Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples.

Immunohistochemical (IHC) staining is an established technique for visualizing proteins in tissue sections for research studies and clinical applications. IHC is increasingly used as a targeting strategy for procurement of labeled cells via tissue microdissection, including immunodissection, computer-aided laser dissection (CALD), expression microdissection (xMD), and other techniques. The initial antigen retrieval (AR) process increases epitope availability and improves staining characteristics; however, the procedure can damage DNA. To better understand the effects of AR on DNA quality and quantity in immunodissected samples, both clinical specimens (KRAS gene mutation positive cases) and model system samples (lung cancer patient-derived xenograft tissue) were subjected to commonly employed AR methods (heat induced epitope retrieval [HIER], protease digestion) and the effects on DNA were assessed by Qubit, fragment analysis, quantitative PCR, digital droplet PCR (ddPCR), library preparation, and targeted sequencing. The data showed that HIER resulted in optimal IHC staining characteristics, but induced significant damage to DNA, producing extensive fragmentation and decreased overall yields. However, neither of the AR methods combined with IHC prevented ddPCR amplification of small amplicons and gene mutations were successfully identified from immunodissected clinical samples. The results indicate for the first time that DNA recovered from immunostained slides after standard AR and IHC processing can be successfully employed for genomic mutation analysis via ddPCR and next-generation sequencing (NGS) short-read methods.

Preoperative nutritional counselling in patients undergoing oesophagectomy.

BACKGROUND: Patients undergoing surgery for oesophageal cancer are at high risk of malnutrition due to pathology and neoadjuvent therapy. This study sought to determine if oesophageal cancer patients undergoing oesophagectomy achieve superior clinical outcomes when preoperative nutritional counselling is performed. METHODS: Oesophageal cancer patients undergoing oesophagectomy were retrospectively divided into cohorts based on those who received (n = 48) and did not receive (n = 58) preoperative nutritional counselling. We compared weight loss, length of stay, 30-day readmission related to nutrition or feeding tube problems, and 90-day mortality. RESULTS: Per cent weight loss was less in patients who received preoperative nutritional counselling. There was a trend toward decreased mean length of stay and there were fewer readmissions for feeding tube-related complications in patients who received counselling. CONCLUSIONS: Nutritional counselling before surgery may lead to decreased weight loss and reduced readmissions for feeding tube-related complications in patients with oesophageal cancer undergoing oesophagectomy.

NPARS-A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science.

Background: Accuracy and reproducibility are vital in science and presents a significant challenge in the emerging discipline of data science, especially when the data are scientifically complex and massive in size. Further complicating matters, in the field of genomic-based science high-throughput sequencing technologies generate considerable amounts of data that needs to be stored, manipulated, and analyzed using a plethora of software tools. Researchers are rarely able to reproduce published genomic studies. Results: Presented is a novel approach which facilitates accuracy and reproducibility for large genomic research data sets. All data needed is loaded into a portable local database, which serves as an interface for well-known software frameworks. These include python-based Jupyter Notebooks and the use of RStudio projects and R markdown. All software is encapsulated using Docker containers and managed by Git, simplifying software configuration management. Conclusion: Accuracy and reproducibility in science is of a paramount importance. For the biomedical sciences, advances in high throughput technologies, molecular biology and quantitative methods are providing unprecedented insights into disease mechanisms. With these insights come the associated challenge of scientific data that is complex and massive in size. This makes collaboration, verification, validation, and reproducibility of findings difficult. To address these challenges the NGS post-pipeline accuracy and reproducibility system (NPARS) was developed. NPARS is a robust software infrastructure and methodology that can encapsulate data, code, and reporting for large genomic studies. This paper demonstrates the successful use of NPARS on large and complex genomic data sets across different computational platforms.

Integration of smoking cessation and lung cancer screening.

The National Lung Screening Trial demonstrated a decrease in both lung cancer mortality and overall mortality in enrollees aged 55-74 with a 30 pack-year smoking history using low-dose computed tomography (LDCT). Lung cancer screening in high-risk groups is supported by the United States Preventive Services Task Force, the National Comprehensive Cancer Network, and multiple other organizations. Inclusion for any lung screening program requires a history of smoking, and many undergoing screening are currently smoking. Screened patients are not only at risk for developing lung cancer, but also carry the risk of developing a host of other smoking related diseases, and cessation at any point is beneficial. Counseling and pharmacotherapy are evidence-based strategies which are well known to help people quit smoking. However, as lung cancer screening is an emerging and evolving field, the integration of cessation resources in screening programs is not uniformly done, and when it is done, there is no standardized approach. The goals of this review are to discuss the rationale for integrating smoking cessation resources in lung cancer screening, review what types of resources may be effective, and discuss different strategies of how integration can be done. Ultimately, the overarching goal of any lung cancer screening program is not merely to find more nodules, or diagnose more cases of cancer, but to help screened patients live longer, better lives. Smoking cessation broadens the impact of any lung cancer screening program well beyond the endpoints of cancer diagnosis and cancer mortality to reduce risk from many other diseases, and can positively impact many more patients than the small percentage that have cancer.

Smoking Cessation in Clinical Practice: How to Get Patients to Stop.

Tobacco use is an etiologic agent for many diseases treated by cardiac, vascular, and thoracic surgeons and contributes to increased perioperative complications and long-term risk. Smoking cessation may be challenging for patients and can be frustrating for clinicians. Lack of familiarity and pessimistic views toward cessation methods lead to underuse by physicians. Evidence-supported measures that increase chances of cessation include direct physician advice, approved pharmacotherapy, structured counseling, and a follow-up plan. Approved pharmacotherapy consists of varenicline, bupropion, or nicotine replacement therapy in the form of long-acting patches and short-acting forms of nicotine such as gum, lozenges, prescription nasal spray, or prescription inhaler. Direct physician advice is critical and strengthened when combined with more in-depth counseling from a specialist who may have more expertise and time. Integrating assessment and referral to counseling services into a clinical workflow can deliver resources in an efficient manner with the goal of providing the best available resources to all patients.

Hyalinizing Clear Cell Carcinoma of the Lung: Case Report and Review of the Literature.

OBJECTIVES: Hyalinizing clear cell carcinoma (HCCC) is common in head and neck sites but extremely rare in the lung. This case report describes an HCCC in the lung of a 54-year-old female patient. METHODS: We summarize the histomorphologic, immunophenotypic, and molecular features for our and three previously reported HCCCs of the lung with emphasis on potential diagnostic pitfalls. RESULTS: Sections of a well-circumscribed 3.5-cm lung mass were characterized by a bronchocentric tumor growing in sheets, nests, and cords in a background of hyalinized stroma. Tumor cell appearance was clear to eosinophilic, lacking significant pleomorphism or mitotic activity. By immunohistochemistry, the tumor cells were strongly positive with antibodies to pan-keratin, p63, and CK5/6 while negative for CK7, CK20, thyroid transcription factor 1, napsin A, chromogranin, and synaptophysin. Next-generation sequencing demonstrated an EWSR1-ATF1 fusion transcript. CONCLUSIONS: Awareness of key morphologic features of pulmonary HCCC is crucial for the recognition of this rare entity in the lung. Ancillary studies, including immunohistochemistry and molecular testing, are essential for the distinction from its mimics.

Successful Treatment of Esophageal Necrosis Secondary to Acute Type B Aortic Dissection.

Esophageal necrosis after descending aortic dissection has been described but with no reports of successful treatment. A 66-year-old man with aortic dissection extending from the left subclavian artery through the common iliac arteries subsequently experienced esophageal necrosis. He underwent thoracic esophagectomy, cervical end esophagostomy, and open gastrostomy tube placement. Gastrointestinal continuity was established with a gastric tube conduit in the substernal plane. An oral diet was tolerated after reconstruction. Treatment of esophageal necrosis after aortic dissection may require esophageal diversion and esophagectomy. Esophageal continuity can later be restored while avoiding the posterior mediastinum.

Cervicothoracic airway injury repair using double-wide intercostal muscle flap.

We present a useful technique for the surgical management of long-segment cervicothoracic tracheobronchial injury using a double-wide intercostal muscle flap. This flap is a modification of a previously endorsed technique extending the ability to reinforce repairs of tracheobronchial injuries not adequately covered by a single intercostal muscle flap.

Accuracy of fine needle aspiration and core lung biopsies to predict histology in patients with non-small cell lung cancer.

Management of advanced non-small cell lung cancer patients is dependent on the histologic diagnosis for both testing and treatment. This study was designed to determine the ability of fine needle aspiration and core biopsies to correctly determine histologic diagnosis in non-small cell lung cancer. Our institutional cardiothoracic surgery database was reviewed for cases of non-small cell lung cancer treated with lobectomy after a preoperative biopsy by CT guidance or bronchoscopy over a 10-year period from 2002 to 2011. The histologic diagnosis of the final lobectomy specimen was compared to the histologic diagnosis from the preoperative biopsy, and the concordance rate was calculated. 119 biopsy specimens from 117 patients were reviewed. Eighty of the 119 biopsies had the same histologic diagnosis as the lobectomy specimen, yielding an overall concordance rate of 67.2 %. Patients with poorly differentiated tumors were at the highest risk of an incorrect histologic diagnosis on preoperative biopsy. Reliance on fine needle aspiration and core biopsies to determine histologic diagnosis in non-small cell lung cancer may put some patients at risk for suboptimal treatment.

Thoracic anesthesia and cross field ventilation for tracheobronchial injuries: a challenge for anesthesiologists.

Tracheobronchial injuries are rare but life threatening sequel of blunt chest trauma. Due to the difficult nature of these injuries and the demanding attributes of the involved surgery, the anesthesiologist faces tough challenges while securing the airway, controlling oxygenation, undertaking one-lung ventilation, maintaining anesthesia during tracheal reconstruction, and gaining adequate postoperative pain control. Amongst the few techniques that can be used with tracheobronchial injuries, cross field ventilation is a remotely described and rarely used technique, especially in injuries around the carina. We effectively applied cross field ventilation in both our cases and the outcome was excellent.

Do HIV-infected non-small cell lung cancer patients receive guidance-concordant care?

BACKGROUND: The incidence of lung cancer cases among HIV-infected individuals is increasing with time. It is unclear whether HIV-infected individuals receive the same care for lung cancer as immunocompetent patients because of comorbidities, the potential for interaction between antiretroviral agents and cancer chemotherapy, and concerns regarding complications related to treatment or infection. OBJECTIVES: The objective of this study was to assess the effect of HIV infection on receipt of guidance-concordant care, and its impact on overall survival among non-small cell lung cancer Medicare beneficiaries. DESIGN: The study design was a matched case-control design where each HIV patient was matched by age group, sex, race, and lung cancer stage at diagnosis with 20 controls randomly selected among those who were not HIV infected. SUBJECTS: The patients included in this study were Medicare beneficiaries diagnosed with non-small cell lung cancer between 1998 and 2007, who qualified for Medicare on the basis of age and were 65 years of age or older at the time of lung cancer diagnosis. HIV infection status was based on Medicare claims data. A total of 174 HIV cases and 3480 controls were included in the analysis. MEASURES: Odds ratios for receiving guidance-concordant care and hazard ratios for overall survival were estimated. RESULTS: HIV infection was not independently associated with the receipt of guidance-concordant care. Among stage I/II patients, median survival times were 26 and 43 months, respectively, for those with and without HIV infection (odds ratio=1.48, P=0.021). CONCLUSIONS: HIV infection was not associated with receipt of guidance-concordant care but reduced survival in early-stage patients.

Epidemiology of lung cancer: smoking, secondhand smoke, and genetics.

The link between smoking and development of lung cancer has been demonstrated, not only for smokers but also for those exposed to secondhand smoke. Despite the obvious carcinogenic effects of tobacco smoking, not all smokers develop lung cancer, and conversely some nonsmokers can develop lung cancer in the absence of other environmental risk factors. A multitude of genetic factors are beginning to be explored that interact with environmental exposure to alter the risk of developing this deadly disease. By more fully appreciating the complex interrelationship between genetics and other risks the development of lung cancer can be more completely understood.