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PubMed1988

Comparison of clonal analysis and DNA restriction analysis for typing of Neisseria meningitidis.

We have formerly described a clonal analysis of 423 serogroup A isolates of Neisseria meningitidis which distinguished 21 clones and 34 electrophoretic types. The clones were found to be uniform within distinct epidemiological situations and distinct between different sets of epidemics. Strains representative of the 34 electrophoretic types have now been analyzed by restriction endonuclease digestion of their genomic DNA's. The results correlated partially with the clonal assignments; the discrepancies were epidemiologically more consistent with the interpretation of the clonal analysis than with that of the restriction endonuclease analysis.

Bacterial Typing Techniques↗
PubMed1994

Clonal analysis of human gynecologic cancers by means of the polymerase chain reaction.

Clonality of human gynecologic cancers was analyzed in small DNA samples prepared from cryostat sections, by means of the polymerase chain reaction (PCR). The method used for clonal analysis was based on restriction fragment length polymorphism of the X-chromosome-linked phosphoglycerokinase (PGK) gene and on the differential methylation of the PGK gene due to random inactivation of 1 of 2 X-chromosomes by methylation in females. Among 52 gynecologic cancers tested, 25 were found to be heterozygous for the BstXI polymorphism of the PGK gene. All the 25 gynecologic cancers (4 cervix, 11 endometrium, 7 ovary and 3 fallopian tube) analyzed by the PCR-based method were monoclonal in origin while adjacent normal tissues were polyclonal. When DNA samples were prepared from widely separated sites of tumors and/or metastatic lesions, every sample was found to be monoclonal, and the same allele of the PGK gene was inactivated in each case. These results demonstrate that clonal analysis by PCR offers a good method for studying clonality in small DNA samples prepared from cryostat sections of tumors. This method could be applied to distinguish between benign and malignant gynecologic lesions.

Adult↗
PubMed1996

Clonal analysis of precancerous lesion of hepatocellular carcinoma.

BACKGROUND & AIMS: It remains to be established whether precancerous lesion (dysplastic nodule) of hepatocellular carcinoma (HCC) is a neoplastic or hyperplastic lesion. Clonal analysis of this lesion was conducted to elucidate this important issue on histogenesis. METHODS: The method for clonal analysis was based on restriction fragment length polymorphism of the X chromosome-linked phosphoglycerokinase gene and on random inactivation of the gene by methylation. Clonal somatic mutations were also analyzed by DNA fingerprinting with two multilocus probes (33.6 and 33.15), and loss of heterozygosity was studied using five single-locus probes (MS1[1p33-p35], MS31[7p22-pter], MS43a[12q24.3-qter], MS8[5q35-qter], and g3[7q36-qter]). RESULTS: Clonal analysis by the phosphoglycerokinase gene-based method showed that all of the five dysplastic nodules and seven HCCs were monoclonal in origin. DNA fingerprinting showed clonal somatic mutations in six of 10 dysplastic nodules and in six of nine HCCs. Loss of heterozygosity was found in one dysplastic nodule (7p22-pter) and two HCCs (1p33-p35 and 12q24.3-qter). CONCLUSIONS: These results confirm monoclonality of HCC and show that hepatic precancerous lesion (dysplastic nodule) is not a hyperplastic but a neoplastic lesion, consisting of monoclonal cells with genetic alterations.

Aged↗
PubMed1994

Discrimination between multicentric and multifocal carcinomas of the breast through clonal analysis.

BACKGROUND: An unanswered, important question concerning multiple breast carcinomas is whether they arise independently in the breast (multicentric) or are metastatic deposits from a single, primary carcinoma (multifocal). This issue was studied by clonal analysis of each focus of multiple breast carcinomas. METHODS: First, the clonality of 30 breast carcinomas was analyzed by the method based on restriction fragment length polymorphism of the X-chromosome-linked phosphoglycerokinase (PGK) gene and on random inactivation of the gene. Second, the clonality of each focus of three multiple breast carcinomas was analyzed by the same method. RESULTS: Clonal analysis of the 30 breast carcinomas revealed that every carcinoma was monoclonal in origin, and one of two alleles of the PGK gene was inactivated at random in these carcinomas. Three patients with multiple breast carcinomas had three, three, and four histologically separate foci of carcinoma in the breast, respectively. Clonal analysis showed that each focus was monoclonal in origin and, in addition, the same allele of the PGK gene was inactivated consistently at each focus in every patient. CONCLUSIONS: The thesis that multiple carcinoma foci arise independently is unlikely to be true, because the probability that every independent focus happens to inactivate the same allele of PGK gene in every patient is very low. It seems more likely that a single primary carcinoma spreads throughout the breast to culminate in multiple secondary carcinoma foci. Therefore, it is concluded that multiple breast carcinomas are multifocal and not multicentric in origin.

Breast Neoplasms↗
PubMed1994

Clonal analysis of regenerative nodules in hepatitis C virus-induced liver cirrhosis.

BACKGROUND/AIMS: Based on histological criteria, regenerative nodules in cirrhotic liver have been generally considered to result from hyperplastic proliferation of hepatocytes. Whether these nodules are hyperplastic or neoplastic has not been determined definitively. This study examined the issue by clonal analysis of each nodule. METHODS: The method for clonal analysis was based on restriction fragment length polymorphism of the X chromosome-linked phosphoglycerokinase gene and on random inactivation of the gene by methylation. RESULTS: Clonality of hepatocellular carcinoma (n = 7) and regenerative nodules (n = 76) induced by hepatitis C virus infection was analyzed. All carcinomas were monoclonal. Clonal analysis of regenerative nodules showed that 43% (33 of 76) were monoclonal in origin. Adjacent monoclonal nodules showed inactivation of the same allele of phosphoglycerokinase gene. Because the gene allele is inactivated at random, it is unlikely that each nodule happens to inactivate the same allele; it is more likely that monoclonal cell expansion is initiated before the nodule is established by septum formation. CONCLUSIONS: Monoclonal cell expansion is seen in a considerable number of regenerative nodules in cirrhotic liver. The results indicate that certain genetic changes, which are required for hepatocarcinogenesis, have already occurred in these nodules.

Base Sequence↗
PubMed1995

Progression of fibroadenoma to phyllodes tumor demonstrated by clonal analysis.

BACKGROUND: The histogeneses of fibroadenoma and phyllodes tumor of the breast appear to be closely related, but it is still unclear whether fibroadenoma can progress directly to phyllodes tumor. METHODS: This issue was studied by conducting clonal analysis of fibroadenoma and phyllodes tumors that were obtained sequentially from the same patient. One patient developed local recurrence of phyllodes tumor twice, and the other two patients each developed a phyllodes tumor after excision of a primary fibroadenoma. The method for clonal analysis was based on trinucleotide repeat polymorphism of the X chromosome-linked androgen receptor (AR) gene and on random inactivation of the gene by methylation. RESULTS: Clonal analysis revealed that all the three primary fibroadenomas were monoclonal and all four recurrent phyllodes tumors were also monoclonal in origin. In addition, the same allele of the AR gene was inactivated in fibroadenoma and phyllodes tumor(s) in each patient. The probability that phyllodes tumors of different origin happen to inactivate the same allele of the AR gene as fibroadenomas in every case is quite low. Rather, it is more reasonable to assume that the phyllodes tumor has the same origin as fibroadenoma. CONCLUSIONS: These results identified monoclonal fibroadenomas that can progress to phyllodes tumors.

Adult↗
PubMed2001

Hepatocellular carcinoma associated with focal nodular hyperplasia. Report of a case with clonal analysis.

We describe a hepatocellular carcinoma partially surrounded by focal nodular hyperplasia in a 65-year-old female patient. In order to clarify the relationship of the hepatocellular carcinoma and the adjacent focal nodular hyperplasia, clonal analysis was conducted. The clonal analysis was based on the methylation pattern of the polymorphic X-chromosome-linked androgen receptor gene (HUMARA). The allelic bands from the amplification of the focal nodular hyperplasia and of the hepatocellular carcinoma showed a significant reduction in the intensity of one of the two alleles as compared with two alleles of equal intensity in the buff coat after HhaI digestion, which indicated that these two parts were monoclonal. However, the inactivated allele in the focal nodular hyperplasia and that in the hepatocellular carcinoma were not identical. Therefore, the focal nodular hyperplasia and hepatocellular carcinoma probably derived from the clonal expansion of two different clones.

Aged↗
PubMed1999

Clonality analysis of granulocytes and T lymphocytes in healthy females by the PCR-based HUMARA method.

Clonality analysis utilizing X-chromosome inactivation has been used in the study of various diseases, including hematological malignancies. The human androgen receptor gene (HUMARA) assay is the newest of such methods, and the majority of the female population can be assessed by this relatively simple procedure. One problem in using these clonality analysis methods, however, is that there may be significant variation in Lyonization in blood cells in normal individuals. To determine the diversity in X-chromosome methylation patterns, which reflect Lyonization, assessed by the HUMARA assay in the supposedly normal population, we analyzed granulocytes and T cells from 97 relatively young (18- to 35-year-old) healthy female volunteers. We found that the methylation patterns in the two HUMARA alleles were distributed even more widely, both in granulocytes and in T cells, than previously reported with other methods. We also found that the deviation of methylation in granulocytes and T cells was well correlated. Thus, we conclude that appropriate controls from the same individuals, such as T cells in the case of stem cell disorders, should always be employed to conclusively determine whether certain cells of hematopoietic origin are clonal.

Adolescent↗
PubMed1999

Consecutively Occurring Multiple Fibroadenomas of the Breast Distinguished from Phyllodes Tumors by Clonality Analysis of Stromal Tissue.

We present a woman with consecutively occurring multiple fibroadenomas of thebreast distinguished from phyllodes tumor by clonality analysis of stromal tissue. Fifty-three masses developed in her right breast in an 11.5 year period since first onset. A clonality analysis, performed by polymerase chain reaction (PCR), focused on the Hpa II site within exon 1 of the androgen receptor (AR) gene. Estrogen receptor (ER) alpha immunohistochemistry was performed with a specific polyclonal antibody against the hormone binding domain of the protein. Since all of the nodules were polyclonal in stromal tissues, they were hyperplastic rather than true neoplasms such as phyllodes tumors. The co-existence of abundant adenosisfoci and numerous sub-clinical small nodules in the adjacent breast tissue alsosuggested proliferative stimuli throughout the breast. ER alpha protein was expressed only in the nuclei of epithelial cells. The possible influence of ER positive epithelial cells on stromal cell growth is discussed.

Journal Article↗
PubMed1993

Use of X-linked clonal analysis in acute promyelocytic leukemia.

X-linked clonal analysis (XLCA) either using Glucose-6-phosphate dehydrogenase (G-6-P-D) polymorphisms or restriction fragment length polymorphisms (RFLP) and methylation analysis has provided considerable understanding of haematologic malignancy. Acute Promyelocytic Leukemia (APL) is characterized by a unique cytogenetic translocation t(15;17), frequent achievement of remission without a preceding phase of marrow hypocellularity after induction chemotherapy and a high rate of clinical response to all-trans retinoic acid (ATRA). In limited studies XLCA has provided insight into the pathogenesis and mechanism of drug action in this disease.

Humans↗
PubMed1997

Clonality analysis in tumours of women by PCR amplification of X-linked genes.

Modifications have been made to two polymerase chain reaction (PCR) methods for clonality analysis based on the inactivation patterns of two highly polymorphic X-linked genes encoding the androgen receptor (AR) and monoamine oxidase A (MAOA). These methods have been used to examine the clonal nature of frozen tissues from 42 tumours and 25 non-tumour controls from female subjects. Unbalanced inactivation patterns of the genes, which indicate monoclonality, were frequently observed in tumours of heterozygous (informative) cases (18/35 = 51.4 per cent for the AR gene, 9/30 = 30 per cent for the MAOA gene, and 21/38 = 55.2 per cent for both). Among 23 informative non-tumour controls, only one (4.3 per cent), a reactive lymph node, showed skewing in the AR gene. Successful detection of monoclonality was found to depend on the proportion of tumour cells in the tissues examined. None of the AR or MAOA informative cases containing less than 50 per cent of tumour cells showed imbalance in inactivation patterns. With more than 50 per cent of tumour cells in the samples, 66.6 per cent (18/27) of AR and 39.1 per cent (9/23) of MAOA informative cases showed allelic imbalance, with a combined frequency of 72.4 per cent (21/29) of both genes. Our results demonstrate that the methods described are useful for clonal analysis of tissue samples from female patients.

Breast Neoplasms↗
PubMed2000

Clonality analysis of defined cell populations in paraffin-embedded tissue sections by RT-PCR amplification of X-linked G6PD gene.

This paper establishes a method of clonality analysis using the reverse transcription-polymerase chain reaction (RT-PCR) to amplify X-linked G6PD transcripts on defined cell populations microdissected from archival, paraffin-embedded tissue sections. Four known monoclonal low-grade B-cell lymphomas from females who were heterozygous (informative) at the 1131 exonic polymorphic locus of the G6PD gene were used to validate the method. Lymphoma and reactive lesions in each case were separated by microdissection. In order to preserve the intact RNA species in the lesion, sections were digested on the slides before microdissection. A one-step RT-PCR was performed with a single pair of primers, one of which contained a mismatched base adjacent to the polymorphic site, to generate a PvuI cutting site. Successful amplification and allele identification by PvuI digestion were achieved from all RNA samples studied. Three of four samples from non-neoplastic reactive lesions showed two bands with equal intensity, representing transcription of the two alleles of the G6PD gene, while the corresponding tumour samples demonstrated a biased intensity in one allele, indicating monoclonality. To assess the method further, the clonal nature of in situ and invasive breast cancers was examined, along with adjacent normal breast tissue and hyperplastic lesions from three informative females from our archives. Apart from the clusters of normal terminal duct-lobular units, all lesions were monoclonal. This result is in agreement with data derived from other X-linked gene studies and loss of heterozygosity (LOH) analyses of pre-invasive breast disease. The results suggest that the clonality analysis method presented here is simple and reliable, and is therefore potentially applicable in a wide range of pathological conditions.

Breast↗
PubMed1998

Clonal analysis helps to differentiate aberrant thyroid tissue from thyroid carcinoma.

A rare case of multiple aberrant of thyroid tissues in the tongue and lymph nodes of the bilateral neck was studied by immunohistochemistry and molecular clonal analysis to determine whether these tissues represent aberrant ectopic thyroid or metastases of a thyroid carcinoma. The thyroid tissues in the tongue and lymph nodes were all of polyclonal origins, consistent with ectopic thyroid in the tongue and bilateral cervical lymph nodes, rather than malignant thyroid tissues. This case shows that molecular clonal analysis can be used to distinguish aberrant thyroid from metastases of thyroid carcinoma.

Adult↗
PubMed1997

Clonal analysis of high-grade squamous intra-epithelial lesions of the uterine cervix.

We previously reported that invasive squamous cell carcinomas of the uterine cervix are of monoclonal composition. In the current study, we extended our previous work to determine the clonal composition of cases of high-grade squamous intra-epithelial lesion (HSIL). Clonal analysis targeting the HUMARA locus was performed on cervical tissue from 9 cases, 8 showing heterozygosity at the HUMARA locus and being, therefore, informative for clonality analysis. Uterine cervices were cut into 12 blocks, fixed with formalin and embedded in paraffin, and DNA was extracted from targeted lesions of each block. A total of 30 samples of cervical intra-epithelial neoplasia 3 (CIN3) (14 samples of carcinoma in situ and 16 samples of severe dysplasia) and 1 sample of CIN2 (moderate dysplasia) were analyzed. Monoclonal composition of the lesions was demonstrated in 30/30 cases of CIN3. Polyclonal composition was seen in the single case of CIN2. In 6 uterine cervices, in which dysplastic lesions were present in more than 3 blocks, the pattern of X-chromosome inactivation was the same in all lesions, suggesting that these individual lesions were derived from a single cell, with intraepithelial extension within the cervical mucosa. By contrast, one uterus contained 2 discontinuous dysplastic foci with different patterns of X-chromosome inactivation, indicating that the 2 lesions developed independently from each other. Our results demonstrate that (i) lesions of CIN3 (severe dysplasia and carcinoma in situ) are composed of a clonal neoplastic population of cells and (ii) most cases of HSIL are unifocal in origin.

Carcinoma in Situ↗
PubMed1998

Clonal analysis of macronodules in cirrhosis.

Several arguments suggest that most hepatocellular carcinomas (HCCs) occurring in human cirrhotic livers arise from large hepatocellular nodules or macronodules. Except for nodules with obvious features of HCC, there exist no consistent criteria enabling the differentiation between benign regenerative and neoplastic, potentially malignant macronodules. Surrogate markers able to accurately discriminate those lesions that will evolve toward a HCC are required. In this study, we investigated the clonality of 26 macronodules isolated from eight cases of explanted cirrhotic livers in women by analyzing X-chromosome inactivation, as indicated by the methylation status of the human androgen receptor gene (HUMARA). For each macronodule, a large set of pathological features was evaluated and used to classify the macronodules into four groups: entirely benign-looking nodule (type 1), low-grade dysplastic nodule (type 2), high-grade dysplastic nodule (type 3), and HCC (type 4). Clonal analysis showed that 14 macronodules (54%) were monoclonal and 12 (46%) were polyclonal. Monoclonality was detected in 5 of 11 (45%) nodules from groups of entirely benign-looking and low-grade dysplastic nodules (types 1 and 2) and in 9 of 15 (60%) nodules from the group of high-grade dysplastic nodule and HCC (types 3 and 4). Neither the etiology of cirrhosis nor the size or histological classification of macronodules was correlated with the clonal status. In conclusion, clonal analysis of macronodules enables the differentiation between mono- and polyclonal macronodules in cirrhosis. Because monoclonal macronodules are prone to evolve to HCC, the determination of the clonal status of a macronodule could provide additional information for evaluating the prognosis of these lesions.

Adult↗
PubMed2000

Limitations of clonality analysis of B cell proliferations using CDR3 polymerase chain reaction.

BACKGROUND/AIMS: Detection of clonal immunoglobulin heavy chain (IgH) rearrangements by the polymerase chain reaction (PCR) is an attractive alternative to Southern blotting in lymphoma diagnostics. However, the advantages and limitations of PCR in clonality analysis are still not fully appreciated. In this study, clonality was analysed by means of PCR, focusing in particular on the sample size requirements when studying extremely small samples of polyclonal and monoclonal lesions. MATERIALS/METHODS: High resolution complementarity determining region 3 (CDR3) PCR was used to investigate the minimum number of cells and the amount of tissue required for the detection of a polyclonal population, both for fresh cells and formalin fixed, paraffin wax embedded tissue. Subsequently, frozen and paraffin wax embedded samples of 76 B cell lymphoproliferative disorders, 43 of which were tested by means of Southern blotting, were analysed to establish the sensitivity of this assay. These specimens included 12 chronic lymphocytic leukaemias (CLLs), nine mantle cell lymphomas (MCLs), 10 follicular lymphomas (FLs), and 45 mucosa associated lymphoid tissue (MALT) lymphomas. The specificity was tested on reactive lymph nodes (n = 19), tonsils (n = 4), peripheral blood lymphocyte fractions (n = 4), and biopsies with gastritis (n = 21). RESULTS: In reactive tissue, 20 ng of high molecular weight DNA derived from 6.5-9 x 10(3) B cells was sufficient to obtain a polyclonal PCR result. With smaller amounts "pseudoclonality" could be induced. When using paraffin wax blocks, undiluted DNA isolated from tonsillar tissue of at least 1 mm2 was necessary to obtain a polyclonal pattern. The sensitivity required to detect clonality in paraffin wax embedded and frozen tissue by PCR for FL (40% and 60%, respectively) was lower than that for MALT lymphomas (60% and 86%, respectively), CLL (78% and 89%, respectively), and MCL (88% and 100%, respectively). PCR specificity was 96% and 100% for frozen and paraffin wax embedded tissue, respectively. CONCLUSION: The minimum amount of template for CDR3 PCR is approximately 20 ng of high molecular weight DNA or 1 mm3 of B cell rich paraffin wax embedded normal tonsillar tissue, but care has to be taken to avoid pseudoclonality when low numbers of B cells are present. Duplicate or triplicate tests should be performed to avoid misinterpretation. The specificity of the PCR assay is almost 100%, whereas sensitivity depends on a combination of factors, such as lymphoma type and tissue fixation. Because frozen samples yield better results, obtaining fresh material for the PCR assay is recommended, especially when analysing FL and MALT lymphomas.

Blotting, Southern↗
PubMed1994

Clonal analysis of parathyroid adenomas by means of the polymerase chain reaction.

Clonality of parathyroid adenomas and normal parathyroid glands was analyzed by a method based on restriction fragment length polymorphism of the X-chromosome-linked phosphoglycerokinase (PGK) gene and on random inactivation of the gene by methylation. Through the introduction of the polymerase chain reaction to this method, clonal analysis could be performed on small DNA samples prepared from cryostat sections of these specimens. Every normal parathyroid gland was found to be polyclonal while every parathyroid adenoma was found to be monoclonal. When DNA samples obtained from four widely separated sites of an adenoma were independently analyzed, each sample was found to be monoclonal and, in addition, the same allele of PGK gene was inactivated. These results suggest that parathyroid adenoma, which has a single cell origin, is a true neoplasm and that its pathogenesis is probably different from that of parathyroid hyperplasia which is polyclonal in origin.

Adenoma↗
PubMed1994

Preoperative Discrimination of Fibroadenoma Which Is Clinically and Cytologically Indistinguishable from Breast Carcinoma through Clonal Analysis of Fine Needle Aspirate of Tumor: Report of a Case.

Recently, it has been demonstrated that breast carcimoma is monoclonal and fibroadenoma is polyclonal in origin. In the present case report, this observation was successfully applied to a preoperative differential diagnosis of a fibroadenoma clinically and cytologically indistinguishable from carcimoma. Case report: A45-year old female presented for clinical examination with a history of breast lump. A firm tumor measuring 2 x 2 cm was palpable in the upper-outer quadrant of @the left breast. The margin of the tumor was partially ill-defined and its mobility was restricted. A tumor shadow with a partially ill-defined margin was revealed by mammography. Ultrasonographic examination showed and irregularly-shaped, hypo-echoic tumor accompanied by an acoustic shadow. Fine needle aspiration biopsy yielded positive cytology. Based on these results, the tumor was diagnosed as breast carcinoma. However, clonal analysis of fine needle aspirates showed a polyclonal pattern, strongly indicating that the tumor was not a carcinoma but benign disease; most probably fibroadenoma. Thus, an open surgical biopsy was performed. Histoglogical examination revealed that the tumor was indeed a fibroadenoma with epithelial hyperplasia. This case suggests the usefulness of clonal analysis of fine needle aspirates in differentiating fibroadenoma from carcinoma of the breast.

Journal Article↗