Chromosomal Copy Number Alterations Research Articles

Phenotypic, genomic, and transcriptomic heterogeneity in a pancreatic cancer cell line.

To evaluate the suitability of the MIA PaCa-2 cell line for studying pancreatic cancer intratumor heterogeneity, we aim to further characterize the nature of MIA PaCa-2 cells' phenotypic, genomic, and transcriptomic heterogeneity. MIA PaCa-2 single-cell clones were established through flow cytometry. For the phenotypic study, we quantified the cellular morphology, proliferation rate, migration potential, and drug sensitivity of the clones. The chromosome copy number and transcriptomic profiles were quantified using SNPa and RNA-seq, respectively. Four MIA PaCa-2 clones showed distinctive phenotypes, with differences in cellular morphology, proliferation rate, migration potential, and drug sensitivity. We also observed a degree of genomic variations between these clones in form of chromosome copy number alterations and single nucleotide variations, suggesting the genomic heterogeneity of the population, and the intrinsic genomic instability of MIA PaCa-2 cells. Lastly, transcriptomic analysis of the clones also revealed gene expression profile differences between the clones, including the uniquely regulated ITGAV, which dictates the morphology of MIA PaCa-2 clones. MIA PaCa-2 is comprised of cells with distinctive phenotypes, heterogeneous genomes, and differential transcriptomic profiles, suggesting its suitability as a model to study the underlying mechanisms behind pancreatic cancer heterogeneity.

Haploinsufficiency of phosphodiesterase 10A activates PI3K/AKT signaling independent of PTEN to induce an aggressive glioma phenotype.

Glioblastoma is universally fatal and characterized by frequent chromosomal copy number alterations harboring oncogenes and tumor suppressors. In this study, we analyzed exome-wide human glioblastoma copy number data and found that cytoband 6q27 is an independent poor prognostic marker in multiple data sets. We then combined CRISPR-Cas9 data, human spatial transcriptomic data, and human and mouse RNA sequencing data to nominate PDE10A as a potential haploinsufficient tumor suppressor in the 6q27 region. Mouse glioblastoma modeling using the RCAS/tv-a system confirmed that Pde10a suppression induced an aggressive glioma phenotype in vivo and resistance to temozolomide and radiation therapy in vitro. Cell culture analysis showed that decreased Pde10a expression led to increased PI3K/AKT signaling in a Pten-independent manner, a response blocked by selective PI3K inhibitors. Single-nucleus RNA sequencing from our mouse gliomas in vivo, in combination with cell culture validation, further showed that Pde10a suppression was associated with a proneural-to-mesenchymal transition that exhibited increased cell adhesion and decreased cell migration. Our results indicate that glioblastoma patients harboring PDE10A loss have worse outcomes and potentially increased sensitivity to PI3K inhibition.

Abstract 1467: Contribution of estrogen metabolites to never-smoking lung cancer

Abstract There has been a consistent rise in the incidence of non-small cell lung cancer (NSCLC) among individuals who have never smoked. Remarkably, over 50% of diagnosed female cases and 15-20% of male cases are never-smokers. Notably, NSCLC in never-smokers exhibits distinctive clinical and pathological features, notably a higher incidence of tumors with EGFR mutations, setting it apart from its counterpart in smokers. Despite the improved disease-free survival observed with EGFR-tyrosine kinase inhibitors, eventual relapse and limited responsiveness to immunotherapy are common, underscoring the urgency to comprehend the molecular mechanisms driving the escalating prevalence of NSCLC in never-smokers and develop targeted preventive and interceptive therapeutic strategies. The preponderance of females among NSCLC patients who never smoked has prompted an exploration into the potential contribution of estrogen to lung tumorigenesis. In contrast to prevailing research focused on estrogen receptor-mediated signaling, our investigations have yielded compelling evidence supporting the involvement of estrogen metabolism in lung carcinogenesis among never-smokers. This group is the first to report that estrogen is metabolized extensively in both mouse and human lungs, resulting in the generation of various derivatives, including the potential carcinogen 4-hydroxyestrogen (4-OHE). Notably, recent findings from our laboratory indicate that prolonged exposure of nonneoplastic human bronchial epithelial cells to 17β estradiol or 4-OHE, at concentrations approximating physiological levels, induces the accumulation of double-strand DNA breaks and cellular transformation. A comprehensive analysis was performed to further elucidate the mechanisms underlying the transformation process. Isolated transformed clones obtained after 9, 18, and 22 wks of exposure to 4-OHE were subjected to karyotyping, F.I.S.H., and RNA and exome sequencing. A longitudinal progression of aberrant chromosomal rearrangements and copy number alterations was observed, that increased with time of 4-OHE exposure. In addition, RNA-Seq analyses revealed the epithelial-mesenchymal transition pathway was highly enriched at the early timepoint (9 wks), while replicative stress-related signaling pathways were induced at all timepoints. To determine if the differentially expressed genes were also dysregulated in clinical lung cancer cases, TCGA lung adenocarcinoma (LUAD) data were examined. Interestingly, many of the genes upregulated after estrogen exposure were similarly overexpressed in the LUAD samples and often associated with a worse prognosis. In conclusion, our data support the role of estrogen metabolites in promoting lung cancer among never-smokers. (Supported by CA217161 and generous contributions from the Hellendall Family Foundation, Gregory G. Lawton and the Timothy and Aurora Hughes Cancer Research Fund.) Citation Format: Mitchell Cheung, Lisa A. Vanderveer, Daniel Krzizike, J. Nicholas Bodor, Joseph Treat, Joseph R. Testa, Margie L. Clapper. Contribution of estrogen metabolites to never-smoking lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1467.

Assessment of Y chromosome copy number alterations in non-neoplastic and neoplastic leukocytes of male dogs

The loss of the Y chromosome (ChrY), also known as LOY, is a common genetic alteration observed in men. It occurs in non-neoplastic cells as an age-related change as well as in neoplastic cells of various cancer types. While well-documented in humans, LOY has not been extensively studied in non-human mammals. In this study, we developed simple digital PCR-based assays to assess the copy number of ChrY relative to the X chromosome (ChrX) and chromosome 8 (Chr8) to evaluate ChrY numerical alterations in male canine DNA specimens. Using these assays, we analyzed non-neoplastic leukocytes from 162 male dogs without hematopoietic neoplasia to investigate the occurrence of age-related LOY in non-neoplastic leukocytes. Additionally, we examined 101 tumor DNA specimens obtained from male dogs diagnosed with various types of lymphoma and leukemia to determine whether copy number alterations of the ChrY occur in canine hematopoietic cancers. Analysis of the 162 non-neoplastic leukocyte DNA specimens from male dogs of varying ages revealed a consistent ∼1:1 ChrY:ChrX ratio. This suggests that age-related LOY in non-neoplastic leukocytes is rare or absent in dogs. Conversely, a decreased or increased ChrY:ChrX ratio was detected in canine neoplastic leukocytes at varying frequencies across different canine hematopoietic malignancies (P = 0.01, Fisher's exact test). Notably, a higher incidence of LOY was observed in more aggressive cancer types. To determine if this relative LOY to ChrX was caused by changes in ChrY or ChrX, we further analyzed their relative copy numbers using Chr8 as a reference. Loss of ChrX relative to Chr8 was found in 21% (9/41) of B-cell lymphomas and 6% (1/18) of non-T-zone/high-grade T-cell lymphomas. In contrast, a subset (29%, 4/14) of T-cell chronic lymphocytic leukemia showed gain of ChrX relative to Chr8. Notably, no relative LOY to Chr8 was detected indolent hematopoietic cancers such as T-zone lymphoma (0/9) and chronic lymphocytic leukemia of B-cell (0/11) and T-cell origins (0/14). However, relative LOY to Chr8 was present in more aggressive canine hematopoietic cancers, with incidences of 24% (10/41) in B-cell lymphoma, 44% (8/18) in non-T-zone/high-grade T-cell lymphoma, and 75% (6/8) in acute leukemia. This study highlights both similarities and differences in LOY between human and canine non-neoplastic and neoplastic leukocytes. It underscores the need for further research into the role of ChrY in canine health and disease, as well as the significance of LOY across various species.

Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns.

Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.

10171-MPC-13 IDH-WILDTYPE LOWER-GRADE ASTROCYTOMA

Abstract BACKGROUND AND PURPOSE In the WHO 2021 classification, glioblastoma is limited to IDH-wildtype and is diagnosed when microvascular proliferation and necrosis are present. Furthermore, even in the presence of morphologically low-grade findings, the diagnosis of glioblastoma is made if there is either EGFR gene amplification, TERT promoter mutation, or +7/-10 chromosome copy number alterations. Therefore, we investigated IDH wild-type lower-grade astrocytoma. CASES 10 patients were included in this study. Sanger sequencing was performed for TERT promoter mutations, and MLPA was further implemented using probes for EGFR and PTEN genes in TERT wild-type cases. The threshold values for copy number change were homozygous deletion (x≤0.4), loss of heterozygosity (LOH) (0.4<x≤0.7), gain (1.3≤x<2.0), and amplification (x≥2.0). EGFR gain and PTEN LOH were used as surrogate markers for +7/-10 chromosome copy-number alterations. RESULTS Seven of these patients were diagnosed with glioblastoma, IDH-wildtype with a TERT promoter mutation. All three did not meet the diagnostic criteria for glioblastoma. All patients received temozolomide combination radiotherapy and maintenance temozolomide therapy. The median survival time of seven glioblastoma, IDH-wildtype patients was 616 days. Two patients who did not meet the diagnostic criteria for glioblastoma survived 510 and 583 days after initial surgery, respectively, and one patient was given the best supportive care policy at 518 days. Genetic analysis of all three cases showed TP53 LOH. CONCLUSION It was suggested that tumors with IDH wild-type low-grade astrocytoma that do not meet the diagnostic criteria for glioblastoma may have a poor prognosis. Although TP53 LOH was common, further investigation of specific genetic abnormalities is needed, and the classification and treatment strategy of these disease groups may be a challenge in the future.

P16 Immunohistochemistry as a Screening Tool for Homozygous CDKN2A Deletions in CNS Tumors.

The 2021 World Health Organization classification of tumors of the central nervous system emphasizes the significance of molecular parameters for an integrated diagnosis. Homozygous deletion of cyclin-dependent kinase inhibitor 2a (CDKN2A) has been associated with an adverse prognosis in IDH -mutant gliomas, supratentorial ependymomas, meningiomas, and MPNST. In this study, we examined the value of p16 protein immunohistochemistry as a rapid and cost-effective screening tool for a homozygous CDKN2A deletion. Genetic analyses for CDKN2A in 30 pleomorphic xanthoastrocytomas, 32 IDH -wild-type high-grade gliomas, 40 supratentorial ependymomas with ZFTA-RELA gene fusion, 21 IDH-mutant astrocytomas, and 24 meningiomas were performed mainly by a molecular inversion probe assay, a high-resolution, quantitative technology for the assessment of chromosomal copy number alterations. Immunohistochemistry for p16 proved to have a high positive predictive value (range 90% to 100%) and an overall low negative predictive value (range 22% to 93%) for a homozygous CDKN2A deletion. In a setting where molecular testing is limited for cost and time reasons, p16 immunohistochemistry serves as a useful and rapid screening tool for identifying cases that should be subjected to further molecular testing for CDKN2A deletions.

Analytical and Clinical Validation of Duoseq, a Novel Assay for Rapid, on-Site Clinical DNA and RNA Sequencing of Hematologic Malignancies

Introduction: Next generation sequencing (NGS) has become a critical component of the workup of malignancies. NGS can provide important diagnostic information including mutations, chromosomal copy number alterations and translocations (from DNAseq) as well as gene expression and fusions (from RNAseq). Incorporation of NGS in the clinic remains difficult. DNAseq and RNAseq remain distinct assays with challenging bioinformatics and turnaround times (TAT) that can last several weeks. Duoseq is a novel assay for combined DNA- and RNAseq in a single workflow that detects single nucleotide variants (SNVs), insertions/deletions (indels), splice site variants (SSVs), structural variants (SVs) and Epstein-Barr virus (EBV) status. Initially implemented for hematologic malignancies, Duoseq assesses nearly all known gene drivers (N=475) and is compatible with both fresh-frozen and formalin-fixed, paraffin-embedded (FFPE) tissues. It is available as a reagent kit and includes cloud-based bioinformatics, enabling any clinical lab with an Illumina sequencer to perform NGS in-house with a TAT of 2-3 days. Methods/Results: Duoseq was validated for concordance with commercial DNA- and RNAseq kits (New England BioLabs (NEB)). Sequencing libraries were prepared on DNA alone, RNA alone and total nucleic acid (TNA) from cell lines in accordance with kit protocols and captured using the Duoseq panel. Results were equivalent between Duoseq and individual (NEB) library preparations with nearly complete concordance in DNA variants (99.4%, P<10 -6) and RNA expression (R 2=0.97, P<10 -6). Separately, copy number alteration calls across 42 cases had high concordance between Duoseq and Affymetrix array approaches (P<10 -6). Analytical validation was performed at two CLIA laboratories to establish assay precision and reproducibility, sensitivity (LoD), and specificity. Analytical validation was performed on well characterized and control samples that were selected to harbor an array of clinically important variants at known allele frequencies. Precision and reproducibility testing confirmed Duoseq's ability to produce accurate results independent of external variables. We tested inter-lab reproducibility, intra-day and inter-day repeatability and technician-to-technician reproducibility. In each case, Duoseq achieved >98% precision and reproducibility for each variant class (SNVs, indels/SSVs and SVs). We confirmed the LoD using TNA from the same samples diluted in normal TNA to create 3-point curves that spanned our expected LoD. We confirmed the assay to be 100% accurate down to ≥5% mutant allele fraction (MAF) for SNVs, ≥10% MAF for indels/SSVs, and ≥20% tumor purity for SVs. Specificity was additionally assessed by including normal cell lines in each run to determine the incidence of cross-contamination indicated by false positives. Analytical specificity was 100%, indicating no instances of sample cross-contamination. We assessed the clinical accuracy of Duoseq using FFPE myeloid and lymphoid specimens (N=153) collected at both laboratories and characterized via orthogonal methods including Foundation Medicine (SNVs and indels/SSVs), fluorescent in situ hybridization (translocations) and in situ hybridization (EBV status). Duoseq achieved a positive predictive agreement of 98% for SNVs (N=139), 96% for indels/SSVs (N=55), 95% for translocations (N=282), and 100% for EBV status (N=58). Cell of origin (COO) for diffuse large B cell lymphoma (n=42) using Hans criteria and had high concordance (90%) with the COO calls rendered from Duoseq expression data. Given Duoseq's array of measurements and short TAT, we plan a potential application in “match” clinical trials where patients are enrolled in treatment arms based on molecular profiling. In ongoing work to test a potential trial workflow, we enrolled four institutions that will provide cases to a central site for pathology review and molecular profiling enabling trial arm assignment. Specimen enrollment is anticipated to be completed to allow for results to be presented at the meeting. Conclusions: Duoseq is comparable to current methods and provides a cost and time effective option for library preparation.The large gene panel enables testing a broad range of clinical features in a single assay, including genes required for diagnosis and prognostication in heme malignancies. These results support clinical use of Duoseq.

Optical Genomic Mapping Provides Unique Findings in Various Types of Myeloid Neoplasms

Introduction: Cytogenomic abnormalities are integral to disease classification, risk stratification, and treatment plans for patients with myeloid neoplasms (MNs). Standard cytogenetic (SCG) techniques, including chromosomal analysis (karyotyping) and fluorescence in situ hybridization (FISH), both carry limitations in detecting certain cytogenomic abnormalities, such as chromoanagenesis, a genomic catastrophe that results in extensive chromosomal rearrangements and copy number alterations. Optical genomic mapping (OGM) is a novel, non-sequencing technique that allows for high-resolution genome wide detection of all classes of structural variants (SVs) and copy number variants (CNVs). This study aimed to investigate cytogenomic alterations across different types of MNs and evaluate the added value of OGM alongside SCG in this context. Materials and methods: OGM was performed using Saphyr from Bionano Genomics (San Diego, USA) on blood or bone marrow from 146 patients diagnosed with various types of MNs over a 9-month period. All patients had karyotype and/or FISH results available. Cases were considered concordant if OGM and SCG both showed normal results or essentially identical cytogenetic abnormalities. Cases were summarized under ‘SCG only’ or ‘OGM only’ if abnormalities were detected by only one assay. Only Tier 1 (pathogenic) and Tier 2 (likely pathogenic) variants were included for a comparison purpose. Abnormalities leading to changes in disease classification, risk stratification, and/or potential patient management were considered as clinically significant. Of note: AML with PML::RARA, RUNX1T1::RUNX1 or MYH11::CBFB rearrangement identified during the fast FISH screen were not included in this study. Results: This study cohort included 90 AML, 26 myelodysplastic syndrome (MDS), 18 myeloproliferative neoplasms (MPN) and 11 MDS/MPN. Overall, 44 (30%) patients showed normal results and 47 (32%) patients showed completely matched cytogenomic abnormalities by OGM and SCG, the remaining 54 (37%) cases showed abnormalities detected by only one assay. Within these 54 cases there were 65 abnormalities detected by only one modality, 11 by SCG only and 54 by OGM only ( Table 1). Of them, 42 were clinically significant: 4 detected by SCG only (in 4 patients) and 38 by OGM only (in 37 patients) ( Table 2). The abnormalities that were detected by SCG but not by OGM were mainly clones or subclones of small (<20%) clonal size, which were below the limit of OGM detection, except one case with tetraploidy in a large clone (65%). The abnormalities detected by OGM but not by SCG mainly included chromoanagenesis (n=17), KMT2A partial tandem duplications (PTD, n=6), chromosomal /gene rearrangement (-R), thirteen being clinically significant: MECOM-R(n=4) , KMT2A-R(n=2) , JAK2-R (n=2) and 5 others in a single case each. Among the various types of MNs, OGM provided additional clinically relevant cytogenomic information in 28 (31%) patients with AML, 8 (31%) patients with MDS, 2 (18%) patients with MDS/MPN, and none (0%) with MPN. Conclusions: Overall, the cytogenomic results completely matched between OGM and SCG in 62% of patients with MNs. The high concordance results seen in MPN suggests OGM may not provide significant additional insight in this setting. OGM identified additional clinically relevant abnormalities in approximately 26% of patients in this cohort. The abnormalities detected by OGM, notably included chromoanagenesis and KMT2A PTDs, were found to occur more frequently in AML and MDS. These abnormalities, undetectable by SCG, are crucial to identify due to their association with significantly poorer prognosis. Additionally, certain abnormalities such as MECOM-R, KMT2A-R, and JAK2-R could potentially guide different therapeutic strategies.

Can Whole Genome and Whole Transcriptome Sequencing Replace Standard Procedures in CLL Diagnostics?

Background: The advantages of genome-wide sequencing approaches over conventional methods in CLL diagnostics are a matter of debate and exact guidelines for the application of next-generation sequencing in a diagnostic context are currently missing. Aim: Compare the accuracy of whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) in determining the presence of point mutations, IGHV mutational status (IGHVms), and chromosomal aberrations to conventional procedures in a clinical setting. Patients and Methods: The cohort comprised 317 CLL patients. Diagnosis was established following WHO guidelines. WGS (100x, 2x151bp) and WTS (5x10 7 reads, 2x101bp) data were generated on NovaSeq instruments. For routine diagnostics, sequencing was carried out by Sanger or targeted panel sequencing (1500x, 2x101bp). Chromosome banding analysis (CBA) and FISH were available for 231 patients. WGS data were analyzed for chromosomal aberrations and copy number alterations using Manta and GATK. IGHVms was determined by Sanger sequencing and/or fragment analysis for 248 patients. Analysis of IGHVms was carried out using IgCaller (WGS) and MiXCR (WTS). Results: Comparing copy number variants (CNV) and balanced structural variants (SV) between CBA and WGS revealed a high concordance. In detail, 297 CNV were detected by both techniques while 32 and 52 were detected only by CBA (small subclones) or by WGS, respectively. 33 balanced SV were detected by both while 8 and 3 were detected only by CBA and WGS, respectively. A complex karyotype (≥ 3 abnormalities) was observed by both techniques in 55 cases, while 5 and 10 cases were categorized as complex by CBA only or WGS only, respectively. Survival analysis of cases with 3 to 5 chromosomal aberrations predicted by routine or WGS revealed similar hazard ratios that were positively correlated with the number of aberrations. For comparing SNV calls from routine and WGS, we investigated genes with validated mutations in at least ten patients in routine diagnostics. This criterion was met by ATM, MYD88, NOTCH1, SF3B1, and TP53. We observed high concordance between routine and WGS data ( ATM 99.4%, MYD88 100%, NOTCH1 97.8%, SF3B1 100%, TP53 99.1%). Five mutations were detected in routine only and three in WGS only (routine only/WGS only: ATM 1/0, MYD88 0/0, NOTCH1 2/2, SF3B1 0/0, TP53 2/1) and found to be caused by low variant allele frequency (5 miscalls, VAF < 5%) and/or filtering out of low quality variants (5 cases). IGHV rearrangements analyzed by Sanger (248 patients), WGS (242/248 patients), and WTS (236/248 patients) data were compared for matches in the rearranged IGHV. IGHVms calling employed 98% of sequence identity as cutoff. Calling the rearranged IGHV was concordant in 93%, 95%, and 92% when comparing Sanger/MiXCR, Sanger/IgCaller, and MiXCR/IgCaller calls, respectively. For IGHVms, the corresponding percentages of concordance were 91%, 86%, and 83%. Mismatches in calling the IGHVms were found in borderline cases. Detection of stereotyped IGHV was fully concordant. In addition to reliably replicating routine results, we find that WGS/WTS data can also outperform routine procedures. In our hands, the highest hazard ratio (4.94) in survival analysis distinguishing mutated CLL (mCLL) from unmutated CLL (uCLL) is observed using WTS for IGHVms determination and 97% sequence identity as cutoff (208 patients, up to 30 years follow up). Survival for borderline cases (97.00-97.99% sequence identity) was statistically indistinguishable from uCLL in routine diagnostics as well as WGS/WTS. Furthermore, using WGS, CN-LOH regions and deletions below the detection limit of CBA (10 MB) can be detected. We observed such regions in samples with mutated TP53 (5 CN-LOH), ATM (2 CN-LOH, 4 deletions < 10MB), and deletions of minimally overlapping region chr8:21,700,000-23,600,000, whose loss was associated with poor survival (3/29 deletions < 3.1 MB). Conclusions: WGS/WTS data reliably replicate results obtained by standard procedures in a diagnostic setting. Sequencing offers advantages such as a unified workflow, better sensitivity for small deletions, CN-LOH detection, genome-wide analyses of coding and non-coding mutations, among others. Challenges of short read based sequencing regard the detection limit for point mutations and specificity/sensitivity in detecting chromosomal aberrations.

The Cancer Genome Atlas for uveal melanoma is predictive of patient outcomes

Uveal melanoma (UM) is the most common primary eye malignancy. Despite excellent local tumor rates, UM is a life-threatening disease with moderate systemic metastatic rates. In the past, certain clinical features were shown to be predictive of patient prognosis, including tumor thickness, tumor diameter, ciliary body involvement, and histopathologic factors. Genetic markers have lately been used to predict patient outcomes. The Cancer Genome Atlas (TCGA) is a worldwide effort developed by the National Cancer Institute and the National Human Genome Research Institute to study numerous mutations in various cancer types. TCGA has explored chromosome copy number alterations in UM, messenger RNA, micro-RNA, and long noncoding RNA expression levels and established four prognostic classes: group A (chromosome 3 and 8 disomy), group B (chromosome 3 disomy and 8q gain), group C (chromosome 3 monosomy and/or 8q gain), and group D (chromosome 3 monosomy and multiple 8q gains). Multiple studies have validated TCGA classification and have reported that it has been highly predictive of UM metastasis and patient survival.

SDPS-27 P16 IMMUNOHISTOCHEMISTRY AS A SCREENING TOOL FOR HOMOZYGOUS CDKN2A DELETIONS IN GLIAL TUMORS

Abstract The 2021 WHO classification of tumors of the central nervous system emphasizes the significance of molecular parameters for an integrated diagnosis. Homozygous deletion of CDKN2A has been associated with an adverse prognosis in IDH-mutant gliomas, supratentorial ependymomas, meningiomas, and MPNST. In this study, we examined the value of p16 protein immunohistochemistry as a screening tool for predicting a homozygous CDKN2A deletion. Genetic analyses for CDKN2A deletion in 30 pleomorphic xanthoastrocytomas, 32 IDH-wildtype high-grade gliomas and 40 supratentorial ependymomas with ZFTA-RELA gene fusion, 10 IDH-mutant astrocytomas, and 10 meningiomas were performed either by a molecular inversion probe assay (MIP), a high-resolution, quantitative technology for the accurate, genome-wide assessment of chromosomal copy number alterations, or by 850k methylation profile-deduced copy number analysis or multiplex ligation-dependent probe amplification analysis. In pleomorphic xanthoastrocytomas and IDH-wildtype high-grade gliomas, p16 immunohistochemistry showed high specificity (100% both), moderate sensitivity (76% and 56%), and a high positive predictive value (PPV; 100% both) for the presence of a homozygous CDKN2A deletion. In supratentorial ependymoma with ZFTA-RELA gene fusion, immunohistochemistry for p16 protein was highly sensitive and specific (90% and 97%) for a homozygous CDKN2A deletion and exhibited a high PPV and NPV (90% and 97%, respectively). For lower-grade meningioma, no correlation between the p16 immunohistochemical status and the CDKN2A deletion status was possible. Therefore, p16 protein expression detected by immunohistochemistry is a useful prescreening tool for detecting a homozygous CDKN2A deletion in glial tumors.

The Clinical Significance of Genetic Variation in Ovarian Cancer.

Genetic variation is a well-known contributor to the onset and progression of cancer. The goal of this study is to provide a comprehensive examination of the nucleotide and chromosomal variation associated with the onset and progression of serous ovarian cancer. Using a variety of computational and statistical methods, we examine the exome sequence profiles of genetic variants present in the primary tumors of 432 ovarian cancer patient samples to compute: (1) the tumor mutational burden for all genes and (2) the chromosomal copy number alterations associated with the onset/progression of ovarian cancer. Tumor mutational burden is reduced in the late vs. early stages, with the highest levels being associated with loss-of-function mutations in DNA-repair genes. Nucleotide variation and copy number alterations associated with known cancer driver genes are selectively favored over ovarian cancer development. The results indicate that genetic variation is a significant contributor to the onset and progression of ovarian cancer. The measurement of the relative levels of genetic variation associated with individual ovarian cancer patient tumors may be a clinically valuable predictor of potential tumor aggressiveness and resistance to chemotherapy. Tumors found to be associated with high levels of genetic variation may help in the clinical identification of high-risk ovarian cancer patients who could benefit from more frequent monitoring.

Primary papillary epithelial tumor of the sella and posterior pituitary tumor show similar (epi)genetic features and constitute a single neuro-oncological entity.

"Primary papillary epithelial tumor of the sella (PPETS)" is a recently described rare tumor entity of the central nervous system (CNS) with stereotypic location in the sella. Comprehensive molecular investigations and epigenetic profiles of PPETS have not been performed to date. We report a comprehensive clinical, histopathologic, and molecular assessment of 5 PPETS cases in comparison with a cohort composed of 7 choroid plexus papilloma (CPP), 7 central neurocytoma (CN), 15 posterior pituitary tumor (PPT) including 4 pituicytoma, 6 granular cell tumors of the sellar region (GCT), and 5 spindle cell oncocytoma. All PPETS had good outcomes. Immunohistochemically, PPETS tumors showed positive staining with TTF1, EMA, AE1/AE3, MAP2, and Vimentin, but were negatively stained with Syn, GFAP, CgA, and S100, and sporadically stained with Ki-67. In unsupervised hierarchical clustering and t-distributed stochastic neighbor embedding analyses of DNA-methylation data, PPETS and PPT tumors formed a distinct cluster irrespective of their histologic types. However, PPETS tumors did not cluster together with CPP and CN samples. Similar findings were obtained when our samples were projected into the reference cohort of the brain tumor classifier. Substantial fractions of the PPETS and PPT tumors shared broadly similar chromosomal copy number alterations. No mutations were detected using targeted next-generation sequencing. Though more cases are needed to further elucidate the molecular pathogenesis of these tumors, our findings indicate that PPETS and PPT tumors may constitute a single neurooncological entity.

Double-checking chromosome segregation.

Enduring chromosome segregation errors represent potential threats to genomic stability due to eventual chromosome copy number alterations (aneuploidy) and formation of micronuclei-key intermediates of a rapid mutational process known as chromothripsis that is found in cancer and congenital disorders. The spindle assembly checkpoint (SAC) has been viewed as the sole surveillance mechanism that prevents chromosome segregation errors during mitosis and meiosis. However, different types of chromosome segregation errors stemming from incorrect kinetochore-microtubule attachments satisfy the SAC and are more frequent than previously anticipated. Remarkably, recent works have unveiled that most of these errors are corrected during anaphase and only rarely result in aneuploidy or formation of micronuclei. Here, we discuss recent progress in our understanding of the origin and fate of chromosome segregation errors that satisfy the SAC and shed light on the surveillance, correction, and clearance mechanisms that prevent their transmission, to preserve genomic stability.

Leveraging homologous recombination repair deficiency in sarcoma.

Personalised oncology is at the forefront of cancer research. The goal of personalised oncology is to selectively kill cancer cells while minimising side effects on normal tissue. This can be achieved by identifying and targeting cancer vulnerabilities that distinguish it from normal cells. Many cancers are deficient in high-fidelity DNA repair pathways that maintain genomic stability, such as homologous recombination (HR). Such cancers are highly sensitive to targeted therapies that induce DNA damage or inhibit DNA repair pathways. A notable example and a poster child of personalised oncology are PARP1/2 inhibitors (PARPi) that selectively kill HR-deficient (HRD) cancer cells by preventing repair of DNA gaps or single-strand breaks (SSBs) (Slade, 2020). Inhibitors of cell cycle checkpoints such as CHK1 and WEE1 can also eliminate HRD cancers by pushing cancer cells through the cell cycle despite unrepaired DNA damage and causing death by mitotic catastrophe (Groelly etal, 2022). PARPi have been approved for the treatment of ovarian, breast, pancreatic, and prostate cancer but other cancer types with an HRD signature (HRDness) may also respond to PARPi treatment. Planas-Paz etal (2023) now show that many sarcomas show HRDness and respond to PARP1/2 and WEE1 inhibitors, thus offering a new personalised oncology approach for this treatment-refractory cancer.

Genomic Profiling of the Craniofacial Ossifying Fibroma by Next-Generation Sequencing.

Ossifying fibroma (OF) of the craniofacial skeleton is a fibro-osseous lesion characterized by various patterns of bone formation in a cellular fibroblastic stroma. The molecular landscape of OF remains mostly unknown. There are a few known pathogenic abnormalities in OF, including HRPT2 mutations in conventional OF and SATB2 translocations in juvenile psammomatoid OF. On the other hand, conflicting reports exist regarding MDM2 gene amplification and chromosomal copy number alterations (CNA) in OF. Surgically removed biopsies and curettage specimens from OF patients were obtained. Clinical, radiographic, and pathologic features of tumors were reviewed. Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue. Capture-based DNA next-generation sequencing targeting the coding regions 529 cancer genes and select introns was performed. We identified 17 OF cases from 8 male and 8 female patients with mean age of 22years (range 1-58years). Nine case occurred in the gnathic bones and 8 in the extragnathic craniofacial bones. These cases included 3 juvenile psammomatoid OF, 6 conventional OF and 8 juvenile trabecular OF. Large-scale CNAs were present in 6 of 17 cases. Seven cases (41%) had focal amplifications including FOSB (n = 2, 11%), FOS (n = 4, 23%), COL1A1 (n = 4, 23%) and TBX3 (n = 5, 29%). Three cases (17%) had pathogenic CDC73 mutations. No cases showed focal MDM2 amplification. Here, we provided a comprehensive molecular characterization of OF that reveals a heterogeneous genetic profile with occasional large-scale CNAs (n = 6, 35%). FOS, FOSB, and TBX3 genes that regulate AP-1 transcriptional complex are frequently altered in OF (n = 7, 41%), chiefly in juvenile trabecular OF. These genes encode transcription factors that act as downstream effectors of the MAP kinase signaling pathway. MDM2 amplification is an exceedingly rare event in OF, if present at all, so identification of this event should continue to raise concern for low-grade gnathic osteosarcoma. In summary, our findings suggest that OF represents a heterogeneous group of tumors at the genetic level but dysregulation of the AP-1 pathway may play a role in pathogenesis of juvenile trabecular OF.

The use of copy number loads to designate mosaicism in blastocyst stage PGT-A cycles: fewer is better.

The use of copy number loads to designate mosaicism in blastocyst stage PGT-A cycles: fewer is better.

Molecular methods for colorectal cancer screening: Progress with next-generation sequencing evolution

Currently, colorectal cancer (CRC) represents the third most common malignancy and the second most deadly cancer worldwide, with a higher incidence in developed countries. Like other solid tumors, CRC is a heterogeneous genomic disease in which various alterations, such as point mutations, genomic rearrangements, gene fusions or chromosomal copy number alterations, can contribute to the disease development. However, because of its orderly natural history, easily accessible onset location and high lifetime incidence, CRC is ideally suited for preventive intervention, but the many screening efforts of the last decades have been compromised by performance limitations and low penetrance of the standard screening tools. The advent of next-generation sequencing (NGS) has both facilitated the identification of previously unrecognized CRC features such as its relationship with gut microbial pathogens and revolutionized the speed and throughput of cataloguing CRC-related genomic alterations. Hence, in this review, we summarized the several diagnostic tools used for CRC screening in the past and the present, focusing on recent NGS approaches and their revolutionary role in the identification of novel genomic CRC characteristics, the advancement of understanding the CRC carcinogenesis and the screening of clinically actionable targets for personalized medicine.

Dimorphic glioblastoma with glial and epithelioid phenotypes: Clonal evolution and immune selection.

Epithelioid glioblastoma is an unusual histologic variant of malignant glioma. The present study investigates both the genomic and transcriptomic determinants that may promote the development of this tumor. Whole-exome sequencing (WES) and whole-transcriptome sequencing (WTS) were performed on an epithelioid glioblastoma, along with a specific bioinformatic pipeline to generate electronic karyotyping and investigate the tumor immune microenvironment. Microdissected sections containing typical glioblastoma features and epithelioid morphology were analyzed separately using the same methodologies. An epithelioid glioblastoma, with immunopositivity for GFAP, Olig-2, and ATRX but negative for IDH-1 and p53, was identified. The tumor cell content from microdissection was estimated to be 85-90% for both histologic tumor components. WES revealed that both glioma and epithelioid sections contained identical point mutations in PTEN, RB1, TERT promoter, and TP53. Electronic karyotype analysis also revealed similar chromosomal copy number alterations, but the epithelioid component showed additional abnormalities that were not found in the glioblastoma component. The tumor immune microenvironments were strikingly different and WTS revealed high levels of transcripts from myeloid cells as well as M1 and M2 macrophages in the glioma section, while transcripts from CD4+ lymphocytes and NK cells predominated in the epithelioid section. Epithelioid glioblastoma may be genomically more unstable and oncogenically more advanced, harboring an increased number of mutations and karyotype abnormalities, compared to typical glioblastomas. The tumor immune microenvironment is also different.