Jason A. Chen

The Emerging Picture of Autism Spectrum Disorder: Genetics and Pathology

Autism spectrum disorder (ASD) is defined by impaired social interaction and communication accompanied by stereotyped behaviors and restricted interests. Although ASD is common, its genetic and clinical features are highly heterogeneous. A number of recent breakthroughs have dramatically advanced our understanding of ASD from the standpoint of human genetics and neuropathology. These studies highlight the period of fetal development and the processes of chromatin structure, synaptic function, and neuron-glial signaling. The initial efforts to systematically integrate findings of multiple levels of genomic data and studies of mouse models have yielded new clues regarding ASD pathophysiology. This early work points to an emerging convergence of disease mechanisms in this complex and etiologically heterogeneous disorder.

An epigenetic signature in peripheral blood associated with the haplotype on 17q21.31, a risk factor for neurodegenerative tauopathy.

Little is known about how changes in DNA methylation mediate risk for human diseases including dementia. Analysis of genome-wide methylation patterns in patients with two forms of tau-related dementia – progressive supranuclear palsy (PSP) and frontotemporal dementia (FTD) – revealed significant differentially methylated probes (DMPs) in patients versus unaffected controls. Remarkably, DMPs in PSP were clustered within the 17q21.31 region, previously known to harbor the major genetic risk factor for PSP. We identified and replicated a dose-dependent effect of the risk-associated H1 haplotype on methylation levels within the region in blood and brain. These data reveal that the H1 haplotype increases risk for tauopathy via differential methylation at that locus, indicating a mediating role for methylation in dementia pathophysiology.

Machine learning for large-scale wearable sensor data in Parkinson's disease: concepts, promises, pitfalls, and futures

For the treatment and monitoring of Parkinsons disease (PD) to be scientific, a key requirement is that measurement of disease stages and severity is quantitative, reliable, and repeatable. The last 50 years in PD research have been dominated by qualitative, subjective ratings obtained by human interpretation of the presentation of disease signs and symptoms at clinical visits. More recently, “wearable,” sensor‐based, quantitative, objective, and easy‐to‐use systems for quantifying PD signs for large numbers of participants over extended durations have been developed. This technology has the potential to significantly improve both clinical diagnosis and management in PD and the conduct of clinical studies. However, the large‐scale, high‐dimensional character of the data captured by these wearable sensors requires sophisticated signal processing and machine‐learning algorithms to transform it into scientifically and clinically meaningful information. Such algorithms that “learn” from data have shown remarkable success in making accurate predictions for complex problems in which human skill has been required to date, but they are challenging to evaluate and apply without a basic understanding of the underlying logic on which they are based. This article contains a nontechnical tutorial review of relevant machine‐learning algorithms, also describing their limitations and how these can be overcome. It discusses implications of this technology and a practical road map for realizing the full potential of this technology in PD research and practice.

Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons

An intronic GGGGCC repeat expansion in C9ORF72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but the pathogenic mechanism of this repeat remains unclear. Using human induced motor neurons (iMNs), we found that repeat-expanded C9ORF72 was haploinsufficient in ALS. We found that C9ORF72 interacted with endosomes and was required for normal vesicle trafficking and lysosomal biogenesis in motor neurons. Repeat expansion reduced C9ORF72 expression, triggering neurodegeneration through two mechanisms: accumulation of glutamate receptors, leading to excitotoxicity, and impaired clearance of neurotoxic dipeptide repeat proteins derived from the repeat expansion. Thus, cooperativity between gain- and loss-of-function mechanisms led to neurodegeneration. Restoring C9ORF72 levels or augmenting its function with constitutively active RAB5 or chemical modulators of RAB5 effectors rescued patient neuron survival and ameliorated neurodegenerative processes in both gain- and loss-of-function C9ORF72 mouse models. Thus, modulating vesicle trafficking was able to rescue neurodegeneration caused by the C9ORF72 repeat expansion. Coupled with rare mutations in ALS2, FIG4, CHMP2B, OPTN and SQSTM1, our results reveal mechanistic convergence on vesicle trafficking in ALS and FTD.

A152T tau allele causes neurodegeneration that can be ameliorated in a zebrafish model by autophagy induction

Mutations in MAPT cause a variety of neurodegenerative disorders. Lopez et al. confirm that A152T-variant tau is associated with increased risk for frontotemporal dementia and progressive supranuclear palsy syndrome. Upregulation of autophagy increases tau clearance and ameliorates pathology in zebrafish expressing A152T-tau, suggesting potential for the treatment of tauopathies.

Suboccipital craniotomy for Chiari I results in evoked potential conduction changes.

Background: Management of Chiari I is controversial, in part because there is no widely used quantitative measurement of decompression. It has been demonstrated that brainstem auditory evoked responses (BAER) and somatosensory evoked potentials (SSEP) have decreased conduction latencies after wide craniectomy. We analyzed these parameters in a suboccipital craniectomy/craniotomy procedure. Methods: Thirteen consecutive patients underwent suboccipital decompression for treatment of symptomatic Chiari I. Craniectomy was restricted to the inferior aspect of the nuchal line, and in most cases the bone flap was replaced. Neuronal conduction was monitored continuously with median nerve somatosensory evoked potentials (M-SEP), posterior tibial nerve somatosensory evoked potentials (T-SEP), BAER, or a combination. The M-SEP N20, T-SEP P37, and BAER V latencies were recorded at four milestones – preoperatively, following craniotomy, following durotomy, and following closure. Results: Five males and eight females, with average age of 9 years, were studied. Clinical improvement was noted in all 13 patients. M-SEP N20 latency decreased from a mean of 18.55 at baseline to 17.75 ms after craniotomy (P = 0.01); to 17.06 ms after durotomy (P = 0.01); and to 16.68 ms after closing (P = 0.02). T-SEP P37 latency did not change significantly. BAER V latency decreased from a mean of 6.25 ms at baseline to 6.14 ms after craniotomy (P = 0.04); to 5.98 ms after durotomy (P = 0.01); and to 5.95 ms after closing (P = 0.45). Conclusion: Significant improvements in conduction followed both craniectomy and durotomy. Bone replacement did not affect these results.

A multiancestral genome-wide exome array study of Alzheimer Disease, frontotemporal dementia, and progressive supranuclear palsy

IMPORTANCE Previous studies have indicated a heritable component of the etiology of neurodegenerative diseases such as Alzheimer disease (AD), frontotemporal dementia (FTD), and progressive supranuclear palsy (PSP). However, few have examined the contribution of low-frequency coding variants on a genome-wide level. OBJECTIVE To identify low-frequency coding variants that affect susceptibility to AD, FTD, and PSP. DESIGN, SETTING, AND PARTICIPANTS We used the Illumina HumanExome BeadChip array to genotype a large number of variants (most of which are low-frequency coding variants) in a cohort of patients with neurodegenerative disease (224 with AD, 168 with FTD, and 48 with PSP) and in 224 control individuals without dementia enrolled between 2005-2012 from multiple centers participating in the Genetic Investigation in Frontotemporal Dementia and Alzheimers Disease (GIFT) Study. An additional multiancestral replication cohort of 240 patients with AD and 240 controls without dementia was used to validate suggestive findings. Variant-level association testing and gene-based testing were performed. MAIN OUTCOMES AND MEASURES Statistical association of genetic variants with clinical diagnosis of AD, FTD, and PSP. RESULTS Genetic variants typed by the exome array explained 44%, 53%, and 57% of the total phenotypic variance of AD, FTD, and PSP, respectively. An association with the known AD gene ABCA7 was replicated in several ancestries (discovery P=.0049, European P=.041, African American P=.043, and Asian P=.027), suggesting that exonic variants within this gene modify AD susceptibility. In addition, 2 suggestive candidate genes, DYSF (P=5.53×10(-5)) and PAXIP1 (P=2.26×10(-4)), were highlighted in patients with AD and differentially expressed in AD brain. Corroborating evidence from other exome array studies and gene expression data points toward potential involvement of these genes in the pathogenesis of AD. CONCLUSIONS AND RELEVANCE Low-frequency coding variants with intermediate effect size may account for a significant fraction of the genetic susceptibility to AD and FTD. Furthermore, we found evidence that coding variants in the known susceptibility gene ABCA7, as well as candidate genes DYSF and PAXIP1, confer risk for AD.

The truth and coherence behind the concept of overdrainage of cerebrospinal fluid in hydrocephalic patients

IntroductionOverdrainage, siphoning, and slit-ventricle syndrome are well-documented complications of shunting in hydrocephalic patients. Despite the prevalence of these conditions, their mechanisms are still not fully understood. In this paper, the authors trace the concept of overdrainage and the related phenomena of siphoning and slit-ventricle syndrome.PurposeTo provide a historical overview of overdrainage and to reignite discussion of a topic that has been settled.Methods and resultsA medical literature search and review were performed via Google Scholar. Of 565 publications, 3 primary papers were identified and a timeline was developed demonstrating the convergence of the aforementioned concepts. From the primary papers, 25 relevant publications were selected and further analyzed searching for hypothesis, evidence, and conclusions.ConclusionOverdrainage, siphoning, and slit-ventricle syndrome are associated concepts that have converged into a pathophysiological theory where siphoning of CSF leads to overdrainage, which is then hypothesized to cause slit-ventricle syndrome in a small subset of patients. Our data suggests that while there have been numerous reports regarding overdrainage and its consequences, the evidence is not as robust as currently presumed and this subject requires prospective exploration.

Experimental evaluation of LANMAR, a scalable ad-hoc routing protocol

Routing protocols for mobile ad-hoc networks have been evaluated extensively through simulation because various network conditions can be easily configured, tested, and replicated across different schemes in simulation than in a real system. Recently, some of these schemes have been implemented in academic, industry and defense testbeds. This gives researchers an opportunity to validate their simulation results with actual implementations. In this paper we report the lessons learned from the implementation of LANMAR (Pei et al. (2000)), a scalable routing protocol that was developed at UCLA as part of large-scale ad hoc network architecture for autonomous unattended agents under ONR support. LANMAR is designed to provide efficient, scalable routing in large ad-hoc wireless networks that exhibit group mobility. In this paper we describe the implementation of this protocol in Linux environments and report on experimental results based on this implementation. The results and lessons from these experiments have enriched our understanding of the LANMAR protocol and its interaction with the other layers and the environment, paving the way to protocol refinements and more efficient implementations.

Genome-wide association study identifies MAPT locus influencing human plasma tau levels

Objective: To identify genetic loci associated with plasma tau concentrations in healthy elders and individuals with Alzheimer disease. Methods: Four hundred sixty-three non-Hispanic white individuals exceeding quality control criteria were included from the Alzheimers Disease Neuroimaging Initiative (ADNI-1) cohort. Association of plasma tau with genetic polymorphisms was performed with a linear regression model. Significant associations were validated in an independent replication cohort consisting of 431 healthy elders or individuals with mild cognitive impairment recruited from the University of California, San Francisco Memory and Aging Center. Results: The minor allele (A) of rs242557 in the microtubule-associated protein tau gene (MAPT) was associated with higher plasma tau levels at genome-wide significance (p = 4.85 × 10−9, empiric family-wise error corrected p = 0.0024) in a dose-dependent fashion. This association was also observed in the replication cohort (p = 1.0 × 10−5; joint analysis p = 1.2 × 10−12). Single nucleotide polymorphisms near PARK2 (rs2187213) (p = 6.15 × 10−6), IL2RA (rs7072793, rs7073236) (p = 7.89 × 10−6), and an intergenic locus on 9p21.3 (rs7047280) (p = 8.13 × 10−6) were identified as suggestive loci associated with plasma tau levels. Conclusions: MAPT H1c haplotype (rs242557) has previously been identified as a genetic risk factor for progressive supranuclear palsy and corticobasal degeneration. The current findings suggest that plasma tau concentration could be an endophenotype for identifying risk for 4-repeat tauopathies in older individuals.