Genome sequencing of idiopathic pulmonary fibrosis in conjunction with a medical school human anatomy course

Serum MUC5AC protein levels are correlated with the development and severity of connective tissue disease-associated pulmonary interstitial lesions

Background

Mucin 5AC (MUC5AC) and mucin 5B (MUC5B) are the major components of airway mucins. The expression levels of MUC5AC and MUC5B are related to connective tissue disease-associated interstitial lung disease (CTD-ILD) in the promoter region of MUC5AC and MUC5B and the relevant bronchoalveolar lavage fluid. However, the serum protein levels of MUC5AC and MUC5B have not been tested in CTD-ILD patients. In this study, we tested the serum levels of MUC5AC and MUC5B proteins in CTD-ILD patients and assessed their relationship with the occurrence and development of ILD.

Methods

Serum samples were obtained from 168 CTD and 80 healthy participants from the First Affiliated Hospital of Xiamen University. The serum levels of MUC5AC and MUC5B proteins were measured by enzyme-linked immunosorbent assay.

Results

Of the 168 individuals with CTD, 70 had primary Sjögren’s syndrome (pSS), 64 had systemic sclerosis (SSc), and 34 had polymyositis/dermatomyositis (PM/DM). There were 116 cases with concurrent ILD; ILD scores were 1 (n=23), 2 (n=41), and 3 (n=52). Serum MUC5AC and MUC5B protein levels were considerably higher in CTD-ILD than CTD-only individuals or healthy controls (both p<0.005). Among the CTD subgroups, MUC5AC was higher in individuals with concurrent ILD than in those without ILD (all p<0.05). MUC5AC was positively correlated with ILD severity in all three CTD subgroups (all R>0.47 and all p<0.05). The MUC5B levels varied substantially between SSc and SSc patients with concurrent ILD (p=0.032) and were related to ILD severity only in PM/DM patients (R=0.346 and p=0.045).

Conclusion

MUC5AC is correlated with the occurrence and development of ILD, while MUC5B is associated with ILD diagnosis and severity in CTD subgroups. Serum MUC5AC levels present a definite diagnostic utility for CTD-ILD and as proxies for its severity.

Genomics Education in the Era of Personal Genomics: Academic, Professional, and Public Considerations

Since the completion of the Human Genome Project in 2003, genomic sequencing has become a prominent tool used by diverse disciplines in modern science. In the past 20 years, the cost of genomic sequencing has decreased exponentially, making it affordable and accessible. Bioinformatic and biological studies have produced significant scientific breakthroughs using the wealth of genomic information now available. Alongside the scientific benefit of genomics, companies offer direct-to-consumer genetic testing which provide health, trait, and ancestry information to the public. A key area that must be addressed is education about what conclusions can be made from this genomic information and integrating genomic education with foundational genetic principles already taught in academic settings. The promise of personal genomics providing disease treatment is exciting, but many challenges remain to validate genomic predictions and diagnostic correlations. Ethical and societal concerns must also be addressed regarding how personal genomic information is used. This genomics revolution provides a powerful opportunity to educate students, clinicians, and the public on scientific and ethical issues in a personal way to increase learning. In this review, we discuss the influence of personal genomics in society and focus on the importance and benefits of genomics education in the classroom, clinics, and the public and explore the potential consequences of personal genomic education.

Ethical Rationales and Guidelines for the Continued Use of Archival Collections of Embryonic and Fetal Specimens

Benefits from the use of cadavers in anatomical education are well described. Historically, human embryos and fetal cadavers were used in anatomy education to understand development and congenital malformations. Recently, three-dimensional printed models produced from archival fetal specimens, and online repositories of images from archival collections of embryos and fetuses, have been used as an educational tool in human development courses. Given that the archival specimens were likely obtained prior to the era of informed consent, this raises questions about their appropriate and ethical use. Because some institutions in the United States retain archival collections of embryonic and fetal specimens that were once used as educational tools, their existence and utility require frequent reexamination against contemporary ethical frameworks to guide appropriate use or utilization. Four ethical rationales for uses of these collections are examined, including destruction, indefinite storage, use in research, and use in health professions education. Guidelines for the use of archival collections of human embryos and fetuses are presented. Indefinite storage and use in health professions education are supported, while use in research is also permitted, however, such use is limited and dependent on circumstance and purpose. The development of current digital repositories and three-dimensionally printed models based on archival collections that were collected without informed consent, or those promoting commercial opportunity, are not supported. New embryonic and fetal donations obtained with informed consent should include reference to potential uses with new technology and virtual, genetic, or imaging applications.

Genome sequencing in a case of Niemann-Pick type C

Adult-onset Niemann–Pick disease type C (NPC) is an infrequent presentation of a rare neurovisceral lysosomal lipid storage disorder caused by autosomal recessive mutations in NPC1 (∼95%) or NPC2 (∼5%). Our patient was diagnosed at age 33 when he presented with a 10-yr history of difficulties in judgment, concentration, speech, and coordination. A history of transient neonatal jaundice and splenomegaly with bone marrow biopsy suggesting a lipid storage disorder pointed to NPC; biochemical (“variant” level cholesterol esterification) and ultrastructural studies in adulthood confirmed the diagnosis. Genetic testing revealed two different missense mutations in the NPC1 gene—V950M and N1156S. Symptoms progressed over >20 yr to severe ataxia and spasticity, dementia, and dysphagia with aspiration leading to death. Brain autopsy revealed mild atrophy of the cerebrum and cerebellum. Microscopic examination showed diffuse gray matter deposition of balloon neurons, mild white matter loss, extensive cerebellar Purkinje cell loss with numerous “empty baskets,” and neurofibrillary tangles predominantly in the hippocampal formation and transentorhinal cortex. We performed whole-genome sequencing to examine whether the patient harbored variants outside of the NPC1 locus that could have contributed to his late-onset phenotype. We focused analysis on genetic modifiers in pathways related to lipid metabolism, longevity, and neurodegenerative disease. We identified no rare coding variants in any of the pathways examined nor was the patient enriched for genome-wide association study (GWAS) single-nucleotide polymorphisms (SNPs) associated with longevity or altered lipid metabolism. In light of these findings, this case provides support for the V950M variant being sufficient for adult-onset NPC disease.

Pneumonia

The lung is constantly exposed to airborne infectious agents due to the large surface area of approximately 100 m². Therefore pneumonia is one of the most common lung diseases. Understanding infection requires understanding the routes of infections, the way invading organisms infect epithelial cells, as well as defense mechanisms of the lung tissue acquired during evolution.

 Different variants of infectious and non-infectious pneumonias are discussed; special types of pneumonias such as granulomatous and fibrosing pneumonias are presented under separate sections. Causing organisms and other causes of pneumonias are included, and their mode of action is included as far as understood.

The Anatomy to Genomics (ATG) Start Genetics medical school initiative: incorporating exome sequencing data from cadavers used for Anatomy instruction into the first year curriculum

BACKGROUND

The increasing use of next generation DNA sequencing in clinical medicine is exposing the need for more genetics education in physician training. We piloted an initiative to determine the feasibility of incorporating exome sequencing data generated from DNA obtained from cadavers used for teaching Anatomy into a first year medical student integrated block-style course.

METHODS

We optimized the procedure to obtain DNA for exome sequencing by comparing the quality and quantity of DNA isolated from several tissues by two different extraction methods. DNA was sequenced using exome capture and analyzed using standard methods. Single nucleotide variants (SNVs), as well as small insertions/deletions, with potential functional impact were selected by faculty for student teams to independently investigate and prepare presentations on their findings.

RESULTS

A total of seven cadaver DNAs were sequenced yielding high quality results. SNVs were identified that were associated, with known physical traits and disease susceptibility, as well as pharmacogenomic phenotypes. Students presented findings based on correlation with known clinical information about the cadavers' diseases and traits.

CONCLUSION

Exome sequencing of cadaver DNA is a useful tool to integrate Anatomy with Genetics and Biochemistry into a first year medical student core curriculum.

Candidate genes of idiopathic pulmonary fibrosis: current evidence and research

Idiopathic pulmonary fibrosis (IPF) is a group of common and lethal forms of idiopathic interstitial pulmonary disease. IPF is characterized by a progressive decline in lung function with a median survival of 2-3 years after diagnosis. Although the pathogenesis of the disease remains unknown, genetic predisposition could play a causal role in IPF. A set of genes have been identified as candidate genes of IPF in the past 20 years. However, the recent technological advances that allow for the analysis of millions of polymorphisms in different subjects have deepened the understanding of the genetic complexity of IPF susceptibility. Genome-wide association studies and whole-genome sequencing continue to reveal the genetic loci associated with IPF risk. In this review, we describe candidate genes on the basis of their functions and aim to gain a better understanding of the genetic basis of IPF. The discovered candidate genes may help to clarify pivotal aspects in the diagnosis, prognosis, and therapies of IPF.