Faculty Bibliography

Success of immune checkpoint inhibitors in advanced non-small-cell lung cancer (NSCLC) has invigorated their use in the neoadjuvant setting for early-stage disease. However, the cellular and molecular mechanisms of the early immune responses to therapy remain poorly understood. Through an integrated analysis of early-stage NSCLC patients and a Kras mutant mouse model, we show a prevalent programmed cell death 1/programmed cell death 1 ligand 1 (PD-1/PD-L1) axis exemplified by increased intratumoral PD-1+ T cells and PD-L1 expression. Notably, tumor progression was associated with spatiotemporal modulation of the immune microenvironment with dominant immunosuppressive phenotypes at later phases of tumor growth. Importantly, PD-1 inhibition controlled tumor growth, improved overall survival, and reprogrammed tumor-associated lymphoid and myeloid cells. Depletion of T lymphocyte subsets demonstrated synergistic effects of those populations on PD-1 inhibition of tumor growth. Transcriptome analyses revealed T cell subset-specific alterations corresponding to degree of response to the treatment. These results provide insights into temporal evolution of the phenotypic effects of PD-1/PD-L1 activation and inhibition and motivate targeting of this axis early in lung cancer progression.

Visual inspection of histopathology slides is one of the main methods used by pathologists to assess the stage, type and subtype of lung tumors. Adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) are the most prevalent subtypes of lung cancer, and their distinction requires visual inspection by an experienced pathologist. In this study, we trained a deep convolutional neural network (inception v3) on whole-slide images obtained from The Cancer Genome Atlas to accurately and automatically classify them into LUAD, LUSC or normal lung tissue. The performance of our method is comparable to that of pathologists, with an average area under the curve (AUC) of 0.97. Our model was validated on independent datasets of frozen tissues, formalin-fixed paraffin-embedded tissues and biopsies. Furthermore, we trained the network to predict the ten most commonly mutated genes in LUAD. We found that six of them-STK11, EGFR, FAT1, SETBP1, KRAS and TP53-can be predicted from pathology images, with AUCs from 0.733 to 0.856 as measured on a held-out population. These findings suggest that deep-learning models can assist pathologists in the detection of cancer subtype or gene mutations. Our approach can be applied to any cancer type, and the code is available at https://github.com/ncoudray/DeepPATH .

BACKGROUND:Critical limb ischemia (CLI) is the most serious complication of peripheral artery disease (PAD). OBJECTIVES/OBJECTIVE:The purpose of this study was to characterize pathology of PAD in below- and above-knee amputation specimens in patients presenting with CLI. METHODS:Peripheral arteries from 95 patients (121 amputation specimens) were examined; 75 patients had presented with CLI, and the remaining 20 had amputations performed for other reasons. The pathological characteristics were separately recorded for femoral and popliteal arteries (FEM-POP), and infrapopliteal arteries (INFRA-POP). RESULTS:A total of 299 arteries were examined. In the 239 arteries from CLI patients, atherosclerotic plaques were more frequent in FEM-POP (23 of 34, 67.6%) compared with INFRA-POP (79 of 205, 38.5%) arteries. Of these 239 arteries, 165 (69%) showed ≥70% stenosis, which was due to significant pathological intimal thickening, fibroatheroma, fibrocalcific lesions, or restenosis in 45 of 165 (27.3%), or was due to luminal thrombi with (39 of 165, 23.6%) or without (81 of 165, 49.1%) significant atherosclerotic lesions. Presence of chronic luminal thrombi was more frequently observed in arteries with insignificant atherosclerosis (OR: 16.7; p = 0.0002), more so in INFRA-POP compared with FEM-POP (OR: 2.14; p = 0.0041) arteries. Acute thrombotic occlusion was less frequently encountered in INFRA-POP than FEM-POP arteries (OR: 0.27; p = 0.0067). Medial calcification was present in 170 of 239 (71.1%) large arteries. CONCLUSIONS:Thrombotic luminal occlusion associated with insignificant atherosclerosis is commonly observed in CLI and suggests the possibility of atherothromboembolic disease. The pathological characteristics of arteries in CLI suggest possible mechanisms of progression of PAD to CLI, especially in INFRA-POP arteries, and may support the preventive role of antithrombotic agents.

Visual inspection of histopathology slides is one of the main methods used by pathologists to assess the stage, type and subtype of lung tumors. Adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) are the most prevalent subtypes of lung cancer, and their distinction requires visual inspection by an experienced pathologist. In this study, we trained a deep convolutional neural network (inception v3) on whole-slide images obtained from The Cancer Genome Atlas to accurately and automatically classify them into LUAD, LUSC or normal lung tissue. The performance of our method is comparable to that of pathologists, with an average area under the curve (AUC) of 0.97. Our model was validated on independent datasets of frozen tissues, formalin-fixed paraffin-embedded tissues and biopsies. Furthermore, we trained the network to predict the ten most commonly mutated genes in LUAD. We found that six of them-STK11, EGFR, FAT1, SETBP1, KRAS and TP53-can be predicted from pathology images, with AUCs from 0.733 to 0.856 as measured on a held-out population. These findings suggest that deep-learning models can assist pathologists in the detection of cancer subtype or gene mutations. Our approach can be applied to any cancer type, and the code is available at https://github.com/ncoudray/DeepPATH .

Systemic lupus erythematosus (SLE) is a major cause of nonbacterial thrombotic endocarditis (NBTE) associated with intracardiac sterile vegetations. It is rare for vegetations to present as an atrial tumor. This report describes a 48-year-old female with SLE and antiphospholipid syndrome complicated by recurrent thrombosis on anticoagulation. A large left atrial mass lesion was detected on echocardiography during a work-up for leg burning. Infective endocarditis could not be confirmed, and hence left atrial mass lesion was the most likely diagnosis. The patient was managed surgically and the pathology report revealed fibrin networks in a pattern similar to that of thrombosis, characteristic of NBTE.

OBJECTIVES/OBJECTIVE:Pulmonary sarcomatoid carcinoma (PSC) is a rare malignant neoplasm that accounts for a small percentage of non-small-cell lung carcinoma (NSCLC). At least 10% of PSCs has a spindle and/or giant cell component, which is often associated with a poor prognosis. We reviewed the Surveillance, Epidemiology, and End Results (SEER) database for the clinicopathological characteristics and surgical outcomes of PSCs. METHODS:The SEER database (1973-2013) was queried for PSC. A comparison between PSC and other NSCLC patients was performed. Cox regression for overall survival (OS) and logistic regression for node-positive predictors were performed. A propensity-matched (1:2) analysis (including age, gender, grade and stage) among surgically treated cases was done to compare OS in PSC versus other NSCLCs. RESULTS:A total of 955 899 NSCLC patients were identified; of these, 4987 patients had been diagnosed with PSC (0.52%). Men represented 60.9% of cases, with a median age of 68 years. The median size of the tumour was 5 cm and 3.5 cm in PSCs and NSCLCs, respectively (P < 0.001). PSC patients had significantly less Stage I, more high-grade tumours, advanced T stage, N+ disease and M1 disease (P < 0.001). In the PSC cohort, the most significant predictor of N+ disease on multivariate analysis was advanced T stage (P < 0.001). Predictors of OS in Stages I/II PSC on multivariate analysis were advanced age [P < 0.001, hazard ratio (HR) = 1.03], male gender (P = 0.024, HR = 1.25), carcinosarcoma (P = 0.002, HR = 1.76), grade (P = 0.033, HR = 1.81), T stage (P = 0.003, HR = 1.75), N status (P = 0.001, HR = 1.90) and surgical resection (P < 0.001, HR = 0.58). Among matched surgically resected cohorts, a poorer prognosis for OS was evident in PSCs in early stages (I/II) than in other NSCLCs (P = 0.009). CONCLUSIONS:PSC patients present with more advanced stage and with worse survival outcomes than other NSCLC patients. While surgical resection conveys a survival advantage in PSC, this group represents a population at a high risk for relapse and should be evaluated for novel adjuvant therapies.