Genetic adaptation of skin pigmentation in highland Tibetans.

Strong ultraviolet (UV) radiation at high altitude imposes a serious selective pressure, which may induce skin pigmentation adaptation of indigenous populations. We conducted skin pigmentation phenotyping and genome-wide analysis of Tibetans in order to understand the underlying mechanism of adaptation to UV radiation. We observe that Tibetans have darker baseline skin color compared with lowland Han Chinese, as well as an improved tanning ability, suggesting a two-level adaptation to boost their melanin production. A genome-wide search for the responsible genes identifies GNPAT showing strong signals of positive selection in Tibetans. An enhancer mutation (rs75356281) located in GNPAT intron 2 is enriched in Tibetans (58%) but rare in other world populations (0 to 18%). The adaptive allele of rs75356281 is associated with darker skin in Tibetans and, under UVB treatment, it displays higher enhancer activities compared with the wild-type allele in in vitro luciferase assays. Transcriptome analyses of gene-edited cells clearly show that with UVB treatment, the adaptive variant of GNPAT promotes melanin synthesis, likely through the interactions of CAT and ACAA1 in peroxisomes with other pigmentation genes, and they act synergistically, leading to an improved tanning ability in Tibetans for UV protection.

Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau.

BACKGROUND: Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products. RESULTS: We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe. CONCLUSIONS: Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.

Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia.

Tibetans are well adapted to the hypoxic environments at high altitude, yet the molecular mechanism of this adaptation remains elusive. We reported comprehensive genetic and functional analyses of EPAS1, a gene encoding hypoxia inducible factor 2α (HIF-2α) with the strongest signal of selection in previous genome-wide scans of Tibetans. We showed that the Tibetan-enriched EPAS1 variants down-regulate expression in human umbilical endothelial cells and placentas. Heterozygous EPAS1 knockout mice display blunted physiological responses to chronic hypoxia, mirroring the situation in Tibetans. Furthermore, we found that the Tibetan version of EPAS1 is not only associated with the relatively low hemoglobin level as a polycythemia protectant, but also is associated with a low pulmonary vasoconstriction response in Tibetans. We propose that the down-regulation of EPAS1 contributes to the molecular basis of Tibetans' adaption to high-altitude hypoxia.

HMOX2 Functions as a Modifier Gene for High-Altitude Adaptation in Tibetans.

Tibetans are well adapted to high-altitude environments. Among the adaptive traits in Tibetans, the relatively low hemoglobin level is considered a blunted erythropoietic response to hypoxic challenge. Previously, EPAS1 and EGLN1, the major upstream regulators in the hypoxic pathway, were reportedly involved in the hemoglobin regulation in Tibetans. In this study, we report a downstream gene (HMOX2) involved in heme catabolism, which harbors potentially adaptive variants in Tibetans. We first resequenced the entire genomic region (45.6 kb) of HMOX2 in Tibetans, which confirmed the previously suspected signal of positive selection on HMOX2 in Tibetans. Subsequent association analyses of hemoglobin levels in two independent Tibetan populations (a total of 1,250 individuals) showed a male-specific association between the HMOX2 variants and hemoglobin levels. Tibetan males with the derived C allele at rs4786504:T>C displayed lower hemoglobin level as compared with the T allele carriers. Furthermore, our in vitro experiments indicated that the C allele of rs4786504 could increase the expression of HMOX2, presumably leading to a more efficient breakdown of heme that may help maintain a relatively low hemoglobin level at high altitude. Collectively, we propose that HMOX2 contributes to high-altitude adaptation in Tibetans by functioning as a modifier in the regulation of hemoglobin metabolism.

Identification of a Tibetan-specific mutation in the hypoxic gene EGLN1 and its contribution to high-altitude adaptation.

Tibetans are well adapted to high-altitude hypoxic conditions, and in recent genome-wide scans, many candidate genes have been reported involved in the physiological response to hypoxic conditions. However, the limited sequence variations analyzed in previous studies would not be sufficient to identify causal mutations. Here we conducted resequencing of the entire genomic region (59.4 kb) of the hypoxic gene EGLN1 (one of the top candidates from the genome-wide scans) in Tibetans and identified 185 sequence variations, including 13 novel variations (12 substitutions and 1 insertion or deletion). There is a nonsynonymous mutation (rs186996510, D4E) showing surprisingly deep divergence between Tibetans and lowlander populations (Fst = 0.709 between Tibetans and Han Chinese). It is highly prevalent in Tibetans (70.9% on average) but extremely rare in Han Chinese, Japanese, Europeans, and Africans (0.56-2.27%), suggesting that it might be the causal mutation of EGLN1 contributing to high-altitude hypoxic adaptation. Neutrality test confirmed the signal of Darwinian positive selection on EGLN1 in Tibetans. Haplotype network analysis revealed a Tibetan-specific haplotype, which is absent in other world populations. The estimated selective intensity (0.029 for the C allele of rs186996510) puts EGLN1 among the known genes that have undergone the strongest selection in human populations, and the onset of selection was estimated to have started at the early Neolithic (∼8,400 years ago). Finally, we detected a significant association between rs186996510 and hemoglobin levels in Tibetans, suggesting that EGLN1 contributes to the adaptively low hemoglobin level of Tibetans compared with acclimatized lowlanders at high altitude.

Genetic evidence of paleolithic colonization and neolithic expansion of modern humans on the tibetan plateau.

Tibetans live on the highest plateau in the world, their current population size is approximately 5 million, and most of them live at an altitude exceeding 3,500 m. Therefore, the Tibetan Plateau is a remarkable area for cultural and biological studies of human population history. However, the chronological profile of the Tibetan Plateau's colonization remains an unsolved question of human prehistory. To reconstruct the prehistoric colonization and demographic history of modern humans on the Tibetan Plateau, we systematically sampled 6,109 Tibetan individuals from 41 geographic populations across the entire region of the Tibetan Plateau and analyzed the phylogeographic patterns of both paternal (n = 2,354) and maternal (n = 6,109) lineages as well as genome-wide single nucleotide polymorphism markers (n = 50) in Tibetan populations. We found that there have been two distinct, major prehistoric migrations of modern humans into the Tibetan Plateau. The first migration was marked by ancient Tibetan genetic signatures dated to approximately 30,000 years ago, indicating that the initial peopling of the Tibetan Plateau by modern humans occurred during the Upper Paleolithic rather than Neolithic. We also found evidences for relatively young (only 7-10 thousand years old) shared Y chromosome and mitochondrial DNA haplotypes between Tibetans and Han Chinese, suggesting a second wave of migration during the early Neolithic. Collectively, the genetic data indicate that Tibetans have been adapted to a high altitude environment since initial colonization of the Tibetan Plateau in the early Upper Paleolithic, before the last glacial maximum, followed by a rapid population expansion that coincided with the establishment of farming and yak pastoralism on the Plateau in the early Neolithic.

High Arterial Oxygen Saturation in the Acclimatized Lowlanders Living at High Altitude.

Blood oxygen saturation (SpO2) is a key indicator of oxygen availability in the body. It is known that a low SpO2 at high altitude is associated with morbidity and mortality risks due to physiological hypoxemia. Previously, it was proposed that the lowlander immigrants living at high altitude should have a lower SpO2 level compared to the highlander natives, but this proposal has not been rigorously tested due to the lack of data from the lowlander immigrants living at high altitude. In this study, we compared arterial oxygen saturation of 5929 Tibetan natives and 1034 Han Chinese immigrants living at altitudes ranging from 1120 m to 5020 m. Unexpectedly, the Han immigrants had a higher SpO2 than the Tibetan natives at the same high altitudes. At the same time, there is a higher prevalence of chronic mountain sickness in Han than in Tibetans at the same altitude. This result suggests that the relatively higher SpO2 level of the acclimatized Han is associated with a physiological cost, and the SpO2 level of Tibetans tends to be sub-optimal. Consequently, SpO2 alone is not a robust indicator of physiological performance at high altitude. Supplementary Information: The online version contains supplementary material available at 10.1007/s43657-023-00117-x.

Polygenic adaptation leads to a higher reproductive fitness of native Tibetans at high altitude.

The adaptation of Tibetans to high-altitude environments has been studied extensively. However, the direct assessment of evolutionary adaptation, i.e., the reproductive fitness of Tibetans and its genetic basis, remains elusive. Here, we conduct systematic phenotyping and genome-wide association analysis of 2,252 mother-newborn pairs of indigenous Tibetans, covering 12 reproductive traits and 76 maternal physiological traits. Compared with the lowland immigrants living at high altitudes, indigenous Tibetans show better reproductive outcomes, reflected by their lower abortion rate, higher birth weight, and better fetal development. The results of genome-wide association analyses indicate a polygenic adaptation of reproduction in Tibetans, attributed to the genomic backgrounds of both the mothers and the newborns. Furthermore, the EPAS1-edited mice display higher reproductive fitness under chronic hypoxia, mirroring the situation in Tibetans. Collectively, these results shed new light on the phenotypic pattern and the genetic mechanism of human reproductive fitness in extreme environments.

Deep phenotyping of 11,880 highlanders reveals novel adaptive traits in native Tibetans.

Tibetans are the ideal population to study genetic adaptation in extreme environments. Here, we performed systematic phenotyping of 11,880 highlanders, covering 133 quantitative traits of 13 organ systems. We provided a comprehensive phenotypic atlas by comparing altitude adaptation and altitude acclimatization. We found the differences between adaptation and acclimatization are quantitative rather than qualitative, with a whole-system "blunted effect" seen in the adapted Tibetans. We characterized twelve different functional changes between adaptation and acclimatization. More importantly, we established a landscape of adaptive phenotypes of indigenous Tibetans, including 45 newly identified Tibetan adaptation-nominated traits, involving specific changes of Tibetans in internal organ state, metabolism, eye morphology, and skin pigmentation. In addition, we observed a sex-biased pattern between altitude acclimatization and adaptation. The generated atlas of phenotypic landscape provides new insights into understanding of human adaptation to high-altitude environments, and it serves as a valuable blueprint for future medical and physiological studies.

Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans.

BACKGROUND: Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting selective signatures in the Tibetan genomes. RESULTS: Here, we present whole-genome sequencing (WGS) data of 1001 indigenous Tibetans, covering the major populated areas of the Qinghai-Tibetan Plateau in China. We identify 35 million variants, and more than one-third of them are novel variants. Utilizing the large-scale WGS data, we construct a comprehensive map of allele frequency and linkage disequilibrium and provide a population-specific genome reference panel, referred to as 1KTGP. Moreover, with the use of a combined approach, we redefine the signatures of Darwinian-positive selection in the Tibetan genomes, and we characterize a high-confidence list of 4320 variants and 192 genes that have undergone selection in Tibetans. In particular, we discover four new genes, TMEM132C, ATP13A3, SANBR, and KHDRBS2, with strong signals of selection, and they may account for the adaptation of cardio-pulmonary functions in Tibetans. Functional annotation and enrichment analysis indicate that the 192 genes with selective signatures are likely involved in multiple organs and physiological systems, suggesting polygenic and pleiotropic effects. CONCLUSIONS: Overall, the large-scale Tibetan WGS data and the identified adaptive variants/genes can serve as a valuable resource for future genetic and medical studies of high-altitude populations.

Genetic variations in Tibetan populations and high-altitude adaptation at the Himalayas.

Modern humans have occupied almost all possible environments globally since exiting Africa about 100,000 years ago. Both behavioral and biological adaptations have contributed to their success in surviving the rigors of climatic extremes, including cold, strong ultraviolet radiation, and high altitude. Among these environmental stresses, high-altitude hypoxia is the only condition in which traditional technology is incapable of mediating its effects. Inhabiting at >3,000-m high plateau, the Tibetan population provides a widely studied example of high-altitude adaptation. Yet, the genetic mechanisms underpinning long-term survival in this environmental extreme remain unknown. We performed an analysis of genome-wide sequence variations in Tibetans. In combination with the reported data, we identified strong signals of selective sweep in two hypoxia-related genes, EPAS1 and EGLN1. For these two genes, Tibetans show unusually high divergence from the non-Tibetan lowlanders (Han Chinese and Japanese) and possess high frequencies of many linked sequence variations as reflected by the Tibetan-specific haplotypes. Further analysis in seven Tibetan populations (1,334 individuals) indicates the prevalence of selective sweep across the Himalayan region. The observed indicators of natural selection on EPAS1 and EGLN1 suggest that during the long-term occupation of high-altitude areas, the functional sequence variations for acquiring biological adaptation to high-altitude hypoxia have been enriched in Tibetan populations.

Identification of the susceptible subpopulations for wide pulse pressure under long-term exposure to ambient particulate matters.

Wide pulse pressure (WPP) is a preclinical indicator for arterial stiffness and cardiovascular diseases. Long-term exposure to ambient particulate matters (PMs) would increase the risk of WPP. Although reducing pollutants emissions and avoiding outdoor activity during a polluted period are effective ways to blunt the adverse effects. Identifying and protecting the susceptible subpopulation is another crucial way to reduce the disease burdens. Therefore, we aimed to identify the susceptible subpopulations of WPP under long-term exposure to PMs. The WPP was defined as pulse pressure over 60 mmHg. Three-year averages of PMs were estimated using random forest approaches. Associations between WPP and PMs exposure were estimated using generalized propensity score weighted logistic regressions. Demographic, socioeconomic characteristics, health-related behaviors, and hematological biomarkers were collected to detect the modification effects on the WPP-PMs associations. Susceptible subpopulations were defined as those with significantly higher risks of WPP under PMs exposures. The PMs-WPP associations were significant with ORs (95%CI) of 1.126 (1.094, 1.159) for PM1, 1.174 (1.140, 1.210) for PM2.5, and 1.111 (1.088, 1.135) for PM10. There were 17 subpopulations more sensitive to WPP under long-term exposure to PMs. The susceptibility was higher in subpopulations with high BMI (Q3-Q4 quartiles), high-intensive physical activity (Q3 or Q4 quartile), insufficient or excessive fruit intake (Q1 or Q5 quartile), insufficient or too long sleep length (<7 or >8 h). Subpopulations with elevated inflammation markers (WBC, LYM, BAS, EOS: Q3-Q4 quartiles) and glucose metabolism indicators (HbA1c, GLU: Q3-Q4 quartiles) were more susceptible. Besides, elder, urban living, low socioeconomic level, and excessive red meat and sodium salt intake were also related to higher susceptibility. Our findings on the susceptibility characteristics would help to develop more targeted disease prevention and therapy strategies. Health resources can be allocated more effectively by putting more consideration to subpopulations with higher susceptibility.

Seasonality and Sex-Biased Fluctuation of Birth Weight in Tibetan Populations.

Birth weight (BW) is a key determinant of infant mortality. Previous studies have reported seasonal fluctuation of BW. However, the responsible environmental factors remain disputable. High-altitude environment provides a great opportunity to test the current hypotheses due to its distinctive climate conditions. We collected BW data of ~ 9000 Tibetan singletons born at Lhasa (elevation: 3660 m) from 2014 to 2018. Using regression models, we analyzed BW seasonality of highland Tibetans. Multivariate models with meteorological factors as independent variables were employed to examine responsible environmental factors accounting for seasonal variation. We compared BW, low-BW prevalence and sex ratio between highland and lowland populations, and we observed a significant seasonal pattern of BW in Tibetans, with a peak in winter and a trough in summer. Notably, there is a marked sex-biased pattern of BW seasonality (more striking in males than in females). Sunlight exposure in the 3rd trimester and barometric pressure exposure in the 2nd trimester are significantly correlated with BW, and the latter can be explained by seasonal change of oxygen partial pressure. In particular, due to the male-biased BW seasonality, we found a more serious BW reduction and higher prevalence of low-BW in males, and a skewed sex ratio in highlanders. The infant BW of highland Tibetans has a clear pattern of seasonality. The winter BW is larger than the summer BW, due to the longer sunlight exposure during the late-trimester. Male infants are more sensitive to hypoxia than female infants during the 2nd trimester, leading to more BW reduction and higher mortality. Supplementary Information: The online version contains supplementary material available at 10.1007/s43657-021-00038-7.

Studies on separating the impedance change components of blood vessels and ventricles in thorax from mixed impedance signals on chest surface.

PURPOSE: The aim of the present study is to separate the impedance change components of the blood vessels and ventricles in thorax from the mixed impedance signals detected on the chest surface. METHODS: The mixed impedance signals on the chest surface are measured with a 15 electrode lead system. The thoracic impedance equations are established and solved iteratively with the algebraic reconstructed technique. Experiments were performed on 80 healthy, otherwise normal, adults. RESULTS: Five impedance change components for the aorta (AO), blood vessel in left lung (PL), blood vessel in right lung (PR), left ventricle (LV), and right ventricle (RV) are separated from the mixed impedance signals. The experiments show that the main waveform of the ventricular components LV and RV is contrary to that of the vascular components AO, PL, and PR, and the negative peak point of the waveform graphs of LV and RV are in phase with the second cardiac sound (S2). The waveform graphs of various components correspond with the physiological activities of the heart and blood vessels in a cardiac cycle. The statistical results for 80 normal adults show that the amplitude of AO is the largest and that of PL and PR is the next, while that of LV and RV is the smallest. There are significant differences between them (P < 0.01). CONCLUSIONS: The mathematical model and the measurement method for the separation in the present paper are feasible.

[Integripetal rhodiola herb attenuates high altitude-induced pulmonary arterial remodeling and expression of vascular endothelial growth factor in rats].

The aim of this study was to investigate the effect of integripetal rhodiola herb on pulmonary arterial remodeling and expression of vascular endothelial growth factor (VEGF) in high altitude pulmonary hypertension in rats. Fifty healthy male Wistar rats were divided into five groups randomly: Plain control group (LC group), 10-day plateau group (H(10) group), 30-day plateau group (H(30) group), 10-day rhodiola-treated plateau group (R(10) group), and 30-day rhodiola-treated plateau group (R(30) group). Each group included 10 rats. The rats in LC group were kept in Chengdu (500 meters above sea level), and rats in H and R groups were kept in Lhasa (3 700 meters above sea level). The rats in R group were daily treated with integripetal rhodiola herb extract (24%, 10 mL/kg) intragastrically for 10 d or 30 d, while rats in LC and H groups were treated with the same volume of saline. Mean pulmonary arterial pressure (mPAP) was detected via a catheter in the pulmonary artery by pressure waveform monitoring. The ratio value of right ventricle weight to left ventricle plus septum weight [RV/(LV + S)] was measured. The microstructure of pulmonary arterioles was examined by electron microscopy. The expression of VEGF in the lung was investigated using immunohistochemistry. The results showed that mPAP and [RV/(LV + S)] in H(10) group and H(30) group were higher than those in LC group (P < 0.05); but there was no significant difference between H(10) group and R(10) group (P < 0.05); and mPAP and [RV/(LV + S)] in H(30) group were lower than those in H(30) group (P < 0.05). Electron microscopy showed that compared to LC group, arteriolar endothelial cells were arranged in a columnar or palisading form, protruding into the lumen, accompanied with luminal stenosis, irregular internal elastic membrane, and proliferation of vascular smooth muscle cells in H groups, which was more obvious in H(30) group than in H(10) group; while these pathological changes were attenuated in the R groups compared to H groups. The levels of VEGF protein in H groups were also higher than those in LC group (P < 0.05); while the expression of VEGF in R(30) group was lower than that in H(30) group. In summary, the results show that the integripetal rhodiola herb can attenuate high altitude-induced pulmonary arterial remodeling in rats, and the inhibition of VEGF protein expression by rhodiola may be one of the mechanisms.

Associations of long-term exposure to ambient air pollution and physical activity with insomnia in Chinese adults.

BACKGROUND: Air pollution is a potential environmental risk for sleep disturbance. However, the evidence is very limited in China. On the other hand, physical activity (PA) is a preventive behavior that can improve insomnia, but whether PA mitigates the negative impact of air pollution on insomnia is unknown. METHODS: We obtained data from the baseline of China Multi-Ethnic Cohort (CMEC) survey, and examined the association between air pollution and insomnia, as well as PA's modification effect of on this association. We included 70,668 respondents and assessed insomnia by self-reported symptoms collected using electronic questionnaires. Using satellite data, we estimated the residence-specified, three-year average PM1, PM2.5, PM10 (particulate matter with aerodynamic diameters of ≤1 µm, ≤2.5 µm and 10 µm, respectively), O3 (ozone), and NO2 (nitrogen dioxide) concentrations. We established the associations between air pollutants and insomnia through logistic regression. We evaluated the modification impact of total and domain-specific PA (leisure, occupation, housework, transportation) by introducing an interaction term. RESULTS: Positive associations were observed between long-term exposure to PM1, PM2.5, PM10, and O3 and insomnia symptoms, with ORs (95% CI) of 1.09 (1.03-1.16), 1.11 (1.07-1.15), 1.07 (1.05-1.10) and 1.15 (1.11-1.20), respectively. As total PA increased, the ORs of air pollution for insomnia tended to decrease and then rise. We observed varying modification effects of domain-specific PA. With an increase in leisure PA, the ORs for PM2.5 and PM10 significantly declined. However, increased ORs of air pollutants were related to insomnia among participants with higher levels of occupational and housework PA. CONCLUSION: Long-term exposure to higher concentrations of PM1, PM2.5, PM10, and O3 increases the risk of insomnia symptoms. Moderate to high levels of leisure PA alleviate the harmful effects of air pollution on insomnia, while high levels of occupation and housework PA intensify such effects.

Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation.

High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.

De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation.

Structural variants (SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%-1.53%) compared to other East Asian genomes (0.70%-0.98%), reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence-a 662-bp intronic insertion in the SCUBE2 gene-is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.

Potential role of proprotein convertase SKI-1 in the mineralization of primary bone.

The biochemical mechanism controlling nucleation of mineral crystals in developing bone, along with the growth and propagation of these crystals once formed, remains poorly understood. To define the nucleation mechanism, a proteomics analysis was begun on isolated biomineralization foci (BMF), sites of initial crystal nucleation in osteoblastic cell cultures and in primary bone. Comparative analyses of the protein profile for mineralized BMF with that for total osteoblast cultures revealed the latter were enriched in several proteins including BAG-75 and BSP, as well as fragments of each. When 12 protease inhibitors were added separately to UMR 106-01 osteoblastic cultures, only the serine protease inhibitor 4-(2-aminoethyl) benzenesulfonyl fluoride hydrochloride (AEBSF) blocked cleavage of BAG-75 and BSP, and prevented mineral crystal nucleation within BMF. Consideration of the specificities of the inhibitors tested and the fact that AEBSF inhibition was not dependent upon inclusion of FBS in the culture media indicated that mineral nucleation does not require serine protease plasmin, thrombin, kallikrein, urokinase, C1s or furin. In contrast, SKI-1 (S1P or site-1) is a membrane-bound serine protease inhibitable by AEBSF. We show here for the first time that mineralizing UMR 106 cells express a 98-kDa active, soluble form of SKI-1 within BMF. In contrast, nonmineralizing UMR cells appear to differentially process SKI-1 into smaller immunoreactive fragments (<35 kDa). These findings suggest that SKI-1 plays a direct or indirect role in assembly of functional nucleation complexes containing BAG-75 and BSP and their fragments, thus facilitating initial mineral nucleation within these biomineralization foci.