ABSTRACT
Systemic mastocytosis (SM) is a myeloproliferative neoplasm displaying abnormal mast cell proliferation. It is subdivided into different forms, including aggressive systemic mastocytosis (ASM) and systemic mastocytosis with an associated hematologic neoplasm (SM-AHN). Oncogenic genetic alterations include point mutations, mainly the KIT D816V, conferring poor prognosis and therapy resistance, and fusion genes, with those involving PDGFRA/PDGFRB as the most recurrent events. We here describe an ASM case negative to the KIT D816V and JAK2 V617F alterations but showing a RUNX1 frameshift heterozygous mutation and the co-occurrence of three fusion transcripts. The first one, PRKG2::PDGFRB, was generated by a balanced t(4;5)(q24;q32) translocation as the sole abnormality. Other two novel chimeras, KAT6A::NCOA2 and RXRA::NOTCH1, originated from cryptic intra-chromosomal abnormalities. The patient rapidly evolved towards SM-AHN, characterized by the persistence of the PRKG2::PDGFRB chimera, due to the presence of an extra copy of the der(5)t(4;5)(q24;q34) chromosome and an increase in the RUNX1 mutation allelic frequency. The results indicated that the transcriptional landscape and the mutational profile of SM deserve attention to predict the evolution and prognosis of this complex disease, whose classification criteria are still a matter of debate.
Subject(s)
Core Binding Factor Alpha 2 Subunit , Frameshift Mutation , Mastocytosis, Systemic , Oncogene Proteins, Fusion , Humans , Core Binding Factor Alpha 2 Subunit/genetics , Mastocytosis, Systemic/genetics , Oncogene Proteins, Fusion/genetics , Receptor, Notch1/genetics , Nuclear Receptor Coactivator 2/genetics , Male , Heterozygote , Female , Middle Aged , Histone AcetyltransferasesABSTRACT
Acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) is a heterogeneous hematological disorder defined by morphological, genetic, and clinical features. Patients with AML-MRC often show cytogenetic changes, which are associated with poor prognosis. Straightforward criteria for AML-MRC diagnosis and a more rigorous characterization of the genetic abnormalities accompanying this disease are needed. Here we describe an informative AML-MRC case, showing two separate, but concurrent, chromothripsis events, occurred at the onset of the tumor, and originating an unbalanced t(5;7) translocation and a derivative chromosome 12 with a highly rearranged short arm. Conversely, despite chromothripsis has been often associated with genomic amplification in cancer, in this case a large marker chromosome harboring amplified sequences from chromosomes 19 and 22 arose from a stepwise mechanism. Notably, the patient also showed a TP53 mutated status, known to be associated with an increased susceptibility towards chromothripsis and a poor prognosis. Our results indicate that multiple chromothripsis events may occur early in neoplastic transformation and act in a synergistic way with progressive chromosomal alterations to determine a dramatic impact on disease outcome, as suggested by the gene expression profile analysis.
Subject(s)
Chromothripsis , Genes, p53 , Leukemia, Myeloid, Acute/genetics , Myelodysplastic Syndromes/genetics , Aged , Aged, 80 and over , Chromosome Aberrations , Female , Humans , Myelodysplastic Syndromes/pathologySubject(s)
Aortic Dissection/etiology , Coronary Aneurysm/etiology , Coronary Artery Bypass/adverse effects , Coronary Stenosis/surgery , Coronary Vessels/injuries , Decision Making , Postoperative Complications , Aged , Aortic Dissection/diagnosis , Aortic Dissection/therapy , Coronary Aneurysm/diagnosis , Coronary Aneurysm/therapy , Coronary Angiography , Coronary Stenosis/diagnostic imaging , Electrocardiography , Humans , Iatrogenic Disease , Male , ReoperationABSTRACT
In NSCLC, the altered expression of some miRNAs in primary tumor tissues has been correlated with diagnosis and prognosis, while the role of circulating miRNAs as cancer biomarkers is currently emerging. MiRNA expression profile through miRNA Affymetrix array was evaluated on a training set formed by the tumor component (n = 30 NSCLC serum, n = 11/30 tumor tissues) and the control component (n = 10 healthy serum and n = 11/30 noncancerous counterparts). Statistical analyses highlighted the following: a = 55 miRNAs deregulated in tumor serum, b = 27 miRNAs deregulated in tumor tissues, and c = 2 miRNAs deregulated both in tumor serum and in tumor tissues. MiRwalk tool and enrichment pathway analyses selected some miRNAs whose target genes are correlated with the main pathways involved in NSCLC tumorigenesis. The altered expression of the selected miR-486-5p (a), miR-29c* (b), and miR-133a (c) was confirmed in the validation set (n = 40). MiR-486-5p had a higher expression in tumor serum than in tumor tissues (P = 0.004), and miR-29c* showed a lower expression in tumor tissues than in tumor serum (P < 0.001). MiR-133a had a not different expression in both tumor serum and tumor tissues (P = 0.07). The low level of miR-486-5p expression in the serum of affected patients was associated with a worse time to progression of disease (P = 0.010), and serum level of miR-486-5p was a significant prognostic indicator of NSCLC (adjusted hazard ratio = 0.179, P = 0.019). These data suggest the possibility to monitor affected patients through serum and/or tissue samples, analyzing the altered expression of specific miRNAs, in order to detect prognostic biomarkers in the NSCLC.
Subject(s)
Biomarkers, Tumor/biosynthesis , Carcinoma, Non-Small-Cell Lung/genetics , MicroRNAs/biosynthesis , Prognosis , Aged , Biomarkers, Tumor/genetics , Carcinogenesis/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Male , MicroRNAs/genetics , Microarray Analysis , Middle AgedABSTRACT
BACKGROUND: Gender-associated epigenetic alterations are poorly investigated in male and female familial breast cancer (fBC). MicroRNAs may contribute to the different biology in men and women particularly related to RASSF1A pathways. METHODS: Microarray technology was used to evaluate miRNA profile in 24 male and 43 female fBC. Key results were validated using RT-qPCR in an external samples set. In vitro studies were carried out to verify microRNA-target gene interaction. RESULTS: Pathway enrichment analysis with the 287 differentially expressed microRNAs revealed several signalling pathways differently regulated in male and female cases. Because we previously hypothesised a peculiar involvement of RASSF1A in male fBC pathogenesis, we focussed on the MAPK and the Hippo signalling pathways that are regulated by RASSF1A. Male miR-152 and miR-497 upregulation and RASSF1A and NORE1A interacting gene downregulation were observed, confirming a possible indirect interaction between miRNAs and the two genes. CONCLUSIONS: For the first time, a different microRNA expression pattern in male and female fBC has been shown. Moreover, the importance of RASSF1A pathway in male fBC carcinogenesis has been confirmed, highlighting a possible role for miR-152 and miR-497 in controlling MAPK and Hippo signalling pathways, regulated by RASSF1A.
Subject(s)
Breast Neoplasms, Male/genetics , Breast Neoplasms, Male/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Male , Microarray Analysis , Signal TransductionABSTRACT
Patients with Silver-Russell syndrome (SRS) show an intrauterine and postnatal growth restriction associated with a variable spectrum of additional features. Genetic or epigenetic alterations on chromosomes 7 and 11 can be detected in several SRS patients; however, a large fraction of cases remains with unknown genetic etiology. Here, we describe the clinical and molecular findings of a patient with a phenotype invoking SRS showing intrauterine and postnatal growth retardation, psychomotor retardation, relative macrocephaly, slightly triangular face with pointed chin, clinodactyly, and a slight body asymmetry, in whom single-nucleotide polymorphism oligonucleotide array analysis led to the identification of a de novo 11p13 duplication containing many genes that could be functionally related with the observed clinical features. Many deletions of chromosome 11p13, resulting in WAGR (Wilms tumor, aniridia, genital anomalies, mental retardation) syndrome, have been described, while only few duplications spanning the same region have been reported so far. To our knowledge, this is the first reported case presenting a SRS carrier of an 11p13 duplication. We propose candidate genes for the observed traits, and in particular, we discuss the possible role of the involvement of 2 noncoding RNAs in the etiology of the phenotype.
ABSTRACT
Mutations in the glucokinase (GCK) gene are the most frequent cause of maturity onset diabetes of the young (MODY) in Italy. We evaluated GCK mutations in 32 unrelated patients younger than 18 years who had been diagnosed with MODY. Eleven different GCK heterozygous mutations were identified in 22 (68.7%) of the 32 probands. Nine mutations were missense and two were nonsense. Three of these mutations (E17X, P59S and E372X) have not been described previously and were shown to be associated with hyperglycaemia. Several prediction methods suggested that the E17X and E372X mutations result in a premature truncated protein and that the P59S mutation is pathogenic. This idea was further supported by evidence suggesting that Proline 59 is a highly conserved amino acid residue and that the P59S mutation does not appear to be present in non-diabetic controls and in sequence variant databases. Furthermore, this mutation was found in six (27.3%) of the patients from the same geographical area, Gargano, pointing to the existence of a founder effect, which was confirmed by microsatellite analysis.
Subject(s)
Diabetes Mellitus, Type 2/genetics , Protein Serine-Threonine Kinases/genetics , Amino Acid Substitution , Codon, Nonsense , Diabetes Mellitus, Type 2/physiopathology , Female , Founder Effect , Germinal Center Kinases , Humans , Italy , Male , Mutation, Missense , Pedigree , Proline/genetics , Proline/metabolismABSTRACT
BACKGROUND: Congenital deletions affecting 3q11q23 have rarely been reported and only five cases have been molecularly characterised. Genotype-phenotype correlation has been hampered by the variable sizes and breakpoints of the deletions. In this study, 14 novel patients with deletions in 3q11q23 were investigated and compared with 13 previously reported patients. METHODS: Clinical data were collected from 14 novel patients that had been investigated by high resolution microarray techniques. Molecular investigation and updated clinical information of one cytogenetically previously reported patient were also included. RESULTS: The molecular investigation identified deletions in the region 3q12.3q21.3 with different boundaries and variable sizes. The smallest studied deletion was 580 kb, located in 3q13.31. Genotype-phenotype comparison in 24 patients sharing this shortest region of overlapping deletion revealed several common major characteristics including significant developmental delay, muscular hypotonia, a high arched palate, and recognisable facial features including a short philtrum and protruding lips. Abnormal genitalia were found in the majority of males, several having micropenis. Finally, a postnatal growth pattern above the mean was apparent. The 580 kb deleted region includes five RefSeq genes and two of them are strong candidate genes for the developmental delay: DRD3 and ZBTB20. CONCLUSION: A newly recognised 3q13.31 microdeletion syndrome is delineated which is of diagnostic and prognostic value. Furthermore, two genes are suggested to be responsible for the main phenotype.
Subject(s)
Chromosome Deletion , Chromosomes, Human, Pair 3 , Developmental Disabilities/genetics , Facies , Genitalia, Male/abnormalities , Growth Disorders/genetics , Developmental Disabilities/diagnosis , Female , Genetic Association Studies , Humans , Male , Nerve Tissue Proteins/genetics , Receptors, Dopamine D3/genetics , Syndrome , Transcription Factors/geneticsABSTRACT
The clock gene machinery controls cellular metabolism, proliferation, and key functions, such as DNA damage recognition and repair. Dysfunction of the circadian clock is involved in tumorigenesis, and altered expression of some clock genes has been found in cancer patients. The aim of this study was to evaluate the expression levels of core clock genes in colorectal cancer (CRC). Quantitative real-time polymerase chain reaction (qPCR) was used to examine ARNTL1, CLOCK, PER1, PER2, PER3, CRY1, CRY2, Timeless (TIM), TIPIN, and CSNK1? expression levels in the tumor tissue and matched apparently healthy mucosa of CRC patients. In the tumor tissue of CRC patients, compared to their matched healthy mucosa, expression levels of ARNTL1 (p=.002), PER1 (p=.002), PER2 (p=.011), PER3 (p=.003), and CRY2 (p=.012) were lower, whereas the expression level of TIM (p=.044) was higher. No significant difference was observed in the expression levels of CLOCK (p=.778), CRY1 (p=.600), CSNK1 (p=.903), and TIPIN (p=.136). As to the clinical and pathological features, a significant association was found between low CRY1 expression levels in tumor mucosa and age (p=.026), and female sex (p=.005), whereas high CRY1 expression levels in tumor mucosa were associated with cancer location in the distal colon (p?=?.015). Moreover, high TIM mRNA levels in the tumor mucosa were prevalent whenever proximal lymph nodes were involved (p= .013) and associated with TNM stages III-IV (p=.005) and microsatellite instability (p=.015). Significantly poorer survival rates were evidenced for CRC patients with lower expression in the tumor tissue of PER1 (p=.010), PER3 (p= .010), and CSNKIE (p=.024). In conclusion, abnormal expression levels of core clock genes in CRC tissue may be related to the process of tumorigenesis and exert an influence on host/tumor interactions.
Subject(s)
CLOCK Proteins/metabolism , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Gene Expression Regulation, Neoplastic/physiology , Aged , CLOCK Proteins/genetics , Female , Gene Expression Profiling , Humans , Male , Microsatellite Instability , Middle Aged , RNA, Messenger/genetics , RNA, Messenger/metabolismABSTRACT
The presence of inflammatory reaction in peri-tumoural connective tissue is generally considered as a defense mechanism against cancer, but inflammation tissue in malignant transformation and early steps of oncogenesis has been recently proven to play a supporting and aggravating role in some carcinomas. Aims of this retrospective study were to evaluate in OSCCs the independent association of peri-tumoral inflammatory infiltrate (PTI) with local recurrence (LR) or survival outcome, and to verify whether PTI can be considered a marker of prognosis. Data from 211 cases of OSCC, only surgically treated between 1990 and 2000, were collected and retrospectively analyzed for PTI and the event LR (5 yrs follow-up at least) by means of univariate-multivariate and neural networks analyses. Patients (mean age 65.3 ± 12.4 yrs, M/F = 2.98) showed presence of PTI in 68.2% (144/211): (+) in 27.0%, (++) in 25.6%, (+++) 15.6%; PTI was found reduced in 24.7% of cases and absent in 7.1%. In overall PTI+ve group (n=144), 66 were TNM Stage I, 33 Stage II, 45 Stage III, none Stage IV. LR (mean 6 ± 4 months) was present in 87/211 (41.2%) patients, of which 43/144 (29.8%) in OSCCs with PTI [23 (+), 13 (++) and 7 (+++)] vs. 44/67 (65.7%) in OSCC with PTI -/+ or PTI-ve ones. By univariate analysis, PTI+ve cases showed a significant lower risk to have LR (p <0.0001; OR= 0.2297; CI= 0.1277:0.4134) vs PTI -/+ or -ve ones, especially among cases with higher PTI value (+++) (OR= 0.1718; CI= 0.0749:0.3939). Multivariate analyses (Logit model and neural networks) confirmed the same datum: presence of PTI was an independent predictive variable accounting for a better tumoural outcome without LR (Logit and neural networks values: OR' 0.226; CI= 0.113:0.454; ROC Area = 0.66, respectively). In terms of prognostic significance, elevated PTI was found to have an independent association with the poorest overall survival rate (P = 0.056). Our findings strongly suggest the importance to investigate routinely PTI in OSCCs, as useful marker of tumoral behavior and prognosis, and warrant further studies.
Subject(s)
Carcinoma, Squamous Cell/pathology , Inflammation/pathology , Mouth Neoplasms/pathology , Adult , Aged , Aged, 80 and over , Female , Humans , Kaplan-Meier Estimate , Male , Middle Aged , Neoplasm Grading , Neoplasm Staging , Neural Networks, Computer , Prognosis , Recurrence , Tumor BurdenABSTRACT
22q11.2 deletion syndrome is mainly characterized by conotruncal congenital heart defects, velopharyngeal insufficiency, hypocalcemia and a characteristic craniofacial appearance. The etiology in the majority of patients is a 3-Mb recurrent deletion in region 22q11.2. Nevertheless, recently some cases of infrequent deletions with various sizes have been reported with a different phenotype. We report on a patient with congenital heart disease (truncus arteriosus type 2) in whom a de novo 1.3-Mb 22q11.2 deletion was detected by array comparative genomic hybridization. The deletion described corresponds to an atypical and distal deletion which spans low copy repeat (LCR) 4 and is associated with breakpoint sites that do not correspond to known LCRs of 22q11.2. We examine the clinical phenotype of our case and compare our findings with those published in the literature. The most prevalent clinical features in this type of deletion are a history of prematurity, pre-natal and post-natal growth retardation, slight facial dysmorphic features, microcephaly and developmental delay, with a speech defect in particular. These are clearly different from those found in the classic 22q11.2 deletion syndrome, and we believe that the main differential diagnosis should be with Silver-Russel syndrome. In our case we observe the cardiac phenotype with truncus arteriosus communis usually seen in the classic 22q11.2 deletion syndrome, and so far associated with the TBX1 gene. Significantly, however, TBX1 is not included in our patient's deletion. The possible roles of a position effect or other genes are discussed.
ABSTRACT
Ganglioneuroma is a rare benign tumor originating from autonomic ganglia and is considered the benign counterpart of neuroblastoma. Ganglioneuromas may be present as an isolated finding and, rarely, in association with neurofibromatosis type 1 (NF1). However, ganglioneuromas of the cervical spine with intradural extension and multiple locations are extremely rare. We describe a 32-year-old woman with multiple ganglioneuromas of the cervical, dorsal and lumbar spine associated with a few café-au-lait spots and subcutaneous nodules. The patient lacked other NF1 stigmata, such as freckling, Lisch nodules and cutaneous neurofibromas. Although our patient did not fulfill the NF1 diagnostic criteria, molecular diagnosis revealed a pathogenic mutation in the NF1 gene. Approximately 30 patients affected by NF1 and ganglioneuromas have been reported: in all these individuals, NF1 diagnosis was made according to the clinical diagnostic criteria and no patients have molecular diagnosis. Therefore, this is the first case with multiple spinal ganglioneuromas associated with a pathogenic NF1 mutation.
Subject(s)
Ganglioneuroma/genetics , Neurofibromin 1/genetics , Spinal Neoplasms/genetics , Adult , Female , Ganglioneuroma/pathology , Humans , Mutation , Pedigree , Spinal Neoplasms/pathologyABSTRACT
AIM: The aim of the study was to evaluate the prevalence of carotid atherosclerosis and endothelial dysfunction in 45 young patients (38 mens and 7 females) with myocardial infarction (MI), age 29-45, mean age 42+/-3 years, to verify its possible role as a marker of coronary atherosclerosis. METHODS: Vascular echography was performed to verify the presence of carotid atherosclerosis and/or endothelial dysfunction in 45 young patients with MI and in 45 healthy control subjects well matched for age and sex. RESULTS: We observed a normal intima media thickness (IMT) only in 30% of patients with juvenile myocardial infarction (JMI) compared with 66% in the control group (P<0.0001) and 34% of patients showed an increased IMT compared with 24% of healthy subjects (P<0.0001). Compared with control subjects, patients with JMI had lower flow-mediated reactivity of the brachial arteries (P<0.05). There was a negative linear relationship between flow-mediated dilation and IMT (P<0.001). The severity of coronary artery disease (CAD) was correlated with increased IMT and with a lower flow-mediated dilation. Finally, multiple regression analysis, demonstrated that both brachial-artery reactivity and carotid IMT were significantly and independently correlated with severity of CAD. CONCLUSIONS: Structural (carotid atherosclerosis) and functional changes (endothelial dysfunction) were present at an early age in the arteries of persons with history of JMI.
Subject(s)
Brachial Artery/physiopathology , Carotid Arteries/pathology , Carotid Artery Diseases/epidemiology , Coronary Artery Disease/epidemiology , Endothelium, Vascular/physiopathology , Myocardial Infarction/epidemiology , Tunica Intima/pathology , Tunica Media/pathology , Adult , Age of Onset , Brachial Artery/diagnostic imaging , Carotid Arteries/diagnostic imaging , Carotid Artery Diseases/diagnosis , Carotid Artery Diseases/physiopathology , Case-Control Studies , Chi-Square Distribution , Coronary Artery Disease/diagnosis , Coronary Artery Disease/physiopathology , Endothelium, Vascular/diagnostic imaging , Female , Humans , Italy/epidemiology , Male , Middle Aged , Myocardial Infarction/diagnosis , Myocardial Infarction/physiopathology , Prevalence , Regression Analysis , Risk Assessment , Risk Factors , Tunica Intima/diagnostic imaging , Tunica Media/diagnostic imaging , Ultrasonography, Doppler, Color , VasodilationABSTRACT
Squamous cell carcinoma (SCC) is one of the most common malignant cancer of the oral cavity encompassing at least 92.8% of all oral malignancies. Despite improved diagnostic and therapeutic methods over the 20 last years, this tumour is still characterized by a high rate of mortality. The latest advances of molecular biological methods have contributed to better understand the mechanisms involved in the oral carcinogenetic process. Deregulation of cell cycle, apoptosis and cell-cell/cell-matrix adhesions are considered the pathways mainly influencing this multistage event and scientific researches over the last decade have been performed in order to investigate the biological diagnostic and prognostic parameters related to these events (i.e. tumour growth markers, markers of tumour suppression and anti-tumour response, angiogenesis markers, markers of tumour invasion and metastatic potential, cell surface markers, intracellular markers, markers derived from arachidonic acid, and enzymatic markers). The aim of the present review was to outline the current knowledge on the role of some of these tumour biological markers in carcinogenesis of oral SCC.
Subject(s)
Carcinoma, Squamous Cell/pathology , Mouth Neoplasms/pathology , Apoptosis , Carcinoma, Squamous Cell/secondary , Cell Adhesion , HumansABSTRACT
MOTIVATION: A major challenge in current biomedical research is the identification of cellular processes deregulated in a given pathology through the analysis of gene expression profiles. To this end, predefined lists of genes, coding specific functions, are compared with a list of genes ordered according to their values of differential expression measured by suitable univariate statistics. RESULTS: We propose a statistically well-founded method for measuring the relevance of predefined lists of genes and for assessing their statistical significance starting from their raw expression levels as recorded on the microarray. We use prediction accuracy as a measure of relevance of the list. The rationale is that a functional category, coded through a list of genes, is perturbed in a given pathology if it is possible to correctly predict the occurrence of the disease in new subjects on the basis of the expression levels of the genes belonging to the list only. The accuracy is estimated with multiple random validation strategy and its statistical significance is assessed against a couple of null hypothesis, by using two independent permutation tests. The utility of the proposed methodology is illustrated by analyzing the relevance of Gene Ontology terms belonging to biological process category in colon and prostate cancer, by using three different microarray data sets and by comparing it with current approaches. AVAILABILITY: Source code for the algorithms is available from author upon request. SUPPLEMENTARY INFORMATION: Colon cancer data set and a complete description of experimental results are available at: ftp://bioftp:76bioftpxxx@marx.ba.issia.cnr.it/supp-info.htm.
Subject(s)
Biomarkers, Tumor/metabolism , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic , Multigene Family , Neoplasm Proteins/metabolism , Neoplasms/metabolism , Oligonucleotide Array Sequence Analysis/methods , Data Interpretation, Statistical , Humans , Male , Neoplasm Proteins/classificationABSTRACT
BACKGROUND: In this paper we present a method for the statistical assessment of cancer predictors which make use of gene expression profiles. The methodology is applied to a new data set of microarray gene expression data collected in Casa Sollievo della Sofferenza Hospital, Foggia--Italy. The data set is made up of normal (22) and tumor (25) specimens extracted from 25 patients affected by colon cancer. We propose to give answers to some questions which are relevant for the automatic diagnosis of cancer such as: Is the size of the available data set sufficient to build accurate classifiers? What is the statistical significance of the associated error rates? In what ways can accuracy be considered dependant on the adopted classification scheme? How many genes are correlated with the pathology and how many are sufficient for an accurate colon cancer classification? The method we propose answers these questions whilst avoiding the potential pitfalls hidden in the analysis and interpretation of microarray data. RESULTS: We estimate the generalization error, evaluated through the Leave-K-Out Cross Validation error, for three different classification schemes by varying the number of training examples and the number of the genes used. The statistical significance of the error rate is measured by using a permutation test. We provide a statistical analysis in terms of the frequencies of the genes involved in the classification. Using the whole set of genes, we found that the Weighted Voting Algorithm (WVA) classifier learns the distinction between normal and tumor specimens with 25 training examples, providing e = 21% (p = 0.045) as an error rate. This remains constant even when the number of examples increases. Moreover, Regularized Least Squares (RLS) and Support Vector Machines (SVM) classifiers can learn with only 15 training examples, with an error rate of e = 19% (p = 0.035) and e = 18% (p = 0.037) respectively. Moreover, the error rate decreases as the training set size increases, reaching its best performances with 35 training examples. In this case, RLS and SVM have error rates of e = 14% (p = 0.027) and e = 11% (p = 0.019). Concerning the number of genes, we found about 6000 genes (p < 0.05) correlated with the pathology, resulting from the signal-to-noise statistic. Moreover the performances of RLS and SVM classifiers do not change when 74% of genes is used. They progressively reduce up to e = 16% (p < 0.05) when only 2 genes are employed. The biological relevance of a set of genes determined by our statistical analysis and the major roles they play in colorectal tumorigenesis is discussed. CONCLUSIONS: The method proposed provides statistically significant answers to precise questions relevant for the diagnosis and prognosis of cancer. We found that, with as few as 15 examples, it is possible to train statistically significant classifiers for colon cancer diagnosis. As for the definition of the number of genes sufficient for a reliable classification of colon cancer, our results suggest that it depends on the accuracy required.
Subject(s)
Algorithms , Oligonucleotide Array Sequence Analysis/methods , Statistics as Topic/methods , Aged , Colonic Neoplasms/classification , Colonic Neoplasms/genetics , Data Interpretation, Statistical , Female , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic/genetics , Humans , Male , Middle Aged , Models, Statistical , Numerical Analysis, Computer-Assisted , Reproducibility of Results , SoftwareABSTRACT
BACKGROUND: Espins are actin bundling proteins present in hair cell stereocilia. A recessive mutation in the espin gene (Espn) has been detected in the jerker mouse and causes deafness, vestibular dysfunction, and hair cell degeneration. More recently mutations in the human espin gene (ESPN) have been described in two families affected by autosomal recessive hearing loss and vestibular areflexia. OBJECTIVE: To report the identification of four additional ESPN mutations (S719R, D744N, R774Q, and delK848) in patients affected by autosomal dominant hearing loss without vestibular involvement. RESULTS: To determine whether the mutated ESPN alleles affected the biological activity of the corresponding espin proteins in vivo, their ability to target and elongate the parallel actin bundles of brush border microvilli was investigated in transfected LLC-PK1-CL4 epithelial cells. For three mutated alleles clear abnormalities in microvillar length or distribution were obtained. CONCLUSIONS: The results further strengthen the causative role of the espin gene in non-syndromic hearing loss and add new insights into espin structure and function.