Report on the Effect of the Implementation of an Early Detection and Prevention of Cancer Program on Families at High Hereditary Risk-Concentrating on Patients Undergoing Genetic Diagnostics and Counseling in Central Poland.

Over a 46-month period, the objectives of the National Cancer Control Program (NCCP, pol. Narodowy Program Zwalczania Chorób Nowotworowych), coordinated by the Ministry of Health, were pursued by conducting genetic diagnostics on individuals at high risk of developing cancer. A total of 1097 individuals were enrolled in the study, leading to the identification of 128 cases of germline mutations. The implementation of the NCCP led to the identification of genetic mutations in 4.43% of the patients qualified for BRCA1 and BRCA2 screening tests, in 18.18% of those qualified for a comprehensive next-generation sequencing (NGS) panel in cases of breast and ovarian cancer, and in 17.36% of cases of colorectal and endometrial cancer. The research conducted allowed us to establish individualized preventive and therapeutic approaches for mutation carriers. However, the results prove that liberalizing the inclusion criteria for high-throughput diagnostics and the use of broad gene panels could significantly increase the percentage of detected carriers. This publication serves as a summary and discussion of the results obtained from the implementation of the NCCP as well as of the role of genetic consulting in personalized medicine.

Genotypic and Phenotypic Changes in Candida albicans as a Result of Cold Plasma Treatment.

We treated Candida albicans cells with a sublethal dose of nonequilibrium (cold) atmospheric-pressure He plasma and studied alterations in the genome of this fungus as well as changes in the phenotypic traits, such as assimilation of carbon from carbohydrates, hydrolytic enzyme activity, and drug susceptibility. There is a general problem if we use cold plasma to kill microorganism cells and some of them survive the process-whether the genotypic and phenotypic features of the cells are significantly altered in this case, and, if so, whether these changes are environmentally hazardous. Our molecular genetic studies have identified six single nucleotide variants, six insertions, and five deletions, which are most likely significant changes after plasma treatment. It was also found that out of 19 tested hydrolytic enzymes, 10 revealed activity, of which nine temporarily decreased their activity and one (naphthol-AS-BI- phosphohydrolase) permanently increased activity as a result of the plasma treatment. In turn, carbon assimilation and drug susceptibility were not affected by plasma. Based on the performed studies, it can be concluded that the observed changes in C. albicans cells that survived the plasma action are not of significant importance to the environment, especially for the drug resistance and pathogenicity of this fungus.

Comparative analysis of 13 HPV genotypes diagnosed in urine sediment cells vs. desquamated cervical epithelial cells

INTRODUCTION: The human papilloma virus (HPV) belongs to double-stranded, DNA circular viruses which infect the epithelial cells. The highest incidence of HPV is identified in malignant processes which affect the uterine cervix, as well as vulvar, penile, rectal and pharyngeal regions. GOAL OF STUDY: An attempt to find correlations between HPV incidence rates in urine sediment cells and in desquamated epithelial cells of the uterine cervix in a group of patients with frequent, recurrent cystitis. MATERIALS AND METHODS: HPV presence was studied, both in urine sediment cells and in uterine cervix epithelial cells of 77 patients. RESULTS: An analysis of urinary sediments brought a total of twenty (25.97%) positive and 57 (74.03%) negative results. In turn, an evaluation of uterine cervix material samples revealed 17 (22.08%) positive and 60 (77.92%) negative results. CONCLUSIONS: The study enabled a comparison between HPV prevalence rates in urine sediment cells and in uterine cervix epithelial cells of an examined patient. The performed observations are likely to trigger a further analysis of the studied issue; however, the obtained results provide arguments for different natural histories of the infection processes.

[Evaluation of genomic imbalance in endometrial hyperplasia and carcinoma]. / Ocena niezrównowaienia genomu w przypadkach rozrostu oraz raka endometrium.

OBJECTIVE: The main goal of our study was to identify the earliest and specific genetic changes which could be associated with an increased risk of neoplastic transformation in a group of patients with endometrial hyperplasia. Another goal was to characterize genetic changes associated with advanced forms of cancer. MATERIAL AND METHODS: The study involved forty-four (44) female patients, including five (5) patients with no histopathologically confirmed hyperplastic features, twenty-six (26) patients with histopathologically confirmed endometrial hyperplasia, and thirteen (13) patients with diagnosed carcinoma of the endometrium. The study was conducted using a custom-made 4x180 K microarray of BlueGnome. RESULTS: Copy number variations (CNV) were found in the cases without endometrial hyperplasia. Such changes occur with varying frequency in the genome of healthy female population. Significant genome imbalance was identified in the twenty-six (26) (100%) patients with diagnosed hyperplasia and in eleven (11) subjects (84.6%) with diagnosed endometrial cancer. Other not yet reported, changes localized in characteristic regions of the genome were also found.

Prenatal diagnosis of rare fetal anomalies--a case report.

Hereby we present a case of a pregnancy in which careful dysmorphology of the fetus in subsequent sonographic evaluation resulted in detection of a very rare anomaly. It allowed explanation of the fetal phenotype, compared then with that of the newborn and estimation of genetic risk for the next pregnancies in this family.

The Usefulness of Cell-Based and Liquid-Based Urine Tests in Clarifying the Diagnosis and Monitoring the Course of Urothelial Carcinoma. Identification of Novel, Potentially Actionable, RB1 and ERBB2 Somatic Mutations.

Bladder cancer is one of the most common cancers in global statistics. One of the issues associated with this disease is the high incidence of cases with delayed diagnosis and what factors correlate with worse treatment outcomes. A possible reason for this may be the rather limited availability of non-invasive diagnostic tools. This short communication presents a case of a 68 year old male patient after an ineffective therapy, carried on for several years with symptoms commonly associated with prostate overgrowth that masked a carcinoma in situ of the urinary bladder. Implementation of several diagnostic techniques, including urine sediment cytology, immunocytochemistry, the fluorescence in situ hybridisation technique, the Bladder EpiCheck test and whole-genome sequencing, enabled the establishment of a correct diagnosis, implementation of appropriate treatment and provision of patient-friendly monitoring. The described case emphasises the usefulness of cell-based and liquid-based urine tests in bladder cancer diagnostic procedures.

P53 mutations in urinary bladder cancer patients from Central Poland.

The present study aimed at detection of P53 gene mutations in cells of urinary bladder neoplasms, as the mutations may be regarded as an independent prognostic factor for progression and recurrence of tumours. In the study, 82 patients with clinically diagnosed urinary bladder tumour were included. The control was composed of DNA samples from urine and blood of 202 healthy patients. Exons 5-8 of the P53 gene were screened for mutations by using multitemperature single-strand conformational polymorphism (MSSCP) analysis. Samples with abnormal MSSCP patterns were subjected to direct sequencing. The frequency of mutations in exons 5-8 of the P53 gene in patients with bladder cancer was lower (3.3% in grade G1, 24% in G2, and 39% in G3) than the data reported in the literature. We found a higher percentage of polymorphism at codon 213 of the P53 gene in bladder cancer patients (6%), compared with the values in the reference group (2.5%). These results were matched with those of the loss of heterozygosity (LOH) analysis. In conclusion, mutations were found mainly in more advanced histopathological and clinical stages of the disease and at the CIS stage (carcinoma in situ). It cannot be excluded that the observed polymorphism at codon 213 may be a predisposing factor for urinary bladder carcinoma development.

Application of multiplex FISH, CGH and MSSCP techniques for cytogenetic and molecular analysis of transitional cell carcinoma (TCC) cells in voided urine specimens.

Multiplex FISH (UroVysion), Comparative Genomic Hybridization (CGH), and Multitemperature Single-Strand Conformation Polymorphism (MSSCP) were applied for non-invasive diagnosis and prognosis of bladder cancer. The UroVysion test was positive in 80% of patients with pT1 and in 100% of patients with either pT2 or pT3 tumours. Tumours with pT3T4 stages were characterized by high numbers of chromosomal imbalances, detected by CGH. The mutation of the p53 gene was detected in 16% of patients, but only in those with pT2 or pT3 tumours.

Diagnostics of SHOX gene rearrangement in 46,XX women with idiopathic short stature.

INTRODUCTION: The SHOX gene has been mapped at the pseudoautosomal region 1 (PAR1) of chromosomes X (Xp22.33) and Y (Yp11.32). The loss of SHOX gene functionality is assumed to be responsible for the Leri-Weill syndrome formation and the disproportionate short stature (DSS). The SHOX gene rearrangements constitute the majority of cases of gene functionality loss. Therefore, a practical application of the method, which allows for the diagnostics of the gene rearrangements, becomes a primary issue. With such an assumption, the MLPA technique (multiplex ligation - dependent probe amplification) becomes the method of choice. MATERIAL AND METHODS: DNA samples were evaluated in the study by means of the MLPA method. The DNA was isolated from peripheral blood of sixty-three (63) 46,XX patients with short stature. RESULTS: Out of the examined patients, deletions within the SHOX gene were found in five (5) patients, and duplication at the PAR1 regulatory region of the SHOX gene in one (1) case. CONCLUSIONS: The obtained results confirm the opinion that the MLPA method, while enabling the diagnostics of the etiopathogenetic factor of short stature, identified in approximately 9.5% of cases, is a useful tool in the diagnostics of SHOX gene deletion and duplication. (Endokrynol Pol 2016; 67 (4): 397-402).

The risk of neoplasm associated with dysgenetic testes in prepubertal and pubertal/adult patients.

INTRODUCTION: In patients with Y-chromosome in the karyotype, partial gonadal dysgenesis and disorders of male reproductive sex organs development are usually resected in childhood because of the high risk of germ cell tumours (GCT). In patients with Y-chromosome, complete gonadal dysgenesis and female genitalia gonadectomy is performed markedly later. However, due to the relatively low number of adult patients with preserved dysgenetic gonads, the true risk of neoplasm is unknown. The aim of the study was to evaluate the prevalence of neoplasia in dysgenetic gonads of children and adults with Y-chromosome in a retrospective study. MATERIAL AND METHODS: A review of medical documentation of 94 patients with disorders of sex development (DSD), Y-chromosome and gonadal dysgenesis (GD), aged 1.2-32 years (47 prepubertal, 1.2-10 years; 47 pubertal/adult, 13-32 years), was conducted. Serum levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH) and testosterone were determined. Bilateral gonadectomy was performed in 73.4% of patients, and unilateral gonadectomy with biopsy of the contralateral gonad in 26.4%. All gonadal tissues were subjected to immunohistochemical evaluation with antibodies against PLAP and OCT3/4 (markers of malignant germ cells, but also foetal multipotent germ cells), while gonads of prepubertal patients were examined by c-KIT, as well. RESULTS: Streak gonads were identified on both sides (complete GD) in 30.8%, a streak gonad on one side and an underdeveloped testis on the other (asymmetric GD) in 38.3%, and underdeveloped testicular structure on both sides (partial GD) in 30.8% of cases. Germ cell neoplasia was found in 53.2% of patients (51.1% in children, 55.3% in pubertal/adults). Invasive GCT were identified in 11.7% of cases, of which 90.9% were in pubertal/adult patients. Other neoplastic lesions included gonadoblastoma (16% prevalence) and testicular carcinoma in situ (25.5%). In younger patients FSH serum levels were increased in 81% of cases (mean 2.82 ± 2.18 IU/L), while LH in 58% (mean 1.82 ± 1.69 IU/L). Hypergonadotropic hypogonadism was diagnosed in most of the pubertal/ /adult patients (mean FSH 54.2 ± 23.3 IU/L, mean LH 21.7 ± 12.1 IU/L, mean testosterone 5.5 ± 4.5 nmol/L). CONCLUSIONS: Dysgenetic gonads in patients with Y chromosome have a high risk of germ cell neoplasia (ca. 50%). If they are preserved until puberty/early adulthood, they may develop overt, invasive GCT. The gonads also have poor hormonal activity (hypergonadotropic hypogonadism) in most of the pubertal/adult patients. Each of these cases must be considered individually and a decision to remove the gonad or not should be based on the comprehensive analysis of the phenotype by a multidisciplinary team of specialists in consultation with the patient and the parents. If dysgenetic gonads are not resected in childhood, these patients need careful ongoing follow-up examination, including biopsy and histopathological evaluation.

Molecular cytogenetic techniques in detecting subtle chromosomal imbalances.

Diagnostic possibilities of CGH and M-FISH techniques for detection of submicroscopic chromosomal imbalancies were compared on the basis of two cases of t(X;Y) and one case of marker chromosome. In cases with t(X;Y), the sequences specific for chromosome Y were detected by PCR and CGH, but the localisation of these sequences on the short arm of chromosome X was confirmed by the FISH technique, employing two Yp-specific probes for SRY and TSPY genes. Significant differences between above cases were revealed in the size of Yp chromosome fragments translocated on chromosome X. An extra material of chromosome marker could not be identified by classical banding and FISH techniques and it was only CGH and M-FISH techniques that enabled detecting the chromosomal origin of the marker. The applied CGH technique enabled finding subtle chromosomal imbalancies in the presented cases with a resolution of approximately 3 Mbp.

Chromosomal mosaicism on amniotic interphase nuclei detected by multiprobe FISH.

So far classical prenatal detection of chromosome aberrations has been limited to the evaluation of metaphase by means of time-consuming cytogenetic techniques. The MultiVision PGT test enables a simultaneous detection of aneuploidies of chromosomes 13,18, 21, X, and Y, even 24 h after amniocentesis. In the presented case, this test detected prenatally a chromosomal mosaicism 69,XYY[35]/46,XY[65]. This result was not confirmed after birth, by the same test on blood smear. The discrepancy is difficult to explain.

Prenatal detection of maternal UPD15 in a new case with i(15p) by Timing Replication Test (TRT) and methylation analysis.

DNA replication kinetics of the Prader-Willi/Angelman Critical Region (PWACR) was studied with and without synchronisation in human amniotic cell cultures obtained from 20 cases with normal karyotype and 4 cases with a marker of chromosome 15, respectively. A Timing Replication Test (TRT) was performed by synchronisation of amniotic cell cultures and followed by interphase FISH to analyse and compare the early/late replication patterns in SNRPN and UBE3A genes between the homologues of chromosome 15. Asynchronous replication patterns of the analysed genes were observed in both amniotic cell cultures but the percentage of interphase nuclei presenting with asynchronous replication was significantly increased in the cultures with synchronisation (40-51%), as compared to those without synchronisation (20-23%). The evaluations, performed by means of TRT, showed asynchronous replication patterns on control values: between 39% and 46% of cells in all the cases with inv dup(15). In contrast, the percentage of cells with asynchronous replication in the case with i(15p) was significantly decreased (3-6%), as compared to the control value, and it may be indicated by uniparental disomy of chromosome 15 (UPD15). In addition, those results have been confirmed by molecular evaluation, using the methylation diagnostic test for diagnosis of the Prader-Willi Syndrome.

Inv(10) in a patient with hypogonadotropic hypogonadism.

Hypogonadotropic hypogonadism (HH) was diagnosed in a 22-year-old patient with 46,XY,inv(10) karyotype. It may be associated with some gene mutations of chromosome X, (KAL-1: Kallman syndrome; and DAX-1: congenital adrenal hypoplasia), as well as of certain autosomes, including chromosome 10. This study aimed to: (1) elucidate the aetiopathogenesis of the disease in the studied case: (2) diagnose chromosome aberrations as accurately as possible: and (3) determine if the observed clinical picture can be referred to the diagnosed chromosomal aberration or it is a mere coincidence. The FISH technique, with the use of non-commercial DNA probes, was applied for a precise description of chromosome breaking points. The application of FISH enabled karyotype description: 46,XY, inv(10)(p15.2q11.22).ish inv(10)(p15.2q21.3)(p15x3)(q21x3)(p15conq21x2). The SSCP method revealed no mutation within the DAX-1 gene and no deletion in the KAL-1 gene.

Molecular diagnostics of promyelocytic leukaemia.

Acute promyelocytic leukaemia (APL) is characterised by proliferation of abnormal promyelocytes. The reciprocal translocation between the long arms of chromosomes 15 and 17, and the fusion between the retinoic acid receptor (RARa) gene, and PML gene, is unique to APL. Because of unsuccessful cytogenetic analysis of conventional G-banding technique (mitoses were not observed), we diagnosed three non-treatment patients with APL by following molecular methods: reverse transcription-polymerase chain reaction (RT-PCR), fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). At the time of diagnosis our patients showed reciprocal translocation t(15;17)(q22;q12) in all cases studied (66-85% of positive bone marrow cells). With the use of CGH we observed the unbalanced chromosomal aberrations: losses of 5q13.1, 5q31.3, 9p21 regions, gain of 5q32 region and trisomy of 18 chromosome.

[Detection of chromosomal aneuploidies in fetus by multiplex Q-PCR method]. / Szybka diagnostyka aneuploidii chromosomowych u plodu za pomoca metody multiplex Q-PCR.

With application of the quantitative PCR, Q-PCR, two cases of aneuploidy: trisomy 18 and trisomy 21 were detected in the course of routine prenatal diagnosis in amniotic cells DNA obtained from 1.5 ml of the amniotic fluid. The conventional cytogenetic methods confirmed the diagnosis and the following karyotypes were established: 47,XY,+21 and 47,XX,+13. The presented results show that by means of the Q-PCR the aneuploidy diagnosis can be obtained within 48 hours.

Molecular subtyping of bladder cancer using Kohonen self-organizing maps.

Kohonen self-organizing maps (SOMs) are unsupervised Artificial Neural Networks (ANNs) that are good for low-density data visualization. They easily deal with complex and nonlinear relationships between variables. We evaluated molecular events that characterize high- and low-grade BC pathways in the tumors from 104 patients. We compared the ability of statistical clustering with a SOM to stratify tumors according to the risk of progression to more advanced disease. In univariable analysis, tumor stage (log rank P = 0.006) and grade (P < 0.001), HPV DNA (P < 0.004), Chromosome 9 loss (P = 0.04) and the A148T polymorphism (rs 3731249) in CDKN2A (P = 0.02) were associated with progression. Multivariable analysis of these parameters identified that tumor grade (Cox regression, P = 0.001, OR.2.9 (95% CI 1.6-5.2)) and the presence of HPV DNA (P = 0.017, OR 3.8 (95% CI 1.3-11.4)) were the only independent predictors of progression. Unsupervised hierarchical clustering grouped the tumors into discreet branches but did not stratify according to progression free survival (log rank P = 0.39). These genetic variables were presented to SOM input neurons. SOMs are suitable for complex data integration, allow easy visualization of outcomes, and may stratify BC progression more robustly than hierarchical clustering.

EORTC risk tables - their usefulness in the assessment of recurrence and progression risk in non-muscle-invasive bladder cancer in Polish patients.

INTRODUCTION: The assessment of risk of recurrence and progression of bladder cancer (BC) is still rather difficult. We decided to check the rates of the changes mentioned above in the group of the Polish patients after a year-long observation and next to compare them with the results calculated in the European Organisation of Research and Treatment of Cancer (EORTC) risk tables. METHODS: The tested group consisted of 91 patients who underwent transurethral resection of bladder tumour (TURBT). When being diagnosed, 60 cases were in the pTa clinical stage, whereas 30 cases were in T1. The coexisting carcinoma in situ (CIS) was observed in four cases. On the basis of the scores obtained from the EORTC tables, the patients were divided into the groups of low, intermediate or high risk of disease recurrence and progression. RESULTS: Recurrence was noticed in 23 patients (25%), while progression was observed in 11 patients (12.1%). The rate of the observed recurrences proved to be lower than it had been predicted in all the groups, except for one of the intermediate-risk group (score 1- 4). Moreover, the rate of the progressions predicted according to the EORTC risk tables was higher in all the risk groups. CONCLUSIONS: It can be noticed that the rate of real recurrences is lower than expected, whereas the rate of the observed progressions is overestimated. Partly, it could be the result of using a relatively small group of patients for observation and applying a different method of treatment.

A novel mutation (c. 341A>G) in the SRY gene in a 46,XY female patient with gonadal dysgenesis.

SRY (sex-determining region Y) gene, MIM 480000, NM_005634) is crucial for sex differentiation which encodes the protein responsible for initiating testis differentiation. SRY mutations are associated with the presence of XY gonadal dysgenesis symptoms. We studied a 46,XY female patient with primary amenorrhoea and negative family history. The clinical, endocrine, histopathologic and cytogenetic data are consistent with gonadal dysgenesis. Using a molecular analysis, a novel (c.341A>G, p. N65D) missense mutation within the HMGbox of SRY gene was detected. Escherichia coli expression of SRY study showed reduced expression of the mutated protein and gel retardation assay method revealed lowered DNA-binding ability in N65D variant of SRY. The novel mutation detected in the SRY gene may be an aetiopathogenic factor in clinically defined 46,XY complete gonadal dysgenesis (CGD). Because of an increased risk of gonadoblastoma, proper early diagnosis and treatment prevent development of malignancies.

Concomitance of oncogenic HPV types, CHEK2 gene mutations, and CYP1B1 gene polymorphism as an increased risk factor for malignancy.

INTRODUCTION: Urinary bladder carcinoma ranks the fourth position in malignancy incidence rates in men (6.1%) and the 17th position in women (1.6%). In general, neoplastic diseases should be approached from two perspectives: prevention with implementation of prophylactic measures and early diagnostics. Prophylactics is possible in the preclinical phase of neoplasm, being both justified and plausible in patients from high-risk groups. Thus, it is particularly important to select such groups, not only by referring to environmental carcinogenic factors (occupational and extra-occupational) but also from genetic predisposition, which may be conductive for neoplasm formation. The mutations / polymorphisms of CHEK2 and CYP1B1 genes predispose to neoplasm via multiorgan mechanisms, while the human papilloma virus (HPV) may participate in the neoplastic transformation as an environmental factor. MATERIAL AND METHODS: 131 patients with diagnosed urinary bladder cancer were qualified to the study. Mutations/polymorphisms of CHEK2 (IVS2 + 1G > A gene, 1100delC, del5395, I157T) and CYP1B1- 355T/T were identified by the PCR in DNA isolated directly from the tumor and from peripheral blood. The ELISA test was used for the studies of 37 HPV genotypes in DNA, isolated tumour tissue. RESULTS: 11 mutations of CHEK2 gene were found, 355T/T polymorphism if CYP1B1 gene occurred in 18 patients (12.9%). Oncogenic HPV was found in 36 (29.3%), out of 123 examined patients. CONCLUSIONS: The concomitance of CHEK2 gene mutations or 355T/T polymorphism of CYP1B1 gene and the presence of oncogenic HPV types statistically significantly correlates with histological malignancy grades of urinary bladder carcinoma.