Patent Application
20080070242
Definitions
As used herein “stringent conditions” means conditions that detect a nucleic acid molecule with at least 90%, preferably at least 95%, nucleotide sequence homology to the probe or primer sequence. See Sambrook et al. Molecular Cloning a Laboratory Manual Cold Spring Harbor Press 2 ed, (1989); PCR Primer: A Laboratorv Manual. Carl Dieffenbach Ed. Cold Spring Harbor Press (1995), for a selection of conditions suitable for washing and hybridizing nucleic acids allowing for stable and specific duplex formation and/or Reverse Transcriptase Polymerase Chain Reaction (RT-PCR). Stringent conditions are those that either employ low ionic strength and high temperature for washing, or employ a denaturing agent during hybridization.
As used herein “Polymerase Chain Reaction” or “PCR” refers to the process or technique of increasing the concentration of a segment of a target sequence of pre-selected genomic material comprised of, but not limited to, DNA, mRNA, cDNA, or fragments thereof, as generally described in U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,965,188.
As used herein “isoenzyme variants” refers to a protein resulting from the alteration of the native HAS1 enzyme arising from post-translational or pre-translational modification.
As used herein “disease” means a state in a mammal which may directly or indirectly lead to a cellular, cell population, or systemic state detrimental to the mammal.
As used herein, the term “probe” refers to an oligonucleotide, single-stranded or double-stranded, produced synthetically or occurring naturally; that is capable of selectively binding to a nucleic acid of interest.
As used herein, the term “primer” refers to an oligonucleotide produced synthetically or naturally occurring, which is capable of acting as a point of initiation of nucleotide synthesis when placed under conditions in which nucleotide synthesis extending from the primer, complimentary to a nucleic acid strand, is possible.
As used herein, “therapeutic” refers to a method or process to vary the expression or transcription of HAS 1 or HAS 1 isoenzyme variants in a cell or cell population; in which the expression, transcription or post-translational modification of HAS1 or HAS1 isoenzyme variants, or lack thereof, is deleterious to the cell or cell population or gives rise to a susceptibility to a condition which is deleterious to the cell or cell population.
As used herein, “microfluidic devices”, sometimes termed “lab on a chip”, “microfluidic chips” or “microsystem platforms” refer to the result of applying microelectronic fabrication technologies to produce a network of wells and channels etched into glass and/or molded into polymers that are bonded to glass or silicon chips. Within these wells and microchannels, cells and reagents can be manipulated by a variety of methods including gravity feed, applying electric or magnetic fields and results detected by, for example, image analysis or optical means. Microfluidic chips provide for PCR reactions and analysis of PCR products (Footz, T. S. et al. Electrophoresis 22:3868 (2001); Obeid, P. J. et al. Analytical Chemistry 75:288 (2003); Backhouse C. J. et al. Electrophoresis 24:1777 (2003)). They enable high resolution separations through polymer-filled microchannels using capillary electrophoresis of e.g. multiple PCR products, and can exhibit a high level of integration by combining multiple functions on a single chip, for example cell sorting and RT-PCR reactions for gene expression or genomic profiles of a given cell or population of cells (Backhouse, C. J. et al. Proceedings of the International Conference on MEMS, NANO and Smart Systems 377 (2003)). Within a microfluidic device, sample processing can be implemented and cells can be separated by a variety of means, including dielectrophoresis, and processed in a variety of ways, including analysis of HAS gene expression as shown here. In the future, microsystem platforms incorporating microfluidics chip-based sample processing and analysis may replace more conventional methodologies for applications such as genotyping.
HAS Abnormalities in Other Cancers
HAS1 is a prognostic factor in MM, ovarian and colon cancer (Adamia, S. et al. Blood 102:5211 (2003); Yamada, Y. et al. Clin. Exp. Metastasis 21:57 (2004); Yabushita, H. Oncol. Rep. 12:739 (2004)). Although as yet there have been no reports of HAS1 splice variant expression in ovarian and colon cancer, based on observations in MM and WM, this would be predicted by one skilled in the art. Overexpressed HAS2 and HAS3 have been identified in prostate cancer (Tsuchiya, N. et al. Am J Pathol 160:1799 (2002); Liu, N. et al. Cancer Res 61:5207 (2001); (Simpson, M. A. et al. J Biol Chem. 276: 17949 (2001)). HAS2 and HAS3 are overexpressed in malignant mesothelioma (Liu, Z. et al. Anticancer Res 24:599 and HAS3 is overexpressed in glioma (Enegd, B. Neurosurgery 50:1311 (2002)). As well, HAS 1 variants are observed to correlate with production of extracelluar HA (Adamia, S. et al. Blood 105:4836 (2005)) (Table 1).
HAS1Vb Predicts for Poor Survival in Multiple Myeloma.
In MM, the presence of HAS isoenzyme variants in the blood correlates with poor survival (Adamia, S. et al. Blood 102:5211 (2003)), but to date no significant correlations have been detected for HAS isoenzyme variants expressed by bone marrow-localized malignant cells. This suggests that HAS isoenzyme variants are upregulated in the blood-borne components of the myeloma clone and are biologically relevant markers of circulating tumor burden. A highly significant correlation between poor survival and expression of HAS genes in blood borne cells is found for the intronic splice variant HAS1Vb, and a strong trend towards clinical correlations with poor outcome is seen for HAS1-FL and HAS1Va (U.S. Pat Application No. 20050003368). The strong association between HAS1Vb and survival, taken together with the rare detection of HAS1Vb in the bone marrow, suggests that HAS1IVb may be preferentially upregulated in circulating malignant cells. Analysis of purified B lineage subsets from MM and WM patients confirms this. HAS1Vb is expressed by circulating B cells as identified by their phenotypic marker profiles, but is not detected in BM-localized B or plasma cells (Adamia, S. et al. Blood 102:5211 (2003)). HAS1 thus represents a new type of prognostic marker that reflects biologically important properties of a malignant clone as it undergoes stepwise oncogenesis and/or disease progression.
HAS1 and Genetic Instability
HAS1 gene expression may promote genetic instability. This idea is supported by the observation that circulating clonal B cells in myeloma patients are extensively DNA aneuploid with, on average, 1.07 excess DNA content, equivalent to an additional 3.2 chromosomes. This provides evidence for genetic instability in the malignant MM B cells that overexpress HAS1 and its variants. Regardless of mechanism, the significant correlation between poor survival and the expression of HAS1 and its splice variants by circulating B cells suggests a key role for expression of HASs by “stem cell” components of the MM clone that circulate in the blood and mediate malignant spread to distant bone marrow sites. The detection of novel HAS1 variants at high levels in MM B cells and their absence from normal B cells, as well as from other cell types, suggests that aberrant HAS1 splicing is characteristic of malignant cells. The detection of HAS1 variants in monoclonal gammopathies of undetermined significance (MGUS) suggests that their expression may be an early event in the genesis of MM.
The enzymatically active part of full length HAS1 protein is intracellular. Based on their sequences and predicted tertiary structures, we speculate that HAS1 variants are intracellular and/or membrane-anchored isoenzymes retaining enzymatically active domains that are likely to synthesize intracellular HA (
Influence on Splicing of Genetic Variation in Genomic DNA
As indicated above, HAS gene expression analysis has demonstrated abnormalities of HAS1 in MM and WM patients. (Adamia, S. et al. Semin Oncol 30:165 (2003); Adamia, S. et al. Blood 105:4836 (2005)). The expression patterns of HAS1 and splice variants in MM and WM patients are likely to occur in other cancers characterized by abnormalities in HASs. HAS1Va (HAS1T) is the result of exon skipping which causes a frame shift (Adamia, S. et al. Semin Oncol 30:165 (2003); Adamia, S. et al. Blood 105:4836 (2005)). However, HAS1Vb and HAS1Vc are the result of intronic splicing, since both of these transcripts retain part of intron 4 either at the 3′ splice site of alternative exon 4 or at the 5′ splice site of exon 5 (Adamia, S. et al. Blood 105:4836 (2005)). These splicing aberrations generate premature stop codons on spliced HAS1 transcripts leading to severe truncation of the encoded proteins. Using bioinformatics analysis in combination with western blotting performed on lysates obtained from MM cell lines, it has been verified that the aberrantly spliced HAS1 transcripts encode proteins which are able to fold properly and produce extracellular and/or intracellular HA. Production of HA has been demonstrated by particle exclusion assay and HA staining. (Adamia, S. et al. Blood 105:4836 (2005)).
Cancer results from aberrations in gene expression and aberrant splicing is a major regulator of gene expression (Adamia, S. et al. Blood 105:4836 (2005); Hastings, M. L. et al Curr Opin Cell Biol 13:302 (2001); Bartel, F. et al. Cancer Cell 2:9 (2002)). Pre-mRNA processing, which occurs in the nucleus of the cell, is a complex process that includes pre-mRNA splicing (Hastings, M. L. et al. Curr Opin Cell Biol 13:302 (2001)). Splicing of a given gene requires activation of more than 100 proteins, including splicing factors and at least 5 small nuclear RNA protein particles (Caballero, O. L. et al. Dis Markers 17:67 (2001)).
Specificity of splicing is known to be defined by the 5′ and 3′ splicing sites and branch points (Nissim-Rafinia, M. et al. Trends Genet 18:123 (2002); Caballero, O. L. et al. Dis Markers 17:67 (2001); Caceres J. F. et al. Trends Genet 18:186 (2002)). However, evidence reported in the literature suggests the importance of other cis-splicing elements, such as exonic splicing enhancers (ESE) and exonic splicing suppressors (ESS) and their intronic counterparts (ISE and ISS), and polypyrimidine tracts. (Caballero O. L. et al. Dis Markers 17:67 (2001); Nissim-Rafinia, M. et al. Trends Genet 18:123 (2002)). Furthermore, mutations occurring in ESE/ISE and ESS/ISS in combination with an aberrant expression of splicing factors (SF) play a significant role in aberrant splicing (Caballero, O. L. et al. Dis Markers 17:67 (2001); Caceres, J. F. et al. Trends Genet 18:186 (2002); Nissim-Rafinia, M. et al. Trends Genet 18:123 (2002)). However, additional mutations on polypyrimidine tracts and on the splicing branch points are required to activate cryptic splice sites and achieve aberrant splicing (Caballero, O. L. et al. Dis Markers 17:67 (2001); Dominski, Z. et al. Mol Cell Biol 11:6075 (1991); Chabot, B. et al. Mol Cell Biol 17:1776 (1997); Cote, J. et al. RNA 3:1248 (1997)).
The current art suggests that high specificity of splice site identification by the splicing machinery can not be fully explained by primary sequence conservation. During splicing, introns fold into secondary structure to localize splicing branch-point at the optimal distance from 5′ splicing site and facilitate assembly of splicing complexes. Alteration of the secondary structure of pre-mRNA, which can be induced by mutations, compromise the splicing pattern of a gene (Buratti et al. Mol Cell Biol 24:10505 (2004)).
To evaluate the factors leading to aberrant HAS1 splicing, ESEs located within the alternatively spliced exon 4 and in the adjacent exon 3 were identified. In addition, the NCBI database was screened to identify mutations and/or single nucleotide polymorphisms (SNPs) on the alternative exon 4 and on exon 3. No mutations were found on alternative exon 4. However, the HAS1 833A/G SNP is located on exon 3. Genetic variation of the 833A/G SNP in exon 3 of HAS1 (Ch19q13.4) in patients was determined using the Taqman SNP Genotyping assay. 86.8% of patients with WM (79/91 tested, p=0.0004) and 85% of MM (230/270 tested, p=0.000002) are homozygous for HAS1 833G/G, as compared to 65% of healthy donors (81/124 tested). No healthy donors or patients have yet been found with homozygous HAS 1 833A/A, suggesting this may be lethal. Homozygosity in WM and MM is statistically significant as measured using three different tests, for WM (p=0.0004 as compared to healthy donors) and for MM (p=0.000002 as compared to healthy donors). HAS1 833A/G homozygosity reflects the germline constitution of the patient, suggesting it may be a predisposing factor for paraproteinemias, perhaps by influencing HAS1 splicing events as discussed below. The HAS1 833A/A genotype was not detected in any patient or healthy donors screened to date, and is presumptively lethal. The same group of WM patients was screened for expression of HAS1 transcripts and splice variants. It was found that increased homozygosity in locus Ch19q13.4 correlated with expression of aberrant splice variants of HAS1, particularly intronic HAS1Vb and HAS1Vc. Only WM patients with HAS1 833G/G genotype expressed either HAS1Vb and/or HAS1Vc with or without full length HAS1. Therefore aberrant splicing of the HAS1 gene in MM and WM patients may be related to the presence of the HAS1 833G/G genotype.
To investigate effects of HAS1 833A/G SNP on HAS1 aberrant splicing ESEs were identified, considering that they are present in constitutive and alternative exons and are required for efficient splicing. Exonic splicing enhancers are recognized by serine/arginine-rich (SR) proteins essential for alternative splicing (Blanchette, M. et al. RNA 3: 405 (1997); Blencowe, B. J. Trends Biochem Sci 25:106 (2000); Zahler A. M. et al. Mol Cell Biol 13:4023 (1993); Zahler A. M. et al. Science 260:219 (1993); Blencowe, B. J. Trends Biochem Sci 25:106 (2000)). A computational approach was used, termed an in silico method, with ESE finder (http://rulai.cshl.edu/tools/ESE/) and exons 3 and 4 were analyzed using SF2/ASF, SC35, SRp40 and SRp55 motif-scoring matrices, derived from pools of the functional enhancer sequences selected from the literature (Cartegni, L. et al. Nucleic Acids Res 31:3568 (2003); Cartegni,l L. et al. Nat Struct Biol 10:120 (2003)). Threshold settings for the analysis were 1.956 for SF2/ASF, 2.383 for SC35, 2.670 for SRp40 and 2.676 for SRp55.
The frequency of the sequence motifs which attract the indicated SF and are most highly expressed in any given human cell nucleus were identified. Screening of both exon 3 and alternative exon 4 of the HAS1 gene demonstrated that the frequency of sequence motifs, which attract the designated SFs, is higher on exon 3 than on alternative exon 4 and exon 5 (
The HAS1 833A/A mutation may disrupt the splicing mechanism, thereby rendering the HAS1 833A/A a lethal genotype. However, for HAS1 833G, the putative ESE remains intact, with the calculated affinity of SRp55 to ESE located on exon 3 being higher than that for SF2, in addition to higher binding affinity of all analyzed SF on exon 3. The HAS1 833G/G genotype may create a “gene dosage” effect in the nucleus of malignant WM cells, perhaps leading to the activation of distal 3′ splicing site and causing exon 4 skipping (Longman, D. et al. Curr Biol 11:1923 (2001); Ring, H. Z. et al. Mol Cell Biol 14:7499 (1994)). However, the population of healthy donors also includes individuals with a HAS1 833G/G genotype who lack expression of HAS1 or its variants. Thus, the increased affinity of SFs for ESE having HAS1 833G appears to be necessary but not sufficient to activate cryptic splice sites in HAS1. Thus the HAS1 833G/G genotype predisposes to WM and MM, and thereby serves as a diagnostic indicator.
Though an exact understanding of the mechanism is not necessary to practise the present invention, based on the evidence described herein, the high affinity of SRp55 is proposed to aggregate specific splicing proteins, thus promoting the skipping of short, alternative exon 4. It is propsed that additional mutations are required to mediate aberrant splicing of this gene (Steiner, B. et al. Hum Mutat 24:120 (2004); Liu, H. X. et al. Nat Genet 27:55 (2001)). This explains why healthy donors with HAS1 833G/G genotype do not express aberrant splice variants of HAS1. The HAS1 833G/G appears insufficient to promote aberrant splicing of this gene. The present invention provides for the HAS1 833G/G genotype as indicating a predisposition of a patient to MM, WM and by correlation other cancers characterized by abnormalities in HASs. Bioinformatics analysis provides that HAS1 833G/G genotype, in combination with additional mutations could activate cryptic splice sites of the HAS1 gene and promote aberrant HAS1 gene splicing. Therefore the HAS1 833G/G genotype is a predictive marker of cancer. In particular, the best mode of the present invention discloses predictors of cancer based in genomic DNA rather than in cDNA or RNA as has been disclosed in the art previously, in particular HAS1 833A/A, HAS1 833 G/G, those listed in Tables 2 and 3; more particularly those listed in Tables 4, 5, 6 and 7 and more particularly in Tables 6 and 7.
Sequencing of genomic DNA from exon 3, intron 3, exon 4, intron 4 and exon 5 of the HAS1 gene.
Exons 3 and 4 and introns 3 and 4, from five WM patients and six MM patients and identified genetic variations not previously known to the art were identified. The genetic variants of HAS1 disclosed herein and those previously reported SNPs, have been mapped to define HAS1 haplotypes, based on their proximity to splice sites and cis splicing elements (ESE/ISE and ESS/ISS) that are important for correct splice-site identification and are distinct from classical splicing signals. These elements can act both as an enhancers or silencers of splicing. In particular, exonic splicing enhancers (ESEs) are prevalent. ESE have been identified using on-line tools ESEfinder release 2 (based on SF2/ASF,SC35, SRp40 and SRp55 motif-scoring matrices), RESCUE-ESE and RESCUE-ISE (httn://genes.mit.edu/burgelab/rescue-ese) Web Server. Using this approach, for the cancer cells from eleven patients, multiple types of genetic variations in HAS1 have been identified and disclosed herein. These include point mutations, nucleotide(s) insertions and deletions, tranversions and transitions. Together these are referred to as genetic variations of a given type, to be inclusive of all categories of variation described above (mutations, insertions and deletions).
Furthermore, based on the distribution of these genetic variations (GV) in HAS1 genomic DNA, four broad categories have been identified:
1) variations that have been previously reported in online databases;
2) variations that are unique to the tumor clone in individual patients;
3) variations that are disease restricted (e.g. recurrent only in MM or only in WM patients); and
4) variations that are recurrent in all WM and MM individuals tested—that is they are present in the HAS1 genomic DNA of the cancer cells from all 11 patients studied.
The present invention discloses novel variations comprising types 2-4 and the detection of variations in a patient comprising types 1-4 as a diagnostic for the existence of cancer or proliferative disease or disorder, in particular MM or WM; and as a diagnostic for a predisposition to cancer or proliferative disease or disorder, in particular MM or WM. As known in the art, genomic variations (including SNPs) can influence spliceosome assembly and thus may contribute to aberrant splicing of HAS1 in cancer patients. Though an exact understanding of the mechanism is not needed to practise the present invention, it is proposed that aberrant splicing of HAS1 results from activation of cryptic splice sites, which lead to exon skipping and/or intron retention. In turn, activation of cryptic donor and/or acceptor splice sites can be promoted by the mutations occurring on ESE/ISE, ESS/ISS and/or at the splicing branch point and polypyrimidine tracts.
The exons and introns were sequenced from 11 different patients (6 with MM and 5 with WM) to identify novel SNPs and identify whether or not recurrent genetic variations of HAS1 are detectable in malignant B cells. Sequencing has been comprehensive, with 3-5 subclones sequenced both directions for each exon or intron of each patient. Genetic variations were identified as already in the NCBI SNP database or as novel variations. Although we identified novel variations that were unique to individual patients, we were surprised to find that many of the genetic variations in exons and introns of HAS1 were recurrent for all malignant clones analyzed (from 11 different patients). These newly identified recurrent variations are indicated in
As can be seen in Table 2, and summarized in Tables 4, 5, 6 and 7; a number of MM in general, and patient specific, genetic variations are observed to occur. As well, as can be seen in Table 3, and summarized in Tables 4, 5, 6 and 7, a number of WM in general and patient specific genetic variations are observed to occur. As will be detailed below, the genetic variations in MM and WM fall into three categories based on the cell types in which they are detected, in any given patient—those that are present in the tumor (tumor specific), those that are present in the hematopoietic lineage (hematopoietic lineage), and those that are present in all cells of the body (germline origin). Genetic variations of germline origin include both novel SNPs first identified here and SNPs that have been previously reported in the art but whose clinical value has not been previously established as predictive markers for disease. For all categories of genetic variation, their use as markers for predicting disease susceptibility, as early indicators of disease stage or for monitoring frank malignancy provides different types of clinically valuable information, as described below.
Diagnostic Application
T The identification of recurrent patterns of genetic variations in genomic HAS1 that characterize cancer cells and are absent from healthy cells (as reported in the NCBI database) provides a cancer cell marker that can be used to detect predisposition to malignancy or malignant cells. In this context, the term “recurrent” is defined as a newly identified genetic variation(s) that is found in more than one patient. Since genomic DNA is very stable, a diagnostic test detecting genetic variations is feasible on samples that must be stored for hours or days or those that are shipped from distant locations for testing. Genetic variations can be tested as single representative variations that define the entire recurrent HAS1 “haplotype” in a population or in individual cells. Alternatively, a battery of simultaneous or sequential tests for multiple variations, particularly well suited for use in association with a microfluidic device, can be used to determine whether or not the recurrent pattern (henceforth referred to as the HAS1 “haplotype”) is present in a population of cells or
The existence of specific, recurrent HAS1 haplotypes in MM and WM, and likely in other cancers or proliferative diseases or disorders, and in particular those characterized by abnormal HASs; provide markers to identify malignant cells and to distinguish between malignant and non-malignant cells. A predisposition to cancer or proliferative diseases or disorders may be ascertained by testing mammalian biological samples for the presence of the HAS1 genomic mutations disclosed herein in general and in Table 2, Table 3, and in particular Tables 4, 5, 6 and 7. This predisposition can be determined by testing DNA from cells removed from any tissue or fluid from the mammal in general or in particular from tissues not involved in the disease (for example buccal cells), from cells of the haematopoietic lineage (for example T cells or polymorphonuclear cells in MM and WM) or from cells thought to be malignant (for example B-Cells in MM and WM), to detect the presence of the genomic variations described above. Combinations of tests detecting the described categories of genetic variation (germline origin, hematopoietic lineage or tumor specific) provide a staging strategy to identify germline predisposition, high risk hematopoietic involvement and frank malignancy, as well as for monitoring response to therapy of malignant cells.
After sequence analysis of exons 3-4 and introns 3 and 4 of the HAS1 gene from 5 WM patients, a number of GV have been detected including tranversions and transitions, deletions and insertions. Among these GV recurrent and unique (specific to individual patients) mutations have been identified, the latter of which are transitions. The reason transitions are more common is indicative of the underlying causes of mutations and to the size of the bases. A purine can be altered so that it base pairs like the other. It is impossible for a purine to be altered to resemble a pyrimidine, or vice versa.
The present invention encompasses any method to detect individual or multiple of the described genetic variation(s) in individual cells or in populations of cells, including but not restricted to allelic discrimination methods, SNP detection methods, PCR and single cell PCR. It also encompasses in situ PCR for detection of DNA encoding the HAS1 protein. The technique is preferred when the copy number of a target nucleic acid is very low, or when different forms of nucleic acids must be distinguished. The method is especially important in detecting and differentiating pre-cancer and cancer cells from normal cells. The method is also useful in detecting subsets of cells destined to become cancer cells. Confirmation of in situ PCR product identity is accomplished by in situ hybridization with a nested 32P-labeled probe or by examining the products using Southern blot analysis to corroborate predicted base pair size.
Mutational Patterns
1. Disease specific: The tumor specific genetic variations (mutations, substitutions, deletions, insertions) are the somatic genetic variations that are detected in B cell linage cells (the malignant cells) of the patients (Table 4). These mutations are associated with MM and/or WM.
These somatic, tumor specific genetic variations provide markers for use in diagnosis and/or monitoring of the disease. They can be used to detect malignant cells at the time of diagnosis and/or during progression of the disease, as a marker for existing disease or as an early marker for emerging disease.
2. Hematopoietic involvement: Genetic variations that are specific to the hematopoietic linage of the patients. These mutations are detected in hematopoietic progenitor cells (stem cells), T cells and other hematopoietic cell types that comprise the healthy hematopoietic cells of the patient (Table 5). They are not germline mutations, as defined by their absence from a representative tissue having the germline sequence, in this case buccal cells (epithelial cells of the patients that are nonmalignant). The mutations identified as being specific to the hematopoietic lineage are detected in hematopoietic cells but not germline tissues (in this case in buccal cells) from patients we have analyzed to date. They are absent from healthy donor hematopoietic cells whose HAS1 gene segments have been sequenced by the inventors and they have not been reported in the NCBI database.
Mutations specific for cells within the hematopoietic lineage of the patients are useful markers for advanced predisposition to malignant disease or impending disease, and can thus be used for diagnosis and monitoring of patients during, for example, “watchful waiting” or as part of continuing monitoring of individuals thought to be at risk of cancer. Individuals with the genetic variations specific to the hematopoietic lineage may be at greater risk and thus require more frequent monitoring than those individuals having only germline genetic variations (see below). They are markers of a second stage of genetic variation that has advanced beyond the germline set of predisposing genetic variations. Most likely, accumulation of these mutations accompany development of MM and/or WM, as evidenced by their presence in the HAS1 gene segments in healthy tissues from these patients.
3. Germline mutations: These mutations are detected in all cells of an individual, in this case a patient, using buccal cells (of the epithelial lineage) as a representative healthy tissue (Table 6). These mutations can also be found in B, T, plasma cells (PC) and stem cells from patients because they are representative of the patient germline that is present in all cells of the body. However, these mutations are absent from cells of healthy donors whose HAS1 gene has been sequenced as disclosed herein, and though reported in the NCBI database have not been previously associated with predisposition to disease. These germline genetic variations predispose individuals to cancer as indicated by their presence in MM and/or WM patients but not in healthy donors (this means these genetic variations are more frequent in patient populations as compared to healthy individuals).
Identifying germline genetic variations in an individual who is not yet a “patient” provides a test for predisposition to MM and/or WM, and a means to identify and monitor individuals at risk of developing disease. Such monitoring provides a test to identify “at risk” individuals. Such identification will facilitate the development of preventive strategies and their application only to those individuals at risk. Knowledge of predisposing mutations may enable prevention in the general population or new therapeutic strategies, by identifying those individuals most likely to benefit. Cost considerations and potential side effects would prevent the use of preventive strategies in all individuals, making an identification strategy a critical and essential element of future disease prevention therapies.
Therefore, these germline genetic variations are predisposing elements for MM and/or WM and can be used for predictive or preventive monitoring strategies.
Together, testing for tumor specific, hematopoietic, and germline genetic variations provides a testing sequence for increasing predisposition to disease and for use as an early maker of emerging malignancy. After identification of “at risk” individuals with germline genetic variations that predispose to cancer, these identified individuals can be followed at regular time points for early detection of emerging hematopoietic lineage mutations, and at a later stage to detect emergence of tumor specific mutations. These events are likely to occur prior to pathological detection of frank malignancy and thus provide a set of valuable early markers for regular follow up of potential patients at risk of developing cancer.
4. Single Nucleotide Polymorphisms (SNPs): SNPs are germline genetic variations detected in every single cell in the body of a given individual, including buccal cells, B, T, PC, stem cells. A genetic variation (mutation) is defined as a SNP if it has a defined frequency in a population of individuals. By definition a polymorphism must be present in more than one individual. Some SNPs in the HAS1 gene are also reported in the NCBI database and are not novel. However, our data showing that these SNPs can be used as markers for identifying individuals at risk of MM and/or WM is novel, as is the observation of the inventors that these SNPs are present at a greatly increased frequency in patient with MM and WM. In these patients we detected increased homozygosity for the HAS1 SNPs reported in NCBI was defined, therefore this work is the first to show that most WM and MM patients are homozygous for these genetic variations.
For the instances reported here, they are frequent in patient populations suffering from cancer or prolfierative disease or disorder but not in healthy individuals.
Unique genetic variations may also become classified as SNPs if additional screening of more individuals indicate these have a definable frequency within the general population.
In the method for diagnosing the existence of cancer or a prolfierative disease or disorder, or a predisposition to cancer or a prolfierative disease or disorder; a genomic nucleic acid sequence isolated from a biological sample taken from a mammal is contacted with the nucleic acid sequence or portion thereof encoding an intronic or exonic genetic variation which is an early marker for cancer or a prolfierative disease or disorder, under stringent conditions that allow hybridization between the sequences and detecting the hybridized sequences. The presence of a genomic nucleic acid sequence or the presence of an altered genomic nucleic acid sequence as compared to a normal nucleic acid sequence is indicative of cancer or a prolfierative disease or disorder, or a predisposition thereto, in the mammal. The increased presence of the DNA, mRNA and/or alternate splice forms of the mRNA in the biological sample is indicative of cancer or a prolfierative disease or disorder, or a predisposition thereto.
A blood sample is provided by a human or other mammalian patient from which B-cells are purified and separated by means known to those skilled in the art. One non-limiting example of such separation and purification means is Fluorescence Activated Cell Sorting (FACS) purification and separation using B-Cell specific antibody (for example including, but not limited to mouse-antihuman CD20) with a flurophore conjugated antibody specific to the B-cell specific antibody (for example including, but not limited to, Flourescein:goat-antimouse antibody). B-cells are then subjected to lysis sufficient to release genomic DNA such means well known in the art and including, but not limited to ultrasonic lysis, heat lysis or Sodium Docenyl Supphate (SDS) lysis. See for example Sambrook et al. Primer: A Laboratory Manual Carl Dieffenbach Ed. Cold Spring Harbor Press (1995).
The presence and quantity of genomic DNA carrying WM or MM in specific, or cancer in general mutations (as disclosed herein in general and in Tables 2 and 3, and in particular Tables 4, 5, 6 and 7) is determined using means known in the art including but not limited to Quantitative PCR, PCR-based DNA sequencing or PCR in general, restriction endonuclease fragment hybridization using mutation specific probes (following or independent of PCR amplification or Restriction Fragment Length Polymorphism) hybridization under stringent conditions with allele specific oligonucleotides (ASO hybridization) of tagged probes, SNP microarray assay or hybridization of labeled DNA or RNA probes (including chemical variants thereof capable of hybridization to genomic DNA and such hybridization being detectable). See for example Sambrook et al. Molecular Cloning a Laboratory Manual Cold Spring Harbor Press 2ed. (1989) or PCR Primer: A Laboratory Manual Carl Dieffenbach Ed. Cold Spring Harbor Press (1995).
The quantity of MM, WM or cancer related genetic mutations (as disclosed herein) compared to total B-cell genomic content is determined and used to assess the prevalence of genetically predisposed B-cells, state of disease progression, metastasis progression, relapse of disease, remission of disease, response of the patient to treatment/chemotherapy, and other beneficial determinations known to those skilled in the art. One can test for a single GV as disclosed herein or a combination of at least two GV as disclosed herein, amounting to the ability to use any of the multiple potential sets of GVs as a cancer or proliferative disease or disorder monitoring tools.
A blood sample is provided by a human or other mammalian patient from which B-cells are purified and separated by means known to those skilled in the art. One non-limiting example of such separation and purification means is Fluorescence Activated Cell Sorting (FACS) purification and separation using B-Cell specific antibody (for example including, but not limited to mouse-antihuman CD20) with a fluorophore conjugated antibody specific to the B-cell specific antibody (for example including, but not limited to, Flourescein:goat-antimouse antibody). Individual B-cells are then subjected to lysis sufficient to release genomic DNA such means well known in the art and including, but not limited to ultrasonic lysis, heat lysis or Sodium Docenyl Supphate (SDS) lysis. See for example Sambrook et al. Molecular Cloning a Laboratory Manual Cold Spring Harbor Press 2ed. (1989) or PCRPrimer: A Laboratory Manual Carl Dieffenbach Ed. Cold Spring Harbor Press (1995).
The presence of genomic DNA carrying WM or MM in specific, or cancer in general, mutations (as disclosed herein in general and in Table 2, Table 3, in particular Tables 4, 5, 6 and 7) is determined using means known in the art including but not limited to Single Cell PCR, generally being PCR with particularly high fidelity in replication and sequencing restriction endonuclease fragment hybridization using mutation specific probes (following or independent of PCR amplification or Restriction Fragment Length Polymorphism), hybridization with allele specific oligonucleotides (ASO hybridization) of tagged probes, SNP microarray assay or hybridization of labeled DNA or RNA probes (including chemical variants thereof capable of hybridization to genomic DNA and such hybridization being detectable). See for example Sambrook et al. Molecular Cloning a Laboratory Manual Cold Spring Harbor Press 2ed. (1989) or PCRPrimer: A Laboratory Manual Carl Dieffenbach Ed. Cold Spring Harbor Press (1995).
Such methods are particularly well suited to the use of microfluidic Devices (as defined herein and generally known in the art). The presence or absence of MM, WM or cancer related genetic mutations (as disclosed herein) is determined and the frequency of the presence of the mutations used to assess the prevalence of genetically predisposed B-cells, state of disease progression, metastasis progression, relapse of disease, remission of disease, response of the patient to treatment/chemotherapy, and other beneficial determinations known to those skilled in the art. In particular this information could be useful for observation and determination of human or mammalian patients progressing from a normal to malignant state of disease, for example detecting progression to WM or MM by observing the presence of WM or MM specific genetic mutations (as disclosed herein in general and Tables 2 and 3, and in particular Tables 4, 5, 6 and 7). Alternatively, the transition from a remissive state of MM to a progressive or relapsed state of MM can be determined using blood samples from the human or mammalian patient and detection of specific genetic mutations (as disclosed herein in general and Tables 2 and 3, and in particular Tables 4, 5, 6 and 7). Example 3: Genetic Tagging Strategy
The method of genetic tagging can be used for identification and induction (if necessary) of point mutations in the genomic sequence and is disclosed more particularly in United States Patent Application #20030119190.; which describes the use of a non-replicating retroviral vector is used as a transporter for randomly introducing mutations into the genome of a host cell. The viral sequence also functions as a tag to identify the mutated gene. Genetic tagging strategy offers the following advantages over other mutagenesis techniques:
1) It can identify and induce point mutations in a localized and controlled manner.
2) It can be used in both uni-celluar and multi-cellular organisms.
3) One can amplify mutated genes from a heterogeneous DNA sample by PCR-based techniques.
4) It is possible to identify, and clone novel genes.
Detection methods for SNP genotyping which can be adapted for point mutation detection and include, but are not limited to, indirect colorimetric, mass spectrometry, fluorescence, fluorescence resonance energy transfer, fluorescence polarization, chemiluminescence. These methods involve hybridization with allele specific probes, oligonucleotide ligation, single nucleotide primer extension, enzymatic cleavage. One skilled in the art would be able to assess the benefits and disadvantages of each method for the particular sample being tested depending on sample quality, quantity and needed accuracy.
The present invention discloses novel genetic mutation indicative of a predisposition to disease and particular disease state (malignancy), in particular MM and WM and more generally cancer. These genetic mutation are further proposed herein to alter RNA splicing. Therefore, use of compounds or factors capable of interfering, inhibiting or otherwise reducing the aberrant RNA splicing resulting in WM, MM, cancer, and proliferative diseases or disorders; specific HAS isoforms disclosed herein and otherwise known in the art, represents a therapeutic target for cancer therapies in general and WM and MM therapies in specific.
Such compounds, factors or methodologies are known to those skilled in the art and include, but are not limited to:
In contrast to the traditional approach to gene therapy, genetic repair strategies attempt to directly correct endogenous genetic mistakes rather than deliver extra copies of genes to cells. Genetic repair strategies attempt to repair defective instructions in a site-specific manner. Processes such as homologous recombination and DNA mismatch repair methods can be used to repair mutant DNA in a site-specific manner.
In the method of treatment, the administration of the oligonucleotides of the invention may be provided prophylactically or therapeutically. The oligonucleotide or mixtures thereof may be provided in a unit dose form, each dose containing a predetermined quantity of oligonucleotides calculated to produce the desired effect in association with a pharmaceutically acceptable diluent or carrier such as phosphate-buffered saline to form a pharmaceutically composition. In addition, the oligonucleotide may be formulated in solid form and redissolved or suspended prior to use. The pharmaceutical composition may optionally contain other chemotherapeutic agents, antibodies, antivirals, exogenous immunomodulators or the like.
The route of administration may be intravenous, intramuscular, subcutaneous, intradermal, intraperitoneal, intrathecal, ex vivo, and the like. Administration may also be by transmucosal or transdermal means, or the compound may be administered orally. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated as used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration bile salts and fusidic acid derivatives. In addition, detergents may be used to facilitate permeation. Transmucosal administration may be through nasal sprays, for example, or using suppositories. For oral administration, the oligonucleotides are formulated into conventional oral administration forms, such as capsules, tablets and tonics. For topical administration, the oligonucleotides of the invention are formulated into ointments, salves, gels, or creams, as is generally known in the art.
In providing a mammal with the compounds or factors of the present invention, preferably a human, the dosage of administered compounds or factors will vary depending upon such factors as the mammal's age, weight, height, sex, general medical condition, previous medical history, disease progression, tumor burden, and the like. Other therapeutic drugs may be administered in conjunction with the compounds or factors.
The efficacy of treatment using the compounds or factors may be assessed by determination of alterations in the presence and quantity of HAS1 genomic DNA containing the mutations as disclosed herein, the concentration or activity of the DNA gene product of the HAS1 isoforms, tumor regression, or a reduction of the pathology or symptoms associated with the cancer.
As disclosed herein in general, and Table 2 and Table 3 in specific, there exist a number of patient specific genomic DNA mutations observed in the HAS1 gene; for cancer patients in general and for MM and WM in particular. Therefore, one skilled in the art is enabled by the present invention to obtain patient specific disease markers allow the monitoring of therapy efficacy, disease state, malignancy presence or state of remission in the patient. One potential methodology would be available to one skilled in the art is as immediately follows:
Prior to, during or following treatment, a human or mammalian patient provides a blood sample from which cells are purified, for example B-cells, as described in Example 1 and Example 2 above. Genomic DNA is isolated and the HAS1 gene sequenced. Sequencing of genomic DNA is well known in the art, both from cell populations or from individual cells: see for example Sambrook et al. Molecular Cloning a Laboratory Manual Cold Spring Harbor Press 2ed. (1989) or PCR Primer: A Laboratory Manual Carl Dieffenbach Ed. Cold Spring Harbor Press (1995).
From the sequence information, both individual specific and disease specific mutations, as taught herein in general and in Tables 2 and 3 in particular, are catalogued. Using the methods described in Example 1 and Example 2 above, the continued presence and/or frequency of occurrence of the genomic mutations may be observed during the course of treatment; specifically prior to, during or after administration of a therapeutic or therapeutic regimen.
While particular embodiments of the present invention have been described in the foregoing, it is to be understood that other embodiments are possible within the scope of the invention and are intended to be included herein. It will be clear to any person skilled in the art that modifications of and adjustments to this invention, not shown, are possible without departing from the spirit of the invention as demonstrated through the exemplary embodiments. The invention is therefore to be considered limited solely by the scope of the appended claims.
This application claims the benefit of U.S. Provisional Application Ser. No. 60/669,368, filed Apr. 8, 2006, under 35 U.S.C. 119(e). The entire disclosure of the prior application is hereby incorporated by reference.
| Number | Date | Country | |
|---|---|---|---|
| 60669368 | Apr 2005 | US |
