Immune Gene Rearrangements: Unique Signatures for Tracing Physiological Lymphocytes and Leukemic Cells.

The tremendous diversity of the human immune repertoire, fundamental for the defense against highly heterogeneous pathogens, is based on the ingenious mechanism of immune gene rearrangements. Rearranged immune genes encoding the immunoglobulins and T-cell receptors and thus determining each lymphocyte's antigen specificity are very valuable molecular markers for tracing malignant or physiological lymphocytes. One of their most significant applications is tracking residual leukemic cells in patients with lymphoid malignancies. This so called 'minimal residual disease' (MRD) has been shown to be the most important prognostic factor across various leukemia subtypes and has therefore been given enormous attention. Despite the current rapid development of the molecular methods, the classical real-time PCR based approach is still being regarded as the standard method for molecular MRD detection due to the cumbersome standardization of the novel approaches currently in progress within the EuroMRD and EuroClonality NGS Consortia. Each of the molecular methods, however, poses certain benefits and it is therefore expectable that none of the methods for MRD detection will clearly prevail over the others in the near future.

Glucocorticoids in T cell development, differentiation and function.

Glucocorticoids (GCs) are small lipid hormones produced by the adrenals that maintain organismal homeostasis. Circadian and stress-induced changes in systemic GC levels regulate metabolism, cardiovascular and neural function, reproduction and immune activity. Our understanding of GC effects on immunity comes largely from administration of exogenous GCs to treat immune or inflammatory disorders. However, it is increasingly clear that endogenous GCs both promote and suppress T cell immunity. Examples include selecting an appropriate repertoire of T cell receptor (TCR) self-affinities in the thymus, regulating T cell trafficking between anatomical compartments, suppressing type 1 T helper (TH1) cell responses while permitting TH2 cell and, especially, IL-17-producing T helper cell responses, and promoting memory T cell differentiation and maintenance. Furthermore, in addition to functioning at a distance, extra-adrenal (local) production allows GCs to act as paracrine signals, specifically targeting activated T cells in various contexts in the thymus, mucosa and tumours. These pleiotropic effects on different T cell populations during development and immune responses provide a nuanced understanding of how GCs shape immunity.

Microbial exposure drives polyclonal expansion of innate γδ T cells immediately after birth.

Starting at birth, the immune system of newborns and children encounters and is influenced by environmental challenges. It is still not completely understood how γδ T cells emerge and adapt during early life. Studying the composition of T cell receptors (TCRs) using next-generation sequencing (NGS) in neonates, infants, and children can provide valuable insights into the adaptation of T cell subsets. To investigate how neonatal γδ T cell repertoires are shaped by microbial exposure after birth, we monitored the γ-chain (TRG) and δ-chain (TRD) repertoires of peripheral blood T cells in newborns, infants, and young children from Europe and sub-Saharan Africa. We identified a set of TRG and TRD sequences that were shared by all children from Europe and Africa. These were primarily public clones, characterized by simple rearrangements of Vγ9 and Vδ2 chains with low junctional diversity and usage of non-TRDJ1 gene segments, reminiscent of early ontogenetic subsets of γδ T cells. Further profiling revealed that these innate, public Vγ9Vδ2+ T cells underwent an immediate TCR-driven polyclonal proliferation within the first 4 wk of life. In contrast, γδ T cells using Vδ1+ and Vδ3+TRD rearrangements did not significantly expand after birth. However, different environmental cues may lead to the observed increase of Vδ1+ and Vδ3+TRD sequences in the majority of African children. In summary, we show how dynamic γδ TCR repertoires develop directly after birth and present important differences among γδ T cell subsets.

Inventories of naive and tolerant mouse CD4 T cell repertoires reveal a hierarchy of deleted and diverted T cell receptors.

Deletion or Treg cell differentiation are alternative fates of autoreactive MHCII-restricted thymocytes. How these different modes of tolerance determine the size and composition of polyclonal cohorts of autoreactive T cells with shared specificity is poorly understood. We addressed how tolerance to a naturally expressed autoantigen of the central nervous system shapes the CD4 T cell repertoire. Specific cells in the tolerant peripheral repertoire either were Foxp3+ or displayed anergy hallmarks and, surprisingly, were at least as frequent as in the nontolerant repertoire. Despite this apparent lack of deletional tolerance, repertoire inventories uncovered that some T cell receptors (TCRs) were lost from the CD4 T cell pool, whereas others mediated Treg cell differentiation. The antigen responsiveness of these TCRs supported an affinity model of central tolerance. Importantly, the contribution of different diverter TCRs to the nascent thymic Treg cell population reflected their antigen reactivity rather than their frequency among precursors. This reveals a multilayered TCR hierarchy in CD4 T cell tolerance that separates deleted and diverted TCRs and assures that the Treg cell compartment is filled with cells of maximal permissive antigen reactivity.

Skewing of the T-cell receptor repertoire in patients receiving rituximab after allogeneic hematopoietic cell transplantation: what lies beneath?

Rituximab is known to affect T cell immune responses. We and others have reported expansions of T large granular lymphocytes (T-LGLs) in lymphoma patients after Rituximab. We report here the immunogenetic profiling of the T cell receptor (TR) gene repertoire in 14 patients who received Rituximab post allo-HCT and explore clinicobiological correlations. All experienced antigenic triggers, CMV, EBV re-activation and chronic GvHD and had been treated with Rituximab. Skewing of TRBV genes was observed: 3 TRBV genes accounted for half of the repertoire. Oligoclonal pattern with expanded clonotypes was common. Patients with oligoclonality exhibited frequently cGvHD. Longitudinal samples in one revealed distinct clonotypes, suggesting clonal drift. T-LGL leukemia of donor origin with mixed chimerism eventually developed. In conclusion, we report development of oligoclonal T-LGLs after Rituximab post allo-HCT, alluding to antigen selection. Persistence of this phenomenon likely reflects strong antigenic stimulation by viruses and/or cGVHD aggravated by Rituximab.

Endogenous T Cell Receptor Rearrangement Represses Aggressive Central Nervous System Autoimmunity in a TcR-Transgenic Model on the Non-Obese Diabetic Background.

The T cell response to central nervous system (CNS) antigen in experimental autoimmune encephalomyelitis (EAE) permits one to model the immune aspects of multiple sclerosis. 1C6 transgenic mice on the non-obese diabetic (NOD) background possess a class II-restricted T cell receptor (TcR; Vα5-Vß7) specific for the encephalitogenic peptide myelin oligodendrocyte glycoprotein (MOG)[35-55]. It remains to be determined what role is played by allelic inclusion in shaping the TcR repertoire of these mice. Here, we show that 1C6 T cells display substantial promiscuity in their expression of non-transgenically derived Vα chains. Further, enforced expression of the transgenic TcR in 1C6 × Rag1-/- mice profoundly disrupted thymic negative selection and led to a sharp decrease in the number of mature peripheral T cells. 1C6 × Rag1-/- mice developed spontaneous EAE at a significant frequency and rapidly developed fatal EAE upon immunization with myelin oligodendrocyte glycoprotein (MOG)[35-55]. Passive transfer of 1C6 × Rag1+/+ CD4+ T cells, but not CD8+ T cells or B cells, partially rescued 1C6 × Rag1-/- mice from severe EAE. FoxP3+ CD4+ Treg cells were present in the CNS of immunized 1C6 mice, as well as immunized 1C6 × Rag1-/- that had been supplemented with 1C6 CD4+ T cells. However, they were not observed in 1C6 × Rag1-/- that did not receive Rag1-sufficient 1C6 CD4+. Further, in vivo blockade of Treg accelerated the onset of symptoms in 1C6 mice immunized with MOG[35-55], indicating the pertinence of Treg-mediated control of autoimmune inflammation in this model. Thus, TcR allelic inclusion is crucial to the generation of FoxP3+ CD4+ T cells necessary for the suppression of severe CNS autoimmunity.

SOX4 controls invariant NKT cell differentiation by tuning TCR signaling.

Natural killer T (NKT) cells expressing the invariant T cell receptor (iTCR) serve an essential function in clearance of certain pathogens and have been implicated in autoimmune and allergic diseases. Complex effector programs of these iNKT cells are wired in the thymus, and upon thymic egress, they can respond within hours of antigenic challenges, classifying iNKT cells as innate-like. It has been assumed that the successful rearrangement of the invariant iTCRα chain is the central event in the divergence of immature thymocytes to the NKT cell lineage, but molecular properties that render the iTCR signaling distinct to permit the T cell lineage diversification remain obscure. Here we show that the High Mobility Group (HMG) transcription factor (TF) SOX4 controls the production of iNKT cells by inducing MicroRNA-181 (Mir181) to enhance TCR signaling and Ca2+ fluxes in precursors. These results suggest the existence of tailored, permissive gene circuits in iNKT precursors for innate-like T cell development.

Influence of immunologic status on age prediction using signal joint T cell receptor excision circles.

Age estimation based on quantifying signal joint T cell receptor excision circle (sjTREC) in T cells has been established to be a promising approach in forensic practice and demonstrated in different ethnic groups. Considering that the homeostasis of T cells carrying sjTRECs is closely related to the immunologic status of a person, it is important to investigate the influence of various immunologic statuses on the age estimation model. In this study, quantification of sjTREC contents was performed for groups of people with various immune system statuses, and the result showed less correlation with chronological age (r 2 = 0.424) than in the healthy group (r 2 = 0.648). The simulation model indicated that this influence could increase the range of prediction in the age estimation model, and the mean absolute deviation (MAD) between chronological age and predicted age. Through this study, it was demonstrated that immunologic status is a factor that affects the accuracy of age prediction using sjTREC quantification.

Reflectance confocal microscopy features of mycosis fungoides and Sézary syndrome: correlation with histopathologic and T-cell receptor rearrangement studies.

BACKGROUND: Mycosis fungoides/Sézary syndrome (MF/SS) often requires multiple skin biopsies for definitive diagnosis. In vivo reflectance confocal microscopy (RCM) visualizes high-resolution cellular detail of the skin. The objective of this study is to evaluate the morphologic features of MF/SS using RCM and to correlate RCM features with histopathology and T-cell receptor (TCR) gene rearrangement studies. METHODS: A cohort of patients with active/recurrent or suspicious MF/SS disease was prospectively recruited for RCM imaging and histopathologic/RCM images were evaluated. Statistical analyses were performed to identify unique RCM features and to correlate RCM features with histopathologic findings and TCR rearrangement studies. RESULTS: Eighty-three lesions were evaluated. Correlation between RCM and histopathology was moderate for all relatable features (κ = 0.41, p<0.001), almost perfect for intraepidermal atypical lymphocytes [prevalence and bias-adjusted kappa (PABAK) = 0.90], and fair for Pautrier collections (κ = 0.32, p = 0.03). Lesions with Pautrier collections identified by RCM were significantly more likely to show TCR clonality (p = 0.04) and diagnostic features of MF/SS on histopathology (p = 0.03). CONCLUSIONS: Our study captures morphologic RCM criteria for a variety of skin lesions. Pautrier collections visualized by RCM are associated with improved histopathologic diagnosis and detection of TCR gene clonality. Although further studies are needed to validate the diagnostic implications of RCM for MF/SS, our study highlights the potential utility of RCM.

Association between lymphocyte antigen receptor gene rearrangements and histopathological evaluation in canine chronic enteropathy.

Although definitive diagnosis of chronic enteropathy (CE) and gastrointestinal (GI) lymphoma requires histopathological evaluation of the GI tract, these conditions are often still difficult to differentiate from each other. Polymerase chain reaction (PCR) for antigen receptor gene rearrangements (PARR) has been applied recently as an adjunctive for diagnosis of lymphoid tumors; however, its clinical value in canine CE and GI lymphoma remains unclear. The purpose of this study was to investigate the relationship between PARR and histopathological diagnosis, degree of enteritis or lymphoma, and long-term prognosis in dogs, in order to evaluate the clinical significance of PARR. Endoscopic biopsy specimens obtained from 96 dogs with chronic enteritis (mild, n=14; moderate, n=20; marked, n=62) and 21 dogs with GI lymphoma were used. Clonality was observed in 51% of the animals with chronic enteritis; interestingly, it was found in 29% of those with only mild enteritis. In dogs with marked enteritis, the rate of PARR was higher in those with lymphocyte epitheliotropism than in those without epitheliotropism. The sensitivity of PARR in animals with GI lymphoma was 76%. There was no significant prognostic difference between chronic enteritis with or without clonal rearrangements. In contrast, dogs histopathologically diagnosed with marked enteritis had a significantly shorter survival time than did those with mild or moderate enteritis. While the significance of PARR in the diagnosis of GI lymphoma remains uncertain, the pathological roles of clonally expanding lymphocytes in canine CE should be investigated further.

[Effects of surgical thymectomy on thymic function and peripheral T cell populations in mice].

OBJECTIVE: To investigate the effect of surgical thymectomy on immune function and peripheral blood T lymphocytes of a mouse model. METHODS: Neonatal (aged 72 hours) and infant (aged 1 week) BALB/c mice were randomly divided into two groups with 20 mice in each group, respectively. The mice of surgical group underwent a surgical thymectomy; the sham operation group excluded the thymectomy procedure. Then surgical group and sham operation group were randomly divided into two subgroups with 10 mice in each group, respectively. One subgroup was sacrificed one month after operation; the other was sacrificed two months after operation. To evaluate thymic function and peripheral T cell populations, T cell receptor rearrangement excision circles (TREC) were assessed by real-time quantitative PCR and T lymphocyte and its subset were detected by flow cytometry. RESULTS: The levels of peripheral T cell populations and TREC of the operation group were significantly lower than those of the sham operation group (P<0.01). There were no significant differences in the measurements between neonatal and infant mice or between one month after operation and two months after operation (P>0.05). CONCLUSION: Thymectomy in young mice can make damage on T cell immune system. The damage may continue in a long term and the age of operation maybe don't have an effect on it.

Receptor revision in CD4 T cells is influenced by follicular helper T cell formation and germinal-center interactions.

Peripheral CD4 T cells in Vß5 transgenic (Tg) C57BL/6J mice undergo tolerance to an endogenous superantigen encoded by mouse mammary tumor virus 8 (Mtv-8) by either deletion or T-cell receptor (TCR) revision. Revision is a process by which surface expression of the Vß5(+) TCR is down-regulated in response to Mtv-8 and recombination activating genes are expressed to drive rearrangement of the endogenous TCRß locus, effecting cell rescue through the expression of a newly generated, non-self-reactive TCR. In an effort to identify the microenvironment in which revision takes place, we show here that the proportion of T follicular helper cells (Tfh) and production of high-affinity antibody during a primary response are increased in Vß5 Tg mice in an Mtv-8-dependent manner. Revising T cells have a Tfh-like surface phenotype and transcription factor profile, with elevated expression of B-cell leukemia/lymphoma 6 (Bcl-6), CXC chemokine receptor 5, programmed death-1, and other Tfh-associated markers. Efficient revision requires Bcl-6 and is inhibited by B lymphocyte-induced maturation protein-1. Revision completes less efficiently in the absence of signaling lymphocytic activation molecule-associated protein although initiation proceeds normally. These data indicate that Tfh formation is required for the initiation of revision and germinal-center interactions for its completion. The germinal center is known to provide a confined space in which B-cell antigen receptors undergo selection. Our data extend the impact of this selective microenvironment into the arena of T cells, suggesting that this fluid structure also provides a regulatory environment in which TCR revision can safely take place.

Self-reactive T cells: suppressing the suppressors.

The immune system is a tightly regulated and complex system. An important part of this immune regulation is the assurance of tolerance toward self-antigens to maintain immune homeostasis. However, in recent years, antigen-specific cellular immune responses toward several normal self-proteins expressed in regulatory immune cells have been reported, especially in patients with cancer. The seemingly lack of tolerance toward such proteins is interesting, as it suggests a regulatory function of self-reactive T (srT) cells, which may be important for the fine tuning of the immune system. In particular, surprising has been the description of cytotoxic srT cells that are able to eliminate normal regulatory immune cells. Such srT cells may be important as effector cells that suppress regulatory suppressor cells. The current knowledge of the nature and function of srT cells is still limited. Still, the therapeutic targeting of srT cells offers a novel approach to harness immune-regulatory networks in cancer.

Epigenetic aspects of lymphocyte antigen receptor gene rearrangement or 'when stochasticity completes randomness'.

To perform their specific functional role, B and T lymphocytes, cells of the adaptive immune system of jawed vertebrates, need to express one (and, preferably, only one) form of antigen receptor, i.e. the immunoglobulin or T-cell receptor (TCR), respectively. This end goal depends initially on a series of DNA cis-rearrangement events between randomly chosen units from separate clusters of V, D (at some immunoglobulin and TCR loci) and J gene segments, a biomolecular process collectively referred to as V(D)J recombination. V(D)J recombination takes place in immature T and B cells and relies on the so-called RAG nuclease, a site-specific DNA cleavage apparatus that corresponds to the lymphoid-specific moiety of the VDJ recombinase. At the genome level, this recombinase's mission presents substantial biochemical challenges. These relate to the huge distance between (some of) the gene segments that it eventually rearranges and the need to achieve cell-lineage-restricted and developmentally ordered routines with at times, mono-allelic versus bi-allelic discrimination. The entire process must be completed without any recombination errors, instigators of chromosome instability, translocation and, potentially, tumorigenesis. As expected, such a precisely choreographed and yet potentially risky process demands sophisticated controls; epigenetics demonstrates what is possible when calling upon its many facets. In this vignette, we will recall the evidence that almost from the start appeared to link the two topics, V(D)J recombination and epigenetics, before reviewing the latest advances in our knowledge of this joint venture.

CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigenic complex.

CD8(+) T cells recognize infected or dysregulated cells via the clonotypically expressed αß TCR, which engages Ag in the form of peptide bound to MHC class I (MHC I) on the target cell surface. Previous studies have indicated that a diverse Ag-specific TCR repertoire can be beneficial to the host, yet the determinants of clonotypic diversity are poorly defined. To better understand the factors that govern TCR repertoire formation, we conducted a comprehensive clonotypic analysis of CD8(+) T cell populations directed against epitopes derived from EBV and CMV. Neither pathogen source nor the restricting MHC I molecule were linked with TCR diversity; indeed, both HLA-A and HLA-B molecules were observed to interact with an overlapping repertoire of expressed TRBV genes. Peptide specificity, however, markedly impacted TCR diversity. In addition, distinct peptides sharing HLA restriction and viral origin mobilized TCR repertoires with distinct patterns of TRBV gene usage. Notably, no relationship was observed between immunodominance and TCR diversity. These findings provide new insights into the forces that shape the Ag-specific TCR repertoire in vivo and highlight a determinative role for the peptide component of the peptide-MHC I complex on the molecular frontline of CD8(+) T cell-mediated immune surveillance.

VDJ recombinase-mediated TCR ß locus gene usage and coding joint processing in peripheral T cells during perinatal and pediatric development.

The generation of TCR proteins is the result of V(D)J recombinase-mediated genomic rearrangements at recombination signal sequences (RSS) in human lymphocytes. V(D)J recombinase can also mediate rearrangements at nonimmune or "cryptic" RSS in normal and leukemic human peripheral T cells. We previously demonstrated age- and gender-specific developmental differences in V(D)J coding joint processing at cryptic RSS within the HPRT locus in peripheral T cells from healthy children (Murray et al. 2006. J. Immunol. 177: 5393-5404). In this study, we investigated developmentally specific V(D)J recombinase TCRß immune gene rearrangements and coding joint processing at RSS in peripheral T cells in the same pediatric population. This approach provided a unique opportunity to investigate site-specific V(D)J recombinase rearrangements and coding joint processing at immune and nonimmune genes from the same individual T cell population. We determined the genomic sequence of 244 TCRß coding junctions from 112 (63 male, 49 female) subjects from the late stages of fetal development through 9 y of age. We observed both age- and gender-specific V(D)J recombinase-mediated TCRß gene usage and coding joint processing at immune RSS. To the best of our knowledge, these data represent the first description of age- and gender-specific developmental differences in TCR gene usage and coding joint processing that could directly influence TCR diversity and immune specificity. It will be important for future studies to ascertain the mechanistic etiology of these developmental and gender differences in TCR diversity and specificity, as well as their importance with respect to the age and gender risks for infectious and autoimmune diseases in humans.

Papulosis linfomatoide: hallazgos clínico-patológicos en 18 pacientes / Lymphomatoid papulosis: Clinical and pathological findings in 18 patients

Introducción: La papulosis linfomatoide (PL) es una dermatosis que se engloba dentro de los procesos linfoproliferativos CD30 positivos de la piel. Se ha descrito su asociación a linfoma de Hogking (LH), así como su progresión a micosis fungoide (MF) y linfoma cutáneo anaplásico de célula grande (LCACG). Objetivos: Investigar los hallazgos clínicos, histológicos y la respuesta al tratamiento en un grupo de pacientes con PL. Material y métodos: Se llevó a cabo un estudio retrospectivo, descriptivo y observacional. Se seleccionaron 18 pacientes con diagnóstico histológico confirmado de PL y con un adecuado seguimiento clínico. Se recopilaron los hallazgos histológicos de las biopsias de piel, la forma de presentación, la evolución y la respuesta a los tratamientos utilizados. Resultados: Se reclutaron un total de 18 pacientes, 10 varones y 8 mujeres. La mayoría de las biopsias, 14 de 18 (78%) mostraban un infiltrado linfocitario en cuña, CD30 positivo, CD3 positivo y CD56 negativo. El tipo histológico más frecuente fue el tipo A, presente en un 83% de las biopsias de los pacientes. La forma clínica de presentación más frecuente fue en forma de pápulas en el tronco (83%). Un 62% de los pacientes sufrió un único brote autorresolutivo. La media de seguimiento fue de 7 años, durante los cuales un 12% de los pacientes desarrolló una micosis fungoide, sin encontrarse otras asociaciones. Discusión: Existen pocas series de pacientes con PL publicadas en los últimos años; sin embargo, globalmente los hallazgos descritos en ellas coinciden con las de nuestro grupo de pacientes. Conclusiones: La PL es un cuadro linfoproliferativo típicamente CD30 positivo que habitualmente tiene un curso benigno con buena respuesta a los tratamientos utilizados (AU)

Background: Lymphomatoid papulosis (LyP) is a CD30+ lymphoproliferative skin disease that has been described in association with Hodgkin lymphoma. It has also been reported to progress to mycosis fungoides or cutaneous anaplastic large-cell lymphoma. Objective: To study the clinical and histologic features of LyP and response to treatment in a patient series. Materials and methods: For this retrospective, descriptive, observational study of patients with histologically confirmed LyP and sufficient follow-up data on record, we extracted histologic findings on skin biopsy, clinical presentation, clinical course, and response to treatments. Results: Eighteen patients (10 male, 8 female) were identified. Most biopsies (14/18, 78%) showed a wedge-shaped lymphocytic infiltrate with CD30+, CD3+, and CD56− cells. A type A histologic pattern was present in the biopsies of 83% of the patients. The most common presentation (83%) consisted of papules on the trunk; for 62% LyP resolved after a single episode. Twelve percent of the patients developed mycosis fungoides (mean follow-up, 7 years); no other associations were noted. Discussion: Although few series of patients with LyP have been published in recent years, the findings reported generally coincide with our observations. Conclusion: LyP is typically a CD30+ lymphoproliferative disorder that usually runs a benign course and responds well to treatment (AU)

Origin and immunophenotype of aberrant IEL in RCDII patients.

OBJECTIVES: Aberrant intra-epithelial lymphocytes (IELs) are the hallmark of refractory coeliac disease type II RCDII and considered a premalignant cell population from which aggressive enteropathy-associated T cell lymphoma (EATL) can evolve. The aim of this study was to gain further insight in the origin and characteristics of aberrant IELs by analysing T-cell receptor (TCR) rearrangements, and by immunophenotypic analysis of aberrant IELs. DESIGN: Duodenal biopsies from 18 RCDII patients and three RCDII cell lines were analysed for the presence of TCR delta, gamma, and beta rearrangements. In addition, IELs isolated from biopsies derived from RCDII patients were phenotypically analysed. RESULTS: Aberrant IELs showed an upregulated expression of granzyme B and decreased expression of PCNA. TCR rearrangements in the aberrant IEL population in biopsies of RCDII patients were heterogenic, which is most likely due to a variation in maturity. Similarly, RCDII cell lines displayed a heterogenic TCR rearrangement pattern. CONCLUSION: Aberrant IELs originate from deranged immature T lymphocytes and display clear differentiation to a cytotoxic phenotype. Aberrant IELs displayed different stages of maturity between RCDII patients, of which only the patients harbouring the most mature aberrant IEL population developed an EATL.

A novel clonality assay for the assessment of canine T cell proliferations.

Polymerase chain reaction (PCR) based clonality assays are an important tool to differentiate neoplastic from reactive lymphocyte populations. A recent description of the canine T cell receptor γ locus identified a large number of formerly unknown genes, and determined the locus topology consisting of 8 cassettes with up to 3 variable (V) genes, 2 joining (J) genes and one constant (C) gene each. Given that these data were not available when existing canine T cell clonality assays were developed, it is likely that they will fail to detect a subset of clonal lymphocyte populations. The objective of this study was to gauge the potential of canine T cell clonality assays to detect all rearranged T cell receptor γ genes and to develop an improved clonality assay. The primer sequences of existing clonality assays were aligned to the reference sequences of all rearranged genes and genes were scored as to the likelihood of being recognized by a primer. All four assays likely recognized subgroup Vγ2 and Vγ6 genes but 3 out of 4 assays were unlikely to detect subgroup Vγ3 and Vγ7 genes. All assays likely recognized Jγx-2 genes, but only two assays were likely to detect most Jγx-1 genes. Two assays had forward primers located as close as four nucleotides to the junctional region. A new multiplex PCR was designed with all primers combined in a single tube. An alternative primer set allowed identification of variable gene usage through gene specific forward primers. The coverage of all rearranged genes facilitated the detection of multiple clonal rearrangements per neoplastic sample. The new assay detected clonal DNA at a concentration of 5% within polyclonal background but detection thresholds were dependent on the gene usage of clonal rearrangements as well as the position of the clonal peak in respect to the polyclonal background. The new multiplex assay recognized 12/12 (100%) of confirmed neoplastic samples as compared to 2/12 (17%) by an existing assay. On a series of 60 diagnostic samples the concordance rate of both assays was 41/60 (68.3%). In 14/60 (23.3%) of the cases, the new multiplex assay yielded a clonal result while the existing assay gave a non-clonal result. In 5/60 (8.3%) of cases, the new assay yielded a non-clonal result while the existing primer set gave a clonal result. These findings suggest that the new multiplex assay has an improved sensitivity over traditional assays and is suited to reduce the rate of false-negative results.