Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma.

BACKGROUND: Genomics-based predictors of drug response have the potential to improve outcomes associated with cancer therapy. Osteosarcoma (OS), the most common primary bone cancer in dogs, is commonly treated with adjuvant doxorubicin or carboplatin following amputation of the affected limb. We evaluated the use of gene-expression based models built in an intra- or interspecies manner to predict chemosensitivity and treatment outcome in canine OS. Models were built and evaluated using microarray gene expression and drug sensitivity data from human and canine cancer cell lines, and canine OS tumor datasets. The "COXEN" method was utilized to filter gene signatures between human and dog datasets based on strong co-expression patterns. Models were built using linear discriminant analysis via the misclassification penalized posterior algorithm. RESULTS: The best doxorubicin model involved genes identified in human lines that were co-expressed and trained on canine OS tumor data, which accurately predicted clinical outcome in 73 % of dogs (p = 0.0262, binomial). The best carboplatin model utilized canine lines for gene identification and model training, with canine OS tumor data for co-expression. Dogs whose treatment matched our predictions had significantly better clinical outcomes than those that didn't (p = 0.0006, Log Rank), and this predictor significantly associated with longer disease free intervals in a Cox multivariate analysis (hazard ratio = 0.3102, p = 0.0124). CONCLUSIONS: Our data show that intra- and interspecies gene expression models can successfully predict response in canine OS, which may improve outcome in dogs and serve as pre-clinical validation for similar methods in human cancer research.

Long-term Outcomes from a Phase 2 Study of Neoadjuvant Chemotherapy for Muscle-invasive Bladder Cancer (SWOG S1314; NCT02177695).

BACKGROUND: The COXEN gene expression model was evaluated for prediction of response to neoadjuvant chemotherapy for muscle-invasive bladder cancer (MIBC). OBJECTIVE: To conduct a secondary analysis of the association of each COXEN score with event-free survival (EFS) and overall survival (OS) and by treatment arm. DESIGN, SETTING, AND PARTICIPANTS: This was a randomized phase 2 trial of neoadjuvant gemcitabine-cisplatin (GC) or dose-dense methotrexate-vinblastine-adriamycin-cisplatin (ddMVAC) in MIBC. INTERVENTION: Patients were randomized to ddMVAC (every 14 d) or GC (every 21 d), both for four cycles. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: EFS events were defined as progression or death before scheduled surgery, a decision to not undergo surgery, recurrence, or death due to any cause after surgery. Cox regression was used to evaluate the COXEN score or treatment arm association with EFS and OS. RESULTS AND LIMITATIONS: A total of 167 evaluable patients were included in the COXEN analysis. The COXEN scores were not significantly prognostic for OS or EFS in the respective arms, but the GC COXEN score had a hazard ratio (HR) of 0.45 (95% confidence interval [CI] 0.20-0.99; p = 0.047) when the arms were pooled. In the intent-to-treat analysis (n = 227), there was no significant difference between ddMVAC and GC for OS (HR 0.87, 95% CI 0.54-1.40; p = 0.57) or EFS (HR 0.86, 95% CI 0.59-1.26; p = 0.45). Among the 192 patients who underwent surgery, pathologic response (pT0 vs downstaging vs no response) was strongly correlated with superior postsurgical survival (5-yr OS 90%, 89% and 52%, respectively). CONCLUSIONS: The COXEN GC score has prognostic value for patients receiving cisplatin-based neoadjuvant treatment. The randomized, prospective design provides estimates of OS and EFS for GC and ddMVAC in this population. Pathologic response (

DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression.

Myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed single-cell RNA sequencing on serial MPN and sAML patient stem and progenitor cells, identifying aberrantly increased expression of DUSP6 underlying disease transformation. Pharmacologic dual-specificity phosphatase (DUSP)6 targeting led to inhibition of S6 and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling while also reducing inflammatory cytokine production. DUSP6 perturbation further inhibited ribosomal S6 kinase (RSK)1, which we identified as a second indispensable candidate associated with poor clinical outcome. Ectopic expression of DUSP6 mediated JAK2-inhibitor resistance and exacerbated disease severity in patient-derived xenograft (PDX) models. Contrastingly, DUSP6 inhibition potently suppressed disease development across Jak2V617F and MPLW515L MPN mouse models and sAML PDXs without inducing toxicity in healthy controls. These findings underscore DUSP6 in driving disease transformation and highlight the DUSP6-RSK1 axis as a vulnerable, druggable pathway in myeloid malignancies.

Of Elephants and Other Mammals: A Comparative Review of Reproductive Tumors and Potential Impact on Conservation.

Reproductive tumors can impact conception, pregnancy, and birth in mammals. These impacts are well documented in humans, while data in other mammals are limited. An urgent need exists to understand the reproductive impact of these lesions in endangered species, because some endangered species have a documented high prevalence of reproductive tumors. This article documents that the prevalence of both benign and malignant neoplasia differs between African and Asian elephants, with Asian elephants more frequently diagnosed and negatively affected by both. The prevalence of these tumors across mammalian species is compared, and impact plus treatment options in human medicine are reviewed to inform decision making in elephants. Evidence suggests that reproductive tumors can negatively impact elephant conservation. Future studies that document reproductive outcomes, including the success of various treatment approaches in elephants with tumors will benefit conservation efforts.

Immune pathways and TP53 missense mutations are associated with longer survival in canine osteosarcoma.

Osteosarcoma affects about 2.8% of dogs with cancer, with a one-year survival rate of approximately 45%. The purpose of this study was to characterize mutation and expression profiles of osteosarcoma and its association with outcome in dogs. The number of somatic variants identified across 26 samples ranged from 145 to 2,697 with top recurrent mutations observed in TP53 and SETD2. Additionally, 47 cancer genes were identified with copy number variations. Missense TP53 mutation status and low pre-treatment blood monocyte counts were associated with a longer disease-free interval (DFI). Patients with longer DFI also showed increased transcript levels of anti-tumor immune response genes. Although, T-cell and myeloid cell quantifications were not significantly associated with outcome; immune related genes, PDL-1 and CD160, were correlated with T-cell abundance. Overall, the association of gene expression and mutation profiles to outcome provides insights into pathogenesis and therapeutic interventions in osteosarcoma patients.

Prospective clinical trial testing COXEN-based gene expression models of chemosensitivity in dogs with spontaneous osteosarcoma.

BACKGROUND: This study is a prospective clinical trial in dogs with osteosarcoma testing a gene expression model (GEM) predicting the chemosensitivity of tumors to carboplatin (CARBO) or doxorubicin (DOX) developed using the COXEN method. PATIENTS AND METHODS: Sixty dogs with appendicular osteosarcoma were enrolled in this trial. RNA isolation and gene expression profiling were conducted with 2 biopsies for 54/63 screened tumors, and with a single biopsy for 9 tumors. Resulting gene expression data were used for calculation of a COXEN score for CARBO and DOX based on a previous study showing the significance of this predictor on patient outcome utilizing retrospective data (BMC Bioinformatics 17:93). Dogs were assigned adjuvant CARBO, DOX or the combination based on the results of the COXEN score following surgical removal of the tumor via amputation and were monitored for disease progression by chest radiograph every 2 months. RESULTS: The COXEN predictor of chemosensitivity to CARBO or DOX was not a significant predictor of progression-free interval or overall survival for the trial participants. The calculation of DOX COXEN score using gene expression data from two independent biopsies of the same tumor were highly correlated (P < 0.0001), whereas the calculated CARBO COXEN score was not (P = 0.3039). CONCLUSION: The COXEN predictor of chemosensitivity to CARBO or DOX is not a significant predictor of outcome when utilized in this prospective study. This trial represents the first prospective trial of a GEM predictor of chemosensitivity and establishes pet dogs with cancer as viable surrogates for prospective trials of prognostic indicators.

A Humanized Animal Model Predicts Clonal Evolution and Therapeutic Vulnerabilities in Myeloproliferative Neoplasms.

Myeloproliferative neoplasms (MPN) are chronic blood diseases with significant morbidity and mortality. Although sequencing studies have elucidated the genetic mutations that drive these diseases, MPNs remain largely incurable with a significant proportion of patients progressing to rapidly fatal secondary acute myeloid leukemia (sAML). Therapeutic discovery has been hampered by the inability of genetically engineered mouse models to generate key human pathologies such as bone marrow fibrosis. To circumvent these limitations, here we present a humanized animal model of myelofibrosis (MF) patient-derived xenografts (PDX). These PDXs robustly engrafted patient cells that recapitulated the patient's genetic hierarchy and pathologies such as reticulin fibrosis and propagation of MPN-initiating stem cells. The model can select for engraftment of rare leukemic subclones to identify patients with MF at risk for sAML transformation and can be used as a platform for genetic target validation and therapeutic discovery. We present a novel but generalizable model to study human MPN biology. SIGNIFICANCE: Although the genetic events driving MPNs are well defined, therapeutic discovery has been hampered by the inability of murine models to replicate key patient pathologies. Here, we present a PDX system to model human myelofibrosis that reproduces human pathologies and is amenable to genetic and pharmacologic manipulation. This article is highlighted in the In This Issue feature, p. 2945.

A Randomized Phase II Study of Coexpression Extrapolation (COXEN) with Neoadjuvant Chemotherapy for Bladder Cancer (SWOG S1314; NCT02177695).

PURPOSE: Dose-dense methotrexate-vinblastine-adriamycin-cisplatin (ddMVAC) and gemcitabine-cisplatin (GC) are accepted neoadjuvant regimens for muscle-invasive bladder cancer. The aim of this study was to validate the score from a coexpression extrapolation (COXEN) algorithm-generated gene expression model (GEM) as a biomarker in patients undergoing radical cystectomy. PATIENTS AND METHODS: Eligibility included cT2-T4a N0 M0, urothelial bladder cancer, ≥ 5 mm of viable tumor, cisplatin eligible, with plan for cystectomy; 237 patients were randomized between ddMVAC, given every 14 days for four cycles, and GC, given every 21 days for four cycles. The primary objective assessed prespecified dichotomous treatment-specific COXEN score as predictive of pT0 rate or ≤ pT1 (downstaging) at surgery. RESULTS: Among 167 evaluable patients, the OR for pT0 with the GC GEM score in GC-treated patients was 2.63 [P = 0.10; 95% confidence interval (CI), 0.82-8.36]; for the ddMVAC COXEN GEM score with ddMVAC treatment, the OR was 1.12 (P = 0.82, 95% CI, 0.42-2.95). The GC GEM score was applied to pooled arms (GC and ddMVAC) for downstaging with an OR of 2.33 (P = 0.02; 95% CI, 1.11-4.89). In an intention-to-treat analysis of eligible patients (n = 227), pT0 rates for ddMVAC and GC were 28% and 30% (P = 0.75); downstaging was 47% and 40% (P = 0.27), respectively. CONCLUSIONS: Treatment-specific COXEN scores were not significantly predictive for response to individual chemotherapy treatment. The COXEN GEM GC score was significantly associated with downstaging in the pooled arms. Additional biomarker development is planned.

Co-evolution of tumor and immune cells during progression of multiple myeloma.

Multiple myeloma (MM) is characterized by the uncontrolled proliferation of plasma cells. Despite recent treatment advances, it is still incurable as disease progression is not fully understood. To investigate MM and its immune environment, we apply single cell RNA and linked-read whole genome sequencing to profile 29 longitudinal samples at different disease stages from 14 patients. Here, we collect 17,267 plasma cells and 57,719 immune cells, discovering patient-specific plasma cell profiles and immune cell expression changes. Patients with the same genetic alterations tend to have both plasma cells and immune cells clustered together. By integrating bulk genomics and single cell mapping, we track plasma cell subpopulations across disease stages and find three patterns: stability (from precancer to diagnosis), and gain or loss (from diagnosis to relapse). In multiple patients, we detect "B cell-featured" plasma cell subpopulations that cluster closely with B cells, implicating their cell of origin. We validate AP-1 complex differential expression (JUN and FOS) in plasma cell subpopulations using CyTOF-based protein assays, and integrated analysis of single-cell RNA and CyTOF data reveals AP-1 downstream targets (IL6 and IL1B) potentially leading to inflammation regulation. Our work represents a longitudinal investigation for tumor and microenvironment during MM progression and paves the way for expanding treatment options.

Identification of functionally primitive and immunophenotypically distinct subpopulations in secondary acute myeloid leukemia by mass cytometry.

BACKGROUND: Background: Mass cytometry (CyTOF) is a powerful tool for analyzing cellular networks at the single cell level. Due to the high-dimensional nature of this approach, analysis algorithms have been developed to visualize and interpret mass cytometry data. In this study, we applied these approaches to a cohort of patients with secondary acute myeloid leukemia (sAML). METHODS: We utilized mass cytometry to interrogate localization and intensity of thrombopoietin-mediated intracellular signaling in sAML. Extracellular and intracellular phenotypes were dissected using SPADE, viSNE, and PhenoGraph. RESULTS: Healthy controls exhibited highly localized signaling responses largely restricted to the hematopoietic stem/progenitor cell (HSPC) compartment. In contrast, sAML samples contained subpopulations outside the HSPC compartment exhibiting thrombopoietin (TPO) sensitivity comparable to or greater than immunophenotypically defined HSPCs. We employed unsupervised clustering by PhenoGraph to elucidate distinct subpopulations within these heterogeneous samples. One metacluster composed almost exclusively of Lin- CD61+ CD34- CD38- CD45low cells was identified. This subpopulation was not readily identified by established manual gating approaches, and generally exhibited greater STAT phosphorylation in response to TPO stimulation than did Lin- CD61- CD34+ CD38- cells. Lin- CD61+ CD34- CD38- CD45low cells were identified in three additional sAML patients analyzed independently using a manual gating approach based upon PhenoGraph results. Each patient exhibited a similar TPO hypersensitivity to the PhenoGraph metacluster. CONCLUSIONS: The identification of this cellular subpopulation highlights the limitations of manual gating in sAML. Our study demonstrates the potential for mass cytometry to elucidate rare subpopulations in highly heterogeneous tumors by utilizing unsupervised high dimensional analysis. © 2018 International Clinical Cytometry Society.

Drug Selection in the Genomic Age: Application of the Coexpression Extrapolation Principle for Drug Repositioning in Cancer Therapy.

The use of patient-specific data in drug and dose selection is becoming an increasingly important component in cancer therapy. Basing drug choice on molecular aspects of the tumor is consistent with the identification of cancer as a molecular disease or diseases, even within the same histological type, and its treatment specific to the background from which it arose and exists. Multiple examples exist of single-gene mutations, and over- or underexpression that convey either sensitivity or resistance to a given agent. What about the picture that global gene expression in a cancer presents regarding drug sensitivity or resistance? Coexpression extrapolation (COXEN) is a methodology that acts as a Rosetta stone between patterns of gene expression that correlate to drug responses in vitro and those in tumors of untreated patients to predict chemosensitivity in such tumors even to drugs that are not specifically indicated for that histotype. Further applications of COXEN in drug discovery allow for in silico screens correlating drug response and gene expression in a genetically diverse cell panel to gene expression patterns in a target tumor with the potential for identifying and repurposing compounds. Here we discuss how COXEN is being developed and tested for application in drug selection, repositioning, and repurposing in oncology.