Genetically Encoded Epoxide Warhead for Precise and Versatile Covalent Targeting of Proteins.

Genetically encoding a proximal reactive warhead into the protein binder/drug has emerged as an efficient strategy for covalently binding to protein targets, enabling broad applications. To expand the reactivity scope for targeting the diverse natural residues under physiological conditions, the development of a genetically encoded reactive warhead with excellent stability and broad reactivity is highly desired. Herein, we reported the genetic encoding of epoxide-containing tyrosine (EPOY) for developing covalent protein drugs. Our study demonstrates that EPOY, when incorporated into a nanobody (KN035), can cross-link with different side chains (mutations) at the same position of PD-L1 protein. Significantly, a single genetically encoded reactive warhead that is capable of covalent and site-specific targeting to 10 different nucleophilic residues was achieved for the first time. This would largely expand the scope of covalent warhead and inspire the development of covalent warheads for both small-molecule drugs and protein drugs. Furthermore, we incorporate the EPOY into a designed ankyrin repeat protein (DarpinK13) to create the covalent binders of KRAS. This covalent KRAS binder holds the potential to achieve pan-covalent targeting of KRAS based on the structural similarity among all oncogenic KRAS mutants while avoiding off-target binding to NRAS/HRAS through a covalent interaction with KRAS-specific residues (H95 and E107). We envision that covalently targeting to H95 will be a promising strategy for the development of covalent pan-KRAS inhibitors in the future.

Benefits of different combinations of aerobic and resistance exercise for improving plasma glucose and lipid metabolism and sleep quality among elderly patients with metabolic syndrome: a randomized controlled trial.

Exercise has beneficial effects on metabolic syndrome (MS). However, the exercise prescriptions that best support plasma glucose and lipid control remain unknown. We evaluated the effects of different combinations of aerobic and resistance training programs on plasma glucose and lipid metabolism and sleep quality in elderly MS patients. Eighty-five elderly MS patients were randomly assigned to five groups: aerobic training (AT), resistance training (RT), high aerobic with low resistance training (HALRT), high resistance with low aerobic training (HRLAT), or control. The exercise groups performed supervised moderate-intensity exercise during three 50-min sessions per week for 12 weeks. Body mass index (BMI), waist circumference (WC), systolic blood pressure (SBP), diastolic blood pressure (DBP), handgrip strength (HGS), fasting plasma glucose (FPG), 2-hour postprandial blood glucose (2hPG), total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) levels and sleep quality were evaluated at baseline and after 12 weeks. All intervention groups showed significant improvements in SBP, HGS, FPG, 2hPG, and Pittsburgh Sleep Quality Index (PSQI) scores compared to baseline (all p < 0.05), while DBP, TC, TG, and LDL-C levels were significantly improved only in the HRLAT and HALRT groups (p < 0.05). The HALRT group showed the largest improvements in WC, SBP, DBP, HGS, FPG, 2hPG, and PSQI score (p < 0.001). The largest improvements in BMI, TC, and LDL-C were observed in the HRLAT group (p < 0.001). The combined exercise prescriptions were more effective than aerobic or resistance training alone at improving plasma glucose and lipid metabolism and sleep quality in elderly MS patients.

Suppression of BMX-ARHGAP fusion gene inhibits epithelial-mesenchymal transition in gastric cancer cells via RhoA-mediated blockade of JAK/STAT axis.

Gastric cancer (GC) is one of the main causes of cancer-related mortality worldwide. Epithelial-mesenchymal transition (EMT) is an important biological process involving the process by which malignant tumor cells obtain the ability of migration, invasion, resistance of apoptosis, and degradation in the extracellular matrix. The current study aimed at investigating whether bone marrow X kinase Rho GTPase activating protein 12 (BMX-ARHGAP) fusion gene affects GC. First, short hairpin RNA (shRNA) against BMX-ARHGAP or BMX-ARHGAP were introduced to treat SGC-7901 cells with the highest BMX-ARHGAP among the five GC cell lines (SGC-7901, MKN-45, NCI-N87, SNU-5, and AGS). Next, cell vitality, drug resistance, migration, and invasion of SGC-7901 cells, activities of Rho and JAK/STAT axis, as well as EMT and lymph node metastasis (LNM) were evaluated. The survival rate of the mice was then determined through the transfection of the specific pathogen-free NOD-SCID mice with treated SGC-7901 cells. The results showed that BMX-ARHGAP expression was associated with the infiltration degree of GC tumor and poor prognosis for patients with GC. BMX-ARHGAP silencing was found to play an inhibitory role in the Rho and JAK/STAT axis to reduce cell vitality, drug resistance, migration and invasion, reverse EMT process, as well as inhibit LNM. BMX-ARHGAP overexpression was observed to have induced effects on GC cells as opposed to those inhibited by BMX-ARHGAP silencing. The survival rate of mice was increased after transfection with silenced BMX-ARHGAP. These findings provided evidence that the suppression of BMX-ARHGAP resulted in the inhibition of RhoA to restraint the development of GC cells by blocking the JAK/STAT axis.

Stratified aspartate aminotransferase-to-platelet ratio index accurately predicts survival in hepatocellular carcinoma patients undergoing curative liver resection.

The aspartate aminotransferase-to-platelet ratio index has been reported to predict prognosis of patients with hepatocellular carcinoma. This study examined the prognostic potential of stratified aspartate aminotransferase-to-platelet ratio index for hepatocellular carcinoma patients undergoing curative liver resection. A total of 661 hepatocellular carcinoma patients were retrieved and the associations between aspartate aminotransferase-to-platelet ratio index and clinicopathological variables and survivals (overall survival and disease-free survival) were analyzed. Higher aspartate aminotransferase-to-platelet ratio index quartiles were significantly associated with poorer overall survival (p = 0.002) and disease-free survival (p = 0.001). Multivariate analysis showed aspartate aminotransferase-to-platelet ratio index to be an independent risk factor for overall survival (p = 0.018) and disease-free survival (p = 0.01). Patients in the highest aspartate aminotransferase-to-platelet ratio index quartile were at 44% greater risk of death than patients in the first quartile (hazard ratio = 1.445, 95% confidence interval = 1.081 - 1.931, p = 0.013), as well as 49% greater risk of recurrence (hazard ratio = 1.49, 95% confidence interval = 1.112-1.998, p = 0.008). Subgroup analysis also showed aspartate aminotransferase-to-platelet ratio index to be an independent predictor of poor overall survival and disease-free survival in patients positive for hepatitis B surface antigen or with cirrhosis (both p < 0.05). Similar results were obtained when aspartate aminotransferase-to-platelet ratio index was analyzed as a dichotomous variable with cutoff values of 0.25 and 0.62. Elevated preoperative aspartate aminotransferase-to-platelet ratio index may be independently associated with poor overall survival and disease-free survival in hepatocellular carcinoma patients following curative resection.

How diversification of overseas subsidiaries affects parent company innovation performance: evidence from China's multinationals.

This paper examines the diversification of overseas subsidiaries on innovation performance of the parent company. Based on theoretical analysis and a combined Chinese firm dataset from 2000 to 2013, we find that diversification of overseas subsidiaries positively promotes the parent company innovation performance through the spillover effect of innovation capabilities. In addition, we determine that both the overseas and domestic investment layout can positively moderate the main effect. But there are differences between them. In concrete terms, the domestic investment layout plays a substitution effect in developed areas and acts a more pronounced moderating role in state-owned sample. Besides, the overseas investment layout plays a more important substitutive moderating role on non-state-owned enterprises. This research provides a special insight for studying the reverse spillover effect of OFDI in terms of the contribution of subsidiary linkages and offers several recommendations for multinational corporations to enhance the global competitiveness.

Metagenomic next-generation sequencing, instead of procalcitonin, could guide antibiotic usage in patients with febrile acute necrotizing pancreatitis: a multicenter, prospective cohort study.

BACKGROUNDS: The effectiveness of procalcitonin-based algorithms in guiding antibiotic usage for febrile acute necrotizing pancreatitis (ANP) remains controversial. Metagenomic next-generation sequencing (mNGS) has been applied to diagnose infectious diseases. The authors aimed to evaluate the effectiveness of blood mNGS in guiding antibiotic stewardship for febrile ANP. MATERIALS AND METHODS: The prospective multicenter clinical trial was conducted at seven hospitals in China. Blood samples were collected during fever (T ≥38.5°C) from ANP patients. The effectiveness of blood mNGS, procalcitonin, and blood culture in diagnosing pancreatic infection was evaluated and compared. Additionally, the real-world utilization of antibiotics and the potential mNGS-guided antimicrobial strategy in febrile ANP were also analyzed. RESULTS: From May 2023 to October 2023, a total of 78 patients with febrile ANP were enrolled and 30 patients (38.5%) were confirmed infected pancreatic necrosis (IPN). Compared with procalcitonin and blood culture, mNGS showed a significantly higher sensitivity rate (86.7% vs. 56.7% vs. 26.7%, P <0.001). Moreover, mNGS outperformed procalcitonin (89.5 vs. 61.4%, P <0.01) and blood culture (89.5 vs. 69.0%, P <0.01) in terms of negative predictive value. Blood mNGS exhibited the highest accuracy (85.7%) in diagnosing IPN and sterile pancreatic necrosis, significantly superior to both procalcitonin (65.7%) and blood culture (61.4%). In the multivariate analysis, positive blood mNGS (OR=60.2, P <0.001) and lower fibrinogen level (OR=2.0, P <0.05) were identified as independent predictors associated with IPN, whereas procalcitonin was not associated with IPN, but with increased mortality (Odds ratio=11.7, P =0.006). Overall, the rate of correct use of antibiotics in the cohort was only 18.6% (13/70) and would be improved to 81.4% (57/70) if adjusted according to the mNGS results. CONCLUSION: Blood mNGS represents important progress in the early diagnosis of IPN, with particular importance in guiding antibiotic usage for patients with febrile ANP.

A real-time respiration position based passive breath gating equipment for gated radiotherapy: a preclinical evaluation.

PURPOSE: To develop a passive gating system incorporating with the real-time position management (RPM) system for the gated radiotherapy. METHODS: Passive breath gating (PBG) equipment, which consists of a breath-hold valve, a controller mechanism, a mouthpiece kit, and a supporting frame, was designed. A commercial real-time positioning management system was implemented to synchronize the target motion and radiation delivery on a linear accelerator with the patient's breathing cycle. The respiratory related target motion was investigated by using the RPM system for correlating the external markers with the internal target motion while using PBG for passively blocking patient's breathing. Six patients were enrolled in the preclinical feasibility and efficiency study of the PBG system. RESULTS: PBG equipment was designed and fabricated. The PBG can be manually triggered or released to block or unblock patient's breathing. A clinical workflow was outlined to integrate the PBG with the RPM system. After implementing the RPM based PBG system, the breath-hold period can be prolonged to 15-25 s and the treatment delivery efficiency for each field can be improved by 200%-400%. The results from the six patients showed that the diaphragm motion caused by respiration was reduced to less than 3 mm and the position of the diaphragm was reproducible for difference gating periods. CONCLUSIONS: A RPM based PBG system was developed and implemented. With the new gating system, the patient's breath-hold time can be extended and a significant improvement in the treatment delivery efficiency can also be achieved.

Impact of leaf motion constraints on IMAT plan quality, deliver accuracy, and efficiency.

PURPOSE: Intensity modulated arc therapy (IMAT) is a radiation therapy delivery technique that combines the efficiency of arc based delivery with the dose painting capabilities of intensity modulated radiation therapy (IMRT). A key challenge in developing robust inverse planning solutions for IMAT is the need to account for the connectivity of the beam shapes as the gantry rotates from one beam angle to the next. To overcome this challenge, inverse planning solutions typically impose a leaf motion constraint that defines the maximum distance a multileaf collimator (MLC) leaf can travel between adjacent control points. The leaf motion constraint ensures the deliverability of the optimized plan, but it also impacts the plan quality, the delivery accuracy, and the delivery efficiency. In this work, the authors have studied leaf motion constraints in detail and have developed recommendations for optimizing the balance between plan quality and delivery efficiency. METHODS: Two steps were used to generate optimized IMAT treatment plans. The first was the direct machine parameter optimization (DMPO) inverse planning module in the Pinnacle(3) planning system. Then, a home-grown arc sequencer was applied to convert the optimized intensity maps into deliverable IMAT arcs. IMAT leaf motion constraints were imposed using limits of between 1 and 30 mm∕deg. Dose distributions were calculated using the convolution∕superposition algorithm in the Pinnacle(3) planning system. The IMAT plan dose calculation accuracy was examined using a finer sampling calculation and the quality assurance verification. All plans were delivered on an Elekta Synergy with an 80-leaf MLC and were verified using an IBA MatriXX 2D ion chamber array inserted in a MultiCube solid water phantom. RESULTS: The use of a more restrictive leaf motion constraint (less than 1-2 mm∕deg) results in inferior plan quality. A less restrictive leaf motion constraint (greater than 5 mm∕deg) results in improved plan quality but can lead to less accurate dose distribution as evidenced by increasing discrepancies between the planned and the delivered doses. For example, the results from our patient-specific quality assurance measurements demonstrated that the average gamma analysis passing rate decreased from 98% to 80% when the allowable leaf motion increased from 3 to 20 mm∕deg. Larger leaf motion constraints also led to longer treatment delivery times (2 to 4 folds) due to the additional MLC leaf motion. CONCLUSIONS: Leaf motion constraints significantly impact IMAT plans in terms of plan quality, delivery accuracy, and delivery efficiency with the impact magnified for more complex cases. Our studies indicate that a leaf motion constraint of 2 to 3 mm∕deg of gantry rotation can provide an optimal balance between plan quality, delivery accuracy, and efficiency.

Comparison of Elekta VMAT with helical tomotherapy and fixed field IMRT: plan quality, delivery efficiency and accuracy.

PURPOSE: Helical tomotherapy (HT) and volumetric modulated arc therapy (VMAT) are arc-based approaches to IMRT delivery. The objective of this study is to compare VMAT to both HT and fixed field IMRT in terms of plan quality, delivery efficiency, and accuracy. METHODS: Eighteen cases including six prostate, six head-and-neck, and six lung cases were selected for this study. IMRT plans were developed using direct machine parameter optimization in the Pinnacle3 treatment planning system. HT plans were developed using a Hi-Art II planning station. VMAT plans were generated using both the Pinnacle3 SmartArc IMRT module and a home-grown arc sequencing algorithm. VMAT and HT plans were delivered using Elekta's PreciseBeam VMAT linac control system (Elekta AB, Stockholm, Sweden) and a TomoTherapy Hi-Art II system (TomoTherapy Inc., Madison, WI), respectively. Treatment plan quality assurance (QA) for VMAT was performed using the IBA MatriXX system while an ion chamber and films were used for HT plan QA. RESULTS: The results demonstrate that both VMAT and HT are capable of providing more uniform target doses and improved normal tissue sparing as compared with fixed field IMRT. In terms of delivery efficiency, VMAT plan deliveries on average took 2.2 min for prostate and lung cases and 4.6 min for head-and-neck cases. These values increased to 4.7 and 7.0 min for HT plans. CONCLUSIONS: Both VMAT and HT plans can be delivered accurately based on their own QA standards. Overall, VMAT was able to provide approximately a 40% reduction in treatment time while maintaining comparable plan quality to that of HT.

MiR-122-5p inhibits cell migration and invasion in gastric cancer by down-regulating DUSP4.

OBJECTIVE: To explore the relationship between miR-122-5p and DUSP4 and their effects on gastric cancer (GC) cell mobility and invasiveness. METHODS: Abnormally expressed miRNAs and mRNAs were analyzed using microarrays. The miR-122-5p and DUSP4 mRNA expression levels in GC tissues and cells were determined by RT-qPCR. The target relationship between miR-122-5p and DUSP4 was validated by dual luciferase reporter assay. GC cell mobility and invasiveness were respectively observed by wound healing assay and transwell invasion assay. Western blot and immunohistochemistry were used for detection of the expressions of DUSP4 protein and MMP2 and MMP9 proteins related to cell invasion and migration. The migration and invasion abilities of gastric cancer cells in vivo were evaluated according to the number of lung metastatic nodules in mice. RESULTS: The expression of miR-122-5p in GC tissues and cells was significantly down-regulated, whereas DUSP4 expression was up-regulated. Bioinformatics prediction strategies and dual luciferase reporter assay verified the binding sites of miR-122-5p on 3'UTR of DUSP4 and the target relationship between miR-122-5p and DUSP4. Overexpression of miR-122-5p and knockdown of DUSP4 in BGC-823 cells observantly suppressed GC cell mobility and invasiveness, whereas downregulation of miR-122-5p expression promoted cell metastasis. MiR-122-5p inhibited GC cell mobility and invasiveness and pulmonary tumor metastasis via downregulation of DUSP4. CONCLUSION: MiR-122-5p restrained migration and invasion abilities of GC cells by repressing DUSP4.

H2AFY is a novel fusion partner of MECOM in acute myeloid leukemia.

The MECOM gene encoding a zinc finger protein that functions as a transcription factor, was located on chromosome 3q26, and rearrangements of MECOM often cause its overexpression in acute myeloid leukemia (AML). We identified H2AFY as a novel fusion gene partner of MECOM in an elderly male AML patient with cryptic 3q26 rearrangement using the whole transcriptome sequencing, who carried out abnormal karyotype of 46,XY,t(3;5)(q27;q31),add(14)(p11). We validated the existence of the unreported H2AFY-MECOM fusion gene by RT-PCR and Sanger DNA sequencing, and detected mutations of NRAS and BCOR in this patient. In addition, we found abnormally elevated expression of MECOM in this patient by quantitative-polymerase chain reaction (RQ-PCR). Further research is needed to investigate functional characterizations of this novel fusion in the development of AML.

Downregulated stromal antigen 2 expression in de novo acute myeloid leukemia patients.

The stromal antigen 2 (STAG2) gene encodes a component of the cohesin complex that participates in the regulation of sister chromatid separation during mitosis. When activated, STAG2 may act as a 'caretaker' tumor suppressor gene. As it is unknown whether STAG2 gene is responsible for the occurrence and associated with the prognosis of acute myeloid leukemia (AML), the present study analyzed the relative expression levels of STAG2 in 127 de novo AML patients and 17 healthy volunteers using reverse transcription-quantitative polymerase chain reaction. In addition, AML patients were divided into three risk groups using cytogenetic and molecular genetic abnormalities to define their risk status. STAG2 gene expression was found to be significantly downregulated in de novo AML patients, when compared with the healthy controls; however, the expression was not significantly different in the various gender and age subgroups. Furthermore, no significant difference between risk groups was detected in AML patients. Thus, the STAG2 gene may serve an important role in AML development, but is not associated with prognosis in AML.

Passive breath gating equipment for cone beam CT-guided RapidArc gastric cancer treatments.

BACKGROUND AND PURPOSE: To report preliminary results of passive breath gating (PBG) equipment for cone-beam CT image-guided gated RapidArc gastric cancer treatments. MATERIAL AND METHODS: Home-developed PBG equipment integrated with the real-time position management system (RPM) for passive patient breath hold was used in CT simulation, online partial breath hold (PBH) CBCT acquisition, and breath-hold gating (BHG) RapidArc delivery. The treatment was discontinuously delivered with beam on during BH and beam off for free breathing (FB). Pretreatment verification PBH CBCT was obtained with the PBG-RPM system. Additionally, the reproducibility of the gating accuracy was evaluated. RESULTS: A total of 375 fractions of breath-hold gating RapidArc treatments were successfully delivered and 233 PBH CBCTs were available for analysis. The PBH CBCT images were acquired with 2-3 breath holds and 1-2 FB breaks. The imaging time was the same for PBH CBCT and conventional FB CBCT (60s). Compared to FB CBCT, the motion artifacts seen in PBH CBCT images were remarkably reduced. The average BHG RapidArc delivery time was 103 s for one 270-degree arc and 269 s for two full arcs. CONCLUSIONS: The PBG-RPM based PBH CBCT verification and BHG RapidArc delivery was successfully implemented clinically. The BHG RapidArc treatment was accomplished using a conventional RapidArc machine with high delivery efficiency.

Characterization of rectal normal tissue complication probability after high-dose external beam radiotherapy for prostate cancer.

PURPOSE: Conformal radiotherapy (RT) has allowed radiation dose escalation to improve the outcome of prostate cancer. With higher doses, concern exists that rectal injury may increase. This study analyzed the utility and limitations of the widely used Lyman-Kutcher- Burman (LKB) normal tissue complication probability model in projecting the hazards of rectal complication with high-dose RT. METHODS AND MATERIALS: A total of 128 patients were included in this study. These patients were treated with three-dimensional conformal RT alone at the University of Texas M.D. Anderson Cancer Center between 1992 and 1999. Patients were treated to 46 Gy with a four-field box technique followed by a six-field arrangement to boost the total dose to 78 Gy. All doses were delivered at 2 Gy/fraction to the isocenter. The minimal follow-up was 2 years. The end point for analysis was Grade 2 or worse rectal bleeding by 2 years. The LKB model was fitted to the data using the maximal likelihood method. RESULTS: Of the 128 patients, 29 experienced Grade 2 or worse rectal bleeding by 2 years. For the entire cohort, the parameters obtained from the fit of the LKB model were as follows: the volume factor was n = 3.91 (95% confidence interval [CI] 0.031 to infinity ), dose associated with 50% chance of complication for uniform whole rectal irradiation [TD50(1)] was 53.6 Gy (95% CI 50.0-75.1), and a determinant of the steepness of the dose-response curve, (m), was 0.156 (95% CI 0.036-0.271). A statistically significant difference was found in the rate of postradiation rectal bleeding in patients with hemorrhoids vs. those without hemorrhoids. The parameters obtained for the patients without hemorrhoids were as follows: n = 0.746 (95% CI 0.026 to infinity ), TD50(1) 56.7 Gy (95% CI 49.9-75.2), and m 0.092 (95% CI 0.019-0.189). CONCLUSION: Our analysis suggests a dose response for rectal bleeding probability along with a volume effect. We found that the LKB model might have limited utility in determining a large volume effect. We further suggest that LKB model should be used with caution in clinical practice.

Near simultaneous computed tomography image-guided stereotactic spinal radiotherapy: an emerging paradigm for achieving true stereotaxy.

PURPOSE: To report treatment setup data from an emerging technique using near-simultaneous computed tomography (CT) image-guided stereotactic radiotherapy for the treatment of spinal and paraspinal tumors. METHODS AND MATERIALS: A targeting system that integrates a CT-on-rails scanner with a linear accelerator (LINAC) was evaluated in the lead-in portion of a Phase I/II protocol for treating patients with paraspinal metastases. Patients were immobilized in supine position by a moldable body cushion vacuum wrapped with a plastic fixation sheet. Planning CT and immediately repeated CT were performed on the LINAC/CT-on-rails unit to assess respiratory-related vertebral body motion. Coplanar intensity-modulated radiotherapy (IMRT) using 7-9 beams was used to deliver 30 Gy in five fractions to the target volume, while limiting the spinal cord dose to <10 Gy. Pretreatment CT scans were fused with the planning CT scans to determine the correct target isocenter by accounting for any translational and roll (axial) rotational discrepancies from the planning CT. (Corrections caused by yaw and pitch rotations have not yet been implemented.) The reproducibility of the treatment isocenter as compared with the planned isocenter was measured with digitally reconstructed radiographs (DRRs), portal film imaging, and immediate post-treatment verification CT scans. Phantom measurements were taken for dose verification for each IMRT plan. RESULTS: Based on a total of 36 CT scans (3 for planning, 3 for respiration study, 15 pretreatment, and 15 post-treatment) from 3 patients, no respiration-associated vertebral body motion was seen. A comparison of the corrected daily anterior-posterior (AP) and lateral (LAT) digital portal images with the planning AP and LAT DRRs confirmed that the isocenter setup accuracy for the 15 treatments was within 1 mm of the planning isocenter. The results from the immediate post-treatment CT scans reconfirmed the findings from the portal images and verified the absence of spinal movement during the treatment. The ion-chamber measurement for the high-dose region was within 2% of the planning dose for three patient treatment plans. Film dose measurement in an IMRT quality assurance phantom demonstrated good agreement from 90% to 30% isodose lines between the planned and measured results. CONCLUSION: Preliminary experience suggests that the near-simultaneous CT image-guided verification technique can be used as a new platform technology for extracranial applications of stereotactic radiotherapy and radiosurgery to spinal and paraspinal tumors.

Identification of a novel gene fusion (BMX-ARHGAP) in gastric cardia adenocarcinoma.

BACKGROUND: Gastric cardia adenocarcinoma (GCA) is one of the major causes of cancer related mortality worldwide. We aim to provide new understanding in the pathogenesis of GCA through investigations on gene expression alterations. METHODS: We preformed RNA-Seq for one pair of GCA and matched non-tumor tissues. Differentially expressed genes (DEGs) and fusion genes were acquired. PCR and gel analysis in additional 14 pairs of samples were performed to validate the chimeric transcripts. RESULTS: 1590 up-regulated and 709 down-regulated genes were detected. Functional analysis revealed that these DEGs were significantly overrepresented in gene ontology items of cell cycle, tumor invasion and proliferation. Moreover, we firstly discovered 3 fusion genes in GCA, including BMX-ARHGAP, LRP5- LITAF and CBX3-C15orf57. The chimeric transcript BMX-ARHGAP was validated and recurrently occurred in 4/15 independent tumor tissues. CONCLUSIONS: Our results may provide new understanding of GCA and biomarkers for further therapeutic studies. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_218.

Incorporating breath holding and image guidance in the adjuvant gastric cancer radiotherapy: a dosimetric study.

BACKGROUND: The respiratory related target motion and setup error will lead to a large margin in the gastric radiotherapy. The purpose of this study is to investigate the dosimetric benefit and the possibility of incorporating the breath-hold (BH) technique with online image-guided radiotherapy in the adjuvant gastric cancer radiotherapy. METHODS: Setup errors and target motions of 22 post-operative gastric cancer patients with surgical clips were analyzed. Clips movement was recorded using the digital fluoroscopics and the probability distribution functions (pdf) of the target motions were created for both the free breathing (FB) and BH treatment. For dosimetric comparisons, two intensity-modulated radiotherapy (IMRT) treatment plans, i.e. the free breathing treatment plan (IMRT(FB)) and the image-guided BH treatment plan (IMRT(IGBH)) using the same beam parameters were performed among 6 randomly selected patients. Different margins for FB and BH plans were derived. The plan dose map was convoluted with various pdfs of the setup errors and the target motions. Target coverage and dose to organs at risk were compared and the dose-escalation probability was assessed. RESULTS: The mean setup errors were 1.2 mm in the superior-inferior (SI), 0.0 mm in the left-right (LR), and 1.4 mm in the anterior-posterior (AP) directions. The mean target motion for the free breathing (vs. BH) was 11.1 mm (vs. 2.2 mm), 1.9 mm (vs. 1.1 mm), and 5.5 mm (vs. 1.7 mm) in the SI, LR, and AP direction, respectively. The target coverage was comparable for all the original plans. IMRT(IGBH) showed lower dose to the liver compared with IMRT(FB) (p = 0.01) but no significant difference in the kidneys. Convolved IMRTIGBH showed better sparing in kidneys (p < 0.01) and similar in liver (p = 0.08). CONCLUSIONS: Combining BH technique with online image guided IMRT can minimize the organ motion and improve the setup accuracy. The dosimetric comparison showed the dose could be escalated to 54 Gy without increasing the critical organs toxicities, although further clinical data is needed.

Dosimetric impact of breathing motion in lung stereotactic body radiotherapy treatment using intensity modulated radiotherapy and volumetric modulated arc therapy [corrected].

PURPOSE: The objective of this study was to investigate the influence of tumor motion on dose delivery in stereotactic body radiotherapy (SBRT) for lung cancer, using fixed field intensity- modulated radiotherapy (IMRT) and volumetric modulated arc therapy (VMAT). METHODS AND MATERIALS: For each of 10 patients with stage I/II non-small-cell pulmonary tumors, a respiration-correlated four-dimensional computed tomography (4DCT) study was carried out. The internal target volume was delineated on the maximum intensity projection CT, which was reconstructed from the 4DCT dataset. A 5-mm margin was used for generation of the planning target volume. VMAT and five-field IMRT plans were generated using Pinnacle(3) SmartArc and direct machine parameter optimization, respectively. All plans were generated for an Elekta Synergy linear accelerator using 6-MV photons. Simulation was performed to study the interplay between multileaf collimator (MLC) sequences and target movement during the delivery of VMAT and IMRT. For each plan, 4D dose was calculated using deformable image registration of the 4DCT images. Target volume coverage and doses to critical structures calculated using 4D methodology were compared with those calculated using 3D methodology. RESULTS: For all patients included in this study, the interplay effect was found to present limited impact (less than 1% of prescription) on the target dose distribution, especially for SBRT, in which fewer fractions (three fractions) are delivered. Dose to the gross tumor volume (GTV) was, on average, slightly decreased (1% of prescription) in the 4D calculation compared with the 3D calculation. The motion impact on target dose homogeneity was patient-dependent and relatively small. CONCLUSIONS: Both VMAT and IMRT plans experienced negligible interplay effects between MLC sequence and tumor motion. For the most part, the 3D doses to the GTV and critical structures provided good approximations of the 4D dose calculations.

Use of kilovoltage X-ray volume imaging in patient dose calculation for head-and-neck and partial brain radiation therapy.

BACKGROUND: To evaluate the accuracy of using kilovoltage x-ray cone-beam computed tomography (kV-CBCT) imaging for in vivo dose calculations. METHODS: A Region-of-Interest (ROI) CT number mapping method was developed to generate the cone-beam CT number vs. relative electron density calibration curve for 3D dose calculations. The stability of the results was validated for three consecutive months. The method was evaluated on three brain tumors and three head-and-neck tumor cases. For each patient, kV-CBCT images were acquired on the first treatment day and two-week intervals on the Elekta XVI system. The delivered dose distributions were calculated by applying the patients' treatment plans to the kV-CBCT images. The resulting dose distributions and dose volume histograms (DVHs) of the tumor and critical structures were compared to the original treatment plan. RESULTS: The kV-CBCT electron density calibration was stable within 1.5% over a three-month period. The DVH and dose distribution comparison based on the planning CT and the initial kV-CBCT showed good agreements for majority of cases. The doses calculated from the planning CT and kV-CBCT were compared on planes perpendicular to the beam axes and passing through the isocenter. Using gamma analysis with a criterion of 2 mm/2% and a threshold of 10%, more than 99.5% of the points on the iso-planes exhibited gamma <1. For one patient, kV-CBCT images detected 5.8% dose variation in the right parotid due to tumor shrinkage and patient weight loss. CONCLUSIONS: ROI mapping method is an effective method for the creation of kV-CBCT electron density calibration curves for head-and-neck and brain tumor patients. Dose variations as monitored using kV-CBCT imaging suggest that some patients can benefit from adaptive treatment plan re-optimization.

Comparison of anatomy-based, fluence-based and aperture-based treatment planning approaches for VMAT.

Volumetric modulated arc therapy (VMAT) has the potential to reduce treatment times while producing comparable or improved dose distributions relative to fixed-field intensity-modulated radiation therapy. In order to take full advantage of the VMAT delivery technique, one must select a robust inverse planning tool. The purpose of this study was to evaluate the effectiveness and efficiency of VMAT planning techniques of three categories: anatomy-based, fluence-based and aperture-based inverse planning. We have compared these techniques in terms of the plan quality, planning efficiency and delivery efficiency. Fourteen patients were selected for this study including six head-and-neck (HN) cases, and two cases each of prostate, pancreas, lung and partial brain. For each case, three VMAT plans were created. The first VMAT plan was generated based on the anatomical geometry. In the Elekta ERGO++ treatment planning system (TPS), segments were generated based on the beam's eye view (BEV) of the target and the organs at risk. The segment shapes were then exported to Pinnacle TPS followed by segment weight optimization and final dose calculation. The second VMAT plan was generated by converting optimized fluence maps (calculated by the Pinnacle TPS) into deliverable arcs using an in-house arc sequencer. The third VMAT plan was generated using the Pinnacle SmartArc IMRT module which is an aperture-based optimization method. All VMAT plans were delivered using an Elekta Synergy linear accelerator and the plan comparisons were made in terms of plan quality and delivery efficiency. The results show that for cases of little or modest complexity such as prostate, pancreas, lung and brain, the anatomy-based approach provides similar target coverage and critical structure sparing, but less conformal dose distributions as compared to the other two approaches. For more complex HN cases, the anatomy-based approach is not able to provide clinically acceptable VMAT plans while highly conformal dose distributions were obtained using both aperture-based and fluence-based inverse planning techniques. The aperture-based approach provides improved dose conformity than the fluence-based technique in complex cases.