INTRODUCTION: Glucocorticoids (GCs) are widely used as a treatment for rheumatoid arthritis (RA), leading to high cumulative doses in long-term treated patients. The impact of a high cumulative GC dose on the systemic inflammatory response in RA remains poorly understood. METHODS: We investigated long-treated patients with RA (n = 72, median disease duration 14 years) through blood counts and the serum levels of 92 inflammation-related proteins, and disease activity was assessed using the Simple Disease Activity Index (SDAI). Patients were grouped based on the cumulative GC dose, with a cut-off value of 20 g (low/high, n = 49/23). RESULTS AND DISCUSSION: Patients with a high cumulative GC dose within the active RA group had elevated serum levels in 23 inflammation-related proteins compared with patients with a low dose (cytokines/soluble receptors: CCL3, CCL20, CCL25, IL-8, CXCL9, IL-17A, IL-17C, IL-18, sIL-18R1, IL-10, sIL-10RB, OSM and sOPG; growth factors: sTGFα and sHGF; other inflammatory mediators: caspase 8, STAMBP, sCDCP1, sirtuin 2, 4E-BP1, sCD40, uPA and axin-1; pcorr < 0.05). In non-active RA, the high and low GC groups did not differ in analysed serum protein levels. Moreover, patients with active RA with a high GC dose had an increased white blood cell count, increased neutrophil-lymphocyte and platelet-lymphocyte ratios and a decreased lymphocyte-monocyte ratio compared with the low dose group (p < 0.05). This is the first study to report elevated serum levels in inflammation-related proteins and deregulated blood counts in patients with active RA with a high cumulative GC dose. The elevated systemic inflammation highlights the importance of improving care for patients receiving high cumulative GC doses.

• MeSH
• biologické markery krev   MeSH
• cytokiny krev   MeSH
• dospělí MeSH
• glukokortikoidy * aplikace a dávkování   terapeutické užití   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mediátory zánětu * krev   metabolismus   MeSH
• revmatoidní artritida * farmakoterapie   krev   imunologie   MeSH
• senioři MeSH
• zánět MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

Germline pathogenic ATM (ataxia-telangiectasia mutated) variants are associated with the risk of multiple cancers; however, genetic testing reveals a large number of ATM variants of uncertain significance (VUS). Here, we studied germline ATM variants occurring in a real-world cohort of 336 patients with chronic lymphocytic leukaemia (CLL) and public cancer whole-exome/genome-sequencing datasets (445 CLL, 75 mantle cell lymphoma, 216 metastatic breast cancer, 140 lung cancer patients). We found that two-thirds of rare germline ATM variants are pathogenic (18%-50%) or VUS-predicted pathogenic (50%-82%), depending on cancer type and reaching a prevalence of up to 8%, and one-third are VUS-predicted benign. Patients with both pathogenic and VUS-predicted pathogenic variants, all heterozygous, mostly missense, are more predisposed to biallelic ATM inactivation by acquiring deletion (del)11q than patients without these variants, similar to patients with somatic ATM variants. A functional assay of ATM activity in primary CLL cells proved that VUS-predicted pathogenic ATM variants partially reduce ATM activity and concurrent del(11q) leads to complete loss of ATM activity. The rare germline variants were associated with reduced progression-free survival in CLL on novel agents, comparable to somatic ATM or TP53 disruptions. Our results highlight the need to determine the pathogenicity of VUS in clinically relevant genes such as ATM.

• MeSH
• ATM protein * genetika   MeSH
• chronická lymfatická leukemie * genetika   MeSH
• kohortové studie MeSH
• lidé MeSH
• lymfom z plášťových buněk genetika   MeSH
• nádory prsu * genetika   MeSH
• zárodečné mutace MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• Publikační typ
• abstrakt z konference MeSH

Richter transformation (RT) is the development of aggressive lymphoma - most frequently diffuse large B-cell lymphoma (DLBCL) and rarely Hodgkin lymphoma (HL) - arising on the background of chronic lymphocytic leukaemia (CLL). Despite recent advances in CLL treatment, RT also develops in patients on novel agents, usually occurring as an early event. RT incidence is lower in CLL patients treated with novel agents in the front line compared to relapsed/refractory cases, with a higher incidence in patients with TP53 disruption. The genetic heterogeneity and complexity are higher in RT-DLBCL than CLL; the genetics of RT-HL are largely unknown. In addition to TP53, aberrations in CDKN2A, MYC, and NOTCH1 are common in RT-DLBCL; however, no distinct RT-specific genetic aberration is recognised yet. RT-DLBCL on ibrutinib is frequently associated with BTK and PLCG2 mutations. Here, we update on genetic analysis, diagnostics and treatment options in RT in the era of novel agents.

• MeSH
• chromozomální aberace MeSH
• cytogenetické vyšetření MeSH
• difúzní velkobuněčný B-lymfom etiologie   genetika   patologie   terapie   MeSH
• Hodgkinova nemoc etiologie   genetika   patologie   terapie   MeSH
• lidé MeSH
• management nemoci MeSH
• rizikové faktory MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

OBJECTIVES: A growing body of evidence highlights the persistent activation of the innate immune system and type I interferon (IFN) signature in the pathogenesis of rheumatoid arthritis (RA) and its association with disease activity. Since the recent study revealed heterogeneity in the IFN signature in RA, we investigated for the first time the heterogeneity in innate signature in RA. METHODS: The innate gene expression signature (10 TLRs, 7 IL1/IL1R family members, and CXCL8/IL8) was assessed in peripheral blood mononuclear cells from RA patients (n=67), both with active (DAS28≥3.2, n=32) and inactive disease (DAS28<3.2, n=35), and in healthy control subjects (n=55). RESULTS: Of the 13 deregulated innate genes (TLR2, TLR3, TLR4, TLR5, TLR8, TLR10, IL1B, IL1RN, IL18, IL18R1, IL1RAP, and SIGIRR/IL1R8) associated with RA, TLR10 and IL1RAP are being reported for the first time. Multivariate analysis based on utilising patient similarity networks revealed the existence of four patient's subsets (clusters) based on different TLR8 and IL1RN expression profiles, two in active and two in inactive RA. Moreover, neural network analysis identified two main gene sets describing active RA within an activity-related innate signature (TLR1, TLR2, TLR3, TLR7, TLR8, CXCL8/IL8, IL1RN, IL18R1). When comparing active and inactive RA, upregulated TLR2, TLR4, TLR6, and TLR8 and downregulated TLR10 (P<0.04) expression was associated with the disease activity. CONCLUSIONS: Our study on the comprehensive innate gene profiling together with multivariate analysis revealed a certain heterogeneity in innate signature within RA patients. Whether the heterogeneity of RA elucidated from diversity in innate signatures may impact the disease course and treatment response deserves future investigations.

• MeSH
• interferon typ I * imunologie   MeSH
• leukocyty mononukleární MeSH
• lidé MeSH
• multivariační analýza MeSH
• revmatoidní artritida * genetika   imunologie   metabolismus   MeSH
• toll-like receptory * genetika   imunologie   metabolismus   MeSH
• transkriptom MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Richterova transformace (Richterův syndrom – RT) představuje transformaci chronické lymfocytární leukemie (CLL) do lymfoproliferace vyšší malignity. Nejčastěji dochází k transformaci do difuzního velkobuněčného B-lymfomu (DLBCL), vzácněji do Hodgkinova lymfomu. K transformaci může dojít kdykoli v průběhu choroby a její výskyt se v literatuře udává v rozmezí 2–10 %. S RT se setkáváme u pacientů léčených imunochemoterapií, ale také u těch, kteří jsou léčeni inhibitory buněčných drah (ibrutinib, idelalisib, venetoklax). Práce se zaměřuje na nejčastější molekulárně genetické aberace asociované s RT-DLBCL vzniklé klonálně z původní CLL. Mezi tyto změny patří disrupce TP53 genu (delece 17p a/nebo mutace) a současně také CDKN2A genu, které se vyskytují u více než poloviny pacientů s RT. S výskytem TP53 a CDKN2A aberací také často souvisí aberantní aktivace genu MYC, která bývá obvykle způsobena strukturálními změnami (zisk 8q, t(8;14)) nebo nepřímo mutacemi v MGA genu. U dalších 30 % pacientů s RT nacházíme aktivační mutace v genu NOTCH1, které bývají často přítomny v CLL klonu ještě před rozvojem RT. Přibližně 20 % případů RT tvoří heterogenní skupina pacientů s dalšími genetickými aberacemi. Také u RT, která vznikla u pacientů léčených ibrutinibem, se setkáváme s disrupcí genu TP53, ztrátou genu CDKN2A, aktivací genu MYC a aktivačními mutacemi v genu NOTCH1. Navíc u 40 % pacientů s RT vzniklou během léčby ibutinibem jsou přítomny mutace v genech BTK a PLCG2, které jsou spojeny s rezistencí k této léčbě. U pacientů s RT vzniklou během léčby idelalisibem a venetoklaxem zatím genetické změny nebyly studovány. I přes popis řady genetických změn u RT nebyla doposud nalezena molekulárně genetická aberace přímo asociovaná s rozvojem RT. Další studie na větších počtech pacientů spolu s rozvojem citlivějších molekulárně diagnostických metod nám v budoucnosti mohou pomoci objasnit molekulární procesy, které vedou k rozvoji této agresivní formy nemoci.

Richter transformation (Richter syndrome - RT) is defined as the transformation of chronic lymphocytic leukaemia (CLL) into high-grade lymphoma. Development of diffuse large B-cell lymphoma (DLBCL) clonally related to CLL is most common, less frequent is transformation to Hodgkin's lymphoma. RT occurs in approximately 2-10% of CLL patients during the disease course. It develops in patients treated with immunochemotherapy as well as in those treated with novel agents (ibrutinib, idelalisib, venetoclax). In this review, we discuss recent discoveries in the understanding of molecular genetic changes associated with RT. The most common molecular events in RT are concurrent disruptions of TP53 and CDKN2A genes that occur in approximately one half of RT patients. The occurrence of TP53 and CDKN2A aberrations is often associated with aberrant activation of the MYC gene, which is usually caused by structural changes (gain 8q, t(8; 14)) or indirectly by mutations in the MGA gene. In 30% RT patients, activating NOTCH1 mutations are detected, which are often present already prior to transformation. Approximately 20% RT patients carry heterogeneous molecular genetic aberrations. RT in ibrutinib-treated patients is also associated with TP53 and CDKN2A disruptions, activation of MYC as well as NOTCH1 mutations. Additionally, in 40% patients who develop RT on ibrutinib, mutations in BTK and PLCG2 genes were identified, known to be associated with treatment resistance. To date, the genetic landscape associated with RT on idelalisib and venetoclax was not studied. Despite improved understanding of molecular genetic changes linked to RT, genetic aberrations driving RT development have not been reported as yet. Further studies on large patient cohorts together with the development of more sensitive molecular technologies may help elucidate the underlying genetic risk factors in these difficult-to-treat patients.

• Klíčová slova
• Richterova transformace, molekulárně genetické aberace,
• MeSH
• chronická lymfatická leukemie * farmakoterapie   komplikace   MeSH
• difúzní velkobuněčný B-lymfom * genetika   MeSH
• lidé MeSH
• mutace genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• přehledy MeSH

• MeSH
• dospělí MeSH
• geny p53 * MeSH
• kostní dřeň patologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mnohočetný myelom genetika   patologie   MeSH
• mutace * MeSH
• nádorový supresorový protein p53 genetika   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• vysoce účinné nukleotidové sekvenování metody   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
• dopisy MeSH
• práce podpořená grantem MeSH

The insufficient standardization of diagnostic next-generation sequencing (NGS) still limits its implementation in clinical practice, with the correct detection of mutations at low variant allele frequencies (VAF) facing particular challenges. We address here the standardization of sequencing coverage depth in order to minimize the probability of false positive and false negative results, the latter being underestimated in clinical NGS. There is currently no consensus on the minimum coverage depth, and so each laboratory has to set its own parameters. To assist laboratories with the determination of the minimum coverage parameters, we provide here a user-friendly coverage calculator. Using the sequencing error only, we recommend a minimum depth of coverage of 1,650 together with a threshold of at least 30 mutated reads for a targeted NGS mutation analysis of ≥3% VAF, based on the binomial probability distribution. Moreover, our calculator also allows adding assay-specific errors occurring during DNA processing and library preparation, thus calculating with an overall error of a specific NGS assay. The estimation of correct coverage depth is recommended as a starting point when assessing thresholds of NGS assay. Our study also points to the need for guidance regarding the minimum technical requirements, which based on our experience should include the limit of detection (LOD), overall NGS assay error, input, source and quality of DNA, coverage depth, number of variant supporting reads, and total number of target reads covering variant region. Further studies are needed to define the minimum technical requirements and its reporting in diagnostic NGS.

• Publikační typ
• časopisecké články MeSH

Overactivation of the innate immune system together with the impaired downstream pathway of type I interferon-responding genes is a hallmark of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic sclerosis (SSc). To date, limited data on the cross-disease innate gene signature exists among those diseases. We compared therefore an innate gene signature of Toll-like receptors (TLRs), seven key members of the interleukin (IL)1/IL1R family, and CXCL8/IL8 in peripheral blood mononuclear cells from well-defined patients with active stages of RA (n = 36, DAS28 ≥ 3.2), SLE (n = 28, SLEDAI > 6), and SSc (n = 22, revised EUSTAR index > 2.25). Emerging diversity and abundance of the innate signature in RA patients were detected: RA was characterized by the upregulation of TLR3, TLR5, IL1RAP/IL1R3, IL18R1, and SIGIRR/IL1R8 when compared to SSc (Pcorr < 0.02) and of TLR2, TLR5, and SIGIRR/IL1R8 when compared to SLE (Pcorr < 0.02). Applying the association rule analysis, six rules (combinations and expression of genes describing disease) were identified for RA (most frequently included high TLR3 and/or IL1RAP/IL1R3) and three rules for SLE (low IL1RN and IL18R1) and SSc (low TLR5 and IL18R1). This first cross-disease study identified emerging heterogeneity in the innate signature of RA patients with many upregulated innate genes compared to that of SLE and SSc.

• MeSH
• dospělí MeSH
• interleukin-1 genetika   metabolismus   MeSH
• interleukin-8 genetika   metabolismus   MeSH
• leukocyty mononukleární metabolismus   MeSH
• lidé středního věku MeSH
• lidé MeSH
• přirozená imunita genetika   MeSH
• receptory interleukinu-1 - typ I genetika   metabolismus   MeSH
• revmatoidní artritida krev   genetika   imunologie   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• systémová sklerodermie krev   genetika   imunologie   MeSH
• systémový lupus erythematodes krev   genetika   imunologie   MeSH
• toll-like receptory genetika   metabolismus   MeSH
• transkriptom 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

BACKGROUND: Systemic lupus erythematosus (SLE) is a remarkably heterogeneous autoimmune disease. Despite tremendous efforts, our knowledge of serum protein patterns in severe SLE phenotypes is still limited. We investigated the serum protein pattern of SLE, with special emphasis on irreversible organ damage and active lupus nephritis (LN) as assessed by renal Systemic Lupus Erythematosus Disease Activity Index. METHODS: We used proximity extension immunoassay (PEA, Proseek Multiplex, Olink) to assess the serum levels of ninety-two inflammation-related proteins in Czech patients with SLE (n = 75) and age-matched healthy control subjects (n = 23). Subgroup analysis was carried out on the basis of organ damage (with/without, 42/33) and biopsy-proven LN (with/without, 27/48; active LN, n = 13; inactive LN, n = 14). RESULTS: Of thirty deregulated proteins between SLE and the healthy controls (Pcorr  < 0.05), the top upregulated proteins in SLE were sirtuin 2, interleukin 18 (IL18), and caspase 8 (Pcorr  < 0.0006). Of these, sirtuin 2 and caspase 8 had not yet been reported with SLE. Elevated levels of IL8, CCL2/MCP1, CCL11, and MMP10 (Pcorr  < 0.05) were detected in patients with organ damage for which the serum levels of CCL11 and MMP10 were particularly informative in organ damage prediction. Comparing patients based on LN, elevated levels of CSF1, sIL15RA, sCD40, sCX3CL1, caspase 8, sIL18R1, bNGF, and GDNF (Pcorr  < 0.05) were detected in active LN. Except GDNF, all LN-associated markers showed usefulness in prediction of active renal disease. CONCLUSIONS: This highly sensitive PEA analysis identified the serum pattern of SLE, organ damage, and active LN, with many novel candidate proteins detected. Their exact role and suitability as biomarkers in SLE deserve further investigation.

• Publikační typ
• časopisecké články MeSH