Evaluation of T cell receptor testing in lymphoid neoplasms: results of a multicenter study of 29 extracted DNA and paraffin-embedded samples

ACVIM consensus statement guidelines on diagnosing and distinguishing low-grade neoplastic from inflammatory lymphocytic chronic enteropathies in cats

BACKGROUND

Lymphoplasmacytic enteritis (LPE) and low-grade intestinal T cell lymphoma (LGITL) are common diseases in older cats, but their diagnosis and differentiation remain challenging.

OBJECTIVES

To summarize the current literature on etiopathogenesis and diagnosis of LPE and LGITL in cats and provide guidance on the differentiation between LPE and LGITL in cats. To provide statements established using evidence-based approaches or where such evidence is lacking, statements based on consensus of experts in the field.

ANIMALS

None.

METHODS

A panel of 6 experts in the field (2 internists, 1 radiologist, 1 anatomic pathologist, 1 clonality expert, 1 oncologist) with the support of a human medical immunologist, was formed to assess and summarize evidence in the peer-reviewed literature and complement it with consensus recommendations.

RESULTS

Despite increasing interest on the topic for clinicians and pathologists, few prospective studies were available, and interpretation of the pertinent literature often was challenging because of the heterogeneity of the cases. Most recommendations by the panel were supported by a moderate or low level of evidence. Several understudied areas were identified, including cellular markers using immunohistochemistry, genomics, and transcriptomic studies.

CONCLUSIONS AND CLINICAL IMPORTANCE

To date, no single diagnostic criterion or known biomarker reliably differentiates inflammatory lesions from neoplastic lymphoproliferations in the intestinal tract of cats and a diagnosis currently is established by integrating all available clinical and diagnostic data. Histopathology remains the mainstay to better differentiate LPE from LGITL in cats with chronic enteropathy.

Validation of a Next-Generation Sequencing-Based T-Cell Receptor Gamma Gene Rearrangement Diagnostic Assay: Transitioning from Capillary Electrophoresis to Next-Generation Sequencing

Assessment of T-cell receptor γ gene (TRG) rearrangements is an importants consideration in the diagnostic workup of lymphoproliferative diseases. Although fragment analysis by PCR and capillary electrophoresis (CE) is the current standard of such assessment in clinical molecular diagnostic laboratories, it does not provide sequence information and is only semi-quantitative. Next-generation sequencing (NGS)-based assays are an attractive alternative to the conventional fragment size-based methods, given that they generate results with specific clonotype sequence information and allow for more accurate quantitation. The present study evaluated various test parameters and performance characteristics of a commercially available NGS-based TRG gene-rearrangement assay by testing 101 clinical samples previously characterized by fragment analysis. The NGS TRG assay showed an overall accuracy of 83% and an analytical specificity of 100%. The concordance rates were 88% to 95% in the V_γ1-8, V_γ10, and V_γ11 gene families, but lower in the V_γ9 gene family. This difference was mostly attributed to the incomplete polyclonal symmetry resulting from the two-tube CE assay versus the one-tube design of the NGS assay. The NGS assay also demonstrated strengths in distinguishing clonotypes of the same fragment size. This clinical validation demonstrated robust performance of the NGS-based TRG assay and identified potential pitfalls associated with CE assay design that are important for understanding the observed discrepancies with the CE-based assay.

The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice

This editorial highlights 20 years of JMD defining professional practice.

The Value of T-Cell Receptor γ (TRG) Clonality Evaluation by Next-Generation Sequencing in Clinical Hematolymphoid Tissues

OBJECTIVES

To evaluate feasibility of assessing T-cell receptor γ (TRG) clonality by next-generation sequencing (NGS) in hematolymphoid tissues.

METHODS

We evaluated TRG clonality using NGS and polymerase chain reaction (PCR) assays in blood, bone marrow, and formalin-fixed, paraffin-embedded tissues in 41 archived cases, including 21 benign cases with no history of any lymphoproliferative disorders (LPDs), 16 LPDs (nine mature T-cell neoplasms, seven mature B-cell neoplasms and immune dysregulation-associated LPDs), and four atypical LPDs from 22 females and 19 males with a median age of 58 (range, 9-87) years.

RESULTS

(1) NGS analyzed TRG sequence and peak ratios, and it had a greater sensitivity than PCR. (2) NGS identified small clones, including biallelic or monoallelic, and minimum clonal percentages (range, ~2.4% to ~69%) within all T cells. (3) We provide our strategy and criteria for evaluating NGS results. (4) We describe every case, with definitive evaluation of TRG clonality in 100% cases by NGS.

CONCLUSIONS

TRG clonality evaluation by NGS provides greater clinical utility than PCR.

Best practices in diagnostic immunohistochemistry: workup of cutaneous lymphoid lesions in the diagnosis of primary cutaneous lymphoma

CONTEXT

Primary cutaneous lymphoma is a common extranodal non-Hodgkin lymphoma. These lesions share common features with their nodal counterparts, but also have differences in morphology, unique clinical presentations, and immunohistochemical features.

OBJECTIVE

To review the 2008 World Health Organization (WHO) and 2005 consensus WHO-EORTC (European Organisation for Research and Treatment of Cancer) classifications, and address the immunohistochemical findings in the most common primary cutaneous T- and B-cell lymphomas. Since clonality testing is commonly used as an ancillary test in the evaluation of cutaneous lymphoma, a brief section in the use and pitfalls of clonality testing is included.

DATA SOURCES

The WHO and EORTC classification publications and the relevant recent literature were used to compile appropriate and practical guidelines in this review.

CONCLUSIONS

The practice of dermatopathology and hematopathology varies widely. Thus, while this review provides an overview and guideline for the workup of lymphoid lesions of the skin, the practitioner should understand the importance of clinical correlation as well as appropriate utility of available resources (such as clonality testing) in arriving at a diagnosis in cutaneous lymphoid lesions.

Molecular diagnostics of T-cell lymphoproliferative disorders

T-cell neoplasms include both mature T-cell leukemias and lymphomas and immature proliferations of precursor T cells. Molecular laboratories routinely assay suspected T-cell proliferations for evidence of clonality. In addition, some T-cell neoplasms are characterized by recurrent structural abnormalities that can be readily identified by such techniques as fluorescence in situ hybridization. New massively parallel sequencing technologies have led to the identification of numerous recurrent gene mutations in T-cell neoplasms. These findings are reviewed. As new technologies become implemented in molecular diagnostic laboratories and as targeted therapies are developed, it is anticipated that more extensive genomic characterization of T-cell neoplasms will be routinely performed in the future.

Lymph node fine needle cytology in the staging and follow-up of cutaneous lymphomas

Background

Lymph nodal involvement is an important clinical-pathological sign in primary cutaneous lymphoma (PCL), as it marks the transformation/evolution of the disease from localized to systemic; therefore the surveillance of lymph nodes is important in the staging and follow up of PCL. Fine needle cytology (FNC) is widely used in the diagnosis of lymphadenopathies but has rarely been reported in PCL staging and follow-up. In this study an experience on reactive and neoplastic lymphadenopathies arisen in PCL and investigated by FNC, combined to ancillary techniques, is reported.

Methods

Twenty-one lymph node FNC from as many PCL patients were retrieved; 17 patients had mycosis fungoides (MF) and 4 a primary cutaneous B-cell lymphoma (PBL). In all cases, rapid on site evaluation (ROSE) was performed and additional passes were used to perform flow cytometry (FC), immunocytochemistry (ICC) and/or polymerase chain reaction (PCR) to assess or rule out a possible clonality of the corresponding cell populations.

Results

FNC combined with FC, ICC, and PCR identified 12 cases of reactive, non specific, hyperplasia (BRH), 4 dermatopathic lymphadenopathy (DL), 4 lymph nodal involvement by MF and 1 lymph nodal involvement by cutaneous B-cell lymphoma.

Conclusions

FNC coupled with ancillary techniques is an effective tool to evaluate lymph node status in PCL patients, provided that ROSE and a rational usage of ancillary techniques is performed according to the clinical context and the available material. The method can be reasonably used as first line procedure in PCL staging and follow up, avoiding expensive and often ill tolerated biopsies when not strictly needed.

Phenotype and TCR-gamma gene rearrangements in a Malaysian cohort of T-cell leukaemia/lymphoma cases

T cells undergo a series of complex phenotypic changes before achieving maturation. Discrete stages of T-cell differentiation are simplified to four stages (pro-, pre-, cortical and mature-T cell) and used in the classification of T-cell leukaemia. HLA-DR has been reported to be expressed in immature T-cell acute lymphoblastic leukemia (ALL) and also confer a poorer treatment outcome. Simultaneously, the genotype goes through distinct pattern changes due to rearrangement of T-cell receptor (TCR) genes. TCR gene rearrangement is important in the diagnosis of clonality and used as markers to detect minimal residual disease in lymphoproliferative disorders. We identified a subset within Pro-T and Pre-T cell cases distinguished by the expression of HLA-DR. These subgroups appeared to be more immature as rearrangement of the TCR-gamma gene was either at germline or involved only the first constant region (C1) unlike a more rearranged pattern in the HLA-DR-subgroups. We also observed a higher incidence of mediastinal mass (67%) in the HLA-DR-subgroup in the Pre-T stage. These characteristics may be useful as markers to further refine staging of T-cell ALL and determine prognosis.

Comparison of BIOMED-2 versus laboratory-developed polymerase chain reaction assays for detecting T-cell receptor-gamma gene rearrangements

Detecting clonal T-cell receptor (TCR)-gamma gene rearrangements (GRs) is an important adjunct test for diagnosing T-cell lymphoma. We compared a recently described assay (BIOMED-2 protocol), which targets multiple variable (V) gene segments in two polymerase chain reaction (PCR) reactions (multi-V), with a frequently referenced assay that targets a single V gene segment in four separate PCR reactions (mono-V). A total of 144 consecutive clinical DNA samples were prospectively tested for T-cell clonality by PCR using laboratory-developed mono-V and commercial multi-V primer sets for TCR-gamma GR. The combination of TCR-beta, mono-V TCR-gamma and multi-V TCR-gamma detected more clonal cases (68/144, 47%) than any individual PCR assay. We detected clonal TCR-beta GR in 47/68 (69%) cases. Using either mono-V or multi-V TCR-gamma primers, the sensitivities for detecting clonality were 52/68 (76%) or 51/68 (75%). Using both mono-V and multi-V TCR-gamma primers improved the sensitivity for detecting clonality, 60/68 (88%). Combining either mono-V or multi-V TCR-gamma primers with TCR-beta primers also improved the sensitivity, 64/68 (94%). Significantly, TCR-gamma V11 GRs could only be detected using the mono-V-PCR primers. We conclude that using more than one T-cell PCR assay can enhance the overall sensitivity for detecting T-cell clonality.

T-cell receptor gene rearrangement and CD30 immunoreactivity in traumatic ulcerative granuloma with stromal eosinophilia of the oral cavity

Traumatic ulcerative granuloma with stromal eosinophilia (TUGSE) is an ulcerative lesion of the oral mucosa with unknown pathogenesis. A few recent case reports have demonstrated molecular evidence of T-cell clonality in TUGSE and CD30 immunoreactivity in the large atypical mononuclear cells, raising the possibility that a TUGSE subset may represent the oral counterpart of primary cutaneous CD30+ T-cell lymphoproliferative disorders. We examined the immunoreactivity for CD30 and T-cell receptor (TCR) gamma gene rearrangement in 37 TUGSE cases. Clonal TCR gene rearrangements were demonstrated in 7 (24%) of 29 cases with amplifiable DNA, and the morphologic features and CD30 immunoreactivity of these cases did not differ from those with polyclonal TCR gene rearrangements. Clinical follow-up was available for 5 of 7 TUGSE cases with clonal TCR gene rearrangement for an average period of 1.75 years after the initial biopsy or excision, and there was no evidence of local recurrence or development of systemic T-cell lymphoproliferative disorder. Without morphologic and/or clinical evidence of lymphoma, T-cell clonality and/or CD30 positivity in these lesions is not indicative of malignancy and should be interpreted with caution.

Cytologic evaluation of lymphadenopathy associated with mycosis fungoides and Sezary syndrome: role of immunophenotypic and molecular ancillary studies

BACKGROUND

The most common presenting site of extracutaneous disease in mycosis fungoides and Sezary syndrome is the peripheral lymph node. Although fine-needle aspiration biopsy has been shown to be a valuable diagnostic technique in evaluating lymphadenopathy, its utility in patients with cutaneous T-cell lymphoma has not been extensively studied. With fine-needle aspiration biopsy, material can be collected for ancillary diagnostic studies and for morphologic evaluation.

METHODS

The authors report a series of 11 fine-needle aspiration biopsy specimens from 10 mycosis fungoides and Sezary syndrome patients. Flow cytometric immunophenotyping and T-cell receptor gamma chain polymerase chain reaction were performed on fine-needle aspiration biopsy material and correlated with cytologic findings.

RESULTS

Seven of 10 patients had lymph node involvement by cutaneous T-cell lymphoma, with 3 cases exhibiting large-cell transformation and 4 cases exhibiting a small-cell pattern. Flow cytometric immunophenotyping identified an abnormal T-cell population in 6 cases. A clonal T-cell rearrangement by T-cell receptor gamma chain polymerase chain reaction (TCR-gamma PCR) was identified in 1 case in which insufficient events were present for evaluation by flow cytometry and in 1 case in which flow cytometry was not diagnostic of T-cell lymphoma. Two cases showed involvement by classic Hodgkin lymphoma diagnosed by immunohistochemistry on cell block material.

CONCLUSIONS

Fine-needle aspiration biopsy in conjunction with immunophenotyping and T-cell receptor gamma chain polymerase chain reaction is significantly useful in evaluation of lymphadenopathy in patients with mycosis fungoides and Sezary syndrome, especially for triaging lymph nodes that would otherwise not be sampled or for evaluating multiple lymph nodes.

The frequency of immunoglobulin heavy chain gene and T-cell receptor gamma-chain gene rearrangements and Epstein-Barr virus in ALK+ and ALK- anaplastic large cell lymphoma and other peripheral T-cell lymphomas

We previously identified a relatively high frequency of B-cell proliferations along with simultaneous T-cell receptor gamma-chain gene (TRG) and immunoglobulin heavy chain gene (IGH) rearrangements in a series of angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma, unspecified. Here, we report on a series of 74 peripheral T-cell lymphoma (PTCL) cases composed entirely of specific PTCL subtypes, including 28 cases of ALK+ anaplastic large-cell lymphoma (ALCL), 35 cases of ALK- ALCL, and 11 cases that represent other specific PTCL subtypes. We performed IGH and TRG gene rearrangement studies and in situ hybridization for Epstein-Barr virus (EBV) to determine the frequency of IGH clonality and to investigate the relationship between EBV, clonality, and associated B-cell proliferations. Using BIOMED-2 PCR assays, we detected TRG clones in 64 of 74 (86%) cases and IGH clones in 6 of 74 (8%) cases, with all IGH-positive cases exhibiting a concurrent TRG clone. Despite the detection of occasional IGH clones, there was no correlation between IGH clonality and EBV, and B-cell proliferations were not identified in any of the cases. These findings suggest that other factors contribute to IGH clonality and demonstrate that, in the absence of an associated B-cell proliferation, IGH clonality occurs infrequently (8%) in specific PTCL subtypes.

Malleable immunoglobulin genes and hematopathology - the good, the bad, and the ugly: a paper from the 2007 William Beaumont hospital symposium on molecular pathology

Immunoglobulin gene rearrangement analysis is one of the more commonly performed assays available on the hematopathology menu of clinical molecular pathology laboratories. The analysis of these rearrangements provides useful information on a number of different levels in the evaluation of lymphoproliferations. An appreciation of the various mechanisms involved in the numerous physiological pathways affecting the immunoglobulin genes, and hence antibody molecules, is central to an understanding of B-cell development vis-à-vis the generation of immunological diversity. Knowledge about the intricate complexities of these mechanisms is also germane to an evaluation of testing methodologies. With this information, it is easier to develop an understanding of how contemporary molecular testing of immunoglobulin gene rearrangements has evolved, from historically quite heterogeneous, fairly flawed, and rather ugly approaches to current more-standardized protocols. In addition, recognition of how such genetic changes with good intentions can turn bad has fostered increasing insights into the pathogenesis of B-cell lymphomas and leukemias. Despite the significant improvements in the design of immunoglobulin gene rearrangement assays, numerous pitfalls and caveats remain. Accordingly, it is crucial to consider such testing a tool, and although most useful, it is one of many tools that may be required to build cogent diagnoses.

CNS T-cell lymphoma: an under-recognized entity?

The incidence of CNS lymphoma has increased significantly in the past 30 years, primarily in the elderly and immunocompromised. While T-cell lymphomas comprise 15-20% of systemic lymphomas, they comprise less than 4% of primary CNS lymphomas, suggesting that they may be under-recognized compared to their systemic counterparts. To investigate this, we studied brain biopsies from three patients who were diagnosed with T-cell lymphoma confined to the brain. They had enhancing lesions by MRI, arising in the cerebellum and brainstem in one and temporal lobe in two. We compared these to biopsies from three patients who had reactive lymphoid infiltrates and who had clinical signs/symptoms and radiographic findings that were indistinguishable from the lymphoma group. Biopsies from both the lymphoma group and reactive group showed considerable cytomorphologic heterogeneity. Although one lymphoma case contained large atypical cells, the other two contained small, mature lymphocytes within a heterogeneous infiltrate of neoplastic and reactive inflammatory cells. Surface marker aberrancies were present in two lymphoma cases, but this alone could not reliably diagnose T-cell lymphoma. The proliferation index was not useful for differentiating lymphoma from reactive infiltrates. In five of the six cases the diagnosis was most influenced by clonality studies for T-cell receptor-gamma gene rearrangements. We conclude that because of the high degree of overlap in cytomorphologic and immunophenotypic features between T-cell lymphoma and reactive infiltrates, T-cell lymphoma may not be recognized unless studies for T-cell receptor gene rearrangements are performed for CNS lesions composed of a polymorphous but predominantly T-cell infiltrate.

Optimization of PCR amplification for B- and T-cell clonality analysis on formalin-fixed and paraffin-embedded samples

In many cases, particularly in retrospective studies, only formalin-fixed and paraffin-embedded (FFPE) tissue samples are available for molecular studies. DNA recovered from FFPE tissues generally consists of fragmented small target sequences with chemical alterations. Clonality analysis is not easy on FFPE samples, in fact, it requires even more experience than that of performed on fresh samples or is more complicated than most genomic PCR amplifications for somatic genes. In our study, we have performed a multi-parameter PCR evaluation investigating immunoglobulin heavy chain gene (IgH) and T-cell receptor gamma gene (TCRgamma) rearrangements on non-purified crude lysates of FFPE samples, in order to establish the significance of different variables on performance of PCR amplification. The results showed that a slight decrease in the concentration of primers in combination with a slight increase in MgCl2 and Taq polymerase concentrations, as well as the use diluted crude template and a standard amount of dNTPs can be the modifications of choice while adjusting IgH and TCRgamma clonality tests on poor quality DNA FFPE samples. Using our improved protocol, 74% (17/23) of the tested B-cell lymphomas and 68% (31/46) of the tested T-cell lymphomas demonstrated monoclonal PCR product, proving the applicability of our optimized method. Our experience may be of help during the optimization process in technically difficult cases as well as to determine which parameters and how should be changed to minimize false-negative and false-positive results.

The frequency of B- and T-cell gene rearrangements and epstein-barr virus in T-cell lymphomas: a comparison between angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma, unspecified with and without associated B-cell proliferations

We report on a series of 58 cases of angioimmunoblastic T-cell lymphoma (AILT) and 59 cases of peripheral T-cell lymphoma, unspecified (PTCL-NOS). Subsets of cases from both diagnostic groups were complicated by associated B-cell proliferations, and we performed B- and T-cell clonality studies and in situ hybridization for Epstein-Barr virus (EBV) to investigate the relationship between B-cell proliferation, B-cell clonality, and EBV. Using multiplex polymerase chain reaction assays based on the BIOMED-2 collaborative study, we detected TCRgamma T-cell clones in 78 and 81% of AILT and PTCL-NOS cases, respectively, and IGH B-cell clones in 34 and 35% of AILT and PTCL-NOS cases, respectively. The majority of cases contained EBV-positive cells, including 50% of AILT and 57% of PTCL-NOS cases, and cases with B-cell proliferations were more often EBV-positive. Although a relatively high rate of B-cell clonality has been shown for AILT, our findings for PTCL-NOS differ from previous reports in that B-cell clonality was relatively frequent. Overall, a positive B-cell clone correlated, in part, with the presence of a B-cell proliferation but not with EBV. Our findings demonstrate that B-cell clonality is a common finding in AILT and PTCL-NOS, and its presence should not negate the diagnosis established by morphologic, immunophenotypic, and clinical findings.

BIOMED-2 multiplex immunoglobulin/T-cell receptor polymerase chain reaction protocols can reliably replace Southern blot analysis in routine clonality diagnostics

To establish the most sensitive and efficient strategy of clonality diagnostics via immunoglobulin and T-cell receptor gene rearrangement studies in suspected lymphoproliferative disorders, we evaluated 300 samples (from 218 patients) submitted consecutively for routine diagnostics. All samples were studied using the BIOMED-2 multiplex polymerase chain reaction (PCR) protocol. In 176 samples, Southern blot (SB) data were also available, and the two types of molecular results were compared. Results of PCR and SB analysis of both T-cell receptor and immunoglobulin loci were concordant in 85% of samples. For discordant results, PCR results were more consistent with the final diagnosis in 73% of samples. No false-negative results were obtained by PCR analysis. In contrast, SB analysis failed to detect clonality in a relatively high number of samples, mainly in cases of low tumor burden. We conclude that the novel BIOMED-2 multiplex PCR strategy is of great value in diagnosing patients with suspected B- and T-cell proliferations. Because of its higher speed, efficiency, and sensitivity, it can reliably replace SB analysis in clonality diagnostics in a routine laboratory setting. Just as with SB results, PCR results should always be interpreted in the context of clinical, immunophenotypical, and histopathological data.

Hepatosplenic γδ T-cell lymphoma

AIM: To investigate the clinicopathologic characteristics, immunophenotype and TCR gene rearrangements of hepatosplenic T-cell lymphoma in eight Chinese patients.

METHODS: Eight Chinese patients with hepatosplenic γδ T-cell lymphomas were studied. Hematoxylin-eosin-stained slides and clinical histories were reviewed. We also carried out immunohistochemical staining for CD3, CD4, CD8, CD20, CD43, CD56, CD79a, UCHL-1, and TCR γδ. Rearrangements of TCR gamma and delta chain genes were also studied.

RESULTS: The spleens were enlarged and the cut surfaces were homogeneous and red-purple in color without identifiable gross lesions or enlarged hilar lymph nodes. Histologically, lymphoma cells infiltrated the cords of Billroth and often packed the sinuses. Liver biopsy showed lymphoma cell infiltrations in the sinusoids, and three cases showed involvements of the portal tracts. Immunohistochemically lymphoma cells were positive for CD3, CD43, and CD56 in all cases. Four of eight cases were positive for CD8, and all cases were negative for CD4 (6/6). Monoclonal rearrangements of TCR γ gene were demonstrated by PCR analysis in five out of the eight cases. TCR δ gene rearrangements were detected in six out of the eight cases, which demonstrated single bands on PAGE gel, and the amplification products in two cases were confirmed by sequencing.

CONCLUSION: The clinicopathology of hepatosplenic γδ T-cell lymphoma in Chinese patients is similar to what was previously reported except that the splenomegaly is not so massive, and CD8 is positive.

A comparison of multiplex and monoplex T-cell receptor gamma PCR

T-cell receptor gamma (TCRgamma) PCR is often used to detect clonal T-cell populations. Because TCRgamma contains a limited number of variable (Vgamma) and joining (Jgamma) regions, a small number of PCR primers can be used to assess T-cell clonality. The seven primers used in the current study were described previously and were split into 2 or 3 multiplex primer sets. In this study, a single 7-primer multiplex (7-plex) PCR reaction was compared with all 12 possible monoplex primer combinations on 18 samples previously analyzed for T-cell receptor rearrangements by TCRbeta Southern blot and/or TCRgamma PCR followed by temporal temperature gradient gel electrophoresis. Using fluorescent Vgamma-region primers, unlabeled Jgamma-region primers, and capillary electrophoresis, we show all TCRgamma rearrangements seen by 7-plex PCR on known positive samples were seen following monoplex PCR. However, additional TCRgamma gene rearrangements were seen in monoplex PCR reactions that were not seen in the 7-plex PCR reactions. Monoplex but not 7-plex PCR of known negative samples occasionally showed TCRgamma gene rearrangements, often with less frequently used Vgamma and Jgamma-region primers, and may have represented false positive results. In summary, the single 7-plex PCR reaction correctly identified specimens with TCRgamma clonal populations and represents an improvement over existing assays that use these same primers split into several smaller multiplex reactions. Monoplex PCR has no advantage over multiplex PCR and has the potential to lead to false positive results.

Molecular methods to distinguish reactive and neoplastic lymphocyte expansions and their importance in transitional neoplastic states

Although lymphoma and leukemia usually can be diagnosed by routine cytology and histology, some cases present a diagnostic challenge for pathologists and clinicians. Often the dilemma lies in determining whether a population of lymphocytes is reactive or neoplastic. We review currently available methods for analyzing lymphocyte populations by immunophenotyping and by identifying clonally rearranged immunoglobulin and T-cell receptor genes and discuss how these tests can be used to clarify such diagnostic dilemmas. We also describe the detection of chromosomal abnormalities and methods on the horizon, such as gene expression profiling, to identify diagnostically useful oncogenes. Finally, we review the emerging concept of transitional neoplastic states, in which reactive lymphocytes transform to neoplastic lymphocytes in the presence of continued antigenic stimulation, such as that caused by infection with Helicobacter pylori. The existence of transitional neoplastic states underscores the need for an array of molecular diagnostic tools that would improve our ability to characterize lymphocyte populations in human and animal patients and enhance early detection of neoplastic lymphocytes such that eradication of the infectious or inflammatory stimulus could lead to cure.

The role of molecular studies in lymphoma diagnosis: a review

Lymphoma classification is based on a multiparametric approach to diagnosis, in which clinical features, morphology, immunophenotype, karyotype and molecular characteristics are important to varying degrees. While in most cases, a diagnosis can be confidently established on the basis of morphology and immunophenotype alone, a small proportion of diagnostically difficult cases will rely on molecular studies to enable a definitive diagnosis. This review discusses the various molecular techniques available including Southern blotting (SB), polymerase chain reaction (PCR), fluorescence in situ hybridisation (FISH)--including multicolour-FISH/spectral karyotyping and comparative genomic hybridisation--and also gene expression profiling using cDNA microarray technology. Emphasis is given to the analysis of antigen receptor gene rearrangements and chromosomal translocations as they relate to lymphoma diagnosis and also in the setting of minimal residual disease (MRD) detection and monitoring. Laboratories performing these tests need to have expertise in these areas of testing, and there is a need for greater standardisation of molecular tests. It is important to know the sensitivity and specificity of each test as well as its limitations and the pitfalls in the interpretation of results. Above all, results of molecular testing should never be considered in isolation, and must always be interpreted in the context of clinical and other laboratory data.

Molecular diagnosis in lymphoma

The evolution of our ability to diagnose and classify lymphomas in an increasingly refined manner has paralleled the development of novel technologic approaches, with contemporary practice dependent upon the harnessing of a plethora of data that include microscopic, immunophenotypic, and genetic information. Although each of these components is currently indispensable, there is a purported progressive improvement in biologic objectivity as one maneuvers through these respective technologies. Accordingly, and in particular given the rapid pace at which key insights into lymphoma biology are emerging with microarray and other cutting-edge technologies, the role of molecular genetic testing is assuming even greater relevance. The ability to diagnose and classify lymphomas more accurately, precisely, and rationally by incorporating molecular data ought to lead to the development of more appropriate directed therapies.

A case of a diffuse large B-cell lymphoma of plasmablastic type associated with the t(2;5)(p23;q35) chromosome translocation

Anaplastic large cell lymphomas are associated with the t(2;5)(p23;q35) chromosome translocation in 40% to 60% of cases, leading to a new chimeric gene NPM-ALK. NPM-ALK positive lymphomas are generally reported to be of either T cell or null phenotype. In this report, we describe a diffuse large B-cell lymphoma associated with the classic t(2;5) translocation and both nuclear and cytoplasmic expression of ALK. The tumor consisted of medium-sized to large immunoblasts and plasmablasts that on immunohistology were negative for CD30, CD20, and CD79a but showed monotypic cytoplasmic expression of lambda light chains. Clonality analysis confirmed B-cell lineage of the tumor cells. The t(2;5)(p23;q35) chromosome translocation was demonstrated as part of a complex karyotypic alteration by classic banding and spectral karyotyping (SKY) analyses. Reverse transcription polymerase chain reaction confirmed rearrangement of NPM and ALK genes. This case exemplifies that the t(2;5) can, albeit rarely, occur in large B-cell lymphomas and is not entirely limited to anaplastic large cell lymphomas of T or null cell phenotypes.

Laboratory strategies for efficient handling of paraffin-embedded tissues for molecular detection of clonality in non-hodgkin lymphomas

We herein present a technical strategy to optimize DNA isolation from paraffin-embedded tissue (PET). This includes the choice of adequate buffers for proteinase K digestion and multiplex PCR amplifications for assessing the appropriateness of DNA extracts for subsequent PCR assays for detecting clonality. We found that the association of proteinase K digestion in nonionic buffer and subsequent extract dilutions accounted for 79% of successful amplifications. A final efficiency of 88% was achieved by additional organic extractions and/or re-extractions. Comparisons were carried out with control DNA extracts from fresh samples to assess the efficiency of each clonality assay. Immunoglobulin CDRIII rearranged region amplification was more efficient for pregerminal center B-cell lymphomas in contrast to CDRII rearrangement detection, which was more effective for germinal and postgerminal lymphomas. T-cell clonality detection by TCRgamma PCR was less efficient in PET samples than in fresh tissues showing that DNA integrity is more critical for TCR than for IGH amplification. Two inconclusive cases without phenotypic markers and two other atypical lymphoproliferations masked by reactive T cells were diagnosed as plasmablastic lymphomas and as monoclonal B-proliferations, respectively, due to IGH rearrangements.

The distribution of gene segments in T-cell receptor gamma gene rearrangements demonstrates the need for multiple primer sets

Limited data exist regarding the distribution of gene segments used in T-cell receptor gamma gene rearrangements (TCR gamma GR) in T-cell lymphoproliferative disorders. The reported efficacy of TCR gamma GR protocols ranges from 60% to greater than 90%. Laboratories reporting a lower detection rate tend to use a limited set of primers. The goal of our study was to provide TCR gamma GR data to demonstrate the molecular biological basis for needing multiple primer sets targeting all gene segments. Sixty cases with a confirmed histological diagnosis of a T-cell lymphoproliferative disorder and TCR gamma GR were identified in our lymphoma registry from 1995 to 2001. DNA was obtained from fresh/frozen tissue, cell lysates, or paraffin-embedded tissue. Variable (V gamma) region gene segments were identified using denaturing gradient gel electrophoresis, which was used to select the cases in the study. Capillary electrophoresis using fluorescent-labeled joining (J gamma) region primers was performed to identify J gamma segments. Sixty cases contained a total of 98 TCR gamma GR, as some cases have more than one rearrangement. The most frequent gene segment combination involved the V gamma 1-8 and J gamma 1/2 segments. If a single primer set directed at these two segments were used for clinical diagnosis, that pair of primers would only diagnose 67% of cases as positive for TCR gamma GR. Our gene segment distribution data emphasize the importance of using a comprehensive set of V gamma and J gamma primers for an optimal detection rate of TCR gamma GR. Protocols with limited numbers of primers should be reconsidered.

Peripheral T-cell lymphoma

Peripheral (post-thymic) T-cell lymphoma consists of a wide spectrum of disorders with marked differences in biology and behavior. Proper classification is pivotal for evaluating treatment results, and most studies performed a decade ago lump together different disease entities and cannot be interpreted. With improved use of immunophenotyping and molecular methods for these disorders, their exact nature is better defined in the Revised European-American Lymphoma and subsequent World Health Organization (WHO) classifications. The WHO classification of post- thymic T/natural killer (NK)-cell lymphoma consists of 15 entities, including about 30% that are unclassified cases. A wide range in incidence exists between different populations, but it is likely to be lower than previously estimated. Certain entities, like nasal/nasal-type T/NK-cell lymphoma and human T-cell leukemia/lymphoma virus 1, are much more prevalent in certain racial groups and show exquisite viral association. In these entities as a group, prognosis and treatment seem inferior to those of their B-cell counterparts, but treatment must be tailored to the exact pathologic diagnosis and prognostic index. Aggressive combination chemotherapy appears to be curative for certain entities (eg, anaplastic lymphoma kinase-positive), whereas purine analogues may be useful for low-grade entities. The role of autologous and allogeneic stem cell transplantation is still poorly defined. Specific antibody-based therapy is also on the horizon.

Effectiveness of capillary electrophoresis using fluorescent-labeled primers in detecting T-cell receptor gamma gene rearrangements

We describe the use of fluorescent-labeled primers to analyze T-cell receptor gamma gene rearrangements (TCR gamma GR) using capillary electrophoresis in the ABI Prism 310 Genetic Analyzer. We also compare the performance with denaturing gradient gel electrophoresis (DGGE). In a single multiplex polymerase chain reaction (PCR) we amplified TCR gamma GR with primers for all known groups of variable region genes, and joining region genes described in lymphoid neoplasms. Ten reactive samples, followed by five cell lines and 25 tumor samples with 41 individual TCR gamma GR (due to many biallelic rearrangements) previously identified by DGGE, were analyzed to validate the technique. The capillary electrophoresis protocol has 92% concordance for both TCR clonal status (23 of 25) and 95% concordance in the number of individual TCR gamma GR (38 of 41) identified by DGGE. The reproducible sensitivity for detecting TCR gamma GR diluted in reactive lymphoid DNA is 2% in clinical applications. Discrimination of predominant rearrangements requires a minimum ratio of two times the height of the normal distribution of polyclonal peaks. Capillary electrophoresis can provide results within 60 minutes for each specimen after PCR is complete. Capillary electrophoresis provides a faster result than sequence-based separation methods and gives an archival electronic record. Fluorescent labeling allows the identification of both the variable and joining gene segments used in a TCR gamma GR. The effectiveness of capillary electrophoresis is similar to DGGE.

Immunoglobulin heavy chain gene analysis in lymphomas: a multi-center study demonstrating the heterogeneity of performance of polymerase chain reaction assays

Determination of monoclonality through an evaluation of immunoglobulin heavy chain (IgH) gene rearrangements is a commonly performed and useful diagnostic assay. Many laboratories that perform this assay do so by the polymerase chain reaction (PCR). To evaluate current methods for performing IgH gene testing, 19 different Association of Molecular Pathology (AMP) member laboratories analyzed 29 blinded B cell and T cell lymphoid neoplasm samples of extracted DNA and formalin-fixed, paraffin-embedded (FFPE) tissue and were asked to complete a technical questionnaire. From this study, it is clear that Southern blot analysis remains the diagnostic gold standard, with a 100% diagnostic sensitivity and specificity. There was, however, remarkable heterogeneity in the performance of, and results obtained from, IgH PCR assays with diagnostic sensitivity ranging from over 90% to as low as 20%, when evaluating the same specimens. Many laboratories overestimate the diagnostic sensitivity of their IgH PCR assay, and there was a significant, and under appreciated, drop-off (from 61.3% to 41.8%) in detection in paired FFPE as compared with fresh/frozen tissues. Fixation has a dramatic impact on the inability to perform the test on FFPE (43.1%) versus DNA already extracted from fresh or frozen tissue (2.8%). A number of variables that affected the outcome of IgH PCR were identified. Strategies that improved the detection of monoclonal IgH rearrangements include: the addition of FRII to the FRIII upstream primer (increasing detection from 57.3% to 73.6%) and the use of the FR3A rather than the FR3 FRIII primer (increasing detection from 54.7% to 69.7%). Although numerous variables (from DNA extraction to PCR product detection) were evaluated, making it difficult to mandate alterations in laboratory practice, these findings ought to prompt diagnostic molecular pathology laboratories to reevaluate their claims of sensitivity, as well as their methodologies. Both pathologists and surgeons need to ensure that not all submitted material is fixed, if there is adequate sample. Importantly, there is a need for greater standardization to reduce the unacceptably high false negative rate of this crucial diagnostic assay.

Spontaneous regression of Kikuchi lymphadenopathy with oligoclonal T-cell populations favors a benign immune reaction over a T-cell lymphoma

To aid in the initial diagnosis of Kikuchi lymphadenitis and to assess whether the composition of the T cells might shed light on the pathogenesis, we used nested polymerase chain reaction tests followed by high-resolution gel electrophoresis to determine the pattern of T-cell antigen receptor rearrangement in 56 consecutive cases. Except for 1 unusual case with recurrent lymphadenopathy, none had a monoclonal beta or gamma rearrangement. Eight cases had a polyclonal pattern at both beta and gamma loci, 20 cases had a mixed polyclonal beta and oligoclonal gamma pattern, and 27 cases had an oligoclonal pattern at both loci. The high frequency of oligoclonality did not indicate an early-stage T-cell lymphoma in evolution, as confirmed by spontaneous resolution of the lymphadenopathy in all cases within 6 months. Rather, it is consistent with reports of oligoclonal T cells in a variety of immune reactions. We conclude that, in the vast majority of cases, absence of a monoclonal T-cell receptor rearrangement excludes the possibility of T-cell lymphoma, and the presence of an oligoclonal pattern implies a benign immune reaction.