Skeletal muscle and visceral adipose radiodensities are pre-surgical, non-invasive markers of aggressive kidney cancer.

INTRODUCTION: Most studies on body composition in kidney cancer have been conducted among patients with metastatic disease. Given that aggressive tumours can adversely impact body composition and even non-metastatic tumours can be aggressive, we evaluated associations between pre-surgical body composition features and tumour pathological features in patients with non-metastatic clear cell renal cell cancer (ccRCC). METHODS: The Resolve Cohort consists of 1239 patients with non-metastatic ccRCC who underwent nephrectomy at Memorial Sloan Kettering Cancer Center between 2000 and 2020. The cross-sectional areas and radiodensities of skeletal muscle, visceral adipose, and subcutaneous adipose tissues were determined from pre-surgical computed tomography (CT) scans at the third lumbar vertebrae using Automatica software. Pearson's correlation coefficients describe inter-relationships among BMI and body composition variables, while odds ratios (OR) and 95% confidence intervals (CI) estimate associations between continuous body composition features (per 1-standard deviation) and advanced stage (Stage III vs. Stages I-II) and high Fuhrman grade (Grades 3-4 vs. 1-2) from multivariable logistic regression models that considered the potential impact of biological sex, contrast enhanced CTs, and early age at onset of ccRCC. RESULTS: The cohort was predominantly male (69%), white (89%), and had a median age of 58. The proportion of patients presenting with advanced stage and high-grade disease were 31% and 51%, respectively. In models that adjusted for demographics and all body composition variables simultaneously, decreasing skeletal muscle radiodensity (i.e., more fat infiltration) but increasing visceral adipose tissue radiodensity (i.e., more lipid depletion) were associated with advanced tumour features. Per 8.4 HU decrease in skeletal muscle radiodensity, the odds of presenting with advanced stage was 1.61 (95% CI: 1.34-1.93). Per 7.22 HU increase in visceral adipose tissue radiodensity, the odds of presenting with advanced stage was 1.45 (95% CI: 1.22-1.74). Skeletal muscle index (i.e., sarcopenia) was not associated with either tumour feature. Similar associations were observed for Fuhrman grade, a more direct marker of tumour aggressiveness. Associations did not differ by sex, contrast use, or age at onset of ccRCC. CONCLUSIONS: Lipid infiltrated skeletal muscle, but lipid depleted visceral adipose tissue were independently associated with advanced tumour features in non-metastatic ccRCC. Findings highlight the importance of evaluating the full range of body composition features simultaneously in multivariable models. Interpreting pre-surgical CTs for body composition for patients may be a novel and non-invasive way to identify patients with aggressive renal tumours, which is clinically relevant as renal biopsies are not routinely performed.

Cannabis use among recently treated cancer patients: perceptions and experiences.

PURPOSE: To characterize cannabis use among cancer patients, we aimed to describe 1) patterns of cannabis use across multiple cancer sites; 2) perceived goals, benefits, harms of cannabis; and 3) communication about cannabis. METHODS: Patients with 9 different cancers treated at Memorial Sloan Kettering Cancer Center between March and August 2021 completed an online or phone survey eliciting cannabis use, attitudes, and communication about cannabis. Multivariable logistic regression estimated the association of cancer type and cannabis use, adjusting for sociodemographic characteristics and prior cannabis use. RESULTS: Among 1258 respondents, 31% used cannabis after diagnosis, ranging from 25% for lung cancer to 59% for testicular cancer. Characteristics associated with cannabis use included younger age, lower education level, and cancer type. In multivariable analysis, compared to lung cancer patients, gastrointestinal cancer patients were more likely to use cannabis (odds ratio [OR] 2.64, 95% confidence interval [CI] 1.25-5.43). Cannabis use in the year prior to diagnosis was strongly associated with cannabis use after diagnosis (OR 19.13, 95% CI 11.92-30.72). Among users, reasons for use included difficulty sleeping (48%); stress, anxiety, or depression (46%); and pain (42%). Among respondents who used cannabis to improve symptoms, 70-90% reported improvement; < 5% reported that any symptom worsened. Only 25% discussed cannabis with healthcare providers. CONCLUSIONS: Almost a third of cancer patients use cannabis, largely for symptom management. Oncologists may not know about their patients' cannabis use. To improve decision making about cannabis use during cancer care, research is needed to determine benefits and harms of cannabis use.

Urologists' Perceptions and Practices Related to Patient Smoking and Cessation: A National Assessment From the 2021 American Urological Association Census.

OBJECTIVE: To assess urologists' perceptions and practices related to smoking and smoking cessation. MATERIALS AND METHODS: Six survey questions were designed to assess beliefs, practices, and determinants related to tobacco use assessment and treatment (TUAT) in outpatient urology clinics. These questions were included in an annual census survey (2021) offered to all practicing urologists. Responses were weighted to represent the practicing US population of nonpediatric urologists (N = 12,852). The primary outcome was affirmative responses to the question, "Do you agree it is important for urologists to screen for and provide smoking cessation treatment to patients in the outpatient clinic?" Practice patterns, perceptions, and opinions of optimal care delivery were assessed. RESULTS: In total, 98% of urologists agreed (27%) or strongly agreed (71%) that cigarette smoking is a significant contributor to urologic disease. However, only 58% agreed that TUAT is important in urology clinics. Most urologists (61%) advise patients who smoke to quit but do not provide additional cessation counseling or medications or arrange follow-up. The most frequently identified barriers to TUAT were lack of time (70%), perceptions that patients are unwilling to quit (44%), and lack of comfort prescribing cessation medications (42%). Additionally, 72% of respondents stated that urologists should provide a recommendation to quit and refer patients for cessation support. CONCLUSION: TUAT does not routinely occur in an evidence-based fashion in outpatient urology clinics. Addressing established barriers and facilitating these practices with multilevel implementation strategies can promote tobacco treatment and improve outcomes for patients with urologic disease.

Genome-wide Association Study of Bladder Cancer Reveals New Biological and Translational Insights.

BACKGROUND: Genomic regions identified by genome-wide association studies (GWAS) for bladder cancer risk provide new insights into etiology. OBJECTIVE: To identify new susceptibility variants for bladder cancer in a meta-analysis of new and existing genome-wide genotype data. DESIGN, SETTING, AND PARTICIPANTS: Data from 32 studies that includes 13,790 bladder cancer cases and 343,502 controls of European ancestry were used for meta-analysis. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSES: Log-additive associations of genetic variants were assessed using logistic regression models. A fixed-effects model was used for meta-analysis of the results. Stratified analyses were conducted to evaluate effect modification by sex and smoking status. A polygenic risk score (PRS) was generated on the basis of known and novel susceptibility variants and tested for interaction with smoking. RESULTS AND LIMITATIONS: Multiple novel bladder cancer susceptibility loci (6p.22.3, 7q36.3, 8q21.13, 9p21.3, 10q22.1, 19q13.33) as well as improved signals in three known regions (4p16.3, 5p15.33, 11p15.5) were identified, bringing the number of independent markers at genome-wide significance (p < 5 × 10-8) to 24. The 4p16.3 (FGFR3/TACC3) locus was associated with a stronger risk for women than for men (p-interaction = 0.002). Bladder cancer risk was increased by interactions between smoking status and genetic variants at 8p22 (NAT2; multiplicative p value for interaction [pM-I] = 0.004), 8q21.13 (PAG1; pM-I = 0.01), and 9p21.3 (LOC107987026/MTAP/CDKN2A; pM-I = 0.02). The PRS based on the 24 independent GWAS markers (odds ratio per standard deviation increase 1.49, 95% confidence interval 1.44-1.53), which also showed comparable results in two prospective cohorts (UK Biobank, PLCO trial), revealed an approximately fourfold difference in the lifetime risk of bladder cancer according to the PRS (e.g., 1st vs 10th decile) for both smokers and nonsmokers. CONCLUSIONS: We report novel loci associated with risk of bladder cancer that provide clues to its biological underpinnings. Using 24 independent markers, we constructed a PRS to stratify lifetime risk. The PRS combined with smoking history, and other established risk factors, has the potential to inform future screening efforts for bladder cancer. PATIENT SUMMARY: We identified new genetic markers that provide biological insights into the genetic causes of bladder cancer. These genetic risk factors combined with lifestyle risk factors, such as smoking, may inform future preventive and screening strategies for bladder cancer.

A comparison of analytic approaches for investigating the obesity paradox in kidney cancer.

PURPOSE: Body mass index (BMI) and kidney cancer mortality are inconsistently associated in the scientific literature. To understand how study design affects results, we contrasted associations between pre-diagnosis BMI and mortality under different analytic scenarios in a large, population-based prospective cohort study. METHODS: Using data from the NIH-AARP Diet and Health Study (1995-2011), we constructed two cohorts: a "full at-risk" cohort with no kidney cancer history at baseline (n = 252,845) and an "incident cancer" subset who developed kidney cancer during follow-up (n = 1,652). Cox Proportional Hazards models estimated hazard ratios (HR) and 95% confidence intervals (CI) between pre-diagnosis BMI and mortality for different outcomes (all-cause and cancer-specific mortality), in the different cohorts (full at-risk vs. incident cancer cohort), and with different covariates (minimally vs. fully adjusted). For the incident cancer cohort, we also examined time to mortality using different timescales: from enrollment or diagnosis. RESULTS: In the full at-risk study population, higher pre-diagnosis BMI was associated with greater cancer-specific mortality in fully adjusted multivariable models, particularly for obese participants [HR, (95% CI): 1.76, (1.38-2.25)]. This association was less pronounced in the incident cancer cohort [1.50, (1.09-2.07)]. BMI was not strongly associated with all-cause mortality in either cohort in fully adjusted models [full cohort: 1.03, (1.01, 1.06); incident cancer cohort: 1.20, (0.97, 1.48)]. CONCLUSIONS: Populations characterized by high adult BMI will likely experience greater population burdens of mortality from kidney cancer, partially because of higher rates of kidney cancer diagnosis. Questions regarding overall mortality burden and post-diagnosis cancer survivorship are distinct and require different study designs.

Smoking cessation pharmacotherapy use during index hospital admission following cystectomy for bladder cancer: A retrospective cohort study.

BACKGROUND: To identify gaps in urologic oncology quality and evidence-based smoking cessation care by assessing how often smoking cessation pharmacotherapy (SCP) is given in the inpatient setting following cystectomy. METHODS: The Premier Healthcare Database (PHD), a deidentified all-payer dataset, was used to generate nationally representative estimates of SCP receipt during hospitalization following cystectomy for patients with bladder cancer who smoke. Regressions were used to model associations between SCP receipt and patient- and hospital-level factors. RESULTS: Of the 21,624 patients who underwent cystectomy for bladder cancer, 3,676 patients (17.0%) were identified as current smokers, representing a weighted estimate of 16,063 admissions. Among these admissions, 27.9% of patients received SCP, the vast majority of which (91.5%) received exclusively nicotine replacement therapy. Rates of SCP receipt varied substantially across hospitals (median: 25.0%, IQR: 20.0-33.3, range: 0.0-60.0). Older age and black race (aOR = 0.59, 95% CI: 0.42-0.82) were associated with lower odds of SCP receipt. Increased patient comorbidity score was associated with higher odds of SCP receipt (aOR = 1.02, 95% CI: 1.01-1.03); specifically, chronic pulmonary disease, alcohol abuse, and depression were independently associated with SCP receipt. Hospital teaching status, bed capacity, and mean annual cystectomy volume were not associated with SCP receipt. SCP receipt was not associated with hospital length of stay nor 90-day readmission or mortality following cystectomy. CONCLUSIONS: SCP is infrequently given to patients who smoke during their hospitalization following cystectomy for bladder cancer, representing a gap in quality urologic oncology care and a missed opportunity to effectively intervene with evidence-based treatment.

Association of Body Mass Index With the Safety Profile of Nivolumab With or Without Ipilimumab.

Importance: Increased survival with immune checkpoint inhibitors has been reported for patients with obesity vs a normal body mass index (BMI). However, the association of obesity with the safety of immune checkpoint inhibitors warrants study. Objective: To investigate associations between BMI and immune-related adverse events (irAEs) among patients with advanced cancers treated with nivolumab monotherapy and nivolumab plus ipilimumab combination therapy. Design, Setting, and Participants: This study was a retrospective pooled analysis of 3772 patients from 14 multicenter CheckMate clinical trials across 8 tumor types. Patients with advanced cancers received nivolumab, 3 mg/kg (n = 2746); nivolumab, 3 mg/kg, plus ipilimumab, 1 mg/kg (n = 713); or nivolumab, 1 mg/kg, plus ipilimumab, 3 mg/kg (n = 313). Baseline BMI was categorized as normal weight or underweight (<25), overweight (25 to <30), or obese (≥30) according to World Health Organization criteria. The studies began patient enrollment between February 9, 2012, and May 21, 2015, and patients were followed up to database lock on May 1, 2019. Data analysis was conducted from May 1 to September 1, 2019. Interventions: Nivolumab, 3 mg/kg; nivolumab, 3 mg/kg, plus ipilimumab, 1 mg/kg; and nivolumab, 1 mg/kg, plus ipilimumab, 3 mg/kg. Main Outcomes and Measures: Odds ratios (ORs) and 95% CIs for incidence of any-grade and grade 3 or 4 irAEs were calculated for patients with obesity vs normal weight or underweight BMI in the overall cohort and in subgroups based on patient and tumor characteristics. Analyses for nivolumab plus ipilimumab cohorts were exploratory. Results: A total of 3772 patients were included, 2600 were male (69%), and median age was 61 years (range, 18-90 years). For patients receiving monotherapy with nivolumab, 3 mg/kg (n = 2746), the incidence of any-grade irAEs was higher in patients with obesity (n = 543) vs those with normal weight or underweight BMI (n = 1266; OR, 1.71; 95% CI, 1.38-2.11). Incidence of grade 3 or 4 irAEs did not differ between patients with obesity and those with normal weight or underweight BMI (OR, 1.21; 95% CI, 0.92-1.61). Risk of any-grade and grade 3 or 4 irAEs appeared consistent with that in the overall population across all subgroups evaluated except for a higher likelihood of grade 3 or 4 irAEs among female patients with obesity vs normal weight or underweight BMI (OR, 1.73; 95% CI, 1.07-2.79). For patients receiving nivolumab plus ipilimumab, the incidence of irAEs appeared consistent across BMI categories. Conclusions and Relevance: Obesity appeared to be associated with an increased incidence of any-grade irAEs among patients treated with nivolumab monotherapy and with grade 3 or 4 irAEs among female patients only. These findings may inform the monitoring of patients at high risk of developing irAEs.

Associations between Pretreatment Body Composition Features and Clinical Outcomes among Patients with Metastatic Clear Cell Renal Cell Carcinoma Treated with Immune Checkpoint Blockade.

PURPOSE: High body mass index (BMI) may lead to improved immune-checkpoint blockade (ICB) outcomes in metastatic clear cell renal cell carcinoma (mccRCC). However, BMI is a crude body size measure. We investigated BMI and radiographically assessed body composition (BC) parameters association with mccRCC ICB outcomes. EXPERIMENTAL DESIGN: Retrospective study of ICB-treated patients with mccRCC. BMI and BC variables [skeletal muscle index (SMI) and multiple adiposity indexes] were determined using pretreatment CT scans. We examined the associations between BMI and BC variables with ICB outcomes. Therapeutic responses per RECIST v1.1 were determined. We compared whole-transcriptomic patterns with BC variables in a separate cohort of 62 primary tumor samples. RESULTS: 205 patients with mccRCC were included in the cohort (74% were male, 71% were overweight/obese, and 53% were classified as low SMI). High-BMI patients experienced longer overall survival (OS) than normal-weight patients [unadjusted HR, 0.66; 95% confidence interval (CI), 0.45-0.97; P = 0.035]. The only BC variable associated with OS was SMI [unadjusted HR comparing low vs. high SMI 1.65 (95% CI: 1.13-2.43); P = 0.009]. However, this OS association became nonsignificant after adjusting for International Metastatic Renal Cell Carcinoma Database Consortium score and line of therapy. No OS association was seen for adiposity and no BC variable was associated with progression-free survival or radiological responses. Tumors from patients with low SMI displayed increased angiogenic, inflammatory, and myeloid signals. CONCLUSIONS: Our findings highlight the relevance of skeletal muscle in the BMI paradox. Future studies should investigate if addressing low skeletal muscle in metastatic patients treated with ICB can improve survival.

Association of Biochemically Verified Post-Diagnosis Smoking and Nonmuscle-Invasive Bladder Cancer Recurrence Risk.

PURPOSE: Our goal was to determine the association between biochemically verified post-diagnosis smoking exposure and nonmuscle-invasive bladder cancer (NMIBC) recurrence risk. MATERIALS AND METHODS: We conducted a prospective study of 354 NMIBC patients with a smoking history undergoing care between 2015 and 2018. Patients contributed at least 2 biospecimens during followup which were tested for cotinine to determine biochemically verified post-diagnosis smoking exposure (yes/no). Our primary endpoint was time to first recurrence after study start date. We examined whether post-diagnosis smoking exposure was associated with recurrence risk in multivariable Cox proportional hazards models that accounted for demographics, clinicopathological variables, time since diagnosis and pack-years. RESULTS: Patients were predominantly White, male and had a median age of 68 years. Most patients had Ta disease (62%) and tumors of high grade (68%). Intravesical bacillus Calmette-Guérin was given to 63% of the cohort. Patients were followed for a median of 3.6 years since study start. Post-diagnosis smoking exposure was detected in 22% of patients, and 38.7% (137) of patients experienced a recurrence during followup. In multivariable models, only bacillus Calmette-Guérin treatment and prior recurrence rate were significantly associated with recurrence. There was no association between post-diagnosis smoking exposure and recurrence risk (HR: 0.73, 95% CI: 0.45-1.20). CONCLUSIONS: In a cohort of patients with predominantly high risk NMIBC, post-diagnosis smoking exposure was not associated with NMIBC recurrence. However, smoking cessation support remains a critical component of cancer care given that the benefits of quitting extend far beyond NMIBC recurrence.

Identification of a Novel Inflamed Tumor Microenvironment Signature as a Predictive Biomarker of Bacillus Calmette-Guérin Immunotherapy in Non-Muscle-Invasive Bladder Cancer.

PURPOSE: Improved risk stratification and predictive biomarkers of treatment response are needed for non-muscle-invasive bladder cancer (NMIBC). Here we assessed the clinical utility of targeted RNA and DNA molecular profiling in NMIBC. EXPERIMENTAL DESIGN: Gene expression in NMIBC samples was profiled by NanoString nCounter, an RNA quantification platform, from two independent cohorts (n = 28, n = 50); targeted panel sequencing was performed in a subgroup (n = 50). Gene signatures were externally validated using two RNA sequencing datasets of NMIBC tumors (n = 438, n = 73). Established molecular subtype classifiers and novel gene expression signatures were assessed for associations with clinicopathologic characteristics, somatic tumor mutations, and treatment outcomes. RESULTS: Molecular subtypes distinguished between low-grade Ta tumors with FGFR3 mutations and overexpression (UROMOL-class 1) and tumors with more aggressive clinicopathologic characteristics (UROMOL-classes 2 and 3), which were significantly enriched with TERT promoter mutations. However, UROMOL subclasses were not associated with recurrence after bacillus Calmette-Guérin (BCG) immunotherapy in two independent cohorts. In contrast, a novel expression signature of an inflamed tumor microenvironment (TME) was associated with improved recurrence-free survival after BCG. Expression of immune checkpoint genes (PD-L1/PD-1/CTLA-4) was associated with an inflamed TME, but not with higher recurrence rates after BCG. FGFR3 mutations and overexpression were both associated with low immune signatures. CONCLUSIONS: Assessment of the immune TME, rather than molecular subtypes, is a promising predictive biomarker of BCG response. Modulating the TME in an immunologically "cold" tumor warrants further investigation. Integrated transcriptomic and exome sequencing should improve treatment selection in NMIBC.

Differences in risk factors for molecular subtypes of clear cell renal cell carcinoma.

The ccA and ccB molecular subtypes of clear cell renal cell carcinoma (ccRCC) have well-characterized prognostic relevance. However, it is not known whether they possess distinct etiologies. We investigated the relationships between these subtypes and RCC risk factors within a case-control study conducted in Eastern Europe. We analyzed risk factor data for ccA (n = 144) and ccB (n = 106) cases and 1476 controls through case-only and case-control comparisons to assess risk factor differences across subtypes using logistic and polytomous regression models. We also performed a meta-analysis summarizing case-only results from our study and three patient cohorts. Patients with ccB tumors had poorer survival than those with ccA tumors and were more likely to be male (case-only odds ratio [OR] 2.68, 95% confidence interval [CI] 1.43-5.03). In case-control analyses, body mass index was significantly associated with ccA tumors (OR 2.45, 95% CI 1.18-5.10 for ≥35 vs <25 kg/m2 ) but not with ccB tumors (1.52, 0.56-4.12), while trichloroethylene was associated with ccB but not ccA (OR 3.09, 95% CI 1.11-8.65 and 1.25, 0.36-4.39 respectively for ≥1.58 ppm-years vs unexposed). A polygenic risk score of genetic variants identified from genome-wide association studies was associated with both ccA and, in particular, ccB (OR 1.82, 1.11-2.99 and 2.87, 95% CI 1.64-5.01 respectively for 90th vs 10th percentile). In a meta-analysis of case-only results including three patient cohorts, we still observed the ccB excess for male sex and the ccA excess for obesity. In conclusion, our findings suggest the existence of etiologic heterogeneity across ccRCC molecular subtypes for several risk factors.

Examining the Accuracy of Self-Reported Smoking-Related Exposure among Recently Diagnosed Nonmuscle Invasive Bladder Cancer Patients.

PURPOSE: Cigarette smoking is a risk factor for developing nonmuscle invasive bladder cancer, and continued smoking exposure after diagnosis may increase the likelihood of adverse clinical outcomes. We compare self-reported vs biochemically verified nicotine exposure to determine the accuracy of self-report among recently diagnosed nonmuscle invasive bladder cancer patients. MATERIALS AND METHODS: This cross-sectional analysis consisted of 517 nonmuscle invasive bladder cancer patients who contributed a urine or saliva specimen the same day as self-reporting their smoking, use of e-cigarettes, nicotine replacement therapy and whether they lived with a smoker. Cotinine, the primary metabolite of nicotine, was used as an objective biomarker of recent nicotine exposure. RESULTS: The prevalence of high, low and no cotinine exposure was 13%, 54% and 33%, respectively. Overall, 7.3% of patients (38/517) reported being a current cigarette smoker, while 13% (65/517) had cotinine levels consistent with active smoking exposure. Of these 65 patients 27 denied current smoking, resulting in a sensitivity of self-reported current smoking of 58%. After considering other sources of nicotine exposure such as e-cigarettes, cigars, nicotine replacement therapy and living with a smoker, the sensitivity was higher, at 82%. Nearly all patients with low cotinine denied any smoking-related exposure. CONCLUSIONS: Our findings suggest either biochemical verification with cotinine or additional questions about other sources of nicotine are needed to accurately identify nonmuscle invasive bladder cancer patients who have smoking-related exposures. Accurate classification of active and passive smoking exposure is essential to allow clinicians to advise cessation and help researchers estimate the association between post-diagnosis smoking-related exposure and nonmuscle invasive bladder cancer recurrence risk.

Targeting Germline- and Tumor-Associated Nucleotide Excision Repair Defects in Cancer.

PURPOSE: Nucleotide excision repair (NER) gene alterations constitute potential cancer therapeutic targets. We explored the prevalence of NER gene alterations across cancers and putative therapeutic strategies targeting these vulnerabilities. EXPERIMENTAL DESIGN: We interrogated our institutional dataset with mutational data from more than 40,000 patients with cancer to assess the frequency of putative deleterious alterations in four key NER genes. Gene-edited isogenic pairs of wild-type and mutant ERCC2 or ERCC3 cell lines were created and used to assess response to several candidate drugs. RESULTS: We found that putative damaging germline and somatic alterations in NER genes were present with frequencies up to 10% across multiple cancer types. Both in vitro and in vivo studies showed significantly enhanced sensitivity to the sesquiterpene irofulven in cells harboring specific clinically observed heterozygous mutations in ERCC2 or ERCC3. Sensitivity of NER mutants to irofulven was greater than to a current standard-of-care agent, cisplatin. Hypomorphic ERCC2/3-mutant cells had impaired ability to repair irofulven-induced DNA damage. Transcriptomic profiling of tumor tissues suggested codependencies between DNA repair pathways, indicating a potential benefit of combination therapies, which were confirmed by in vitro studies. CONCLUSIONS: These findings provide novel insights into a synthetic lethal relationship between clinically observed NER gene deficiencies and sensitivity to irofulven and its potential synergistic combination with other drugs.See related commentary by Jiang and Greenberg, p. 1833.

An approach for normalization and quality control for NanoString RNA expression data.

The NanoString RNA counting assay for formalin-fixed paraffin embedded samples is unique in its sensitivity, technical reproducibility and robustness for analysis of clinical and archival samples. While commercial normalization methods are provided by NanoString, they are not optimal for all settings, particularly when samples exhibit strong technical or biological variation or where housekeeping genes have variable performance across the cohort. Here, we develop and evaluate a more comprehensive normalization procedure for NanoString data with steps for quality control, selection of housekeeping targets, normalization and iterative data visualization and biological validation. The approach was evaluated using a large cohort ($N=\kern0.5em 1649$) from the Carolina Breast Cancer Study, two cohorts of moderate sample size ($N=359$ and$130$) and a small published dataset ($N=12$). The iterative process developed here eliminates technical variation (e.g. from different study phases or sites) more reliably than the three other methods, including NanoString's commercial package, without diminishing biological variation, especially in long-term longitudinal multiphase or multisite cohorts. We also find that probe sets validated for nCounter, such as the PAM50 gene signature, are impervious to batch issues. This work emphasizes that systematic quality control, normalization and visualization of NanoString nCounter data are an imperative component of study design that influences results in downstream analyses.

Impact of body size and body composition on bladder cancer outcomes: Risk stratification and opportunity for novel interventions.

Body size is emerging as a novel and clinically-relevant patient factor in bladder cancer research. Historically, a patient's body mass index (BMI) has been used as a proxy for obesity but it shows inconsistent associations with risk of developing the disease as well as with most clinical outcomes. More specific body composition features can be derived for patients using a variety of methods. To date, skeletal muscle measurements derived from preoperative computed tomography scans have shown the most consistent associations with clinical outcomes. Importantly, skeletal muscle can potentially be modified through resistance training and/or nutritional interventions. Large scale studies that evaluate the prognostic impact of not only body composition features at baseline but also describe changes in body composition post-treatment are needed to move the field forward to ultimately improve clinical outcomes for bladder cancer patients.

Automated body composition analysis of clinically acquired computed tomography scans using neural networks.

BACKGROUND & AIMS: The quantity and quality of skeletal muscle and adipose tissue is an important prognostic factor for clinical outcomes across several illnesses. Clinically acquired computed tomography (CT) scans are commonly used for quantification of body composition, but manual analysis is laborious and costly. The primary aim of this study was to develop an automated body composition analysis framework using CT scans. METHODS: CT scans of the 3rd lumbar vertebrae from critically ill, liver cirrhosis, pancreatic cancer, and clear cell renal cell carcinoma patients, as well as renal and liver donors, were manually analyzed for body composition. Ninety percent of scans were used for developing and validating a neural network for the automated segmentation of skeletal muscle and adipose tissues. Network accuracy was evaluated with the remaining 10 percent of scans using the Dice similarity coefficient (DSC), which quantifies the overlap (0 = no overlap, 1 = perfect overlap) between human and automated segmentations. RESULTS: Of the 893 patients, 44% were female, with a mean (±SD) age and body mass index of 52.7 (±15.8) years old and 28.0 (±6.1) kg/m2, respectively. In the testing cohort (n = 89), DSC scores indicated excellent agreement between human and network-predicted segmentations for skeletal muscle (0.983 ± 0.013), and intermuscular (0.900 ± 0.034), visceral (0.979 ± 0.019), and subcutaneous (0.986 ± 0.016) adipose tissue. Network segmentation took ~350 milliseconds/scan using modern computing hardware. CONCLUSIONS: Our network displayed excellent ability to analyze diverse body composition phenotypes and clinical cohorts, which will create feasible opportunities to advance our capacity to predict health outcomes in clinical populations.

Transcriptomic signatures related to the obesity paradox in patients with clear cell renal cell carcinoma: a cohort study.

BACKGROUND: Obesity is associated with an increased risk of developing clear cell renal cell carcinoma (RCC) but, paradoxically, obesity is also associated with improved oncological outcomes in this cancer. Because the biological mechanisms underlying this paradoxical association are poorly understood, we aimed to identify transcriptomic differences in primary tumour and peritumoral adipose tissue between obese patients and those at a normal weight. METHODS: In this cohort study, we assessed data from five independent clinical cohorts of patients with clear cell RCC aged 18 years and older. Overweight patients were excluded from each cohort for our analysis. We assessed patients from the COMPARZ phase 3 clinical trial, a cohort from the Cancer Genome Atlas (TCGA), and a Memorial Sloan Kettering (MSK) observational immunotherapy cohort for their inclusion into our study. We assessed overall survival in obese patients (those with a body-mass index [BMI] ≥30 kg/m2) and in patients with a normal weight (BMI 18·5-24·9 kg/m2, as per WHO's BMI categories), defined as the time from treatment initiation (in the COMPARZ and MSK immunotherapy cohorts) or surgery (in the TCGA cohort) to the date of any-cause death or of censoring on the day of the last follow-up. We also evaluated and validated transcriptomic differences in the primary tumours of obese patients compared with those of a normal weight. We compared gene-expression differences in peritumoral adipose tissue and tumour tissue in an additional, prospectively collected cohort of patients with non-metastatic clear cell RCC (the MSK peritumoral adipose tissue cohort). We analysed differences in gene expression between obese patients and those at a normal weight in the COMPARZ, TCGA, and peritumoral adipose tissue cohorts. We also assessed the tumour immune microenvironment in a prospective cohort of patients who had nephrectomy for localised RCC at MSK. FINDINGS: Of the 453 patients in the COMPARZ trial, 375 (83%) patients had available microarray data, pretreatment BMI measurements, and overall survival data for analyses, and we excluded 119 (26%) overweight patients, leaving a final cohort of 256 (68%) patients from this study for our analyses. From 332 patients in the TCGA cohort, we evaluated clinical and demographic data from 152 (46%) patients with advanced (ie, stages III and IV) clear cell RCC treated by nephrectomy; after exclusion of 59 (39%) overweight patients, our final cohort consisted of 93 (61%) patients. After exclusion of 74 (36%) overweight patients from the initial MSK immunotherapy study population of 203 participants, our final cohort for overall survival analysis comprised 129 (64%) participants. We found that overall survival was longer in obese patients than in those with normal weight in the TCGA cohort, after adjustment for stage or grade (adjusted HR 0·41, 95% CI 0·22-0·75), and in the COMPARZ clinical trial after adjustment for International Metastatic RCC Database (IMDC) risk score (0·68, 0·48-0·96). In the MSK immunotherapy cohort, the inverse association of BMI with mortality (HR 0·54, 95% CI 0·31-0·95) was not significant after adjustment for IMDC risk score (adjusted HR 0·72, 95% CI 0·40-1·30). Tumours of obese patients showed higher angiogenic scores on gene-set enrichment analysis-derived hallmark gene set angiogenesis signatures than did those of patients at a normal weight, but the degree of immune cell infiltration did not differ by BMI. We found increased peritumoral adipose tissue inflammation in obese patients relative to those at a normal weight, especially in peritumoral fat near the tumour. INTERPRETATION: We found aspects of the tumour microenvironment that vary by BMI in the tumour and peritumoral adipose tissue, which might contribute to the apparent survival advantage in obese patients with clear cell RCC compared with patients at a normal weight. The complex interplay between the clear cell RCC tumour and peritumoral adipose tissue microenvironment might have clinical relevance and warrants further investigation. FUNDING: Ruth L Kirschstein Research Service Award, American Society of Clinical Oncology Young Investigator Award, MSK's Ludwig Center, Weiss Family Kidney Research Fund, Novartis, The Sidney Kimmel Center for Prostate and Urologic Cancers, and the National Institutes of Health (National Cancer Institute) Cancer Center Support Grant.