Methylation profiling of human cancers in blood: molecular monitoring and prognostication (review)

Cancer is a polygenetic and polyepigenetic disease. Circulating tumor cells in peripheral blood have been demonstrated to reflect the biological characteristics of tumors including the potential of metastasis development and tumor recurrence. Aberrant promoter methylation has emergingly become a fundamental molecular abnormality leading to transcriptional silencing of tumor suppressor genes, DNA repair genes and metastasis inhibitor genes, and is linked to the predisposition of genetic alterations of other cancer-associated genes. This epigenetic inheritance has significant biological implications for cancer progression and metastasis formation. Of significance, DNA hypermethylation of multiple genes successfully detected in circulating tumor cells from cancer patients may prove valuable for disease monitoring. A number of epigenetic markers may feasibly enable the detection of circulating tumor cells from patients with different cancer types. The prognostic and therapeutic implications of aberrant DNA methylation could eventually bring forth improved outcome of cancer patients. A growing body of evidence and future advances in understanding cancer epigenetics may fuel us to monitor and treat cancers in alternative ways.

Epigenetic tumor markers in plasma and serum: biology and applications to molecular diagnosis and disease monitoring

Circulating tumor DNA in plasma and serum has been demonstrated to reflect the biological characteristics of tumors, including the rates of apoptosis and necrosis. Aberrant promoter methylation has increasingly emerged as a fundamental molecular abnormality associated with loss of critical gene functions during carcinogenesis. This epigenetic inheritance has significant biological implications for early tumor initiation and cancer progression or metastasis formation. The promoter-region methylation is crucial in transcriptional silencing of tumor suppressor genes, DNA repair genes, and metastasis inhibitor genes, and is linked to the predisposition of genetic alterations of other cancer-associated genes. Of clinical relevance, epigenetic markers in plasma and serum have recently been established as specific and sensitive biomarkers for early and noninvasive screening, risk assessment, and monitoring of neoplastic diseases. A panel of epigenetic markers may possibly allow the detection of circulating tumor DNA in virtually all patients with different cancer types. Furthermore, the prognostic value of aberrant DNA methylation and therapeutic implications of demethylation of methylated genes could further improve the management of patients with different kinds of cancer.

Circulating tumor cell mRNAs in peripheral blood from hepatocellular carcinoma patients under radiotherapy, surgical resection or chemotherapy: a quantitative evaluation

We assessed whether current therapies could lead to hematogenous dissemination of malignant hepatocytes in hepatocellular carcinoma (HCC) patients using semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) for alpha-fetoprotein (afp) and albumin (alb) mRNAs. We analyzed 137 peripheral blood samples before, during and after treatment from 84 patients under radiotherapy, surgical resection or chemotherapy. As compared to the upper limit for 53 healthy/non-HCC controls, alb- mRNA levels increased 2-10-fold in 6% of patients pre-treatment and 2-2.6x10(4)-fold in 32% post-treatment. Levels of afp- mRNA increased 3-210-fold in 17% pre-treatment and 4-5x10(5)-fold in 30% post-treatment. During a longitudinal follow-up of eight patients under radiotherapy or radiotherapy/resection, alb-mRNA levels were normal before treatment, whereas afp-mRNA levels increased 10-fold in two patients. During treatment, alb-mRNA and afp-mRNA levels increased 2-61-fold in three patients and 2.5-5-fold in two patients, respectively. After treatment, alb-mRNA levels declined to normal in all three patients within 3.5 months, but afp-mRNA levels increased 127-5x10(5)-fold in three patients within 5 months. We show evidence that HCC cells disseminating mostly post-treatment may be the 'seed' of recurrence/metastasis. In conjunction with the serum alpha-fetoprotein test, sequential afp-mRNA quantification could predict clinical metastasis/recurrence in 56% of patients during a 4-year follow-up.

Quantitative correlation of cytokeratin 19 mRNA level in peripheral blood with disease stage and metastasis in breast cancer patients: potential prognostic implications

Mortality among patients with breast cancer (BC) is mainly caused by metastasis. We determined the circulating tumor burden in BC patients by semiquantitative reverse transcription-polymerase chain reaction using carcinoembryonic antigen (CEA) and cytokeratin 19 (CK19) mRNAs as molecular markers. We distinguished the mRNA levels in circulation between BC patients and healthy controls with reference to a BC-derived cell line, SK-BR-3. We prospectively analyzed peripheral blood samples from 33 BC patients and 26 healthy controls. We found CEA mRNA in 97% of patients and 92% of normal controls, and CK19 mRNA in 72% of patients and 19% of controls. CEA and CK19 mRNAs in normal peripheral blood were most likely derived from illegitimate transcription. In 10 patients, of whom 9 (90%) developed systemic metastases, the upper limit of CK19 mRNA of normal controls was exceeded. As compared with normal controls, significantly elevated CK19 mRNA levels in the patients appeared to originate from circulating malignant BC cells (P<0.0001). It was clinically significant that the mean CK19 mRNA level increased with advancing disease stage. Of prognostic value, we report for the first time that BC patients with CK19 mRNA elevation had notably shorter (approximately 3-year reduction) overall survival than patients with normal CK19 mRNA levels (P=0.045). Quantification of CK19 mRNA may prove useful for cancer staging, disease monitoring and prognostic assessment among BC patients.

Quantitative relationship of the circulating tumor burden assessed by reverse transcription-polymerase chain reaction for cytokeratin 19 mRNA in peripheral blood of colorectal cancer patients with Dukes' stage, serum carcinoembryonic antigen level and tumor progression

We prospectively analyzed the circulating tumor burden in colorectal cancer patients using semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) for carcinoembryonic antigen (CEA) and cytokeratin 19 (CK19 ). We distinguished the mRNA levels in peripheral blood between 33 patients and 26 healthy controls with reference to SK-BR-3 cell line. We found CEA-mRNA in 88% of patients and 92% of controls, and CK19 mRNA in 64% of patients and 19% of controls. Our CK19 mRNA assay was sufficiently sensitive to detect one SK-BR-3 cell among 10(6) normal blood cells. The upper limit of CK19 mRNA among controls was exceeded by 14 patients, and 12 patients (86%) developed systemic metastases/recurrence. Significantly elevated CK19 mRNA levels appeared to originate from circulating malignant cells (P<0.0001). Of relevance, the CK19 mRNA level increased with advancing Dukes' stage and correlated directly with the serum CEA level (P=0.016). CK19 mRNA quantification may prove valuable for cancer staging and disease monitoring.

Molecular analysis of circulating tumor cells in peripheral blood from patients with germ cell tumor: a quantitative approach

Germ cell tumor (GCT) is one of the few malignancies in which recurrent patients would have a good chance of cure by chemotherapy. Using semiquantitative reverse transcription polymerase chain reaction for alpha-fetoprotein (alphafp) mRNA, we measured the circulating tumor load in 54 peripheral blood samples from 7 GCT patients at diagnosis and 47 healthy controls. Clinicopathological information of GCT patients was obtained during a 12-month follow-up. As compared to the upper limit among healthy controls, alphafp mRNA levels increased 23-3.4x103-fold pre-treatment in all 7 patients, and 2.8x103-1.4x104-fold post-treatment in 2 patients studied. All 7 patients with substantially elevated alphafp mRNA levels developed recurrence or metastasis within 12 months of diagnosis. We present evidence that alphafp-expressing tumor cells disseminating in GCT patients before treatment may possibly be the source of recurrence or metastasis. Sequential quantification of alphafp mRNA during the clinical course may provide crucial information for identifying GCT patients at high risk for metastasis.

Frequent p15 promoter methylation in tumor and peripheral blood from hepatocellular carcinoma patients

We prospectively analyzed p15 methylation patterns in 25 surgically resected tumors and 130 plasma, serum, and buffy coat samples from hepatocellular carcinoma (HCC) patients, controls with chronic hepatitis/cirrhosis, and healthy subjects. Using methylation-specific PCR, we demonstrated for the first time p15 promoter methylation in 64% of tumors and 25% (4 of 16) of patients' plasma and serum samples. Concurrent p15 and p16 methylation was shown in 48% of tumors, and p15/p16 methylation was detected in the plasma/serum of 92% (11 of 12) of patients. Of note, 75% of 12 patients with concurrent tumor methylation developed clinical metastasis/recurrence (P = 0.027). In buffy coat samples, p15 methylation was detected in all eight patients with tumor p15 methylation, suggesting the presence of circulating tumor cells. None of the control samples were methylation positive. Our data underscore the important role(s) of p15 and p16 methylation in hepatocarcinogenesis and tumor progression. Among 92% (23 of 25) of patients with tumor p15/p16 methylation, circulating tumor DNA and HCC cells were detected in the peripheral blood of 87% (20 of 23) of patients. The combination of these epigenetic markers may prove valuable for noninvasive HCC diagnosis and disease monitoring.

Quantitative comparison of alpha-fetoprotein and albumin mRNA levels in hepatocellular carcinoma/adenoma, non-tumor liver and blood: implications in cancer detection and monitoring

Early detection of recurrence is valuable for monitoring hepatocellular carcinoma (HCC) progression. By quantitative reverse transcriptase polymerase chain reaction (RT-PCR), we derived calibration curves for alpha-fetoprotein (afp) and albumin (alb) mRNAs using 40 matched tumors and non-tumor liver tissues from HCC/adenoma patients. We prospectively quantified tumor cells and non-tumor liver cells in 62 patients' blood samples before, during and after surgery. Expression of both mRNAs was heterogeneous (1-10(5)-fold) between tumors and HepG2 cell line. The alb-mRNA levels in non-tumor liver cells were 2-10-fold higher than in tumor cells. The afp-mRNA levels in HCC cells were 30-1000-fold higher than in non-tumor cells. The alb-mRNA level in blood may reflect the number of liver cells, whereas the afp-mRNA level may represent mostly the number of HCC cells. We found different ratios of circulating HCC cells to non-tumor liver cells during the clinical course of patients, in association with the subsequent development of recurrence/metastasis. This approach may prove useful for detecting and monitoring HCC progression.

Quantitative analysis of circulating tumor cells in peripheral blood of osteosarcoma patients using osteoblast-specific messenger RNA markers: a pilot study

Metastasis is a major cause of mortality and morbidity in osteosarcoma (OS) patients. To monitor tumor dissemination, we assessed the circulating tumor burden in OS patients by semiquantitative reverse transcription-PCR using osteocalcin, osteonectin, osteopontin, and type I collagen (COLL) mRNAs as molecular markers. We distinguished levels of the mRNAs in peripheral blood between OS patients and healthy subjects using an OS-derived cell line (Saos-2) as a reference standard. We prospectively analyzed 40 peripheral blood samples from 11 OS patients at diagnosis and 29 healthy subjects. In all 29 (100%) healthy subjects, we detected osteocalcin, osteonectin, and osteopontin mRNAs that were most likely attributed to illegitimate transcription in normal hematopoietic cells. In contrast, we found low COLL mRNA levels in only 35% (10 of 29) of healthy subjects, but significantly higher COLL mRNA levels in 91% (10 of 11) of OS patients (P < 0.0001). The reverse transcription-PCR assay for COLL mRNA was sensitive down to the detection of 10 Saos-2 cells among 10(6) normal peripheral blood nucleated cells. The upper limit of COLL mRNA determined among the healthy subjects was found exceeded by six OS patients. The substantially elevated COLL mRNA levels in peripheral blood seemed to originate from circulating malignant cells in these six OS patients, all of whom subsequently developed clinical metastases within 12 months of diagnosis (P = 0.002). Conversely, no metastases were detected in the remaining OS patients with normal COLL mRNA levels. Quantification of COLL mRNA may prove valuable for diagnosing OS micrometastasis and assessing prognosis.

Aberrant p15 promoter methylation in adult and childhood acute leukemias of nearly all morphologic subtypes: potential prognostic implications

We prospectively analyzed p15 and p16 promoter methylation patterns using methylation-specific polymerase chain reaction (PCR) in patients with adult and childhood acute leukemias and studied the association of methylation patterns with chromosomal abnormalities and prognostic variables. In nearly all French-American-British leukemia subtypes, we found p15 methylation in bone marrow or peripheral blood cells from 58% (46/79) of patients with acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), or acute biphenotypic leukemia (ABL). An identical alteration was detected in blood plasma from 11 of 12 of these patients (92%). We also demonstrated for the first time concomitant p16 and p15 methylation in 22% (8/37) of adults with AML or ALL, exclusively in those with M2, M4, or L2 subtypes. According to cytogenetic data from 35 patients with ALL, AML, or ABL, 82% (14/17) of those with unmethylated p15 alleles had normal karyotypes or hyperdiploidies associated with a favorable prognosis. Conversely, 44% (8/18) of patients with p15 methylation had chromosomal translocations, inversions, or deletions, suggesting an interplay of these abnormalities with p15 methylation. As a prognostic marker for disease monitoring, p15 methylation appears to be more widely applicable than BCR-ABL, AF4-MLL, and AML1-ETO transcripts, which were detectable in only 8% (4/48) of patients by reverse transcriptase-PCR. Thirty-nine of 43 blood samples (91%) sequentially collected from 12 patients with AML, ALL, or ABL showed p15 methylation status in excellent concordance with morphologic disease stage. Early detection of p15 methylation at apparent remission or its acquisition during follow-up may prove valuable for predicting relapse. Overall survival of patients with p15 methylation was notably shortened among 38 adults with AML and 12 adults with ALL. Aberrant p15 methylation may have important prognostic implications for clinical monitoring and risk assessment. (Blood. 2000;95:1942-1949)

Hematogenous dissemination of hepatocytes and tumor cells after surgical resection of hepatocellular carcinoma: a quantitative analysis

The only hope of long-term survival for patients with hepatocellular carcinoma (HCC) is surgical resection or liver transplantation. However, recurrence or metastasis formation is common after surgery. We aim to assess whether surgical resection leads to hematogenous dissemination of malignant and nontumor hepatocytes and determine the quantity and timing of hepatocyte shedding into the circulation. Using semiquantitative reverse transcription-PCR for alpha-fetoprotein (afp) and albumin (alb) mRNAs, we measured the mass of malignant and nontumor hepatocytes in 53 peripheral blood samples collected preoperatively, intraoperatively, and postoperatively from 13 HCC patients. We compared these data with those in 54 control samples collected from 24 healthy subjects and patients with chronic hepatitis/cirrhosis and 10 hepatocellular adenoma patients who underwent resection. Clinicopathological information of HCC patients was obtained during 3-year follow-up. In 100% (23 of 23) of HCC and adenoma patients, alb mRNA levels increased 10-10(6)-fold intraoperatively and then markedly declined within 8 weeks after operation. Levels of afp mRNA increased 5-7600-fold preoperatively in 8% (1 of 13) and postoperatively in 70% (9 of 13) of HCC patients. All five HCC patients with persistently elevated afp mRNA levels died from intrahepatic/extrahepatic metastasis, liver recurrence, or persistent HCC within 1 year after surgery. The absence/clearance of afp mRNA in 75 % (six of eight) of survivors was strongly associated with the absence of metastasis/recurrence (P = 0.02). We present evidence that alb-expressing hepatocytes are released intraoperatively into the circulation, and afp-expressing tumor cells are disseminated mostly postoperatively that may potentially be the source of recurrence or metastasis. Sequential quantification of both alb and afp mRNAs may provide insights for risk assessment and prognostic indication.

Quantitative analysis of aberrant p16 methylation using real-time quantitative methylation-specific polymerase chain reaction

We have developed a quantitative method for methylation analysis of the p16 gene based on real-time methylation-specific PCR (MSP). Real-time MSP is sensitive enough to detect down to 10 genome equivalents of the methylated p16 sequence. Application of real-time MSP to DNA from tumor-derived cell lines revealed complete concordance with conventional MSP analysis. Quantitative data generated by real-time MSP were expressed as the methylation index, which was defined as the percentage of bisulfite-converted DNA that consisted of methylated target sequences. The methylation index was shown to be inversely correlated with p16 gene transcription during demethylation treatment of cell lines with 5-aza-2'-deoxycytidine. The application of real-time MSP to bone marrow aspirates from patients with multiple myeloma revealed complete concordance with conventional MSP analysis. Real-time quantitative MSP may have applications in elucidating diverse biological processes involving DNA methylation and may become a valuable diagnostic tool for detecting tumor-associated epigenetic changes in cancer patients.

DNA methylation changes and multiple myeloma

In contrast to classical mutations, DNA methylation is a mechanism of changing the base sequence without altering the coding function of a gene. The interplay between this epigenetic modification and classical mutations plays an important role in tumorigenesis. Global genomic hypomethylation has been associated with the induction of chromosomal instability, which is commonly seen in solid tumors and multiple myeloma. De novo methylation of CpG islands on the promoter region may contribute to the progressive inactivation of growth-inhibitory genes resulting in the clonal selection of cells with growth advantage. Recently, alteration of p16 and p15 solely by hypermethylation has been detected in high frequencies hitherto unreported in multiple myeloma (MM). Hypermethylation of p16 has been shown to be associated with plasmablastic disease (p=0.026) in primary MM and transcriptional silencing of p16 and p15 has also been found to correlate with hypermethylation of these genes in MM-derived cell lines. Our results in studies with cell lines and primary MM support the fact that hypermethylation of p16 and p15 plays an important role in MM tumorigenesis. Because of its high frequency, the presence of hypermethylation of p16 may prove to be a useful tumor marker for the majority of MM patients. Promoters silenced by methylation can be reactivated by treatment with the demethylating agent 5-aza-2'deoxycytidine. The reversibility of this epigenetic inactivation of the p16 and p15 genes in MM may also provide a broad clinical application in the development of new therapeutic interventions in this uniformly fatal form of cancer.

Combined morphological and interphase fluorescence in situ hybridization study in multiple myeloma of Chinese patients

To gain insight into the real incidence of the numeric chromosomal aberrations and the cell lineage involvement of the neoplastic process in multiple myeloma (MM), we examined 18 Chinese MM patients by May-Grunwald-Giemsa (MGG) staining and fluorescence in situ hybridization using three DNA centromeric probes specific for chromosomes 3, 7, and 9. In this investigation, cytogenetic abnormalities were detected in plasma cells (PCs), myeloid cells (MCs), and lymphoid cells (LCs) in all of the MM patients studied. This is the first demonstration of the cytogenetic aberration involved in the myeloid series. Furthermore, the MCs and PCs of 16 MM patients had the same aneuploidies in one or more of the chromosomes analyzed. These data suggest that the neoplastic transformation of MM may occur early in the hematopoietic development. Chromosomal aberrations involving mainly subclones and considerable cellular heterogeneity with gain of a variety of copy numbers of the same chromosome were demonstrated within PCs, which may possibly be the result of an underlying defect of PCs in the control of their number of chromosomes. Whereas PCs showed evidence suggestive of increased polyploidization, MCs and LCs, which exhibited similar chromosomal patterns as the former, rarely did. Thus, the clonal evolution from LC to PC, if that happens in MM, is characterized by chromosomal instability favoring growth of tumor cells with polysomies and polyploidies.

Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients

We have studied the feasibility of detecting tumor-associated aberrant p16 methylation in the circulation of patients with hepatocellular carcinoma (HCC). We extracted DNA from the tumor tissues and peripheral blood plasma or serum of 22 HCC patients. p16 methylation was found in 73% (16 of 22) of HCC tissues using methylation-specific PCR. Among the 16 cases with aberrant methylation in the tumor tissues, similar changes were also detected in the plasma/serum samples of 81% (13 of 16) of the cases. No methylated p16 sequences were detected in the peripheral plasma/serum of the six HCC cases without these changes in the tumor, in 38 patients with chronic hepatitis/cirrhosis, or in 10 healthy control subjects. These results suggest that circulating liver tumor DNA may be detected using tumor-associated DNA methylation changes. Because methylation abnormalities have been found in many other genes and tumor types, this approach may have implications for the noninvasive detection of a wide variety of cancers.

Transcriptional silencing of the p16 gene in human myeloma-derived cell lines by hypermethylation

Recently, p16 and p15 have been identified as commonly inactivated tumour suppressor genes in haematological malignancies. We previously reported that these genes were frequently hypermethylated in multiple myeloma (MM). To investigate how p16 and p15 inactivation are associated with hypermethylation, methylation status and transcription of these genes in six MM-derived cell lines were studied by Southern blot analysis and RT-PCR. Aberrant methylation of p16 was found in ARH-77, HS-Sultan, IM-9, RPMI-8226, U266-B1 and NCI-H929 MM cell lines. However, loss of p16 transcription was demonstrated only in HS-Sultan, RPMI-8226, U266-B1 and NCI-H929 with extensive methylation at the 5' upstream region of p16. Conversely, only HS-Sultan showed extensive methylation at the 5' upstream region of p15, which was associated with p15 transcriptional block. These results suggest that extensive methylation within a critical domain may be crucial in silencing p16 or p15 transcription. To demonstrate the reversibility of methylation and its relationship with transcription, HS-Sultan, RPMI-8226 and NCI-H929 were demethylated with 5-aza-2'-deoxycytidine. Restoration of gene transcription was observed and correlated with partial demethylation of the genes. The present data show that the p16 and p15 genes are silenced in MM by hypermethylation, which may play an important role in MM pathogenesis.

Semiquantification of circulating hepatocellular carcinoma cells by reverse transcriptase polymerase chain reaction

Hepatocellular carcinoma (HCC) is one of the most common and rapidly fatal malignancies worldwide. Treatment options are severely limited by the frequent presence of metastases. If hepatocyte-specific mRNAs are detected in the circulation, it is possible to infer the presence of circulating, presumably malignant, liver cells. If these can be quantified, it is possible to predict the likelihood of haematogenous metastasis. In this investigation, we have attempted to gain an index of the mass of circulating HCC cells (with reference to the number of hepatoblastoma cells) by measuring the amounts of PCR products for albumin (alb) mRNA and alpha-fetoprotein (afp) mRNA by reverse transcriptase polymerase chain reaction (RT-PCR) and Southern blot analysis. For calibration, total RNA from 1-10(6) HepG2 cells was mixed with total RNA from 10(6) normal peripheral mononuclear cells. A linear relationship was demonstrated between the amount of alb- or afp PCR product and the level of HepG2 total RNA spiked. The assay is sensitive down to a detection level of one HepG2 cell. Alb mRNA was detected in 50% of 18 normal subjects and afp mRNA in only two normal subjects. The alb mRNA cut-off level for the normal was exceeded by seven normal subjects and 34 out of 64 HCC patients, and that for afp mRNA was exceeded by six HCC patients but none of the normal subjects. The level of alb mRNA detected was not linearly proportional to the amount of afp mRNA detected in peripheral blood of the same patients, suggesting heterogeneous expression of alb and afp genes in different circulating tumour cells. In addition, no significant linear association between the levels of afp mRNA and serum AFP was observed. Semiquantification of both mRNA markers for HCC cell detection may prove useful in prediction of metastases.

Isolation and sequence analysis of a cDNA encoding an adenine nucleotide translocator from Plasmodium falciparum

A cDNA clone encoding the polypeptide for Plasmodium falciparum adenine nucleotide translocator (ANT) was isolated by screening a cDNA library with a 150 base pair fragment of genomic DNA which had been enzymatically amplified using two oligonucleotide primers designed from conserved regions of ANT's from other sources. The deduced amino acid sequence of the P. falciparum cloned insert was highly homologous to ANT of other organisms. Features of the sequence are discussed with reference to the targeting and membrane insertion of ANT. The protein has a molecular mass of 35 kDa as predicted from the 303 amino acids encoded in the open reading frame.