Melbourne Medical School Collected Works - Research Publications

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Uncovering the Molecular Drivers of NHEJ DNA Repair-Implicated Missense Variants and Their Functional Consequences

Al-Jarf, R ; Karmakar, M ; Myung, Y ; Ascher, DB (MDPI, 2023-10)

Variants in non-homologous end joining (NHEJ) DNA repair genes are associated with various human syndromes, including microcephaly, growth delay, Fanconi anemia, and different hereditary cancers. However, very little has been done previously to systematically record the underlying molecular consequences of NHEJ variants and their link to phenotypic outcomes. In this study, a list of over 2983 missense variants of the principal components of the NHEJ system, including DNA Ligase IV, DNA-PKcs, Ku70/80 and XRCC4, reported in the clinical literature, was initially collected. The molecular consequences of variants were evaluated using in silico biophysical tools to quantitatively assess their impact on protein folding, dynamics, stability, and interactions. Cancer-causing and population variants within these NHEJ factors were statistically analyzed to identify molecular drivers. A comprehensive catalog of NHEJ variants from genes known to be mutated in cancer was curated, providing a resource for better understanding their role and molecular mechanisms in diseases. The variant analysis highlighted different molecular drivers among the distinct proteins, where cancer-driving variants in anchor proteins, such as Ku70/80, were more likely to affect key protein-protein interactions, whilst those in the enzymatic components, such as DNA-PKcs, were likely to be found in intolerant regions undergoing purifying selection. We believe that the information acquired in our database will be a powerful resource to better understand the role of non-homologous end-joining DNA repair in genetic disorders, and will serve as a source to inspire other investigations to understand the disease further, vital for the development of improved therapeutic strategies.
Acute effects of single and repeated mild traumatic brain injury on levels of neurometabolites, lipids, and mitochondrial function in male rats.

Allen, J ; Pham, L ; Bond, ST ; O'Brien, WT ; Spitz, G ; Shultz, SR ; Drew, BG ; Wright, DK ; McDonald, SJ (Frontiers Media SA, 2023)

INTRODUCTION: Mild traumatic brain injuries (mTBIs) are the most common form of acquired brain injury. Symptoms of mTBI are thought to be associated with a neuropathological cascade, potentially involving the dysregulation of neurometabolites, lipids, and mitochondrial bioenergetics. Such alterations may play a role in the period of enhanced vulnerability that occurs after mTBI, such that a second mTBI will exacerbate neuropathology. However, it is unclear whether mTBI-induced alterations in neurometabolites and lipids that are involved in energy metabolism and other important cellular functions are exacerbated by repeat mTBI, and if such alterations are associated with mitochondrial dysfunction. METHODS: In this experiment, using a well-established awake-closed head injury (ACHI) paradigm to model mTBI, male rats were subjected to a single injury, or five injuries delivered 1 day apart, and injuries were confirmed with a beam-walk task and a video observation protocol. Abundance of several neurometabolites was evaluated 24 h post-final injury in the ipsilateral and contralateral hippocampus using in vivo proton magnetic resonance spectroscopy (1H-MRS), and mitochondrial bioenergetics were evaluated 30 h post-final injury, or at 24 h in place of 1H-MRS, in the rostral half of the ipsilateral hippocampus. Lipidomic evaluations were conducted in the ipsilateral hippocampus and cortex. RESULTS: We found that behavioral deficits in the beam task persisted 1- and 4 h after the final injury in rats that received repetitive mTBIs, and this was paralleled by an increase and decrease in hippocampal glutamine and glucose, respectively, whereas a single mTBI had no effect on sensorimotor and metabolic measurements. No group differences were observed in lipid levels and mitochondrial bioenergetics in the hippocampus, although some lipids were altered in the cortex after repeated mTBI. DISCUSSION: The decrease in performance in sensorimotor tests and the presence of more neurometabolic and lipidomic abnormalities, after repeated but not singular mTBI, indicates that multiple concussions in short succession can have cumulative effects. Further preclinical research efforts are required to understand the underlying mechanisms that drive these alterations to establish biomarkers and inform treatment strategies to improve patient outcomes.
Factors Associated with Participation in a Multidomain Web-Based Dementia Prevention Trial: Evidence from Maintain Your Brain (MYB)

Welberry, HJ ; Chau, T ; Heffernan, M ; San Jose, JC ; Jorm, LR ; Singh, MF ; Sachdev, PS ; Anstey, KJ ; Lautenschlager, NT ; Valenzuela, M ; McNeil, JJ ; Brodaty, H ; Fairley, A (IOS PRESS, 2023)

BACKGROUND: The Maintain Your Brain (MYB) trial aims to prevent cognitive decline and dementia through multidomain, web-based risk-reduction. To facilitate translation, it is important to understand drivers of participation. OBJECTIVE: To describe characteristics associated with participation in MYB. METHODS: This was an observational ancillary study of MYB, a randomized controlled trial nested within the 45 and Up Study in New South Wales, Australia. We linked 45 and Up Study survey and MYB participation data. The study cohort comprised 45 and Up Study participants, aged 55-77 years at 1 January 2018, who were invited to participate in MYB. 45 and Up Study participant characteristics and subsequent MYB consent and participation were examined. RESULTS: Of 98,836 invited, 13,882 (14%) consented to participate and 6,190 participated (6%). Adjusting for age and sex, a wide range of factors were related to participation. Higher educational attainment had the strongest relationship with increased MYB participation (university versus school non-completion; AdjOR = 5.15; 95% CI:4.70-5.64) and lower self-rated quality of life with reduced participation (Poor versus Excellent: AdjOR = 0.19; 95% CI:0.11-0.32). A family history of Alzheimer's disease was related to increased participation but most other dementia risk factors such as diabetes, obesity, stroke, high blood pressure, and current smoking were associated with reduced participation. CONCLUSION: Higher socio-economic status, particularly educational attainment, is strongly associated with engagement in online dementia prevention research. Increasing population awareness of dementia risk factors, and better understanding the participation barriers in at-risk groups, is necessary to ensure online interventions are optimally designed to promote maximum participation.
Study protocol for development and validation of a single tool to assess risks of stroke, diabetes mellitus, myocardial infarction and dementia: DemNCD-Risk

Kootar, S ; Huque, MH ; Kiely, KM ; Anderson, CS ; Jorm, L ; Kivipelto, M ; Lautenschlager, NT ; Matthews, F ; Shaw, JE ; Whitmer, RA ; Peters, R ; Anstey, KJ (BMJ PUBLISHING GROUP, 2023-09)

INTRODUCTION: Current efforts to reduce dementia focus on prevention and risk reduction by targeting modifiable risk factors. As dementia and cardiometabolic non-communicable diseases (NCDs) share risk factors, a single risk-estimating tool for dementia and multiple NCDs could be cost-effective and facilitate concurrent assessments as compared with a conventional single approach. The aim of this study is to develop and validate a new risk tool that estimates an individual's risk of developing dementia and other NCDs including diabetes mellitus, stroke and myocardial infarction. Once validated, it could be used by the public and general practitioners. METHODS AND ANALYSIS: Ten high-quality cohort studies from multiple countries were identified, which met eligibility criteria, including large representative samples, long-term follow-up, data on clinical diagnoses of dementia and NCDs, recognised modifiable risk factors for the four NCDs and mortality data. Pooled harmonised data from the cohorts will be used, with 65% randomly allocated for development of the predictive model and 35% for testing. Predictors include sociodemographic characteristics, general health risk factors and lifestyle/behavioural risk factors. A subdistribution hazard model will assess the risk factors' contribution to the outcome, adjusting for competing mortality risks. Point-based scoring algorithms will be built using predictor weights, internally validated and the discriminative ability and calibration of the model will be assessed for the outcomes. Sensitivity analyses will include recalculating risk scores using logistic regression. ETHICS AND DISSEMINATION: Ethics approval is provided by the University of New South Wales Human Research Ethics Committee (UNSW HREC; protocol numbers HC200515, HC3413). All data are deidentified and securely stored on servers at Neuroscience Research Australia. Study findings will be presented at conferences and published in peer-reviewed journals. The tool will be accessible as a public health resource. Knowledge translation and implementation work will explore strategies to apply the tool in clinical practice.
Understanding the complementarity and plasticity of antibody-antigen interfaces.

Myung, Y ; Pires, DEV ; Ascher, DB ; Valencia, A (Oxford University Press (OUP), 2023-07-01)

MOTIVATION: While antibodies have been ground-breaking therapeutic agents, the structural determinants for antibody binding specificity remain to be fully elucidated, which is compounded by the virtually unlimited repertoire of antigens they can recognize. Here, we have explored the structural landscapes of antibody-antigen interfaces to identify the structural determinants driving target recognition by assessing concavity and interatomic interactions. RESULTS: We found that complementarity-determining regions utilized deeper concavity with their longer H3 loops, especially H3 loops of nanobody showing the deepest use of concavity. Of all amino acid residues found in complementarity-determining regions, tryptophan used deeper concavity, especially in nanobodies, making it suitable for leveraging concave antigen surfaces. Similarly, antigens utilized arginine to bind to deeper pockets of the antibody surface. Our findings fill a gap in knowledge about the antibody specificity, binding affinity, and the nature of antibody-antigen interface features, which will lead to a better understanding of how antibodies can be more effective to target druggable sites on antigen surfaces. AVAILABILITY AND IMPLEMENTATION: The data and scripts are available at: https://github.com/YoochanMyung/scripts.
LEGO-CSM: a tool for functional characterization of proteins

Nguyen, TB ; de Sa, AGC ; Rodrigues, CHM ; Pires, DE ; Ascher, DB ; Valencia, A (OXFORD UNIV PRESS, 2023-07-01)

MOTIVATION: With the development of sequencing techniques, the discovery of new proteins significantly exceeds the human capacity and resources for experimentally characterizing protein functions. Localization, EC numbers, and GO terms with the structure-based Cutoff Scanning Matrix (LEGO-CSM) is a comprehensive web-based resource that fills this gap by leveraging the well-established and robust graph-based signatures to supervised learning models using both protein sequence and structure information to accurately model protein function in terms of Subcellular Localization, Enzyme Commission (EC) numbers, and Gene Ontology (GO) terms. RESULTS: We show our models perform as well as or better than alternative approaches, achieving area under the receiver operating characteristic curve of up to 0.93 for subcellular localization, up to 0.93 for EC, and up to 0.81 for GO terms on independent blind tests. AVAILABILITY AND IMPLEMENTATION: LEGO-CSM's web server is freely available at https://biosig.lab.uq.edu.au/lego_csm. In addition, all datasets used to train and test LEGO-CSM's models can be downloaded at https://biosig.lab.uq.edu.au/lego_csm/data.
Direct inference and control of genetic population structure from RNA sequencing data

Fachrul, M ; Karkey, AM ; Shakya, M ; Judd, L ; Harshegyi, T ; Sim, KS ; Tonks, S ; Dongol, S ; Shrestha, R ; Salim, A ; Adhikari, A ; Banda, HCC ; Blohmke, C ; Darton, T ; Farooq, Y ; Ghimire, M ; Hill, J ; Hoang, NT ; Jere, TM ; Kamzati, M ; Kao, Y-H ; Masesa, C ; Mbewe, M ; Msuku, H ; Munthali, P ; Nga, TVTJ ; Nkhata, R ; Saad, N ; Tan, TV ; Thindwa, D ; Khanam, FD ; Meiring, J ; Clemens, JE ; Dougan, G ; Pitzer, VS ; Qadri, FA ; Heyderman, R ; Gordon, M ; Voysey, MJ ; Baker, S ; Pollard, A ; Khor, CC ; Dolecek, CJ ; Basnyat, BE ; Dunstan, S ; Holt, K ; Inouye, M (NATURE PORTFOLIO, 2023-08-02)

RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data.
PCPro: a clinically accessible, circulating lipid biomarker signature for poor-prognosis metastatic prostate cancer

Scheinberg, T ; Lin, H-M ; Fitzpatrick, M ; Azad, AAA ; Bonnitcha, P ; Davies, A ; Heller, G ; Huynh, K ; Mak, B ; Mahon, K ; Sullivan, D ; Meikle, PJJ ; Horvath, LGG (SPRINGERNATURE, 2023-05-05)

BACKGROUND: Using comprehensive plasma lipidomic profiling from men with metastatic castration-resistant prostate cancer (mCRPC), we have previously identified a poor-prognostic lipid profile associated with shorter overall survival (OS). In order to translate this biomarker into the clinic, these men must be identifiable via a clinically accessible, regulatory-compliant assay. METHODS: A single regulatory-compliant liquid chromatography-mass spectrometry assay of candidate lipids was developed and tested on a mCRPC Discovery cohort of 105 men. Various risk-score Cox regression prognostic models of OS were built using the Discovery cohort. The model with the highest concordance index (PCPro) was chosen for validation and tested on an independent Validation cohort of 183 men. RESULTS: PCPro, the lipid biomarker, contains Cer(d18:1/18:0), Cer(d18:1/24:0), Cer(d18:1/24:1), triglycerides and total cholesterol. Within the Discovery and Validation cohorts, men who were PCPro positive had significantly shorter OS compared to those who were PCPro negative (Discovery: median OS 12.0 months vs 24.2 months, hazard ratio (HR) 3.75 [95% confidence interval (CI) 2.29-6.15], p < 0.001, Validation: median OS 13.0 months vs 25.7 months, HR = 2.13 [95% CI 1.46-3.12], p < 0.001). CONCLUSIONS: We have developed PCPro, a lipid biomarker assay capable of prospectively identifying men with mCRPC with a poor prognosis. Prospective clinical trials are required to determine if men who are PCPro positive will benefit from therapeutic agents targeting lipid metabolism.
Studying the Synergistic Effect of Substrate Stiffness and Cyclic Stretch Level on Endothelial Cells Using an Elastomeric Cell Culture Chamber

Sekar, NC ; Suarez, SA ; Nguyen, N ; Lai, A ; Thurgood, P ; Zhou, Y ; Chheang, C ; Needham, S ; Pirogova, E ; Peter, K ; Khoshmanesh, K ; Baratchi, S (AMER CHEMICAL SOC, 2023-01-18)

Endothelial cells lining blood vessels are continuously exposed to biophysical cues that regulate their function in health and disease. As we age, blood vessels lose their elasticity and become stiffer. Vessel stiffness alters the mechanical forces that endothelial cells experience. Despite ample evidence on the contribution of endothelial cells to vessel stiffness, less is known about how vessel stiffness affects endothelial cells. In this study, we developed a versatile model to study the cooperative effect of substrate stiffness and cyclic stretch on human aortic endothelial cells. We cultured endothelial cells on elastomeric wells covered with fibronectin-coated polyacrylamide gel. Varying the concentrations of acrylamide and bis-acrylamide enabled us to produce soft and stiff substrates with elastic modules of 40 and 200 kPa, respectively. Using a customized three-dimensional (3D) printed cam-driven system, the cells were exposed to 5 and 10% cyclic stretch levels. This enabled us to mimic the stiffness and stretch levels that endothelial cells experience in young and aged arteries. Using this model, we found that endothelial cells cultured on a soft substrate had minimal cytoskeletal alignment to the direction of the stretch compared to the ones cultured on the stiff substrate. We also observed an increase in the cellular area and aspect ratio in cells cultured on the stiff substrate, both of which are positively regulated by cyclic stretch. However, neither cyclic stretch nor substrate stiffness significantly affected the nuclear circularity. Additionally, we found that the accumulation of NF-κB in the nucleus, endothelial proliferation, tube formation, and expression of IL1β depends on the stretch level and substrate stiffness. Our model can be further used to investigate the complex signaling pathways associated with vessel stiffening that govern the endothelial responses to mechanical forces.
Dynamic Vortex Generation, Pulsed Injection, and Rapid Mixing of Blood Samples in Microfluidics Using the Tube Oscillation Mechanism

Thurgood, P ; Needham, S ; Pirogova, E ; Peter, K ; Baratchi, S ; Khoshmanesh, K (AMER CHEMICAL SOC, 2023-01-24)

Here, we describe the generation of dynamic vortices in micro-scale cavities at low flow rates. The system utilizes a computer-controlled audio speaker to axially oscillate the inlet tube of the microfluidic system at desired frequencies and amplitudes. The oscillation of the tube induces transiently high flow rates in the system, which facilitates the generation of dynamic vortices inside the cavity. The size of the vortices can be modulated by varying the tube oscillation frequency or amplitude. The vortices can be generated in single or serial cavities and in a wide range of cavity sizes. We demonstrate the suitability of the tube oscillation mechanism for the pulsed injection of water-based solutions or whole blood into the cavity. The injection rate can be controlled by the oscillation characteristics of the tube, enabling the injection of liquids at ultralow flow rates. The dynamic vortices facilitate the rapid mixing of the injected liquid with the main flow. The controllability and versatility of this technology allow for the development of programmable inertial microfluidic systems for performing multistep biological assays.

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