Establishment of a Multi-Analyte Serum Biomarker Panel to Identify Lymph Node Metastases in Non-small Cell Lung Cancer

IntroductionIn non-small cell lung cancer (NSCLC), the presence of locoregional lymph node metastases remains the most important prognostic factor and significantly guides treatment regimens. Unfortunately, currently-available noninvasive staging modalities have limited accuracy. The objective of this study was to create a multianalyte blood test capable of discriminating a patient's true (pathologic) nodal status preoperatively.MethodsPretreatment serum specimens collected from 107 NSCLC patients with localized disease were screened with 47 biomarkers implicated in disease presence or progression. Multivariate statistical algorithms were then used to identify the optimal combination of biomarkers for accurately discerning each patient's nodal status.ResultsWe identified 15 candidate biomarkers that met our criteria for statistical relevance in discerning a patient's preoperative nodal status. A ‘random forest’ classification algorithm was used with these parameters to define a 6-analyte panel, consisting of macrophage inflammatory protein-1α, carcinoembryonic antigen, stem cell factor, tumor necrosis factor-receptor I, interferon-γ, and tumor necrosis factor-α, that was the optimum combination of biomarkers for identifying a patient's pathologic nodal status. A Classification and Regression Tree analysis was then created with this panel that was capable of correctly classifying 88% of the patients tested, relative to the pathologic assessments. This value is in contrast to our observed 85% classification rate using conventional clinical methods.ConclusionsThis study establishes a serum biomarker panel with efficacy in discerning preoperative nodal status. With further validation, this blood test may be useful for assessing nodal status (including occult disease) in NSCLC patients facing tumor resection therapy

Soil methane sink capacity response to a long-term wildfire chronosequence in Northern Sweden

Boreal forests occupy nearly one fifth of the terrestrial land surface and are recognised as globally important regulators of carbon (C) cycling and greenhouse gas emissions. Carbon sequestration processes in these forests include assimilation of CO2 into biomass and subsequently into soil organic matter, and soil microbial oxidation of methane (CH4). In this study we explored how ecosystem retrogression, which drives vegetation change, regulates the important process of soil CH4 oxidation in boreal forests. We measured soil CH4 oxidation processes on a group of 30 forested islands in northern Sweden differing greatly in fire history, and collectively representing a retrogressive chronosequence, spanning 5000 years. Across these islands the build-up of soil organic matter was observed to increase with time since fire disturbance, with a significant correlation between greater humus depth and increased net soil CH4 oxidation rates. We suggest that this increase in net CH4 oxidation rates, in the absence of disturbance, results as deeper humus stores accumulate and provide niches for methanotrophs to thrive. By using this gradient we have discovered important regulatory controls on the stability of soil CH4 oxidation processes that could not have not been explored through shorter-term experiments. Our findings indicate that in the absence of human interventions such as fire suppression, and with increased wildfire frequency, the globally important boreal CH4 sink could be diminished

Bilobectomy for non–small cell lung cancer: A search for clinical factors that may affect perioperative morbidity and long-term survival

ObjectiveThe resection of two lobes for non–small cell lung cancer has the potential for significant morbidity and mortality as well as a negative impact on survival. The purpose of this study is to analyze our bilobectomy experience.MethodsAge, gender, diagnosis, bilobectomy type, bilobectomy indication, operative technique, pathologic condition, major complications, stage, and survival were reviewed from 1984 through 2007. Major complications were compared by Fisher's exact testing. Kaplan–Meier survival curves were compared by log–rank and likelihood ratio analysis.ResultsBilobectomies were performed on 92 patients with non–small cell lung cancer. A total of 35 upper–middle and 57 middle–lower bilobectomies were performed. Indications for bilobectomy were bronchial involvement (n = 49), extension across the fissure (n = 36), or other reasons (n = 7). The 5-year survival for all patients was 42%. Significant differences in survival were observed among the different stages (stage I, 65%; stage II, 42%; stage III, 13%; P < .0001). Squamous cell carcinomas had a higher 5-year survival than adenocarcinomas (54% vs 32%), a difference that approached significance by log–rank test (P < .079) and reached significance by likelihood ratios (P < .048). When bilobectomy was performed for extension across the fissure, survival approached significance for squamous cell carcinomas (71%) over adenocarcinomas (42%) by log–rank test (P < .089) and was significant by likelihood ratio (P < .048) when comparing survival between adenocarcinoma and squamous cell carcinoma. Multivariate analysis demonstrated that increasing age (P = .0102) and upper&middle bilobectomy (P = .0285) adversely affected 5-year survival, whereas early-stage disease (P = .0245) beneficially affected 5-year survival.ConclusionBilobectomy can be performed with acceptable morbidity and mortality. Survival relates to disease stage. Optimal survival benefit occurs when the indication for bilobectomy is squamous cell carcinoma extending across the fissure

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Intraoperative Sentinel Node Mapping with Technitium-99 in Lung Cancer: Results of CALGB 140203 Multicenter Phase II Trial

Introduction:Sentinel node mapping with radioactive technetium in non-small cell lung cancer has been shown to be feasible in several single institution reports. The Cancer and Leukemia Group B designed a phase II trial to test a standardized method of this technique in a multi-institutional setting. If validated, the technique could provide a more accurate and sensitive way to identify lymph node metastases.Methods:Patients with clinical stage I non-small cell lung cancer amenable to resection were candidates for this trial. Intraoperatively, tumors were injected with technetium sulfur colloid (0.25 mCi). The tumor and lymph nodes were measured in vivo with a hand held Geiger counter and resection of the tumor and nodes was carried out. Sentinel nodes, all other nodes and the tumor were analyzed with standard histologic assessment. Negative sentinel nodes were also evaluated with immunohistochemistry.Results:In this phase II trial, 8 surgeons participated (1-13 patients enrolled per surgeon), and 46 patients (out of a planned 150) were enrolled. Of these, 43 patients had cancer and an attempted complete resection, and 39 patients underwent sentinel node mapping. One or more sentinel nodes were identified in 24 of the 39 patients (61.5%). The sentinel node(s) were found to be accurate (no other nodes were positive for cancer if the sentinel node was negative) in 20/24 patients (83.3%). In the overall group the sentinel node mapping procedure was found to be accurate in 20/39 patients (51.2%).Conclusions:Intraoperative sentinel node mapping in lung cancer with radioisotope yielded lower accrual and worse accuracy than expected. The multi-institutional attempt at validating this technique was unsuccessful

Wedge resection versus lobectomy for stage I (T1 N0 M0) non-small-cell lung cancer

AbstractBackground: The role of nonanatomic wedge resection in the management of stage I (T1 N0 M0) non-small-cell lung cancer continues to be debated against the present gold standard of care—anatomic lobectomy.Methods: We analyzed the results of 219 consecutive patients with pathologic stage I (T1 N0 M0) non-small-cell lung cancer who underwent open wedge resection (n = 42), video-assisted wedge resection (n = 60), and lobectomy (n = 117) to assess morbidity, recurrence, and survival differences between these approaches.Results: There were no differences among the three groups with regard to histologic tumor type. Analysis demonstrated the wedge resection groups to be significantly older and to have reduced pulmonary function despite a higher incidence of treatment for chronic obstructive pulmonary disease when compared with patients having lobectomy. The mean hospital stay was significantly less in the wedge resection groups. There were no operative deaths among patients having wedge resection; however, a 3% operative mortality occurred among patients having lobectomy (p = 0.20). Kaplan-Meier survival curves were nearly identical at 1 year (open wedge resection, 94%; video-assisted wedge resection, 95%; lobectomy, 91%). At 5 years survival was 58% for patients having open wedge resection, 65% for those having video-assisted wedge resection, and 70% for those having lobectomy. Log rank testing demonstrated significant differences between the survival curves during the 5-year period of study (p = 0.02). This difference was a result of a significantly greater non-cancer-related death rate by 5 years among patients having wedge resection (38% vs 18% for those having lobectomy; p = 0.014).Conclusion: Wedge resection, done by open thoracotomy or video-assisted techniques, appears to be a viable “compromise” surgical treatment of stage I (T1 N0 M0) non-small-cell lung cancer for patients with cardiopulmonary physiologic impairment. Because of the increased risk for local recurrence, anatomic lobectomy remains the surgical treatment of choice for patients with stage I non-small-cell lung cancer who have adequate physiologic reserve. (J Thorac Cardiovasc Surg 1997;113:691-700