Evaluation of the deliverability of dynamic conformal arc therapy (DCAT) by gantry wobble and its influence on dose.

We aimed to investigate the deliverability of dynamic conformal arc therapy (DCAT) by gantry wobble owing to the intrinsic inter-segment break of the Elekta linear accelerator (LINAC) and its adverse influence on the dose to the patient. The deliverability of DCAT was evaluated according to the plan parameters, which affect the gantry rotation speed and resultant positional inaccuracies; the deliverability according to the number of control points and dose rates was investigated by using treatment machine log files and dosimetry devices, respectively. A non-negligible degradation in DCAT deliverability due to gantry wobble was observed in both the treatment machine log files and dosimetry devices. The resulting dose-delivery error occurred below a certain number of control points or above a certain dose rate. Dose simulations in the patient domain showed a similar impact on deteriorated deliverability. For targets located primarily in the isocenter, the dose differences were negligible, whereas for organs at risk located mainly off-isocenter, the dose differences were significant up to - 8.77%. To ensure safe and accurate radiotherapy, optimal plan parameters should be selected, and gantry angle-specific validations should be conducted before treatment.

Comparison of outcomes between fungal and non-fungal periprosthetic joint infections in total knee arthroplasty.

Aims: Fungal periprosthetic joint infections (PJIs) are rare, but their diagnosis and treatment are highly challenging. The purpose of this study was to investigate the clinical outcomes of patients with fungal PJIs treated with two-stage exchange knee arthroplasty combined with prolonged antifungal therapy. Methods: We reviewed our institutional joint arthroplasty database and identified 41 patients diagnosed with fungal PJIs and treated with two-stage exchange arthroplasty after primary total knee arthroplasty (TKA) between January 2001 and December 2020, and compared them with those who had non-fungal PJIs during the same period. After propensity score matching based on age, sex, BMI, American Society of Anesthesiologists grade, and Charlson Comorbidity Index, 40 patients in each group were successfully matched. The surgical and antimicrobial treatment, patient demographic and clinical characteristics, recurrent infections, survival rates, and relevant risk factors that affected joint survivorship were analyzed. We defined treatment success as a well-functioning arthroplasty without any signs of a PJI, and without antimicrobial suppression, at a minimum follow-up of two years from the time of reimplantation. Results: The fungal PJI group demonstrated a significantly worse treatment success rate at the final follow-up than the non-fungal PJI group (65.0% (26/40) vs 85.0% (34/40); p < 0.001). The mean prosthesis-free interval was longer in the fungal PJI group than in the non-fungal PJI group (6.7 weeks (SD 5.8) vs 4.1 weeks (SD 2.5); p = 0.020). The rate of survivorship free from reinfection was worse in the fungal PJI group (83.4% (95% confidence interval (CI) 64.1 to 92.9) at one year and 76.4% (95% CI 52.4 to 89.4) at two years) than in the non-fungal PJI group (97.4% (95% CI 82.7 to 99.6) at one year and 90.3% (95% CI 72.2 to 96.9) at two years), but the differences were not significant (p = 0.270). Cox proportional hazard regression analysis identified the duration of the prosthesis-free interval as a potential risk factor for failure (hazard ratio 1.128 (95% CI 1.003 to 1.268); p = 0.043). Conclusion: Fungal PJIs had a lower treatment success rate than non-fungal PJIs despite two-stage revision arthroplasty and appropriate antifungal treatment. Our findings highlight the need for further developments in treating fungal PJIs.

Effect of diabetes mellitus on the outcomes of total ankle arthroplasty: is controlled diabetes mellitus a risk factor?

BACKGROUND: It is still uncertain whether diabetes mellitus (DM) is a risk factor for poor outcomes and increased complications after total ankle arthroplasty (TAA). The objective of this study was to compare clinical outcomes and complication rates of TAA in patients with and without DM. METHODS: This study enrolled patients with symptomatic end-stage ankle osteoarthritis with a minimum follow-up period of 24 months after TAA. A total of 252 patients (266 ankles) were classified into two groups according to the presence of DM: (1) DM group (59 patients, 67 ankles) and (2) non-DM group (193 patients, 199 ankles). We defined controlled diabetes as (1) HbA1c level < 7.0%, or (2) fasting glucose level < 130 mg/dL with HbA1c level ≥ 7.0% for hospitalization period. Clinical outcomes data (Ankle Osteoarthritis Scale, American Orthopedic Foot and Ankle Society ankle-hindfoot score, Short Form-36 Physical Component Summary score, and visual analog scale for pain) were compared preoperatively and at the final follow-up between the two groups. Complications following TAA were also compared between the two groups. RESULTS: All clinical variables had improved in both groups by the final follow-up (mean follow-up = 77.8 months). There was no significant difference in any clinical variable between the two groups at the final follow-up (P > 0.05). Of the 266 ankles, 73 ankles (19 in the DM group, 54 in the non-DM group) developed periprosthetic osteolysis. Although the DM group showed a higher prevalence of aseptic loosening or subsidence, the difference between the two groups was not statistically significant (P = 0.236). CONCLUSIONS: In the intermediate-term follow-up, TAA in patients with controlled DM showed clinical outcomes and complication rates comparable to patients without DM. Our results suggest that TAA can be done safely in diabetic patients if the DM is controlled in the perioperative period. LEVEL OF EVIDENCE: Therapeutic Level III.

Recording of elapsed time and temporal information about biological events using Cas9.

DNA has not been utilized to record temporal information, although DNA has been used to record biological information and to compute mathematical problems. Here, we found that indel generation by Cas9 and guide RNA can occur at steady rates, in contrast to typical dynamic biological reactions, and the accumulated indel frequency can be a function of time. By measuring indel frequencies, we developed a method for recording and measuring absolute time periods over hours to weeks in mammalian cells. These time-recordings were conducted in several cell types, with different promoters and delivery vectors for Cas9, and in both cultured cells and cells of living mice. As applications, we recorded the duration of chemical exposure and the lengths of elapsed time since the onset of biological events (e.g., heat exposure and inflammation). We propose that our systems could serve as synthetic "DNA clocks."

Mid-term results of total hip arthroplasty with modified trochanteric osteotomy in Crowe type IV developmental dysplasia of the hip.

BACKGROUND: This study aimed to explore mid-term clinical results of cementless total hip arthroplasty (THA) with modified trochanteric osteotomy in Crowe type IV developmental dysplasia of the hip (DDH). METHODS: Thirteen patients (13 hips) with Crowe type IV DDH who underwent THA with modified trochanteric osteotomy between May 2013 and October 2015 were retrospectively analyzed. The mean follow-up duration was 5.2 years (range, 4.9-6.1 years). RESULTS: The mean Harris Hip Score (HHS) significantly (p < 0.05) improved from 30.7 (range, 22-38) to 87.5 (range, 83-93). The mean leg length discrepancy (LLD) was 53.4 mm (range, 42.1-68.5 mm) preoperatively. The final LLD was 5.6 mm (range, 2.4-9.1 mm; p < 0.05). The mean leg length after surgery was 47.4 mm (range, 33.6-67.2 mm) and the femur shortening distance was 43.8 mm (range, 31.2-53.4 mm). The average duration of bone union for the greater trochanter (GT) was 2.5 months (range, 1.5-3.6 months). There was no infection, GT non-union, or loosening (septic or aseptic) of the stem or cup in any case. CONCLUSIONS: THA with modified trochanteric osteotomy with a cementless cup is an effective treatment for Crowe type IV DDH. It can rebuild complex biomechanics and biology of hip dysplasia without increasing complications.

Comparison of Preoperative Bone Density in Patients With and Without Periprosthetic Osteolysis Following Total Ankle Arthroplasty.

BACKGROUND: Modern total ankle arthroplasty (TAA) prostheses are uncemented press-fit designs whose stability is dependent on bone ingrowth. Preoperative insufficient bone density reduces initial local stability at the bone-implant interface, and we hypothesized that this may play a role in periprosthetic osteolysis. We aimed to investigate the preoperative bone density of the distal tibia and talus and compare these in patients with and without osteolysis. METHODS: We enrolled 209 patients (218 ankles) who underwent primary TAA using the HINTEGRA prosthesis. The overall mean follow-up duration was 66 (range, 24-161) months. The patients were allocated into 2 groups according to the presence of periprosthetic osteolysis: the osteolysis group (64 patients, 65 ankles) and nonosteolysis group (145 patients, 153 ankles). Between the 2 groups, we investigated and compared the radiographic outcomes, including the Hounsfield unit (HU) value around the ankle joint and the coronal plane alignment. RESULTS: HU values of the tibia and talus measured at 5 mm from the reference points were higher than those at 10 mm in each group. However, comparing the osteolysis and nonosteolysis groups, we found no significant intergroup difference in HU value at every measured level in the tibia and talus (P > .05). Concerning the coronal plane alignment, there were no significant between-group differences in the tibiotalar and talar tilt angles (P > .05). CONCLUSION: Patients with osteolysis showed similar preoperative bone density of the distal tibia and talus compared with patients without osteolysis. Our results suggest that low bone density around the ankle joint may not be associated with increased development of osteolysis. LEVEL OF EVIDENCE: Level III, retrospective cohort study.

Bone marrow aspirate concentration provided better results in cartilage regeneration to microfracture in knee of osteoarthritic patients.

PURPOSE: To determine whether microfracture with bone marrow aspirate concentrate (BMAC) improves functional outcome and cartilage regeneration better than microfracture alone in patients undergoing high tibial osteotomy (HTO) for medial unicompartmental osteoarthritis (OA). METHODS: Among 436 patients treated with HTO for medial unicompartmental OA with varus deformity between 2010 and 2016, clinical outcomes were retrospectively compared between the microfracture alone group (group I, 43 cases) and microfracture with BMAC augmentation group (group II, 48 cases). Of these, 64 patients underwent a second-look arthroscopic assessment. Clinical outcomes were compared based on the Knee Society Score (KSS), International Knee Documentation Committee (IKDC) subjective score, and Western Ontario and McMaster Universities Arthritis Index (WOMAC). Cartilage regeneration was assessed according to Koshino's staging system and the International Cartilage Repair Society (ICRS) Cartilage Repair Assessment (CRA) grading system. RESULTS: At the last follow-up, there were no significant intergroup differences in terms of KSS for pain and function (p > 0.05). Moreover, WOMAC scores were similar between the two groups (p > 0.05). Regarding second-look arthroscopy findings, according to Koshino's staging system, there was no significant intergroup difference in terms of defect coverage (p = 0.187). However, group II showed a significantly better mean CRA score than group I (p = 0.035). CONCLUSION: There were no significant differences in clinical outcomes and cartilage regeneration between the groups. However, the CRA score was significantly higher with BMAC augmentation and microfracture than microfracture alone. Therefore, BMAC augmentation had a synergistic effect for a better cartilage regeneration, although studies with a longer follow-up might help to confirm whether microfracture with BMAC augmentation would ensure better clinical outcomes than microfracture alone for the treatment of knee OA.

The results of screw augmentation of acetabular cement spacers for the treatment of periprosthetic hip joint infection.

INTRODUCTION: Prosthesis of antibiotic-loaded acrylic cement (PROSTALAC) is widely used in two-stage revision arthroplasty in periprosthetic joint infection (PJI) after total hip arthroplasty (THA). In our institution, we encountered several cases of acetabular cement spacer dislodgement. The aim of this study was to compare the results of two-stage revision arthroplasties with antibiotic-loaded cement spacers with or without screws on the acetabulum for PJI. PATIENTS AND METHODS: This retrospective study included 44 patients who underwent a two-stage revision THA for PJI from June 2007 to May 2017. We divided the patients into two groups: group 1 consisted of 21 patients (21 hips) who underwent two-stage revision arthroplasty with screw augmentation, while group 2 consisted of 23 patients (23 hips) who underwent the same surgery without screw augmentation at the acetabular cement spacer. We compared the migration and dislodgement of the acetabular cement spacer between the two groups. RESULTS: Before the second-stage surgery, there was less vertical migration of the cement spacer in group 1 compared to group 2 (1.2 mm vs 3.1 mm, p < 0.001). There was also less medial migration of the cement spacer in group 1 (0.6 mm vs 1.6 mm, p = 0.001). After the first stage, the mean Harris Hip score was significantly higher in group 1 than in group 2 (75 vs 65, p = 0.033). Cement spacer rotation or total movement out of the acetabular area occurred in six patients, all in group 2. After first stage reinfection occurred in two patients, one in each group. CONCLUSIONS: Screw augmentation to the acetabulum in the first-stage surgery provides better stability of acetabular antibiotic cement spacers without increasing reinfection rate.

Correction: Molecular subtypes of oropharyngeal cancer show distinct immune microenvironment related with immune checkpoint blockade response.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Molecular subtypes of oropharyngeal cancer show distinct immune microenvironment related with immune checkpoint blockade response.

BACKGROUND: Oropharyngeal cancer (OPC) exhibits diverse immunological properties; however, their implications for immunotherapy are unknown. METHODS: We analysed 37 surgically resected and nine recurrent or metastatic anti-programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1)-treated OPC tumours. OPCs were classified into immune-rich (IR), mesenchymal (MS) and xenobiotic (XB) subtypes based on RNA-sequencing data. RESULTS: All IR type tumours were human papillomavirus (HPV) positive, most XB types were HPV negative, and MS types showed mixed HPV status. The IR type showed an enriched T cell exhaustion signature with PD-1+ CD8+ T cells and type I macrophages infiltrating the tumour nest on multiplex immunohistochemistry. The MS type showed an exclusion of CD8+ T cells from the tumour nest and high MS and tumour growth factor-ß signatures. The XB type showed scant CD8+ T cell infiltration and focal CD73 expression. The IR type was associated with a favourable response signature during anti-PD-1/PD-L1 therapy and showed a high APOBEC mutation signature, whereas the MS and XB types showed resistance signature upregulation. Among anti-PD-1/PD-L1-treated OPC patients, the IR type showed a favourable clinical response (3/4 patients), whereas the XB type showed early progression (3/3 patients). CONCLUSION: Our analysis classified OPCs into three subtypes with distinct immune microenvironments that are potentially related to the response to anti-PD-1/PD-L1 therapy.

ShinyGO: a graphical gene-set enrichment tool for animals and plants.

MOTIVATION: Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene lists with underlying molecular pathways and functional categories such as gene ontology (GO) and other databases. RESULTS: To complement existing tools, we developed ShinyGO based on a large annotation database derived from Ensembl and STRING-db for 59 plant, 256 animal, 115 archeal and 1678 bacterial species. ShinyGO's novel features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for the retrieval of pathway diagrams and protein-protein interaction networks. ShinyGO is an intuitive, graphical web application that can help researchers gain actionable insights from gene-sets. AVAILABILITY AND IMPLEMENTATION: http://ge-lab.org/go/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Patient-Derived Cells to Guide Targeted Therapy for Advanced Lung Adenocarcinoma.

Adequate preclinical model and model establishment procedure are required to accelerate translational research in lung cancer. We streamlined a protocol for establishing patient-derived cells (PDC) and identified effective targeted therapies and novel resistance mechanisms using PDCs. We generated 23 PDCs from 96 malignant effusions of 77 patients with advanced lung adenocarcinoma. Clinical and experimental factors were reviewed to identify determinants for PDC establishment. PDCs were characterized by driver mutations and in vitro sensitivity to targeted therapies. Seven PDCs were analyzed by whole-exome sequencing. PDCs were established at a success rate of 24.0%. Utilizing cytological diagnosis and tumor colony formation can improve the success rate upto 48.8%. In vitro response to a tyrosine kinase inhibitor (TKI) in PDC reflected patient treatment response and contributed to identifying effective therapies. Combination of dabrafenib and trametinib was potent against a rare BRAF K601E mutation. Afatinib was the most potent EGFR-TKI against uncommon EGFR mutations including L861Q, G719C/S768I, and D770_N771insG. Aurora kinase A (AURKA) was identified as a novel resistance mechanism to olmutinib, a mutant-selective, third-generation EGFR-TKI, and inhibition of AURKA overcame the resistance. We presented an efficient protocol for establishing PDCs. PDCs empowered precision medicine with promising translational values.

SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance.

We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing single-guide RNA-encoding and target sequence pairs. Deep learning-based training on this large dataset of SpCas9-induced indel frequencies led to the development of a SpCas9 activity-predicting model named DeepSpCas9. When tested against independently generated datasets (our own and those published by other groups), DeepSpCas9 showed high generalization performance. DeepSpCas9 is available at http://deepcrispr.info/DeepSpCas9.

Molecular characterization of lung adenocarcinoma from Korean patients using next generation sequencing.

The treatment of Lung adenocarcinoma (LUAD) could benefit from the incorporation of precision medicine. This study was to identify cancer-related genetic alterations by next generation sequencing (NGS) in resected LUAD samples from Korean patients and to determine their associations with clinical features. A total of 201 tumors and their matched peripheral blood samples were analyzed using targeted sequencing via the Illumina HiSeq 2500 platform of 242 genes with a median depth of coverage greater than 500X. One hundred ninety-two tumors were amenable to data analysis. EGFR was the most frequently mutated gene, occurring in 106 (55%) patients, followed by TP53 (n = 67, 35%) and KRAS (n = 11, 6%). EGFR mutations were strongly increased in patients that were female and never-smokers. Smokers had a significantly higher tumor mutational burden (TMB) than never-smokers (average 4.84 non-synonymous mutations/megabase [mt/Mb] vs. 2.84 mt/Mb, p = 0.019). Somatic mutations of APC, CTNNB1, and AMER1 in the WNT signaling pathway were highly associated with shortened disease-free survival (DFS) compared to others (median DFS of 89 vs. 27 months, p = 0.018). Patients with low TMB, annotated as less than 2 mt/Mb, had longer DFS than those with high TMB (p = 0.041). A higher frequency of EGFR mutations and a lower of KRAS mutations were observed in Korean LUAD patients. Profiles of 242 genes mapped in this study were compared with whole exome sequencing genetic profiles generated in The Cancer Genome Atlas Lung Adenocarcinoma. NGS-based diagnostics can provide clinically relevant information such as mutations or TMB from readily available formalin-fixed paraffin-embedded tissue.

Indoor radon exposure increases tumor mutation burden in never-smoker patients with lung adenocarcinoma.

OBJECTIVES: Radon, a natural radiation, is the leading environmental cause of lung cancer in never-smokers. However, the radon exposure impact on the mutational landscape and tumor mutation burden (TMB) of lung cancer in never-smokers has not been explored. The aim of this study was to investigate the mutational landscape of lung adenocarcinoma in never-smokers who were exposed to various degrees of residential radon. MATERIALS AND METHODS: To investigate the effect of indoor radon exposure, we estimated the cumulative exposure to indoor radon in each house of patients with lung cancer with a never-smoking history. Patients with at least 2 year-duration of residence before the diagnosis of lung adenocarcinoma were included. Patients were subgrouped based on the median radon exposure level (48 Bq/m3): radon-high vs. radon-low and targeted sequencing of tumor and matched blood were performed in all patients. RESULTS: Among 41 patients with lung adenocarcinoma, the TMB was significantly higher in the radon-high group than it was in the radon-low group (mean 4.94 vs. 2.6 mutations/Mb, P = 0.01). The recurrence rates between radon-high and radon-low group did not differ significantly. Mutational signatures of radon-high tumors showed features associated with inactivity of the base excision repair and DNA replication machineries. The analysis of tumor evolutionary trajectories also suggested a series of mutagenesis induced by radon exposure. In addition, radon-high tumors revealed a significant protein-protein interaction of genes involved in DNA damage and repair (P < 0.001). CONCLUSIONS: Indoor radon exposure increased the TMB in never-smoker patients with lung adenocarcinoma and their mutational signature was associated with defective DNA mismatch repair.

Comprehensive analysis of the characteristics and treatment outcomes of patients with non-small cell lung cancer treated with anti-PD-1 therapy in real-world practice.

PURPOSE: Immune checkpoint inhibitors (ICI) have shown marked responses in patients with non-small cell lung cancer (NSCLC) in clinical trials. However, because such trials comprise cohorts selected based on specific criteria, it is unclear if their results represent routine clinical practice. METHODS: We examined 155 patients with advanced NSCLC who were administered either nivolumab or pembrolizumab at Yonsei Cancer Center, Korea between March 2014 and January 2019. Patient characteristics, EGFR/ALK mutation status, metastatic locations, response to ICIs, and adverse events were retrospectively analyzed. RESULTS: The median age was 64 years and 72.9% of patients were male; former or current smokers constituted 67.1% of the subjects. Adenocarcinoma was predominant (67.7%), and 50.3% of the patients underwent ≥ 2 previous treatments. Twenty-three patients (14.8%) were EGFR mutation- or ALK rearrangement-positive. The objective response rate (ORR) was 23.9% [95% confidence interval (CI) 17.4-31.4%]; the median progression-free survival (PFS) and overall survival (OS) were 3.06 (95% CI 1.893-4.21) and 10.25 (95% CI 5.39-15.11) months, respectively. Multivariate analysis identified ECOG performance status, EGFR mutation/ALK rearrangement status, liver metastasis and PD-L1 proportion as independent predictors of OS. Furthermore, 61.9% of the patients had adverse events of any grade; 38.1% had immune-related adverse events that were associated with PFS and OS on multivariate analysis. CONCLUSIONS: The real-world ORR, PFS, OS, and adverse event profiles were comparable to previous clinical trials despite the patients' different baseline characteristics. Our findings can aid in establishing effective immunotherapeutic management of NSCLC in routine clinical practice.

Investigating the Feasibility of Targeted Next-Generation Sequencing to Guide the Treatment of Head and Neck Squamous Cell Carcinoma.

PURPOSE: Head and neck squamous cell carcinoma (HNSCC) is a deadly disease in which precision medicine needs to be incorporated. We aimed to implement next-generation sequencing (NGS) in determining actionable targets to guide appropriate molecular targeted therapy in HNSCC patients. MATERIALS AND METHODS: Ninety-three tumors and matched blood samples underwent targeted sequencing of 244 genes using the Illumina HiSeq 2500 platform with an average depth of coverage of greater than 1,000×. Clinicopathological data from patients were obtained from 17 centers in Korea, and were analyzed in correlation with NGS data. RESULTS: Ninety-two of the 93 tumors were amenable to data analysis. TP53 was the most common mutation, occurring in 47 (51%) patients, followed by CDKN2A (n=23, 25%), CCND1 (n=22, 24%), and PIK3CA (n=19, 21%). The total mutational burden was similar between human papillomavirus (HPV)-negative vs. positive tumors, although TP53, CDKN2A and CCND1 gene alterations occurred more frequently in HPV-negative tumors. HPV-positive tumors were significantly associated with immune signature-related genes compared to HPV-negative tumors. Mutations of NOTCH1 (p=0.027), CDKN2A (p < 0.001), and TP53 (p=0.038) were significantly associated with poorer overall survival. FAT1 mutations were highly enriched in cisplatin responders, and potentially targetable alterations such as PIK3CA E545K and CDKN2A R58X were noted in 14 patients (15%). CONCLUSION: We found several targetable genetic alterations, and our findings suggest that implementation of precision medicine in HNSCC is feasible. The predictive value of each targetable alteration should be assessed in a future umbrella trial using matched molecular targeted agents.

Exercise-Induced Intrapulmonary Arteriovenous Shunt in a Patient Complaining of Dyspnea during Strenuous Exercise.

A 51-year-old highly fit man presented for dyspnea with strenuous aerobic exercise. The patient was asymptomatic and all tests were normal at rest. With increasing exercise intensity, he suddenly complained of dyspnea and showed a severe exercise-induced hypoxemia with an excessive alveolar-arterial oxygen tension difference. In agitated saline contrast echocardiography at peak exercise, a large amount of left to right shunt was identified after > 5 cardiac cycles, which suggests the presence of exercise-induced intrapulmonary arteriovenous shunt in this patient.