Optimisation of postmortem tissue preservation and alternative protocol for serotonin transporter gene polymorphisms amplification in SIDS and SIUD cases

Simultaneous Evaluation of the Preservative Effect of RNAlater on Different Tissues by Biomolecular and Histological Analysis

A major concern in biomedical research is the quality of biological samples. RNAlater is a stabilizer, which was originally developed for RNA preservation in fresh tissues and is important for collection and transportation. However, this reagent lacks a comprehensive and systematic evaluation of its preservative effect on different mammalian tissues under consistent experimental conditions. In this study, we collected liver, kidney, testis, brain, and colon tissues from mice and divided the samples into the following respective groups: fresh, RNAlater preserved, and liquid nitrogen snap frozen. Biomolecules (RNA, DNA, and protein) were extracted from each tissue in each group, and samples were formalin fixed and paraffin embedded for quality assessment. Our results revealed that high-quality (yield, purity, and integrity) nucleic acids could be extracted from all samples. Gene expression determined by quantitative real-time polymerase chain reaction exhibited no major difference among the three groups. Notably, we observed significant protein degradation in brain tissue preserved by RNAlater compared with fresh and snap-frozen tissue. Protein expression of the other four tissues was similar among the three groups. Hematoxylin and eosin staining of all tissue types indicated no apparent difference among the three groups. We concluded that high-quality nucleic acids can be obtained and tissue morphology conserved when tissues are preserved with RNAlater. However, there are tissue-specific differences in protein preservation when using RNAlater, which should be evaluated before extensive storage.

KIT exon 11 and PDGFRA exon 18 gene mutations in gastric GIST: proposal of a short panel for predicting therapeutic response

Background

GIST is the most common mesenchymal tumor of gastrointestinal tract and is more frequent in stomach. Its main mutations affect KIT and PDGFRA genes. Full genetic analysis panels are currently used to study mutations in GIST and other tumors. Considering that in gastric GIST KIT gene mutations in exon 11 are sensitive to IM whereas PDGFRΑ gene mutations in exon 18 (D842V) are resistant to the same drug, the aim of this study is to focus on these two molecular targets as a short alternative panel for predicting therapeutic response in gastric GIST which might optimize resources.

Methods

The genotypes of 38 cases of primary GIST were determined by performing bidirectional DNA sequencing.

Results

Exon 11 of KIT gene showed mutations in 65.3% and the exon 18 of PDGFRA gene showed 9% of cases. So it was possible to determine a subgroup of tumors which presented mutations in KIT exon 11 and PDGFRA exon 18.

Conclusion

Considering all of the foregoing analyzed globally, the application of short panel has impact on the cost and time of release of results to the physician, allowing a rapid approach to patients eligible for treatment with the target therapy.

A review of the optimisation of the use of formalin fixed paraffin embedded tissue for molecular analysis in a forensic post-mortem setting

Molecular analyses in a post-mortem setting are becoming increasingly common, particularly in cases of sudden unexplained death, with the aim of identifying genetic mutations which may be responsible for causing death. In retrospective investigations, the access to suitable autopsy biological samples may be limited, and often formalin fixed paraffin embedded (FFPE) tissue is the only sample available. The preservation of tissue in formalin is known to damage DNA through crosslinking activity. This results in the extraction of severely fragmented DNA of variable yields, which subsequently reduces the ability to perform downstream molecular analyses. Numerous studies have investigated possible improvements to various aspects of the DNA extraction and amplification procedures from FFPE tissue and this review aims to collate these optimization steps in a cohesive manner. A systematic review was performed of three major databases, which identified 111 articles meeting the inclusion criteria. Five main areas for optimization and improvements were identified in the workflow: (1) tissue type, (2) fixation process, (3) post-fixation, (4) DNA extraction procedure and (5) amplification. It was found that some factors identified, for example tissue type and fixation process, could not be controlled by the researcher when conducting retrospective analyses. For this reason, optimization should be performed in other areas, within the financial means of the laboratories, and in accordance with the purposes of the investigation. Implementation of one or more of the optimization measures described here is anticipated to assist in the extraction of higher quality DNA. Despite the challenges posed by FFPE tissue, it remains a valuable source of DNA in retrospective molecular forensic investigations.

Variants in TSPYL1 are not associated with sudden infant death syndrome in a cohort of deceased infants from Switzerland

Sudden infant death syndrome (SIDS) is currently the major cause of an unexpected and unexplained death of infants in the first year of lifetime in industrialized countries. Besides environmental factors also genetic factors have been identified as risk factors for SIDS. Notably, the mutation c.457dupG (p.Glu153Glyfs*17) in the TSPYL1 gene has been reported to cause autosomal recessive sudden infant death with dysgenesis of the testes syndrome (SIDDT) in an Old Order Amish community in Pennsylvania. The purpose of this study was to analyze whether variants of TSPYL1 are associated with the sudden infant death syndrome (SIDS) in the area of Europe from which the Amish descended. Mutation analysis of the entire TSPYL1 gene was performed in a cohort of 165 SIDS cases with mostly Swiss ethnic origin, in comparison to 163 German controls. Eight known polymorphisms were detected, none of which was significantly associated with SIDS. One deceased girl was heterozygous for the hitherto unreported TSPYL1 variant c.106C>G (p.Leu36Val), and two affected girls were heterozygous for the rare known TSPYL1 variant rs140756663 (c.1098C>A, p.Phe366Leu). In addition, one deceased boy was heterozygous for the rare common silent nucleotide substitution c.718C>T (p.Leu240Leu, rs150144081), while one control was heterozygous for the rare silent nucleotide substitution rs56190632 (c.760C>T; p.Leu254Leu). In silico analyses predicted a likely non-pathogenic effect for p.Leu36Val and p.Phe366Leu, respectively, although protein features might be affected. The Amish founder mutation was not detected in the analyzed SIDS cases and controls. Mutations and polymorphisms in the TSPYL1 gene were not associated with SIDS in a cohort of 165 deceased Swiss infants.

Gene expression profiling in human neurodegenerative disease

Transcriptome study in neurodegenerative disease has advanced considerably in the past 5 years. Increasing scientific rigour and improved analytical tools have led to more-reproducible data. Many transcriptome analysis platforms assay the expression of the entire genome, enabling a complete biological context to be captured. Gene expression profiling (GEP) is, therefore, uniquely placed to discover pathways of disease pathogenesis, potential therapeutic targets, and biomarkers. This Review summarizes microarray human GEP studies in the common neurodegenerative diseases amyotrophic lateral sclerosis (ALS), Parkinson disease (PD) and Alzheimer disease (AD). Several interesting reports have compared pathological gene expression in different patient groups, disease stages and anatomical areas. In all three diseases, GEP has revealed dysregulation of genes related to neuroinflammation. In ALS and PD, gene expression related to RNA splicing and protein turnover is disrupted, and several studies in ALS support involvement of the cytoskeleton. GEP studies have implicated the ubiquitin-proteasome system in PD pathogenesis, and have provided evidence of mitochondrial dysfunction in PD and AD. Lastly, in AD, a possible role for dysregulation of intracellular signalling pathways, including calcium signalling, has been highlighted. This Review also provides a discussion of methodological considerations in microarray sample preparation and data analysis.

Investigation of 5-HTT expression using quantitative real-time PCR in the human brain in SIDS Italian cases

The sudden infant death syndrome (SIDS) is the main cause of postneonatal infant death, being defined as the sudden death of an infant under one year of age that remains unexplained after a complete clinical review, autopsy and death scene investigation. The neurotransmitter serotonin (5-HT) is involved in the regulation of a broad array of behavioral and biological functions. By controlling the reuptake of 5-HT from the extracellular space, the serotonin transporter (5-HTT) regulates the duration and strength of the interactions between 5-HT and its receptors. It has been shown that the activity of the human 5-HTT gene promoter is regulated by polymorphic repetitive elements, resulting in differences in the efficacy of 5-HTT reuptake among the allelic variants: the short (S) allele is associated with lower transcriptional efficiency of the promoter compared with the long (L) allele. Using qRT-PCR we studied the gene expression of 5-HTT in ten SIDS cases, previously analyzed at a molecular level and which showed the genetic S/S profile. In nine cases we observed 5-HTT expression levels comparable to those seen in the control case, while in one case there was a remarkable reduction in the expression of the gene. It is presumable that, despite the presence of the same S/S genotype, the different genetic background could influence the transcript stability and that the polimorphic variant of the 5-HTT gene could respond differently to the external environmental stimuli.

Gene expression analysis characterizes antemortem stress and has implications for establishing cause of death

Within the field of forensic pathology, determination of the cause of death depends upon identifying physical changes in the corpse or finding diagnostic laboratory abnormalities. When such perturbations are absent, definitive assignment of a cause of death may be difficult or impossible. An example of such a problem is sudden infant death syndrome (SIDS), a common cause of neonatal mortality that does not produce physical findings or laboratory abnormalities. Although respiratory failure as a cause of SIDS represents the most widely held hypothesis, sudden cardiac death and hyperthermia have also been advanced as possible causes. We hypothesize that each of these physiological stresses would produce a different pattern of premortem gene expression and that these patterns of gene expression would remain evident in tissues collected postmortem. If these patterns were sufficiently distinctive, they could be used to identify the cause of death. Using an infant mouse model, we compared gene expression patterns in liver tissue after sudden death, lethal hyperthermia, and lethal hypoxia. Each of these conditions produced readily distinguishable differences in gene expression patterns. With the K-nearest neighbor classification algorithm, only 10 genes are necessary to correctly classify samples. If the liver tissue was not harvested immediately after death, additional alteration in gene expression patterns resulted; however, these alterations did not affect the group of genes used to classify the samples. Our findings suggest that gene expression analysis from tissues collected postmortem may provide useful clues about certain physiologic stresses that may precede death.

Post-mortem echocardiography as a guide to cardiac autopsy-a worthwhile concept?

Sudden and unexpected death in the young is a common and worldwide problem. Sudden, unexpected death in infancy (SUDI), clinically unexpected death in an infant between one week and one year of age, affects around 1 in 1000 infants. Autopsy will reveal a specific cause of death in only one third of cases. This has led to various ancillary examinations in an effort to increase the diagnostic yield of the autopsy.

In this case report it is suggested that another diagnostic modality, that of the post-mortem echocardiogram might be a worthwhile concept to explore.