Implementation of Rapid Genome Sequencing for Critically Ill Infants With Complex Congenital Heart Disease.

BACKGROUND: Rapid genome sequencing (rGS) has been shown to improve care of critically ill infants. Congenital heart disease (CHD) is a leading cause of infant mortality and is often caused by genetic disorders, yet the utility of rGS has not been prospectively studied in this population. METHODS: We conducted a prospective evaluation of rGS to improve the care of infants with complex CHD in our cardiac neonatal intensive care unit. RESULTS: In a cohort of 48 infants with complex CHD, rGS diagnosed 14 genetic disorders in 13 (27%) individuals and led to changes in clinical management in 8 (62%) cases with diagnostic results. These included 2 cases in whom genetic diagnoses helped avert intensive, futile interventions before cardiac neonatal intensive care unit discharge, and 3 cases in whom eye disease was diagnosed and treated in early childhood. CONCLUSIONS: Our study provides the first prospective evaluation of rGS for infants with complex CHD to our knowledge. We found that rGS diagnosed genetic disorders in 27% of cases and led to changes in management in 62% of cases with diagnostic results. Our model of care depended on coordination between neonatologists, cardiologists, surgeons, geneticists, and genetic counselors. These findings highlight the important role of rGS in CHD and demonstrate the need for expanded study of how to implement this resource to a broader population of infants with CHD.

Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program.

Copy number variations (CNVs) play a significant role in human disease. While chromosomal microarray has traditionally been the first-tier test for CNV detection, use of genome sequencing (GS) is increasing. We report the frequency of CNVs detected with GS in a diverse pediatric cohort from the NYCKidSeq program and highlight specific examples of its clinical impact. A total of 1052 children (0-21 years) with neurodevelopmental, cardiac, and/or immunodeficiency phenotypes received GS. Phenotype-driven analysis was used, resulting in 183 (17.4%) participants with a diagnostic result. CNVs accounted for 20.2% of participants with a diagnostic result (37/183) and ranged from 0.5 kb to 16 Mb. Of participants with a diagnostic result (n = 183) and phenotypes in more than one category, 5/17 (29.4%) were solved by a CNV finding, suggesting a high prevalence of diagnostic CNVs in participants with complex phenotypes. Thirteen participants with a diagnostic CNV (35.1%) had previously uninformative genetic testing, of which nine included a chromosomal microarray. This study demonstrates the benefits of GS for reliable detection of CNVs in a pediatric cohort with variable phenotypes.

Antimicrobial peptides in mucosal secretions: the importance of local secretions in mitigating infection.

The antimicrobial activity of the collective molecules comprising human milk reflects an evolutionarily successful paradigm for preventing and limiting microbial infection. Understanding the molecules that participate in this process and how they work can yield insight into potentially new antimicrobial therapies. Upon proteolytic processing, antimicrobial peptides can be derived from milk proteins, such as lactoferrin, casein, and lysozyme. Similarly, using the HIV-1 gp41 protein template, we have demonstrated that the 28-residue C-terminus, when produced as an independent peptide, exhibits selective toxicity for bacteria over eukaryotic cells. Upon optimizing this sequence for cationic charge and hydrophobic character presented as a alpha-helical structure, we show improved capability of the parent LLP1 sequence to selectively kill bacteria in the host environment and that this activity is increased by the inclusion of Trp residues on the hydrophobic face. We report that it is possible to (i) design de novo antimicrobial peptides that demonstrate optimal antimicrobial activity with minimal inflammatory activity and (ii) design antimicrobial peptides to function in a defined environment. In the end, we describe a de novo designed antimicrobial peptide, WLBU2, which is selectively toxic to microbial pathogens in complex environments and does not stimulate a significant immunomodulatory response. In spite of these properties, WLBU2 activity against Pseudomonas aeruginosa in human milk is inferior to the host peptide LL37 with regard to antimicrobial potency. These studies demonstrate that antimicrobial peptides can be engineered for greater potency in one medium but may not be optimal for working in a different medium such as human milk.

De novo generation of cationic antimicrobial peptides: influence of length and tryptophan substitution on antimicrobial activity.

Comparison of human immunodeficiency virus lentiviral lytic peptide 1 with other host-derived peptides indicates that antimicrobial properties of membrane-active peptides are markedly influenced by their cationic, hydrophobic, and amphipathic properties. Many common themes, such as Arg composition of the cationic face of an amphipathic helix and the importance of maintaining the hydrophobic face, have been deduced from these observations. These studies suggest that a peptide with these structural properties can be derived de novo by using only a few strategically positioned amino acids. However, the effects of length and helicity on antimicrobial activity and selectivity have not been objectively evaluated in the context of this motif. To address these structure-function issues, multimers of a 12-residue lytic base unit (LBU) peptide composed only of Arg and Val residues aligned to form idealized amphipathic helices were designed. Bacterial killing assays and circular dichroism analyses reveal a strong correlation between antibacterial activity, peptide length, and propensity to form a helix in solvent mimicking the environment of a membrane. Increasing peptide length beyond two LBUs (24-residue peptides) resulted in no appreciable increase in antimicrobial activity. Derivatives (WLBU) of the LBU series were further engineered by substituting Trp residues in the hydrophobic domains. The 24-residue WLBU2 peptide was active at physiologic NaCl concentrations against Staphylococcus aureus and mucoid and nonmucoid strains of Pseudomonas aeruginosa. Further, WLBU2 displayed the highest antibacterial selectivity of all peptides evaluated in the present study by using a coculture model of P. aeruginosa and primary human skin fibroblasts. These findings provide fundamental information toward the de novo design of an antimicrobial peptide useful for the management of infectious diseases.

Mortality after pediatric lung transplantation: autopsies vs. clinical impression.

Appreciable mortality accompanies pediatric lung and heart-lung transplantation. The objective of this investigation was to compare the clinical impression of causes of death with autopsy findings in all pediatric lung or heart lung transplant recipients who had an autopsy performed between 1985-2002 at the Children's Hospital of Pittsburgh. Medical records and autopsy findings were reviewed. Thirty recipients with autopsies had 33 transplant procedures: heart-lung (16), double lung (14), repeat lung (2), and repeat heart-lung (1). Perioperative deaths occurred in 8 children, most often precipitated by graft dysfunction. Early deaths (2 weeks-1 year) occurred in 12 children resulting from infection. Late deaths (greater than 1 year) occurred in 10 children. Bronchiolitis obliterans complicated by infection was the major cause of death in these recipients. An autopsy confirmed the clinical impression of cause of death in 29/30 and added significant supplemental information in 16 cases. Unsuspected factors contributing to death included donor lung abnormalities, concurrent infection, and cardiovascular disease. Postmortem examination remains a critical component to augment the understanding of causes of death following pediatric thoracic transplantation.

Post-transplant complications.

Lung transplantation carries the potential of great benefit to patients with chronic, end-stage lung disease; but it comes with significant medical, social, financial, and psychosocial costs that differ from those experienced prior to transplantation. Further understanding of its limitations, especially the development of acute and chronic rejection, will continue to lead to better immunosuppressive regimens and therapies. Success of the transplant procedure involves not only interventions to improve graft survival, but also those to improve the patient's quality of life.

Selective toxicity of engineered lentivirus lytic peptides in a CF airway cell model.

Lentivirus lytic peptides (LLPs) are derived from HIV-1 and have antibacterial properties. LLP derivatives (eLLPs) were engineered for greater potency against Staphylococcus aureus (SA) and Pseudomonas aeruginosa (PA). Minimum bactericidal concentration (MBC) was determined in low and physiologic salt concentrations. MBC was decreased against SA and equivalent against PA in physiologic salt when compared to the parent compound LLP1. In a novel cystic fibrosis (CF) airway cell model, one derivative, WLSA5, reduced the number of adherent PA and only moderately affected CF cell viability. Overall, eLLPs are selectively toxic to bacteria and may be useful against CF airway infections.

Relapsed non-Hodgkin's lymphoma diagnosed by flexible bronchoscopy.

Pulmonary relapse of non-Hodgkin's lymphoma (NHL) occurred in a 10-year-old girl who presented with cough, blood-tinged sputum, and chest tightness. The diagnosis of Ki-1 (CD30) anaplastic large-cell lymphoma was established using bronchoalveolar lavage (BAL) and transbronchial biopsy (TBB). These procedures demonstrated malignant cells that stained positive for CD30 and had the t(2;5) translocation, thereby avoiding the need for an open lung biopsy.

Lentivirus lytic peptide 1 perturbs both outer and inner membranes of Serratia marcescens.

Bis-lentivirus lytic protein 1 (Bis-LLP1) and polymyxin B exhibited similar killing activities against Serratia marcescens. By electron microscopy, bis-LLP1 interacted with the outer and cytoplasmic bacterial membranes, while polymyxin B affected only the outer membrane. The results of standard biochemical probes supported the findings of the electron microscopy studies, suggesting that these antimicrobial peptides have different mechanisms of action.