Fred G. Biddle

The degree of lateralization of paw usage (handedness) in the mouse is defined by three major phenotypes

Lateralization of paw usage in the laboratory mouse may be a useful model system in which to assess the genetic and developmental cause of asymmetry of hand usage. With a set number of paw reaches from a centrally placed food tube, individual mice from an inbred strain will exhibit a reliable number of left and right paw reaches. For a single inbred strain, there are approximately equal numbers of left-pawed and right-pawed mice, but strain differences have been reported in the degree of lateralization of paw preference. We reported a preliminary strain survey in which the strains appeared to fall into two groups of highly lateralized and weakly lateralized paw preference (Biddleet al., 1993). We review here our expanded survey of genetically different strains and stocks of the laboratory mouse, including different species and subspecies. The major genetic trait is the degree of lateralization of paw preference and the strain differences appear to fall into three major classes of highly lateralized, weakly lateralized, and ambilateral preference. The trait exhibits both additivity and dominance in preliminary reciprocal crosses, depending on which strain pairs are used. The wide difference between strains that have highly lateralized and ambilateral paw preference suggests specific genetic tools that could be used to begin a genetic dissection of the causes of this trait. Preliminary assessment of the size of the corpus callosum in three strains with significantly different degrees of lateralization suggests that genetically determined deficiencies and absence of this structure are not the direct cause of the strain differences in the trait of degree of lateralization. In the expanded survey, some strains appear to exhibit a directional deviation from equal numbers of mice with left and right paw usage. Therefore, direction of paw usage may not be a genetically neutral trait, but replicate assessments and genetic tests are needed to confirm this.

Increased dopamine synthesis in aging substantia nigra neurons

Striatal dopamine (DA) and metabolite (DOPAC) levels in 8-, 21-, 52- and 104-week-old C57BL mice were compared with those in 11-week-old mice, 20 days after 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) treatment. DA and DOPAC concentrations expressed relative to striatal wet weight did not change with age. In contrast, DA and DOPAC levels increased almost linearly when values were expressed relative to the proportion of remaining tyrosine hydroxylase-positive (TH+) SNc neurons, reaching a 5-7-fold increase per average remaining TH+ neuron by 104 weeks of age (corresponding to neuronal loss of 70%) relative to that found per average neuron in 8-week-old mice. DA and DOPAC levels per average remaining TH+ SNc neuron following MPTP increased for low doses (neuronal losses less than 42%) but decreased for higher doses (55 and 70% losses) but the DOPAC/DA ratio per SNc neuron increased and was 9-fold higher in the 300 mg/kg MPTP-treated animals in comparison to saline controls. Cytoplasmic TH protein (estimated by somal TH immunodensity) was increased by 45% in SNc somata from mice treated with 150 mg/kg MPTP in comparison to saline controls, and by 63% in 104-week-old mice in comparison to 8-week-old animals. This study provides evidence that an average surviving TH+ SNc neuron compensates for the age-related loss of other SNc neurons by increasing dopamine synthesis similar to younger SNc neurons surviving low levels of toxically induced damage and that the compensation may be in part mediated by increased synthesis of TH.

Integrated analysis of long noncoding RNA and coding RNA expression in esophageal squamous cell carcinoma.

Tumorigenesis is a complex dynamic biological process that includes multiple steps of genetic and epigenetic alterations, aberrant expression of noncoding RNA, and changes in the expression profiles of coding genes. We call the collection of those perturbations in genome space the “cancer initiatome.” Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome and they have key regulatory functions in chromatin remodeling and gene expression. Spatiotemporal variation in the expression of lncRNAs has been observed in development and disease states, including cancer. A few dysregulated lncRNAs have been studied in cancers, but the role of lncRNAs in the cancer initiatome remains largely unknown, especially in esophageal squamous cell carcinoma (ESCC). We conducted a genome-wide screen of the expression of lncRNAs and coding RNAs from ESCC and matched adjacent nonneoplastic normal tissues. We identified differentially expressed lncRNAs and coding RNAs in ESCC relative to their matched normal tissue counterparts and validated the result using polymerase chain reaction analysis. Furthermore, we identified differentially expressed lncRNAs that are co-located and co-expressed with differentially expressed coding RNAs in ESCC and the results point to a potential interaction between lncRNAs and neighboring coding genes that affect ether lipid metabolism, and the interaction may contribute to the development of ESCC. These data provide compelling evidence for a potential novel genomic biomarker of esophageal squamous cell cancer.

Multiple region whole-exome sequencing reveals dramatically evolving intratumor genomic heterogeneity in esophageal squamous cell carcinoma

Cancer is a disease of genome instability and genomic alterations; now, genomic heterogeneity is rapidly emerging as a defining feature of cancer, both within and between tumors. Motivation for our pilot study of tumor heterogeneity in esophageal squamous cell carcinoma (ESCC) is that it is not well studied, but the highest incidences of esophageal cancers are found in China and ESCC is the most common type. We profiled the mutations and changes in copy number that were identified by whole-exome sequencing and array-based comparative genomic hybridization in multiple regions within an ESCC from two patients. The average mutational heterogeneity rate was 90% in all regions of the individual tumors in each patient; most somatic point mutations were nonsynonymous substitutions, small Indels occurred in untranslated regions of genes, and copy number alterations varied among multiple regions of a tumor. Independent Sanger sequencing technology confirmed selected gene mutations with more than 88% concordance. Phylogenetic analysis of the somatic mutation frequency demonstrated that multiple, genomically heterogeneous divergent clones evolve and co-exist within a primary ESCC and metastatic subclones result from the dispersal and adaptation of an initially non-metastatic parental clone. Therefore, a single-region sampling will not reflect the evolving architecture of a genomically heterogeneous landscape of mutations in ESCC tumors and the divergent complexity of this genomic heterogeneity among patients will complicate any promise of a simple genetic or epigenetic diagnostic signature in ESCC. We conclude that any potential for informative biomarker discovery in ESCC and targeted personalized therapies will require a deeper understanding of the functional biology of the ontogeny and phylogeny of the tumor heterogeneity.

Genetic variability of purine nucleoside phosphorylase activity in the mouse: Relationship to Np-1 and Np-2

A survey of 37 inbred strains for erythrocyte purine nucleoside phosphorylase activity showed a greater than threefold range. Six of these strains had significantly greater activity than the others, and all of the high-activity strains had the Np-2 electrophoretic band. The high-purine nucleoside phosphorylase activity trait corresponding to Np-2 was inherited in an autosomal codominant manner and minor differences were apparent in thermal and kinetic properties between low- and high-activity strains. This work provides further support for there being either two structural loci for purine nucleoside phosphorylase, Np-1 and Np-2, or a regulatory-modifier locus.

Learning of paw preference in mice is strain dependent, gradual and based on short-term memory of previous reaches

We studied the dynamics of paw preference learning in unbiased symmetrical test chambers where mice, Mus musculus, could freely choose which paw to use. When compared to nonlearner model mice, three strains exhibited different degrees of learning within and between two training sessions 1 week apart. While paw preference was probabilistic, positive autocorrelation between paw choices made by individual mice in a training session showed that bias in paw preference changed gradually with successive paw reaches and was concordant between sessions. Within a session, the degree of positive autocorrelation between consecutive paw choices differed between strains and decreased faster with increasing lag between reaches in stronger than in weak learners, suggesting that the degree of learning is the genetic variable in mice. We propose that strong biases in individual mice result from weak biases that appear by chance early in training and increase by a positive feedback mechanism because of learning during training. This explains how individual mice of each strain were strongly biased when there was almost no bias at the population level. The decrease in autocorrelation with lag shows that constitutive behaviours play a minor role and, hence, paw preference can adapt to environmental changes. We conclude that paw preference learning in mice is genetically dependent on past experience, changes gradually within training sessions, and is based on short-term memory; it also has long-term effects, provided there is time for memory consolidation.

Purine nucleoside phosphorylase heterogeneity in the mouse as analyzed by isoelectric focusing and specific activity

1. Isoelectric focusing in polyacrylamide gels identified three erythrocytic electrophoretic patterns of purine nucleoside phosphorylase in a survey of 16 mouse strains. 2. Three strain-specific electrophoretic types were also evident in liver, kidney and spleen leukocytes. 3. There are 3-fold differences in purine nucleoside phosphorylase activities between strains for several tissues; C57BL/6J and Mus spretus having the greatest and the least activity, respectively. 4. Within strains there were up to 8-fold tissue-specific differences in activity with the order from greatest to least being: liver, kidney, spleen leukocyte, erythrocyte, heart.

Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse

Using a new agent-based model that mimics the learning process in hand-reaching behavior of individual mice, we show that mouse hand preference is probabilistic, dependent on the environment and prior learning. We quantify the learning capabilities of three inbred strains and show that population distributions of hand preference emerge from the properties of individual mice. The model informs our understanding of gene—environment interactions because it accommodates genotypic differences in learning and memory abilities, and environmental biases. We tuned each strain’s model to match their experimental hand-preference distributions in unbiased worlds and, by comparing simulations and experiments, identified and quantified a constitutive left-bias in hand preference of one strain. The models, tuned for unbiased worlds, match experimental measures in left- and right-biased worlds and in biased worlds after previous training. New measures quantitatively assess this matching, revealing that two strains, previously considered non-learners of hand preference, actually have significant learning ability and we confirm this with new experiments. Model mice match the kinetics of hand-preference learning of one strain and predict the limits of learning. We conclude that genetically evolved hand-preference behavior in mice is inherently probabilistic to provide robustness and allow constant adaptability to ever-changing environments.

Purine nucleoside phosphorylase (Np) in the mouse: Linkage relationship of Np-2 to esterase-10 (Es-10) and Np-1 on chromosome 14

An improved method for detecting four Np-1 (purine nucleoside phosphorylase) alleles in mouse erythrocytes by cellulose acetate electrophoresis is described. The previous linkage of Np-1 and Es-10 (esterase-10) was confirmed, with a map distance of 13.0±2.6 cM. Np-2 was detected by either specific activity assay or starch gel electrophoresis and shown to be linked to Es-10, 15.9 ± 3.1 cM, on chromosome 14. No recombinants between Np-1 and Np-2 were observed in 52 offspring, indicating either that these loci are either closely associated or that Np-2 represents simply a property of existing allelic products of the Np-1 locus.

Autosomal Dominant Corneal Dystrophy with TGFBI Mutations: Lessons Learned from a Chinese Pedigree

Corneal dystrophies are rare autosomal dominant genetic diseases with diverse anatomic classification. The complexity of this disease reflects both the heterogeneity of causative gene mutations and the diversity of clinical presentations. Here, we studied and report a four-generation Chinese pedigree with corneal dystrophy, in which the clinical symptoms resemble Meesmann corneal dystrophy without the characteristic gene mutations of either KRT3 or KRT12. Targeted exon sequencing with PCR methods identified an Arg124Cys mutation in the TGFBI gene that concordant with phenotype in all affected individuals. This TGFBI mutation has been associated with multiple subtypes of corneal dystrophy. We reviewed the global reported TGFBI mutations in different ethnic groups and geographically mapped TGFBI mutations previously reported in China. The distribution of TGFBI allelic mutations may assist the clinical diagnosis of the heterogeneous, autosomal dominant corneal dystrophies.