Comprehensive Genetic and Histopathologic Study Reveals Three Types of Neuroblastoma Tumors

PURPOSE: To determine the relationship between multiple genetic features, tumor morphology, and prognosis in neuroblastoma. PATIENTS AND METHODS: The genetic alterations and morphologic features that underpin three histopathologic risk classifications were analyzed in 108 neuroblastoma patients. Tumors were subdivided into four groups based on the three most frequent and prognostically significant genetic alterations (17q gain, 1p deletion, and MYCN amplification), and all other genetic, morphologic, and clinical data were analyzed with respect to these groups. RESULTS: Our analyses identify three nonoverlapping tumor types with distinct genetic and morphologic features, defined here as types 1, 2, and 3. Type 1 tumors show none of the three significant genetic alterations and have good prognosis. Both type 2 (17q gain only or 17q gain and 1p del) and type 3 (17q gain, 1p del, and MYCN amplification) tumors progress. However, these tumor types are distinguished clinically by having significantly different median age at diagnosis and median progression-free survival (PFS). Multivariate analysis indicates that 17q gain is the only independent prognostic factor among all genetic, histopathologic, and clinical factors analyzed. Among histopathologic risk systems, the International Neuroblastoma Pathology Classification was the best predictor of PFS. CONCLUSION: Our results indicate that specific combinations of genetic changes in neuroblastoma tumors contribute to distinct morphologic and clinical features. Furthermore, the identification of two genetically and morphologically distinct types of progressing tumors suggests that possibilities for different therapeutic regimens should be investigated.

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Association of TP53 mutation status and GATA6 amplification with clinical outcome of pancreatic cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e16224 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e16224-e16224

Author(s):

Jung-In Yang ◽

Taehoon Ha ◽

Edward Zhou ◽

Chris Tzanavaris ◽

Craig E. Devoe ◽

...

Keyword(s):

Clinical Outcome ◽

Retrospective Analysis ◽

Tp53 Mutation ◽

Progression Free Survival ◽

Tp53 Gene ◽

Genetic Alterations ◽

Cancer Prognosis ◽

General Belief ◽

Genetic Changes ◽

Survival Estimate

e16224 Background: Recent advances in pancreatic adenocarcinoma (PDAC) research unveiled that molecular subtypes reflect cancer prognosis and chemosensitivity. Here, we examined the possible use of genomic profiling of PDAC in the clinic by assessing retrospective clinical outcomes and treatment responsiveness based on genetic alterations. Methods: All patients treated for PDAC with Next-Generation Sequencing (NGS) data available between 2014 to 2020 at Northwell Health Cancer Institute were included in a retrospective analysis. Patients were subdivided into resectable and unresectable cancer. Genetic findings frequently reported in NGS were used to compare progression-free survival (PFS) and overall survival (OS) within subgroups. Survival probability was compared using Peto-Peto’s modified survival estimate followed by pairwise comparisons using Peto-Peto’s modified survival estimate. Family-wise error rate was adjusted using Benjamini & Hochberg method. Results: A total 115 patients were qualified for the evaluation. In all cases of PDAC, TP53 mutation (n = 89) was associated with poor OS compared to the wild-type TP53 gene (n = 19) (median OS 20.2 months, 95% CI 10.2 to 39.7, vs. 41.1 months, 95% CI 20.9 to 81.0, HR 1.98, p = 0.028). In unresectable PDAC, tumors with GATA6 amplification (n = 11) were associated with a significantly better OS over patients whose tumors harbored a TP53 mutation (n = 57) (median OS 22.9 months, 95% CI 9.6 to 54.5, vs. 10.0 months, 95% CI 4.2 to 23.8, HR 0.48, p = 0.048) . Within the TP53 mutation group, FOLFIRINOX (n = 21) did not show improved OS compare to Gem/NabP (n = 30) (mean OS 13.8 months, 95% CI 6.8 to 28.2, vs. 8.5 months, 95% CI 4.17 to 17.4, HR 0.84, p = 0.25). Other genetic alterations were not associated with OS. There was no difference in PFS in all PDACs. Conclusions: Our retrospective analysis showed that genetic changes in TP53 and GATA6 were significantly associated with the clinical outcome for PDAC. Mutation of TP53 was associated with poor OS in general. However, in unresectable PDAC, GATA6 amplification was associated with better clinical outcome than tumors with TP53 mutation. In contrary to general belief, FOLFIRINOX did not result in better OS than Gem/NabP.

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Oncogenic PKA signaling stabilizes MYC oncoproteins via an aurora kinase A-dependent mechanism

10.1101/2021.04.16.438110 ◽

2021 ◽

Author(s):

Gary K. L. Chan ◽

Samantha Maisel ◽

Yeonjoo C. Hwang ◽

Rebecca R. B. Wolber ◽

Phuong Vu ◽

...

Keyword(s):

Drug Targets ◽

Human Cancer ◽

Aurora Kinase ◽

Genetic Alterations ◽

Genetic Changes ◽

Aurora Kinase A ◽

Protein Levels ◽

Cancer Models ◽

Tumor Types ◽

Kinase A

AbstractGenetic alterations that activate protein kinase A (PKA) signaling are found across many tumor types, but their downstream oncogenic mechanisms are poorly understood. We used global phosphoproteomics and kinome activity profiling to map the conserved signaling outputs driven by diverse genetic changes that activate PKA in human cancer, including melanoma and fibrolamellar carcinoma (FLC). We define two consensus networks of effectors downstream of PKA in cancer models. One is centered on RAS/MAPK components, and a second involves Aurora Kinase A (AURKA). We find that AURKA stabilizes c-MYC and n-MYC protein levels and expression programs in PKA-dependent tumor models, in part via a positive feedback loop mediated by the oncogenic kinase PIM2. This process can be suppressed by conformation-disrupting AURKA inhibitors such as CD-532. Our findings elucidate two independent mechanisms of PKA-driven tumor cell growth and offer insight into drug targets for study in FLC and other PKA-dependent malignancies.

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PATH-66. THE GENOMIC LANDSCAPE OF SPINAL CORD EPENDYMOMA

Neuro-Oncology ◽

10.1093/neuonc/noz175.661 ◽

2019 ◽

Vol 21 (Supplement_6) ◽

pp. vi158-vi158

Author(s):

Biswarathan Ramani ◽

Javier Villanueva-Meyer ◽

Christine Glastonbury ◽

Ece Meram ◽

Kyle Walsh ◽

...

Keyword(s):

Spinal Cord ◽

Progression Free Survival ◽

Suppressor Gene ◽

Tumor Location ◽

Genetic Alterations ◽

Lumbar Spinal Cord ◽

Small Subset ◽

Mycn Amplification ◽

Chromosome 22Q ◽

Significant Difference

Abstract INTRODUCTION Ependymomas are seen throughout the neural axis but spinal cord is most common in adults. A subset arises in the setting of neurofibromatosis 2, whereas most are sporadic, potentially with somatic NF2 inactivation. The genetic drivers in NF2 wildtype tumors are unknown, as is the spectrum of cooperating genetic alterations. METHODS We performed targeted next-generation sequencing (NGS) to assess mutations, rearrangements, and chromosomal copy number alterations in 46 adult spinal cord ependymomas. RESULTS The 24 females and 22 males ranged from 20–73 (median 46) years of age. Tumors were in the cervical (n=24), thoracic (n=12), and lumbar (n=10) spinal cord. Nine tumors (20%) harbored truncating NF2 mutations with loss of the remaining wildtype allele, with frequent monosomy 13q. Thirteen NF2-wildtype tumors (28%) showed monosomy 22q with frequent monosomy 13q and trisomy 7, 9, and 12. Seventeen tumors (37%) carried a near-tetraploid genome, likely due to genomic reduplication with frequent preservation of diploidy in chromosomes 13q (77%), 14q (88%), 21q (53%) and 22q (65%). Remaining cases did not show a recurrent pattern, but one harbored focal high-level MYCN amplification. Three of the six recurrences were seen in the last subgroup; however, there was no significant difference for progression-free survival between four subgroups. None of the NF2-mutant tumors were in lumbar spinal cord, but there was no difference for tumor location or patient age between four subgroups. DISCUSSION Biallelic NF2 mutational inactivation characterizes only a subset of spinal cord ependymomas, and MYCN amplification is likely a genetic driver in a small subset of NF2 wildtype cases. The high frequency of chromosome 22q loss even in NF2-wildtype tumors raises the possibility of cryptic alterations in the NF2 gene not detected by our panel, or perhaps implicates the presence of another as yet unidentified tumor suppressor gene on chromosome 22q.

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Typical numerical alterations in genome identified by array CGH analysis in neuroblastoma tumors

AIMS Molecular Science ◽

10.3934/molsci.2021019 ◽

2021 ◽

Vol 8 (4) ◽

pp. 248-256

Author(s):

Katarzyna Szewczyk ◽

◽

Keyword(s):

Array Cgh ◽

Positive Impact ◽

Good Prognosis ◽

Chromosome 17 ◽

Mycn Amplification ◽

Chromosome 14 ◽

Genetic Changes ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Tumor Genome

<abstract><sec> <title>Introduction</title> The clinical variability in the course of neuroblastoma (NB) is closely linked to diverse genetic changes acquired by tumor cells. Rapid NB progression is associated with oncogene MYCN amplification (MNA) and segmental chromosomal aberrations (SCA). Alternatively, numerical chromosomal alterations (NCA) have positive impact on treatment. So far, no studies have been undertaken to identify NCA that may group NB patients. Therefore, the aim of the study was to identify NCA typical for NB. </sec><sec> <title>Materials and methods</title> Copy number alterations in NB tumor genome (fresh samples N = 94; formalin-fixed paraffin-embedded specimens N = 66) were analyzed with a pangenomic array CGH technique. </sec><sec> <title>Results</title> The profile with NCA was observed in 72 (45%) cases, NCA+SCA in 37 (23%), normal in 35 (22%) and MNA in 16 (10%). Samples with NCA were characterized by whole chromosome gains: 17, 7, 6 (78%, 65%, 51%, respectively) and copy loss of chromosome 14 (57%). Similarly to NCA, patients with a combined NCA and SCA profile were also characterized by gain of whole chromosome 17 and 7 (35% both) and loss of chromosome 14 (38%), but with lower frequency. In the combined NCA and SCA profiles, typical NB changes such as deletion 1p36 (27%) and gain 17q (41%) were observed, as well as deletion 11q (24%). The same alterations were detected in MNA samples (44%, 44%, 19%, respectively). A difference was found in spanning 11q deletion between MNA and NCA+SCA subgroup, which may suggest new prognostic markers in NB. In MNA subgroup specific NCA was not indicated. </sec><sec> <title>Conclusions</title> The hypothesis that NCA in NB tumors are more frequent in younger children with good prognosis was confirmed. To gain new insights into the pathogenesis of NB and to establish molecular targets for diagnosis and therapy, candidate genes in the altered chromosomal regions must be investigated. </sec></abstract>

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Comprehensive study of genetic features of pancreatic neuroendocrine tumors.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.e16699 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. e16699-e16699

Author(s):

Vladimir S. Trifanov ◽

Oleg I. Kit ◽

Dmitry Yu. Gvaldin ◽

Natalya N. Timoshkina ◽

Sergey V. Sanamyants ◽

...

Keyword(s):

Candidate Genes ◽

Neuroendocrine Tumors ◽

Molecular Genetic ◽

Genetic Alterations ◽

Pancreatic Neuroendocrine Tumors ◽

Loss Of Function ◽

Rare Type ◽

Genetic Changes ◽

Genetic Features ◽

American Society

e16699 Background: Pancreatic neuroendocrine tumors (panNETs) are a heterogeneous, relatively rare type of neoplasm which distinguishes a long clinical course in a large number of cases, that leads to the fact that the prevalence rate of NETs is one of the highest. The purpose of this study was a research the mutational profiles of panNETs of various grades of malignancy and to search for new candidate genes involved in the oncogenic processes of this pathology. Methods: The study included a retrospective group of 24 patients (10 men, 14 women, median age - 60 years old) with a diagnosis of panNET, treated in the RRIO from 2011 to 2018. Comprehensive cancer panel (409 genes) were used for NGS procedure on the NextSeq 550 platform(Illumina, USA). To work with raw data, we used the standard pipeline proposed by BaseSpace (Illumina, USA). Interpretation of the identified variants was carried out in accordance with the recommendations of the Association for Molecular Pathology, American Society of Clinical Oncology and College of American Pathologists. Results: 119 mutations in 54 genes were detected in samples of panNETs. 26 genetic variations were characterized as new, not previously described for panNETs. 18% of the mutations were activating, 35% of the variants led to a loss of function of the encoded protein, 52% were not classified. Candidate genes that have not been previously described in the literature and which are potentially involved in pancreatic oncogenesis are identified: CREB1, TCF12, PRKAR1A, BCL11A and BUB1B. The largest number of mutational events occurred in the genes responsible for histone methylation; in addition, 38% described genetic alterations in the regulation of the SMAD2/3 signaling pathway. Conclusions: According to the NGS study of panNETs of low and moderate malignancy in the Russian cohort, a unique spectrum of 119 mutations was obtained, of which 26 were not previously described. The discovered molecular genetic changes in the signaling pathways underline the importance of impaired epigenetic control of transcription in pancreatic oncogenesis and open up new prospects for targeted therapy.

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PATH-13. PLEOMORPHIC XANTHOASTROCYTOMA INTEGRATED GENOMIC CHARACTERIZATION - WHAT HAVE WE LEARNED?

Neuro-Oncology ◽

10.1093/neuonc/noaa222.648 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii426-iii427

Author(s):

Rachael Vaubel ◽

Valentina Zschernack ◽

Alissa Caron ◽

Dragana Milosevic ◽

Robert Jenkins ◽

...

Keyword(s):

Overall Survival ◽

Strong Predictor ◽

Progression Free Survival ◽

Genetic Alterations ◽

Pleomorphic Xanthoastrocytoma ◽

Who Grade ◽

Targeted Next Generation Sequencing ◽

Genomic Characterization ◽

Promoter Mutations ◽

Methylation Profiling

Abstract Pleomorphic xanthoastrocytoma (PXA) is a rare astrocytoma occurring predominantly in children and young adults. It is characterized histologically by large pleomorphic, spindled and lipidized cells with frequent eosinophilic granular bodies and pericellular reticulin deposition. BRAF p.V600E mutation and CKDN2A/B deletion are the most common genetic alterations. We report the integrated genomic characterization of a cohort of 67 patients (37 F, 30 M; median age 20.3 years (interquartile 13.4–32.9) with histologically defined PXA (52, 78%) or anaplastic PXA (A-PXA) (15, 22%), using genome-wide cytogenetic (ThermoFisher Oncoscan, n=67), methylation profiling (Illumina EPIC array, n=43), and targeted next generation sequencing (n=32). BRAF p.V600E mutation (n=51, 76.1%) and CDKN2A/B deletion (n=63; 94%) were the most frequent alterations. Of 16 BRAF p.V600E negative cases, 7 showed an alternative BRAF activating mutation (n=2), NF1 (n=3) mutation or ATG7-RAF1 fusion (n=2). Targeted TERT analysis found promoter mutations in 3 (of 58) cases, but TERT amplification was absent. Supervised and unsupervised methylation profiling against a comprehensive reference cohort demonstrated consensus grouping with the PXA class in 36 of 43 cases; while the minority grouped with a ganglioglioma class (n=3), with reactive brain or had no resolvable subgroup (n=4). Follow-up was available in 61 patients (91.0%) (median 63 months). Overall survival was significantly different between PXA and A-PXA (5-year:80.4% vs. 55.1%; p=0.001), but not progression-free survival (5-year:61.7% vs. 39.8%; p=0.128). Our data confirm the high frequency of MAP-K abnormalities and CDKN2A/B deletion in PXA. WHO grade remains a strong predictor of patient overall survival.

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A phase 2 study of defactinib (VS-6063) in patients with NF2 altered tumors: Results from NCI-match (EAY131) subprotocol U.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.3087 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 3087-3087

Author(s):

David Michael Jackman ◽

Opeyemi Jegede ◽

Marjorie Glass Zauderer ◽

Edith P. Mitchell ◽

James Zwiebel ◽

...

Keyword(s):

Solid Tumors ◽

Stable Disease ◽

Objective Response ◽

Genomic Analysis ◽

Progression Free Survival ◽

Genetic Alterations ◽

Outcome Analysis ◽

Clinical Activity ◽

Match Trial ◽

Best Response

3087 Background: The NCI-MATCH trial assigns patients (pts) with solid tumors, lymphomas, or multiple myeloma to targeted therapies based on genetic alterations identified in tumor biopsies. Neurofibromatosis 2 (NF2)-inactivated tumors demonstrate increased sensitivity to FAK inhibition in preclinical models. Arm U evaluated the FAK inhibitor defactinib in pts with NF2 altered tumors. Methods: Patients found to harbor an inactivating NF2 mutation on NGS were assigned to the ARM U substudy MATCH. Defactinib 400 mg was given by mouth twice daily until progression or intolerable toxicity. The primary endpoint was objective response rate (ORR). Secondary endpoints included toxicity, progression-free survival (PFS), and 6-month PFS. Results: Of 5,548 cases with sufficient tissue for genomic analysis, 51 pts were found to have NF2 alterations (< 1% of the total analyzed). While NF2 alterations are known to occur more commonly in meningiomas and mesotheliomas, alterations were also detected in an array of other tumor types, including renal cell carcinomas and ovarian cancers. Thirty-five pts were ultimately enrolled; 33 patients were started on therapy, with 2 of those determined to be ineligible for outcome analysis. All pts had received at least one prior therapy, with 52% (16/31) having received 3 or more prior lines of therapy. Median follow-up was 35.9 months. ORR [90% CI] was 3% (1/31, [0.16, 14.86]), with the one partial response in a pt with choroid meningioma. Of the twelve pts whose best response was stable disease (39%, 12/31), 8 demonstrated some degree of tumor shrinkage (Table) with a disease control rate of 42% (13/31). Median PFS was 1.9 months for the 31 eligible pts who received study treatment, with median PFS of 9.3 months for the 9 patients who had a best response of stable disease or better. Six pts achieved a PFS of greater than 5.5 months. Among all treated pts (n=33), the most common treatment-related toxicities were fatigue (36%), nausea (33%), and hyperbilirubinemia (27%). There were no grade 4 or 5 toxicities; 27% of pts had grade 3 toxicities. No correlation could be made between clinical outcomes and tumor histology or specific NF2 genotype. Conclusions: Defactinib monotherapy had limited clinical activity in this cohort of previously treated patients with solid tumors exhibiting NF2 loss. Clinical trial information: NCT04439331. [Table: see text]

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Treatments after Immune Checkpoint Inhibitors in Patients with dMMR/MSI Metastatic Colorectal Cancer

Cancers ◽

10.3390/cancers14020406 ◽

2022 ◽

Vol 14 (2) ◽

pp. 406

Author(s):

Quang Loc Bui ◽

Léo Mas ◽

Antoine Hollebecque ◽

David Tougeron ◽

Christelle de la Fouchardière ◽

...

Keyword(s):

Colorectal Cancer ◽

Disease Control ◽

Metastatic Colorectal Cancer ◽

Checkpoint Inhibitors ◽

Progression Free Survival ◽

Immune Checkpoints ◽

Repair Deficiency ◽

Improved Outcomes ◽

Number Of Patients ◽

Tumor Types

Background: Several studies reported improved outcomes with conventional treatments (CT, i.e., chemotherapy ± targeted therapy) administered after immune checkpoints inhibitors (ICI) in certain tumor types. No data are available concerning patients (pts) with metastatic colorectal cancer (mCRC) harboring mismatch repair deficiency/microsatellite instability (dMMR/MSI). We aimed to assess the outcomes of dMMR/MSI mCRC pts receiving CT after ICI failure. Methods: We conducted a retrospective multicenter study investigating the outcomes of all dMMR/MSI mCRC pts who received post-ICI CT between 2015 and 2020. Results: 31 pts (male 61%, median age 56 years) were included. ICI was an anti-PD(L)1 monotherapy in 71% of pts, and 61% received >2 lines before post-ICI CT. The overall response rate and disease control rate were 13% and 45%, with a median progression-free survival (PFS) and overall survival of 2.9 and 7.4 months, respectively. No association of the outcomes with either ICI efficacy or anti-angiogenic agents was observed. Prolonged PFS (range 16.1–21.3 months) was observed in 4 pts (13%). Conclusions: Although conducted on a limited number of patients, our results do not support an association of previous ICI treatment with an enhanced efficacy of CT in dMMR/MSI mCRC. However, prolonged disease control was observed in several cases, suggesting that some pts might derive an unexpected benefit from post-ICI treatments.

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Adenoid cystic carcinoma of the breast: case report

Mastology ◽

10.29289/2594539420210009 ◽

2021 ◽

Vol 31 ◽

Author(s):

Matheus Lavigne Marinho ◽

Alexandre Tafuri ◽

Carlos Alberto da Silva Ramos ◽

Antônio Alexandre Lisbôa Ladeia ◽

Luciana de Carvalho Azevedo

Keyword(s):

Breast Cancer ◽

Adenoid Cystic Carcinoma ◽

Triple Negative ◽

Breast Conserving Surgery ◽

Genetic Alterations ◽

Good Prognosis ◽

Carcinoma Of The Breast ◽

Adenoid Cystic ◽

Molecular Aspects ◽

Peculiar Behavior

Adenoid cystic carcinoma (AdCC) of the breast is an uncommon invasive lobular neoplasm whose morphology is similar to the homonymous tumor of salivary glands and with a peculiar behavior toward the “triple-negative” (TN) profile. Tumors belonging to this family do not immunohistochemically express three of the main prognostic biomarkers and tend to show a more aggressive behavior. However, this rare histological pattern of breast cancer is generally associated with good prognosis. In this study, the authors describe the case of a 49-year-old woman diagnosed with this rare malignant tumor and who underwent breast-conserving surgery. Recent studies have aimed to understand the genes, genetic alterations, and etiological aspects related to the still obscure etiopathogenesis of AdCC. Thus, morphological and molecular aspects relevant to AdCC and reported in the literature will be discussed.

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Chimeric RNA:DNA Donorguide Improves HDR in vitro and in vivo

10.1101/2021.05.28.446234 ◽

2021 ◽

Author(s):

Brandon W Simone ◽

Han B Lee ◽

Camden L Daby ◽

Santiago Restrepo-Castillo ◽

Hirotaka Ata ◽

...

Keyword(s):

Cell Types ◽

Repair Process ◽

Strand Break ◽

Genetic Alterations ◽

Precise Integration ◽

Genetic Changes ◽

Area Of Interest ◽

Temporal Localization

Introducing small genetic changes to study specific mutations or reverting clinical mutations to wild type has been an area of interest in precision genomics for several years. In fact, it has been found that nearly 90% of all human pathogenic mutations are caused by small genetic variations, and the methods to efficiently and precisely correct these errors are critically important. One common way to make these small DNA changes is to provide a single stranded DNA (ssDNA) donor containing the desired alteration together with a targeted double-strand break (DSB) at the genomic target. The donor is typically flanked by regions of homology that are often ~30-100bp in length to leverage the homology directed repair (HDR) pathway. Coupling a ssDNA donor with a CRISPR-Cas9 to produce a targeted DSB is one of the most streamlined approaches to introduce small changes. However, in many cell types this approach results in a low rate of incorporation of the desired alteration and has undesired imprecise repair at the 5' or 3' junction due to artifacts of the DNA repair process. We herein report a technology that couples the spatial temporal localization of an ssDNA repair template and leverages the nucleic acid components of the CRISPR-Cas9 system. We show that by direct fusion of an ssDNA template to the trans activating RNA (tracrRNA) to generate an RNA-DNA chimera, termed Donorguide, we recover precise integration of genetic alterations, with both increased integration rates and decreased imprecision at the 5' or 3' junctions relative to an ssODN donor in vitro in HEK293T cells as well as in vivo in zebrafish. Further, we show that this technology can be used to enhance gene conversion with other gene editing tools such as TALENs.

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