The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis

Selective cardiac surveillance in patients with gynecologic cancer undergoing treatment with pegylated liposomal doxorubicin (PLD)

The study objective was to examine the safety and cost savings of selective cardiac surveillance (CS) during treatment with pegylated liposomal doxorubicin (PLD). A retrospective, dual institution study of women receiving PLD for the treatment of a gynecologic malignancy was performed. The study period was 2002–2014. At both institutions, a selective strategy for CS was implemented in which only high-risk women with a cardiac history or with symptoms suggestive of cardiac toxicity during PLD treatment underwent a cardiac evaluation. Patient demographics, clinical and treatment history were evaluated. Cost analyses were performed utilizing professional/technical fee rates for echocardiogram and multi-gated acquisition scan for each state. PLD was administered in 184 women. The mean patient age was 62.7years, and 79% were treated for recurrent ovarian or peritoneal carcinoma. The median cumulative administered dose of PLD was 300mg/m2; 24 received >550mg/m2. The median follow-up time was 20months. Of the 184 patients, the majority (n=157, 85.3%) did not undergo either an initial cardiac evaluation or surveillance during or post-PLD treatment. Fifty-three patients considered high risk for anthracycline-induced cardiotoxicity underwent CS. Only three patients (1.6%) in the entire cohort developed CHF that was possibly related to PLD treatment; all had significant pre-existing cardiac risk factors. Selective instead of routine use of CS in the study population resulted in a cost savings of $182,552.28. Utilizing cardiac surveillance in select women undergoing PLD treatment for gynecologic malignancies resulted in significant health care cost savings without adversely impacting clinical outcomes

A randomized phase II/III study to assess the efficacy of trametinib in patients with recurrent or progressive low-grade serous ovarian or peritoneal cancer

Background: Low-grade serous carcinoma of the ovary/peritoneum (LGSOC) is a rare subtype, accounting for 5-10% of all serous cancers, and is characterized by alterations in the MAPK pathway, relative chemoresistance, and prolonged overall survival (OS) compared to high-grade serous carcinoma. NRG Oncology in the US and the National Cancer Research Network (NCRN) in the UK collaborated on a phase II/III trial to assess the efficacy of a MEK inhibitor trametinib (TRAM) compared to physician’s choice standard of care (SOC) in recurrent LGSOC. Methods: Patients (pts) were randomized 1:1 to receive either TRAM 2 mg daily or 1 of 5 SOC options (weekly paclitaxel, PLD, topotecan, letrozole, or tamoxifen) until disease progression. Pts who progressed on SOC were allowed to crossover to TRAM. The primary objective tested the progression-free survival (PFS) superiority of TRAM vs SOC. Secondary objectives included toxicity, QoL, and objective response rate (ORR) by RECIST 1.1. Exploratory objectives were OS and PFS and ORR after crossover. PFS and OS curves were estimated using the Kaplan-Meier method and compared by a 1-sided, α = 0.025 log-rank test. Results: 260 pts (48.1% had >3 prior lines of therapy) were enrolled between Feb 2014 and Apr 2018. Median follow-up was 31.4 months (mo). PFS was significantly improved for TRAM compared to SOC (median, 13.0 vs 7.2 mo; HR 0.48; 95% CI, 0.36-0.64; P < .0001). ORR was 26.2% for TRAM vs 6.2% for SOC (OR 5.4; 95% CI, 2.39-12.21; P< .0001). Response duration for TRAM was significantly better than for SOC (median, 13.63 mo; 95% CI, 8.08-18.76; vs 5.88 mo; 95% CI, 2.76-12.19). Preliminary analysis of QoL patient reported outcomes shows no significant therapy effects. Main Grade >3 AE in TRAM vs SOC were hematologic toxicity (13.4% vs 9.4%), GI toxicity (27.6% vs 29%), skin toxicity (15% vs 3.9%), and vascular toxicity (18.9% vs 8.6%). Median OS for TRAM vs SOC was 37.0 mo (95% CI, 30.3-NE) vs 29.2 mo (95% CI, 23.5-51.6) (HR 0.75; 95% CI, 0.51-1.11). For 88 pts who crossed over to TRAM, median PFS = 10.8 mo (95% CI, 7.3-12.0), and ORR = 15% (95% CI, 0.07-0.22). Conclusions: Compared to physician’s choice SOC, TRAM was associated with significantly improved PFS and ORR in women with recurrent LGSOC

The Phase-I trigger readout electronics upgrade of the ATLAS Liquid Argon calorimeters

International audienceThe Phase-I trigger readout electronics upgrade of the ATLAS Liquid Argon calorimeters enhances the physics reach of the experiment during the upcoming operation at increasing Large Hadron Collider luminosities. The new system, installed during the second Large Hadron Collider Long Shutdown, increases the trigger readout granularity by up to a factor of ten as well as its precision and range. Consequently, the background rejection at trigger level is improved through enhanced filtering algorithms utilizing the additional information for topological discrimination of electromagnetic and hadronic shower shapes. This paper presents the final designs of the new electronic elements, their custom electronic devices, the procedures used to validate their proper functioning, and the performance achieved during the commissioning of this system

The Phase-I Trigger Readout Electronics Upgrade of the ATLAS Liquid Argon Calorimeters

The Phase-I trigger readout electronics upgrade of the ATLAS Liquid Argon calorimeters enhances the physics reach of the experiment during the upcoming operation at increasing Large Hadron Collider luminosities. The new system, installed during the second Large Hadron Collider Long Shutdown, increases the trigger readout granularity by up to a factor of ten as well as its precision and range. Consequently, the background rejection at trigger level is improved through enhanced filtering algorithms utilizing the additional information for topological discrimination of electromagnetic and hadronic shower shapes. This paper presents the final designs of the new electronic elements, their custom electronic devices, the procedures used to validate their proper functioning, and the performance achieved during the commissioning of this system

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival. Ricketts et al. find distinctive features of each RCC subtype, providing the foundation for development of subtype-specific therapeutic and management strategies. Somatic alteration of BAP1, PBRM1, and metabolic pathways correlates with subtype-specific decreased survival, while CDKN2A alteration, DNA hypermethylation, and Th2 immune signature correlate with decreased survival within all subtypes