Comprehensive molecular characterization of adenoid cystic carcinoma reveals tumor suppressors as novel drivers and prognostic biomarkers.

Adenoid cystic carcinoma (ACC) is a MYB-driven head and neck malignancy with high rates of local recurrence and distant metastasis and poor long-term survival. New effective targeted therapies and clinically useful biomarkers for patient stratification are needed to improve ACC patient survival. Here, we present an integrated copy number and transcriptomic analysis of ACC to identify novel driver genes and prognostic biomarkers. A total of 598 ACCs were studied. Clinical follow-up was available from 366 patients, the largest cohort analyzed to date. Copy number losses of 1p36 (70/492; 14%) and of the tumor suppressor gene PARK2 (6q26) (85/343; 25%) were prognostic biomarkers; patients with concurrent losses (n = 20) had significantly shorter overall survival (OS) than those with one or no deletions (p < 0.0001). Deletion of 1p36 independently predicted short OS in multivariate analysis (p = 0.02). Two pro-apoptotic genes, TP73 and KIF1B, were identified as putative 1p36 tumor suppressor genes whose reduced expression was associated with poor survival and increased resistance to apoptosis. PARK2 expression was markedly reduced in tumors with 6q deletions, and PARK2 knockdown increased spherogenesis and decreased apoptosis, indicating that PARK2 is a tumor suppressor in ACC. Moreover, analysis of the global gene expression pattern in 30 ACCs revealed a transcriptomic signature associated with short OS, multiple copy number alterations including 1p36 deletions, and reduced expression of TP73. Taken together, the results indicate that TP73 and PARK2 are novel putative tumor suppressor genes and potential prognostic biomarkers in ACC. Our studies provide new important insights into the pathogenesis of ACC. The results have important implications for biomarker-driven stratification of patients in clinical trials. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Diffuse leptomeningeal glioneuronal tumor with distinct neuronal and glial components but identical diagnostic molecular and genetic features.

The 2021 World Health Organization (WHO) classification of the central nervous system (CNS) tumors has classified diffuse leptomeningeal glioneuronal tumor (DLGNT) as a mixed neuronal and glial tumor. Here, we report a DLGNT with two distinct morphological tumor components but identical molecular features. A four-year-old female child presented with progressive right upper extremity weakness. Magnetic resonance imaging (MRI) revealed the leptomeningeal enhancement over the brain stem and cervicothoracic spine. The histological examination of surgical specimens revealed two distinct tumor components: approximately half of the tumor is composed of oligodendroglioma-like tumor intermingled with nodules of ganglioglioma-like tumor. Immunohistochemistry confirmed the oligodendroglioma and ganglioglioma features. The molecular genetic studies demonstrated the features of DLGNT, including fusion of KIAA1549::BRAF, deletion of chromosome 1p, and absence of isocitrate dehydrogenase 1/2 (IDH1/2) mutation in both tumor components. Interestingly, the genetic studies also revealed the distinct chromosomal abnormalities of the loss of chromosome 4 only in oligodendroglioma-like tumor and copy neutral loss of heterozygosity of 7Q34Q36.3 in the ganglioglioma-like tumor component. This case highlights the critical role of molecular testing in the diagnosis of rare cases of DLGNT with diverse morphological components as well as in the identification of unique molecular alternations responsible for morphological phenotypes of the distinct tumors in DLGNT.

Chromosome 1 instability in multiple myeloma: Aberrant gene expression, pathogenesis, and potential therapeutic target.

Multiple myeloma (MM), the terminally differentiated B cells malignancy, is widely considered to be incurable since many patients have either developed drug resistance or experienced an eventual relapse. To develop precise and efficient therapeutic strategies, we must understand the pathogenesis of MM. Thus, unveiling the driver events of MM and its further clonal evolution will help us understand this complicated disease. Chromosome 1 instabilities are the most common genomic alterations that participate in MM pathogenesis, and these aberrations of chromosome 1 mainly include copy number variations and structural changes. The chromosome 1q gains/amplifications and 1p deletions are the most frequent structural changes of chromosomes in MM. In this review, we intend to focus on the genes that are affected by chromosome 1 instability: some tumor suppressors were lost or down regulated in 1p deletions, and others that contributed to tumorigenesis were upregulated in 1q gains/amplifications. We have summarized their biological function as well as their roles in the MM pathogenesis, hoping to uncover potential novel therapeutical targets and promote the development of future therapeutic approaches.

Diffuse leptomeningeal glioneuronal tumor without KIAA1549-BRAF fusion and 1p detection: a case report and review of literature.

BACKGROUND: Diffuse leptomeningeal glioneuronal tumor (DLGNT) is a rare mixed neuronal-glial tumor of central nervous system. Chromosome microarray usually identifies co-deletion of the short arm of chromosome 1 and the long arm of chromosome 19 as well as fusion of the KIAA1549 and BRAF genes. METHODS: We describe a case of a 3-year-old boy with typical imaging and histopathological features, but without KIAA1549-BRAF fusion and 1p deletion. Additionally, a literature review is performed summarizing the clinical features, management, and prognosis of this rare entity. RESULTS: A 3-year-old boy presented with chronic headache and vomiting. On initial MRI scanning, diffuse thickening with enhancement of the cerebral and spinal leptomeninges could be detected after contrast injection. Multiple cystic lesions were found located on infratentorial leptomeninges, with progressive thickening of leptomeninges and increasing cysts on follow-up MRI after 9 months. Meningeal biopsy was carried out, showing that most of tumor cells were composed of oligodendroglioma-like cells. The tumor cells were immunopositive for GFAP, Olig-2, and synaptophysin but negative for IDH-1 and H3k27M. Molecular genetic testing did not detect KIAA1549-BRAF fusion, 1p deletion, or 1p/19q co-deletion. The patient was finally diagnosed as DLGNT after multidisciplinary team consultation. CONCLUSIONS: Given that the clinical and pathological mechanism of DLGNTs remains unclear, our case gives supplement about the diversity of molecular genetic characteristics. Combination of clinical, neuroradiological, and histopathological data is particularly important for the diagnosis of DLGNTs, till now.

Coexpression network analysis identifies transcriptional modules associated with genomic alterations in neuroblastoma.

Neuroblastoma is a highly complex and heterogeneous cancer in children. Acquired genomic alterations including MYCN amplification, 1p deletion and 11q deletion are important risk factors and biomarkers in neuroblastoma. Here, we performed a co-expression-based gene network analysis to study the intrinsic association between specific genomic changes and transcriptome organization. We identified multiple gene coexpression modules which are recurrent in two independent datasets and associated with functional pathways including nervous system development, cell cycle, immune system process and extracellular matrix/space. Our results also indicated that modules involved in nervous system development and cell cycle are highly associated with MYCN amplification and 1p deletion, while modules responding to immune system process are associated with MYCN amplification only. In summary, this integrated analysis provides novel insights into molecular heterogeneity and pathogenesis of neuroblastoma. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.

Diffuse leptomeningeal glioneuronal tumor (DLGNT) mimicking Whipple's disease: a case report and literature review.

INTRODUCTION: Diffuse leptomeningeal glioneuronal tumor is a new entity under the neuronal and mixed neuronal-glial tumors in the WHO 2016 updated classification and commonly found in children and adolescents. The initial diagnosis is challenging because of its non-specific radiologic feature and negative CSF cytology analysis. A 17 years male was presented with intractable headache subsequently followed by back pain and joint pain. MRI showed enhancement of arachnoid membrane at basal cistern, bilateral sylvian fissure and cerebral cistern with slight enlargement of ventricles. There were no evidences of infection in CSF and blood samples. Based on the duodenal biopsy and prodromal symptom of joint pain, the patient was suspected of having Whipple's disease. Eleven months after the onset, a small mass lesion was observed at the anterior horn of right lateral ventricle. The histology was remarkable for anaplastic oligodendroglioma. Immunostainings revealed positivity for GFAP, Olig2, synaptophysin and negativity for IDH1 mutation, H3K27M. MIB1 labeling index was 40% and 1p19q FISH analysis showed only 1p deletion. Therefore, a final diagnosis of DLGNT was made. CONCLUSION: DLGNT should be included as a differential diagnosis of patients with leptomeningeal-enhanced and high CSF protein level with normal white blood cell count.

Intellectual disability secondary to a 16p13 duplication in a 1;16 translocation. Extended phenotype in a four-generation family.

We describe a large family from the Gaza Strip presented with multiple congenital anomalies. The proband was presented with intellectual disability and multiple congenital anomalies including cleft palate, low-set ears, everted upper lip, diaphragmatic hernia, and arthrogryposis. Pedigree analysis showed 19 affected patients over five generations, only 6 were alive and 11 individuals were obligate carriers. The proband had an apparently normal karyotype, although FISH studies showed a derivative chromosome 1 with duplication of 16p13.3 and deletion of the 1p subtelomere. Her father however had a balanced translocation. The seven affected patients had a similar phenotype, one of them died before genetic testing was carried out and the living six patients had the same unbalanced translocation. Array CGH revealed an 8.8 Mb duplication in 16p13 and 200,338 bp deletion in 1p36.3. Accordingly, intellectual disability, hypertelorism, cupped ears, everted upper lip, and limb anomalies were presenting clinical features of the 16p13 duplication syndrome while deep set eyes were perhaps related to the 1p terminal deletion. Prevention of recurrent intellectual disability in this family can be achieved through carrier detection and prenatal genetic diagnosis.

Oncocytoma-Like Angiomyolipoma of the Kidney: A Closer Look into the Clinicopathologic, Immunohistochemical, and Molecular Characteristics of a Rare Entity with Review of the Literature.

Introduction. Angiomyolipoma (AML) is a mesenchymal neoplasm that belongs to the perivascular epithelioid cell tumor family (PEComa). AMLs can be subtyped into several patterns dependent on cell type, morphology, and tissue composition. One of the patterns, oncocytoma-like AML is a rare entity with only three cases published in the literature. Case presentation. We present a case of a previously healthy 29-year-old woman who underwent a left partial nephrectomy secondary to a 4.6 cm heterogeneous renal neoplasm. Gross examination demonstrated a well-circumscribed renal mass. Modified Giemsa stain preparation showed oncocytic cells in syncytial pattern with ample granular cytoplasm and round nuclei with prominent nucleoli. Histology assessment showed an oncocytic neoplasm with interspersed adipose tissue. The tumor exhibited tubular architecture with the tubules lined by eosinophilic epithelioid cells with nuclear atypia and prominent nucleoli. Thick blood vessels with emanating epithelioid cells were present. High-grade histology features were not identified. The tumor cells were positive for HMB-45 and SMA and negative for PAX8, keratins, KIT, and vimentin. A diagnosis of oncocytoma-like AML was rendered. Next-generation sequencing (NGS) and RNA fusion were performed. NGS revealed no pathogenic variants and RNA fusion identified no rearrangements. Chromosomal copy number alterations were present in the long arm of chromosome 1 (1p) and chromosome 22. Conclusions. We describe and discuss the clinical, cytomorphologic, histologic, and molecular findings of oncocytoma-like AML, a rare renal neoplasm, and provide a review of the literature.

Chromosome 1p status in neuroblastoma correlates with higher expression levels of miRNAs targeting neuronal differentiation pathway.

Neuroblastoma (NB) is characterized by acquired segmental and numerical chromosome aberrations. Although deletions of distal 1p and 11q are frequent alterations, no candidate tumor suppressor gene residing in these chromosomal sites could be identified so far. In the present study, we detected the genomic imbalances of six neuroblastoma cell lines using the multiplex ligation-dependent probe amplification (MLPA) technique and the microRNA (miRNA) expression profiles of the cell lines by a microarray study. According to MLPA results, we aimed to assess the miRNA expression profiles of the cell lines harboring 11q and 1p deletions. The cell lines with 1p deletions revealed statistically significant higher levels of expression for 29 miRNAs in contrast to the cell lines without 1p deletion in microarray study. We also performed GO enrichment analysis for predicted targets of the differentially expressed miRNAs. According to GO enrichment analysis, miRNAs that showed the high change in expression was associated with neuronal differentiation. We showed that hsa-miR-494, hsa-miR-495, and hsa-miR-543 target most of mRNAs in neuronal differentiation pathway. Although limited to the cell lines, our results highly suggest that NBs with different segmental chromosome abnormalities may have different dysregulated miRNA expression signatures that target the genes involved in neuronal differentiation.

Chromosome 1p36 candidate gene ZNF436 predicts the prognosis of neuroblastoma: a bioinformatic analysis.

BACKGROUND: Genetic 1p deletion is reported in 30% of all neuroblastoma and is associated with the unfavorable prognosis of neuroblastoma. The expressions and prognosis of 1p candidate genes in neuroblastoma are unclear. METHODS: Public neuroblastoma cohorts were obtained for secondary analysis. The prognosis of 1p candidate genes in neuroblastoma was determined using Kaplan-Meier and cox regression analysis. The prediction of the nomogram model was determined using timeROC. RESULTS: First, we confirmed the bad prognosis of 1p deletion in neuroblastoma. Moreover, zinc finger protein 436 (ZNF436) located at 1p36 region was down-regulated in 1p deleted neuroblastoma and higher ZNF436 expression was associated with the longer event free survival and overall survival of neuroblastoma. The expression levels of ZNF436 were lower in neuroblastoma patients with MYCN amplification or age at diagnosis ≥ 18months, or with stage 4 neuroblastoma. ZNF436 had robust predictive values of MYCN amplification and overall survival of neuroblastoma. Furthermore, the prognostic significance of ZNF436 in neuroblastoma was independent of MYCN amplification and age of diagnosis. Combinations of ZNF436 with MYCN amplification or age of diagnosis achieved better prognosis. At last, we constructed a nomogram risk model based on age, MYCN amplification and ZNF436. The nomogram model could predict the overall survival of neuroblastoma with high specificity and sensitivity. CONCLUSIONS: Chromosome 1p36 candidate gene ZNF436 was a prognostic maker of neuroblastoma.

Optical Genome Mapping Reveals the Complex Genetic Landscape of Myeloma.

Fluorescence in situ hybridization (FISH) on enriched CD138 plasma cells is the standard method for identification of clinically relevant genetic abnormalities in multiple myeloma. However, FISH is a targeted analysis that can be challenging due to the genetic complexity of myeloma. The aim of this study was to evaluate the potential of optical genome mapping (OGM) to detect clinically significant cytogenetic abnormalities in myeloma and to provide larger pangenomic information. OGM and FISH analyses were performed on CD138-purified cells of 20 myeloma patients. OGM successfully detected structural variants (SVs) (IGH and MYC rearrangements), copy number variants (CNVs) (17p/TP53 deletion, 1p deletion and 1q gain/amplification) and aneuploidy (gains of odd-numbered chromosomes, monosomy 13) classically expected with myeloma and led to a 30% increase in prognosis yield at our institution when compared to FISH. Despite challenges in the interpretation of OGM calls for CNV and aneuploidy losses in non-diploid genomes, OGM has the potential to replace FISH as the standard of care analysis in clinical settings and to efficiently change how we identify prognostic and predictive markers for therapies in the future. To our knowledge, this is the first study highlighting the feasibility and clinical utility of OGM in myeloma.

Comparison of Next-Generation Sequencing and Fluorescence In Situ Hybridization for Detection of Segmental Chromosomal Aberrations in Neuroblastoma.

The aim of this study was to compare next-generation sequencing (NGS) with the traditional fluorescence in situ hybridization (FISH) for detecting segmental chromosomal aberrations (SCAs) such as 1p deletion, 11q deletion and 17q gain, which are well-known predictive markers for adverse outcome in neuroblastoma. The tumor tissue obtained from 35 patients with neuroblastoma was tested by FISH and targeted NGS, which is specially designed to detect copy number alterations across the entire chromosomal region in addition to mutations in 353 cancer-related genes. All chromosomal copy number alterations were analyzed using the copy number variation plot derived from targeted NGS. FISH was performed to detect 1p deletion, 11q deletion and 17q gain. The copy numbers of 1p, 11q, and 17q obtained via NGS were correlated with those acquired via FISH. The SCAs determined by NGS were matched with those by FISH. Most 17q gain of mismatched cases detected by NGS alone showed a subsegmental gain of 17q. FISH revealed 11q deletion and 17q gain in a few tumor cells of two cases, which were not detected by NGS. NGS can be a sensitive complementary and alternative method to the conventional FISH for detecting SCAs.

Paediatric diffuse leptomeningeal tumor with glial and neuronal differentiation harbouring chromosome 1p/19q co-deletion and H3.3 K27M mutation: unusual molecular profile and its therapeutic implications.

Diffuse leptomeningeal glioneuronal tumor (DL-GNT) is a newly introduced tumor entity of uncertain prognosis characterised by a primary diffuse leptomeningeal growth pattern, oligodendroglial-like morphology and dual glial/neuronal differentiation. Predominantly occurring in children, these tumors present as chronic meningitis and mimic infectious/inflammatory diseases. They are surgically challenging tumors with a high incidence of delayed morbidity and mortality despite low-grade histology. Their molecular genetic profile is not fully elucidated and few reports have identified chromosome 1p and 19q deletions, and BRAF alterations. We present a rare instance of a DL-GNT in a 13-year-old female who presented with slowly progressive and sequential neurological deficits over a 12-month duration. Imaging showed leptomeningeal thickening and spinal lesions. Biopsy from the spinal mass showed histomorphological features characteristic of DL-GNT. Further molecular analysis revealed 1p and 19q co-deletion and H3K27M mutation, while no mutation were identified in IDH, TERT, or BRAF genes. Patient died 4 months after diagnosis. Only one previous case of DL-GNT has been reported to harbour H3K27M mutation. Although H3K27M mutations have been described in rare examples of low-grade glial and glioneuronal tumors, whether DL-GNTs with H3K27M represent a rare growth pattern of the aggressive H3K27M-mutant diffuse midline gliomas needs further clarification.

Prognostic value of 1p deletion for multiple myeloma: a meta-analysis.

INTRODUCTION: Previous studies have indicated that a deletion on the short arm of chromosome 1 negatively predicts survival in patients with multiple myeloma (MM). Due to the small sample size in each study, we performed this meta-analysis to comprehensively investigate the association between the 1p deletion and survival in patients with MM. METHODS: A literature search was conducted in both foreign and Chinese databases, including SinoMed, CNKI, Wanfang, PubMed, EMBASE, and Scopus. Hazard ratios (HR) with 95% confidence intervals (CI) for overall survival (OS) and progression-free survival (PFS) in 11 eligible articles were extracted or calculated to analyze the pooled HR, which was estimated by fixed-effect or random-effect models based on the heterogeneity between included articles. A subgroup analysis and a meta-regression were conducted, and Galbraith plots were generated to examine any possible heterogeneity. RESULTS: The HRs for OS were available in nine articles, whereas five articles discussed HRs for PFS. The HR with 95%CI was 1.989 (95%CI 1.522-2.600, P = 0.017, I(2)  = 57.1%) when comparing the OS of patients with 1p deletion with the OS of those without this deletion. For PFS, 1p deletion still predicted a poor prognosis (HR 2.11, 95%CI 1.54-2.88, P = 0.292, I(2)  = 19.3%). Moreover, the subgroup analysis suggested that either the deleted gene on 1p or techniques for detecting chromosome abnormalities contributed to the heterogeneity, which was partially consistent with the results derived from a meta-regression analysis and the Galbraith plot method. CONCLUSION: Our meta-analysis provides globally quantifiable confirmation of the adverse prognostic role of 1p deletion in OS and PFS for patients with MM.