Rapid detection of IgH/BCL2 rearrangement in follicular lymphoma by interphase fluorescence in situ hybridization with bacterial artificial chromosome probes

High Resolution Fiber-Fluorescence In Situ Hybridization

High resolution fiber-Fluorescence in situ hybridization (FISH) is an advanced FISH technology that can effectively bridge the resolution gap between probe hybridizing on DNA molecules and chromosomal regions. Since various types of DNA and chromatin fibers can be generated reflecting different degrees of DNA/chromatin packaging status, fiber-FISH technology has been successfully used in diverse molecular cytogenetic/cytogenomic studies. Following a brief review of this technology, including its major development and increasing applications, typical protocols to generate DNA/chromatin fiber will be described, coupled with rationales, as well as technical tips. These released DNA/chromatin fibers are suitable for an array of cytogenetic/cytogenomic analyses.

CD10 down expression in follicular lymphoma correlates with gastrointestinal lesion involving the stomach and large intestine

Follicular lymphoma (FL) shows co-expression of B-cell lymphoma 2 (BCL2) and CD10, whereas downexpression of CD10 is occasionally experienced in gastrointestinal (GI) FL with unknown significance. Gastrointestinal FL is a rare variant of FL, and its similarity with mucosa-associated lymphoid tissue lymphoma was reported. We investigated the clinicopathological and genetic features of CD10 downexpressed (CD10^down ) GI-FL. The diagnosis of CD10^down FL was carried out with a combination of pathological and molecular analyses. The incidence of CD10^down GI-FL was shown in 35/172 (20.3%) cases, which was more frequent than nodal FL (3.5%, P < 0.001). The difference was additionally significant between GI-FL and nodal FL when the analysis was confined to primary GI-FL (55.2% vs 3.5%, P < 0.001). Compared to CD10⁺ GI-FL, CD10^down GI-FL significantly involved the stomach or large intestine (P = 0.015), and additionally showed the downexpression of BCL6 (P < 0.001). The follicular dendritic cell meshwork often showed a duodenal pattern in the CD10^down group (P = 0.12). Furthermore, a lymphoepithelial lesion was observed in 5/12 (40%) gastric FL cases, which indicated caution in the differentiation of mucosa-associated lymphoid tissue lymphoma. Molecular analyses were undertaken in seven cases of CD10^down GI-FL, and an identical clone was found between CD10^down follicles and CD10⁺ BCL2⁺ neoplastic follicles. In the diagnosis of cases with CD10^down BCL2⁺ follicles, careful examination with molecular studies should be carried out.

The complex translocation (9;14;14) involving IGH and CEBPE genes suggests a new subgroup in B-lineage acute lymphoblastic leukemia

Many subtypes of acute lymphoblastic leukemia (ALL) are associated with specific chromosomal rearrangements. The complex translocation t(9;14;14), a variant of the translocation (14;14)(q11;q32), is a rare but recurrent chromosomal abnormality involving the immunoglobulin heavy-chain (IGH) and CCAAT enhancer-binding protein (CEBPE) genes in B-lineage ALL (B-ALL) and may represent a new B-ALL subgroup. We report here the case of a 5-year-old girl with B-ALL, positive for CD19, CD38 and HLA-DR. A direct technique and G-banding were used for chromosomal analysis and fluorescentin situ hybridization (FISH) with BAC probes was used to investigate a possible rearrangement of the IGH andCEBPE genes. The karyotype exhibit the chromosomal aberration 46,XX,del(9)(p21),t(14;14)(q11;q32). FISH with dual-color break-apartIGH-specific and CEPBE-specific bacterial artificial chromosome (BAC) probes showed a complex t(9;14;14) associated with a deletion of cyclin-dependent kinase inhibitor 2A (CDKN2A) and paired box gene 5 (PAX5) at 9p21-13 and duplication of the fusion gene IGH-CEBPE.

Fine needle aspiration: past, current practice and recent developments

Fine needle aspiration (FNA) is a diagnostic technique that has become widely used. The procedure may be performed by interventional radiologists, endoscopists, pathologists and cytotechnologists; diagnostic interpretation of FNA samples is performed by pathologists and cytotechnologists. I provide here an introduction to the technique and applications of FNA with a review of current practice parameters and recent developments in the molecular application of FNA.

Biology and treatment of follicular lymphoma

Follicular lymphoma (FL) is the second most common lymphoid tumor. It is composed of elements resembling those of normal germinal centers. In particular, it is constituted by small centrocytes and large centroblasts, typically CD10+, CD19+, CD20+, CD79a+ and BCL6+, with follicular growth pattern. The molecular hallmark of FL is the t(14;18)(q32;q21) translocation, which leads to inappropriate BCL2 expression. This feature, other than representing a pathogenetic primary event, constitutes a suitable diagnostic marker, as well as a target for minimal residual disease monitoring and, hopefully, future therapies. Clinically, FL presents with indolent behavior, characterized by prompt response to initial therapy but almost invariably subsequent relapses. Novel approaches, including stem cell transplantation, monoclonal antibodies and innovative agents, should be then considered for improving long-term results.

Molecular genetic analysis of haematological malignancies II: mature lymphoid neoplasms

Molecular genetic techniques have become an integral part of the diagnostic assessment for many lymphomas and other chronic lymphoid neoplasms. The demonstration of a clonal immunoglobulin or T cell receptor gene rearrangement offers a useful diagnostic tool in cases where the diagnosis is equivocal. Molecular genetic detection of other genomic rearrangements may not only assist with the diagnosis but can also provide important prognostic information. Many of these rearrangements can act as molecular markers for the detection of low levels of residual disease. In this review, we discuss the applications of molecular genetic analysis to the chronic lymphoid malignancies. The review concentrates on those disorders for which molecular genetic analysis can offer diagnostic and/or prognostic information.

Genetic deletions in sputum as diagnostic markers for early detection of stage I non-small cell lung cancer

PURPOSE

Analysis of molecular genetic markers in biological fluids has been proposed as a powerful tool for cancer diagnosis. We have characterized in detail the genetic signatures in primary non-small cell lung cancer, which provided potential diagnostic biomarkers for lung cancer. The aim of this study was to determine whether the genetic changes can be used as markers in sputum specimen for the early detection of lung cancer.

EXPERIMENTAL DESIGN

Genetic aberrations in the genes HYAL2, FHIT, and SFTPC were evaluated in paired tumors and sputum samples from 38 patients with stage I non-small cell lung cancer and in sputum samples from 36 cancer-free smokers and 28 healthy nonsmokers by using fluorescence in situ hybridization.

RESULTS

HYAL2 and FHIT were deleted in 84% and 79% tumors and in 45% and 40% paired sputum, respectively. SFTPC was deleted exclusively in tumor tissues (71%). There was concordance of HYAL2 or FHIT deletions in matched sputum and tumor tissues from lung cancer patients (r = 0.82, P = 0.04; r = 0.84, P = 0.03), suggesting that the genetic changes in sputum might indicate the presence of the same genetic aberrations in lung tumors. Furthermore, abnormal cells were found in 76% sputum by detecting combined HYAL2 and FHIT deletions whereas in 47% sputum by cytology, of the cancer cases, implying that detecting the combination of HYAL2 and FHIT deletions had higher sensitivity than that of sputum cytology for lung cancer diagnosis. In addition, HYAL2 and FHIT deletions in sputum were associated with smoking history of cancer patients and smokers (both P < 0.05).

CONCLUSIONS

Tobacco-related HYAL2 and FHIT deletions in sputum may constitute diagnostic markers for early-stage lung cancer.

FISH detection of t(14;18) in follicular lymphoma on Papanicolaou-stained archival cytology slides

BACKGROUND

The t(14;18)(q32;q21) translocation is present in about 85% of follicular lymphomas (FL) and can be identified using fluorescence in situ hybridization (FISH). In the diagnostic laboratory setting, the cytologic archival material consists of stained slides, and only rarely is material saved for molecular testing. The authors proposed FISH for FL using Papanicolaou-stained archival cytology material as a practical ancillary technique for diagnosing FL.

METHODS

Cases included 35 FL, 6 small lymphocytic lymphomas/chronic lymphocytic leukemias (SLL/CLL), 4 mantle cell lymphomas (MCL), 4 marginal zone lymphomas (MZL), 1 lymphoplasmacytic lymphoma (LPL), and 10 reactive lymphoid tissues (RLT). FISH was performed on Papanicolaou-stained archival cytology slides using probes for immunoglobulin heavy chain (IGH) on chromosome 14 and BCL2 on chromosome 18.

RESULTS

In all, 25 of 32 (81%) FL cases exhibited the t(14;18) translocation, whereas 7 of 32 (19%) lacked the translocation. No cases of non-FL were positive for t(14;18). This series shows a sensitivity of 81% and specificity of 100% for detecting the t(14;18) translocation as a diagnostic tool in FL.

CONCLUSIONS

When performed on Papanicolaou-stained cytology slides, FISH for t(14;18) is relatively sensitive and quite specific for FL. These findings are similar to those reported on other specimens, such as paraffin-embedded tissue and unstained cytology slides. The authors proposed that their technique would allow the pathologist and clinician the flexibility to utilize previously stained fine-needle aspiration slides for FISH evaluation.

Identification of putative oncogenes in lung adenocarcinoma by a comprehensive functional genomic approach

Amplification and overexpression of putative oncogenes confer growth advantages for tumor development. We used a functional genomic approach that integrated simultaneous genomic and transcript microarray, proteomics, and tissue microarray analyses to directly identify putative oncogenes in lung adenocarcinoma. We first identified 183 genes with increases in both genomic copy number and transcript in six lung adenocarcinoma cell lines. Next, we used two-dimensional polyacrylamide gel electrophoresis and mass spectrometry to identify 42 proteins that were overexpressed in the cancer cells relative to normal cells. Comparing the 183 genes with the 42 proteins, we identified four genes - PRDX1, EEF1A2, CALR, and KCIP-1 - in which elevated protein expression correlated with both increased DNA copy number and increased transcript levels (all r > 0.84, two-sided P < 0.05). These findings were validated by Southern, Northern, and Western blotting. Specific inhibition of EEF1A2 and KCIP-1 expression with siRNA in the four cell lines tested suppressed proliferation and induced apoptosis. Parallel fluorescence in situ hybridization and immunohistochemical analyses of EEF1A2 and KCIP-1 in tissue microarrays from patients with lung adenocarcinoma showed that gene amplification was associated with high protein expression for both genes and that protein overexpression was related to tumor grade, disease stage, Ki-67 expression, and a shorter survival of patients. The amplification of EEF1A2 and KCIP-1 and the presence of overexpressed protein in tumor samples strongly suggest that these genes could be oncogenes and hence potential targets for diagnosis and therapy in lung adenocarcinoma.

A novel multiple FISH array for the detection of genetic aberrations in cancer

Interphase multicolor fluorescence in situ hybridization (IM-FISH) has great promise for improving cancer diagnosis because it can directly visualize multiple changes in chromosomes and gene copy number on a cell-to-cell basis. However, no more than four targets can be detected simultaneously by current commercially available IM-FISH protocols, and the DNA probes used are too large to detect the single-gene aberrations that characterize tumorigenesis. As a result, multiple FISH has a low sensitivity in detecting cancer cells. To overcome such limitations, we first developed specific genomic probes for the genes relevant to primary lung cancer. We next designed a multiple FISH array by arranging four different compositions of cocktails of four probes for each gene on a coverslip, which allowed four four-color FISH experiments to be performed in parallel on a single slide. We then tested the multiple FISH array on bronchial brushing samples from lung cancer patients to determine its ability to detect genetic abnormalities. A comparison of the data with the results of cytology and commercial four-color FISH suggested that the multiple FISH array had the highest sensitivity for cancer detection. The technique may thus be a powerful laboratory strategy for cancer prevention and early detection and for improved patient management.

Genomic profiles in stage I primary non small cell lung cancer using comparative genomic hybridization analysis of cDNA microarrays

To investigate the genomic aberrations that are involved in lung tumorigenesis and therefore may be developed as biomarkers for lung cancer diagnosis, we characterized the genomic copy number changes associated with individual genes in 14 tumors from patients with primary non small cell lung cancer (NSCLC). Six squamous cell carcinomas (SQCAs) and eight adenocarcinomas (ADCAs) were examined by high-resolution comparative genomic hybridization (CGH) analysis of cDNA microarray. The SQCAs and ADCAs shared common frequency distributions of recurrent genomic gains of 63 genes and losses of 72 genes. Cluster analysis using 57 genes defined the genomic differences between these two major histologic types of NSCLC. Genomic aberrations from a set of 18 genes showed distinct difference of primary ADCAs from their paired normal lung tissues. The genomic copy number of four genes was validated by fluorescence in situ hybridization of 32 primary NSCLC tumors, including those used for cDNA microarray CGH analysis; a strong correlation with cDNA microarray CGH data emerged. The identified genomic aberrations may be involved in the initiation and progression of lung tumorigenesis and, most importantly, may be developed as new biomarkers for the early detection and classification of lung cancer.

Cytologic differential diagnosis of follicular lymphoma grades 1 and 2 from reactive follicular hyperplasia: Cytologic features of fine-needle aspiration smears with Pap stain and fluorescence in situ hybridization analysis to detect t(14;18)(q32;q21) chromosomal translocation

Fine-needle aspiration cytology (FNAC) is a well-established technique for diagnosis of malignant lymphoma (ML). Generally, Giemsa but not Pap stain is used in FNAC. However, cytologic features obtained from Pap stain are also valuable. Very few studies on the cytologic characteristics of ML, as determined by Pap stain, are available. It is easier to observe nuclear irregularity and to identify nucleoli in ML cells by Pap stain than by Giemsa stain. Here, we applied Pap stain for cytomorphologic differential diagnosis of follicular lymphoma (FL) from reactive follicular hyperplasia (RFH). Eighteen biopsy-confirmed cases of FL grades 1 and 2, with available FNAC smears, and six cases of RFH were selected for this study. Low-power magnification showed well-known features, and tingible body macrophages and lymphoid cell aggregates were observed frequently in RFH and FL, respectively. In addition, the so-called two-nuclei-like cleaved cells were observed frequently in FL. These cells showed notably cleaved nuclei, and therefore, appeared to possess two nuclei. Under high-power magnification, the occurrence of cells with nucleoli >1 microm and of cleaved cells was high in FL compared to RFH. It is believed that FL derives from centrocytes and that FL cells are slightly larger than non-neoplastic small lymphocytes. However, analysis of cell diameter in this study indicated that small lymphoma cells were predominant in half the cases of FL grades 1 and 2, and the percentage of these cells was similar to that in RFH, showing why false-negative diagnosis of FL grades 1 and 2 occasionally occurs. There are limitations of FNAC in the diagnosis of FL. However, we believe that the appearance of two-nuclei-like cleaved cells and the high percentage of nucleoli-possessing cells, which we describe here, provide significant and valuable clues for the differential diagnosis of FL from RFH. Of 18 cases of FL grades 1 and 2, t(14;18)(q32;q21) was found in 13 cases with the use of destained FNAC smears. Our study suggests that, together with the cytomorphologic findings described earlier, FISH analysis for the chromosomal translocation, t(14;18)(q32;q21), is crucial for final cytologic diagnosis of FL grades 1 and 2.

Retinoblastoma protein is frequently absent or phosphorylated in anaplastic large-cell lymphoma

The possible role of retinoblastoma protein (Rb) in the pathogenesis of anaplastic large-cell lymphoma (ALCL) is unknown. We investigated Rb protein expression, both total (phosphorylated and underphosphorylated) and active (underphosphorylated), in four anaplastic lymphoma kinase (ALK)-positive ALCL cell lines (Karpas 299, JB-6, SU-DHL1, and SR-786) by Western blot analysis, and in 67 ALCL tumors (30 ALK-positive, 37 ALK-negative) using immunohistochemical methods. We also used fluorescence in situ hybridization and polymerase chain reaction methods to assess for loss of heterozygosity of the rb gene. The findings were correlated with apoptotic rate assessed by the terminal dUTP nick-end labeling assay. Immunoblots showed high total Rb levels in Karpas 299, SU-DHL1 and SR-786 and relatively lower levels in and JB-6. Underphosphorylated Rb was negative or expressed at low levels in all cell lines. In ALCL tumors, total Rb was detected in 44 (66%) and absent in 23 (34%). The mean apoptotic rate was 3.2% in Rb-negative tumors compared with 2.7%, 2.2%, and 1.2% in tumors with <10%, 10 to 50%, and >50% Rb-positive cells, respectively (P = 0.2, Kruskall-Wallis test). In a subset of 25 total Rb-positive tumors we assessed for underphosphorylated Rb, which was detected in 12 tumors. The detection of only total Rb in the remaining 13 tumors suggests that Rb was phosphorylated. Fluorescence in situ hybridization showed allelic loss of the rb gene in 10 (40%) of 25 tumors analyzed and was significantly associated with absence of Rb expression (P = 0.003). Similar results were obtained for loss of heterozygosity of the 13q14 locus. Five-year progression-free survival for patients with Rb-negative ALCL was 89.4% compared with 47.7% for patients with total Rb-positive ALCL (P = 0.006, log-rank test). Similar trends for progression-free survival held true for patients with ALK-positive and ALK-negative tumors analyzed separately. In conclusion, Rb is absent or phosphorylated in most ALCL cell lines and tumors and absence of Rb expression is associated with better clinical outcome in patients with ALCL.

Evaluation of interphase fluorescence in situ hybridization for the t(14;18)(q32;q21) translocation in the diagnosis of follicular lymphoma on fine-needle aspirates

BACKGROUND

Diagnosing lymphoproliferative disorders on fine-needle aspiration (FNA) can be challenging due to variable cellularity and lack of architecture. Ancillary studies often are required for diagnosis. Follicular lymphoma (FL) is characterized by a monoclonal B-cell proliferation with coexpression of CD19/CD10 and a t(14;18)(q32;q21) reciprocal translocation, resulting in the immunoglobulin heavy chain/BCL-2 fusion gene. These features also can be found, with much lower frequency, in diffuse large B-cell lymphoma (DLBCL) of follicle center cell origin. The objective of the current study was to compare the accuracy in detecting FL and DLBCL of follicle center cell origin by interphase fluorescence in situ hybridization (I-FISH) versus flow cytometry immunophenotyping (FCM) on FNAs.

METHODS

Concurrent testing by FISH for t(14;18)(q32;q21) and FCM was performed on 84 FNAs, including 40 FLs and 44 non-FLs (de novo DLBCLs, mantle cell lymphomas, small lymphocytic lymphomas/chronic lymphocytic leukemias [SLLs/CLLs], small B-cell lymphomas, and reactive lymphoid hyperplasias). The final diagnosis was rendered based on the combined information from cytomorphology, FCM, FISH, immunocytochemical staining for Ki-67, monoclonality for kappa and lambda light chains, and, if available, corresponding tissue biopsy, cytogenetic analysis, and polymerase chain reaction analysis.

RESULTS

Among 40 FLs, FISH produced positive results for the t(14;18) translocation in 85.0%, negative results in 7.5%, and insufficient results in 7.5%; whereas, with FCM, 75% of cases exhibited a CD19-positive (CD19+)/CD10+ population (28 monoclonal, 2 nonclonal), 12.5% of cases exhibited a CD19+/CD10-negative population (3 monoclonal, 2 nonclonal), and 12.5% of cases were insufficient. All of nonclonal results from FCM and all of the insufficient results from FCM analysis exhibited unequivocal t(14;18) translocation by FISH. In contrast, the three negative results and the three insufficient results from FISH were monoclonal and CD19+/CD10+ on FCM. The results from FISH and FCM were concordant in 75% cases. Of 44 non-FLs, FISH produced positive results for the t(14;18) translocation in 5 DLBCLs and 2 SLLs/CLLs. The latter showed single fusion signals just above the cutoff level. All cases in the non-FL group that failed to show clonality or had insufficient results from FCM were DLBCLs. Among 17 DLBCLs, FISH detected a t(14;18) translocation in 29.4%, whereas FCM demonstrated a CD19+/CD10+ population in 23.5%.

CONCLUSIONS

I-FISH for the t(14;18)(q32;q21) translocation provided high overall accuracy in detecting FLs on FNAs. This test can be used for diagnosing or monitoring FL on FNAs when cellularity is limited or when FCM results are noncontributory. For detecting a follicle center cell origin in DLBCLs, I-FISH for the t(14;18) translocation appeared to be slightly more sensitive than FCM for the CD19+/CD10+ immunophenotype.

Molecular Diagnostics

It is increasingly evident that molecular diagnostics, that is, the use of diagnostic testing to understand the molecular mechanisms of an individual patient’s disease, will be pivotal in the delivery of safe and effective therapy for many diseases in the future. A huge body of new information on the genetic, genomic and proteomic profiles of different hematopoietic diseases is accumulating. This chapter focuses on new technologies and advancements in understanding the molecular basis of hematologic disorders, providing an overview of new information and its significance to patient care.

In Section I, Dr. Braziel discusses the impact of new genetic information and research technologies on the actual practice of diagnostic molecular hematopathology. Recent and projected changes in methodologies and analytical strategies used by clinical molecular diagnostics laboratories for the evaluation of hematologic disorders will be discussed, and some of the challenges to clinical implementation of new molecular information and techniques will be highlighted.

In Section II, Dr. Shipp provides an update on current scientific knowledge in the genomic profiling of malignant lymphomas, and describes some of the technical aspects of gene expression profiling. Analysis methods and the actual and potential clinical and therapeutic applications of information obtained from genomic profiling of malignant lymphomas are discussed.

In Section III, Dr. Liotta presents an update on proteomic analysis, a new and very active area of research in hematopoietic malignancies. He describes new technologies for rapid identification of different important proteins and protein networks, and the potential therapeutic and prognostic value of the elucidation of these proteins and protein pathways in the clinical care of patients with malignant lymphomas.