Human retinoblastoma susceptibility gene: genomic organization and analysis of heterozygous intragenic deletion mutants

The mouse double minute 2 309T>G polymorphism and retinoblastoma risk: A meta-analysis

PURPOSE

Mouse double minute 2 (MDM2) homolog is a protein that in humans is encoded by the MDM2 gene. It is expressed in retinoblastoma (Rb) cells and acts as a key negative regulator of the p53 tumor suppressor gene. Several studies have investigated the association of Rb with MDM2 309T>G polymorphism, but the results were conflicting. To derive a more precise estimation of the association, we performed a meta-analysis of the relationship between MDM2 309T>G polymorphism with Rb in all published studies.

METHODS

Published literature from PubMed and other databases were retrieved. All the reported studies evaluating the association between MDM2 309T>G polymorphism and Rb risk were included. The pooled odds ratio (OR) and 95% confidence interval (CI) were calculated using the fixed-effect model. A total of four case-control studies, including 520 cases and 745 controls were included.

RESULTS

This meta-analysis found that MDM2 309T>G polymorphism was significantly associated with Rb risk in the dominant model, TG+GG versus TT (OR = 1.43, 95% CI = 1.11-1.84, P = 0.006).

CONCLUSION

The present meta-analysis suggested that MDM2 309T>G polymorphism has a significant association with increased Rb risk.

Histone deacetylase inhibitors differentially regulate c-Myc expression in retinoblastoma cells

Retinoblastoma (RB) is the most prevalent childhood intraocular cancer type. Previous studies have demonstrated that c-myc (a proto-oncogene) is associated with tumorigenesis. However, at present, the influence of the expression profile and bioactivity of c-Myc on RB occurrence and progression is yet to be characterised. Notably, the present study demonstrated that c-myc is downregulated in the RB cell line WERI-Rb1. However, treatment with the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) was revealed to significantly upregulate the expression of c-Myc mRNA and protein in WERI-Rb1 cells. Moreover, TSA increased the activity of the c-myc promoter in WERI-Rb1 cells, and the expression of c-Myc was also regulated by other HDAC inhibitors, including vorinostat (SAHA), valproic acid sodium salt (VPA) and entinostat. Notably, although c-myc was silenced in the Y79 cell line, the HDAC inhibitor TSA did not induce upregulation of mRNA and protein in Y79 cells. By contrast, certain HDAC inhibitors (TSA, VPA and SAHA) were discovered to significantly decrease the activity of the c-myc promoter in Y79 cells. Furthermore, the current data indicated that exogenous c-myc expression has a mild inhibitory effect on WERI-Rb1 and Y79 cell viability. Therefore, the present study revealed novel insights into the expression mechanism and bioactivity of c-Myc in RB cells.

Molecular Diagnostics in Clinical Oncology

There are multiple applications of molecular tests in clinical oncology. Mutation analysis is now routinely utilized for the diagnosis of hereditary cancer syndromes. Healthy carriers of cancer-predisposing mutations benefit from tight medical surveillance and various preventive interventions. Cancers caused by germ-line mutations often require significant modification of the treatment strategy. Personalized selection of cancer drugs based on the presence of actionable mutations has become an integral part of cancer therapy. Molecular tests underlie the administration of EGFR, BRAF, ALK, ROS1, PARP inhibitors as well as the use of some other cytotoxic and targeted drugs. Tumors almost always shed their fragments (single cells or their clusters, DNA, RNA, proteins) into various body fluids. So-called liquid biopsy, i.e., the analysis of circulating DNA or some other tumor-derived molecules, holds a great promise for non-invasive monitoring of cancer disease, analysis of drug-sensitizing mutations and early cancer detection. Some tumor- or tissue-specific mutations and expression markers can be efficiently utilized for the diagnosis of cancers of unknown primary origin (CUPs). Systematic cataloging of tumor molecular portraits is likely to uncover a multitude of novel medically relevant DNA- and RNA-based markers.

Genome-wide analysis of pancreatic cancer using microarray-based techniques

BACKGROUND/AIMS

Microarray-based comparative genomic hybridisation (CGH) has allowed high-resolution analysis of DNA copy number alterations across the entire cancer genome. Recent advances in bioinformatics tools enable us to perform a robust and highly sensitive analysis of array CGH data and facilitate the discovery of novel cancer-related genes.

METHODS

We analysed a total of 29 pancreatic ductal adenocarcinoma (PDAC) samples (6 cell lines and 23 microdissected tissue specimens) using 1-Mb-spaced CGH arrays. The transcript levels of all genes within the identified regions of genetic alterations were then screened using our Pancreatic Expression Database.

RESULTS

In addition to 238 high-level amplifications and 35 homozygous deletions, we identified 315 minimal common regions of 'non-random' genetic alterations (115 gains and 200 losses) which were consistently observed across our tumour samples. The small size of these aberrations (median size of 880 kb) contributed to the reduced number of candidate genes included (on average 12 Ensembl-annotated genes). The database has further specified the genes whose expression levels are consistent with their copy number status. Such genes were UQCRB, SQLE, DDEF1, SLA, ERICH1 and DLC1, indicating that these may be potential target candidates within regions of aberrations.

CONCLUSION

This study has revealed multiple novel regions that may indicate the locations of oncogenes or tumour suppressor genes in PDAC. Using the database, we provide a list of novel target genes whose altered DNA copy numbers could lead to significant changes in transcript levels in PDAC.

Similarity classifier in diagnosis of bladder cancer

In this article a similarity classifier's performance is studied in the diagnosis of bladder cancer. It is demonstrated that good classification results in diagnosis of bladder cancer are already achieved with a very small amount of data in the training set with the use of similarity classifier. When a new disease is initially discovered, the amount of samples are always quite limited (due to a fact that amount of patients is few), and this situation makes clinical work very difficult. A similarity classifier is a fast and accurate tool for medical diagnosis and it is capable of accurate performance already with a limited amount of data. This is quite important because there is a very limited amount of techniques available even to deal with such small sample sizes and especially in the diagnosis of cancer, high diagnosis accuracy is most important. In this study similarity classifier is used in diagnosis of bladder cancer. A good accuracy (of 100%) is already achieved with very small amount of samples in training the classifier. Here only four samples (two persons with bladder cancer and two persons without bladder cancer) were needed to train classifier managing the diagnosis of bladder cancer with 100% accuracy.

Altered structure and expression of RB1 gene and increased phosphorylation of pRb in human vestibular schwannomas

Tumor-specific alterations at the RB1 gene locus in 30 human vestibular schwannomas including 10 NF2 and 20 sporadic cases were analysed. Southern blot analysis of DNA from these samples revealed loss of heterozygosity (LOH) at the RB1 locus in 6 of 24 informative cases (25%) compared to normal blood DNAs from the same patients. Northern blot analysis showed normal size RB1 mRNA in all the tumor samples. However, there was a 2-5-fold increase in the level of expression of the RB1 gene in all the tumor samples compared to the WI38 cell line which was used as control. Western blot analysis of the RB1 protein, pRb showed a 2.5-5-fold increase in the level of total pRb as compared to normal WI38 cell line. Sixty five to seventy five percent of the total pRb were in phosphorylated form in most tumors. The LOH at the RB1 gene locus suggests genetic instability in these patients. Further, increased levels of RB1 mRNA, total pRb and the phosphorylated form of pRb suggests that RB1 gene in these tumors may have anti-apoptotic function. These results suggest that the RB1 gene has a major role in the development of human vestibular schwannomas.

Molecular prognostication in bladder cancer--a current perspective

The optimal management of bladder cancer depends on the accurate assessment of the tumour's biological potential. Advances in molecular biology and cytogenetics have spurred intense research in identifying and characterising prognostic markers for patients with transitional cell carcinoma (TCC) of the bladder. The molecular changes that occur can be categorised into (1) chromosomal alterations leading to carcinogenesis, (2) cellular proliferation as a result of dysregulation of cell cycle control, and (3) growth control processes such as angiogenesis leading to metastasis. The accumulation of these changes ultimately determines a tumour's clinical behaviour and response to therapy. As the understanding of bladder cancer evolves, novel molecular markers for prognostication will make their way from the research laboratory to the clinical setting with the promise to improve patient care and outcomes.

Loss of heterozygosity at 13q14 and 13q21 in high grade, high stage prostate cancer

BACKGROUND

Loss of heterozygosity (LOH) at chromosome 13q has been frequently detected in prostate cancer, and three regions (i.e., 13q14, 13q21, and 13q33) may harbor tumor suppressor genes important in this neoplasm. In this study, we examined the frequency of 13q LOH in advanced prostate cancers, in order to determine the clinicopathologic relevance of 13q LOH.

METHODS

LOH was determined by analyzing microsatellite markers in 41 cases of microdissected predominantly high grade prostate cancer tissues and their matched nonneoplastic cells. The results were compared with those generated previously for lower grade, asymptomatic cancers.

RESULTS

The frequencies of LOH at 13q14, 13q21, and 13q33 were 62% (21/34), 57% (20/35), and 34% (11/32), respectively. In comparison to previous results, LOH at 13q14 and 13q21 but not 13q33 was more frequent in prostate cancers that produced local clinical symptoms (bladder outlet obstruction) than those that did not (P < 0.05). LOH at 13q14 was also significantly more frequent in high grade and high stage cancers than those that were lower grade and lower stage (P < 0.05).

CONCLUSIONS

Although the target genes on 13q have not been identified in carcinomas of the prostate, LOH at 13q14 in particular is associated with clinically significant prostate cancers. Further fine mapping of these loci may lead to identification of tumor suppressor genes that are deleted in aggressive carcinomas of the prostate.

An 800-kb region of deletion at 13q14 in human prostate and other carcinomas

Deletions of regions at 13q14 have been detected by various genetic approaches in human cancers including prostate cancer. Several studies have defined one region of loss of heterozygosity (LOH) at 13q14 that seems to reside in a DNA segment of 7.1 cM between genetic markers D13S263 and D13S153. To define the smallest region of overlap (SRO) for deletion at 13q14, we first applied tissue microdissection and multiplex PCR to detect homozygous deletion and/or hemizygous deletion at 13q14 in 134 prostate cancer specimens from 114 patients. We detected deletions at markers D13S1227, D13S1272, and A005O48 in 13 (10%) of these tumor specimens. Of the 13 tumors with deletions, 12 were either poorly differentiated primary tumors or metastases of prostate cancer. To fine-map the deletion region, we then constructed a high-resolution YAC/BAC/STS/EST physical map based on experimental and database analyses. Several markers encompassing the deletion region were analyzed for homozygous deletion and/or hemizygous deletion in 61 cell lines/xenografts derived from human cancers of the prostate, breast, ovary, endometrium, cervix, and bladder, and a region of deletion was defined by duplex PCR assay between markers A005X38 and WI-7773. We also analyzed LOH at 13q14 in the 61 cell lines/xenografts using the homozygosity mapping of deletion approach and 26 microsatellite markers. We found 24 (39%) of the cell lines/xenografts to show LOH at 13q14 and defined a region of LOH by markers M1 and M5. Combination of homozygous or hemizygous deletion and LOH results defined the SRO for deletion to be an 800-kb DNA interval between A005X38 and M5. There are six known genes located in or close to the SRO for deletion. This region of deletion is at least 2 Mb centromeric to the RB1 tumor-suppressor gene and the leukemia-associated genes 1 and 2, each of which is located at 13q14. These data suggest that the 800-kb DNA segment with deletion contains a gene whose deletion may be important for the development of prostate and other cancers. This study also provides a framework for the fine-mapping, cloning, and identification of a novel tumor-suppressor gene at 13q14.

Ionizing radiation and genetic risks. XII. The concept of "potential recoverability correction factor" (PRCF) and its use for predicting the risk of radiation-inducible genetic disease in human live births

Genetic risks of radiation exposure of humans are generally expressed as expected increases in the frequencies of genetic diseases over those that occur naturally in the population as a result of spontaneous mutations. Since human data on radiation-induced germ cell mutations and genetic diseases remain scanty, the rates derived from the induced frequencies of mutations in mouse genes are used for this purpose. Such an extrapolation from mouse data to the risk of genetic diseases will be valid only if the average rates of inducible mutations in human genes of interest and the average rates of induced mutations in mice are similar. Advances in knowledge of human genetic diseases and in molecular studies of radiation-induced mutations in experimental systems now question the validity of the above extrapolation. In fact, they (i) support the view that only in a limited number of genes in the human genome, induced mutations may be compatible with viability and hence recoverable in live births and (ii) suggest that the average rate of induced mutations in human genes of interest from the disease point of view will be lower than that assumed from mouse results. Since, at present, there is no alternative to the use of mouse data on induced mutation rates, there is a need to bridge the gap between these and the risk of potentially inducible genetic diseases in human live births. In this paper, we advance the concept of what we refer to here as "the potential recoverability correction factor" (PRCF) to bridge the above gap in risk estimation and present a method to estimate PRCF. In developing the concept of PRCF, we first used the available information on radiation-induced mutations recovered in experimental studies to define some criteria for assessing potential recoverability of induced mutations and then applied these to human genes on a gene-by-gene basis. The analysis permitted us to estimate unweighted PRCFs (i.e. the fraction of genes among the total studied that might contribute to recoverable induced mutations) and weighted PRCFs (i.e. PRCFs weighted by the incidences of the respective diseases). The estimates are: 0.15 (weighted) to 0.30 (unweighted) for autosomal dominant and X-linked diseases and 0.02 (weighted) to 0.09 (unweighted) for chronic multifactorial diseases. The PRCF calculations are unnecessary for autosomal recessive diseases since the risks projected for the first few generations even without using PRCFs are already very small. For congenital abnormalities, PRCFs cannot be reliably estimated. With the incorporation of PRCF into the equation used for predicting risk, the risk per unit dose becomes the product of four quantities (risk per unit dose=Px(1/DD)xMCxPRCF) where P is the baseline frequency of the genetic disease, 1/DD is the relative mutation risk per unit dose, MC is the mutation component and PRCF is the disease-class-specific potential recoverability correction factor instead of the first three (as has been the case thus far). Since PRCF is a fraction, it is obvious that the estimate of risk obtained with the revised risk equation will be smaller than previously calculated values.

Expression and phosphorylation status of retinoblastoma protein in adult T-cell leukemia/lymphoma

The deletion or hyperphosphorylation of the retinoblastoma protein (pRB), is reported to progress various tumors. But its relevance to adult T-cell leukemia/lymphoma (ATL) remains to be elucidated. To better understand the role of pRB in ATL, we examined the expression and phosphorylation status of pRB in three ATL cell lines and 43 clinical samples, eight peripheral blood samples and 35 lymph node samples, from patients with ATL by Western blotting. In addition, 30 lymph node sections were also evaluated immunohistochemically. As a result, Western blotting analysis revealed that the pRB in the ATL cell lines was in the hyperphosphorylated, but that in 39 of 43 clinical samples, pRB was exclusively in the hypophosphorylated form. Four peripheral blood samples were negative for pRB. Immunohistochemistry revealed that the lymph nodes of all of 30 patients tested were positive for pRB at various staining levels, weak, mild, and strong. But weak expression may be essentially negative for pRB function. Patients with weak pRB expression in their lymph nodes lived significantly shorter lives than those with mild expression. Surprisingly, patients with strong expression also showed a significantly worse prognosis than those with mild expression. Although only the absence of pRB expression was considered previously to be indicative of RB functional loss, it has been reported recently that overexpression of pRB is correlated with progression of disease in patients with advanced bladder carcinoma or follicular lymphoma. These findings indicate that pRB controls tumor proliferation not only as a cell cycle regulator but also by other mechanisms, possibly through the inhibition of apoptosis, as suggested by recent findings in an osteosarcoma cell line, Saos-2. In conclusion, pRB may play an essential role in its hypophosphorylated form for progression of ATL, as well as a cell cycle promoter in hyperphosphorylated or negative/excessive reduced form.

Retinoblastoma

BACKGROUND: Retinoblastoma is the most common intraocular malignancy of infants and children. With early diagnosis and treatment, survival is greater than 90%; however, patients with a germline retinoblastoma mutation have a substantial risk of having a second high-grade malignancy. METHODS: The recent developments in the diagnosis and treatment of retinoblastoma are reviewed. RESULTS: Identification of the retinoblastoma germline mutation is now possible with the discovery of the retinoblastoma gene. Patients with the germline mutation have a 51% cumulative risk over 50 years of developing a second malignancy. Several pilot studies using primary chemotherapy for retinoblastoma have shown promising results. CONCLUSIONS: Risk assessment and genetic counseling have become more precise with the development of laboratory methods to identify the retinoblastoma gene. The development of primary chemotherapy regimens to reduce the size of retinoblastoma tumors may decrease the need for radiation therapy and thereby reduce the risk of radiation-related malignancies in patients with the germline mutation.

Frequency of somatic and germ-line mosaicism in retinoblastoma: implications for genetic counseling

Although mosaicism can have important implications for genetic counseling of families with hereditary disorders, information regarding the incidence of mosaicism is available for only a few genetic diseases. Here we describe an evaluation of 156 families with retinoblastoma; the initial oncogenic mutation in the retinoblastoma gene had been identified in these families. In 15 ( approximately 10%) families, we were able to document mosaicism for the initial mutation in the retinoblastoma gene, either in the proband or in one of the proband's parents. The true incidence of mosaicism in this group of 156 families is probably higher than our findings indicate; in some additional families beyond the 15 we identified, mosaicism was likely but could not be proven, because somatic or germ-line DNA from key family members was unavailable. Germ-line DNA from two mosaic fathers was analyzed: in one of these, the mutation was detected in both sperm and leukocyte DNA; in the other, the mutation was detected only in sperm DNA. Our data suggest that mosaicism is more common than is generally appreciated, especially in disorders such as retinoblastoma, in which a high proportion of cases represent new mutations. The possibility of mosaicism should always be considered during the genetic counseling of newly identified families with retinoblastoma. As demonstrated here, genetic tests of germ-line DNA can provide valuable information that is not available through analysis of somatic (leukocyte) DNA.

p21WAF-1 reorganizes the nucleus in tumor suppression

Interphasic nuclear organization has a key function in genome biology. We demonstrate that p21WAF-1, by influencing gene expression and inducing chromosomal repositioning in tumor suppression, plays a major role as a nuclear organizer. Transfection of U937 tumor cells with p21WAF-1 resulted in expression of the HUMSIAH (human seven in absentia homologue), Rb, and Rbr-2 genes and strong suppression of the malignant phenotype. p21(WAF-1) drastically modified the compartmentalization of the nuclear genome. DNase I genome exposure and fluorescence in situ hybridization show, respectively, a displacement of the sensitive sites to the periphery of the nucleus and repositioning of chromosomes 13, 16, 17, and 21. These findings, addressing nuclear architecture modulations, provide potentially significant perspectives for the understanding of tumor suppression.

Retinoblastoma protein family in cell cycle and cancer: a review

Two genes, p107 and Rb2/p130, are strictly related to RB, the most investigated tumor suppressor gene, responsible for susceptibility to retinoblastoma. The products of these three genes, namely pRb, p107, and pRb2/p130 are characterized by a peculiar steric conformation, called "pocket," responsible for most of the functional interactions characterizing the activity of these proteins in the homeostasis of the cell cycle. The interest in these genes and proteins springs from their ability to regulate cell cycle processes negatively, being able, for example, to dramatically slow down neoplastic growth. So far, among these genes, only RB is firmly established to act as a tumor suppressor, because its lack-of-function is clearly involved in tumor onset and progression. It has been found deleted or mutated in most retinoblastomas and sarcomas, but its inactivation is likely to play a crucial role in other types of human cancers. The two other members of the family have been discovered more recently and are currently under extensive investigation. We review analogies and differences among the pocket protein family members, in an attempt to understand their functions in normal and cancer cells.

Frequency and parental origin of hypermethylated RB1 alleles in retinoblastoma

The retinoblastoma susceptibility (RB1) gene contains an unmethylated CpG-rich island at its 5' end. Using methylation-sensitive restriction enzymes, we have investigated the methylation status of this island in 21 sporadic unilateral retinoblastomas and 30 hereditary retinoblastomas. Three sporadic unilateral tumors were found to have hypermethylated RB1 alleles. In two tumors, the paternal allele was methylated, whereas the maternal allele had been lost. Cultured cells from one of these tumors were studied by the reverse transcription polymerase chain reaction and found to have a reduced level of RB1 mRNA. The third tumor had retained constitutional heterozygosity, and the paternal allele was specifically methylated. The combined data from previously published reports and from this study show that hypermethylation of the RB1 gene occurs in 13% of sporadic unilateral tumors and may reduce gene activity.

Cloning and chromosomal localization of the gene coding for human protein kinase CK1

A cDNA clone coding for human protein kinase CK1 (casein kinase 1) has been isolated and sequenced demonstrating that it corresponds to a homolog of the CK1 alpha form found in bovine brain. The derived amino acid sequence of the human CK1 alpha is identical to the bovine counterpart except that it contains 12 extra amino acids at the carboxyl end. Using this cDNA sequence and PCR amplification, YAC genomic clones that contain this human CK1 alpha sequence have been isolated. These YACs have been used for fluorescent in situ hybridization in order to localize the human CK1 alpha gene to chromosome 13q13.

Unbiased transmission of mutant alleles at the human retinoblastoma locus

The preferential transmission of the mutant allele to offspring from fathers who carry a germline mutation in the retinoblastoma gene was examined by analyzing 46 consecutive pedigrees. Among 75 offspring from 29 fathers, the ratio of carriers to noncarriers was 49%. Among the 106 offspring from 55 mothers the ratio was 57%. Neither ratio differs statistically from the expected 50%. When the analysis was limited to only those families with low-penetrance retinoblastoma, we still did not observe a biased transmission of alleles from fathers, although mothers did have an excess of carrier offspring of borderline statistical significance (the P-value was approximately 0.03). While we cannot rule out a biased transmission of alleles from some parents, there appears to be no such bias overall.

Isolation and characterisation of a panel of cosmids which allows unequivocal identification of chromosome deletions involving the RB1 gene using fluorescence in situ hybridisation

A series of cosmids covering the majority of the RB1 gene have been isolated from a flow sorted human chromosome 13 specific library. Using fluorescence in situ hybridisation these cosmids were all shown to hybridise to the 13q14 region but not to chromosomes known to carry subband deletions involving the RB1 gene. This panel of cosmids, therefore, can be used objectively for identification of RB1 gene deletions in tumour and normal cells.

Diagnosis of retinoblastoma in a presymptomatic stage after detection of interstitial chromosomal deletion 13q

In a newborn with only minor malformations the finding of an extended interstitial chromosome deletion 13q was unexpectedly found [46,XY,del(13) (q14.11q22.2)]. The included deletion of chromosome band 13q14, which is known to be predisposing for retinoblastoma (Rb), gave rise to subsequent ophthalmological inspection. A multifocal tumor was detected immediately in the right eye and 11 months later contralaterally. In contrast to the Knudson hypothesis, which suggests a high risk of a multifocal and bilateral tumor in patients with an inherited mutation of the RB-1 gene, literature data indicate a reduced tumorigenesis in patients with a cytogenetic deletion of the critical Rb region of chromosome 13. However, the authors' patient shows that even with a cytogenetic deletion early, bilateral, and multifocal tumor formation is possible. Reliable risk estimates of tumorigenesis for patients with a chromosome deletion cannot be given, since most of these were ascertained by their tumor.

The transcription factor E2F-1 mediates the autoregulation of RB gene expression

The retinoblastoma (RB) gene is the prototype tumor suppressor gene. Mutations in this gene are often associated with the occurrence of various tumors. Several mutations have been found in the promoter region of the gene, suggesting that inappropriate transcriptional regulation of the RB gene contributes to tumorigenesis. Sequence analysis of the RB promoter has revealed a potential E2F recognition site within a region critical for RB gene transcription. By using the cloned E2F-1 gene, here we report that (i) RB expression is negatively regulated by its own gene product, (ii) E2F-1 binds specifically to an E2F recognition sequence in the RB promoter and transactivates the RB promoter, (iii) overexpression of RB suppresses E2F-1-mediated stimulation of RB promoter activity, and (iv) the expression of the RB gene is paralleled by the expression of the E2F-1 gene during cell cycle progression. These results demonstrate that expression of RB is negatively autoregulated through E2F-1.

The transcription factor E2F-1 mediates the autoregulation of RB gene expression

The retinoblastoma (RB) gene is the prototype tumor suppressor gene. Mutations in this gene are often associated with the occurrence of various tumors. Several mutations have been found in the promoter region of the gene, suggesting that inappropriate transcriptional regulation of the RB gene contributes to tumorigenesis. Sequence analysis of the RB promoter has revealed a potential E2F recognition site within a region critical for RB gene transcription. By using the cloned E2F-1 gene, here we report that (i) RB expression is negatively regulated by its own gene product, (ii) E2F-1 binds specifically to an E2F recognition sequence in the RB promoter and transactivates the RB promoter, (iii) overexpression of RB suppresses E2F-1-mediated stimulation of RB promoter activity, and (iv) the expression of the RB gene is paralleled by the expression of the E2F-1 gene during cell cycle progression. These results demonstrate that expression of RB is negatively autoregulated through E2F-1.

Molecular etiology of low-penetrance retinoblastoma in two pedigrees

In one family with low-penetrance retinoblastoma, a germ-line deletion is shared by affected and unaffected, obligate carriers. The deletion encompasses exon 4 of the retinoblastoma gene and corresponds to a mutant protein without residues 127-166. In a second family, RFLP analysis shows that two distant relatives have independently derived mutations. These families, together with others reported elsewhere, indicate that attributes of alleles at the retinoblastoma locus specify penetrance.

Isolation of DNA sequences deleted in lung cancer by genomic difference cloning

To identify DNA sequences that are deleted in human lung cancer, genomic subtraction hybridization was used to construct plasmid libraries that are enriched for DNA sequences deleted in the small cell lung carcinoma cell line SK-LC-17. The clones of the libraries contained predominantly single copy sequences, allowing direct screening of normal and tumor DNA by genomic Southern blotting. Of 150 clones tested, three independent clones (del-27, del-118, and del-109) were identified that specifically hybridized with normal human DNA but not with tumor DNA from the cell line SK-LC-17. The corresponding DNA sequences are localized on human chromosomes 5, 8, and X/Y. The DNA regions identified by del-109 and del-118 were also found to be deleted in several other lung carcinoma cell lines. Moreover, del-118 was deleted in a freshly isolated lymph node metastasis of a human lung adenocarcinoma. It is therefore reasonable to speculate that the identified clones are derived from independent genetic loci encoding potential tumor suppressor genes.

Molecular mechanisms in the evolution of chronic myelocytic leukemia

Chronic myelocytic or Ph1-positive acute lymphoblastic leukemias have been analyzed for alterations in a variety of proto-oncogenes and anti-oncogenes implicated in the progression of chronic myeloid leukemia (CML) from its chronic phase to blast crisis. The most frequent genetic change found in disease evolution is an alteration of the p53 gene involving a point mutation, a rearrangement or a deletion. These gene changes are common in myeloid and undifferentiated variants of blast crisis but are usually undetectable in lymphoid leukemic transformants. Other molecular changes also occur in the clonal evolution of CML. The retinoblastoma-susceptibility (Rb) gene is an anti-oncogene. Structural abnormalities of Rb are frequent in all types of human acute leukemia, but are particularly common in Ph1-positive leukemia of lymphoid phenotype including both Ph1-positive ALL and lymphoid blast crisis of CML. Changes in Rb occur early in the transition to blast crisis with loss of Rb protein being the common factor. Mutations in the N-RAS gene also occur, but are rare in typical blast crisis. They are sometimes seen in Ph1-negative myeloid blast crisis. Since changes in the p53 gene are generally associated with progression of disease of a myeloid phenotype and changes in the Rb gene occur more often with a lymphoid phenotype, a particular molecular alteration may influence the character of disease evolution in CML.

Paternal selection favoring mutant alleles of the retinoblastoma susceptibility gene

Penetrance and segregation rates of mutant Rb-1 alleles were assessed in all 51 members of eight kindreds with hereditary retinoblastoma by concomitant ophthalmologic examination and determination of seven intragenic restriction fragment length polymorphisms (RFLPs). Penetrance was in the range reported in the literature except for one family in which it was only 42.8%. However, the odds of transmitting a mutant Rb-1 allele from one generation to the next were 25:9 in this population, much above the Mendelian 1:1 ratio (P less than 0.025). This preferential transmission was discovered through the use of molecular information. Further analysis revealed that this distortion was due to preferential inheritance among children of male carriers (18:4, P less than 0.005). No difference from a 1:1 segregation ratio could be detected among the children of female carriers (7:5). These findings were consistent with a review of relevant data in the literature.

Follow-up of retinoblastoma patients having prenatal and perinatal predictions for mutant gene carrier status using intragenic polymorphic probes from the RB1 gene

We have carried out presymptomatic prediction of mutant gene carrier status in ten individuals with a family history of retinoblastoma. In all cases standard linkage studies were employed using intragenic DNA probes which recognise restriction fragment length polymorphisms. In four cases foetal DNA samples were obtained by chorionic villus sampling, the remaining six were derived from either cord blood samples or venipuncture of neonates. We demonstrated that the mutant gene was inherited by only one of these patients who has subsequently developed bilateral tumours. Six of the other cases have now reached the age beyond which it might have been expected that tumours would develop and are all disease free. It must be concluded that repeated ophthalmological examination of these and future patients shown not to have inherited the mutant gene, is unnecessary.

Loss of heterozygosity on chromosome 17p13 in breast carcinomas identifies tumors with high proliferation index

The capacity of breast tumor cells to proliferate is considered a potential prognostic factor together with other histopathologic parameters. The authors determined the proliferation index on a large panel of human primary breast tumors by measuring the levels of incorporation of bromodeoxyuridine (BrdU) by fresh tumor specimens in culture. Previous analysis showed that the percentage of cells entering the S-phase of the cell cycle strongly correlates with tumor grade, tumor size, and estrogen and progesterone receptor status. The capacity of tumor cells to proliferate might be associated with specific genetic mutations in primary tumors. To test this hypothesis, a panel of 96 human breast carcinomas, for which the BrdU labeling index (LI) was known, were tested for loss of heterozygosity (LOH) or increased copy number (ICN) at chromosomes 1q, 3p, 13q, 17p, and 18q. On chromosome 17p, LOH and ICN were observed in 27% and 12%, respectively, of the informative breast tumors. The LOH on chromosome 17p was significantly associated with tumors having an elevated BrdU proliferation index (P = 0.022). No association (P = 0.45) was observed between BrdU LI and tumor size (T2 + T3 compared with T1), tumor grade, and lymph node status. Increased copy number on chromosome 17p, LOH or ICN on 1q, and LOH on 13q14, 18q, and 3p also showed no significant correlation with cell kinetic parameters. These data are consistent with the presence of a gene or genes on chromosome 17p13 near the YNZ22.1 locus whose normal functioning is necessary for controlling breast tumor cells proliferation in vivo.

Genes associated with tumor suppression and growth control in the human nervous system

Cancer, the uncontrolled proliferation of a population of somatic cells, is fundamentally a genetic disorder. Although the specific array of genetic changes causing individual tumor types remains largely obscure, the past two decades have witnessed a tremendous increase in our understanding of the specific genes regulating cell differentiation, proliferation, and senescence. There appear to be two distinct fundamental genetic mechanisms of tumorigenesis. One mechanism is associated with the activation of growth-promoting factors such as proto-oncogenes. Alternatively, tumor formation may be induced as the result of the loss or inactivation of genes which normally regulate or suppress cell growth. These genes have been termed 'tumor suppressor' genes or 'anti-oncogenes'. This review focuses on the role of 'tumor suppressor' genes in tumor formation and growth control of the human nervous system.

Molecular mechanisms of cancer

Cancer is caused by specific DNA damage. Several common mechanisms that cause DNA damage result in specific malignant disorders: First, proto-oncogenes can be activated by translocations. For example, translocation of the c-myc proto-oncogene from chromosome 8 to one of the immunoglobulin loci on chromosomes 2, 14, or 22 results in Burkitt's lymphomas. Translocation of the c-abl proto-oncogene from chromosome 9 to the BCR gene located on chromosome 22 produces a hybrid BCR/ABL protein resulting in chronic myelogenous leukemia. Second, proto-oncogenes can be activated by point mutations. For example, point mutations of genes coding for guanosine triphosphate-binding proteins, such as H-, K-, or N-ras or G proteins, can be oncogenic as noted in a large variety of malignant neoplasms. Proteins from these mutated genes are constitutively active rather than being faithful second messengers of periodic extracellular signals. Third, mutations that inactivate a gene can result in tumors if the product of the gene normally constrains cellular proliferation. Functional loss of these "tumor suppressor genes" is found in many tumors such as colon and lung cancers. The diagnosis, classification, and treatment of cancers will be greatly enhanced by understanding their abnormalities at the molecular level.

Recombination by sequence repeats with formation of suppressive or residual mitochondrial DNA in Neurospora

Recombination junctions of several Neurospora mitochondrial DNA (mtDNA) mutants and their revertants were identified. Their nucleotide sequences and putative secondary structures were determined in order to understand the nature of the elements involved in intramolecular recombination. Multiple deletions, involving the same portion of Neurospora mtDNA, were identified in six independently isolated mutants. A 9-nucleotide repeat element, CCCCNCCCC, was found to be involved in these and other Neurospora mitochondrial recombination events. The repeat elements were clustered as hot spots on the Neurospora mtDNA and were associated with palindromic DNA sequences. The palindromes have a potential to generate hairpin structures. A much lower free energy of the putative hairpins at the 5' end of the recombination site, and the possible formation of non-B-DNA structure by polypyrimidine tracks, may be important in the initiation of recombination. Using PCR, we found low levels of a specific mitochondrial deletion in certain Neurospora mutants. Their presence in low amounts in a population with a much larger number of normal mtDNA is unexpected. Contrary to earlier belief, this finding supports the view that deleted, smaller DNA molecules are not always suppressive relative to normal mtDNAs.

Esterase D and retinoblastoma gene loci are tightly linked to Wilson's disease in Chinese pedigrees from Taiwan

Wilson's disease (WD) is a rare autosomal recessive disorder and has been mapped to the long arm of chromosome 13 (q14.1). We have analyzed the segregation of esterase D (ESD) and retinoblastoma (RB) gene loci in ten families of Chinese WD subjects living in Taiwan. The polymorphic information content (PIC) for ESD and RB was 0.18 and 0.31, respectively. We confirmed a tight linkage between these loci and WD with a lod score of 3.33 by multipoint linkage analysis. The data from this limited number of pedigrees also suggested the following order: centromere-WD-RB-ESD or centromere-ESD-RB-WD. ESD in conjunction with RB polymorphism would be useful in prenatal and presymptomatic diagnosis, as well as in carrier detection in informative pedigrees.

Molecular detection of constitutional deletions in patients with retinoblastoma

The recent cloning of the retinoblastoma (RB) gene as well as the identification of intragenic polymorphisms afford the necessary tools for the analysis of rearrangements using molecular hybridization. We searched for constitutional deletions by Southern blotting in 67 independent patients with normal karyotype comprising 15 familial and 52 sporadic cases. Among the latter, 33 were bilaterally and 19 unilaterally affected. We detected 6 deletions using cDNA probes covering almost all of the RB gene, as well as a genomic probe of the 5' part of the gene. With this approach, the incidence of detectable deletions was around 10%. No hot spots for deletion breakpoints were found. Asymptomatic carriers were detected in 2 families. The effectiveness of genetic counselling was largely improved by this approach.

Allele-specific hypermethylation of the retinoblastoma tumor-suppressor gene

Inactivation of the retinoblastoma gene appears to have a fundamental role in the genesis of retinoblastoma, osteosarcoma, and other malignant tumors. The gene is generally inactivated because of loss-of-function mutations, although epigenetic phenomena, such as hypermethylation of the promoter region, could possibly have the same effect. We investigated the methylation pattern at the 5' end of the retinoblastoma gene, including its promoter region and exon 1, in DNA purified from 56 primary retinoblastomas. We found five tumors with evidence for hypermethylation, all from unilateral, simplex patients. No methylation abnormalities were detected in DNA purified from the leukocytes from these patients. It is interesting that in one of these tumors the hypermethylation was confined to one allele. There were no mutations in a 1,306-bp sequence including the hypermethylated region that might account for the allele-specific hypermethylation. We believe that the hypermethylation of the retinoblastoma gene that we found in these tumors corresponds to the allelic inactivation of the gene, and we speculate that erroneous hypermethylation without alteration of nucleotide sequence occasionally plays a role in the genesis of this cancer. If this is true, then retinoblastomas with hypermethylation might be treatable with chemotherapeutic agents that interfere with methylation of DNA.

Characterization of deletions at the retinoblastoma locus in patients with bilateral retinoblastoma

DNA samples from 92 unrelated patients with bilateral retinoblastoma were analyzed by Southern blot hybridization with cDNA and genomic clones of the retinoblastoma (RB-1) gene. Qualitative and quantitative evaluation of the Southern blot patterns showed a deletion of all or part of the RB-1 gene in 15 patients. Deletion hot spots were not detected. The study shows that 16% of germ cell mutations are detectable by Southern blot hybridization, but that densitometric analysis is required in most cases.

Retinoblastoma cell lines Y79, RB355 and WERI-Rb27 are genetically related

Genesis of the childhood ocular tumor retinoblastoma results from the mutational inactivation of a single gene, RB, located on chromosome 13. Cultured cells or cell lines derived from retinoblastomas have been extensively studied for insight into mutational mechanisms of RB inactivation, functional properties of wild-type RB alleles, and pathways of retinal differentiation. Three such cell lines (Y79, RB355 and WERI-Rb27) were previously shown to have similar, heterozygous rearrangements of their RB genes, suggesting a common mutational mechanism affecting a specific region of the gene. This proposal was based on the premise that all three mutations occurred independently. By using molecular analyses of human genetic polymorphisms, we now show that these three cell lines are in fact genetically related, despite their different origins, morphologies, growth characteristics, and karyotypes. Interpretation of these and other published data suggest that both RB355 and WERI-Rb27 are probably sublines of Y79.

No evidence for sequences structurally related to the RB1 gene in the human genome

The retinoblastoma (RB1) gene is a ubiquitously expressed gene encoding a cell-cycle control protein. Inactivation of this gene plays a crucial role in the development of retinoblastoma, osteosarcoma, and other tumors. In a search for structurally related gene sequences we identified a 5.5-kb BamHI fragment strongly cross-hybridizing with the 5' end of the RB1 cDNA. Molecular cloning, in situ hybridization, restriction mapping, and sequence analysis identified this DNA segment as the 28S rRNA gene. The absence of other cross-hybridizing sequences suggests that the RB1 gene is not part of a structurally related gene family.

Stromelysin in tumor progression and metastasis

There are several characteristics of stromelysin that suggest that expression of this enzyme may play an important role in tumor invasion and metastasis; the stromelysin gene is expressed in response to stimulation by oncogenes and tumor promoters, and the protein product of this gene is a metalloproteinase capable of degrading multiple components of the extracellular matrix. Experimental evidence to support this hypothesis has been derived from several animal model systems, in which a positive correlation has been observed between stromelysin expression and tumor progression and metastasis. In addition, in vivo experiments in which the levels of TIMP, the tissue inhibitor of metalloproteinases, were altered also strongly suggest a causal role for metalloproteinases in tumor metastases. The expression of active stromelysin in tumor cells requires the fulfillment of several criteria, and this multistep process is reminiscent of the molecular events that are currently understood to contribute to tumor progression and carcinogenesis. Expression of stromelysin mRNA requires both a stimulus, a step which may correspond to the activation of an oncogene in multistep carcinogenesis, as well as the lifting of transcriptional repression, which may correspond to the loss of tumor suppressor function. Both positive and negative modulation of stromelysin transcription appear to utilize pathways that involve the protooncogenes c-fos and/or c-jun. The expression of active stromelysin enzyme also requires conversion of the proenzyme to an active form, and a proper balance between the expression of inhibitors and the levels of active enzyme. The multiple levels of stromelysin regulation support the concept of multistep carcinogenesis and may provide a tool for further understanding of the molecular nature of the events that lead to tumor progression, invasion, and metastasis.

Cloning and sequence of the human adrenodoxin reductase gene

Adrenodoxin reductase (ferrodoxin:NADP+ oxidoreductase, EC 1.18.1.2) is a flavoprotein mediating electron transport to all mitochondrial forms of cytochrome P450. We cloned the human adrenodoxin reductase gene and characterized it by restriction endonuclease mapping and DNA sequencing. The entire gene is approximately 12 kilobases long and consists of 12 exons. The first exon encodes the first 26 of the 32 amino acids of the signal peptide, and the second exon encodes the remainder of signal peptide and the apparent FAD binding site. The remaining 10 exons are clustered in a region of only 4.3 kilobases, separated from the first two exons by a large intron of about 5.6 kilobases. Two forms of human adrenodoxin reductase mRNA, differing by the presence or absence of 18 bases in the middle of the sequence, arise from alternate splicing at the 5' end of exon 7. This alternately spliced region is directly adjacent to the NADPH binding site, which is entirely contained in exon 6. The immediate 5' flanking region lacks TATA and CAAT boxes; however, this region is rich in G + C and contains six copies of the sequence GGGCGGG, resembling promoter sequences of "housekeeping" genes. RNase protection experiments show that transcription is initiated from multiple sites in the 5' flanking region, located about 21-91 base pairs upstream from the AUG translational initiation codon.

Molecular genetics in the pathology and diagnosis of retinoblastoma

Retinoblastoma, the most common intraocular malignancy of children, has served as an important paradigm for understanding the events involved in neoplastic transformation. Much of the contemporary molecular description of human cancers stems directly from experimental approaches first developed to study this childhood tumour. This analytical methodology has demonstrated a major role for heritable predisposition in tumourigenesis, provided evidence for tissue pleiotropy of cancer genes, and revealed a more precise estimation of the number, activity, and location of other tumour suppressor loci.