Genome characterization of the selected long- and short-sleep mouse lines

Whole‑exome sequencing reveals Lewis lung carcinoma is a hypermutated Kras/Nras-mutant cancer with extensive regional mutation clusters in its genome

Lewis lung carcinoma (LLC), as a widely used preclinical cancer model, has still not been genetically and genomically characterized. Here, we performed a whole-exome sequencing analysis on the LLC cell line to elucidate its molecular characteristics and etiologies. Our data showed that LLC originated from a male mouse belonging to C57BL/6L (a transitional strain between C57BL/6J and C57BL/6N) and contains substantial somatic SNV and InDel mutations (> 20,000). Extensive regional mutation clusters are present in its genome, which were caused mainly by the mutational processes underlying the SBS1, SBS5, SBS15, SBS17a, and SBS21 signatures during frequent structural rearrangements. Thirty three deleterious mutations are present in 30 cancer genes including Kras, Nras, Trp53, Dcc, and Cacna1d. Cdkn2a and Cdkn2b are biallelically deleted from the genome. Five pathways (RTK/RAS, p53, cell cycle, TGFB, and Hippo) are oncogenically deregulated or affected. The major mutational processes in LLC include chromosomal instability, exposure to metabolic mutagens, spontaneous 5-methylcytosine deamination, defective DNA mismatch repair, and reactive oxygen species. Our data also suggest that LLC is a lung cancer similar to human lung adenocarcinoma. This study lays a molecular basis for the more targeted application of LLC in preclinical research.

Neurotensin and Neurotensin Receptors in Stress-related Disorders: Pathophysiology & Novel Drug Targets

Neurotensin (NT) is a 13-amino acid neuropeptide widely distributed in the CNS that has been involved in the pathophysiology of many neural and psychiatric disorders. There are three known neurotensin receptors (NTSRs), which mediate multiple actions, and form the neurotensinergic system in conjunction with NT. NTSR1 is the main mediator of NT, displaying effects in both the CNS and the periphery, while NTSR2 is mainly expressed in the brain and NTSR3 has a broader expression pattern. In this review, we bring together up-to-date studies showing an involvement of the neurotensinergic system in different aspects of the stress response and the main stress-related disorders, such as depression and anxiety, post-traumatic stress disorder (PTSD) and its associated symptoms, such as fear memory and maternal separation, ethanol addiction, and substance abuse. Emphasis is put on gene, mRNA, and protein alterations of NT and NTSRs, as well as behavioral and pharmacological studies, leading to evidence-based suggestions on the implicated regulating mechanisms as well as their therapeutic exploitation. Stress responses and anxiety involve mainly NTSR1, but also NTSR2 and NTSR3. NTSR1 and NTSR3 are primarily implicated in depression, while NTSR2 and secondarily NTSR1 in PTSD. NTSR1 is interrelated with substance and drug abuse and NTSR2 with fear memory, while all NTSRs seem to be implicated in ethanol consumption. Some of the actions of NT and NTSRs in these pathological settings may be driven through interactions between NT and corticotrophin releasing factor (CRF) in their regulatory contribution, as well as by NT's pro-inflammatory mediating actions.

Prediction of Locomotor Activity by Infrared Motion Detector on Sleep-wake State in Mice

Objective

Behavioral assessments that effectively predict sleep-wake states were tried in animal research. This study aimed to examine the prediction power of an infrared locomotion detector on the sleep-wake states in ICR (Institute Cancer Research) mice. We also explored the influence of the durations and ways of data processing on the prediction power.

Methods

The locomotor activities of seven male mice in home cages were recorded by infrared detectors. Their sleep-wake states were assessed by video analysis. Using the receiver operating characteristic curve analysis, the cut-off score was determined, then the area under the curve (AUC) values of the infrared motion detector that predicted sleep-wake states were calculated. In order to improve the prediction power, the four ways of data processing on the prediction power were performed by Matlab 2013b.

Results

In the initial analysis of raw data, the AUC value was 0.785, but it gradually reached to 0.942 after data summation. The simple data averaging and summation among four different methods showed the maximal AUC value. The 10-minute data summation improved sensitivity (0.889) and specificity (0.901) significantly from the baseline value (sensitivity 0.615; specificity 0.936) (p < 0.001).

Conclusion

This study suggests that the locomotor activity measured by an infrared motion detector might be useful to predict the sleep-wake states in ICR mice. It also revealed that only simple data summation may improve the predictive power. Using daily locomotor activities measured by an infrared motion detector is expected to facilitate animal research related to sleep-wake states.

Quantitative trait loci for sensitivity to acute ethanol and ethanol consummatory behaviors in rats

Individuals with a low initial response to alcohol (i.e., ethanol) are at greater risk of developing alcohol abuse or dependence later in life. Similar to humans, individual differences in ethanol sensitivity also can be seen in rats, and several laboratories have used these individual differences to generate selectively bred rats that differ in acute ethanol sensitivity. We have worked with two sets of such rats (Inbred High or Low Alcohol Sensitivity strains, IHAS or ILAS, respectively; Inbred Alcohol Tolerant or Non-Tolerant strains, IAT and IANT, respectively) and have confirmed previously mapped quantitative trait loci (QTL) for these acute differences with the use of recombinant congenic lines; however, the relationship between acute sensitivity and ethanol drinking in these rats has yet to be determined. Thus, here we tested the hypothesis that QTLs underlying variation in initial low sensitivity to ethanol also will modulate variation in ethanol drinking behaviors. Separate groups of selectively inbred parent and congenic rats were tested for the loss of righting response (LORR) and also assessed for ethanol consummatory behavior using either operant self-administration or an intermittent-access two-bottle choice procedure. LORR testing confirmed the presence of a LORR duration QTL in all of the congenics; however, the lack of a corresponding difference in blood ethanol concentration at the regaining of the righting response suggests that these QTLs may be mediating a difference in ethanol metabolism rather than in neuronal sensitivity. IHAS/ILAS-derived congenic rats did not differ from parent rats at any point during operant self-administration. IAT/IANT-derived congenic rats showed small, but significant, increases in ethanol consumption relative to the parent strains only during the initial stages of operant self-administration. In contrast to operant testing, IHAS/ILAS-derived congenic rats showed significantly greater ethanol consumption and preference than parent rats during intermittent-access testing. There were not differences, however, between IAT/IANT congenic and parent rats during intermittent access. These data support the hypothesis that there is a genetic relationship between initial ethanol sensitivity and ethanol consumption, at least for the IHAS/ILAS-derived congenic rats. Our current studies, however, cannot eliminate pharmacokinetic or taste preference factors as contributing to the rats' responses, nor can we eliminate the possibility of a linkage effect because of the fairly large size of the QTL intervals; i.e., distinct genes may be mediating the acute sensitivity and drinking responses.

Model based heritability scores for high-throughput sequencing data

Background

Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available for calculating heritability for traits derived from high-throughput sequencing.

Results

We propose several statistical models and different methods to compute and test a heritability measure for such data based on linear and generalized linear mixed effects models. We also provide methodology for hypothesis testing and interval estimation. Our analyses show that, among the methods, the negative binomial mixed model (NB-fit), compound Poisson mixed model (CP-fit), and the variance stabilizing transformed linear mixed model (VST) outperform the voom-transformed linear mixed model (voom). NB-fit and VST appear to be more robust than CP-fit for estimating and testing the heritability scores, while NB-fit is the most computationally expensive. CP-fit performed best in terms of the coverage of the confidence intervals. In addition, we applied the methods to both microRNA (miRNA) and messenger RNA (mRNA) sequencing datasets from a recombinant inbred mouse panel. We show that miRNA and mRNA expression can be a highly heritable molecular trait in mouse, and that some top heritable features coincide with expression quantitative trait loci.

Conclusions

The models and methods we investigated in this manuscript is applicable and extendable to sequencing experiments where some biological replicates are available and the environmental variation is properly controlled. The CP-fit approach for assessing heritability was implemented for the first time to our knowledge. All the methods presented, as well as the generation of simulated sequencing data under either negative binomial or compound Poisson mixed models, are provided in the R package HeritSeq.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1539-6) contains supplementary material, which is available to authorized users.