Comparison and Functional Genetic Analysis of Striatal Protein Expression Among Diverse Inbred Mouse Strains

C57BL/6J (B6) and DBA/2J (D2) inbred mouse strains are highly variable genetically and differ in a large number of behavioral traits related to striatal function, including depression, anxiety, stress response, and response to drugs of abuse. The genetic basis of these phenotypic differences are, however, unknown. Here, we present a comparison of the striatal proteome between B6 and D2 and relate differences at the protein level to strain differences at the mRNA level. We also leverage a recombinant inbred BXD population derived from B6 and D2 strains to investigate the role of genetic variation on the regulation of mRNA and protein levels. Finally, we test the hypothesis that differential protein expression contributes to differential behavioral responses between the B6 and D2 strain. We detected the expression of over 2,500 proteins in membrane-enriched protein fractions from B6 and D2 striatum. Of these, 160 proteins demonstrated significant differential expression between B6 and D2 strains at a 10% false discovery level, including COMT, GABRA2, and cannabinoid receptor 1 (CNR1)—key proteins involved in synaptic transmission and behavioral response. Similar to previous reports, there was little overlap between protein and transcript levels (25%). However, the overlap was greater (51%) for proteins demonstrating genetic regulation of cognate gene expression. We also found that striatal proteins with significantly higher or lower relative expression in B6 and D2 were enriched for dopaminergic and glutamatergic synapses and processes involved in synaptic plasticity [e.g., long-term potentiation (LTP) and long-term depression (LTD)]. Finally, we validated higher expression of CNR1 in B6 striatum and demonstrated greater sensitivity of this strain to the locomotor inhibiting effects of the CNR1 agonist, Δ9-tetrahydrocannabinol (THC). Our study is the first comparison of differences in striatal proteins between the B6 and D2 strains and suggests that alterations in the striatal proteome may underlie strain differences in related behaviors, such as drug response. Furthermore, we propose that genetic variants that impact transcript levels are more likely to also exhibit differential expression at the protein level.

Structural divergence of essential triad ribbon synapse proteins among placental mammals - Implications for preclinical trials in photoreceptor transplantation therapy

As photoreceptor transplantation rapidly moves closer to the clinic, verifying graft efficacy in animal models may have unforeseen xenogeneic barriers. Although photoreceptor transplants have most convincingly exhibited functional synaptogenesis in conspecific studies, such evidence (while ruling out false-positives due to: viral graft labeling, fusion/cytosolic transfer, or neuroprotection) has not yet been shown for discordant xenografts. From this, a fundamental question should be raised: is useful xenosynaptogenesis likely between human photoreceptors and mouse retina? The triad ribbon synapse (TRS) that would normally form is unique and contains trans-synaptic proteins essential to its formation and function. Thus, could interspecific structural divergence be present that may inhibit this trans-synaptic bridge in discordant xenografts? In an effort to address this question computationally, we compared eight recently confirmed (including subcellular location) TRS specific (or predominantly expressed at the TRS) proteins among placental mammals (1-to-1 orthologs) using HyPhy selection analysis (a predictive measure of structural divergence) and by using Phyre2 tertiary structural modeling. Here, selection analysis revealed strong positive (diversifying) selection acting on a particularly important TRS protein: pikachurin. This positive selection was localized to its second Laminin-G (LG)-like domain and on its N-terminal domain - a putative region of trans-synaptic interaction. Localization of structural divergence to the N-terminus of each putative post-translational cleavage (PTC) product may suggest neofunctionalization from ancestral uncleaved pikachurin - this would be consistent with a recent counter-paradigm report of pikachurin cleavage predominating at the TRS. From this, we suggest a dual role after cleavage where the N-terminal fragment can still mediate the trans-synaptic bridge, while the C-terminal fragment may act as a diffusible trophic or "homing" factor for bipolar cell dendrite migration. Tertiary structural models mirrored the conformational divergence predicted by selection analysis. With human and mouse pikachurin (as well as other TRS proteins) likely to diverge considerably in structure among placental mammals - alongside known inter-mammalian variation in TRS phenotype and protein repertoire, high levels of diversifying selection acting on genes involving sensation, considerable timespans allowing for genetic drift that can create xenogeneic epistasis, and uncertainty surrounding the extent of xenosynaptogenesis in PPC transplant studies to date - use of distantly related hosts to test human photoreceptor graft therapeutic efficacy should be considered with caution.

Screening the Molecular Framework Underlying Local Dendritic mRNA Translation

In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches.