Specific Loss Of Heterozygosity Research Articles

Analysis of tumor samples from SOLO2: Concordance of BRCA mutation (BRCAm) detection in tumor vs. blood and frequency of BRCA-specific loss of heterozygosity (LOH) and loss of function somatic mutations.

12017Background: The PARP inhibitor olaparib is approved for maintenance treatment of platinum-sensitive relapsed ovarian cancer (PSR OC) in the USA based on pivotal studies (Study 19, SOLO2) that ...

Detecting Accumulated Somatic Mutations in Healthy Aged Female Myeloid Cells

Background: Acute Myeloid Leukemia and Myelodysplasia are diseases associated with age and with genetic mutations driving evolution of clonal dominance. The earliest steps leading to genetic variation occur in a milieu of normal hematopoiesis by as a matter of course because genomic divergence is a fundamental element of biology. Organism speciation implicates genetic variation is the first step of evolution, followed by resource restriction pressure (a bottleneck). Such conditions create an environment where competitive advantages arise for genetically unique sub-species. Our work is based on the hypothesis that these rules also apply to the rise of pathologic clonal dominance. Consequentially, a low level of mutations in normal hematopoietic stem cells should be detectable and increase with age. Mutations can serve as lineage markers to allow the definition of the kinetics of competing myeloid sub-clones. Also, individual clones with higher rates of mutation might serve as a pre-condition for pathological clonal dominance and disease initiation.Methods: Healthy 78 year old female myeloid progenitors were single cell sorted and cultured for 6 weeks in expansion media. Clones were harvested and typed apropos X-Chromosome Inactivation state (XCI state) as either "Xa" or "Xb" using a methylation specific polymerase chain reaction strategy after DNA was bisulfite modified. Remaining unmodified DNA was whole genome amplified and placed on an Affymetrix 6.0 Single Nucleotide Polymorphism (SNP) array (2.5 million SNP calls/array). Partek Genome Suite software interpreted raw SNP intensity signals as copy number variants (CNV) or loss of heterozygosity (LOH) calls using a stringent search strategy of a > 30 SNP markers, and an average variance of 0.5 (p<0.001). Mutations were compared between XCI states and within XCI states (i.e: individual Xa or Xb clones).Results: SNP comparison between XCI defined phylogenetic lineages showed significant somatic LOH and CNV variance, as did comparison of clones within specific XCI states (e.g: between Xa clones). Mutations represent accumulated genetic drift over the 78.75 years since subject conception and are summarized in Table 1. Regarding call parameters, LOH analysis was unpaired, using Partek internal references. For CNV calls, subtractive comparison was made between related data sets. For example, raw Xa data from clones A1 and A2 were averaged, CNV calls were generated and compared to Xb averaged clone data (B1 and B2) to reveal specific XCI state variance (i.e.: A-Ave vs B-Ave). Individual clones were compared within the XCI state (i.e.: clone A1 compared directly to A2 to reveal unique A1 calls). An example of our data interpretation: 8 LOH and 558 CNV are specific to and shared among XCI state Xa clones (i.e.: A-both). Clone A1 had 35 specific, unique LOH and 1402 CNV calls, while clone A2 had 15 unique, specific LOH and 650 CNV calls. Xb clone data (B1, B2, B-both) are displayed in Table 1.Conclusions: Recent studies reveal frequent mutations in the blood of healthy individuals; however within a person there a no model to identify normal myeloid sub-clones. Therefore we have no accurate data on stem cell kinetics or clonal evolution in healthy marrow. Herein we describe the feasibility of using SNP calls variation in un-diseased aged human myeloid cells to define stem cell specific progeny. To our knowledge, this is the first use of both inclusive (somatic mutations) and exclusive (XCI state) markers to develop a phylogenetic lineage map of normal aged marrow. Importantly, all clones had progenitors with an identical genetic background (the fertilized egg) at a single time point (conception). Therefore, this innovative approach allows for the somatic variation rate to be monitored in primary cells occupying the same organism environment as a function of age and stress events (i.e.: chemo, radiation, etc). [Display omitted] [Display omitted] [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Erlotinib and the Risk of Oral Cancer: The Erlotinib Prevention of Oral Cancer (EPOC) Randomized Clinical Trial.

Standard molecularly based strategies to predict and/or prevent oral cancer development in patients with oral premalignant lesions (OPLs) are lacking. To test if the epidermal growth factor receptor inhibitor erlotinib would reduce oral cancer development in patients with high-risk OPLs defined by specific loss of heterozygosity (LOH) profiles. Secondary objectives included prospective determination of LOH as a prognostic marker in OPLs. The Erlotinib Prevention of Oral Cancer (EPOC) study was a randomized, placebo-controlled, double-bind trial. Accrual occurred from November 2006 through July 2012, with a median follow-up time of 35 months in an ambulatory care setting in 5 US academic referral institutions. Patients with OPLs were enrolled in the protocol, and each underwent LOH profiling (N = 379); they were classified as high-risk (LOH-positive) or low-risk (LOH-negative) patients based on their LOH profiles and oral cancer history. The randomized sample consisted of 150 LOH-positive patients. Oral erlotinib treatment (150 mg/d) or placebo for 12 months. Oral cancer-free survival (CFS). A total of 395 participants were classified with LOH profiles, and 254 were classified LOH positive. Of these, 150 (59%) were randomized, 75 each to the placebo and erlotinib groups. The 3-year CFS rates in placebo- and erlotinib-treated patients were 74% and 70%, respectively (hazard ratio [HR], 1.27; 95% CI, 0.68-2.38; P = .45). The 3-year CFS was significantly lower for LOH-positive compared with LOH-negative groups (74% vs 87%, HR, 2.19; 95% CI, 1.25-3.83; P = .01). Increased EGFR gene copy number correlated with LOH-positive status (P < .001) and lower CFS (P = .01). The EGFR gene copy number was not predictive of erlotinib efficacy. Erlotinib-induced skin rash was associated with improved CFS (P = .01). In this trial, LOH was validated as a marker of oral cancer risk and found to be associated with increased EGFR copy number (the target of the intervention). Erlotinib did not, however, improve CFS in high-risk patients with LOH-positive or high-EGFR-gene-copy-number OPLs. These results support incorporation of LOH testing as a prognostic tool in routine clinical practice but do not support erlotinib use in this setting. clinicaltrials.gov Identifier: NCT00402779.

Specific TP53 Mutants Overrepresented in Ovarian Cancer Impact CNV, TP53 Activity, Responses to Nutlin-3a, and Cell Survival

Evolutionary Action analyses of The Cancer Gene Atlas data sets show that many specific p53 missense and gain-of-function mutations are selectively overrepresented and functional in high-grade serous ovarian cancer (HGSC). As homozygous alleles, p53 mutants are differentially associated with specific loss of heterozygosity (R273; chromosome 17); copy number variation (R175H; chromosome 9); and up-stream, cancer-related regulatory pathways. The expression of immune-related cytokines was selectively related to p53 status, showing for the first time that specific p53 mutants impact, and are related to, the immune subtype of ovarian cancer. Although the majority (31%) of HGSCs exhibit loss of heterozygosity, a significant number (24%) maintain a wild-type (WT) allele and represent another HGSC subtype that is not well defined. Using human and mouse cell lines, we show that specific p53 mutants differentially alter endogenous WT p53 activity; target gene expression; and responses to nutlin-3a, a small molecular that activates WT p53 leading to apoptosis, providing “proof of principle” that ovarian cancer cells expressing WT and mutant alleles represent a distinct ovarian cancer subtype. We also show that siRNA knock down of endogenous p53 in cells expressing homozygous mutant alleles causes apoptosis, whereas cells expressing WT p53 (or are heterozygous for WT and mutant p53 alleles) are highly resistant. Therefore, despite different gene regulatory pathways associated with specific p53 mutants, silencing mutant p53 might be a suitable, powerful, global strategy for blocking ovarian cancer growth in those tumors that rely on mutant p53 functions for survival. Knowing p53 mutational status in HGSC should permit new strategies tailored to control this disease.

Association of loss of heterozygosity with shorter survival in primary glioblastoma patients

Loss of heterozygosity (LOH) co-deletion 1p/19q, MGMT promoter methylation and/or IDH1 mutation generally signify a better prognosis for patients with glioma. However, the influence of 1p/19q co-deletion and the LOH on other chromosomes in primary glioblastoma on survival is still debatable. The aim of our study was to identify LOH on chromosomes 1p, 19q, 9p, 10q, 13q, and 17p, and evaluate their impact either alone or 1p/19q co-deletion or by groups of LOH on the overall survival of 42 primary glioblastoma patients without an oligodendroglial component. These patients were additionally molecularly characterized for EGFR amplification, IDH1 mutations and TP53 mutations. We assessed their influence on the overall survival of glioblastoma patients. LOH in at least one of the loci on all examined chromosomes was detected in 65% of cases and was significantly associated with shorter overall survival (hazard ratio 3.07; 95% CI: 1.29-7.31, p = 0.006). 1p/19q co-deletion was infrequent (7.14%) and had no impact on overall survival. Our results indicate that in primary glioblastoma a specific LOH group analysis may be important for the prognosis. LOH 1p/19q co-deletion is rare in glioblastoma without an oligodendroglial component and has no impact on patient survival.

Abstract 4158: MEKK1 regulates DMP1 transcriptional activity via phosphorylation and predicts breast cancer patient outcome

Abstract Breast cancer remains a significant public health issue in the industrialized countries. Physicians depend on surgery, cytotoxic adjuvant chemotherapy, or radiation for treatment of breast cancer patients. Few novel therapies are approved for clinical use. Although existing therapies are effective in controling the disease in many patients, the cytotoxic side-effects make them limited. This is especially the case in the patients with early stage breast cancer whose prognosis with surgery alone is good and avoiding adjuvant chemotherapy would spare them toxic side effects. On the other hand, significant fraction of patients relapses and develops metastasis. Therefore, it is critical to identify markers for better breast cancer patient stratification based on their prognosis that would guide physicians in selection and aggressiveness of therapies. Recently, we linked transcription factor DMP1 (cyclin D binding protein 1, Dmtf1) as a critical tumor suppressor that blocks proliferative signals from ErbB2 and oncogenic Ras by activating p14Arf-p53 pathway. hDMP1 is hemizygously deleted in ∼50% of human breast tumors that retain wild-type ARF and p53. In this study we identified an upstream kinase, MEKK1, which cooperates with Dmp1 to activate Arf transcription. In constitutively active form (C-terminal kinase domain or CA-MEKK1), MEKK1 increased transcriptional activity of Dmp1 via direct phosphorylation, while the full length (regulatory and kinase domain) form behaved as a feedback inhibitor by increasing Dmp1 ubiquitination. Phosphorylation sites on DMP1 that increase its transcriptional activity were mapped to the C-terminal transactivation domain. Expression of CA-MEKK1 in breast cancer cell lines activated endogenous Arf-p53 pathway. hMEKK1 is located on human 5q11 chromosome, a locus frequently deleted in breast and lung cancer. Since MEKK1 appeared to be an activator of p53 tumor suppressor pathway, we wondered if MEKK1 is involved in human cancer. Using DNA from breast cancer patient tumors and matched normal tissue, we analyzed hMEKK1 gene deletion using specific loss of heterozygosity (LOH) primers. MEKK1 was found hemizygously deleted in ∼20% of patients. Immunohistochemistry confirmed reduction of MEKK1 protein intensity to LOH(+) compared to LOH (-) patients. In the independent cohort of breast cancer patients, we show that low MEKK1 mRNA expression is associated with adverse outcome. Here we show that constitutively active MEKK1 is a novel activator of Dmp1-Arf-p53 pathway via Dmp1 phosphorylation. The MEKK1 gene was frequently deleted in breast tumor tissue and its expression was correlated with disease outcome. Overall, MEKK1 is a potential prognostic/predictive indicator for breast cancer and could be used by physicians to better stratify patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4158. doi:1538-7445.AM2012-4158

27-OR: Leukemia Specific Loss of Heterozygosity at MHC Locus Detected at Confirmatory Typing of HSCT Recipient with CLL

27-OR: Leukemia Specific Loss of Heterozygosity at MHC Locus Detected at Confirmatory Typing of HSCT Recipient with CLL

T1502: Performance Characteristics of K-RAS and LOH Mutation Patterns in Predicting Mucinous Pancreatic Cyst Histology

Commercially available pancreatic cyst fluid DNA analysis (RedPath) maybe helpful in the evaluation of pancreatic cysts (PCs). Early studies have demonstrated that a k-ras mutation has a high predictive value for mucinous histology and that multiple high amplitude loss of heterozygosity (LOH) mutations may be predictive of malignancy. However, few data exist regarding the prevalence of specific LOH mutations and the predictive value of specific LOH mutations for mucinous histology.

Loss of Heterozygosity in Endometrial Carcinoma

Inactivation of a tumor suppressor gene typically occurs in two steps, thus fulfilling Knudson hypothesis. One "hit" is frequently a point mutation or a small deletion. The other alteration is usually a large genomic loss of part of a gene, or even part of a chromosome, or the whole chromosome. However, it is not clear which of these two events occurs first. Loss of heterozygosity (LOH) analysis allows the identification of one of the 2 hits. Although microsatellite polymerase chain reaction is the technique most frequently used to assess LOH, other different approaches can also be used. The LOH can also be assessed by restriction fragment length polymorphism analysis, single strand conformation polymorphism analysis, oligonucleotide microarrays capable to simultaneously determine the genotype of thousands of single-nucleotide polymorphism (single-nucleotide polymorphism arrays), comparative genomic hybridization, multiplex amplification and probe hybridization, and multiplex ligation-dependent probe amplification. In this article, the authors review the results obtained with molecular analysis of LOH in the understanding of development and progression of endometrial carcinoma. Particular attention is given to: (1) the presence of widespread LOH in nonendometrioid carcinoma, probably reflecting the existence of chromosomal instability; and (2) specific LOH patterns associated with some clinicopathologic features.

Genome-Wide Analysis for Loss of Heterozygosity in Primary and Recurrent Phyllodes Tumor and Fibroadenoma of Breast using Single Nucleotide Polymorphism Arrays

Phyllodes tumors of the breast are biphasic stromal and epithelial tumors histologically similar to benign fibroadenomas, but with a neoplastic stromal component. In contrast to fibroadenoma, phyllodes tumors can recur and be locally aggressive or be malignant. This study uses SNP array analysis to present a genome-wide map of loss of heterozygosity (LOH) in a cohort of phyllodes tumors and fibroadenomas. LOH is frequent and sometimes extensive in phyllodes tumors, but is rarely seen in fibroadenomas. There is heterogeneity between phyllodes tumors of different patients and no one LOH marker identifies a majority of these lesions. However, a subset of LOH loci occur in multiple cases of phyllodes tumors and are not found in fibroadenomas. Primary phyllodes tumors and paired recurrences from the same patient share common regions of LOH. In contrast, metachronous fibroadenomas from the same patient have different LOH patterns with no indication of a shared origin. Specific LOH loci may be associated with pathologic progression in recurrent phyllodes tumors. In a single case of phyllodes tumor containing a malignant epithelial component the malignant epithelium and stroma partially share an LOH genotype, suggesting a common precursor cell for the biphasic malignant components.

STRAD in Peutz-Jeghers syndrome and sporadic cancers

Background/Aims:LKB1 is a tumour suppressor gene that is associated with Peutz-Jeghers syndrome (PJS), a rare autosomal dominant cancer predisposition syndrome. However, germline mutations in the LKB1 gene are found in...

High frequency of allelic losses in high-grade prostate cancer is associated with biochemical progression after radical prostatectomy

Loss of heterozygosity (LOH) is the most consistent genetic change in prostate cancer (CaP). We aimed, to correlate specific LOH and the overall LOH frequency, to disease progression after radical prostatectomy (RP) in high-grade CaP. Between January 1990 through December 1998, 126 patients who underwent RP (cT1-T2), Gleason 8–10, were pT3, or pN1, or SM(+) (surgical margins). Nine were lost of follow-up, 39/117 (33%) had no biochemical progression (mean follow-up: 45 months). After exclusion for preoperative PSA >50 ng/mL, a case-control study was designed by matching 26 of these cases with 26 similar patients without biochemical progression (criteria: pT, pN, year of surgery). Using microsatellite markers, LOH were assessed on six chromosomal regions (7q31, 8p22, 12p13, 13q14, 16q23.2, 18q21). No prognostic value was associated with LOH at any one specific locus. However, the overall LOH frequency (five classes, cutoff of 60%), was significantly higher if progression ( P = 0.02; P = 0.03) in SM(+) patients, and was near statistical significance ( P = 0.08; P = 0.07) for the overall case-control population. In multivariate analysis (overall population), the overall LOH rate ≥60% was independently associated with progression [ P = 0.035; Odds Ratio (OR) = 5.54]. An overall LOH rate ≥60% predicted poor outcome in 85% of SM(+) patients and 69% of the whole population. Our results suggest that the overall rate of LOH at chromosomal “hot spots” is more likely to be predictive of recurrence than the presence of LOH at any one particular locus. Moreover, the identification of a threshold of LOH could help in predicting patients with poor outcome who may be candidates for local or systemic adjuvant therapies.

Clinical and molecular analysis of combined hepatocellular-cholangiocarcinomas

Background/Aims Combined hepatocellular-cholangiocarcinoma (HCC-CC) show dual hepatocellular and biliary epithelial differentiation. To better understand the relations between cholangiocarcinoma (CC), HCC-CC and hepatocellular carcinoma (HCC), we screened for genetic alterations. Methods A series of nine CC, 15 HCC-CC and three separated HCC and CC lesions (‘collision tumors’) were screened for loss of heterozygosity (LOH) using 400 microsatellite markers and for p53 and β-catenin mutations. A comparison with a previously characterized series of 137 HCC was performed. Results In six cases of CC and HCC-CC, we identified TP53 gene mutations. A CTNNB1/β-catenin was identified in two patients presenting collision tumors, but no mutations were found in CC or in HCC-CC. A high level of chromosome instability in both CC and HCC-CC was found. Recurrent specific LOH were identified at 3p and 14q in more than 50% of the CC and the HCC-CC cases, whereas these chromosomal regions were deleted in less than 10% of the HCC cases ( P<10 −5). Minimal common regions of deletion (MCRD) were defined at 3p24-p14 and 14q24-q32, respectively. Conclusions These results suggest that combined HCC-CC are genetically closer to CC than HCC and common carcinogenesis pathways may be altered in HCC-CC and CC.

Clinical and molecular analysis of combined hepatocellular-cholangiocarcinomas

<h2>Abstract</h2><h3>Background/Aims</h3> Combined hepatocellular-cholangiocarcinoma (HCC-CC) show dual hepatocellular and biliary epithelial differentiation. To better understand the relations between cholangiocarcinoma (CC), HCC-CC and hepatocellular carcinoma (HCC), we screened for genetic alterations. <h3>Methods</h3> A series of nine CC, 15 HCC-CC and three separated HCC and CC lesions (‘collision tumors') were screened for loss of heterozygosity (LOH) using 400 microsatellite markers and for p53 and β-catenin mutations. A comparison with a previously characterized series of 137 HCC was performed. <h3>Results</h3> In six cases of CC and HCC-CC, we identified <i>TP53</i> gene mutations. A CTNNB1/β-catenin was identified in two patients presenting collision tumors, but no mutations were found in CC or in HCC-CC. A high level of chromosome instability in both CC and HCC-CC was found. Recurrent specific LOH were identified at 3p and 14q in more than 50% of the CC and the HCC-CC cases, whereas these chromosomal regions were deleted in less than 10% of the HCC cases (<i>P</i><10⁻⁵). Minimal common regions of deletion (MCRD) were defined at 3p24-p14 and 14q24-q32, respectively. <h3>Conclusions</h3> These results suggest that combined HCC-CC are genetically closer to CC than HCC and common carcinogenesis pathways may be altered in HCC-CC and CC.

Microsatellite analysis of breast carcinoma and corresponding local recurrences.

Local recurrence is a serious complication of breast carcinoma that reduces quality of life and influences prognosis. The aim of this study was to determine whether local recurrences of breast carcinoma are genetically related to the primary tumours. Forty cases of locally recurrent breast carcinomas (median onset: 3.6 years after primary surgery) were analysed: 22 patients had undergone breast-conserving therapy and 18 mastectomy. Eighteen microsatellites on chromosomes 2p, 3p, 5q, 10q, 11p, 11q, 13q, 17q, 17p, 18p were amplified by PCR using fluorescent-labelled primers, automatically detected after polyacrylamide gel electrophoresis and analysed for loss of heterozygosity (LOH) or microsatellite instability (MSI). Follow-up data were available for 39 cases with a median value of 89 months. All LOH and MSI found in the primary tumours were also present in the corresponding recurrences, indicating that they are genetically related to the primary tumours and not secondary malignancies in the same breast. MSI was found in three cases, of which one harboured MSI at more than two loci. The median value of LOH per case was significantly higher in the recurrent (four per case) compared to the primary tumours (two per case; p < 0.001, Mann-Whitney test), reflecting the genotype of tumour progression. Early local recurrence was associated with specific LOH for TP53.15 (p = 0.018, log-rank test) in the primary tumours. LOH on D13S1699 or D17S855 was associated with lymph node metastases (p = 0.024 and p = 0.019, respectively; chi-square test). In addition, tumour grade, lack of oestrogen or progesterone receptor expression, young patient age and early appearance of local recurrence significantly correlated with poor survival. The development of local recurrence despite clear resection margins may result from residual DCIS distant from the invasive carcinoma, homing of circulating tumour cells, or genetically altered, histologically normal breast tissue not immediately adjacent to the invasive carcinoma.

Loss of heterozygosity at 1p, 8p, 10p, 13q, and 17p in advanced urothelial cancer and lack of relation to chemotherapy response and outcome

Studies of urothelial tumors have identified structural abnormalities in a number of chromosomes. This study aimed to identify specific genetic changes of patients with advanced urothelial cancers, and relate these changes to increased chemotherapy sensitivity or good prognosis. We screened 56 muscle-invasive bladder cancer tumors for loss of heterozygosity (LOH) at chromosome 1p, 8p, 10p, 13q, and 17p with PCR using 6 microsatellite markers. All patients had recurrent locally advanced or metastatic disease. DNA was extracted after microdissection of the primary tumor and normal tissue from paraffin-embedded specimens. The PCR products were electrophoresed in an ABI Prism 377 DNA sequencer and the alleles from tumor DNA and normal tissue DNA were analyzed using the GeneScan program. The LOH findings were correlated with response to chemotherapy and survival. Allelic loss of specific markers was present in 26–50% of the informative tumors. The most frequent LOH was observed at 17p, supporting the notion that this region may contain genes of importance to urothelial cancer progression. The overall rate of response to chemotherapy was 48%, and ranged from 40% to 56% according to specific LOH changes. The median survival of all patients from start of chemotherapy was 5.8 months and ranged from 5.3 to 7.9 months for patients with specific LOH changes. Response and survival of patients with no lost markers was the same size, compared to patients with one, two, or more lost markers. Specific genetic changes were detected in a significant number of tumors from patients with advanced urothelial cancer. These changes were not predictive of response to chemotherapy or of the duration of survival.

Frequent allelic imbalance of tumor suppressor gene loci in cervical dysplasia.

In addition to human papillomavirus (HPV) infection, loss of heterozygosity (LOH) at tumor suppressor gene loci has been frequently observed in cervical cancer. Thus, it may be assumed that detection and characterization of specific LOH profiles in preneoplastic lesions, in addition to HPV typing, might facilitate assessment of progression risk of cervical dysplasia. In this study, the type and frequency of allelic imbalance (allelic loss or allelic reduction) were analyzed in 24 unrelated cervical lesions using 14 polymorphic microsatellite markers at different tumor suppressor gene loci. No allelic loss was observed in four condylomatous lesions, whereas 2 of 13 (15%) CIN I lesions displayed allelic loss at 3p25 and 5q11-13. In high-grade lesions, however, allelic loss occurred in four of six (66%) cases at multiple chromosomal regions (3p14-25, 5p15, 5q11, 5q21, 11p15, and 17q21). Allelic reduction was observed in 4 of 13 (30%) low-grade lesions and 3 of 6 (50%) high-grade lesions. LOH was confined to lesions infected by high-risk HPV types. These data suggest that chromosomal instability is an early event in cervical carcinogenesis. The detection of LOH on multiple chromosome 3p loci in 50% of high-grade lesions suggests that a specific marker panel encompassing this region might enable better assessment of which lesions are likely to regress, persist, or progress.

Mutation analysis of the Fanconi anaemia A gene in breast tumours with loss of heterozygosity at 16q24.3.

The recently identified Fanconi anaemia A (FAA) gene is located on chromosomal band 16q24.3 within a region that has been frequently reported to show loss of heterozygosity (LOH) in breast cancer. FAA mutation analysis of 19 breast tumours with specific LOH at 16q24.3 was performed. Single-stranded conformational polymorphism (SSCP) analysis on cDNA and genomic DNA, and Southern blotting failed to identify any tumour-specific mutations. Five polymorphisms were identified, but frequencies of occurrence did not deviate from those in a normal control population. Therefore, the FAA gene is not the gene targeted by LOH at 16q24.3 in breast cancer. Another tumour suppressor gene in this chromosomal region remains to be identified. © 1999 Cancer Research Campaign

Specificity of loss of heterozygosity in radiation-induced mouse myeloid and lymphoid leukaemias

Purpose : To determine whether loss of heterozygosity (LOH) at specific chromosomal loci in radiation-induced leukaemias, arising in a similar genetic background, is leukaemia-type specific (myeloid versus lymphoid) or common to both. Materials and methods : Leukaemias that arose in 3Gy X-irradiated (CBA/H C57BL/6)F1 intercross and backcross mice were diagnosed as acute myeloid leukaemia (AML) or thymic lymphoma (TL). LOH was determined using 28 polymorphic microsatellite markers distributed over seven chromosomes using control and leukaemic DNA from individual mice. Results : LOH incidences of 0-20% were observed at most loci in both leukaemia types. Specific LOH incidences of 38-76% were observed for myeloid (chromosome 2) and lymphoid (chromosomes 11 and 14) leukaemias. Chromosome 4 LOH was frequently (38-50%) observed in both types, although the commonly deleted regions differed. LOH was detected at either chromosome 2 or 4 in AML and either chromosome 4 or 11 in TL. Conclusions : LOH incidences of 38-76% suggest a causal role of particular loci which is mainly, but not exclusively, dependent on leukaemia type. LOH incidences of 0-20% at other loci in both leukaemias suggest that many genetic deletions are noncausal and incidental in radiation-leukaemogenesis.

Human bladder cancers and normal bladder mucosa present the same hot spot of heterozygous chromosome-9 deletion.

Loss of heterozygosity (LOH) on chromosome 9 is the most frequent genetic alteration in bladder cancer identified to date, suggesting the presence of key gene(s) for this pathology. In this study, we examined 44 bladder tumors and 21 normal bladder samples for LOH on both arms of chromosome 9. Sixteen microsatellite markers, 12 on the short arm (encompassing 9p21-22) and 4 on the long arm (encompassing 9q33-34), were chosen for their highly frequent alterations in bladder cancer. LOH for at least one marker was identified in 42 tumor samples (95.5%), and 14 tumors (32%) displayed LOH for all informative tested markers. Detailed analysis showed that 2 markers on chromosome 9p (D9S157 and D9S156) had the highest frequencies of allelic loss (about 70%), independent of tumor grade and stage. The same study was performed on the 21 normal bladder mucosa samples: 50% of informative cases presented a single specific LOH at the D9S156 locus. Normal samples showing LOH at this locus were therefore screened with 3 novel microsatellite markers in the 810-kb region incorporating D9S156. Using this marker, we found no further heterozygous loss in this region. This result allows different interpretations of the D9S156 loss in normal bladder mucosa, and suggests that D9S156 may be more an indicator of bladder epithelium impairment than a tumor-initiation marker. Similarly, this unexpected result calls in question the interpretation of LOH studies.