A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging.

Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7× increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca2+ responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca2+ concentration using fluorescence lifetime imaging microscopy (FLIM).

Two B-box proteins orchestrate vegetative and reproductive growth in summer chrysanthemum.

Floral transition, the switch from vegetative to reproductive growth, is extremely important for the growth and development of flowering plants. In the summer chrysanthemum, CmBBX8, a member of the subgroup II B-box (BBX) family, positively regulates the transition by physically interacting with CmERF3 to inhibit CmFTL1 expression. In this study, we show that CmBBX5, a B-box subgroup I member comprising two B-boxes and a CCT domain, interacts with CmBBX8. This interaction suppresses the recruitment of CmBBX8 to the CmFTL1 locus without affecting its transcriptional activation activity. CmBBX5 overexpression led to delayed flowering under both LD (long-day) and SD (short-day) conditions, while lines expressing the chimeric repressor gene-silencing (CmBBX5-SRDX) exhibited the opposite phenotype. Subsequent genetic evidence indicated that in regulating flowering, CmBBX5 is partially dependent on CmBBX8. Moreover, during the vegetative growth period, levels of CmBBX5 expression were found to exceed those of CmBBX8. Collectively, our findings indicate that both CmERF3 and CmBBX5 interact with CmBBX8 to dampen the regulation of CmFTL1 via distinct mechanisms, which contribute to preventing the premature flowering of summer chrysanthemum.

Plasma parameters correction method based on plasma image-spectrum fusion for matrix effect elimination in LIBS.

Matrix effect is one of the obstacles that hinders the rapid development of laser-induced breakdown spectroscopy (LIBS), and it is currently a hot, challenging, and focal point in research. To eliminate the matrix effect, this study proposed a plasma parameters correction method based on plasma image-spectrum fusion (PPC-PISF). This method corrects the total number density, plasma temperature, and electron number density variations caused by matrix effect using effective features in plasma images and spectra. To verify the feasibility of this method, experiments were conducted on pressed and metal samples, and the results were compared with those corrected by image-assisted LIBS (IA-LIBS). For the pressed samples, after correction by PPC-PISF, the R2 of the calibration curves all improved to above 0.993, the average root-mean-square error (RMSE) decreased by 41.05%, and the average relative error (ARE) decreased by 59.35% evenly in comparison to IA-LIBS. For the metal samples, after correction by PPC-PISF, the R2 of the calibration curves all increased to above 0.997. Additionally, the RMSE decreased by 29.63% evenly, the average ARE decreased by 38.74% compared to IA-LIBS. The experimental results indicate that this method is an effective method for eliminating the matrix effect, promoting the further development of LIBS in industrial detection.

Individual Micron-Sized Aerosol Qualitative Analysis-Combined Raman Spectroscopy and Laser-Induced Breakdown Spectroscopy by Optical Trapping in Air.

The attribution of single particle sources of atmospheric aerosols is an essential problem in the study of air pollution. However, it is still difficult to qualitatively analyze the source of a single aerosol particle using noncontact in situ techniques. Hence, we proposed using optical trapping to combine gated Raman spectroscopy with laser-induced breakdown spectroscopy (LIBS) in a single levitated micron aerosol. The findings of the spectroscopic imaging indicated that the particle plasma formed by a single particle ablation with a pulsed laser within 7 ns deviates from the trapped particle location. The LIBS acquisition field of view was expanded using the 19-bundle fiber, which also reduces the fluctuation of a single particle signal. In addition, gated Raman was utilized to suppress the fluorescence and increase the Raman signal-to-noise ratio. Based on this, Raman can measure hard-to-ionize substances with LIBS, such as sulfates. The LIBS radical can overcome the restriction that Raman cannot detect ionic chemicals like fluoride and chloride in halogens. To test the capability of directly identifying distinctive feature compounds utilizing spectra, we detected anions using Raman spectroscopy and cations using LIBS. Four typical mineral aerosols are subjected to precise qualitative evaluations (marble, gypsum, baking soda, and activated carbon adsorbed potassium bicarbonate). To further validate the application potential for substances with indistinctive feature discrimination, we employed machine learning algorithms to conduct a qualitative analysis of the coal aerosol from ten different origin regions. Three data fusion methodologies (early fusion, intermediate fusion, and late fusion) for Raman and LIBS are implemented, respectively. The accuracy of the late fusion model prediction using StackingClassifier is higher than that of the LIBS data (66.7%) and Raman data (86.1%) models, with an average accuracy of 90.6%. This research has the potential to provide online single aerosol analysis as well as technical assistance for aerosol monitoring and early warning.

Self-absorption correction method for one-point calibration laser-induced breakdown spectroscopy.

As an important variant of calibration-free laser-induced breakdown spectroscopy (CF-LIBS), one-point calibration LIBS (OPC-LIBS) corrects the Boltzmann plot of the unknown sample by using one known sample and obtains higher quantitative accuracy than CF-LIBS. However, the self-absorption effect restricts its accuracy. In this work, a new self-absorption correction (SAC) method for OPC-LIBS is proposed to solve this problem. This method uses an algorithm to correct the self-absorption and does not require the calculation of the self-absorption coefficient. To verify the effectiveness of this SAC method, Ti, V, and Al elements in two titanium alloys were determined by classical OPC-LIBS and OPC-LIBS with SAC. The average relative errors (AREs) of all elements in the two samples were decreased from 8.78% and 9.28% to 8.07% and 7.56%, respectively. The results demonstrated the effectiveness of this SAC method for OPC-LIBS.

PDHA1 Alleviates Myocardial Ischemia-Reperfusion Injury by Improving Myocardial Insulin Resistance During Cardiopulmonary Bypass Surgery in Rats.

OBJECTIVE: Cardiopulmonary bypass (CPB) is a requisite technique for thoracotomy in advanced cardiovascular surgery. However, the consequent myocardial ischemia-reperfusion injury (MIRI) is the primary culprit behind cardiac dysfunction and fatal consequences post-operation. Prior research has posited that myocardial insulin resistance (IR) plays a vital role in exacerbating the progression of MIRI. Nonetheless, the exact mechanisms underlying this phenomenon remain obscure. METHODS: We constructed pyruvate dehydrogenase E1 α subunit (PDHA1) interference and overexpression rats and used ascending aorta occlusion in an in vivo model of CPB-MIRI. We devised an in vivo model of CPB-MIRI by constructing rat models with both pyruvate dehydrogenase E1α subunit (PDHA1) interference and overexpression through ascending aorta occlusion. We analyzed myocardial glucose metabolism and the degree of myocardial injury using functional monitoring, biochemical assays, and histological analysis. RESULTS: We discovered a clear downregulation of glucose transporter 4 (GLUT4) protein content expression in the CPB I/R model. In particular, cardiac-specific PDHA1 interference resulted in exacerbated cardiac dysfunction, significantly increased myocardial infarction area, more pronounced myocardial edema, and markedly increased cardiomyocyte apoptosis. Notably, the opposite effect was observed with PDHA1 overexpression, leading to a mitigated cardiac dysfunction and decreased incidence of myocardial infarction post-global ischemia. Mechanistically, PDHA1 plays a crucial role in regulating the protein content expression of GLUT4 on cardiomyocytes, thereby controlling the uptake and utilization of myocardial glucose, influencing the development of myocardial insulin resistance, and ultimately modulating MIRI. CONCLUSION: Overall, our study sheds new light on the pivotal role of PDHA1 in glucose metabolism and the development of myocardial insulin resistance. Our findings hold promising therapeutic potential for addressing the deleterious effects of MIRI in patients.

Global enhancement of cortical excitability following coactivation of large neuronal populations.

Correlated activation of cortical neurons often occurs in the brain and repetitive correlated neuronal firing could cause long-term modifications of synaptic efficacy and intrinsic excitability. We found that repetitive optogenetic activation of neuronal populations in the mouse cortex caused enhancement of optogenetically evoked firing of local coactivated neurons as well as distant cortical neurons in both ipsilateral and contralateral hemispheres. This global enhancement of evoked responses required coactivation of a sufficiently large population of neurons either within one cortical area or distributed in several areas. Enhancement of neuronal firing was saturable after repeated episodes of coactivation, diminished by inhibition of N-methyl-d-aspartic acid receptors, and accompanied by elevated excitatory postsynaptic potentials, all consistent with activity-induced synaptic potentiation. Chemogenetic inhibition of neuronal activity of the thalamus decreased the enhancement effect, suggesting thalamic involvement. Thus, correlated excitation of large neuronal populations leads to global enhancement of neuronal excitability.

Insulin reduces pyroptosis-induced inflammation by PDHA1 dephosphorylation-mediated NLRP3 activation during myocardial ischemia-reperfusion injury.

BACKGROUND: Previous studies proved that pyrin domain-containing protein 3 (NLRP3)-induced pyroptosis plays an important role in Myocardial ischemia-reperfusion injury (MIRI). Insulin can inhibit the activation of NLRP3 inflammasome, although the exact mechanism remains unclear. The aim of this study was to determine whether insulin reduces NLRP3-induced pyroptosis by regulating pyruvate dehydrogenase E1alpha subunit (PDHA1) dephosphorylation during MIRI. METHODS: Rat hearts were subject to 30 min global ischemia followed by 60 min reperfusion, with or without 0.5 IU/L insulin. Myocardial ischemia-reperfusion injury was evaluated by measuring myocardial enzymes release, Cardiac hemodynamics, pathological changes, infarct size, and apoptosis rate. Cardiac aerobic glycolysis was evaluated by measuring ATP, lactic acid content, and pyruvate dehydrogenase complex (PDHc) activity in myocardial tissue. Recombinant adenoviral vectors for PDHA1 knockdown were constructed. Pyroptosis-related proteins were measured by Western blotting analysis, immunohistochemistry staining, and ELISA assay, respectively. RESULTS: It was found that insulin significantly reduced the area of myocardial infarction, apoptosis rate, and improved cardiac hemodynamics, pathological changes, energy metabolism. Insulin inhibits pyroptosis-induced inflammation during MIRI. Subsequently, Adeno-associated virus was used to knock down cardiac PDHA1 expression. Knockdown PDHA1 not only promoted the expression of NLRP3 but also blocked the inhibitory effect of insulin on NLRP3-mediated pyroptosis in MIRI. CONCLUSIONS: Results suggest that insulin protects against MIRI by regulating PDHA1 dephosphorylation, its mechanism is not only to improve myocardial energy metabolism but also to reduce the NLRP3-induced pyroptosis.

[Origin identification of Poria cocos based on hyperspectral imaging technology].

To realize the non-destructive and rapid origin discrimination of Poria cocos in batches, this study established the P. cocos origin recognition model based on hyperspectral imaging combined with machine learning. P. cocos samples from Anhui, Fujian, Guangxi, Hubei, Hunan, Henan and Yunnan were used as the research objects. Hyperspectral data were collected in the visible and near infrared band(V-band, 410-990 nm) and shortwave infrared band(S-band, 950-2 500 nm). The original spectral data were divided into S-band, V-band and full-band. With the original data(RD) of different bands, multiplicative scatter correction(MSC), standard normal variation(SNV), S-G smoothing(SGS), first derivative(FD), second derivative(SD) and other pretreatments were carried out. Then the data were classified according to three different types of producing areas: province, county and batch. The origin identification model was established by partial least squares discriminant analysis(PLS-DA) and linear support vector machine(LinearSVC). Finally, confusion matrix was employed to evaluate the optimal model, with F1 score as the evaluation standard. The results revealed that the origin identification model established by FD combined with LinearSVC had the highest prediction accuracy in full-band range classified by province, V-band range by county and full-band range by batch, which were 99.28%, 98.55% and 97.45%, respectively, and the overall F1 scores of these three models were 99.16%, 98.59% and 97.58%, respectively, indicating excellent performance of these models. Therefore, hyperspectral imaging combined with LinearSVC can realize the non-destructive, accurate and rapid identification of P. cocos from different producing areas in batches, which is conducive to the directional research and production of P. cocos.

[Origin identification of Polygonatum cyrtonema based on hyperspectral data].

In this study, visual-near infrared(VNIR), short-wave infrared(SWIR), and VNIR + SWIR fusion hyperspectral data of Polygonatum cyrtonema from different geographical origins were collected and preprocessed by first derivative(FD), second derivative(SD), Savitzky-Golay smoothing(S-G), standard normalized variate(SNV), multiplicative scatter correction(MSC), FD+S-G, and SD+S-G. Three algorithms, namely random forest(RF), linear support vector classification(LinearSVC), and partial least squares discriminant analysis(PLS-DA), were used to establish the identification models of P. cyrtonema origin from three spatial scales, i.e., province, county, and township, respectively. Successive projection algorithm(SPA) and competitive adaptive reweighted sampling(CARS) were used to screen the characteristic bands, and the P. cyrtonema origin identification models were established according to the selected characteristic bands. The results showed that(1)after FD preprocessing of VNIR+SWIR fusion hyperspectral data, the accuracy of recognition models established using LinearSVC was the highest, reaching 99.97% and 99.82% in the province origin identification model, 100.00% and 99.46% in the county origin identification model, and 99.62% and 98.39% in the township origin identification model. The accuracy of province, county, and township origin identification models reached more than 98.00%.(2)Among the 26 characteristic bands selected by CARS, after FD pretreatment, the accuracy of origin identification models of different spatial scales was the highest using LinearSVC, reaching 98.59% and 97.05% in the province origin identification model, 97.79% and 94.75% in the county origin identification model, and 90.13% and 87.95% in the township origin identification model. The accuracy of identification models of different spatial scales established by 26 characteristic bands reached more than 87.00%. The results show that hyperspectral imaging technology can realize accurate identification of P. cyrtonema origin from different spatial scales.

Enhancing the nonlinearity of optomechanical system via multiple mechanical modes.

We theoretically investigate the nonlinear dynamics of an optomechanical system, where the system consists of N identical mechanical oscillators individually coupled to a common cavity field. We find that the optomechanical nonlinearity can be enhanced N times through theoretical analysis and numerical simulation in such a system. This leads to the power thresholds to observe the nonlinear behaviors (bistable, period-doubling, and chaotic dynamics) being reduced to 1/N. In addition, we find that changing the sign (positive or negative) of the coupling strength partly does not affect the threshold of driving power for generating corresponding nonlinear phenomena. Our work may provide a way to engineer optomechanical devices with a lower threshold, which has potential applications in implementing secret information processing and optical sensing.

Accuracy improvement of single-sample calibration laser-induced breakdown spectroscopy with self-absorption correction.

The single sample calibration laser-induced breakdown spectroscopy (SSC-LIBS) is quite suitable for the fields where the standard sample is hard to obtain, including space exploration, geology, archaeology, and jewelry identification. But in practice, the self-absorption effect of plasma destroys the linear relationship of spectral intensity and element concentration based on the Lomakin-Scherbe formula which is the guarantee of the high accuracy of the SSC-LIBS. Thus, the self-absorption effect limits the quantitative accuracy of SSC-LIBS greatly. In this work, an improved SSC-LIBS with self-absorption correction (SSC-LIBS with SAC) is proposed for the promotion of quantitative accuracy of SSC-LIBS. The SSC-LIBS with SAC can correct the intensity ratio of spectral lines in the calculation of SSC-LIBS through relative self-absorption coefficient K without complicated preparatory information. The alloy samples and pressed ore samples were used to verify the effect of the SSC-LIBS with SAC. Compared with SSC-LIBS, for alloy samples, the average RMSEP and average ARE of SSC-LIBS with SAC decreased from 0.83 wt.% and 13.75% to 0.40 wt.% and 4.06%, respectively. For the pressed ore samples, the average RMSEP and average ARE of SSC-LIBS with SAC decreased from 4.77 wt.% and 90.48% to 2.34 wt.% and 14.60%. The experimental result indicates that SSC-LIBS with SAC has a great improvement of quantitative accuracy and better universality compared with traditional SSC-LIBS, which is a mighty promotion of the wide application of SSC-LIBS.

Major osteoporosis fracture prediction in type 2 diabetes: a derivation and comparison study.

The widely recommended fracture prediction tool FRAX was developed based on and for the general population. Although several adjusted FRAX methods were suggested for type 2 diabetes (T2DM), they still need to be evaluated in T2DM cohort. INTRODUCTION: This study was undertaken to develop a prediction model for Chinese diabetes fracture risk (CDFR) and compare its performance with those of FRAX. METHODS: In this retrospective cohort study, 1730 patients with T2DM were enrolled from 2009.08 to 2013.07. Major osteoporotic fractures (MOFs) during follow-up were collected from Electronic Health Records (EHRs) and telephone interviews. Multivariate Cox regression with backward stepwise selection was used to fit the model. The performances of the CDFR model, FRAX, and adjusted FRAX were compared in the aspects of discrimination and calibration. RESULTS: 6.3% of participants experienced MOF during a median follow-up of 10 years. The final model (CDFR) included 8 predictors: age, gender, previous fracture, insulin use, diabetic peripheral neuropathy (DPN), total cholesterol, triglycerides, and apolipoprotein A. This model had a C statistic of 0.803 (95%CI 0.761-0.844) and calibration χ2 of 4.63 (p = 0.86). The unadjusted FRAX underestimated the MOF risk (calibration χ2 134.5, p < 0.001; observed/predicted ratio 2.62, 95%CI 2.17-3.08), and there was still significant underestimation after diabetes adjustments. Comparing FRAX, the CDFR had a higher AUC, lower calibration χ2, and better reclassification of MOF. CONCLUSION: The CDFR model has good performance in 10-year MOF risk prediction in T2DM, especially in patients with insulin use or DPN. Future work is needed to validate our model in external cohort(s).

Oxymatrine Alleviates Hyperglycemic Cerebral Ischemia/Reperfusion Injury via Protecting Microvessel.

Hyperglycemia aggravates cerebral ischemia/reperfusion (I/R) injury via vascular injury. There is still a lack of effective pharmaceutical preparations for cerebral I/R injury under hyperglycemia. This study aimed to investigate the effects of oxymatrine (OMT) on hyperglycemia-exacerbated cerebral I/R injury in vitro and in vivo. The middle cerebral artery occlusion (MCAO) and reperfusion was established in the rats under hyperglycemia. Meanwhile, oxygen-glucose deprivation and reoxygenation (OGD/R) with high glucose was used as an in vitro model of hyperglycemic cerebral I/R injury. The results showed that the neurological deficit score, mortality, infarct volume and penumbra apoptosis in hyperglycemia group were significantly higher than those in normal glucose group. OMT pre-treated obviously reduced the degree of neurological deficit, mortality, infarct volume, improve cerebral blood flow after I/R in rats with hyperglycemia, and increase the survival rate of human brain microvascular endothelial cells (HBMECs) in high glucose and OGD/R group. OMT significantly improved the ultrastructure changes of endothelial cells, and maintain the migration and angiogenesis potency of HBMECs in high glucose and OGD/R group. OMT obviously alleviated the down-regulating CD31 and CD105 expression in cerebral microvessels caused by hyperglycemia. It is concluded that OMT treatment might alleviate cerebral I/R injury under hyperglycemia via protecting microvessels.

Abscisic acid induces the expression of AsKIN during the recovery period of garlic cryopreservation.

KEY MESSAGE: Abscisic acid induced the expression of AsKIN during the recovery period of garlic cryopreservation. AsKIN was identified as a gene involved in cold and osmotic stress resistance. Cryopreservation has been proven to be effective in removing viruses from garlic. However, oxidative damage in cryopreservation has a significant impact on the survival after preservation. Abscisic acid (ABA) has been shown to reduce oxidative stress and promote the survival after cryopreservation. However, it is not clear which genes play important roles in this process. In this study, we added ABA to the dehydration step and analyzed the transcriptomic divergences between the ABA-treated group and the control group in three cryogenic steps (dehydration, unloading and recovery). By short time-series expression miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), the recovery step was identified as the period of significant changes in gene expression levels in cryopreservation. The addition of ABA promoted the upregulated expression of microtubule-related genes in the recovery step. We further identified AsKIN as a hub gene in the recovery step and verified its function. The results showed that overexpression of AsKIN enhanced the tolerance of Arabidopsis to oxidative stress in cryopreservation, influenced the expression of genes in response to cold and osmotic stress and promoted plant growth after stress. The AsKIN gene is likely to be involved in the plant response to cold stress and osmotic stress. These results reveal the molecular mechanisms of ABA in cryopreservation and elucidate the potential biological functions of the kinesin-14 subfamily.

Ascorbic acid addition during dehydration improves garlic shoot tip cryopreservation but does not affect viral load.

Cryopreservation is known be an effective method for virus elimination in garlic. However, oxidative damage during the cryopreservation seriously affects the survival of garlic after cryopreservation. Ascorbic acid (AsA) can reduce oxidative damage and improve regrowth following cryopreservation, and its effect may be influenced by the step during which it is added. In this study, AsA was added at the osmoprotection (O) and dehydration (DE) steps of cryopreservation. By observing the dynamic changes in cell viability and reactive oxygen species (ROS) components with different AsA treatments, AsA has been linked to the reduced accumulation of ROS in the shoot tips. Increased gene expression levels of antioxidant enzymes also explained the ROS scavenging effect of AsA. The correlation analysis between cell viability, ROS, membrane lipid peroxidation-related indicators and antioxidant-related indicators showed that membrane lipid peroxidation caused by excess ROS was the main factor affecting cell viability. Ascorbic acid added during dehydration minimized the accumulation of ROS from dehydration to dilution and alleviated the oxidative damage during cryopreservation. Thus, the survival and regrowth of the garlic was significantly improved after cryopreservation. Dehydration was found to be the suitable step for the addition of AsA during garlic cryopreservation. We further evaluated the virus elimination effect under optimal AsA treatment. However, there was no significant difference in virus content in regenerated plants when compared with the control.

Indirect quantitative analysis of soluble solid content in citrus by the leaves using hyperspectral imaging combined with machine learning.

Due to the effect of bagging on fruit growth, non-destructive and in situ soluble solid content (SSC) in citrus detection remains a challenge. In this work, a new method for accurately quantifying SSC in citrus using hyperspectral imaging of citrus leaves was proposed. Sixty-five Ehime Kashi No. 28 citruses with surrounding leaves picked at two different times were picked for the experiment. Using the principal components analysis combined with Gaussian process regression model, the correlation coefficients of prediction-real value by citrus and its leaves in cross-validation were 0.972 and 0.986, respectively. In addition, the relationship between citrus leaves and SSC content was further explored, and the possible relationship between chlorophyll in leaves and SSC of citrus was analyzed. Comparing the quantitative analysis results by citrus and its leaves, the results show that the proposed method is a non-destructive and reliable method for determining the SSC by citrus leaves and has broad application prospects in indirect detection of citrus.

A new POLH mutation in a consanguineous Chinese family with xeroderma pigmentosum variant type.

We report a Chinese consanguineous family with a variant type of xeroderma pigmentosum (XPV), and identified one novel mutation in the patient. Our study expands the mutational spectrum of XPV. Click here for the corresponding questions to this CME article.

Prenatal diagnosis of fetal inferior vena cava malformation using HDlive flow combined with spatiotemporal image correlation.

OBJECTIVES: This study aimed to examine the application value of high-definition live (HDlive) flow combined with spatiotemporal image correlation (STIC) in the diagnosis of fetal inferior vena cava malformation (IVCM). METHODS: Twenty cases of IVCMs were diagnosed using two-dimensional HDlive flow and HDlive flow combined with STIC and retrospectively analyzed to examine the impact of using HDlive flow combined with STIC in the diagnosis of IVCM. RESULTS: HDlive flow combined with STIC detected one case of duplicated IVC, four cases of left IVC (two cases with complex malformations), and 15 cases of interrupted IVC (two cases of isolated IVC disconnection, five cases with left atrial heterogeneous syndrome, and eight cases with other complex malformations). CONCLUSION: HDlive flow combined with STIC can help in the diagnosis of IVCM, and this technique has important clinical value.

Missense Variants in HIF1A and LACC1 Contribute to Leprosy Risk in Han Chinese.

Genome-wide association studies (GWASs) and genome-wide linkage studies (GWLSs) have identified numerous risk genes affecting the susceptibility to leprosy. However, most of the reported GWAS hits are noncoding variants and account for only part of the estimated heritability for this disease. In order to identify additional risk genes and map the potentially functional variants within the GWAS loci, we performed a three-stage study combining whole-exome sequencing (WES; discovery stage), targeted next-generation sequencing (NGS; screening stage), and refined validation of risk missense variants in 1,433 individuals with leprosy and 1,625 healthy control individuals from Yunnan Province, Southwest China. We identified and validated a rare damaging variant, rs142179458 (c.1045G>A [p.Asp349Asn]) in HIF1A, as contributing to leprosy risk (p = 4.95 × 10-9, odds ratio [OR] = 2.266). We were able to show that affected individuals harboring the risk allele presented with multibacillary leprosy at an earlier age (p = 0.025). We also confirmed the association between missense variant rs3764147 (c.760A>G [p.Ile254Val]) in the GWAS hit LACC1 (formerly C13orf31) and leprosy (p = 6.11 × 10-18, OR = 1.605). By using the population attributable fraction, we have shown that HIF1A and LACC1 are the major genes with missense variants contributing to leprosy risk in our study groups. Consistently, mRNA expression levels of both HIF1A and LACC1 were upregulated in the skin lesions of individuals with leprosy and in Mycobacterium leprae-stimulated cells, indicating an active role of HIF1A and LACC1 in leprosy pathogenesis.