👤 Tracy Chew

Hepatocellular carcinoma (HCC) exhibits diverse aetiologies and molecular heterogeneity, with a median 5-year overall survival of <70% due to high recurrence rates following curative-intent surgery. This study investigated the complex tumour microenvironment (TME) in HCC and explored interactions between various cell types and their roles in disease recurrence. Using a multi-omics approach on multi-region samples of surgically resected HCC from the PLANet 1.0 cohort (NCT03267641), we performed spatial transcriptomics on 17 tissue samples from four patients and bulk RNA sequencing on 329 sectors from 90 patients. Findings were validated using immunofluorescence and multiplex immunohistochemistry. Our analysis revealed extensive intra- and intertumour gene expression heterogeneity and identified a specific subset of endothelial cells (ECs), INTS6 INTS6 The spatial co-localisation of cell types plays a significant role in the recurrence of hepatocellular carcinoma. In this study, we have pinpointed a particular group of endothelial cells, known as INTS6+ endothelial cells, which are spatially colocalised with tumour cells and enriched in microvascular invasion regions in patients experiencing recurrence. These discoveries highlight novel therapeutic targets that focus on endothelial cell interactions within the tumour microenvironment to prevent recurrence and enhance overall patient survival. Show less

Lp(a) is an independent risk factor for a variety of cardiovascular (CV) outcomes. However, it remains unclear whether its prognostic value differs between individuals with varying baseline traditional CV risk. This study aims to evaluate the association between Lp(a) levels and all-cause & CV mortality, stratified by baseline CV risk. Using data from NHANES III (1988-1994) with mortality follow-up through 2019, we analysed a nationally representative cohort of U.S. adults. Baseline CV risk was stratified into low, borderline-intermediate, and high groups using the PREVENT equations. Associations between Lp(a) levels and outcomes were assessed using multivariable Cox and Fine-Gray competing risk models. A total of 55,050,155 survey-weighted records (4,707 unweighted) were analysed. The mean age was 48 (±13) years, with 51% female. Over a mean follow-up of 22.4 years (±7.07), there were 17,301,805 all-cause and 4,965,456 CV deaths. Elevated Lp(a) (>50 mg/dL) was present in 15% overall, more commonly in the high-risk group (15% vs 11% in low-risk). In the high-risk group, Lp(a) >75 mg/dL was associated with higher all-cause (HR: 1.25; 95% CI: 1.02-1.53) and CV mortality (sHR: 1.21; 95% CI: 1.09-1.36). Lp(a) 50-75 mg/dL showed a borderline association with all-cause mortality (HR: 1.16; 95% CI: 1.00-1.34) but not CV mortality (sHR: 1.06; 95% CI: 0.98-1.15). No significant associations were observed in lower-risk groups. Elevated Lp(a) levels (> 75 mg/dL) are associated with increased all-cause and CV mortality among individuals with high baseline traditional CV risk, as defined by the AHA's PREVENT score, independent of traditional risk factors. Our findings highlight the value of Lp(a) particularly among those with elevated baseline risk, where its prognostic utility appears greatest. Show less

To evaluate whether integrating Apolipoprotein B (ApoB) into the Systematic Coronary Risk Evaluation 2 (SCORE2) cardiovascular risk prediction framework improves its predictive accuracy and clinical applicability within the UK Biobank population. A 10-year prospective cohort study was conducted with 448 303 UK Biobank participants eligible for SCORE2 calculation. Three approaches were employed: (i) threshold analysis to determine the optimal ApoB cutoff for cardiovascular disease (CVD) risk prediction using Youden's Index, (ii) assessment of the synergistic effect of SCORE2 and ApoB through concordant and discordant classifications, and (iii) recalibration of the SCORE2 model by incorporating ApoB as an additional predictor. Each 0.2 g/L increase in ApoB was associated with an increased subdistribution hazard for CVD events [subdistribution hazard ratio (SHR): 1.13; 95% CI: 1.11-1.14, P < 0.001], accounting for non-cardiovascular death as a competing risk. Threshold analysis identified an optimal ApoB cutoff at 1.18 g/L; however, it demonstrated limited discriminatory performance (area under the curve 0.54), with low sensitivity (32.4%), and moderate specificity (74.4%). Individuals with both low ApoB (<1.18 g/L) and low SCORE2 risk (<5%) had a lower CVD incidence rate (232.51 per 100 000 person-years) compared with those identified as low risk by SCORE2 alone (253.69 per 100 000 person-years). Integration of ApoB into the SCORE2 model did not significantly improve the model discrimination, calibration, and net reclassification improvement. Apolipoprotein B exhibited a dose-response relationship with cardiovascular risk but had limited standalone predictive utility within the UK Biobank population. However, combining ApoB with SCORE2 thresholds improved the identification of low-risk individuals, suggesting a complementary role for ApoB in refining cardiovascular risk stratification. Show less

Atopic dermatitis (AD) is a complex inflammatory disease with a strong genetic component. A singular approach of genome wide association studies (GWAS) can identify AD-associated genetic variants, but is unable to explain their functional relevance in AD. This study aims to characterize AD-associated genetic variants and elucidate the mechanisms leading to AD through a multi-omics approach. GWAS identified an association between genetic variants at 6p21.32 locus and AD. Genotypes of 6p21.32 locus variants were evaluated against Minor alleles of rs116160149 and rs115388857 at 6p21.32 locus were associated with increased AD risk ( Genetic variants at 6p21.32 locus increase AD susceptibility through raising Show less

Transcriptomic changes in the essential tremor (ET)-associated cerebello-thalamo-cortical "tremor network" and their association to brain structure have not been investigated. The aim was to characterize molecular changes associated with network-level imaging-derived phenotypes (IDP) found in ET. We performed an imaging-transcriptomic study in British adults using imaging-genome-wide association study summary statistics (UK Biobank "BIG40" cohort; n = 33,224, aged 40-69 years). We imputed imaging-transcriptomic associations for 184 IDPs and analyzed functional enrichment of gene modules and aggregate network-level phenotypes. Validation was performed in cerebellar-tissue RNA-sequencing data from ET patients and controls (n = 55). Among 237,896 individual predicted gene expression levels for 6063 unique genes/transcripts, we detected 2269 genome-wide significant associations (Bonferroni P < 2.102e-7, 0.95%). These were concentrated in intracellular volume fraction measures of white matter pathways and in genes with putative links to tremor (MAPT, ARL17A, KANSL1, SPPL2C, LRRC37A4P, PLEKHM1, and FMNL1). Whole-tremor-network cortical thickness was associated with a gene module linked to mitochondrial organization and protein quality control (r = 0.91, P = 2e-70), whereas white-gray T1-weighted magnetic resonance imaging (MRI) contrast in the tremor network was associated with a gene module linked to sphingolipid synthesis and ethanolamine metabolism (r = -0.90, P = 2e-68). Imputed association effect sizes and RNA-sequencing log-fold change in the validation dataset were significantly correlated for cerebellar peduncular diffusion MRI phenotypes, and there was a close overlap of significant associations between both datasets for gray matter phenotypes (χ The identified genes and processes are potential treatment targets for ET, and our results help characterize molecular changes that could in future be used for patient treatment selection or prognosis prediction. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. Show less

Focal adhesions (FAs) connect inner workings of cell to the extracellular matrix to control cell adhesion, migration and mechanosensing. Previous studies demonstrated that FAs contain three vertical layers, which connect extracellular matrix to the cytoskeleton. By using super-resolution iPALM microscopy, we identify two additional nanoscale layers within FAs, specified by actin filaments bound to tropomyosin isoforms Tpm1.6 and Tpm3.2. The Tpm1.6-actin filaments, beneath the previously identified α-actinin cross-linked actin filaments, appear critical for adhesion maturation and controlled cell motility, whereas the adjacent Tpm3.2-actin filament layer beneath seems to facilitate adhesion disassembly. Mechanistically, Tpm3.2 stabilizes ACF-7/MACF1 and KANK-family proteins at adhesions, and hence targets microtubule plus-ends to FAs to catalyse their disassembly. Tpm3.2 depletion leads to disorganized microtubule network, abnormally stable FAs, and defects in tail retraction during migration. Thus, FAs are composed of distinct actin filament layers, and each may have specific roles in coupling adhesions to the cytoskeleton, or in controlling adhesion dynamics. Show less

WWP2 expression is elevated in the tubulointerstitium of fibrotic kidneys and contributes to CKD pathogenesis and progression. WWP2 uncouples the profibrotic activation and cell proliferation in renal myofibroblasts. WWP2 controls mitochondrial respiration in renal myofibroblasts through the metabolic regulator peroxisome proliferator-activated receptor gamma coactivator 1-alpha. Renal fibrosis is a common pathologic end point in CKD that is challenging to reverse, and myofibroblasts are responsible for the accumulation of a fibrillar collagen–rich extracellular matrix. Recent studies have unveiled myofibroblasts' diversity in proliferative and fibrotic characteristics, which are linked to different metabolic states. We previously demonstrated the regulation of extracellular matrix genes and tissue fibrosis by WWP2, a multifunctional E3 ubiquitin–protein ligase. Here, we investigate WWP2 in renal fibrosis and in the metabolic reprograming of myofibroblasts in CKD. We used kidney samples from patients with CKD and The tubulointerstitial expression of WWP2 was associated with fibrotic progression in patients with CKD and in murine kidney disease models. WWP2 deficiency promoted myofibroblast proliferation and halted profibrotic activation, reducing the severity of renal fibrosis WWP2 regulates the metabolic reprogramming of profibrotic myofibroblasts by a WWP2-PGC-1 Show less

Non-ischemic cardiomyopathy (NICM) can cause left ventricular dysfunction through interstitial fibrosis, which corresponds to the failure of cardiac tissue remodeling. Recent evidence implicates monocytes/macrophages in the etiopathology of cardiac fibrosis, but giving their heterogeneity and the antagonizing roles of macrophage subtypes in fibrosis, targeting these cells has been challenging. Here we focus on WWP2, an E3 ubiquitin ligase that acts as a positive genetic regulator of human and murine cardiac fibrosis, and show that myeloid specific deletion of WWP2 reduces cardiac fibrosis in hypertension-induced NICM. By using single cell RNA sequencing analysis of immune cells in the same model, we establish the functional heterogeneity of macrophages and define an early pro-fibrogenic phase of NICM that is driven by Ccl5-expressing Ly6c Show less

Eukaryotic cells assemble actomyosin rings during cytokinesis to function as force-generating machines to drive membrane invagination and to counteract the intracellular pressure and the cell surface tension. How the extracellular matrix affects actomyosin ring contraction has not been fully explored. While studying the Show less

To evaluate the 3D static articulation accuracy of 3 model scanner-CAD systems (Ceramill Map400 [AG], inEos X5 [SIR], Scanner S600 Arti [ZKN]) using a coordinate measuring machine (CMM). Trueness and precision for each system will be reported in Part I. The master model simulated a single crown opposing a 3-unit fixed dental prosthesis. Five mounted stone cast sets were prepared, and one set was randomly selected. Reference values were obtained by measuring interarch and interocclusal reference features with the CMM. The stone cast set was scanned 5 times consecutively and articulated virtually with each system (3 test groups, n = 5). STL files of the virtual models were measured with CMM software. dR For trueness values, mean interarch global distortions ranged from 13.1 to 40.3 μm for dR The overall interarch global distortion of all three model scanner-CAD systems was low and did not exceed 0.6%. Variations in scanner technology, virtual articulation algorithm, and use of physical articulators contributed to the differences in distortion observed among all three groups. Show less

Accurate maxillomandibular relationship transfer is important for CAD/CAM prostheses. This study compared the 3D-accuracy of virtual model static articulation in three laboratory scanner-CAD systems (Ceramill Map400 [AG], inEos X5 [SIR], Scanner S600 Arti [ZKN]) using two virtual articulation methods: mounted models (MO), interocclusal record (IR). The master model simulated a single crown opposing a 3-unit fixed partial denture. Reference values were obtained by measuring interarch and interocclusal reference features with a coordinate measuring machine (CMM). MO group stone casts were articulator-mounted with acrylic resin bite registrations while IR group casts were hand-articulated with poly(vinyl siloxane) bite registrations. Five test model sets were scanned and articulated virtually with each system (6 test groups, 15 data sets). STL files of the virtual models were measured with CMM software. dR Mean interarch 3D distortion ranged from -348.7 to 192.2 μm for dR Interarch and interocclusal distances increased in MO groups, while they decreased in IR groups. AG-IR had the greatest interarch distortion as well as interocclusal superior-inferior distortion. The other groups performed similarly to each other, and the overall interarch distortion did not exceed 0.7%. In these systems and articulation methods, interocclusal distortions may result in hyper- or infra-occluded prostheses. Show less

Family- and population-based genetic studies have successfully identified multiple disease-susceptibility loci for Age-related macular degeneration (AMD), one of the first batch and most successful examples of genome-wide association study. However, most genetic studies to date have focused on case-control studies of late AMD (choroidal neovascularization or geographic atrophy). The genetic influences on disease progression are largely unexplored. We assembled unique resources to perform a genome-wide bivariate time-to-event analysis to test for association of time-to-late-AMD with ∼9 million variants on 2721 Caucasians from a large multi-center randomized clinical trial, the Age-Related Eye Disease Study. To our knowledge, this is the first genome-wide association study of disease progression (bivariate survival outcome) in AMD genetic studies, thus providing novel insights to AMD genetics. We used a robust Cox proportional hazards model to appropriately account for between-eye correlation when analyzing the progression time in the two eyes of each participant. We identified four previously reported susceptibility loci showing genome-wide significant association with AMD progression: ARMS2-HTRA1 (P = 8.1 × 10-43), CFH (P = 3.5 × 10-37), C2-CFB-SKIV2L (P = 8.1 × 10-10) and C3 (P = 1.2 × 10-9). Furthermore, we detected association of rs58978565 near TNR (P = 2.3 × 10-8), rs28368872 near ATF7IP2 (P = 2.9 × 10-8) and rs142450006 near MMP9 (P = 0.0006) with progression to choroidal neovascularization but not geographic atrophy. Secondary analysis limited to 34 reported risk variants revealed that LIPC and CTRB2-CTRB1 were also associated with AMD progression (P < 0.0015). Our genome-wide analysis thus expands the genetics in both development and progression of AMD and should assist in early identification of high risk individuals. Show less

Progressive retinal atrophy is a common cause of blindness in the dog and affects >100 breeds. It is characterized by gradual vision loss that occurs due to the degeneration of photoreceptor cells in the retina. Similar to the human counterpart retinitis pigmentosa, the canine disorder is clinically and genetically heterogeneous and the underlying cause remains unknown for many cases. We use a positional candidate gene approach to identify putative variants in the Hungarian Puli breed using genotyping data of 14 family-based samples (CanineHD BeadChip array, Illumina) and whole-genome sequencing data of two proband and two parental samples (Illumina HiSeq 2000). A single nonsense SNP in exon 2 of Show less

Genome-wide association studies (GWAS) on Parkinson's disease (PD) have mostly been done in Europeans and Japanese. No study has been done in Han Chinese, which make up nearly a fifth of the world population. We conducted the first Han Chinese GWAS analysing a total of 22,729 subjects (5,125 PD cases and 17,604 controls) from Singapore, Hong Kong, Malaysia, Korea, mainland China and Taiwan. We performed imputation, merging and logistic regression analyses of 2,402,394 SNPs passing quality control filters in 779 PD cases, 13,227 controls, adjusted for the first three principal components. 90 SNPs with association P < 10-4 were validated in 9 additional sample collections and the results were combined using fixed-effects inverse-variance meta-analysis. We observed strong associations reaching genome-wide significance at SNCA, LRRK2 and MCCC1, confirming their important roles in both European and Asian PD. We also identified significant (P < 0.05) associations at 5 loci (DLG2, SIPA1L2, STK39, VPS13C and RIT2), and observed the same direction of associations at 9 other loci including BST1 and PARK16. Allelic heterogeneity was observed at LRRK2 while European risk SNPs at 6 other loci including MAPT and GBA-SYT11 were non-polymorphic or very rare in our cohort. Overall, we replicate associations at SNCA, LRRK2, MCCC1 and 14 other European PD loci but did not identify Asian-specific loci with large effects (OR > 1.45) on PD risk. Our results also demonstrate some differences in the genetic contribution to PD between Europeans and Asians. Further pan-ethnic meta-analysis with European GWAS cohorts may unravel new PD loci. Show less

HIV-associated sensory neuropathy (HIV-SN) is a common neurological complication of HIV infection. The TNF block is a region within the central MHC that contains many immunoregulatory genes. Polymorphisms and haplotypes of the TNF block have been associated with increased risk of HIV-SN in Asians and whites. Here we investigated genetic associations with HIV-SN in 342 black Southern Africans (190 cases and 152 neuropathy-free controls) using single nucleotide polymorphisms (SNPs) spanning the TNF block and a set of haplotypes defined by 31 SNPs in Asian and white populations (denoted FVa). We included population-appropriate tagSNPs derived from an African population (Yoruban, YRI, HapMap) and derived extended haplotypes comprising 61 SNPs (denoted FVa_ext b). We found no association between HIV-SN and carriage of two SNPs (TNF-1031/rs1799964*C and BAT1 (intron10)/rs9281523*C) associated with HIV-SN in whites and Asians. Additionally, a haplotype containing TNF-1031/rs1799964*C associated with increased risk of HIV-SN in Asians, but was not present in this African population. However, alleles of seven SNPs associated with reduced risk of HIV-SN (corrected for age, height and multiple comparisons). These were rs11796*A, rs3130059*G, rs2071594*C, NFKBIL1-62/rs2071592*A, rs2071591*A, LTA+252/rs909253*G, rs1041981*C. One haplotype (FV18_ext1), not containing these alleles, was associated with increased risk of HIV-SN after correction for age, height and multiple comparisons. Our results confirm the involvement of genes in the TNF block in altering risk for HIV-SN, but genotypes critical in this African population differed from those affecting HIV-SN in whites and Asians. These differences support the need for genetic association studies in diverse populations. Show less

Singapore comprises three ethnic groups: Chinese (76.7%), Malays (14%), and Asian-Indians (7.9%). Overall, Singaporeans experience coronary heart disease rates similar to those found in the United States. However, there is a dramatic interethnic gradient, with Asian-Indians having significantly higher risk than Chinese and Malays. These differences are associated with HDL cholesterol levels and cannot be solely explained by environmental exposure, and may be driven by genetic factors. The gene encoding apolipoprotein A-V (APOA5) has been located on chromosome 11, and it is emerging as an important candidate gene for lipoprotein metabolism. We investigated associations between APOA5 polymorphisms and plasma lipids in 3,971 Singaporeans to establish whether they accounted for some of the ethnic differences in plasma lipids. We found significant associations between the minor alleles at each of four common polymorphisms and higher plasma triglycerides (TGs) across ethnic groups. Haplotype analyses showed significant associations with TGs, explaining 6.9%, 5.2%, and 2.7% of the TG variance in Malays, Asian-Indians, and Chinese, respectively. Conversely, we observed significant inverse associations between the minor alleles and HDL cholesterol concentrations for Chinese and Malays. These data suggest that APOA5 plays a role in the ethnic differences observed for plasma TG and HDL cholesterol concentrations. Show less