Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data

BACKGROUND

Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Historically, gene targeting was first done in embryonic stem cells (ESCs) derived from the 129 family of inbred strains, leading to a mixed background or congenic mice when crossed with C57BL/6 mice. Depending on the number of backcrosses and breeding strategies, genomic segments from 129-derived ESCs can be introgressed into the C57BL/6 genome, establishing a unique genetic makeup that needs characterization in order to obtain valid conclusions from experiments using GEM lines. Currently, SNP genotyping is used to detect the extent of 129-derived ESC genome introgression into C57BL/6 recipients; however, it fails to detect novel/rare variants.

RESULTS

Here, we present a computational pipeline implemented in the Galaxy platform and in BASH/R script to determine genetic introgression of GEM using next generation sequencing data (NGS), such as whole genome sequencing (WGS), whole exome sequencing (WES) and RNA-Seq. The pipeline includes strategies to uncover variants linked to a targeted locus, genome-wide variant visualization, and the identification of potential modifier genes. Although these methods apply to congenic mice, they can also be used to describe variants fixed by genetic drift. As a proof of principle, we analyzed publicly available RNA-Seq data from five congenic knockout (KO) lines and our own RNA-Seq data from the Sall2 KO line. Additionally, we performed target validation using several genetics approaches.

CONCLUSIONS

We revealed the impact of the 129-derived ESC genome introgression on gene expression, predicted potential modifier genes, and identified potential phenotypic interference in KO lines. Our results demonstrate that our new approach is an effective method to determine genetic introgression of GEM.

Molecular diagnosis in patients with retinoblastoma: Report of a series of cases

OBJECTIVES

To report the benefits of genetic diagnosis in patients with retinoblastoma.

METHOD

Observational study. Patients with retinoblastoma and their families were included. Demographic and clinical data were recorded. Blood and tumour samples were obtained. Next generation sequencing was performed on the samples. When deletion 13 q syndrome was suspected, cytogenetics microarray was performed (Cytoscan® HD, Affymetrix, Santa Clara, CA, USA), with a high density chip of 1.9 million of non-polymorphic probes and 750 thousand SNP probes.

RESULTS

Of the 7 cases were analysed 4 were male. The mean age at diagnosis was 21 months (range 5-36). Three cases had bilateral retinoblastoma, and 4 unilateral. None had family history. In all patients, blood was analysed, and a study was performed on the tissue from 2 unilateral enucleated tumours, in which 6 mutations were identified, all de novo. Just one was novel (c.164delC; case 1). One case of unilateral tumour revealed blood mosaicism, showing that his condition was inheritable, and that there is a high risk of developing retinoblastoma in the unaffected eye. The patient also has an increased risk of presenting with other primary tumours.

CONCLUSION

Molecular diagnosis of RB1 in patients with retinoblastoma impacts on the decision process, costs, treatment, and prognosis of patients, as well as their families.

Cyclin D2 and cyclin D3 play opposite roles in mouse skin carcinogenesis

D-type cyclins are components of the cell-cycle engine that link cell signaling pathways and passage throughout G1 phase. We previously described the effects of overexpression cyclin D1, D2 or D3 in mouse epidermis and tumor development. We now asked whether cyclin D2 and/or cyclin D3 play a relevant role in ras-dependent tumorigenesis. Here, we described the effect of cyclin D3 and cyclin D2 overexpression in mouse skin tumor development. Notably, overexpression of cyclin D3 results in reduced tumor development and malignant progression to squamous cell carcinomas (SCC). Biochemical analysis of keratinocytes shows that overexpression of cyclin D3 results in strong reduction of cyclin D2 and its associated kinase activity. Furthermore, we found that reinstatement of cyclin D2 level in the cyclin D3/cyclin D2 bigenic mice results in a complete reversion of the inhibitory action of cyclin D3. Supporting these results, ablation of cyclin D2 results in reduced tumorigenesis and malignant progression. On the other hand, overexpression of cyclin D2 results in an increased number of papillomas and malignant progression. We conclude that cyclin D3 and cyclin D2 play opposite roles in mouse skin tumor development and that the suppressive activity of cyclin D3 is associated with cyclin D2 downregulation.

A variant of pulmonary alveolar microlithiasis in nackt mice

Four adult mutant nackt mice, which demonstrate alopecia and CD4+ T-cell deficiency, and two outbred SENCAR mice (sentinels) were presented for routine health surveillance. Lesions were not observed at necropsy. Microscopically, all four nackt mice demonstrated multiple concretions that were 30-100 microm in diameter, irregularly rounded to oval, nonbirefringent, and amphophilic to basophilic. Many of the concretions appeared attached to or within the alveolar walls of all lung lobes. Approximately half of the concretions had irregular fracture lines. All concretions were periodic acid-Schiff positive, and Von Kassa staining revealed diffuse calcification. None of the concretions were associated with inflammatory cell infiltrates, and metaplastic ossification was not evident. A diagnosis of pulmonary alveolar microlithiasis, a rare disease in both humans and animals, was made based on the size and location of the concretions and the lack of an inflammatory response. This is the first report of a laboratory mouse demonstrating pulmonary alveolar microlithiasis.

PCR-based microsatellite analysis for differentiation and genetic monitoring of nine inbred SENCAR mouse strains

Sixteen DNA microsatellites or simple sequence length polymorphisms (SSLPs), generated by polymerase chain reaction (PCR) were selected for use in the genetic quality control of the nine inbred SENCAR strains currently available. The SENCAR strains constitute a powerful tool for mechanistic studies of multi-stage skin carcinogenesis, as well as for studies to understand the underlying genetic basis of resistance to tumour promotion and progression. SSLP analysis is a fast and economical way for detecting genetic contamination (unexpected outcrosses) among these closely-related albino strains, where standard immunological and biochemical markers have been shown to be insufficient.

The CD4 T cell-deficient mouse mutation nackt (nkt) involves a deletion in the cathepsin L (CtsI) gene

We recently reported a novel autosomal recessive mouse mutation designated nackt (nkt). Homozygous mutant mice have diffuse alopecia and a marked reduction in the proportion of CD4+ T cells in the thymus and peripheral lymphoid tissues. Here we show that the CD4 T-cell deficiency is due to a defect in the thymic microenvironment rather than the hematopoietic compartment. Furthermore, we identified the molecular basis of the mutant phenotype by demonstrating that the nkt mutation represents a 118-bp deletion of the cathepsin L (Ctsl) gene which is required for degradation of the invariant chain, a critical chaperone for major histocompatibility complex class II molecules. This finding explains the similarities in skin and immune defects observed in nkt/nkt and Ctsl -/- mice. The data reported here provide further in vivo evidence that the lysosomal cysteine protease cathepsin L plays a critical role in CD4+ T-cell selection in the thymus.

[Murine models for human diseases]

This article is a bibliographic review concerning mouse mutations, spontaneous, induced or genetically engineered, as models of human genetic diseases. Since the beginning of the last century, mouse models have been instrumental in the understanding of the pathogenesis of many diseases and designing of new therapies. A number of recent technological advances in embryo manipulation and many large-scale mutagenesis screens will dramatically increase the availability of new mouse models in the near future. In the "post-genomic" era, mouse mutants will have a significant role as a model system for functional genome analysis of the upcoming whole-genome information of the human and mouse genomes projects.

Microsatellite DNA variants between the inbred SENCAR mouse strains

The two-stage model, initiation with 7,12-dimethylbenz[a]anthracene and promotion with 12-O-tetradecanoylphorbol-13-acetate, of mouse skin carcinogenesis has been the protocol of choice to study the genetic susceptibility to carcinogens, the outbred SENCAR mouse being the most widely used skin tumor-sensitive animal model. Squamous cell carcinomas (SCCs) develop from many of the papillomas, making these mice a useful model for epithelial tumorigenesis and for the progression to malignant tumors. Nine different inbred strains derived from outbred SENCAR mice have been recently reported. Interestingly, these strains display different sensitivities to two-stage carcinogenesis, and, in particular, some of them show a dissociation between susceptibility to papilloma development and the malignant conversion of these into SCC. However, the utility of these SENCAR strains for genetic mapping is limited by the lack of information regarding DNA variant alleles among them. Therefore, we analyzed the nine inbred strains with microsatellite markers distributed along the 20 chromosomes and in this article report the variant alleles found. The information presented is likely to be helpful for linkage analysis and marker-assisted development of congenic strains between SENCAR-derived inbred strains.

Allelotype analysis of chemically induced squamous cell carcinomas in F(1) hybrids of two inbred mouse strains with different susceptibility to tumor progression

Loss of heterozygosity (LOH) at specific chromosomal loci is generally considered indirect evidence for the presence of putative suppressor genes. Allelotyping of tumors using polymorphic markers distributed throughout the entire genome allows the analysis of specific allelic losses. In the field of chemical carcinogenesis, the outbred SENCAR mouse has been commonly used to analyze the multistage nature of skin tumor development. In the study reported here we generated F(1) hybrids between two inbred strains (SENCARB/Pt and SSIN/Sprd) derived from the SENCAR stock that differ in their susceptibility to tumor progression. We typed 24 7, 12-dimethylbenz[a]anthracene and 12-O-tetradecanoylphorbol-13-acetate-induced squamous cell carcinomas for LOH using 56 microsatellite markers distributed among all autosomal chromosomes. The highest percentage of LOH, 78%, was found on chromosome 7, but there was no preferential loss of one particular allele, indicating that the putative suppressor genes found in this area are not involved in genetic susceptibility. High levels of LOH were also found on chromosomes 16 (39%), 6 (29%), 4 (25%), 9 (25%), 14 (22%), 10 (20%) and 19 (20%), but with no preferential loss of the alleles of one strain. The chromosomal regions with LOH on mouse chromosomes 4, 6, 7, 9, 10, 14, 16 and 19 correspond to regions in the human genome where LOH has been reported and have been suggested to harbor tumor suppressor genes.

[Types of employment and health: analysis of the Second European Survey on Working Conditions]

OBJECTIVES

To investigate the relationships among types of employment and several health self-perceived outcomes in a sample of active workers from the 15 state members of the European Union.

METHODS

Cross-sectional study with data drawn from the Second European Survey on Working Conditions (n = 15,146 individuals). The predictive variable was the types of employment aggregated in: permanent workers, sole traders, small employers (less than 10 employees) and temporary workers (full-and part-time). Unconditional logistic regression models were adjusted by age, gender and several indications of working conditions. Permanent workers was used as the baseline category.

RESULTS

Employees with permanent (69,3%) and temporary (12,5%) contracts notified the highest level of a job absenteeism while temporary employees reported the highest level of job dissatisfaction. On the other hand, sole traders (12,2%) and small employees (6.1%) notified the most frequent level of overall fatigue, backache and muscular pains. Having permanent workers as baseline category, temporary employees was associated with high dissatisfaction (OR = 1.68), and and overall fatigue (OR = 1.16), but with lower frequency of stress (OR = 0.74) and job absenteeism (OR = 0.87). Small employers showed a low frequency of absenteeism (OR = 0.68), but a high stress (OR = 1.77) and overall fatigue (OR = 1.27). Finally, sole traders reported more frequently overall fatigue (OR = 1.40), and stress (OR = 1.33), but less job absenteeism (OR = 0.58).

CONCLUSIONS

These findings suggest that types of employment may have an independent effect on several health self-perceive outcomes. Further research is necessary to overcome various shortcoming of this study, and to assess the role either job security or level of income and social protection.

[Temporary disability: analysis strategies]

OBJECTIVES

To apply different regression models to estimate rate ratios for temporary sick-leave (TSL) which may occur several times in the same individual during a period, and the frequency is not constant for the observation period.

SUBJECTS AND METHODS

All workers employed more than 30 days between January 1st of 1992 and June 1st of 1995 were included into the population study. The following period was 1,259 days and the total number of workers included in the study was 2,306. During that period 2,649 TSL episodes were notified, which meant 85,947 lost days. Poisson regression, Generalised Estimating Equations (GEE) and Andersen-Gill modification of Cox regression modify by Wei (WLW) were applied.

RESULTS

The highest TSL incidence rates were seen in women, lesser than 30 years old, cleaners, maintenance workers and auxiliary nurses, and those involved in shiftwork. This profile was not modified after applying GEE and WLW regression models, although confidence intervals were widened.

CONCLUSIONS

TSL data does not fit Poisson regression assumptions, but GEE and WLW regression models do not appear as alternatives. Other conditional regression models would need to be explored to suitably analyse this data.

Nackt (nkt), a new hair loss mutation of the mouse with associated CD4 deficiency

A spontaneous recessive mutation named nackt (symbol: nkt) affecting hair growth and T-cell development was discovered in a moderately inbred stock of mice. Skin lesions were characterized by sparse rough coat, bare patches around the eyes and neck, and a scratching behavior throughout life. Fluorescence-activated cell sorter analysis indicated a deficiency in the CD4(+) 8(-) T-cell subset in the thymus and a marked decrease in CD4(+) T cells in peripheral lymphoid organs. Linkage analysis using a set of molecular markers and an F2 intersubspecific cross indicated that the mutation maps to the central region of mouse chromosome 13, in a region homologous to human chromosome 5q22-q35.

Evidence of genetic heterogeneity in a BALB/c mouse colony as determined by DNA fingerprinting

A genetic monitoring of the BALB/c mouse foundation colony in our animal facility was carried out. The techniques of choice were skin grafting, coat colour test, flow cytometric analysis for H2 antigens (loci H2-D and H2-A), electrophoretic analysis of isoenzymes (loci Idh1, Pep3, Es3 and Mod1), PCR-amplified microsatellites (loci Igh-V, Ngfg, Plau, Crp, Igh, D16Mit5, D3Mit49 and D17Mit16) and DNA fingerprinting (multilocus probes 33.6, 33.15 and (CAC)5). No evidence of genetic contamination was found, ruling out the possibility of an outcross with AKR, the other albino strain maintained at the facility. Nevertheless, DNA fingerprint patterns revealed evidence of genetic heterogeneity in four out of nine lines of the nucleus colony, interpreted as minisatellite mutations favoured for a single line system with more than 40 generations of separation from the ancestral pair. These mice are mainly used in cancer and immunological research within the institute.