Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys

Hypobaric hypoxia (HH) exposure can cause serious brain injury as well as life-threatening cerebral edema in severe cases. Previous studies on the mechanisms of HH-induced brain injury have been conducted primarily using non-primate animal models that are genetically distant to humans, thus hindering the development of disease treatment. Here, we report that cynomolgus monkeys (Macaca fascicularis) exposed to acute HH developed human-like HH syndrome involving severe brain injury and abnormal behavior. Transcriptome profiling of white blood cells and brain tissue from monkeys exposed to increasing altitude revealed the central role of the HIF-1 and other novel signaling pathways, such as the vitamin D receptor (VDR) signaling pathway, in co-regulating HH-induced inflammation processes. We also observed profound transcriptomic alterations in brains after exposure to acute HH, including the activation of angiogenesis and impairment of aerobic respiration and protein folding processes, which likely underlie the pathological effects of HH-induced brain injury. Administration of progesterone (PROG) and steroid neuroprotectant 5α-androst-3β,5,6β-triol (TRIOL) significantly attenuated brain injuries and rescued the transcriptomic changes induced by acute HH. Functional investigation of the affected genes suggested that these two neuroprotectants protect the brain by targeting different pathways, with PROG enhancing erythropoiesis and TRIOL suppressing glutamate-induced excitotoxicity. Thus, this study advances our understanding of the pathology induced by acute HH and provides potential compounds for the development of neuroprotectant drugs for therapeutic treatment.

Author Correction: Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys

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A novel mutation in PRPF31,causative of autosomal dominant retinitis pigmentosa,using the BGISEQ-500 sequencer

AIM： To study the genes responsible for retinitis pigmentosa.METHODS： A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were captured using the Target_Eye_365_V3 chip and sequenced using the BGISEQ-500 sequencer, according to the manufacturer＇s instructions. Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. Local realignment was performed with the Genome Analysis Toolkit（GATK v.3.3.0） Indel Realigner, and variants were called with the Genome Analysis Toolkit Haplotypecaller, without any use of imputation. Variants were filtered against a panel derived from 1000 Genomes Project, 1000 G_ASN, ESP6500, Ex AC and db SNP138. In all members of Family ONE and Family TWO with available DNA samples, the genetic variant was validated using Sanger sequencing.RESULTS： A novel, pathogenic variant of retinitis pigmentosa, c.357_358 del AA（p.Ser119 Serfs X5） was identified in PRPF31 in 2 of 15 autosomal-dominant retinitis pigmentosa（ADRP） families, as well as in one, sporadic case. Sanger sequencing was performed uponprobands, as well as upon other family members. This novel, pathogenic genotype co-segregated with retinitis pigmentosa phenotype in these two families. CONCLUSION： ADRP is a subtype of retinitis pigmentosa, defined by its genotype, which accounts for 20%-40% of the retinitis pigmentosa patients. Our study thus expands the spectrum of PRPF31 mutations known to occur in ADRP, and provides further demonstration of the applicability of the BGISEQ500 sequencer for genomics research.

A Cysteinyl-tRNA Synthetase Mutation Causes Novel Autosomal-Dominant Inheritance of a Parkinsonism/Spinocerebellar-Ataxia Complex

This study aimed to identify possible pathogenic genes in a 90-member family with a rare combination of multiple neurodegenerative disease phenotypes,which has not been depicted by the known neurodegenerative disease.We performed physical and neurological examinations with International Rating Scales to assess signs of ataxia,Parkinsonism,and cognitive function,as well as brain magnetic resonance imaging scans with seven sequences.We searched for co-segregations of abnormal repeat-expansion loci,pathogenic variants in known spinocerebellar ataxiarelated genes,and novel rare mutations via whole-genome sequencing and linkage analysis.A rare co-segregating missense mutation in the CARS gene was validated by Sanger sequencing and the aminoacylation activity of mutant CARS was measured by spectrophotometric assay.This pedigree presented novel late-onset core characteristics including cerebellar ataxia,Parkinsonism,and pyramidal signs in all nine affected members.Brain magnetic resonance imaging showed cerebellar/pons atrophy,pontine-midline linear hyperintensity,decreased rCBF in the bilateral basal ganglia and cerebellar dentate nucleus,and hypo-intensities of the cerebellar dentate nuclei,basal ganglia,mesencephalic red nuclei,and substantia nigra,all of which suggested neurodegeneration.Whole-genome sequencing identified a novel pathogenic heterozygous mutation(E795V)in the CARS gene,meanwhile,exhibited none of the known repeat-expansions or point mutations in pathogenic genes.Remarkably,this CARS mutation causes a 20%decrease in aminoacylation activity to charge tRNA^(Cys) with L-cysteine in protein synthesis compared with that of the wild type.All family members carrying a heterozygous mutation CARS(E795V)had the same clinical manifestations and neuropathological changes of Parkinsonism and spinocerebellar-ataxia.These findings identify novel pathogenesis of Parkinsonismspinocerebellar ataxia and provide insights into its genetic architecture.

A Mitochondrial Genome Sequence of the Tibetan Antelope(Pantholops hodgsonii)

To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis ames and Capra hircus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii （16,498 bp） revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. ames and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. ames and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P. hodgsonii and O. ames is about 2.25 million years ago. Eutther analysis on natural selection indicated that the COXI （cytochrome c oxidase subunit I） gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.

Clinical Auditory Phenotypes Associated with GATA3 Gene Mutations in Familial Hypoparathyroidism-deafness-renal Dysplasia Syndrome

Background： Hypoparathyroidism-deafness-renal dysplasia （HDR） syndrome is an autosomal dominant disorder primarily caused by haploinsufficiency of GATA binding protein 3 （GATA3） gene mutations, and hearing loss is the most frequent phenotypic feature. This study aimed at identifying the causative gene mutation for a three-generation Chinese t;amily with HDR syndrome and analyzing auditory phenotypes in all familial HDR syndrome cases. Methods： Three affected family members underwent otologic examinations, biochemistry tests, and other clinical evaluations. Targeted genes capture combining next-generation sequencing was pertbrmed within the family. Sanger sequencing was used to confirm the causative mutation. The auditory phenotypes of all reported familial H DR syndrome cases analyzed were provided. Results： In Chinese family 712 l, a heterozygous nonsense mutation c.826C〉T （p.R276＊） was identified in GA TA3. All the three affected members suffered from sensorineural deafness and hypocalcemia; however, renal dysplasia only appeared in the youngest patient. Furthermore, an overview of thirty HDR syndrome families with corresponding GATA3 mutations revealed that hearing impairment occurred earlier in the younger generation in at least nine familial cases （30%） and two thirds of them were found to carry premature stop mutations. Conclusions： This study highlights the phenotypic heterogeneity of HDR and points to a possible genetic anticipation in patients with HDR, which needs to be further investigated.

NEIGHBORING-NUCLEOTIDE EFFECTS ON THE MUTATION PATTERNS OF THE RICE GENOME

DNA composition dynamics across genomes of diverse taxonomy is a major subject of genome analyses. DNA composition changes are characteristics of both replication and repair machineries. We investigated 3,611,007 single nucleotide polymorphisms （SNPs） generated by comparing two sequenced rice genomes from distant inbred lines （subspecies）, including those from 242,811 introns and 45,462 protein-coding sequences （CDSs）. Neighboring-nucleotide effects （NNEs） of these SNPs are diverse, depending on structural content-based classifications （genomewide, intronic, and CDS） and sequence context-based categories （A/C, A/G, A/T, C/G, C/T, and G/T substitutions） of the analyzed SNPs. Strong and evident NNEs and nucleotide proportion biases surrounding the analyzed SNPs were observed in 1-3 bp sequences on both sides of an SNP. Strong biases were observed around neighboring nucleotides of protein-coding SNPs, which exhibit a periodicity of three in nucleotide content, constrained by a combined effect of codon-related rules and DNA repair mechanisms. Unlike a previous finding in the human genome, we found negative correlation between GC contents of chromosomes and the magnitude of corresponding bias of nucleotide C at -1 site and G at ＋1 site. These results will further our understanding of the mutation mechanism in rice as well as its evolutionary implications.

PRELIMINARY DNA IDENTIFICATION FOR THE TSUNAMI VICTIMS IN THAI-LAND

The 2004 Southeast Asia Tsunami killed nearly 5,400 people in Southern Thailand, including foreign tourists and local residents. To recover DNA evidence as much as possible from the seriously decomposed bodies, we explored procedures of sample preparation from both bone and tooth samples as well as both mitochondrial and nuclear markers. Despite having failed to recover enough DNA for nuclear marker typing, we succeeded in obtaining fully informative results for mitochondrial markers （HV1 and HV2） from 258 tooth samples with a success rate of 51% （258/507）. Using an organic DNA extraction method coupled with an ultrafiltration step, we obtained 16 STR （including 13 CODIS loci, one sex discrimination locus, and two Identifiler loci） profiles for 834 samples with a success rate of 79% （834/1,062）. In addition, by comparing the allelic frequencies between the typed samples as a group and other index populations, we conclude that the Thai tsunami victims are a combined group of several populations. Our results provide valuable evidence and protocols for the future forensic practice.

A special issue to mark the 90th Anniversary ofCollege of Life Sciences, Zhejiang University

The College of Life Sciences (CLS) remains one of the most prestigious—and the oldest—colleges in Zhejiang University. This special issue, which includes 16 reviews contributed by our alumni and faculties, is dedicated to mark the 90th Anniversary of CLS.