Corinna Ludwig

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.

Frequent and Focal FGFR1 Amplification Associates with Therapeutically Tractable FGFR1 Dependency in Squamous Cell Lung Cancer

FGFR1 amplification provides a therapeutic target for squamous cell lung cancer, which is resistant to other targeted lung cancer drugs. A Smoking Gun for Lung Cancer Detectives and scientists alike need strong evidence to take their cases to the judge, who for scientists is often a patient with a deadly disease. Yet, new culprits are sometimes found that can break a case wide open. Lung cancer, which accounts for more than 10% of the global cancer burden, has a poor prognosis and inadequately responds to chemotherapy and radiotherapy. New targeted treatments for lung adenocarcinomas inhibit the oncogenic versions of signaling protein kinases that arise from mutations typically found in lung cancer patients who have never smoked. However, smokers frequently suffer from a different deviant, squamous cell lung cancers, for which there are no known molecular genetic targets for therapy. Now, Weiss et al. have fingered a new suspect in smoking-related lung cancer: amplification of the FGFR1 gene, which encodes the fibroblast growth factor receptor 1 tyrosine kinase (FGFR1). To identify therapeutically viable genetic alterations that may influence squamous cell lung cancer, Weiss et al. performed genomic profiles on a large set of lung cancer specimens. Squamous cell lung cancer samples showed FGFR1 amplification, which was not found in other lung cancer subtypes. The authors then determined that a molecule that broadly inhibits FGF receptor function could block tumor growth and cause cell death in the cancers that expressed high amounts of the FGFR1 gene product in a manner that was dependent on FGFR1 expression. Moreover, FGFR1 inhibition resulted in a considerable decrease in tumor size in a mouse model of FGFR1-amplified lung cancer. This culmination of evidence implies that inhibition of this receptor tyrosine kinase should be explored as a candidate therapy for corralling squamous cell lung cancer in smokers. Lung cancer remains one of the leading causes of cancer-related death in developed countries. Although lung adenocarcinomas with EGFR mutations or EML4-ALK fusions respond to treatment by epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) inhibition, respectively, squamous cell lung cancer currently lacks therapeutically exploitable genetic alterations. We conducted a systematic search in a set of 232 lung cancer specimens for genetic alterations that were therapeutically amenable and then performed high-resolution gene copy number analyses. We identified frequent and focal fibroblast growth factor receptor 1 (FGFR1) amplification in squamous cell lung cancer (n = 155), but not in other lung cancer subtypes, and, by fluorescence in situ hybridization, confirmed the presence of FGFR1 amplifications in an independent cohort of squamous cell lung cancer samples (22% of cases). Using cell-based screening with the FGFR inhibitor PD173074 in a large (n = 83) panel of lung cancer cell lines, we demonstrated that this compound inhibited growth and induced apoptosis specifically in those lung cancer cells carrying amplified FGFR1. We validated the FGFR1 dependence of FGFR1-amplified cell lines by FGFR1 knockdown and by ectopic expression of an FGFR1-resistant allele (FGFR1V561M), which rescued FGFR1-amplified cells from PD173074-mediated cytotoxicity. Finally, we showed that inhibition of FGFR1 with a small molecule led to significant tumor shrinkage in vivo. Thus, focal FGFR1 amplification is common in squamous cell lung cancer and associated with tumor growth and survival, suggesting that FGFR inhibitors may be a viable therapeutic option in this cohort of patients.

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype with poor prognosis. We sequenced 29 SCLC exomes, 2 genomes and 15 transcriptomes and found an extremely high mutation rate of 7.4 ± 1 protein-changing mutations per million base pairs. Therefore, we conducted integrated analyses of the various data sets to identify pathogenetically relevant mutated genes. In all cases, we found evidence for inactivation of TP53 and RB1 and identified recurrent mutations in the CREBBP, EP300 and MLL genes that encode histone modifiers. Furthermore, we observed mutations in PTEN, SLIT2 and EPHA7, as well as focal amplifications of the FGFR1 tyrosine kinase gene. Finally, we detected many of the alterations found in humans in SCLC tumors from Tp53 and Rb1 double knockout mice. Our study implicates histone modification as a major feature of SCLC, reveals potentially therapeutically tractable genomic alterations and provides a generalizable framework for the identification of biologically relevant genes in the context of high mutational background.

Chest wall resection for lung cancer: indications and techniques.

Lung cancer invasion of the chest wall is not a common challenge and represents only about 5% of all patients resected for lung cancer. In T3N0M0 tumours, long-term survival reaches 40-50%, provided certain conditions are fulfilled. The number of explorative thoracotomies and the rate of non-radical resections might be high due to the local extension of an aggressive tumour. Mortality after resection is as high as for pneumonectomy. For historical and anatomical reasons, we have to divide the patients into two groups: infiltration of, and above, the second rib (Pancoast) and tumours located caudally to the second rib. We have to define the two entities. There is a problem concerning correct diagnosis: many tumours reach the chest wall. If the lung is not adherent to the parietal pleura, a standard lobectomy can be performed. However, in the case of adhesions, the differentiation between tumour invasion and inflammation may be difficult. We do not want to perform over-treatment since lung resection en bloc with the chest wall has a higher morbidity and mortality than lobectomy. But we have to avoid opening the tumour intraoperatively or perform a non-radical resection. Therefore, we need a preoperative diagnostic tool answering the question of extrapulmonary infiltration. In this context, we will discuss whether extrapleural lung resection is acceptable in the case of pleural invasion without chest wall involvement. The prognosis of patients with tumours invading the chest wall and mediastinal lymph node metastasis is worse. But patients with ipsilateral supraclavicular lymph node metastasis are not excluded. Thus, careful clinical investigations are necessary. To achieve complete resection, the surgeon should use anatomical knowledge to choose the best form of access to make radical resection more feasible. The problem of pain after thoracotomy is accentuated after chest wall resection, especially after paravertebral resection. The use of modern pain treatment is very important.

Comparison of the number of pre-, intra- and postoperative lung metastases

AIM To compare the number of lung metastases seen preoperatively on computed tomography in patients with a previous history of malignant disease with the number of resected pulmonary nodules and the number of histologically proven lung metastases. PATIENTS AND METHODS Between 1998 and 2003, we operated on 281 patients with suspected lung metastases. The histology of the primary tumour, the number of preoperatively diagnosed nodules, the number of lesions removed during surgery and the number of histologically confirmed metastases of 276 patients are presented. RESULTS Resection of lung metastases was performed in 276 patients. The median age was 62 years (21-86 years). The mean number of nodules seen on the CT scan was 1.9 (total: 515 nodules), 2.9 pulmonary lesions were removed (total: 835 nodules) and 2.1 nodules were confirmed as lung metastases (total: 560). In 39%, the number of lesions found and removed during the operation was higher than counted on the preoperative CT scan. These extra nodules found during the operation were confirmed as lung metastases in 16% of all patients. A benign solitary lesion was found in 15.2% of the patients and in 7.9% a primary carcinoma of the lung was diagnosed. In patients with a solitary nodule we found no metastasis in 16.4%, one lung metastasis in 76.7% and more than one lung metastasis in 6.9%. In patients with more than one nodule on the preoperative CT scan, an identical number of lung metastases were histologically confirmed in 35% of the patients, a larger number in 27.4% and a smaller number in 37.6%. CONCLUSIONS In patients with a previous history of malignant disease, 15.2% of the pulmonary lesions are benign. Video-assisted thoracoscopic surgery (VATS) is a safe diagnostic and therapeutic method for solitary lesions, with little discomfort for the patient. In patients with more than one nodule on the CT scan, manual exploration of the lung is necessary to detect further lesions.

Intermittent positive-pressure breathing after lung surgery.

Intermittent positive-pressure breathing is thought to avoid atelectasis and improve pulmonary function after major lung resections. Since no clear scientific data was available to confirm this, our objective was to determine whether atelectasis can be avoided and if postoperative lung function is improved. Prospective analysis was carried out in 135 patients operated on between 2007 and 2009; 55 received intermittent positive-pressure breathing. Pre- and postoperative lung function tests were similar in both groups. Pulmonary complications were observed in 19% of patients without intermittent positive-pressure breathing and 27% of those who received this treatment. We were unable to find evidence that additional improvement in postoperative pulmonary function is achieved when adding intermittent positive-pressure breathing to the standard physical therapy.

Inhalation with Tobramycin® to improve healing of tracheobronchial reconstruction

OBJECTIVE Sleeve resections were introduced to preserve lung function in patients with limited pulmonary reserve. Ischaemia and infection of the distal part of the anastomosis is the leading cause of bronchial anastomotic leakage. We have learned from our experience in lung transplantation that inhalation with Tobramycin helps prevent anastomotic insufficiency. We would like to present our experience in patients with tracheobronchial sleeve and prophylactic Tobramycin inhalation. PATIENTS AND METHODS Retrospective analysis of 114 patient records, between 01.01.2005 and 31.12.2006, where a bronchial anastomosis (patients with tracheal resection were excluded) was performed. All patients received Tobramycin inhalation (2 x 80 mg) for 7 days. Data analysed were; length of chest tube drainage in days, complications, morbidity and hospital mortality. RESULTS In 694 patients, an anatomic resection was performed. Of these, 114 (16%) were sleeve resections and 63 (9%) pneumonectomies. In 21 women and 93 men, between 25 and 84 years old, sleeve lobectomy was performed 104 times and carinal resection 10 times. A preoperative neoadjuvant therapy had been given in 26%. Radical (R0) resection was possible in 94%. The duration of the operation was between 83 and 225 min (median: 127 min). Chest tubes were removed on average after 6 days. Patients were discharged after 11 days. The rate of bronchial anastomotic leakage was 4.4%. There were two patients with postoperative respiratory insufficiency and mechanical ventilation, two patients with technical failure required early correction of the suture and one patient with a necrosis of the anastomosis. Thirty-day hospital mortality was 2.6% (3/114). CONCLUSIONS Increasing experience with sleeve resection has reduced the rate of pneumonectomy below 10%, although a number of the patients had received neoadjuvant therapy and the carinal resection rate of necrosis and infection of the anastomosis was low. We therefore recommend use of local antibiotic inhalation after sleeve resection.

Combined point mutation in KRAS or EGFR genes and EML4–ALK translocation in lung cancer patients

A total of three cases with novel constellations regarding mutation patterns in non-small-cell lung cancer (NSCLC) are reported. The mutation patterns that are observed are novel and unexpected. First, a combined simultaneous KRAS mutation and EML4-ALK translocation, both in the main tumor and a bone metastasis, were observed, these mutations are assumed to mutually exclude each other. A further two cases include a father and a daughter, both of whom are suffering from NSCLC with different EGFR mutation patterns. A common cause was assumed; however, could not be deduced to mutations in the KRAS, BRAF and EGFR genes. The aforementioned cases are important, as it must be taken into account that mutations previously assumed to be exclusive can occur in combination, may influence the clinical outcome and may require different therapy compared with single mutated tumors. It has to be discussed whether diagnostic algorithms need to be adapted. The cases of father and daughter show that further unknown factors can influence development of NSCLC.

Benign stenosis of the trachea.

Benign stenosis of trachea results mainly from tracheotomy, ventilation, or trauma. The combination of a defect of the mucosa or the tracheal wall and infection produce secondary scar tissue healing with shrinkage of the tracheal lumen or instability of the tracheal wall. Standard of treatment consists of resection of the pathologic segment of the trachea with end-to-end anastomosis. In case of involvement of the larynx, partial resections of the anterior cricoid cartilage or division of the larynx with tracheolaryngeal silicone stents are used. Short-term and long-term results are satisfying considering some technical recommendations.

A new classification of bronchial anastomosis after sleeve lobectomy.

OBJECTIVE Ischemia and infection of the distal part of the tracheobronchial anastomosis are the leading causes of bronchial anastomotic leakage with a high morbidity and mortality. To improve interpretation of healing of the anastomosis and the consequences, we have developed a classification scheme that allows quality control and defines early and standardized treatment of complications. PATIENTS AND METHOD We conducted a retrospective analysis of the records of 202 patients treated in our institution between January 1, 2006 and December 31, 2010 after sleeve lobectomy. All patients received prophylactic inhalation with tobramycin 80 mg twice a day. Neoadjuvant treatment was given in 21% of the patients. Routine bronchoscopy on day 7 was performed with classification of the anastomosis as follows: X, unknown; 1, healing well with no fibrin deposits; 2, focal fibrin deposits and superficial (mucosal) necrosis; 3, circular fibrin deposits, superficial (mucosal) necrosis, and/or ischemia of the distal mucosa; 4, transmural necrosis with instability of the anastomosis; and 5, perforation, necrosis of the anastomosis, and insufficiency. RESULTS The anastomosis was graded as satisfactory (1 and 2) in 86% of the patients. In 14%, it was regarded as critical (≥3-5) leading to systemic antibiotic treatment and control bronchoscopy. The overall 30-day mortality was 1%. CONCLUSIONS Quality control of the tracheobronchial anastomosis comprised bronchoscopy performed before patients were dismissed. Inasmuch as postoperative bronchoscopy is not always performed by the operating surgeon, this classification is an aid to improve the description of endobronchial healing and to commence treatment of critical bronchial healing.