Influence of Cytochrome P450, ABC and SLC Gene Polymorphisms on Imatinib Therapy Outcome of Patients with Gastrointestinal Stromal Tumours (GIST).

The efficacy of imatinib-based therapy depends on the proteins involved in its metabolism and transportation. Therefore, the aim of our study was to investigate the possible correlation of selected P450, ABC and SLC polymorphic variants and the outcome of imatinib therapy. A total of 101 patients with advanced, KIT/PDGFRA(+) GIST treated with imatinib were enrolled to the study. DNA was extracted from peripheral blood samples and genotypes were determined by PCR-RFLP and direct sequencing. Deviation from the Hardy-Weinberg equilibrium was only observed for rs2740574. None of the studied SNPs was associated with GIST time to progression. No significant correlation between any specific variant and time to progression was found in the group with KIT exon 11 mutation. However, individuals of at least three potentially unfavourable genotypes presented significantly shorter time to progression in comparison to patients with two or less unfavourable genotypes.

Aberrant DNA methylation of alternative promoter of DLC1 isoform 1 in meningiomas.

DLC1 encodes GTPase-activating protein with a well-documented tumor suppressor activity. This gene is downregulated in various tumors through aberrant promoter hypermethylation. Five different DLC1 isoforms can be transcribed from alternative promoters. Tumor-related DNA methylation of the DLC1 isoform 1 alternative promoter was identified as being hypermethylated in meningiomas in genome-wide DNA methylation profiling. We determined the methylation pattern of this region in 50 meningioma FFPE samples and sections of 6 normal meninges, with targeted bisulfite sequencing. All histopathological subtypes of meningiomas showed similar and significant increase of DNA methylation levels. High DNA methylation was associated with lack of DLC1 protein expression in meningiomas as determined by immunohistochemistry. mRNA expression levels of 5 isoforms of DLC1 transcript were measured in an additional series of meningiomas and normal meninges. The DLC1 isoform 1 was found as the most expressed in normal control tissue and was significantly downregulated in meningiomas. Transfection of KT21 meningioma cell line with shRNA targeting DLC1 isoform 1 resulted in increased activation of RHO-GTPases assessed with pull-down assay, enhanced cell migration observed in scratch assay as well as slight increase of cell metabolism determind by MTT test. Results indicate that isoform 1 represents the main pool of DLC1 protein in meninges and its downregulation in meningiomas is associated with hypermethylation of CpG dinucleotides within the corresponding promoter region. This isoform is functional GAP protein and tumor suppressor and targeting of its expression results in the increase of DLC1 related cell processes: RHO activation and cell migration.

Long-term follow-up of patients with GIST undergoing metastasectomy in the era of imatinib -- analysis of prognostic factors (EORTC-STBSG collaborative study).

BACKGROUND: Long-term complete remissions remain a rare exception in patients with metastatic gastrointestinal stromal tumors (GIST) treated with IM (imatinib). To date the therapeutic relevance of surgical resection of metastatic disease remains unknown except for the use in palliative intent. PATIENTS AND METHODS: We analyzed overall survival (OS) and progression-free survival (PFS) in consecutive patients with metastatic GIST who underwent metastasectomy and received IM therapy (n = 239). RESULTS: Complete resection (R0+R1) was achieved in 177 patients. Median OS was 8.7 y for R0/R1 and 5.3 y in pts with R2 resection (p = 0.0001). In the group who were in remission at time of resection median OS was not reached in the R0/R1 surgery and 5.1 y in the R2-surgery (p = 0.0001). Median time to relapse/progression after resection of residual disease was not reached in the R0/R1 and 1.9 years in the R2 group of patients, who were resected in response. No difference in mPFS was seen in patients progressing at time of surgery. CONCLUSIONS: Our analysis implicates possible long-term survival in patients in whom surgical complete remission can be achieved. Incomplete resection, including debulking surgery does not seem to prolong survival. Despite the retrospective character and likely selection bias, this analysis may help in decision making for surgical approaches in metastatic GIST.

Surgical resection of residual disease in initially inoperable imatinib-resistant/intolerant gastrointestinal stromal tumor treated with sunitinib.

AIM: Sunitinib malate therapy in inoperable and/or metastatic gastrointestinal stromal tumor (GIST) resistant to imatinib mesylate may facilitate surgical removal of residual disease. We explored this possibility in the course of treating patients as part of a treatment-use trial, the objective of which was to provide access to sunitinib treatment. METHODS: Four patients with inoperable and/or metastatic GIST resistant to imatinib who had responded to sunitinib therapy administered at a starting dose of 50 mg daily in 6-week cycles of 4 weeks on treatment followed by 2 weeks off underwent surgical removal of residual disease. Disease progression on or clinical response to treatment was defined based on Response Evaluation Criteria in Solid Tumors. RESULTS: In three of four cases it was possible to perform macroscopically complete resection of residual disease, resulting in surgical complete clinical responses, two with durations of 13 months. The fourth patient achieved a dramatic partial response to sunitinib that required emergency surgical resection of the necrotic tumor mass, with the partial response having been maintained for 15 months. In all cases, viable GIST cells were detected histologically in the resection specimens, and sunitinib treatment was resumed post-surgery. None of the patients experienced any postoperative complications during 13-16 months of follow-up. CONCLUSIONS: Combining sunitinib treatment with surgical removal of residual disease may allow selected imatinib-resistant GIST patients who have shown a favorable response to sunitinib to achieve complete and sustained remission or durable control of previously progressive disease beyond that expected for sunitinib treatment alone.

Presence of t(14;18) positive cells in blood and bone marrow does not predict outcome in follicular lymphoma.

Follicular Lymphoma International Prognostic Index-FLIPI is an established clinical predictor for outcome in follicular lymphoma. The role of molecular abnormalities in blood and bone marrow of follicular lymphoma patients including t(14;18) is less clear. Seventy-five patients from a single institution diagnosed with follicular lymphoma between1999 and 2005 were included into the study. Diagnosis was based on lymph node biopsy in 62 cases (83%). Thirty-nine patients (52%) had G1 histological grade and 47 (63%) had entirely follicular growth pattern, as well as 9 patients (12%) had systemic symptoms and 33 (44%) were assigned to a good risk according to FLIPI. Median age of patients was 53 years. During a median observation time of 3 years 63 patients (84%) required initiating anti-lymphoma treatment. Seventy-five samples of peripheral blood and 65 samples of bone marrow were collected at the diagnosis. Bcl2 rearrangements including major breakpoint region and minor breakpoint cluster region were investigated using nested polymerase chain reaction technique. The primary end points of the study were time to first line lymphoma treatment and progression-free survival. Cells carrying t(14;18) were found in 31 cases (41%) including 29 samples of peripheral blood and 26 samples of bone marrow. Detection of t(14;18) in blood and bone marrow at diagnosis had no influence on clinical outcome. Age, follicular growth pattern systemic symptoms, and FLIPI score above 1 were predictive for initiation of the first lymphoma therapy. Follicular growth pattern, initial nodal involvement, serum LDH level, and FLIPI score above 1 were predictive for longer progression-free survival.

Molecular and biochemical testing in stage III melanoma: multimarker reverse transcriptase-polymerase chain reaction assay of lymph fluid after lymph node dissection and preoperative serum lactate dehydrogenase level.

BACKGROUND: There is a need for biomarkers to identify patients at risk for disease progression after resection of melanoma regional lymph node metastasis. OBJECTIVES: This study assessed the prognostic value of multimarker reverse transcriptase-polymerase chain reaction (RT-PCR) assay in lymphatic drainage (LY) after lymph node dissection (LND) and of preoperative serum lactate dehydrogenase (LDH) levels in American Joint Committee on Cancer (AJCC) stage III melanoma patients. METHODS: We collected 24-h LY from 255 stage III melanoma patients after radical LND [114, completion LND after positive sentinel node biopsy (CLND); 141, therapeutic LND for clinically/cytologically detected regional nodal metastases (TLND)]. For detection of melanoma cells, RT-PCR assays with primers specific for tyrosinase, MART1 (MelanA) and uMAGE mRNA were conducted. The LY sample was deemed positive if at least one marker was detected. In 244 patients, the preoperative serum LDH level was available. Median follow-up time was 25 months (range 5-60). RESULTS: The LY multimarker RT-PCR assay results were positive in 82 of 255 patients (32%). A significantly higher rate of melanoma recurrence was observed in patients with positive LY multimarker RT-PCR results (P = 0.01). Significant relationships were observed between positive LY multimarker RT-PCR results and shorter 3-year overall survival (OS) and disease-free survival (DFS), both in univariate and multivariate analyses (P = 0.007). Preoperative serum LDH level was increased in 79 of 244 patients (32%) [40.5% in TLND group and 23.0% in CLND group (P = 0.003)]. There were significant differences in OS between patients with normal and high preoperative LDH levels (P = 0.007), and these differences were seen mainly in patients in the TLND group. CONCLUSIONS: The multimarker RT-PCR assay detected melanoma cells in approximately 32% of LY after LND, which correlated significantly with early melanoma recurrence and shorter survival. Increased pre-LND serum LDH level had an additional negative impact on OS of melanoma patients with palpable nodal metastases after TLND.

Detection of circulating melanoma cells in peripheral blood by a two-marker RT-PCR assay.

The aim of this study was to develop a highly sensitive two-marker assay for the detection of circulating melanoma cells in patients' blood using a reverse transcriptase-polymerase chain reaction (RT-PCR). We analysed the usefulness of two different sets of markers: tyrosinase and MUC-18 (TYR/MUC-18), and tyrosinase and MART 1 (TYR/MART 1). Total cellular RNA was isolated from 337 blood samples from 80 melanoma patients at different stages of the disease. All patients had undergone primary surgery. Assay sensitivity and specificity were confirmed using three different melanoma cell lines and two different fibroblast lines. In addition, blood from 47 healthy subjects and 10 patients with non-melanoma cancer was used as a negative control. We found that two-marker analysis is more accurate than the single tyrosinase assay. The frequency of melanoma cell detection in patients' blood was about 10% higher when the TYR/MART 1 two-marker assay was used. Using this assay we did not find any statistical correlation between the molecular markers and the UICC stage of disease or the Breslow thickness or Clark level of the primary melanoma. The frequency of melanoma cell detection with the TYR/MUC-18 two-marker assay was even higher than the TYR/MART 1 assay, but unfortunately the MUC-18 transcript was also present in about 20% of healthy subjects. Therefore we do not recommend the use of MUC-18 as a standard value marker.

[Molecular diagnosis of neoplasms]. / Diagnostyka molekularna chorób nowotworowych.

Based on general biological features of cancer cells, different aspects of cancer diagnostics are discussed.

Alternative splicing of DNA polymerase beta mRNA is not tumor-specific.

Mammalian DNA polymerase beta is a crucial enzyme in cell genomic maintenance. Its structure is highly conserved. Some splice variants of beta-pol mRNA were observed. One alternative splice DNA polymerase beta mRNA, generated by 87 nt deletion (exon 11) in the catalytic domain of this enzyme, was suggested to be responsible for genomic instability in tumorigenesis and in genetic disorder (Werner syndrome). Here, we show that exon-11-deleted beta-pol mRNA is present in all examined normal and tumor tissues as well as in resting or PHA-stimulated peripheral-blood mononuclear cells. This finding proves that the presence of the exon-11 alternative splicing variant of beta-pol mRNA is not tumor-specific.

Alternative polyadenylation of the gene transcripts encoding a rat DNA polymerase beta.

Rat cells produce two different transcripts of DNA polymerase beta (beta-Pol). The low-molecular-weight transcript (1.4 kb) was already sequenced. We report here the cloning and sequencing of the full-length cDNA, corresponding to the high-molecular-weight (HMW) transcript (4.0 kb) of beta-Pol. Sequence data strongly suggest that both transcripts are produced from a single gene by alternative polyadenylation. The HMW transcript contains the entire 1.4 kb transcript sequence and additional 2.2 kb on the 3' end. The 3' UTR of the HMW transcript contains some regulatory sequences which are not present in the 1.4-kb transcript. The A + U-rich fragment and (GU)21 sequence are believed to influence the stability of the mRNA. The functional significance of the A-rich region locally destabilizing double-stranded secondary structure remains unknown.

Cloning and characterization of the 5' part of the high molecular weight transcript of rat DNA polymerase beta.

A rat brain cDNA library has been constructed. Three identical clones of about 2.2 kb representing high molecular weight DNA polymerase beta transcript were found. Sequencing proved our earlier suggestion that both high and low molecular weight DNA polymerase beta transcripts have the same open reading frame and differ mainly at the 3' end. Because of that, alternative polyadenylation is discussed as a possible mechanism for tissue- and development-specific regulation of the DNA polymerase beta gene expression.

[Myelodysplastic syndrome associated with clonal proliferation of B lymphocytes]. / Zespól mielodysplastyczny przebiegajacy z klonalna proliferacja limfocytów B.

We present an unusual case of the myelodysplastic syndrome (subtype refractory anemia with the excess of blasts in transformation--RAEB-t) associated with significant increase of IgG (4,700 mg/dl), lambda (160 U/dl) in blood serum and circulating clone of B lymphocytes SIgG, lambda, manifesting clonal rearrangement of JH domain. Peripheral blood cells of the patient showed two different chromosomal abnormalities: 47,XY, + del/8/p? and 47,XY, +22, +14, -19. We suppose that two independent neoplastic clones are developed in the described case, i.e. a population displaying markers of myeloblasts and monoblasts, and a clone of B lymphocytes.

Effect of busulphan treatment and elevated temperature on the expression of the beta-pol gene in rat testis.

Changes in the expression pattern of the DNA polymerase beta gene during inhibition of spermatogenesis by busulphan and by temperature (artificial cryptorchidism) have been studied. Transient arrest of spermatogenesis in two-month-old rats after injection of a single dose of busulphan (10 mg/kg) resulted in parallel but transient decrease in the 1.4 kb of beta-pol mRNA level to an undetectable value, followed by its reappearance after resumption of spermatogenesis. An artificial cryptorchidism also caused a drastic decrease of beta-pol mRNA level. Both results as well as morphological examination of testis after busulphan injection and artificial cryptorchidism revealed that spermatocytes and spermatids represent the testicular cell fraction containing the elevated amount of beta-pol mRNA. Involvement of DNA polymerase beta in meiotic recombination is discussed.

Changes in the DNA polymerase beta gene expression during development of lung, brain, and testis suggest an involvement of the enzyme in DNA recombination.

Changes in the expression pattern of DNA polymerase beta gene during rat lung, brain, and testis development have been investigated. A decrease in the level of beta-pol mRNA was observed during postnatal development of lung and brain. By contrast, an almost 20-fold increase in the level of beta-pol mRNA was observed during spermatogenesis. For most adult rat tissues the abundance of beta-pol mRNA was low compared with that of beta-actin mRNA. Northern blot analysis revealed four distinct transcripts hybridizing to beta-pol probes. At least two of them, 1.4 kb and 4.0 kb, were products of a beta-polymerase gene. The changes in the expression pattern during lung and brain development, and during spermatogenesis, suggest involvement of DNA polymerase beta in gap-filling DNA synthesis during recombination.

Levels and size complexity of DNA polymerase beta mRNA in rat regenerating liver and other organs.

A cDNA probe encoding DNA polymerase beta (beta-pol) was used to study the level and size complexity of beta-pol mRNA in regenerating rat liver and other rat tissues. An almost 2-fold increase in beta-pol mRNA was observed 18-24 h after partial hepatectomy. In most adult rat tissues (liver, heart, kidney, stomach, spleen, thymus, lung and brain) the abundance of beta-pol mRNA was low. In contrast, young brain and testes exhibited beta-pol mRNA levels 5- and 15-times higher, respectively. The observed changes in the level of beta-pol mRNA in regenerating rat liver and in developing brain are correlated with reported changes in DNA polymerase beta activity. Four different (4.0, 2.5, 2.2, 1.4 kb) transcripts hybridizing to beta-pol probe were found in all tissues examined. The 4.0 kb transcript was dominant for young and adult brain, whereas the 1.4 kb transcript was dominant for testes. The significance of these transcripts is discussed.

Proto-oncogene c-fos induction in rat hippocampus.

The apparently non-specific accumulation of c-fos proto-oncogene mRNA was found in rat hippocampus as a result of injection of either glutamate, noradrenaline, or physiological saline. There was no c-fos gene induction following an electroconvulsive shock.