Whole-Genome Sequencing Analysis of Male Breast Cancer Unveils Novel Structural Events and Potential Therapeutic Targets

The molecular characterization of male breast cancer (MaBC) has received limited attention in research, mostly because of its low incidence rate, accounting for only 0.5% to 1% of all reported cases of breast cancer each year. Managing MaBC presents significant challenges, with most treatment protocols being adapted from those developed for female breast cancer. Utilizing whole-genome sequencing (WGS) and state-of-the-art analyses, the genomic features of 10 MaBC cases (n = 10) were delineated and correlated with clinical and histopathologic characteristics. Using fluorescence in situ hybridization, an additional cohort of 18 patients was interrogated to supplement WGS findings. The genomic landscape of MaBC uncovered significant genetic alterations that could influence diagnosis and treatment. We found common somatic mutations in key driver genes, such as FAT1, GATA3, SMARCA4, and ARID2. Our study also mapped out structural variants that impact cancer-associated genes, such as ARID1A, ESR1, GATA3, NTRK1, and NF1. Using a WGS-based classifier, homologous recombination deficiency (HRD) was identified in 2 cases, both presenting with deleterious variants in BRCA2. Noteworthy was the observation of FGFR1 amplification in 21% of cases. Altogether, we identified at least 1 potential therapeutic target in 8 of the 10 cases, including high tumor mutational burden, FGFR1 amplification, and HRD. Our study is the first WGS characterization of MaBC, which uncovered potentially relevant variants, including structural events in cancer genes, HRD signatures, and germline pathogenic mutations. Our results demonstrate unique genetic markers and potential treatment targets in MaBC, thereby underlining the necessity of tailoring treatment strategies for this understudied patient population. These WGS-based findings add to the growing knowledge of MaBC genomics and highlight the need to expand research on this type of cancer.

The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis

The molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are not well understood, and there is a lack of knowledge regarding the genomic and transcriptomic differences between primary and metastatic UTUC. To address these gaps, we integrate whole-exome sequencing, RNA sequencing, and Imaging Mass Cytometry using lanthanide metal-conjugated antibodies of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. We perform a spatially-resolved single-cell analysis of cancer, immune, and stromal cells to understand the evolution of primary to metastatic UTUC. We discover that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature are stable across primary and matched metastatic UTUC. Molecular and immune subtypes are consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single cells. Molecular subtypes at the single-cell level are highly conserved between primary and metastatic UTUC tumors within the same patient.

NIPBL::NACC1 Fusion Hepatic Carcinoma

Several reports describing a rare primary liver tumor with histologic features reminiscent of follicular thyroid neoplasms have been published under a variety of descriptive terms including thyroid-like, solid tubulocystic, and cholangioblastic cholangiocarcinoma. Although these tumors are considered to represent histologic variants, they lack classic features of cholangiocarcinoma and have unique characteristics, namely immunoreactivity for inhibin and NIPBL::NACC1 fusions. The purpose of this study is to present clinicopathologic and molecular data for a large series of these tumors to better understand their pathogenesis. We identified 11 hepatic tumors with these features. Immunohistochemical and NACC1 and NIPBL fluorescence in situ hybridization assays were performed on all cases. Four cases had available material for whole-genome sequencing (WGS) analysis. Most patients were adult women (mean age: 42 y) who presented with abdominal pain and large hepatic masses (mean size: 14 cm). Ten patients had no known liver disease. Of the patients with follow-up information, 3/9 (33%) pursued aggressive behavior. All tumors were composed of bland cuboidal cells with follicular and solid/trabecular growth patterns in various combinations, were immunoreactive for inhibin, showed albumin mRNA by in situ hybridization, and harbored the NIPBL::NACC1 fusion by fluorescence in situ hybridization. WGS corroborated the presence of the fusion in all 4 tested cases, high tumor mutational burden in 2 cases, and over 30 structural variants per case in 3 sequenced tumors. The cases lacked mutations typical of conventional intrahepatic cholangiocarcinoma. In this report, we describe the largest series of primary inhibin-positive hepatic neoplasms harboring a NIPBL::NACC1 fusion and the first WGS analysis of these tumors. We propose to name this neoplasm NIPBL:NACC1 fusion hepatic carcinoma.

Deciphering the origin and therapeutic targets of cancer of unknown primary: a case report that illustrates the power of integrative whole-exome and transcriptome sequencing analysis

Cancer of unknown primary (CUP) represents a significant diagnostic and therapeutic challenge, being the third to fourth leading cause of cancer death, despite advances in diagnostic tools. This article presents a successful approach using a novel genomic analysis in the evaluation and treatment of a CUP patient, leveraging whole-exome sequencing (WES) and RNA sequencing (RNA-seq). The patient, with a history of multiple primary tumors including urothelial cancer, exhibited a history of rapid progression on empirical chemotherapy. The application of our approach identified a molecular target, characterized the tumor expression profile and the tumor microenvironment, and analyzed the origin of the tumor, leading to a tailored treatment. This resulted in a substantial radiological response across all metastatic sites and the predicted primary site of the tumor. We argue that a comprehensive genomic and molecular profiling approach, like the BostonGene© Tumor Portrait, can provide a more definitive, personalized treatment strategy, overcoming the limitations of current predictive assays. This approach offers a potential solution to an unmet clinical need for a standardized approach in identifying the tumor origin for the effective management of CUP.

The importance of escalating molecular diagnostics in patients with low-grade pediatric brain cancer

Pilocytic astrocytomas are the most common pediatric brain tumors, typically presenting as low-grade neoplasms. We report two cases of pilocytic astrocytoma with atypical tumor progression. Case 1 involves a 12-yr-old boy with an unresectable suprasellar tumor, negative for BRAF rearrangement but harboring a BRAF p.V600E mutation. He experienced tumor size reduction and stable disease following dabrafenib treatment. Case 2 describes a 6-yr-old boy with a thalamic tumor that underwent multiple resections, with no actionable driver detected using targeted next-generation sequencing. Whole-genome and RNA-seq analysis identified an internal tandem duplication in FGFR1 and RAS pathway activation. Future management options include FGFR1 inhibitors. These cases demonstrate the importance of escalating molecular diagnostics for pediatric brain cancer, advocating for early reflexing to integrative whole-genome sequencing and transcriptomic profiling when targeted panels are uninformative. Identifying molecular drivers can significantly impact treatment decisions and improve patient outcomes.

Evolution of structural rearrangements in prostate cancer intracranial metastases

Intracranial metastases in prostate cancer are uncommon but clinically aggressive. A detailed molecular characterization of prostate cancer intracranial metastases would improve our understanding of their pathogenesis and the search for new treatment strategies. We evaluated the clinical and molecular characteristics of 36 patients with metastatic prostate cancer to either the dura or brain parenchyma. We performed whole genome sequencing (WGS) of 10 intracranial prostate cancer metastases, as well as WGS of primary prostate tumors from men who later developed metastatic disease (n = 6) and nonbrain prostate cancer metastases (n = 36). This first whole genome sequencing study of prostate intracranial metastases led to several new insights. First, there was a higher diversity of complex structural alterations in prostate cancer intracranial metastases compared to primary tumor tissues. Chromothripsis and chromoplexy events seemed to dominate, yet there were few enrichments of specific categories of structural variants compared with non-brain metastases. Second, aberrations involving the AR gene, including AR enhancer gain were observed in 7/10 (70%) of intracranial metastases, as well as recurrent loss of function aberrations involving TP53 in 8/10 (80%), RB1 in 2/10 (20%), BRCA2 in 2/10 (20%), and activation of the PI3K/AKT/PTEN pathway in 8/10 (80%). These alterations were frequently present in tumor tissues from other sites of disease obtained concurrently or sequentially from the same individuals. Third, clonality analysis points to genomic factors and evolutionary bottlenecks that contribute to metastatic spread in patients with prostate cancer. These results describe the aggressive molecular features underlying intracranial metastasis that may inform future diagnostic and treatment approaches.

Immunogenomic Landscape of Neuroendocrine Prostate Cancer

PURPOSE

Patients with neuroendocrine prostate cancer (NEPC) are often managed with immunotherapy regimens extrapolated from small-cell lung cancer (SCLC). We sought to evaluate the tumor immune landscape of NEPC compared with other prostate cancer types and SCLC.

EXPERIMENTAL DESIGN

In this retrospective study, a cohort of 170 patients with 230 RNA-sequencing and 104 matched whole-exome sequencing data were analyzed. Differences in immune and stromal constituents, frequency of genomic alterations, and associations with outcomes were evaluated.

RESULTS

In our cohort, 36% of the prostate tumors were identified as CD8+ T-cell inflamed, whereas the remaining 64% were T-cell depleted. T-cell-inflamed tumors were enriched in anti-inflammatory M2 macrophages and exhausted T cells and associated with shorter overall survival relative to T-cell-depleted tumors (HR, 2.62; P < 0.05). Among all prostate cancer types in the cohort, NEPC was identified to be the most immune depleted, wherein only 9 out of the 36 total NEPC tumors were classified as T-cell inflamed. These inflamed NEPC cases were enriched in IFN gamma signaling and PD-1 signaling compared with other NEPC tumors. Comparison of NEPC with SCLC revealed that NEPC had poor immune content and less mutations compared with SCLC, but expression of checkpoint genes PD-L1 and CTLA-4 was comparable between NEPC and SCLC.

CONCLUSIONS

NEPC is characterized by a relatively immune-depleted tumor immune microenvironment compared with other primary and metastatic prostate adenocarcinoma except in a minority of cases. These findings may inform development of immunotherapy strategies for patients with advanced prostate cancer.

Abstract 2149: A whole genome sequencing classifier of homologous recombination deficiency

Homologous recombination deficiency (HRd) is a DNA repair defect prevalent in but not exclusive to breast and ovarian cancer most commonly associated with BRCA1 or BRCA2 alterations. HRd results in accumulation of small and large scale genetic alterations across the genome, including allele specific copy number alterations (aCNAs), small nucleotide variants (SNVs), deletions, and structural variants (SVs). Detection of HRd in tumors predicts response to genotoxic drugs such as PARP inhibitors and platinum.

Genome wide aCNAs such as large state transitions (LST), loss of heterozygosity (LOH), and telomeric allelic imbalances (TAI) in conjunction with BRCA1/2 mutation detection have been implemented in routine diagnostic testing to identify HRd in tumors. However, these features represent a subset of the genetic signatures predictive of HRd, and we hypothesize that a significant portion of tumors with HRd are missed using these existing assays.

Whole genome sequencing (WGS) enables the detection of the full spectrum of genetic lesions that arise in an HRd tumor in a single assay. To demonstrate the added value of WGS to identify HRd, we trained and validated a pan-cancer classifier of HRd. A tumor/normal matched cohort of 321 cancer patients sequenced by WGS was assembled and analyzed as part of a retrospective study, representing 62 tumor types. An unbiased analysis of HRd associated SV signatures revealed the top quartile of samples harboring tandem duplications (Dups) and deletions (Dels) in the size range of 1-10kbp were enriched with BRCA1, BRCA2, and RAD51C/D alterations. Through curating Dels, Dups, HRd SNV/InDel signatures, and alteration of HRd associated genes, 37 unique patients were found to have high confidence HRd, out of which 13% had no alterations in BRCA1, BRCA2, or other HRd genes. We then trained a random forest classifier to identify HRd tumors. The most important predictive features were WGS-specific, namely small deletions with microhomology, SV Dels, and SV Dups. The HRd classifier was validated using an independent cohort of 556 samples from the Pan-Cancer Analysis of Whole Genomes (PCAWG) study. Of 46 samples with biallelic BRCA1/2 alterations, the classifier achieved high areas under receiver-operator characteristic (AUROC, 0.99) and precision recall curves (AUPRC, 0.96). The aCNA score, the number of segments harboring LST, LOH, and TAI, had similar AUROC (0.96) but lower AUPRC (0.87). There were 11 BRCA1/2 non-altered cases predicted to be HRd with the classifier which were not identified by CNA scores, in which 10 had at least 1 alteration in an HRd gene, including RAD51C, CHEK2 biallelic alterations and SVs in PALB2, Fanconi pathway genes, and ATM/ATR. We conclude that a classifier incorporating the additional mutational features which can only be detected using WGS can achieve superior precision in identifying HRd tumors and, in the future, uncover additional patients for therapeutic options.

Citation Format: Kevin Hadi, Gunes Gundem, Max F. Levine, Aditya Deshpande, Minal Patel, Stan Skzrypczak, Majd Al Assaad, Juan Miguel Mosquera, Olivier Elemento, Andrew L. Kung, Juan S. Medina-Martínez, Elli Papaemmanuil. A whole genome sequencing classifier of homologous recombination deficiency [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2149.

Abstract NG10: Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets

Untreated prostate cancers rely on androgen receptor (AR) signaling for growth and survival, forming the basis for the initial efficacy of androgen deprivation therapy (ADT). Yet the disease can relapse and progress to a lethal stage termed castration-resistant prostate cancer (CRPC). Reactivation of AR signaling represents the most common driver of CRPC growth, and next-generation AR signaling inhibitors (ARSIs) are now used in combination with ADT as first-line therapy. However, ARSIs can result in selective pressure, thereby generating AR-independent tumors. The transition from AR dependence frequently accompanies a change in a phenotype resembling developmental transdifferentiation or “lineage plasticity”. Neuroendocrine prostate cancer, which lacks a defined pathologic classification, is the most studied type of lineage plasticity. However, most AR-null tumors do not exhibit neuroendocrine features and are classified as “double-negative prostate cancer”, the drivers of which are poorly defined. Lineage plasticity studies in CRPC are limited by the lack of genetically defined patient-derived models that recapitulate the disease spectrum. To address this, we developed a biobank of organoids generated from patient biopsies to study the landscape of metastatic CRPC and allow for functional validation assays. Proteins called transcription factors (TFs) are drivers of tumor lineage plasticity. To identify the key TFs that drive the growth of AR-independent tumors, we integrated epigenetic and transcriptomic data generated from CRPC models. We generated ATAC-seq (assay for transposase-accessible chromatin sequencing) and RNA-seq data from 22 metastatic human prostate cancer organoids, six patient-derived xenografts (PDXs), and 12 derived or traditional cell lines. We classified the 40 models into four subtypes and predicted key TFs of each subtype. Besides the well-characterized AR-dependent (CRPC-AR) and neuroendocrine subtypes (CRPC-NE), we identified two novel AR-negative/low groups, including a Wnt-dependent subtype (CRPC-WNT), driven by TCF/LEF TFs, and a stem cell-like (SCL) subtype (CRPC-SCL), driven by the AP-1 family of TFs. To apply the subtype classification to patient samples, we derived RNA-seq signatures from the organoids and applied them to 366 patient samples from two independent CRPC cohorts. The generated signatures recapitulated the four-subtype classification and revealed that CRPC-SCL is the second most prevalent group. Patients from CRPC-SCL are also associated with shorter time under ARSI treatment compared to CRPC-AR, indicating that the ARSI treatments were less effective for CRPC-SCL patients. Additional chromatin immunoprecipitation sequencing (ChIP-seq) analysis indicated that AP-1 (FOSL1) collaboratively binds with TEAD and transcription coactivators, YAP and TAZ. Knocking down of AP-1 (FOSL1), YAP/TAZ decreased cell growth of CRPC-SCL and showed a decrease of chromatin accessibility at CRPC-SCL-specific open chromatin sites and down-regulation of YAP/TAZ target gene expression. In addition, the expression of AP-1 (FOSL1) decreased upon YAP/TAZ knockdown suggesting a positive feedback loop as well as YAP/TAZ as actional targets in CRPC-SCL. We used two small-molecule inhibitors, verteporfin and T-5224, that act on the YAP/TAZ/AP-1 pathway for their potential use as therapeutics for CRPC-SCL tumors, both inhibited the growth of samples from CRPC-SCL but not CRPC-AR. By overexpressing an AP-1 family gene (FOSL1) in AR-high cells, we observed an increase in chromatin accessibility at CRPC-SCL-specific open chromatin sites as well as significant up-regulation of CRPC-SCL signature genes, suggesting that AP-1 functions as a pioneering factor and master regulator for CRPC-SCL. All this work was recently published in Science (Tang, Xu et al. Science, 2022) where I am the co-first author. In summary, by using a diverse biobank of organoids, PDXs, and cell lines that recapitulate the heterogeneity of metastatic prostate cancer, we created a map of the chromatin accessibility and transcriptomic landscape of CRPC. We validated the CRPC-AR and CRPC-NE subtypes and report two novel subtypes of AR-negative/low samples, CRPC-SCL and CRPC-WNT, as well as their respective key TFs. Additional analysis revealed a model in which YAP, TAZ, TEAD, and AP-1 function together and drive oncogenic growth in CRPC-SCL samples. In addition, we proposed small inhibitors of YAP and TAZ that can potentially be used to treat CRPC-SCL patients. Overall, our results show how the stratification of CRPC patients into four subtypes using their transcriptomes can potentially inform appropriate clinical decisions.

Citation Format: Fanying Tang, Duo Xu, Shangqian Wang, Chen Khuan Wong, Alexander Martinez-Fundichely, Cindy J. Lee, Sandra Cohen, Jane Park, Corinne E. Hill, Kenneth Eng, Rohan Bareja, Teng Han, Eric Minwei Liu, Ann Palladino, Wei Di, Dong Gao, Wassim Abida, Shaham Beg, Loredana Puca, Maximiliano Meneses, Elisa de Stanchina, Michael F. Berger, Anuradha Gopalan, Lukas E. Dow, Juan Miguel Mosquera, Himisha Beltran, Cora N. Sternberg, Ping Chi, Howard I. Scher, Andrea Sboner, Yu Chen, Ekta Khurana. Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr NG10.

Use of a navigable interface for integrated whole genome and transcriptome sequencing as a platform for pursuit of therapeutic targets in advanced prostate cancers

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Background: Metastatic, castration-resistant prostate cancer (mCRPC) is commonly the deadly form of PC. Among these, a subset of tumors are androgen-indifferent with the most aggressive often manifesting variant histology, including neuroendocrine or small cell changes. Neuroendocrine PC can be de novo (NEPC) or develop in response to therapy as treatment emergent (CRPC-NE). Currently effective durable treatments for NEPC are lacking. Hence, we sought to identify additional targets in CRPC/NEPC using an integrative platform of whole genome (WGS) and transcriptome sequencing (RNAseq). Methods: WGS was performed on55 tumor/normal pairs (CRPC-Ad, n= 32; CRPC-NE, n=13; de novo NEPC, n=7; metastatic hormone naïve, PC n=3) from 48 patients. RNAseq data was available in a subset of 21 samples. We employed the Isabl GxT analytic platform and manually curated single base substitution (SBS, COSMIC v3) molecular signatures and structural variants (SV) that involved tumor suppressor genes and oncogenes. Results: We observed 184 events in cancer-associated genes and targets in 38 cases. Non-canonical ETS fusions were identified in 2 CRPC-Ad patients ( MSMB-ERG and YWHAE-ETV4). Other rare events included SVs affecting ALK ( SLC45A3-ALK) and FGFR1 amplification in 1 patient each. Pathogenic germline alterations in 15% of patients with equal frequency in each clinicopathological state. These variants included genes such as BRCA1, BRCA2, and ATM, and other genes of uncertain relevance for prostate cancer ( e.g., PPM1D and MUTYH). SBS genomic signatures associated with homologous recombination deficiency (HRD) were observed in 15% of the patients (7 cases): 3 harbored germline BRCA1/2mutations, 2 with somatic BRCA2 mutations, and 2 without alteration in BRCA1/2 (1 of these CRPC-Ad had a complex SV disrupting RAD51B) without apparent enrichment for any histology, and a majority of both histologies were enriched in Mismatch repair (MMR)-associated SBS. One subject CRPC-NE and amphicrine character, which displayed a complete response to immune checkpoint blockade, harbored driver mutations in AR and CTNNB1, and homozygous loss of MSH2/6. Further, molecular signatures of potential clinical relevance were detected at varying contributions and included CDK12-type genomic instability (CRPC-Ad, n=2) (4%) and MMR deficiency with POLD1 proofreading (CRPC-Ad) who also experienced a durable response to pembrolizumab. Conclusions: WGS/RNAseq in CRPC and NEPC elucidates genomic signatures associated with HRD and MMR, complex SVs in oncogenes, and non-canonical ETS fusions. Expansion of our analysis is underway with enhanced integration of clinical metadata and RNAseq for rational trial design for aggressive variant CRPC and NEPC.

GLI1 -Rearranged Enteric Tumor : Expanding the Spectrum of Gastrointestinal Neoplasms With GLI1 Gene Fusions

GLI1 encodes a transcription factor that targets cell cycle regulators affecting stem cell proliferation. GLI1 gene fusions were initially described in pericytomas with a t[7;12] translocation and more recently in gastric plexiform fibromyxomas and gastroblastomas. This study describes the clinicopathologic, immunohistochemical, and molecular features of three intestinal-based neoplasms harboring GLI1 gene fusions. We studied three unique mesenchymal small bowel tumors. Paraffin embedded tumor tissues from these cases and 62 additional tumor samples that included a plexiform fibromyxoma were sequenced using a targeted RNAseq method to detect fusion events. The study patients included two women and one man who were 52, 80, and 22 years of age at the time of diagnosis. The tumors involved the submucosa and muscularis propria of the duodenum, jejunum, and ileum. All 3 tumors contained a proliferation of monotonous oval or spindle cells with scattered, somewhat dilated vessels. Two cases showed epithelioid structures such as glands, tubules, or nests. Immunohistochemical analysis revealed cytokeratin expression in the epithelioid components of both tumors displaying these features, and variable numbers of mesenchymal cells. Diffuse CD56 positivity was seen in the mesenchymal component of 2 tumors and desmin and smooth muscle actin staining in the other tumor. Immunostains for S-100 protein, DOG-1, and CD117 were negative in all cases. GLI1 fusions with different partner genes were detected in all tumors, and in the plexiform fibromyxoma, used as a control. Validation by fluorescence in situ hybridization was performed. None of the tumors have recurred or metastasize after surgery. We describe novel GLI1 fusions in 3 mesenchymal neoplasms of the small intestine, including 2 with biphenotypic features. Thus far, all cases have pursued indolent clinical courses. We propose the term " GLI1 -rearranged enteric tumor" to encompass this group of unique neoplasms of the small intestine that harbor GLI1 gene fusions and expand the spectrum of gastrointestinal neoplasms with these alterations.

Abstract B026: Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets

In castration-resistant prostate cancer (CRPC), the loss of androgen receptor (AR) dependence leads to clinically aggressive tumors with few therapeutic options. We used ATAC-seq (assay for transposase-accessible chromatin sequencing), RNA-seq, and DNA sequencing to investigate 22 organoids, six patient-derived xenografts, and 12 cell lines. We identified the well-characterized AR-dependent and neuroendocrine subtypes, as well as two AR-negative/low groups: a Wnt-dependent subtype, and a stem cell–like (SCL) subtype driven by activator protein–1 (AP-1) transcription factors. We used transcriptomic signatures to classify 366 patients, which showed that SCL is the second most common subtype of CRPC after AR-dependent. Our data suggest that AP-1 interacts with the YAP/TAZ and TEAD proteins to maintain subtype-specific chromatin accessibility and transcriptomic landscapes in this group. Together, this molecular classification reveals drug targets and can potentially guide therapeutic decisions.

Citation Format: Fanying Tang, Duo Xu, Shangqian Wang, Chen Khuan Wong, Alexander Martinez-Fundichely, Cindy Lee, Sandra Cohen, Jane Park, Corinne Hill, Kenneth Eng, Rohan Bareja, Teng Han, Eric Minwei Liu, Ann Palladino, Wei Di, Dong Gao, Wassim Abida, Shaham Beg, Loredana Puca, Maximiliano Meneses, Elisa De Stanchina, Michael Berger, Anuradha Gopalan, Lukas Dow, Juan Miguel Mosquera, Himisha Beltran, Cora Sternberg, Ping Chi, Howard Scher, Andrea Sboner, Yu Chen, Ekta Khurana. Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B026.

Whole-genome characterization of myoepithelial carcinomas of the soft tissue

Myoepithelial carcinomas (MECs) of soft tissue are rare and aggressive tumors affecting young adults and children, but their molecular landscape has not been comprehensively explored through genome sequencing. Here, we present the whole-exome sequencing (WES), whole-genome sequencing (WGS), and RNA sequencing findings of two MECs. Patients 1 and 2 (P1, P2), both male, were diagnosed at 27 and 37 yr of age, respectively, with shoulder (P1) and inguinal (P2) soft tissue tumors. Both patients developed metastatic disease, and P2 died of disease. P1 tumor showed a rhabdoid cytomorphology and a complete loss of INI1 (SMARCB1) expression, associated with a homozygous SMARCB1 deletion. The tumor from P2 showed a clear cell/small cell morphology, retained INI1 expression and strong S100 positivity. By WES and WGS, tumors from both patients displayed low tumor mutation burdens, and no targetable alterations in cancer genes were detected. P2's tumor harbored an EWSR1::KLF15 rearrangement, whereas the tumor from P1 showed a novel ASCC2::GGNBP2 fusion. WGS evidenced a complex genomic event involving mainly Chromosomes 17 and 22 in the tumor from P1, which was consistent with chromoplexy. These findings are consistent with previous reports of EWSR1 rearrangements (50% of cases) in MECs and provide a genetic basis for the loss of SMARCB1 protein expression observed through immunohistochemistry in 10% of 40% of MEC cases. The lack of additional driver mutations in these tumors supports the hypothesis that these alterations are the key molecular events in MEC evolution. Furthermore, the presence of complex structural variant patterns, invisible to WES, highlights the novel biological insights that can be gained through the application of WGS to rare cancers.

Case report: Metastatic urothelial cancer with an exceptional response to immunotherapy and comprehensive understanding of the tumor and the tumor microenvironment

Although immune checkpoint inhibitors (ICIs) are increasingly used as second-line treatments for urothelial cancer (UC), only a small proportion of patients respond. Therefore, understanding the mechanisms of response to ICIs is critical to improve clinical outcomes for UC patients. The tumor microenvironment (TME) is recognized as a key player in tumor progression and the response to certain anti-cancer treatments. This study aims to investigate the mechanism of response using integrated genomic and transcriptomic profiling of a UC patient who was part of the KEYNOTE-045 trial and showed an exceptional response to pembrolizumab. Diagnosed in 2014 and receiving first-line chemotherapy without success, the patient took part in the KEYNOTE-045 trial for 2 years. She showed dramatic improvement and has now been free of disease for over 6 years. Recently described by Bagaev et al., the Molecular Functional (MF) Portrait was utilized to dissect genomic and transcriptomic features of the patient's tumor and TME. The patient's tumor was characterized as Immune Desert, which is suggestive of a non-inflamed microenvironment. Integrated whole-exome sequencing (WES) and RNA sequencing (RNA-seq) analysis identified an ATM mutation and high TMB level (33.9 mut/mb), which are both positive biomarkers for ICI response. Analysis further revealed the presence of the APOBEC complex, indicating the potential for use of APOBEC signatures as predictive biomarkers for immunotherapy response. Overall, comprehensive characterization of the patient's tumor and TME with the MF Portrait revealed important insights that could potentially be hypothesis generating to identify clinically useful biomarkers and improve treatment for UC patients.

Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer

Genetic alterations in RET lead to activation of ERK and AKT signaling and are associated with hereditary and sporadic thyroid cancer and lung cancer. Highly selective RET inhibitors have recently entered clinical use after demonstrating efficacy in treating patients with diverse tumor types harboring RET gene rearrangements or activating mutations. In order to understand resistance mechanisms arising after treatment with RET inhibitors, we performed a comprehensive molecular and genomic analysis of a patient with RET-rearranged thyroid cancer. Using a combination of drug screening and proteomic and biochemical profiling, we identified an adaptive resistance to RET inhibitors that reactivates ERK signaling within hours of drug exposure. We found that activation of FGFR signaling is a mechanism of adaptive resistance to RET inhibitors that activates ERK signaling. Combined inhibition of FGFR and RET prevented the development of adaptive resistance to RET inhibitors, reduced cell viability, and decreased tumor growth in cellular and animal models of CCDC6-RET-rearranged thyroid cancer.

Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets

In castration-resistant prostate cancer (CRPC), the loss of androgen receptor (AR) dependence leads to clinically aggressive tumors with few therapeutic options. We used ATAC-seq (assay for transposase-accessible chromatin sequencing), RNA-seq, and DNA sequencing to investigate 22 organoids, six patient-derived xenografts, and 12 cell lines. We identified the well-characterized AR-dependent and neuroendocrine subtypes, as well as two AR-negative/low groups: a Wnt-dependent subtype, and a stem cell-like (SCL) subtype driven by activator protein-1 (AP-1) transcription factors. We used transcriptomic signatures to classify 366 patients, which showed that SCL is the second most common subtype of CRPC after AR-dependent. Our data suggest that AP-1 interacts with the YAP/TAZ and TEAD proteins to maintain subtype-specific chromatin accessibility and transcriptomic landscapes in this group. Together, this molecular classification reveals drug targets and can potentially guide therapeutic decisions.

Molecular Evaluation of Low-grade Low-stage Endometrial Cancer With and Without Recurrence

Low-grade, low-stage endometrioid carcinomas (LGLS EC) demonstrate 5-yr survival rates up to 95%. However, a small subset of these tumors recur, and little is known about prognostic markers or established mutation profiles associated with recurrence. The goal of the current study was to identify the molecular profiles of the primary carcinomas and the genomic differences between primary tumors and subsequent recurrences. Four cases of LGLS EC with recurrence and 8 cases without recurrence were evaluated via whole-exome sequencing. Three of the 4 recurrent tumors were evaluated via Oncomine Comprehensive Assay. The resulting molecular profiles of the primary and recurrent tumors were compared. Two of the 3 recurrent cases showed additional mutations in the recurrence. One recurrent tumor included an additional TP53 mutation and the other recurrent tumor showed POLE and DDR2 kinase gene mutation. The POLE mutation occurred outside the exonuclease domain. PIK3CA mutations were detected in 4 of 4 primary LGLS EC with recurrence and in 3 of 8 disease-free cases. LGLS EC with recurrence showed higher MSIsensor scores compared with LGLS without recurrence. The level of copy number gains in LGLS EC with recurrence was larger than LGLS EC without recurrence. This pilot study showed 1 of 3 recurrent cases gained a mutation associated with genetic instability (TP53) and 1 of them also acquired a mutation in the DDR2 kinase, a potential therapeutic target. We also noted a higher level of copy number gains, MSIsensor scores and PIK3CA mutations in the primary tumors that later recurred.

Tumor-immune microenvironment revealed by Imaging Mass Cytometry in a metastatic sarcomatoid urothelial carcinoma with a prolonged response to pembrolizumab

Sarcomatoid urothelial carcinoma (SUC) is a rare subtype of urothelial carcinoma (UC) that typically presents at an advanced stage compared to more common variants of UC. Locally advanced and metastatic UC have a poor long-term survival following progression on first-line platinum-based chemotherapy. Antibodies directed against the programmed cell death 1 protein (PD-1) or its ligand (PD-L1) are now approved to be used in these scenarios. The need for reliable biomarkers for treatment stratification is still under research. Here, we present a novel case report of the first Imaging Mass Cytometry (IMC) analysis done in SUC to investigate the immune cell repertoire and PD-L1 expression in a patient who presented with metastatic SUC and experienced a prolonged response to the anti-PD1 immune checkpoint inhibitor pembrolizumab after progression on first-line chemotherapy. This case report provides an important platform for translating these findings to a larger cohort of UC and UC variants.

The genomic landscape of metastatic clear cell renal cell carcinoma after systemic therapy

Primary clear cell renal cell carcinoma (ccRCC) has been previously characterized, but the genomic landscape of metastatic ccRCC is largely unexplored. Here, we performed whole exome sequencing (WES) in 68 samples from 44 patients with ccRCC, including 52 samples from a metastatic site. SETD2, PBRM1, APC and VHL were the most frequently mutated genes in the metastatic ccRCC cohort. RBM10 and FBXW7 were also among the 10 most frequently mutated genes in metastatic tissues. Recurrent somatic copy number variations (CNV) were observed at the previously identified regions 3p25, 9p21 and 14q25, but also at 6p21 (CDKN1A) and 13q14 (RB1). No statistically significant differences were found between samples from therapy‐naïve and pretreated patients. Clonal evolution analyses with multiple samples from 13 patients suggested that early appearance of CNVs at 3p25, 9p21 and 14q25 may be associated with rapid clinical progression. Overall, the genomic landscapes of primary and metastatic ccRCC seem to share frequent CNVs at 3p25, 9p21 and 14q25. Future work will clarify the implication of RBM10 and FBXW7 mutations and 6p21 and 13q14 CNVs in metastatic ccRCC.

RET Fusion-Positive Papillary Thyroid Cancers are Associated with a More Aggressive Phenotype

BACKGROUND

It is unclear if different genetic drivers in papillary thyroid cancer (PTC) confer different phenotypic tumor behavior leading to more aggressive disease. We hypothesized that RET-driven cancers are more aggressive.

PATIENTS AND METHODS

We reviewed records of consecutive patients treated for newly diagnosed PTC at this single institution from 2015 to 2016. Tumor samples from these patients were genotyped to identify RET-translocated, BRAFV600E mutant, and HRAS, KRAS, and NRAS mutant tumors. Patient demographic, clinicopathologic, and outcomes data were compared to identify genotype-specific patterns of disease.

RESULTS

Of the 327 patients who underwent initial surgery for PTC during the study period, 192 (58.7%) had BRAFV600E mutant tumors (BRAF), 14 (4.3%) had RET-rearranged tumors (RET), 46 (14.1%) had RAS mutant tumors (RAS), and 75 (22.9%) had BRAF, RET, and RAS wildtype tumors. RET-driven tumors were more likely to have extrathyroidal extension (50.0% versus 27.0% for BRAF and 2.2% for RAS, P < 0.001), multifocal disease (85.7% versus 60.3%, and 44.4%, respectively, P = 0.017), and distant metastases (14.3% versus 1.1%, and 0%, respectively, P = 0.019). RET and BRAF patients also had worse disease-free survival than RAS patients (Kaplan-Meier log rank, P = 0.027).

CONCLUSIONS

Patients with RET-driven PTCs had higher rates of extrathyroidal extension, multifocal disease, and distant metastases than patients whose tumors had BRAFV600E or RAS mutations. Patients with RET-rearranged tumors had similar disease-free survival to patients with BRAFV600E mutant tumors. RET rearrangement may confer an aggressive phenotype in PTC.

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. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Genomic instability is enriched in localized prostate cancers from men of African ancestry

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Background: Whole genome sequencing (WGS) of prostate cancers (PC) from American men of African ancestry (AA) is limited despite AA men having twice the incidence of and mortality from PC as compared to their European ancestry (EA) men. Herein we describe analysis of AA PC WGS to identify genomic contributions to incidence and outcome disparities. Methods: WGS data from AA localized hormone naïve (HN) PCs (n = 23) from our institution were combined with publicly available WGS HNPC datasets (n = 5); quantitative predominant genome-wide ancestry was approximated via RFMix. A comparable EA cohort (n = 224) was similarly assembled. Ancestry groups were compared via regression models correcting for Gleason grade, PSA, and pathologic stage. Results: Analysis of known HNPC driver genes revealed lower frequency of PTEN (2/28 v 70/224, 7% v 31%, p = 0.006) and higher frequency of MYC (5/28 v 13/224, 18% v 5%, p = 0.014) and FOXA1 (7/28 v 24/224, 25% v 11%, p = 0.018) alterations in AA tumors relative to EA. An unbiased search for coding and noncoding drivers uncovered recurrent FOXA1 promoter (n = 8, p = 1.1e-8, RR = 3.92) and gene body protein-coding (n = 5, p = 1.2e-6, RR = 7.83) mutations, as targets of somatic selection and affecting nearly half of AA cases. Despite comparable tumor mutational burdens in each group, analysis of genome-wide mutational signatures revealed an AA-specific enrichment of SNVs in trinucleotide contexts associated with mismatch repair deficiency (SBS6, p = 1.68e-2, RR = 49.1). AA tumors also had significantly more small deletions (sig. ID2) relative to EA samples (p = 2.25e-31, RR = 9.47), implying replication slippage at lagging strands. Finally, AA PC genomes had consistently higher MSI scores relative to EA (median [IQR]: 4.03 [3.8-4.53] v 1.52 [1.21-1.85], p = 2.95e-44), yet lower than MSI-H colon cancers. These associations were independent of tissue preservation method or source, suggesting they reflect an ancestry-specific mutational process. Comparison of germline and somatic variants between AA and EA uncovered candidate DNA damage response genes (DDR) for further functional validation. Conclusions: Analysis of the largest AA cohort to date of WGS HNPC has revealed an ancestry-specific somatic mutational processes resulting in elevated rate of MMR-linked SNVs, replication-slippage associated small deletions, and MSI, relative to EA. The uniformity of these data suggest that AAs may harbor an inherited factor contributing to increased somatic genomic instability in the HNPC context. These results are compatible with published analyses demonstrating lower expression of DDR genes in AA versus EA PCs. Greater MSI and indels (via neoantigen formation) may explain the higher response proportions in AA PC patients treated with immune- and radiotherapies. Studies are ongoing to define mechanisms via associations between germline predisposition, somatic modification, and transcriptional outcome.

Serial ctDNA evaluation to predict clinical progression in patients with advanced urothelial carcinoma

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Background: It is not known whether serial circulating tumor DNA (ctDNA) can augment imaging for assessing treatment response in patients (pts.) with advanced urothelial carcinoma (UC). We hypothesized that serial ctDNA measurements predict the clinical progression of advanced UC and map its evolutionary trajectories. Methods: We analyzed 182 serial ctDNA samples from 53 pts. with advanced UC sequenced by the Guardant360 ctDNA platform. The aggregate variant allele frequency (aVAF) was defined as the sum of VAFs of all genomic alterations (GAs) in a ctDNA sample. Clinical response status was categorized into progressive disease (PD) and non-PD based on imaging. Progression-free survival (PFS) was defined as the time from treatment start till PD or death. The Mann-Whitney test was used to compare radiologic response status (PD vs. non-PD) and the ctDNA aVAF collected within 4 weeks of restaging imaging. Results: Pts. with lower initial ctDNA aVAF (≤0.2) had longer overall survival (OS) (hazard ratio (HR): 0.31, 95%CI: 0.11-0.90, p = 0.03). Pts. who achieved clearance of their ctDNA aVAF at the time of any subsequent ctDNA sample (n = 19/53) had longer OS (HR: 0.26, 95%CI: 0.08-0.85, adjusted p = 0.027). Combining ctDNA aVAF values from two consecutive samples improved the performance of a clinical prognostic model based on age, sex, and liver metastasis (C-statistic improved from 0.65 to 0.84). The mean ctDNA aVAF and the median number of GAs per ctDNA sample significantly increased at the time of PD vs. non-PD (12.31 vs. 2.10, p < 0.0001, and 3 vs. 1, p = 0.0006, respectively). Delta ctDNA aVAF increases predicted radiologic PD with an area under the receiver operating characteristic curve of 0.84 (95%CI: 0.65-0.95, p < 00.1). Delta ctDNA aVAF improved the patient risk stratification, pts with both decreased delta ctDNA aVAF and non-PD had the longest overall survival (Log-rank p = 0.05). A subgroup of 20 pts. had increasing ctDNA aVAF and ≥ 1 available subsequent radiologic scans within six months. Increasing ctDNA VAF ≥1 predicted PD in 90% (18/20) of pts with a median lead time of 92 days over imaging. APOBEC3-induced mutations (A3-m) were identified in ctDNA samples of (23%) 12/53 pts. Pts. with ctDNA A3-m had longer median PFS on immune checkpoint blockade than pts. without (17 vs. 3 months, Log-rank p = 0.01). There was no significant difference in OS according to ctDNA A3m status (Log-rank p = 0.37). Serial ctDNA provided insights into the clonal dynamics of treatment resistance, including the acquisition of ERBB2 S653C resistance mutation at the time of PD on lapatinib. Conclusions: Serial ctDNA predicts clinical outcomes and provides real-time assessment of treatment effectiveness in pts. with advanced UC. This has the potential to guide future adaptive therapy paradigms.

Extracellular Matrix in Synthetic Hydrogel-Based Prostate Cancer Organoids Regulate Therapeutic Response to EZH2 and DRD2 Inhibitors

Following treatment with androgen receptor (AR) pathway inhibitors, ≈20% of prostate cancer patients progress by shedding their AR-dependence. These tumors undergo epigenetic reprogramming turning castration-resistant prostate cancer adenocarcinoma (CRPC-Adeno) into neuroendocrine prostate cancer (CRPC-NEPC). No targeted therapies are available for CRPC-NEPCs, and there are minimal organoid models to discover new therapeutic targets against these aggressive tumors. Here, using a combination of patient tumor proteomics, RNA sequencing, spatial-omics, and a synthetic hydrogel-based organoid, putative extracellular matrix (ECM) cues that regulate the phenotypic, transcriptomic, and epigenetic underpinnings of CRPC-NEPCs are defined. Short-term culture in tumor-expressed ECM differentially regulated DNA methylation and mobilized genes in CRPC-NEPCs. The ECM type distinctly regulates the response to small-molecule inhibitors of epigenetic targets and Dopamine Receptor D2 (DRD2), the latter being an understudied target in neuroendocrine tumors. In vivo patient-derived xenograft in immunocompromised mice showed strong anti-tumor response when treated with a DRD2 inhibitor. Finally, we demonstrate that therapeutic response in CRPC-NEPCs under drug-resistant ECM conditions can be overcome by first cellular reprogramming with epigenetic inhibitors, followed by DRD2 treatment. The synthetic organoids suggest the regulatory role of ECM in therapeutic response to targeted therapies in CRPC-NEPCs and enable the discovery of therapies to overcome resistance.

Fine-needle aspiration biopsy of growing teratoma syndrome as a diagnostic pitfall of metastatic adenocarcinoma

Growing teratoma syndrome (GTS) is a rare clinical entity that can occur in patients with a history of treatment for germ cell tumors (GCTs) and normalized serum tumor markers. Owing to the assortment of tissue types found in teratomas that may exhibit atypical features, distinguishing GTS from metastatic cancer in extragonadal masses can be challenging. Fine-needle aspiration biopsy (FNAB) can be useful for the rapid diagnosis of metastatic masses and has been effective in distinguishing GCTs from one another. However, discrepancies in cytologic and histologic diagnoses have been reported in the evaluation of GCTs by FNAB. The potential incomplete sampling of metastatic teratomas in GTS by FNAB along with features of cellular atypia commonly found in teratomas can lead to a misdiagnosis of metastatic carcinoma and drastically affect treatment. Correlation of cytologic, histologic, clinical, and radiographic findings are essential in evaluating metastatic masses in patients with a history of GCT. We report a case of a 46-year-old man with GTS originally diagnosed on FNAB as metastatic adenocarcinoma compatible with a colorectal primary tumor.

Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing

BACKGROUND

Characterization of circulating tumor DNA (ctDNA) has been integrated into clinical practice. Although labs have standardized validation procedures to develop single locus tests, the efficacy of on-site plasma-based next-generation sequencing (NGS) assays still needs to be proved.

MATERIALS AND METHODS

In this retrospective study, we profiled DNA from matched tissue and plasma samples from 75 patients with cancer. We applied an NGS test that detects clinically relevant alterations in 33 genes and microsatellite instability (MSI) to analyze plasma cell-free DNA (cfDNA).

RESULTS

The concordance between alterations detected in both tissue and plasma samples was higher in patients with metastatic disease. The NGS test detected 77% of sequence alterations, amplifications, and fusions that were found in metastatic samples compared with 45% of those alterations found in the primary tumor samples (p = .00005). There was 87% agreement on MSI status between the NGS test and tumor tissue results. In three patients, MSI-high ctDNA correlated with response to immunotherapy. In addition, the NGS test revealed an FGFR2 amplification that was not detected in tumor tissue from a patient with metastatic gastric cancer, emphasizing the importance of profiling plasma samples in patients with advanced cancer.

CONCLUSION

Our validation experience of a plasma-based NGS assay advances current knowledge about translating cfDNA testing into clinical practice and supports the application of plasma assays in the management of oncology patients with metastatic disease. With an in-house method that minimizes the need for invasive procedures, on-site cfDNA testing supplements tissue biopsy to guide precision therapy and is entitled to become a routine practice.

IMPLICATIONS FOR PRACTICE

This study proposes a solution for decentralized liquid biopsy testing based on validation of a next-generation sequencing (NGS) test that detects four classes of genomic alterations in blood: sequence mutations (single nucleotide substitutions or insertions and deletions), fusions, amplifications, and microsatellite instability (MSI). Although there are reference labs that perform single-site comprehensive liquid biopsy testing, the targeted assay this study validated can be established locally in any lab with capacity to offer clinical molecular pathology assays. To the authors' knowledge, this is the first report that validates evaluating an on-site plasma-based NGS test that detects the MSI status along with common sequence alterations encountered in solid tumors.

Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors

The availability of fresh frozen (FF) tissue is a barrier for implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. However, these methods have not been systematically compared. We performed transcriptomic analysis of 32 FFPE tumor samples from 11 patients using three exome capture-based methods: Agilent SureSelect V6, TWIST NGS Exome, and IDT XGen Exome Research Panel. We compared these methods to the TruSeq RNA-seq of fresh frozen (FF-TruSeq) tumor samples from the same patients. We assessed the recovery of clinically relevant biological features. The Spearman's correlation coefficients between the global expression profiles of the three capture-based methods from FFPE and matched FF-TruSeq were high (rho = 0.72-0.9, p < 0.05). A significant correlation between the expression of key immune genes between individual capture-based methods and FF-TruSeq (rho = 0.76-0.88, p < 0.05) was observed. All exome capture-based methods reliably detected outlier expression of actionable gene transcripts, including ERBB2, MET, NTRK1, and PPARG. In urothelial cancer samples, the Agilent assay was associated with the highest molecular subtype concordance with FF-TruSeq (Cohen's k = 0.7, p < 0.01). The Agilent and IDT assays detected all the clinically relevant fusions that were initially identified in FF-TruSeq. All FFPE exome capture-based methods had comparable performance and concordance with FF-TruSeq. Our findings will enable the implementation of RNA-seq in the clinic to guide precision oncology approaches.

Targeting the epichaperome as an effective precision medicine approach in a novel PML-SYK fusion acute myeloid leukemia

The epichaperome is a new cancer target composed of hyperconnected networks of chaperome members that facilitate cell survival. Cancers with an altered chaperone configuration may be susceptible to epichaperome inhibitors. We developed a flow cytometry-based assay for evaluation and monitoring of epichaperome abundance at the single cell level, with the goal of prospectively identifying patients likely to respond to epichaperome inhibitors, to measure target engagement, and dependency during treatment. As proof of principle, we describe a patient with an unclassified myeloproliferative neoplasm harboring a novel PML-SYK fusion, who progressed to acute myeloid leukemia despite chemotherapy and allogeneic stem cell transplant. The leukemia was identified as having high epichaperome abundance. We obtained compassionate access to an investigational epichaperome inhibitor, PU-H71. After 16 doses, the patient achieved durable complete remission. These encouraging results suggest that further investigation of epichaperome inhibitors in patients with abundant baseline epichaperome levels is warranted.

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g., deletion) or complex (e.g., chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early-replicating regions, superenhancers, and breast or ovarian cancers. Rigma comprise "chasms" of low-JCN deletions enriched in late-replicating fragile sites and gastrointestinal carcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold-back inversions associated with expressed protein-coding fusions, breakend hypermutation, and acral, but not cutaneous, melanomas. Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis.

Incorporating cytologic adequacy assessment into precision oncology workflow using telepathology: An institutional experience

BACKGROUND

Tumor sample quality and quantity determine the success of somatic mutation analysis. Thus, a rapid on-site evaluation (ROSE) tumor cytology adequacy assessment was incorporated into the workflow of precision oncology at Weill Cornell Medicine in New York City. Optimal samples were obtained from 68 patients with metastatic cancer.

METHODS

Cytopathologists performed ROSE on fine-needle aspirate samples via telepathology, and subsequently core-needle biopsies were obtained. In a retrospective manner, the concordance between adequacy assessment and the success rate of the procedure was evaluated to obtain sufficient tumor tissue for next-generation sequencing (NGS).

RESULTS

Out of the 68 procedures, 43 were documented as adequate and 25 were documented as inadequate. The diagnostic yield of adequate procedures was 100%. Adequacy evaluation predicted the success rate of molecular profiling in 40 of 43 procedures (93%; 95% CI, 80.9-98.5 procedures). The success rate of molecular testing was significantly higher in the adequate group: 93% compared with 32% in the inadequate group (P < .0005). Seven procedures that failed to provide quality material for mutational analysis and pathological diagnosis were evaluated as inadequate. Cell block provided sufficient DNA for NGS in 6 cases. In 2 cases, a core biopsy could not be performed; hence, the fine-needle aspirate material confirmed the diagnosis and was used for NGS testing.

CONCLUSION

These results support the incorporation of ROSE into the workflow of precision oncology to obtain high-quality tissue samples from metastatic lesions. In addition, NGS testing of concurrent cytology specimens with adequate cellularity can be a surrogate for NGS testing of biopsy specimens.

Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome

CONTEXT.—

An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology.

OBJECTIVE.—

To describe the validation studies as per New York State-Department of Health (NYS-DOH) guidelines for the Oncomine Comprehensive Panel v2, which was originally tailored to the National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) trial.

DESIGN.—

Accuracy, precision, and reproducibility were investigated by using 130 DNA and 18 RNA samples from cytology cell blocks; formalin-fixed, paraffin-embedded tissues; and frozen samples. Analytic sensitivity and specificity were tested by using ATCC and HapMap cell lines.

RESULTS.—

High accuracy and precision/reproducibility were observed for single nucleotide variants and insertion/deletions. We also share our experience in the detection of gene fusions and copy number alterations from an amplicon-based sequencing platform. After sequencing analysis, variant annotation and report generation were performed by using the institutional knowledgebase.

CONCLUSIONS.—

This study serves as an example for validating a comprehensive targeted next-generation sequencing assay with both DNASeq and RNASeq components for NYS-DOH.

Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer

Loss of androgen receptor (AR) signaling dependence occurs in approximately 15%-20% of advanced treatment-resistant prostate cancers, and this may manifest clinically as transformation from a prostate adenocarcinoma histology to a castration-resistant neuroendocrine prostate cancer (CRPC-NE). The diagnosis of CRPC-NE currently relies on a metastatic tumor biopsy, which is invasive for patients and sometimes challenging to diagnose due to morphologic heterogeneity. By studying whole-exome sequencing and whole-genome bisulfite sequencing of cell free DNA (cfDNA) and of matched metastatic tumor biopsies from patients with metastatic prostate adenocarcinoma and CRPC-NE, we identified CRPC-NE features detectable in the circulation. Overall, there was markedly higher concordance between cfDNA and biopsy tissue genomic alterations in patients with CRPC-NE compared with castration-resistant adenocarcinoma, supporting greater intraindividual genomic consistency across metastases. Allele-specific copy number and serial sampling analyses allowed for the detection and tracking of clonal and subclonal tumor cell populations. cfDNA methylation was indicative of circulating tumor content fraction, reflective of methylation patterns observed in biopsy tissues, and was capable of detecting CRPC-NE-associated epigenetic changes (e.g., hypermethylation of ASXL3 and SPDEF; hypomethylation of INSM1 and CDH2). A targeted set combining genomic (TP53, RB1, CYLD, AR) and epigenomic (hypo- and hypermethylation of 20 differential sites) alterations applied to ctDNA was capable of identifying patients with CRPC-NE.

Common germline-somatic variant interactions in advanced urothelial cancer

The prevalence and biological consequences of deleterious germline variants in urothelial cancer (UC) are not fully characterized. We performed whole-exome sequencing (WES) of germline DNA and 157 primary and metastatic tumors from 80 UC patients. We developed a computational framework for identifying putative deleterious germline variants (pDGVs) from WES data. Here, we show that UC patients harbor a high prevalence of pDGVs that truncate tumor suppressor proteins. Deepening somatic loss of heterozygosity in serial tumor samples is observed, suggesting a critical role for these pDGVs in tumor progression. Significant intra-patient heterogeneity in germline-somatic variant interactions results in divergent biological pathway alterations between primary and metastatic tumors. Our results characterize the spectrum of germline variants in UC and highlight their roles in shaping the natural history of the disease. These findings could have broad clinical implications for cancer patients.

Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology

BACKGROUND

Frequency of clinically relevant mutations in solid tumors by targeted and whole-exome sequencing is ∼30%. Transcriptome analysis complements detection of actionable gene fusions in advanced cancer patients. Goal of this study was to determine the added value of anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) assay to identify further potential drug targets, when coupled with whole-exome sequencing (WES).

METHODS

Selected series of fifty-six samples from 55 patients enrolled in our precision medicine study were interrogated by WES and AMP-based NGS. RNA-seq was performed in 19 cases. Clinically relevant and actionable alterations detected by three methods were integrated and analyzed.

RESULTS

AMP-based NGS detected 48 fusions in 31 samples (55.4%); 31.25% (15/48) were classified as targetable based on published literature. WES revealed 29 samples (51.8%) harbored targetable alterations. TMB-high and MSI-high status were observed in 12.7% and 1.8% of cases. RNA-seq from 19 samples identified 8 targetable fusions (42.1%), also captured by AMP-based NGS. When number of actionable fusions detected by AMP-based NGS were added to WES targetable alterations, 66.1% of samples had potential drug targets. When both WES and RNA-seq were analyzed, 57.8% of samples had targetable alterations.

CONCLUSIONS

This study highlights importance of an integrative genomic approach for precision oncology, including use of different NGS platforms with complementary features. Integrating RNA data (whole transcriptome or AMP-based NGS) significantly enhances detection of potential targets in cancer patients. In absence of fresh frozen tissue, AMP-based NGS is a robust method to detect actionable fusions using low-input RNA from archival tissue.

Neurofibroma originating from a urachal mass

Urachal anomalies are rare in the adult population and when diagnosed, are typically malignant. Herein, we report a case of a 61-year-old male who underwent an excision of a urachal mass for a presumed malignancy. Pathologic evaluation demonstrated a neurofibroma. Neurofibromas are benign peripheral nerve sheath tumors that mostly appear as localized skin tumors and rarely involve the genitourinary system. Neoplastic transformation of neurofibromas is rare but not unheard. To our knowledge, this is the first description of a neurofibroma originating from the urachus.

Contemporary Results and Clinical Utility of Renal Mass Biopsies in the Setting of Ablative Therapy: A single center experience

PURPOSE

Clinical guidelines have recently included renal mass biopsy (RMB) in management algorithms, especially in the setting of small renal masses ≤ 4 cm (SRM) and ablative therapy. We sought to evaluate the diagnostic rates of RMB, factors associated with a non-diagnostic biopsy, its clinical utility, and its safety profile in the setting of ablative therapy.

MATERIALS AND METHODS

A total of 174 RMB from 167 patients, performed in a tertiary academic center from 01/2015 to 01/2019, were included. Patient demographics, radiographic mass size, RMB diagnoses, subsequent clinical management, and complications were retrospectively reviewed. RMBs were classified as diagnostic or non-diagnostic based on set criteria.

RESULTS

The mean mass size was 3.0 cm (range: 0.5-15.3 cm) and 140 biopsies (80%) were SRM. Among all RMB, 159 (91%) were diagnostic and 15 (9%) were non-diagnostic. Non-diagnostic biopsies were associated with small mass size, the presence of a cystic component (p < 0.00001) and fewer number of cores submitted (p = 0.0046). All non-diagnostic biopsies occurred in SRMs, where the mean mass size was significantly smaller than diagnostic biopsies (1.3 versus 3.2 cm, p = 0.001). RMB with concurrent ablation yielded non-diagnostic results more frequently than isolated RMBs (15% vs 2%, respectively).

CONCLUSIONS

RMB is useful for definitive diagnosis and clinical management in the setting of ablative therapy. Small mass size, cystic lesions, and fewer number of passes obtained are associated with non-diagnostic biopsies. When a renal mass diagnosis is particularly critical, a separate biopsy procedure prior to ablative therapy is recommended.

Neuroendocrine differentiation in usual-type prostatic adenocarcinoma: Molecular characterization and clinical significance

BACKGROUND

Small cell neuroendocrine (NE) carcinomas of the prostate classically lose androgen receptor (AR) expression, may harbor loss of the RB1, TP53, and PTEN tumor suppressor genes, and are associated with a poor prognosis. However usual-type adenocarcinomas may also contain areas of NE differentiation, and in this context the molecular features and biological significance are less certain.

METHODS

We examined the molecular phenotype and oncologic outcomes of primary prostate adenocarcinomas with ≥5% NE differentiation (≥5% chromogranin A-positive NE cells in any given tumor spot on tissue microarray) using three independent study sets: a set of tumors with paneth cell-like NE differentiation (n = 26), a retrospective case-cohort of intermediate- and high-risk patients enriched for adverse outcomes (n = 267), and primary tumors from a retrospective series of men with eventual castration-resistant metastatic prostate cancer (CRPC) treated with abiraterone or enzalutamide (n = 55).

RESULTS

Benign NE cells expressed significantly lower quantified AR levels compared with paired benign luminal cells (P < .001). Similarly, paneth-like NE carcinoma cells or carcinoma cells expressing chromogranin A expressed significantly lower quantified AR levels than paired non-NE carcinoma cells (P < .001). Quantified ERG protein expression, was also lower in chromogranin A-labeled adenocarcinoma cells compared with unlabeled cells (P < .001) and tumors with NE differentiation showed lower gene expression scores for AR activity compared with those without. Despite evidence of lower AR signaling, adenocarcinomas with NE differentiation did not differ by prevalence of TP53 missense mutations, or PTEN or RB1 loss, compared with those without NE differentiation. Finally, NE differentiation was not associated with time to metastasis in intermediate- and high-risk patients (P = .6 on multivariate analysis), nor with progression-free survival in patients with CRPC treated with abiraterone or enzalutamide (P = .9).

CONCLUSION

NE differentiation in usual-type primary prostate adenocarcinoma is a molecularly and clinically distinct form of lineage plasticity from that occurring in small cell NE carcinoma.

Abstract 5310: Chromatin accessibility landscape and transcriptome of castration resistant prostate cancers reveals novel subtypes and diverse master regulators

Castration-resistant prostate cancer (CRPC) is a heterogeneous disease with diverse drivers and mechanisms of resistance to androgen receptor (AR) therapy.

We generated ATAC-seq and RNA-seq data for twenty-four metastatic human prostate cancer organoids and cell lines. Integration of chromatin accessibility profiles and transcriptomes revealed four subtypes: androgen-receptor(AR)-dependent, neuroendocrine, Wnt-dependent and epithelial mesenchymal transition (EMT). The transcriptomic signatures obtained from these four subtypes enable the classification of 100 metastatic prostate cancer patient samples from Institute Precision Medicine (IPM) and 270 published samples from SU2C study, revealing potential therapeutic vulnerabilities. Furthermore, using novel computational algorithms we constructed regulatory networks and identified the master regulators of each subtype. Currently we're carrying out western blot and quantitative PCR to confirm the subtypes of all prostate cancer models we use, and using drug sensitivity test, CRISPR knockout and cell competition assay to validate the functions of candidates in each subtype.

Our study has characterized global chromatin accessibility landscape and transcriptome in the largest number of metastatic prostate cancer models, which revealed novel subtypes and corresponding tumor drivers. Collectively, these organoids, cell lines and matching sequence data provide a resource to the community to study various CRPC models. The molecular classification and corresponding master regulators reveal new drug targets and could potentially guide future therapeutic studies.

Citation Format: Fanying Tang, Chen Khuan Wong, Sandra Cohen, Cindy Lee, Minwei Liu, Rohan Bareja, Kenneth Eng, Shaham Beg, Loredana Puca, Cora Sternberg, Juan Miguel Mosquera, Himisha Beltran, Andrea Sboner, Yu Chen, Ekta Khurana. Chromatin accessibility landscape and transcriptome of castration resistant prostate cancers reveals novel subtypes and diverse master regulators [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5310.

Oncogenic Addiction to ERBB2 Signaling Predicts Response to Trastuzumab in Urothelial Cancer

Urothelial carcinoma (UC) is a common and frequently lethal cancer. Despite the presence of genomic alterations creating dependency on particular signaling pathways, the use of targeted therapies in advanced and metastatic UC has been limited. We performed an integrated analysis of whole-exome and RNA sequencing of primary and metastatic tumors in a patient with platinum-resistant UC. We found a strikingly high ERBB2 mRNA expression and enrichment of downstream oncogenic ERBB2 signaling in this patient's tumors compared with tumors from an unselected group of patients with UC (N=17). This patient had an exceptional sustained response to trastuzumab. Our findings show that oncogenic addiction to ERBB2 signaling potentially predicts response to ERBB2-directed therapy of UC.

Next-generation sequencing of residual cytologic fixative preserved DNA from pancreatic lesions: A pilot study

BACKGROUND

Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is a sensitive and specific tool in the risk stratification of pancreatic lesions, including cysts. The sensitivity and specificity of EUS-FNA has been shown to improve when cytology is combined with next-generation sequencing (NGS). Ideally, fresh cyst fluid is used for NGS. In this pilot study, we explore the possibility of sequencing DNA derived from residual alcohol-fixed pancreatic aspirates.

METHODS

Residual cytologic fixatives (n = 42) from 39 patients who underwent EUS-FNA for pancreatic lesions were collected along with demographics, imaging, and laboratory studies. Samples were designated as nonneoplastic/nonmucinous benign (NB), mucinous cyst (MC), pancreatic ductal adenocarcinoma (PDAC), or well-differentiated neuroendocrine tumor (NET) on the basis of cytopathologic evaluation and sequenced on the Oncomine platform (ThermoFisher Scientific, Waltham, Massachusetts).

RESULTS

Ten of 14 (71.4%) MCs exhibited clinically significant variants, including KRAS, GNAS, and TP53. Ten of 15 (66.7%) PDACs had KRAS alterations, and 9 of 15 (60%) showed variants in TP53. No variants were detected in any NETs. Only 1 of 9 (11.1%) NB aspirates showed variants in KRAS and MAP2K. Sequencing of formalin-fixed, paraffin-embedded tissue revealed variants identical to those detected in fixative-derived DNA in 4 of 5 cases (80%).

CONCLUSION

Residual DNA from alcohol-fixed aspirates are an underutilized source for NGS. Sequencing residual fixative-derived DNA has the potential to be integrated into the workup of pancreatic aspirates, possibly impacting management.

Fusions involving BCOR and CREBBP are rare events in infiltrating glioma

BCOR has been recognized as a recurrently altered gene in a subset of pediatric tumors of the central nervous system (CNS). Here, we describe a novel BCOR-CREBBP fusion event in a case of pediatric infiltrating astrocytoma and further probe the frequency of related fusion events in CNS tumors. We analyzed biopsy samples taken from a 15-year-old male with an aggressive, unresectable and multifocal infiltrating astrocytoma. We performed RNA sequencing (RNA-seq) and targeted DNA sequencing. In the index case, the fused BCOR-CREBBP transcript comprises exons 1-4 of BCOR and exon 31 of CREBBP. The fused gene thus retains the Bcl6 interaction domain of BCOR while eliminating the domain that has been shown to interact with the polycomb group protein PCGF1. The fusion event was validated by FISH and reverse transcriptase PCR. An additional set of 177 pediatric and adult primary CNS tumors were assessed via FISH for BCOR break apart events, all of which were negative. An additional 509 adult lower grade infiltrating gliomas from the publicly available TCGA dataset were screened for BCOR or CREBBP fusions. In this set, one case was found to harbor a CREBBP-GOLGA6L2 fusion and one case a CREBBP-SRRM2 fusion. In a third patient, both BCOR-L3MBTL2 and EP300-BCOR fusions were seen. Of particular interest to this study, EP300 is a paralog of CREBBP and the breakpoint seen involves a similar region of the gene to that of the index case; however, the resultant transcript is predicted to be completely distinct. While this gene fusion may play an oncogenic role through the loss of tumor suppressor functions of BCOR and CREBBP, further screening over larger cohorts and functional validation is needed to determine the degree to which this or similar fusions are recurrent and to elucidate their oncogenic potential.

Abstract IA33: Precision medicine at Weill Cornell Medicine/New York Presbyterian: Breaking silos, integrating resources, being inclusive

Genomic testing with next-generation sequencing (NGS) has become a pillar of precision medicine, whose aim is to identify the genomic alterations of a patient’s tumor and provide guidelines to clinicians for optimal treatment. Clinical testing is typically performed with targeted panels interrogating a limited set of genes, selected based on our best scientific knowledge on their diagnostic or prognostic role. Despite more recent efforts to be more inclusive, most genomic databases have a limited representation of non-European populations, resulting in a biased selection of those genes, and the potential exclusion of under-represented groups from the benefit of precision medicine. At the Englander Institute for Precision Medicine (EIPM), we developed a whole-exome sequencing (WES) clinical test, EXaCT-1, which interrogates about 21,000 protein coding genes for single-nucleotide variants, indels, and copy number. EXaCT-1 enables an unbiased view of the genomic landscape of a patient’s tumor and allows for the collection of data to investigate genomic diversity. We also tackled one of the major barriers of precision medicine: the infrastructure to execute clinical sequencing. From ordering a test, collecting and processing samples, to the analysis and review of the data and generation of reports, several systems, procedures, and expertise are involved, and their effective coordination is a key component for the timely delivery of results. We have built a framework supporting the entire process of clinical genomic testing: a Laboratory Information Management System (LIMS) helps the clinical lab to receive orders, acquire and process specimens, and seamlessly communicate with the sequencers and the computational pipelines. Molecular pathologists use NGSReporter, a secure web application, to review the data and sign-out reports. NGSReporter integrates the results of a test with our Precision Medicine Knowledge Base (PMKB – https://pmkb.weill.cornell.edu), which classifies variants based on their relevance to clinical management and provides standardized interpretations. Reports are sent to the electronic health record (EHR) as PDFs as well as discrete entities, enabling queries such as: “Which Hispanic patients with KRAS mutations are diabetic?” Sharing de-identified data is also a key aspect of precision medicine. To this end, we provide our investigators and collaborators with a protected cBioPortal instance that, in addition to publicly available datasets, includes internal data, thus enabling the exploration of hypotheses about the role of alterations across different cohorts and clinical features. Being in the center of New York City has the added benefit of an ethnically diverse patient population. Finding the “right treatment for the right person and at the right time” requires a concerted effort of multiple partners. The EIPM infrastructure facilitates these efforts, with the goal of making precision medicine accessible to everyone.

Citation Format: Andrea Sboner, Cora Sternberg, Juan Miguel Mosquera, Wei Song, Michael Kluk, Wayne Tam, Hanna Rennert, David Pisapia, Jeffrey Catalano, Gloria Cheang, David Wilkes, Danielle Bulaon, M. Laura Martin, Alexandros Sigaras, Kenneth Eng, Rohan Bareja, Rob Kim, Massimo Loda, Olivier Elemento. Precision medicine at Weill Cornell Medicine/New York Presbyterian: Breaking silos, integrating resources, being inclusive [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr IA33.

Integrative multiplatform molecular profiling of benign prostatic hyperplasia identifies distinct subtypes

Benign prostatic hyperplasia (BPH), a nonmalignant enlargement of the prostate, is among the most common diseases affecting aging men, but the underlying molecular features remain poorly understood, and therapeutic options are limited. Here we employ a comprehensive molecular investigation of BPH, including genomic, transcriptomic and epigenetic profiling. We find no evidence of neoplastic features in BPH: no evidence of driver genomic alterations, including low coding mutation rates, mutational signatures consistent with aging tissues, minimal copy number alterations, and no genomic rearrangements. At the epigenetic level, global hypermethylation is the dominant process. Integrating transcriptional and methylation signatures identifies two BPH subgroups with distinct clinical features and signaling pathways, validated in two independent cohorts. Finally, mTOR inhibitors emerge as a potential subtype-specific therapeutic option, and men exposed to mTOR inhibitors show a significant decrease in prostate size. We conclude that BPH consists of distinct molecular subgroups, with potential for subtype-specific precision therapy.

Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer

Histologic transformation to small cell neuroendocrine prostate cancer occurs in a subset of patients with advanced prostate cancer as a mechanism of treatment resistance. Rovalpituzumab tesirine (SC16LD6.5) is an antibody-drug conjugate that targets delta-like protein 3 (DLL3) and was initially developed for small cell lung cancer. We found that DLL3 is expressed in most of the castration-resistant neuroendocrine prostate cancer (CRPC-NE) (36 of 47, 76.6%) and in a subset of castration-resistant prostate adenocarcinomas (7 of 56, 12.5%). It shows minimal to no expression in localized prostate cancer (1 of 194) and benign prostate (0 of 103). DLL3 expression correlates with neuroendocrine marker expression, RB1 loss, and aggressive clinical features. DLL3 in circulating tumor cells was concordant with matched metastatic biopsy (87%). Treatment of DLL3-expressing prostate cancer xenografts with a single dose of SC16LD6.5 resulted in complete and durable responses, whereas DLL3-negative models were insensitive. We highlight a patient with neuroendocrine prostate cancer with a meaningful clinical and radiologic response to SC16LD6.5 when treated on a phase 1 trial. Overall, our findings indicate that DLL3 is preferentially expressed in CRPC-NE and provide rationale for targeting DLL3 in patients with DLL3-positive metastatic prostate cancer.