Because of the complexity of cancer‐immune system interactions, combinations of biomarkers will be required for predicting individual patient responses to treatment and for monitoring combination ...strategies to overcome treatment resistance. To this end, the “immunogram” has been proposed as a comprehensive framework to capture all relevant immunological variables. Here, we developed a method to convert transcriptomic data into immunogram scores (IGS). This immunogram includes 10 molecular profiles, consisting of innate immunity, priming and activation, T cell response, interferon γ (IFNG) response, inhibitory molecules, regulatory T cells, myeloid‐derived suppressor cells (MDSCs), recognition of tumor cells, proliferation, and glycolysis. Using genes related to these 10 parameters, we applied single‐sample gene set enrichment analysis (ssGSEA) to 9417 bulk RNA‐Seq data from 9362 cancer patients with 29 different solid cancers in The Cancer Genome Atlas (TCGA). Enrichment scores were z‐score normalized (Z) for each cancer type or the entire TCGA cohort. The IGS was defined by the formula IGS = 3 + 1.5 × Z so that patients would be well distributed over a range of scores from 1 to 5. The immunograms constructed in this way for all individual patients in the entire TCGA cohort can be accessed at “The RNA‐Seq based Cancer Immunogram Web” (https://yamashige33.shinyapps.io/immunogram/).
We propose a novel scoring and visualization method for “immunogram” to assess the cancer immunity status of individual patients using the large TCGA dataset and RNA‐Seq of each patient. Immunograms for each individual will be a useful tool for precision immuno‐oncology, although their application needs to be validated in clinical trials.
Understanding the tumor microenvironment (TME) and anti-tumor immune responses in gastric cancer are required for precision immune-oncology. Taking advantage of next-generation sequencing technology, ...the feasibility and reliability of transcriptome-based TME analysis were investigated. TME of 30 surgically resected gastric cancer tissues was analyzed by RNA-Seq, immunohistochemistry (IHC) and flow cytometry (FCM). RNA-Seq of bulk gastric cancer tissues was computationally analyzed to evaluate TME. Computationally analyzed immune cell composition was validated by comparison with cell densities established by IHC and FCM from the same tumor tissue. Immune cell infiltration and cellular function were also validated with IHC and FCM. Cell proliferation and cell death in the tumor as assessed by RNA-Seq and IHC were compared. Computational tools and gene set analysis for quantifying CD8
T cells, regulatory T cells and B cells, T cell infiltration and functional status, and cell proliferation and cell death status yielded an excellent correlation with IHC and FCM data. Using these validated transcriptome-based analyses, the immunological status of gastric cancer could be classified into immune-rich and immune-poor subtypes. Transcriptome-based TME analysis is feasible and is valuable for further understanding the immunological status of gastric cancer.
Background. The epidemiology of human herpesvirus 6 (HHV-6) encephalitis after allogeneic hematopoietic cell transplantation (HCT) and its relationship with HHV-6 reactivation have not been ...sufficiently characterized. Methods. This prospective, multicenter study of 230 allogeneic HCT recipients investigated the epidemiology of HHV-6 reactivation and HHV-6 encephalitis. Plasma HHV-6 DNA load was prospectively evaluated twice weekly until 70 days after HCT. Results. Cumulative incidence of positive HHV-6 DNA and high-level HHV-6 reactivation (plasma HHV-6 DNA ≥10 4 copies/mL) at day 70 after HCT was 72.2% and 37.0%, respectively. Multivariate analysis identified myeloablative conditioning (hazard ratio HR, 1.9; P = .004), umbilical cord blood transplantation (UCBT) (HR, 2.0; P = .003), and male sex (HR, 1.6; P = .04) as risk factors for displaying high-level HHV-6 reactivation. HHV-6 encephalitis occurred in 7 patients, and cumulative incidence at day 70 was 3.0%. None of the144 patients without high-level HHV-6 reactivation and 7 of 86 patients (8.1%) with high-level HHV-6 reactivation developed HHV-6 encephalitis (P = .0009). Prevalence of HHV-6 encephalitis was significantly higher among patients receiving UCBT than in patients with other sources (cumulative incidence at day 70, 7.9% vs 1.2%, P = .008). In each of 7 patients with HHV-6 encephalitis, central nervous system (CNS) symptoms developed concomitant with peak plasma HHV-6 DNA (range, 21 656–433 639 copies/mL). Conclusions. High levels of plasma HHV-6 DNA are associated with higher risk of HHV-6 encephalitis. UCBT is a significant risk factor for HHV-6 encephalitis. HHV-6 encephalitis should be considered if CNS dysfunction develops concomitant to high-level plasma HHV-6 DNA after allogeneic HCT.
Acute myelogenous leukemia (AML) is the most common adult leukemia, characterized by the clonal expansion of immature myeloblasts initiating from rare leukemic stem (LS) cells. To understand the ...functional properties of human LS cells, we developed a primary human AML xenotransplantation model using newborn nonobese diabetic/severe combined immunodeficient/interleukin (NOD/SCID/IL)2rγnull mice carrying a complete null mutation of the cytokine γc upon the SCID background. Using this model, we demonstrated that LS cells exclusively recapitulate AML and retain self-renewal capacity in vivo. They home to and engraft within the osteoblast-rich area of the bone marrow, where AML cells are protected from chemotherapy-induced apoptosis. Quiescence of human LS cells may be a mechanism underlying resistance to cell cycle-dependent cytotoxic therapy. Global transcriptional profiling identified LS cell-specific transcripts that are stable through serial transplantation. These results indicate the potential utility of this AML xenograft model in the development of novel therapeutic strategies targeted at LS cells.
a-Axis-oriented undoped n-BaSi2 epitaxial films were grown on Si(111) substrates by molecular beam epitaxy, and the crystalline quality and grain boundaries were investigated by means of reflection ...high-energy electron diffraction, X-ray diffraction, and transmission electron microscopy (TEM). The grain size of the BaSi2 films was estimated to be approximately 0.1–0.3μm, and straight grain boundaries (GBs) were observed in the plan-view TEM images. Dark-field TEM images under a two-beam diffraction condition showed that these GBs consist mostly of BaSi2 {011} planes. The diffusion length of minority carriers in n-BaSi2 was found to be approximately 10μm by an electron-beam-induced current technique.
► Undoped n-type BaSi2 layers were grown epitaxially on Si(111). ► Grain size of the BaSi2 was found to be 0.1–0.3μm. ► Grain boundaries were found to consist of {011} plane of BaSi2. ► Diffusion length of minority carriers in the n-BaSi2 was estimated to be about 10μm.
Although splenomegaly is one of the important signs of primary myelofibrosis, the differential diagnosis varies from malignant disorders to benign disorders, including malignant lymphoma and ...sarcoidosis. The patient was a 67-year-old male who developed anemia and huge splenomegaly. The laboratory findings include human T-cell leukemia virus type 1 (HTLV-1) antibody, elevated soluble interleukin-2 receptor, hypocellular bone marrow, and uptake in the spleen on positron emission tomography/computed tomography scan. Additionally, we performed laparoscopic splenectomy to alleviate the clinical symptoms and to rule out malignant lymphoma. Histological findings revealed extramedullary hematopoiesis, characterized by the presence of erythroid islands and clusters of dysplastic megakaryocytes with increased reticulin fibrosis. Immunohistochemical staining revealed the presence of von Willebrand factor, dysplastic megakaryocytes, myeloperoxidase, myeloid-predominant proliferations, and CD34 immature myeloid cells. Furthermore, regarding the angiogenesis in the spleen, the endothelial cells of the capillaries and those of the sinusoidal vascular system that were reactive for CD34 and CD8, respectively, were also detected. Consequently, the histological findings revealed both extramedullary hematopoiesis and angiogenesis in spleen. Based on the histological findings and the identification of Janus activating kinase 2 (JAK-2) mutation, the patient was diagnosed with primary myelofibrosis. Splenectomy reduces blood transfusion requirements after surgery. The patient was carefully followed-up without further treatments. Thus, primary myelofibrosis is the crucial differential diagnosis of huge splenomegaly.
We investigated the tumor immune response in gastric cancer patients receiving third-line nivolumab monotherapy to identify immune-related biomarkers for better patient selection. Nineteen patients ...(10 males, median age 67 years) who received nivolumab as a third- or later-line therapy were enrolled. We analyzed the tumor immune response in durable clinical benefit (DCB) and non-DCB patients. Pre-treatment and early-on-treatment tumor transcriptomes were examined, and gene expression profiles, immunograms, and T cell receptor (TCR) repertoire were analyzed. DCB was observed in 15.8% of patients, with comparable secondary endpoints (ORR; objective response rate, OS; overall survival, PFS; progression-free survival) to previous trials. The immunograms of individual subjects displayed no significant changes before or early in the treatment, except for the regulatory T cell (Treg) score. Moreover, there were no consistent alterations observed among cases experiencing DCB. The intratumoral immune response was suppressed by previous treatments in most third- or later-line nivolumab recipients. TCR repertoire analysis revealed newly emerged clonotypes in early-on-treatment tumors, but clonal replacement did not impact efficacy. High T cell/Treg ratios and a low UV-radiation-response gene signature were linked to DCB and treatment response. This study emphasizes the tumor immune response's importance in nivolumab efficacy for gastric cancer. High T cell/Treg ratios and specific gene expression signatures show promise as potential biomarkers for treatment response. The tumor-infiltrating immune response was compromised by prior treatments in third-line therapy, implying that, to enhance immunotherapeutic outcomes, commencing treatment at an earlier stage might be preferable. Larger cohort validation is crucial to optimize immune-checkpoint inhibitors in gastric cancer treatment.
Cancer histological images contain rich biological and clinical information, but quantitative representation can be problematic and has prevented the direct comparison and accumulation of large-scale ...datasets. Here, we show successful universal encoding of cancer histology by deep texture representations (DTRs) produced by a bilinear convolutional neural network. DTR-based, unsupervised histological profiling, which captures the morphological diversity, is applied to cancer biopsies and reveals relationships between histologic characteristics and the response to immune checkpoint inhibitors (ICIs). Content-based image retrieval based on DTRs enables the quick retrieval of histologically similar images using The Cancer Genome Atlas (TCGA) dataset. Furthermore, via comprehensive comparisons with driver and clinically actionable gene mutations, we successfully predict 309 combinations of genomic features and cancer types from hematoxylin-and-eosin-stained images. With its mounting capabilities on accessible devices, such as smartphones, universal encoding for cancer histology has a strong impact on global equalization for cancer diagnosis and therapies.
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•DTR is a universal encoder for cancer histology using a deep neural network•DTR enables quick and accurate retrieval of histologically similar images•DTR enables genomic feature prediction from histology images in various cancer types•DTR-based image retrieval system is publicly accessible from PC and smartphone
Komura et al. develop a method to encode cancer histology using a deep neural network. The utility of the method is validated in three clinically useful applications: unsupervised analysis of cancer morphology to detect histological subtypes, retrieving histologically similar images among large datasets, and predicting genomic features from histology images
An attempt was made to grow BaSi2 epitaxial films on Si(001) substrates using molecular beam epitaxy. The structure and morphology of the films were investigated using reflection high-energy electron ...diffraction, X-ray diffraction, electron backscatter diffraction, atomic force microscopy, and transmission electron microscopy. The BaSi2 film grown was a-axis oriented, despite a large lattice mismatch. The measurements indicated that there are two possible epitaxial relationships of BaSi2(100)//Si(001) with BaSi2010//Si110 and BaSi2001//Si110, due to the fourfold symmetry of Si(001). X-ray reciprocal space mapping revealed that the BaSi2 film was almost strain-free. Plan-view transmission electron microscopy clarified the grain size and the existence of grain boundaries in the BaSi2 film.
► BaSi2 layers were grown epitaxially on Si(001), despite the large lattice mismatch. ► a-Axis-oriented BaSi2 layers were grown. ► The grain size of BaSi2 on Si(001) was found to be as large as 1μm. ► The grain size of BaSi2 on Si(001) is much larger than that on Si(111).
Background
Although percutaneous endoscopic gastrostomy (PEG) offers better access to the gastrointestinal system, in patients with previous abdominal surgery, PEG can be unsuccessful. ...Laparoscopically assisted percutaneous endoscopic gastrostomy (LAPEG) is indicated for such patients. However, patients with amyotrophic lateral sclerosis (ALS) may be more susceptible to anesthesia-related complications than other patients, requiring the indications for LAPEG, along with perioperative management, to be considered carefully.
Case presentation
A 70-year-old, male patient with ALS was referred to our hospital for a gastrostomy for progressive dysphagia. He had undergone an open distal gastrectomy for gastric ulcer perforation in his twenties. Upper gastrointestinal endoscopy denied the transillumination sign and focal finger invagination. Because the risk of respiratory complications caused by general anesthesia was not considered serious, the decision was made to perform a LAPEG. Under careful, intraoperative airway management and neuromuscular monitoring, adhesiolysis was performed to increase mobility of the remnant stomach. A gastrostomy tube was inserted through the abdominal wall and into the remnant stomach under laparoscopic and endoscopic guidance. The patient was discharged in stable condition on postoperative day 3 without any respiratory complications.
Conclusions
LAPEG was able to be performed in a patient with ALS with a previous gastrectomy. A perioperative team comprised of neurologists, endoscopists, surgeons, anesthesiologists, and nurses who are fully conversant with ALS must be assembled to deal with potentially complex medical issues related to the procedure and anesthetic and perioperative management.
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