Beata Grygalewicz

Chordoma, a rare sarcoma of notochordal origin, exhibits slow growth and local aggressiveness. While copy-number (CN) events are recognized as key chordoma drivers, no comprehensive classification, based on CN, has yet been developed. Here, we establish a robust, reproducible genomic subtyping of chordoma, based on CN events. Two independent skull base chordoma cohorts (N=32,N=71) were analyzed, utilizing distinct analytical platforms, DNA methylation microarrays and whole-genome sequencing, both controlled for B-allele frequencies. Samples were clustered using unsupervised hierarchical methods. The CN events defined four consistent molecular clusters across both cohorts: C1 (CN-stable), C9 (chromosomal losses, especially of chr9/ CDKN2A ), C7 (chr7 gain), and C2 (gains of chr2 and chr7). The findings were validated in fluorescence in situ hybridization (FISH) with concordance of 84-89%. The CN clusters explain 31-33% of the RNA-sequencing transcriptional variance. Moreover, the C2 cluster showed up-regulation of Sonic Hedgehog signaling and clusters C2 and C9 were enriched in cell-cycle-related genes. The proposed CN clusters correlate with existing chordoma classificators e.g. chromosomal instability (CIN), mutation burden, immune score, and methylation clusters. Furthermore, comparison with over 2,000 sarcomas highlighted CN patterns more common in chordoma (i.e. chr1q, chr2, chr7 gains and chr1p, chr3, chr9, chr10, chr13, chr14, chr18 losses) but also revealed shared aberrations, e.g. chr22 loss shared with Gastrointestinal Stromal Tumours (GISTs). This study provides a unifying classification for skull base chordoma, linking distinct genomic architectures to specific transcriptional programs and potential therapeutic vulnerabilities.

Recent progress in understanding the etiopathogenesis of lymphoid neoplasms, together with advances in treatment strategies, has led to a revision of diagnostic algorithms. The 5th edition of the WHO Classification of Lymphoid Neoplasms introduced new entities among mature B-cell lymphomas, such as diffuse large B-cell lymphoma/high-grade B-cell lymphoma (DLBCL/HGBCL) with MYC and BCL2 rearrangements, and high-grade B-cell lymphoma with 11q aberration, as well as precursor B-cell leukemia/lymphoma with TCF3::HLF or ETV6::RUNX1-like fusions. These updates necessitate modifications to standard cytogenetic testing procedures. In addition, recurrent chromosomal abnormalities not yet included in the WHO classification, such as MYC rearrangement in HGBCL with 11q aberration, may contribute to redefining existing entities. Another significant development is the adoption of the mSMART 4.0 classification for prognostic stratification in plasma cell myeloma. The clinical importance of cytogenetic markers continues to evolve — an example being the use of venetoclax in patients with t(11;14), which has further highlighted the prognostic relevance of this translocation. Currently, standard cytogenetic diagnostics rely on conventional karyotyping and fluorescence in situ hybridization (FISH). Despite their usefulness, both methods have notable limitations. Optical Genome Mapping (OGM) is an emerging technology capable of detecting both numerical and structural chromosomal alterations, as well as gene fusions, within a single assay. With a resolution approximately 10,000 times higher than that of karyotyping, OGM can identify cryptic aberrations and small clones that traditional techniques may miss. Although still undergoing validation, comparative analyses across karyotyping, FISH, and OGM may soon confirm the future diagnostic role of OGM in lymphoid malignancies. Keywords: cytogenetics lymphoma cytogenetic diagnostic algorithms optical genome mapping

Chromosome number abnormalities is one of the hallmarks of cancer. DNA copy number alterations (CNA) are studied using various genome-wide methods. In our

High-grade B-cell lymphoma with 11q aberration (HGBCL-11q) is a rare germi-nal centre lymphoma characterised by a typical gain/loss pattern on chromo-some 11q but without MYC translocation. It shares some features with Burkitt lymphoma (BL), HGBCLs and germinal centre-derived diffuse large B-cell lym-phoma, not otherwise specified (GCB-DLBCL-NOS). Since microRNA expression in HGBCL-11q remains unknown, we aimed to identify and compare the mi-croRNA expression profiles in HGBCL-11q, BL and in GCB-DLBCL-NOS. Next-generation sequencing (NGS)-based microRNA profiling of HGBCL-11q (n = 6), BL (n = 8), and GCB-DLBCL-NOS without (n = 3) and with MYC rearrange-ment (MYC-R) (n = 7) was performed. We identified sets of 39, 64, and 49 mi-croRNAs differentiating HGBCL-11q from BL, and from GCB-DLBCL-NOS without MYC-R, respectively. The expression levels of miR-223-3p, miR-193b-3p, miR-29b-3p, and miR-146a-5p consistently differentiated HGBCL-11q from both BL, GCB-DLBCL-NOS without MYC-R. In addition, HGBCL-11q presented greater heterogeneity in microRNA expression than BL. The expression profile of MYC-regulated microRNAs differed in HGBCL-11q and in BL, while also clearly distinguishing HGBCL-11q and BL from GCB-DLBCL-NOS. The microRNA pro-file of HGBCL-11q differs from those of BL and GCB-DLBCL-NOS, exhibiting greater heterogeneity compared to BL. The microRNA profile further supports that HGBCL-11q is a distinct subtype of B-cell lymphoma.

(1) Background: The aim of our study was the complex assessment of WT1 variants and their expression in relation to chromosomal changes and molecular prognostic markers in acute myeloid leukemia (AML). It is the first multidimensional study in Polish AML patients; (2) Methods: Bone marrow aspirates of 90 AML patients were used for cell cultures (banding techniques and fluorescence in situ hybridization), and to isolate DNA (WT1 genotyping, array comparative genomic hybridization), and RNA (WT1 expression). Peripheral blood samples from 100 healthy blood donors were used to analyze WT1 rs16754; (3) Results: Allele frequency and distribution of WT1 variant rs16754 (A;G) did not differ significantly among AML patients and controls. Higher expression of WT1 gene was observed in AA genotype (of rs16754) in comparison with GA or GG genotypes—10,556.7 vs. 25,836.5 copies (p = 0.01), respectively. WT1 mutations were more frequent in AML patients under 65 years of age (p < 0.0001) and affected relapse-free survival (RFS). The presence of NPM1 or CEBPA mutations decreased the risk of WT1 mutation presence, odds ratio (OR) = 0.11, 95% CI 0.02–0.46, p = 0.002 or OR = 0.05, 95% CI 0.006–0.46, p = 0.002, respectively. We observed significantly higher WT1 expression in AML CD34+ vs. CD34−, −20,985 vs. 8304 (p = 0.039), respectively. The difference in WT1 expression between patients with normal and abnormal karyotype was statistically insignificant; (4) Conclusions: WT1 gene expression and its rs16754 variant at diagnosis did not affect AML outcome. WT1 mutation may affect RFS in AML.

Background: MYC, BCL2 and BCL6 are known to be altered in high grade B-cell lymphoma (HGBL). Double/triple-hit lymphomas (D/THLs) are characterized by chromosomal rearrangementsof MYC, BCL2 and/or BCL6. D/THLs have been included in the updated 2016 WHO classification, as a new category of "High grade B-cell lymphoma with rearrangements" (HGBL-R) or Diffuse Large B-cell lymphoma (DLBCL) entity, depending on morphology/cytogenetic features. BCL2 protein is expressed in a much higher proportion of DLBCL and HGBL, not otherwise specified (HGBL,NOS), and is often associated with a concomitant expression of MYC and BCL6. Most of HGBLs do not carry BCL2/MYC/BCL6 rearrangements and are referred to as "double/triple-expressor lymphomas" (D/TELs). D/THLs patients usually progress rapidly, are resistant to R-CHOP immunochemotherapy, and have very poor prognosis. D/TELs also have a worse outcome than other DLBCL,NOS. BCL2 overexpression is observed in both germinal centre B-cell-like (GCB) and non-GCB HGBL. We have previously described a diagnostic algorithm for subtypes of HGBL based on flow-cytometry immunphenotyping (FCM) with CD38 overexpression, which correlates with MYC rearrangement assessed in fine needle aspiration biopsy (FNAB) samples. Here, we propose that patients with HGBL/DLBCL,NOS, with BCL2 overexpression, especially those with D/THLs and D/TELs, may benefit from DA-EPOCH-R (dose-adjusted cyclophosphamide, doxorubicin, etoposide, vincristine, prednisone with rituximab) treatment. Methods: 30 patients (male/female 18/12, median age/range 51/35-76/) diagnosed with DLBCL,NOS (13 pts), HGBL-R (11 pts), HGBL,NOS (2 pts), primary mediastinal B-cell lymphoma - PMBL (3 pts) and DLBCL,leg type (1 pt), based on 2016 WHO classification, were treated with DA-EPOCH-R as first-line therapybetween January 2015 - July 2016. Clinical stage III or IV and IPI 3 or more were found in 27 pts (90%) and 22 pts (73%), respectively. All cases were evaluated by histopathological/immunohistochemical/flow-cytometry examination (HP/IHC/FCM), with panels of antibodies, including also CD5/CD10/CD20/CD38/BCL2/BCL6/MYC. In most cases, MYC, BCL2, BCL6 and, in case of relapse, also TP53 status was evaluated by karyotyping (CC) and FISH. Results: Considering the cell-of-origin, there were 20 pts with GCB, 3 non-GCB, 4 CD5+ and 3 PMBL. In addition, 15 pts were DEL, 12 - TEL, 3 - one-expressor lymphoma, 8 - D/THL, 12 - one-hit lymphoma and 10 - non-hit lymphoma, mostly with BCL2 overexpression. Karyotype was successfully assessed in 70%, while BCL2 overexpression was found in 83% of HGBL pts. MYC, BCL2, and BCL6 rearrangement was found in 48%, 35% and 21%, respectively. In 50%, 46% and 54% of cases there was an increase in copy number/amplification of MYC, BCL2 and BCL6, respectively. In 15 evaluable pts., overall and complete response was 80% and 53%, respectively. Median follow-up of HGBL pts treated with DA-EPOCH-R was 5 months (range 1-17), and the probability of one year overall survival was 91%, 95% C.I. (80%,100%). Progression free survival at 1 year was 62%, 95C.I. (36%,90%). 3 of 4 patients with progressive disease had TP53 deletion. The main toxicity was pancytopenia with neutropenia grade 3 or more in 24 pts (80%). Treatment-related mortality due to septic shock occurred in 2 patients (7%). Conclusions: DA-EPOCH-R regimen shows a promising activity considering D/THL and D/TEL-associated drug resistance. DA-EPOCH-R regimen seems to overcome drug resistance associated with BCL2/MYC/BCL6 overexpression, but not with TP53 deletion. Combining HP/IHC with FNAB/FCM/CC/FISH is a reliable method for D/THL and D/TEL diagnosis but the most sensitive method for fast MYC/BCL2 rearrangement assessment in DHL is FNAB/FCM CD38 and BCL2 overexpression.