Our work along with number of collaborations has successfully identified genes, pathways, regulators and drugs associated with neural repair and neuronal degeneration by applying and establishing various in vitro and in vivo model systems. Our unique approach is by integrating various omics functional studies, extensive experimental applications and systems analyses to understand various complex questions in translational and basic science research.
The repair of traumatic injuries to the central nervous system (CNS) presents a significant therapeutic challenge. Currently there are no effective therapies to treat brain and spinal cord injuries. The regenerative capacity of injured adult mammalian CNS is extremely limited, which leads to neurological deficits. However, the injured axons in the adult peripheral nervous system (PNS) maintain the capacity to regenerate, which leads to substantial functional recovery after injury.
We performed the first systems approach to study neural repair mechanism by pioneering work in functional genomics via the application of genome wide transcriptomics in neurons and the development of systems biology methods for analysis and data integration.
From our previous work we have shown that, by applying systems analyses we have identified core regeneration associated gene and protein networks which are differentially expressed after PNS injury (where regeneration occurs) but not after CNS injury (where regeneration fails). These gene networks responsible for PNS regeneration after injury are reproducible across various datasets. From these reproducible networks we have characterized: (a) core gene expression changes after PNS injury, (b) regulators responsible for regeneration after PNS injury, (c) convergent pathways responsible for PNS recovery after injury, (d) small molecule recapitulating the PNS intrinsic growth program. In future, we plan to extend these initial findings to a new level by analyzing, validating and integrating additional transcriptome profiling data generated from sorted neurons and other cell types after nerve injury to examine pathways, identify novel regulators and small molecules associated with neural repair, and ultimately generate mouse models which can regenerate their CNS neurons after injury.
Reduced expression of frataxin (Fxn) is the cause of Friedreich's ataxia (FRDA), an early-onset neurodegenerative disease resulting in early mortality (median age of death, 35 years). Studies in mouse have shown that Fxn plays an important role during embryonic development (homozygous frataxin knockout mice display embryonic lethality). Existing transgenic and knockout FRDA animal models are designed to reduce frataxin either temporally, or selectively by targeting tissues that are severely affected in FRDA patients. These FRDA animal models are either mildly symptomatic due to insufficient reduction of frataxin (greater than 75%) or engineered to be tissue-specific conditional knockouts.
We have developed an inducible mouse model for FRDA that permits reversible frataxin knockdown and detailed studies of the temporal progression or recovery following restoration of frataxin expression. We targeted a single copy shRNA against the Fxn transgene (doxycycline-inducible) under the control of H1 promoter gene into the rosa26 genomic locus. This allowed us to circumvent the lethal effect of organism-wide knockout, while permitting significant frataxin reduction in all tissues. Fxn knockdown was achieved to control the onset and progression of the disease depending on the dose of doxycycline (Dox).
We found that systemic knockdown of Fxn in adult mice led to multiple features paralleling those observed in human patients, including electrophysiologic, cellular, biochemical and structural phenotypes associated with cardiomyopathy, as well as dorsal root ganglion and retinal neuronal degeneration and reduced axonal size and myelin sheath thickness in the spinal cord. Fxn knockdown mice also exhibited other abnormalities similar to patients, including weight loss, reduced locomotor activity, ataxia, reduced muscular strength, and reduced survival, as well as genome-wide transcriptome changes. The reversibility of knockdown also allowed us to determine to what extent observed phenotypes represent neurodegenerative cell death, or reversible cellular dysfunction. Remarkably, upon restoration of near wild-type Fxn levels, we observed significant recovery of function, pathology and associated transcriptomic changes, even after significant motor dysfunction was observed. This inducible model of FRDA is likely to be of broad utility in therapeutic development and in understanding the relative contribution of reversible cellular dysfunction to the devastating phenotypes observed in this condition.
We have established meta-analyses system biology pipelines for meaningful interpretation of complex biological process. Utilizing these pipelines we have integrated multi-layer datasets and have identified novel genes, regulators, pathways and small molecules associated with various biological questions.
By applying these pipelines to nerve injury datasets, we have identified, (1) a transcriptional program observed after PNS, but not CNS injury, (2) this program links known signaling pathways via a core set of transcription factors, (3) we experimentally and bio-informatically validated several network predictions and (4) used the core transcriptional profile to identify a drug that promotes CNS regeneration. By applying these approaches to transcriptomic studies obtained from autism spectrum disorder (ASD) samples, we have demonstrated the presences of pathway convergence and identified critical transcriptional regulators associated with ASD. We have also applied genomic, proteomics and metabolomics framework to understand evolutionary process in Escherichia coli, and demonstrated how a network framework facilitates hypothesis generation and permits evolving beyond network predictions to experimental validation of network models.