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Objectives: Several studies rely on archived tissue blocks to assess the PD‐L1 scores; however, a detailed analysis of potential variations of scores between fresh and archived tissue blocks still lacks. In addition, the prognostic implications of PD‐L1 in lung cancers have not yet been completely understood. Here, we aimed to investigate the temporal variation in PD‐L1 scores from clinical samples and the clinical implications of PD‐L1 in non–small cell lung cancer (NSCLC). Methods: NSCLC cases from January 2005 to June 2023 were considered for this study, and PD‐L1 scores in archived and fresh tissue blocks were analyzed. Association of PD‐L1 with various driver mutations was explored, and implications of PD‐L1 in progression‐free survival (PFS) and overall survival (OS) were analyzed. Results: Our study revealed a significant disparity in PD‐L1 scores between archived and fresh tissue blocks, and a temporal variation in scores within 6 months of tissue acquisition. Advanced‐stage primary tumors, metastatic lymph nodes, and visceral pleural invasion revealed higher PD‐L1 expression as presented by tumor proportion score (TPS). Notably, in fully resected stage I/II NSCLC cases, OS was better in the high PD‐L1 (≥ 50% TPS) cohort with driver mutations compared to cases without driver mutations (hazard ratio—0.5129, 95% confidence interval 0.2058–1.084, p = 0.0779). In contrast, high PD‐L1 was associated with worse OS compared to no PD‐L1 (< 1% TPS) (hazard ratio—2.431, 95% confidence interval 1.144–6.656, p = 0.0242) in the cohort without driver mutations. Furthermore, the presence of a KRAS mutation favored the outcome of anti‐PD‐L1/PD1 immunotherapy in advanced NSCLC. Conclusion: PD‐L1 detection from tissue blocks was found to vary temporally, urging for a prioritized consideration for patients with marginal scores when archived blocks are employed for its detection. Prognostic roles of PD‐L1 were associated with driver mutations, and KRAS mutations favored the outcome of anti‐PD‐L1/PD1 therapy in advanced NSCLC. [ABSTRACT FROM AUTHOR]

Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer.

Abstract Background Pulmonary sarcomatoid carcinoma is a rare tumor that is resistant to cytotoxic agents. This observational study aimed to evaluate the detection rate of driver gene alteration and the efficacy of targeted therapy for pulmonary sarcomatoid carcinoma. Methods We established a database of patients with pulmonary sarcomatoid carcinoma and their clinical information, including EGFR mutation, ALK fusion gene, ROS1 fusion gene, BRAF mutation, and MET exon 14 skipping mutation. The present study retrieved and analyzed the data of patients with pulmonary sarcomatoid carcinoma in whom driver gene alterations were evaluated, and the survival duration after the initiation of treatment with targeted therapy was examined. Results A total of 44 patients were included in the present study. The EGFR mutation, ALK fusion gene, and MET exon 14 skipping mutation were detected in 2/43 patients (4.7%), 2/34 patients (5.9%), and 2/16 patients (12.5%), respectively. The ROS1 fusion gene (0/18 patients) and BRAF mutation (0/15 patients) were not detected. Female patients (P = 0.063, Fisher’s exact test) and patients without smoking history (P = 0.025, Fisher’s exact test) were the dominant groups in which any driver mutation was detected. Five patients with driver gene alterations were treated with targeted therapy. Progression-free survival (PFS) was 1.3 months and 1.6 months in 2 of the patients treated with gefitinib. Two patients with the ALK fusion gene showed 2.1 and 14.0 months of PFS from the initiation of treatment with crizotinib, and a patient with the MET exon 14 skipping mutation showed 9.7 months of PFS from the initiation of treatment with tepotinib. Conclusion The EGFR mutation, ALK fusion gene, and MET exon 14 skipping mutation were detected in patients with pulmonary sarcomatoid carcinoma in clinical practice, and some patients achieved long survival times after receiving targeted therapy. Further investigation is necessary to evaluate the efficacy of targeted therapy for pulmonary sarcomatoid carcinoma.

Abstract Background Targeted therapy is now the standard of care in driver–oncogene-positive non-small cell lung cancer (NSCLC). Its initial clinical effects are remarkable. However, almost all patients experience treatment resistance to targeted therapy. Hence, chemotherapy is considered a subsequent treatment option. In patients with driver–oncogene-negative NSCLC, combined immune checkpoint inhibitors (ICIs) and chemotherapy as the first-line therapy has been found to be beneficial. However, the efficacy of ICI plus chemotherapy against driver–oncogene-positive NSCLC other than epidermal growth factor receptor mutation and anaplastic lymphoma kinase fusion is unclear. Methods Using the hospital medical records, we retrospectively reviewed advanced or recurrent NSCLC patients who were treated with chemotherapy with or without ICIs at Aichi Cancer Center Hospital between January 2014 and January 2023. Patients with druggable rare mutations such as KRAS-G12C, MET exon 14 skipping, HER2 20 insertion, BRAF-V600E mutations, and ROS1 and RET rearrangements were analyzed. Results In total, 61 patients were included in this analysis. ICI plus chemotherapy was administered in 36 patients (the ICI-chemo group) and chemotherapy in 25 patients (the chemo group). The median progression-free survival (PFS) rates were 14.0 months in the ICI-chemo group and 4.8 months in the chemo group (hazard ratio [HR] = 0.54, 95% confidence interval [CI] = 0.28–1.01). The median overall survival rates were 31.3 and 21.7 months in the ICI-chemo and chemo groups, respectively (HR = 0.70, 95% CI = 0.33–1.50). Multivariate Cox regression analysis of PFS revealed that HER2 exon 20 insertion mutation was significantly associated with a poorer PFS (HR: 2.39, 95% CI: 1.19–4.77, P = 0.014). Further, ICI-chemo treatment was significantly associated with a better PFS (HR: 0.48, 95% CI: 0.25–0.91, P = 0.025). Conclusion ICI plus chemotherapy improves treatment efficacy in rare driver–oncogene-positive NSCLC.

Background: Pulmonary sarcomatoid carcinoma is a rare tumor that is resistant to cytotoxic agents. This observational study aimed to evaluate the detection rate of driver gene alteration and the efficacy of targeted therapy for pulmonary sarcomatoid carcinoma. Methods: We established a database of patients with pulmonary sarcomatoid carcinoma and their clinical information, including EGFR mutation, ALK fusion gene, ROS1 fusion gene, BRAF mutation, and MET exon 14 skipping mutation. The present study retrieved and analyzed the data of patients with pulmonary sarcomatoid carcinoma in whom driver gene alterations were evaluated, and the survival duration after the initiation of treatment with targeted therapy was examined. Results: A total of 44 patients were included in the present study. The EGFR mutation, ALK fusion gene, and MET exon 14 skipping mutation were detected in 2/43 patients (4.7%), 2/34 patients (5.9%), and 2/16 patients (12.5%), respectively. The ROS1 fusion gene (0/18 patients) and BRAF mutation (0/15 patients) were not detected. Female patients (P = 0.063, Fisher's exact test) and patients without smoking history (P = 0.025, Fisher's exact test) were the dominant groups in which any driver mutation was detected. Five patients with driver gene alterations were treated with targeted therapy. Progression-free survival (PFS) was 1.3 months and 1.6 months in 2 of the patients treated with gefitinib. Two patients with the ALK fusion gene showed 2.1 and 14.0 months of PFS from the initiation of treatment with crizotinib, and a patient with the MET exon 14 skipping mutation showed 9.7 months of PFS from the initiation of treatment with tepotinib. Conclusion: The EGFR mutation, ALK fusion gene, and MET exon 14 skipping mutation were detected in patients with pulmonary sarcomatoid carcinoma in clinical practice, and some patients achieved long survival times after receiving targeted therapy. Further investigation is necessary to evaluate the efficacy of targeted therapy for pulmonary sarcomatoid carcinoma. [ABSTRACT FROM AUTHOR]

Background: Targeted therapy is now the standard of care in driver–oncogene-positive non-small cell lung cancer (NSCLC). Its initial clinical effects are remarkable. However, almost all patients experience treatment resistance to targeted therapy. Hence, chemotherapy is considered a subsequent treatment option. In patients with driver–oncogene-negative NSCLC, combined immune checkpoint inhibitors (ICIs) and chemotherapy as the first-line therapy has been found to be beneficial. However, the efficacy of ICI plus chemotherapy against driver–oncogene-positive NSCLC other than epidermal growth factor receptor mutation and anaplastic lymphoma kinase fusion is unclear. Methods: Using the hospital medical records, we retrospectively reviewed advanced or recurrent NSCLC patients who were treated with chemotherapy with or without ICIs at Aichi Cancer Center Hospital between January 2014 and January 2023. Patients with druggable rare mutations such as KRAS-G12C, MET exon 14 skipping, HER2 20 insertion, BRAF-V600E mutations, and ROS1 and RET rearrangements were analyzed. Results: In total, 61 patients were included in this analysis. ICI plus chemotherapy was administered in 36 patients (the ICI-chemo group) and chemotherapy in 25 patients (the chemo group). The median progression-free survival (PFS) rates were 14.0 months in the ICI-chemo group and 4.8 months in the chemo group (hazard ratio [HR] = 0.54, 95% confidence interval [CI] = 0.28–1.01). The median overall survival rates were 31.3 and 21.7 months in the ICI-chemo and chemo groups, respectively (HR = 0.70, 95% CI = 0.33–1.50). Multivariate Cox regression analysis of PFS revealed that HER2 exon 20 insertion mutation was significantly associated with a poorer PFS (HR: 2.39, 95% CI: 1.19–4.77, P = 0.014). Further, ICI-chemo treatment was significantly associated with a better PFS (HR: 0.48, 95% CI: 0.25–0.91, P = 0.025). Conclusion: ICI plus chemotherapy improves treatment efficacy in rare driver–oncogene-positive NSCLC. [ABSTRACT FROM AUTHOR]

Lung cancer is the leading cause of cancer deaths in the United States and the world. It is divided into two major types: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). In the tumor-node-metastasis (TNM) cancer-staging classification system (Stages I/II/III/IV), the severity of neoplastic growth is characterized by the size of the tumor (T1 to T4), the extent of lymph node involvement (N0 to N3), and whether (M1) or not (M0) distant metastasis has occurred. Surgery is the treatment of choice for medically fit patients with Stage I/II NSCLC. Combination chemoradiotherapy and immune checkpoint inhibitor therapy are used across all NSCLC types. Oncogene-addicted tumors with sensitizing EGFR or BRAF mutations or activating ALK, ROS1 or NTRK translocations are treated with their cognate orally active small molecule protein kinase blockers. On the order of 20 % of NSCLCs bear activating mutations in EGFR and are treated with osimertinib and other kinase antagonists. SCLC, which accounts for approximately 15 % of lung cancer cases, is a deadly high-grade neuroendocrine carcinoma with a poor prognosis. Limited-stage SCLC is confined to one hemi-thorax and one radiation port and extensive-stage disease signifies those cancers that do not meet the criteria for limited-stage disease. Local treatment options to control thoracic disease include radiotherapy and surgery. In patients with extensive-stage disease, a platinum agent (cisplatin or carboplatin) combined with etoposide and an anti-PDL1 inhibitor (atezolizumab or durvalumab) for four cycles followed by anti-PDL1 maintenance therapy is the recommended first-line regimen.

ABSTRACT Objectives Several studies rely on archived tissue blocks to assess the PD‐L1 scores; however, a detailed analysis of potential variations of scores between fresh and archived tissue blocks still lacks. In addition, the prognostic implications of PD‐L1 in lung cancers have not yet been completely understood. Here, we aimed to investigate the temporal variation in PD‐L1 scores from clinical samples and the clinical implications of PD‐L1 in non–small cell lung cancer (NSCLC). Methods NSCLC cases from January 2005 to June 2023 were considered for this study, and PD‐L1 scores in archived and fresh tissue blocks were analyzed. Association of PD‐L1 with various driver mutations was explored, and implications of PD‐L1 in progression‐free survival (PFS) and overall survival (OS) were analyzed. Results Our study revealed a significant disparity in PD‐L1 scores between archived and fresh tissue blocks, and a temporal variation in scores within 6 months of tissue acquisition. Advanced‐stage primary tumors, metastatic lymph nodes, and visceral pleural invasion revealed higher PD‐L1 expression as presented by tumor proportion score (TPS). Notably, in fully resected stage I/II NSCLC cases, OS was better in the high PD‐L1 (≥ 50% TPS) cohort with driver mutations compared to cases without driver mutations (hazard ratio—0.5129, 95% confidence interval 0.2058–1.084, p = 0.0779). In contrast, high PD‐L1 was associated with worse OS compared to no PD‐L1 (

The presence of molecular mutations in colorectal cancer (CRC) is a decisive factor in selecting the most effective first-line therapy. However, molecular analysis is routinely performed only in a limited number of patients with remote metastases. We propose to use tissue stiffness as a marker of the presence of molecular mutations in CRC samples. For this purpose, we applied compression optical coherence elastography (C-OCE) to calculate stiffness values in regions corresponding to specific CRC morphological patterns (n = 54). In parallel to estimating stiffness, molecular analysis from the same zones was performed to establish their relationships. As a result, a high correlation between the presence of KRAS/NRAS/BRAF driver mutations and high stiffness values was revealed regardless of CRC morphological pattern type. Further, we proposed threshold stiffness values for label-free targeted detection of molecular alterations in CRC tissues: for KRAS, NRAS, or BRAF driver mutation—above 803 kPa (sensitivity—91%; specificity—80%; diagnostic accuracy—85%), and only for KRAS driver mutation—above 850 kPa (sensitivity—90%; specificity—88%; diagnostic accuracy—89%). To conclude, C-OCE estimation of tissue stiffness can be used as a clinical diagnostic tool for preliminary screening of genetic burden in CRC tissues. [ABSTRACT FROM AUTHOR]

In invasive lung adenocarcinoma (LUAD), patients with micropapillary (MIP) or solid (SOL) components had a significantly poorer prognosis than those with only lepidic (LEP), acinar (ACI) or papillary (PAP) components. It is interesting to explore the genetic features of different histologic subtypes, especially the highly aggressive components.Based on a cohort of 5,933 patients, this study observed that in different tumor size groups, LUAD with MIP/SOL components showed a different prevalence, and patients with ALK alteration or TP53 mutations had a higher probability of developing MIP/SOL components. To control individual differences, this research used spatial whole-exome sequencing (WES) via laser-capture microdissection of five patients harboring these five coexistent components and identified genetic features among different histologic components of the same tumor. In tracing the evolution of components, we found that titin (TTN) mutation might serve as a crucial intratumor potential driver for MIP/SOL components, which was validated by a cohort of 146 LUAD patients undergoing bulk WES. Functional analysis revealed that TTN mutations enriched the complement and coagulation cascades, which correlated with the pathway of cell adhesion, migration, and proliferation.Collectively, the histologic subtypes of invasive LUAD were genetically different, and certain trunk genotypes might synergize with branching TTN mutation to develop highly aggressive components.

Cancer is the result of continuous accumulation of gene mutations in normal cells. The number of mutations is different in different types of cancer and even in different patients with the same type of cancer. Therefore, studying all possible numbers of gene mutations in malignant cells is of great value for the understanding of tumorigenesis and the treatment of cancer. To this end, we applied a stochastic mathematical model considering the clonal expansion of any premalignant cells with different mutations to analyze the number of gene mutations in colorectal cancer. The age-specific colorectal cancer incidence rates from the Surveillance, Epidemiology and End Results (SEER) registry in the United States and the Life Span Study (LSS) in Nagasaki and Hiroshima, Japan are chosen to test the reasonableness of the model. Our fitting results indicate that the transformation from normal cells to malignant cells may undergo two to five driver mutations for colorectal cancer patients without radiation-exposed environment, two to four driver mutations for colorectal cancer patients with low level radiation-exposure, and two to three driver mutations for colorectal cancer patients with high level radiation-exposure. Furthermore, the net growth rate of the mutated cells with radiation-exposure was is higher than that of the mutated cells without radiation-exposure for the models with two to five driver mutations. These results suggest that radiation environment may affect the clonal expansion of cells and significantly affect the development of tumors.

PurposePatients with non-small cell lung cancer (NSCLC) that harbor driver mutations are associated with a cancer diagnosis at a younger age. While targeted therapies provide deep remissions and durable benefit in a subset of patients, it is unclear whether targeted therapies bridge the gap in years of life lost (YLL) in these younger NSCLC patients with targetable mutations in comparison to generally older NSCLC patients without actionable driver mutations.Materials and methodsRetrospective cross-sectional study using landmark trials leading to the approval of targeted therapies in NSCLC with actionable mutations. We evaluated all targeted therapies as well as chemotherapy and IO regimens for the treatment of NSCLC through FDA Oncology Announcements and NCCN Guidelines for NSCLC (version 4.2021).ResultsWe estimated the YLL for each driver mutation, cumulative median duration of response (DOR) with targeted therapies by mutation type, and percentage of estimated improvement in YLL from NSCLC targeted therapies. The median ages at diagnosis (in years) for patients whose tumors express targetable mutations were: 47.6 (NTRK); 52.0 (ALK); 62.0 (HER2); 57.0 (ROS1); 61.4 (RET); 63.0 (BRAF); 69.0 (EGFR); and 72.0 (MET). For comparison, the median age at diagnosis for patients without driver mutations, regardless of PD-L1 status was 71 years. The median DOR (in years) for patients whose tumors express the same mutations include: 0.9 (NTRK); 3.9 (ALK); 0.6 (HER2); 6.2 (ROS1); 2.2 (RET); 1.5 (BRAF); 3.1 (EGFR); and 2.4 (MET). The median DOR for patients without driver mutations was 1.2 years. The cumulative estimated survival time (years; median age at diagnosis plus the median DOR or OS) for patients whose tumors express targetable mutations were: 48.5 (NTRK); 55.9 (ALK); 62.6 (HER2); 63.2 (ROS1); 63.6 (RET); 64.5 (BRAF); 72.1 (EGFR); and 74.4 (MET). The cumulative estimated survival time for patients without driver mutations, regardless of PD-L1 status, was 72.2 years of age. We calculated the number of years NSCLC is diagnosed earlier in patients with targetable mutations as follows: 23.4 (NTRK), 19 (ALK), 14 (ROS1), 11 (EGFR), 9.6 (RET), 9 (HER2), and 8 (BRAF). The percent difference (%) ameliorated in YLL by mutation type is as follows: 44.3 (ROS1), 28.2 (EGFR), 22.9 (RET), 20.5 (ALK), 18.8 (BRAF), 6.4 (HER2), and 3.7 (NTRK).ConclusionAlthough targeted therapies have paved the way for significant progress toward providing a survival benefit to many young patients with advanced NSCLC with actionable mutations, it is evident that these therapies still leave a wide gap in the YLL in these younger patients compared to generally older individuals with advanced NSCLC without targetable mutations.

Background: Intrahepatic cholangiocarcinoma (iCCA) is often diagnosed at an advanced stage, leading to limited treatment options and a poor prognosis. So far, standard systemic therapy for advanced iCCA has been a combination of gemcitabine and cisplatin. However, recent advancements in the understanding of the molecular characteristics of iCCA have opened new possibilities for molecular-targeted therapies and immunotherapy. Summary: Reportedly, 9–36% of iCCA cases have an inflamed tumor immune microenvironment (TME) based on the immune gene expression signature, which is characterized by the presence of immune cells involved in anti-tumor immune responses. The majority of iCCA cases have a non-inflamed TME with a lack of effector T cells, rendering immune checkpoint inhibitors (ICIs) ineffective in these cases. Interestingly, alterations in the fibroblast growth factor receptor (FGFR2) gene and IDH1/2 gene mutations are often observed in the non-inflamed TME in iCCA. Several mechanisms have been reported for the role of driver mutations on the establishment of TME unique for iCCA. For example, IDH1/2 mutations, which cause an increase in DNA methylation, are associated with the downregulation and hypermethylation of antigen processing and presentation machinery, which may contribute to the establishment of a non-inflamed TME. Therefore, inhibitors targeting IDH1/2 may restore the DNA methylation and expression status of molecules involved in antigen presentation, potentially improving the efficacy of ICIs. FGFR inhibitors may also have the potential to modulate immunosuppressive TME by inhibitingthe suppressor of cytokine signaling 1 and activating the interferon-γ signaling as a consequence of inhibition of the FGFR signal. From this perspective, understanding the molecular characteristics of iCCA, including the TME and driver mutations, is essential for the effective application of ICIs and molecular-targeted therapies. Key Messages: Combination approaches that target both the tumor and immune system hold promise for improving the outcomes of patients with iCCA. Further research and clinical trials are needed to validate these approaches and optimize the treatment strategies for iCCA. [ABSTRACT FROM AUTHOR]

Purpose: Various molecular profiles are needed to classify malignant brain tumors, including gliomas, based on the latest classification criteria of the World Health Organization, and their poor prognosis necessitates new therapeutic targets. The Todai OncoPanel 2 RNA Panel (TOP2-RNA) is a custom-target RNA-sequencing (RNA-seq) using the junction capture method to maximize the sensitivity of detecting 455 fusion gene transcripts and analyze the expression profiles of 1,390 genes. This study aimed to classify gliomas and identify their molecular targets using TOP2-RNA. Methods: A total of 124 frozen samples of malignant gliomas were subjected to TOP2-RNA for classification based on their molecular profiles and the identification of molecular targets. Results: Among 55 glioblastoma cases, gene fusions were detected in 11 cases (20%), including novel MET fusions. Seven tyrosine kinase genes were found to be overexpressed in 15 cases (27.3%). In contrast to isocitrate dehydrogenase (IDH) wild-type glioblastoma, IDH-mutant tumors, including astrocytomas and oligodendrogliomas, barely harbor fusion genes or gene overexpression. Of the 34 overexpressed tyrosine kinase genes, MDM2 and CDK4 in glioblastoma, 22 copy number amplifications (64.7%) were observed. When comparing astrocytomas and oligodendrogliomas in gene set enrichment analysis, the gene sets related to 1p36 and 19q were highly enriched in astrocytomas, suggesting that regional genomic DNA copy number alterations can be evaluated by gene expression analysis. Conclusions: TOP2-RNA is a highly sensitive assay for detecting fusion genes, exon skipping, and aberrant gene expression. Alterations in targetable driver genes were identified in more than 50% of glioblastoma. Molecular profiling by TOP2-RNA provides ample predictive, prognostic, and diagnostic biomarkers that may not be identified by conventional assays and, therefore, is expected to increase treatment options for individual patients with glioma. [ABSTRACT FROM AUTHOR]

Simple Summary: Molecular targeted therapies are very effective as a treatment for postoperative recurrence of non-small cell lung cancer (NCSLC) with driver mutations. On the other hand, the efficacy of local therapies for oligo-recurrence has also been reported. To investigate the optimal treatment strategy for oligo-recurrence in NSCLC patients with driver mutations, we retrospectively evaluated 66 NSCLC patients with driver mutations who were treated with local or molecular targeted therapies as the initial treatment after recurrence. Patients treated with local therapies as a first-line treatment did not show statistically significant differences in post-recurrence survival and progression-free survival compared with those treated with molecular targeted therapies. However, local therapies as an initial treatment should be considered preferably, as they can be curative after recurrence and can delay the start of the administration of molecular targeted therapies. Background: The efficacy of local therapies for lung cancer patients with postoperative oligo-recurrence has been reported. However, whether local therapies should be chosen over molecular targeted therapies for oligo-recurrence patients with driver mutations remains controversial. Therefore, we aimed to investigate the optimal initial treatment strategy for oligo-recurrence in lung cancer patients with driver mutations. Methods: Among 2152 patients with lung adenocarcinoma who underwent surgical resection at our institute between 2008 and 2020, 66 patients with driver mutations who experienced cancer oligo-recurrence after surgery and were treated with local or molecularly targeted therapy as an initial therapy after recurrence were evaluated. Oligo-recurrence was characterized by the presence of 1 to 3 recurrent lesions. These patients were investigated, focusing on their post-recurrence therapies and prognoses. Results: The median follow-up period was 71 months. Local and molecular targeted therapies were administered to 41 and 25 patients, respectively. The number of recurrence lesions tended to be lower in the initial local therapy group than in the molecular targeted therapy group. In the initial local therapy group, 23 patients (56%) subsequently received molecular targeted therapies. The time from recurrence to the initiation of molecular targeted therapy was significantly longer in the local therapy group than in the molecular targeted therapy group (p < 0.001). There was no significant difference in post-recurrence overall survival (hazard ratio, 1.429; 95% confidence interval, 0.701–2.912; log-rank, p = 0.324) and post-recurrence progression-free survival (hazard ratio, 0.799; 95% confidence interval, 0.459–1.390; log-rank, p = 0.426) in the initial local ablative therapy group compared with the initial molecular targeted therapy group. Conclusions: Local therapies as a first-line treatment did not show statistically significant differences in post-recurrence survival or progression-free survival compared with molecular targeted therapies. However, local therapies as an initial treatment should be considered preferably, as they can cure the recurrence and can delay the start of administration of molecular targeted therapies. [ABSTRACT FROM AUTHOR]

Unlike drug selection, radiation parameters (field, dose) are not based on driver gene mutations in patients with metastatic non-small cell lung cancer (NSCLC). This study aimed to compare radiosensitivity in NSCLC with and without EGFR driver gene mutations using clinical and in vitro data. The clinical study included 42 patients who underwent whole-brain radiotherapy for brain metastases from NSCLC; of these, 13 patients had EGFR mutation-positive tumors. The Kaplan–Meier method was used to calculate the cranial control rate without intracranial recurrence. In the in vitro study, colony formation and double-strand DNA breaks were examined in two EGFR mutation-negative and three EGFR mutation-positive NSCLC-derived cell lines. Colony formation was assessed 14 days after irradiation with 0 (control), 2, 4, or 8 Gy. DNA double-strand breaks were evaluated 0.5 and 24 h after irradiation. EGFR mutation-positive patients had a significantly better cranial control rates than EGFR mutation-negative patients (p = 0.021). EGFR mutation-positive cells formed significantly fewer colonies after irradiation with 2 or 4 Gy than EGFR mutation-negative cells (p = 0.002, respectively) and had significantly more DNA double-strand breaks at 24 h after irradiation (p < 0.001). Both clinical and in vitro data suggest that EGFR mutation-positive NSCLC is radiosensitive. [ABSTRACT FROM AUTHOR]

Malignant tumors derived from the epithelium lining the nasal cavity region are termed sinonasal cancers, a highly heterogeneous group of rare tumors accounting for 3 – 5 % of all head and neck cancers. Progress with next-generation molecular profiling has improved our understanding of the complexity of sinonasal cancers and resulted in the identification of an increasing number of distinct tumor entities. Despite these significant developments, the treatment of sinonasal cancers has hardly evolved since the 1980s, and an advanced sinonasal cancer presents a poor prognosis as targeted therapies are usually not available. To gain insights into potential targeted therapeutic opportunities, we performed a multiomics profiling of patient-derived functional tumor models to identify molecular characteristics associated with pharmacological responses in the different subtypes of sinonasal cancer. Methods: Patient-derived ex vivo tumor models representing four distinct sinonasal cancer subtypes: sinonasal intestinal-type adenocarcinoma, sinonasal neuroendocrine carcinoma, sinonasal undifferentiated carcinoma and SMARCB1 deficient sinonasal carcinoma were included in the analyses. Results of functional drug screens of 160 anti-cancer therapies were integrated with gene panel sequencing and histological analyses of the tumor tissues and the ex vivo cell cultures to establish associations between drug sensitivity and molecular characteristics including driver mutations. Results: The different sinonasal cancer subtypes display considerable differential drug sensitivity. Underlying the drug sensitivity profiles, each subtype was associated with unique molecular features. The therapeutic vulnerabilities correlating with specific genomic background were extended and validated with in silico analyses of cancer cell lines representing different human cancers and with reported case studies of sinonasal cancers treated with targeted therapies. Conclusion: The results demonstrate the importance of understanding the differential biology and the molecular features associated with the different subtypes of sinonasal cancers. Patient-derived ex vivo tumor models can be a powerful tool for investigating these rare cancers and prioritizing targeted therapeutic strategies for future clinical development and personalized medicine.

Background: Intrahepatic cholangiocarcinoma (iCCA) is often diagnosed at an advanced stage, leading to limited treatment options and a poor prognosis. So far, standard systemic therapy for advanced iCCA has been a combination of gemcitabine and cisplatin. However, recent advancements in the understanding of the molecular characteristics of iCCA have opened new possibilities for molecular-targeted therapies and immunotherapy. Summary: Reportedly, 9–36% of iCCA cases have an inflamed tumor immune microenvironment (TME) based on the immune gene expression signature, which is characterized by the presence of immune cells involved in anti-tumor immune responses. The majority of iCCA cases have a non-inflamed TME with a lack of effector T cells, rendering immune checkpoint inhibitors (ICIs) ineffective in these cases. Interestingly, alterations in the fibroblast growth factor receptor (FGFR2) gene and IDH1/2 gene mutations are often observed in the non-inflamed TME in iCCA. Several mechanisms have been reported for the role of driver mutations on the establishment of TME unique for iCCA. For example, IDH1/2 mutations, which cause an increase in DNA methylation, are associated with the downregulation and hypermethylation of antigen processing and presentation machinery, which may contribute to the establishment of a non-inflamed TME. Therefore, inhibitors targeting IDH1/2 may restore the DNA methylation and expression status of molecules involved in antigen presentation, potentially improving the efficacy of ICIs. FGFR inhibitors may also have the potential to modulate immunosuppressive TME by inhibitingthe suppressor of cytokine signaling 1 and activating the interferon-γ signaling as a consequence of inhibition of the FGFR signal. From this perspective, understanding the molecular characteristics of iCCA, including the TME and driver mutations, is essential for the effective application of ICIs and molecular-targeted therapies. Key Messages: Combination approaches that target both the tumor and immune system hold promise for improving the outcomes of patients with iCCA. Further research and clinical trials are needed to validate these approaches and optimize the treatment strategies for iCCA.

Recent advances in molecular biology have led to the identification of molecules associated with carcinogenesis and the development of molecular-targeted drugs that selectively attack qualitative or quantitative molecular changes in cancer cells. Molecular targeted drugs are classified into "low molecular weight compounds" and "monoclonal antibody drugs" according to the difference in molecular weight. Molecular targeted drugs often have clinically meaningful biomarkers, such as gain- or loss-of-function in cancer-related target genes caused by point mutations, amplification, fusion, and deletion. High therapeutic effects can be expected by detecting driver mutations, which are directly related to carcinogenesis, and by using the corresponding molecular-targeted drugs. In recent years, the development of next-generation sequencing has enabled the simultaneous measurement of hundreds of gene sequences, and an oncogene panel containing cancer-related genes has been covered by the National Health Insurance. Precision medicine is defined as medical care designed to optimize the efficiency or therapeutic benefit for specific patient groups, especially using genetic or molecular profiling. This article is based on a study reported in the Journal of Tokyo Women's Medical University (in Japanese) 2022;92 (1):1-7.

Patients with inflammatory bowel disease (IBD) are exposed to chronic systemic inflammation and are at risk for secondary malignancies. Here we review the literature on the risk of myeloid neoplasms (MN) in IBD and present the disease profiles of patients at a single institution with IBD who later developed MN, comparing them to those in the literature. No IBD characteristic was found to associate with MN disease severity, including the previously-identified association between MNs and thiopurine exposure. Of the somatic mutations identified in out cohort's MN, mutations in TET2 were most prevalent, followed by FLT3-ITD, BCR-ABL, and NPM1 mutations.

Ovarian clear cell carcinoma (OCCC) has distinct clinical and molecular features and heterogeneous prognosis. Insights into the somatic genomic abnormalities of OCCC provide the basis for deeper understanding and potential therapeutic avenues. Herein, we performed extensive genomic profiling in Chinese patients to illustrate the mutation landscape and genetic prognostic biomarkers of OCCC. We used targeted DNA sequencing on 61 OCCC cases with a panel of 520 cancer-related genes. Correlations between clinicopathological features and survival were evaluated. Nomogram-based models were constructed to predict progress-free survival (PFS). We detected 763 somatic mutations spanning 286 genes. The most frequent genetic alterations, ARID1A (49%) and PIK3CA (48%), were concurrently mutated. Comprehensive copy number alterations (CNAs) were identified in chromosomes 20q13.2 and 8q. Most (73.7%) patients harboured potentially targetable driver mutations. The mean and median tumour mutational burden were 7.0 and 3.0 mutations/Mb, respectively. Microsatellite instability (high) was identified in 8.2% of patients. Mutation of the base-excision repair pathway was significantly higher in patients of stage II/III/IV. ATM mutation was associated with platinum sensitivity (p <.05). Survival analysis identified chr8q CNAs in all patients, PIK3CA mutations in stage I patients and SWI/SNF complex (ARID1A and SMARCA4) mutations in stage II/III/IV patients as potential prognosticators (p <.05). Integration of genetic alterations (SWI/SNF complex mutations, ATM mutations and chr8q CNAs) improved the performance of a nomogram based on tumour stage and residual disease (concordance index 0.75 vs. 0.70, p <.05). We described somatic genomic alterations in Chinese OCCC patients and observed different genomic alterations between stage I and stage II/III/IV tumours. Genetic factors may supplement clinical factors in nomogram modelling for PFS prediction. We performed extensive genomic profiling in a well-annotated cohort of 61 Chinese ovarian clear cell carcinoma (OCCC) patients. PIK3CA mutations were associated with worse overall survival (OS) in stage I OCCC, and SWI/SNF gene mutations were associated with improved OS in stage II/III/IV disease. We propose an easy-to-use nomogram using clinical factors (tumour stage and residual disease) and genetic alterations (SWI/SNF complex mutations, ATM mutations and chr8q CNAs) to predict the progress-free survival (PFS) of OCCC. [ABSTRACT FROM AUTHOR]

Background: Tertiary hyperparathyroidism (THPT) is a peculiar subtype of hyperparathyroidism that usually develops from chronic kidney disease (CKD) and persists even after kidney transplantation. Unlike its precursor, secondary hyperparathyroidism (SHPT), THPT is characterized by uncontrolled high levels of calcium in the blood, which suggests the monoclonal or oligoclonal proliferation of parathyroid cells. However, the molecular abnormalities leading to THPT have not yet been fully understood. Methods: In this study, we analyzed DNA samples from hyperplastic parathyroid and corresponding blood cells of 11 patients with THPT using whole-exome sequencing (WES). We identified somatic single nucleotide variants (SNV) and insertions or deletions variants (INDEL) and performed driver mutation analysis, KEGG pathway, and GO functional enrichment analysis. To confirm the impact of selected driver mutated genes, we also tested their expression level in these samples using qRT-PCR. Results: Following quality control and mutation filtering, we identified 17,401 mutations, comprising 6690 missense variants, 3078 frameshift variants, 2005 stop-gained variants, and 1630 synonymous variants. Copy number variants (CNV) analysis showed that chromosome 22 copy number deletion was frequently observed in 6 samples. Driver mutation analysis identified 179 statistically significant mutated genes, including recurrent missense mutations on TBX20, ATAD5, ZNF669, and NOX3 genes in 3 different patients. KEGG pathway analysis revealed two enriched pathways: non-homologous endjoining and cell cycle, with a sole gene, PRKDC, involved. GO analysis demonstrated significant enrichment of various cellular components and cytobiological processes associated with four genes, including GO items of positive regulation of developmental growth, protein ubiquitination, and positive regulation of the apoptotic process. Compared to blood samples, THPT samples exhibited lower expression levels of PRKDC, TBX20, ATAD5, and NOX3 genes. THPT samples with exon mutations had relatively lower expression levels of PRKDC, TBX20, and NOX3 genes compared to those without mutations, although the difference was not statistically significant. Conclusion: This study provides a comprehensive landscape of the genetic characteristics of hyperplastic parathyroids in THPT, highlighting the involvement of multiple genes and pathways in the development and progression of this disease. The dominant mutations identified in our study depicted new insights into the pathogenesis and molecular characteristics of THPT. [ABSTRACT FROM AUTHOR]

Abstract Background Pancreatic cancer (PC) is one of the most aggressive cancers worldwide. Although many studies have investigated genomic alterations, the genomic landscape of Japanese PC patients has not been fully elucidated. Methods We used whole‐exome sequencing, cancer gene panel deep‐sequencing, and microarray gene expression profiling data derived from the Japanese version of the Cancer Genome Atlas (JCGA) in 93 PC cases. Results Somatic driver mutations were identified in 65.6% of samples in 19 genes. The median tumor mutation burden (TMB) value was 0.24 Muts/Mb (interquartile range, 0.15–0.64 Muts/Mb). The commonly mutated genes were KRAS (58%), TP53 (40%), CDKN2A (10%), SMAD4 (10%), FGFR2 (9%), and PKHD1 (9%). Frequent germline variation genes were BRCA1 (8%), CDH1 (5%), MET (5%), MSH6 (5%), and TEK (5%). Frequent chromosomal arm alterations included copy number gains in 2q (42%), 7q (24%), and 3q (24%), and copy number losses in 19p (62%), 19q (47%), 12q (34%), and 7q (30%). A prognostic analysis according to the presence of driver mutations showed that overall survival (OS) in the driver mutation‐positive group was significantly worse in comparison to that of the driver mutation‐negative group (median, 23.1 vs 46.7 mo; P = .010). A Cox proportional hazards analysis for OS identified driver mutation (hazard ratio [HR], 1.89; P = .025) and lymph node metastasis (HR, 3.27; P = .002) as independent prognostic factors. Conclusion The present results from the JCGA dataset constitute a fundamental resource for genomic medicine for PC patients, especially in Japan.

Background: Fluorine-18 (isotope)-Fluoro-deoxyglucose positron emission tomography computed tomography (F-18-FDG PET/CT) as a non-invasive method could predict driver mutation status in pulmonary adenocarcinoma. Aim: To assess whether F-18 FDG PET/CT can differentiate between positive and negative driver mutation status of pulmonary adenocarcinoma. Settings and Design: Hundred biopsy proven, untreated pulmonary adenocarcinoma patients tested for EGFR and ALK gene mutations underwent staging F-18 FDG PET/CT scan at our institute. Methods and Material: Metabolic parameters like SUVmax of the primary (pSUVmax), SULpeak, SUVmean, Metabolic tumor volume (MTV) and total lesion glycolysis (TLG) of primary lesion, SUVmax of the most avid metastatic regional lymph node (nSUVmax) and extra thoracic metastasis (mSUVmax) and average SUVmax of the primary lesion, regional nodal metastasis and extra thoracic metastasis were calculated. Statistical Analysis Used: The independent sample ‘T’ test and Mann-Whitney U test were used for analysis. Receiver operating characteristic (ROC) curves were used to determine the cut-off value of pSUVmax for predicting ALK mutation status. Results: Fourty one patients showed EGFR mutations, 14 showed ALK rearrangements and 45 were wild-type. Patients with ALK rearrangements showed a lower pSUVmax, SULpeak, SUVmean and TLG compared to wild type patients. ROC curve analysis showed a pSUVmax cutoff of < 11.0 yielding an area under the curve (AUC) of 0.709. Patients with EGFR mutations showed a lower mSUVmax, MTV, and TLG compared to wild type. Conclusions: FDG- PET/CT can be a useful non- invasive tool if tumor tissue is not available, although genetic testing continues to be the gold standard.

AbstractIntroduction Ovarian clear cell carcinoma (OCCC) has distinct clinical and molecular features and heterogeneous prognosis. Insights into the somatic genomic abnormalities of OCCC provide the basis for deeper understanding and potential therapeutic avenues. Herein, we performed extensive genomic profiling in Chinese patients to illustrate the mutation landscape and genetic prognostic biomarkers of OCCC.Patients and methods We used targeted DNA sequencing on 61 OCCC cases with a panel of 520 cancer-related genes. Correlations between clinicopathological features and survival were evaluated. Nomogram-based models were constructed to predict progress-free survival (PFS).Results We detected 763 somatic mutations spanning 286 genes. The most frequent genetic alterations, ARID1A (49%) and PIK3CA (48%), were concurrently mutated. Comprehensive copy number alterations (CNAs) were identified in chromosomes 20q13.2 and 8q. Most (73.7%) patients harboured potentially targetable driver mutations. The mean and median tumour mutational burden were 7.0 and 3.0 mutations/Mb, respectively. Microsatellite instability (high) was identified in 8.2% of patients. Mutation of the base-excision repair pathway was significantly higher in patients of stage II/III/IV. ATM mutation was associated with platinum sensitivity (p

Abstract Introduction Considerable differences of treatment response and pattern of failure may exist between definitive chemoradiation (CRT) treated locally advanced non‐small cell lung cancer (LA‐NSCLC) patients. The clinical value of additional tyrosine kinase inhibitors (TKIs) before disease recurrence and salvage local therapy after initial recurrent disease remain controversial. Methods and Materials Consecutive LA‐NSCLC patients receiving definitive CRT and having definite results about driver mutations (EGFR, ALK and ROS1) were retrospectively reviewed. Initial recurrent disease was classified as in‐field recurrence, out‐of‐field recurrence and distant metastasis. Recurrent disease occurred only in the brain or limited to ≤3 extra‐cranial organs and ≤5 extra‐cranial lesions, was defined as oligo‐recurrence. Progression free survival and overall survival (OS) were calculated from diagnosis to disease progression or death, and to death, respectively. OS2 was measured from initial disease recurrence to death among patients who had recurrent disease. Results Of the 153 enrolled patients, 39 had driver mutations and 13 received additional TKI therapy besides definitive CRT. Patients harboring driver mutations but without additional TKI therapy had a similar PFS and significantly longer OS (p = 0.032) than those without driver mutations. Additional TKI therapy prolonged PFS (p = 0.021) but not OS among patients with driver mutations. No significant difference of pattern of failure was observed between patient subgroups stratified by the status of driver mutations and the usage of additional TKI therapy. Furthermore, 57 of the 95 patients with initial recurrent disease developed oligo‐recurrence and salvage local therapy significantly improved OS2 (p = 0.01) among patients with oligo‐recurrence disease. Conclusion LA‐NSCLC patients receiving definitive CRT generally had similar PFS and pattern of treatment failure, regardless of driver mutation status. Additional TKI therapy besides definitive CRT could prolong PFS but not OS. The majority of recurrent disease after definitive CRT belongs to oligo‐recurrence and salvage local therapy may provide survival benefit.

Regional lymph node metastasis (LNM) increases the risk of distant metastasis in papillary thyroid cancer (PTC) patients. However, it remains unclear how tumor cells in PTC patients with LNM evade immune system surveillance and proceed to colonize distant organs. Here, we comprehensively characterize the tumor-infiltrating immune cell landscape in PTC with LNM. LNM-related genes include multiple important soluble mediators such as CXCL6, IL37, MMP10, and COL11A1, along with genes involved in areas such as extracellular matrix organization and TLR regulation by endogenous ligands. In PTC without LNM, the tumor infiltration of activated dendritic cells and M0 macrophages showed increases from normal cells, but with yet greater increases and correspondingly worse prognosis in PTC with LNM. Conversely, the tumor infiltration of activated NK cells and eosinophils was decreased in PTC without LNM, as compared to normal cells, and yet further decreased in PTC with LNM, with such decreases associated with poor prognosis. We further demonstrate that mutations of driver genes in tumor cells influence the infiltration of surrounding immune cells in the tumor microenvironment (TME). Particularly, patients carrying TG mutations tend to show increased filtration of M2 macrophages and activated NK cells in the TME, whereas patients carrying HRAS mutations tend to show reduced filtration of M0 macrophages and show enhanced filtration of activated dendritic cells in the TME. These findings increase our understanding of the mechanisms of regional lymph node metastasis in PTC and its associated tumor microenvironment, potentially facilitating the development of personalized treatment regimens to combat immunotherapy failure.

Abstract Background Bladder cancer (BCa) is the most common malignant tumor of the urinary system, with transitional cell carcinoma (TCC) being the predominant type. EP300 encodes a lysine acetyltransferase that regulates a large subset of genes by acetylating histones and non-histone proteins. We previously identified several bladder cancer-associated mutations in EP300 using high-throughput sequencing; however, the functional consequences of these mutations remain unclear. Methods Bladder cancer cells T24 and TCC-SUP were infected with shEP300 lentiviruses to generate stable EP300 knockdown cell lines. The expression levels of EP300, p16 and p21 were detected by real-time PCR and western blots. The transcriptional activity of p16 and p21 were detected by dual luciferase assay. Cell proliferation assay, flow cytometric analyses of cell cycle, invasion assay and xenograft tumor model were used to measure the effect of EP300-R1627W mutation in bladder cancer. Immunoprecipitation was used to explore the relationship between EP300-R1627W mutation and p53. Structural analysis was used to detect the structure of EP300-R1627W protein compared to EP300-wt protein. Results we screened the mutations of EP300 and found that the EP300-R1627W mutation significantly impairs EP300 transactivation activity. Notably, we demonstrated that the R1627W mutation impairs EP300 acetyltransferase activity, potentially by interfering with substrate binding. Finally, we show that EP300-R1627W is more aggressive in growth and invasion in vitro and in vivo compared to cells expressing EP300-wt. We also found that the EP300-R1627W mutation occurs frequently in seven different types of cancers. Conclusion In summary, our work defines a driver role of EP300-R1627W in bladder cancer development and progression.

Background: Pancreatic cancer (PC) is one of the most aggressive cancers worldwide. Although many studies have investigated genomic alterations, the genomic landscape of Japanese PC patients has not been fully elucidated. Methods: We used whole‐exome sequencing, cancer gene panel deep‐sequencing, and microarray gene expression profiling data derived from the Japanese version of the Cancer Genome Atlas (JCGA) in 93 PC cases. Results: Somatic driver mutations were identified in 65.6% of samples in 19 genes. The median tumor mutation burden (TMB) value was 0.24 Muts/Mb (interquartile range, 0.15–0.64 Muts/Mb). The commonly mutated genes were KRAS (58%), TP53 (40%), CDKN2A (10%), SMAD4 (10%), FGFR2 (9%), and PKHD1 (9%). Frequent germline variation genes were BRCA1 (8%), CDH1 (5%), MET (5%), MSH6 (5%), and TEK (5%). Frequent chromosomal arm alterations included copy number gains in 2q (42%), 7q (24%), and 3q (24%), and copy number losses in 19p (62%), 19q (47%), 12q (34%), and 7q (30%). A prognostic analysis according to the presence of driver mutations showed that overall survival (OS) in the driver mutation‐positive group was significantly worse in comparison to that of the driver mutation‐negative group (median, 23.1 vs 46.7 mo; P =.010). A Cox proportional hazards analysis for OS identified driver mutation (hazard ratio [HR], 1.89; P =.025) and lymph node metastasis (HR, 3.27; P =.002) as independent prognostic factors. Conclusion: The present results from the JCGA dataset constitute a fundamental resource for genomic medicine for PC patients, especially in Japan. [ABSTRACT FROM AUTHOR]

Simple Summary: Cholangiocarcinoma (CCA) is a chemotherapy-resistant cancer. Reportedly, combination chemotherapy that includes immune checkpoint inhibitors (ICIs) showed superior effects compared to conventional chemotherapy for the treatment of advanced CCA. Although the efficacy of ICIs is considered to be affected by the tumor immune microenvironment (TME), the genetic/epigenetic background associated with TME in CCA is unknown. Here, we find that downregulations of genes involved in antigen presentation are associated with a "non-inflamed" tumor; the downregulations are inversely correlated with their DNA methylation levels. All tumors in the "inflamed" group exhibited an upregulation/low-methylation pattern. In contrast, the majority of CCAs in the non-inflamed group represent a downregulation/high-methylation pattern in antigen-presenting machineries. In addition, unique gene mutations of CCA that should induce DNA methylation events, like those in IDH1/2, are exclusively observed in CCAs carrying a non-inflamed tumor phenotype. These results may prove to be a clue to develop novel biomarkers and combination therapies for the treatment of CCA using ICIs. Cholangiocarcinoma (CCA) is a refractory cancer; a majority of CCAs represents a non-inflamed tumor phenotype that should be resistant to treatment, including immune checkpoint inhibitors (ICIs). In this study, we aimed to understand the molecular characteristics associated with non-inflamed CCAs. The genetic/epigenetic status of 36 CCAs was obtained from the Cancer Genome Atlas (PanCancerAtlas). CCAs were classified based on immune class using hierarchical clustering analysis of gene expressions related to tumor-infiltrating lymphocytes. The associations between immune class and genetic/epigenetic events were analyzed. We found that the tumors with alterations in FGFR2 and IDH1/2 had a "non-inflamed" tumor phenotype. A significant association was observed between the non-inflamed group and the downregulation of genes involved in antigen presentation (p = 0.0015). The expression of antigen-presenting machineries was inversely correlated with their DNA methylation levels, where 33.3% of tumors had an upregulation/low-methylation pattern, and 66.7% of tumors had a downregulation/high-methylation pattern. All tumors in the "inflamed" group exhibited an upregulation/low-methylation pattern. In contrast, 24 of 30 tumors in the non-inflamed group represent the downregulation/high-methylation pattern (p = 0.0005). Methylation with downregulation of antigen-presenting machineries is associated with the "non-inflamed" tumor phenotype of CCAs. This evidence provides important insights for developing new strategies for treating CCA. [ABSTRACT FROM AUTHOR]

Background: Hepatitis B virus (HBV) infection is one of the major causes of chronic liver disease, which progresses from chronic hepatitis B (CHB) to fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Early detection and laboratory-based screening of hepatocellular carcinoma are still major challenges. This study was undertaken to determine whether the cancer hallmark gene signatures that are released into circulation as circulating tumour DNA (ctDNA) can be used as a liquid biopsy marker for screening, early detection, and prognosis of HCC.Methods: A total of 130 subjects, including HBV-HCC (n = 80), HBV-cirrhotic and non-cirrhotic (n = 35), and healthy (n = 15) controls, were evaluated for TP53 and beta-catenin (CTNNB1) gene hotspot mutations in ctDNA by Sanger-based cycle sequencing and droplet digital PCR (ddPCR) assays. Mutation detection frequency, percentage mutant fractions, and their association with tumour stage, mortality, and smoking habits were determined.Results: Sanger-based cycle sequencing was carried out for 32 HCC patients. Predict SNP Tools analysis indicated several pathogenic driver mutations in the ctDNA sequence, which include p.D228N, p.C229R, p.H233R, p.Y234D, p.S240T, p.G245S, and p.R249M for TP53 gene exon 7 and p.S33T for CTNNB1 gene exon 3. The TP53 c.746G>T (p.R249M) mutation was detected predominately (25% cases) by sequencing, but there was no dominant mutation at position c.747G>T (p.R249S) that was reported for HBV-HCC patients. A dual-probe ddPCR assay was developed to determine mutant and wild-type copy numbers of TP53 (p.R249M and p.R249S) and CTNNB1 (p.S45P) and their percentage mutant fraction in all 130 subjects. The TP53 R249M and CTNNB1 S45P mutations were detected in 31.25% and 26.25% of HCC patients, respectively, with a high mutant-to-wild-type fraction percentage (1.81% and 1.73%), which is significant as compared to cirrhotic and non-cirrhotic patients. Poor survival was observed in HCC patients with combined TP53 and CTNNB1 gene driver mutations. The TP53 R249M mutation was also significantly (p < 0.0001) associated with smoking habits (OR, 11.77; 95% CI, 3.219–36.20), but not the same for the TP53 R249S mutation.Conclusion: Screening of ctDNA TP53 and CTNNB1 gene mutations by ddPCR may be helpful for early detection and identifying the risk of HCC progression.

Abstract Purpose Patients with non‐small cell lung cancer (NSCLC) that harbor driver mutations are associated with a cancer diagnosis at a younger age. While targeted therapies provide deep remissions and durable benefit in a subset of patients, it is unclear whether targeted therapies bridge the gap in years of life lost (YLL) in these younger NSCLC patients with targetable mutations in comparison to generally older NSCLC patients without actionable driver mutations. Materials and Methods Retrospective cross‐sectional study using landmark trials leading to the approval of targeted therapies in NSCLC with actionable mutations. We evaluated all targeted therapies as well as chemotherapy and IO regimens for the treatment of NSCLC through FDA Oncology Announcements and NCCN Guidelines for NSCLC (version 4.2021). Results We estimated the YLL for each driver mutation, cumulative median duration of response (DOR) with targeted therapies by mutation type, and percentage of estimated improvement in YLL from NSCLC targeted therapies. The median ages at diagnosis (in years) for patients whose tumors express targetable mutations were: 47.6 (NTRK); 52.0 (ALK); 62.0 (HER2); 57.0 (ROS1); 61.4 (RET); 63.0 (BRAF); 69.0 (EGFR); and 72.0 (MET). For comparison, the median age at diagnosis for patients without driver mutations, regardless of PD‐L1 status was 71 years. The median DOR (in years) for patients whose tumors express the same mutations include: 0.9 (NTRK); 3.9 (ALK); 0.6 (HER2); 6.2 (ROS1); 2.2 (RET); 1.5 (BRAF); 3.1 (EGFR); and 2.4 (MET). The median DOR for patients without driver mutations was 1.2 years. The cumulative estimated survival time (years; median age at diagnosis plus the median DOR or OS) for patients whose tumors express targetable mutations were: 48.5 (NTRK); 55.9 (ALK); 62.6 (HER2); 63.2 (ROS1); 63.6 (RET); 64.5 (BRAF); 72.1 (EGFR); and 74.4 (MET). The cumulative estimated survival time for patients without driver mutations, regardless of PD‐L1 status, was 72.2 years of age. We calculated the number of years NSCLC is diagnosed earlier in patients with targetable mutations as follows: 23.4 (NTRK), 19 (ALK), 14 (ROS1), 11 (EGFR), 9.6 (RET), 9 (HER2), and 8 (BRAF). The percent difference (%) ameliorated in YLL by mutation type is as follows: 44.3 (ROS1), 28.2 (EGFR), 22.9 (RET), 20.5 (ALK), 18.8 (BRAF), 6.4 (HER2), and 3.7 (NTRK). Conclusion Although targeted therapies have paved the way for significant progress toward providing a survival benefit to many young patients with advanced NSCLC with actionable mutations, it is evident that these therapies still leave a wide gap in the YLL in these younger patients compared to generally older individuals with advanced NSCLC without targetable mutations.

Abstract Background We previously reported a familial thyroid follicular cell carcinoma (FCC) in a large number of Dutch German longhaired pointers and identified two deleterious germline mutations in the TPO gene associated with disease predisposition. However, the somatic mutation profile of the FCC in dogs has not been investigated at a genome-wide scale. Results Herein, we comprehensively investigated the somatic mutations that potentially contribute to the inherited tumor formation and progression using high depth whole-genome sequencing. A GNAS p.A204D missense mutation was identified in 4 out of 7 FCC tumors by whole-genome sequencing and in 20 out of 32 dogs’ tumors by targeted sequencing. In contrast to this, in the human TC, mutations in GNAS gene have lower prevalence. Meanwhile, the homologous somatic mutation in humans has not been reported. These findings suggest a difference in the somatic mutation landscape between TC in these dogs and human TC. Moreover, tumors with the GNAS p.A204D mutation had a significantly lower somatic mutation burden in these dogs. Somatic structural variant and copy number alterations were also investigated, but no potential driver event was identified. Conclusion This study provides novel insight in the molecular mechanism of thyroid carcinoma development in dogs. German longhaired pointers carrying GNAS mutations in the tumor may be used as a disease model for the development and testing of novel therapies to kill the tumor with somatic mutations in the GNAS gene.

Bulk sequencing is commonly used to characterize the genetic diversity of cancer cell populations in tumors and the evolutionary relationships of cancer clones. However, bulk sequencing produces aggregate information on nucleotide variants and their sample frequencies, necessitating computational methods to predict distinct clone sequences and their frequencies within a sample. Interestingly, no methods are available to measure the statistical confidence in the variants assigned to inferred clones. We introduce a bootstrap resampling approach that combines clone prediction and statistical confidence calculation for every variant assignment. Analysis of computer-simulated datasets showed the bootstrap approach to work well in assessing the reliability of predicted clones as well downstream inferences using the predicted clones (e.g., mapping metastatic migration paths). We found that only a fraction of inferences have good bootstrap support, which means that many inferences are tentative for real data. Using the bootstrap approach, we analyzed empirical datasets from metastatic cancers and placed bootstrap confidence on the estimated number of mutations involved in cell migration events. We found that the numbers of driver mutations involved in metastatic cell migration events sourced from primary tumors are similar to those where metastatic tumors are the source of new metastases. So, mutations with driver potential seem to keep arising during metastasis. The bootstrap approach developed in this study is implemented in software available at https://github.com/SayakaMiura/CloneFinderPlus.

Introduction: Driver mutations play a critical role in the occurrence and development of human cancers. Most studies have focused on missense mutations that function as drivers in cancer. However, accumulating experimental evidence indicates that synonymous mutations can also act as driver mutations. Methods: Here, we proposed a computational method called PredDSMC to accurately predict driver synonymous mutations in human cancers. We first systematically explored four categories of multimodal features, including sequence features, splicing features, conservation scores, and functional scores. Further feature selection was carried out to remove redundant features and improve the model performance. Finally, we utilized the random forest classifier to build PredDSMC. Results: The results of two independent test sets indicated that PredDSMC outperformed the state-of-the-art methods in differentiating driver synonymous mutations from passenger mutations. Discussion: In conclusion, we expect that PredDSMC, as a driver synonymous mutation prediction method, will be a valuable method for gaining a deeper understanding of synonymous mutations in human cancers. [ABSTRACT FROM AUTHOR]

Introduction: Considerable differences of treatment response and pattern of failure may exist between definitive chemoradiation (CRT) treated locally advanced non‐small cell lung cancer (LA‐NSCLC) patients. The clinical value of additional tyrosine kinase inhibitors (TKIs) before disease recurrence and salvage local therapy after initial recurrent disease remain controversial. Methods and Materials: Consecutive LA‐NSCLC patients receiving definitive CRT and having definite results about driver mutations (EGFR, ALK and ROS1) were retrospectively reviewed. Initial recurrent disease was classified as in‐field recurrence, out‐of‐field recurrence and distant metastasis. Recurrent disease occurred only in the brain or limited to ≤3 extra‐cranial organs and ≤5 extra‐cranial lesions, was defined as oligo‐recurrence. Progression free survival and overall survival (OS) were calculated from diagnosis to disease progression or death, and to death, respectively. OS2 was measured from initial disease recurrence to death among patients who had recurrent disease. Results: Of the 153 enrolled patients, 39 had driver mutations and 13 received additional TKI therapy besides definitive CRT. Patients harboring driver mutations but without additional TKI therapy had a similar PFS and significantly longer OS (p = 0.032) than those without driver mutations. Additional TKI therapy prolonged PFS (p = 0.021) but not OS among patients with driver mutations. No significant difference of pattern of failure was observed between patient subgroups stratified by the status of driver mutations and the usage of additional TKI therapy. Furthermore, 57 of the 95 patients with initial recurrent disease developed oligo‐recurrence and salvage local therapy significantly improved OS2 (p = 0.01) among patients with oligo‐recurrence disease. Conclusion: LA‐NSCLC patients receiving definitive CRT generally had similar PFS and pattern of treatment failure, regardless of driver mutation status. Additional TKI therapy besides definitive CRT could prolong PFS but not OS. The majority of recurrent disease after definitive CRT belongs to oligo‐recurrence and salvage local therapy may provide survival benefit. [ABSTRACT FROM AUTHOR]

Non-small cell lung cancer (NSCLC) is the most common lung cancer diagnosis, among which epidermal growth factor receptor (EGFR), Kirsten rat sarcoma (KRAS), and anaplastic lymphoma kinase (ALK) mutations are the common genetic drivers. Their relative tyrosine kinase inhibitors (TKIs) have shown a better response for oncogene-driven NSCLC than chemotherapy. However, the development of resistance is inevitable following the treatments, which need a new strategy urgently. Although immunotherapy, a hot topic for cancer therapy, has shown an excellent response for other cancers, few responses for oncogene-driven NSCLC have been presented from the existing evidence, including clinical studies. Recently, the tumor microenvironment (TME) is increasingly thought to be a key parameter for the efficacy of cancer treatment such as targeted therapy or immunotherapy, while evidence has also shown that the TME could be affected by multi-factors, such as TKIs. Here, we discuss changes in the TME in NSCLC after TKI treatments, especially for EGFR-TKIs, to offer information for a new therapy of oncogenedriven NSCLC. [ABSTRACT FROM AUTHOR]

Objective: This study aimed to examine the mutation panel studied with liquid biopsy in patients diagnosed with lung adenocancer and to investigate its relationship with survival. Materials and Methods: The study comprised 24 patients diagnosed with lung adenocarcinoma between the ages of 18 and 80 who were metastatic and had not yet received treatment. Using the next-generation sequencing commercial kit 56G Oncology Panel, the cfDNAs (cell-free DNAs) isolated from the patient's blood were analyzed. SOPHiA DDM® (Saint-Sulpice, Switzerland) bioinformatics program was used to classify the detected genetic variants. The patients were followed for 3 years in terms of survival. For the statistical analysis, R Version 4.1.3 (https://rstudio.com/) and TURCOSA Analytical (https://turcosa.com.tr/) software was used. Results: Mutation was found in liquid biopsy in 16 (66.7%) of the patients, and more than one mutation was detected in seven (29.1%) patients. The relationship between the variables and mortality was examined in the cases included in the study; there was a significant relationship between age and mortality (p=0.029), and mortality was increasing with aging. In the survival analysis, no statistically significant relationship was found between gender, smoking status, mutation status, and survival according to Kaplan--Meier graphs and log-rank tests. Conclusion: Therefore, driver mutation was detected in 66.7% of the patients. Liquid biopsy may be essential in the progression of lung adenocarcinoma to detect the driver mutations, which are targets for treatments. [ABSTRACT FROM AUTHOR]

Regional lymph node metastasis (LNM) increases the risk of distant metastasis in papillary thyroid cancer (PTC) patients. However, it remains unclear how tumor cells in PTC patients with LNM evade immune system surveillance and proceed to colonize distant organs. Here, we comprehensively characterize the tumor-infiltrating immune cell landscape in PTC with LNM. LNM-related genes include multiple important soluble mediators such as CXCL6, IL37, MMP10, and COL11A1, along with genes involved in areas such as extracellular matrix organization and TLR regulation by endogenous ligands. In PTC without LNM, the tumor infiltration of activated dendritic cells and M0 macrophages showed increases from normal cells, but with yet greater increases and correspondingly worse prognosis in PTC with LNM. Conversely, the tumor infiltration of activated NK cells and eosinophils was decreased in PTC without LNM, as compared to normal cells, and yet further decreased in PTC with LNM, with such decreases associated with poor prognosis. We further demonstrate that mutations of driver genes in tumor cells influence the infiltration of surrounding immune cells in the tumor microenvironment (TME). Particularly, patients carrying TG mutations tend to show increased filtration of M2 macrophages and activated NK cells in the TME, whereas patients carrying HRAS mutations tend to show reduced filtration of M0 macrophages and show enhanced filtration of activated dendritic cells in the TME. These findings increase our understanding of the mechanisms of regional lymph node metastasis in PTC and its associated tumor microenvironment, potentially facilitating the development of personalized treatment regimens to combat immunotherapy failure. [ABSTRACT FROM AUTHOR]

Background: Primary liver cancer (PLC) is classified into hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC), and combined hepatocellular and intrahepatic cholangiocarcinoma (CHC). We investigated the genomic landscape of PLC according to the histological classification and established a cross-histological molecular subtyping for PLC by a multi-omics analysis. Methods: We analyzed 265 PLC cases with whole-exome sequencing and DNA copy number analyses and 251 cases with gene expression profiling. Results: The cohort included HCC (n = 223, 84%), ICC (n = 34, 13%), and CHC (n = 8, 3%). Mutation analyses identified histological type-specific driver genes, such as CTNNB1 in HCC and KRAS, IDH1, and PIK3CA in ICC, and ARID1A and KMT2C in CHC. The tumor suppressor gene TP53 mutation was detected in 21.1% of HCC, 16.1% of ICC, and 25.0% of CHC cases. Other well- characterized tumor suppressor genes included RB1, which was mutated in 2.8% of HCC and 3.2% of ICC; and PTEN, which was mutated in 1.4% of HCC, 3.2% of ICC, and 12.5% of CHC cases. DNA copy number analyses identified focal amplifications, with NUF2 (1q23.3) the most frequently detected as an amplified gene in all 3 types (HCC, 3.8%; CHC, 12.5%, ICC, 3.2%). Molecular subtyping for PLC based on the multi-omics analysis identified three subtypes, one of which was associated with recurrence after resection and amplified genes located at chromosome 8q. Conclusions: Our dataset serves as a fundamental resource for genomic medicine for PLC in Japan and identified amplified genes located at chromosome 8q as promising therapeutic targets for the subgroup with a poor prognosis. [ABSTRACT FROM AUTHOR]

Background: Bladder cancer (BCa) is the most common malignant tumor of the urinary system, with transitional cell carcinoma (TCC) being the predominant type. EP300 encodes a lysine acetyltransferase that regulates a large subset of genes by acetylating histones and non-histone proteins. We previously identified several bladder cancer-associated mutations in EP300 using high-throughput sequencing; however, the functional consequences of these mutations remain unclear. Methods: Bladder cancer cells T24 and TCC-SUP were infected with shEP300 lentiviruses to generate stable EP300 knockdown cell lines. The expression levels of EP300, p16 and p21 were detected by real-time PCR and western blots. The transcriptional activity of p16 and p21 were detected by dual luciferase assay. Cell proliferation assay, flow cytometric analyses of cell cycle, invasion assay and xenograft tumor model were used to measure the effect of EP300-R1627W mutation in bladder cancer. Immunoprecipitation was used to explore the relationship between EP300-R1627W mutation and p53. Structural analysis was used to detect the structure of EP300-R1627W protein compared to EP300-wt protein. Results: we screened the mutations of EP300 and found that the EP300-R1627W mutation significantly impairs EP300 transactivation activity. Notably, we demonstrated that the R1627W mutation impairs EP300 acetyltransferase activity, potentially by interfering with substrate binding. Finally, we show that EP300-R1627W is more aggressive in growth and invasion in vitro and in vivo compared to cells expressing EP300-wt. We also found that the EP300-R1627W mutation occurs frequently in seven different types of cancers. Conclusion: In summary, our work defines a driver role of EP300-R1627W in bladder cancer development and progression. [ABSTRACT FROM AUTHOR]

Lung cancer is the leading cause of cancer deaths in the United States and the world. It is divided into two major types: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). In the tumor-node-metastasis (TNM) cancer-staging classification system (Stages I/II/III/IV), the severity of neoplastic growth is characterized by the size of the tumor (T1 to T4), the extent of lymph node involvement (N0 to N3), and whether (M1) or not (M0) distant metastasis has occurred. Surgery is the treatment of choice for medically fit patients with Stage I/II NSCLC. Combination chemoradiotherapy and immune checkpoint inhibitor therapy are used across all NSCLC types. Oncogene-addicted tumors with sensitizing EGFR or BRAF mutations or activating ALK , ROS1 or NTRK translocations are treated with their cognate orally active small molecule protein kinase blockers. On the order of 20 % of NSCLCs bear activating mutations in EGFR and are treated with osimertinib and other kinase antagonists. SCLC, which accounts for approximately 15 % of lung cancer cases, is a deadly high-grade neuroendocrine carcinoma with a poor prognosis. Limited-stage SCLC is confined to one hemi-thorax and one radiation port and extensive-stage disease signifies those cancers that do not meet the criteria for limited-stage disease. Local treatment options to control thoracic disease include radiotherapy and surgery. In patients with extensive-stage disease, a platinum agent (cisplatin or carboplatin) combined with etoposide and an anti-PDL1 inhibitor (atezolizumab or durvalumab) for four cycles followed by anti-PDL1 maintenance therapy is the recommended first-line regimen. [Display omitted] [ABSTRACT FROM AUTHOR]

We report a rare case of stage IV pulmonary combined large-cell neuroendocrine carcinoma (LCNEC) and adenocarcinoma (ACA), both demonstrating anaplastic lymphoma kinase (ALK) rearrangement by IHC and FISH. This 61-year-old lifelong nonsmoking Asian woman presented with a cough, and after diagnosis and surgical treatment, completed four cycles of adjuvant cisplatin and etoposide chemotherapy. She subsequently developed recurrence with bony metastases of exclusively ALK-positive LCNEC. Alectinib was started, and the patient experienced a partial response.

Hippo signaling has been recognized as a key tumor suppressor pathway. Here, we perform a comprehensive molecular characterization of 19 Hippo core genes in 9,125 tumor samples across 33 cancer types using multidimensional "omic" data from The Cancer Genome Atlas. We identify somatic drivers among Hippo genes and the related microRNA (miRNA) regulators, and using functional genomic approaches, we experimentally characterize YAP and TAZ mutation effects and miR-590 and miR-200a regulation for TAZ. Hippo pathway activity is best characterized by a YAP/TAZ transcriptional target signature of 22 genes, which shows robust prognostic power across cancer types. Our elastic-net integrated modeling further reveals cancer-type-specific pathway regulators and associated cancer drivers. Our results highlight the importance of Hippo signaling in squamous cell cancers, characterized by frequent amplification of YAP/TAZ, high expression heterogeneity, and significant prognostic patterns. This study represents a systems-biology approach to characterizing key cancer signaling pathways in the post-genomic era.

Over the last decade there has been a rapid expansion of clinically actionable driver mutations in non-small cell lung cancer (NSCLC), with an unprecedented number of corresponding targeted therapies approved and funded for use in the clinic. Here we summarise the approach taken in Wales to embed a NSCLC biomarker testing pathway within the National Optimal Pathway for Lung Cancer. The Welsh Thoracic Oncology Group established a working group tasked with progressing the standardisation of genomic testing. In July 2021, the 10 lung cancer multidisciplinary teams (MDTs) were invited to take part in a national survey of current biomarker testing practices and a retrospective audit of the next generation sequencing (NGS) pathway in Wales was conducted. Seventy per cent of MDTs completed the survey, which confirmed variability in the approach to testing with respect to timing of requests, patient selection and testing technologies used. Only 43% reported having pathology-initiated reflex testing, but 87% had adopted DNA and RNA NGS testing as their standard-of-care genomic testing strategy. Data from 53 patients with stage III–IV NSCLC with genomic testing requested between October 2020 and May 2021 were analysed in the NGS pathway audit. Forty (75.5%) patients had both DNA and RNA NGS requested, with a median turnaround time from biopsy to results of 26 days (range 19–37 days) and 25 days (range 16–38 days), respectively. The geographical location of MDT did not influence turnaround times and MDTs with reflex testing had shorter biopsy-to-result times. DNA NGS testing was successful in 51 (96.2%) patients; in those who had RNA NGS, testing was successful in 30 (75%) patients. Significant progress has been made within Wales to implement a national biomarker testing pathway, with reflex testing becoming standard of care. However, challenges remain in optimising the quantity and quality of tissue available for testing, together with a need to reduce turnaround times. This will need to be addressed to ensure all eligible patients are tested at the right time in the diagnostic pathway to facilitate optimal treatment strategies and ultimately improve outcomes. [ABSTRACT FROM AUTHOR]

The incidence and mortality of lung cancer rank top three of all cancers worldwide. Accounting for 85% of the total number of lung cancer, non-small cell lung cancer (NSCLC) is an important factor endangering human health. Recently, targeted therapies against driver mutations and epigenetic alterations have made encouraging advances that benefit NSCLC patients. Druggable driver mutations, which mainly occur in EGFR, KRAS, MET, HER2, ALK, ROS1, RET and BRAF, have been identified in more than a quarter of NSCLC patients. A series of highly selective mutant targeting inhibitors, such as EGFR tyrosine kinase inhibitors and KRAS inhibitors, have been well studied and applied in clinical treatments, which greatly promote the overall survival of NSCLC patients. However, drug resistance has become a major challenge for targeted treatment, and a variety of methods to overcome drug resistance are constantly being developed, including inhibitors against new mutants, combination therapy with other pathway inhibitors, etc. In addition, epigenetics-based therapy is emerging. Epigenetic regulators such as histone deacetylases and non-coding RNA play a crucial role in the development of cancer and drug resistance by affecting multiple signaling pathways. Epigenetics-based therapeutic strategies combined with targeted drugs show great clinical potential. Many agents targeting epigenetic changes are being investigated in preclinical studies, with some already under clinical trials. This article focuses on driver mutations and epigenetic alterations in association with relevant epidemiological data. We introduce the current status of targeted inhibitors and known drug resistance, review advances in major targeted therapies with recent data from preclinical and clinical trials, and discuss the possibility of combination therapy against driver mutations and epigenetic alterations in overcoming drug resistance. [ABSTRACT FROM AUTHOR]

Background: We previously reported a familial thyroid follicular cell carcinoma (FCC) in a large number of Dutch German longhaired pointers and identified two deleterious germline mutations in the TPO gene associated with disease predisposition. However, the somatic mutation profile of the FCC in dogs has not been investigated at a genome-wide scale. Results: Herein, we comprehensively investigated the somatic mutations that potentially contribute to the inherited tumor formation and progression using high depth whole-genome sequencing. A GNAS p.A204D missense mutation was identified in 4 out of 7 FCC tumors by whole-genome sequencing and in 20 out of 32 dogs' tumors by targeted sequencing. In contrast to this, in the human TC, mutations in GNAS gene have lower prevalence. Meanwhile, the homologous somatic mutation in humans has not been reported. These findings suggest a difference in the somatic mutation landscape between TC in these dogs and human TC. Moreover, tumors with the GNAS p.A204D mutation had a significantly lower somatic mutation burden in these dogs. Somatic structural variant and copy number alterations were also investigated, but no potential driver event was identified. Conclusion: This study provides novel insight in the molecular mechanism of thyroid carcinoma development in dogs. German longhaired pointers carrying GNAS mutations in the tumor may be used as a disease model for the development and testing of novel therapies to kill the tumor with somatic mutations in the GNAS gene. [ABSTRACT FROM AUTHOR]

Simple Summary: There are growing data on targeting HER2 alterations, which include gene mutations, gene amplifications, and protein overexpression, for non-small cell lung cancer (NSCLC). Currently, there are limited targeted therapies approved for NSCLC patients with HER2 alterations, and this remains an unmet clinical need. There has been an influx of research on antibody–drug conjugates, monoclonal antibodies, and tyrosine kinase inhibitors. This review discusses the diagnostic challenges of HER2 alterations in NSCLC and summarizes recent progress in HER2 targeted drugs for both clinicians and researchers treating this patient population. Human epidermal growth factor receptor 2 (HER2), a member of the ERBB family of tyrosine kinase receptors, has emerged as a therapeutic target of interest for non-small cell lung cancer (NSCLC) in recent years. Activating HER2 alterations in NSCLC include gene mutations, gene amplifications, and protein overexpression. In particular, the HER2 exon 20 mutation is now a well clinically validated biomarker. Currently, there are limited targeted therapies approved for NSCLC patients with HER2 alterations. This remains an unmet clinical need, as HER2 alterations are present in 7–27% of de novo NSCLC and may serve as a resistance mechanism in up to 10% of EGFR mutated NSCLC. There has been an influx of research on antibody–drug conjugates (ADCs), monoclonal antibodies, and tyrosine kinase inhibitors (TKIs) with mixed results. The most promising therapies are ADCs (trastuzumab-deruxtecan) and novel TKIs targeting exon 20 mutations (poziotinib, mobocertinib and pyrotinib); both have resulted in meaningful anti-tumor efficacy in HER2 mutated NSCLC. Future studies on HER2 targeted therapy will need to define the specific HER2 alteration to better select patients who will benefit, particularly for HER2 amplification and overexpression. Given the variety of HER2 targeted drugs, sequencing of these agents and optimizing combination therapies will depend on more mature efficacy data from clinical trials and toxicity profiles. This review highlights the challenges of diagnosing HER2 alterations, summarizes recent progress in novel HER2-targeted agents, and projects next steps in advancing treatment for the thousands of patients with HER2 altered NSCLC. [ABSTRACT FROM AUTHOR]

Summary: The biology of non-small cell lung cancer (NSCLC) is driven by a complex mutational landscape, and the detection of driver molecular alterations by next-generation sequencing is key for identification of druggable alterations. Thus, broad molecular profiling displays a standard-of-care approach particularly in patients with advanced adenocarcinoma at the time of the initial diagnosis, but also at the time of acquired resistance to tyrosine kinase inhibitors, guiding further treatment choices. Sequencing of plasma-circulating tumor DNA is of increasing importance in NSCLC diagnostics due to the easy accessibility, representing an optimal tool for longitudinal monitoring of the disease course. [ABSTRACT FROM AUTHOR]