Allelotyping in mycosis fungoides and Sézary syndrome: common regions of allelic loss identified on 9p, 10q, and 17p

Unraveling the Structural Variations of Early-Stage Mycosis Fungoides-CD3 Based Purification and Third Generation Sequencing as Novel Tools for the Genomic Landscape in CTCL

Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma (CTCL). At present, knowledge of genetic changes in early-stage MF is insufficient. Additionally, low tumor cell fraction renders calling of copy-number variations as the predominant mutations in MF challenging, thereby impeding further investigations. We show that enrichment of T cells from a biopsy of a stage I MF patient greatly increases tumor fraction. This improvement enables accurate calling of recurrent MF copy-number variants such as ARID1A and CDKN2A deletion and STAT5 amplification, undetected in the unprocessed biopsy. Furthermore, we demonstrate that application of long-read nanopore sequencing is especially useful for the structural variant rich CTCL. We detect the structural variants underlying recurrent MF copy-number variants and show phasing of multiple breakpoints into complex structural variant haplotypes. Additionally, we record multiple occurrences of templated insertion structural variants in this sample. Taken together, this study suggests a workflow to make the early stages of MF accessible for genetic analysis, and indicates long-read sequencing as a major tool for genetic analysis for MF.

DNA copy number imbalances in primary cutaneous lymphomas

BACKGROUND

Cutaneous lymphomas (CL) represent a clinically defined group of extranodal non-Hodgkin lymphomas harbouring heterogeneous and incompletely delineated molecular aberrations. Over the past decades, molecular studies have identified several chromosomal aberrations, but the interpretation of individual genomic studies can be challenging.

OBJECTIVE

With a comprehensive meta-analysis, we aim to delineate genomic alterations for different types of CL and propose a more accurate classification in line with their various pathogenicity.

METHODS

We searched PubMed and ISI Web of Knowledge for publications from 1996 to 2016 reporting the investigation of CL for genome-wide copy number alterations, by means of comparative genomic hybridization techniques and whole-genome sequencing and whole-exome sequencing. We then extracted and remapped the available copy number variation (CNV) data from these publications with the same pipeline and performed clustering and visualisation to aggregate samples of similar CNV profiles.

RESULTS

For 449 samples from 22 publications, CNV data were accessible for sample based meta-analysis. Our findings illustrate structural and numerical chromosomal imbalance patterns. Most frequent CNAs were linked to oncogenes or tumour suppressor genes with important roles in the course of the disease.

CONCLUSION

Summary profiles for genomic imbalances, generated from case-specific data, identified complex genomic imbalances, which could discriminate between different subtypes of CL and promise a more accurate classification. The collected data presented in this study are publicly available through the 'Progenetix' online repository.

Sézary Syndrome in a 17-Year-Old Boy: Clinicopathologic Features and Genomic Profile

We describe the case of a 17-year-old Hispanic boy who had had erythroderma and diffuse lymphadenopathy for approximately 6 months. A diagnosis of Sézary syndrome was made on the basis of the histologic features of the skin; the presence of the same T-cell clone on the skin, blood, and bone marrow; and the high CD4(+) lymphocyte count with an aberrant phenotype in peripheral blood; bone marrow involvement was also present. The patient was treated with systemic gemcitabine and achieved partial remission.

Genomic analyses reveal recurrent mutations in epigenetic modifiers and the JAK-STAT pathway in Sézary syndrome

Sézary syndrome (SS) is an aggressive leukaemia of mature T cells with poor prognosis and limited options for targeted therapies. The comprehensive genetic alterations underlying the pathogenesis of SS are unknown. Here we integrate whole-genome sequencing (n=6), whole-exome sequencing (n=66) and array comparative genomic hybridization-based copy-number analysis (n=80) of primary SS samples. We identify previously unknown recurrent loss-of-function aberrations targeting members of the chromatin remodelling/histone modification and trithorax families, including ARID1A in which functional loss from nonsense and frameshift mutations and/or targeted deletions is observed in 40.3% of SS genomes. We also identify recurrent gain-of-function mutations targeting PLCG1 (9%) and JAK1, JAK3, STAT3 and STAT5B (JAK/STAT total ∼11%). Functional studies reveal sensitivity of JAK1-mutated primary SS cells to JAK inhibitor treatment. These results highlight the complex genomic landscape of SS and a role for inhibition of JAK/STAT pathways for the treatment of SS.

Sézary syndrome is a T cell malignancy that has been poorly characterized at the genome level. In this study, Kiel et al. perform whole-genome analyses and identify mutations in the JAK–STAT pathway and show that primary cells are sensitive to JAK inhibitors.

Mycosis fungoides and Sézary syndrome

The development of array comparative genomic hybridization (aCGH) techniques has allowed to characterize more precisely several human neoplasms with the aim of providing prognostic markers and targets for directed therapeutic intervention. Recently, several studies applying aCGH technique have been reported in which an exhaustive genetic characterization of mycosis fungoides (MF) and Sézary syndrome (SS) has been performed. Regarding MF, a genomic profile characterized by the gains of 7q, 17q, and 8q and losses in 9p, 13q, 17p, and 10q has been described. In SS, the most common abnormalities are gains in 8q and 17q and losses at 17p and 10q. One of the main contributions of the aCGH studies in MF and SS has been the description of genetic markers associated with a poor prognosis. In MF, three specific chromosomal regions, 9p21.3 (CDKN2A, CDKN2B, and MTAP), 8q24.21 (MYC), and 10q26qter (MGMT and EBF3) have been defined as prognostic markers exhibiting a significant correlation with overall survival (P = 0.042, P = 0.017, and P = 0.022, respectively). Moreover, two MF genomic subgroups have been described, distinguishing a stable group (0-5 DNA aberrations) and an unstable group (>5 DNA aberrations), showing that the genomic unstable group had a shorter overall survival (P = 0.05).

Integrated genomic analysis of sézary syndrome

Sézary syndrome (SS) is a rare variant of primary cutaneous T-cell lymphoma. Little is known about the underlying pathogenesis of S. To address this issue, we used Affymetrix 10K SNP microarray to analyse 13 DNA samples isolated from 8 SS patients and qPCR with ABI TaqMan SNP genotyping assays for the validation of the SNP microarray results. In addition, we tested the impact of SNP loss of heterozygosity (LOH) identified in SS cases on the gene expression profiles of SS cases detected with Affymetrix GeneChip U133A. The results showed: (1) frequent SNP copy number change and LOH involving 1, 2p, 3, 4q, 5q, 6, 7p, 8, 9, 10, 11, 12q, 13, 14, 16q, 17, and 20, (2) reduced SNP copy number at FAT gene (4q35) in 75% of SS cases, and (3) the separation of all SS cases from normal control samples by SNP LOH gene clusters at chromosome regions of 9q31q34, 10p11q26, and 13q11q12. These findings provide some intriguing information for our current understanding of the molecular pathogenesis of this tumour and suggest the possibility of presence of functional SNP LOH in SS tumour cells.

Genetic alterations in Sezary syndrome

Sezary syndrome (SS) is a rare form of cutaneous T-cell lymphoma characterized by erythroderma and the presence of Sezary cells in the skin, lymph nodes, and peripheral blood. Over the past few decades, cytogenetic and molecular cytogenetic findings have revealed many genetic alterations in patients with SS. The most frequent genetic lesions include monosomy 10, losses of 10q and 17p, gains of 8q24 and 17q, and diverse structural alterations involving these regions. Expression patterns in regions of genomic imbalance show that a large number of genes in SS are deregulated, and this might have a causative role in oncogenesis. Overall, chromosomal instability is characteristic of this lymphoma and related to a poor prognosis, but no specific abnormalities that may be directly involved in development of the disease have yet been found.

CDKN2A-CDKN2B deletion defines an aggressive subset of cutaneous T-cell lymphoma

Inactivation of the CDKN2A-CDKN2B locus has been reported in the most frequent subtypes of cutaneous T-cell lymphomas (CTCLs), mycosis fungoides, Sézary syndrome (SS) and CD30+ cutaneous anaplastic large cell lymphoma. To investigate whether genetic or epigenetic inactivation of CDKN2A-CDKN2B is more specifically observed in certain CTCL subtypes with clinical impact, we used array-comparative genomic hybridization, quantitative PCR, interphase fluorescent in situ hybridization and methylation analyses of p14(ARF) p16(INK4A) and p15(INK4B) promoters. We studied 67 samples from 58 patients with either transformed mycosis fungoides (n=24), SS (n=16) or CD30+ cutaneous anaplastic large cell lymphoma (n=18). We observed combined CDKN2A-CDKN2B deletion in both transformed mycosis fungoides (n=17, 71%) and SS patients (n=7, 44%), but, surprisingly, in only one CD30+ cutaneous anaplastic large cell lymphoma case. Interphase fluorescent in situ hybridization showed 9p21 loss in 17 out of 19 cases, with 9p21 deletion indicating either hemizygous (n=4) or homozygous (n=2) deletion, with mixed patterns in most patients (n=11). The limited size of 9p21 deletion was found to account for false-negative detection by either BAC arrays (n=9) or fluorescent in situ hybridization (n=2), especially in patients with Sézary syndrome (n=6). Methylation was found to be restricted to the p15(INK4B) gene promoter in patients with or without 9p21 deletion and did not correlate with prognosis. In contrast, CDKN2A-CDKN2B genetic loss was strongly associated with a shorter survival in CTCL patients (P=0.002) and more specifically at 24 months in transformed mycosis fungoides and SS patients (P=0.02). As immunohistochemistry for p16(INK4A) protein was not found to be informative, the genetic status of the CDKN2A-CDKN2B locus would be relevant in assessing patients with epidermotropic CTCLs in order to identify those cases where the disease was more aggressive.

Genome-wide analysis of cutaneous T-cell lymphomas identifies three clinically relevant classes

This study was undertaken to identify recurrent genetic alterations of the three main types of cutaneous T-cell lymphomas (CTCLs): mycosis fungoides (MF), Sézary syndrome (SS), and cutaneous anaplastic large-cell lymphoma (CALCL). Using array-based comparative genomic hybridization, the molecular cytogenetic profiles of 72 samples obtained from 58 patients with CTCL corresponding to 24 transformed MF (T-MF), 16 SS, and 18 CALCLs were determined. T-MF was characterized by gains of 1q25-31, 7p22-11.2, 7q21, 7q31, and 17q12, and losses of 9p21, 10p11.2, and 10q26. SS exhibited gains of 8q23-24.3 and 17q23-24, as well as losses of 9p21, 10p12-11.2, 10q22-24, 10q25-26, and 17p13-q11.1. Finally, CALCL exhibited 6q27 and 13q34 losses. Such imbalances were statistically associated with one CTCL subtype. Unsupervised hierarchical clustering defined three categories of clinical relevance: (1) CALCL apart from epidermotropic-CTCL, (2) an SS-only category, and (3) a mixed category with T-MF and SS cases, with both primary and secondary SS cases. In rare cases, the genetic classification did not correspond to the inclusion diagnosis, possibly reflecting the association of two diseases in the same patient or initial misdiagnosis according to follow-up. Finally, different samples in the same patient clustered together, showing reproducibility of such a classifier.

Loss of Heterozygosity Analysis Identifies Genetic Abnormalities in Mycosis Fungoides and Specific Loci Associated With Disease Progression

Mycosis fungoides (MF) exhibits a variety of underlying molecular defects. Loss of heterozygosity (LOH) is a technique used to detect chromosomal imbalances in neoplastic disorders using archival tissue. We analyzed skin biopsies of MF in different stages for the presence of LOH at specific loci to evaluate underlying genetic aberrations involved in MF and its progression. Twenty-five skin biopsies (15 plaque stage and 10 tumor stage) from 19 patients were evaluated. LOH was examined at 1p22 (D1S2766), 9p21 [IFNA, p15 (D9S1748), p16 (D9S171)], 10q23 [PTEN (D10S185, D10S541, D10S2491)], and 17p13 [p53 (TP53)]. Abnormal lymphocytes were microdissected from formalin-fixed, paraffin-embedded tissue sections. Sixteen of the 25 (64%) specimens evaluated had at least one abnormal LOH locus and LOH was identified in 7 of 15 (47%) plaque and in 9 of 10 (90%) tumor stage lesions, respectively. All 3 patients with sequential biopsies (plaque followed by tumor lesions) had additional LOH abnormalities in tumor specimens compared with plaque stage lesions. LOH most frequently involved chromosome 10, including 7 of 10 (70%) tumor stage lesions. Loss of multiple alleles was only identified in tumor stage cases, with 3 tumors undergoing allelic losses at 3 separate loci. Our results suggest that LOH studies are a robust method for evaluating genetic abnormalities in MF. Tumor stage lesions manifest increasing allelic losses compared with plaque stage. Further, in this series, several loci associated with the tumor suppressor gene PTEN on chromosome 10 appear to be associated with progression from plaque to tumor stage.

Spectral karyotyping demonstrates genetically unstable skin-homing T lymphocytes in cutaneous T-cell lymphoma

We initially established cell lines from skin biopsies from four patients (MF8, MF18, MF19 and MF31) in early stages of cutaneous T-cell lymphoma (CTCL) in 1999. After 3 weeks of culture, skin-homing T lymphocytes were stimulated with phytohaemagglutinin. Metaphase spreads were analysed using spectral karyotyping (SKY), a molecular cytogenetic technique. MF18 and MF19 had predominantly normal karyotypes. MF8 had recurrent numerical aberrations resulting in two T lymphocyte clones: one with trisomy 21 (12/20 cells) and the other with monosomy chromosome 22 (3/20 cells). MF8 also exhibited a clonal deletion, del(5)(p15.1), as well as multiple non-clonal structural aberrations. MF31 had a clonal deletion, del(17)(p12) and other non-clonal deletions involving chromosomes 2, 5, 10, 11. MF18 had a single abnormal cell that contained two reciprocal translocations t(1;2)(q32;p21) and t(4;10)(p15.2;q24). In 2001, three of the original patients had new skin biopsies taken and cell lines were established. SKY analysis revealed the continued presence of a T-cell clone in MF8 with trisomy 21 (4/20 cells). Additionally, a new clone was seen with a del(18)(p11.2) (17/20 cells). MF31 had only one aberrant cell with a del(17)(p12). MF18 had a clonal deletion, [del(1)(p36.1) in 3/20 cells] and non-clonal aberrations involving chromosomes 3, 4, 5, 6, 12, 13, 17 and 18. Thus, three of four patients continued to show numerous numerical and structural aberrations, both clonal and non-clonal, with only MF8 having a recurring T lymphocyte clone (+21). Our findings demonstrate high genetic instability among skin-homing T lymphocytes even in early stages of CTCL. We did not see genetic instability or evidence of clones in cell lines from a patient with atopic dermatitis and one with psoriasis.

Common chromosomal abnormalities in mycosis fungoides transformation

To identify cytogenetic features of large cell transformation in mycosis fungoides (T-MF), we selected in 11 patients, 16 samples either from skin tumors (13), lymph node (1), or peripheral blood cells (2) collected at the time of the transformation. Comparative genomic hybridization (CGH), G-banding, fluorescence in situ hybridisation (FISH), multicolour FISH (mFISH), and DNA content analysis were used. Fifteen samples displayed unbalanced CGH profiles, with gains more frequently observed than losses. Recurrent chromosomal alterations were observed for chromosomes 1, 2, 7, 9, 17, and 19. The most common imbalances were gain of chromosome regions 1p36, 7, 9q34, 17q24-qter, 19, and loss of 2q36-qter, 9p21, and 17p. In six samples 1p36-pter gain was associated with 9q34-qter gain and whole chromosome 19 gain. In five of these samples whole or partial gain of chromosome 17 was also observed. No specific pattern was seen with regard to the expression of the CD30 antigen by tumor cells. Cytogenetics and/or DNA content analysis of skin tumor cells revealed an abnormal chromosome number in all tested cases (n = 7) with DNA ploidy ranging from hyperdiploid (2.78) to hypotetraploid (3.69) (mean 3.14+/-0.38). Thus, T-MF displayed frequent chromosomal imbalances associated with hypotetraploidy.

Alemtuzumab in T-cell lymphoproliferative disorders

The humanized monoclonal antibody alemtuzumab binds to the CD52 antigen, a glycoprotein which is widely expressed on normal and malignant B and T lymphocytes. Recently it has been demonstrated in a number of clinical trials that alemtuzumab has clinical activity in mature T-cell diseases such as T-prolymphocytic leukaemia and cutaneous T-cell lymphoma, inducing responses in up to two thirds of heavily pre-treated relapsed/refractory patients. Response was associated with improved survival. The toxicity profile for the antibody is manageable. The major complications are infusional reactions associated with initial injections, and prolonged lymphopenia associated with reactivation of viruses. Future studies will be directed towards alternative (subcutaneous) routes and schedules of administration, use as first-line therapy, combination strategies, and role of alemtuzumab to purge minimal residual bone-marrow disease prior to stem-cell transplantation.

Multicolor fluorescence in situ hybridization (SKY) in mycosis fungoides and Sézary syndrome: search for recurrent chromosome abnormalities

Cutaneous T-cell lymphoma (CTCL) is a clonally derived lymphoproliferative disorder that preferentially involves the skin. The two major clinical expressions of CTCL, mycosis fungoides (MF) and Sézary syndrome (SS), have poorly understood pathogenesis. Chromosome abnormalities, mostly complex karyotypes, are seen in about 50% of patients with MF/SS, and there have only been a few instances of recurrent rearrangements. We analyzed 19 blood samples from patients with MF/SS with cytogenetics and multicolor FISH (SKY) to better describe the complex karyotypes and search for recurrent abnormalities or breakpoints. Comparison of phytohemagglutinin (PHA)-stimulated cultures versus a combination of interleukin 2 plus interleukin 7 showed similar efficiency in detecting abnormal clones; however, the PHA cultures yielded more analyzable metaphases. Nine of 19 patients (47%) had an abnormal karyotype. The most frequent abnormalities, in 7 of 9 cases, involved chromosome 10; followed by chromosome 6, in 6 of 9 cases; chromosomes 3, 7, 9, 17, and 19, in 5 of 9 cases; chromosomes 1 and 12, in 4 of 9 cases; and chromosomes 8, 11, and 13, in 3 of 9 cases. Most abnormalities were structural. Recurrent rearrangements included deleted chromosomes 6 and 13, in three cases each, and recurrent breakpoints at 1p32-36, 6q22-25, 17p11.2-13, 10q23-26, and 19p13.3, occurring in three or more cases. One patient had a pseudodicentric translocation between the short arms of chromosomes 8 and 17, confirmed by dual-color FISH and interpreted as psu dic(17;8)(p11.2;p11.2). Two patients with SS reported in the literature seem to have a similar translocation. If confirmed, a psu dic(17;8) could be the first recurring translocation detected in at least three patients with MF/SS.

The Role of Alemtuzumab in the Management of T-Cell Malignancies

T-cell malignancies are rare, making up 10% to 15% of all lymphoid neoplasms in adults. They include many different types of disorders such as T-cell prolymphocytic leukemia, T-cell large granular lymphocytic leukemia, adult T-cell leukemia/lymphoma, cutaneous T-cell lymphoma, and peripheral T-cell lymphoma, which are themselves divided into multiple subcategories. Most T-cell malignancies arise as a result of chromosomal abnormalities, including T-cell receptor rearrangement anomalies. Viral infections are implicated in the development of adult T-cell leukemia/lymphoma and some cases of peripheral T-cell lymphoma have been linked to Epstein-Barr virus or human immunodeficiency virus infection. With the possible exception of T-cell large granular lymphocytic leukemia, which often has an indolent course, T-cell malignancies have not responded well to conventional chemotherapeutic treatment. The introduction of monoclonal antibodies for the treatment of cancer has changed the outlook for patients with T-cell malignancies. Recent studies with single-agent alemtuzumab, an anti-CD52 monoclonal antibody, have shown improved response rates and survival in patients with T-cell prolymphocytic leukemia and cutaneous T-cell lymphoma. Preliminary data also suggest that alemtuzumab may have activity in patients with heavily pretreated peripheral T-cell lymphoma who are refractory to conventional chemotherapy. Preclinical studies with mice bearing human adult T-cell leukemia/lymphoma cells suggest that alemtuzumab may have a potential therapeutic role in this setting. Treatment of T-cell hematologic malignancies with alemtuzumab appears promising. Earlier treatment and combination with chemotherapeutic agents may improve treatment outcome for patients with these malignancies and allow for consolidation with stem cell transplant strategies in selected patients.

Biological Insights into the Pathogenesis of Cutaneous T-Cell Lymphomas (CTCL)

Mycosis fungoides and Sezary syndrome, collectively known as cutaneous T-cell lymphomas (CTCLs), are low-grade, indolent, clonal, non-Hodgkin's lymphomas consisting of CD4+ CD45RO+ T cells with a CLA+ CCR4+ skin-homing phenotype. There are several variants of primary CTCLs with differences in clinical behavior and prognosis. Currently, the precise etiologies of mycosis fungoides and Sezary syndrome are unknown. This article reviews our current understanding of the pathogenetic abnormalities involving genomic mutations, abnormal cDNA expression, and dysregulation of signaling pathways in CTCL.

Additional Her 2/neu gene copies in patients with Sézary syndrome

BACKGROUND

Her 2/neu gene amplification has been reported in several types of cancer. Monoclonal antibodies against the Her 2/neu receptor are used as a treatment in e.g. metastatic breast cancer.

AIM

The aim of this study was to determine the frequency of additional Her 2/neu gene copies in relations to the number of chromosome 17 centromeres of patients with Sézary syndrome.

METHODS

Fluorescence in situ hybridization (FISH) with probes specific for the Her 2/neu gene locus and the centromere of chromosome 17 was performed on nuclei from peripheral blood cells of 9 patients with Sézary syndrome. For analysis of Her 2/neu protein expression immunostaining was performed. In addition, FISH was used to analyze distribution of typical lymphocytes on cryo-cut sections of affected skin of two patients.

RESULTS

7/9 cases showed additional Her 2/neu gene copies in relation to the number of chromosome 17 centromeres. 4/5 cases with additional Her 2/neu gene copies in which immunostaining was performed expressed Her 2/neu protein. On cryo-cut sections atypical lymphocytes with additional Her 2/neu gene copies were detected in the dermis as well as in the epidermis of affected skin.

DISCUSSION

These data suggest that Her 2/neu might be involved in the pathogenesis of Sézary syndrome and that Her 2/neu might be a promising target for antitumor therapy in a subgroup of patients.

Large cell transformation of mycosis fungoides: tetraploidization within skin tumor large cells

Little is known about the molecular or cytogenetic alterations of mycosis fungoides (MF) large cell transformation. We report our findings on chromosomal rearrangement, based on peripheral blood and skin examination before and after cutaneous MF large cell transformation, using both conventional and molecular cytogenetic techniques. Blood cells exhibited a similar hypodiploid karyotype before and after MF transformation. A near-tetraploid karyotype with complex structural rearrangements was established from a skin tumor after MF large cell transformation. Both recurrent chromosome abnormalities and an identical T-cell receptor gamma-chain rearrangement were shared by blood and skin cells, suggesting that MF large cell transformation derived from a common monoclonal ancestor detected at MF stage. A complex hypotetraploid karyotype was established only from the skin tumor, however. MF large cell transformation may be associated with chromosome duplication followed by chromosome losses and interchromosomal rearrangements. Accordingly, additional parallel blood and skin tumor cytogenetic studies are required to further identify the recurrent cytogenetic changes associated with the aggressiveness of the disease after large cell transformation.

Fine mapping of chromosome 10q deletions in mycosis fungoides and sezary syndrome: Identification of two discrete regions of deletion at 10q23.33-24.1 and 10q24.33-25.1

Previous cytogenetic studies in mycosis fungoides (MF) and Sezary syndrome (SS) have identified a large and poorly defined area of chromosomal deletion on chromosome 10q. We report an extensive fine-mapping allelotyping study using 19 microsatellite markers in the region 10q22.3-10q26.13. Allelic loss was identified by loss of heterozygosity analysis in 26 of 60 (43%) cases: 15 of 45 (33%) with MF and 11 of 15 (73%) with SS. MF and SS samples showed similar patterns of allelic loss with the identification of two discrete regions of deletion which were mutually exclusive in all but two cases. Within the first region of deletion at 10q23.33-10q24.1, around microsatellite marker D10S185 (2.77 Mb), 23 genes were identified, including three (KIF11, HHEX, and HELLS) with functions that, if dysregulated, could be critical in MF and SS. The second region of deletion, 10q24.33-10q25.1, around microsatellite marker D10S530 (3.92 Mb), encodes 11 genes, the majority of which have poorly identified functions. This extensive allelotyping study provides the basis for future highly selective candidate gene analyses.

Heterozygote AG variant of -596 A/G IL-6 gene polymorphism is a marker for cutaneous T-cell lymphoma (CTCL)

The aim of the study was to investigate possible associations of IL-6 gene polymorphisms (-596 A/G and -174 C/G) with cutaneous T-cell lymphoma (CTCL). In the case-control study, genotype distributions and allelic frequencies in two promoter IL-6 gene polymorphisms in the group of 63 Czech patients with CTCL were compared to those of 105 control non-CTCL subjects matched for age and sex. The IL-6 gene polymorphisms were determined by PCR with following restriction analysis. A significant difference of -596 A/G IL-6 genotype distribution was found between the CTCL patients and the controls (P = 0.002) with almost threefold odds ratio for the heterozygote (AG) genotype in CTCL patients (OR = 2.64, P = 0.002). No significant differences in genotype distribution and/or allelic frequency of functional -174 C/G IL-6 gene polymorphism were observed. The double heterozygote AGCG of both IL-6 promoter polymorphisms was associated with CTCL (OR = 2.24, 95% confidence interval 1.17-4.28, P = 0.01). Thus, the heterozygote variant of -596 A/G promoter IL-6 polymorphism could be considered as a genotype marker for CTCL.

Multilineage progression of genetically unstable tumor subclones in cutaneous T-cell lymphoma

Molecular analysis of solid malignant tumors has suggested multilineage progression of genetically unstable subclones during early stages of tumorigenesis as a common mechanism of tumor cell evolution. We have investigated whether multilineage progression is a feature of cutaneous T-cell lymphoma (CTCL). To identify individual tumor cell subclones, we determined the pattern of mutations within microsatellite DNA obtained from multiple histomorphologically confined tumor cell nests of mycosis fungoides (MF) and lymphomatoid papulosis (LyP) lesions. Tumor cells were isolated by laser microdissection, and allelotypes were determined at microsatellite markers D6S260, D9S162, D9S171, D10S215, TP53.PCR15, and D18S65. Nine cases of MF and one patient with anaplastic large cell lymphoma (ALCL) originating from LyP were analyzed at 277 different microdissected areas obtained from 31 individual lesions. Three specimens of cutaneous lichen planus microdissected at 26 areas served as the control tissue. Microsatellite instability in microdissected tissue [MSI(md-tissue)] was detected in tumor tissues of all CTCL patients. One hundred and fifty-seven of 469 analyzed polymerase chain reaction (PCR) amplifications contained mutated microsatellite alleles (34%). In lichen planus, MSI(md-tissue) was seen in only four of 76 PCR products (5%) (P < 0.0001). The distribution of allelotypes in tumor cells from different disease stages was consistent with multilineage progression in five MF cases, as well as in the LyP/ALCL patient. Our results suggest that CTCL may evolve by multilineage progression and that tumor subclones in MF can be detected in early disease stages by mutation analysis of microsatellite DNA obtained from multiple microdissected areas.

Genomic Aberrations and Survival in Cutaneous T Cell Lymphomas

Information on chromosomal aberrations in cutaneous T cell lymphomas (CTCL), is scarce. In this study, comparative genomic hybridization (CGH) was used to analyze chromosomal imbalances (CI) in 32 patients with CTCL. CI were detected in 21 patients (66%). Euchromatic loss (dim) was localized most frequently (>16%) at the chromosomal regions 17p (28%), 13q (25%), 10q (16%), and 6q (19%), and gain of chromatin (enh) at 7 (25%), 8q (25%), and 17q (16%). The pattern dim6q-enh7-enh8-dim13 was the most frequent combination of CI. The number of aberrations per tumor sample varied between 0 and 19 and correlated with clinical tumor stages: from none in stage Ia to 8.75+/-1.8 (mean+/-SEM) in stage IVa. CI occurred more frequently in aggressive subtypes (9.33+/-2.16) than in indolent (2.88+/-0.8) subtypes. A high number of CI (>/=5) was associated with shorter survival. Gain of chromatin in 8q and loss of 6q and 13q correlated with a significantly shorter survival, whereas the most frequently observed aberrations (loss in 17p and gain in 7) did not influence the prognosis. In summary, CGH analysis revealed a characteristic pattern of recurring chromosomal gains and losses in CTCL. The association of the imbalances with the clinical course of the disease suggests that genes encoded at these loci may influence tumor development and progression.

Cutaneous T-cell lymphomas: a review with emphasis on new treatment approaches

Primary cutaneous T-cell lymphomas represent a wide variety of non-Hodgkin lymphomas that are characterized by a distinct clinical presentation. Advanced molecular and biological techniques have enhanced the recognition of cutaneous T-cell lymphomas. The most common subtypes of cutaneous T-cell lymphomas are the epidermotropic variants mycosis fungoides and Sézary syndrome. At present, a stage-adjusted therapy is the best concept available, since early aggressive treatment options did not improve the prognosis of patients with cutaneous T-cell lymphomas. Accurate diagnostic and clinical assessment as well as identification of prognostic factors provides a helpful basis for treatment strategies. Current medical literature on diagnosis, prognosis, and treatment is reviewed with emphasis on new biologic response-modifying treatment options.

Histopathology and genetics of cutaneous T-cell lymphoma

There is emerging evidence that genomic and chromosomal instability are features of CTCL, including variants such as MF, Sézary syndrome, and primary cutaneous CD30+ LCAL, and that specific chromosomal abnormalities are common. Additional resolution of specific regions of chromosomal loss and gain are required to define putative genes that may be of fundamental pathogenetic importance in CTCL. Inactivation of well-defined cell cycle and TSG are common as for other types of NHL. The prognostic significance of these abnormalities in CTCL has yet to be determined. The dysregulation of specific transcription factors is of interest, but requires further study. It is hoped that greater understanding of these molecular abnormalities will permit the development of CTCL-specific therapies that alleviate suffering and prolong survival.

Microsatellite Instability Is Associated with Hypermethylation of the hMLH1 Gene and Reduced Gene Expression in Mycosis Fungoides

Fifty-one mycosis fungoides samples were analyzed for microsatellite instability (MSI) using the panel of markers recommended for hereditary nonpolyposis colorectal cancer kindred and a panel we designed for cutaneous T cell lymphoma in order to compare detection rates and determine if MSI is a genome-wide phenomenon. Samples demonstrating MSI were analyzed for abnormalities of the hMLH1 gene including loss of heterozygosity, mutations, and promoter hypermethylation. MSI was detected in 16% using the hereditary nonpolyposis colorectal cancer panel and 22% with the cutaneous T cell lymphoma panel. Overall, 27% demonstrated MSI and 73% had a stable phenotype. hMLH1 gene studies did not detect loss of heterozygosity or reveal any mutations. Promoter hypermethylation was detected in nine of 14 patients with MSI, however (64%). In addition hMLH1 and hMSH2 protein expression was studied using immunohistochemical techniques. Five of nine patients with MSI and hMLH1 promoter methylation showed abnormal hMLH1 protein expression with normal hMSH2 gene expression. All other patients tested demonstrated normal hMLH1 and hMSH2 protein expression. MSI was found to be more prevalent in tumor stage mycosis fungoides (47%) than early stage disease (20%) and was associated with an older age of onset of mycosis fungoides. MSI may be a consequence of hMLH1 promoter hypermethylation in mycosis fungoides patients and may prevent transcription in a subset of patients. This suggests that the development of a mutator phenotype may contribute to disease progression in mycosis fungoides.

Molecular cytogenetic characterization of Sézary syndrome

Sézary syndrome (SS) is a rare form of erythrodermic cutaneous T-cell lymphoma with hematological involvement and a poor prognosis. At present little is known about the molecular pathogenesis of this malignancy. To address this issue, we analyzed 28 SS cases through the use of molecular cytogenetic techniques. Conventional cytogenetic analysis showed 12 of 28 cases with clonal chromosome abnormalities (43%). Seven cases had aberrations affecting chromosomes 1 and 17; five demonstrated rearrangement of chromosomes 10 and 14; four presented with an abnormality of 6q. Multiplex-fluorescence in situ hybridization (M-FISH) revealed complex karyotypes in 6 of 17 cases (35%), and recurrent der(1)t(1;10)(p2;q2) and der(14)t(14;15)(q;q?) translocations were each identified in two cases, and confirmed by dual-color FISH. There was an overall difference in the incidence of clonal abnormalities detected by G-banded karyotyping and M-FISH. In addition, comparative genomic hybridization studies revealed chromosome imbalances (CIs) in 9 of 20 cases (45%), with a mean DNA copy number change per sample of 1.95 +/- 2.74, and losses (mean: 1.25 +/- 1.77) more frequent than gains (mean: 0.7 +/- 1.26). The most common CIs noted were loss of 1p, followed by losses of 10/10q, 17p, and 19, and gains of 17q and 18. Furthermore, in conjunction with this study a systematic literature review was conducted, which showed a high frequency and consistent pattern of chromosome changes in SS. These findings suggest that chromosomal instability is common in SS, although there are specific chromosomal abnormalities that appear to be characteristic, and the identification of two different recurrent chromosome translocations provides the basis for further studies.

Amplification and overexpression of JUNB is associated with primary cutaneous T-cell lymphomas

Primary cutaneous lymphomas (PCLs) represent a heterogeneous group of extranodal T- and B-cell malignancies. The underlying molecular pathogenesis of this malignancy remains unclear. This study aimed to characterize oncogene abnormalities in PCLs. Using genomic microarray, we detected oncogene copy number gains of RAF1 (3p25), CTSB (8p22), PAK1 (11q13), and JUNB (19p13) in 5 of 7 cases of mycosis fungoides (MF)/Sezary syndrome (SS) (71%), gains of FGFR1 (8p11), PTPN (20q13), and BCR (22q11) in 4 cases (57%), and gains of MYCL1 (1p34), PIK3CA (3q26), HRAS (11p15), MYBL2 (20q13), and ZNF217 (20q13) in 3 cases (43%). Amplification of JUNB was studied in 104 DNA samples from 78 PCL cases using real-time polymerase chain reaction. Twenty-four percent of cases, including 7 of 10 cases of primary cutaneous CD30(+) anaplastic large-cell lymphoma (C-ALCL), 4 of 14 MF, 4 of 22 SS, and 2 of 23 primary cutaneous B-cell lymphoma (PCBCL) showed amplification of JUNB, and high-level amplification of this oncogene was present in 3 C-ALCL and 2 MF cases. JUNB protein expression was analyzed in tissue sections from 69 PCL cases, and 44% of cases, consisting of 21 of 23 SS, 6 of 8 C-ALCL, 5 of 10 MF, and 9 of 21 PCBCL, demonstrated nuclear expression of JUNB by tumor cells. Overexpression of JUNB also was detected in 5 C-ALCL and 2 SS cases. These results have revealed, for the first time, amplification and expression patterns of JUNB in PCL, suggesting that JUNB may be critical in the pathogenesis of primary cutaneous T-cell lymphomas.

Molecular cytogenetic analysis of cutaneous T-cell lymphomas: identification of common genetic alterations in Sézary syndrome and mycosis fungoides

BACKGROUND

Data on genome-wide surveys for chromosome aberrations in primary cutaneous T-cell lymphoma (CTCL) are limited.

OBJECTIVE

To investigate genetic aberrations in CTCL.

METHODS

We analysed 18 cases of Sézary syndrome (SS) and 16 cases of mycosis fungoides (MF) by comparative genomic hybridization (CGH) analysis, and correlated findings with the results of additional conventional cytogenetics, fluorescent in situ hybridization (FISH) and allelotyping studies.

RESULTS

CGH analysis showed chromosome imbalances (CIs) in 19 of 34 CTCL cases (56%). The mean +/- SD number of CIs per sample was 1.8 +/- 2.4, with losses (1.2 +/- 2.0) slightly more frequent than gains (0.6 +/- 1.0). The most frequent losses involved chromosomes 1p (38%), 17p (21%), 10q/10 (15%) and 19 (15%), with minimal regions of deletion at 1p31p36 and 10q26. The commonly detected chromosomal gains involved 4/4q (18%), 18 (15%) and 17q/17 (12%). Both SS and late stages of MF showed a similar pattern of CIs, but no chromosomal changes were found in three patients with T1 stage MF. Of the 18 SS cases also analysed by cytogenetics, seven showed clonal chromosome abnormalities (39%). Five cases had structural aberrations affecting chromosomes 10 and 17, four demonstrated rearrangement of 1p and three revealed an abnormality of either 6q or 14q consistent with CGH findings. FISH analysis showed chromosome 1p and 17q rearrangements in five of 15 SS cases, and chromosome 10 abnormalities in four SS cases consistent with both the G-banded karyotype and the CGH results. In addition, allelotyping analysis of 33 MF patients using chromosome 1 markers suggested minimal regions of deletion at D1S228 (1p36), D1S2766 (1p22) and D1S397 (1q25).

CONCLUSIONS

These findings provide a comprehensive assessment of genetic abnormalities in CTCL and a rational approach for further studies.