Molecular cytogenetic characterization of head and neck squamous cell carcinoma and refinement of 3q amplification.

We applied a combination of molecular cytogenetic methods, including comparative genomic hybridization (CGH), spectral karyotyping (SKY), and fluorescence in situ hybridization, to characterize the genetic aberrations in a panel of 11 cell lines derived from head and neck squamous cell carcinoma and 1 cell line derived from premalignant oral epithelium. CGH identified recurrent chromosomal losses at 1p, 3p, 4, 8p, 10p, and 18q; gains at 3q, 5p, 8q, 9q, and 14q; and high-level amplification at 3q13, 3q25-q26, 5q22-q23, 7q21, 8q24, 11q13-q14, 12p13, 14q24, and 20q13.1. Several recurrent translocations including t(1;13)(q10;q10), t(13;13)(q10;q10), t(14;14)(q10;q10), i(8)(q10), and i(9)(q10) and breakpoint clusters at 1p11, 1q21, 3p11, 5q11, 5q13, 6q23, 8p11, 8q11, 9p13, 9q13, 10q11, 11q13, 13q10, 14q10, and 15q10 were identified by SKY. There was a good correlation between the number of aberrations identified by CGH and SKY (r = 0.69), and the analyses were both confirmatory and complementary in their assessment of genetic aberrations. Amplification at 3q26-q27 was identified in 42% of cases. Although SKY defined the derivation of 3q gain, the precise breakpoint remained unassigned. Positional cloning efforts directed at the amplified region at 3q26-q27 identified three highly overlapping nonchimeric yeast artificial chromosome clones containing the apex of amplification. The use of these yeast artificial chromosome clones as a probe for fluorescence in situ hybridization analysis allowed a detailed characterization and quantification of the 3q amplification and refinement of unassigned SKY breakpoints.

Pericentromeric heteromorphism of human chromosome 18 as revealed by FISH-technique.

The pericentromeric heterochromatin contains tandemly repeated alphoid DNA sequences of about 171 bp in length. They are highly divergent from one chromosome to another due to chromosome specific alphoid subsets. In the present investigation, we used chromosome 18-specific centromeric probe (D18Z1) to evaluate the extent of pericentromeric heteromorphism classified by FISH-technique among 25 normal individuals. The hybridization signals were arbitrarily classified into five sizes when compared with the length of the short arm of chromosome 18. These are: negative (1), small (2), medium (3), large (4), and very large (5), with incidence of 0, 12, 24, 42, and 22 percent, respectively. Based on limited data, there were no chromosomes with negative signals while 42% of chromosome 18 had large-sized pericentromeric heterochromatin. The incidence observed earlier by restriction endonuclease Alu1 was different as compared to the present approach suggesting the complex heterogeneity of pericentric region of chromosome 18.

Highly complex chromosomal aberrations in bone marrow of a patient with metastatic prostate neoplasm.

Prostate cancer is the single most common malignancy among men in North America. Nevertheless, cytogenetic evaluation of bone marrow in patients with metastatic prostate neoplasm has been rare and, to date, only five such patients have been reported. We report an additional case where chromosomal abnormalities of a bizarre nature were found in the bone marrow. Though cytogenetic findings in prostate cancer are heterogeneously complex, the chromosome regions involved include 1p, 1q, 7q, 8p, 10q, 12p, and 17q and are considered hot spots. What is the significance of these so-called hot spots in metastasis of prostatic cancer to the bone marrow? At present, no meaningful conclusion can be drawn, as data are limited, but accumulation of such cases may provide valuable information concerning the role of chromosomal abnormalities in patients--specifically with metastatic stage--and may help urologists during therapeutic decision making, particularly if a genetic marker for aggressiveness can be determined.

Characterisation of a satellited non-fluorescent Y chromosome (Y[nfqs]) by FISH.

A fetus was prenatally diagnosed as having a Y(nfqs) chromosome which was inherited from the father. With the QFQ technique, the Yqh was observed to be nonfluorescent and contained cytological satellites which were attached to the terminal long arm. The satellites were positively stained by the Ag-NOR technique suggesting that the NORs were active. A battery of DNA probes was used to characterise the Y(nfqs). Hybridisation experiments using a chromosome 15 specific classical satellite DNA probe (D15Z1) and a Yq telomere DNA probe showed that the additional satellited material on Yq originated from 15p, and that the Yq terminal region had been lost. This is the first reported case in which the origin of cytological satellites on Yq has been determined by FISH, but this does not imply that all satellited Y chromosomes are derived from 15p. However, the clinical significance of this Y(nfqs) chromosome remains obscure.

Variant complex translocations involving chromosomes 1, 9, 9, 15 and 17 in acute promyelocytic leukemia without RAR alpha/PML gene fusion rearrangement.

Acute promyelocytic leukemia (APL;M3) is specifically characterized by a predominance of malignant promyelocytes having atypical reciprocal translocation involving chromosome 15 and 17 [t(15;17)(q22;q11)] resulting in the fusion of retinoic acid receptor alpha (RAR alpha) on chromosome 17 and the putative transcription factor gene PML, ie the translocation generates two fusion transcripts, PML/RAR alpha and RAR alpha/PML. We describe a patient with clinical and morphologic characteristics of atypical APL but with a previously undescribed variant translocation. A 35-year-old Hispanic having atypical APL was referred for cytogenetic evaluation. The cytogenetic findings with GTG-banding coupled with FISH analysis revealed the following karyotype: 46,XX,der(9)t(1;9)(q25;q34)der(9)t(9;?)(q34;?), t(15;17)(q22;q11)ish. der(9)t(1;9)(q25;q34)(WCP1+,WCP9+),t(9;17;15)(q34;q11;q22) (WCP9+,WCP15+,PML+;WCP17+,RAR alpha +;WCP15+,WCP17+,PML-)[20]/46,XX[5]. The chromosome 17q was translocated to the chromosome 15q. However, chromosome 15q including the PML gene normally translocating to 17q and creating the RAR alpha/PML fusion gene, translocated to chromosome 9q. Does this patient have another subset of APL? Or is the genetics of APL different in cases with variant translocations as opposed to those with atypical t(15;17) translocation, though in the majority of the cases their clinical presentation remains the same.

Centromeric alphoid DNA heteromorphisms of chromosome 21 revealed by FISH-technique.

The centromeric heterochromatin of chromosome 21 has been evaluated by the fluorescence in situ hybridization (FISH) technique. It was found that the alphoid DNA sequences of pericentromeric regions of chromosome 21 were highly heteromorphic when a centromeric specific probe was hybridized to these sequences. The variations were so extreme that they could even be arbitrarily classified into at least five sizes by comparison with the length of the short arm (p) of chromosome 18. They are negative (1); small (2); medium (3); large (4); and very large (5). We used 15 normal cases and 12 individuals with trisomy 21 (Down syndrome), and the incidences for these five classes were 3.0%, 22.7%, 59.2%, 13.6% and 1.5%, respectively. At least 3% of the chromosomes no. 21 did not show any trace of hybridization signals, which apparently escape detection at interphase level as well. Although, the variations observed in the present study are continuous, the proposed classification may yield some implications for future investigations.

Characterization of a complex translocation [t(4;9;22)(p16;q34;q11)] in chronic myelogenous leukemia by fluorescence in situ hybridization technique.

A patient was referred with a high leukocyte count and diagnosed with chronic myelogenous leukemia (CML). Although practically asymptomatic since the time of diagnosis, he had a variable and inconsistent response to treatment. All of his bone marrow cells had a complex, three-way translocation, involving chromosomes 4, 9 and 22. Translocation of chromosome 4 to chromosome 9 was undetectable by routine cytogenetic techniques; however, by the fluorescence in situ hybridization technique, a three-way translocation was identified, 46,XY,t(4;9;22)(p16;q34;q11). Although, other chromosomes are frequently involved in complex or variant translocations with chromosome 9 and 22, participation of chromosome 4 is a very rare event. So far, two previous cases have been described in the literature with translocations involving chromosome 4p16. We present a third case of CML having similar break points whose clinical presentation is unusual.

A new translocation, t(5;21)(q13;q22) in acute myelogenous leukemia.

We report a case of acute myelogenous leukemia with a variant translocation involving chromosomes 5 and 21 with breakpoints on 5q13 and 21q22 as revealed by various techniques including fluorescence in situ hybridization. The unusual presentation of t(5;21)(q13;q22), as the sole abnormality in acute myelogenous leukemia, is atypical.

T-cell receptor J beta 1/J beta 2 locus rearrangements in an HTLV-1-positive T-cell lymphoma with complex chromosomal aberrations.

We report a case of human T-cell lymphotropic virus type 1 (HTLV-1)-infected adult T-cell lymphoma that has multiple chromosomal abnormalities, including the presence of an additional 7q22-36, which contains the locus of the T-cell receptor (TCR) beta chain gene. Specific TCR J beta 1/J beta 2 gene rearrangements were detected in both marrow and peripheral blood DNA, with evidence of further evolution of the transformed clonal population within the peripheral lymphocytes. To our knowledge, this is the first case in which gene rearrangements have been associated with additional TCR loci. Consequently, it is advised that every effort should be made to correlate chromosomal abnormalities with gene rearrangement by molecular methods.

Retrieval of aneuploidy by FISH-technique in a case with 46,XX/47,XXX/47,XX,+8.

We report on a 46 year old female with a new chromosomal finding [46,XX/47,XXX/47,XX,+8] who was referred for ovarian failure. The clinical presentation was highly unusual and the patient does not exhibit the characteristic phenotype of trisomy 8 syndrome. Interphase cytogenetics using FISH-technique revealed discrepancies with a different population of cells when compared with its metaphase index. Therefore, it is advised that patients with mosaic karyotypes should be evaluated by analyzing metaphase as well as interphase nuclei labeled with chromosome specific molecular tags, especially in the situations where the incidence of a mosaic cell line is very low. Nevertheless, in a cost-conscious environment, we must exercise caution prior to making universal recommendations concerning the usefulness of medical devices which are increasing at a logarithmic rate.

Characterization of 7q--by FISH technique of a case with acute myelogenous leukemia evolving from agnogenic myeloid metaplasia.

We present a new case of acute myelogenous leukemia (AML) which evolved from agnogenic myeloid metaplasia (AMM). Routine cytogenetic techniques revealed a terminal deletion of one chromosome 7 (del (7) (q21)). When metaphases were hybridized with the 7q specific telomeric probe, a signal was detected at the distal q arm of the deleted chromosome 7 suggesting an interstitial deletion and the cytogenetic diagnosis was changed to 46,XY, del(7) (q21.1q36.2). Apparently, precise characterization of such deletions may have gone undetected, owing to the lack of technology, and deletions that have been previously regarded as terminal may very well be interstitial. Undoubtedly, precise identification of genetic abnormalities may lead to a better classification which may help to assign patients into sub-subgroups within the specific chromosomal abnormalities to initiate better therapeutic modalities and decisions.

New translocations [t(6;15)(p25;q22) and t(6;19)(q16;q13.3)] with t(9;22)(q34;q11) in a Ph-positive chronic myelogenous leukemia.

A case with typical features of chronic myelogenous leukemia (CML) with two complex aberrations in addition to the standard t(9;22) is reported. Cytogenetic evaluation of the patient's bone marrow cells (BMC) showed 46,XX,t(6;19)(q16;p13.3),t(9;22)(q34;q11) in 60% of the mitotic cells and 46,XX,idem, t(6;15)(p25;q22) in the remaining 40% dividing cells. The patient's peripheral blood smear exhibited the usual differential observed in chronic-phase CML and was clinically indistinguishable from patients with the t(9;22) as the only translocation. We performed Southern blotting on BglII-digested DNA with the Trans-Probe (OSI) and in addition to the 4.8-, 2.3-, and 1.1-kilobase (kb) germline fragments, we detected an additional fragment at 7 kb. This probe spans the entire 5.8-kb M-breakpoint cluster region (BCR), and a single breakpoint in this region will appear as either one or two additional fragments. Because only one additional fragment was observed, both cell lines apparently share the same breakpoint in the ABL/BCR gene. Apparently the second aberrant cell line with the additional t(6;15) represents clonal evolution of the original abnormal clone.

New translocation involving homologous chromosome 3 in acute myelogenous leukemia (M2)

An apparent balanced translocation involving the long arms of homologous chromosomes is described for the first time in a patient with acute myelogenous leukemia (AML) (M2), i.e., 46,XY,t(3;3) (q21;q26). After reviewing the literature, it was noted that a breakpoint involving band 3q26 is a frequent anomaly in other translocations. Thus, we are tempted to hypothesize that 3q26 band may also play an important role in the pathogenesis of AML (M2).

Trisomy 8 and 11 in refractory anemia with excess blasts in transformation (RAEB-T).

There are no specific chromosomal abnormalities associated with refractory anemia with excess blasts in transformation [RAEB-T]. An 80-year-old white male with RAEB-T was found to have trisomies of chromosomes 8 and 11, i.e., 48,XY,+8,+11. To our knowledge, this chromosomal abnormality in RAEB-T has not been previously reported.