Targeted RNA-Sequencing Enables Detection of Relevant Translocations and Single Nucleotide Variants and Provides a Method for Classification of Hematological Malignancies-RANKING

BACKGROUND: Patients with hematological malignancies (HMs) carry a wide range of chromosomal and molecular abnormalities that impact their prognosis and treatment. Since no current technique can detect all relevant abnormalities, technique(s) are chosen depending on the reason for referral, and abnormalities can be missed. We tested targeted transcriptome sequencing as a single platform to detect all relevant abnormalities and compared it to current techniques. MATERIAL AND METHODS: We performed RNA-sequencing of 1385 genes (TruSight RNA Pan-Cancer, Illumina) in bone marrow from 136 patients with a primary diagnosis of HM. We then applied machine learning to expression profile data to perform leukemia classification, a method we named RANKING. Gene fusions for all the genes in the panel were detected, and overexpression of the genes EVI1, CCND1, and BCL2 was quantified. Single nucleotide variants/indels were analyzed in acute myeloid leukemia (AML), myelodysplastic syndrome and patients with acute lymphoblastic leukemia (ALL) using a virtual myeloid (54 genes) or lymphoid panel (72 genes). RESULTS: RANKING correctly predicted the leukemia classification of all AML and ALL samples and improved classification in 3 patients. Compared to current methods, only one variant was missed, c.2447A>T in KIT (RT-PCR at 10(-4)), and BCL2 overexpression was not seen due to a t(14; 18)(q32; q21) in 2% of the cells. Our RNA-sequencing method also identified 6 additional fusion genes and overexpression of CCND1 due to a t(11; 14)(q13; q32) in 2 samples. CONCLUSIONS: Our combination of targeted RNA-sequencing and data analysis workflow can improve the detection of relevant variants, and expression patterns can assist in establishing HM classification

Health professionals’ perspective on the applicability of AO Spine PROST (patient reported outcome Spine trauma) in people with a motor-complete traumatic or non-traumatic spinal cord injury

Purpose: The AO Spine PROST (Patient Reported Outcome Spine Trauma) was developed for people with spine trauma and minor or no neurological impairment. The purpose is to investigate health professionals’ perspective on the applicability of the AO Spine PROST for people with motor-complete traumatic or non-traumatic spinal cord injury (SCI), using a discussion meeting and international survey study. Methods: A discussion meeting with SCI rehabilitation physicians in the Netherlands was performed, followed by a worldwide online survey among the AO Spine International community, involved in the care of people with SCI. Participants rated the comprehensibility, relevance, acceptability, feasibility and completeness of the AO Spine PROST on a 1–5 point scale (5 most positive). Comments could be provided per question. Results: The discussion meeting was attended by 13 SCI rehabilitation physicians. The survey was completed by 196 participants. Comprehensibility (mean ± SD: 4.1 ± 0.8), acceptability (4.0 ± 0.8), relevance (3.9 ± 0.8), completeness (3.9 ± 0.8), and feasibility (4.1 ± 0.7) of the AO Spine PROST were rated positively for use in people with motor-complete traumatic or non-traumatic SCI. Only a few participants questioned the relevance of items on the lower extremities (e.g., walking) or missed items on pulmonary functioning and complications. Some recommendations were made for improvement in instructions, terminology and examples of the tool. Conclusion: Health professionals found the AO Spine PROST generally applicable for people with motor-complete traumatic or non-traumatic SCI. This study provides further evidence for the use of the AO Spine PROST in spine trauma care, rehabilitation and research, as well as suggestions for its further development.</p

Feasibility of Follow-Up Studies and Reclassification in Spinocerebellar Ataxia Gene Variants of Unknown Significance

Spinocerebellar ataxia (SCA) is a heterogeneous group of neurodegenerative disorders with autosomal dominant inheritance. Genetic testing for SCA leads to diagnosis, prognosis and risk assessment for patients and their family members. While advances in sequencing and computing technologies have provided researchers with a rapid expansion in the genetic test content that can be used to unravel the genetic causes that underlie diseases, the large number of variants with unknown significance (VUSes) detected represent challenges. To minimize the proportion of VUSes, follow-up studies are needed to aid in their reclassification as either (likely) pathogenic or (likely) benign variants. In this study, we addressed the challenge of prioritizing VUSes for follow-up using (a combination of) variant segregation studies, 3D protein modeling, in vitro splicing assays and functional assays. Of the 39 VUSes prioritized for further analysis, 13 were eligible for follow up. We were able to reclassify 4 of these VUSes to LP, increasing the molecular diagnostic yield by 1.1%. Reclassification of VUSes remains difficult due to limited possibilities for performing variant segregation studies in the classification process and the limited availability of routine functional tests

Appraisals and coping mediate the relationship between resilience and distress among significant others of persons with spinal cord injury or acquired brain injury: A cross-sectional study

Background: Many significant others of persons with serious conditions like spinal cord injury (SCI) and acquired brain injury (ABI) report high levels of psychological distress. In line with the stress-coping model, the aim of the present study was to investigate the relationship between personal resource resilience and psychological distress, and whether appraisals of threat and loss, and passive coping mediate this relationship. Methods: Significant others (n = 228) of persons with SCI or ABI completed questionnaires shortly after admission to first inpatient rehabilitation after onset of the condition. The questionnaire included measures to assess psychological distress (Hospital Anxiety and Depression Scale), resilience (Connor-Davidson Resilience Scale-10), appraisals (Appraisals of Life Events scale, threat and loss) and passive coping (Utrecht Coping List). The PROCESS tool was used to test the presence of mediation. Confounding and differences between SCI and ABI were investigated. Results: High levels of psychological distress among significant others were found (34-41%). Fifty-five percent of the variance in psychological distress was explained by the relationship between resilience and psychological distress. This relationship was mediated by appraisals of threat and loss, and passive coping. The relationship between resilience and psychological distress was similar in the SCI and ABI groups. Conclusions: The results of our study indicate that appraisals of threat and loss and passive coping are mediating factors in the relationship between resilience and psychological distress. It seems useful to investigate if interventions focussing on psychological factors like resilience, appraisal and coping are effective to prevent or reduce psychological distress among significant others of persons with SCI or ABI

Long-term air pollution exposure, genome-wide DNA methylation and lung function in the lifelines cohort study

BACKGROUND: Long-term air pollution exposure is negatively associated with lung function, yet the mechanisms underlying this association are not fully clear. Differential DNA methylation may explain this association. OBJECTIVES: Our main aim was to study the association between long-term air pollution exposure and DNA methylation. METHODS: We performed a genome-wide methylation study using robust linear regression models in 1,017 subjects from the LifeLines cohort study to analyze the association between exposure to nitrogen dioxide (NO2) and particulate matter (PM2.5, fine particulate ma

Norepinephrine Augments Salmonella enterica-Induced Enteritis in a Manner Associated with Increased Net Replication but Independent of the Putative Adrenergic Sensor Kinases QseC and QseE

Stress has long been correlated with susceptibility to microbial infection. One explanation for this phenomenon is the ability of pathogens to sense and respond to host stress-related catecholamines, such as norepinephrine (NE). In Gram-negative enteric pathogens, it has been proposed that NE may facilitate growth by mediating iron supply, or it may alter gene expression by activating adrenergic sensor kinases. The aim of this work was to investigate the relative importance of these processes in a model in which NE alters the outcome of Salmonella enterica serovar Typhimurium infection. A bovine ligated ileal loop model was used to study the effect of NE on enteritis induced by S. Typhimurium and on the bacterial in vivo replication rate. Mutants lacking putative adrenergic receptor genes were assessed in the loop model, in a calf intestinal colonization model, and in vitro. S. Typhimurium-induced enteritis was significantly enhanced by addition of 5 mM NE. This effect was associated with increased net bacterial replication in the same model. Exogenous ferric iron also stimulated bacterial replication in the medium used but not transcription of enteritis-associated loci. The putative adrenergic sensors QseC and QseE were not required for NE-enhanced enteritis, intestinal colonization of calves, or NE-dependent growth in iron-restricted medium and did not influence expression or secretion of enteritis-associated virulence factors. Our findings support a role for stress-related catecholamines in modulating the virulence of enteric bacterial pathogens in vivo but suggest that bacterial adrenergic sensors may not be the vital link in such interkingdom signaling in Salmonella

Pooled resequencing of 122 ulcerative colitis genes in a large Dutch cohort suggests population-Specific associations of rare variants in MUC2

Genome-wide association studies have revealed several common genetic risk variants for ulcerative colitis (UC). However, little is known about the contribution of rare, large effect genetic variants to UC susceptibility. In this study, we performed a deep targeted resequencing of 122 genes in Dutch UC patients in order to investigate the contribution of rare variants to the genetic susceptibility to UC. The selection of genes consists of 111 established human UC susceptibility genes and 11 genes that lead to spontaneous colitis when knocked-out in mice. In addition, we sequenced the promoter regions of 45 genes where known variants exert cis-eQTL-effects. Targeted pooled re-sequencing was performed on DNA of 790 Dutch UC cases. The Genome of the Netherlands project provided sequence data of 500 healthy controls. After quality control and prioritization based on allele frequency and pathogenicity probability, follow-up genotyping of 171 rare variants was performed on 1021 Dutch UC cases and 1166 Dutch controls. Single-variant association and gene-based analyses identified an association of rare variants in the MUC2 gene with UC. The associated variants in the Dutch population could not be replicated in a German replication cohort (1026 UC cases, 3532 controls). In conclusion, this study has identified a putative role for MUC2 on UC susceptibility in the Dutch population and suggests a populationspecific contribution of rare variants to UC

Exome sequencing in patient-parent trios suggests new candidate genes for early-onset primary sclerosing cholangitis

BACKGROUND & AIMS Primary sclerosing cholangitis (PSC) is a rare bile duct disease strongly associated with inflammatory bowel disease (IBD). Whole-exome sequencing (WES) has contributed to understanding the molecular basis of very early-onset IBD, but rare protein-altering genetic variants have not been identified for early-onset PSC. We performed WES in patients diagnosed with PSC METHODS In this multicentre study, WES was performed on 87 DNA samples from 29 patient-parent trios with early-onset PSC. We selected rare (minor allele frequency <2%) coding and splice-site variants that matched recessive (homozygous and compound heterozygous variants) and dominant (de novo) inheritance in the index patients. Variant pathogenicity was predicted by an in-house developed algorithm (GAVIN), and PSC-relevant variants were selected using gene expression data and gene function. RESULTS In 22 of 29 trios we identified at least 1 possibly pathogenic variant. We prioritized 36 genes, harbouring a total of 54 variants with predicted pathogenic effects. In 18 genes, we identified 36 compound heterozygous variants, whereas in the other 18 genes we identified 18 de novo variants. Twelve of 36 candidate risk genes are known to play a role in transmembrane transport, adaptive and innate immunity, and epithelial barrier function. CONCLUSIONS The 36 candidate genes for early-onset PSC need further verification in other patient cohorts and evaluation of gene function before a causal role can be attributed to its variants.Peer reviewe