Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

This corrects the article DOI: 10.1038/nature22364.

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.

BAP1 and YY1 regulate expression of death receptors in malignant pleural mesothelioma.

Malignant pleural mesothelioma (MPM) is a rare, aggressive, and incurable cancer arising from the mesothelial lining of the pleura, with few available treatment options. We recently reported that loss of function of the nuclear deubiquitinase BRCA1-associated protein 1 (BAP1), a frequent event in MPM, is associated with sensitivity to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-mediated apoptosis. As a potential underlying mechanism, here we report that BAP1 negatively regulates the expression of TRAIL receptors: death receptor 4 (DR4) and death receptor 5 (DR5). Using tissue microarrays of tumor samples from MPM patients, we found a strong inverse correlation between BAP1 and TRAIL receptor expression. BAP1 knockdown increased DR4 and DR5 expression, whereas overexpression of BAP1 had the opposite effect. Reporter assays confirmed wt-BAP1, but not catalytically inactive BAP1 mutant, reduced promoter activities of DR4 and DR5, suggesting deubiquitinase activity is required for the regulation of gene expression. Co-immunoprecipitation studies demonstrated direct binding of BAP1 to the transcription factor Ying Yang 1 (YY1), and chromatin immunoprecipitation assays revealed BAP1 and YY1 to be enriched in the promoter regions of DR4 and DR5. Knockdown of YY1 also increased DR4 and DR5 expression and sensitivity to TRAIL. These results suggest that BAP1 and YY1 cooperatively repress transcription of TRAIL receptors. Our finding that BAP1 directly regulates the extrinsic apoptotic pathway will provide new insights into the role of BAP1 in the development of MPM and other cancers with frequent BAP1 mutations.

Tracking the Evolution of Non-Small-Cell Lung Cancer.

BACKGROUND: Among patients with non-small-cell lung cancer (NSCLC), data on intratumor heterogeneity and cancer genome evolution have been limited to small retrospective cohorts. We wanted to prospectively investigate intratumor heterogeneity in relation to clinical outcome and to determine the clonal nature of driver events and evolutionary processes in early-stage NSCLC. METHODS: In this prospective cohort study, we performed multiregion whole-exome sequencing on 100 early-stage NSCLC tumors that had been resected before systemic therapy. We sequenced and analyzed 327 tumor regions to define evolutionary histories, obtain a census of clonal and subclonal events, and assess the relationship between intratumor heterogeneity and recurrence-free survival. RESULTS: We observed widespread intratumor heterogeneity for both somatic copy-number alterations and mutations. Driver mutations in EGFR, MET, BRAF, and TP53 were almost always clonal. However, heterogeneous driver alterations that occurred later in evolution were found in more than 75% of the tumors and were common in PIK3CA and NF1 and in genes that are involved in chromatin modification and DNA damage response and repair. Genome doubling and ongoing dynamic chromosomal instability were associated with intratumor heterogeneity and resulted in parallel evolution of driver somatic copy-number alterations, including amplifications in CDK4, FOXA1, and BCL11A. Elevated copy-number heterogeneity was associated with an increased risk of recurrence or death (hazard ratio, 4.9; P=4.4×10-4), which remained significant in multivariate analysis. CONCLUSIONS: Intratumor heterogeneity mediated through chromosome instability was associated with an increased risk of recurrence or death, a finding that supports the potential value of chromosome instability as a prognostic predictor. (Funded by Cancer Research UK and others; TRACERx ClinicalTrials.gov number, NCT01888601 .).

Identification of antibiotic resistance patterns in Helicobacter pylori strains isolated from gastric biopsies using real-time PCR and genotypic analysis.

BACKGROUND: Helicobacter pylori (H. pylori) is associated with dyspepsia, mucus-associated lymphoid tissue lymphoma, gastritis, and peptic ulcer disease. Treatment in Malta consists of triple therapy, which consists of a proton pump inhibitor and 2 of the antibiotics amoxicillin, clarithromycin, metronidazole and fluoroquinolones. We aimed to determine the resistance rates for clarithromycin and fluoroquinolones in patients with H. pylori, and its incidence, in patients undergoing an esophagogastroduodenoscopy (EGD) using real-time polymerase chain reaction (RT-PCR). METHODS: Patients undergoing an EGD were recruited. A rapid urease test (RUT) was performed, and 4 gastric biopsies were also taken (2 from antrum, 2 from corpus) and analyzed using RT-PCR. Positive samples were tested for antibiotic resistance using amplification and reverse hybridization techniques. RESULTS: Two hundred patients (mean age 53.6 [range 20-92] years; 53.1% female) were recruited; the majority were (78%) non-smokers. H. pylori was identified in 21.0% of the patients. Fluoroquinolone resistance was detected in 21.4% of the patients. Clarithromycin resistance was observed in 26.2%, with dual resistance identified in 4.8% of the patients. A high concordance was present with patients testing negative for H. pylori with both RUT and RT-PCR (94.3%). Only 57.6% of patients tested positive with both tests. However, 92.9% of RT-PCR positive patients had a positive genotype HelicoDR test. CONCLUSIONS: This data demonstrates a high rate of H. pylori resistance to both clarithromycin and fluoroquinolones. These should be avoided when treating H. pylori by utilizing different treatment regimes. Furthermore, we derived important data on the role of RT-PCR, which may be implemented in routine clinical practice.

Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma.

ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.

Retrospective response analysis of BAP1 expression to predict the clinical activity of systemic cytotoxic chemotherapy in mesothelioma.

Introduction BRCA1 associated protein-1 (BAP1) is a key tumor driver in mesothelioma and a potential biomarker predicting response to several targeted therapies in clinical testing. Whether it also modulates response to cytotoxic chemotherapy is undetermined. This study used retrospective response analysis of BAP1 expression in archival tumor biopsies taken from patients in the MS01 trial (NCT00075699). We aimed to determine if BAP1 expression correlated with overall survival within the three treatment arms in this trial, namely active symptom control (ASC); ASC plus mitomycin, vinblastine and cisplatin (MVP); and ASC plus vinorelbine. Materials and methods We used immunohistochemical analysis of tumor samples from the MS01 trial to identify subgroups with and without nuclear BAP1 expression. We performed correlative analysis of clinical characteristics (age at diagnosis, sex and histological subtype) and overall survival within treatment arms with nuclear BAP1 expression. Results 89 tumor samples from the 409 patients originally in the trial were available for analysis. Of these, 60 samples harbored a positive internal control, in the form of positive staining of inflammatory cells for BAP1, and were carried forward for analysis. Correlative analysis suggested no significant association between loss of nuclear BAP1 expression and age at diagnosis, sex and histological subtype. Kaplan Meier survival analysis revealed a small, though non-significant, overall survival disadvantage associated with BAP1 expression in tumors from patients treated with vinorelbine. Discussion This exploratory analysis suggests BAP1 expression may modify response to vinorelbine in MPM, possibly due to prevention of mitotic microtubule formation. We suggest ongoing and planned clinical studies of vinorelbine in MPM assess BAP1 expression as a predictive biomarker of response.

Preinvasive disease of the airway.

Squamous cell carcinoma of the lung arises from preinvasive progenitors in the central airways. The archetypal model appears to be a stepwise morphological progression until there is invasion of the basement membrane. However, not every lesion appears to follow this course and many individuals can have stable disease, or indeed regress to normal epithelium. From our increased understanding of the molecular pathology it is becoming apparent that the respiratory epithelium accumulates progressive genetic and epigenetic insults in response to carcinogens. Still, little is known about how to predict those 'at risk' of progression, and it is likely that in the future molecular signatures will underpin prediction models of developing invasive lung cancer. Currently, autofluorescence bronchoscopy gives us the ability to follow the natural history of these lesions, with the prospect that detecting and treating lesions early may improve survival. However, treatment remains controversial, and radical therapies are offered to individuals with carcinoma in situ who may never develop invasive cancer. This has paved the way for the use of minimally invasive bronchoscopic treatments, which, while apparently effective, have not been tested in randomised controlled trials. In this paper we describe the known biology and natural history of preinvasive lesions and review the current treatment strategies.

An unusual late onset of pulmonary alveolar microlithiasis: A case report and literature review.

Pulmonary alveolar microlithiasis (PAM) is an uncommon genetic disorder associated with alveolar cell injury. This injury is caused in most cases by inactivating mutations in SLC34A2 gene, which is responsible for the production of a sodium-dependent phosphate co-transporter. The dysfunction or deficiency of this transporter leads to the aggregation of local phosphate intra-alveolarly and formation of microliths. Most of the patients are asymptomatic at the time of the diagnosis but as the disease progress it leads to fatal respiratory or cardiac failure. We describe a case of a 63-year-old man referred to our department for a surgical lung biopsy. He has been symptomatic for one year with progressive shortness of breath and deteriorating exercise tolerance. The imaging was suggestive of extensive interstitial bilateral lung disease. Histological findings after the lung biopsy by video-assisted thoracic surgery (VATS) established the diagnosis of pulmonary alveolar microlithiasis. His sister suffered from the same disease and passed away at the age of 54. It is remarkably rare for PAM to have such a late onset with a previous normal X-ray and only a few cases have been reported worldwide.

Mediastinal hemangioendothelioma: Case report and review of the literature.

BACKGROUND: Epithelioid haemangioendothelioma (EHE) is a rare low-grade vascular neoplasm that can arise in the lung, liver, soft tissues or, less commonly, bone. Due to its low prevalence of less than one in a million and its non-specific clinical features, EHE is often misdiagnosed and managed inappropriately. Here we discuss the case of a 58 year-old gentleman with mediastinal EHE and review existing literature on pulmonary EHE (PEH). CASE HISTORY: A 58 year-old gentleman presented to our outpatient Clinic with chest discomfort and palpitations. A whole-body FDG-CT-PET showed an FDG-avid single 6.3cm nodule in the superior anterior mediastinum which was fully excised by robotic approach. Histology showed a nodular structure with clusters of epithelioid and spindled cells with a low proliferative index and mitotic count, suspended in a sclerotic stroma. Immunohistochemistry staining was positive for CD3 and CD34, confirming endothelial lineage, and SMA, identifying smooth muscle clusters. DISCUSSION: PEH typically presents in young Caucasian women, either incidentally as multiple small pulmonary nodules on CT or with respiratory symptoms that include cough, dyspnoea, chest pain and occasionally pleural effusions. Aetiology and prognosis remain unclear, although indicators of poor prognosis include the presence of respiratory symptoms, male gender, older age and multi-organ disease. Diagnosis is difficult and PEH is often misidentified as chronic granulomatous disease, amyloidosis or other malignancy of the lung. Histological features suggestive of PEH include nodules of hypocellular sclerotic stroma containing spindle-shaped tumour cells with abundant eosinophilic cytoplasm, vacuoles containing erythrocytes and low mitotic counts. CD31, CD34 and Fli-1 positive immunohistochemistry is strongly indicative of epithelioid lineage. There is no standard treatment for PEH but curative resection is the preferred treatment option where possible, with chemotherapy being used as adjuvant treatment or in widespread inoperable disease. CONCLUSION: This case report outlines the clinicopathological features that are characteristic of EHE with the hope of facilitating correct and early diagnosis in the future.

Sclerosing hemangioma of the lung showing strong FDG avidity on PET scan: Case report and review of the current literature.

Sclerosing Hemangioma is a rare lung tumor with polymorphic histologic features that usually occurs in middle aged women. Based on many immunohistochemical and ultrastructural studies, it is most probably derived from undifferentiated respiratory epithelial cells. Symptoms are usually due to enlargement of the tumor and compression of the surrounding tissues. Occurrence of multiple lesions or metastasis is extremely rare although some authors consider sclerosing hemangioma as a potentially low grade malignancy tumor. It usually presents with low to moderate uptake on FDG PET imaging. We present a case of sclerosing hemangioma with strong FDG avidity on PET scan in a 41 year old lady with history of haemoptysis. A full review of the literature on this topic was performed.

Key Features in the Management of Pulmonary Carcinosarcoma.

Pulmonary carcinosarcoma represents a category of extremely rare tumours accounting for 0.1% of all lung malignancies. It is defined as a poorly differentiated non-small-cell carcinoma that contains a component of sarcoma or sarcoma-like elements. These biphasic tumours typically have a poor prognosis due to late diagnosis and early metastases. Preoperative tissue diagnosis is usually difficult due to the heterogeneity of the tumour, with biopsies often just reflecting one element of the tumour. By means of a case illustration and review of the literature, we discuss the optimal management of patients with pulmonary carcinosarcoma.

IgG4 related lung disease extending to the thoracic vertebrae.

IgG4-related disease (IgG4-RD) is a fibroinflammatory condition that can affect practically every organ. Although it was first identified in pancreas and salivary glands, major organs like liver, biliary tree, kidney, thyroid glands and lungs are commonly involved, sometimes resulting in organ failure. We describe a case of an 41-year-old man presented with back pain after a rotator cuff injury. A Computed Tomography (CT) revealed incidentally a right lower lobe paravertebral lesion extending across the T5 and T6 vertebral levels and invading into the adjacent pleural surface. The laboratory findings and the CT guided biopsy were inconclusive. Morphological and immunohistochemical findings after a lung biopsy by video-assisted thoracic surgery (VATS) were suggestive to IgG4-related lung disease (IgG4-RLD), which was confirmed with high serum levels of IgG4. This represents the first case of a IgG4-RLD lesion located in the mediastinum and extending to the adjacent pleural surface and vertebrae and should be included in the differential diagnosis of posterior mediastinal masses.

The Potential Malignancy of a Solitary Fibrous Tumour of the Lung.

Solitary fibrous tumours (SFTs) are rare neoplasms that in the majority of cases are benign. We present the case of a 52-year-old male, with a 23-year history of a slow growing pleural mass, presenting to our department with worsening dyspnoea and localised chest discomfort. The purpose of this case report is to highlight the potential malignancy of a solitary fibrous tumour of the lung along with the key features in diagnosis and management.

Inflammatory myofibroblastic tumour of the lung: a reactive lesion or a true neoplasm?

Inflammatory myofibroblastic tumour (IMT) of the lung represents an extremely rare type of inflammatory pseudo tumor that appears most commonly in children and young individuals. There has been an ongoing controversy whether an IMT is a reactive lesion or a true neoplasm making the further management extremely challenging. Purpose of the paper is through a literature review to highlight the existence of this rare tumour along with its key features and the management options available.

The challenging management of lung choriocarcinoma.

The purpose of this paper is to highlight the existence and the management of lung choriocarcinoma (CCA), a rare category of lung tumors. We present a 42-year-old female that presented to our department with a PET positive lesion in the left upper lobe and a history of pregnancy 6 months prior to onset of symptoms. CT guided biopsy was inconclusive for diagnosis and the patient underwent a left thoracotomy and lingula sparing upper lobectomy. Histology revealed CCA of the lung and subsequently blood results confirmed the elevated b-HCG. CCA of the lung is a clinical entity that should be considered in the differential diagnosis of lung lesions in women after pregnancy.

Primary synovial sarcoma of the lung: can haemothorax be the first manifestation?

Primary pulmonary synovial sarcomas represent a rare clinical entity and account for approximately 0.5% of lung malignancies. We report the case of a 30-year-old male who presented clinically with haemothorax. Imaging revealed a complex collection obscuring a multi-lobulated mass in the right lower lobe of the lung. He underwent a right thoracotomy for evacuation of collection and surgical resection of his pulmonary mass. Histological analysis confirmed a grade 3 monophasic fibrous synovial sarcoma of the lung with infiltration to adjacent pleura, causing his initial haemothorax. Postoperative period was uneventful and patient was referred to the oncology team for further management. Primary pulmonary synovial sarcoma, though rare, should remain an important differential when considering lung malignancies, as complete surgical resection is the mainstay of treatment.