ALEX) method evaluates the impact of genomic abnormalities on the RNA transcription of nearby genes to inform the formulation of biological hypotheses on molecular mechanisms. The projection onto the most interesting statistical evidence (PROMISE) method identifies omic features that consistently associate with better prognosis or consistently associate with worse prognosis across multiple measures of clinical outcome. We have shown that these methods are statistically robust and powerful in the statistical bioinformatic literature and successfully used these methods to make fundamental biological discoveries that have formed the scientific rationale for ongoing clinical trials. We describe these methods and illustrate their application on a publicly available T-cell acute lymphoblastic leukemia (T-ALL) data set. A companion github site ( https://github.com/stjude/TALL-example ) provides the R code and data necessary to recapitulate the example data analyses of this chapter.

Down-regulation ofASY/Nogo transcription associated with progression of adult T-cell leukemia/lymphoma

Adult T-cell leukemia/lymphoma (ATLL) is an aggressive form of human leukemia/lymphoma. Although this disease is initiated by infection with human T-lymphotropic virus type 1 (HTLV-1), many HTLV-1 carriers survive for a long period without aggressive illness, suggesting that other factors may play roles in the progression of ATLL to an aggressive state. However, the mechanism involved in this progression still remains unclear. Previously, we have reported that ASY/Nogo mRNA was markedly down-regulated in human small-cell lung carcinomas, whereas it was expressed in normal tissues and other lung carcinomas, such as adenocarcinoma and squamous cell carcinoma. To understand whether or not ASY/Nogo gene is involved in the progression of ATLL, we examined the expression of ASY/Nogo mRNA in smoldering, chronic and aggressive ATLL, and found that the expression level of ASY/Nogo mRNA was markedly reduced in clinically aggressive ATLL. HTLV-1 Tax expression was not affected by the down-regulation of ASY/Nogo mRNA. These results indicate that the ASY/Nogo gene may act as a suppressor against ATLL progression, independent of Tax expression.

Human leukocyte antigen-class II-negative long-term cultured human T-cell leukemia virus type-I-infected T-cell lines with progressed cytological properties significantly induce superantigen-dependent normal T-cell proliferation

While most human T-cell leukemia virus type-I (HTLV-I)-infected T cells express abundant class II antigens, some aggressive-type adult T-cell leukemia (ATL) cells lose their expression. To investigate the significance of the class II antigen of HTLV-I infected cells, the progressiveness of HTLV-I-infected long-term cultured T-cell lines was evaluated, and then their antigen-presenting capacity was examined using a superantigen, staphylococcus enterotoxin B (SEB). Among the cell lines derived from peripheral blood, HPB-ATL-T (ATL-T), HPB-ATL-2 (ATL-2) and HPB-ATL-O were more progressed than Tax exclusively expressing HPB-CTL-I (CTL-I), because the former deleted p16 gene (polymerase chain reaction (PCR)) and strongly transcribed survivin (reverse transcriptase-PCR). Notably, interferon gamma-independent loss of class II expression of ATL-T and ATL-2 was found. In antigen-presenting experiments, however, both cell lines induced SEB-dependent significant T-cell proliferation estimated by [(3)H] thymidine uptake. No class II-re-expressed ATL-2 cells were observed in the SEB-presenting cultures by indirect immunofluorescence, and only minimum inhibition of SEB-dependent T-cell response by anti-human leukocyte antigen (HLA)-DR monoclonal antibody was observed. These findings suggest that both ATL-T and ATL-2 very effectively present SEB to T cells less dependently on class II molecules. These less immunogenic leukemic cells of aggressive ATL may contribute to disease aggression.

HTLV-I Tax protein inhibits apoptosis induction but not G1 arrest by pyrrolidinedithiocarbamate, an anti-oxidant, in adult T cell leukemia cells

OBJECTIVE

We examined the anti-tumor effect of pyrrolidinedithiocarbamate (PDTC) on HTLV-1-infected T clones and the mechanism of HTLV-1 Tax protein inhibition of PDTC-induced apoptosis.

MATERIALS AND METHODS

Tax-nonproducing clones S1T and Su9T01, Tax-producing clones K3T and F6T, and Tax cDNA stably transfected S1TcTax clones S1TcTax04 and S1TcTax05 were examined for PDTC inhibition of thymidine incorporation and apoptosis induction by ISEL method. In addition, S1TcTax clones were analyzed by DNA histography and DNA fragmentation and also examined for p53, p21, or Bax protein expression by Western blot.

RESULTS

PDTC inhibited thymidine incorporation of all four HTLV-1-infected T cells in a similar dose-dependent manner, but K3T and F6T were more resistant than S1T and Su9T01 in apoptosis induction. S1TcTax clones also showed resistance to PDTC-induced apoptosis as compared to Tax-nonproducing S1T and S1Tneo. DNA histography demonstrated that PDTC induces G1 arrest and apoptosis in S1T and S1Tneo, and that S1TcTax clones are also sensitive to PDTC in G1 arrest but resistant in apoptosis induction. DNA fragmentation also demonstrated ladder formation only in S1Tneo but not in S1TcTax04. Western blots demonstrated higher expression of p53 and p21 proteins in S1Tneo than in S1TcTax04 during whole phase after PDTC stimulation with moderate enhancement in S1Tneo but small in S1TcTax04. Bax protein expression was detected only at early phase in S1Tneo but was not detected in S1TcTax04.

CONCLUSION

These findings suggest that PDTC-induced apoptosis is related with Bax, and that G1 arrest is possibly related with p21. Tax might inhibit apoptosis induction mainly via inhibition of Bax expression preceded at least in part by p53 inhibition.

T-Cell Control by Human T-Cell Leukemia/Lymphoma Virus Type 1

Human T-cell leukemia/lymphoma virus type 1 (HTLV-1) causes neoplastic transformation of human T-cells in a small number of infected individuals several years from infection. Collective evidence from in vitro studies indicates that several viral proteins act in concert to increase the responsiveness of T-cells to extracellular stimulation, modulate proapoptotic and antiapoptotic gene signals, enhance T-cell survival, and avoid immune recognition of the infected T-cells. The virus promotes T-cell proliferation by usurping several signaling pathways central to immune T-cell function, such as antigen stimulation and receptor-ligand interaction, suggesting that extracellular signals are important for HTLV-1 oncogenesis. Environmental factors such as chronic antigen stimulation may therefore be of importance, as also suggested by epidemiological data. Thus genetic and environmental factors together with the virus contribute to disease development. This review focuses on current knowledge of the mechanisms regulating HTLV-1 replication and the T-cell pathways that are usurped by viral proteins to induce and maintain clonal proliferation of infected T-cells. The relevance of these laboratory findings is related to clonal T-cell proliferation and adult T-cell leukemia/lymphoma development in vivo.

Interruption of p16 gene expression in adult T-cell leukaemia/lymphoma: clinical correlation

We previously reported that p16 gene deletion is involved in the development and progression of adult T-cell leukaemia/lymphoma (ATLL). To further investigate the significance of this gene in ATLL, we examined its expression status in 63 patients. Samples were analysed at DNA, mRNA and protein levels using real-time polymerase chain reaction (PCR), reverse transcription (RT)-coupled real-time PCR and Western blot respectively. Twenty-four patients (38.1%) were p16 gene negative, and they showed significantly shorter survival than p16-gene-positive patients. The expression of p16 mRNA in p16-gene-positive patients varied greatly, and cells from some patients showed up to several hundredfold higher expression than normal lymphocytes. Surprisingly, among 17 patients examined for p16 protein expression, all four patients with unusually high mRNA lacked p16 protein expression, indicating that p16 protein production in these patients was interrupted at the translational level. Moreover, these patients showed significantly shorter survival than p16-protein-positive patients. These results indicate that the presence of p16 gene and p16 mRNA do not necessarily indicate the production of p16 protein in ATLL, and that loss of p16 protein function is involved in progression of ATLL.

Seizing of T Cells by Human T-Cell Leukemia⧸Lymphoma Virus Type 1

Human T-cell leukemia/lymphoma virus type 1 (HTLV-1) causes neoplastic transformation of human T-cells in a small number of infected individuals several years from infection. Several viral proteins act in concert to increase the responsiveness of T-cells to extracellular stimulation, modulate proapoptotic and antiapoptotic gene signals, enhance T-cell survival, and avoid immune recognition of the infected T-cells. The virus promotes T-cell proliferation by usurping several signaling pathways central to immune T-cell function. Viral proteins modulate the downstream effects of antigen stimulation and receptor-ligand interaction, suggesting that extracellular signals are important for HTLV-1 oncogenesis. Environmental factors such as chronic antigen stimulation are therefore important, as also suggested by epidemiological data. The ability of a given individual to respond to specific antigens is determined genetically. Thus, genetic and environmental factors, together with the virus, contribute to disease development. As in the case of other virus-associated cancers, HTLV-1-induced leukemia/lymphoma can be prevented by avoiding viral infection or by intervention during the asymptomatic phase with approaches able to interrupt the vicious cycle of virus-induced proliferation of a subset of T-cells. This review focuses on current knowledge of the mechanisms regulating HTLV-1 replication and the T-cell pathways that are usurped by viral proteins to induce and maintain clonal proliferation of infected T-cells in vitro. The relevance of these laboratory findings will be related to clonal T-cell proliferation and adult T-cell leukemia/lymphoma development in vivo.

Role of tumor suppressor genes in the development of adult T cell leukemia/lymphoma (ATLL)

Adult T cell leukemia/lymphoma (ATLL) is one of the peripheral T cell malignant neoplasms strongly associated with human T cell leukemia virus type-I (HTLV-I). Although the viral transactivating protein Tax has been proposed to play a critical role in leukemogeneis as shown by its transforming activity in various experimental systems, additional cellular events are required for the development of ATLL. One of the genetic events in ATLL is inactivation of tumor suppressor genes. Among many candidates for tumor suppressor genes, the main genetic events have been reported to center around the cyclin-dependent kinase inhibitors ((CDKIs) p15INK4A, p16INK4B, p18INK4C, p19INK4D, p21WAF1, p27KIP1, and p57KIP2), p53 and Rb genes; all of them play a major regulatory role during G1 to S transition in the cell cycle. Acute/lymphomatous ATLL has frequent alterations of p15 (20%) and p16 (28-67%), while chronic/smoldering ATLL has fewer abnormalities of p15 (0-13%) and p16 (5-26%). Most of these changes are deletion of the genes; fewer samples have mutations. ATLL patients with deleted p15 and/or p16 genes have significantly shorter survival than those individuals with both genes preserved. Although genetic alterations of p18, p19, p21, p27 have rarely been reported, inactivation of these genes may contribute to the development of ATLL because low expression levels of these genes seem to mark ATLL. The p53 gene is mutated in 10-50% of acute/lymphomatous ATLL. Functional impairment of the p53 protein, even if the gene has wild-type sequences, has been suggested in HTLV-I infected cells. Each of these genetic events are mainly found in acute/lymphomatous ATLL, suggesting that alterations of these genes may be associated with transformation to an aggressive phenotype. The Rb tumor suppressor gene is infrequently structurally altered, but one half of ATLL cases have lost expression of this key protein. Notably, alterations of one of the CDKIs, p53 and Rb genes appear to obviate the need for inactivation of other genes in the same pathway. A novel tumor suppressor gene on chromosome 6q may also have a critical role in the pathogenesis of ATLL. Taken together, tumor suppressor genes are frequently altered in acute/lymphomatous ATLL and their alteration is probably the driving force fueling the transition from chronic/smoldering to acute/lymphomatous ATLL.

Lack of sequence variation in sporadic bovine leucosis in regions of tumour suppressor genes p53 and p16

Regions of the promoter and exons 5-8 of the tumour suppressor gene p53 were analysed in 25 cases of sporadic bovine leucosis. The study included 17 cases of juvenile leucosis, five cases of adult leucosis and three cases of skin leucosis. Exon 2 of tumour suppressor gene p16 was also investigated in the same samples. No sequence variations were present in the analysed areas of the genes. In p53, this fact represents a clear difference in comparison with enzootic bovine leucosis. In p16, no comparative data are available.

HTLV-I Tax related dysfunction of cell cycle regulators and oncogenesis of adult T cell leukemia

HTLV-I is causually related to the oncogenesis of adult T cell leukemia (ATL). However, the precise mechanism of HTLV-I oncogenesis is unclear. HTLV-I Tax protein functions as an activator of various cellular genes, including IL-2, IL-2 receptor-alpha, and c-fos through the activation of nuclear transfer factors such as NF-kappaB and SRF, and also potently activates trascription of viral genes through CREB/ATF sites in the viral LTR. However, Tax activation of HTLV-I infected T cells through the above pathways induces polyclonal proliferation of the cells in vitro; Tax however may function only transiently in the immediate post-infection period following infection in vivo. The long latent period of 60 years from infection to onset of disease suggests other mechanisms for ATL oncogenesis. Recent studies suggest that the malignant transformation of ATL is a multi-hit phenomena, suggesting that discrete genetic events are responsible for ATL oncogenesis. These genetic events could be responsible for the different stages of ATL: smoldering, chronic, lymphoma, and acute type, p16 and p53 genes are important negative regulators of the cell cycle and are often found to be mutated in neoplasms. Recent studies including ours demonstrated a high frequency of alteration of these two genes in primary ATL cells. Furthermore, alteration of the two genes is associated with acute but not chronic type ATL. In addition, p16 gene alteration is linked to the growth rate of ATL cells, suggesting that the alteration of these cell cycle regulatory genes may be related to progression from smoldering or chronic to acute or lymphoma type ATL. Tax may be involved in mutagenesis of these genes through suppression of DNA-beta polymerase gene expression during the process from latent period to acute/lymphoma type. Once transformation occurs, activation of the pathway between Tax and the three nuclear transfer factors, NF-kappaB, SRF, and CREB/ATF, contributes to establish the aggressive manifestations of acute/lymphoma type ATL cells.

Deletion of the p16INK4A gene in ex vivo acute adult T cell lymphoma/leukemia cells and methylation of the p16INK4A promoter in HTLV type I-infected T cell lines

The stoichiometry of the p16INK4A and p15INK4B proteins bound to the cyclin D-CDK4/6 complex regulates the entry of cells into the G1 phase of the cell cycle. Thus, their level of expression is essential in maintaining regulated cell growth. In several tumors, deletion of these genes has been reported and, more recently, promoter methylation has been suggested as an alternative mechanism to decrease the expression of these cell cycle inhibitor proteins. Here, we studied the methylation status and the integrity of the p16INK4A and p15INK4B genes in 8 chronically HTLV-I-infected T cell lines and in ex vivo cells from 14 ATLL patients. Deletion of the locus carrying both genes was not found in the HTLV-I-infected T cell lines but was found in seven of eight acute ATLL cases and in none of the PBMCs from the chronic cases or the affected lymph nodes of the lymphoma type. In contrast, partial or complete methylation of one or both genes was found only in chronically HTLV-I T cells. Thus, HTLV-I infection targets the p16INK4A and p15INK4B loci both in vitro and in vivo, although the mechanisms may differ.