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PubMed2004

Prediction of chemotherapeutic response in ovarian cancer with DNA microarray expression profiling.

Ovarian carcinoma is a leading cause of gynecologic cancer death in women. Despite treatment, a large number of women with ovarian cancer eventually relapse and die of the disease. Hence, recurrent ovarian cancer continues to be a therapeutic dilemma, possibly a result of the emergence of drug resistance during relapse. Recent advances in expression genomics enable global transcript analysis that leads to molecular classification of cancers and prediction of outcome and treatment response. We did a cDNA microarray examination of the expression profiles of eight primary ovarian cancers stratified into two groups based on their chemotherapeutic response. We applied a voice-speech-pattern recognition algorithm for microarray data analysis and were able to model and predict the response of these patients to chemotherapy from their expression profiles. Hence, gene expression profiling by means of DNA microarray may be applied diagnostically for predicting treatment response in ovarian cancer.

Adult↗

PubMed2026

SCLC TumorMiner: A genomics platform for small cell lung cancer precision oncology.

Small cell lung cancer (SCLC) is among the most aggressive malignancies. Unlike many other cancers, it is not represented in The Cancer Genome Atlas, and available datasets are fragmented across institutions, disease stages, and treatment settings. RNA sequencing provides a powerful and cost-effective approach, but the high dimensionality of transcriptomic data and the heterogeneity of patient cohorts pose significant challenges. To address such challenges, we developed SCLC TumorMiner (https://discover.nci.nih.gov/SclcTumorMinerCDB/), which includes 50 tumor samples from relapsed patients at the National Cancer Institute (NCI) and 154 samples from untreated patients at the University of Cologne and Tongji University. SCLC TumorMiner enables molecular classification, genomic pathway analyses, risk stratification, identification of predictive cell-surface biomarkers such as DLL3 or TROP2, and drug-response biomarkers such as SLFN11. SCLC TumorMiner illustrates profound differences between untreated and relapsed patient samples. Additionally, "MyPatient", one of SCLC TumorMiner's modules, is presented as a medical assistant application prototype.

SCLC↗

PubMed2026

Proteomic and metabolomic profiling reveals dysregulation of immune states, mucin-type glycosylation and steroid metabolism in extramammary Paget's disease.

BACKGROUND: Extramammary Paget's disease is a rare cutaneous adenocarcinoma characterized by mucin-rich Paget cells and chronic inflammation, yet its molecular basis remains unclear. OBJECTIVE: To systematically characterize the proteomic and metabolomic landscape of EMPD, uncover immune heterogeneity, and identify molecular pathways underlying tumor progression and microenvironment remodeling. METHODS: We performed integrated proteomic and metabolomic analyses on 92 male tumor patients and 30 healthy controls, identifying 10,217 proteins and 1466 metabolites. RESULTS: Extramammary Paget's disease lesions exhibited broad activation of inflammatory pathways. Immune profiling further uncovered substantial inflammatory heterogeneity, delineating immune-cold and immune-hot subtypes, with the latter associated with stronger invasive potential. Aberrant mucin-type glycosylation was also prominent, featuring Tn-modified MUC1 and MUC5AC accompanied by elevated GALNT7, GALNT6, GALNT4, and ST6GAL1, which correlated with inflammatory intensity. Metabolomic data demonstrated elevated levels of testosterone, dehydroepiandrosterone, and related intermediates in tumor tissues, indicating an androgen-enriched metabolic profile in extramammary Paget's disease. CONCLUSION: These findings reveal immune, glycoproteomic, and metabolomic pathways in extramammary Paget's disease pathogenesis and provide novel insights for molecular classification and therapeutic targeting.

Humans↗

PubMed2005

Gene expression profile in oral squamous cell carcinoma: a pilot study.

PURPOSE: To study the gene expression profile of oral squamous cell carcinomas. MATERIALS AND METHODS: Gene expression profile was investigated in oral squamous cell carcinomas in 5 patients using the Atlas Glass Human 3.8 I Microarray (which detects cDNA obtained from cellular total RNA) (Clontech Laboratories, Palo Alto, CA). Data were normalized by the LOWESS method. Statistical significances of deviations from a 1:1 ratio were evaluated by t tests, with P<.05. RESULTS: Of the 3,757 genes analyzed, 322 (8.6%) were significantly overexpressed in tumoral tissue with respect to normal tissue, while 104 (2.8%) were significantly underexpressed. The affected genes fell into a wide range of functional categories. CONCLUSION: We consider that cDNA microarrays are of clear value for investigating the biology of these tumors, and that this technology may help in the molecular classification of oral squamous cell carcinomas and in the identification of targets for gene therapy.

Aged↗

PubMed2005

Expression of IFITM1 in chronic myeloid leukemia patients.

We investigated the peripheral blood gene expression profile of interferon induced transmembrane protein 1 (IFITM1) in sixty chronic myeloid leukemia (CML) patients classified according to new prognostic score (NPS). IFITM1 is a component of a multimeric complex involved in the trunsduction of antiproliferative and cell adhesion signals. Expression level of IFITM1 was found significantly different between the high- and low-risk groups (P = 9.7976 x 10(-11)) by real-time reverse transcription polymerase chain reaction (RT-PCR). Higher IFITM1 expression correlated with improved survival (P = 0.01). These results indicate that IFITM1 expression profiling could be used for molecular classification of CML, which may also predict survival.

Adult↗

PubMed2005

New approaches to pathogenic gene function discovery with human squamous cell cervical carcinoma by gene ontology.

PURPOSE: This study utilized mRNA differential display and the Gene Ontology (GO) analysis to characterize the multiple interactions of a number of genes with gene expression profile involved in squamous cell cervical carcinoma. METHODS: mRNA differential displays were used to identify potential transcripts that were differentially expressed between cervix cancers of 13 patients (invasive cancer stages Ib-IIb) and universal reference RNAs comprised of 17 different normal cervixes. Aberrant bands were excised and used to make cDNA, which was sequenced. DNA sequences were compared to other nucleic acids in the NCBR database for homology. Transcript expression was verified in select samples using RT-PCR and North blotting. The specific functions were correlated with gene expression patterns via gene ontology. RESULTS: Fifty-eight genes were up- or down-regulated above 2-fold and organized into reciprocally dependent sub-function sets depending on the cervical cancer pathway. The GO analysis showed that squamous cell cervical carcinogenesis underwent complete up-regulation of cell cycle, transport, epidermal differentiation, protein biosynthesis, and RNA metabolism. Also, genes belonging to protein metabolism and catabolism activity were significantly up-regulated. In contrast, significant down-regulation was shown in muscle development, cell adhesion, and damaged DNA binding activity. CONCLUSION: The GO analysis can overcome the complexity of the gene expression profile of the squamous cell cervical carcinoma-associated pathway and identify several cancer-specific cellular processes as well as genes of unknown function. Also, GO analysis can serve as a powerful basis for a molecular classification of carcinogenesis.

Apoptosis↗

PubMed2006

Differential gene expression profiling in genetic and multifactorial cardiovascular diseases.

Gene expression profiling by microarray technologies has been successfully applied to study the transcriptional changes that occur in tissues such as heart, vessels and blood cells in different cardiovascular disorders. Such studies have been performed in human cardiovascular syndromes and in animal models with the aim of unraveling the complex molecular pictures underlying human pathophysiology. As already observed in cancer research, gene expression studies in humans may provide a finer molecular classification of patients with cardiovascular diseases and indicate new markers useful for prognostic and therapeutic strategies. In this paper, we present the findings obtained with microarray platforms to explore transcriptome alterations in cardiovascular diseases. To describe the potential of global expression profiling approach in this field, we have chosen to review the genomic findings obtained in some classic heart diseases with genetic transmission such as hyperthrophic cardiomyopathy and Fabry disease, together with findings obtained in common multifactorial cardiovascular disorders such as heart failure, atherosclerosis and infarction. Wherever feasible, we present the results obtained in patients together with those obtained in the corresponding animal and cellular models.

Animals↗

PubMed2003

Distinct transcriptional profiles of adrenocortical tumors uncovered by DNA microarray analysis.

Comprehensive expression profiling of tumors using DNA microarrays has been used recently for molecular classification and biomarker discovery, as well as a tool to identify and investigate genes involved in tumorigenesis. Application of this approach to a cohort of benign and malignant adrenocortical tissues would be potentially informative in all of these aspects. In this study, we generated transcriptional profiles of 11 adrenocortical carcinomas (ACCs), 4 adrenocortical adenomas (ACAs), 3 normal adrenal cortices (NCs), and 1 macronodular hyperplasia (MNH) using Affymetrix HG_U95Av2 oligonucleotide arrays representing approximately 10,500 unique genes. The expression data set was used for unsupervised hierarchical cluster analysis as well as principal component analysis to visually represent the expression data. An analysis of variance on the three classes (NC, ACA plus MNH, and ACC) revealed 91 genes that displayed at least threefold differential expression between the ACC cohort and both the NC and ACA cohorts at a significance level of P < 0.01. Included in these 91 genes were those known to be up-regulated in adrenocortical tumors, such as insulin-like growth factor (IGF2), as well as novel differentially expressed genes such as osteopontin (SPP) and serine threonine kinase 15 (STK15). Increased expression of IGF2 was identified in 10 of 11 ACCs (90.9%) and was verified by quantitative reverse transcriptase-polymerase chain reaction. Select proliferation-related genes (TOP2A and Ki-67) were validated at the protein level using immunohistochemistry and adrenocortical tissue microarrays. Our results demonstrated significant and consistent gene expression changes in ACCs compared to benign adrenocortical lesions. Moreover, we identified several genes that represent potential diagnostic markers and may play a role in the pathogenesis of ACC.

Adenoma↗

PubMed1998

Endogenous proteolytic cleavage of normal and disease-associated isoforms of the human prion protein in neural and non-neural tissues.

We have investigated the proteolytic cleavage of the cellular (PrPC) and pathological (PrPSc) isoforms of the human prion protein (PrP) in normal and prion-affected brains and in tonsils and platelets from neurologically intact individuals. The various PrP species were resolved after deglycosylation according to their electrophoretic mobility, immunoreactivity, Sarkosyl solubility, and, as a novel approach, resistance to endogenous proteases. First, our data show that PrPC proteolysis in brain originates amino-truncated peptides of 21 to 22 and 18 (C1) kd that are similar in different regions and are not modified by the PrP codon 129 genotype, a polymorphism that affects the expression of prion disorders. Second, this proteolytic cleavage of PrPC in brain is blocked by inhibitors of metalloproteases. Third, differences in PrPC proteolysis, and probably in Asn glycosylation and glycosylphosphatidylinositol anchor composition, exist between neural and non-neural tissues. Fourth, protease-resistant PrPSc cores in sporadic Creutzfeldt-Jakob disease (CJD) and Gerstmann-Sträussler-Scheinker F198S disease brains all have an intact C1 cleavage site (Met111-His112), which precludes disruption of a domain associated with toxicity and fibrillogenesis. Fifth, the profile of endogenous proteolytic PrPSc peptides is characteristic of each disorder studied, thus permitting the molecular classification of these prion diseases without the use of proteinase K and even a recognition of PrPSc heterogeneity within type 2 CJD patients having different codon 129 genotype and neuropathological phenotype. This does not exclude the role of additional factors in phenotypic expression; in particular, differences in glycosylation that may be especially relevant in the new variant CJD. Proteolytic processing of PrP may play an important role in the neurotropism and phenotypic expression of prion diseases, but it does not appear to participate in disease susceptibility.

Aged↗

PubMed2001

Familial occurrence of pigment dispersion syndrome.

BACKGROUND: Pigment dispersion syndrome affects up to 4% of the white population. It is characterized by the presence of transillumination defects, Krukenberg's spindle and dense trabecular meshwork pigmentation. Open-angle glaucoma will develop in as many as 50% of affected patients. In this study we describe the familial occurrence of pigment dispersion syndrome in six North American pedigrees and the phenotypic characteristics with respect to pigment dispersion syndrome and glaucoma. METHODS: Probands with pigment dispersion syndrome were identified in glaucoma clinics at university eye centres in Ottawa and Durham, NC. Families with two or more affected members were evaluated. All willing members in each family underwent a thorough clinical examination and were classified as affected with pigment dispersion syndrome, suspect or unaffected. The previous medical records were reviewed to obtain the past medical and ocular history, including risk factors for glaucoma. RESULTS: All six families are white. Three families show at least two generations of affected members. Of the 43 subjects examined 58% were women. All 14 affected members showed moderate to heavy trabecular meshwork pigmentation and either Krukenberg's spindle or transillumination defects. The affected members were also considerably more myopic (mean spherical equivalent for the right eye -4.72 dioptres) than the suspect group or the unaffected group (mean spherical equivalent -0.79 D and +1.19 D respectively) (p < or = 0.001), and the intraocular pressure was higher for the affected than the unaffected group (mean for the right eye 20 mm Hg vs. 16 mm Hg) (p = 0.004). Half of those affected also had open-angle glaucoma. INTERPRETATION: We have identified and phenotypically characterized six North American families with autosomal dominant pigment dispersion syndrome. Our ultimate goal is to identify the gene(s) that causes this disorder in order to clarify its molecular etiology and pathophysiology. This may give rise to a molecular classification of the disease as well as provide the foundation for genetic testing and new treatment approaches.

Adult↗

PubMed2003

Gene expression profiling as a tool for the diagnosis of acute leukemias.

The standard methods to diagnose leukemia are cytomorphology and, in some cases, histology, which both are supplemented by cytochemistry and multiparameter immunophenotyping. Cytogenetics, fluorescence in situ hybridisation (FISH), and polymerase chain reaction (PCR) assays add important information and allow comprehensive diagnosis of well-defined subentities today. In the clinic, better understanding of the course of distinct, biologically defined disease subtypes is the basis for a selection of specific therapeutic approaches. As knowledge on deregulated pathways in leukemia accelerates the development of new therapeutics, a detailed and comprehensive diagnostic tool is required. The microarray technology that quantifies gene expression intensities of thousands of genes in a single analysis has the potential to become essential for the molecular classification of leukemias. Microarrays may be used routinely for diagnostic purposes in the near future. Gene expression profiling should also lead to the detection of new biological and clinically relevant subtypes in leukemia and therefore guide therapeutic decisions.

Acute Disease↗

PubMed2002

Rapid detection of the prion protein M129V polymorphism with the LightCycler.

The common single nucleotide polymorphism at codon 129 of the prion protein gene is a key determinant of the genetic susceptibility to Creutzfeldt-Jakob disease (CJD). Recently, a molecular classification of sporadic CJD based on the M129V genotype in conjunction with other determinants was proposed. In the present study, we describe the development and evaluation of a rapid fluorescent-based assay to detect this polymorphism using the LightCycler system. The two polymorphic alleles could be clearly distinguished by their melting points at 52.1 and 60.4 degrees C, representing the 129V and 129M alleles, respectively. These results were confirmed by DNA sequencing. We evaluated our test in 400 patient samples and found no deviations from the expected melting patterns. The calculated allele frequency for the M-allele was 0.66. Thus, we have established a rapid, reliable fluorescent assay for high-throughput detection of the prion protein M129V polymorphism.

Creutzfeldt-Jakob Syndrome↗

PubMed2003

Molecular profiles of invasive mucinous and ductal carcinomas of the breast: a molecular case study.

Expression profiling using cDNA microarrays have redefined the molecular classification of some cancers. The comprehensive genetic analysis also permits the identification of novel pathways that might determine subtle differences in tumor phenotype. Herein, we analyzed the tissues from a patient with bilateral cancer of different histologies in each breast (pure invasive mucinous and pure invasive ductal), thus providing a unique opportunity to assess the expression profiles determined by histology in an isogenic human background. Our results show that the mucinous phenotype is associated with the expression of immunostimulatory and inhibitory genes, consistent with the cellular infiltration of lymphocytes and with the expression of enzymes involved in mucin production. Moreover, the panel of matrix metallo-proteinases are distinctly different between the mucinous and the invasive tumors, suggesting that therapeutic targets to this class of compounds may need to be tailored for the varying histologies. Taken together, these data suggest that expression profiling can be used diagnostically to distinguish individual histologic subclassifications and may guide the selection of target therapeutics.

Adenocarcinoma, Mucinous↗

PubMed2003

Epigenetic gene silencing in cancer initiation and progression.

Hypermethylation of CpG islands, an epigenetic event that is not accompanied by changes in DNA sequence, represents an alternative mechanism to deletions or mutations to inactivate tumor suppressor genes. Recent evidence supports the notion that CpG island hypermethylation, by silencing key cancer-related genes, plays a major causal role in cancer. However, a long-standing issue in the field is the sequence of molecular events leading to epigenetic gene silencing. A new model has been proposed that chromatin remodeling, as a result of histone deacetylation and methylation, is the primary event in abrogating transcriptional initiation; subsequently, CpG island hypermethylation establishes a permanent state of gene silencing. Accumulating evidence indicates that CpG island hypermethylation is an early event in cancer development and, in some cases, may precede the neoplastic process. Because of their heritable nature, hypermethylated CpG islands leave 'molecular footprints' in evolving cancer cells and can be used as molecular markers to reconstruct epigenetic progression during tumorigenesis. Furthermore, hypermethylated CpG islands are proving to be useful for molecular classification of different cancer types.

CpG Islands↗

PubMed2003

Patients with a novel neurofilamentopathy: dementia with neurofilament inclusions.

We report a new disease, dementia with neurofilament inclusions, characterized clinically by early-onset dementia with frontal lobe signs, focal atrophy of the frontal and temporal lobes, and microscopically by the presence in many brain regions of intraneuronal, cytoplasmic, neurofilament inclusions. The neuronal inclusions are immunoreactive to all three molecular weight neurofilament subunits: heavy (NF-H), light, and medium subunits, including the phosphorylated and non-phosphorylated forms of NF-H. Prion protein and beta-amyloid deposits were absent. The inclusions do not contain tau or alpha-synuclein protein aggregates known to characterize many neurodegenerative disorders. In addition to delineating a new disease entity, the identification of intraneuronal, cytoplasmic, neurofilament inclusions extends the molecular classification of neurodegenerative diseases and implicates new mechanisms of neurodegeneration in diseases affecting the human brain.

Adult↗

PubMed1999

Neuropathology of prion diseases.

Prion diseases include sporadic forms such as Creutzfeldt-Jakob disease (CJD), familial forms (familial CJD), fatal familial insomnia, Gerstmann-Sträussler-Scheinker disease, and acquired forms (i.e., kuru, iatrogenic CJD). The most frequent of the latter include acquired forms secondary to injections of human cadaveric pituitary-derived growth hormone and the new variant of CJD--probably related to bovine spongiform encephalopathy. The communal lesions are neuronal loss, spongiosis and gliosis and, inconstantly, the presence of amyloid plaques and different kinds of small deposits immunolabeled with anti-prion (PrP) antibodies. Their number and topography are variable. Recent works have shown the role of the host genotype, especially of codon 129, in the susceptibility to these diseases. We have tried to correlate neuropathology with the genotype of codon 129 and the type of PrP to establish a molecular classification.

Animals↗

PubMed2001

Recent advances in melanoma research.

Recent advancement in the research of malignant melanoma is reviewed. Among many gene alterations detected in human melanoma, defect of CDKN2A located at chromosome 9p21 seems to be most important in the earlier developmental phase, though significance of this gene in the evolution of melanoma in situ has not been confirmed yet. Deletions of PTEN/MMAC1 on 10q23.3 and AIM1 on 6q21 as well as mutations of ras gene are involved in the later progression stages of melanoma. Adhesion molecules relevant to development and progression of melanoma have been intensely investigated in recent years, revealing crucial roles of cadherins and alpha(v)beta(3) integrin in the biologic behaviors of melanoma cells. Melanoma is characterized by extremely high potential of developing metastases. Dynamic changes of matrix metalloproteinase activity during invasion and movement of melanoma cells may be a major concern in this field. Fragility of blood vessels in melanoma lesions is another important point related to hematogeneous metastases. Acral lentiginous melanoma is a unique subtype of melanoma, because, in contrast to other subtypes, ultraviolet irradiation is not a major factor in its development. Investigation of pathogenesis of acral lentiginous melanoma surely provides us with new information about mechanism of melanocyte transformation. Recent advances in the management of malignant melanoma are also briefly reviewed, such as biochemotherapy, immunotherapy, and gene therapy. Finally, the concept of molecular classification of melanoma by gene expression profile is introduced, which possibly enables us to give the tailor-made therapy for each melanoma patient in the near future.

Chromosomes, Human, Pair 10↗

PubMed2001

[Cerebellar vermis hypoplasia with extracerebral involvement (retina, kidney, liver): difficult to classify syndromes].

UNLABELLED: Congenital cerebellar vermis hypoplasias diversely associated with retinopathy, nephropathy and hepatopathy are rare syndromes of uncertain nosology. We report three new cases. CASE REPORTS: Case 1. A 3-month-old boy presented a brief nystagmus. At the age of 2 years, he had facial dysmorphia, hypotonia, ataxia, ocular motor apraxia and neurodevelopmental impairment with cerebellar vermis hypoplasia. The electroretinogram showed asymptomatic retinal involvement. At the age of 6 years, he developed chronic renal failure. The diagnosis of familial juvenile nephronophthisis was made by detection of a large homozygous deletion of the NPH1 region. Case 2. A term newborn boy presented apnea, tachypnea, hypotonia, nystagmus, ptosis, lack of visual contact and hepatomegaly. He had facial dysmorphia, bilateral optic coloboma with chorioretinal dysplasia and cerebellar vermis hypoplasia. There were cysts in the kidneys with increased echogenicity and lack of demarcation between the pyramids and the cortex. The liver was hyperechoic with fibrosis. At the age of 15 months, the child had severe developmental delay. He had bouts of fever. A search for a large homozygous deletion of the NPH1 region was negative. Case 3. A term newborn girl presented difficulty to suck, cyanosis, hypotonia and ptosis. Later, the child had a developmental delay. At the age of 6 years, she developed chronic renal failure (nephronophthisis). At the age of 23 years, she presented divergent strabismus, ataxia, mental retardation, slow ocular pursuit and facial dysmorphia. The neuroimaging showed a cerebellar vermis hypoplasia. A search for a large homozygous deletion of the NPH1 region was negative. CONCLUSION: The diagnosis of cerebellar vermis hypoplasia requires searching for retina, kidney and liver involvement. The large homozygous deletion of the NPH1 region has to be investigated if typical familial juvenile nephronophthisis is associated. Because cerebellar vermis hypoplasia with extracerebral involvements (retina, kidney, liver) is part of many different closely related syndromes, a clear molecular classification is necessary for accurate genetic counselling and an early prenatal diagnosis.

Abnormalities, Multiple↗