Using Portuguese BRCA pathogenic variation as a model to study the impact of human admixture on human health.

BACKGROUND: Admixture occurs between different ethnic human populations. The global colonization in recent centuries by Europeans led to the most significant admixture in human history. While admixture may enhance genetic diversity for better fitness, it may also impact on human health by transmitting genetic variants for disease susceptibility in the admixture population. The admixture by Portuguese global exploration initiated in the 15th century has reached over 20 million of Portuguese-heritage population worldwide. It provides a valuable model to study the impact of admixture on human health. BRCA1 and BRCA2 (BRCA) are two of the important tumor suppressor genes. The pathogenic variation (PV) in BRCA is well determined to cause high risk of hereditary breast and ovarian cancer. Tracing the distribution of Portuguese BRCA PV in Portuguese-heritage population will help to understand the impact of admixture on cancer susceptibility in modern humans. In this study, we analyzed the distribution of the Portuguese-originated BRCA variation in Brazilian population, which has high degree Portuguese-heritage. METHODS: By comprehensive data mining, standardization and annotation, we generated a Portuguese-derived BRCA variation dataset and a Brazilian-derived BRCA variation dataset. We compared the two BRCA variation datasets to identify the BRCA variants shared between the two populations. RESULTS: The Portuguese-derived BRCA variation dataset consists of 220 BRCA variants including 78 PVs from 11,482 Portuguese cancer patients, 93 (42.2%) in BRCA1 and 127 (57.7%) in BRCA2. Of the 556 Portuguese BRCA PV carriers carrying the 78 PVs, 331 (59.5%) carried the three Portuguese-BRCA founder PVs of BRCA1 c.2037delinsCC, BRCA1 c.3331_3334del and BRCA2 c.156_157insAlu. The Brazilian-derived BRCA variation dataset consists of 255 BRCA PVs from 7,711 cancer patients, 136 (53.3%) in BRCA1 and 119 (46.6%) in BRCA2. We developed an open database named dbBRCA-Portuguese ( https://genemutation.fhs.um.edu.mo/dbbrca-portuguese/ ) and an open database named dbBRCA-Brazilian ( https://genemutation.fhs.um.edu.mo/dbbrca-brazilian ) to host the BRCA variation data from Portuguese and Brazilian populations. We compared the BRCA PV datasets between Portuguese and Brazilian populations, and identified 29 Portuguese-specific BRCA PVs shared between Portuguese and Brazilian populations, 14 in BRCA1 including the Portuguese founder BRCA1 c.3331_3334del and BRCA1 c.2037delinsCC, and 15 in BRCA2 including the Portuguese founder BRCA2 c.156_157insAlu. Searching the 78 Portuguese BRCA PVs in over 5,000 ancient human genomes identified evolution origin for only 8 PVs in Europeans dated between 37,470 and 3,818 years before present, confirming the Portuguese-specificity of Portuguese BRCA PVs; comparing the 78 Portuguese BRCA PVs Portuguese, 255 Brazilian BRCA PVs, and 134 African BRCA PVs showed little overlapping, ruling out the possibility that the BRCA PVs shared between Portuguese and Brazilian may also be contributed by African. CONCLUSION: Our study provides evidence that the admixture in recent human history contributed to cancer susceptibility in modern humans.

Pathogenic variants in human DNA damage repair genes mostly arose in recent human history.

BACKGROUND: Genome stability is maintained by the DNA damage repair (DDR) system composed of multiple DNA repair pathways of hundreds of genes. Germline pathogenic variation (PV) in DDR genes damages function of the affected DDR genes, leading to genome instability and high risk of diseases, in particular, cancer. Knowing evolutionary origin of the PVs in human DDR genes is essential to understand the etiology of human diseases. However, answer to the issue remains largely elusive. In this study, we analyzed evolutionary origin for the PVs in human DDR genes. METHODS: We identified 169 DDR genes by referring to various databases and identified PVs in the DDR genes of modern humans from ClinVar database. We performed a phylogenetic analysis to analyze the conservation of human DDR PVs in 100 vertebrates through cross-species genomic data comparison using the phyloFit program of the PHAST package and visualized the results using the GraphPad Prism software and the ggplot module. We identified DDR PVs from over 5000 ancient humans developed a database to host the DDR PVs ( https://genemutation.fhs.um.edu.mo/dbDDR-AncientHumans ). Using the PV data, we performed a molecular archeological analysis to compare the DDR PVs between modern humans and ancient humans. We analyzed evolution selection of DDR genes across 20 vertebrates using the CodeML in PAML for phylogenetic analysis. RESULTS: Our phylogenic analysis ruled out cross-species conservation as the origin of human DDR PVs. Our archeological approach identified rich DDR PVs shared between modern and ancient humans, which were mostly dated within the last 5000 years. We also observed similar pattern of quantitative PV distribution between modern and ancient humans. We further detected a set of ATM, BRCA2 and CHEK2 PVs shared between human and Neanderthals. CONCLUSIONS: Our study reveals that human DDR PVs mostly arose in recent human history. We propose that human high cancer risk caused by DDR PVs can be a by-product of human evolution.

Classification of MLH1 Missense VUS Using Protein Structure-Based Deep Learning-Ramachandran Plot-Molecular Dynamics Simulations Method.

Pathogenic variation in DNA mismatch repair (MMR) gene MLH1 is associated with Lynch syndrome (LS), an autosomal dominant hereditary cancer. Of the 3798 MLH1 germline variants collected in the ClinVar database, 38.7% (1469) were missense variants, of which 81.6% (1199) were classified as Variants of Uncertain Significance (VUS) due to the lack of functional evidence. Further determination of the impact of VUS on MLH1 function is important for the VUS carriers to take preventive action. We recently developed a protein structure-based method named "Deep Learning-Ramachandran Plot-Molecular Dynamics Simulation (DL-RP-MDS)" to evaluate the deleteriousness of MLH1 missense VUS. The method extracts protein structural information by using the Ramachandran plot-molecular dynamics simulation (RP-MDS) method, then combines the variation data with an unsupervised learning model composed of auto-encoder and neural network classifier to identify the variants causing significant change in protein structure. In this report, we applied the method to classify 447 MLH1 missense VUS. We predicted 126/447 (28.2%) MLH1 missense VUS were deleterious. Our study demonstrates that DL-RP-MDS is able to classify the missense VUS based solely on their impact on protein structure.

Impact of Preoperative Mapping and Intraoperative Neuromonitoring in Minimally Invasive Parafascicular Surgery for Deep-Seated Lesions.

BACKGROUND: Transsulcal tubular retractor-assisted minimally invasive parafascicular surgery changes the surgical strategy for deep-seated lesions by promoting a deficit-sparing approach. When integrated with preoperative brain mapping and intraoperative neuromonitoring (IONM), this approach may potentially improve patient outcomes. In this study, we assessed the impact of preoperative brain mapping and IONM in tubular retractor-assisted neuro-oncological surgery. METHODS: This retrospective single-center cohort study included patients who underwent transsulcal tubular retractor-assisted minimally invasive parafascicular surgery for resection of deep-seated brain tumors from 2016 to 2022. The cohort was divided into 3 groups: group 1, no preoperative mapping or IONM (17 patients); group 2, IONM only (25 patients); group 3, both preoperative mapping and IONM (38 patients). RESULTS: We analyzed 80 patients (33 males and 47 females) with a median age of 46.5 years (range: 1-81 years). There was no significant difference in mean tumor volume (26.2 cm3 [range 1.07-97.4 cm3]; P = 0.740) and mean preoperative depth of the tumor (31 mm [range 3-65 mm], P = 0.449) between the groups. A higher proportion of high-grade gliomas and metastases was present within group 3 (P = 0.003). IONM was related to fewer motor (P = 0.041) and language (P = 0.032) deficits at hospital discharge. Preoperative mapping and IONM were also related to shorter length of stay (P = 0.008). CONCLUSIONS: Preoperative and intraoperative brain mapping and monitoring enhance transsulcal tubular retractor-assisted minimally invasive parafascicular surgery in neuro-oncology. Patients had a reduced length of stay and prolonged overall survival. IONM alone reduces postoperative neurological deficit.

Classification of PTEN missense VUS through exascale simulations.

Phosphatase and tensin homolog (PTEN), a tumor suppressor with dual phosphatase properties, is a key factor in PI3K/AKT signaling pathway. Pathogenic germline variation in PTEN can abrogate its ability to dephosphorylate, causing high cancer risk. Lack of functional evidence lets numerous PTEN variants be classified as variants of uncertain significance (VUS). Utilizing Molecular Dynamics (MD) simulations, we performed a thorough evaluation for 147 PTEN missense VUS, sorting them into 66 deleterious and 81 tolerated variants. Utilizing replica exchange molecular dynamic (REMD) simulations, we further assessed the variants situated in the catalytic core of PTEN's phosphatase domain and uncovered conformational alterations influencing the structural stability of the phosphatase domain. There was a high degree of agreement between our results and the variants classified by Variant Abundance by Massively Parallel Sequencing, saturation mutagenesis, multiplexed functional data and experimental assays. Our extensive analysis of PTEN missense VUS should benefit their clinical applications in PTEN-related cancer. SIGNIFICANCE STATEMENT: Classification of PTEN variants affecting its lipid phosphatase activity is important for understanding the roles of PTEN variation in the pathogenesis of hereditary and sporadic malignancies. Of the 3000 variants identified in PTEN, 1296 (43%) were assigned as VUS. Here, we applied MD and REMD simulations to investigate the effects of PTEN missense VUS on the structural integrity of the PTEN phosphatase domain consisting the WPD, P and TI active sites. We classified a total of 147 missense VUS into 66 deleterious and 81 tolerated variants by referring to the control group comprising 54 pathogenic and 12 benign variants. The classification was largely in concordance with these classified by experimental approaches.

Butterfly gliomas: a time for stratified management?

Butterfly glioblastomas (bGBM) are a rare subset of WHO grade IV tumours that carry a poor prognosis with a median survival ranging between 3.3 to 6 months. Given their poor prognosis, there is debate over whether histological diagnosis with a biopsy or any surgical or oncological intervention alters disease progression. With this in mind, we reviewed our experience as a high-volume unit to evaluate management decisions and outcomes. A retrospective analysis was undertaken (January 2009 to June 2021) of the electronic patient records of a large neurosurgical centre. We assessed patient demographics, initial clinical presentation, tumour characteristics, clinical management and overall survival (Kaplan-Meier estimator, log-rank analysis and cox proportional hazard analysis). Eighty cases of bGBM were identified. These patients were managed with biopsy ± adjuvant therapy (36), with radiotherapy alone without biopsy (3), or through surgical resection (3). Thirty-eight cases of suspected bGBM were managed conservatively, receiving no oncological treatment or surgical resection/biopsy for histological diagnosis. Those managed conservatively and with radiotherapy without biopsy were diagnosed at neuro-oncology multidisciplinary meeting (MDT) based on clinical presentation and radiological imaging. No significant difference in survival was seen between conservative management compared with single adjuvant treatment (p = 0.69). However, survival was significantly increased when patients received dual adjuvant chemoradiotherapy following biopsy or resection (p = 0.002). A Cox Proportional Hazards model found that survival was significantly impacted by the oncology treatment (p < 0.001), but was not significantly related to potential confounding variables such as the patient's age (p = 0.887) or KPS (p = 0.057). Butterfly glioblastoma have a poor prognosis. Our study would suggest that unless a patient is planned for adjuvant chemoradiotherapy following biopsy, they should be managed conservatively. This avoids unnecessary procedural interventions with the associated morbidities and costs.

Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population.

Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.

The Fate of Nonoperative Management in Patients with Lytic Spondylolisthesis.

BACKGROUND: There is a lack of consensus within the current literature about the role of nonoperative management in lytic spondylolisthesis. Our objective was to assess the fate that nonoperative management plays in patients diagnosed with lytic spondylolisthesis. METHODS: Data were collected between May 2015 and February 2020 from 41 patients who were initially referred specifically for instrumented lumbar fixation but were instead planned for nonoperative management as they opted to avoid surgery. Magnetic resonance imaging (MRI) scans were used to determine spondylolisthesis grade, type of deformity, and radiologic features. Patient notes were reviewed to establish management plans. Furthermore, patients were also contacted via telephone to assess their symptoms and disease progression. RESULTS: Twenty-six of the 41 patients had lytic spondylolisthesis (63.4%). Of these patients, the male-to-female ratio was 10:16. The median age was 60 (range: 22-76) years. A total of 12 patients were managed nonoperatively for 5 years or longer, with 2 patients showing progression from grade I to II. CONCLUSION: Nonoperative management of lytic spondylolisthesis is a reasonable option in a selected cohort of patients. The longer in duration patients are managed conservatively, the less likely they are to require a surgical intervention. Even severe radiologic foraminal stenosis without radicular pain does not seem to push patients toward surgery. Management decisions must be made on an individual basis. These data can give some reassurance to patients who wish to consider nonoperative management and help guide clinicians.

High fidelity simulation of the endoscopic transsphenoidal approach: Validation of the UpSurgeOn TNS Box.

Objective: Endoscopic endonasal transsphenoidal surgery is an established technique for the resection of sellar and suprasellar lesions. The approach is technically challenging and has a steep learning curve. Simulation is a growing training tool, allowing the acquisition of technical skills pre-clinically and potentially resulting in a shorter clinical learning curve. We sought validation of the UpSurgeOn Transsphenoidal (TNS) Box for the endoscopic endonasal transsphenoidal approach to the pituitary fossa. Methods: Novice, intermediate and expert neurosurgeons were recruited from multiple centres. Participants were asked to perform a sphenoidotomy using the TNS model. Face and content validity were evaluated using a post-task questionnaire. Construct validity was assessed through post-hoc blinded scoring of operative videos using a Modified Objective Structured Assessment of Technical Skills (mOSAT) and a Task-Specific Technical Skill scoring system. Results: Fifteen participants were recruited of which n = 10 (66.6%) were novices and n = 5 (33.3%) were intermediate and expert neurosurgeons. Three intermediate and experts (60%) agreed that the model was realistic. All intermediate and experts (n = 5) strongly agreed or agreed that the TNS model was useful for teaching the endonasal transsphenoidal approach to the pituitary fossa. The consensus-derived mOSAT score was 16/30 (IQR 14-16.75) for novices and 29/30 (IQR 27-29) for intermediate and experts (p < 0.001, Mann-Whitney U). The median Task-Specific Technical Skill score was 10/20 (IQR 8.25-13) for novices and 18/20 (IQR 17.75-19) for intermediate and experts (p < 0.001, Mann-Whitney U). Interrater reliability was 0.949 (CI 0.983-0.853) for OSATS and 0.945 (CI 0.981-0.842) for Task-Specific Technical Skills. Suggested improvements for the model included the addition of neuro-vascular anatomy and arachnoid mater to simulate bleeding vessels and CSF leak, respectively, as well as improvement in materials to reproduce the consistency closer to that of human tissue and bone. Conclusion: The TNS Box simulation model has demonstrated face, content, and construct validity as a simulator for the endoscopic endonasal transsphenoidal approach. With the steep learning curve associated with endoscopic approaches, this simulation model has the potential as a valuable training tool in neurosurgery with further improvements including advancing simulation materials, dynamic models (e.g., with blood flow) and synergy with complementary technologies (e.g., artificial intelligence and augmented reality).

Applications of Molecular Dynamics Simulation in Protein Study.

Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein-protein interaction, enzymatic reactions and drug-protein interactions, and membrane proteins. In this review, we provide a brief review for the history of MD Simulations application and the current status of MD Simulations applications in protein studies.

Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations.

Large quantity of variants of uncertain significance (VUS) has been identified in cancer predisposition genes, but classification of VUS remains a big challenge. We proposed that the impact of VUS on protein structure stability can be used to identify these with deleterious effects by using molecular dynamics simulation (MDS)-based approach and developed a MDS-based method for missense VUS classification. In the current study, we applied the system to classify the missense VUS in BRCA2. BRCA2 plays an important role in maintaining genome stability by repairing double-strand DNA damage through homologous recombination. BRCA2 BRC repeats bring RAD51 from cytoplasm to the break sites in nucleus to initiate the repairing process. Missense variants in BRCA2 BRC repeats can interfere the interaction between BRCA2 and RAD51, impair double-strand break repair, cause genome instability and increase cancer risk. We characterized the missense VUS in BRCA2 BRC4 repeat, the primary site of BRCA2 interacting with RAD51. Based on the well-determined BRC4 structure, we applied MDS to measure the impact of BRC4 missense VUS on the stability of BRC4 structure by testing the equilibrium state, flexibility, compactness, hydrogen bonds and surface accessibility. Of the 46 missense VUS analyzed, we were able to differentiate them into 24 Deleterious and 22 Tolerated variants. Comparison between the MDS-based and other 24 existing computational methods for variant classification showed that the MDS-based approach is highly sensitive and specific for classifying missense VUS in cancer predisposition genes.

Surgical management and outcomes in spinal intradural arachnoid cysts: the experience from two tertiary neurosurgical centres.

PURPOSE: Evaluation of the presentation and outcomes of different surgical treatment approaches for spinal intradural arachnoid cysts (SIAC). METHODS: Cases were identified from electronic records of two major neurosurgical centres in London over the last 10 years (October 2009-October 2019) that have been surgically treated in both institutions. Clinical findings, surgical technique, and recurrence by procedure were statistically analysed. Statistical analysis was performed with STATA 13.1 Software. RESULTS: A total of 42 patients with SIAC were identified for this study with a mean age at the time of surgery of 53.6 years and a male:female ratio of 8:13. There were 31 patients with primary SIACs and 11 with secondary SIACs. The most common presenting symptom was paraesthesia (n = 27). The most common location of the cyst was in the thoracic region (n = 33). Syrinx was present in 26.2% of SIACs (n = 11). Resection was associated with significantly better postoperative pain compared to other surgical techniques (p = 0.01), significantly poorer postoperative urinary function (p = 0.029), and lower rates of sensory recovery in patients who presented preoperatively with sensory deficit (p = 0.041). No significant difference was seen in symptomatic outcomes between patients with primary and secondary SIACs. CONCLUSION: Resection and drainage are both effective methods of managing SIACs. In this observational study, resection was associated with significantly reduced pain postoperatively when compared with drainage, however also with significantly less improvement in postoperative urinary function. Therefore, resection should be the gold standard management option for SIACs, with drainage as an option where resection is unsafe, and drainage should also be considered in patients presenting with urinary dysfunction.

Twelve tips to organise a mock OSCE.

The objective structured clinical examination (OSCE) is central to assessing clinical competence in undergraduate and postgraduate exams for medical and allied healthcare professions. A mock OSCE on the other hand is a simulation of the OSCE and a unique learning experience for the examinee. They benefit in a variety of ways; from enhancing their time management skills to receiving feedback that can improve their clinical skills. Unfortunately, opportunities to participate in simulated OSCEs remain limited. Reasons include difficulty in fulfilling organisational requirements and equipment-related costs. Mock OSCEs can be set up by undergraduate students or junior trainees for peers, without senior supervision or direct guidance. This article will discuss 12 tips regarding the arrangement of mock OSCEs to guide organisers, including accessing resources and establishing the content of the exam.

Experiences with Cyclical User-Centered Design for Patient and Clinician Facing Medication Reconciliation mHealth Applications.

Accurate medication lists are essential data required to make clinically informed decisions. Obtaining a comprehensive, up-to-date medication list is difficult for clinicians. Patients have limited input into reviewing and reconciling their own medication data. Ideally, a medication list would comprise a 360-degree view of all prescribed, dispensed, purchased medications and would seamlessly connect patients and providers to medication data from multiple sources. While an ideal medication list would capture every aspect of medication management, in reality a Best-Possible Medication History (BPMH) is a more achievable goal. In an effort to realize a BPMH and to facilitate the goals of the State of Connecticut's Office of Health Strategy's Medication Reconciliation and Polypharmacy Committee (MRPC), we engaged stakeholders (patients, clinicians, advocates) in focus-groups and interviews to solicit feedback on the user interface requirements for a BPMH. Feedback was obtained via facilitated discussions that occurred in-person, via virtual meetings, and through online surveys.

Comprehensive Identification of Deleterious TP53 Missense VUS Variants Based on Their Impact on TP53 Structural Stability.

TP53 plays critical roles in maintaining genome stability. Deleterious genetic variants damage the function of TP53, causing genome instability and increased cancer risk. Of the large quantity of genetic variants identified in TP53, however, many remain functionally unclassified as variants of unknown significance (VUS) due to the lack of evidence. This is reflected by the presence of 749 (42%) VUS of the 1785 germline variants collected in the ClinVar database. In this study, we addressed the deleteriousness of TP53 missense VUS. Utilizing the protein structure-based Ramachandran Plot-Molecular Dynamics Simulation (RPMDS) method that we developed, we measured the effects of missense VUS on TP53 structural stability. Of the 340 missense VUS tested, we observed deleterious evidence for 193 VUS, as reflected by the TP53 structural changes caused by the VUS-substituted residues. We compared the results from RPMDS with those from other in silico methods and observed higher specificity of RPMDS in classification of TP53 missense VUS than these methods. Data from our current study address a long-standing challenge in classifying the missense VUS in TP53, one of the most important tumor suppressor genes.

BRCA1 and BRCA2 Variation in Taiwanese General Population and the Cancer Cohort.

BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. Rapidly evolving human BRCA generates oncogenic variants causing high cancer risk. BRCA variation is ethnic-specific in reflecting adaptation and/or effects of genetic drift. Taiwanese population of 23.8 million is an admixture of multiple ethnic origins; Taiwan's subtropical and tropical climate and geographically islandic location provide a unique natural environment. Therefore, Taiwanese population provides a unique model to study human BRCA variation. Through collecting, standardizing, annotating, and classifying publicly available BRCA variants derived from Taiwanese general population and the cancer cohort, we identified 335 BRCA variants, of which 164 were from 1,517 non-cancer individuals, 126 from 2,665 cancer individuals, and 45 from both types of individuals. We compared the variant data with those from other ethnic populations such as mainland Chinese, Macau Chinese, Japanese, Korean, Indian, and non-Asians. We observed that the sharing rates with other Asian ethnic populations were correlated with its genetic relationship. Over 60% of the 335 Taiwanese BRCA variants were VUS, unclassified variants, or novel variants, reflecting the ethnic-specific features of Taiwanese BRCA variation. While it remains challenging to classify these variants, our structural and in silico analyses predicted their enrichment of BRCA deleterious variants. We further determined the 3.8% prevalence of BRCA pathogenic variants in the Taiwanese breast cancer cohort, and determined 0.53% prevalence of the BRCA pathogenic variants in Taiwanese general population, with the estimated 126,140 BRCA pathogenic variant carriers. We identified BRCA2 c.5164_5165delAG at BRCA2 BRC6 motif as a potential founder mutation in Taiwanese population. Our study on BRCA variation in Taiwanese and other East Asian populations demonstrates that ethnic specificity is a common phenomenon for BRCA variation in East Asian population; the data generated from the study provide a reference for clinical applications in BRCA-related cancer in Taiwanese population.

The impact of COVID-19 on neurosurgical head trauma referrals and admission at a tertiary neurosurgical centre.

BACKGROUND: COVID-19 has greatly impacted surgical specialities throughout the globe leading to a decrease in hospital admissions and referrals. Neurosurgery has seen a great decline in cases including head trauma leading to a negative impact on the development of neurosurgical trainees. The main objective of this study is to the identify changes in neurosurgical referrals, admissions and management during the COVID-19 pandemic. We also aim to assess how current practise could be adapted to help manage future pandemic peaks. METHODS: Data was collected for the first 31 days of lockdown during 2020 (23rd March - 22nd April) and compared to the same time period in the years 2016-2019. We assessed the number of referrals, admissions and clinical information of patients during this period with a key emphasis on head trauma. RESULTS: Neurosurgical head injury referrals and admissions reduced by 57.5% and 48.3% respectively during the first 31 days of lockdown when compared to the mean figures for the same period in the previous 4 years. This was also seen with head trauma with a 21.9% decline in referrals and 39.1% reduction in admissions for the period of interest. A significant decrease in length of stay (P < 0.001) was seen between 2020 and the years 2017-19. CONCLUSION: The impact of COVID-19 makes it imperative that we plan for future pandemics to lessen the impact on neurosurgery. Special considerations need to be taken so that trainees are sufficiently prepared for completion of training whilst still priotising patient safety and providing high quality care.

RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor.

The COVID-19 pandemic, caused by SARS-CoV-2, has led to catastrophic damage for global human health. The initial step of SARS-CoV-2 infection is the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Constant evolution of SARS-CoV-2 generates new mutations across its genome including the coding region for the RBD in the spike protein. In addition to the well-known single mutation in the RBD, the recent new mutation strains with an RBD "double mutation" are causing new outbreaks globally, as represented by the delta strain containing RBD L452R/T478K. Although it is considered that the increased transmissibility of double-mutated strains could be attributed to the altered interaction between the RBD and ACE2 receptor, the molecular details remain to be elucidated. Using the methods of molecular dynamics simulation, superimposed structural comparison, free binding energy estimation, and antibody escaping, we investigated the relationship between the ACE2 receptor and the RBD double mutants of L452R/T478K (delta), L452R/E484Q (kappa), and E484K/N501Y (beta, gamma). The results demonstrated that each of the three RBD double mutants altered the RBD structure and enhanced the binding of the mutated RBD to ACE2 receptor. Together with the mutations in other parts of the virus genome, the double mutations increase the transmissibility of SARS-CoV-2 to host cells.

Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition.

BACKGROUND: Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important component in the genome, the core promoter in the human genome could be under evolutionary selection, as reflected by its highly diversification in order to adjust gene expression for better adaptation to the different environment. RESULTS: Applying the "Exome-based Variant Detection in Core-promoters" method, we analyzed human core-promoter diversity by using the 2682 exome data sets of 25 worldwide human populations sequenced by the 1000 Genome Project. Collectively, we identified 31,996 variants in the core promoter region (- 100 to + 100) of 12,509 human genes ( https://dbhcpd.fhs.um.edu.mo ). Analyzing the rich variation data identified highly ethnic-specific patterns of core promoter variation between different ethnic populations, the genes with highly variable core promoters, the motifs affected by the variants, and their involved functional pathways. eQTL test revealed that 12% of core promoter variants can significantly alter gene expression level. Comparison with GWAS data we located 163 variants as the GWAS identified traits associated with multiple diseases, half of these variants can alter gene expression. CONCLUSION: Data from our study reals the highly diversified nature of core promoter in the human genome, and highlights that core promoter variation could play important roles not only in gene expression regulation but also in disease predisposition.

Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model.

The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural stability of their affected proteins, information from structural change caused by genetic variants can be used to identify the variants with deleterious effects. In order to measure the structural change for proteins with large size, we designed a method named RP-MDS composed of Ramachandran plot (RP) and Molecular Dynamics Simulation (MDS). Ramachandran plot captures the variant-caused secondary structural change, whereas MDS provides a quantitative measure for the variant-caused globular structural change. We tested the method using variants in TP53 DNA binding domain of 219 residues as the model. In total, RP-MDS identified 23 of 38 (60.5%) TP53 known Pathogenic variants and 17 of 42 (41%) TP53 VUS that caused significant changes of P53 structure. Our study demonstrates that RP-MDS method provides a powerful protein structure-based tool to screen deleterious genetic variants affecting large-size proteins.