Clinical and Diagnostic Utility of Genomic Profiling for Digestive Cancers: Real-World Evidence from Japan.

The usefulness of comprehensive genomic profiling (CGP) in the Japanese healthcare insurance system remains underexplored. Therefore, this large-scale study aimed to determine the usefulness of CGP in diagnosing digestive cancers. Patients with various cancer types recruited between March 2020 and October 2022 underwent the FoundationOne® CDx assay at the Keio PleSSision Group (19 hospitals in Japan). A scoring system was developed to identify potentially actionable genomic alterations of biological significance and actionable genomic alterations. The detection rates for potentially actionable genomic alterations, actionable genomic alterations, and alterations equivalent to companion diagnosis (CDx), as well as the signaling pathways associated with these alterations in each digestive cancer, were analyzed. Among the 1587 patients, 547 had digestive cancer. The detection rates of potentially actionable genomic alterations, actionable genomic alterations, and alterations equivalent to CDx were 99.5%, 62.5%, and 11.5%, respectively. APC, KRAS, and CDKN2A alterations were frequently observed in colorectal, pancreatic, and biliary cancers, respectively. Most digestive cancers, except esophageal cancer, were adenocarcinomas. Thus, the classification flowchart for digestive adenocarcinomas proposed in this study may facilitate precise diagnosis. CGP has clinical and diagnostic utility in digestive cancers.

Clinical utility of the Oncomine Dx Target Test multi-CDx system and the possibility of utilizing those original sequence data.

BACKGROUND: Companion diagnostic tests play a crucial role in guiding treatment decisions for patients with non-small cell lung cancer (NSCLC). The Oncomine Dx Target Test (ODxTT) Multi-CDx System has emerged as a prominent companion diagnostic method. However, its efficacy in detecting driver gene mutations, particularly rare mutations, warrants investigation. AIMS: This study aimed to assess the performance of the ODxTT in detecting driver gene mutations in NSCLC patients. Specifically, we aimed to evaluate its sensitivity in detecting epidermal growth factor receptor (EGFR) mutations, a key determinant of treatment selection in NSCLC. MATERIALS AND METHODS: We conducted a retrospective analysis of NSCLC patients who underwent testing with the ODxTT at Keio University Hospital between May 2020 and March 2022. Patient samples were subjected to both DNA and RNA tests. Driver gene mutation status was assessed, and instances of missed mutations were meticulously examined. RESULTS: Of the 90 patients, five had nucleic acid quality problems, while 85 underwent both DNA and RNA tests. Driver gene mutations were detected in 56/90 (62.2%) patients. Of the 34 patient specimens, driver mutations were not detected using the ODxTT; however, epidermal growth factor receptor (EGFR) mutations were detected using polymerase chain reaction-based testing in two patients, and a KRAS mutation was detected by careful examination of the sequence data obtained using the ODxTT in one patient. For the above three cases, carefully examining the gene sequence information obtained using the ODxTT could identify driver mutations that were not mentioned in the returned test results. Additionally, we confirmed comparable instances of overlook results for EGFR mutations in the dataset from South Korea, implying that this type of oversight could occur in other countries using the ODxTT. EGFR mutation was missed in ODxTT in Japan (6.3%, 2/32), South Korea (2.0%, 1/49), and overall (3.7%, 3/81). CONCLUSION: Even if sufficient tumor samples are obtained, rare EGFR mutations (which are excluded from the ODxTT's genetic mutation list) might not be detected using the current ODxTT system due to the program used for sequence analysis. However, such rare EGFR mutations can still be accurately detected on ODxTT's sequence data using next-generation sequencing.

Germline BRCA2 variant with low variant allele frequency detected in tumor-only comprehensive genomic profiling.

Germline BRCA1/2 variants in comprehensive genomic profiling (CGP) often exhibit variant allele frequency (VAF) exceeding 50%. However, when genomic loss occurs at the ipsilateral allele, including the germline variant in tumor cells, the VAF is low. This case report presents a patient with uterine sarcoma with a pathogenic BRCA2 mutation and low VAF in tumor-only CGP, which was later identified as a germline variant. When genomic alterations in BRCA1/2 are identified in tumor-only CGP, the possible germline origin of the variants should be considered, even if their VAF is very low.

BRCA1/2 reversion mutations in a pan-cancer cohort.

Tumor sensitivity to platinum (Pt)-based chemotherapy and poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors is increased by homologous recombination deficiency-causing mutations; in particular, reversion mutations cause drug resistance by restoring protein function. Treatment response is predicted by breast cancer susceptibility gene 1/2 (BRCA1/2) mutations; however, BRCA1/2 reversion mutations have not been comprehensively studied in pan-cancer cohorts. We aimed to characterize BRCA1/2 reversion mutations in a large pan-cancer cohort of Japanese patients by retrospectively analyzing sequencing data for BRCA1/2 pathogenic/likely pathogenic mutations in 3738 patients with 32 cancer types. We identified somatic mutations in tumors or circulating cell-free DNA that could restore the ORF of adverse alleles, including reversion mutations. We identified 12 (0.32%) patients with somatic BRCA1 (n = 3) and BRCA2 (n = 9) reversion mutations in breast (n = 4), ovarian/fallopian tube/peritoneal (n = 4), pancreatic (n = 2), prostate (n = 1), and gallbladder (n = 1) cancers. We identified 21 reversion events-BRCA1 (n = 3), BRCA2 (n = 18)-including eight pure deletions, one single-nucleotide variant, six multinucleotide variants, and six deletion-insertions. Seven (33.3%) reversion deletions showed a microhomology length greater than 1 bp, suggesting microhomology-mediated end-join repair. Disease course data were obtained for all patients with reversion events: four patients acquired mutations after PARP-inhibitor treatment failure, two showed somatic reversion mutations after disease progression, following Pt-based treatment, five showed mutations after both treatments, one patient with pancreatic cancer and BRCA1 reversion mutations had no history of either treatment. Although reversion mutations commonly occur in BRCA-associated cancers, our findings suggest that reversion mutations due to Pt-chemotherapy might be correlated with BRCA1/2-mediated tumorigenesis even in non-BRCA-associated histologies.

Correlation between choline kinase alpha expression and 11C-choline accumulation in breast cancer using positron emission tomography/computed tomography: a retrospective study.

Choline kinase (CK) is reportedly overexpressed in various malignancies. Among its isoforms, CKα overexpression is presumably related to oncogenic change. Choline positron emission tomography (PET) is reportedly useful for detecting and evaluating therapy outcomes in malignancies. In this study, we investigated the correlation between CKα expression and 11C-choline accumulation in breast cancer cells. We also compared the CKα expression level with other pathological findings for investigating tumour activity. Fifty-six patients with breast cancer (mean age: 51 years) who underwent their first medical examination between May 2007 and December 2008 were enrolled. All the patients underwent 11C-choline PET/computed tomography imaging prior to surgery. The maximum standardised uptake value was recorded for evaluating 11C-choline accumulation. The intensity of CKα expression was classified using immunostaining. A significant correlation was observed between CKα expression and 11C-choline accumulation (P < 0.0001). A comparison of breast cancer mortality demonstrated that strong CKα expression was associated with a shorter survival time (P < 0.0001). 11C-choline accumulation was also negatively correlated with survival time (P < 0.0001). Tumours with strong CKα expression are reportedly highly active in breast cancer. A correlation was observed between CKα expression and 11C-choline accumulation, suggesting their role as prognostic indicators of breast cancer.

Clinical predominance of whole-exome sequencing to evaluate microsatellite instability status.

The microsatellite instability (MSI)/mismatch repair (MMR) status is one of the critical genomic biomarkers for predicting patient response to immune checkpoint inhibitors (ICIs). In this study, we aimed to investigate the concordance among the MSIsensor score obtained from whole-exome sequencing (WES), which could be a futuristic clinical cancer sequencing method, using only tumor tissues, MSI-PCR results, and immunohistochemistry (IHC) results to analyze various solid cancer types. We first endeavored to set the cut-off value of MSIsensor to determine functional deficient mismatch repair (f-dMMR) status. The MSI status of 1054 patients analyzed using WES was evaluated using MSIsensor. In addition, 87 of these patients were further analyzed using MSI-PCR and MMR IHC to calculate the sensitivity and specificity of the MSIsensor cut-off score. Our results showed that score 12.5 was an adequate cut-off score equivalent to PCR-confirmed MSS/MSI-low and MSI-high statuses, with sensitivity, specificity, and area under the curve values of 95.2%, 100%, and 0.998, respectively. Moreover, we identified false-positive cases of tumors with high mutational burden with an MSIsensor score <12.5, and optional IHC examination could rescue these cases. In conclusion, the MSIsensor score obtained using WES with tumor tissue showed a high clinical validity, with a cut-off value of 12.5 for f-dMMR detection, in combination with optional IHC analysis for MMR. Our novel algorithm will provide insights into the development of ICIs for cancer treatment, particularly when WES becomes a more common cancer genomic test in the near future.

Immunohistochemical staining patterns of p53 predict the mutational status of TP53 in oral epithelial dysplasia.

Next-generation sequencing of oral squamous cell carcinoma (OSCC) has revealed TP53 as the most frequently mutated gene in OSCC mutually exclusive with human papillomavirus infection. Oral epithelial dysplasia (OED) is defined as a precancerous lesion of OSCC by the current World Health Organization (WHO) classification; therefore, it is assumed that TP53 mutations occur in early precancerous conditions such as OED. Here, we conducted an integrated analysis of TP53, including whole coding sequencing of TP53, FISH analysis of the 17p13.1 locus, and immunohistochemical analysis for p53 (p53-IHC), in 40 OED cases. We detected 20 mutations in 16 (40%) OED cases, and four cases, each harbored two mutations. FISH analysis revealed six of 24 cases (25%) had a deletion on 17p13.1, and four cases had concurrent TP53 mutations and 17p13.1 deletion (2-hit). Also, the increased frequency of TP53 mutations in higher degrees of OED implies acquisition of the mutation is a major event toward OSCC. p53-IHC revealed that overall cases could be categorized into four patterns that correlate well with the mutational status of TP53. Especially, two patterns, broad p53 expression type (pattern HI) and p53 null type (pattern LS), strongly correlated with a missense mutation and nonsense mutation, respectively. Furthermore, seven of the 40 cases progressed to SCC, and six of these seven cases presented pattern HI or LS. Therefore, patterns HI and LS have a high risk for malignant transformation if excisional treatment is not performed irrespective of the dysplasia grade. Although the current WHO classification mainly focuses on morphological criteria for the diagnosis of OED, interobserver discrepancy appears in some instances of the OED diagnosis. Our immunohistochemical analysis supports a more accurate pathological diagnosis for OED in cases of low dysplastic changes or of differential diagnosis with non-dysplastic lesions.

A Rare Case of Pyogenic Granuloma in the Tooth Extraction Socket.

Pyogenic granuloma (PG) refers to a common, acquired, benign, and vascular tumor that arises in tissues such as the skin and mucous membranes. However, it is extremely rare for PG to arise from an empty socket after tooth extraction. Herein, we describe a rare case of PG that arose from the empty extraction socket of the second molar adjacent to a dentigerous cyst of the left mandibular wisdom tooth in a 57-year-old man. The patient's second molar was extracted during the same procedure in which the wisdom tooth and cyst were removed. Subsequently, at 42 days after surgery, an exophytic mass was found in the socket of the second molar. An excisional biopsy was performed, and the histopathological diagnosis was PG. Since the PG recurred 90 days after the surgery, a complete excision with bone curettage was performed. During the 12 months of follow-up, there has been no recurrence observed. In conclusion, as tooth extraction is a routine dental practice, clinicians should be aware that PGs can also develop from an extraction socket.

Thoracic spine hemangioma causing rapidly progressive myelopathy and mimicking a malignant tumor: A case report.

Vertebral hemangiomas are common benign tumors that are mostly asymptomatic and are discovered incidentally. Only 0.9-1.2% of all vertebral hemangiomas, termed aggressive vertebral hemangiomas, expand to cause pain and neural compression. We present an extremely rare case of a 49-year-old woman who had an aggressive vertebral hemangioma of the thoracic spine that caused rapidly progressive myelopathy with remarkable irregular extraosseous bone proliferation, which mimicked a malignant vertebral tumor. In this case, despite the lesion's hostile appearance during imaging, the pathological diagnosis was benign and symptom-based surgical treatment with posterior decompression and stabilization provided good clinical outcomes during the postoperative 18 months follow-up period. In this case, despite the use of standard imaging modalities (radiograph, CT, and MRI), making a preoperative imaging diagnosis of an aggressive vertebral hemangioma was difficult, and although aggressive vertebral hemangiomas with atypical radiological features are rare, they should be considered as a differential diagnosis.

Anaplastic large cell lymphoma with TP63 rearrangement: A dismal prognosis.

Anaplastic large cell lymphoma (ALCL) with TP63 rearrangement is a new entity and has the most dismal prognosis in all types of ALCL. This might be due to the resulting fusion protein having N-terminal truncated p63 with high oncogenic ability. Since this N-terminal domain has the function of tumor suppressor activity, the mechanism for high oncogenic capacity is thought to be the dominant negative function. Here, we report two ALCL cases with TP63 rearrangement that was each given too short a prognosis (Case 1 and 2: four and six months) in spite of intensive treatment. Immunohistochemically, p63 was highly expressed, and a sprit signal was detected using a TP63 break apart fluorescence in situ hybridization (FISH) in each case. Additionally, a poor prognostic marker of ALCL, all cytotoxic molecules (TIA-1, Granzyme B, and Perforin) were also expressed in almost all ALCL cells. Taken together, we suggest that not only the dominant negative function of N-truncated p63 but also the effect of cytotoxic molecules may influence the dismal prognosis of ALCL with TP63 rearrangement.

Development of three-dimensional hollow elastic model for cerebral aneurysm clipping simulation enabling rapid and low cost prototyping.

OBJECTIVE: We developed a method for fabricating a three-dimensional hollow and elastic aneurysm model useful for surgical simulation and surgical training. In this article, we explain the hollow elastic model prototyping method and report on the effects of applying it to presurgical simulation and surgical training. METHODS: A three-dimensional printer using acrylonitrile-butadiene-styrene as a modeling material was used to produce a vessel model. The prototype was then coated with liquid silicone. After the silicone had hardened, the acrylonitrile-butadiene-styrene was melted with xylene and removed, leaving an outer layer as a hollow elastic model. RESULTS: Simulations using the hollow elastic model were performed in 12 patients. In all patients, the clipping proceeded as scheduled. The surgeon's postoperative assessment was favorable in all cases. This method enables easy fabrication at low cost. CONCLUSION: Simulation using the hollow elastic model is thought to be useful for understanding of three-dimensional aneurysm structure.

Mannequin simulation improves the confidence of medical students performing tube thoracostomy: a prospective, controlled trial.

This study was undertaken to determine the educational benefits of mannequin simulation for performance of tube thoracostomy in a porcine model by medical students. Thirty medical students were randomized into two groups; the first performed tube thoracostomy on a mannequin simulator and then a porcine model; the second used only the porcine model. Performance measures included completion of subtasks, time to perform the procedure, a global score assigned by faculty raters, and a self-evaluation survey. Subtask completion rate was similar in both groups (P > 0.05). Mean time to perform the procedure was 9.8 minutes (+/- 0.9, simulator), and 9.3 minutes (+/- 1.0, nonsimulator, P > 0.05). Global scores were 12.3 (+/- 1.3, simulator) and 11.0 (+/- 1.4, non-simulator, P > 0.05). Self-evaluation of confidence (1 = "very", 7 = "not at all") showed the simulator group was significantly more confident (3.4 +/- 0.42) than the nonsimulator group (4.7 +/- 0.49, P < 0.05). All students met basic competencies to perform tube thoracostomy. The simulator group felt significantly more confident to subsequently perform the procedure on a patient, whereas performance was not statistically significantly different for the two groups. Further trials may be needed to delineate the optimal role for these simulators in teaching tube thoracostomy.

Angina bullosa hemorrhagica of the soft palate: a clinical study of 16 cases.

Angina bullosa hemorrhagica (ABH) is an oral mucosal blood blister that develops without blood dyscrasia or vesiculobullous disorder. Although a minor mucosal trauma has been suggested as a triggering factor for ABH, its etiopathogenesis, especially the causative role of systemic conditions, is largely unknown. We investigated the presence or absence of local factors as well as systemic background disease in 16 patients with ABH arising in the soft palate. All the lesions were solitary, and 75% of them (n = 12) appeared during the ingestion of hard or crispy food. With regard to underlying systemic conditions, hypertension was the most common (n = 6), and asthma, insomnia, diabetes mellitus, rheumatoid arthritis, gastrointestinal disorder and hyperuricemia were also recorded (n = 1 each). Five patients had no significant background disease. There were no recalcitrant or recurrent cases. In conclusion, the present study has revealed that scratching of the oral mucosa during eating plays an important role in the formation of ABH. Hypertension appears to be the most frequent background condition, but its pathogenic relationship with ABH remains speculative, as hypertension is fairly common in adults.