BACKGROUND: Telomeres are protective structures at chromosome ends which shorten gradually with increasing age. In chronic lymphocytic leukemia (CLL), short telomeres have been associated with unfavorable disease outcome, but the link between clonal evolution and telomere shortening remains unresolved. METHODS: We investigated relative telomere length (RTL) in a well-characterized cohort of 198 CLL patients by qPCR and focused in detail on a subgroup 26 patients who underwent clonal evolution of TP53 mutations (evolTP53). In the evolTP53 subgroup we explored factors influencing clonal evolution and corresponding changes in telomere length through measurements of telomerase expression, lymphocyte doubling time, and BCR signaling activity. RESULTS: At baseline, RTL of the evolTP53 patients was scattered across the entire RTL spectrum observed in our CLL cohort. RTL changed in the follow-up samples of 16/26 (62%) evolTP53 cases, inclining to reach intermediate RTL values, i.e., longer telomeres shortened compared to baseline while shorter ones prolonged. For the first time we show that TP53 clonal shifts are linked to RTL change, including unexpected RTL prolongation. We further investigated parameters associated with RTL changes. Unstable telomeres were significantly more frequent among younger patients (P = 0.032). Shorter telomeres were associated with decreased activity of the B-cell receptor signaling components p-ERK1/2, p-ZAP-70/SYK, and p-NFκB (P = 0.04, P = 0.01, and P = 0.02, respectively). CONCLUSIONS: Our study revealed that changes of telomere length reflect evolution in leukemic subclone proportion, and are associated with specific clinico-biological features of the explored cohort.
- MeSH
- chronická lymfatická leukemie genetika MeSH
- klonální evoluce genetika MeSH
- lidé středního věku MeSH
- lidé MeSH
- mutace MeSH
- nádorový supresorový protein p53 genetika MeSH
- protoonkogenní proteiny c-bcr metabolismus MeSH
- signální transdukce MeSH
- telomerasa genetika MeSH
- telomery ultrastruktura MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (≥6 Mb) and recurrent chromosomal aberrations (≥300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel represents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
- MeSH
- chromozomální aberace MeSH
- diagnostické techniky molekulární MeSH
- genetická predispozice k nemoci * MeSH
- genetická variace MeSH
- genomika metody MeSH
- lidé MeSH
- lymfoidní leukemie diagnóza genetika MeSH
- lymfom diagnóza genetika MeSH
- mutace INDEL MeSH
- nádorové biomarkery * MeSH
- prognóza MeSH
- translokace genetická MeSH
- variabilita počtu kopií segmentů DNA MeSH
- výpočetní biologie metody MeSH
- vysoce účinné nukleotidové sekvenování * metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
AIMS: This is a nation-wide survey of chronic lymphocytic leukemia (CLL) patients at six large hematology centers in the Czech Republic. The aim was to identify specific populations, social, and health characteristics of CLL subgroups divided according to the immunogenetic features of their B cell receptors (BCRs) and clonality. PATIENTS AND METHODS: Questionnaires directed to specific health, social, and environmental conditions were collected in a cohort of 573 CLL patients. For these patients, immunoglobulin heavy chain gene rearrangements were also analyzed in order to gain information about their clonality, IGHV mutational status, and the presence of stereotyped BCRs. Data extracted from the questionnaires were analyzed statistically in the context of immunogenetic features of the cohort. RESULTS: There were no statistically significant differences in the data collected in the survey between patients with mutated and patients with unmutated IGHV. However, patients with oligoclonal CLL reported health conditions such as hypercholesterolemia, hypertension, herpes simplex, tumors, and also, separately, CLL in 1st degree relatives, more often than their monoclonal counterparts. In patients with stereotyped BCRs, we found more frequent alcohol consumption and gastric infections in subset #1 cases and frequent cholecystectomies and familial CLL in subset #2 cases. CONCLUSION: To the best of our knowledge, this study is the first to investigate CLL immunogenetic features and clonality in the context of epidemiological data. We reported statistically significant associations suggesting the influence of certain health and social conditions on a number of clonal populations expanding in CLL and also on characteristic BCR features, especially stereotypy.
- MeSH
- biologické faktory * MeSH
- chronická lymfatická leukemie epidemiologie genetika imunologie MeSH
- dospělí MeSH
- genetická variace * MeSH
- genetika člověka MeSH
- genotyp MeSH
- imunogenetika * MeSH
- kohortové studie MeSH
- lidé středního věku MeSH
- lidé MeSH
- receptory antigenů B-buněk genetika MeSH
- rizikové faktory MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- Geografické názvy
- Česká republika MeSH
Activation-induced cytidine deaminase (AID) is a mutator enzyme essential for somatic hypermutation (SHM) and class switch recombination (CSR) during effective adaptive immune responses. Its aberrant expression and activity have been detected in lymphomas, leukemias, and solid tumors. In chronic lymphocytic leukemia (CLL) increased expression of alternatively spliced AID variants has been documented. We used real-time RT-PCR to quantify the expression of AID and its alternatively spliced transcripts (AIDΔE4a, AIDΔE4, AIDivs3, and AIDΔE3E4) in 149 CLL patients and correlated this expression to prognostic markers including recurrent chromosomal aberrations, the presence of complex karyotype, mutation status of the immunoglobulin heavy chain variable gene, and recurrent mutations. We report a previously unappreciated association between higher AID transcript levels and trisomy of chromosome 12. Functional analysis of AID splice variants revealed loss of their activity with respect to SHM, CSR, and induction of double-strand DNA breaks. In silico modeling provided insight into the molecular interactions and structural dynamics of wild-type AID and a shortened AID variant closely resembling AIDΔE4, confirming its loss-of-function phenotype.
- MeSH
- alternativní sestřih * MeSH
- biologické modely * MeSH
- chronická lymfatická leukemie * enzymologie genetika patologie MeSH
- cytidindeaminasa * biosyntéza chemie genetika MeSH
- lidé středního věku MeSH
- lidé MeSH
- lidské chromozomy, pár 12 enzymologie genetika MeSH
- myši knockoutované MeSH
- myši MeSH
- nádorové proteiny * biosyntéza chemie genetika MeSH
- počítačová simulace MeSH
- regulace genové exprese enzymů * MeSH
- regulace genové exprese u nádorů * MeSH
- senioři MeSH
- simulace molekulární dynamiky MeSH
- trizomie * genetika patologie MeSH
- zvířata MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- myši MeSH
- senioři MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.
- MeSH
- genetické markery genetika MeSH
- genová přestavba genetika MeSH
- imunoglobuliny genetika MeSH
- lidé MeSH
- receptory antigenů T-buněk genetika MeSH
- reprodukovatelnost výsledků MeSH
- reziduální nádor genetika MeSH
- řízení kvality MeSH
- výpočetní biologie metody MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Východiska: Chronická lymfocytární leukemie (CLL) se vyznačuje vysokou klinickou i biologickou variabilitou. Ta je úzce spjata s řadou buněčných a molekulárních znaků, mezi něž patří sekvenční motivy B buněčných receptorů. Tyto motivy se u třetiny pacientů s CLL vyskytují v téměř identické (stereotypní) podobě, což je umožňuje zařadit do homogenních skupin, tzv. stereotypních subsetů CLL. Homogenita stereotypních subsetů není určena pouze sekvenčními motivy B buněčných receptorů, ale odráží se i v klinicko-biologických charakteristikách onemocnění. Pro zjednodušení přístupu k informacím o jednotlivých subsetech byl vytvořen veřejně dostupný webový nástroj Encyclopedia of CLL Subsets. Materiál a metody: Encyklopedie subsetů CLL vznikla jako součást bioinformatické platformy Antigen Receptor Research Tool (ARResT) vyvinuté speciálně pro analýzu, shlukování a anotaci imunoglobulinových sekvencí. Datový soubor od 7 500 CLL pacientů, na kterém je systém Encyklopedie postaven, pochází z mezinárodní studie Agathangelidis et al publikované v roce 2012 [1]. Analýzou tohoto souboru vznikl přehled hlavních stereotypních subsetů a jejich charakteristik. Další související klinické a cytogenomické informace o jednotlivých subsetech byly získány strojovým zpracováním dostupné literatury ze serveru PubMed a jsou pravidelně doplňovány a aktualizovány. Výsledky: Vytvořili jsme unikátní webovou aplikaci Encyklopedie subsetů CLL dostupnou na http: //arrest.tools/subsets. Ta umožňuje interaktivní přístup k informacím o stereotypních subsetech CLL. Uživatel může získat a porovnávat základní informace o hlavních subsetech, vč. jejich klinických a cytogenomických vlastností. Tyto informace byly ručně zkontrolovány a vybrány ze strojově zpracovaných výsledků z databáze PubMed za pomoci odborníků v oblasti výzkumu CLL. V rámci Encyklopedie mají uživatelé také možnost přímo použít publikovaný nástroj ARResT/AssignSubsets a přiřadit vlastní sekvence B buněčných receptorů do hlavních subsetů. Závěr: Encyklopedie subsetů CLL je veřejně dostupný online nástroj, který usnadňuje přístup k nejnovějším poznatkům z oblasti výzkumu stereotypních subsetů u CLL a navíc umožňuje analýzu vlastních dat a interpretaci získaných výsledků. To má velký potenciál pro využití Encyklopedie v běžné praxi.
Background: Chronic lymphocytic leukemia (CLL) is clinically and biologically highly variable disease which is closely related with multiple cellular and molecular markers, including sequence motifs of B-cell receptors. These motifs are highly similar (stereotyped) within one third of CLL patients and create homogeneous groups called stereotyped CLL subsets. The homogeneity is reflected also in clinical and biological characteristics of the disease. To facilitate access to the information about individual subsets, we have created a publicly available web-based tool Encyclopedia of CLL Subsets. Materials and methods: The Encyclopedia of CLL subsets belongs to our bioinformatics platform Antigen Receptor Research Tool (ARResT) developed for analysis, clustering, and annotation of immunoglobulin sequences. To gather primary knowledge about the subsets, we have analyzed a dataset of 7,500 CLL patients published by Agathangelidis et al in 2012 [1]. We have created an overview of major stereotyped subsets and their characteristics. Additional clinical and cytogenomic information about individual subsets has been obtained by machine text processing of available literature from server PubMed and is regularly updated. Results: We have created a unique web-based application Encyclopedia of CLL Subsets available from http: //arrest.tools/subsets for an interactive access to the information about stereotyped CLL subsets. A user can obtain and compare basic information about the major subsets including their clinical and cytogenomic characteristics. These have been manually curated from machine processed results from PubMed database by experts in CLL research. Through the Encyclopedia‘s user interface, user can also directly use our published tool ARResT/AssignSubsets to assign new immunoglobulin sequences to the major subsets. Conclusion: The Encyclopedia of CLL Subsets is a publicly available online tool facilitating access to the most recent research knowledge about stereotyped CLL subsets and enabling analysis of own data and interpretation of the results. This gives the Encyclopedia a great potential for its use in clinical routine.
- MeSH
- B-lymfocyty cytologie patologie MeSH
- chronická lymfatická leukemie * genetika MeSH
- imunogenetika MeSH
- lidé MeSH
- výpočetní biologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
Telomeres are repetitive DNA sequences protecting physical ends of linear chromosomes against degradation and end-to-end chromosomal fusion. Telomeres shorten with each cell division, which regulates the cellular lifespan in somatic cells and limits their renewal capacity. Cancer cells are often able to overcome this physiological barrier and become immortal with unlimited replicative capacity. In this review, we present current knowledge on the role of telomeres in human aging with a focus on their behavior in hematological malignancies of adults. Associations of telomere length to age-related diseases and to the prevention of telomere shortening are also discussed.
- MeSH
- buněčné dělení MeSH
- chromozomální nestabilita genetika MeSH
- dospělí MeSH
- hematologické nádory genetika patofyziologie MeSH
- lidé MeSH
- nádorové biomarkery metabolismus MeSH
- stárnutí buněk genetika fyziologie MeSH
- stárnutí genetika fyziologie MeSH
- telomerasa metabolismus MeSH
- telomery fyziologie MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
