A Phase 2 Trial of Talazoparib and Avelumab in Genomically Defined Metastatic Kidney Cancer.

BACKGROUND: Although different kidney cancers represent a heterogeneous group of malignancies, multiple subtypes including Von Hippel-Lindau (VHL)-altered clear cell renal cell carcinoma (ccRCC), fumarate hydratase (FH)- and succinate dehydrogenase (SDH)-deficient renal cell carcinoma (RCC), and renal medullary carcinoma (RMC) are affected by genomic instability. Synthetic lethality with poly ADP-ribose polymerase inhibitors (PARPis) has been suggested in preclinical models of these subtypes, and paired PARPis with immune checkpoint blockade (ICB) may achieve additive and/or synergistic effects in patients with previously treated advanced kidney cancers. OBJECTIVE: To evaluate combined PARPi + ICB in treatment-refractory metastatic kidney cancer. DESIGN, SETTING, AND PARTICIPANTS: We conducted a single-center, investigator-initiated phase 2 trial in two genomically selected advanced kidney cancer cohorts: (1) VHL-altered RCC with at least one prior ICB agent and one vascular endothelial growth factor (VEGF) inhibitor, and (2) FH- or SDH-deficient RCC with at least one prior ICB agent or VEGF inhibitor and RMC with at least one prior line of chemotherapy. INTERVENTION: Patients received talazoparib 1 mg daily plus avelumab 800 mg intravenously every 14 d in 28-d cycles. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The primary endpoint was objective response rate (ORR) by Immune Response Evaluation Criteria in Solid Tumors at 4 mo, and the secondary endpoints included progression-free survival (PFS), overall survival, and safety. RESULTS AND LIMITATIONS: Cohort 1 consisted of ten patients with VHL-altered ccRCC. All patients had previously received ICB. The ORR was 0/9 patients; one patient was not evaluable due to missed doses. In this cohort, seven patients achieved stable disease (SD) as the best response. The median PFS was 3.5 mo (95% confidence interval [CI] 1.0, 3.9 mo). Cohort 2 consisted of eight patients; four had FH-deficient RCC, one had SDH-deficient RCC, and three had RMC. In this cohort, six patients had previously received ICB. The ORR was 0/8 patients; two patients achieved SD as the best response and the median PFS was 1.2 mo (95% CI 0.4, 2.9 mo). The most common treatment-related adverse events of all grades were fatigue (61%), anemia (28%), nausea (22%), and headache (22%). There were seven grade 3-4 and no grade 5 events. CONCLUSIONS: The first clinical study of combination PARPi and ICB therapy in advanced kidney cancer did not show clinical benefit in multiple genomically defined metastatic RCC cohorts or RMC. PATIENT SUMMARY: We conducted a study to look at the effect of two medications, talazoparib and avelumab, in patients with metastatic kidney cancer who had disease progression on standard treatment. Talazoparib blocks the normal activity of molecules called poly ADP-ribose polymerase, which then prevents tumor cells from repairing themselves and growing, while avelumab helps the immune system recognize and kill cancer cells. We found that the combination of these agents was safe but not effective in specific types of kidney cancer.

A new flow cytometry assay identifies recipient IgG subtype antibodies binding donor cells: increasing donor availability for highly sensitised patients.

Objectives: There are four immunoglobulin (IgG) subtypes that have varying complement-activating ability: strong (IgG3 and IgG1) and weak (IgG2 and IgG4). The standard flow cytometric crossmatch (FCM) assay does not distinguish between the various subtypes of the IgG molecule. This study outlines the development and use of a novel cell-based IgG subtype-specific FCM assay that is able to detect the presence of and quantitate the IgG subtypes bound to donor cells. Methods: A six-colour lyophilised reagent was designed that specifically detects the four IgG subtypes, as well as distinguishes between T cells and B cells in the lymphocyte population. To test the efficacy of this reagent, a retrospective evaluation of a group of highly sensitised patients awaiting heart and kidney transplant was carried out, who, because of positive standard FCM results, had been deemed incompatible with numerous prior potential donors. Results: Observations in this study demonstrate that the positive standard FCM results were mainly because of the presence of noncomplement-activating IgG2 or IgG4 antibodies. The results were supported by the absence of C3d-binding donor-specific antibodies (DSA) and a negative complement-dependent cytotoxicity crossmatch (CDC). Conclusion: Preliminary data presented in this study demonstrate the reliability of the novel IgG subtype assay to detect the presence of pretransplant, complement-activating antibodies bound to donor cells. The knowledge gained from the IgG subtype assay and the C3d-binding specificities of DSAs provides improved identification of donor suitability in pretransplant patients, potentially increasing the number of transplants.

Molecular Characterization of the Tumor Microenvironment in Renal Medullary Carcinoma.

Renal medullary carcinoma (RMC) is a highly aggressive disease associated with sickle hemoglobinopathies and universal loss of the tumor suppressor gene SMARCB1. RMC has a relatively low rate of incidence compared with other renal cell carcinomas (RCCs) that has hitherto made molecular profiling difficult. To probe this rare disease in detail we performed an in-depth characterization of the RMC tumor microenvironment using a combination of genomic, metabolic and single-cell RNA-sequencing experiments on tissue from a representative untreated RMC patient, complemented by retrospective analyses of archival tissue and existing published data. Our study of the tumor identifies a heterogenous population of malignant cell states originating from the thick ascending limb of the Loop of Henle within the renal medulla. Transformed RMC cells displayed the hallmarks of increased resistance to cell death by ferroptosis and proteotoxic stress driven by MYC-induced proliferative signals. Specifically, genomic characterization of RMC tumors provides substantiating evidence for the recently proposed dependence of SMARCB1-difficient cancers on proteostasis modulated by an intact CDKN2A-p53 pathway. We also provide evidence that increased cystine-mTORC-GPX4 signaling plays a role in protecting transformed RMC cells against ferroptosis. We further propose that RMC has an immune landscape comparable to that of untreated RCCs, including heterogenous expression of the immune ligand CD70 within a sub-population of tumor cells. The latter could provide an immune-modulatory role that serves as a viable candidate for therapeutic targeting.

Genomic and Metabolic Hallmarks of SDH- and FH-deficient Renal Cell Carcinomas.

BACKGROUND: Succinate dehydrogenase-deficient and fumarate hydratase-deficient renal cell carcinomas (SDHRCC and FHRCC) are rare kidney cancers driven by loss of TCA cycle enzymes. OBJECTIVE: To define and compare the genomic and metabolomic hallmarks of SDHRCC and FHRCC. DESIGN, SETTING, AND PARTICIPANTS: We analyzed SDHRCC and FHRCC tumors with either immunohistochemical evidence of loss of protein expression or genomically confirmed biallelic inactivation of SDHA/B/C/D/AF2 or FH. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Somatic alterations were identified using clinical pipelines, with allele-specific copy number alterations (CNAs) identified using FACETS. Mass spectrometry-based metabolomic profiling was performed on available SDHRCC and FHRCC tumors. RESULTS AND LIMITATIONS: Tumors were analyzed for 42 patients (25 FHRCC, 17 SDHRCC). In the germline analysis, 16/17 SDHRCCs harbored a germline alteration in SDHB, whereas only 17/22 FHRCCs had pathogenic germline FH variants. SDHRCCs had a lower mutation burden (p = 0.02) and CNA burden (p = 0.0002) than FHRCCs. All SDHRCCs presented with deletion of chromosome 1p (overlapping SDHB), whereas FHRCCs demonstrated high but not ubiquitous loss of 1q (FH locus). Both SDHRCCs and FHRCCs exhibited significant idiopathic accumulation of the metabolite guanine. FHRCC tumors had elevated levels of urea cycle metabolites (argininosuccinate, citrulline, and fumarate), whereas SDHRCC tumors had elevation of numerous acylcarnitines. These characteristic metabolic changes allowed identification of a previously unrecognized SDH-deficient RCC. CONCLUSIONS: Despite sharing similar genetic etiology, SDHRCC and FHRCC represent distinct molecular entities with unique genetic and metabolic abnormalities. PATIENT SUMMARY: Kidney cancers driven by loss of the gene encoding either the succinate dehydrogenase or fumarate hydratase enzyme are rare. We sought to define and compare the genetic and metabolic features of these cancer entities.

Phase II Trial of Cabozantinib Plus Nivolumab in Patients With Non-Clear-Cell Renal Cell Carcinoma and Genomic Correlates.

PURPOSE: To assess the efficacy and safety of cabozantinib plus nivolumab in a phase II trial in patients with non-clear-cell renal cell carcinoma (RCC). PATIENTS AND METHODS: Patients had advanced non-clear-cell renal carcinoma who underwent 0-1 prior systemic therapies excluding prior immune checkpoint inhibitors. Patients received cabozantinib 40 mg once daily plus nivolumab 240 mg once every 2 weeks or 480 mg once every 4 weeks. Cohort 1 enrolled patients with papillary, unclassified, or translocation-associated RCC; cohort 2 enrolled patients with chromophobe RCC. The primary end point was objective response rate (ORR) by RECIST 1.1; secondary end points included progression-free survival, overall survival, and safety. Next-generation sequencing results were correlated with response. RESULTS: A total of 47 patients were treated with a median follow-up of 13.1 months. Objective response rate for cohort 1 (n = 40) was 47.5% (95% CI, 31.5 to 63.9), with median progression-free survival of 12.5 months (95% CI, 6.3 to 16.4) and median overall survival of 28 months (95% CI, 16.3 to not evaluable). In cohort 2 (n = 7), no responses were observed; one patient had stable disease > 1 year. Grade 3/4 treatment-related adverse events were observed in 32% treated patients. Cabozantinib and nivolumab were discontinued because of toxicity in 13% and 17% of patients, respectively. Common mutations included NF2 and FH in cohort 1 and TP53 and PTEN in cohort 2. Objective responses were seen in 10/12 patients with either NF2 or FH mutations. CONCLUSION: Cabozantinib plus nivolumab showed promising efficacy in most non-clear-cell RCC variants tested in this trial, particularly those with prominent papillary features, whereas treatment effects were limited in chromophobe RCC. Genomic findings in non-clear-cell RCC variants warrant further study as predictors of response.

Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers.

Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes. The HPV oncoproteins E6 and E7 are necessary but insufficient for cancer formation, indicating that additional secondary genetic events are required. Here, we investigate potential oncogenic impacts of virus integration. Analysis of 105 HPV-positive oropharyngeal cancers by whole-genome sequencing detects virus integration in 77%, revealing five statistically significant sites of recurrent integration near genes that regulate epithelial stem cell maintenance (i.e., SOX2, TP63, FGFR, MYC) and immune evasion (i.e., CD274). Genomic copy number hyperamplification is enriched 16-fold near HPV integrants, and the extent of focal host genomic instability increases with their local density. The frequency of genes expressed at extreme outlier levels is increased 86-fold within ±150 kb of integrants. Across 95% of tumors with integration, host gene transcription is disrupted via intragenic integrants, chimeric transcription, outlier expression, gene breaking, and/or de novo expression of noncoding or imprinted genes. We conclude that virus integration can contribute to carcinogenesis in a large majority of HPV-positive oropharyngeal cancers by inducing extensive disruption of host genome structure and gene expression.

Comprehensive Molecular Characterization and Response to Therapy in Fumarate Hydratase-Deficient Renal Cell Carcinoma.

PURPOSE: Fumarate hydratase-deficient renal cell carcinoma (FH-RCC) is a rare, aggressive form of RCC associated with hereditary leiomyomatosis and RCC syndrome. Evidence for systemic therapy efficacy is lacking. EXPERIMENTAL DESIGN: We studied clinical and genomic characteristics of FH-RCC, including response [objective response rate (ORR)] to systemic therapies and next-generation sequencing (NGS). Patients with metastatic FH-RCC, defined by presence of pathogenic germline or somatic FH mutation plus IHC evidence of FH loss, were included. RESULTS: A total of 28 of 32 included patients (median age 46; range, 20-74; M:F, 20:12) underwent germline testing; 23 (82%) harbored a pathogenic FH germline variant. Five (16%) were negative for germline FH mutations; all had biallelic somatic FH loss. Somatic NGS (31/32 patients) revealed co-occurring NF2 mutation most frequently (n = 5). Compared with clear-cell RCC, FH-RCC had a lower mutation count (median 2 vs. 4; P < 0.001) but higher fraction of genome altered (18.7% vs. 10.3%; P = 0.001). A total of 26 patients were evaluable for response to systemic therapy: mTOR/VEGF combination (n = 18, ORR 44%), VEGF monotherapy (n = 15, ORR 20%), checkpoint inhibitor therapy (n = 8, ORR 0%), and mTOR monotherapy (n = 4, ORR 0%). No complete responses were seen. Median overall and progression-free survival were 21.9 months [95% confidence interval (CI): 14.3-33.8] and 8.7 months (95% CI: 4.8-12.3), respectively. CONCLUSIONS: Although most FH-RCC tumors are due to germline FH alterations, a significant portion result from biallelic somatic FH loss. Both somatic and germline FH-RCC have similar molecular characteristics, with NF2 mutations, low tumor mutational burden, and high fraction of genome altered. Although immunotherapy alone produced no objective responses, combination mTOR/VEGF therapy showed encouraging results.

Outcomes of Obese Patients Bridged to Heart Transplantation with a Left Ventricular Assist Device.

The current study aims to investigate the impact of left ventricular assist device (LVAD) implantation on weight loss and functional status in obese patients bridged to transplantation (BTT). The United Network for Organ Sharing (UNOS) database was queried to identify patients with body mass index (BMI) ≥ 30 who underwent LVAD implantation as BTT from 2008 to 2018. Patients were divided into three groups based the World Health Organization classification of obesity: obesity class I (BMI, 30.0-34.9 kg/m2), obesity class II (BMI, 35-39.9 kg/m2), and obesity class III (BMI, >40 kg/m2). Patients with incomplete data on BMI were excluded. The primary outcome was a change in BMI while listed. Secondary outcomes included a change in functional status after LVAD implantation and posttransplant morbidity and survival. Out of 14,191 patients who had an LVAD while listed within the study period, 5,354 (37.7%) had a BMI ≥30 kg/m2. Obesity was classified as class I in 3,909 (73%), class II in 1,275 (23.8%), and class III in 170 (3.2%) patients. Among patients with complete data on BMI, 18.9% (n = 394) reported a change in BMI, leading to an improvement in their obesity class, and this was similar for all obesity classes (22% [n = 331], 50% [n = 111], and 60% [n = 43] for classes I, II, and III, respectively). All groups reported an improvement in functional status (65% vs. 62% and 61% for classes I, II, and III, respectively). Posttransplant survival was not significantly different between obese groups (p = 0.787). Compared with classes I and II, the incidence of thrombosis (p = 0.0006) and device malfunction (p = 0.036) was significantly higher in the class III group. About one out of every five obese patients listed for heart transplantation with an LVAD loses weight, leading to a change in their BMI class. Most patients reported a significant improvement in their functional status. Among those successfully BTT, posttransplant survival was similar.

Emergent TandemHeart-ECMO for acute severe mitral regurgitation with cardiogenic shock and hypoxaemia: a case series.

BACKGROUND: Acute severe mitral regurgitation (MR) associated with cardiogenic shock is a life-threatening emergency. Traditional teaching has focused on the need for emergent coronary angiography and/or intra-aortic balloon counterpulsation in preparation for emergent open-heart surgery for repair/replacement. Unfortunately, emergent open-heart surgery in patients with acute MR complicated by cardiogenic shock is associated with 25-46% perioperative mortality. New devices have provided additional options for stabilization prior to emergent surgery which facilitate improved outcomes. CASE SUMMARY: We present two cases of acute severe MR resulting in cardiogenic shock and profound hypoxaemia. TandemHeart® mechanical circulatory support with an oxygenator spliced into the circuit, akin to veno-arterial extracorporeal membrane oxygenation (ECMO), facilitated haemodynamic stabilization and decongestion of the lungs facilitating successful bridge to mitral valve surgery. Successful discharge to home was achieved in both patients with good neurological outcomes and sustained long-term functional recovery at 18 and 14 months, respectively. DISCUSSION: Selective use of the TandemHeart®, with or without ECMO, facilitates management of the critically ill cardiogenic shock patient with acute severe MR.

Evaluation for Heart Transplantation and LVAD Implantation: JACC Council Perspectives.

Timely referrals for transplantation and left ventricular assist device implantation play a key role in favorable outcomes in patients with advanced heart failure. Nonetheless, evaluation usually occurs at advanced heart failure centers and is obscured from referring physicians. The purposes of this review are to explain the decision-making process for candidacy for advanced therapies and to describe the potential impact of the new organ allocation algorithm on center decision making. The document first addresses the signs of advanced heart failure, specifically focusing on the importance of the syndrome of low cardiac output as a key feature of advanced heart failure, and then summarizes the evaluation as a 3-step process addressing the following questions: 1) Is transplantation or durable assist device placement indicated? 2) Are there contraindications to either intervention? 3) How can one choose between transplantation and left ventricular assist device implantation if advanced therapies are indicated and not contraindicated?

Differential gene expression in non-adherent heart transplant survivors: Implications for regulatory T-cell expression.

Survival despite prolonged non-adherence with immunosuppression is rare but has been reported in kidney, lung, and liver transplantation. Its occurrence in heart transplantation is quite rare. Our study was prompted by an index patient who survived despite prolonged medication non-adherence. Prospective consent and blood collection were conducted for seven additional patients who presented in a similar fashion. The blood of patients who were diagnosed with rejection, stable early post-transplant, and stable more than 5 years post-transplant were all compared with a custom gene array focusing on T-regulatory cell processes. The two genes that were differentially expressed in every comparison were TGF beta and RNASEN with very low expression in the rejector group. The prolonged non-adherent group had the maximum expression for TGF beta but average RNASEN expression as compared to the low expression for rejectors and high for post-5 years patients. The patients presented survived for varying lengths of time without immunosuppression. The gene array analysis showed intriguing differences between these rare patients and important patient cohorts. Further efforts should be directed to finding and studying more patients who survive despite lack of prescribed immunosuppression. The mechanisms underlying this phenomenon may inform future advances in transplant immunosuppression.

Safety of Outpatient Milrinone Infusion in End-Stage Heart Failure: ICD-Level Data on Atrial Fibrillation and Ventricular Tachyarrhythmias.

BACKGROUND: Milrinone infusion is one of a few select "non-device" therapies for patients with New York Heart Association (NYHA) class IV, stage D heart failure, which has been associated with an increase in ventricular tachyarrhythmia and atrial fibrillation. Milrinone improves hemodynamics and provides symptomatic relief. Many patients with end-stage heart failure die from cardiac pump failure, and the impact of ventricular tachyarrhythmia and atrial fibrillation on their mortality is unclear. METHODS: This is a retrospective study of 98 consecutive patients receiving outpatient milrinone in a single center from 2008 to 2016. The primary endpoint of the study was overall survival on milrinone. Secondary endpoints were incidence of post-milrinone implantable cardioverter defibrillator (ICD) shocks and development of ventricular tachyarrhythmia or atrial fibrillation. RESULTS: Median survival was 581 ± 96 days with no difference between those with prior ventricular tachyarrhythmia and those without at 1 month (92% vs 97%, P = 0.34), 6 months (67% vs 73%, P = 0.75), and 12 months (67% vs 61%, P = 0.88). Seven out of 12 (58%) patients with prior ventricular tachyarrhythmia had ICD shocks, as compared to 5 out of 78 (6.4%) (P <0.001). Thirty-five patients had atrial fibrillation prior to starting milrinone, which decreased to 72% (P <0.05) by the third follow-up time period (7-9 months). Amiodarone use was protective against new onset atrial fibrillation. CONCLUSIONS: Patients with stage D heart failure with a history of ventricular tachyarrhythmia have similar survival on outpatient milrinone compared to those without. However, those with prior ventricular tachyarrhythmia received more ICD shocks for more ventricular tachyarrhythmias. Milrinone remains a viable therapy for patients with stage D heart failure with limited therapeutic options.

Racial Disparities and Outcomes After Left Ventricular Assist Device Implantation as Bridge to Transplantation or Destination Therapy.

OBJECTIVE: We sought to investigate outcomes after left ventricular assist device (LVAD) implantation in advanced heart failure patients stratified by race. METHODS: Patients who had LVADs inserted at a single center as a bridge to transplant (BTT) or destination therapy (DT) were divided into 3 groups based on race: Caucasian, African American (AA), and Hispanic. Postoperative outcomes including complications, discharge disposition, and survival at defined time points were compared. Cox proportional hazards were used to identify factors associated with 1-year all-cause survival. RESULTS: A total of 158 patients who had LVADs as BTT (n = 63) and DT (n = 95) were studied. Of these, 56% (n = 89) were Caucasians, 35% (n = 55) were AA, and 9% (n = 14) were Hispanics. AA patients had higher BMI and lower socioeconomic status and educational level, and were more likely to be single or divorced. Operative outcomes were similar among all 3 groups. Unadjusted 30-day, 6-month, 1-year, and 2-year survival rates for Caucasians versus AA versus Hispanics were 82% versus 89% versus 93%, P = 0.339; 74% versus 80% versus 71%, P = 0.596; 67% versus 76% versus 71%, P = 0.511; and 56% versus 62% versus 68%, P = 0.797. On multivariate analysis, device-related infection, malfunction, and abnormal rhythm were factors associated with overall all-cause mortality. CONCLUSION: AA patients who undergo LVAD implantation as BTT or DT have lower socioeconomic status and educational level compared to their Caucasian or Hispanic counterparts. These differences, however, do not translate into postimplant survival outcomes.

Venoarterial ECMO for Adults: JACC Scientific Expert Panel.

Venoarterial extracorporeal membrane oxygenation (ECMO) is a rescue therapy that can stabilize patients with hemodynamic compromise, with or without respiratory failure, for days or weeks. In cardiology, the main indications for ECMO include cardiac arrest, cardiogenic shock, post-cardiotomy shock, refractory ventricular tachycardia, and acute management of complications of invasive procedures. The fundamental premise underlying ECMO is that it is a bridge-to recovery, to a more durable bridge, to definitive treatment, or to decision. As a very resource- and effort-intensive intervention, ECMO should not be used on unsalvageable patients. As the use of this technology continues to evolve rapidly, it is important to understand the indications and contraindications; the logistics of ECMO initiation, management, and weaning; the general infrastructure of the program (including the challenges associated with transferring patients supported by ECMO); and ethical considerations, areas of uncertainty, and future directions.

Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing.

MOTIVATION: Clonal heterogeneity is common in many types of cancer, including chronic lymphocytic leukemia (CLL). Previous research suggests that the presence of multiple distinct cancer clones is associated with clinical outcome. Detection of clonal heterogeneity from high throughput data, such as sequencing or single nucleotide polymorphism (SNP) array data, is important for gaining a better understanding of cancer and may improve prediction of clinical outcome or response to treatment. Here, we present a new method, CloneSeeker, for inferring clinical heterogeneity from sequencing data, SNP array data, or both. RESULTS: We generated simulated SNP array and sequencing data and applied CloneSeeker along with two other methods. We demonstrate that CloneSeeker is more accurate than existing algorithms at determining the number of clones, distribution of cancer cells among clones, and mutation and/or copy numbers belonging to each clone. Next, we applied CloneSeeker to SNP array data from samples of 258 previously untreated CLL patients to gain a better understanding of the characteristics of CLL tumors and to elucidate the relationship between clonal heterogeneity and clinical outcome. We found that a significant majority of CLL patients appear to have multiple clones distinguished by copy number alterations alone. We also found that the presence of multiple clones corresponded with significantly worse survival among CLL patients. These findings may prove useful for improving the accuracy of prognosis and design of treatment strategies. AVAILABILITY AND IMPLEMENTATION: Code available on R-Forge: https://r-forge.r-project.org/projects/CloneSeeker/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Human papillomavirus and the landscape of secondary genetic alterations in oral cancers.

Human papillomavirus (HPV) is a necessary but insufficient cause of a subset of oral squamous cell carcinomas (OSCCs) that is increasing markedly in frequency. To identify contributory, secondary genetic alterations in these cancers, we used comprehensive genomics methods to compare 149 HPV-positive and 335 HPV-negative OSCC tumor/normal pairs. Different behavioral risk factors underlying the two OSCC types were reflected in distinctive genomic mutational signatures. In HPV-positive OSCCs, the signatures of APOBEC cytosine deaminase editing, associated with anti-viral immunity, were strongly linked to overall mutational burden. In contrast, in HPV-negative OSCCs, T>C substitutions in the sequence context 5'-ATN-3' correlated with tobacco exposure. Universal expression of HPV E6*1 and E7 oncogenes was a sine qua non of HPV-positive OSCCs. Significant enrichment of somatic mutations was confirmed or newly identified in PIK3CA, KMT2D, FGFR3, FBXW7, DDX3X, PTEN, TRAF3, RB1, CYLD, RIPK4, ZNF750, EP300, CASZ1, TAF5, RBL1, IFNGR1, and NFKBIA Of these, many affect host pathways already targeted by HPV oncoproteins, including the p53 and pRB pathways, or disrupt host defenses against viral infections, including interferon (IFN) and nuclear factor kappa B signaling. Frequent copy number changes were associated with concordant changes in gene expression. Chr 11q (including CCND1) and 14q (including DICER1 and AKT1) were recurrently lost in HPV-positive OSCCs, in contrast to their gains in HPV-negative OSCCs. High-ranking variant allele fractions implicated ZNF750, PIK3CA, and EP300 mutations as candidate driver events in HPV-positive cancers. We conclude that virus-host interactions cooperatively shape the unique genetic features of these cancers, distinguishing them from their HPV-negative counterparts.

Thirty biologically interpretable clusters of transcription factors distinguish cancer type.

BACKGROUND: Transcription factors are essential regulators of gene expression and play critical roles in development, differentiation, and in many cancers. To carry out their regulatory programs, they must cooperate in networks and bind simultaneously to sites in promoter or enhancer regions of genes. We hypothesize that the mRNA co-expression patterns of transcription factors can be used both to learn how they cooperate in networks and to distinguish between cancer types. RESULTS: We recently developed a new algorithm, Thresher, that combines principal component analysis, outlier filtering, and von Mises-Fisher mixture models to cluster genes (in this case, transcription factors) based on expression, determining the optimal number of clusters in the process. We applied Thresher to the RNA-Seq expression data of 486 transcription factors from more than 10,000 samples of 33 kinds of cancer studied in The Cancer Genome Atlas (TCGA). We found that 30 clusters of transcription factors from a 29-dimensional principal component space were able to distinguish between most cancer types, and could separate tumor samples from normal controls. Moreover, each cluster of transcription factors could be either (i) linked to a tissue-specific expression pattern or (ii) associated with a fundamental biological process such as cell cycle, angiogenesis, apoptosis, or cytoskeleton. Clusters of the second type were more likely also to be associated with embryonically lethal mouse phenotypes. CONCLUSIONS: Using our approach, we have shown that the mRNA expression patterns of transcription factors contain most of the information needed to distinguish different cancer types. The Thresher method is capable of discovering biologically interpretable clusters of genes. It can potentially be applied to other gene sets, such as signaling pathways, to decompose them into simpler, yet biologically meaningful, components.

Corticosteroid Weaning in Stable Heart Transplant Patients: Guidance by Serum Cortisol Level.

BACKGROUND: Despite earlier studies describing the feasibility of steroid weaning in heart transplant patients, the majority of patients are maintained on steroid therapy for life. We examined a strategy based on a single morning serum cortisol measurement. METHODS: We assigned stable posttransplant patients, who were maintained on tacrolimus, mycophenolate mofetil, and corticosteroids, into one of two groups based on a screening morning cortisol level. Patients with a cortisol < 8 micrograms/deciliter were assigned to a "maintenance" group and the others were assigned to the weaning group and steroids were tapered off over 4-6 weeks. Patients were monitored on subsequent office visits for adrenal insufficiency and allograft rejection. RESULTS: Thirty-one patients were enrolled (6 patients in the maintenance group and 25 in the steroid-weaning group). Mean follow-up was 10.2 ± 4 years for the weaning group and 9.0 ± 4.9 years in the maintenance group (p = 0.6). No cases of rejection were noted, nor did any patient resume steroid treatment following discontinuation. CONCLUSION: Steroids can be safely discontinued in stable heart transplant patients with an AM serum cortisol ≥ 8 micrograms/deciliter with appropriate outpatient follow-up. In this study, no patient suffered late rejection or clinically noted adrenal insufficiency.

Circulating T-Cell Subsets, Monocytes, and Natural Killer Cells in Peripartum Cardiomyopathy: Results From the Multicenter IPAC Study.

OBJECTIVE: The aim of this work was to evaluate the hypothesis that the distribution of circulating immune cell subsets, or their activation state, is significantly different between peripartum cardiomyopathy (PPCM) and healthy postpartum (HP) women. BACKGROUND: PPCM is a major cause of maternal morbidity and mortality, and an immune-mediated etiology has been hypothesized. Cellular immunity, altered in pregnancy and the peripartum period, has been proposed to play a role in PPCM pathogenesis. METHODS: The Investigation of Pregnancy-Associated Cardiomyopathy (IPAC) study enrolled 100 women presenting with a left ventricular ejection fraction of <0.45 within 2 months of delivery. Peripheral T-cell subsets, natural killer (NK) cells, and cellular activation markers were assessed by flow cytometry in PPCM women early (<6 wk), 2 months, and 6 months postpartum and compared with those of HP women and women with non-pregnancy-associated recent-onset cardiomyopathy (ROCM). RESULTS: Entry NK cell levels (CD3-CD56+CD16+; reported as % of CD3- cells) were significantly (P < .0003) reduced in PPCM (6.6 ± 4.9% of CD3- cells) compared to HP (11.9 ± 5%). Of T-cell subtypes, CD3+CD4-CD8-CD38+ cells differed significantly (P < .004) between PPCM (24.5 ± 12.5% of CD3+CD4-CD8- cells) and HP (12.5 ± 6.4%). PPCM patients demonstrated a rapid recovery of NK and CD3+CD4-CD8-CD38+ cell levels. However, black women had a delayed recovery of NK cells. A similar reduction of NK cells was observed in women with ROCM. CONCLUSIONS: Compared with HP control women, early postpartum PPCM women show significantly reduced NK cells, and higher CD3+CD4-CD8-CD38+ cells, which both normalize over time postpartum. The mechanistic role of NK cells and "double negative" (CD4-CD8-) T regulatory cells in PPCM requires further investigation.