Evaluation of a New Method for CyberKnife Treatment for Central Lung and Mediastinal Tumors by Tracheobronchial Tracking.

BACKGROUND: CyberKnife treatment for central lung tumors and mediastinal tumors can be difficult to perform with marker less. PURPOSE: We aimed to evaluate a novel tracheobronchial-based method (ie, tracheobronchial tracking) for the purpose of minimally invasive CyberKnife treatment for central lung and mediastinal tumors. METHODS: Five verification plans were created using an in-house phantom. Each plan included five irradiation sessions. The reference plan irradiated and tracked the simulated tumor (using the target tracking volume, TTV). Trachea plans tracked the simulated tracheo-bronchus and irradiated the simulated tumor and included two types of subplans: correlated plans in which the displacement of the simulated tracheobronchial and the simulated tumor were correlated, and non-correlated plans in which these factors were not correlated. Moreover, 15 mm and 25 mm TTVs were evaluated for each plan. The sin waveform and the patient's respiratory waveform were prepared as the respiratory model. Evaluations were performed by calculating the dose difference between the radiophotoluminescent glass dosimeter (RPLD)-generated mean dose values (generated by the treatment planning system, TPS) and the actual absorbed RPLD dose. Statistical analyses were performed to evaluate findings for each plan. Correlation and prediction errors were calculated for each axis of each plan using log files to evaluate tracking accuracy. RESULTS: Dose differences were statistically significant only in comparisons with the non-correlated plan. When evaluated using the sin waveform, the mean values for correlation and prediction errors in each axis and for all plans were less than 0.6 mm and 0.1 mm, respectively. In the same manner, they were less than 1.1 mm and 0.2 mm when evaluated using the patient's respiratory waveform. CONCLUSION: Our newly-developed tracheobronchial tracking method would be useful in facilitating minimally invasive CyberKnife treatment in certain cases of central lung and mediastinal tumors.

Cycle-generative adversarial network-based bone suppression imaging for highly accurate markerless motion tracking of lung tumors for cyberknife irradiation therapy.

PURPOSE: Lung tumor tracking during stereotactic radiotherapy with the CyberKnife can misrecognize tumor location under conditions where similar patterns exist in the search area. This study aimed to develop a technique for bone signal suppression during kV-x-ray imaging. METHODS: Paired CT images were created with or without bony structures using a 4D extended cardiac-torso phantom (XCAT phantom) in 56 cases. Subsequently, 3020 2D x-ray images were generated. Images with bone were input into cycle-consistent adversarial network (CycleGAN) and the bone suppressed images on the XCAT phantom (BSIphantom ) were created. They were then compared to images without bone using the structural similarity index measure (SSIM) and peak signal-to-noise ratio (PSNR). Next, 1000 non-simulated treatment images from real cases were input into the training model, and bone-suppressed images of the patient (BSIpatient ) were created. Zero means normalized cross correlation (ZNCC) by template matching between each of the actual treatment images and BSIpatient were calculated. RESULTS: BSIphantom values were compared to their paired images without bone of the XCAT phantom test data; SSIM and PSNR were 0.90 ± 0.06 and 24.54 ± 4.48, respectively. It was visually confirmed that only bone was selectively suppressed without significantly affecting tumor visualization. The ZNCC values of the actual treatment images and BSIpatient were 0.763 ± 0.136 and 0.773 ± 0.143, respectively. The BSIpatient showed improved recognition accuracy over the actual treatment images. CONCLUSIONS: The proposed bone suppression imaging technique based on CycleGAN improves image recognition, making it possible to achieve highly accurate motion tracking irradiation.

Rapid and high throughput assessment of cellular immunity against SARS-CoV-2 based on the ex vivo activation of genes in leukocyte assay with whole blood.

During the novel coronavirus outbreak and vaccine development, antibody production garnered major focus as the primary immunogenic response. However, cellular immunity's recent demonstration of comparable or greater significance in controlling infection demands the re-evaluation of the importance of T-cell immunity in SARS-CoV-2 infection. Here, we developed a novel assay, the ex vivo activation of genes in leukocytes (EAGL), which employs short-term whole blood stimulation with the LeukoComplete™ system, to measure ex vivo SARS-CoV-2-specific T cell responses (cellular immunity). This assay measures upregulated mRNA expression related to leukocyte activation 4 h after antigen stimulation. LeukoComplete™ system uses whole blood samples, eliminating the need for pretreatment before analysis. Furthermore, this system's high reproducibility is ensured through a series of operations from mRNA extraction to cDNA synthesis on a 96-well plate. In the performance evaluation using fresh blood from previously SARS-CoV-2-infected and COVID-19-vaccinated individuals, the EAGL assay had a comparable sensitivity and specificity to the ELISpot assay (EAGL: 1.000/1.000; ELISpot: 0.900/0.973). As a simple, high-throughput assay, the EAGL assay is also a quantitative test that is useful in studies with large sample numbers, such as monitoring new vaccine efficacies against novel coronaviruses or epidemiologic studies that require cellular immune testing during viral infection.

Relationship between microorganisms and volatile components in each fermentation process in the kusaya gravy that plays an important role in the manufacturing of kusaya, a traditional Japanese fermented fish product.

The relationship between the microbiota and volatile components of kusaya gravy involved in the manufacturing of kusaya, a traditional Japanese fermented fish product, in the Izu Islands (Niijima and Hachijojima) and the fermentation processes are not clear. In this study, we aimed to investigate the relationship between the microbiota and volatile compounds involved in the manufacturing and management of kusaya gravy. 16S ribosomal RNA (rRNA) gene-based amplicon sequencing revealed that the microbiota in kusaya gravy was significantly different between the two islands, and the microbiota hardly changed during each fermentation process. Gas chromatography-mass spectrometry analysis also revealed that the volatile components were strongly related to the microbiota in kusaya gravy, with Hachijojima samples containing sulfur-containing compounds and Niijima samples containing short-chain fatty acids. Therefore, our findings suggest that kusaya gravy is a characteristic fermented gravy with a stable microbiota, and the fermented pickling gravy is fermented by microorganisms.

Evaluation of computed tomography metal artifact and CyberKnife fiducial recognition for novel size fiducial markers.

PURPOSE: This study aimed to compare fiducial markers used in CyberKnife treatment in terms of metal artifact intensity observed in CT images and fiducial recognition in the CyberKnife system affected by patient body thickness and type of marker. METHODS: Five markers, ACCULOC 0.9 mm × 3 mm, Ball type Gold Anchor (GA) 0.28 mm × 10 mm, 0.28 mm × 20 mm, and novel size GA 0.4 mm × 10 mm, 0.4 mm × 20 mm were evaluated. To evaluate metal artifacts of CT images, two types of CT images of water-equivalent gels with each marker were acquired using Aquilion LB CT scanner, one applied SEMAR (SEMAR-on) and the other did not apply this technique (SEMAR-off). The evaluation metric of artifact intensity (MSD ) which represents a variation of CT values were compared for each marker. Next, 5, 15, and 20 cm thickness of Tough Water (TW) was placed on the gel under the condition of overlapping the vertebral phantom in the Target Locating System, and the live image of each marker was acquired to compare fiducial recognition. RESULTS: The mean MSD of SEMAR-off was 78.80, 74.50, 97.25, 83.29, and 149.64 HU for ACCULOC, GA0.28 mm × 10 mm, 20 mm, and 0.40 mm × 10 mm, 20 mm, respectively. In the same manner, that of SEMAR-on was 23.52, 20.26, 26.76, 24.89, and 33.96 HU, respectively. Fiducial recognition decreased in the order of 5, 15, and 20 cm thickness, and GA 0.4 × 20 mm showed the best recognition at thickness of 20 cm TW. CONCLUSIONS: We demonstrated the potential to reduce metal artifacts in the CT image to the same level for all the markers we evaluated by applying SEMAR. Additionally, the fiducial recognition of each marker may vary depending on the thickness of the patient's body. Particularly, we showed that GA 0.40 × 20 mm may have more optimal recognition for CyberKnife treatment in cases of high bodily thickness in comparison to the other markers.

Common clinicopathological and immunological features of sarcomatoid carcinoma across organs: A histomorphology-based cross-organ study.

Sarcomatoid carcinoma (SC), which can occur in any organ, is a rare disease. To elucidate common characteristics of SC beyond organs, we evaluated clinicopathological and immunological features of SC defined by the single histological criterion beyond organs compared to randomly matched conventional carcinoma (non-SC) adjusted for the disease stage. Immunological features were assessed by multiplex immunohistochemistry, comparing immune cell density in tumor tissues and tumor programmed death-ligand 1 (PD-L1) expression. A total of 101 patients with SC or non-SC (31 lung, 19 esophagus, 22 pancreas, 15 liver, 4 bile duct, 6 kidney, 2 uterus and 2 ovary) were identified among 7197 patients who underwent surgery at our institute (1997-2020). SC was significantly associated with worse survival (HR: 1.571; 95% CI: 1.084-2.277; P = .017). The frequency of postoperative progression within 6 months was significantly higher for SC patients (54% vs 28%; P = .002). The immune profiling revealed the densities of CD8+ T cells (130 vs 72 cells/mm2 ; P = .004) and tumor-associated macrophages (566 vs 413 cells/mm2 ; P < .0001) and the tumor PD-L1 expression score (40% vs 5%; P < .0001) were significantly higher in SCs than in non-SCs. Among 73 SC patients with postoperative progression, multivariate Cox regression analysis showed that immunotherapy tended to be associated with favorable survival (HR: 0.256; 95% CI: 0.062-1.057; P = .060). Collectively, SCs shared clinicopathological and immunological features across organs. Our study can initiate to standardize the pathological definition of SC and provide a rationale for the investigation and development for this rare disease in a cross-organ manner.

BioQuant: Data Processing Software for Simultaneous Imaging Analysis for Elements and Molecules Using Two Mass Spectrometers.

Simultaneous imaging analysis for both elements and molecules was conducted by introducing laser-induced sample particles into two separate mass spectrometers (i.e., an inorganic spectrometer and an organic mass spectrometer) through the split-flow protocol. The timing of ion detections for elements and molecules can be different, reflecting the differences in mass scan rates, lengths for transport tubing, and flow rates of carrier gases, and thus, the timing of ion detections must be carefully aligned to discuss abundance correlations between elements and molecules. To achieve this, a new data processing software "BioQuant" was developed to correct the time difference of the signal intensities for components obtained by the two mass spectrometers. With the BioQuant software, signal intensity data obtained from several unit cells were merged into a newly defined unit cell, calculated by the common time intervals from both mass spectrometers. With the newly defined unit cells, correlation analysis between the elements and molecules can be conducted. Combination of the BioQuant software and laser ablation system connected to two separated mass spectrometers can become a benchmark technique for simultaneous imaging analysis for both the elements and molecules from single sample material.

Application of the relative molar sensitivity method using GC-FID to quantify safranal in saffron (Crocus sativus L.).

Safranal is one flavor component of saffron, which is used as a spice, food additive, and crude drug. In ISO3632, safranal is defined as the compound that contributes to the quality of saffron, and many quantitative determination methods for safranal have been reported. However, safranal is volatile and degrades easily during storage, and an analytical standard with an exact known purity is not commercially available, making it difficult to quantify accurately the content of safranal in saffron. Here, we developed a method for quantifying safranal using relative molar sensitivity (RMS), called the RMS method, using a GC-flame ionization detector (GC-FID). We determined the RMS of safranal to 1,4-bis(trimethylsilyl)benzene-d4, a certified reference material commercially available, by a combination of quantitative NMR and chromatography. Using two GC-FID instruments made by different manufacturers to evaluate inter-instrument effect, the resultant RMS was 0.770, and the inter-instrument difference was 0.6%. The test solution, with a known safranal concentration, was measured by the RMS method, with an accuracy of 99.4-101%, repeatability of 0.81%, and reproducibility of 0.81-1.3%. Given the ease of degradation, high volatility, and uncertain purity of safranal reagents, the RMS method is a more accurate quantification approach compared to the calibration curve method and methods based on absorption spectrophotometry. Moreover, our findings revealed that the GC-FID makeup gas affected the RMS and quantitative values.

Relationships between physical and immunological tumor microenvironment in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is physically palpated as a hard tumor with an unfavorable prognosis. Assessing physical features and their association with pathological features could help to elucidate the mechanism of physical abnormalities in cancer tissues. A total of 93 patients who underwent radical surgery for pancreatic and bile duct cancers at a single center hospital during a 28-month period were recruited for this study that aimed to estimate the stiffness of PDAC tissues compared to the other neoplasms and assess relationships between tumor stiffness and pathological features. Physical alterations and pathological features of PDAC, with or without preoperative therapy, were analyzed. The immunological tumor microenvironment was evaluated using multiplexed fluorescent immunohistochemistry. The stiffness of PDAC correlated with the ratio of Azan-Mallory staining, α-smooth muscle actin, and collagen I-positive areas of the tumors. Densities of CD8+ T cells and CD204+ macrophages were associated with tumor stiffness in cases without preoperative therapy. Pancreatic ductal adenocarcinoma treated with preoperative therapy was softer than that without, and the association between tumor stiffness and immune cell infiltration was not shown after preoperative therapy. We observed the relationship between tumor stiffness and immunological features in human PDAC for the first time. Immune cell densities in the tumor center were smaller in hard tumors than in soft tumors without preoperative therapies. Preoperative therapy could alter physical and immunological aspects, warranting further study. Understanding of the correlations between physical and immunological aspects could lead to the development of new therapies.

Development of a dynamic motion platform with two independent drive systems for radiotherapy.

BACKGROUND: There are some motion platforms for radiotherapy quality assurance. However, no platform with two drive systems that can move along three axes is available. PURPOSE: The purpose of this study is to develop a dynamic motion platform with two drive systems capable of three-axis motion and to evaluate its motion performance. METHODS: The developed moving platform had two drive systems that use the same equipment. Each axis of the platform used can support a maximum load of 10 kg. The motors for moving the platform in each direction are capable of a drive stroke up to 40 mm. The drive speed is 30 mm/s at maximum load fluctuation. To evaluate the static positional accuracy of this system with an arbitrary input movement, the XYZ position of each axis was measured using a coordinate measuring machine operating from 0 to 40 mm at 10 mm intervals. In addition, the accuracy of dynamic motion was verified with Sine waveform inputs of different patterns to the three axes for approximately 60 s, and they were compared with the resulting detected signals by SyncTrax. RESULTS: The two drive systems were successfully operated on three axes by using independent control systems. For static position, the accuracies were within 0.2 mm, 0.05 mm, and 0.14 mm for lateral, longitudinal, and vertical directions, respectively. For dynamic motion, the mean absolute errors in the X, Y, and Z axes between the platform inputs and SyncTrax detected signals were 0.14 ± 0.10 mm, 0.16 ± 0.12 mm, and 0.16 ± 0.11 mm, respectively. CONCLUSIONS: A new dynamic platform for radiation therapy with two drive systems capable of three-axis motion was developed, and the positional accuracy of the drive axes was confirmed to be less than 0.2 mm.

Changes in blood pressure and arterial stiffness monitored using the cardio-ankle vascular index during hemodialysis.

During hemodialysis (HD), blood pressure (BP) changes are frequently observed. However, the mechanism of BP changes during HD has not been fully clarified. The cardio-ankle vascular index (CAVI) reflects the arterial stiffness of the arterial tree from the origin of the aorta to the ankle independent from BP during measurement. Additionally, CAVI reflects functional stiffness in addition to structural stiffness. We aimed to clarify the role of CAVI in regulating the BP system during HD. We included 10 patients undergoing 4-hour HD (total 57 HD sessions). Changes in the CAVI and various hemodynamic parameters were evaluated during each session. During HD, BP decreased and CAVI significantly increased (CAVI, median [interquartile range]; 9.1 [8.4-9.8] [0 min] to 9.6 [9.2-10.2] [240 min], p < 0.05). Changes in CAVI from 0 min to 240 min were significantly correlated with water removal rate (WRR) (r = -0.42, p = 0.002). Changes in CAVI at each measurement point were negatively correlated with ΔBP (Δsystolic BPeach MP, r = -0.23, p < 0.0001; Δdiastolic BPeach MP, r = -0.12, p = 0.029). Whereas one patient exhibited a simultaneous decrease in BP and CAVI during the initial 60 min of HD. Arterial stiffness monitored with CAVI generally increased during HD. CAVI elevation is associated with decreased WWR and BP. An increase in CAVI during HD may reflect the contraction of smooth muscle cells and play an important role in BP maintenance. Hence, measuring CAVI during HD may distinguish the cause of BP changes.

An online internal standard technique for high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS).

An online internal standard correction technique for high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS) was designed using an autosampler system equipped with HPLC to improve the analytical precision. The autosampler was programed to operate in the following sequence: it first takes up a portion of sample solution, rinses the nozzle, sucks air as a spacer, takes an internal standard solution and finally injects all of them into a sampling loop through an injection valve. The repeatability of the sampling (amount 20 µL) was improved from 2.5 to 1.2% using the online internal standard technique. This technique was applied to As speciation in food samples, since food safety monitoring requires high precision and high sample throughput. Rhenium was very suitable as an internal standard element due to its retention time, peak shape and water solubility. This technique effectively improved the analytical precision of the As speciation and got rid of the operation of adding an internal standard solution into samples.

Characterization of the surugamide biosynthetic gene cluster of TUA-NKU25, a Streptomyces diastaticus strain isolated from Kusaya, and its effects on salt-dependent growth.

Kusaya, a traditional Japanese fermented fish product, is known for its high preservability, as it contains natural antibiotics derived from microorganisms, and therefore molds and yeasts do not colonize it easily. In this study, the Streptomyces diastaticus strain TUA-NKU25 was isolated from Kusaya, and its growth as well as the production of antibiotics were investigated. Strain TUA-NKU25 showed advantageous growth characteristics in the presence, but not in the absence, of sodium chloride (NaCl). Antimicrobial assay, high-performance liquid chromatography, and electrospray ionization-mass spectrometry analysis showed that this strain produced surugamide A and uncharacterized antimicrobial compound(s) during growth in the presence of NaCl, suggesting that the biosynthesis of these compounds was upregulated by NaCl. Draft genomic analysis revealed that strain TUA-NKU25 possesses a surugamide biosynthetic gene cluster (sur BGC), although it is incomplete, lacking surB/surC. Phylogenetic analysis of strain TUA-NKU25 and surugamide-producing Streptomyces showed that sur BGC formed a clade distinct from other known groups.

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses.

Flavor characteristics of ripened cheese are established by various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, which spontaneously develop during the cheese-manufacturing process. We previously revealed the relationship between bacterial microbiota and flavor components in soft-type ripened cheeses by using a multiomics approach that combined metagenomics and metabolomics; however, we could not establish a causal relationship. This study aimed to substantiate the causal nature of the correlations revealed by the multiomics approach by using cheese-ripening tests with single isolate inoculation. The bacterial diversity and composition in surface mold-ripened cheeses from Japan and France varied, depending on the differences between the milks (pasteurized or raw), cheese positions (core or rind), and manufacturers. Although the volatile compounds did not clearly reflect the distinctive characteristics of the cheese samples, nonstarter lactic acid bacteria, Actinobacteria, and Proteobacteria positively correlated with ketones and sulfur compounds, as evidenced by a Spearman's correlation analysis. Cheese-ripening tests conducted after inoculation with single bacterial strains belonging to the above-mentioned taxa confirmed that these bacteria formed volatile compounds, in agreement with the correlations observed. In particular, various flavor compounds, such as acids, esters, ketones, and sulfur compounds, were detected in cheese inoculated with Pseudoalteromonas sp. TS-4-4 strain. These findings provide important insights into the role of nonstarter bacteria in the development of cheese flavor and into the effectiveness of the multiomics approach in screening for bacteria that can improve the quality of cheese products. IMPORTANCE Our previous study revealed that the existence of various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, clearly correlated with the abundance of flavor components, such as volatile compounds, in soft-type ripened cheeses via a multiomics approach that used 16S rRNA gene amplicon sequencing and headspace gas chromatography-mass spectrometry. However, this approach only showed correlations derived from statistical analyses rather than causal relationships. Therefore, in the present study, we performed cheese-ripening tests using nonstarter bacteria to substantiate the correlations revealed by the multiomics approach in soft-type ripened cheese. Our results suggest the capability of nonstarter bacteria, such as Proteobacteria, to impart flavor to cheese and the effectiveness of the multiomics approach in screening for microbial isolates that can improve the quality of cheese. Overall, our research provides new insights into the importance of bacteria in cheese production.

Usefulness of serum BUN or BUN/creatinine ratio as markers for citrin deficiency in positive cases of newborn screening.

Citrin deficiency belongs to a group of urea cycle disorders that can be identified during newborn screening by measuring citrulline, phenylalanine, methionine, and galactose levels. Early diagnosis of citrin deficiency is beneficial as disease-specific interventions such as permission of food preference and/or supplementation of medium-chain triglyceride can prevent metabolic decompensation. However, there are currently no laboratory tests for the diagnosis of citrin deficiency in routine clinical practice. Our retrospective study investigated the diagnostic characteristics of citrin deficiency during infancy at secondary newborn screening. The present study included 10 patients with citrin deficiency and 35 controls without the condition. The positive likelihood ratios for serum levels of blood urea nitrogen (BUN) levels were 6.8 at the first visit, 3.2 at age ≤ 60 days, and 17.5 at age ≤ 100 days. The serum BUN/creatinine ratio also showed a high positive likelihood ratio (3.9 at first visit, 16.0 at age ≤ 60 days, and 24.5 at age ≤ 100 days). Therefore, the serum BUN or BUN/creatinine ratio may help to identify patients with citrin deficiency during newborn screening. Further studies are required to confirm its diagnostic accuracy in a larger cohort and elucidate the underlying mechanisms involved.

Transcriptomic Profiling of MSI-H/dMMR Gastrointestinal Tumors to Identify Determinants of Responsiveness to Anti-PD-1 Therapy.

PURPOSE: Transcriptomic profiling was performed for microsatellite instability-high (MSI-H)/mismatch repair-deficient (dMMR) gastrointestinal tumors to determine the predictors of response to PD-1 blockade. EXPERIMENTAL DESIGN: Thirty-six patients with MSI-H/dMMR gastrointestinal tumors, including gastric cancer, colorectal cancer, cholangiocarcinoma, small intestine cancer, and pancreatic cancer, being treated with PD-1 blockade were analyzed. We conducted the transcriptomic analysis of gastrointestinal tumors using RNA sequencing data, including the consensus molecular subtypes (CMS) of colorectal cancer. RESULTS: Gene set enrichment analysis (GSEA) demonstrated that non-responders had upregulations of epithelial-mesenchymal transition, angiogenesis, hypoxia, mTORC1, TNF-α, KRAS, Wnt/ß-catenin, TGF-ß, and various metabolism-related signaling pathways. Meanwhile, the IFNγ pathway was enriched in responders. On the basis of the leading-edge analysis of GSEA, VEGF-A was significantly correlated with enriched pathways in non-responders. Patients with high VEGF-A expression, compared with those with low expression, had significantly shorter progression-free survival [PFS; median 4.8 months vs. not reached (NR), P = 0.032] and overall survival (median 11.1 months vs. NR, P = 0.045). Among 13 patients with colorectal cancer evaluable for CMS classification, the objective response rate was 100%, 0%, 0%, and 16.7% in CMS1, CMS2, CMS3, and CMS4, respectively. Patients with CMS1 had significantly longer PFS (NR vs. 4.8 months, P = 0.017) than those with CMS2, CMS3, or CMS4. CONCLUSIONS: Several transcriptomic features, including CMS classification and related genes, were associated with response to PD-1 blockade in MSI-H/dMMR gastrointestinal tumors. These findings can help develop predictive biomarkers or combination immunotherapies.

Development of antigen-prediction algorithm for personalized neoantigen vaccine using human leukocyte antigen transgenic mouse.

Immunotherapy is currently recognized as the fourth modality in cancer therapy. CTL can detect cancer cells via complexes involving human leukocyte antigen (HLA) class I molecules and peptides derived from tumor antigens, resulting in antigen-specific cancer rejection. The peptides may be predicted in silico using machine learning-based algorithms. Neopeptides, derived from neoantigens encoded by somatic mutations in cancer cells, are putative immunotherapy targets, as they have high tumor specificity and immunogenicity. Here, we used our pipeline to select 278 neoepitopes with high predictive "SCORE" from the tumor tissues of 46 patients with hepatocellular carcinoma or metastasis of colorectal carcinoma. We validated peptide immunogenicity and specificity by in vivo vaccination with HLA-A2, A24, B35, and B07 transgenic mice using ELISpot assay, in vitro and in vivo killing assays. We statistically evaluated the power of our prediction algorithm and demonstrated the capacity of our pipeline to predict neopeptides (area under the curve = 0.687, P < 0.0001). We also analyzed the potential of long peptides containing the predicted neoepitopes to induce CTLs. Our study indicated that the short peptides predicted using our algorithm may be intrinsically present in tumor cells as cleavage products of long peptides. Thus, we empirically demonstrated that the accuracy and specificity of our prediction tools may be potentially improved in vivo using the HLA transgenic mouse model. Our data will help to design feedback algorithms to improve in silico prediction, potentially allowing researchers to predict peptides for personalized immunotherapy.

Component with abundant immune-related cells in combined hepatocellular cholangiocarcinoma identified by cluster analysis.

Combined hepatocellular cholangiocarcinoma (cHCC-CCA) is a heterogeneous tumor sharing histological features with hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). The tumor immune microenvironment (TIME) of cHCC-CCA is unclear. We compared the TIME of cHCC-CCA with that of HCC and iCCA. Twenty-three patients with cHCC-CCA after hepatectomy were evaluated in this study. Twenty-three patients with iCCA and HCC were also included. iCCA was matched for size, and HCC was matched for size and hepatitis virus infection with cHCC-CCA. Immune-related cells among the iCCA-component of cHCC-CCA (C-com), HCC-component of cHCC-CCA (H-com), iCCA, and HCC were assessed using multiplex fluorescence immunohistochemistry. Among C-com, H-com, iCCA, and HCC, multiple comparisons and cluster analysis with k-nearest neighbor algorithms were performed using immunological variables. Although HCC had more T lymphocytes and lower PD-L1 expression than iCCA (P < 0.05), there were no significant differences in immunological variables between C-com and H-com. C-com tended to have more T lymphocytes than iCCA (P = 0.09), and C-com and H-com had fewer macrophages than HCC (P < 0.05). In cluster analysis, all samples were classified into two clusters: one cluster had more immune-related cells than the other, and 12 of 23 H-com and eight of 23 C-com were identified in this cluster. The TIME of C-com and H-com may be similar, and some immunological features in these components were different from those in HCC and some iCCA. Cluster analysis identified components with abundant immune-related cells in cHCC-iCCA.