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1.
Hum Mol Genet ; 27(21): 3669-3674, 2018 11 01.
Article in English | MEDLINE | ID: mdl-30124836

ABSTRACT

The Neurofascins (NFASCs) are a family of proteins encoded by alternative transcripts of NFASC that cooperate in the assembly of the node of Ranvier in myelinated nerves. Differential expression of NFASC in neurons and glia presents a remarkable example of cell-type specific expression of protein isoforms with a common overall function. In mice there are three NFASC isoforms: Nfasc186 and Nfasc140, located in the axonal membrane at the node of Ranvier, and Nfasc155, a glial component of the paranodal axoglial junction. Nfasc186 and Nfasc155 are the major isoforms at mature nodes and paranodes, respectively. Conditional deletion of the glial isoform Nfasc155 in mice causes severe motor coordination defects and death at 16-17 days after birth. We describe a proband with severe congenital hypotonia, contractures of fingers and toes, and no reaction to touch or pain. Whole exome sequencing revealed a homozygous NFASC variant chr1:204953187-C>T (rs755160624). The variant creates a premature stop codon in 3 out of four NFASC human transcripts and is predicted to specifically eliminate Nfasc155 leaving neuronal Neurofascin intact. The selective absence of Nfasc155 and disruption of the paranodal junction was confirmed by an immunofluorescent study of skin biopsies from the patient versus control. We propose that the disease in our proband is the first reported example of genetic deficiency of glial Neurofascin isoforms in humans and that the severity of the condition reflects the importance of the Nfasc155 in forming paranodal axoglial junctions and in determining the structure and function of the node of Ranvier.


Subject(s)
Cell Adhesion Molecules/genetics , Intercellular Junctions/metabolism , Muscle Hypotonia/genetics , Mutation , Nerve Growth Factors/genetics , Nervous System Diseases/genetics , Neuroglia/metabolism , Animals , Conditioning, Psychological , DNA Mutational Analysis , Female , Homozygote , Humans , Infant , Intercellular Junctions/genetics , Mice , Muscle Hypotonia/metabolism , Nervous System Diseases/metabolism , Poland , Protein Isoforms , Syndrome
2.
Genet Res (Camb) ; 102: e6, 2020 08 10.
Article in English | MEDLINE | ID: mdl-32772980

ABSTRACT

PURPOSE: To characterize the spectrum of BRCA1 and BRCA2 pathogenic germline variants in women from south-west Poland and west Ukraine affected with breast or ovarian cancer. Testing in women at high risk of breast and ovarian cancer in these regions is currently mainly limited to founder mutations. METHODS: Unrelated women affected with breast and/or ovarian cancer from Poland (n = 337) and Ukraine (n = 123) were screened by targeted sequencing. Excluded from targeted sequencing were 34 Polish women who had previously been identified as carrying a founder mutation in BRCA1. No prior testing had been conducted among the Ukrainian women. Thus, this study screened BRCA1 and BRCA2 in the germline DNA of 426 women in total. RESULTS: We identified 31 and 18 women as carriers of pathogenic/likely pathogenic (P/LP) genetic variants in BRCA1 and BRCA2, respectively. We observed five BRCA1 and eight BRCA2 P/LP variants (13/337, 3.9%) in the Polish women. Combined with the 34/337 (10.1%) founder variants identified prior to this study, the overall P/LP variant frequency in the Polish women was thus 14% (47/337). Among the Ukrainian women, 16/123 (13%) women were identified as carrying a founder mutation and 20/123 (16.3%) were found to carry non-founder P/LP variants (10 in BRCA1 and 10 in BRCA2). CONCLUSIONS: These results indicate that genetic testing in women at high risk of breast and ovarian cancer in Poland and Ukraine should not be limited to founder mutations. Extended testing will enhance risk stratification and management for these women and their families.


Subject(s)
BRCA1 Protein/genetics , BRCA2 Protein/genetics , Breast Neoplasms/genetics , Genetic Predisposition to Disease , Genetic Testing/methods , Germ-Line Mutation , Ovarian Neoplasms/genetics , Breast Neoplasms/epidemiology , Breast Neoplasms/pathology , Female , High-Throughput Nucleotide Sequencing/methods , Humans , Ovarian Neoplasms/epidemiology , Ovarian Neoplasms/pathology , Poland/epidemiology , Ukraine/epidemiology
3.
Int J Mol Sci ; 21(19)2020 Sep 26.
Article in English | MEDLINE | ID: mdl-32993062

ABSTRACT

The role of autophagy in colorectal cancer (CRC) pathogenesis appears to be crucial. Autophagy acts both as a tumor suppressor, by removing redundant cellular material, and a tumor-promoting factor, by providing access to components necessary for growth, metabolism, and proliferation. To date, little is known about the expression of genes that play a basal role in the autophagy in CRC. In this study, we aimed to compare the expression levels of 46 genes involved in the autophagy pathway between tumor-adjacent and tumor tissue, employing large RNA sequencing (RNA-seq) and microarray datasets. Additionally, we verified our results using data on 38 CRC cell lines. Gene set enrichment analysis revealed a significant deregulation of autophagy-related gene sets in CRC. The unsupervised clustering of tumors using the mRNA levels of autophagy-related genes revealed the existence of two major clusters: microsatellite instability (MSI)-enriched and -depleted. In cluster 1 (MSI-depleted), ATG9B and LAMP1 genes were the most prominently expressed, whereas cluster 2 (MSI-enriched) was characterized by DRAM1 upregulation. CRC cell lines were also clustered according to MSI-enriched/-depleted subgroups. The moderate deregulation of autophagy-related genes in cancer tissue, as compared to adjacent tissue, suggests a prominent field cancerization or early disruption of autophagy. Genes differentiating these clusters are promising candidates for CRC targeting therapy worthy of further investigation.


Subject(s)
Autophagy , Colorectal Neoplasms , Databases, Nucleic Acid , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Neoplasm Proteins , Transcriptome , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Humans , Neoplasm Proteins/biosynthesis , Neoplasm Proteins/genetics
4.
BMC Med Genet ; 19(1): 12, 2018 01 19.
Article in English | MEDLINE | ID: mdl-29351780

ABSTRACT

BACKGROUND: FANCM and RECQL have recently been reported as breast cancer susceptibility genes and it has been suggested that they should be included on gene panel tests for breast cancer predisposition. However, the clinical value of testing for mutations in RECQL and FANCM remains to be determined. In this study, we have characterised the spectrum of FANCM and RECQL mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine. METHODS: We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron-exon junctions of FANCM and RECQL in germline DNA from unrelated women affected with breast cancer (n = 338) and ovarian cancer (n = 89) from Poland (n = 304) and Ukraine (n = 123). These women were at high-risk of carrying a genetic predisposition to breast and/or ovarian cancer due to a family history and/or early-onset disease. RESULTS: Among 427 women screened, we identified one carrier of the FANCM:c.1972C > T nonsense mutation (0.23%), and two carriers of the frameshift insertion FANCM:c.1491dup (0.47%). None of the variants we observed in RECQL were predicted to be loss-of-function mutations by standard variant effect prediction tools. CONCLUSIONS: Our study of the Polish and Ukrainian populations has identified a carrier frequency of truncating mutations in FANCM consistent with previous reports. Although initial reports suggesting that mutations in RECQL could be associated with increased breast cancer risk included women from Poland and identified the RECQL:c.1667_1667 + 3delAGTA mutation in 0.23-0.35% of breast cancer cases, we did not observe any carriers in our study cohort. Continued screening, both in research and diagnostic settings, will enable the accumulation of data that is needed to establish the clinical utility of including RECQL and FANCM on gene panel tests.


Subject(s)
DNA Helicases/genetics , Genetic Predisposition to Disease , RecQ Helicases/genetics , White People/genetics , Adult , Aged , Aged, 80 and over , Breast Neoplasms/genetics , Case-Control Studies , Codon, Nonsense , Exons , Female , Gene Frequency , Genetic Variation , Humans , Middle Aged , Ovarian Neoplasms/genetics , Pedigree , Poland , Risk Factors , Ukraine , Young Adult
5.
Contemp Oncol (Pozn) ; 22(1A): 1-2, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29628786

ABSTRACT

Studies on genetic and epigenetic mechanisms of carcinogenesis have led to the discovery of crucial genetic events for many of particular malignancies. This was followed by invention of new therapeutic approaches based on molecular mechanisms underlying cancer development and progression that bears the name of personalised medicine. In the case of gliomas, ascertainment of genetic/epigenetic markers was the basis for re-classification of tumours that until now depended on histopathological analysis. This article reviews recent advances in personalised medicine and the new World Health Organisation classification of gliomas.

6.
J Craniofac Surg ; 28(5): e422-e431, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28570402

ABSTRACT

Mandibular prognathism is defined as an abnormal forward projection of the mandible beyond the standard relation to the cranial base and it is usually categorized as both a skeletal Class III pattern and Angle Class III malocclusion. The etiology of mandibular prognathism is still uncertain, with various genetic, epigenetic, and environmental factors possibly involved. However, many reports on its coexistence in both twins and segregation in families suggest the importance of genetic influences. A multifactorial and polygenic background with a threshold for expression or an autosomal dominant mode with incomplete penetrance and variable expressivity are the most probable inheritance patterns. Linkage analyses have, thus far, shown the statistical significance of such loci as 1p22.1, 1p22.3, 1p32.2, 1p36, 3q26.2, 4p16.1, 6q25, 11q22, 12pter-p12.3, 12q13.13, 12q23, 12q24.11, 14q24.3 to 31.2, and 19p13.2. The following appear among candidate genes: MATN1, EPB41, growth hormone receptor, COL2A1, COL1A1, MYO1H, DUSP6, ARHGAP21, ADAMTS1, FGF23, FGFR2, TBX5, ALPL, HSPG2, EVC, EVC2, the HoxC gene cluster, insulin-like growth factor 1, PLXNA2, SSX2IP, TGFB3, LTBP2, MMP13/CLG3, KRT7, and FBN3. On the other hand, MYH1, MYH2, MYH3, MYH7, MYH8, FOXO3, NFATC1, PTGS2, KAT6B, HDAC4, and RUNX2 expression is suspected to be involved in the epigenetic regulations behind the mandibular prognathism phenotype.


Subject(s)
Malocclusion, Angle Class III/genetics , Mandible , Prognathism/genetics , Cephalometry/methods , Cytoskeletal Proteins/genetics , Fibroblast Growth Factor-23 , Genetic Linkage , Humans , Image Processing, Computer-Assisted/methods , Imaging, Three-Dimensional/methods , Malocclusion, Angle Class III/diagnosis , Mandible/abnormalities , Mandible/diagnostic imaging , Prognathism/diagnosis
7.
Brain Behav Immun ; 54: 194-200, 2016 May.
Article in English | MEDLINE | ID: mdl-26872421

ABSTRACT

Overwhelming evidence indicates that subthreshold inflammatory state might be implicated in the pathophysiology of schizophrenia (SCZ) and bipolar disorder (BPD). It has been reported that both groups of patients might be characterized by abnormal lymphocyte counts. However, little is known about alterations in lymphocyte proportions that may differentiate SCZ and BPD patients. Therefore, in this study we investigated blood cell proportions quantified by means of microarray expression deconvolution using publicly available data from SCZ and BPD patients. We found significantly lower counts of natural killer (NK) cells in drug-naïve and medicated SCZ patients compared to healthy controls across all datasets. In one dataset from SCZ patients, there were no significant differences in the number of NK cells between acutely relapsed and remitted SCZ patients. No significant difference in the number of NK cells between BPD patients and healthy controls was observed in all datasets. Our results indicate that SCZ patients, but not BPD patients, might be characterized by reduced counts of NK cells. Future studies looking at lymphocyte counts in SCZ should combine the analysis of data obtained using computational deconvolution and flow cytometry techniques.


Subject(s)
Bipolar Disorder/blood , Killer Cells, Natural/pathology , Schizophrenia/blood , Adult , Bipolar Disorder/genetics , Bipolar Disorder/immunology , Bipolar Disorder/pathology , Case-Control Studies , Female , Flow Cytometry , Genetic Predisposition to Disease , Humans , Inflammation/immunology , Killer Cells, Natural/immunology , Lymphocyte Count , Male , Middle Aged , Schizophrenia/genetics , Schizophrenia/immunology , Schizophrenia/pathology , Transcriptome
8.
Am J Med Genet A ; 170(12): 3265-3270, 2016 12.
Article in English | MEDLINE | ID: mdl-27605359

ABSTRACT

Epileptic encephalopathies (EE) include a range of severe epilepsies in which intractable seizures or severe sub-clinical epileptiform activity are accompanied by impairment of motor and cognitive functions. Mutations in several genes including ion channels and other genes whose function is not completely understood have been associated to some EE. In this report, we provide a detailed clinical description of a sporadic male patient with early-onset epilepsy and epileptic encephalopathy in whom we performed complete exome sequencing (WES) and identified a GRIN2B mutation. The GRIN2B splicing mutation in intron 10 (c.2011-1G>A) was revealed in a WES study. The result was confirmed by Sanger sequencing. No mutation was found in both parents. Our finding confirms that early-onset EE may be caused not only by gain-of-function variants but also by splice site mutations-in particular those affecting the splice acceptor site of the 10th intron of the GRIN2B gene. © 2016 Wiley Periodicals, Inc.


Subject(s)
Epilepsy/diagnosis , Epilepsy/genetics , Genetic Association Studies , Mutation , Phenotype , Receptors, N-Methyl-D-Aspartate/genetics , Biomarkers , Child , Chromosome Deletion , Chromosomes, Human, Pair 4 , Comparative Genomic Hybridization , DNA Mutational Analysis , Electroencephalography , Exome , High-Throughput Nucleotide Sequencing , Humans , Magnetic Resonance Imaging , Male , Neuroimaging , Physical Examination , RNA Splice Sites
9.
Birth Defects Res A Clin Mol Teratol ; 106(4): 304-7, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26879631

ABSTRACT

BACKGROUND: A clinical case is described of growth retardation, severe developmental delay, facial dysmorphic features with microcephaly, as well as congenital cataract, schizencephaly, periventricular calcifications, and epilepsy. METHODS: TORCH infection was suspected, but all tests for toxoplasmosis, rubella, cytomegalovirus, and herpes simplex virus were negative for the child and her mother; however, an increased level of antibodies against parvovirus B19 was detected in the proband. RESULTS: Chromosomal analysis and array-CGH showed no aberration. Target capture sequencing for COL4A1 and COL4A2 revealed a de novo COL4A1 mutation (c.2123G>T [p.Gly708Val]). The mutation occurred at a highly conserved Gly residue in the Gly-X-Y repeat of the collagen triple helical domain, suggesting that these mutations may alter the collagen IV α1α1α2 heterotrimers. The mutation was predicted to be damaging. CONCLUSION: We suggest that COL4A1 testing should be considered in patients with schizencephaly as well as with phenotype suggesting TORCH infection without any proven etiological factors.


Subject(s)
Body Dysmorphic Disorders , Cataract , Collagen Type IV/genetics , Mutation , Parvoviridae Infections , Parvovirus B19, Human , Schizencephaly , Body Dysmorphic Disorders/genetics , Body Dysmorphic Disorders/pathology , Cataract/genetics , Cataract/pathology , Female , Humans , Infant, Newborn , Schizencephaly/genetics , Schizencephaly/pathology
10.
Ginekol Pol ; 86(9): 694-9, 2015 Sep.
Article in Polish | MEDLINE | ID: mdl-26665572

ABSTRACT

UNLABELLED: The aim of the study was to assess whether commercial kit QF-PCR can be used as the only method for rapic prenatal dia gnosis of chromosomes 13, 18, 21, X and Y aneuploidies, omitting cell culture and complete cyt6genetik analysis of fetal chromosomes. MATERIAL AND METHODS: DNA from amniocytes (94 cases) and trophoblast cells (6 cases) was analyzed witt QF-PCR according to the manufacturer's protocol. The obtained products were separated using ABI 310 Genetic Analyzer and the resulting data were analyzed using GeneMarker software. RESULTS: The results of QF-PCR were obtained in 95 out of 100 cases (95%). Abnormalities were found in 28 casea (29.5%). All these results were confirmed in subsequent cytogenetic analysis. Normal results were obtained in 62 patients (70.5%). However in that group, we found three chromosomal aberrations other than those analyzed b3 QF-PCR. Additionally two abnormal and three normal karyotypes were found in patients with inconclusive QF-POF results. CONCLUSIONS: QF-PCR is a fast and reliable tool for chromosomal aneuploidy analysis and can be used as the only method without a full analysis of the karyotype, but only in cases of suspected fetal 13, 18, 21 trisomy or numerica aberrations of X chromosome. In other cases, fetal karyotype analysis from cells obtained after cell culture should be offered to the patient.


Subject(s)
Aneuploidy , Chromosome Disorders/diagnosis , Polymerase Chain Reaction/methods , Prenatal Diagnosis/methods , Chromosome Disorders/genetics , Chromosomes, Human, 21-22 and Y , Chromosomes, Human, Pair 13 , Chromosomes, Human, Pair 18 , DNA/analysis , Female , Humans , Karyotyping/methods , Pregnancy , Sex Chromosome Disorders/diagnosis , Time Factors , Trisomy/diagnosis , Trisomy 13 Syndrome
11.
Tumour Biol ; 35(12): 12397-401, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25195132

ABSTRACT

The protective effect of vitamin D against several cancers including colorectal cancer is modulated by the vitamin D receptor (VDR) and its ligand, the active form of vitamin D. VDR response has been found to play a role in various genes encoding proteins involved in crucial cellular pathways. Single nucleotide polymorphisms (SNPs) of the VDR gene that modulate its activity are located in the promoter region, exons 2-9, and their vicinity and also in the 3'UTR region. Some of them have been previously studied in relation to cancer susceptibility and prognosis. The aim of our study was to investigate four polymorphisms, BsmI, ApaI, TaqI, and FokI, of the VDR gene in Polish patients with sporadic colorectal cancer and to evaluate their association with susceptibility to cancer. We found a significant association between the BsmI genotype and cancer (individuals with the bb genotype are more susceptible to cancer compared to those with other genotypes, p = 0.025, Fisher's exact test for 2 × 2 table). Also, the TT genotype at TaqI and the AA genotype at ApaI are correlated with a higher risk of cancer (p = 0.00071 and p = 1.0 × 10(-5), respectively). We found relatively strong linkage disequilibrium between the TaqI and ApaI loci (T with A and t with a, respectively). Both of these loci are associated with cancer. We do not observe any such association for the FokI polymorphism. In conclusion, a small modification in VDR expression may play a role in such a multipathway process as tumorigenesis.


Subject(s)
Colorectal Neoplasms/genetics , Genetic Predisposition to Disease , Polymorphism, Genetic , Receptors, Calcitriol/genetics , Adult , Aged , Aged, 80 and over , Alleles , Case-Control Studies , Female , Genotype , Humans , Linkage Disequilibrium , Male , Middle Aged , Odds Ratio , Poland , Polymorphism, Single Nucleotide , Risk
12.
Genes Chromosomes Cancer ; 52(3): 237-49, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23124995

ABSTRACT

MircoRNAs as a new class of regulatory molecules have been investigated in many specific cells and organs in healthy and diseased conditions. Although miRNA signatures can be directly assessed in patients' affected tissues such as tumor sections, recent studies revealed that miRNA profiles can also be obtained indirectly, that is, from the patients' peripheral blood. For better understanding of miRNA's contribution to gastric carcinoma (one of the leading causes of cancer-related mortality worldwide), we screened for deregulated miRNAs in blood collected from human cancer patients and compared the expression patterns with a gastric carcinoma mouse model (Tff1 knock-out). The profiles were assessed using species-specific miRNA microarrays. Among many dozens of deregulated miRNAs (219 in H. sapiens; 75 in M. musculus), a subset of eight miRNAs comparable in sequence from both species was noted. By in silico analysis, their involvement in targeting neoplastic and MAPkinase pathways was demonstrated. We found a high probability of linkage of all noted miRNAs to pathways in cancer with P-values of 0.013 and 0.018 in mice and humans, respectively. Linkage to the MAPK-signaling pathway in mice was observed with a P-value of 0.01. Moreover, when comparing the 219 deregulated miRNAs obtained from blood with deregulated miRNAs derived from gastric cancer (GC) tissues, as published previously, 24 miRNAs were identical. If confirmed in a larger patient pool, these miRNAs could constitute appropriate blood-born biomarkers for GC.


Subject(s)
MicroRNAs/genetics , Stomach Neoplasms/genetics , Animals , Disease Models, Animal , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Male , Mice , Mice, Knockout , Stomach Neoplasms/pathology
13.
J Hum Genet ; 58(1): 11-5, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23096495

ABSTRACT

The activity of phosphatases could be influenced by genetic, as well as epigenetic alterations. In our study, we have investigated the methylation status of four PTPRs: PTPRM, PTPRT, PTPRR and PTPRZ1, which were pre-selected using microarray techniques as being alternatively methylated in sporadic colorectal cancer (CRC). The analyses were carried out on 131 surgical specimens obtained from sporadic CRC patients. The methylation status of the four genes was examined using methyl specific PCR (MSP). The analysis of promoter methylation using an Illumina 27K microarray revealed four protein tyrosine phosphatases PTPRM, PTPRT, PTPRR and PTPRZ1 as being hypermethylated with ß-value ≥0.2 and P≤0.05. Subsequent analysis using MSP confirmed these observations-the frequency of promoter methylation was significantly higher in tumor cells compared with matched normal tissue for each of the analyzed genes. There was no association observed between the methylation status of PTPRs and either CIMP, K-ras (codon 12) and BRAF (exon 15, V600E) mutations or tumor localization (proximal/distal). The results of our study show a statistically significant difference between promoter methylation in cancerous and healthy tissue. This result supports the hypothesis that the PTPR family has an important role in the etiology of CRC.


Subject(s)
Colorectal Neoplasms/genetics , DNA Methylation , Promoter Regions, Genetic/genetics , Receptor-Like Protein Tyrosine Phosphatases/genetics , Aged , Colorectal Neoplasms/pathology , Epigenomics , Female , Gene Expression Regulation, Neoplastic , Humans , Male , Middle Aged , Mutation , Oligonucleotide Array Sequence Analysis/methods , Phenotype , Polymerase Chain Reaction , Receptor-Like Protein Tyrosine Phosphatases, Class 2/genetics , Receptor-Like Protein Tyrosine Phosphatases, Class 5/genetics , Receptor-Like Protein Tyrosine Phosphatases, Class 7/genetics
14.
J Pediatr Gastroenterol Nutr ; 57(6): 688-93, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23857338

ABSTRACT

Esophageal atresia (EA) is one of the most frequent congenital malformations of the gastrointestinal tract. Many genetic alterations in patients with EA have been described in the literature. It is thought that the etiology of EA is heterogeneous. This review of the literature provides detailed information about chromosomal aberrations, gene mutations, and clinical features of neonates with EA, and serves as an excellent source to compare newly diagnosed patients with those described in the literature.


Subject(s)
Chromosome Aberrations , Esophageal Atresia/genetics , Esophagus/abnormalities , Mutation , Humans , Tracheoesophageal Fistula/genetics
15.
J Cutan Pathol ; 40(1): 25-9, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23072482

ABSTRACT

Basal cell carcinoma (BCC) of the skin is considered to be the most common malignancy in people of European ancestry. It is often not clinically aggressive and has been regarded as genetically stable. However, histopathologic subtypes of BCC differ in their ability to invade surrounding tissues and recur. The aim of this work was to present a comprehensive study of chromosomal imbalances of cutaneous BCC and to correlate the findings with their histopathologic and clinical features. In all, 101 tumor samples were classified according to the current microscopic classification of BCC and then analyzed by comparative genomic hybridization (CGH). Over 60% of BCC were found to carry chromosomal imbalances - partial or whole chromosome gains and losses. Different subtypes of BCC presented common chromosomal alterations. No single chromosomal imbalance was found to be characteristic of a particular subtype of BCC, although the frequency of some chromosomal changes differed from one group to the other. The significance of chromosome 2 gains as a phenomenon that does not coexist with the losses in 9q is discussed.


Subject(s)
Carcinoma, Basal Cell/genetics , Chromosome Aberrations , Comparative Genomic Hybridization , Skin Neoplasms/genetics , Adult , Aged , Aged, 80 and over , Chromosomes, Human, Pair 2 , Chromosomes, Human, Pair 9 , DNA Copy Number Variations/genetics , Female , Genetic Testing , Genome, Human , Humans , Male , Middle Aged , Young Adult
16.
Pol Arch Intern Med ; 133(2)2023 02 27.
Article in English | MEDLINE | ID: mdl-36779516

ABSTRACT

The immense progress in molecular biology observed in the last decades has led to a fundamental change in our understanding of the etiology of human diseases. Whole genome analyses, both DNA sequencing and microarray comparative genomic hybridization, allowed for identification of previously unknown diseases and syndromes. Therefore, in difficult­to­diagnose cases, clinical diagnosis is being replaced by molecular diagnosis (molecular dysmorphology, genomic medicine). For both scientific development of human genetics and clinical characteristics of rare genetic diseases, the construction and sharing of internationally available large databases has become crucial. However, genetic data have to be considered on the individual level too; therefore, they have to be treated as sensitive personal information. The context of ethical and legal risks involved in genetic testing has been long analyzed, although recognition of personal data protection issues is a more recent topic. The respective legal acts and protective measures should take into account several different aspects. The present paper explores major benefits and risks associated with international sharing of vast databases of genetic material, and presents legal provisions applied in the European Union, the United States, and China. The latter part is based on the respective acts themselves, as well as on analyses and commentaries by other scholars.


Subject(s)
Genetic Testing , Genomic Medicine , Humans , United States , Comparative Genomic Hybridization , Computer Security
17.
Mol Carcinog ; 51(12): 1003-8, 2012 Dec.
Article in English | MEDLINE | ID: mdl-22006538

ABSTRACT

Recent investigations have demonstrated the clear heterogeneity of sporadic colorectal cancer (CRC) with regard to CpG island methylation. Two unsupervised cluster analyses revealed that CRCs form three distinct DNA methylation subsets, which are referred to as the high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME, respectively). A recent study by Yagi et al. found a fairly sensitive and specific identification of HME, IME, and LME using two marker panels analyzed by MALDI-TOF mass spectrometry (MassARRAY). However, the expensive equipment required for this method substantially increases the cost and complexity of the assay. In this article, we demonstrate the assessment of HME, IME, and LME in a group of 233 sporadic CRCs using seven markers proposed by Yagi et al. The DNA methylation of each marker was quantified using combined bisulfite restriction analysis (COBRA) and analyzed along with various genetic factors associated with CRC [the BRAF and KRAS mutations, MLH1 methylation and microsatellite instability (MSI)]. The baseline methylation of each marker was generated from pooled DNA isolated from 50 normal colon tissues. We demonstrate that the correlation of HME, IME, and LME epigenotyped by COBRA using different molecular classifiers is similar to that achieved by MassARRAY. Therefore, epigenotyping CRCs using COBRA is a simple, specific, and cost-effective method that has the potential to be widely used in CRC research.


Subject(s)
Colorectal Neoplasms/genetics , Epigenesis, Genetic , Adaptor Proteins, Signal Transducing/genetics , Aged , Base Sequence , Cluster Analysis , DNA Methylation , DNA Primers , Female , Genes, ras , Genotype , Humans , Male , Middle Aged , MutL Protein Homolog 1 , Nuclear Proteins/genetics , Polymerase Chain Reaction , Proto-Oncogene Proteins B-raf/genetics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
18.
Tumour Biol ; 33(4): 1015-9, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22274926

ABSTRACT

Data presented in a number of recent studies have revealed a negative correlation between CpG island methylator phenotype (CIMP) and chromosomal instability (CIN) measured by a loss of heterozygosity (LOH) of selected loci, suggesting that CIN and CIMP represent two independent mechanisms in sporadic colorectal cancer (CRC) carcinogenesis. However, CIN is a heterogeneous phenomenon, which may be studied not only by employing LOH analysis but also by observing chromosomal imbalances (gains and deletions). The current study aimed to investigate the relationship between CIMP and chromosomal gains and deletions (assessed by comparative genomic hybridization) in a group of 20 CIMP-high and 79 CIMP-low/CIMP-0 CRCs. Our results revealed that the mean numbers of gains and of total chromosomal imbalances were significantly greater (p = 0.004 and p = 0.007, respectively) in the CIMP-low/CIMP-0 group compared to the CIMP-high group, while no significant difference was observed between the mean numbers of losses (p = 0.056). The analysis of copy number changes of 41 cancer-related genes by multiplex ligation-dependent probe amplification showed that CRK gene was exclusively deleted in CIMP-low/CIMP-0 tumors (p = 0.02). Given that chromosomal losses play an important role in tumor suppressor inactivation and chromosomal gains, in the activation of proto-oncogenes, we hypothesize that tumor suppressor inactivation plays similar roles in both CIMP-high and CIMP-low/CIMP-0 CRCs, while the predominance of chromosomal gains in CIMP-low/CIMP-0 tumors may suggest that the activation of proto-oncogenes is the underlying mechanism of CIMP-low/CIMP-0 CRC progression.


Subject(s)
Chromosome Aberrations , Colorectal Neoplasms/genetics , CpG Islands/genetics , DNA Methylation , Adult , Aged , Comparative Genomic Hybridization , DNA Copy Number Variations , Female , Humans , Loss of Heterozygosity , Male , Middle Aged , Multiplex Polymerase Chain Reaction/methods , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins B-raf/genetics , Proto-Oncogene Proteins c-crk/genetics , Proto-Oncogene Proteins p21(ras) , Tumor Suppressor Protein p53/genetics , ras Proteins/genetics
19.
Anticancer Res ; 40(10): 5667-5671, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32988891

ABSTRACT

BACKGROUND: Renal cell carcinoma (RCC) is a common urological cancer, and its risk correlates with environmental factors such as obesity, smoking and hypertension. Microarray technology enables analysis of the expression pattern of the whole phosphatome, members of which are involved in many cellular pathways and may act as either tumour suppressors or oncogenes in cancers. MATERIALS AND METHODS: We analysed data for the expression level of 87 out of 107 known protein phosphatase genes included in the Hugo Gene Nomenclature Committee Website for 72 RCC tissues and paired healthy tissues obtained from the GEO Database. RESULTS: Our analysis revealed overexpression of DUSP1, DUSP4, PTP4A3, PTPRC and PTPRE genes at all examined stages of RCC. Moreover, we found overexpression of PTPN12 at stage 2, overexpression of CDKN3 at stages 3 and 4, and overexpression of DUSP10 and PTPN22 at stages 2, 3 and 4. Lower expression of DUSP9, PTPR9 and PTPRO was also observed at all stages. CONCLUSION: Significant changes in expression patterns of protein tyrosine phosphatase genes confirm the involvement of this group in crucial carcinogenesis pathways underlying RCC. Thus, we postulate that protein tyrosine phosphatases play an important role in RCC promotion and progression, and may be considered as potential therapeutic targets.


Subject(s)
Carcinoma, Renal Cell/genetics , Cell Proliferation/genetics , Oncogenes/genetics , Protein Tyrosine Phosphatases/genetics , Carcinoma, Renal Cell/pathology , Cell Line, Tumor , Cyclin-Dependent Kinase Inhibitor Proteins/genetics , Dual Specificity Phosphatase 1/genetics , Dual-Specificity Phosphatases/genetics , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic/genetics , Humans , Leukocyte Common Antigens/genetics , Male , Mitogen-Activated Protein Kinase Phosphatases/genetics , Neoplasm Proteins/genetics , Neoplasm Staging , Receptor-Like Protein Tyrosine Phosphatases, Class 3/genetics , Receptor-Like Protein Tyrosine Phosphatases, Class 4/genetics , Risk Factors , Signal Transduction/genetics , Smoking/adverse effects
20.
J Immunol Res ; 2020: 8758090, 2020.
Article in English | MEDLINE | ID: mdl-33282963

ABSTRACT

Current immunotherapies are effective only in a subset of patients, likely due to several factors including defects in tumor cell antigen presentation, decreased response to immune effectors, and molecular heterogeneity of cancers. Recent molecular classifications enable the categorization of many tumor types. However, deregulation of major histocompatibility complex (MHC) gene expression is poorly characterized in the context of molecular cancer subtypes. To suppress the confounding effect of immune infiltrates on expression patterns of immunoregulators, we identified and removed genes with strong correlation to estimated immune compartment levels in each tumor type. Next, we reanalyzed a total of 13 TCGA cancer types encompassing 5651 tumors and 485 normal adjacent tissues by performing unsupervised clustering of 14 MHC genes. Subsequently, resultant clusters were statistically compared in terms of expression of other immune-related genes. Three MHC expression clusters were discovered by unsupervised clustering. We identified concordantly decreased expression of MHC genes (MHC-low) in 26 out of 55 molecular subtypes. Consequently, our study underlines the urgent need for designing strategies to enhance tumor MHC expression that could improve immune cold tumor rejection by cytotoxic T lymphocytes.


Subject(s)
Genetic Therapy , Immunomodulation/genetics , Immunotherapy , Major Histocompatibility Complex/genetics , Major Histocompatibility Complex/immunology , Neoplasms/therapy , Animals , Biomarkers , Biomarkers, Tumor , DNA Methylation , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Genetic Therapy/methods , High-Throughput Nucleotide Sequencing , Humans , Immunologic Factors , Immunotherapy/methods , Neoplasms/diagnosis , Neoplasms/etiology , Transcriptome
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