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Background: Prospective randomized trials have not yet identified baseline features predictive of organ preservation in locally advanced rectal cancers treated with total neoadjuvant therapy and a selective watch-and-wait strategy. Methods: This was a secondary analysis of the OPRA trial, which randomized patients with stage II–III rectal adenocarcinoma to receive either induction or consolidation total neoadjuvant therapy. Patients were recommended for total mesorectal excision, or watch and wait based on clinical response at 8 ± 4 weeks after completing treatment. Standardized baseline clinical and radiological variables were collected prospectively. Survival outcomes, including total mesorectal excision-free survival, disease-free survival, and overall survival, were assessed by intention-to-treat analysis. Cox proportional hazards models were used to evaluate associations between baseline variables and survival outcomes. Results: Of the 324 patients randomized for the OPRA trial, 38 (11.7%) had cT4 tumours, 230 (71.0%) cN-positive disease, 101 (32.5%) mesorectal fascia involvement, and 64 (19.8%) extramural venous invasion. Several baseline features were independently associated with recommendation for total mesorectal excision on multivariable analysis: nodal disease (HR 1.66, 95% c.i. 1.12 to 2.48), extramural venous invasion (HR 1.57, 1.07 to 2.29), mesorectal fascia involvement (HR 1.45, 1.01 to 2.09), and tumour length (HR 1.11, 1.00 to 1.22). Of these, nodal disease (HR 2.02, 1.15 to 3.53) and mesorectal fascia involvement (HR 2.02, 1.26 to 3.26) also predicted worse disease-free survival. Age (HR 1.03, 1.00 to 1.06) was associated with overall survival. Conclusion: Baseline MRI features, including nodal disease, extramural venous invasion, mesorectal fascia involvement, and tumour length, independently predict the likelihood of organ preservation after completion of total neoadjuvant therapy. Mesorectal fascia involvement and nodal disease are associated with disease-free survival. Prospective randomized studies have not yet evaluated baseline features that predict organ preservation in locally advanced rectal cancer treated with total neoadjuvant therapy and a selective watch-and-wait strategy. This secondary analysis of the OPRA trial demonstrated that baseline MRI features, including nodal status, extramural venous invasion, mesorectal fascia involvement, and tumour length, independently predict total mesorectal excision-free survival. Nodal status and mesorectal fascia involvement are associated with disease-free survival. [ABSTRACT FROM AUTHOR]

PURPOSE: Cure models are a useful alternative to Cox proportional hazards models in oncology studies when there is a subpopulation of patients who will not experience the event of interest. Although software is available to fit cure models, there are limited tools to evaluate, report, and visualize model results. This article introduces the cureit R package, an end-to-end pipeline for building mixture cure models, and demonstrates its use in a data set of patients with primary extremity and truncal liposarcoma. METHODS: To assess associations between liposarcoma histologic subtypes and disease-specific death (DSD) in patients treated at Memorial Sloan Kettering Cancer Center between July 1982 and September 2017, mixture cure models were fit and evaluated using the cureit package. Liposarcoma histologic subtypes were defined as well-differentiated, dedifferentiated, myxoid, round cell, and pleomorphic. RESULTS: All other analyzed liposarcoma histologic subtypes were significantly associated with higher DSD in cure models compared with well-differentiated. In multivariable models, myxoid (odds ratio [OR], 6.25 [95% CI, 1.32 to 29.6]) and round cell (OR, 16.2 [95% CI, 2.80 to 93.2]) liposarcoma had higher incidences of DSD compared with well-differentiated patients. By contrast, dedifferentiated liposarcoma was associated with the latency of DSD (hazard ratio, 10.6 [95% CI, 1.48 to 75.9]). Pleomorphic liposarcomas had significantly higher risk in both incidence and the latency of DSD (P <.0001). Brier scores indicated comparable predictive accuracy between cure and Cox models. CONCLUSION: We developed the cureit pipeline to fit and evaluate mixture cure models and demonstrated its clinical utility in the liposarcoma disease setting, shedding insights on the subtype-specific associations with incidence and/or latency. [ABSTRACT FROM AUTHOR]

PURPOSE: Cure models are a useful alternative to Cox proportional hazards models in oncology studies when there is a subpopulation of patients who will not experience the event of interest. Although software is available to fit cure models, there are limited tools to evaluate, report, and visualize model results. This article introduces the cureit R package, an end-to-end pipeline for building mixture cure models, and demonstrates its use in a data set of patients with primary extremity and truncal liposarcoma. METHODS: To assess associations between liposarcoma histologic subtypes and disease-specific death (DSD) in patients treated at Memorial Sloan Kettering Cancer Center between July 1982 and September 2017, mixture cure models were fit and evaluated using the cureit package. Liposarcoma histologic subtypes were defined as well-differentiated, dedifferentiated, myxoid, round cell, and pleomorphic. RESULTS: All other analyzed liposarcoma histologic subtypes were significantly associated with higher DSD in cure models compared with well-differentiated. In multivariable models, myxoid (odds ratio [OR], 6.25 [95% CI, 1.32 to 29.6]) and round cell (OR, 16.2 [95% CI, 2.80 to 93.2]) liposarcoma had higher incidences of DSD compared with well-differentiated patients. By contrast, dedifferentiated liposarcoma was associated with the latency of DSD (hazard ratio, 10.6 [95% CI, 1.48 to 75.9]). Pleomorphic liposarcomas had significantly higher risk in both incidence and the latency of DSD (P <.0001). Brier scores indicated comparable predictive accuracy between cure and Cox models. CONCLUSION: We developed the cureit pipeline to fit and evaluate mixture cure models and demonstrated its clinical utility in the liposarcoma disease setting, shedding insights on the subtype-specific associations with incidence and/or latency. Cure models are useful in settings with high rates of long-term survivors. The "cureit" pipeline can simplify cure analyses, as shown with a liposarcoma example. [ABSTRACT FROM AUTHOR]

Reproducible translation of transcriptomics data has been hampered by the ubiquitous presence of batch effects. Statistical methods for managing batch effects were initially developed in the setting of sample group comparison and later borrowed for other settings such as survival outcome prediction. The most notable such method is ComBat, which adjusts for batches by including it as a covariate alongside sample groups in a linear regression. In survival prediction, however, ComBat is used without definable groups for survival outcome and is done sequentially with survival regression for a potentially batch‐confounded outcome. To address these issues, we propose a new method called BATch MitigAtion via stratificatioN (BatMan). It adjusts batches as strata in survival regression and uses variable selection methods such as the regularized regression to handle high dimensionality. We assess the performance of BatMan in comparison with ComBat, each used either alone or in conjunction with data normalization, in a resampling-based simulation study under various levels of predictive signal strength and patterns of batch-outcome association. Our simulations show that (1) BatMan outperforms ComBat in nearly all scenarios when there are batch effects in the data and (2) their performance can be worsened by the addition of data normalization. We further evaluate them using microRNA data for ovarian cancer from the Cancer Genome Atlas and find that BatMan outforms ComBat while the addition of data normalization worsens the prediction. Our study thus shows the advantage of BatMan and raises caution about the use of data normalization in the context of developing survival prediction models. The BatMan method and the simulation tool for performance assessment are implemented in R and publicly available at LXQin/PRECISION.survival—GitHub. A new method BatMan is developed to deal with transcriptomics batch effects in the setting of survival prediction. [ABSTRACT FROM AUTHOR]

We present a new R package PRECISION.seq for assessing the performance of depth normalization in microRNA sequencing data. It provides a pair of microRNA sequencing data sets for the same set of tumor samples, additional pairs of data sets simulated by re-sampling under various patterns of differential expression, and a collection of numerical and graphical tools for assessing the performance of normalization methods. Users can easily assess their chosen normalization method and compare its performance to nine methods already included in the package. PRECISION.seq enables an objective and systematic evaluation of normalization methods in microRNA sequencing using realistically distributed and robustly benchmarked data under a wide range of differential expression patterns. To our best knowledge, this is the first such tool available. The data sets and source code of the R package can be found at https://github.com/LXQin/PRECISION.seq. [ABSTRACT FROM AUTHOR]

Purpose: The aim of this study was to determine outcomes and prognostic factors for patients with primary and locally recurrent extra-abdominal desmoid tumors who underwent percutaneous cryoablation, and to compare with patients treated with surgery. Methods: Group characteristics were compared using Fisher's exact test, and propensity score matching was performed using the nearest-neighbor approach. Kaplan–Meier and log-rank analyses were used to evaluate the variation in first local recurrence and disease control, while multivariate Cox regression was used to identify factors associated with first local recurrence. All statistical tests were two-sided and a p-value of 0.05 was considered statistically significant. Results: Twenty-two cryoablation patients were matched with 33 surgical patients (n = 55). Median follow-up after cryoablation was 16.3 months versus 14.9 months after surgery. Two-year local recurrence-free survival (LRFS) was 59% after cryoablation and 71% after surgery, and median LRFS was 26.6 months after cryoablation but was not reached after surgery. Two-year disease control for all patients was 85%, however median disease control was not reached in either the cryoablation or surgery groups. There was no significant difference in LRFS or disease control between matched cryoablation and surgical patients. No local recurrences occurred after the first cryoablation in patients with zero or one of the following risk factors: tumor size > 5 cm, age ≤ 25 years, or locally recurrent disease. All patients with two or more of these risk factors recurred locally after the first cryoablation. Conclusion: Percutaneous cryoablation of primary and locally recurrent extra-abdominal desmoid tumors provides freedom from first local recurrence and long-term disease control comparable with surgery. [ABSTRACT FROM AUTHOR]

One pivotal feature of transcriptomics data is the unwanted variations caused by disparate experimental handling, known as handling effects. Various data normalization methods were developed to alleviate the adverse impact of handling effects in the setting of differential expression analysis. However, little research has been done to evaluate their performance in the setting of survival outcome prediction, an important analysis goal for transcriptomics data in biomedical research. Leveraging a unique pair of datasets for the same set of tumor samples—one with handling effects and the other without, we developed a benchmarking tool for conducting such an evaluation in microRNA microarrays. We applied this tool to evaluate the performance of three popular normalization methods—quantile normalization, median normalization and variance stabilizing normalization—in survival prediction using various approaches for model building and designs for sample assignment. We showed that handling effects can have a strong impact on survival prediction and that quantile normalization, a most popular method in current practice, tends to underperform median normalization and variance stabilizing normalization. We demonstrated with a small example the reason for quantile normalization's poor performance in this setting. Our finding highlights the importance of putting normalization evaluation in the context of the downstream analysis setting and the potential of improving the development of survival predictors by applying median normalization. We make available our benchmarking tool for performing such evaluation on additional normalization methods in connection with prediction modeling approaches. [ABSTRACT FROM AUTHOR]

PURPOSE: Accurate assessment of a molecular classifier that guides patient care is of paramount importance in precision oncology. Recent years have seen an increasing use of external validation for such assessment. However, little is known about how it is affected by ubiquitous unwanted variations in test data because of disparate experimental handling and by the use of data normalization for alleviating such variations. METHODS: In this paper, we studied these issues using two microarray data sets for the same set of tumor samples and additional data simulated by resampling under various levels of signal-to-noise ratio and different designs for array-to-sample allocation. RESULTS: We showed that (1) unwanted variations can lead to biased classifier assessment and (2) data normalization mitigates the bias to varying extents depending on the specific method used. In particular, frozen normalization methods for test data outperform their conventional forms in terms of both reducing the bias in accuracy estimation and increasing robustness to handling effects. We make available our benchmarking tool as an R package on GitHub for performing such evaluation on additional methods for normalization and classification. CONCLUSION: Our findings thus highlight the importance of proper test-data normalization for valid assessment by external validation and call for caution on the choice of normalization method for molecular classifier development. [ABSTRACT FROM AUTHOR]

PURPOSE: Accurate assessment of a molecular classifier that guides patient care is of paramount importance in precision oncology. Recent years have seen an increasing use of external validation for such assessment. However, little is known about how it is affected by ubiquitous unwanted variations in test data because of disparate experimental handling and by the use of data normalization for alleviating such variations. METHODS: In this paper, we studied these issues using two microarray data sets for the same set of tumor samples and additional data simulated by resampling under various levels of signal-to-noise ratio and different designs for array-to-sample allocation. RESULTS: We showed that (1) unwanted variations can lead to biased classifier assessment and (2) data normalization mitigates the bias to varying extents depending on the specific method used. In particular, frozen normalization methods for test data outperform their conventional forms in terms of both reducing the bias in accuracy estimation and increasing robustness to handling effects. We make available our benchmarking tool as an R package on GitHub for performing such evaluation on additional methods for normalization and classification. CONCLUSION: Our findings thus highlight the importance of proper test-data normalization for valid assessment by external validation and call for caution on the choice of normalization method for molecular classifier development. [ABSTRACT FROM AUTHOR]

PURPOSE: To detect alterations in DNA damage repair (DDR) genes, measure homologous recombination deficiency (HRD), and correlate these findings with clinical outcome in patients with leiomyosarcoma (LMS). PATIENTS AND METHODS: Patients with LMS treated at Memorial Sloan Kettering (MSK) Cancer Center who consented to prospective targeted next-generation sequencing with MSK-IMPACT were screened for oncogenic somatic variants in one of 33 DDR genes; where feasible, an experimental HRD score was calculated from IMPACT data. Progression-free survival (PFS) and overall survival (OS) were estimated after stratifying patients by DDR gene alteration status and HRD score. RESULTS: Of 211 patients with LMS, 20% had an oncogenic DDR gene alteration. Univariable analysis of PFS in 117 patients who received standard frontline chemotherapy in the metastatic setting found that an altered homologous recombination pathway gene was significantly associated with shorter PFS (hazard ratio [HR], 1.79; 95% CI, 1.04 to 3.07; P =.035). Non- BRCA homologous recombination gene alteration was associated with shorter PFS (HR, 2.61; 95% CI, 1.35 to 5.04; P =.004) compared with BRCA -altered and wild-type homologous recombination genes. Univariable analysis of OS from diagnosis in the entire cohort of 211 patients found that age, tumor size, number of metastatic sites, localized disease, and non- BRCA homologous recombination gene alteration were significantly associated with OS. On multivariable analysis, non- BRCA homologous recombination pathway gene alteration remained significant (HR, 4.91; 95% CI, 2.47 to 9.76; P <.001). High HRD score was not associated with a different PFS or OS. CONCLUSION: Patients with LMS with homologous recombination pathway gene alterations have poor clinical outcomes, particularly those with non- BRCA gene alterations. HRD score calculated from a targeted exome panel did not discern disparate clinical outcomes. [ABSTRACT FROM AUTHOR]

PURPOSE: Methods for depth normalization have been assessed primarily with simulated data or cell-line–mixture data. There is a pressing need for benchmark data enabling a more realistic and objective assessment, especially in the context of small RNA sequencing. METHODS: We collected a unique pair of microRNA sequencing data sets for the same set of tumor samples; one data set was collected with and the other without uniform handling and balanced design. The former provided a benchmark for evaluating evidence of differential expression and the latter served as a test bed for normalization. Next, we developed a data perturbation algorithm to simulate additional data set pairs. Last, we assembled a set of computational tools to visualize and quantify the assessment. RESULTS: We validated the quality of the benchmark data and showed the need for normalization of the test data. For illustration, we applied the data and tools to assess the performance of 9 existing normalization methods. Among them, trimmed mean of M-values was a better scaling method, whereas the median and the upper quartiles were consistently the worst performers; one variation of remove unwanted variation had the best chance of capturing true positives but at the cost of increased false positives. In general, these methods were, at best, moderately helpful when the level of differential expression was extensive and asymmetric. CONCLUSION: Our study (1) provides the much-needed benchmark data and computational tools for assessing depth normalization, (2) shows the dependence of normalization performance on the underlying pattern of differential expression, and (3) calls for continued research efforts to develop more effective normalization methods. [ABSTRACT FROM AUTHOR]

Background: Sorafenib and dacarbazine have low single‐agent response rates in metastatic sarcomas. As angiogenesis inhibitors can enhance the efficacy of chemotherapy, we investigated the combination of sorafenib and dacarbazine in select sarcoma subtypes. Materials and Methods: Patients with leiomyosarcoma (LMS), synovial sarcoma (SS), or malignant peripheral nerve sheath tumors (MPNST) with up to two previous lines of therapy and adequate hepatic, renal, and marrow function received 3‐week cycles of sorafenib at 400 mg oral twice daily and dacarbazine 1,000 mg/m2 intravenously (later reduced to 850 mg/m2). Patients were evaluated for response every 6 weeks. The primary objective was to determine the disease control rate (DCR) of sorafenib plus dacarbazine in the selected sarcoma subtypes. Results: The study included 37 patients (19 female); median age was 55 years (range 26–87); and histologies included LMS (22), SS (11), and MPNST (4). The DCR was 46% (17/37). Median progression‐free survival was 13.4 weeks. The RECIST response rate was 14% (5/37). The Choi response rate was 51% (19/37). Median overall survival was 13.2 months. Of the first 25 patients, 15 (60%) required dacarbazine dose reductions for hematologic toxicity, with one episode of grade 5 neutropenic fever. After reducing the starting dose of dacarbazine to 850 mg/m2, only 3 of the final 12 (25%) patients required dose reduction. Conclusion: This phase II study met its primary endpoint with an 18‐week DCR of 46%. The clinical activity of dacarbazine plus sorafenib in patients with these diagnoses is modest. Implications for Practice: Metastatic soft tissue sarcomas are a heterogeneous group of relatively rare malignancies. Most patients are treated with cytotoxic chemotherapy or targeted therapy in the form of tyrosine kinase inhibitors. Response rates are relatively low, and there is a need for better therapies. This clinical trial demonstrates that combining a cytotoxic therapy (dacarbazine) with an antiangiogenic small molecule (sorafenib) is feasible and associated with favorable disease‐control rates; however, it also increases the potential for significant toxicity. Sorafenib and dacarbazine have low single agent response rates in metastatic sarcomas. This article reports results of a clinical trial using a combination of sorafenib and dacarbazine in select sarcoma subtypes. [ABSTRACT FROM AUTHOR]

Summary: Background Preclinical studies suggest that imatinib resistance in gastrointestinal stromal tumor (GIST) can be mediated by MAP-kinase activation via fibroblast growth factor (FGF) signaling. In FGF stimulated GIST cell lines, BGJ398, a pan-FGFR kinase inhibitor in combination with imatinib, was cytotoxic and superior to imatinib therapy alone. In FGF-dependent GIST, the combination of BGJ398 and imatinib may provide a mechanism to overcome imatinib resistance. Methods This phase Ib study of BGJ398 and imatinib was performed in patients with imatinib refractory advanced GIST. A standard 3 + 3 dosing schema was utilized to determine the recommended phase II dose (RP2D). Two treatment schedules were evaluated incorporating imatinib 400 mg daily in combination with (A) BGJ398 daily 3 weeks on, 1 week off or (B) BGJ398 daily 1 week on, 3 weeks off. Results 16 patients enrolled. The median age was 54 years (range: 44–77), 81% were male, and the median number of lines of prior therapy was 4 [range: 2–6, 13 patients had ≥3 prior therapies]. 12 patients received treatment on schedule A [BGJ398 dose range: 25 – 75 mg]: 2 patients experienced dose limiting toxicities (DLT) (n = 1, myocardial infarction & grade (G)4 CPK elevation; n = 1, G3 ALT elevation) on schedule A (BGJ398 75 mg), significant hyperphosphatemia, an on-target effect, was not observed, implying the maximum tolerated dose was below the therapeutic dose. Following protocol amendment, 4 patients enrolled on schedule B [BGJ398 dose range: 75 − 100 mg]: no DLTs were observed. The most common treatment related adverse events occurring in >15% of patients included CPK elevation (50%), lipase elevation (44%), hyperphosphatemia (24%), anemia (19%), and peripheral edema (19%). Among the 12 evaluable patients, stable disease (SD) was the best response observed in 7 patients by RECIST v1.1 and 9 patients by CHOI. Stable disease ≥ 32 weeks was observed in 3 patients (25%). Median progression free survival was 12.1 weeks (95% CI 4.7–19.5 weeks). Conclusions Toxicity was encountered with the combination therapy of BGJ398 and imatinib. Due to withdrawal of sponsor support the study closed before the RP2D or dosing schedule of the combination therapy was identified. In heavily pre-treated patients, stable disease ≥ 32 weeks was observed in 3 of 12 evaluable patients. Trial Registration: NCT02257541. [ABSTRACT FROM AUTHOR]

Background: Desmoid-type fibromatosis can arise in patients with familial adenomatous polyposis (FAP), therefore patients with desmoids often undergo colonoscopy to rule out FAP. Because finding FAP is uncommon, we sought to define subsets of desmoid patients in whom colonoscopy frequently identified FAP.Methods: Patients with desmoid-type fibromatosis were identified from surgery and pathology databases at a single institution, and information on colonoscopy and FAP diagnosis was collected retrospectively. CTNNB1 mutation status was defined by Sanger sequencing and digital polymerase chain reaction of archived specimens.Results: Among 626 patients with desmoids, 26 were diagnosed with FAP. In 20 patients, FAP diagnosis predated the desmoid diagnosis. Among patients without prior FAP diagnosis, 161 underwent colonoscopy, which identified only six cases of FAP (diagnostic yield 3.7%). Yields were substantially higher among patients with four characteristics: age < 40 years (11% yield), intra-abdominal or retroperitoneal tumors (5.4%), multifocal disease (29%), and family history (8%) (all p < 0.001). All cases of FAP were detected in patients younger than 40 years of age and with at least one of the other three characteristics. CTNNB1 mutation status was available in 82 patients with known FAP status. None of the 61 patients with CTNNB1 mutations were diagnosed with FAP, while 7 of the 21 patients with no CTNNB1 mutation detected (24%) were FAP patients.Conclusions: Patients with desmoid-type fibromatosis and undiagnosed FAP generally have multiple risk factors, which may be used to selectively recommend colonoscopic screening. Routine CTNNB1 sequencing may also rule out FAP and allow for deferral of colonoscopy. [ABSTRACT FROM AUTHOR]

Background: Myxofibrosarcoma and undifferentiated pleomorphic sarcoma (UPS) are aggressive, genetically complex sarcomas. The minimum myxoid component used as a criterion for myxofibrosarcoma varies widely, so we determined the optimal myxoid component cutpoints for stratifying outcomes of UPS and myxofibrosarcoma. We also analyzed clinicopathologic factors associated with outcome. Methods: Review of a prospective, single-institution database identified 197 patients with primary, high-grade extremity/truncal myxofibrosarcoma or UPS resected during 1992-2013. Histology was reviewed and percent myxoid component determined for each tumor. Disease-specific survival (DSS) and distant recurrence-free survival (DRFS) were analyzed using the Kaplan-Meier method, log-rank test, and Cox regression. Results: Median follow-up for survivors was 6.4 years. In minimum p value analysis of myxoid component, the best cutpoint for both DSS and DRFS was 5 % (adjusted p ≤ 0.001), followed by 70 %. Therefore, sarcomas with <5 % myxoid component ( n = 69) were classified as UPS and those with ≥5 % myxoid component ( n = 128) as myxofibrosarcoma. Five-year DRFS was 24 % for UPS, 51 % for 5-69 % myxoid component myxofibrosarcoma, and 65 % for ≥70 % myxoid component myxofibrosarcoma. Myxoid component, tumor size, and age were independently associated with DSS; myxoid component and tumor size were associated with DRFS. Only tumor site was associated with local recurrence. Conclusions: Percent myxoid component and tumor size are the two most important predictors of DSS and DRFS in high-grade myxofibrosarcoma and UPS. A 5 % myxoid component cutpoint is an improved criterion for classifying myxofibrosarcoma. Myxoid component-based classification improves stratification of patient outcome and will aid in selection of patients for systemic therapy and clinical trials. [ABSTRACT FROM AUTHOR]

Gemcitabine (G) and docetaxel (D) are commonly used to treat recurrent/metastatic soft tissue sarcoma. This study tested the hypothesis that outcomes would be improved by addition of bevacizumab (B). The initial design was randomized double-blind trial of G + D + B versus G + D + placebo. Due to slow accrual this was modified to single-arm open-label G + D + B. Eligible patients had diagnosis of leiomyosarcoma, pleomorphic undifferentiated sarcoma, pleomorphic liposarcoma, or angiosarcoma. Treatment was B 15 mg/kg on d1, G 900 mg/m2 on d1 and d8, and D 75 mg/m2 on d8, q21d. Primary endpoint was progression-free survival (PFS) at 6 months and would be met if ≥17 patients were progression-free at 6 m. Secondary endpoints are response rate, PFS at 3 m, overall survival, and toxicity. Of 44 patients enrolled, 35 were treated with GDB and evaluable for safety and efficacy. Median age was 55, 50% male, most ECOG 0. Toxicity is mostly myelosuppression with one deep vein thrombosis and one small bowel perforation possibly related to B. There were 17 partial responses (49%) by RECIST 1.1. Among 35 patients, the number who remained on study and progression-free was 24 at 3 m and 15 at 6 m. 9 withdrew prior to 6 m for reasons other than toxicity or progression. PFS at 6 m was 65% (95% CI: 51–85%). The primary endpoint of 6 m PFS was not met due to censoring of patients who withdrew. However PFS at 3 m (76%) was promising and response rate was higher than expected from G + D. [ABSTRACT FROM AUTHOR]

Malignant peripheral nerve sheath tumors (MPNSTs) represent a group of highly aggressive soft-tissue sarcomas that may occur sporadically, in association with neurofibromatosis type I (NF1 associated) or after radiotherapy. Using comprehensive genomic approaches, we identified loss-of-function somatic alterations of the Polycomb repressive complex 2 (PRC2) components (EED or SUZ12) in 92% of sporadic, 70% of NF1-associated and 90% of radiotherapy-associated MPNSTs. MPNSTs with PRC2 loss showed complete loss of trimethylation at lysine 27 of histone H3 (H3K27me3) and aberrant transcriptional activation of multiple PRC2-repressed homeobox master regulators and their regulated developmental pathways. Introduction of the lost PRC2 component in a PRC2-deficient MPNST cell line restored H3K27me3 levels and decreased cell growth. Additionally, we identified frequent somatic alterations of CDKN2A (81% of all MPNSTs) and NF1 (72% of non-NF1-associated MPNSTs), both of which significantly co-occur with PRC2 alterations. The highly recurrent and specific inactivation of PRC2 components, NF1 and CDKN2A highlights their critical and potentially cooperative roles in MPNST pathogenesis. [ABSTRACT FROM AUTHOR]

MicroRNA arrays possess a number of unique data features that challenge the assumption key to many normalization methods. We assessed the performance of existing normalization methods using two microRNA array datasets derived from the same set of tumor samples: one dataset was generated using a blocked randomization design when assigning arrays to samples and hence was free of confounding array effects; the second dataset was generated without blocking or randomization and exhibited array effects. The randomized dataset was assessed for differential expression between two tumor groups and treated as the benchmark. The non-randomized dataset was assessed for differential expression after normalization and compared against the benchmark. Normalization improved the true positive rate significantly in the non-randomized data but still possessed a false discovery rate as high as 50%. Adding a batch adjustment step before normalization further reduced the number of false positive markers while maintaining a similar number of true positive markers, which resulted in a false discovery rate of 32% to 48%, depending on the specific normalization method. We concluded the paper with some insights on possible causes of false discoveries to shed light on how to improve normalization for microRNA arrays. [ABSTRACT FROM AUTHOR]

Rhabdomyosarcoma, a cancer of skeletal muscle lineage, is the most common soft-tissue sarcoma in children. Major subtypes of rhabdomyosarcoma include alveolar (ARMS) and embryonal (ERMS) tumors. Whereas ARMS tumors typically contain translocations generating PAX3-FOXO1 or PAX7-FOXO1 fusions that block terminal myogenic differentiation, no functionally comparable genetic event has been found in ERMS tumors. Here we report the discovery, through whole-exome sequencing, of a recurrent somatic mutation encoding p.Leu122Arg in the myogenic transcription factor MYOD1 in a distinct subset of ERMS tumors with poor outcomes that also often contain mutations altering PI3K-AKT pathway components. Previous mutagenesis studies had shown that MYOD1 with a p.Leu122Arg substitution can block wild-type MYOD1 function and bind to MYC consensus sequences, suggesting a possible switch from differentiation to proliferation. Our functional data now confirm this prediction. Thus, MYOD1 p.Leu122Arg defines a subset of rhabdomyosarcomas eligible for high-risk protocols and the development of targeted therapeutics. [ABSTRACT FROM AUTHOR]

Purpose: The aim of this study was to build a molecular prognostic model based on gene signatures for patients with completely resected hepatic metastases from colorectal cancer (MCRC). Methods: Using the Illumina HumanHT-12 gene chip, RNA samples from the liver metastases of 96 patients who underwent R0 liver resection were analyzed. Patients were randomly assigned to a training (n = 60) and test (n = 36) set. The genes associated with disease-specific survival (DSS) and liver-recurrence-free survival (LRFS) were identified by Cox-regression and selected to construct a molecular risk score (MRS) using the supervised principle component method on the training set. The MRS was then evaluated in the independent test set. Results: Nineteen and 115 genes were selected to construct the MRS for DSS and LRFS, respectively. Each MRS was validated in the test set; 3-year DSS/LRFS rates were 42/32% and 79/80% for patients with high and low MRS, respectively (p = 0.007 for DSS and p = 0.046 for LRFS). In a multivariate model controlling for a previously validated clinical risk score (CRS), the MRS remained a significant predictor of DSS (p = 0.001) and LRFS (p = 0.03). When CRS and MRS were combined, the patients were discriminated better with 3-year DSS/LRFS rates of 90/89% in the low risk group (both risk scores low) vs 42/26% in the high risk group (both risk scores high), respectively (p = 0.002/0.004 for DSS/LRFS). Conclusion: MRS based on gene expression profiling has high prognostic value and is independent of CRS. This finding provides a potential strategy for better risk-stratification of patients with liver MCRC. [ABSTRACT FROM AUTHOR]

Background: Leiomyosarcoma is a soft tissue sarcoma whose outcome has historically been confounded by the inclusion of gastrointestinal stromal tumors. Thus, we sought to determine the factors that predict survival and recurrence in patients with primary leiomyosarcoma alone. Methods: During 1982-2006, a total of 353 patients with primary resectable leiomyosarcoma were identified from a prospective database. Multivariate analysis was used to assess clinicopathologic factors for association with disease-specific survival (DSS). Competing risk survival analysis was used to determine factors predictive for local and distant recurrence. Results: Of 353 patients, 170 (48 %) presented with extremity, 144 (41 %) with abdominal/retroperitoneal, and 39 (11 %) with truncal tumors. Median age was 57 (range, 18-88) years, and median follow-up was 50 (range, 1-270) months. Most tumors were high grade (75 %), deep (73 %), and completely resected (97 %); median size was 6.0 (range, 0.3-45) cm. Abdominal/retroperitoneal location was associated with worse long-term DSS compared to extremity or trunk ( P = 0.005). However, by multivariate analysis, only high grade and size were significant independent predictors of DSS. Overall, 139 patients (39 %) had recurrence: 51 % of those with abdominal/retroperitoneal, 33 % of extremity, and 26 % of truncal disease. Significant independent predictors for local recurrence were size and margin, whereas predictors for distant recurrence were size and grade. Site was not an independent predictor of recurrence; however, late recurrence (>5 years) occurred in 9 % of abdominal/retroperitoneal and 4 % of extremity lesions. Conclusions: Grade and size are significant independent predictors of DSS and distant recurrence. Long-term follow-up in leiomyosarcoma is important, as late recurrence continues in 6-9 % patients. [ABSTRACT FROM AUTHOR]

Background: Malignant peripheral nerve sheath tumors (MPNSTs) occur sporadically, after prior radiation therapy (RT), or in association with neurofibromatosis type 1 (NF1). It is controversial whether patients with NF1-associated MPNST have worse outcomes. We investigated the prognostic significance of sporadic, NF1-associated, and RT-induced MPNST. Methods: Patients with primary high-grade MPNST from 1982 to 2011 were identified from a prospectively maintained database. Patients with sporadic MPNST were included only if the MPNST was not associated with NF1 or a neurofibroma or if it was immunohistochemically S100-positive. Results: We studied 105 patients; 42 had NF1-associated tumors, 49 sporadic, and 14 RT-induced. Median age at diagnosis was 38 years. Median follow-up for surviving patients was 4 years. Mean tumor diameter was 5.5 cm for RT-induced tumors and 9.7 cm for NF1-associated and sporadic tumors ( P = 0.004). In multivariate analysis, factors associated with worse disease-specific survival (DSS) were larger size (HR 1.08; 95 % CI 1.04-1.13; P < 0.001) and positive margin (HR 3.30; 95 % CI 1.74-6.28; P < 0.001). Age, gender, site of disease, and S100 staining were not associated with DSS. The 3-year and median DSS were similar for NF1 and sporadic cases; combined 3-year DSS was 64 % and median DSS was 8.0 years. For RT-induced tumors, 3-year DSS was 49 % and median DSS was 2.4 years. The relationship between RT association and DSS approached statistical significance (HR 2.29; 95 % CI 0.93-5.67; P = 0.072). Conclusions: Margin status and size remain the most important predictors of DSS in patients with MPNST. NF1-associated and sporadic MPNSTs may be associated with improved DSS compared with RT-induced tumors. [ABSTRACT FROM AUTHOR]

Background: Dermatofibrosarcoma protuberans (DFSP) is an uncommon soft tissue malignancy that typically presents with local invasion but rarely metastasizes. We examine clinicopathologic factors associated with disease-free survival (DFS) in patients with primary and recurrent DFSP and evaluate responses to multimodality therapy. Materials and Methods: Patients treated for DFSP were identified in a prospectively maintained database. Clinicopathologic factors associated with DFS were analyzed using univariate and multivariate analysis. Results: A total of 244 patients with DFSP were identified. Median follow-up was 50 months. A total of 14 patients had local recurrence (LR), and 2 patients had distant recurrence (DR), with a median time to recurrence of 35 months. At time of last follow-up, 70% and 47% of patients showed no evidence of disease (NED) in the primary ( n = 197) and recurrent groups ( n = 47), respectively. On univariate analysis, tumor location and depth were associated with DFS in the primary group, while margin status (R1 vs. R0) was associated with DFS in the LR group. On multivariate analysis, only depth (primary group) and margin status (LR group), remained significant. Also, 22 patients had therapy other than surgical resection: 14 radiotherapy, 4 tyrosine kinase inhibitor (TKI) only, 2 conventional chemotherapy only, and 2 chemotherapy plus TKI. Responses to other therapies were variable. Conclusions: DFS after treatment for DFSP is strongly predicted by tumor depth in the primary setting and margin status in recurrent tumors. The treatment for DFSP in the primary or recurrent setting is excision with negative margins, resulting in low recurrence rates and infrequent metastatic spread. Multimodality treatment, especially TKI use, can be effective, but is not curative. [ABSTRACT FROM AUTHOR]

Background: In colorectal cancer (CRC), microsatellite instability (MSI) is a valuable marker of defective DNA mismatch repair that identifies cancers with distinct phenotypic properties, including favorable survival. However, the optimal assay for MSI status is unknown. We have evaluated a simplified 3-marker assay for MSI and compared it with the 5-marker (NCI) assay to see if technical variations in MSI testing are important. Materials and Methods: DNA samples from 357 CRCs were evaluated for MSI using the 5 microsatellite markers recommended for the NCI assay (BAT 25, BAT26, D2S123, D5S346, and D17S250). Results were compared with a simplified 3-marker assay (BAT25, BAT26, and D2S123). CRCs identified as MSI were evaluated for their clinical, pathological, and genetic characteristics. Results: The 5-marker assay identified 96 cancers as MSI. Only 56 of these were MSI by the 3-marker assay (3-marker+ group), leaving 40 cases identified as MSI only by NCI criteria (3-marker− group). The remaining 261 cancers were microsatellite stable (MSS). The 3-marker+ MSI tumors had features characteristic of MSI tumors: more proximal, poorly differentiated, associated with hereditary nonpolyposis colorectal cancer (HNPCC), more BRAF mutations, fewer KRAS mutations, better 5-year disease-specific survival, more frequent mismatch repair (MMR) protein loss, and less likely to be metastatic on presentation ( P < .05). Chromosomal arm loss was observed only in 3-marker− MSI and MSS cancers ( P < .05). Conclusion: The 3-marker MSI assay outperforms the traditional 5-marker assay for identifying patients with favorable prognosis and homogeneous clinical and genetic features. More accurate MSI testing should improve prognostic and predictive scoring systems for colorectal cancer. [ABSTRACT FROM AUTHOR]

Peripheral neuroblastic tumors (PNTs) share a common origin in the sympathetic nervous system, but manifest variable differentiation and growth potential. Malignant neuroblastoma (NB) and benign ganglioneuroma (GN) stand at opposite ends of the clinical spectrum. We hypothesize that a common PNT progenitor is driven to variable differentiation by specific developmental signaling pathways. To elucidate developmental pathways that direct PNTs along the differentiation spectrum, we compared the expression of genes related to neural crest development in GN and NB. In GNs, we found relatively low expression of sympathetic markers including adrenergic biosynthesis enzymes, indicating divergence from sympathetic fate. In contrast, GNs expressed relatively high levels of enteric neuropeptides and key constituents of the Hedgehog (HH) signaling pathway, including Dhh, Gli1 and Gli3. Predicted HH targets were also differentially expressed in GN, consistent with transcriptional response to HH signaling. These findings indicate that HH signaling is specifically active in GN. Together with the known role of HH activity in enteric neural development, these findings further suggested a role for HH activity in directing PNTs away from the sympathetic lineage toward a benign GN phenotype resembling enteric ganglia. We tested the potential for HH signaling to advance differentiation in PNTs by transducing NB cell lines with Gli1 and determining phenotypic and transcriptional response. Gli1 inhibited proliferation of NB cells, and induced a pattern of gene expression that resembled the differential pattern of gene expression of GN, compared to NB (p<0.00001). Moreover, the transcriptional response of SY5Y cells to Gli1 transduction closely resembled the transcriptional response to the differentiation agent retinoic acid (p,0.00001). Notably, Gli1 did not induce N-MYC expression in neuroblastoma cells, but strongly induced RET, a known mediator of RA effect. The decrease in NB cell proliferation induced by Gli1, and the similarity in the patterns of gene expression induced by Gli1 and by RA, corroborated by closely matched gene sets in GN tumors, all support a model in which HH signaling suppresses PNT growth by promoting differentiation along alternative neural crest pathways. [ABSTRACT FROM AUTHOR]

The patterns of failure and mechanisms of sarcoma-specific death are poorly characterized among the minority of patients with low-grade soft tissue sarcoma (STS) who succumb to disease. Between 1982 and 2006, 2,041 patients aged ≥16 years with low-grade STS of all sites were treated with curative intent and prospectively followed at a single institution. Among this cohort, 181 (9%) died from disease (DOD). Overall, 105 patients (58%) died from locally recurrent disease (DOLR), and 59 (32%) died from distant disease (DODR). In 17 patients (9%), the mechanism of sarcoma-related death could not be verified. DOD occurred at a median of 62 months, while median disease-specific survival for the entire cohort was not reached. Median follow-up was 66 months (range 2–431 months). On multivariate analysis, DOD was associated with site, size, and less than R0 resection. For DOLR, site, size, positive margins, liposarcoma histology, and local recurrence (by definition) were significant factors. For DODR, site, histology, and positive margins were not significant factors, while size and local recurrence were. Of DOLR, 80% were retroperitoneal, 68% were liposarcoma, and only 2% were extremity. Conversely, of DODR, extremity (47%) and trunk (18%) were the most common sites, but histology was more variable [liposarcoma 35%, malignant fibrous histiocytoma (MFH) 20%, fibrosarcoma 12%, extraskeletal myxoid chondrosarcoma 10%]. High-grade recurrence rates were comparable between DOLR (27%) and DODR (25%). Among patients with low-grade STS, DOD occurs in approximately 9% of patients. Nonextremity site, larger size, and less than R0 resection are the most important risk factors for DOD, and distinct patterns of recurrence and death are predicted by primary tumor site. [ABSTRACT FROM AUTHOR]

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Background. For extremity soft tissue sarcomas (STS), surgical resection remains the standard of care, and the addition of chemotherapy is controversial. This was a phase Ib/II trial of neoadjuvant therapy for patients with STS. Methods. Patients with high grade, extremity STS of >8 cm and amenable to definitive resection were treated with up to four 21-day cycles of 900 mg/m² gemcitabine on days 1 and 8, 75 mg/m² docetaxel on day 8, and 400 mg of pazopanib daily (GDP), followed by surgery and, if indicated, radiation therapy. Primary and secondary endpoints (phase Ib portion) were the safety and rate of pathologic response. Results. The trial was discontinued because of slow accrual after inclusion of five patients (leiomyosarcoma: two; undif-ferentiated pleomorphic sarcoma: three). Two patients completed four treatment cycles: one underwent surgery and one had insufficient response and received additional therapies. Three patients discontinued treatment because of toxicity. Grade 3 adverse events included hypertension, fatigue, aspartate aminotransferase(AST)or alanine aminotransferase (ALT) elevation, hoarseness, and myelotoxicity. There were no complete or partial responses. One patient had ≥90% pathologic response. Among four patients who underwent resection, three remain free of disease, and one patient eventually relapsed. Conclusion. GDP combination used in the neoadjuvant setting resulted in significanttoxicity; despite pathologic responses, no objective responses occurred. [ABSTRACT FROM AUTHOR]