Gene expression profile in cases of infectious death in infancy.

BACKGROUND: Genetic predispositions in cases suffering sudden unexpected infant death have been a research focus worldwide during the past decade. Despite large efforts, there is still uncertainty concerning the molecular pathogenesis of these deaths. With genetic technology in constant development, the possibility of an alternative approach into this research field has become available, like mRNA expression studies. METHODS: In this study, we investigated mRNA gene expression in 14 cases who died suddenly and unexpectedly from infection without a history of severe illness prior to death. The control group included eight accidents, two cases of natural death, one undetermined, one case of medical malpractice, and two homicides. The study included tissue from liver, heart, and brain using Illumina whole-genome gene expression assay. RESULTS: From the array, 19 genes showed altered expression in the infectious deaths compared to controls. Tissue from the heart showed 15 genes with altered mRNA expression compared to the control group. CONCLUSIONS: Downregulation of KCNE5 in heart tissue from cases of infectious death was of particular interest. Variants of KCNE5 are associated with Brugada syndrome and sudden death and could be responsible for the fatal outcome in the group of infectious death. IMPACT: KCNE5 is downregulated in tissue from the heart in cases of infectious death in infancy. This study provides knowledge about the gene expression profile in cases of infectious death. Variants of a gene known to give increased risk of cardiac arrhythmia is downregulated in cases of infectious death in infancy. The results could give us better knowledge as to why some infants do not survive an infection. This study provides a candidate gene for future studies.

Polymorphisms in the myeloid differentiation primary response 88 pathway do not explain low expression levels in sudden infant death syndrome.

AIM: The aim of this study was to investigate if a range of known rare and common genetic variants in the Toll-like receptor 4 (TLR4)/myeloid differentiation primary response 88 (MyD88) pathway were present or overrepresented in sudden infant death syndrome (SIDS) compared to controls. METHODS: Genetic variations in the genes encoding TLR4, MyD88 and Interleukin-1 receptor-associated kinase 4 were analysed. The subjects investigated included 158 SIDS cases with a median age of 15.25 weeks (2-47 weeks), 80 cases of infectious death with a median age of 24.9 weeks (0-285 weeks) and 199 adult controls with a median age of 50 years (11-86 years). The cases were collected in the years 1988-2017, and the autopsies were performed at the Department of Forensic Sciences at Oslo University Hospital, Oslo, Norway. RESULTS: The results showed that none of the genetic variants selected from the MyD88 pathway were associated with neither SIDS nor infectious death. Most of the rare genetic variants were homozygote for the common allele in all groups, while the rest revealed allelic variation. CONCLUSION: The genetic variations investigated in this study did not appear to be involved in the pathogenesis of SIDS.

Inconsistent classification of unexplained sudden deaths in infants and children hinders surveillance, prevention and research: recommendations from The 3rd International Congress on Sudden Infant and Child Death.

This report details the proceedings and conclusions from the 3rd International Congress on Unexplained Deaths in Infants and Children, held November 26-27, 2018 at the Radcliffe Institute at Harvard University. The Congress was motivated by the increasing rejection of the diagnosis Sudden Infant Death Syndrome (SIDS) in the medical examiner community, leading to falsely depressed reported SIDS rates and undermining the validity and reliability of the diagnosis, which remains a leading cause of infant and child mortality. We describe the diagnostic shift away from SIDS and the practical issues contributing to it. The Congress was attended by major figures and opinion leaders in this area from countries significantly engaged in this problem. Four categories (International Classification of Diseases (ICD)-11 categories of MH11, MH12, MH14, PB00-PB0Z) were recommended for classification, and explicit definitions and guidance were provided for death certifiers. SIDS was reframed as unexplained sudden death in infancy or SIDS/MH11 to emphasize that either term signifies the lack of explanation following a rigorous investigation. A distinct category for children over the age of 1 was recommended (MH12). Definitions and exclusions were provided for the alternative categories of accidental asphyxia and undetermined. As recommended, unexplained sudden death in infancy or SIDS on a death certificate will code a unique, trackable entity, accurately reflecting the inability to determine a definitive explanation, while satisfying surveillance needs and reliable identification for research efforts. The conclusions will be submitted to the World Health Organization for inclusion in the upcoming ICD-11.

The gene encoding the inwardly rectifying potassium channel Kir4.1 may be involved in sudden infant death syndrome.

AIM: Disturbances in brain function and development may play a role in sudden infant death syndrome (SIDS). This Norwegian study aimed to test the hypothesis that specific variants of genes involved in water transport and potassium homeostasis would be predisposing factors for SIDS. METHODS: Genetic variation in the genes encoding aquaporin-4 (AQP4), Kir4.1 (KCNJ10) and α-syntrophin was analysed in 171 SIDS cases (62.6% male) with a median age of 15.5 (2-52) weeks and 398 adult controls (70.6% male) with a median age of 44 (11-91) years. All the subjects were Caucasians who were autopsied from 1988 to 2013. RESULTS: The CC genotype of rs72878794 in the AQP4 gene and a combination of the CC genotype in rs17375748, rs1130183, rs12133079 and rs1186688 in KCNJ10 (4xCC) were found to be associated with SIDS. The SIDS cases with the 4xCC SNP combination were younger than the SIDS cases with other genotype combinations (p = 0.006). CONCLUSION: This study indicates that genetic variations in KCNJ10 and AQP4 may be predisposing factors for SIDS. Alterations in the expression of the AQP4/Kir4.1 complex can disrupt water and ion homeostasis, which may influence brain development and facilitate brain oedema formation This may be especially unfavourable during the first weeks of life.

Altered gene expression and possible immunodeficiency in cases of sudden infant death syndrome.

BACKGROUND: A large number of studies have tried to uncover a genetic predisposition for sudden infant death syndrome (SIDS), but there is still uncertainty concerning the pathogenesis of these deaths. The purpose of this study was to investigate mRNA gene expression in SIDS cases and controls, in order to uncover genes that are differentially expressed in the two groups. METHODS: Tissue from brain, heart, and liver from 15 SIDS cases and 15 controls were included in the study, and mRNA expression was determined using the Illumina whole genome gene expression DASL HT assay. RESULTS: Seventeen genes showed significantly altered expression compared to controls, after correction for multiple testing. Three genes involved in the immune system were of particular interest, including the downregulation of MyD88 in tissue from SIDS brains, as well as the downregulation of the genes encoding CCL3 and UNC13 in the liver. CONCLUSION: These findings indicate that there is an altered expression of genes involved in the inflammatory process in a proportion of SIDS cases, which further strengthen the hypothesis that impaired immune response play a role in this syndrome.

The novel colorectal cancer biomarkers CDO1, ZSCAN18 and ZNF331 are frequently methylated across gastrointestinal cancers.

We have previously shown that gastrointestinal cancers display similar epigenetic aberrations. In a recent study, we identified frequently methylated genes for cholangiocarcinoma (CDO1, DCLK1, SFRP1 and ZSCAN18), where one of these genes, DCLK1, was also confirmed to be highly methylated in colorectal cancer. The aim of the present study was to determine whether these four genes, in addition to one gene found to be methylated in colon cancer cell lines (ZNF331), are commonly methylated across gastrointestinal malignancies, as well as explore their role as potential biomarkers. Quantitative methylation specific PCR (qMSP) of colorectal cancer (n=164) and normal colorectal mucosa (n=106) samples showed that all genes were frequently methylated in colorectal cancer (71-92%) with little or no methylation in normal mucosa (0-3%). Methylation of minimum two of these five genes identified 95% of the tumors with a specificity of 98%, and an area under the receiver operating characteristics curve (AUC) of 0.98. For gastric (n=25) and pancreatic (n=20) cancer, the same panel detected 92% and 90% of the tumors, respectively. Seventy-four cancer cell lines were further analyzed by qMSP and real time RT-PCR. In addition to the previously reported DCLK1, a high negative correlation between promoter DNA methylation and gene expression was observed for CDO1, ZNF331 and ZSCAN18. In conclusion, the high methylation frequency of these genes in colorectal- as well as in gastric-, pancreatic- and bile duct cancer confirmed an epigenetic similarity between gastrointestinal cancer types, and simultaneously demonstrated their potential as biomarkers, particularly for colorectal cancer detection.

A novel transcript, VNN1-AB, as a biomarker for colorectal cancer.

Colorectal cancer is a global health challenge with high incidence rate and mortality. The patients' prognosis is strongly associated with disease stage and currently there is a need for improved prognostic and predictive biomarkers. In this study, novel colorectal cancer-specific transcript structures were nominated from whole transcriptome sequencing of seven colorectal cancer cell lines, two primary colorectal carcinomas with corresponding normal colonic mucosa and 16 normal tissues. The nominated transcripts were combined with gene level outlier expression analyses in a cohort of 505 colorectal cancers to identify biomarkers with capacity to stratify colorectal cancer subgroups. The transcriptome sequencing data and outlier expression analysis revealed 11 novel colorectal cancer-specific exon-exon junctions, of which 3 were located in the gene VNN1. The junctions within VNN1 were further characterized using rapid amplification of cDNA ends (RACE) and the prevalence of the subsequently characterized novel transcript, VNN1-AB, was investigated by real-time RT-PCR in 291 samples of miscellaneous origins. VNN1-AB was not present in any of the 43 normal colorectal tissue samples investigated, but in 5 of the 6 polyps, and 102 of the 136 (75%) colorectal cancers. We have identified a novel transcript of the VNN1 gene, with an organ-confined complete specificity for colorectal neoplasia.

Genetic variation in the monoamine oxidase A and serotonin transporter genes in sudden infant death syndrome.

AIM: The purpose of this study was to investigate common polymorphisms in the genes encoding monoamine oxidase A (MAOA) and serotonin transporter (5-HTT) in Norwegian cases of sudden infant death syndrome (SIDS). This was done to further elucidate the role of genetic variation in these genes and SIDS. METHODS: A variable number of tandem repeat area in the promoter of the MAOA gene and rs25531 in the promoter region of the gene encoding 5-HTT were investigated in 193 SIDS cases and 335 controls. The methods used were polymerase chain reaction, restriction fragment analysis and gel electrophoresis. RESULTS: There were no differences between SIDS cases and controls for any of the investigated polymorphisms. This was also true when male and female SIDS cases were analysed separately. CONCLUSION: This article indicates that neither the VNTR in the promoter of the MAOA gene, nor rs25531 in the gene encoding 5-HTT, is involved in SIDS. However, as medullary serotonergic abnormalities most likely contribute to the death in at least some SIDS cases, it is important to investigate these genes, as well as other genes involved in the serotonergic network, in more detail.

Is there any correlation between HLA-DR expression in laryngeal mucosa and interleukin gene variation in sudden infant death syndrome?

AIM: The mucosal immune system and cytokines are activated in a large proportion of cases of sudden infant death syndrome (SIDS). Our aim was to search for a possible association between cytokine polymorphisms and immune stimulation of the laryngeal mucosal in SIDS. METHODS: HLA-DR expression in laryngeal mucosal glands and surface epithelium in 97 SIDS victims was evaluated applying a semi-quantitative scoring system. The findings were related to cytokine gene polymorphisms as well as to the level of various cytokines in the cerebrospinal fluid (CSF). A risk score was established: a score of 0 prepresenting negative HLA-DR, supine position and no fever prior to death. RESULTS: The IL-6 -176CG/CC genotype was found in 92.3% of the SIDS cases with positive score for all risk factors (p = 0.01). Infants with high HLA-DR score had high levels of IL-6 in the cerebrospinal fluid (>30 µg/L) (p = 0.005). Furthermore, the IL-8 SNPs -781 CT/TT genotypes and -251 AA/AT genotypes were observed in 93% of the SIDS cases with one or more of the risk factors present compared with SIDS cases no risk factors reported (p = 0.003 and p = 0.016, respectively). CONCLUSION: This study adds further evidence to the hypothesis that there are genetically associated disturbances of immunological homoeostasis in SIDS.

The exon-level biomarker SLC39A14 has organ-confined cancer-specificity in colorectal cancer.

An alternative transcript variant of SLC39A14, caused by pre-mRNA splicing, was recently suggested as a biomarker for colorectal cancer (CRC). In our study, we have validated the cancer-specific splicing pattern of the mutually exclusive exons 4A and 4B in altogether 244 colorectal tissue samples. Exon-specific quantitative RT-PCR analyses across 136 Stage I-IV CRC samples and 44 normal colonic mucosa samples showed complete cancer-specificity, as well as 94% sensitivity of SLC39A14-exon4B relative to SLC39A14-exon4A expression. However, across 20 samples from a range of healthy tissues, 18 expressed the CRC variant. This was true also for ten benign lymph nodes, demonstrating that the cancer-specificity is mainly confined to the colon and rectum. Hence, clinical use of SLC39A14-exon4B as a detection marker for CRC other than in samples taken from the bowel wall is diminished. Prognostic value by detection of metastasis to lymph nodes is also abated, elucidating an important pitfall to biomarker discovery. However, analyses of ten nondysplastic biopsies from patients with active inflammatory bowel disease showed negative results in seven samples and only weakly positive results in three samples, suggesting value of SLC39A14-exon4B as a marker to distinguish CRC from other pathologic conditions of the colon. In conclusion, the SLC39A14-exon4B transcript variant is a CRC biomarker with high sensitivity and organ-confined specificity. Further use of the transcript and its encoded protein isoform should be explored in an organ-confined context.

Sudden and unexpected death in early life: proceedings of a symposium in honor of Dr. Henry F. Krous.

Reported here are the proceedings of a symposium given in honor of Dr. Henry F. Krous upon his retirement as Clinical Professor of Pathology and Pediatrics at the University of California Schools of Medicine, and as Director of the San Diego SIDS/SUDC Research Project. Dr. Krous' distinguished 37-year-career was dedicated to research into sudden unexpected death in infancy and childhood, notably the sudden infant death syndrome (SIDS) and sudden unexplained death in childhood (SUDC). The presentations were given at the International Conference on Stillbirth, SIDS, and infant survival on October 5, 2012, in Baltimore, MD, USA. Eight colleagues of Dr. Krous whose own professional careers were touched by his efforts discussed forensic issues related to SIDS, tissue banking, animal models in SIDS, brainstem studies in SIDS, genetic studies in SIDS, establishment of a SUDC registry, neuropathologic research in SUDC, and potential shared mechanisms underlying sudden and unexpected death in early life. The wide scope of the presentations crossed the disciplines of forensic pathology, pediatric pathology, neuropathology, neuroscience, physiology, genetics, and bereavement, and attest to Dr. Krous' far-reaching influence upon SIDS and SUDC research.

Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas.

BACKGROUND: The presence of cancer-specific DNA methylation patterns in epithelial colorectal cells in human feces provides the prospect of a simple, non-invasive screening test for colorectal cancer and its precursor, the adenoma. This study investigates a panel of epigenetic markers for the detection of colorectal cancer and adenomas. METHODS: Candidate biomarkers were subjected to quantitative methylation analysis in test sets of tissue samples from colorectal cancers, adenomas, and normal colonic mucosa. All findings were verified in independent clinical validation series. A total of 523 human samples were included in the study. Receiver operating characteristic (ROC) curve analysis was used to evaluate the performance of the biomarker panel. RESULTS: Promoter hypermethylation of the genes CNRIP1, FBN1, INA, MAL, SNCA, and SPG20 was frequent in both colorectal cancers (65-94%) and adenomas (35-91%), whereas normal mucosa samples were rarely (0-5%) methylated. The combined sensitivity of at least two positives among the six markers was 94% for colorectal cancers and 93% for adenoma samples, with a specificity of 98%. The resulting areas under the ROC curve were 0.984 for cancers and 0.968 for adenomas versus normal mucosa. CONCLUSIONS: The novel epigenetic marker panel shows very high sensitivity and specificity for both colorectal cancers and adenomas. Our findings suggest this biomarker panel to be highly suitable for early tumor detection.

Gene variants predisposing to SIDS: current knowledge.

Genetic risk factors play a role in sudden unexpected infant death; either as a cause of death, such as in cases with medium-chain acyl-coenzyme A dehydrogenase deficiency and cardiac arrest due to long QT syndrome, or as predisposing factors for sudden infant death syndrome (SIDS). Most likely genetic predisposition to SIDS represent a polygenic inheritance pattern leading to sudden death when combined with other risk factors, such as a vulnerable developmental stage of the central nervous system and/or the immune system, in addition to environmental risk factors, such as a common cold or prone sleeping position. Genes involved in the regulation of the immune system, cardiac function, the serotonergic network and brain function and development have so far emerged as the most important with respect to SIDS. The purpose of the present paper is to survey current knowledge on SIDS and possible genetic contributions.

Aquaporin-4 gene variation and sudden infant death syndrome.

The purpose of this study was to investigate the aquaporin-4 (AQP4) gene in cases of sudden infant death syndrome (SIDS) and controls and to elucidate the hypothesis that a genetically determined disturbed water homeostasis in the brain is involved as a predisposing factor in SIDS. The single nucleotide polymorphisms (SNPs) rs2075575, rs4800773, rs162004, and rs3763043 in the AQP4 gene were investigated in 141 SIDS cases and 179 controls. For each SIDS case, a brain/body weight ratio was calculated. The study revealed an association between the T allele and the CT/TT genotypes of rs2075575 and SIDS (C versus T, p < 0.01; CC versus CT/TT, p = 0.03). For the other three investigated SNPs, there were no differences in genotype frequencies between SIDS cases and controls. For the SNP rs2075575, it was also found an association between brain/body weight ratio and genotype in the SIDS cases aged 0.3-12 wk (p = 0.014, median ratio CC 10.6, CT/TT 12.1). In conclusion, this study indicates that rs2075575 may be of significance as a predisposing factor for SIDS, and that the CT/TT genotypes are associated with an increased brain/body weight ratio in infants dying from SIDS during the vulnerable period from birth up to 3 mo of age.

Interleukin-6 and the serotonergic system of the medulla oblongata in the sudden infant death syndrome.

Mild infection may trigger sudden death in the vulnerable infant by cytokine interactions with a compromised medullary serotonergic (5-HT) system, leading to disrupted cardiorespiratory regulation and sleep-related sudden death. The cytokine interleukin (IL)-6 is elevated in the cerebrospinal fluid in SIDS. We tested the hypothesis that the expression of IL-6 receptors (IL-6R) and/or gp130 (involved in IL-6R signaling) is altered in the medullary 5-HT system in SIDS. Immunohistochemistry of IL-6R and gp130 was performed on medullae from 25 SIDS infants, 20 infectious deaths, and 14 controls using a semi-quantitative grading system. In the SIDS cases, mean IL-6R intensity grade in the arcuate nucleus (major component of medullary 5-HT system) was significantly higher than in the control group (2.00 +/- 0.07 vs. 1.77 +/- 0.08, P = 0.04), with no other differences in IL-6R or gp130 expression at any other site. Arcuate 5-HT neurons expressed IL-6R, indicating a site of IL-6/5-HT interaction. In SIDS, IL-6R expression is abnormal in the arcuate nucleus, the putative human homolog of rodent ventral medullary chemosensitivity sites involving 5-HT. Aberrant interactions between IL-6 and the arcuate nucleus may contribute to impaired responses to hypercapnia generated by infection (hyper-metabolism) combined with rebreathing.

Novel mutations of the suppressor gene PTEN in colorectal carcinomas stratified by microsatellite instability- and TP53 mutation- status.

PTEN regulates cell homeostasis by inhibiting growth signals transduced through PI3-kinases. The gene is mutated in several cancer types, but so far, only a limited number of mutations have been reported in colorectal cancer. In the present study, direct sequencing was used to analyze the whole coding region and exon-intron boundaries of PTEN in a series of microsatellite stable (n=34) and microsatellite unstable (n=30) colorectal carcinomas with known TP53 mutation status. We detected 21 PTEN mutations in altogether 13 tumors (20%), including 19 mutations in the coding sequence and two in the exon-intron boundaries. Sixteen of these alterations have not been previously reported in colorectal cancer. Furthermore, seven out of the 13 altered tumors harbored more than one mutation, potentially leading to loss of gene function. Finally, all PTEN mutations found were in tumors harboring wild-type TP53. In conclusion, PTEN is mutated in a significant subgroup of colorectal carcinomas, and our findings further extend the previously small spectrum of reported PTEN changes. Additionally, it seems that mutations in PTEN and TP53 are mutually exclusive for this cancer type.

Prevalence of long-QT syndrome gene variants in sudden infant death syndrome.

BACKGROUND: The hypothesis that some cases of sudden infant death syndrome (SIDS) could be caused by long-QT syndrome (LQTS) has been supported by molecular studies. However, there are inadequate data regarding the true prevalence of mutations in arrhythmia-susceptibility genes among SIDS cases. Given the importance and potential implications of these observations, we performed a study to more accurately quantify the contribution to SIDS of LQTS gene mutations and rare variants. METHODS AND RESULTS: Molecular screening of 7 genes (KCNQ1, KCNH2, SCN5A, KCNE1, KCNE2, KCNJ2, CAV3) associated with LQTS was performed with denaturing high-performance liquid chromatography and nucleotide sequencing of genomic DNA from 201 cases diagnosed as SIDS according to the Nordic Criteria, and from 182 infant and adult controls. All SIDS and control cases originated from the same regions in Norway. Genetic analysis was blinded to diagnosis. Mutations and rare variants were found in 26 of 201 cases (12.9%). On the basis of their functional effect, however, we considered 8 mutations and 7 rare variants found in 19 of 201 cases as likely contributors to sudden death (9.5%; 95% CI, 5.8 to 14.4%). CONCLUSIONS: We demonstrated that 9.5% of cases diagnosed as SIDS carry functionally significant genetic variants in LQTS genes. The present study demonstrates that sudden arrhythmic death is an important contributor to SIDS. As these variants likely modify ventricular repolarization and QT interval duration, our results support the debated concept that an ECG would probably identify most infants at risk for sudden death due to LQTS either in infancy or later on in life.

Gene methylation profiles of normal mucosa, and benign and malignant colorectal tumors identify early onset markers.

BACKGROUND: Multiple epigenetic and genetic changes have been reported in colorectal tumors, but few of these have clinical impact. This study aims to pinpoint epigenetic markers that can discriminate between non-malignant and malignant tissue from the large bowel, i.e. markers with diagnostic potential. The methylation status of eleven genes (ADAMTS1, CDKN2A, CRABP1, HOXA9, MAL, MGMT, MLH1, NR3C1, PTEN, RUNX3, and SCGB3A1) was determined in 154 tissue samples including normal mucosa, adenomas, and carcinomas of the colorectum. The gene-specific and widespread methylation status among the carcinomas was related to patient gender and age, and microsatellite instability status. Possible CIMP tumors were identified by comparing the methylation profile with microsatellite instability (MSI), BRAF-, KRAS-, and TP53 mutation status. RESULTS: The mean number of methylated genes per sample was 0.4 in normal colon mucosa from tumor-free individuals, 1.2 in mucosa from cancerous bowels, 2.2 in adenomas, and 3.9 in carcinomas. Widespread methylation was found in both adenomas and carcinomas. The promoters of ADAMTS1, MAL, and MGMT were frequently methylated in benign samples as well as in malignant tumors, independent of microsatellite instability. In contrast, normal mucosa samples taken from bowels without tumor were rarely methylated for the same genes. Hypermethylated CRABP1, MLH1, NR3C1, RUNX3, and SCGB3A1 were shown to be identifiers of carcinomas with microsatellite instability. In agreement with the CIMP concept, MSI and mutated BRAF were associated with samples harboring hypermethylation of several target genes. CONCLUSION: Methylated ADAMTS1, MGMT, and MAL are suitable as markers for early tumor detection.