PATH-54. MULTI-DIMENSIONAL MOLECULAR CHARACTERIZATION OF PATIENT-MATCHED MEDULLOBLASTOMA AT DIAGNOSIS AND RELAPSE

Abstract INTRODUCTION Recurrent medulloblastoma (MB) confers an abysmal prognosis with ~10% 5-year overall survival. Optimal treatment paradigms for relapsed disease are largely unknown. Conservation of molecular subgroup at relapse has been described and divergent clonal evolution implicated, yet multi-dimensional molecular characterization of larger cohorts are warranted to substantiate these findings and to disclose potential mechanisms underlying treatment failure and disease recurrence. METHODS A multi-institutional series of 85 patient-matched, primary MBs and their relapses was profiled by DNA methylation array (Illumina 450K/850K). Entity and molecular subgroup classifications were assigned using random forest tumor classifiers (Molecular Neuropathology v.11b4). Genome-wide copy-number aberrations were also inferred from these data while parallel next-generation (whole-exome or targeted panel) sequencing on the majority of the cohort facilitated inference of somatic driver mutations. RESULTS Comprised of WNT (1%), SHH (41%), Group 3 (22%), Group 4 (35%), primary tumors largely retained subgroup affiliation at relapse with the notable exception of 14% of cases. The majority (8/12) of discrepant classifications were determined to be secondary glioblastomas, while three Group 4 primary tumors relapsed as Group 3. Amongst conserved pairs, copy-number analyses suggest somatic clonal divergence between primary MBs and their respective relapses with an average of 0.8 (range 0–5) primary-specific and 2.0 (range 0–11) relapse-specific cytogenetic alterations. Despite high global methylation correlations between primary/relapse pairs (median 0.95), epigenetic evolution at relapse is suggested by the lower degree of conservation amongst promoter-associated probes (median 0.83, p < 2.2e-16). CONCLUSION Secondary malignancy, particularly glioblastoma, may masquerade as relapsed MB, highlighting the utility of molecular characterization for relapsed disease and necessity for vigilant clinical surveillance. By deciphering the evolution of MB from diagnosis to relapse, a fundamental understanding of disease pathogenesis may be garnered, motivating rational and targeted clinical interventions in early therapy and at the time of relapse.

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MBCL-08. INTEGRATIVE MOLECULAR ANALYSIS OF PATIENT-MATCHED DIAGNOSTIC AND RELAPSED MEDULLOBLASTOMAS

Neuro-Oncology ◽

10.1093/neuonc/noaa222.484 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii389-iii389

Author(s):

Rahul Kumar ◽

Maximilian Deng ◽

Kyle Smith ◽

Anthony Liu ◽

Girish Dhall ◽

...

Keyword(s):

Molecular Analysis ◽

Copy Number ◽

Driver Mutations ◽

P Value ◽

Next Generation ◽

Driver Genes ◽

Methylation Array ◽

Primary Tumors ◽

Group 4 ◽

Group 3

Abstract INTRODUCTION The next generation of clinical trials for relapsed medulloblastoma demands a thorough understanding of the clinical behavior of relapsed tumors as well as the molecular relationship to their diagnostic counterparts. METHODS A multi-institutional molecular cohort of patient-matched (n=126 patients) diagnostic MBs and relapses/subsequent malignancies was profiled by DNA methylation array. Entity, subgroup classification, and genome-wide copy-number aberrations were assigned while parallel next-generation (whole-exome or targeted panel) sequencing on the majority of the cohort facilitated inference of somatic driver mutations. RESULTS Comprised of WNT (2%), SHH (41%), Group 3 (18%), Group 4 (39%), primary tumors retained subgroup affiliation at relapse with the notable exception of 10% of cases. The majority (8/13) of discrepant classifications were determined to be secondary glioblastomas. Additionally, rare (n=3) subgroup-switching events of Group 4 primary tumors to Group 3 relapses were identified coincident with MYC/MYCN pathway alterations. Amongst truly relapsing MBs, copy-number analyses suggest somatic clonal divergence between primary MBs and their respective relapses with Group 3 (55% of alterations shared) and Group 4 tumors (63% alterations shared) sharing a larger proportion of cytogenetic alterations compared to SHH tumors (42% alterations shared; Chi-square p-value < 0.001). Subgroup- and gene-specific patterns of conservation and divergence amongst putative driver genes were also observed. CONCLUSION Integrated molecular analysis of relapsed MB discloses potential mechanisms underlying treatment failure and disease recurrence while motivating rational implementation of relapse-specific therapies. The degree of genetic divergence between primary and relapsed MBs varied by subgroup but suggested considerably higher conservation than prior estimates.

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MBRS-47. RAPID MOLECULAR SUBGROUPING OF MEDULLOBLASTOMA BASED ON DNA METHYLATION BY NANOPORE SEQUENCING

Neuro-Oncology ◽

10.1093/neuonc/noaa222.556 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii406-iii406

Author(s):

Julien Masliah-Planchon ◽

Elodie Girard ◽

Philipp Euskirchen ◽

Christine Bourneix ◽

Delphine Lequin ◽

...

Keyword(s):

Dna Methylation ◽

Single Molecule ◽

Nanopore Sequencing ◽

Molecular Subgroup ◽

Group Assignment ◽

Group 4 ◽

Methylation Assay ◽

Tumor Group ◽

Long Read ◽

Group 3

Abstract Medulloblastoma (MB) can be classified into four molecular subgroups (WNT group, SHH group, group 3, and group 4). The gold standard of assignment of molecular subgroup through DNA methylation profiling uses Illumina EPIC array. However, this tool has some limitation in terms of cost and timing, in order to get the results soon enough for clinical use. We present an alternative DNA methylation assay based on nanopore sequencing efficient for rapid, cheaper, and reliable subgrouping of clinical MB samples. Low-depth whole genome with long-read single-molecule nanopore sequencing was used to simultaneously assess copy number profile and MB subgrouping based on DNA methylation. The DNA methylation data generated by Nanopore sequencing were compared to a publicly available reference cohort comprising over 2,800 brain tumors including the four subgroups of MB (Capper et al. Nature; 2018) to generate a score that estimates a confidence with a tumor group assignment. Among the 24 MB analyzed with nanopore sequencing (six WNT, nine SHH, five group 3, and four group 4), all of them were classified in the appropriate subgroup established by expression-based Nanostring subgrouping. In addition to the subgrouping, we also examine the genomic profile. Furthermore, all previously identified clinically relevant genomic rearrangements (mostly MYC and MYCN amplifications) were also detected with our assay. In conclusion, we are confirming the full reliability of nanopore sequencing as a novel rapid and cheap assay for methylation-based MB subgrouping. We now plan to implement this technology to other embryonal tumors of the central nervous system.

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Clinical Outcomes and Patient-Matched Molecular Composition of Relapsed Medulloblastoma

Journal of Clinical Oncology ◽

10.1200/jco.20.01359 ◽

2021 ◽

Vol 39 (7) ◽

pp. 807-821

Author(s):

Rahul Kumar ◽

Kyle S. Smith ◽

Maximilian Deng ◽

Colt Terhune ◽

Giles W. Robinson ◽

...

Keyword(s):

Clinical Outcomes ◽

Local Relapse ◽

Genetic Alterations ◽

Driver Genes ◽

Methylation Array ◽

Molecular Subgroup ◽

Term Survival ◽

Molecular Features ◽

Group 4 ◽

Group 3

PURPOSE We sought to investigate clinical outcomes of relapsed medulloblastoma and to compare molecular features between patient-matched diagnostic and relapsed tumors. METHODS Children and infants enrolled on either SJMB03 (NCT00085202) or SJYC07 (NCT00602667) trials who experienced medulloblastoma relapse were analyzed for clinical outcomes, including anatomic and temporal patterns of relapse and postrelapse survival. A largely independent, paired molecular cohort was analyzed by DNA methylation array and next-generation sequencing. RESULTS A total of 72 of 329 (22%) SJMB03 and 52 of 79 (66%) SJYC07 patients experienced relapse with significant representation of Group 3 and wingless tumors. Although most patients exhibited some distal disease (79%), 38% of patients with sonic hedgehog tumors experienced isolated local relapse. Time to relapse and postrelapse survival varied by molecular subgroup with longer latencies for patients with Group 4 tumors. Postrelapse radiation therapy among previously nonirradiated SJYC07 patients was associated with long-term survival. Reirradiation was only temporizing for SJMB03 patients. Among 127 patients with patient-matched tumor pairs, 9 (7%) experienced subsequent nonmedulloblastoma CNS malignancies. Subgroup (96%) and subtype (80%) stabilities were largely maintained among the remainder. Rare subgroup divergence was observed from Group 4 to Group 3 tumors, which is coincident with genetic alterations involving MYC, MYCN, and FBXW7. Subgroup-specific patterns of alteration were identified for driver genes and chromosome arms. CONCLUSION Clinical behavior of relapsed medulloblastoma must be contextualized in terms of up-front therapies and molecular classifications. Group 4 tumors exhibit slower biological progression. Utility of radiation at relapse is dependent on patient age and prior treatments. Degree and patterns of molecular conservation at relapse vary by subgroup. Relapse tissue enables verification of molecular targets and identification of occult secondary malignancies.

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Vegetative Characterization of Wild Grapevines (Vitis spp.) Native to Puebla, Mexico

HortScience ◽

10.21273/hortsci.43.7.1991 ◽

2008 ◽

Vol 43 (7) ◽

pp. 1991-1995 ◽

Cited By ~ 2

Author(s):

Omar Franco-Mora ◽

Edgar Jesús Morales-Rosales ◽

Andrés González-Huerta ◽

Juan Guillermo Cruz-Castillo

Keyword(s):

Euclidean Distance ◽

Principal Component ◽

Dorsal Side ◽

General Shape ◽

Group 4 ◽

Total Variability ◽

Group 3 ◽

Group 2 ◽

Group 1

Thirty-four accessions of wild grapevines, native to three regions of the state of Puebla, Mexico, that is Teziutlán, Tehuacán, and Atlixco, were vegetatively characterized with 32 suggested IPGRI, UPOV, and OIV descriptors related to young shoot (YS), mature shoot (MS), young leaf (YL), mature leaf (ML), and woody shoot (WS). Excepting profile and absence of sinus teeth in ML, the remaining parameters showed variation among the accessions. After the performance of a correlation analysis among the 32 characters, only those closely correlated were used; that is, for MS: color of dorsal side of node, density of prostrate trichomes of internode; for YL: density of prostrate trichomes between veins and density of erect trichomes on main veins; and for ML: general shape of petiole sinus and the density of erect trichomes on veins in mature leaves. With those six characters, six principal components explained the total variability observed. The most closely related descriptors for principal Component 1 were the ML general shape of petiole sinus (−0.735) and the YL density of erect trichomes on main veins (0.659), whereas for principal Component 2, the MS color of the dorsal side of the node (0.677) and the density of erect trichomes in ML (0.596) were the most highly related. A cluster analysis identified four groups with a euclidean distance of 18; except for plant 183, the other six included in Group 1 were native to the regions Atlixco and Tehuacán; Group 2 was formed by plants native to the three regions, whereas Group 3 was formed by plants native to Teziutlán and Atlixco; Group 4 was formed only by Plant 36, native to Atlixco. These results show that variation among accessions occurs within and among the three states of the Puebla region.

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Molecular characterization of luminal breast tumors in African American women.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.550 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 550-550

Author(s):

Yael Simons ◽

Mohamed Hassan ◽

George Chlipala ◽

Oana Cristina Danciu ◽

Vijayakrishna K. Gadi ◽

...

Keyword(s):

African American ◽

Racial Disparities ◽

Molecular Characterization ◽

Endocrine Resistance ◽

Breast Tumors ◽

Driver Gene ◽

Gene Fusions ◽

Primary Tumors ◽

Gene Alterations

550 Background: Racial disparities in breast cancer (BC) mortality are attributed to later stage diagnoses and a higher incidence of triple-negative BC among African American (AA) women. In previous work, we showed that AA women with ER+ BC are more likely to develop biologically aggressive disease and are more likely to die from early stage, ER+ BC than non-Hispanic White women (Hoskins et al, JAMA Oncol, 2021). The underlying molecular drivers of this disparity are unknown. Here we report the molecular characterization of a series of luminal BC from AA women. Methods: Consecutive breast tumor specimens received in the Pathology Department underwent next generation sequencing (NGS). Unstained FFPE tissue sections were macro-dissected to isolate tumor cells, and nucleic acids were extracted using commercially available kits. DNA and RNA sequencing libraries were prepared with the Oncomine Comprehensive Assay v3 (OCAv3) (Thermo Fisher), which includes 161 driver genes and detects SNVs, CNVs, INDELs and gene fusions. Sequencing was performed on the Ion S5XL sequencer. Sequencing reads were mapped to the UCSC human genome build GRCh37/hg19 using Torrent Suite™ software (version 5.10; Thermo Fisher). Data analysis and variant calling was performed using the Ion Reporter analysis tool. Results: We identified 60 somatic driver gene alterations in luminal tumors from 35 AA patients (primary tumors, n = 26; metastatic tumors, n = 9). Recurrently altered genes identified in > 5% of tumors are listed in the Table. The most frequently altered gene was PIK3CA (42% of tumors). ESR1 gene fusions were seen in 25% of tumors. Interestingly, an equal frequency of ESR1 fusions were detected in primary (27%) and metastatic (22%) tumors, in contrast to activating mutations which are found in recurrent tumors following treatment with aromatase inhibitors. ARID1A alterations were identified in 17% of primary tumors. ARID1A encodes a subunit of the SWI/SNF chromatin remodeling complex. Alterations in ARID1A confer endocrine resistance, and are enriched in recurrent tumors in the literature. We also found a high number of CNVs in members of the FGF gene family (36% of tumors), which are also associated with resistance to endocrine therapy. An in silico analysis comparing our findings with publicly available datasets will be presented. Conclusions: This study of somatic driver gene alterations in a consecutive series of luminal breast tumors from AA patients found a higher than expected frequency of alterations in genes associated with endocrine resistance in untreated primary tumors, suggesting a partial explanation for racial disparities in survival.[Table: see text]

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Clinical Characteristic and Molecular Subgroups of Thai Pediatric Medulloblastomas at Queen Sirikit National Institute of Child Health

Journal of the Medical Association of Thailand ◽

10.35755/jmedassocthai.2021.10.12989 ◽

2021 ◽

Vol 104 (10) ◽

pp. 1648-1657

Keyword(s):

Child Health ◽

Signaling Pathway ◽

Survival Rates ◽

Large Cell ◽

Disease Classification ◽

Molecular Subgroups ◽

Molecular Subgroup ◽

Group 4 ◽

Group 3 ◽

Clinical Records

Objective: To determine the correlation between clinical characteristics and molecular subgroups of medulloblastoma (MB) in Thai pediatric patients at the Queen Sirikit National Institute of Child Health (QSNICH), Thailand. Materials and Methods: MB specimens operated between 2004 and 2018 were classified by Nanostring into four molecular subgroups, including Wingless signaling pathway (WNT), Sonic Hedgehog signaling pathway (SHH), Group 3, and Group 4. For the present cases, the clinical records were retrospectively analyzed. Results: Twenty-two MB cases with complete clinical records were analyzed. Group 4 was the most common molecular subgroup (31.82%), followed by WNT (27.27%), SHH (22.73%), and Group 3 (18.18%). The histologic subtypes included 18, three, and one cases of classic MB, MB with extensive nodularity (MBEN), and large cell MB, respectively. All SHH MBs were found in infants. All MBENs belonged to SHH subgroup, and the large cell MB was Group 3. All six WNT MB cases did not experience tumor recurrence. Five-year cause specific survival rates were 100% in WNT, 60% in SHH, 57.1% in Group 4, and 0% in Group 3. Five-year recurrence-free survival rates were 100% in WNT, 42.9% in Group 4, and 0% in SHH and Group 3. Conclusion: MB is a heterogeneous disease. Classification of MB, especially at the molecular subtype, is helpful for the management and prognostication. Keywords: Medulloblastoma; Molecular subgroup

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Molecular characterization of SMN copy number derived from carrier screening and from core families with SMA in a Chinese population

European Journal of Human Genetics ◽

10.1038/ejhg.2010.54 ◽

2010 ◽

Vol 18 (9) ◽

pp. 978-984 ◽

Cited By ~ 34

Author(s):

Zhu Sheng-Yuan ◽

Fu Xiong ◽

Ya-Jun Chen ◽

Ti-Zhen Yan ◽

Jian Zeng ◽

...

Keyword(s):

Molecular Characterization ◽

Copy Number ◽

Chinese Population ◽

Carrier Screening

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Integrative Genomic Analysis of Medulloblastoma Identifies a Molecular Subgroup That Drives Poor Clinical Outcome

Journal of Clinical Oncology ◽

10.1200/jco.2010.28.5148 ◽

2011 ◽

Vol 29 (11) ◽

pp. 1424-1430 ◽

Cited By ~ 434

Author(s):

Yoon-Jae Cho ◽

Aviad Tsherniak ◽

Pablo Tamayo ◽

Sandro Santagata ◽

Azra Ligon ◽

...

Keyword(s):

Clinical Outcome ◽

Copy Number ◽

Single Nucleotide Polymorphism Array ◽

Genomic Analysis ◽

Molecular Characteristics ◽

Molecular Subgroups ◽

Poor Clinical Outcome ◽

Molecular Subgroup ◽

Primary Tumors ◽

Relative Contribution

Purpose Medulloblastomas are heterogeneous tumors that collectively represent the most common malignant brain tumor in children. To understand the molecular characteristics underlying their heterogeneity and to identify whether such characteristics represent risk factors for patients with this disease, we performed an integrated genomic analysis of a large series of primary tumors. Patients and Methods We profiled the mRNA transcriptome of 194 medulloblastomas and performed high-density single nucleotide polymorphism array and miRNA analysis on 115 and 98 of these, respectively. Non-negative matrix factorization–based clustering of mRNA expression data was used to identify molecular subgroups of medulloblastoma; DNA copy number, miRNA profiles, and clinical outcomes were analyzed for each. We additionally validated our findings in three previously published independent medulloblastoma data sets. Results Identified are six molecular subgroups of medulloblastoma, each with a unique combination of numerical and structural chromosomal aberrations that globally influence mRNA and miRNA expression. We reveal the relative contribution of each subgroup to clinical outcome as a whole and show that a previously unidentified molecular subgroup, characterized genetically by c-MYC copy number gains and transcriptionally by enrichment of photoreceptor pathways and increased miR-183∼96∼182 expression, is associated with significantly lower rates of event-free and overall survivals. Conclusion Our results detail the complex genomic heterogeneity of medulloblastomas and identify a previously unrecognized molecular subgroup with poor clinical outcome for which more effective therapeutic strategies should be developed.

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