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PubMed1994

Characterization of a microdissection library from human chromosome region 3p14.

Structural alterations in human chromosome region 3p14-p23 resulting in the inactivation of one or more tumor suppressor genes are thought to play a pathogenic role in small cell lung cancer, renal cell carcinoma, and other human neoplasms. To identify putative tumor suppressor genes, 428 recombinant clones from a microdissection library specific for human chromosome region 3p14 were isolated and characterized. Ninety-six of these (22.5%) were human single-copy DNA sequences, 57 of which were unique sequence clones. Forty-four of these were mapped to the microdissected region using a cell hybrid mapping panel. Within this mapping panel, four probes detected two new chromosome breakpoints that were previously indistinguishable from the translocation breakpoint t(3;8) in 3p14.2 in hereditary renal cell carcinoma. One probe maps to the homozygously deleted region of the small cell lung cancer cell line U2020. In addition, microdissection clones have been shown to be suitable for isolation of yeast artificial chromosomes.

Animals↗

PubMed1994

Microdissected double-minute DNA detects variable patterns of chromosomal localizations and multiple abundantly expressed transcripts in normal and leukemic cells.

Double-minute (dm) chromosomes are cytogenetically resolvable DNA amplification-mediating acentric extrachromosomal structures that are commonly seen in primary tumors, tumor cell lines, and drug-resistant cells grown in vitro. Selective isolation of dm DNAs with standard molecular biological techniques is difficult, and thus, detailed studies to elucidate their structure, site of chromosomal origin, and chromosomal reintegration patterns have been limited. In those instances in which a gene has been localized on dms, characterization of the remainder of the DNA, which far exceeds the size of the gene identified, has remained inconclusive, dms seen in the acute myeloid leukemia cell line HL-60 have been shown to harbor the c-myc protooncogene. In this paper, we report the successful isolation of the dm-specific DNAs from these cells by the microdissection/polymerase chain reaction technique and demonstrate that the dm DNAs derived from a single discrete normal chromosome segment 8q24.1-q24.2 reintegrate at various specific locations in the leukemic cells. The microdissected dm DNA detects multiple abundantly expressed transcripts distinct from c-myc mRNA on Northern blots. By devising a "transcript selection" strategy, we cloned the partial genomic sequence of a gene from the microdissected DNA that encodes two of these RNAs. This strategy will be generally applicable for rapid cloning of unknown amplified genes harbored on dms. With DNA from 20 microdissected dms, we constructed a genomic library of about 20,000 recombinant microclones with an average insert size of about 450 bp.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1996

Isolation of a cosmid sublibrary for a region of chromosome 12 frequently amplified in human cancers using a complex chromosome microdissection probe.

Chromosome-specific cosmid libraries are an extremely useful resource for positional cloning projects. Once a particular region of interest has been identified, it would be of value to have an approach for isolating chromosome band-specific cosmids that could be assembled into a sublibrary for rapid screening. We constructed a region-specific sublibrary of 700 cosmids by screening a chromosome 12-specific cosmid library with a complex probe generated by degenerate oligonucleotide-primed PCR of a microdissected homogeneously staining region containing sequences amplified from chromosome 12q13-q15. Based on fluorescence in situ hybridization, approximately 60% of the cosmids in the sublibrary were derived from the microdissected region. To demonstrate further the utility of this sublibrary, a 150-kb contig containing the SAS and CDK4 genes was constructed, as well as several additional contigs between CDK4 and MDM2. This study demonstrates the possibility of utilizing probes generated by microdissection for assembling band-specific sublibraries that are amenable to rapid screening with multiple markers.

Base Sequence↗

PubMed1995

Coverage of chromosome 6 by chromosome microdissection: generation of 14 subregion-specific probes.

Human chromosome 6 has been subdivided by chromosome microdissection into 14 unique regions. Following microdissection, polymerase chain reaction (PCR) amplification of dissected DNA was performed using a universal primer to generate subregion-specific probes that provided complete coverage of chromosome 6. All 16 microdissections have been regionally assigned along chromosome 6 by fluorescence in situ hybridization (FISH) using biotin-labeled dissected DNA hybridized to G-banded normal metaphase chromosomes. These probes can be used as region-specific paints to generate unique "bar codes" and for analysis of chromosome alterations involving chromosome 6 that are unidentifiable by conventional banding analysis.

Base Sequence↗

PubMed1995

Mouse chromosome-specific painting probes generated from microdissected chromosomes.

Using degenerate primer amplification of chromosomes microdissected from banded cytogenetic preparations, we constructed both whole chromosome painting probes for mouse Chromosomes (Chrs) 1, 2, 3, and 11 and a centromere probe that strongly paints most mouse centromeres. We also amplified a Robertsonian translocation chromosome microdissected from unstained preparations to construct a painting probe for Chrs 9 and 19. The chromosome probes uniformly painted the respective chromosomes of origin. We demonstrated the utility of the Chr 11 probe in aberration analysis by staining mutants that we had previously identified as containing a Chr 11 translocation, and in some mutant cell lines we observed chromosome rearrangements not previously detected in stained cytogenetic preparations. The technology of microdissection and amplification applies to all mouse chromosomes or to specific subchromosomal regions and will be useful in mouse genetics, in aberration analysis, and for chromosome identification.

Animals↗

PubMed1994

Analysis of region-specific library constructed by sequence-independent amplification of microdissected fragments surrounding weaver (wv) gene on mouse chromosome 16.

The C3-C4 region of mouse chromosome 16 was microdissected and amplified directly by sequence-independent amplification (SIA). The SIA product was proved to originate from the microdissected region by fluorescence in situ hybridization (FISH) and was cloned into the PCR II vector (mean insert size 506 bp). Colony hybridization showed that about 59% of the clones contained either unique or low copy number sequences. Southern blot analysis of 100 unique clones demonstrated that 50 clones hybridized with single (33 clones) or multiple (17 clones) bands on blots of DNA from a hamster-mouse hybrid cell line that contains mouse chromosome 16, 13 clones hybridized with mouse but not with the hamster-mouse hybrid DNA, 19 clones contained repetitive sequences, and the remaining 18 clones failed to yield bands. One third of the 100 unique clones hybridized to human genomic DNA. Thirty-three clones were sequenced. None of them was found in GenBank. Our results demonstrate that this relatively simple method of microdissection and cloning can produce a library of good quality.

Animals↗

PubMed1996

Differential epithelial outgrowth of plucked and microdissected human hair follicles in explant culture.

In the present study we prepared explant cultures of plucked total hair follicles and of fragments microdissected from the following regions: B1 (bulb region), B2 (intermediate region), B3-1 (lower central outer root sheath, ORS), B3-2 (upper central ORS) and B4 (area of fracture). The growth capacities, the start of epithelial outgrowth, the stages of differentiation and apoptosis were studied immunohistochemically in early and late explant cultures using a battery of antibodies against cytokeratins, growth factor receptors and cell adhesion molecules and proliferation markers. Whole plucked hair follicles showed epithelial outgrowths exclusively in the upper central ORS (B3-2) starting early, mostly by day 3. In microdissected fragments, in contrast, outgrowths were more widespread, mostly in B3-2 and B3-1, and started early, but were also of late onset in some cases of B2 and B4. Epithelial outgrowths exhibited a basal layer of small cuboidal cells in a low stage of differentiation and one to two suprabasal layers of large prickle-like cells expressing late differentiation markers. The former expressed the receptor of nerve growth factor (NGF) heterogeneously whereas epidermal growth factor (EGF) receptor was not detectable. This is similar to ORS cells of this area in vivo. The proliferative activity of the outgrowths was always restricted to peripheral cells. Thus no essential differences in differentiation of outgrowing cells were detected. These results suggest that keratinocytes with the highest growth capacities in plucked human hair follicles are localized in the lower central ORS (corresponding to B3-2) and some with a lower capacity in the upper central ORS (corresponding to B3-1) as established after microdissection. This is in agreement with the bulge activation theory. NGF may also play a role in hair growth.

Adult↗

PubMed1999

[Microdissection. Use in molecular oncologic dermatology].

Microdissection allows the procurement of selective cell populations or single cells of archival sections or frossen tissue. Most cutaneous tumors can not be cultivated or consist of heterogeneous cell populations. Thus, microdissection is an important pre-requisite for molecular genetic analyses of cutaneous neoplasms. This review describes the microdissection and its application in dermatologic oncology is demonstrated.

Cell Transformation, Neoplastic↗

PubMed2001

Directed isolation and mapping of microsatellites from swine Chromosome 1q telomeric region through microdissection and RH mapping.

Several quantitative trait loci (QTLs) (vertebrate number, birth weight, age at puberty, growth rate, gestation length, and backfat depth) have been independently mapped to the distal region of swine Chromosome (SSC) 1q in several resource populations. In order to improve the map resolution and refine these QTLs more precisely on SSC1q, we have isolated and mapped additional microsatellites (ms), using chromosome microdissection and radiation hybrid (RH) mapping. Five copies of the telomeric region of SSC1q were microdissected from metaphase spreads and pooled. The chromosomal fragment DNA was randomly amplified by using degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR), enriched for ms, and subcloned into a PCR vector. Screening of subsequent clones with ms probes identified 23 unique ms sequences. Fifteen of these (65%) were subjected to radiation hybrid (RH) mapping by using the INRA-University of Minnesota porcine RH panel (IMpRH); and the remaining eight were not suited for the RH mapping. Twelve microsatellites were assigned to SSC1q telomeric region of IMpRH map (LOD >6), and three remain unlinked (LOD <6). Out of the 15 microsatellite markers, 9 were polymorphic in NIAI reference population based on the Meishan and Göttingen miniature pig. In summary, we have used microdissection and radiation hybrid mapping to clone and map 12 new microsatellites to the swine gene map to increase the resolution of SSC1q in the region of known QTLs.

Animals↗

PubMed1999

The need for microdissectional tumor cell preparation during the molecular genetic analysis of prostate cancer.

For clinically localized prostate cancer, recent studies strongly indicate that the determination of p53 inactivation allows the identification of a highly aggressive subgroup of prostatic tumors associated with decreased recurrence-free and long-term survival following radical prostatectomy. However, several questions regarding the determination of p53 alterations in prostate cancer, such as the poor correlation between immunohistochemistry and molecular genetic analysis, remain to be clarified. On the DNA level, p53 gene alterations have been identified in only up to 64% of tumors exhibiting immunohistochemically detected overexpression of the p53 oncoprotein. This discrepancy can be explained either by the genetic microheterogeneity of prostate cancer or by stabilization of the wild-type protein due to posttranslational events. In the present study we tried to determine the concordance between an immunohistochemically detected p53 overexpression and the result of molecular genetic analysis. Therefore, tumor tissue obtained by microdissection from 40 prostate cancer specimens was subjected to DNA-sequence analysis. Microdissection was based either only on histopathologic criteria or on the result of the immunohistochemical staining reaction. In 8 of 14 (57%) tumors a positive immunohistochemical reaction could be confirmed by DNA sequencing, which revealed a missense point mutation at the p53 gene locus, mainly in the form of G-->A transversion in exon 5 of the p53 gene. Following the micropreparation of tumor cells exhibiting p53 oncoprotein overexpression, missense point mutation could be detected in an additional 4 cases. Following a microscopically guided tumor cell dissection according to the result of immunohistochemistry, DNA sequencing confirmed an immunohistochemically detected p53 overexpression in 86% of cases investigated. This result indicates that a microdissectional tumor cell preparation is recommended for molecular genetic analysis of histologically heterogeneous tissue specimens such as prostate cancer and should be performed according to and in addition to the result of immunohistochemistry when an immunohistochemical approach is available.

Adenocarcinoma↗

PubMed1996

Characterization of familial partial 10p trisomy by chromosomal microdissection, FISH, and microsatellite dosage analysis.

Unbalanced translocations are a frequent cause of multiple congenital anomalies in children. Translocations as small as 2-5 Mb of DNA are detectable by G-banding under optimal conditions. Some of these small translocations are visible but cannot be characterized cytogenetically due to the lack of characteristic banding on Giemsa preparations. We have combined chromosomal microdissection and fluorescence in situ hybridization (FISH) to identify the origin of a small translocated segment in three members of a family with a derivative chromosome 9 and multiple anomalies, including several ophthalmologic anomalies. We microdissected the abnormal region of the derivative 9 chromosome and used this DNA to generate a FISH probe. This probe hybridized to distal 10p on the metaphase spread of the proband, indicating the origin of the translocated segment. A whole 10p FISH probe confirmed the origin by hybridizing to the translocated segment of the derivative chromosome. FISH was then performed with a whole chromosome 9 painting probe and excluded the presence of a reciprocal, balancing translocation. We then studied the chromosome 10 partial duplication with microsatellite markers to better characterize the chromosomal segment that caused these phenotypic features. By examining the involved areas with distal 10p and 9p microsatellite markers, we were able to demonstrate a minimum of 9 Mb of trisomic 10p DNA with a chromosomal breakpoint between 10p14-10p15. We then compared this family's clinical findings to those of individuals with partial 10p trisomy who had been reported in the literature. The clinical phenotypes seen in this family are similar to, but milder than, the phenotypes of persons with the larger partial trisomies of 10p that were diagnosable by cytogenetic analysis alone. This study shows that microdissection and DNA markers can be used to precisely define small translocations that are difficult to identify by conventional G-banded chromosome analysis.

Abnormalities, Multiple↗

PubMed1987

A new microdissection technique for regional biochemical analysis of the rat spinal cord: serotonin, norepinephrine, dopamine and uric acid.

This report described a new microdissection procedure to evaluate the regional distribution of neuromediators in the rat spinal cord. Different segments are first divided into sagittal slices. From these, different grey and white matter regions can be microdissected. This permits selective biochemical measurements in different laminae, including the area around the central canal. White and grey matter can also be differentially analysed. Using HPLC with electrochemical detection, we report on the regional analysis of biogenic amines as well as uric acid. An increase in 5-hydroxytryptamine (5-HT) levels was observed from cervical to lumbar segments. 5-HT levels were highest in the motoneurone samples (lamina IX) of the lumbar cord. The next highest levels were found in lamina X, followed by the intermediate grey matter laminae and the dorsal horn. Small amounts of 5-HT were detected in the white matter. Interestingly, the ratio of 5-hydroxyindoleacetic acid (5-HIAA) to 5-HT was greatest in the white matter and least in the motoneurone sample. Norepinephrine (NE) levels were higher in the thoracic than in the cervical or the lumbar cord. The highest levels were found in the lamina X in thoracic segments. With this exception, no marked laminar difference in NE levels was observed. Dopamine (DA) levels were highest in the dorsal horn of the cervical and the thoracic cord, the next highest levels were found in the intermediate grey matter and lamina X in the same segments. The distribution of uric acid (UA) was comparable to that of NE: UA levels were highest in the thoracic cord, but no marked laminar difference was observed. On the other hand, UA levels in white matter generally exceeded those in the grey matter. These data indicate the value of a sagittal regional microdissection of the spinal cord. The ability to separately analyse different laminae of the cord (as well as differentiating grey and white matter) should prove useful in future studies of experimentally evoked changes in neurotransmitters within functionally distinct regions of the spinal cord.

Animals↗

PubMed1991

Laser microdissection and single unique primer PCR allow generation of regional chromosome DNA clones from a single human chromosome.

We have developed an argon laser chromosome microdissection technique in conjunction with a polymerase chain reaction (PCR) approach to directly amplify microdissected chromosomes. The single 22-mer primer used in PCR, although unique in sequence (5'-TAGATCTGA-TATCTGAATTCCC-3'), randomly primed and amplified any target DNA. These methods were applied to the distal half of the short arm of human chromosome 4 containing the Huntington disease (HD) locus. Forty-four percent of representative clones from this library identify single-copy DNA sequences. This calculation suggests that the resulting chromosome-specific DNA library contains approximately 600 nonoverlapping sequences with an average size 350 bp at an average spacing of 30 kbp along chromosome 4. This microdissection and PCR cloning procedure is a simple and general approach for constructing a chromosome region-specific DNA library from a single metaphase spread.

Base Sequence↗

PubMed2004

Intrahepatic hepatitis C virus RNA quantification in microdissected hepatocytes.

BACKGROUND/AIMS: Debate continues on whether serum and intrahepatic HCV viral loads are correlated and if HCV viral load correlates with the severity of liver disease. These difficulties may at least in part be linked to liver cell heterogeneity, when total liver extracts from HCV-infected individuals are tested for HCV RNA quantification. We have therefore investigated the feasibility of quantifying HCV replication using a laser-based microdissection technique. METHODS: We compared the results with those obtained for serum HCV RNA quantification and immunochemistry in the case of HCV antigen detection in the liver. Twenty-one HCV-positive patients with chronic active hepatitis (n=10) or cirrhosis (n=11) were analyzed. RESULTS: A positive correlation (P=0.0019) was observed between HCV RNA quantifications in sera and microdissected cells. Immunohistochemistry demonstrated that HCV antigen hepatocytes were randomly distributed within liver lobules. Their percentage varied in different patients (0-40%), but did not correlate with the HCV viral load. CONCLUSIONS: We have designed a sensitive methodology to evaluate the intrahepatic HCV viral load by combining a standardized RNA quantification method with microdissected hepatocytes from frozen liver needle biopsies. Our results directly demonstrate a positive correlation between serum and intrahepatic viral loads, which therefore provides a reliable reflection of intrahepatic HCV replication.

Adult↗

PubMed2001

Expression profiling of ductal carcinoma in situ by laser capture microdissection and high-density oligonucleotide arrays.

Gene expression profiling through the use of nucleic acid arrays is a powerful method for the molecular classification of human neoplasms. Laser capture microdissection is an equally useful technique to selectively isolate defined cell populations from heterogeneous histological tissue sections. In this report, we demonstrate how a modest use of laser capture microdissection is sufficient to isolate nanogram quantities of high-quality RNA. Together with the use of several internal standards and microcapillary electrophoresis of input RNA, two rounds of linear molecular amplification have been used to generate sufficient quantities of labeled target for hybridization to high-density oligonucleotide expression arrays. Results demonstrate that the technique is reproducible, generates only modest biasing of the original transcript population, and is comparable to the sensitivity achieved with standard methodology. Using this approach, we have compared the expression profiles of nonmalignant human breast epithelium and adjacent ductal carcinoma in situ lesions from breast cancer patients. Several genes, previously implicated in human breast cancer progression, demonstrate differential expression among the microdissected cell populations.

Breast↗

PubMed2003

PCR-based quantification of amplified RNA from laser microdissected mouse liver samples.

New molecular methods such as quantitative reverse transcription-polymerase chain reaction (RT-PCR) and microarray gene expression analysis have been established recently to quantify gene expression in tissue samples. Such methods, although highly sensitive, require RNA quantities of at least several micrograms. These amounts are not available in many experiments concerning microdissected embryonic or regenerating structures. We combined laser-assisted tissue preparation, RNA amplification, and quantitative RT-PCR to estimate both accuracy and linearity of gene expression in small tissue samples. Our results show that mRNA isolated from laser-microdissected fetal liver tissue or regenerative nodules, which originated from EGFP-marked transplanted fetal cells, can be significantly increased with the amplification protocol. The quantitative expression ratio of the genes albumin and GAPDH was conserved after one and two rounds of amplification compared to nonamplified material. Furthermore, genes expressed at low levels such as the transcription factor C/EBPbeta become detectable after two rounds of amplification in small microdissected tissue samples.

Albumins↗

PubMed2003

Resolution of clonal origins for endometriotic lesions using laser capture microdissection and the human androgen receptor (HUMARA) assay.

OBJECTIVE: To determine the clonal origins of endometriotic lesions using laser capture microdissection and PCR-based HUMARA assay. DESIGN: Molecular genetic study of human tissue. SETTING: Molecular genetics laboratory in an academic setting. PATIENT(S): Twenty patients with endometriosis. Forty specimens of endometriotic lesions from these patients and one specimen of normal endometrium were analyzed. INTERVENTION(S): Laser capture microdissection was used to harvest epithelial cells from single and multifocal endometrial lesions from paraffin-embedded and frozen tissues, and their clonality was determined with the HUMARA assay. MAIN OUTCOME MEASURE(S): Polymerase chain reaction-based HUMARA assay of clonality. RESULT(S): Thirty-eight specimens were polymorphic and thus informative. Most specimens were monoclonal, as determined by the HUMARA assay. In four specimens of multifocal lesions, polyclonality was detected, but upon more refined microdissections and further analyses, we found that each focus was monoclonal individually. CONCLUSION(S): Previously reported polyclonality is very likely to be attributed to the pooling of multifocal lesions or contamination of normal tissues. These results suggest that endometriotic lesions were monoclonal in origin, and in the case of multifocal lesions, each focus originates monoclonally; hence, different foci have independent origins. The monoclonality of endometriotic lesions suggests that they may carry neoplastic potentials, and the apparent independent origins of multifocal lesions suggest that reconstruction of individual lesion histories may help us to understand the initiation and progression of endometriosis.

Adult↗

PubMed1996

von Hippel-Lindau disease gene deletion detected in microdissected sporadic human colon carcinoma specimens.

The progression of human malignancies is thought to involve the inactivation or loss of tumor suppressor genes. Previous studies have suggested that inactivation of tumor suppressor genes on chromosomes 5q, 17p, 18q, and 8p play a role in the development of colorectal carcinoma. However, chromosome 3p at the von Hippel-Lindau disease (VHL) gene locus (3p25-26) has not been previously implicated in the development or progression of sporadic colorectal carcinoma. The authors have analyzed VHL gene alterations on chromosome 3p in sporadic human colon carcinomas and adenomas using modified microdissection techniques. These techniques allow for procurement and analysis of selected subpopulations of cells from both paraffin-embedded and frozen human tumor specimens. VHL disease gene deletion was detected by polymerase chain reaction (PCR) and single-strand conformation polymorphism (SSCP) analysis in microdissected colon carcinoma specimens. Allelic loss of VHL gene was detected in 7 of 11 (64%) informative patients who underwent colectomy for primary sporadic colon carcinoma. However, no allelic loss of VHL gene was shown in colonic adenomas of eight informative patients. These results indicate that VHL disease gene deletion frequently occurs in sporadic colon carcinoma. Because this deletion was not present in adenomas, VHL gene may play a role in colonic carcinogenesis and represent a relatively late event in colonic neoplasia progression. Additionally, microdissection of tissue sections may be especially useful in detecting allelic loss in PCR-based studies of infiltrating tumors, particularly when the tumor cells represent a relatively small percentage of the total cell population.

Adenocarcinoma↗