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.

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.

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.

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.

Abstract 1434: Uncovering the mechanism of adaptive resistance to RET inhibitors in RET rearranged thyroid cancer

Kinase inhibitors are a critical tool for cancer treatment, but their efficacy is limited by resistance mechanisms. In thyroid and lung cancer RET gene rearrangements result in constitutive MAPK pathway activation and drive malignancy. While treatment with new selective RET inhibitors has been associated with significant clinical responses, a majority of patients experience a partial response or disease stabilization as their best clinical outcome. Resistance to RET inhibitors has emerged as a clinical problem requiring new treatment strategies. Using a combination of drug screening, proteomic, and biochemical profiling we identified a strategy to overcome adaptive resistance to RET inhibitors in human thyroid cancer cell lines and vertebrate animal models. The identification of alternative signaling pathways that reactivates ERK signaling as a mechanism of resistance to RET inhibitors provides an opportunity to anticipate resistance to selective RET inhibitors and use combination therapy that leads to more significant and durable anti-tumor responses in patients with RET rearranged cancers.

Citation Format: Renuka Raman, Jacques Villefranc, Timothy Ullmann, Jessica Thiesmeyer, Viviana Anelli, Chantal Pauli, Rohan Bareja, Kenneth Wha Eng, Princesca Dorsaint, David Wilkes, Shaham Beg, Reid Shaw, Michael Churchill, Naveen Gumpeni, Theresa Scognamiglio, Mark Rubin, Carla Grandori, Juan Mosquera, Juan Mosquera, Juan Mosquera, Noah Dephoure, Andrea Sboner, Olivier Elemento, Yariv Houvras. Uncovering the mechanism of adaptive resistance to RET inhibitors in RET rearranged thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1434.

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.

Transient flow-driven distortion of a nematic liquid crystal in channel flow with dissipative weak planar anchoring

Motivated by the one-drop-filling (ODF) method for the industrial manufacturing of liquid crystal displays, we analyze the pressure-driven flow of a nematic in a channel with dissipative weak planar anchoring at the boundaries of the channel. We obtain quasisteady asymptotic solutions for the director angle and the velocity in the limit of small Leslie angle, in which case the key parameters are the Ericksen number and the anchoring strength parameter. In the limit of large Ericksen number, the solution for the director angle has narrow reorientational boundary layers and a narrow reorientational internal layer separated by two outer regions in which the director is aligned at the positive Leslie angle in the lower half of the channel and the negative Leslie angle in the upper half of the channel. On the other hand, in the limit of small Ericksen number, the solution for the director angle is dominated by splay elastic effects with viscous effects appearing at first order. As the Ericksen number varies, there is a continuous transition between these asymptotic behaviors, and in fact the two asymptotic solutions capture the behavior rather well for all values of the Ericksen number. The steady-state value of the director angle at the boundaries and the timescale of the evolution toward this steady-state value in the asymptotic limits of large and small Ericksen number are determined. In particular, using estimated parameter values for the ODF method, it is found that the boundary director rotation timescale is substantially shorter than the timescale of the ODF method, suggesting that there is sufficient time for significant transient flow-driven distortion of the nematic molecules at the substrates from their required orientation to occur.

Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity

Advanced prostate cancer initially responds to hormonal treatment, but ultimately becomes resistant and requires more potent therapies. One mechanism of resistance observed in around 10–20% of these patients is lineage plasticity, which manifests in a partial or complete small cell or neuroendocrine prostate cancer (NEPC) phenotype. Here, we investigate the role of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complex in NEPC. Using large patient datasets, patient-derived organoids and cancer cell lines, we identify mSWI/SNF subunits that are deregulated in NEPC and demonstrate that SMARCA4 (BRG1) overexpression is associated with aggressive disease. We also show that SWI/SNF complexes interact with different lineage-specific factors in NEPC compared to prostate adenocarcinoma. These data point to a role for mSWI/SNF complexes in therapy-related lineage plasticity, which may also be relevant for other solid tumors.

The differentiation of prostate adenocarcinoma to neuroendocrine prostate cancer (CRPC-NE) is a mechanism of resistance to androgen deprivation therapy. Here the authors show that SWI/SNF chromatin-remodeling complex is deregulated in CRPC-NE and that the complex interacts with different lineage specific factors throughout prostate cancer transdifferentiation.

Novel homozygous variant in WISP3 in a family with unrecognized progressive pseudorheumatoid dysplasia

We present the use of whole-genome sequencing to correctly diagnose progressive pseudorheumatoid dysplasia in patients with atypical clinical and radiologic findings and prior diagnosis of juvenile idiopathic arthritis.

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 Molecular Analysis of Patients With Advanced and Metastatic Cancer

PURPOSE

We developed a precision medicine program for patients with advanced cancer using integrative whole-exome sequencing and transcriptome analysis.

PATIENTS AND METHODS

Five hundred fifteen patients with locally advanced/metastatic solid tumors were prospectively enrolled, and paired tumor/normal sequencing was performed. Seven hundred fifty-nine tumors from 515 patients were evaluated.

RESULTS

Most frequent tumor types were prostate (19.4%), brain (16.5%), bladder (15.4%), and kidney cancer (9.2%). Most frequently altered genes were TP53 (33%), CDKN2A (11%), APC (10%), KTM2D (8%), PTEN (8%), and BRCA2 (8%). Pathogenic germline alterations were present in 10.7% of patients, most frequently CHEK2 (1.9%), BRCA1 (1.5%), BRCA2 (1.5%), and MSH6 (1.4%). Novel gene fusions were identified, including a RBM47-CDK12 fusion in a metastatic prostate cancer sample. The rate of clinically relevant alterations was 39% by whole-exome sequencing, which was improved by 16% by adding RNA sequencing. In patients with more than one sequenced tumor sample (n = 146), 84.62% of actionable mutations were concordant.

CONCLUSION

Integrative analysis may uncover informative alterations for an advanced pan-cancer patient population. These alterations are consistent in spatially and temporally heterogeneous samples.

Quantitative Evidence for Revising the Definition of Primary Graft Dysfunction after Lung Transplant

RATIONALE

Primary graft dysfunction (PGD) is a form of acute lung injury that occurs after lung transplantation. The definition of PGD was standardized in 2005. Since that time, clinical practice has evolved, and this definition is increasingly used as a primary endpoint for clinical trials; therefore, validation is warranted.

OBJECTIVES

We sought to determine whether refinements to the 2005 consensus definition could further improve construct validity.

METHODS

Data from the Lung Transplant Outcomes Group multicenter cohort were used to compare variations on the PGD definition, including alternate oxygenation thresholds, inclusion of additional severity groups, and effects of procedure type and mechanical ventilation. Convergent and divergent validity were compared for mortality prediction and concurrent lung injury biomarker discrimination.

MEASUREMENTS AND MAIN RESULTS

A total of 1,179 subjects from 10 centers were enrolled from 2007 to 2012. Median length of follow-up was 4 years (interquartile range = 2.4-5.9). No mortality differences were noted between no PGD (grade 0) and mild PGD (grade 1). Significantly better mortality discrimination was evident for all definitions using later time points (48, 72, or 48-72 hours; P < 0.001). Biomarker divergent discrimination was superior when collapsing grades 0 and 1. Additional severity grades, use of mechanical ventilation, and transplant procedure type had minimal or no effect on mortality or biomarker discrimination.

CONCLUSIONS

The PGD consensus definition can be simplified by combining lower PGD grades. Construct validity of grading was present regardless of transplant procedure type or use of mechanical ventilation. Additional severity categories had minimal impact on mortality or biomarker discrimination.

Abstract IA19: Phenotype plasticity—a novel mechanism of targeted therapy resistance

Prostate cancer (PCa) is the most commonly diagnosed cancer and the third highest cause of cancer-related death in men in Europe, where it is responsible for over 90,000 deaths a year. The mainstay of treatment for metastatic PCa is androgen-deprivation therapy (ADT). Although initially effective, the treatment ultimately fails and progression to castration-resistant prostate cancer (CRPC) occurs. Given that CRPC is still driven by hormonal signaling through aberrant activation of the androgen receptor (AR), improved, more potent AR-targeting therapies have been developed for CRPC patients. However, resistance to these therapies ultimately occurs as well. One form of resistance identified by my group results in a phenotypic switch leading to androgen receptor indifference and progression to neuroendocrine prostate cancer (NEPC), which shows a distinct histomorphology and expresses neural-like markers. Unlike more commonly recognized mechanisms of ADT resistance due to AR mutations or amplification, NEPC no longer responds to AR-targeting therapy and has a mean survival of 7 months. There is mounting evidence supporting the role of epigenetic events as a mechanism for transdifferentiation of PCa to an androgen signaling-indifferent state under specific genomic conditions, involving but not limited to TP53, RB1, and PTEN loss. However, the epigenetic regulators at work and the specific changes in the epigenetic landscape are unknown. The SWI/SNF complex is a major epigenetic player, both in regulating normal cell differentiation and in cancer biology. This presentation will focus on novel data supporting the role of alterations in this complex that could contribute to PCa phenotype plasticity.

Citation Format: Joanna Cyrta, David Wilkes, Sung Suk Chae, Matteo Benelli, Rohan Bareja, Davide Prandi, Paola Maria Giovanna Cavaliere, Himisha Beltran, Andrea Sboner, Francesca Demichelis, Mark A. Rubin. Phenotype plasticity—a novel mechanism of targeted therapy resistance [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr IA19.

Asymmetric band gap shift in electrically addressed blue phase photonic crystal fibers

In this paper, we present electrooptic experiments on photonic crystal fibers filled with a liquid crystalline blue phase. These fibers guide light via photonic band gaps (PBGs). The blue phase is isotropic in the field-off state but becomes birefringent under an electric field. This leads to a polarization dependent shift of the PBGs. Interestingly, the effect on the PBGs is asymmetrical: while the short wavelength edges of the PBGs shift, the long wavelength edges are almost unaffected. By performing band gap and modal analyses via the finite element simulations, we find that the asymmetric shift is the result of the mixed polarization of the involved photonic bands. Finally, we use the band gap shifts to calculate effective Kerr constants of the blue phase.

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response

IMPORTANCE

Understanding molecular mechanisms of response and resistance to anticancer therapies requires prospective patient follow-up and clinical and functional validation of both common and low-frequency mutations. We describe a whole-exome sequencing (WES) precision medicine trial focused on patients with advanced cancer.

OBJECTIVE

To understand how WES data affect therapeutic decision making in patients with advanced cancer and to identify novel biomarkers of response.

DESIGN, SETTING, AND PATIENTS

Patients with metastatic and treatment-resistant cancer were prospectively enrolled at a single academic center for paired metastatic tumor and normal tissue WES during a 19-month period (February 2013 through September 2014). A comprehensive computational pipeline was used to detect point mutations, indels, and copy number alterations. Mutations were categorized as category 1, 2, or 3 on the basis of actionability; clinical reports were generated and discussed in precision tumor board. Patients were observed for 7 to 25 months for correlation of molecular information with clinical response.

MAIN OUTCOMES AND MEASURES

Feasibility, use of WES for decision making, and identification of novel biomarkers.

RESULTS

A total of 154 tumor-normal pairs from 97 patients with a range of metastatic cancers were sequenced, with a mean coverage of 95X and 16 somatic alterations detected per patient. In total, 16 mutations were category 1 (targeted therapy available), 98 were category 2 (biologically relevant), and 1474 were category 3 (unknown significance). Overall, WES provided informative results in 91 cases (94%), including alterations for which there is an approved drug, there are therapies in clinical or preclinical development, or they are considered drivers and potentially actionable (category 1-2); however, treatment was guided in only 5 patients (5%) on the basis of these recommendations because of access to clinical trials and/or off-label use of drugs. Among unexpected findings, a patient with prostate cancer with exceptional response to treatment was identified who harbored a somatic hemizygous deletion of the DNA repair gene FANCA and putative partial loss of function of the second allele through germline missense variant. Follow-up experiments established that loss of FANCA function was associated with platinum hypersensitivity both in vitro and in patient-derived xenografts, thus providing biologic rationale and functional evidence for his extreme clinical response.

CONCLUSIONS AND RELEVANCE

The majority of advanced, treatment-resistant tumors across tumor types harbor biologically informative alterations. The establishment of a clinical trial for WES of metastatic tumors with prospective follow-up of patients can help identify candidate predictive biomarkers of response.

Protein Quantitative Trait Loci Analysis Identifies Genetic Variation in the Innate Immune Regulator TOLLIP in Post-Lung Transplant Primary Graft Dysfunction Risk

The authors previously identified plasma plasminogen activator inhibitor-1 (PAI-1) level as a quantitative lung injury biomarker in primary graft dysfunction (PGD). They hypothesized that plasma levels of PAI-1 used as a quantitative trait could facilitate discovery of genetic loci important in PGD pathogenesis. A two-stage cohort study was performed. In stage 1, they tested associations of loci with PAI-1 plasma level using linear modeling. Genotyping was performed using the Illumina CVD Bead Chip v2. Loci meeting a p < 5 × 10(-4) cutoff were carried forward and tested in stage 2 for association with PGD. Two hundred ninety-seven enrollees were evaluated in stage 1. Six loci, associated with PAI-1, were carried forward to stage 2 and evaluated in 728 patients. rs3168046 (Toll interacting protein [TOLLIP]) was significantly associated with PGD (p = 0.006). The increased risk of PGD for carrying at least one copy of this variant was 11.7% (95% confidence interval 4.9-18.5%). The false-positive rate for individuals with this genotype who did not have PGD was 6.1%. Variants in the TOLLIP gene are associated with higher circulating PAI-1 plasma levels and validate for association with clinical PGD. A protein quantitative trait analysis for PGD risk prioritizes genetic variations in TOLLIP and supports a role for Toll-like receptors in PGD pathogenesis.

A comparison of non-contrast and contrast-enhanced MRI in the initial stage of Legg-Calvé-Perthes disease

BACKGROUND

A prognostic indicator of outcome for Legg-Calvé-Perthes disease (LCP) is needed to guide treatment decisions during the initial stage of the disease (stage 1), before deformity occurs. Radiographic prognosticators are applicable only after fragmentation (stage II).

OBJECTIVE

We investigated pre- and postcontrast MRI in depicting stage I femoral head involvement.

MATERIALS AND METHODS

Thirty children with stage I LCP underwent non-contrast coronal T1 fast spin-echo (FSE) and corresponding postcontrast fat-suppressed T1-weighted fast spin-echo (FSE) sequences to quantify the extent of femoral head involvement. Three pediatric radiologists and one pediatric orthopedic surgeon independently measured central head involvement.

RESULTS

Interobserver reliability of percent head involvement using non-contrasted MR images had intraclass correlation coefficient (ICC) of 0.72. Postcontrast MRI improved interobserver reliability (ICC 0.82). Qualitatively, the area of involvement was more clearly visible on contrast-enhanced MRI. A comparison of results obtained by each observer using the two MRI techniques showed no correlation. ICC ranged from -0.08 to 0.03 for each observer. Generally, greater head involvement was depicted by contrast compared with non-contrast MRI (Pearson r = -0.37, P = 0.04).

CONCLUSION

Pre- and postcontrast MRI assess two different components of stage I LCP. However, contrast-enhanced MRI more clearly depicts the area of involvement.

Chemically induced twist-bend nematic liquid crystals, liquid crystal dimers, and negative elastic constants

Here we report the chemical induction of the twist-bend nematic phase in a nematic mixture of ether-linked liquid crystal dimers by the addition of a dimer with methylene links; all dimers have an odd number of groups in the spacer connecting the two mesogenic groups. The twist-bend phase has been identified from its optical texture and x-ray scattering pattern as well as NMR spectroscopy, which demonstrates the phase chirality. Theory predicts that the key macroscopic property required for the stability of this chiral phase formed from achiral molecules is for the bend elastic constant to tend to be negative; in addition the twist elastic constant should be smaller than half the splay elastic constant. To test these important aspects of the prediction we have measured the bend and splay elastic constants in the nematic phase preceding the twist-bend nematic using the classic Frederiks methodology and all three elastic constants employing the dynamic light scattering approach. Our results show that, unlike the splay, the bend elastic constant is small and decreases significantly as the transition to the induced twist-bend nematic phase is approached, but then exhibits unexpected behavior prior to the phase transition.

Variation in PTX3 is associated with primary graft dysfunction after lung transplantation

RATIONALE

Elevated long pentraxin-3 (PTX3) levels are associated with the development of primary graft dysfunction (PGD) after lung transplantation. Abnormalities in innate immunity, mediated by PTX3 release, may play a role in PGD pathogenesis.

OBJECTIVES

Our goal was to test whether variants in the gene encoding PTX3 are risk factors for PGD.

METHODS

We performed a candidate gene association study in recipients from the multicenter, prospective Lung Transplant Outcomes Group cohort enrolled between July 2002 and July 2009. The primary outcome was International Society for Heart and Lung Transplantation grade 3 PGD within 72 hours of transplantation. Targeted genotyping of 10 haplotype-tagging PTX3 single-nucleotide polymorphisms (SNPs) was performed in lung transplant recipients. The association between PGD and each SNP was evaluated by logistic regression, adjusting for pretransplantation lung disease, cardiopulmonary bypass use, and population stratification. The association between SNPs and plasma PTX3 levels was tested across genotypes in a subset of recipients with idiopathic pulmonary fibrosis.

MEASUREMENTS AND MAIN RESULTS

Six hundred fifty-four lung transplant recipients were included. The incidence of PGD was 29%. Two linked 5' region variants, rs2120243 and rs2305619, were associated with PGD (odds ratio, 1.5; 95% confidence interval, 1.1 to 1.9; P = 0.006 and odds ratio, 1.4; 95% confidence interval, 1.1 to 1.9; P = 0.007, respectively). The minor allele of rs2305619 was significantly associated with higher plasma PTX3 levels measured pretransplantation (P = 0.014) and at 24 hours (P = 0.047) after transplantation in patients with idiopathic pulmonary fibrosis.

CONCLUSIONS

Genetic variants of PTX3 are associated with PGD after lung transplantation, and are associated with increased PTX3 plasma levels.

Allergic lung inflammation decreases the anti-viral response to vaccinia virus (175.3)

Despite the global eradication of smallpox following widespread vaccination with vaccinia virus (VV), other members of the poxviridae family persist and continue to infect animal and human hosts. Although the lung is the most lethal route of poxvirus infection, there is little known about the local immune response to pulmonary VV infection. Moreover, VV vaccination is contraindicated in patients with atopic dermatitis as the pro-allergic milieu diminishes anti-VV responses. Our goal was to determine the role of allergic airway disease (AAD) on the local immune response to VV infection. Our studies demonstrated increased weight loss, airway hyperreactivity, mucus gene expression, lung pathology and virus titer in mice with AAD. In contrast to observations from cells exposed to pro-allergic cytokines, expression of antimicrobial peptide genes in the lung tissue of infected mice was similar in control mice, and mice with AAD. At 4 days post infection (dpi) there was a more robust innate response in mice with AAD as evidenced by increased infiltration of lung macrophages and granulocytes. By 10 dpi, there were increased numbers of IL-10+CD8+ and IFNγ+CD8+ T cells and enhanced secretion of IL-10 and IFNγ in the bronchoalveolar lavage fluid of mice with AAD, compared to controls. Mice with AAD also had increased VV-specific IgG1 and IgM serum antibodies. These studies suggest the allergic lung microenvironment may influence the anti-viral immune response to pulmonary VV infection.

Elevated plasma long pentraxin-3 levels and primary graft dysfunction after lung transplantation for idiopathic pulmonary fibrosis

Primary graft dysfunction (PGD) after lung transplantation may result from ischemia reperfusion injury (IRI). The innate immune response to IRI may be mediated by Toll-like receptor and IL-1-induced long pentraxin-3 (PTX3) release. We hypothesized that elevated PTX3 levels were associated with PGD. We performed a nested case control study of lung transplant recipients with idiopathic pulmonary fibrosis (IPF) or chronic obstructive pulmonary disease (COPD) from the Lung Transplant Outcomes Group cohort. PTX3 levels were measured pretransplant, and 6 and 24 h postreperfusion. Cases were subjects with grade 3 PGD within 72 h of transplantation and controls were those without grade 3 PGD. Generalized estimating equations and multivariable logistic regression were used for analysis. We selected 40 PGD cases and 79 non-PGD controls. Plasma PTX3 level was associated with PGD in IPF but not COPD recipients (p for interaction < 0.03). Among patients with IPF, PTX3 levels at 6 and 24 h were associated with PGD (OR = 1.6, p = 0.02 at 6 h; OR = 1.4, p = 0.008 at 24 h). Elevated PTX3 levels were associated with the development of PGD after lung transplantation in IPF patients. Future studies evaluating the role of innate immune activation in IPF and PGD are warranted.

Alterations in pulmonary immunity in response to vaccinia virus (103.8)

Vaccinia virus (VV) infection in mice is an accepted model to study the pathogenesis of variola virus, the causative agent of human smallpox. Although the lung is a key site of poxvirus infection, there is little known about the local immune response to intrapulmonary VV infection. Additionally, because vaccination with VV is contraindicated in patients with atopic allergic skin conditions it is very important to determine the role of atopic lung disease on local vaccinia immunity. We have found that established allergic lung disease results in significantly increased numbers of eosinophils, myeloid dendritic cells (mDCs) and alveolar macrophages. Interestingly, an intrapulmonary VV infection in mice with allergic lung disease does not further increase the number of mDCs or alveolar macrophages, but does trigger a significant increase in plasmacytoid DCs (pDCs) and a significant decrease in eosinophils. Moreover, pulmonary eosinophils, mDCs and macrophages from mice with allergic lung disease were less susceptible to an in vitro VV infection than the respective cells from naïve mice. Whereas pulmonary pDCs and B cells from mice with allergic lung disease were more susceptible to an in vitro VV infection. Alterations in antigen presentation were also observed using splenocytes from animals with induced hypersensitivity. Taken together, these studies strongly suggest that the allergic lung microenvironment may influence anti-viral immunity to an intrapulmonary VV infection.

Diversifying Biomedical Training: A Synergistic Intervention

For over three decades, the scientific community has expressed concern over the paucity of African American, Latino and Native American researchers in the biomedical training pipeline. Concern has been expressed regarding what is forecasted as a shortage of these underrepresented minority (URM) scientists given the demographic shifts occurring worldwide and particularly in the United States. Increased access to graduate education has made a positive contribution in addressing this disparity. This article describes the multiple pathway approaches that have been employed by a school of medicine at an urban Midwest research institution to increase the number of URM students enrolled in, and graduating from, doctoral programs within basic science departments, through the combination of R25 grants and other grant programs funded by the National Institutes of Health (NIH). This article outlines the process of implementing a strong synergistic approach to the training of URM students through linkages between the NIH-funded "Bridges to the Doctorate (BRIDGES)" and "Initiative for Maximizing Graduate Student Diversity (IMGSD)" programs. The article documents the specific gains witnessed by this particular institution and identifies key components of the interventions that may prove useful for institutions seeking to increment the biomedical pipeline with scientists from diverse backgrounds.

Intraobserver and interobserver reliability of two ultrasound measures of humeral head position in infants with neonatal brachial plexus palsy

BACKGROUND

Ultrasonographic evaluation of the hip in infants is considered both reliable and reproducible in the diagnosis of developmental dysplasia of the hip. Ultrasonographic evaluation of the shoulder in infants has been reported as a valuable diagnostic aid in dysplastic development following neonatal brachial plexus palsy. To our knowledge, there has been no study of the intraobserver reproducibility and interobserver reliability of sonography of the shoulder in infants with and without suspected posterior shoulder dislocation.

METHODS

Two identical but randomly ordered sets of the same deidentified sonographic images of shoulders in infants were given to radiologists, pediatric orthopaedists and orthopaedic residents, and fellows with varying degrees of experience in the evaluation of shoulder pathology in infants, who measured the position of the humeral head relative to the axis of the scapula. Intraobserver reproducibility and interobserver reliability of the measurements were assessed.

RESULTS

For the position of the humeral head with respect to the glenoid in both normal and abnormal conditions, the Pearson correlation coefficient for intraobserver reproducibility was 0.91 and the intraclass correlation coefficient for interobserver reliability was 0.875. For estimating the percentage of the humeral head posterior to the axis of the scapula, the Pearson correlation was 0.85 and the intraclass correlation coefficient was 0.77.

CONCLUSIONS

Ultrasonographic examination of the shoulder in infants to assess for the position of the humeral head with respect to the scapula showed high intraobserver reproducibility and interobserver reliability. It is recommended as a reliable technique for evaluating shoulder position in infants with neonatal brachial plexus palsy.

Structural and Functional Genetic Disorders of the Great Vessels and Outflow Tracts

Development of the aorta and pulmonary artery is a complex process involving multiple molecular genetic pathways that modulate morphogenesis of the outflow tracts and the anastomosis of branch vessels. Recent genetic studies of the cardiovascular system demonstrate that congenital and adult onset progressive disorders of the great vessels such as aneurysms are components of generalized vascular, cardiac, and extracardiovascular syndromes. Current paradigms suggest that aortic disease is founded in patterning anomalies of the conotruncus that occur in utero. These aberrations can be consequences of genetic aberrations in transcriptional regulation of signal transduction both within and outside the developing great vessels.

Hepatobiliary disease in sarcoidosis

BACKGROUND AND AIM

Sarcoidosis is a multisystem granulomatous disease of unknown etiology. Little is known about the prevalence, pattern, and risk factors for hepatobiliary disease in patients with sarcoidosis.

METHODS

We retrieved the records of all patients diagnosed with sarcoidosis at a tertiary care referral hospital and a county hospital between 1976 and 2002. Liver disease was defined as abnormal liver tests (AST > 45 U/L, ALT > 35 U/L, alkaline phosphatase > 125 U/L, total bilirubin > 1.3 mg/dL) in the setting of sarcoidosis. Patients with sarcoidosis and normal liver tests constituted a comparison group.

RESULTS

A total of 1,436 patients with presumed sarcoidosis were identified (66% female, 57% African-American). Three hundred and forty patients had abnormalities in liver tests, and 40 with confirmed sarcoidosis underwent a liver biopsy. Biopsy specimens were available for review for 34 patients; 29 (85%) of 34 exhibited various degrees of portal inflammation, bile duct depletion was noted in 17 (50%), and 9 (26%) had bridging fibrosis or cirrhosis. One hundred and thirty patients with sarcoidosis and normal liver tests were compared to the 40 with sarcoid-related hepatic dysfunction. Male gender, hepatomegaly, splenomegaly, and normal chest radiograph were associated with hepatic sarcoidosis. On multivariate analysis, male gender (OR 2.8, p = 0.012), and splenomegaly (OR 9.2, p < 0.0001) were more prevalent in the group with liver disease.

CONCLUSIONS

Hepatobiliary disease in sarcoidosis is rarely clinically overt. When present, it ranges from asymptomatic liver tests abnormalities to cirrhosis. Male gender and splenomegaly were significantly associated with sarcoid-related liver disease.

Haploinsufficiency at the protein kinase A RI alpha gene locus leads to fertility defects in male mice and men

Carney complex (CNC) is a familial multiple neoplasia syndrome characterized by spotty skin pigmentation, cardiac and cutaneous myxomas, and endocrine tumors. CNC is inherited as an autosomal dominant trait and is transmitted with greater frequency by women vs. men. Nearly two thirds of CNC patients are heterozygous for inactivating mutations in the gene encoding the protein kinase A (PKA) type I alpha regulatory subunit (RI alpha), PRKAR1. We report here that male mice heterozygous for the Prkar1a gene have severely reduced fertility. Sperm from Prkar1a heterozygous mice are morphologically abnormal and reduced in number. Genetic rescue experiments reveal that this phenotype results from elevated PKA catalytic activity in germ cells as early as the pachytene stage of spermatogenesis. Consistent with this defect in the male mutant mice, sperm from CNC patients heterozygous for PRKAR1A mutations were also found to be morphologically aberrant and decreased in number. We conclude that unregulated PKA activity in male meiotic or postmeiotic germ cells leads to structural defects in mature sperm and results in reduced fertility in mice and humans, contributing to the strikingly reduced transmission of PRKAR1A inactivating mutations by male patients with CNC.

Inherited disposition to cardiac myxoma development

Carney complex is a genetic condition in which affected individuals develop benign tumours in various tissues, including the heart. Most individuals with Carney complex have a mutation in the PRKAR1A gene, which encodes the regulatory R1alpha subunit of protein kinase A - a significant component of the cyclic-AMP signalling pathway. Genetically engineered mutant Prkar1a mouse models show an increased propensity to develop tumours, and have established a role for R1alpha in initiating tumour formation and, potentially, in maintaining cell proliferation. Ongoing investigations are exploring the intersection of R1alpha-dependent cell signalling with other gene products such as perinatal myosin, mutation of which can also cause cardiac myxomas.

Clinical phenotypes and molecular genetic mechanisms of Carney complex

Carney complex is a familial multiple neoplasia disorder with characteristic features such as cardiac and cutaneous myxomas and spotty pigmentation of the skin. Clinical genetic analyses have shown that Carney complex is transmitted in an autosomal dominant way and can present with a wide array of other tumours, such as psammomatous melanotic schwannoma, testicular Sertoli-cell tumours, and pituitary adenomas. Molecular genetic studies show that mutations in the PRKAR1A gene, encoding the R1alpha regulatory subunit of cyclic-AMP-dependent protein kinase A, are the cause of Carney complex in most patients. Investigation of genetically engineered animal models confirms the role of PRKAR1A as a tumour suppressor and has begun to elaborate mechanisms underlying tumorigenesis in this disorder. Further genetic studies in human beings have highlighted novel variant phenotypes, such as congenital contractures, which are potentially associated with Carney complex, and have identified alternative genetic pathways to cardiac tumorigenesis, including mutation of the MYH8 gene that encodes perinatal myosin.