Work-related head injury and industry sectors in Finland: causes and circumstances

OBJECTIVE

Despite the continuous development of occupational safety, the prevalence of work-related head injuries is excessive. To promote prevention, we conducted a study evaluating the risks and pathways that precede head injuries in different economic activity sectors.

METHODS

In Finland, more than 90% of employees are covered by inclusive statutory workers' compensation. We obtained data on occupational head injuries in 2010-2017 from an insurance company database. The European Statistics on Accidents at Work (ESAW) variables represented the characteristics of the accidents and the injury. We analysed the risk factors, contributing events and injury mechanisms in 20 industry sectors, based on the Statistical Classification of Economic Activities in the European Community (NACE).

RESULTS

In the 32,898 cases, the most commonly affected area was the eyes (49.6%). The highest incidence of head injuries was in construction (15.7 per 1000 insurance years). Construction, manufacturing, and human health and social work activities stood out due to their distinctive ESAW category counts. 'Working with hand-held tools' [risk ratio (RR) 2.23, 95% confidence interval (CI) 2.14-2.32] in construction and 'operating machines' (RR 3.32, 95% CI 3.01-3.66) and 'working with hand-held tools' (1.99, 1.91-2.07) in manufacturing predicted head injury. The risk related to parameters of violence and threats in health and social work activities was nearly ninefold the risk of other sectors.

CONCLUSION

The risks and pathways preceding head injuries varied considerably. The highest head injury rates were in construction and manufacturing. Violence emerged as a major risk factor in human health and social work activities.

snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions

Motivation

Co-localization of trait associated SNPs for specific transcription-factor binding sites or regulatory regions in the genome can yield profound insight into underlying causal mechanisms. Analysis is complicated because the truly causal SNPs are generally unknown and can be either SNPs reported in GWAS studies or other proxy SNPs in their linkage disequilibrium. Hence, a comprehensive pipeline for SNP co-localization analysis that utilizes all relevant information about both the genotyped SNPs and their proxies is needed.

Results

We developed an R package snpEnrichR for SNP co-localization analysis. The software integrates different tools for random SNP generation and genome co-localization analysis to automatize and help users to create custom SNP co-localization analysis. We show via an example that including proxy SNPs in SNP co-localization analysis enhances the sensitivity of co-localization detection.

Availability and implementation

The software is available at https://github.com/kartiek/snpEnrichR.

Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells

The transcriptional network and protein regulators that govern T helper 17 (Th17) cell differentiation have been studied extensively using advanced genomic approaches. For a better understanding of these biological processes, we have moved a step forward, from gene- to protein-level characterization of Th17 cells. Mass spectrometry–based label-free quantitative (LFQ) proteomics analysis were made of in vitro differentiated murine Th17 and induced regulatory T (iTreg) cells. More than 4,000 proteins, covering almost all subcellular compartments, were detected. Quantitative comparison of the protein expression profiles resulted in the identification of proteins specifically expressed in the Th17 and iTreg cells. Importantly, our combined analysis of proteome and gene expression data revealed protein expression changes that were not associated with changes at the transcriptional level. Our dataset provides a valuable resource, with new insights into the proteomic characteristics of Th17 and iTreg cells, which may prove useful in developing treatment of autoimmune diseases and developing tumor immunotherapy.

T helper 17 (Th17) cells and induced regulatory T (iTreg) cells are two subsets of T helper cells differentiated from naïve cells that play important roles in autoimmune diseases, immune homeostasis, and tumor immunity. The differentiation process is achieved by changes in numerous proteins, including transcription regulators, enzymes, membrane receptors, and cytokines, which are critical in lineage commitment. To profile protein expression changes in Th17 and iTreg cells, we polarized murine naïve CD4+ T (Thp) cells in vitro to Th17 and iTreg cells and performed quantitative proteomic analysis of these cells. More than 4,000 proteins, covering almost all subcellular compartments, were detected. Quantitative comparison of the protein expression profiles resulted in the identification of proteins specifically expressed in the Th17 and iTreg cells. Importantly, our combined analysis of proteome and gene expression data revealed protein expression changes that were not associated with changes at the transcriptional level. The present study serves as a valuable resource that may prove useful in developing treatment of autoimmune diseases and cancer.

Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks

Motivation: Mechanistic models based on ordinary differential equations provide powerful and accurate means to describe the dynamics of molecular machinery which orchestrates gene regulation. When combined with appropriate statistical techniques, mechanistic models can be calibrated using experimental data and, in many cases, also the model structure can be inferred from time–course measurements. However, existing mechanistic models are limited in the sense that they rely on the assumption of static network structure and cannot be applied when transient phenomena affect, or rewire, the network structure. In the context of gene regulatory network inference, network rewiring results from the net impact of possible unobserved transient phenomena such as changes in signaling pathway activities or epigenome, which are generally difficult, but important, to account for.

Results: We introduce a novel method that can be used to infer dynamically evolving regulatory networks from time–course data. Our method is based on the notion that all mechanistic ordinary differential equation models can be coupled with a latent process that approximates the network structure rewiring process. We illustrate the performance of the method using simulated data and, further, we apply the method to study the regulatory interactions during T helper 17 (Th17) cell differentiation using time–course RNA sequencing data. The computational experiments with the real data show that our method is capable of capturing the experimentally verified rewiring effects of the core Th17 regulatory network. We predict Th17 lineage specific subnetworks that are activated sequentially and control the differentiation process in an overlapping manner.

Availability and Implementation: An implementation of the method is available at http://research.ics.aalto.fi/csb/software/lem/.

Contacts:jukka.intosalmi@aalto.fi or harri.lahdesmaki@aalto.fi

Abstract 5089: Evaluation of BMP4 and BMP7 induced gene expression changes in breast cancer cells reveals time-dependent transcription patterns and a common synexpression group of genes

Bone morphogenetic proteins (BMPs) are members of the transforming growth factor beta superfamily of growth factors. They are well-known for their key roles in the regulation of various developmental processes and bone formation, but in recent years, evidence has also accumulated of their crucial contribution in tumor biology. In particular, BMP4 and BMP7 have been implicated in breast cancer pathogenesis. However, little is known about BMP target genes in the context of tumor cells. Here, we used whole-genome microarrays to explore the effects of BMP4 and BMP7 treatment on global gene expression levels in seven breast cancer cell lines during a 6-point time series. Several complementary methods, including hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data, were used for data analysis. Both BMP ligands had a strong influence on gene expression levels, although the response to BMP4 treatment was more pronounced as compared to BMP7. As might have been expected, the cellular functions most strongly affected by the stimulation of BMP signaling were regulation of transcription and development. The observed transcriptional response, as well as its functional outcome, followed a temporal sequence, where the regulation of gene expression and signal transduction was followed by changes in transcripts involved in metabolism and cell proliferation. Hierarchical clustering analysis revealed distinct differences in the response of individual cell lines to BMPs, but also underlined a common synexpression group of genes for both ligands. Remarkably, the majority of the genes within these synexpression groups were shared by the two ligands, and thus these genes are likely to represent the core molecular responses common to BMP4 and BMP7 signaling pathways. Taken together, our data demonstrate that BMP signaling has a substantial effect on gene transcription in breast cancer cells and that the cellular functions affected follow a logical temporal pattern. Our results also reveal components of the cellular transcriptional response that are common to BMP4 and BMP7. Finally, our study provides a list of putative novel BMP target genes relevant in breast cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5089. doi:1538-7445.AM2012-5089

Analysis of BMP4 and BMP7 signaling in breast cancer cells unveils time-dependent transcription patterns and highlights a common synexpression group of genes

Background

Bone morphogenetic proteins (BMPs) are members of the TGF-beta superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP4 and BMP7, in particular, have been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We explored the effects of BMP4 and BMP7 treatment on global gene transcription in seven breast cancer cell lines during a 6-point time series, using a whole-genome oligo microarray. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data.

Results

Both ligands had a strong effect on gene expression, although the response to BMP4 treatment was more pronounced. The cellular functions most strongly affected by BMP signaling were regulation of transcription and development. The observed transcriptional response, as well as its functional outcome, followed a temporal sequence, with regulation of gene expression and signal transduction leading to changes in metabolism and cell proliferation. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMPs, but also highlighted a synexpression group of genes for both ligands. Interestingly, the majority of the genes within these synexpression groups were shared by the two ligands, probably representing the core molecular responses common to BMP4 and BMP7 signaling pathways.

Conclusions

All in all, we show that BMP signaling has a remarkable effect on gene transcription in breast cancer cells and that the functions affected follow a logical temporal pattern. Our results also uncover components of the common cellular transcriptional response to BMP4 and BMP7. Most importantly, this study provides a list of potential novel BMP target genes relevant in breast cancer.

Candidate driver genes in microsatellite-unstable colorectal cancer

Defects in the mismatch repair system lead to microsatellite instability (MSI), a feature observed in ∼ 15% of all colorectal cancers (CRCs). Microsatellite mutations that drive tumourigenesis, typically inactivation of tumour suppressors, are selected for and are frequently detected in MSI cancers. Here, we evaluated somatic mutations in microsatellite repeats of 790 genes chosen based on reduced expression in MSI CRC and existence of a coding mononucleotide repeat of 6-10 bp in length. All the repeats were initially sequenced in 30 primary MSI CRC samples and whenever frameshift mutations were identified in >20%, additional 70 samples were sequenced. To distinguish driver mutations from passengers, we similarly analyzed the occurrence of frameshift mutations in 121 intronic control repeats and utilized a statistical regression model to determine cut-off mutation frequencies for repeats of all types (A/T and C/G, 6-10 bp). Along with several know target genes, including TGFBR2, ACVR2, and MSH3, six novel candidate driver genes emerged that harbored significantly more mutations than identical control repeats. The mutation frequencies in 100 MSI CRC samples were 51% in G8 of GLYR1, 47% in T9 of ABCC5, 43% in G8 of WDTC1, 33% in A8 of ROCK1, 30% in T8 of OR51E2, and 28% in A8 of TCEB3. Immunohistochemical staining of GLYR1 revealed defective protein expression in tumors carrying biallelic mutations, supporting a loss of function hypothesis. This is a large scale, unbiased effort to identify genes that when mutated are likely to contribute to MSI CRC development.

High frequency of TTK mutations in microsatellite-unstable colorectal cancer and evaluation of their effect on spindle assembly checkpoint

Frameshift mutations frequently accumulate in microsatellite-unstable colorectal cancers (MSI CRCs) typically leading to downregulation of the target genes due to nonsense-mediated messenger RNA decay. However, frameshift mutations that occur in the 3' end of the coding regions can escape decay, which has largely been ignored in previous works. In this study, we characterized nonsense-mediated decay-escaping frameshift mutations in MSI CRC in an unbiased, genome wide manner. Combining bioinformatic search with expression profiling, we identified genes that were predicted to escape decay after a deletion in a microsatellite repeat. These repeats, located in 258 genes, were initially sequenced in 30 MSI CRC samples. The mitotic checkpoint kinase TTK was found to harbor decay-escaping heterozygous mutations in exon 22 in 59% (105/179) of MSI CRCs, which is notably more than previously reported. Additional novel deletions were found in exon 5, raising the mutation frequency to 66%. The exon 22 of TTK contains an A(9)-G(4)-A(7) locus, in which the most common mutation was a mononucleotide deletion in the A(9) (c.2560delA). When compared with identical non-coding repeats, TTK was found to be mutated significantly more often than expected without selective advantage. Since TTK inhibition is known to induce override of the mitotic spindle assembly checkpoint (SAC), we challenged mutated cancer cells with the microtubule-stabilizing drug paclitaxel. No evidence of checkpoint weakening was observed. As a conclusion, heterozygous TTK mutations occur at a high frequency in MSI CRCs. Unexpectedly, the plausible selective advantage in tumourigenesis does not appear to be related to SAC.

Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme

Background

Coordinated efforts to collect large-scale data sets provide a basis for systems level understanding of complex diseases. In order to translate these fragmented and heterogeneous data sets into knowledge and medical benefits, advanced computational methods for data analysis, integration and visualization are needed.

Methods

We introduce a novel data integration framework, Anduril, for translating fragmented large-scale data into testable predictions. The Anduril framework allows rapid integration of heterogeneous data with state-of-the-art computational methods and existing knowledge in bio-databases. Anduril automatically generates thorough summary reports and a website that shows the most relevant features of each gene at a glance, allows sorting of data based on different parameters, and provides direct links to more detailed data on genes, transcripts or genomic regions. Anduril is open-source; all methods and documentation are freely available.

Results

We have integrated multidimensional molecular and clinical data from 338 subjects having glioblastoma multiforme, one of the deadliest and most poorly understood cancers, using Anduril. The central objective of our approach is to identify genetic loci and genes that have significant survival effect. Our results suggest several novel genetic alterations linked to glioblastoma multiforme progression and, more specifically, reveal Moesin as a novel glioblastoma multiforme-associated gene that has a strong survival effect and whose depletion in vitro significantly inhibited cell proliferation. All analysis results are available as a comprehensive website.

Conclusions

Our results demonstrate that integrated analysis and visualization of multidimensional and heterogeneous data by Anduril enables drawing conclusions on functional consequences of large-scale molecular data. Many of the identified genetic loci and genes having significant survival effect have not been reported earlier in the context of glioblastoma multiforme. Thus, in addition to generally applicable novel methodology, our results provide several glioblastoma multiforme candidate genes for further studies.

Anduril is available at http://csbi.ltdk.helsinki.fi/anduril/

The glioblastoma multiforme analysis results are available at http://csbi.ltdk.helsinki.fi/anduril/tcga-gbm/

Mutations in the circadian gene CLOCK in colorectal cancer

The circadian clock regulates daily variations in physiologic processes. CLOCK acts as a regulator in the circadian apparatus controlling the expression of other clock genes, including PER1. Clock genes have been implicated in cancer-related functions; in this work, we investigated CLOCK as a possible target of somatic mutations in microsatellite unstable colorectal cancers. Combining microarray gene expression data and public gene sequence information, we identified CLOCK as 1 of 790 putative novel microsatellite instability (MSI) target genes. A total of 101 MSI colorectal carcinomas (CRC) were sequenced for a coding microsatellite in CLOCK. The effect of restoring CLOCK expression was studied in LS180 cells lacking wild-type CLOCK by stably expressing GST-CLOCK or glutathione S-transferase empty vector and testing the effects of UV-induced apoptosis and radiation by DNA content analysis using flow cytometry. Putative novel CLOCK target genes were searched by using ChIP-seq. CLOCK mutations occurred in 53% of MSI CRCs. Restoring CLOCK expression in cells with biallelic CLOCK inactivation resulted in protection against UV-induced apoptosis and decreased G(2)-M arrest in response to ionizing radiation. Using ChIP-Seq, novel CLOCK-binding elements were identified near DNA damage genes p21, NBR1, BRCA1, and RAD50. CLOCK is shown to be mutated in cancer, and altered response to DNA damage provides one plausible mechanism of tumorigenesis.

Abstract A57: Nonsense-mediated decay escaping mutations in microsatellite-unstable colorectal cancer

Genomic instability drives tumorigenesis by allowing the accumulation of genetic alterations that provide cells with growth advantage. Microsatellite-instability (MSI) and the underlying mutator phenotype caused by a defect in mismatch repair (MMR) functions is the hallmark of Lynch syndrome, and is also observed in a subset of all colorectal cancers (CRC). In cells with a defective MMR system, spontaneous length changes of repetitive microsatellite sequences accumulate all over the genome at highly increased rates. At coding regions instability may lead to frameshift mutations and altered protein products. Genes that mutate this way under MMR deficiency giving selective advantage to cells in tumorigenesis are called MSI target genes. It is generally anticipated that the frameshift mutation-containing transcripts that lead to prematurely terminated proteins undergo nonsense-mediated decay (NMD), followed by a reduction in gene expression levels. However, when a premature stop occurs in the carboxyl-terminal end of the gene it might escape decay mechanisms, which may lead to either dominant-negative or oncogenic effects. Aim of this study was a genome-wide unbiased identification of new MSI CRC target genes that escape NMD. By combining bioinformatic search to expression profiling, we created a list of 330 genes that contained mononucleotide repeats from 6 to 10 base pairs and were likely to be translated despite potential mutations. A novel frameshift predictor software was developed to search all repeat-containing transcripts in the human genome that would escape NMD after one nucleotide deletion. To enhance the odds of identifying oncogenic mutants, the analysis was restricted to genes that were overexpressed in MSI CRC versus normal colonic mucosa. All of these genes were screened initially by sequencing the given repeat in a panel of 30 MSI CRCs.Whenever the mutation frequency exceeded 20% in the tumor set, which was considered evidence for possible selection in MSI tumorigenesis, an additional set of 70 MSI CRCs was sequenced. The great majority of the successfully sequenced genes had no mutations. Altogether four genes were mutated in over 20% of the samples in the extended 100 MSI tumor panel. These candidate driver target genes are being evaluated further by various methods, including sequencing of MSI CRC cell lines and microsatellite-stable (MSS) CRCs, statistical analyses, and functional in vitro experiments.

Citation Information: Cancer Res 2009;69(23 Suppl):A57.

Allelic imbalance at rs6983267 suggests selection of the risk allele in somatic colorectal tumor evolution

A common single nucleotide polymorphism (SNP), rs6983267, at 8q24.21 has recently been shown to associate with colorectal cancer (CRC). Three independent SNP association studies showed that rs6983267 contributes to CRC with odds ratios (OR) of 1.17 to 1.22. Here, we genotyped a population-based series of 1,042 patients with CRC and 1,012 healthy controls for rs6983267 and determined the contribution of SNP to CRC in Finland, using germ line DNA, as well as the respective cancer DNA in heterozygous patients. The comprehensive clinical data available from the 1,042 patients and their first-degree relatives enabled us to thoroughly examine the possible association of this variant with different clinical features. As expected, a significant association between the G allele of rs6983267 and CRC [OR, 1.22; 95% confidence interval (CI), 1.08-1.38; P = 0.0018] was found, confirming the previous observations. A trend towards association of the G allele with microsatellite-stable cancer (OR, 1.37; 95% CI, 1.02-1.85; P = 0.04) and family history of cancers other than CRC was seen (OR, 1.20; 95% CI, 1-1.43; P = 0.05). Four hundred and sixty-six GT heterozygotes identified in this study were analyzed for allelic imbalance at rs6983267 in the respective cancer DNA. One hundred and one tumors showed allelic imbalance (22%). The risk allele G was favored in 67 versus 34 tumors (P = 0.0007). This finding implicates that the underlying germ line genetic defect in 8q24.21 is a target in the somatic evolution of CRC.