Comprehensive serial molecular profiling of an “N of 1” exceptional non-responder with metastatic prostate cancer progressing to small cell carcinoma on treatment

Abstract Importance Small cell carcinoma/neuroendocrine prostate cancer (NePC) is a lethal, poorly understood prostate cancer (PCa) subtype. Controversy exists about the origin of NePC in this setting. Objective To molecularly profile archived biopsy specimens from a case of early-onset PCa that rapidly progressed to NePC to identify drivers of the aggressive course and mechanisms of NePC origin and progression. Design, setting, and participants A 47-year-old patient presented with metastatic prostatic adenocarcinoma (Gleason score 9). After a 6-month response to androgen deprivation therapy, the patient developed jaundice and liver biopsy revealed exclusively NePC. Targeted next generation sequencing (NGS) from formalin-fixed paraffin-embedded (FFPE)-isolated DNA was performed from the diagnostic prostate biopsy and the liver biopsy at progression. Intervention Androgen deprivation therapy for adenocarcinoma followed by multiagent chemotherapy for NePC. Main outcomes and measures Identification of the mutational landscape in primary adenocarcinoma and NePC liver metastasis. Whether the NePC arose independently or was derived from the primary adenocarcinoma was considered based on mutational profiles. Results A deleterious somatic SMAD4 L535fs variant was present in both prostate and liver specimens; however, a TP53 R282W mutation was exclusively enriched in the liver specimen. Copy number analysis identified concordant, low-level alterations in both specimens, with focal MYCL amplification and homozygous PTEN, RB1, and MAP2K4 losses identified exclusively in the NePC specimen. Integration with published genomic profiles identified MYCL as a recurrently amplified in NePC. Conclusions and relevance NGS of routine biopsy samples from an exceptional non-responder identified SMAD4 as a driver of the aggressive course and supports derivation of NePC from primary adenocarcinoma (transdifferentiation).http://deepblue.lib.umich.edu/bitstream/2027.42/113670/1/13045_2015_Article_204.pd

Discordant and heterogeneous clinically relevant genomic alterations in circulating tumor cells vs plasma DNA from men with metastatic castration resistant prostate cancer

Circulating tumor cell (CTC) and cellâ free (cf) DNAâ based genomic alterations are increasingly being used for clinical decisionâ making in oncology. However, the concordance and discordance between paired CTC and cfDNA genomic profiles remain largely unknown. We performed comparative genomic hybridization (CGH) on CTCs and cfDNA, and lowâ pass whole genome sequencing (lpWGS) on cfDNA to characterize genomic alterations (CNA) and tumor content in two independent prospective studies of 93 men with mCRPC treated with enzalutamide/abiraterone, or radiumâ 223. Comprehensive analysis of 69 patient CTCs and 72 cfDNA samples from 93 men with mCRPC, including 64 paired samples, identified common concordant gains in FOXA1, AR, and MYC, and losses in BRCA1, PTEN, and RB1 between CTCs and cfDNA. Concordant PTEN loss and discordant BRCA2 gain were associated with significantly worse outcomes in Epic ARâ V7 negative men with mCRPC treated with abiraterone/enzalutamide. We identified and externally validated CTCâ specific genomic alternations that were discordant in paired cfDNA, even in samples with high tumor content. These CTC/cfDNAâ discordant regions included key genomic regulators of lineage plasticity, osteomimicry, and cellular differentiation, including MYCN gain in CTCs (31%) that was rarely detected in cfDNA. CTC MYCN gain was associated with poor clinical outcomes in ARâ V7 negative men and small cell transformation. In conclusion, we demonstrated concordance of multiple genomic alterations across CTC and cfDNA platforms; however, some genomic alterations displayed substantial discordance between CTC DNA and cfDNA despite the use of identical copy number analysis methods, suggesting tumor heterogeneity and divergent evolution associated with poor clinical outcomes.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153751/1/gcc22824.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153751/2/gcc22824_am.pd

Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy.

Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~0.01x) tumor content determination through genome-wide copy number alteration (CNA) profiling. We applied PRINCe to a retrospective cohort of 124 cfDNA samples from 100 patients with advanced cancers, including 76 men with metastatic castration-resistant prostate cancer (mCRPC), enabling cfDNA tumor content approximation and actionable focal CNA detection, while facilitating concordance analyses between cfDNA and tissue-based NGS profiles and assessment of cfDNA alteration associations with mCRPC treatment outcomes. Therapeutically relevant focal CNAs were present in 42 (34%) cfDNA samples, including 36 of 93 (39%) mCRPC patient samples harboring AR amplification. PRINCe identified pre-treatment cfDNA CNA profiles facilitating disease monitoring. Combining PRINCe with routine targeted NGS of cfDNA enabled mutation and CNA assessment with coverages tuned to cfDNA tumor content. In mCRPC, genome-wide PRINCe cfDNA and matched tissue CNA profiles showed high concordance (median Pearson correlation = 0.87), and PRINCe detectable AR amplifications predicted reduced time on therapy, independent of therapy type (Kaplan-Meier log-rank test, chi-square = 24.9, p < 0.0001). Our screening approach enables robust, broadly applicable cfDNA-based precision oncology for patients with advanced cancer through scalable identification of therapeutically relevant CNAs and pre-/post-treatment genomic profiles, enabling cfDNA- or tissue-based precision oncology workflow optimization

Minimum Technical Data Elements for Liquid Biopsy Data Submitted to Public Databases

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154656/1/cpt1747.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154656/2/cpt1747-sup-0001-FigS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154656/3/cpt1747_am.pd

Precision Oncology Opportunities And Disease Insights From Next-Generation-Sequencing Profiling Of Routine Clinical Biospecimens

Rapid technological developments in next-generation sequencing (NGS) and inter-institutional collaborations including The Cancer Genome Atlas (TCGA) have enabled comprehensive characterization of the genomic, transcriptomic, and epigenetic landscapes from bulk tissue specimens in a wide range of cancers. Emerging work has focused on scaling NGS-based profiling strategies to guide precision medicine approaches in clinical oncology using routine clinical biospecimens such as formalin-fixed, paraffin-embedded (FFPE) tissue or less-invasive liquid (e.g., blood or urine) samples. Technical challenges associated with limited tumor lesion size, low nucleic acid quantities, disease-specificity applications, and disease and histological heterogeneity present hurdles to widespread adoption and utility of extant NGS-based precision oncology approaches. Here, several analytical advances are described supporting democratization of precision oncology approaches from clinical tissue and liquid biospecimens, while revealing disease insights and important clinical considerations in the context of both localized and advanced (including multifocal and/or heterogeneous) disease. First, development and validation of a targeted DNA and RNA NGS assay compatible with small quantities of DNA and RNA isolated from routine, archived FFPE tissue specimens is described. This assay, targeting recurrently mutated oncogenic hotspots, tumor suppressors, copy-number-altered genes, and recurrent gene fusions is applied to a cohort of >300 FFPE tissue samples, revealing high sensitivity with orthogonal molecular diagnostic assays for BRAF, KRAS, and EGFR oncogenic alterations. Second, I describe a rapid, inexpensive, low-pass cell-free DNA (cfDNA) whole-genome sequencing (WGS) copy-number profiling approach, including a novel heuristic tumor content approximation method, capable of establishing genome-wide copy-number profiles from 0.01-0.1x sequencing coverage. Application of our approach in plasma samples from patients with advanced cancer with matched comprehensive tissue NGS revealed high concordance with tissue-based molecular profiles, while highlighting important areas of potential utility from noninvasive profiling of overall disease burden. Third, I describe the systematic assessment of expression-based molecular subtypes in histologically heterogenous bladder cancers, revealing robust identification of basal/luminal molecular subtypes in a cohort of >100 bladder cancer cell lines and tumor tissue specimens, and recapitulation of basal/luminal subtypes in >400 samples profiled by TCGA using selected marker subsets. Importantly, I describe divergent expression profiles in the context of shared genomic alterations for individual histologically divergent tumor components from the same tumor, confounding proposed clinical utility of expression-based subtypes for disease prediction and prognosis. Fourth, I describe the development of a targeted RNAseq panel capable of assessing major transcriptional programs and disease biomarkers across the full spectrum of prostate cancer disease, while deriving commercially available prognostic scores that show limited robustness to disease multifocality. Lastly, I describe extensions of our cfDNA WGS approach to urine cfDNA samples from patients with advanced cancer, while exploring the potential utility of pairing described analytic tools with existing and emerging molecular profiling strategies to improve our understanding of disease biology and maximize clinical utility.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/140890/1/hovelson_1.pd

Bulletin officiel des contributions directes et du cadastre / Direction générale des impôts

19361936 (A1936,N7,PART2)

Comparative genomics of primary prostate cancer and paired metastases: insights from 12 molecular case studies

Primary prostate cancer (PCa) can show marked molecular heterogeneity. However, systematic analyses comparing primary PCa and matched metastases in individual patients are lacking. We aimed to address the molecular aspects of metastatic progression while accounting for the heterogeneity of primary PCa. In this pilot study, we collected 12 radical prostatectomy (RP) specimens from men who subsequently developed metastatic castration-resistant prostate cancer (mCRPC). We used histomorphology (Gleason grade, focus size, stage) and immunohistochemistry (IHC) (ERG and p53) to identify independent tumors and/or distinct subclones of primary PCa. We then compared molecular profiles of these primary PCa areas to matched metastatic samples using whole-exome sequencing (WES) and amplicon-based DNA and RNA sequencing. Based on combined pathology and molecular analysis, seven (58%) RP specimens harbored monoclonal and topographically continuous disease, albeit with some degree of intratumor heterogeneity; four (33%) specimens showed true multifocal disease; and one displayed monoclonal disease with discontinuous topography. Early (truncal) events in primary PCa included SPOP p.F133V (one patient), BRAF p.K601E (one patient), and TMPRSS2:ETS rearrangements (eight patients). Activating AR alterations were seen in nine (75%) mCRPC patients, but not in matched primary PCa. Hotspot TP53 mutations, found in metastases from three patients, were readily present in matched primary disease. Alterations in genes encoding epigenetic modifiers were observed in several patients (either shared between primary foci and metastases or in metastatic samples only). WES-based phylogenetic reconstruction and/or clonality scores were consistent with the index focus designated by pathology review in six out of nine (67%) cases. The three instances of discordance pertained to monoclonal, topographically continuous tumors, which would have been considered as unique disease in routine practice. Overall, our results emphasize pathologic and molecular heterogeneity of primary PCa, and suggest that comprehensive IHC-assisted pathology review and genomic analysis are highly concordant in nominating the 'index' primary PCa area