Comprehensive Characterization of Cancer Driver Genes and Mutations.

Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%-85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors.

Clonal Deletion of Tumor-Specific T Cells by Interferon-γ Confers Therapeutic Resistance to Combination Immune Checkpoint Blockade.

Resistance to checkpoint-blockade treatments is a challenge in the clinic. We found that although treatment with combined anti-CTLA-4 and anti-PD-1 improved control of established tumors, this combination compromised anti-tumor immunity in the low tumor burden (LTB) state in pre-clinical models as well as in melanoma patients. Activated tumor-specific T cells expressed higher amounts of interferon-γ (IFN-γ) receptor and were more susceptible to apoptosis than naive T cells. Combination treatment induced deletion of tumor-specific T cells and altered the T cell repertoire landscape, skewing the distribution of T cells toward lower-frequency clonotypes. Additionally, combination therapy induced higher IFN-γ production in the LTB state than in the high tumor burden (HTB) state on a per-cell basis, reflecting a less exhausted immune status in the LTB state. Thus, elevated IFN-γ secretion in the LTB state contributes to the development of an immune-intrinsic mechanism of resistance to combination checkpoint blockade, highlighting the importance of achieving the optimal magnitude of immune stimulation for successful combination immunotherapy strategies.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.

Active Pulsatile Gels: From a Chemical Microreactor to a Polymeric Actuator.

We report on a synthesis protocol, experimental characterization, and theoretical modeling of active pulsatile Belousov-Zhabotinsky (BZ) hydrogels. Our two-step synthesis technique allows independent optimization of the geometry, the chemical, and the mechanical properties of BZ gels. We identify the role of the surrounding medium chemistry and gel radius for the occurrence of BZ gel oscillations, quantified by the Damköhler number, which is the ratio of chemical reaction to diffusion rates. Tuning the BZ gel size to maximize its chemomechanical oscillation amplitude, we find that its oscillatory strain amplitude is limited by the time scale of gel swelling relative to the chemical oscillation period. Our experimental findings are in good agreement with a Vanag-Epstein model of BZ chemistry and a Tanaka Fillmore theory of gel swelling dynamics.

High-Quality Surface Plasmon Polaritons in Large-Area Sodium Nanostructures.

Sodium (Na) is predicted to be an ideal plasmonic material with ultralow optical loss across visible to near-infrared (NIR). However, there has been limited research on Na plasmonics. Here we develop a scalable fabrication method for Na nanostructures by combining phase-shift photolithography and a thermo-assisted spin-coating process. Using this method, we fabricated Na nanopit arrays with varying periodicities (300-600 nm) and with tunable surface plasmon polariton (SPP) modes spanning visible to NIR. We achieved SPP resonances as narrow as 9.3 nm. In addition, Na nanostructures showed line width narrowing from visible toward NIR, showing their prospect operating in the NIR. To address the challenges associated with the high reactivity of Na, we designed a simple encapsulation strategy and stabilized the Na nanostructures in ambient conditions for more than two months. As a low-cost and low-loss plasmonic material, Na offers a competitive option for nanophotonic devices and plasmon-enhanced applications.

Low-Loss Plasmonics with Nanostructured Potassium and Sodium-Potassium Liquid Alloys.

Alkali metals have low optical losses in the visible to near-infrared (NIR) compared with noble metals. However, their high reactivity prohibits the exploration of their optical properties. Recently sodium (Na) has been experimentally demonstrated as a low-loss plasmonic material. Here we report on a thermo-assisted nanoscale embossing (TANE) technique for fabricating plasmonic nanostructures from pure potassium (K) and NaK liquid alloys. We show high-quality-factor resonances from K as narrow as 15 nm in the NIR, which we attribute to the high material quality and low optical loss. We further demonstrate liquid Na-K plasmonics by exploiting the Na-K eutectic phase diagram. Our study expands the material library for alkali metal plasmonics and liquid plasmonics, potentially enabling a range of new material platforms for active metamaterials and photonic devices.

CNCDatabase: a database of non-coding cancer drivers.

Most mutations in cancer genomes occur in the non-coding regions with unknown impact on tumor development. Although the increase in the number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies making it difficult to understand their roles in tumorigenesis of different cancer types. We have developed CNCDatabase, Cornell Non-coding Cancer driver Database (https://cncdatabase.med.cornell.edu/) that contains detailed information about predicted non-coding drivers at gene promoters, 5' and 3' UTRs (untranslated regions), enhancers, CTCF insulators and non-coding RNAs. CNCDatabase documents 1111 protein-coding genes and 90 non-coding RNAs with reported drivers in their non-coding regions from 32 cancer types by computational predictions of positive selection using whole-genome sequences; differential gene expression in samples with and without mutations; or another set of experimental validations including luciferase reporter assays and genome editing. The database can be easily modified and scaled as lists of non-coding drivers are revised in the community with larger whole-genome sequencing studies, CRISPR screens and further experimental validations. Overall, CNCDatabase provides a helpful resource for researchers to explore the pathological role of non-coding alterations in human cancers.

Clinical Frailty Scale is a better predictor for adverse post-operative complications and functional outcomes than Modified Frailty Index and Charlson Comorbidity Index after total knee arthroplasty.

PURPOSE: Studies have demonstrated correlations between frailty and comorbidity scores with adverse outcomes in total knee replacement (TKR). However, there is a lack of consensus on the most suitable pre-operative assessment tool. This study aims to compare Clinical Frailty Scale (CFS), Modified Frailty Index (MFI), and Charlson Comorbidity Index (CCI) in predicting adverse post-operative complications and functional outcomes following a unilateral TKR. METHODS: In total, 811 unilateral TKR patients from a tertiary hospital were identified. Pre-operative variables were age, gender, body mass index (BMI), American Society of Anesthesiologists (ASA) class, CFS, MFI, and CCI. Binary logistic regression analysis was performed to ascertain odd ratios of pre-operative variables on adverse post-operative complications (length of stay < LOS >, complications, ICU/HD admission, discharge location, 30-day readmission, 2-year reoperation). Multiple linear regression analyses were used to estimate the standardized effects of pre-operative variables on the Knee Society Functional Score (KSFS), Knee Society Knee Score (KSKS), Oxford Knee Score (OKS), and 36-Item Short Form Survey (SF-36). RESULTS: CFS is a strong predictor for LOS (OR 1.876, p < 0.001), complications (OR 1.83-4.97, p < 0.05), discharge location (OR 1.84, p < 0.001), and 2-year reoperation rate (OR 1.98, p < .001). ASA and MFI were predictors for ICU/HD admission (OR:4.04, p = 0.002; OR 1.58, p = 0.022, respectively). None of the scores was predictive for 30-day readmission. A higher CFS was associated with a worse outcome for 6-month KSS, 2-year KSS, 6-month OKS, 2-year OKS, and 6-month SF-36. CONCLUSION: CFS is a superior predictor for post-operative complications and functional outcomes than MFI and CCI in unilateral TKR patients. This suggests the importance of assessing pre-operative functional status when planning for TKR. LEVEL OF EVIDENCE: Diagnostic, II.

Interactome Mapping Uncovers a General Role for Numb in Protein Kinase Regulation.

Cellular functions are frequently regulated by protein-protein interactions involving the binding of a modular domain in one protein to a specific peptide sequence in another. This mechanism may be explored to identify binding partners for proteins harboring a peptide-recognition domain. Here we report a proteomic strategy combining peptide and protein microarray screening with biochemical and cellular assays to identify modular domain-mediated protein-protein interactions in a systematic manner. We applied this strategy to Numb, a multi-functional protein containing a phosphotyrosine-binding (PTB) domain. Through the screening of a protein microarray, we identified >100 protein kinases, including both Tyr and Ser/Thr kinases, that could potentially interact with the Numb PTB domain, suggesting a general role for Numb in regulating kinase function. The putative interactions between Numb and several tyrosine kinases were subsequently validated by GST pull-down and/or co-immunoprecipitation assays. Furthermore, using the Oriented Peptide Array Library approach, we defined the specificity of the Numb PTB domain which, in turn, allowed us to predict binding partners for Numb at the genome level. The combination of the protein microarray screening with computer-aided prediction produced the most expansive interactome for Numb to date, implicating Numb in regulating phosphorylation signaling through protein kinases and phosphatases. Not only does the data generated from this study provide an important resource for hypothesis-driven research to further define the function of Numb, the proteomic strategy described herein may be employed to uncover the interactome for other peptide-recognition domains whose consensus motifs are known or can be determined.

Pathogenesis and treatment of autoimmune rheumatic diseases.

PURPOSE OF REVIEW: Autoimmune diseases are of unknown origin, and they represent significant causes of morbidity and mortality. Here, we review new developments in the understanding of their pathogenesis that have led to development of well tolerated and effective treatments. RECENT FINDINGS: In addition to the long-recognized genetic impact of the HLA locus, interferon regulatory factors, PTPN22, STAT4, and NOX have been implicated in pathogenesis of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Smoking, ultraviolet light, diet, and microbiota exert strong environmental influence on development of RA and SLE. Metabolism has been recognized as a critical integrator of genetic and environmental factors, and it controls immune cell differentiation both under physiological and pathological conditions. SUMMARY: With the advent of high-throughput genetic, proteomic, and metabolomic technologies, the field of medicine has been shifting towards systems-based and personalized approaches to diagnose and treat common conditions, including rheumatic diseases. Regulatory checkpoints of metabolism and signal transduction, such as glucose utilization, mitochondrial electron transport, JAK, mTOR, and AMPK pathway activation, and production of pro-inflammatory cytokines IL-1, IL-6, and IL-17 have presented new targets for therapeutic intervention. This review amalgamates recent discoveries in genetics and metabolomics with immunological pathways of pathogenesis in rheumatic diseases.

Assessment of NETest Clinical Utility in a U.S. Registry-Based Study.

BACKGROUND: The clinical relevance of molecular biomarkers in oncology management has been recognized in breast and lung cancers. We evaluated a blood-based multigene assay for management of neuroendocrine tumors (NETs) in a real-world study (U.S. registry NCT02270567). Diagnostic accuracy and relationship to clinical disease status in two cohorts (treated and watch-and-wait) were evaluated. MATERIALS AND METHODS: Patients with NETs (n = 100) were followed for 6-12 months. Patients' primary tumors were gastroenteropancreatic (68%), lung 20%, and of unknown origin (12%). Characteristics included well-differentiated, low-grade tumors (97%), stage IV disease (96%); treatment with surgery (70%); and drug treatment (56%). NETest was measured at each visit and disease status determined by RECIST. Scores categorized as low (NETest 14%-40%) or high (≥80%) defined disease as stable or progressive. Multivariate analyses determined the strength of the association with progression-free survival (PFS). RESULTS: NETest diagnostic accuracy was 96% and concordant (95%) with image-demonstrable disease. Scores were reproducible (97%) and concordant with clinical status (98%). The NETest was the only feature linked to PFS (odds ratio, 6.1; p < .0001). High NETest correlated with progressive disease (81%; median PFS, 6 months), and low NETest correlated with stable disease (87%; median PFS, not reached). In the watch-and-wait cohort, low NETest was concordant with stable disease in 100% of patients, and high NETest was associated with management changes in 83% of patients. In the treated cohort, all low NETest patients (100%) remained stable. A high NETest was linked to intervention and treatment stabilization (100%). Use of NETest was associated with reduced imaging (biannual to annual) in 36%-38% of patients. CONCLUSION: Blood NETest is an accurate diagnostic and can be of use in monitoring disease status and facilitating management change in both watch-and-wait and treatment cohorts. IMPLICATIONS FOR PRACTICE: A circulating multigene molecular biomarker to guide neuroendocrine tumor (NET) management has been developed because current biomarkers have limited clinical utility. NETest is diagnostic (96%) and in real time defines the disease status (>95%) as stable or progressive. It is >90% effective in guiding treatment decisions in conjunction with diagnostic imaging. Monitoring was effective in watch-and-wait or treatment groups. Low levels supported no management change and reduced the need for imaging. High levels indicated the need for management intervention. Real-time liquid biopsy assessment of NETs has clinical utility and can contribute additional value to patient management strategies and outcomes.

Fungal dysbiosis in cirrhosis.

OBJECTIVE: Cirrhotics have a high rate of infections, which are increasingly fungal or culture-negative in nature. While infected cirrhotics have bacterial dysbiosis, the role of fungi is unclear. We aimed to evaluate gut bacterial and fungal dysbiosis in cross-sectional and longitudinal analyses of outpatient and inpatient cirrhotics and prediction of hospitalisations. METHODS: Cross-sectional: Age-matched controls, outpatients (with/without antibiotics) and hospitalised uninfected, culture-negative and culture-positive cirrhotics were included and followed for 90 days. Longitudinal: Three studies were conducted: (1) cirrhotics followed over 6 months, (2) outpatient cirrhotics administered antibiotics per standard of care for 5 days and (3) cirrhotics and controls administered omeprazole over 14 days. In all studies, stool bacterial/fungal profiles were analysed. RESULTS: Cross-sectional: In 143 cirrhotics and 26 controls, bacterial and fungal diversities were significantly linked. Outpatients on antibiotics and patients with culture-positive infections had the lowest diversities. Bacterial and fungal correlations were complex in uninfected, outpatient and control groups but were markedly skewed in infected patients. 21% were admitted on 90-day follow-up. A lower Bacteroidetes/Ascomycota ratio was associated with lower hospitalisations. Longitudinal: Fungal and bacterial profiles were stable on follow-up (5 days and 6 months). After antibiotics, a significantly reduced bacterial and fungal diversity, higher Candida and lower autochthonous bacterial relative abundance were seen. After omeprazole, changes in bacterial diversity and composition were seen but fungal metrics remained stable. CONCLUSION: There is a significant fungal dysbiosis in cirrhosis, which changes differentially with antibiotics and proton pump inhibitor use, but is otherwise stable over time. A combined bacterial-fungal dysbiosis metric, Bacteroidetes/Ascomycota ratio, can independently predict 90-day hospitalisations in patients with cirrhosis. CLINICAL TRIAL NUMBER: NCT01458990.

Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: A randomized clinical trial.

Recurrent hepatic encephalopathy (HE) is a leading cause of readmission despite standard of care (SOC) associated with microbial dysbiosis. Fecal microbiota transplantation (FMT) may improve dysbiosis; however, it has not been studied in HE. We aimed to define whether FMT using a rationally derived stool donor is safe in recurrent HE compared to SOC alone. An open-label, randomized clinical trial with a 5-month follow-up in outpatient men with cirrhosis with recurrent HE on SOC was conducted with 1:1 randomization. FMT-randomized patients received 5 days of broad-spectrum antibiotic pretreatment, then a single FMT enema from the same donor with the optimal microbiota deficient in HE. Follow-up occurred on days 5, 6, 12, 35, and 150 postrandomization. The primary outcome was safety of FMT compared to SOC using FMT-related serious adverse events (SAEs). Secondary outcomes were adverse events, cognition, microbiota, and metabolomic changes. Participants in both arms were similar on all baseline criteria and were followed until study end. FMT with antibiotic pretreatment was well tolerated. Eight (80%) SOC participants had a total of 11 SAEs compared to 2 (20%) FMT participants with SAEs (both FMT unrelated; P = 0.02). Five SOC and no FMT participants developed further HE (P = 0.03). Cognition improved in the FMT, but not the SOC, group. Model for End-Stage Liver Disease (MELD) score transiently worsened postantibiotics, but reverted to baseline post-FMT. Postantibiotics, beneficial taxa, and microbial diversity reduction occurred with Proteobacteria expansion. However, FMT increased diversity and beneficial taxa. SOC microbiota and MELD score remained similar throughout. CONCLUSION: FMT from a rationally selected donor reduced hospitalizations, improved cognition, and dysbiosis in cirrhosis with recurrent HE. (Hepatology 2017;66:1727-1738).

Frequent BRAF mutations suggest a novel oncogenic driver in colonic neuroendocrine carcinoma.

BACKGROUND AND OBJECTIVES: The World Health Organization (WHO) 2010 has classified GI neuroendocrine neoplasms into neuroendocrine tumor (NET) and high-grade neuroendocrine carcinoma (NEC). The genetic underpinnings of NEC are poorly understood. The aim of the study was to perform genomic profiling of NEC to better characterize this aggressive disease. METHODS: We identified nine patients with colonic NEC between January 1, 2005 and June 30, 2013. Whole exome sequencing (WES) was performed on tumor DNA from two patients with ≥80% tumor cellularity and matched normal tissue available. Focused BRAF mutational analysis was performed on an additional seven patients via sanger sequencing of BRAF exons 11 and 15. RESULTS: We identified BRAF exon 15 mutations (c.A1781G: p.D594G and c.T1799A: p.V600E) by WES in two patients. Upon additional screening of seven colonic NECs for BRAF exon 11 and 15 mutations, we identified BRAF V600E mutations in two of seven specimens (29%). Overall, BRAF exon 15 mutations were present in four of nine colonic NECs. CONCLUSION: Colonic NEC is a rare but aggressive tumor with high frequency (44%) of BRAF mutations. Further investigation is warranted to ascertain the incidence of BRAF mutations in a larger population as BRAF inhibition may be a potential avenue of targeted treatment for these patients.

Effects of CPAP therapy on visceral fat thickness, carotid intima-media thickness and adipokines in patients with obstructive sleep apnoea.

BACKGROUND AND OBJECTIVE: Obstructive sleep apnoea (OSA) is associated with an increased prevalence of metabolic syndrome. This study explores the effects of continuous positive airway pressure (CPAP) for patients with OSA on visceral and mesenteric fat thickness, carotid intima-media thickness (IMT) and adipokines. METHODS: A randomized controlled study was conducted at a teaching hospital on 90 patients newly diagnosed with OSA to receive either therapeutic CPAP or subtherapeutic CPAP for 3 months. Visceral fat thickness and carotid IMT were measured with B-mode ultrasound; adipokine levels were assessed at baseline and 3 months. RESULTS: Altogether, 45 patients received therapeutic CPAP and 45 received subtherapeutic CPAP without significant differences in age 50.3 (10.1) versus 48.7 (9.0) years, BMI 28.2 (3.9) versus 28.2 (4.5) kg/m2 , Epworth Sleepiness Scale (ESS) 12.4 (5.9) versus 11.3 (4.7), apnoea-hypopnoea index (AHI) 30.6 (21.4) versus 35.2 (25.5) /h, minimum SaO2 79.6 (10.8) versus 76.7 (12.4) % and existing co-morbidities. CPAP usage was therapeutic 4.2 (2.1) versus subtherapeutic 4.1 (2.0) h/night over 3 months. Adiponectin and irisin levels changed significantly following therapeutic CPAP for 3 months versus subtherapeutic CPAP (-1.6 vs 7.3, P = 0.042; 0.1 vs -0.1, P = 0.028 respectively) while only serum level of monocyte chemotactic protein 1 (MCP-1) at baseline was positively correlated with AHI (r = 0.278). No significant changes were observed in other adipokines, visceral fat thickness and IMT. CONCLUSION: Short-term therapeutic CPAP versus subtherapeutic CPAP does not significantly reduce visceral fat thickness and IMT, although it reduces adiponectin and increases irisin.

Improved Protein Conjugation with Uniform, Macroporous Poly(acrylamide-co-acrylic acid) Hydrogel Microspheres via EDC/NHS Chemistry.

We demonstrate a robust and tunable micromolding method to fabricate chemically functional poly(acrylamide-co-acrylic acid) (p(AAm-co-AA)) hydrogel microspheres with uniform dimensions and controlled porous network structures for rapid biomacromolecular conjugation. Specifically, p(AAm-co-AA) microspheres with abundant carboxylate functional groups are fabricated via surface-tension-induced droplet formation in patterned poly(dimethylsiloxane) molds and photoinduced radical polymerization. To demonstrate the chemical functionality, we enlisted rapid EDC/NHS (1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC) and N-hydroxysuccinimide (NHS)) chemistry for fluorescent labeling of the microspheres with small-molecule dye fluorescein glycine amide. Epifluorescence imaging results illustrate the uniform incorporation of carboxylate groups within the microspheres and rapid conjugation kinetics. Furthermore, protein conjugation results using red fluorescent protein R-phycoerythrin demonstrate the highly porous nature of the microspheres as well as the utility of the microspheres and the EDC/NHS scheme for facile biomacromolecular conjugation. Combined, these results illustrate the significant potential for our fabrication-conjugation strategy in the development of biofunctionalized polymeric hydrogel microparticles toward rapid biosensing, bioprocess monitoring, and biodiagnostics.