Gone FISHing: clinical lessons learned in brain tumor molecular diagnostics over the last decade

Fluorescence in situ hybridization (FISH) is a powerful, morphology-based technique to assess targeted copy number alterations or gene rearrangements in formalin-fixed, paraffin-embedded tissues. It has a wide range of applications in routine clinical contexts to identify cytogenetic biomarkers for more accurate diagnosis and prognostic stratification. This review and update addresses practical uses of FISH as a molecular diagnostic tool in the setting of brain tumors, including gliomas, embryonal neoplasms, ependymomas and meningiomas, focusing on key genetic biomarkers, such as 1p19q codeletion, epidermal growth factor receptor (EGFR) gene amplification, BRAF rearrangement and many others. Also discussed are lessons learned over the past decade, including common technical issues to consider when implementing and interpreting FISH results in a clinical setting.     

Cancer vaccines in colon and rectal cancer over the last decade: lessons learned and future directions

Introduction: Great advances have been made in screening for and treatment of colorectal cancer (CRC), but recurrence rates remain high and additional therapies are needed. There is great excitement around the field of immunotherapy and many attempts have been made to bring immunotherapy to CRC through a cancer vaccine.

Areas covered: This is a detailed review of the last decade’s significant CRC vaccine trials.

Expert commentary: Monotherapy with a CRC vaccine is likely best suited for adjuvant therapy in disease free patients. Vaccine therapy elicits crucial tumor infiltrating lymphocytes, which are lacking in microsatellite-stable tumors, and therefore may be better suited for these patients. The combination of CRC vaccines with checkpoint inhibitors may unlock the potential of immunotherapy for a much broader range of patients. Future studies should focus on vaccine monotherapy in correctly selected patients and combination therapy in more advanced disease.     

Smoking cessation: what have we learned over the past decade?

This article discusses developments in understanding smoking and smoking cessation, methodological issues, and intervention approaches over the past 10 years. Although effective multisession clinic interventions have been developed, such programs reach relatively few smokers. This has led to self-help, work site, health care setting, and community interventions aimed at delivering less intensive programs to larger populations. Conceptual and empirical developments and trends within these above delivery contexts are reviewed, and avenues of research are identified. Nicotine replacement strategies have benefited from technological advances (e.g., transdermal patches) and present continuing challenges with respect to integration with behavioral strategies and incorporation into primary care medical settings. Research over the next decade should focus on the development of cost-effective interventions that can reach representative and high-risk smokers.     

Cystic fibrosis screening: lessons learned from the first 320,000 patients.

PURPOSE: To examine the data from > 335,000 Cystic fibrosis (CF) tests to detect unsuspected findings and obtain clinical data when indicated to optimize genetic counseling. METHODS: A proprietary database containing 335,204 consecutive CF DNA tests and 445 CF prenatal diagnostic tests was queried. Clinical information was obtained for prenatal and selected nonprenatal cases by telephone contact with physician offices. RESULTS: The mutation 1078delT was found in much lower frequency than expected with rates of only 1:55,867 tests and 0.06% of CF mutations. This level is below the threshold set by the American College of Medical Genetics. Homozygosity was observed for 2789+5G>A in a 29-year-old women and compound heterozygosity with delta F408 in a 40-year-old woman with isolated chronic sinusitis. Many patients elected prenatal diagnosis when not at a 1:4 risk due to echogenic bowel or IVS-8 5T issues. CONCLUSIONS: With the exception of 1078delT, all CF mutations in the ACMG panel were detected with a frequency of > 0.1% of CF chromosomes. When ACMG guidelines are strictly adhered to, population-based CF carrier screening will accurately identify couples at risk for having children with CF.     

HIT: lessons learned

The peculiar pathogenesis of heparin-induced thrombocytopenia (HIT), involving a "self" antigen-platelet factor 4 (PF4) bound to heparin-and resulting antibody-mediated platelet activation, is a model for thrombosis triggered by drug-induced autoimmunity. The high probability of forming an immune response to heparin, and the highly-variable clinical significance of a positive laboratory test-depending on the type of assay and the magnitude of a given positive test result-provides lessons regarding appropriate interpretation of diagnostic laboratory testing in the context of pretest probability. The relatively high risk of inducing microvascular thrombosis due to coumarin-induced vitamin K antagonism attests to the dangers of a compromised protein C natural anticoagulant system in the setting of a hypercoagulability state such as HIT. Unusual immunologic features of HIT, such as the dissociation between immunogenicity (induction of immune response) and cross-reactivity (capacity to form the antigens recognized by HIT antibodies)of the implicated polysaccharide anticoagulants, and the generally rapid formation and disappearance of anti-PF4/heparin antibodies, suggest that further lessons regarding HIT immunopathogenesis remain to be learned.     

The EGAPP initiative: lessons learned

The Evaluation of Genomic Applications in Practice and Prevention Working Group was first convened in 2005 to develop and test evidence-based methods for the evaluation of genomic tests in transition from research to clinical and public health practice. Over the ensuing years, the Working Group has met 26 times, publishing eight recommendation statements, two methods papers, and one outcomes paper, as well as planning and serving as technical experts on numerous associated systematic reviews. Evaluation of Genomic Applications in Practice and Prevention methods have evolved to address implications of the proliferation of genome-wide association studies and are currently expanding to face challenges expected from clinical implementation of whole-genome sequencing tests. In this article, we review the work of the Evaluation of Genomic Applications in Practice and Prevention Working Group over the first 8 years of its existence with an emphasis on lessons learned throughout the process. It is hoped that in addition to the published methods of the Working Group, the lessons we have learned along the way will be informative to others who are producers and consumers of evidence-based guidelines in the field of genomic medicine.Genet Med 2014:16(3):217–224.     

Childhood Asthma Management Program: lessons learned

The National Heart, Lung, and Blood Institute Childhood Asthma Management Program was initiated in 1991 and is now the largest and most comprehensive study of long-term intervention with anti-inflammatory therapy in children with mild to moderate asthma. The purpose of this perspective is to review key findings of the study and lessons learned in conducting research in more than 1000 children with persistent asthma for more than 10 years. A key lesson was absence of a continued effect of inhaled corticosteroid on lung growth during long-term follow-up even as symptoms and airway responsiveness remained improved.     

SARS: lessons learned from other coronaviruses

The identification of a new coronavirus as the etiological agent of severe acute respiratory syndrome (SARS) has evoked much new interest in the molecular biology and pathogenesis of coronaviruses. This review summarizes present knowledge on coronavirus molecular biology and pathogenesis with particular emphasis on mouse hepatitis virus (MHV). MHV, a member of coronavirus group 2, is a natural pathogen of the mouse; MHV infection of the mouse is considered one of the best models for the study of demyelinating disease, such as multiple sclerosis, in humans. As a result of the SARS epidemic, coronaviruses can now be considered as emerging pathogens. Future research on SARS needs to be based on all the knowledge that coronavirologists have generated over more than 30 years of research.     

An evidence-based approach for laparoscopic inguinal hernia repair: lessons learned from over 1,000 repairs

In this educational article, we aim to provide a literature review on laparoscopic anatomy of the inguinal region. We share the lessons learnt from the 1,194 laparoscopic hernia operations we have performed in 16 years of experience, trying to provide an anatomical and physiological basis for surgeons. The current study reports a personal experience with a transabdominal preperitoneal (TAPP) hernioplasty procedure. A literature review using the keywords "hernia," "laparoscopic approach," and "hernia repair" was performed using the electronic biomedical database PubMed, Medline Extra, Embase, Biosis, Science Citation Index, Ovid and text books. Between January 1994 and December 2010, a total of 1,194 patients, males and females (average age, 56.7 years), underwent laparoscopic TAPP inguinal hernia repair. Following reduction of the hernia sac and creation of the preperitoneal flap, a polypropylene mesh (10 × 16) and four spiral tacks were placed. TAPP is easy to learn and perform. Through this approach, a much better view from the inguinal anatomy is achieved, and the procedure also offers a brief learning curve. Our patients reported minimal postoperative pain and returned to work after 5-10 days, which is in accordance with the general anesthesia series. During the follow-up period, 10% of seromas, 3% of scrotal hematomas, 1% of hemorrhages, and 3% of recurrent hernias were observed. It should be emphasized that we have not observed abscess formation or acute infection related to the presence of mesh.     

HIV vaccine research in Thailand: lessons learned

Thailand is the only country that has conducted two Phase III efficacy trials and ten other Phase I/II studies using various HIV-1 vaccine constructs. This outstanding record is the result of strong efforts and commitment among various partners, including policy makers, regulators, researchers and foreign collaborators. Recently, it has become apparent that hardly any new HIV/AIDS candidate vaccines are in the pipeline reaching the stage of clinical testing, especially a candidate vaccine that is suitable for Thailand and the surrounding region. However, many lessons learned can be utilized or modified for other vaccine trials, particularly vaccines against other infectious diseases prevalent in developing countries.     

Immunity against cancer: lessons learned from melanoma

Most major advances in human cancer immunology and immunotherapy have come from studies in melanoma. We are beginning to understand the immune repertoire of T cells and antibodies that are active against melanoma, with recent glimpses of the CD4(+) T cell repertoire. The view of what the immune system can see is extending to mutations and parts of the genome that are normally invisible.     

Gifts from the grave: lessons learned for living well

Often expected to work institutional miracles although under resourced, most hospice and palliative care nurses excel in meeting consistently intense and demanding clinical and human challenges. They do so by staying focused and being grounded, highly accountable, responsive, and empathetic. With time and experience, they often master the art of advocacy, and through developing a capacity for "organization-with-heart," they navigate very complex institutional, systemic, cultural, and societal waters. Nurses are present to patient and familial wounds; the sights, sounds, smells of chaos and beauty; gladness and grief; intimacy and numbness. Our guest author today distills years of nursing experience into a very few words that can be shared in classrooms, homes, and clinics. It is clear that she not only knows of what she speaks, but, having died many times to that which is not fruitful, she separates the essential from the nonessential and, in so doing, is renewed and full of life. Isn't this an ultimate demonstration of integration and embodiment? Therese Schroeder-Sheker, The Chalice of Repose Project.     

Molecular pathogenesis of lymphangioleiomyomatosis: lessons learned from orphans

Lymphangioleiomyomatosis (LAM) is a rare progressive cystic lung disease affecting young women. The pivotal observation that LAM occurs both spontaneously and as part of the tuberous sclerosis complex (TSC) led to the hypothesis that these disorders share common genetic and pathogenetic mechanisms. In this review we describe the evolution of our understanding of the molecular and cellular basis of LAM and TSC, beginning with the discovery of the TSC1 and TSC2 genes and the demonstration of their involvement in sporadic (non-TSC) LAM. This was followed by rapid delineation of the signaling pathways in Drosophila melanogaster with confirmation in mice and humans. This knowledge served as the foundation for novel therapeutic approaches that are currently being used in human clinical trials.     

Immunity to intestinal pathogens: lessons learned from Salmonella

Salmonella are a common source of food- or water-borne infection and cause a wide range of clinical disease in human and animal hosts. Salmonella are relatively easy to culture and manipulate in a laboratory setting, and the infection of laboratory animals induces robust innate and adaptive immune responses. Thus, immunologists have frequently turned to Salmonella infection models to expand understanding of host immunity to intestinal pathogens. In this review, I summarize current knowledge of innate and adaptive immunity to Salmonella and highlight features of this response that have emerged from recent studies. These include the heterogeneity of the antigen-specific T-cell response to intestinal infection, the prominence of microbial mechanisms to impede T- and B-cell responses, and the contribution of non-cognate pathways for elicitation of T-cell effector functions. Together, these different issues challenge an overly simplistic view of host–pathogen interaction during mucosal infection, but also allow deeper insight into the real-world dynamic of protective immunity to intestinal pathogens.     

The genetics of autoimmune thyroiditis: the first decade

Most of our current understanding of the genetic predisposition to autoimmune disease can be traced to experiments performed in the decade from 1971 to 1981. Chella David was a key contributor to this research. Many of these early steps came from studies of experimental autoimmune thyroiditis. This model has been especially valuable because essentially the same disease can occur spontaneously in selected strains of animals or can be induced by deliberate immunization. From a genetic point of view, the disease has been investigated in three different species: mice, rats and chickens. The same antigen, thyroglobulin, initiates the disease in all three species. Among the main discoveries were the relationship of autoimmune disease to the major histocompatibility complex (MHC), the interplay of different subregions within the MHC in promoting or retarding development of disease, the differing roles of MHC class II and MHC I class genes in induction and effector phases, respectively, and the cumulative effect of non-MHC genes, each of which represents a small addition to overall susceptibility. Other experiments revealed that genetic differences in thyroglobulin allotypes influence susceptibility to thyroiditis. Thyroid glands differed in different strains in vulnerability to passive transfer of antibody. The first evidence of modulatory genes on the sex-related X chromosome emerged. All of these genetic findings were concurrently translated to the human disease, Hashimoto’s thyroiditis, where thyroglobulin is also the initiating antigen.