An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns

More than 90% of genetic variants are rare in most modern sequencing studies, such as the Alzheimer''s Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data. Furthermore, 54% of the rare variants in ADSP WES are singletons. However, both single variant and unit-based tests are limited in their statistical power to detect an association between rare variants and phenotypes. To best use missense rare variants and investigate their biological effect, we examine their association with phenotypes in the context of protein structures. We developed a protein structure–based approach, protein optimized kernel evaluation of missense nucleotides (POKEMON), which evaluates rare missense variants based on their spatial distribution within a protein rather than their allele frequency. The hypothesis behind this test is that the three-dimensional spatial distribution of variants within a protein structure provides functional context to power an association test. POKEMON identified three candidate genes (TREM2, SORL1, and EXOC3L4) and another suggestive gene from the ADSP WES data. For TREM2 and SORL1, two known Alzheimer''s disease (AD) genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low-frequency risk variants within these genes. EXOC3L4 is a novel AD risk gene that has a cluster of variants primarily shared by case subjects around the Sec6 domain. This cluster is also validated in an independent replication data set and a validation data set with a larger sample size.

High-throughput DNA sequencing of diverse humans has identified millions of genetic variants, the vast majority of which are exceptionally rare. A survey of ∼60,000 individuals from the Exome Aggregation Consortium (ExAC) found that out of ∼7 million variants, 99% have a frequency <1% and 54% are singletons (Taliun et al. 2021). Similarly, in the Alzheimer''s Disease Sequencing Project (ADSP) whole-exome sequencing (WES) of ∼10,000 individuals, 97% of identified variants have a minor allele frequency <1%, and 23% are singletons (Butkiewicz et al. 2018). However, the effect of most rare variants on diseases of interest remains unknown because of insufficient statistical power to detect the associations between these variants and phenotypes.We hypothesized that rare missense variants contribute to common diseases by disrupting the protein function and are likely to form clustered or dispersed patterns within protein structures when examined in population-based studies. Therefore, incorporating spatial context will improve rare variant association tests. Prior studies have shown that missense variants show nonrandom patterns in protein structures, such as cancer-associated hotspot regions with a high density of missense somatic mutations (Tokheim et al. 2016). Our group (Sivley et al. 2018) also found that germline causal missense variants for Mendelian diseases show nonrandom patterns in three-dimensional (3D) space. These patterns include clusters that likely reflect disruption of a key functional region and dispersions that likely reflect depletion of variants within a sensitive protein core.To test this hypothesis within sequencing studies of disease traits, we developed a kernel function to quantify genetic similarity among individuals by using protein structure information. When two individuals have different missense variants distal in genomic coordinates but close in 3D protein structure, these individuals will be assigned a high genetic similarity through our kernel function. When applied over an entire data set, our kernel function captures differences in the spatial patterns of rare missense variants among cases and controls or over continuous traits. Using a statistical framework similar to SKAT (Wu et al. 2011), we test the association of rare variants with quantitative and dichotomous phenotypes using this structure-based kernel. We call this approach protein optimized kernel evaluation of missense nucleotides (POKEMON). We validated that POKEMON can identify trait associations with spatial patterns formed by missense variants both in simulation studies and real-world data.     

Secondary vestibulocerebellar projections to flocculonodular lobe in a prosimian primate,Galago senegalensis

The organization of vestibulocerebellar projections to the flocculonodular and adjacent cortices were studied in Galago using horseradish peroxidase (HRP). Implants of HRP pellets or injections (0.14–0.95μI) were placed in floccular, parafloccular, nodular, and uvular cortices. Following survival times of 18–25 hours animals were killed via transcardiac perfusion of heparinized saline followed by a buffered solution of paraformaldehyde and glutaraldehyde. Tissues were processed using DAB as the chromogen. Consequent to floccular implants HRP-positive cells are found bilaterally in medial (MVN), spinal (SpVN), and superior (SVN) vestibular nuclei. Labeled neurons are present in the ipsilateral subgroup y and interstitial nucleus of the eighth nerve. The prepositus hypoglossal nuclei also contained HRP-positive somata. A column of labeled cells is present exclusively in dorsomedial MVN subsequent to injection of the paraflocculus. Injections of nodular cortex reveal a distinct bilateral projection to this cortical area. Many labeled cells are located in SpVN, MVN, SVN, subgroups x and y, the interstitial nucleus, and the ganglion of the eighth nerve. Labeled somata are concentrated in dorsal and dorsolateral SpVN and in a bandlike configuration in subgroup x. HRP-reactive cells appear to have a differential rostrocaudal distribution in MVN, while the majority of positive cells in SVN are found in central portions of the nucleus. After HRP injection into the transition area between nodular and uvular cortices, labeled neurons are present in MVN, SpVN, and the prepositus hypoglossal nucleus. A similar distribution of HRP-positive cells is seen following injections of ventral uvula; however, cells are markedly fewer in number. In no case, subsequent to injection of the flocculonodular lobe and adjacent cortices, are HRP-labeled neurons found in the lateral vestibular nucleus.     

Neuropeptides and inflammation. A somatostatin analog as a selective antagonist of neutrophil activation by substance P

Objective. Substance P and somatostatin are neuropeptides found in peripheral sensory nerves. In vitro, these have opposing effects on inflammatory cells. We compared the effects of these peptides on the activation of neutrophils. Methods. Neutrophils were isolated from healthy volunteers, and chemotaxis, superoxide anion generation, aggregation, and changes in cytosolic calcium and GTPase activity were measured in the presence of substance P, somatostatin, and the chemoattractant FMLP. Results. Substance P was an effective chemoattractant, 20% as potent as FMLP at equimolar concentrations. Substance P also stimulated GTPase activity in neutrophil plasma membranes. Somatostatin did not activate neutrophils; however, it effectively inhibited neutrophil chemotaxis and GTPase activity provoked substance P, but not by FMLP. Conclusions. These studies demonstrate that substance P can effectively stimulate chemotaxis, possible via effects on a GTP-binding protein distinct from that triggered by FMLP, and that somatostatin is a selective antagonist of substance P. The biochemical specificities of these peptides on cells may modulate neurogenic inflammation at the local level.     

腹泻标本中同时分离类志贺邻单胞菌和豚鼠气单胞菌1例

0　引言　腹泻标本中同时检出类志贺邻单胞菌和豚鼠气单胞菌 ,在国内尚未见报道 .现报告如下 .1　临床资料　患者 ,女 ,45岁 .主诉于 12 h前因食不洁冷冻鱼类食品后 ,出现腹痛伴腹泻 ,为黄色稀水便转为血水样便 ,9次 / d,每次量约 2 0 0 m L.伴轻度乏力、恶心、里急后重 .腹痛以上腹部及左下腹部为著 ,呈持续隐痛伴有阵发性加重 .于2 0 0 0 - 0 3- 2 7就诊 .体检 :T37.2℃ ,P78次 / min,R16次 /min,BP13/ 8KPa.实验室检查 :WBC10 .8× 10 9· L- 1 ,N0 .84,L 0 .16 .大便常规 :RBC +++/ HP,WBC 3- 9/ HP,便隐血阳性 .取粪便送检做…     

Evidence-based neurosurgery

OBJECTIVE: The evidence-based medicine movement is gaining influence in many medical specialties. Although many think that clinical medicine always has been based on evidence, the discipline of evidence-based medicine places particular emphasis on a defined set of principles of critical analysis of individual research reports, methodologically rigorous synthesis of multiple reports, and the collection and dissemination of evidence repositories that allow rapid application of evidence in practice. This article provides a selective introduction to the discipline of evidence-based medicine as it applies to neurological surgery. METHODS: The vast literature on evidence-based medicine has been reviewed selectively to identify resources that are readable, accessible, and relevant to neurosurgery. RESULTS: The history, concepts, and techniques of evidence-based medicine are presented in brief, and educational and methodological resources, as well as evidence repositories, are introduced. CONCLUSION: The techniques of evidence-based medicine are relevant to neurological surgery. There is a relatively large repository of critically analyzed and summarized evidence that is useful to the neurosurgical practitioner. Familiarity with these techniques and repositories can help the neurosurgeon bring the best available evidence to bear on the care of individual patients.