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LOH and copy number changes. SNP analysis of SS tumor samples and matched constitutional DNA showing LOH on the left and copy number on the right of each chromosome ideogram representing chromosomes 9 (A), 10 (B), and 17 (C). Each sample is depicted as a series of vertical bars in both the LOH and copy number panels. Blue areas, regions of LOH; yellow areas, retention of heterozygosity. The color intensities of inferred markers decline to the white as the distance from the nearest informative markers increases (18). Copy number is marked by shades of red ranging from light red for copy of ≤1 to dark red for copies of ≥3 (see scale at the bottom of the panel); white color is for 0 copies corresponding to HD. Boxed regions, UPD events.
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In this study, we used single nucleotide polymorphism and comparative genomic hybridization array to study DNA copy number changes and loss of heterozygosity for 28 patients affected by Sézary syndrome (SS), a rare form of cutaneous T-cell lymphoma (CTCL). Our data identified, further confirming previous studies, recurrent losses of 17p13.2-p11.2 a...
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... copy number regions were determined according to the hybridization intensity data generated from each genotype probe on the mapping array comparing normal and tumor samples. The result of the genome-wide analysis of CNAs, showing the most frequent regions involved in gain or loss of genetic material is represented, as summary plot, in Supplementary Fig. S2. The computed copy number summary score identified three regions of copy number loss and three regions of gain as highly re- current (>30%). ...
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... deletions (HD) that are of particular interest as they may unveil the presence of tumor suppressor genes. Two HDs were unequivocally identified in patient P28: the first one, encompassing 34 consecutive SNP loci with inferred copy number of 0.2 over 6.4 Mb, occurred on 9p21.3-p21.2 locus and included tumor suppressor genes CDKN2A and CDKN2B (Fig. 2); the second HD (∼2 Mb segment with three consecutive SNPs of inferred copy number values of 0.2) was identified on chromosome 13q14.2 encompassing the RB1 locus (data not shown). Both these HDs have been confirmed by quantitative RT-PCR experiments performed on tumor DNA from patient P28 (Supplementary Table S2). Furthermore, a ...
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... us to assess the concurrent status of LOH and CNAs. We included in the LOH analysis tumor samples displaying consistent regions of deletion defined as more than three contiguous deleted SNPs (22). We found a good correlation between LOH and copy number data for all the above-described recurrent deletions affecting chromosomes 9, 10, and 17 (Fig. 2). However, we observed that some individuals, displaying LOH, do not exhibit copy number changes, a condition that might be ex- plained with copy-neutral LOH events also known as UPD (23). The highest incidence, with six samples displaying UPD events, was detected for chromosome 10, whereas not more than two cases have been detected for ...
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... displaying LOH, do not exhibit copy number changes, a condition that might be ex- plained with copy-neutral LOH events also known as UPD (23). The highest incidence, with six samples displaying UPD events, was detected for chromosome 10, whereas not more than two cases have been detected for other chromosomes such as 17 and 9 (boxed areas in Fig. 2). These regions generally span interstitial areas of LOH or telomeric ends and they usually interest relatively small areas (∼10-60 SNP markers), with the exception of UPDs exhibited by patient P28 for 10p12.1-q24.3 (303 SNPs over 78 Mb; Fig. 2) and 13q12.11-q14.2 (143 SNPs in ∼29 Mb; data not shown). Besides UPD, we found one case ...
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... not more than two cases have been detected for other chromosomes such as 17 and 9 (boxed areas in Fig. 2). These regions generally span interstitial areas of LOH or telomeric ends and they usually interest relatively small areas (∼10-60 SNP markers), with the exception of UPDs exhibited by patient P28 for 10p12.1-q24.3 (303 SNPs over 78 Mb; Fig. 2) and 13q12.11-q14.2 (143 SNPs in ∼29 Mb; data not shown). Besides UPD, we found one case (P23) showing a chromosomal area of ∼7.3 Mb (24 SNPs) on 10p12.31-p12.1 with inferred copy number value of >5. This patient, however, exhibits concomitant LOH of this region (Fig. 2), suggesting that the LOH might be due to the amplification, ...
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... of UPDs exhibited by patient P28 for 10p12.1-q24.3 (303 SNPs over 78 Mb; Fig. 2) and 13q12.11-q14.2 (143 SNPs in ∼29 Mb; data not shown). Besides UPD, we found one case (P23) showing a chromosomal area of ∼7.3 Mb (24 SNPs) on 10p12.31-p12.1 with inferred copy number value of >5. This patient, however, exhibits concomitant LOH of this region (Fig. 2), suggesting that the LOH might be due to the amplification, rather than loss, of one of the allele. The use of SNP technique allowed for a more complete understanding of the complex genetic rearrangements underlying SS ...
Citations
... Comprehensive genomic analyses on large CTCL patient cohorts failed to identify recurrent driver mutations, but chromosomal instability was revealed as a key disease feature associated with adverse clinical outcomes (Karenko et al, 2007;van Doorn et al, 2009;Kiel et al, 2015). Specifically, chromosome 17 copy number alterations (CNA) were frequently detected (Caprini et al, 2009(Caprini et al, , 2018van Doorn et al, 2009;Lin et al, 2012;Choi et al, 2015;da Silva Almeida et al, 2015;Kiel et al, 2015;Wang et al, 2015;Prasad et al, 2016;Woollard et al, 2016;Fanok et al, 2018). They present either as chromosome 17p deletions, resulting in the loss of TP53, and/or duplications of chromosomal segments, or the entire arm of chromosome 17q, where STAT3 and STAT5A/B genes are located. ...
... Expression of STAT3 and STAT5B was significantly increased in L-CTCL samples compared to healthy controls (Fig 2D-F). Extracted expression and clinical data from a previously published study corroborated these results (Caprini et al, 2009). It showed a significant positive correlation between STAT3/5 gene expression and the percentage of clonal CD3 + malignant cells in the blood of patients with 17q gains (n = 12; STAT3: Spearman r = 0.73, P = 0.009; STAT5A: Spearman r = 0.63, P = 0.03 and STAT5B: Spearman r = 0.68, P = 0.02; Fig EV1F-H). ...
... Expression data were extracted from the Oncomine TM Platform (Thermo Fisher Scientific) Caprini Lymphoma dataset, which includes 32 Sezary syndrome patients (Caprini et al, 2009;www. oncomine.org). ...
Leukemic cutaneous T-cell lymphomas (L-CTCL) are lymphoproliferative disorders of skin-homing mature T-cells causing severe symptoms and high mortality through chronic inflammation, tissue destruction, and serious infections. Despite numerous genomic sequencing efforts, recurrent driver mutations have not been identified , but chromosomal losses and gains are frequent and dominant. We integrated genomic landscape analyses with innovative pharmacologic interference studies to identify key vulnerable nodes in L-CTCL. We detected copy number gains of loci containing the STAT3/5 oncogenes in 74% (n = 17/23) of L-CTCL, which correlated with the increased clonal T-cell count in the blood. Dual inhibition of STAT3/5 using small-molecule degraders and multi-kinase blockers abolished L-CTCL cell growth in vitro and ex vivo, whereby PAK kinase inhibition was specifically selective for L-CTCL patient cells carrying STAT3/5 gains. Importantly, the PAK inhibitor FRAx597 demonstrated encouraging anti-leukemic activity in vivo by inhibiting tumor growth and disease dissemination in intrader-mally xenografted mice. We conclude that STAT3/5 and PAK kinase interaction represents a new therapeutic node to be further explored in L-CTCL.
... Currently, 11 immortalized patient-derived cell lines are used to study CTCL (Table 1) [18][19][20]. CTCL cells have been studied extensively with the aim to explore their genomic and transcriptomic similarities among cell lines (as a group) as well as between cell lines and patient samples [21][22][23][24][25][26]. Netchiporouk et al., (2017) studied the CTCL cell lines by using spectral karyotyping. ...
... The highlighted studies based on karyotyping of cell lines [21][22][23][24][25][39][40][41][42][43][44][45][46][47][48] were correlated with chromosomal aberrations seen in patients. SS and MF patient studies demonstrated similar chromosomal gains and losses, balanced and unbalanced translocations and other structural aberrations as observed in patient-derived cell lines indicating commonality of alterations in cell lines and clinical samples together with disease heterogeneity [36]. ...
Cutaneous T cell lymphoma (CTCL) is a spectrum of lymphoproliferative disorders caused by the infiltration of malignant T cells into the skin. The most common variants of CTCL include mycosis fungoides (MF), Sézary syndrome (SS) and CD30+ Lymphoproliferative disorders (CD30+ LPDs). CD30+ LPDs include primary cutaneous anaplastic large cell lymphoma (pcALCL), lymphomatoid papulosis (LyP) and borderline CD30+ LPD. The frequency of MF, SS and CD30+ LPDs is ~40–50%, <5% and ~10–25%, respectively. Despite recent advances, CTCL remains challenging to diagnose. The mechanism of CTCL carcinogenesis still remains to be fully elucidated. Hence, experiments in patient-derived cell lines and xenografts/genetically engineered mouse models (GEMMs) are critical to advance our understanding of disease pathogenesis. To enable this, understanding the intricacies and limitations of each individual model system is highly important. Presently, 11 immortalized patient-derived cell lines and different xenograft/GEMMs are being used to study the pathogenesis of CTCL and evaluate the therapeutic efficacy of various treatment modalities prior to clinical trials. Gene expression studies, and the karyotyping analyses of cell lines demonstrated that the molecular profile of SeAx, Sez4, SZ4, H9 and Hut78 is consistent with SS origin; MyLa and HH resemble the molecular profile of advanced MF, while Mac2A and PB2B represent CD30+ LPDs. Molecular analysis of the other two frequently used Human T-Cell Lymphotropic Virus-1 (HTLV-1)+ cell lines, MJ and Hut102, were found to have characteristics of Adult T-cell Leukemia/Lymphoma (ATLL). Studies in mouse models demonstrated that xenograft tumors could be grown using MyLa, HH, H9, Hut78, PB2B and SZ4 cells in NSG (NOD Scid gamma mouse) mice, while several additional experimental GEMMs were established to study the pathogenesis, effect of drugs and inflammatory cytokines in CTCL. The current review summarizes cell lines and xenograft/GEMMs used to study and understand the etiology and heterogeneity of CTCL.
... 12 In addition to the genes above, deletions of RPA1, HIC1, and DUSP5 and gain of STAT3/STAT5 and IL-2 (receptor) genes were reported. 2 Caprini et al 13 noted that more than 3 of these recurrent chromosomal alterations (gain or loss) are significantly correlated with Sz prognosis. ...
... Choi et al 14 not only identified identical regions as being recurrently deleted and gained in Sz but, strikingly, also with a similar prevalence as described earlier. 2,13 This hallmark CNA signature, also in agreement with results from Wang et al, 15 is depicted in Figure 1 and, on the one hand, underscores the heterogeneity of the genetic alterations in this disease, but on the other hand, illustrates the similarity (in terms of tumor genetics) of seemingly heterogenous patients in cohorts analyzed in different centers using different platforms. Based on the NGS data, an 11-probe fluorescence in situ hybridization panel was developed that largely confirmed the findings for Sz and thus may offer the capacity to facilitate diagnosis. ...
Primary cutaneous T-cell lymphomas (CTCL) constitute a heterogeneous group of non-Hodgkin T-cell lymphomas that present in the skin. In recent years significant progress has been made in the understanding of the pathogenesis of CTCL. Progress in CTCL classifications combined with technical advances, in particular next generation sequencing (NGS), enabled a more detailed analysis of the genetic and epigenetic landscape and transcriptional changes in clearly defined diagnostic entities. These studies not only demonstrated extensive heterogeneity between different CTCL subtypes but also identified recurrent alterations that are highly characteristic for diagnostic subgroups of CTCL. The identified alterations in particular involve epigenetic remodelling, cell cycle regulation, and the constitutive activation of targetable, oncogenic pathways. In this respect, aberrant JAK-STAT signaling is a recurrent theme, however not universal for all CTCL and with seemingly different underlaying causes in different entities. A number of the mutated genes identified are potentially actionable targets for the development of novel therapeutic strategies. Moreover, these studies have produced an enormous amount of information that will be critically important for the further development of improved diagnostic and prognostic biomarkers that can assist in the clinical management of CTCL patients. In the present review the main findings of these studies in relation to their functional impact on the malignant transformation process are discussed for different subtypes of CTCL.
... Besides Chka, we detected altered expression levels of several other enzymes of the choline metabolic pathway, including up-regulated expression of Lpcat1, Faah and Plcd3 as well as down-regulated expression of Dgka, Gdpd3 and Pip5k1b in Traf3 −/− B cells [59] ( Figure 2). In line with our finding, up-regulation of Lpcat1 and Faah or down-regulation of Dgka and Pip5k1b has been reported in other human cancers [84][85][86][87][88][89]. Among these, Lpcat1, a key enzyme of the Lands Cycle (an alternative pathway of PC synthesis) that converts LPC to PC, has been shown to play important roles in cancer pathogenesis and progression [84][85][86]. ...
Aberrant choline metabolism, characterized by an increase in total choline-containing compounds, phosphocholine and phosphatidylcholine (PC), is a metabolic hallmark of carcinogenesis and tumor progression. This aberration arises from alterations in metabolic enzymes that control PC biosynthesis and catabolism. Among these enzymes, choline kinase α (CHKα) exhibits the most frequent alterations and is commonly overexpressed in human cancers. CHKα catalyzes the phosphorylation of choline to generate phosphocholine, the first step in de novo PC biosynthesis. CHKα overexpression is associated with the malignant phenotype, metastatic capability and drug resistance in human cancers, and thus has been recognized as a robust biomarker and therapeutic target of cancer. Of clinical importance, increased choline metabolism and CHKα activity can be detected by non-invasive magnetic resonance spectroscopy (MRS) or positron emission tomography/computed tomography (PET/CT) imaging with radiolabeled choline analogs for diagnosis and treatment monitoring of cancer patients. Both choline-based MRS and PET/CT imaging have also been clinically applied for lymphoid malignancies, including non-Hodgkin lymphoma, multiple myeloma and central nervous system lymphoma. However, information on how choline kinase is dysregulated in lymphoid malignancies is very limited and has just begun to be unraveled. In this review, we provide an overview of the current understanding of choline kinase in B cell and T cell malignancies with the goal of promoting future investigation in this area.
... Les CS sont des cellules tumorales, présentant fréquemment des anomalies de leur contenu en ADN(Lima et al. 2003), avec une instabilité chromosomique et microsatellitaire, attestée par la présence de marqueurs de cassures double-brin de l'ADN (Tsang et al. 2018).La technique de CGH-array (comparative genomic hybridization) a permis de dégager dans le MF/SS de fréquentes délétions touchant les bras chromosomiques 1p et 17p(Caprini et al. 2009 ;Salgado et al. 2010 ; van Doorn et al. 2009 ; Vermeer et al. 2008), mais les caryotypes sont complexes et hétérogènes (Mao et al. 2002). De nombreux gènes, dont des suppresseurs de tumeurs et oncogènes, sont ainsi remaniés par délétion, duplication, ou translocation, engendrant des variations de leur nombre de copies (CNV pour copy number variation) (Choi et al. 2015 ; Iżykowska et al. 2017 ; Prasad et al. 2016 ; Wang et al. 2015). ...
Les lymphomes T cutanés primitifs (CTCL) sont un groupe de néoplasies cutanées dérivant de cellules T à tropisme cutané. Le mycosis fongoïde (MF) est le CTCL le plus fréquent, d’évolution généralement indolente, alors que le syndrome de Sézary est une forme proche mais rare, leucémisée et agressive, qui se caractérise par une érythrodermie prurigineuse généralisée, une lymphadénopathie, et la présence de nombreux lymphocytes atypiques circulants au noyau cérébriforme, dénommés cellules de Sézary. Le diagnostic des formes leucémisées selon les critères internationaux reste encore complexe, du fait de l’absence de marqueur positif universel de cellule de Sézary. Néanmoins, le récepteur KIR3DL2/CD158k a été identifié en 2001 à leur surface, et validé comme marqueur pour le diagnostic et le suivi des patients Sézary à l’hôpital Saint-Louis de Paris depuis 2014. Le premier objectif de ce travail était de comparer et faire connaître les performances du KIR3DL2 par rapport aux critères diagnostiques actuellement admis, depuis son utilisation sur notre site. Par ailleurs, la pathogenèse de ces lymphomes n’est pas entièrement élucidée, en particulier l’origine cellulaire du clone malin, ainsi que les relations entre les compartiments cutanés et sanguins au cours de la maladie. Nous avons pu caractériser les cellules de Sézary grâce au KIR3DL2, et mettre en évidence une hétérogénéité phénotypique et moléculaire inattendue des clones naïfs/mémoires circulants et cutanés dans le syndrome de Sézary. Ces phénotypes peuvent évoluer in vitro après stimulation, et in vivo au cours du temps et des lignes de traitement chez les patients, suggérant un potentiel plastique de ces cellules tumorales. Enfin sur le plan thérapeutique, les traitements actuels ne sont pas curatifs, mais de nouvelles molécules sont en cours de développement. Le pronostic du syndrome de Sézary est grevé d’une forte mortalité infectieuse, les patients présentant des signes d’immunodépression. Les enjeux de demain seront donc de sélectionner les patients pour la thérapie la plus adaptée, tout en préservant leur immunité anti-tumorale et anti-infectieuse. Dans la dernière partie de ce travail, nous avons exploité nos résultats pour apprécier rétrospectivement l’impact de l’hétérogénéité tumorale, et de l'évolution des profils immunitaires T bénins, sur la réponse et la survenue de toxicités au cours de l'immunothérapie anti-CCR4 par mogamulizumab, des patients MF et Sézary. Nos résultats sont en faveur d’une utilisation plus systématique du KIR3DL2 pour l’identification des cellules malignes de Sézary, en pratique de soins comme en recherche. Une hétérogénéité inter- et intra-individuelle de la population clonale a été mise en évidence concernant les phénotypes naïfs/mémoires, l’expression de récepteurs de chimiokines et cytokines ainsi que des molécules « immune checkpoints ». Elle n’est pas figée dans le temps, mais peut évoluer sous traitement et être responsable de phénomènes de résistance thérapeutique, ce qui sous-tend l’importance d’une caractérisation tumorale fine avant mise sous immunothérapie ou thérapie ciblée. D’autre part, la contrepartie T bénigne est altérée chez ces patients immunodéprimés, et est remaniée sous immunothérapie anti-CCR4, ce qui suggère l’intérêt de nouvelles combinaisons thérapeutiques avec des agents immunomodulateurs et immunothérapies spécifiques.
... While SS is a moderately aggressive peripheral T-cell lymphoma with a 5-year overall survival rate of 36% [7], L-HES is typically indolent [25,35]. Chronic L-HES is infrequently associated with cytogenetic changes [23,25], whereas SS T cells harbor frequent chromosomal abnormalities and widespread changes in epigenetic status that can alter gene expression and prognosis (Table 2) [36][37][38][39][40][41]. Despite these important differences, SS and L-HES have similarities in a number of clinical and molecular findings (Table 2). ...
Sézary syndrome (SS), an aggressive cutaneous T-cell lymphoma (CTCL) with poor prognosis, is characterized by the clinical hallmarks of circulating malignant T cells, erythroderma and lymphadenopathy. However, highly variable clinical skin manifestations and similarities with benign mimickers can lead to significant diagnostic delay and inappropriate therapy that can lead to disease progression and mortality. SS has been the focus of numerous transcriptomic-profiling studies to identify sensitive and specific diagnostic and prognostic biomarkers. Benign inflammatory disease controls (e.g., psoriasis, atopic dermatitis) have served to identify chronic inflammatory phenotypes in gene expression profiles, but provide limited insight into the lymphoproliferative and oncogenic roles of abnormal gene expression in SS. This perspective was recently clarified by a transcriptome meta-analysis comparing SS and lymphocytic-variant hypereosinophilic syndrome, a benign yet often clonal T-cell lymphoproliferation, with clinical features similar to SS. Here we review the rationale for selecting lymphocytic-variant hypereosinophilic syndrome (L-HES) as a disease control for SS, and discuss differentially expressed genes that may distinguish benign from malignant lymphoproliferative phenotypes, including additional context from prior gene expression studies to improve understanding of genes important in SS.
... ATP6V1A was a critical gene related to autophagy, which can induce autophagy through binding with a smallmolecule compound EN6 and activating the mTOR signaling pathway (35). PSMD is considered an important cancer-related gene in the NF-kb pathway, which was shown to be consistently activated in Sezary Syndrome (36). Furthermore, some studies indicate that the singlenucleotide polymorphism (SNP) variations of PSMD3 in European individuals are related to the number of immune cells in peripheral blood and inflammatory diseases such as asthma (37). ...
Background:
Acute myeloid leukemia (AML) is a type of cancer that consists of a group of hematological malignancies with high heterogeneity. DNA methyltransferase 3A (DNMT3A)-mutated AML patients have a poor prognosis. Some long non-coding RNAs (lncRNAs) have been reported to enhance therapeutic sensitivity, and so could affect the overall survival rate of elderly cytogenetically normal acute myeloid leukemia (CN-AML) patients; however, studies on the lncRNA signature in DNMT3A-mutated AML are rare.
Method:
The DNMT3A R878H conditional knock-in mouse model was constructed to explore the lncRNAs of DNMT3A mutation by using the Cuffcomparison method. Cis and trans regulation networks were used to predict candidate genes. The expression levels in leukemic cell lines and the prognostic index of these candidate genes were analyzed with the Broad Institute Cancer Cell Line Encyclopedia (CCLE) and OncoLnc databases. The data for each sample were statistically analyzed using GraphPad Prism.
Results:
In this study, we applied the DNMT3A R878H conditional knock-in mouse model to explore the lncRNA epigenetic landscape of DNMT3A mutation by using the Cuffcomparison method. Twenty-three differentially expressed lncRNAs were identified in Dnmt3aR878H/WTMx1-Cre+ mice. We next predicted the downstream targetable genes regulated by these lncRNAs through cis and trans regulation networks and found 124 candidate genes are related to these lncRNAs. In further analysis of 124 genes, we found that increased mRNA expression levels of interleukin 1 receptor type 2 (IL1R2), Krüppel-like factor 13 (KLF13), ATPase H+ transporting V1 subunit A (ATP6V1A), proteasome 26S Subunit, non-ATPase 3 (PSMD3), and pyrroline-5-carboxylate reductase 2 (PYCR2) were associated with poor prognosis in AML. Functional analysis of these genes demonstrated that the pathways involved in autophagy, cell cycle, and hematopoietic stem cell differentiation were more enriched in Dnmt3aR878H/WTMx1-Cre+ mice.
Conclusion:
Our study was the first to use DNMT3A R878H conditional knock-in mouse model to predict the specific lncRNAs regulated by the DNMT3A mutation in AML. Six candidate genes were found to be associated with DNMT3A mutation with poor prognosis. Our results provided a possible treatment strategy for this disease.
... In addition to Chka, we also discovered TRAF3-mediated regulation of several other enzymes that catalyze the anabolic or catabolic pathways of phospholipids in B cells, including Lpcat1, Faah, Gdpd3, Plcd3, Dgka, Lacc1, and Pip5k1b. Among these, upregulation of LPCAT1 and FAAH, as well as downregulation of DGKA and PIP5K1B, has been documented in human cancers (70)(71)(72)(73)(74)(75). In particular, the key enzyme of an alternative pathway of PC synthesis, LPCAT1 of the Lands Cycle that converts lysophosphatidylcholine (LPC) to PC, has been shown to play important roles in cancer pathogenesis and progression (70)(71)(72). ...
Specific deletion of the tumor suppressor TRAF3 from B lymphocytes in mice leads to the prolonged survival of mature B cells and expanded B cell compartments in secondary lymphoid organs. In the current study, we investigated the metabolic basis of TRAF3-mediated regulation of B cell survival by employing metabolomic, lipidomic, and transcriptomic analyses. We compared the polar metabolites, lipids, and metabolic enzymes of resting splenic B cells purified from young adult B cell-specific Traf3-/- and littermate control mice. We found that multiple metabolites, lipids, and enzymes regulated by TRAF3 in B cells are clustered in the choline metabolic pathway. Using stable isotope labeling, we demonstrated that phosphocholine and phosphatidylcholine biosynthesis was markedly elevated in Traf3-/- mouse B cells and decreased in TRAF3-reconstituted human multiple myeloma cells. Furthermore, pharmacological inhibition of choline kinase α, an enzyme that catalyzes phosphocholine synthesis and was strikingly increased in Traf3-/- B cells, substantially reversed the survival phenotype of Traf3-/- B cells both in vitro and in vivo. Taken together, our results indicate that enhanced phosphocholine and phosphatidylcholine synthesis supports the prolonged survival of Traf3-/- B lymphocytes. Our findings suggest that TRAF3-regulated choline metabolism has diagnostic and therapeutic value for B cell malignancies with TRAF3 deletions or relevant mutations.
... The clonal expansion was calculated as a percentage of the TCR-Vβ clonal cells in the CD3+/CD4+ fraction. Isolation of peripheral blood mononuclear cells (PBMCs) from blood was performed by density gradient centrifugation (Ficoll-Histopaque Sigma-Aldrich, USA) as previously described (Caprini et al., 2009). An enrichment in the total T lymphocytes was performed using the Pan-T isolation kit ( ...
The PI3K/AKT/mTOR pathway is hyperactivated in many tumors, as well as in cutaneous T-cell lymphoma (CTCL) which includes mycosis fungoides (MF) and the aggressive variant known as Sezary syndrome (SS). TORC1 signaling is activated in SS cells by cytokines and chemokines, which are overexpressed in SS tissues. Furthermore, the recurrent copy number variation (CNV) of genes belonging to this cascade, such as PTEN, LKB1, and P70S6K, contributes to the hyperactivation of the pathway. The aim of this study was to investigate the therapeutic potential of mTOR inhibitors in CTCL. We compared the efficacy of three rapalogs (rapamycin, temsirolimus and everolimus) and the dual-mTOR/PI3K inhibitor PF-04691502 (hereinafter PF-502) in four CTCL cell lines. PF-502 showed to be the most effective inhibitor of cell growth. Interestingly, PF-502 confirmed its antitumor activity also in patient-derived CTCL cells and in a xenograft mouse model, where it induced significant apoptosis and increased survival of treated mice. Furthermore, we found an inverse correlation between PTEN gene expression and the ability of PF-502 to induce apoptosis in SS cells. Our data strongly support the therapeutic potential of dual PI3K/mTOR inhibitors in CTCL.
... L-HES gene expression data based on Affimetrix HG U133 Plus 2 microarrays from Ravoet, et al. [12] was obtained from the Gene Expression Omnibus (https:// www.ncbi.nlm.nih.gov/geo/) using accession number GSE12079. While several microarray studies for SS have been published [13,16,17,58,59], no other data set using the Affymetrix HG U133 Plus 2.0 platform is publicly available. The work flow for raw data processing, quality control measures, and analysis is summarized in the Supplementary Figure 2. Data analysis was performed in R version 3.4 (https://www.R-project.org/) ...
Sézary syndrome (SS) is an aggressive cutaneous T cell lymphoma with pruritic skin inflammation and immune dysfunction, driven by neoplastic, clonal memory T cells in both peripheral blood and skin. To gain insight into abnormal gene expression promoting T cell dysfunction, lymphoproliferation and transformation in SS, we first compared functional transcriptomic profiles of both resting and activated CD4+CD45RO+ T cells from SS patients and normal donors to identified differential expressed genes. Next, a meta-analysis was performed to compare our SS data to public microarray data from a novel benign disease control, lymphocytic-variant hypereosinophilic syndrome (L-HES). L-HES is a rare, clonal lymphoproliferation of abnormal memory T cells that produces similar clinical symptoms as SS, including severe pruritus and eosinophilia. Comparison revealed gene sets specific for either SS (370 genes) or L-HES (519 genes), and a subset of 163 genes that were dysregulated in both SS and L-HES T cells compared to normal donor T cells. Genes confirmed by RT-qPCR included elevated expression of PLS3, TWIST1 and TOX only in SS, while IL17RB mRNA was increased only in L-HES. CDCA7 was increased in both diseases. In an L-HES patient who progressed to peripheral T cell lymphoma, the malignant transformation identified increases in the expression of CDCA7, TIGIT, and TOX, which are highly expressed in SS, suggesting that these genes contribute to neoplastic transformation. In summary, we have identified gene expression biomarkers that implicate a common transformative mechanism and others that are unique to differentiate SS from L-HES.
