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Cystic fibrosis [keywords]
- Analytical Validation Considerations of Multiplex Mass Spectrometry-based Proteomic Platforms for Measuring Protein Biomarkers. [JOURNAL ARTICLE]
- J Proteome Res 2014 Aug 29.
Protein biomarker discovery and validation in current omics era are vital for healthcare professionals to improve diagnosis, detect cancers at an early stage, identify the likelihood of cancer recurrence, stratify stages with differential survival outcomes, and monitor therapeutic responses. The success of such biomarkers would have a huge impact on how we improve the diagnosis and treatment of patients, and alleviate the financial burden of healthcare systems. In the past, the genomics community (mostly through large-scale, deep genomic sequencing technologies) has been steadily improving our understanding of the molecular basis of disease, with a number of biomarker panels already authorized by the US Food and Drug Administration (FDA) for clinical use (e.g., MammaPrint, two recently cleared devices using next-generation sequencing platforms to detect DNA changes in the cystic fibrosis transmembrane conductance regulator (CFTR) gene). Clinical proteomics, on the other hand, albeit its ability to delineate the functional units of a cell, more likely driving the phenotypic differences of a disease (i.e., proteins and protein-protein interaction networks and signaling pathways underlying the disease), "staggers" to make a significant impact with only an average ~1.5 protein biomarkers per year approved by the FDA over the past 15-20 years. This statistic itself raises the concern that major roadblocks have been impeding an efficient transition of protein marker candidates in biomarker development in spite of major technological advances in proteomics in recent years. The National Cancer Institute's Clinical Proteomic Technologies for Cancer initiative (NCI-CPTC) that launched the Clinical Proteomic Tumor Analysis Consortium - (CPTAC) has tackled many issues that plagued the clinical proteomics field in order to ensure a more streamlined transition from research to the clinic by (1) introducing "verification" between discovery and validation using analytically robust, multiplexed targeted proteomic technologies ; (2) developing open-access regulatory science pre-submission documents (mock 510k) with the FDA on how to appropriately validate multiplex proteomic assays, and thus creating a framework to inform the proteomics community regarding analytical validation requirements sought by all international regulatory agencies; (3) generating and well-characterizing renewable affinity reagents for assay validation for the community; and (4) implementing data metrics for proteomic datasets to be more transparent and accessible by the public.
- Aerosolized Antibiotics for Non-Cystic Fibrosis Bronchiectasis. [JOURNAL ARTICLE]
- Respiration 2014 Aug 22.:177-184.
Patients with non-cystic fibrosis bronchiectasis (NCFB) share many of the respiratory symptoms and the disease progression of cystic fibrosis (CF). As there are no approved therapies for the management of NCFB, an approach has been to use therapies similar to those used to treat CF. In many cases, however, this is ineffective or detrimental. The reason for this has not been determined, but it may be due to key differences in pathogenesis. The questions arising from this have spurred dedicated investigation into the effective management of NCFB. Patients with NCFB have chronic bacterial infection, and bacterial load correlates with symptoms and quality of life. Treatment with systemic antibiotics decreases bacterial load and can have a favorable effect on outcomes. Chronic or frequent use of systemic antibiotics, however, is impractical and sometimes unsafe, so aerosol as a means of delivery is seen as an attractive alternative. The clinical response to and tolerability of inhaled antibiotics have differed significantly between NCFB and CF. New delivery technology, novel antibiotic formulations and a better understanding of the bacterial burden of NCFB are now changing the approach to disease management. © 2014 S. Karger AG, Basel.
- Resolution of Cystic Fibrosis-related Diabetes with Ivacaftor Therapy. [JOURNAL ARTICLE]
- Am J Respir Crit Care Med 2014 Sep 1; 190(5):590-591.
- Pancreatic ductal adenocarcinoma: Risk factors, screening, and early detection. [REVIEW]
- World J Gastroenterol 2014 Aug 28; 20(32):11182-11198.
Pancreatic cancer is the fourth most common cause of cancer-related deaths in the United States, with over 38000 deaths in 2013. The opportunity to detect pancreatic cancer while it is still curable is dependent on our ability to identify and screen high-risk populations before their symptoms arise. Risk factors for developing pancreatic cancer include multiple genetic syndromes as well as modifiable risk factors. Genetic conditions include hereditary breast and ovarian cancer syndrome, Lynch Syndrome, familial adenomatous polyposis, Peutz-Jeghers Syndrome, familial atypical multiple mole melanoma syndrome, hereditary pancreatitis, cystic fibrosis, and ataxia-telangiectasia; having a genetic predisposition can raise the risk of developing pancreatic cancer up to 132-fold over the general population. Modifiable risk factors, which include tobacco exposure, alcohol use, chronic pancreatitis, diet, obesity, diabetes mellitus, as well as certain abdominal surgeries and infections, have also been shown to increase the risk of pancreatic cancer development. Several large-volume centers have initiated such screening protocols, and consensus-based guidelines for screening high-risk groups have recently been published. The focus of this review will be both the genetic and modifiable risk factors implicated in pancreatic cancer, as well as a review of screening strategies and their diagnostic yields.
- Cystic fibrosis-related bone disease explored using a four step algorithm. [JOURNAL ARTICLE]
- J Cyst Fibros 2014 Aug 26.
A suboptimal bone accrual in young individuals with cystic fibrosis (CF) may be related to the development of a premature CF-related bone disease. Dual energy X-ray absorptiometry (DXA) is the mainstream measure of bone health; however, the influence of body size and lean tissue mass (LTM) on bone data is poorly interpreted.Total body dual-energy X-ray absorptiometry (DXA) measurements of bone mineral content (BMC) and LTM in 53 individuals with CF (7.00-17.99years) were compared to 53 sex-matched controls. BMC, height, and LTM in relation to height and BMC Z-scores were calculated and used in a 4-step algorithm.Pubertal females with CF had less total body BMC for age (p=0.02); pre-pubertal males (p=0.05) and pubertal females with CF (p=0.03) were shorter; and pubertal females with CF showed less total body BMC for LTM (p=0.01).The algorithm showed the following: (1) prior to puberty lowered total body BMC was primarily due to short stature, (2) LTM was appropriate for body size, and (3) pubertal females with CF had significantly less total body BMC for their LTM. Longer controlled trials are needed to clinically interpret CF-related bone disease using DXA derived data that considers patient size and body composition.
- Ivacaftor and sinonasal pathology in a cystic fibrosis patient with genotype deltaF508/S1215N. [JOURNAL ARTICLE]
- J Cyst Fibros 2014 Aug 25.
In patients with Cystic Fibrosis and a type III mutation, ivacaftor (Kalydeco®, Vertex) can increase the opening time of the CFTR channel and improve chloride transport. Research showed significant improvement of lung function and increase in weight following ivacaftor use. However, ivacaftor showed to have adverse events on the sinonasal system as well, such as upper respiratory tract infections, nasal congestion and headaches. This case report showed a positive effect of ivacaftor on the sinonasal pathology in a 17year old patient with CF. After 5months of ivacaftor use, the CT-sinus showed complete resolution of the opacification of the paranasal sinuses and a decrease in symptoms of sinonasal disease. This positive effect of ivacaftor on sinonasal pathology seems promising, therefore more research is needed to evaluate the effect of ivacaftor on the upper airways in CF.
- Antibiotic Management of Lung Infections in Cystic Fibrosis: Part II. Nontuberculous Mycobacteria, Anaerobic Bacteria, and Fungi. [JOURNAL ARTICLE]
- Ann Am Thorac Soc 2014 Aug 28.
Airway infections are a key component of cystic fibrosis (CF) lung disease. While the approach to common pathogens such as Pseudomonas aeruginosa is guided by a significant body of evidence, other infections often pose a considerable challenge to treating physicians. In Part I of this series on the antibiotic management of difficult lung infections, we discussed bacterial organisms including MRSA, Gram-negative bacterial infections and treatment of multiple bacterial pathogens. Here, we summarize the approach to infections with nontuberculous mycobacteria, anaerobic bacteria and fungi. Nontuberculous mycobacteria can significantly impact the course of lung disease in CF patients, but differentiation between colonization and infection is difficult clinically as co-infection with other micro-organisms is common. Treatment consists of different classes of antibiotics, varies in intensity, and is best guided by a team of specialized clinicians and microbiologists. The ability of anaerobic bacteria to contribute to CF lung disease is less clear, even though clinical relevance has been reported in individual patients. Anaerobes detected from CF sputum are often resistant to multiple drugs, and treatment has not yet been shown to positively affect patient outcome. Fungi have gained significant interest as potential CF pathogens in recent years. While the role of Candida is largely unclear, there is mounting evidence that Scedosporium species and Aspergillus fumigatus, beyond the classical presentation of allergic bronchopulmonary aspergillosis, can be relevant in CF patients and treatment should be considered. Currently, however there remains limited information on how best to select patients that could benefit from antifungal therapy.
- A Novel Signal Transduction Pathway that Modulates rhl Quorum Sensing and Bacterial Virulence in Pseudomonas aeruginosa. [JOURNAL ARTICLE]
- PLoS Pathog 2014 Aug; 10(8):e1004340.
The rhl quorum-sensing (QS) system plays critical roles in the pathogenesis of P. aeruginosa. However, the regulatory effects that occur directly upstream of the rhl QS system are poorly understood. Here, we show that deletion of gene encoding for the two-component sensor BfmS leads to the activation of its cognate response regulator BfmR, which in turn directly binds to the promoter and decreases the expression of the rhlR gene that encodes the QS regulator RhlR, causing the inhibition of the rhl QS system. In the absence of bfmS, the Acka-Pta pathway can modulate the regulatory activity of BfmR. In addition, BfmS tunes the expression of 202 genes that comprise 3.6% of the P. aeruginosa genome. We further demonstrate that deletion of bfmS causes substantially reduced virulence in lettuce leaf, reduced cytotoxicity, enhanced invasion, and reduced bacterial survival during acute mouse lung infection. Intriguingly, specific missense mutations, which occur naturally in the bfmS gene in P. aeruginosa cystic fibrosis (CF) isolates such as DK2 strains and RP73 strain, can produce BfmS variants (BfmSL181P, BfmSL181P/E376Q, and BfmSR393H) that no longer repress, but instead activate BfmR. As a result, BfmS variants, but not the wild-type BfmS, inhibit the rhl QS system. This study thus uncovers a previously unexplored signal transduction pathway, BfmS/BfmR/RhlR, for the regulation of rhl QS in P. aeruginosa. We propose that BfmRS TCS may have an important role in the regulation and evolution of P. aeruginosa virulence during chronic infection in CF lungs.
- P. aeruginosa SGNH Hydrolase-Like Proteins AlgJ and AlgX Have Similar Topology but Separate and Distinct Roles in Alginate Acetylation. [JOURNAL ARTICLE]
- PLoS Pathog 2014 Aug; 10(8):e1004334.
The O-acetylation of polysaccharides is a common modification used by pathogenic organisms to protect against external forces. Pseudomonas aeruginosa secretes the anionic, O-acetylated exopolysaccharide alginate during chronic infection in the lungs of cystic fibrosis patients to form the major constituent of a protective biofilm matrix. Four proteins have been implicated in the O-acetylation of alginate, AlgIJF and AlgX. To probe the biological function of AlgJ, we determined its structure to 1.83 Å resolution. AlgJ is a SGNH hydrolase-like protein, which while structurally similar to the N-terminal domain of AlgX exhibits a distinctly different electrostatic surface potential. Consistent with other SGNH hydrolases, we identified a conserved catalytic triad composed of D190, H192 and S288 and demonstrated that AlgJ exhibits acetylesterase activity in vitro. Residues in the AlgJ signature motifs were found to form an extensive network of interactions that are critical for O-acetylation of alginate in vivo. Using two different electrospray ionization mass spectrometry (ESI-MS) assays we compared the abilities of AlgJ and AlgX to bind and acetylate alginate. Binding studies using defined length polymannuronic acid revealed that AlgJ exhibits either weak or no detectable polymer binding while AlgX binds polymannuronic acid specifically in a length-dependent manner. Additionally, AlgX was capable of utilizing the surrogate acetyl-donor 4-nitrophenyl acetate to catalyze the O-acetylation of polymannuronic acid. Our results, combined with previously published in vivo data, suggest that the annotated O-acetyltransferases AlgJ and AlgX have separate and distinct roles in O-acetylation. Our refined model for alginate acetylation places AlgX as the terminal acetlytransferase and provides a rationale for the variability in the number of proteins required for polysaccharide O-acetylation.