Genetic drivers of heterogeneity in type 2 diabetes pathophysiology.

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes1,2 and molecular mechanisms that are often specific to cell type3,4. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10-8) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.

Stroke genetics informs drug discovery and risk prediction across ancestries.

Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries.

Extracting immunological and clinical heterogeneity across autoimmune rheumatic diseases by cohort-wide immunophenotyping.

OBJECTIVE: Extracting immunological and clinical heterogeneity across autoimmune rheumatic diseases (AIRDs) is essential towards personalised medicine. METHODS: We conducted large-scale and cohort-wide immunophenotyping of 46 peripheral immune cells using Human Immunology Protocol of comprehensive 8-colour flow cytometric analysis. Dataset consisted of >1000 Japanese patients of 11 AIRDs with deep clinical information registered at the FLOW study, including rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). In-depth clinical and immunological characterisation was conducted for the identified RA patient clusters, including associations of inborn human genetics represented by Polygenic Risk Score (PRS). RESULTS: Multimodal clustering of immunophenotypes deciphered underlying disease-cell type network in immune cell, disease and patient cluster resolutions. This provided immune cell type specificity shared or distinct across AIRDs, such as close immunological network between mixed connective tissue disease and SLE. Individual patient-level clustering dissected patients with AIRD into several clusters with different immunological features. Of these, RA-like or SLE-like clusters were exclusively dominant, showing immunological differentiation between RA and SLE across AIRDs. In-depth clinical analysis of RA revealed that such patient clusters differentially defined clinical heterogeneity in disease activity and treatment responses, such as treatment resistance in patients with RA with SLE-like immunophenotypes. PRS based on RA case-control and within-case stratified genome-wide association studies were associated with clinical and immunological characteristics. This pointed immune cell type implicated in disease biology such as dendritic cells for RA-interstitial lung disease. CONCLUSION: Cohort-wide and cross-disease immunophenotyping elucidate clinically heterogeneous patient subtypes existing within single disease in immune cell type-specific manner.

Optimization of extreme ultra-violet light emitted from the CO2 laser-irradiated tin plasmas using 2D radiation hydrodynamic simulations.

We studied Extreme Ultra-Violet (EUV) emission characteristics of the 13.5 nm wavelength from CO2 laser-irradiated pre-formed tin plasmas using 2D radiation hydrodynamic simulations. Our results indicate that when a CO2 laser irradiates pre-formed tin plasma, the heated plasma expands towards the surrounding plasma, steepening the density at the ablation front and lowering the density near the laser axis due to the transverse motion of the plasma. Consequently, the laser absorption fraction decreases, and the contribution to EUV output from the ablation front becomes dominant over that from the low-density plasmas. We estimated that an EUV conversion efficiency of 10% from laser to EUV emission could be achieved with a larger laser spot size, shortened laser pulse width, and longer pre-formed plasma density scale length. Our results offer one optimizing solution to achieve an efficient and powerful EUV light source for the next-generation semiconductors.

Multi-trait and cross-population genome-wide association studies across autoimmune and allergic diseases identify shared and distinct genetic component.

OBJECTIVES: Autoimmune and allergic diseases are outcomes of the dysregulation of the immune system. Our study aimed to elucidate differences or shared components in genetic backgrounds between autoimmune and allergic diseases. METHODS: We estimated genetic correlation and performed multi-trait and cross-population genome-wide association study (GWAS) meta-analysis of six immune-related diseases: rheumatoid arthritis, Graves' disease, type 1 diabetes for autoimmune diseases and asthma, atopic dermatitis and pollinosis for allergic diseases. By integrating large-scale biobank resources (Biobank Japan and UK biobank), our study included 105 721 cases and 433 663 controls. Newly identified variants were evaluated in 21 778 cases and 712 767 controls for two additional autoimmune diseases: psoriasis and systemic lupus erythematosus. We performed enrichment analyses of cell types and biological pathways to highlight shared and distinct perspectives. RESULTS: Autoimmune and allergic diseases were not only mutually classified based on genetic backgrounds but also they had multiple positive genetic correlations beyond the classifications. Multi-trait GWAS meta-analysis newly identified six allergic disease-associated loci. We identified four loci shared between the six autoimmune and allergic diseases (rs10803431 at PRDM2, OR=1.07, p=2.3×10-8, rs2053062 at G3BP1, OR=0.90, p=2.9×10-8, rs2210366 at HBS1L, OR=1.07, p=2.5×10-8 in Japanese and rs4529910 at POU2AF1, OR=0.96, p=1.9×10-10 across ancestries). Associations of rs10803431 and rs4529910 were confirmed at the two additional autoimmune diseases. Enrichment analysis demonstrated link to T cells, natural killer cells and various cytokine signals, including innate immune pathways. CONCLUSION: Our multi-trait and cross-population study should elucidate complex pathogenesis shared components across autoimmune and allergic diseases.

Polygenic risk scores for prediction of breast cancer risk in Asian populations.

PURPOSE: Non-European populations are under-represented in genetics studies, hindering clinical implementation of breast cancer polygenic risk scores (PRSs). We aimed to develop PRSs using the largest available studies of Asian ancestry and to assess the transferability of PRS across ethnic subgroups. METHODS: The development data set comprised 138,309 women from 17 case-control studies. PRSs were generated using a clumping and thresholding method, lasso penalized regression, an Empirical Bayes approach, a Bayesian polygenic prediction approach, or linear combinations of multiple PRSs. These PRSs were evaluated in 89,898 women from 3 prospective studies (1592 incident cases). RESULTS: The best performing PRS (genome-wide set of single-nucleotide variations [formerly single-nucleotide polymorphism]) had a hazard ratio per unit SD of 1.62 (95% CI = 1.46-1.80) and an area under the receiver operating curve of 0.635 (95% CI = 0.622-0.649). Combined Asian and European PRSs (333 single-nucleotide variations) had a hazard ratio per SD of 1.53 (95% CI = 1.37-1.71) and an area under the receiver operating curve of 0.621 (95% CI = 0.608-0.635). The distribution of the latter PRS was different across ethnic subgroups, confirming the importance of population-specific calibration for valid estimation of breast cancer risk. CONCLUSION: PRSs developed in this study, from association data from multiple ancestries, can enhance risk stratification for women of Asian ancestry.

Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancer.

The silencing of tumor suppressor genes by promoter CpG island (CGI) methylation is an important cause of oncogenesis. Silencing of MLH1 and BRCA1, two examples of oncogenic events, results from promoter CGI methylation. Interestingly, both MLH1 and BRCA1 have a divergent promoter, from which another gene on the opposite strand is also transcribed. Although studies have shown that divergent transcription is an important factor in transcriptional regulation, little is known about its implication in aberrant promoter methylation in cancer. In this study, we analyzed the methylation status of CGI in divergent promoters using a recently enriched transcriptome database. We measured the extent of CGI methylation in 119 colorectal cancer (CRC) clinical samples (65 microsatellite instability high [MSI-H] CRC with CGI methylator phenotype, 28 MSI-H CRC without CGI methylator phenotype and 26 microsatellite stable CRC) and 21 normal colorectal tissues using Infinium MethylationEPIC BeadChip. We found that CGI within divergent promoters are less frequently methylated than CGI within unidirectional promoters in normal cells. In the genome of CRC cells, CGI within unidirectional promoters are more vulnerable to aberrant methylation than CGI within divergent promoters. In addition, we identified three DNA sequence motifs that correlate with methylated CGI. We also showed that methylated CGI are associated with genes whose expression is low in normal cells. Thus, we here provide fundamental observations regarding the methylation of divergent promoters that are essential for the understanding of carcinogenesis and development of cancer prevention strategies.

Soft X-ray spectral analysis of laser produced molybdenum plasmas using the fundamental and second harmonics of a Nd:YAG laser.

Our measurement of the soft X-ray emission of Mo plasmas produced by picosecond Nd:YAG lasers emitting on the fundamental (1064 nm, 150 ps) and second (532 nm, 130 ps) harmonics is presented. The contrast in intensity between spectral peaks and the intensity outside them is lower for the second harmonic produced plasmas probably due to the presence more intense satellite emission and higher optical thickness. The measured spectra are absolutely calibrated and the observed output photon flux was (7 - 9) × 1013 photons/sr in the water-window (2.3 - 4.4 nm) spectral range for a laser energy of 160 mJ independent of laser wavelength. However, in the short wavelength range 1.5 - 2 nm, the emission using the second harmonic is strongly enhanced and is even higher than for the maximum energy of 220 mJ of the fundamental wavelength, so despite inevitable energy losses, laser wavelength conversion may lead to emission enhancement in certain spectral ranges. This enhancement is attributed to higher absorption of short wavelength laser light and higher charge state generation in denser plasmas.

Enhancement of water-window soft x-ray emission from laser-produced Au plasma under low-pressure nitrogen atmosphere.

To generate bright water-window (WW) soft x rays (2.3-4.4 nm), gold slab targets were irradiated with laser pulses (1064 nm, 7 ns, 1 J). Emission spectroscopy showed that the introduction of low-pressure nitrogen enhanced the soft x-ray yield emitted from the laser-produced Au plasma. The intensity of the WW x-ray transported in a 400-Pa N2 atmosphere from the laser-produced plasma increased by 3.8 times over that in vacuum. Considering a strong x-ray absorption, the x-ray yield emitted directly from the Au plasma in the N2 gas was evaluated to be 13 times higher than that in vacuum. Although similar measurements were made for various gases, only N2 gas causes an increase in a soft x-ray yield. The processes leading to this enhancement mechanism were revealed by using hydrodynamic simulation and atomic structure codes.

Intense water-window soft x-ray emission by spectral control using dual laser pulses.

We demonstrate intense emission in the water-window soft x-ray spectral region by controlling the spectral behavior through changing the balance between emissivity and self-absorption in an expanding plasma. The number of photons obtained from a dual laser irradiated target with a 150-ps pre-pulse was maximized at 3.8 × 1014 photons/sr in λ = 2.34 - 4.38 nm at a pulse separation time of 7 - 10 ns. Enhancement of the number of photons is attributed to efficient coupling with the main laser pulse while maintaining a tiny source size.

Emission of water-window soft x-rays under optically thin conditions using low-density foam targets.

The effect of optical thickness in a bismuth water-window soft x-ray source is considered by comparing the emission from laser-produced plasmas of a 7.5% atomic density foam target and a solid-density target. The number of photons recorded in the 4 nm region was comparable for both targets at a plasma-initiating laser pulse duration of 6 ns. From experiments at different pulse durations of 150 ps and 6 ns, self-absorption (opacity) effects were found to be relatively small for bismuth plasmas as compared to those of tin, based on the same emission mechanism and which are used in 13.5 nm sources for extreme ultraviolet lithography.

Experiments on laser cleaning of sooted optical windows.

To develop laser-ignition technology, transparent glass plates were artificially sooted and irradiated repetitively by laser from the front (sooted) and back sides separately. Generally, the back-side irradiation was more effective at soot removal. However, the cleaning effect was saturated after thousands of laser shots. Although the saturated soot quantity was a decreasing function of the laser fluence per pulse, its magnitude remained the same for both front-side and back-side irradiations. In examining several soot-removal mechanisms proposed so far, it was found that the aerodynamic force produced by the flow induced by the laser heating of the soot was the most plausible mechanism.

Attosecond sublevel beating and nonlinear dressing on the 3d-to-5p and 3p-to-5s core-transitions at 91.3 eV and 210.4 eV in krypton.

Applying extreme ultraviolet (XUV) transient absorption spectroscopy, the dynamics of the two laser dressed transitions 3d5/2-to-5p3/2 and 3p3/2-to-5s1/2 at photon energies of 91.3 eV and 210.4 eV were examined with attosecond temporal resolution. The dressing process was modeled with density matrix equations which are found to describe very accurately both the experimentally observed transmission dynamics and the linear and nonlinear dressing oscillations at 0.75 PHz and 1.5 PHz frequencies. Furthermore, using Fourier transform XUV spectroscopy, quantum beats from the 3d5/2-3d3/2 and 3p3/2-3p1/2 sublevels at 0.3 PHz and 2.0 PHz were experimentally identified and resolved.

Avalanche of stimulated forward scattering in high harmonic generation.

Optical amplifiers in all ranges of the electromagnetic spectrum exhibit an essential characteristic, namely the input signal during the propagation in the amplifier medium is multiplied by the avalanche effect of the stimulated emission to produce exponential growth. We perform a theoretical study motivated and supported by experimental data on a He gas amplifier driven by intense 30-fs-long laser pulses and seeded with attosecond pulse trains generated in a separated Ne gas jet. We demonstrate that the strong-field theory in the frame of high harmonic generation fully supports the appearance of the avalanche effect in the amplification of extreme ultraviolet attosecond pulse trains. We theoretically separate and identify different physical processes taking part in the interaction and we demonstrate that X-ray parametric amplification dominates over others. In particular, we identify strong-field mediated intrapulse X-ray parametric processes as decisive for amplification at the single-atom level. We confirm that the amplification takes place at photon energies where the amplifier is seeded and when the seed pulses are perfectly synchronized with the driving strong field in the amplifier. Furthermore, propagation effects, phase matching and seed synchronization can be exploited to tune the amplified spectral range within the seed bandwidth.

Reinjection of transmitted laser light into laser-produced plasma for efficient laser ignition.

For improving the laser absorption efficiency in laser ignition, the transmitted laser light was returned to the laser-produced plasma by using a corner cube. In the experiments, the transmitted light was reinjected into the plasma at different times. The laser absorption efficiency was found to be substantially improved when the transmitted light was reinjected into the plasma after adequate plasma expansion. Furthermore, through visualization experiments on gas-dynamics phenomena, it was found that the reinjection of the transmitted light affected not only the laser absorption efficiency but also the gas dynamics after breakdown, and thereby the initial flame kernel development.

Body mass index stratification optimizes polygenic prediction of type 2 diabetes in cross-biobank analyses.

Type 2 diabetes (T2D) shows heterogeneous body mass index (BMI) sensitivity. Here, we performed stratification based on BMI to optimize predictions for BMI-related diseases. We obtained BMI-stratified datasets using data from more than 195,000 individuals (nT2D = 55,284) from BioBank Japan (BBJ) and UK Biobank. T2D heritability in the low-BMI group was greater than that in the high-BMI group. Polygenic predictions of T2D toward low-BMI targets had pseudo-R2 values that were more than 22% higher than BMI-unstratified targets. Polygenic risk scores (PRSs) from low-BMI discovery outperformed PRSs from high BMI, while PRSs from BMI-unstratified discovery performed best. Pathway-specific PRSs demonstrated the biological contributions of pathogenic pathways. Low-BMI T2D cases showed higher rates of neuropathy and retinopathy. Combining BMI stratification and a method integrating cross-population effects, T2D predictions showed greater than 37% improvements over unstratified-matched-population prediction. We replicated findings in the Tohoku Medical Megabank (n = 26,000) and the second BBJ cohort (n = 33,096). Our findings suggest that target stratification based on existing traits can improve the polygenic prediction of heterogeneous diseases.

Poor accuracy and sustainability of the first-step FIB4 EASL pathway for stratifying steatotic liver disease risk in the general population.

BACKGROUND AND AIMS: The European Association for the Study of the Liver introduced a clinical pathway (EASL CP) for screening significant/advanced fibrosis in people at risk of steatotic liver disease (SLD). We assessed the performance of the first-step FIB4 EASL CP in the general population across different SLD risk groups (MASLD, Met-ALD and ALD) and various age classes. METHODS: We analysed a total of 3372 individuals at risk of SLD from the 2017-2018 National Health and Nutrition Examination Survey (NHANES17-18), projected to 152.3 million U.S. adults, 300,329 from the UK Biobank (UKBB) and 57,644 from the Biobank Japan (BBJ). We assessed liver stiffness measurement (LSM) ≥8 kPa and liver-related events occurring within 3 and 10 years (3/10 year-LREs) as outcomes. We defined MASLD, MetALD, and ALD according to recent international recommendations. RESULTS: FIB4 sensitivity for LSM ≥ 8 kPa was low (27.7%), but it ranged approximately 80%-90% for 3-year LREs. Using FIB4, 22%-57% of subjects across the three cohorts were identified as candidates for vibration-controlled transient elastography (VCTE), which was mostly avoidable (positive predictive value of FIB4 ≥ 1.3 for LSM ≥ 8 kPa ranging 9.5%-13% across different SLD categories). Sensitivity for LSM ≥ 8 kPa and LREs increased with increasing alcohol intake (ALD>MetALD>MASLD) and age classes. For individuals aged ≥65 years, using the recommended age-adjusted FIB4 cut-off (≥2) substantially reduced sensitivity for LSM ≥ 8 kPa and LREs. CONCLUSIONS: The first-step FIB4 EASL CP is poorly accurate and feasible for individuals at risk of SLD in the general population. It is crucial to enhance the screening strategy with a first-step approach able to reduce unnecessary VCTEs and optimise their yield.