Rare germline ATM variants of uncertain significance in chronic lymphocytic leukaemia and other cancers.

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.

Comparison of structural variants detected by optical mapping with long-read next-generation sequencing.

MOTIVATION: Recent studies have shown the potential of using long-read whole-genome sequencing (WGS) approaches and optical mapping (OM) for the detection of clinically relevant structural variants (SVs) in cancer research. Three main long-read WGS platforms are currently in use: Pacific Biosciences (PacBio), Oxford Nanopore Technologies (ONT) and 10x Genomics. Recently, whole-genome OM technology (Bionano Genomics) has been introduced into human diagnostics. Questions remain about the accuracy of these long-read sequencing platforms, how comparable/interchangeable they are when searching for SVs and to what extent they can be replaced or supplemented by OM. Moreover, no tool can effectively compare SVs obtained by OM and WGS. RESULTS: This study compared optical maps of the breast cancer cell line SKBR3 with AnnotSV outputs from WGS platforms. For this purpose, a software tool with comparative and filtering features was developed. The majority of SVs up to a 50 kbp distance variance threshold found by OM were confirmed by all WGS platforms, and ∼99% of translocations and ∼80% of deletions found by OM were confirmed by both PacBio and ONT, with ∼70% being confirmed by 10x Genomics in combination with PacBio and/or ONT. Interestingly, long deletions (>100 kbp) were detected only by 10x Genomics. Regarding insertions, ∼74% was confirmed by PacBio and ONT, but none by 10x Genomics. Inversions and duplications detected by OM were not detected by WGS. Moreover, the tool enabled the confirmation of SVs that overlapped in the same gene(s) and was applied to the filtering of disease-associated SVs. AVAILABILITY AND IMPLEMENTATION: https://github.com/novosadt/om-annotsv-svc.

Determining optical mapping errors by simulations.

MOTIVATION: Optical mapping is a complementary technology to traditional DNA sequencing technologies, such as next-generation sequencing (NGS). It provides genome-wide, high-resolution restriction maps from single, stained molecules of DNA. It can be used to detect large and small structural variants, copy number variations and complex rearrangements. Optical mapping is affected by different kinds of errors in comparison with traditional DNA sequencing technologies. It is important to understand the source of these errors and how they affect the obtained data. This article proposes a novel approach to modeling errors in the data obtained from the Bionano Genomics Inc. Saphyr system with Direct Label and Stain (DLS) chemistry. Some studies have already addressed this issue for older instruments with nicking enzymes, but we are unaware of a study that addresses this new system. RESULTS: The main result is a framework for studying errors in the data obtained from the Saphyr instrument with DLS chemistry. The framework's main component is a simulation that computes how major sources of errors for this instrument (a false site, a missing site and resolution errors) affect the distribution of fragment lengths in optical maps. The simulation is parametrized by variables describing these errors and we are using a differential evolution algorithm to evaluate parameters that best fit the data from the instrument. Results of the experiments manifest that this approach can be used to study errors in the optical mapping data analysis. AVAILABILITY AND IMPLEMENTATION: Source codes supporting the presented results are available at: https://github.com/mvasinek/olgen-om-error-prediction. The data underlying this article are available on the Bionano Genomics Inc. website, at: https://bionanogenomics.com/library/datasets/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Serum protein pattern associated with organ damage and lupus nephritis in systemic lupus erythematosus revealed by PEA immunoassay.

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.

Correlation Network Analysis Reveals Relationships between MicroRNAs, Transcription Factor T-bet, and Deregulated Cytokine/Chemokine-Receptor Network in Pulmonary Sarcoidosis.

Sarcoidosis is an inflammatory granulomatous disease with unknown etiology driven by cytokines and chemokines. There is limited information regarding the regulation of cytokine/chemokine-receptor network in bronchoalveolar lavage (BAL) cells in pulmonary sarcoidosis, suggesting contribution of miRNAs and transcription factors. We therefore investigated gene expression of 25 inflammation-related miRNAs, 27 cytokines/chemokines/receptors, and a Th1-transcription factor T-bet in unseparated BAL cells obtained from 48 sarcoidosis patients and 14 control subjects using quantitative RT-PCR. We then examined both miRNA-mRNA expressions to enrich relevant relationships. This first study on miRNAs in sarcoid BAL cells detected deregulation of miR-146a, miR-150, miR-202, miR-204, and miR-222 expression comparing to controls. Subanalysis revealed higher number of miR-155, let-7c transcripts in progressing (n = 20) comparing to regressing (n = 28) disease as assessed by 2-year follow-up. Correlation network analysis revealed relationships between microRNAs, transcription factor T-bet, and deregulated cytokine/chemokine-receptor network in sarcoid BAL cells. Furthermore, T-bet showed more pronounced regulatory capability to sarcoidosis-associated cytokines/chemokines/receptors than miRNAs, which may function rather as "fine-tuners" of cytokine/chemokine expression. Our correlation network study implies contribution of both microRNAs and Th1-transcription factor T-bet to the regulation of cytokine/chemokine-receptor network in BAL cells in sarcoidosis. Functional studies are needed to confirm biological relevance of the obtained relationships.

Expression of the active caspase-3 in children and adolescents with classical Hodgkin lymphoma.

UNLABELLED: The aim of the study was to determine whether the expression of active caspase-3 in neoplastic Hodgkin and Reed-Sternberg (H/RS) cells correlates with the treatment response and provides prognostic information on treatment outcome. In this retrospective study, we included 56 patients with classical Hodgkin lymphoma treated at the Department of Paediatric Haematology and Oncology between January 2000 and June 2005. Active caspase-3 was detected by immunohistochemistry in primary biopsy specimens. Seventeen patients (29.3%) were evaluated as caspase-3 positive and remained alive in the first complete remission. This stood in contrast to patients with less than 5% caspase-3 positive cells, five of whom experienced relapse and three patients died. Adequate treatment response was achieved in 11 patients (19.6%). Comparison of event-free survival with regard to the percentage of caspase-3 positive tumour cells showed a tendency for a better clinical outcome in patients with 5% or more active caspase-3 positive cells. KEYWORDS: classical Hodgkin lymphoma - apoptosis - active caspase-3 - therapy response - clinical outcome.

Comparing Deep Learning Performance for Chronic Lymphocytic Leukaemia Cell Segmentation in Brightfield Microscopy Images.

Objectives: This article focuses on the detection of cells in low-contrast brightfield microscopy images; in our case, it is chronic lymphocytic leukaemia cells. The automatic detection of cells from brightfield time-lapse microscopic images brings new opportunities in cell morphology and migration studies; to achieve the desired results, it is advisable to use state-of-the-art image segmentation methods that not only detect the cell but also detect its boundaries with the highest possible accuracy, thus defining its shape and dimensions. Methods: We compared eight state-of-the-art neural network architectures with different backbone encoders for image data segmentation, namely U-net, U-net++, the Pyramid Attention Network, the Multi-Attention Network, LinkNet, the Feature Pyramid Network, DeepLabV3, and DeepLabV3+. The training process involved training each of these networks for 1000 epochs using the PyTorch and PyTorch Lightning libraries. For instance segmentation, the watershed algorithm and three-class image semantic segmentation were used. We also used StarDist, a deep learning-based tool for object detection with star-convex shapes. Results: The optimal combination for semantic segmentation was the U-net++ architecture with a ResNeSt-269 background with a data set intersection over a union score of 0.8902. For the cell characteristics examined (area, circularity, solidity, perimeter, radius, and shape index), the difference in mean value using different chronic lymphocytic leukaemia cell segmentation approaches appeared to be statistically significant (Mann-Whitney U test, P < .0001). Conclusion: We found that overall, the algorithms demonstrate equal agreement with ground truth, but with the comparison, it can be seen that the different approaches prefer different morphological features of the cells. Consequently, choosing the most suitable method for instance-based cell segmentation depends on the particular application, namely, the specific cellular traits being investigated.

Whole-genome optical mapping of bone-marrow myeloma cells reveals association of extramedullary multiple myeloma with chromosome 1 abnormalities.

Extramedullary disease (EMM) represents a rare, aggressive and mostly resistant phenotype of multiple myeloma (MM). EMM is frequently associated with high-risk cytogenetics, but their complex genomic architecture is largely unexplored. We used whole-genome optical mapping (Saphyr, Bionano Genomics) to analyse the genomic architecture of CD138+ cells isolated from bone-marrow aspirates from an unselected cohort of newly diagnosed patients with EMM (n = 4) and intramedullary MM (n = 7). Large intrachromosomal rearrangements (> 5 Mbp) within chromosome 1 were detected in all EMM samples. These rearrangements, predominantly deletions with/without inversions, encompassed hundreds of genes and led to changes in the gene copy number on large regions of chromosome 1. Compared with intramedullary MM, EMM was characterised by more deletions (size range of 500 bp-50 kbp) and fewer interchromosomal translocations, and two EMM samples had copy number loss in the 17p13 region. Widespread genomic heterogeneity and novel aberrations in the high-risk IGH/IGK/IGL, 8q24 and 13q14 regions were detected in individual patients but were not specific to EMM/MM. Our pilot study revealed an association of chromosome 1 abnormalities in bone marrow myeloma cells with extramedullary progression. Optical mapping showed the potential for refining the complex genomic architecture in MM and its phenotypes.

Treatment and outcome of patients after cardiopulmonary resuscitation admitted to the intensive cardiac care unit.

OBJECTIVES: Sudden circulatory arrest is most often of cardiac origin. Our aim was to evaluate circulatory arrest etiology and treatment strategies in patients after cardiopulmonary resuscitation (CPR) with persistent impairment of consciousness in relation to survival and the subsequent quality of life. DESIGN: Retrospective analysis of patients after CPR treated according to the local protocol including mild hypothermia in the intensive cardiac care unit. RESULTS: Over 2 years, we admitted 57 mechanically ventilated patients after CPR. 47 patients (82%) were resuscitated outside the hospital. In 33 patients (58%) the initial rhythm was ventricular fibrillation; in the remaining patients (42%) asystole/pulseless electrical activity. Urgent coronary angiography was performed in 36 patients and percutaneous coronary intervention in 25 of them. The admission APACHE II score was 32,4 +/- 3,4 with predicted mortality of 77,1%. The hospital survival rate was 54% and 47% of the patients were discharged home in a good state of health (Glasgow outcome score 4-5). CONCLUSION: Our results suggest that comprehensive post-resuscitation care including therapeutic hypothermia and percutaneous coronary intervention in selected cases may have a positive impact on the prognosis of patients after CPR.

Dynamic changes in HLA-DR expression during short-term and long-term ibrutinib treatment in patients with chronic lymphocytic leukemia.

There is the first evidence of changes in the kinetics of B cell antigen receptor (BCR) internalisation of neoplastic cells in chronic lymphocytic leukemia (CLL) after the short-term and long-term administration of ibrutinib. We aimed to assess the influence of short-term and long-term ibrutinib treatment on the HLA-DR expression on CLL cells, T cells and monocytes. The immunophenotyping of CLL and immune cells in peripheral blood was performed on 16 high-risk CLL patients treated with ibrutinib. After early ibrutinib administration, the HLA-DR expression on CLL cells reduced (P = 0.032), accompanied by an increase in CLL cell counts in peripheral blood (P = 0.001). In vitro culturing of CLL cells with ibrutinib also revealed the reduction in the HLA-DR expression at protein and mRNA levels (P < 0.01). The decrease in HLA-DR on CLL cells after the first month was followed by the gradual increase of its expression by the 12th month (P = 0.001). A one-month follow-up resulted in elevated absolute counts of CD4+ (P = 0.002) and CD8+ (P < 0.001) T cells as well as CD4+ and CD8+ cells bearing HLA-DR (P < 0.01). The long-term administration of ibrutinib was associated with the increased numbers of CD4+ bearing HLA-DR (P = 0.006) and elevation of HLA-DR expression on all monocyte subsets (P ≤ 0.004). Our results provide the first evidence of the time-dependent immunomodulatory effect of ibrutinib on CLL and T cells and monocytes. The clinical consequences of time-dependent changes in HLA-DR expression in ibrutinib treated patients deserve further investigation.

Serum protein fingerprinting by PEA immunoassay coupled with a pattern-recognition algorithms distinguishes MGUS and multiple myeloma.

Serum protein fingerprints associated with MGUS and MM and their changes in MM after autologous stem cell transplantation (MM-ASCT, day 100) remain unexplored. Using highly-sensitive Proximity Extension ImmunoAssay on 92 cancer biomarkers (Proseek Multiplex, Olink), enhanced serum levels of Adrenomedullin (ADM, Pcorr= .0004), Growth differentiation factor 15 (GDF15, Pcorr= .003), and soluble Major histocompatibility complex class I-related chain A (sMICA, Pcorr= .023), all prosurvival and chemoprotective factors for myeloma cells, were detected in MM comparing to MGUS. Comparison of MGUS and healthy subjects revealed elevation of angiogenic and antia-poptotic midkine (Pcorr= .0007) and downregulation of Transforming growth factor beta 1 (TGFB1, Pcorr= .005) in MGUS. Importantly, altered serum pattern was associated with MM-ASCT compared to paired MM at the diagnosis as well as to healthy controls, namely by upregulated B-Cell Activating Factor (sBAFF) (Pcorr< .006) and sustained elevation of other pro-tumorigenic factors. In conclusion, the serum fingerprints of MM and MM-ASCT were characteristic by elevated levels of prosurvival and chemoprotective factors for myeloma cells.

Neutrophils in chronic lymphocytic leukemia are permanently activated and have functional defects.

A growing body of studies highlights involvement of neutrophils in cancer development and progression. Our aim was to assess the phenotypic and functional properties of circulating neutrophils from patients with chronic lymphocytic leukemia (CLL). The percentage of CD54+ and CD64+ neutrophils as well as CD54 expression on these cells were higher in CLL patients than in age-matched healthy controls. Neutrophils from CLL produced more reactive oxygen species (ROS) compared to controls in both resting and activated conditions. Lipopolysaccharide-induced production of IL-1ß and TNF-a as well as reduced TLR2 expression in neutrophils from CLL than in neutrophils from controls suggesting their tolerant state. Finally, phenotypic alterations of neutrophils, particularly elevation of CD64 and CD54 markers, correlated with disease activity and treatment, and low percentage of neutrophils. Taken together, the alterations in percentage and functional characteristics of neutrophils reflect the clinical course of CLL. Our data provide first evidence that neutrophils in CLL are permanently primed and have functional defects.

Utilization of the Discrete Differential Evolution for Optimization in Multidimensional Point Clouds.

The Differential Evolution (DE) is a widely used bioinspired optimization algorithm developed by Storn and Price. It is popular for its simplicity and robustness. This algorithm was primarily designed for real-valued problems and continuous functions, but several modified versions optimizing both integer and discrete-valued problems have been developed. The discrete-coded DE has been mostly used for combinatorial problems in a set of enumerative variants. However, the DE has a great potential in the spatial data analysis and pattern recognition. This paper formulates the problem as a search of a combination of distinct vertices which meet the specified conditions. It proposes a novel approach called the Multidimensional Discrete Differential Evolution (MDDE) applying the principle of the discrete-coded DE in discrete point clouds (PCs). The paper examines the local searching abilities of the MDDE and its convergence to the global optimum in the PCs. The multidimensional discrete vertices cannot be simply ordered to get a convenient course of the discrete data, which is crucial for good convergence of a population. A novel mutation operator utilizing linear ordering of spatial data based on the space filling curves is introduced. The algorithm is tested on several spatial datasets and optimization problems. The experiments show that the MDDE is an efficient and fast method for discrete optimizations in the multidimensional point clouds.

Profile of Inflammation-Associated Proteins in Early Post-Transplant Samples of Patients After Allogeneic Hematopoietic Stem Cell Transplantation: a Preliminary Study.

Allogeneic hematopoietic stem cell transplantation (aHSCT) is used as a curative treatment in severe hematological and immunological disorders. Despite clear improvement of the aHSCT outcome, substantial proportion of patients still suffers from severe complications, including graft-versus-host disease (GvHD). The aim of this study was, therefore, to identify inflammation-associated molecules deregulated in the early serum samples of the patients after aHSCT and nominate markers associated with particular aHSCT parameters/complications. Serum concentrations of 92 inflammation-associated proteins were measured in samples obtained from 80 aHSCT patients 14 days after transplantation and from 23 healthy control subjects by a novel sensitive proximity extension assay technology using Proseek Multiplex Inflammation I kit. Serum profiles of inflammatory proteins in patients after aHSCT were substantially different from those observed in control subjects and related to underlying disease status before transplantation. Particularly, the difference between aHSCT patients and controls reached significance level for 57 analytes (40 upregulated, 17 downregulated in aHSCT patients). The concentration of several markers was associated with the level of donor/recipient HLA match (TGF-α: p corr = 0.025, HGF: p corr = 0.036) and with complete donor chimerism at day +30 after allografting (DNER: p corr = 0.042). None of the markers was significantly associated with acute and chronic GvHD after correction. More than half of investigated proteins significantly differed between the samples from aHSCT patients and healthy control subjects as a consequence of the "cytokine storm" after aHSCT. Comparisons of patient's subgroups based on specific biological/clinical parameters revealed much less evident differences; nevertheless, we nominated several markers associated with the level of donor/recipient HLA match and post-transplant chimerism.

Phototoxicity of essential oils intended for cosmetic use.

The aim of this study, linked-up with a previous study on bergamot oils, was the evaluation of phototoxic potential of essential oils (orange, lemon and Litsea cubeba), used as cosmetic ingredients. The applied tiered testing strategy included chemical analysis of the substances (by means of capillary gas chromatography/mass spectrometry), in vitro 3T3 NRU phototoxicity test and EpiDerm™ skin phototoxicity test. In order to clarify the situation in man, the highest non-phototoxic/non-cytotoxic concentrations and concentrations 10 x lower (safety factor 10) were tested xin vivo by means of human skin photopatch test in a limited group of human volunteers. The study revealed, that phototoxicity of the essential oils was dependent on the content of photoactive components and the solvent used. The highest non-phototoxic concentrations obtained by the skin model assay proved to be a useful starting point for subsequent confirmatory human photopatch test aimed to identify safe concentration for human use. However, the highest non-phototoxic concentration obtained in the skin model assay cannot be applied directly for human practice (3 of 8 tested oils evoked a phototoxic reaction). A safety factor of 10 should be applied for extrapolation of experimental data from the skin model assay to man.