Chromosome 22q11 Research Articles

Cholangioblastic Cholangiocarcinoma (NIPBL::NACC1 cholangiocarcinoma): Expanded Morphologic Spectrum and Further Genetic Characterization.

The cholangioblastic variant of intrahepatic cholangiocarcinoma is a distinctive neoplasm that typically affects young women without underlying liver disease. Morphologically, it demonstrates solid, trabecular, and tubulocystic architecture, biphasic small cell-large cell cytology, and immunoreactivity for inhibin, neuroendocrine markers, and biliary but not hepatocellular markers. In 2021, our group identified a characteristic NIPBL::NACC1 gene fusion in cholangioblastic cholangiocarcinoma, and since then ~20 genetically confirmed cases have been reported in the literature. We report 2 additional cases, both of which caused diagnostic challenges. The first was previously published as a "biliary adenofibroma with malignant features" which we now show recurred as a high-grade adenocarcinoma. Re-review of the original lesion demonstrated the morphologic and immunohistochemical features of highly cystic cholangioblastic cholangiocarcinoma, whereas the high-grade recurrence lacked many of these features. In addition to the characteristic NIPBL::NACC1 gene fusion, the recurrence demonstrated loss of the RB1 and PTEN genes which were found in the highly cystic, bland areas of the original tumor, suggesting that the recurrence was derived from this bland component. The second case was originally misclassified as metastatic well-differentiated neuroendocrine neoplasm and only focally demonstrated the characteristic biphasic small cell-large cell cytology. In addition, a review of 7 cholangioblastic cholangiocarcinomas in our files demonstrates that loss of chromosome 13q14.2 (where the RB1 gene resides) and loss of chromosome 6q15-q16.3 are recurrent secondary changes in these neoplasms. Expression profiling demonstrated alterations in the transforming growth factor receptor beta superfamily, and overexpression of MYC which was validated by immunohistochemistry. Our findings expand the morphologic and genetic spectrum of this neoplasm and provide insight into secondary genetic changes associated with progression.

Blood DNA virome associates with autoimmune diseases and COVID-19

Aberrant immune responses to viral pathogens contribute to pathogenesis, but our understanding of pathological immune responses caused by viruses within the human virome, especially at a population scale, remains limited. We analyzed whole-genome sequencing datasets of 6,321 Japanese individuals, including patients with autoimmune diseases (psoriasis vulgaris, rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), pulmonary alveolar proteinosis (PAP) or multiple sclerosis) and coronavirus disease 2019 (COVID-19), or healthy controls. We systematically quantified two constituents of the blood DNA virome, endogenous HHV-6 (eHHV-6) and anellovirus. Participants with eHHV-6B had higher risks of SLE and PAP; the former was validated in All of Us. eHHV-6B-positivity and high SLE disease activity index scores had strong correlations. Genome-wide association study and long-read sequencing mapped the integration of the HHV-6B genome to a locus on chromosome 22q. Epitope mapping and single-cell RNA sequencing revealed distinctive immune induction by eHHV-6B in patients with SLE. In addition, high anellovirus load correlated strongly with SLE, RA and COVID-19 status. Our analyses unveil relationships between the human virome and autoimmune and infectious diseases.

Somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma.

Deletion of the long q arm of chromosome 22 (22qDEL) is the most frequently identified recurrent somatic copy number alteration (SCNA) observed in papillary thyroid carcinoma (PTC). Since its role in PTC is not fully understood, we conducted a pooled analysis of genomic characteristics and clinical correlates in 1094 primary tumors from four published PTC genomic studies. The majority of PTC with 22qDEL exhibited arm-level loss of heterozygosity (86%); nearly all PTC with 22qDEL had losses in 22q12 and 13, which together constitute 70% of the q arm. Our analysis confirmed that 22qDEL occurs more frequently with RAS point mutations (50.4%), particularly HRAS (70.3%), compared with other PTC drivers (9.3%), supporting the conclusion that 22qDEL is unlikely to be a solitary driver of PTC but possibly an important co-factor in carcinogenesis, particularly in PTC with RAS driver mutations. Differential RNA expression analyses revealed downregulation of most genes located on chromosome 22 in those with 22qDEL compared to those without 22qDEL. Many differentially expressed genes are drawn from immune response and regulation pathways. These findings highlight the value of further investigations into the contributions of 22qDEL events to PTC, perhaps mediated through immune perturbations.

GENETIC ANALYSIS OF BMP-4 GENE IN BADDI GOAT BREED OF DISTRICT KHAIRPUR MIR'S SINDH PAKISTAN

Bone morphogentic protein 4 is a protein that found in goat, cattle, and human are encoded by BMP4 gene. the candidate gene is found on chromosome 10q in goats. BMP4 gene is the subfamily of the superfamily named as transforming growth factor beta. it is an evolutionary conserved member of BMPs family. BMP4 is a protein coding gene that concern with connective and soft tissues of the body structure . it play main role in goats, cattle, human and other animal's bodies for maintaining the body activities such as cell proliferation, differentiation, apoptosis and migration. Present study was aimed to investigate the mutational variations found with same area of indigenous goat breed. The Genomic DNA was extracted from blood samples of Baddi goat breed. The samples were transported and stored at 4 degree for further processing of DNA extraction. The targeted region of BMP4 gene that was amplified by the specific set of primers. The amplified products were sequenced by the ABI Genetic Anayzer 3500 and sequencing data was analyzed by Bio Edit v 7.2 and blasting was performed on ensemble.org. Result revealed that about 4 missense mutations found the breed with help of PCR, gel electrophoresis and DNA sequencing. The missense mutation was identified by the replacement of genetic codon from original codon such as first missense mutation found in replacement of Serine by Threonine at 157Bp, second and third from Glycine to isolecucine at 159 Bp and 173 Bp respectively. while fourth mutational variation occured from Arginine to Serine at 177 Bp. However, the percentage of mutation in Baddi breed was greater than 1% it means there was polymorphism has been found with replacement of original amino acids with variate amino acids that play a significant role in improvement of goat characteristic such as body, muscles, milk and meat quantities. Obtained result revealed a great heterogeneity in genetic makeup of Baddi breed and hence could be used in genetic marker which assisted the selection of Baddi breed than other breeds.

MicroRNA Profile of High-Grade B-Cell Lymphoma with 11q Aberration.

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.

CRKL Gene Deletion in Familial Zinner (OSVIRA) and OHVIRA Syndromes.

We present the first description of a family in which 2 siblings show alternative expression of CRKL gene deletion as the phenotypes of Zinner (OSVIRA, obstructed seminal vesicle and ipsilateral renal agenesis) and OHVIRA (obstructed hemivagina with an ipsilateral renal anomaly) syndromes. The male infant with Zinner syndrome and his sister aged 5years with OHVIRA syndrome both have a paternally inherited 703-kb deletion at chromosome 22q11.21 that includes CRKL. This observation supports Acien's hypothesis that the upper vagina has an embryological dual origin and furthermore substantiates the theory that Zinner (OSVIRA) is the male equivalent of OHVIRA in females.

Swedish Genome-Wide Haplotype Association Analysis Suggests Breast Cancer Loci with Varying Risk-Modifying Effects.

Background: To find support for risk-modifying genes in breast cancer, a haplotype GWAS in sporadic breast cancer cases was undertaken. The results were compared with the results from previous analyses in familial cases and all cases from the same Swedish cohort. Methods: In total, 2550 women with sporadic invasive breast cancer and 5021 healthy controls were included in a sliding-window haplotype GWAS using PLINK 1.07. Results: The analysis of sporadic cases confirmed the loci on chromosomes 10q26.13, 11q13.3, and 16q12.1 and suggested one novel locus on chromosome 12p11.21 (OR = 1.42 p = 4.55 × 10-8). A comparison between these loci and the same loci in the analyses of familial cases and all breast cancer cases was undertaken. Conclusions: Haplotype GWAS in sporadic cases of Swedish breast cancer cases supported known risk loci and suggested another risk locus. The loci identified in the analysis of sporadic and all breast cancer cases were suggested to act as modifiers of the risk of breast cancer. Haplotype analysis identified other loci with higher odds ratios than single-variant analysis. Further studies are needed to find out how to best include the findings in breast cancer prevention.

Retrospective longitudinal study on the long-term impact of COVID-19 infection on polysomnographic evaluation in patients with Prader-Willi syndrome

BackgroundTo evaluate the impact of coronavirus disease 2019 (COVID-19) on polysomnographic evaluation in patients with Prader-Willi syndrome (PWS).Patients and methodsA retrospective cohort study of two consecutive overnight polysomnograms (PSG) in 92 PWS patients (mean age 9.1, range 3.1–22 years). 57/92 participants (35 female) had a COVID-19 infection between the two consecutive examinations. 35 patients (21 female) had no infection (control group). Distribution of genetics was as follows: 13/57 (22.8%) deletion, 19/57 (33.3%) uniparental disomy, 2/57 (3,5%) imprinting defect, 3/57 (5.3%) non-deletion, 20/57 (35.1%) diagnosed by analyses of the methylation pattern of chromosome 15q11-13. Mean time interval between COVID-19 infection and post-COVID-19 evaluation was 96.2 days.ResultsCourse of COVID-19 infection was asymptomatic 8/82 (9.8%), mild 63/82 (76.8%), medium 11/84 (13.4%). The five most frequently experienced symptoms in PWS patients were fever (56.1%); headache (45.1%); cold (42.7%); cough (31.7%) and body aches (21.95%). PWS patients who had COVID-19 infection had significantly lower mean oxygen saturation (SpO2) measured by pulse oximetry (post 94.8% vs. pre 95.7%, p = 0.001), lower detected lowermost SpO2 (post 86.2 vs. pre 87.3%, p = 0.003), and higher occurrence of hypopnoea (post 13.9 vs. pre 10.7, p = 0.001). Time in optimal SpO2 (95–100%) decreased significantly (post 54.3% vs. pre 73.8%, p = 0.001), whereas an increase was observed in time in suboptimal SpO2 (90–95%) (post 45.5% vs. 25.8%, p = 0.001) and in time in poor SpO2 (< 90%) (post 0.7% vs. pre 0.2%, p = 0.030). Body-Mass-Index (BMI)-SDS for PWS showed no differences between the groups at any time. BMI-SDS-differences showed no influence on differences in SpO2 evaluations. In the genetic subgroup with deletion there was a statistically significant effect on an increased number of OSA (p = 0.027). The genetic subgroup with uniparental disomy (UPD) was associated with a reduced risk of higher HF (p = 0.035) and less hypopnea (p = 0.011).ConclusionPWS patients predominantly experienced only mild to medium symptoms during COVID-19 infection without necessity of hospitalisation. However, on average three months after infection, differences in PSG evaluations were still apparent, manifesting in lower SpO2 and more frequent hypopnea. A long-lasting impairment of the pulmonary system due to the COVID-19 infection might be responsible.

Classification and Prognostic Stratification Based on Genomic Features in Myelodysplastic and Myeloproliferative Neoplasm- and Their Overlapping Conditions.

Background/Objectives: Myeloid neoplasms encompass a diverse group of disorders. In this study, we aimed to analyze the clinical and genomic data of patients with myeloproliferative neoplasm (MPN), myelodysplastic neoplasm (MDS), and their overlapping conditions, such as MDS/MPN and aplastic anemia (AA), to help redefine the disease classification. Methods: Clinico-genomic data of 1585 patients diagnosed with MPN (n = 715), MDS (n = 698), MDS/MPN (n = 78), and AA (n = 94) were collected. Patterns of 53 recurrent genomic abnormalities were compartmentalized into 10 groups using a Dirichlet process (DP). Results: These genomic groups were correlated with specific genomic features, survival outcomes, and disease subtypes. Groups DP1 and DP5, characterized by JAK2 and CALR mutations, respectively, showed very favorable prognoses among the patients with MPN. Groups DP2, DP7, and DP9 demonstrated very adverse prognoses across the disease subtypes. DP2 included patients with MDS harboring TP53 mutations and complex karyotypes; DP9 comprised patients with acute myeloid leukemia-related mutations, including NPM1; and DP7 included patients with SETBP1 mutations. Groups DP10 and DP8, linked to SF3B1 and DDX41 mutations or chromosome 1q derivatives, presented a favorable risk profile. Improved survival was observed with transplantation in groups DP2, DP7, and DP9. Conclusions: These findings highlight the role of genomic classifications in guiding personalized treatment strategies, ultimately enhancing the understanding and management of myeloid neoplasms.

Chromosome 1 Alterations in Multiple Myeloma: Considerations for Precision Therapy.

Multiple myeloma (MM) is an incurable blood malignancy characterized by the clonal expansion of plasma cells and the secretion of monoclonal immunoglobulins. High-risk MM, defined by specific cytogenetic abnormalities, poses significant therapeutic challenges and is associated with inferior survival outcomes compared to standard-risk disease. Although molecularly targeted therapies have shown efficacy in other hematologic malignancies, currently venetoclax is the only targeted therapy approved for MM (t(11;14)). However, chromosome 1q gains, amplifications, and 1p deletions are frequently observed in MM, and have been linked to drug resistance and poor patient prognosis. Accordingly, this review focuses on emerging MM precision therapies capable of targeting dysregulated genes within these regions. It addresses gene therapies, small molecule inhibitors and monoclonal antibodies currently under investigation to antagonize oncogenic drivers including MCL-1, BCL9, F11R, and CKS1B, all of which are implicated in cell survival, proliferation or drug resistance. In conclusion, the link between chromosome 1 abnormalities and high-risk disease in MM patients offers a compelling rationale to identify and explore therapeutic targeting of chromosome 1 gene products as a novel precision medicine approach for a poorly served patient population.

Genetic complexity in myelodysplastic syndromes: Insights from a case with complex karyotype and renal manifestations

Myelodysplastic syndrome (MDS) is a heterogeneous disorder with a significant risk of progression to acute myeloid leukemia. We present a case initially suspected of acute leukemia, subjected to comprehensive cytogenetic, immunophenotypic, and molecular evaluations. Cytogenetic analysis revealed a complex karyotype including translocation t (1;3) (q42;q21), near-tetraploidy, and deletions on chromosomes 5q and 20q. Fluorescence in situ hybridization confirmed the 5q and 20q deletions, along with trisomy 8. Immunophenotyping identified 7.5% abnormal myeloid blasts. Next-generation sequencing detected pathogenic TP53 mutations: c.569 (p.Pro190LeufsTer57) and c.464C&gt;A (p.Thr155Asn). In addition, renal imaging showed mildly raised echotexture. This case underscores the value of integrated multimodal analysis for precise diagnosis and management of MDS, offering insights into its complex genetic landscape.

Patient identified with interrupted aortic arch and 22q11.2 deletion syndrome in late pregnancy: a case report

Interrupted aortic arch (IAA) is an uncommon congenital heart malformation that can be fatal with no surgical intervention. Most patients have IAA discovered as newborns because of cardiac symptoms, and atypical adult patients are relatively rare. We report a case of atypical adult IAA in a woman in her 20s. Her first pregnancy and childbirth did not show any obvious abnormalities. Although this patient did not have any major clinical manifestations, she developed tachycardia during her second pregnancy and was diagnosed with IAA by echocardiography. The etiology of IAA was chromosome 22q11.2 deletion syndrome based on the results of whole-exome sequencing. After interdisciplinary diagnosis and treatment to reduce the pulmonary artery pressure and cardiac burden, the patient and her newborn had a favorable prognosis. This case highlights the importance of not overlooking cardiovascular concerns in patients who develop symptoms in pregnancy. Echocardiography can detect IAA, and genetic testing may assist in an etiological diagnosis, which improves the maternal and fetal prognosis.

Aortopathy in repaired tetralogy of Fallot and David procedure.

Tetralogy of Fallot (TOF) is a condition that often leads to long-term enlargement of the aortic root in after surgery. The aortic dilation is believed to be caused by histological abnormalities of the aortic media and the hemodynamic characteristics of increased aortic flow, compared to pulmonary flow. Severe cyanosis, severe right ventricular outflow tract (RVOT) obstruction, older age at repair, a larger aortic size at the time of repair, and a history of an aortopulmonary shunt parameters related to long-standing volume overload of the aortic root were the reported risk factors. Right aortic arch, male sex, and the association of chromosome 22q11 deletion were also reported to be risk factors. The enlargement of the aortic root can cause aortic regurgitation (AR), leading to left ventricular dysfunction and an increased risk of aortic dissection, necessitating surgical intervention. The outcomes of aortic valve repair for AR have improved, leading to an increasing trend of choosing this approach, particularly in younger patients who would otherwise require mechanical valve replacement, thereby avoiding the need for anticoagulation therapy. The indications and timing of prophylactic aortic root replacement in adult patients with congenital heart disease have not been described, and the current consensus recommends surgical intervention for an ascending aorta with a diameter of ≥55 mm. In this review article, we focus on valve-sparing root replacement (VSRR) in TOF.

A self-reported Brazilian registry of 5q-spinal muscular atrophy: data on natural history, genetic characteristics, and multidisciplinary care.

Spinal muscular atrophy linked to chromosome 5q (SMA-5q) is a neurodegenerative disorder caused by mutations in the SMN1 gene. To describe the key demographic, clinical and genetic characteristics, as well as natural history data of patients with SMA-5q. Up to January 2022, 706 patients with confirmed genetic diagnosis of SMA-5q, or their parents, completed a self-reported questionnaire on natural history, genetic characteristics, drug treatments, and multidisciplinary care. Most patients had type 1 SMA-5q (42%); with 33% having type 2, and 23% type 3. There were 667 patients (94.4%) with a homozygous SMN1-exon 7 deletion. Of the total, 131 (18.6%) patients had a previous family history of the disease, and the familial recurrence rate was higher in type 3 (25.6%). Type 1 patients had a mean age of 3 months at the onset of symptoms and a delay of more than 3 months until genetic diagnosis. The median survival of patients with type 1 without invasive ventilation was 27 months. Before 2018, the median age of use of invasive ventilation was 16 months and, after, most patients (71%) were not submitted to invasive ventilation. About 50% of patients with type 3 lost their walking ability by 37 years of age. Further, 384 (54.4%) patients had access to disease-modifying therapy, and 62.3% of type 1 patients were in treatment, compared with only 47.2% of type 2 and 31.9% of type 3 patients. There is still a substantial diagnostic delay, especially in those patients with types 2 and 3 SMA-5q. However, the present study demonstrated prolonged survival, especially in type 1 patients.

Loss of chromosome cytoband 13q14.2 orchestrates breast cancer pathogenesis and drug response

Breast cancer (BCa) is a major global health challenge. The BCa genome often carries extensive somatic copy number alterations (CNAs), including gains/amplifications and losses/deletions. These CNAs significantly affect tumor development, drug response and patient survival. However, how individual CNAs contribute is mostly elusive. We identified loss of chromosome 13q14.2 as a key CNA in BCa, occurring in up to 63% of patients, depending on the subtype, and correlating with poor survival. Through multi-omics and in vitro analyses, we uncover a paradoxical role of 13q14.2 loss, promoting both cell cycle and pro-apoptotic pathways in cancer cells, while also associating with increased NK cell and macrophage populations in the tumor microenvironment. Notably, 13q14.2 loss increases BCa susceptibility to BCL2 inhibitors, both in vitro and in patient-derived xenografts. Thus, 13q14.2 loss could serve as a biomarker for BCa prognosis and treatment, potentially improving outcomes for BCa patients.Graphical abstract

Abstract B021: Aneuploidy-associated cohesin RAD21 gains promote immune evasion in prostate cancers

Abstract Aneuploidy, characterized by imbalanced chromosome numbers, is a hallmark of cancer and is strongly correlated with lethal progression in prostate cancer. Our recent work identified that gains of chromosome 8q, the most frequently gained chromosome in aneuploidy prostate cancers, drive cancer progression, partially through the cohesin RAD21 gene located on the chr8q24 region. We demonstrated that increased RAD21 expression accelerates lethal progression and oncogenesis in both prostate cancer and Ewing sarcoma by alleviating oncogenic stress during early-stage oncogenesis in both cell line and organoid models. Therefore, we hypothesize that elevated RAD21 levels could enable cancer cells to evade immune surveillance by mitigating oncogenic stress and DNA damage. In this study, we developed isogenic prostate and breast cancer cell culture models with varying levels of RAD21. Using a natural killer (NK) cell co-culture assay, we observed that cells with elevated RAD21 expression were significantly less susceptible to NK-mediated cytotoxicity and exhibited increased survivorship when co-cultured with NK cells. These findings align with publicly available data showing that tumors with high RAD21 levels have reduced NK cell infiltration in prostate cancer. Our results suggest that increased RAD21 expression, commonly associated with chr8q gains, facilitates immune evasion in cancer cells, thereby promoting early-stage oncogenesis. Understanding the role of RAD21 in immune evasion could reveal novel therapeutic strategies targeting immune surveillance mechanisms in prostate cancer. Citation Format: Elise G. DeArment, Ruoxi W. Wang, Kate Lu, Xiaofeng A. Su, Andrew Elliott, Nicholas A. Zorko, Justin H. Hwang, Xiaofeng A. Su. Aneuploidy-associated cohesin RAD21 gains promote immune evasion in prostate cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B021.

Extra-Axial Poorly Differentiated Chordoma Initially Misdiagnosed as Epithelioid Sarcoma.

Poorly differentiated chordoma is an exceedingly rare, aggressive subtype of chordoma. These tumors typically arise in the axial skeleton of young patients, most commonly the skull base, followed by the cervical spine. Herein, we present a 60-year-old patient with longstanding knee pain and nondiagnostic imaging, initially thought to be due to osteoarthritis. No discrete mass-forming lesion was identified by radiology. Synovial histology at the time of arthroplasty revealed a multinodular proliferation of epithelioid-to-histiocytoid cells with a moderate amount of eosinophilic-to-clear, vacuolated cytoplasm. Scattered cells with high-grade nuclear atypia were present. A diagnosis of metastatic carcinoma was considered due to immunohistochemical positivity for keratin and GATA3. However, a diagnosis of epithelioid sarcoma was rendered based on clinical context, morphology, and loss of immunohistochemical expression for SMARCB1 (INI1). However, upon re-review of the tumor, brachyury was retrospectively added to the immunohistochemistry panel and showed strong positivity, thus prompting amendment of the initial diagnosis of epithelioid sarcoma to extra-axial poorly differentiated chordoma. Given the rarity of this diagnosis, molecular testing was performed which revealed a unique SMARCB1 molecular profile with a single-nucleotide variant in addition to the commonly reported loss of chromosome 22q. This report of an ultra-rare sarcoma in an uncommon anatomic site highlights multiple potential pitfalls in the diagnosis of poorly differentiated chordoma, emphasizes the importance of brachyury immunohistochemistry in rendering a correct interpretation, and underscores an opportunity for further molecular analysis to better define the molecular profile of this entity.

EPCO-54. MULTIOMIC ANALYSIS OF SPINAL EPENDYMOMAS REVEALS MECHANISMS OF TUMOR AGGRESSIVENESS WITH MYCN AMPLIFICATION

Abstract Grade-3 spinal ependymomas, particularly those harboring MYCN amplification, have dismal prognoses despite optimal treatment regimens. MYCN functions as a transcription factor (TF) to drive the expression of key tumor driver genes. Our aim is to identify mechanisms underlying tumor aggressiveness and treatment resistance in MYCN-amplified ependymomas. MYCN amplification in spinal ependymomas was identified with custom next generation sequencing panels and bulk methylation analysis. We then conducted paired single-nucleus RNA (snRNA-seq) and chromatin accessibility (snATAC-seq) sequencing of grade-2 (n=2, 1 patient) and grade-3 spinal ependymomas (n=6, 6 patients, 4 MYCN-amplified). Comparator snRNA-seq datasets (grade-2/grade-3; 8/2) were included from a publicly available dataset (GSE163686; all non-MYCN-amplified). Canonical cell classes were identified with a combination of cluster- and cell-based strategies. Downstream analysis was conducted using R 4.3 (Seurat, Signac, clusterProfiler, CellChat), and Python 3.11 (scanpy) packages. We identified ependymoma tumor cells distinct from canonical immune cell classes with gene expression analysis and confirmed a distinct copy-number-variation pattern in these cells with chromosome 1 and 2p gain, and chromosome 6p and 22q loss. MYCN-amplified tumor cells (compared to non-MYCN-amplified grade2/3 tumor cells) showed increased differential accessibility at genes including VEGFA. Increased MYCN TF activity was confirmed with gene overexpression of downstream targets including NOTCH3, CREB5, PLK1, and VEGFA. Other genes that were highly accessible and overexpressed in MYCN-amplified tumor cells were related to oxidative stress, differentiation, and anti-apoptotic pathways. MYCN-amplified tumor cells modified the tumor microenvironment with increased VISTA signaling between MYCN-amplified tumor cells and tumor-associated macrophages, creating an immunosuppressive environment. We confirmed these effects by observing a higher proportion of M2-like macrophages in MYCN-amplified tumors (29.6% vs 18.2%). In conclusion, MYCN amplification in spinal ependymomas upregulates tumor cell proliferation, angiogenesis, and M2-like macrophage recruitment/programming.

BIOM-60. UNDERSTANDING THE INTERSECTION OF RACE, SEX, AND GENOMIC PROFILES IN MENINGIOMA PATHOPHYSIOLOGY

Abstract BACKGROUND While meningioma incidence and outcomes vary by sex and race, the potential underlying molecular differences possibly contributing to these disparities are less understood. Herein, we explore the clinical and genomic characteristics of meningiomas across groups characterized by age and sex. METHODS We analyzed adult patients with primary meningiomas resected from 2012 to 2023. Patients underwent whole exome sequencing, and demographic data were categorized into four groups based on self-reported race and sex, which included White females, White Males, Black females, and Black males. The primary analyses involved comparisons of tumor characteristics, socioeconomic status (median zip code income, % with high school diploma, health insurance status, distance from hospital), genomics, and recurrence rates. RESULTS The study included 509 primary meningiomas. White females exhibited low-risk genomic profiles characterized by driver mutations in KLF4 (+/- TRAF7) (p=0.010) and POLR2A (p=0.045), with no associated CNVs (p=0.410). This benign molecular profile correlated with lower WHO grades (p=0.013) and a lower incidence of recurrence (p=0.0003). Black females had meningiomas enriched with Hedgehog pathway mutations (p=0.0035) and a predilection for the anterior skull base (p=0.034), leading to an increased risk of recurrence (p=0.026). White males showed an aggressive genomic profile, including chromosome 1p loss (p=0.025) and 10q loss (p=0.067), associated with a high risk of recurrence (p=0.0002). Black males had meningiomas with chromosome 14q loss (p=0.0002), the highest incidence of high-grade meningiomas (p=0.048), and a 4.5-fold increased risk of recurrence (OR 4.5 [1.6-11.8]; p=0.006). Black males also experienced the worst progression-free survival (HR 5.5 [2.5-12.4]; p&amp;lt;0.0001), independent of WHO grade, extent of resection, and socioeconomic status. CONCLUSIONS Each demographic has a distinct molecular profile that correlates with clinical behavior in a race and sex-specific manner. Black males are disproportionately affected by biologically aggressive meningiomas, leading to higher tumor grade and recurrence rates.

PATH-64. UNDERSTANDING MECHANISTIC UNDERPINNINGS OF MOLECULAR SUBGROUPS OF MENINGIOMA

Abstract Meningiomas are the most common intracranial tumors. In the past, they were thought to be indolent and could be treated by resection. The current standard of care utilizes WHO histopathological grading to identify malignant potential. Our lab identified three molecular groups (MenG A, B, and C) using CNVs, methylation, and/or expression profiling with different biological characteristics. These groups were independently validated and predicted recurrence more reliably than WHO grade. MenG A is genomically stable but harbors tumors with point mutations, mainly in TRAF7, KLF4, and AKT1. On the other hand, MenG B and C tumors have chromosome 22q arm deletion or loss of merlin, the protein product of the NF2 gene. Moreover, MenG B is characterized by DNA hypomethylation, while MenG C tumors show DNA hypermethylation and have additional chromosomal losses, most notably in chromosome 1p. Lastly, while MenG A/B are indolent, MenG C – comprising approximately 28% of meningiomas – recur frequently and are refractory to radiotherapy and/or surgery. How can two groups of tumors with the same driver mutation behave so differently? Hence, our lab is interested in (1) what molecular pathway/factor(s) are necessary for becoming any meningioma, and (2) what mechanisms are critical for the aggressiveness of MenG C. Here, we investigate the role of TRAF7 in meningioma biology. Toward this end, we study interactors, modulators, and individual mutations in cell culture. In addition, we use published exome sequencing and expression data to reveal possible connections between chromatin state and individual genes. In conclusion, a variety of underlying mechanisms drive meningioma tumorigenicity and aggressiveness. Elucidating these mechanisms could provide future therapeutic targets for currently untreatable meningiomas.