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1.
Drug Metab Dispos ; 49(3): 179-187, 2021 03.
Article in English | MEDLINE | ID: mdl-33376147

ABSTRACT

CYP2D6 is a major drug metabolizing enzyme with a buried active site. Channels leading to the active site from various enzyme surfaces are believed to facilitate ligand egress and access to the active site. The present study used molecular dynamics (MD) and in vitro studies with CYP2D6*1 and a Trp75-to-Ala mutant to examine channel gating in CYP2D6 by Trp75. MD simulations measured energy landscapes of Trp75 conformations and simulated substrate passage within channel 2b using bufuralol as a model substrate. Trp75 alternated between multiple stable states that supported substrate transport along channel 2b with low-energy barriers between states (∼ -1 kcal/mol). Trp75 conformations were stabilized primarily by hydrogen bonding between Trp75 and Glu222, Asn226, Ala225, or Gln72. Energy barriers were low between Trp75 conformations, allowing Trp75 to easily move between various conformations over time and to function in both binding to and moving substrates in the 2b channel of CYP2D6. Michaelis-Menten kinetic studies completed with purified enzyme in a reconstituted system showed overall reduced enzyme efficiency for metabolism of bufuralol and dextromethorphan by the Trp75Ala mutant compared with CYP2D6*1. In stopped-flow measurements, k off for dextromethorphan was decreased in the absence of Trp75. Our results support a role for Trp75 in substrate shuttling to the active site of CYP2D6. SIGNIFICANCE STATEMENT: Using combined molecular dynamics and in vitro assays, this study shows for the first time a role for Trp75 as a channel entrance gating residue in the mechanism of substrate binding/unbinding in CYP2D6. Energy landscapes derived from molecular dynamics were used to quantitate the strength of gating, and kinetics assays showed the impact on enzyme efficiency and k off of a Trp75Ala mutation.


Subject(s)
Cytochrome P-450 CYP2D6/metabolism , Ion Channel Gating/physiology , Tryptophan/metabolism , Animals , Crystallography, X-Ray/methods , Cytochrome P-450 CYP2D6/chemistry , Ethanolamines/metabolism , Ethanolamines/pharmacology , Ion Channel Gating/drug effects , Protein Structure, Secondary , Rats , Substrate Specificity/drug effects , Substrate Specificity/physiology , Tryptophan/chemistry
2.
Drug Metab Dispos ; 47(6): 567-573, 2019 06.
Article in English | MEDLINE | ID: mdl-30952677

ABSTRACT

Rolapitant [(Varubi), 5S,8S)-8-[[(1R)-1-[3,5 bis(trifluoromethyl phenyl]ethoxy]methyl]-8-phenyl-1,7-diazaspiro[4.5]decan-2-one] is a high-affinity NK1 receptor antagonist that was approved in September 2015 as a treatment for nausea and vomiting caused by chemotherapy. In vivo rolapitant moderately inhibits CYP2D6 for at least 7 days after one 180 mg dose. Due to the long inhibition time, we investigated rolapitant as a possible mechanism-based inactivator of CYP2D6. Rolapitant docked in the active site of CYP2D6 and displayed type I binding to CYP2D6 with a K s value of 1.2 ± 0.4 µM. However, in NADPH-, time-, and concentration-dependent assays of CYP2D6 activity, no evidence for mechanism-based inactivation and no metabolites of rolapitant were observed. Stopped-flow binding studies yielded a kon /koff (K d) value of 6.2 µM. The IC50 value for rolapitant inhibition of CYP2D6 activity was 24 µM, suggesting that inhibition is not due to tight binding of rolapitant to CYP2D6. By Lineweaver-Burk analysis, rolapitant behaved as a mixed, reversible inhibitor. The K i values of 20 and 34 µM were determined by Dixon analysis, with bufuralol and dextromethorphan as reporter substrates, respectively, and drug-drug interaction modeling did not predict the reported in vivo inhibition. The interaction of rolapitant with CYP2D6 was also examined in 1 microsecond molecular dynamics simulations. Rolapitant adopted multiple low-energy binding conformations near the active site, but at distances not consistent with metabolism. Given these findings, we do not see evidence that rolapitant is a mechanism-based inactivator. Moreover, the reversible inhibition of CYP2D6 by rolapitant may not fully account for the moderate inhibition described in vivo.


Subject(s)
Cytochrome P-450 CYP2D6 Inhibitors/therapeutic use , Cytochrome P-450 CYP2D6/metabolism , Spiro Compounds/therapeutic use , Catalytic Domain/physiology , Dextromethorphan/therapeutic use , Drug Interactions/physiology , Ethanolamines/therapeutic use , Humans
3.
Nature ; 469(7331): 539-42, 2011 Jan 27.
Article in English | MEDLINE | ID: mdl-21248752

ABSTRACT

The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of ∼3,500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (also known as KDM6A), JARID1C (also known as KDM5C) and SETD2 (ref. 2). These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control. However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodelling complex gene PBRM1 (ref. 4) as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology.


Subject(s)
Carcinoma, Renal Cell/genetics , Kidney Neoplasms/genetics , Mutation/genetics , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Animals , Cell Line, Tumor , DNA-Binding Proteins , Disease Models, Animal , Gene Expression Regulation , Gene Knockdown Techniques , Humans , Mice , Pancreatic Neoplasms/genetics
4.
Nature ; 463(7279): 360-3, 2010 Jan 21.
Article in English | MEDLINE | ID: mdl-20054297

ABSTRACT

Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.


Subject(s)
Carcinoma, Renal Cell/genetics , Genes, Neurofibromatosis 2 , Histone-Lysine N-Methyltransferase/genetics , Histones/metabolism , Kidney Neoplasms/genetics , Nuclear Proteins/genetics , Oxidoreductases, N-Demethylating/genetics , Carcinoma, Renal Cell/pathology , Cell Hypoxia/genetics , Chromatin/metabolism , Gene Expression Regulation, Neoplastic , Histone Demethylases , Humans , Kidney Neoplasms/pathology , Mutation/genetics , Sequence Analysis, DNA
5.
Kidney Int ; 88(5): 1057-69, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26083655

ABSTRACT

The study of kidney cancer pathogenesis and its treatment has been limited by the scarcity of genetically defined animal models. The FLCN gene that codes for the protein folliculin, mutated in Birt-Hogg-Dubé syndrome, presents a new target for mouse modeling of kidney cancer. Here we developed a kidney-specific knockout model by disrupting the mouse Flcn in the proximal tubules, thus avoiding homozygous embryonic lethality or neonatal mortality, and eliminating the requirement of loss of heterozygosity for tumorigenesis. This knockout develops renal cysts and early onset (6 months) of multiple histological subtypes of renal neoplasms featuring high tumor penetrance. Although the majority of the tumors were chromophobe renal cell carcinomas in affected mice under 1 year of age, papillary renal cell carcinomas predominated in the kidneys of older knockout mice. This renal neoplasia from cystic hyperplasia at 4 months to high-grade renal tumors by 16 months represented the progression of tumorigenesis. The mTOR and TGF-ß signalings were upregulated in Flcn-deficient tumors, and these two activated pathways may synergetically cause renal tumorigenesis. Treatment of knockout mice with the mTOR inhibitor rapamycin for 10 months led to the suppression of tumor growth. Thus, our model recapitulates human Birt-Hogg-Dubé kidney tumorigenesis, provides a valuable tool for further study of Flcn-deficient renal tumorigenesis, and tests new drugs/approaches to their treatment.


Subject(s)
Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/pathology , Cysts/pathology , Disease Models, Animal , Kidney Neoplasms/genetics , Kidney Neoplasms/pathology , Kidney Tubules, Proximal/pathology , Proto-Oncogene Proteins/genetics , Tumor Suppressor Proteins/genetics , Animals , Antibiotics, Antineoplastic/therapeutic use , Carcinogenesis/genetics , Carcinoma, Renal Cell/drug therapy , Carcinoma, Renal Cell/metabolism , Cysts/genetics , Hyperplasia/pathology , Kidney Neoplasms/drug therapy , Kidney Neoplasms/metabolism , Mice , Mice, Knockout , Signal Transduction , Sirolimus/therapeutic use , TOR Serine-Threonine Kinases/antagonists & inhibitors , TOR Serine-Threonine Kinases/metabolism , Transforming Growth Factor beta/metabolism
6.
Proc Natl Acad Sci U S A ; 108(4): 1439-44, 2011 Jan 25.
Article in English | MEDLINE | ID: mdl-21220347

ABSTRACT

The receptor tyrosine kinase MET is frequently amplified in human tumors, resulting in high cell surface densities and constitutive activation even in the absence of growth factor stimulation by its endogenous ligand, hepatocyte growth factor (HGF). We sought to identify mechanisms of signaling crosstalk that promote MET activation by searching for kinases that are coordinately dysregulated with wild-type MET in human tumors. Our bioinformatic analysis identified leucine-rich repeat kinase-2 (LRRK2), which is amplified and overexpressed in papillary renal and thyroid carcinomas. Down-regulation of LRRK2 in cultured tumor cells compromises MET activation and selectively reduces downstream MET signaling to mTOR and STAT3. Loss of these critical mitogenic pathways induces cell cycle arrest and cell death due to loss of ATP production, indicating that MET and LRRK2 cooperate to promote efficient tumor cell growth and survival in these cancers.


Subject(s)
Protein Serine-Threonine Kinases/genetics , Proto-Oncogene Proteins c-met/genetics , Receptors, Growth Factor/genetics , Signal Transduction , Adenosine Triphosphate/metabolism , Carcinoma, Papillary/genetics , Carcinoma, Papillary/metabolism , Carcinoma, Papillary/pathology , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/metabolism , Carcinoma, Renal Cell/pathology , Cell Cycle , Cell Line, Tumor , Cell Proliferation , Cell Survival , Gene Amplification , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Immunoblotting , Immunohistochemistry , In Situ Hybridization, Fluorescence , Kidney Neoplasms/genetics , Kidney Neoplasms/metabolism , Kidney Neoplasms/pathology , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 , Protein Serine-Threonine Kinases/metabolism , Proto-Oncogene Proteins c-met/metabolism , RNA Interference , Receptors, Growth Factor/metabolism , Thyroid Neoplasms/genetics , Thyroid Neoplasms/metabolism , Thyroid Neoplasms/pathology
7.
Pediatr Res ; 73(4 Pt 1): 450-6, 2013 Apr.
Article in English | MEDLINE | ID: mdl-23269123

ABSTRACT

BACKGROUND: Gene expression in archived newborn blood spots remaining from newborn screening may reflect pathophysiological disturbances useful in understanding the etiology of cerebral palsy (CP). METHODS: We quantified the expression of gene sets representing four physiological pathways hypothesized to contribute to CP in archived unfrozen residual newborn blood spot specimens from 53 children with CP and 53 age-, gender-, and gestational age-matched controls. We selected four empirical and three canonical gene sets representing the inflammatory, hypoxic, coagulative, and thyroidal pathways and examined mRNA expression using an 8 × 60,000 oligonucleotide microarray. The log2 fold change of gene expression between matched cases and controls was analyzed using the generally applicable gene set enrichment method. RESULTS: The empirical inflammatory and empirical hypoxic gene sets were significantly downregulated in term-born CP cases (n = 33) as compared with matched controls (P = 0.0007 and 0.0009, respectively), whereas both gene sets were significantly upregulated (P =0.0055 and 0.0223, respectively) in preterm-born CP cases (n = 20). The empirical thyroidal gene set was significantly upregulated in preterm-born CP cases (P = 0.0023). CONCLUSION: The newborn blood spot transcriptome can serve as a platform for investigating distinctive gene expression patterns in children who later develop CP.


Subject(s)
Cerebral Palsy/genetics , Dried Blood Spot Testing , Gene Expression Profiling , Genetic Testing , Neonatal Screening/methods , Adolescent , Case-Control Studies , Cerebral Palsy/blood , Cerebral Palsy/diagnosis , Child , Child, Preschool , Female , Gene Regulatory Networks , Genetic Markers , Genetic Predisposition to Disease , Gestational Age , Humans , Infant, Newborn , Male , Phenotype , Polymerase Chain Reaction , Predictive Value of Tests , Reproducibility of Results
8.
Am J Pathol ; 178(2): 853-60, 2011 Feb.
Article in English | MEDLINE | ID: mdl-21281817

ABSTRACT

Molecular pathways associated with pathogenesis of sporadic papillary renal cell carcinoma (PRCC), the second most common form of kidney cancer, are poorly understood. We analyzed primary tumor specimens from 35 PRCC patients treated by nephrectomy via gene expression analysis and tissue microarrays constructed from an additional 57 paraffin-embedded PRCC samples via immunohistochemistry. Gene products were validated and further studied by Western blot analyses using primary PRCC tumor samples and established renal cell carcinoma cell lines, and potential associations with pathologic variables and survival in 27 patients with follow-up information were determined. We show that the expression of E2-EPF ubiquitin carrier protein, which targets the principal negative regulator of hypoxia-inducible factor (HIF), von Hippel-Lindau protein, for proteasome-dependent degradation, is markedly elevated in the majority of PRCC tumors exhibiting increased HIF1α expression, and is associated with poor prognosis. In addition, we identified multiple hypoxia-responsive elements within the E2-EPF promoter, and for the first time we demonstrated that E2-EPF is a hypoxia-inducible gene directly regulated via HIF1. These findings reveal deregulation of the oxygen-sensing pathway impinging on the positive feedback mechanism of HIF1-mediated regulation of E2-EPF in PRCC.


Subject(s)
Ubiquitin-Conjugating Enzymes/metabolism , Base Sequence , Carcinoma, Renal Cell/diagnosis , Carcinoma, Renal Cell/enzymology , Carcinoma, Renal Cell/pathology , Cell Hypoxia , Disease Progression , Female , HEK293 Cells , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Male , Molecular Sequence Data , Mutation/genetics , Prognosis , Response Elements/genetics , Von Hippel-Lindau Tumor Suppressor Protein/genetics
9.
Curr Oncol Rep ; 14(3): 240-8, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22535504

ABSTRACT

Renal cell carcinoma (RCC) is the most common type of renal cancer in adults. RCC is notoriously resistant to current therapies suggesting the need to improve our knowledge and create more effective therapies. The molecular genetic defects that occur in RCC are extensive and complex ranging from single DNA changes, to large chromosomal defects, to signature disruptions in the transcription of hundreds of genes. These changes are often shared within each histological RCC subtype, illustrating their significance to the disease phenotype. This review presents an overview of the genetic abnormalities that occur within the most common subtypes of RCC. We discuss the recent molecular findings that have advanced our understanding of the somatic architecture of renal tumors and their impact on disease therapeutics.


Subject(s)
Carcinoma, Renal Cell/genetics , Kidney Neoplasms/genetics , Mutation/genetics , Carcinoma, Renal Cell/pathology , Carcinoma, Renal Cell/therapy , Cytogenetic Analysis , Gene Expression Profiling , Humans , Kidney Neoplasms/pathology , Kidney Neoplasms/therapy , Transcriptome
10.
Proc Natl Acad Sci U S A ; 106(31): 12909-14, 2009 Aug 04.
Article in English | MEDLINE | ID: mdl-19567831

ABSTRACT

Understanding the signaling pathways that drive aggressive breast cancers is critical to the development of effective therapeutics. The oncogene MET is associated with decreased survival in breast cancer, yet the role that MET plays in the various breast cancer subtypes is unclear. We describe a knockin mouse with mutationally activated Met (Met(mut)) that develops a high incidence of diverse mammary tumors with basal characteristics, including metaplasia, absence of progesterone receptor and ERBB2 expression, and expression of cytokeratin 5. With gene expression and tissue microarray analysis, we show that high MET expression in human breast cancers significantly correlated with estrogen receptor negative/ERBB2 negative tumors and with basal breast cancers. Few treatment options exist for breast cancers of the basal or trastuzumab-resistant ERBB2 subtypes. We conclude from these studies that MET may play a critical role in the development of the most aggressive breast cancers and may be a rational therapeutic target.


Subject(s)
Breast Neoplasms/etiology , Mammary Neoplasms, Experimental/etiology , Proto-Oncogene Proteins c-met/physiology , Adenocarcinoma/etiology , Adenocarcinoma/genetics , Animals , Breast Neoplasms/genetics , Female , Gene Amplification , Humans , Immunohistochemistry , Mammary Neoplasms, Experimental/genetics , Mice , Mice, Inbred C57BL , Proto-Oncogene Proteins c-met/genetics , Receptor, ErbB-2/analysis , Receptors, Progesterone/analysis , Signal Transduction
11.
Int J Mol Sci ; 13(8): 9599-9608, 2012.
Article in English | MEDLINE | ID: mdl-22949818

ABSTRACT

Screening newborns for treatable serious conditions is mandated in all US states and many other countries. After screening, Guthrie cards with residual blood (whole spots or portions of spots) are typically stored at ambient temperature in many facilities. The potential of archived dried blood spots (DBS) for at-birth molecular studies in epidemiological and clinical research is substantial. However, it is also challenging as analytes from DBS may be degraded due to preparation and storage conditions. We previously reported an improved assay for obtaining global RNA gene expression from blood spots. Here, we evaluated sex-specific gene expression and its preservation in DBS using oligonucleotide microarray technology. We found X inactivation-specific transcript (XIST), lysine-specific demethylase 5D (KDM5D) (also known as selected cDNA on Y, homolog of mouse (SMCY)), uncharacterized LOC729444 (LOC729444), and testis-specific transcript, Y-linked 21 (TTTY21) to be differentially-expressed by sex of the newborn. Our finding that trait-specific RNA gene expression is preserved in unfrozen DBS, demonstrates the technical feasibility of performing molecular genetic profiling using such samples. With millions of DBS potentially available for research, we see new opportunities in using newborn molecular gene expression to better understand molecular pathogenesis of perinatal diseases.


Subject(s)
Biomarkers/analysis , Blood Specimen Collection , Cerebral Palsy/genetics , Gene Expression Profiling , Neonatal Screening , Adolescent , Animals , Case-Control Studies , Cerebral Palsy/blood , Cerebral Palsy/diagnosis , Child , Child, Preschool , Female , Histone Demethylases/genetics , Humans , Infant, Newborn , Male , Mice , Minor Histocompatibility Antigens , Oligonucleotide Array Sequence Analysis , RNA, Long Noncoding/genetics , Real-Time Polymerase Chain Reaction
12.
Chin J Cancer ; 31(9): 413-20, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22776233

ABSTRACT

Biallelic inactivation of fumarate hydratase(FH) causes type 2 papillary renal cell carcinoma (PRCC2), uterine fibroids, and cutaneous leimyomas, a condition known as hereditary leiomyomatosis and renal cell cancer(HLRCC). The most direct effect of FH inactivation is intracellular fumarate accumulation. A majority of studies on FH inactivation over the past decade have focused on the theory that intracellular fumarate stabilizes hypoxia-inducible factor 1α(HIF1A) through competitive inhibition of HIF prolyl hydroxylases. Recently, a competing theory that intracellular fumarate activates nuclear factor (erythroid-derived 2)-like 2(NRF2) through post-translational modification of its negative regulator. Kelch-like ECH-associated protein 1(KEAP1) has emerged from a computational modeling study and mouse model studies. This review dissects the origin of these two governing theories and highlights the presence of chromatin-structure-regulated targets of transcription factors, which we refer to as "cryptic targets" of transcription factors. One such cryptic target is heme oxygenase I(HMOX1), the expression of which is known to be modulated by the gene product of SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as BRG1).


Subject(s)
Fumarate Hydratase/genetics , Hypoxia-Inducible Factor 1, alpha Subunit , Kidney Neoplasms/metabolism , Leiomyomatosis/metabolism , NF-E2-Related Factor 2 , Neoplastic Syndromes, Hereditary/metabolism , Animals , DNA Helicases/metabolism , Fumarate Hydratase/metabolism , Fumarates/metabolism , Heme Oxygenase-1/metabolism , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Kelch-Like ECH-Associated Protein 1 , Kidney Neoplasms/genetics , Leiomyomatosis/genetics , NF-E2-Related Factor 2/genetics , NF-E2-Related Factor 2/metabolism , Neoplastic Syndromes, Hereditary/genetics , Nuclear Proteins/metabolism , Procollagen-Proline Dioxygenase/metabolism , Protein Processing, Post-Translational , Skin Neoplasms , Transcription Factors/metabolism , Uterine Neoplasms
13.
Breast Cancer Res Treat ; 129(2): 319-29, 2011 Sep.
Article in English | MEDLINE | ID: mdl-20945089

ABSTRACT

Phyllodes tumors of the breast are rare fibroepithelial neoplasms with a potential for recurrence. Current histological classification is not always predictive of clinical behavior. The aim of this study was to identify genetic changes associated with the development of borderline and malignant phyllodes tumors in an Asian population, and to assess if genetic data supported the categorization of these tumors into the existing three grades of benign, borderline, and malignant. Expression profiling of 21 phyllodes tumors (6 benign, 10 borderline, 5 malignant) was performed using Affymetrix U133Plus 2.0 GeneChips(®). Gene expression among benign, borderline, and malignant tumors was compared and a 29 gene list was able to classify them according to their histologic grade. Among these 29 genes are those responsible for matrix formation, cell adhesion, epidermis formation, and cell proliferation. Comparative genomic microarray analysis showed that the most common chromosomal alteration associated with borderline and malignant tumors was 1q gain, and an increasing number of chromosomal changes was noted with increasing histological grade. Upregulation of HOXB13 was seen in malignant relative to borderline phyllodes tumors and further investigated by immunohistochemistry in a corresponding set of formalin-fixed, paraffin-embedded tumors. HOXB13 protein overexpression was found to be correlated with stromal hypercellularity and atypia (P = 0.03, P = 0.039, respectively) and may be implicated in the development of malignant phyllodes tumors.


Subject(s)
Breast Neoplasms/genetics , Phyllodes Tumor/genetics , Adult , Aged , Asian People/genetics , Breast Neoplasms/chemistry , Breast Neoplasms/classification , Breast Neoplasms/ethnology , Breast Neoplasms/mortality , Breast Neoplasms/pathology , Chi-Square Distribution , Comparative Genomic Hybridization , Disease Progression , Female , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Homeodomain Proteins/analysis , Homeodomain Proteins/genetics , Humans , Immunohistochemistry , Middle Aged , Neoplasm Grading , Oligonucleotide Array Sequence Analysis , Phyllodes Tumor/chemistry , Phyllodes Tumor/classification , Phyllodes Tumor/ethnology , Phyllodes Tumor/mortality , Phyllodes Tumor/pathology , Prognosis , Singapore/epidemiology , Survival Rate , Time Factors
14.
PLoS Genet ; 4(9): e1000176, 2008 Sep 05.
Article in English | MEDLINE | ID: mdl-18773095

ABSTRACT

Chromosomal abnormalities, such as structural and numerical abnormalities, are a common occurrence in cancer. The close association of homologous chromosomes during interphase, a phenomenon termed somatic chromosome pairing, has been observed in cancerous cells, but the functional consequences of somatic pairing have not been established. Gene expression profiling studies revealed that somatic pairing of chromosome 19 is a recurrent chromosomal abnormality in renal oncocytoma, a neoplasia of the adult kidney. Somatic pairing was associated with significant disruption of gene expression within the paired regions and resulted in the deregulation of the prolyl-hydroxylase EGLN2 [corrected] a key protein that regulates the oxygen-dependent degradation of hypoxia-inducible factor (HIF). Overexpression of EGLN2 [corrected] in renal oncocytoma increased ubiquitin-mediated destruction of HIF and concomitantly suppressed the expression of several HIF-target genes, including the pro-death BNIP3L gene. The transcriptional changes that are associated with somatic pairing of chromosome 19 mimic the transcriptional changes that occur following DNA amplification. Therefore, in addition to numerical and structural chromosomal abnormalities, alterations in chromosomal spatial dynamics should be considered as genomic events that are associated with tumorigenesis. The identification of EGLN2 as a significantly deregulated gene that maps within the paired chromosome region directly implicates defects in the oxygen-sensing network to the biology of renal oncocytoma.


Subject(s)
Adenoma, Oxyphilic/genetics , Adenoma, Oxyphilic/metabolism , Chromosome Pairing/genetics , Chromosomes, Human, Pair 19 , Dioxygenases/genetics , Kidney Neoplasms/genetics , Kidney Neoplasms/metabolism , Nuclear Proteins/genetics , Oxygen/metabolism , Procollagen-Proline Dioxygenase/genetics , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/metabolism , Cell Hypoxia/genetics , Cell Line, Tumor , Chromosomes, Human, Pair 19/metabolism , Dioxygenases/metabolism , Down-Regulation , Gene Expression Profiling , Humans , Hypoxia-Inducible Factor 1/genetics , Hypoxia-Inducible Factor 1/metabolism , Hypoxia-Inducible Factor-Proline Dioxygenases , Nuclear Proteins/metabolism , Procollagen-Proline Dioxygenase/metabolism
15.
Lancet Oncol ; 11(6): 571-8, 2010 Jun.
Article in English | MEDLINE | ID: mdl-20381423

ABSTRACT

Renal-cell carcinoma is a heterogeneous group of tumours that arise in the adult kidneys. Irrespective of the type of renal tumour, traditional chemotherapeutic and radiation-based therapies have been largely ineffective at treating advanced tumours, with long-term survival being very low. Molecularly-targeted inhibitors of protein kinases are effective in delaying progression of advanced renal tumours. These therapies revolve around inhibition of the vascular endothelial growth factor receptor tyrosine kinase and the mammalian target of rapamycin serine or threonine kinase signalling pathways. The genetic complexity of renal tumours revealed by gene-expression profiling and other molecular-genetic technologies indicate that inhibition of additional kinase-associated pathways could also prevent renal tumour growth. In this review, we discuss the use of molecularly-targeted kinase inhibitors in the treatment of renal-cell carcinoma and identify the next generation of kinase inhibitors that show promise for treatment.


Subject(s)
Carcinoma, Renal Cell/drug therapy , Kidney Neoplasms/drug therapy , Protein Kinase Inhibitors/therapeutic use , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/metabolism , Cell Cycle Proteins/metabolism , Enzyme Activation , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Kidney Neoplasms/genetics , Kidney Neoplasms/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Protein Kinases/metabolism , Protein Serine-Threonine Kinases/metabolism , Receptor Protein-Tyrosine Kinases/metabolism , Receptors, Vascular Endothelial Growth Factor/metabolism , Signal Transduction , TOR Serine-Threonine Kinases , Vascular Endothelial Growth Factor A/metabolism
16.
BMC Cancer ; 10: 196, 2010 May 12.
Article in English | MEDLINE | ID: mdl-20462447

ABSTRACT

BACKGROUND: Chromophobe renal cell carcinoma (chRCC) and renal oncocytoma are two distinct but closely related entities with strong morphologic and genetic similarities. While chRCC is a malignant tumor, oncocytoma is usually regarded as a benign entity. The overlapping characteristics are best explained by a common cellular origin, and the biologic differences between chRCC and oncocytoma are therefore of considerable interest in terms of carcinogenesis, diagnosis and clinical management. Previous studies have been relatively limited in terms of examining the differences between oncocytoma and chromophobe RCC. METHODS: Gene expression profiling using the Affymetrix HGU133Plus2 platform was applied on chRCC (n = 15) and oncocytoma specimens (n = 15). Supervised analysis was applied to identify a discriminatory gene signature, as well as differentially expressed genes. High throughput single-nucleotide polymorphism (SNP) genotyping was performed on independent samples (n = 14) using Affymetrix GeneChip Mapping 100 K arrays to assess correlation between expression and gene copy number. Immunohistochemical validation was performed in an independent set of tumors. RESULTS: A novel 14 probe-set signature was developed to classify the tumors internally with 93% accuracy, and this was successfully validated on an external data-set with 94% accuracy. Pathway analysis highlighted clinically relevant dysregulated pathways of c-erbB2 and mammalian target of rapamycin (mTOR) signaling in chRCC, but no significant differences in p-AKT or extracellular HER2 expression was identified on immunohistochemistry. Loss of chromosome 1p, reflected in both cytogenetic and expression analysis, is common to both entities, implying this may be an early event in histogenesis. Multiple regional areas of cytogenetic alterations and corresponding expression biases differentiating the two entities were identified. Parafibromin, aquaporin 6, and synaptogyrin 3 were novel immunohistochemical markers effectively discriminating the two pathologic entities. CONCLUSIONS: Gene expression profiles, high-throughput SNP genotyping, and pathway analysis effectively distinguish chRCC from oncocytoma. We have generated a novel transcript predictor that is able to discriminate between the two entities accurately, and which has been validated both in an internal and an independent data-set, implying generalizability. A cytogenetic alteration, loss of chromosome 1p, common to renal oncocytoma and chRCC has been identified, providing the opportunities for identifying novel tumor suppressor genes and we have identified a series of immunohistochemical markers that are clinically useful in discriminating chRCC and oncocytoma.


Subject(s)
Adenoma, Oxyphilic/genetics , Biomarkers, Tumor/genetics , Carcinoma, Renal Cell/genetics , Chromosomes, Human, Pair 1 , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Genetic Testing/methods , Kidney Neoplasms/genetics , Polymorphism, Single Nucleotide , Adenoma, Oxyphilic/chemistry , Adenoma, Oxyphilic/diagnosis , Aquaporin 6/analysis , Biomarkers, Tumor/analysis , Carcinoma, Renal Cell/chemistry , Carcinoma, Renal Cell/diagnosis , Cytogenetic Analysis , Diagnosis, Differential , Gene Dosage , Gene Regulatory Networks , Humans , Immunohistochemistry , Kidney Neoplasms/chemistry , Kidney Neoplasms/diagnosis , Membrane Proteins/analysis , Nerve Tissue Proteins/analysis , Odds Ratio , Oligonucleotide Array Sequence Analysis , Predictive Value of Tests , Reproducibility of Results , Synaptogyrins , Tumor Suppressor Proteins/analysis
17.
BJU Int ; 106(1): 62-5, 2010 Jul.
Article in English | MEDLINE | ID: mdl-20002663

ABSTRACT

STUDY TYPE: Aetiology (case series) Level of Evidence 4. OBJECTIVE: To present the molecular rationale and potential clinical benefit of topoisomerase II (TopoII)-inhibiting therapy for renal medullary carcinoma (RMC), a rare but extremely lethal form of kidney cancer that classically afflicts young men with sickle-cell trait. The current therapeutic approach with these aggressive tumours is radical nephrectomy followed by systemic chemotherapy, but the prognosis remains dismal. MATERIALS AND METHODS: The whole-genome expression was analysed in four RMC tumours. We also report a case of metastatic RMC in which a complete response was achieved for 9 months using a TopoII-inhibiting therapy. RESULTS: Expanded whole-genome expression analysis showed increases of TopoII in all cases. There was also overall deregulation of DNA remodelling and repair, and an ontological association between RMC and urothelial carcinoma. Using a TopoII-inhibiting agent, there was a complete response for 9 months in a patient with metastatic RMC. CONCLUSION: This report provides molecular evidence for the rational use of TopoII inhibitors in the treatment of RMC.


Subject(s)
Anemia, Sickle Cell/complications , Carcinoma, Medullary/therapy , Carcinoma, Renal Cell/therapy , DNA-Binding Proteins/antagonists & inhibitors , Enzyme Inhibitors/therapeutic use , Kidney Neoplasms/therapy , Topoisomerase II Inhibitors , Adult , Antigens, Neoplasm/metabolism , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Carcinoma, Medullary/enzymology , Carcinoma, Medullary/genetics , Carcinoma, Renal Cell/genetics , Combined Modality Therapy , DNA Topoisomerases, Type II/metabolism , DNA-Binding Proteins/metabolism , Humans , Immunohistochemistry , Kidney Neoplasms/enzymology , Kidney Neoplasms/genetics , Male , Nephrectomy , Prognosis , Treatment Outcome , Young Adult
18.
Int J Oncol ; 35(1): 109-14, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19513557

ABSTRACT

Although the functions of most of the identified microRNAs (miRNAs) have yet to be determined, their use as potential biomarkers has been considered in several human diseases and cancers. In order to understand their role in renal tumorigenesis, we screened the expression levels of miRNAs in four subtypes of human renal neoplasms: clear cell, papillary, and chromophobe renal cell carcinomas (RCC) as well as benign renal oncocytomas. We found a unique miRNA signature for each subtype of renal tumor. Furthermore, we identified unique patterns of miRNA expression distinguishing clear cell RCC cases with favorable vs. unfavorable outcome. Specifically, we documented the overexpression of miRs 424 and 203 in clear cell RCC relative to papillary RCC, as well as the inversion of expression of miR-203 in the benign oncocytomas (where it is underexpressed relative to normal kidney) as compared to the malignant chromophobe RCC (where it is overexpressed relative to normal kidney). Our results further suggest that overexpression of S-has-miR-32 is associated with poor outcome. While previous studies have identified unique miRNA expression pattern distinguishing tumors from different anatomical locations, here we extend this principle to demonstrate the utility of miRNA expression profiling to identify a signature unique to various tumor subtypes at a single anatomic locus.


Subject(s)
Adenoma, Oxyphilic/genetics , Carcinoma, Renal Cell/genetics , Gene Expression Profiling/methods , Kidney Neoplasms/genetics , MicroRNAs/analysis , Adenoma, Oxyphilic/pathology , Carcinoma, Renal Cell/pathology , Cluster Analysis , Gene Expression Regulation, Neoplastic , Humans , Kidney Neoplasms/pathology , Prognosis
19.
Cancer Res ; 67(7): 3171-6, 2007 Apr 01.
Article in English | MEDLINE | ID: mdl-17409424

ABSTRACT

Papillary renal cell carcinoma (RCC) represents 10% to 15% of adult renal neoplasms; however, the molecular genetic events that are associated with the development and progression of sporadic papillary RCC remain largely unclear. Papillary RCCs can be divided into two subtypes based on histologic, cytogenetic, and gene expression differences. Type 1 tumors ( approximately 60-70%) are generally low grade with favorable outcome, whereas type 2 tumors ( approximately 30-40%) are associated with increased cytogenetic complexity, high tumor grade, and poor prognosis. In this study, computational analysis of gene expression data derived from papillary RCC revealed that a transcriptional signature indicative of MYC pathway activation is present in high-grade type 2 papillary RCC. The MYC signature is associated with amplification of chromosome 8q and overexpression of MYC that maps to chromosome 8q24. The importance of MYC activation was confirmed by both pharmacologic and short interfering RNA-mediated inhibition of active Myc signaling in a cell line model of type 2 papillary RCC. These results provide both computational and genetic evidence that activation of Myc is associated with the aggressiveness of papillary type 2 RCC. Therefore, it will be useful to consider inhibition of components of the MYC signaling pathway as avenues for therapeutic intervention in high-grade papillary RCC.


Subject(s)
Carcinoma, Papillary/genetics , Carcinoma, Renal Cell/genetics , Gene Expression Regulation, Neoplastic , Genes, myc , Kidney Neoplasms/genetics , Carcinoma, Papillary/metabolism , Carcinoma, Papillary/pathology , Carcinoma, Renal Cell/metabolism , Carcinoma, Renal Cell/pathology , Cell Growth Processes/physiology , Cell Line, Tumor , Chromosomes, Human, Pair 8/genetics , Gene Dosage , Humans , Kidney Neoplasms/metabolism , Kidney Neoplasms/pathology , Proto-Oncogene Proteins c-myc/biosynthesis , Proto-Oncogene Proteins c-myc/genetics , Signal Transduction
20.
Mol Cancer Ther ; 7(3): 648-58, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18319331

ABSTRACT

We hypothesized that signaling through multiple mitogen-activated protein kinase (MAPK) kinase (MKK) pathways is essential for the growth and vascularization of soft-tissue sarcomas, which are malignant tumors derived from mesenchymal tissues. We tested this using HT-1080, NCI, and Shac fibrosarcoma-derived cell lines and anthrax lethal toxin (LeTx), a bacterial toxin that inactivates MKKs. Western blots confirmed that LeTx treatment reduced the levels of phosphorylated extracellular signal-regulated kinase and p38 MAPK in vitro. Although short treatments with LeTx only modestly affected cell proliferation, sustained treatment markedly reduced cell numbers. LeTx also substantially inhibited the extracellular release of angioproliferative factors including vascular endothelial growth factor, interleukin-8, and basic fibroblast growth factor. Similar results were obtained with cell lines derived from malignant fibrous histiocytomas, leiomyosarcomas, and liposarcomas. In vivo, LeTx decreased MAPK activity and blocked fibrosarcoma growth. Growth inhibition correlated with decreased cellular proliferation and extensive necrosis, and it was accompanied by a decrease in tumor mean vessel density as well as a reduction in serum expression of angioproliferative cytokines. Vital imaging using high-resolution ultrasound enhanced with contrast microbubbles revealed that the effects of LeTx on tumor perfusion were remarkably rapid (<24 h) and resulted in a marked reduction of perfusion within the tumor but not in nontumor tissues. These results are consistent with our initial hypothesis and lead us to propose that MKK inhibition by LeTx is a broadly effective strategy for targeting neovascularization in fibrosarcomas and other similar proliferative lesions.


Subject(s)
Cell Division , Fibrosarcoma/blood supply , Mitogen-Activated Protein Kinases/metabolism , Neovascularization, Pathologic , Signal Transduction , Antigens, Bacterial/pharmacology , Bacterial Toxins/pharmacology , Cell Cycle , Cell Line, Tumor , Cell Proliferation , Fibrosarcoma/pathology , Humans
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