Genetic mutations in recurrent and/or metastatic squamous cell carcinoma of unknown primary – an analysis of the Japanese national genomic profiling database

<b>Introduction:</b> Although genetic mutations have been reported in nasopharyngeal carcinoma (NPC), there are currently no scientifically validated treatments targeting these mutations. Furthermore, cancer genomic profiling tests are underutilized in clinical practice. This highlights an urgent need to explore the genomic landscape of NPC and its potential therapeutic implications.<b>Aim:</b> The aim of this study is to investigate the genetic mutational landscape of recurrent and/or metastatic nasopharyngeal carcinoma (NPC).<b>Materials and methods:</b> Data were analyzed for 67 consecutive patients with NPC registered at the Japan National Cancer Center, Center for Cancer Genomics and Advanced Therapeutics (C-CAT) between June 2019 and May 2024. Genetic mutations were determined by FoundationOne CDx or Liquid CDx next-generation sequencing. Survival of patients was determined by the log-rank test and a Cox proportional hazards model.<b>Results:</b> The top 10 mutations in NPC were <i>CDKN2A</i> (41.8%), <i>CDKN2B</i> (31.3%), <i>TP53</i> (20.9%), <i>KMT2D</i> (20.9%), <i>DNMT3A</i> (19.4%), <i>NOTCH1</i> (17.9%), <i>STK11</i> (17.9%), <i>MTAP</i> (17.9%), <i>EP300</i> (17.9%), <i>TSC1</i> (13.4%), with 11.1 6.1 (mean SEM) mutations/individual. Mutations in <i>KMT2D</i> (p = 0.0127), <I>DNMT3A</i> (p = 1.41×10<sup>-7</sup>), <i>GNAS</i> (p = 3.64×10<sup>-11</sup>), <i>SPEN</i> (p = 0.0167), <i>BRCA1</i> (p = 0.0379), and <i>KMT2A</i> (p = 2.06×10<sup>-5</sup>) were associated with a significantly worse prognosis, as determined by the log-rank test. The hazard ratios for cases with these mutations were 0.0122 (95% CI, 1.58×10<sup>-4</sup>-0.936, p = 0.046) for <i>TP53</i>, 1847.0 (95% CI, 4.619-7.386×10<sup>5</sup>, p = 0.014) for <i>DNMT3A</i>, 126.7 (95% CI, 1.262-12720, p = 0.039) for <i>BRCA2</i>, 197.9 (95% CI, 2.844-13770, p = 0.015) for <i>ALK</i>, 34.22 (95% CI, 1.256-932.7, p = 0.036) for <i>SPEN</i>, and 6.445×10<sup>-4</sup> (95% CI, 2.913×10<sup>-6</sup>-0.143, p = 7.6×10<sup>-3</sup>) for <i>MYCL</i>.<b>Conclusions:</b> This study identified genetic mutations in recurrent and/or metastatic NPC. Even in advanced cases, prognosis-related mutations were identified, underscoring the importance of cancer genomic profiling tests.

Squamous cell carcinoma of unknown primary (SCCUP): a genomic landscape study

Background/ObjectivesCervical squamous cell carcinoma of unknown primary (SCCUP) is a rare entity within head and neck cancer and both treatment regimens as well as identified potential predictors for oncological outcomes vary between published series. In this study, we evaluated oncological outcomes and identified potential prognostic factors for outcome.Patients and methodsThis retrospective monocentric cohort study includes 82 SCCUP patients diagnosed and treated between January 2000 and June 2021. Overall survival (OS), disease-specific survival (DSS), disease-free survival (DFS) and locoregional recurrence-free survival (LRFS) were evaluated. The Cox proportional hazards model was used to analyze the prognostic effect of patient and tumor characteristics on oncological outcomes.ResultsFive year OS, DSS, DFS and LRFS were respectively 53.9%, 72.2%, 68.9% and 67.3%. The p16 status was evaluated in 55 patients with 40% being p16 positive. On univariable analysis, p16 negative SCCUPs had significantly worse survival and recurrence rates in the presence of clinical extranodal extension (cENE) (OS: p=0.0013, DSS: p=0.0099, DFS: p=0.0164, LRFS: p=0.0099) and radiological extranodal extension (rENE) (OS: p=0.0034, DSS: p=0.0137, DFS: p=0.0167, LRFS: p=0.0100). In p16 positive SCCUP patients, rENE had a significantly negative prognostic effect on DFS (p=0.0345) and LRFS (p=0.0367). Total group multivariate analysis identified rENE as an independent negative predictor for all oncological outcomes. The “number of positive lymph nodes” was a second independent predictor for DSS (p=0.0257) and DFS (p=0.0435).ConclusionsWe report favorable oncological outcomes, comparable to previously published results. Although the presence of rENE seems associated with poor oncological outcomes, the differential effect of clinical, radiological and pathological ENE in both p16 positive and negative subgroups remain to be elucidated by further prospective research.

Chromosomal aberrations are known to drive metastatic spread, but their profile is still elusive in carcinoma of unknown primary (CUP). Therefore, the aim of this study was to characterize the chromosomal aberration pattern in CUP depending on histological and clinical features and to assess its prognostic impact together with chromothripsis, tumor mutational burden (TMB), microsatellite instability (MSI), and mutational profiles as potential prognostic biomarkers. Chromosomal aberrations and chromothripsis were detected by methylation-based copy number variation (CNV) analysis, whereas TMB and MSI were calculated based on large next-generation sequencing (NGS) panels. Putative primaries were assigned by consensus between two independent oncologists. CNV losses varied depending on putative primaries and were more abundant in patients harboring TP53 mutations and/or deletions 17p. CNV loss was prognostically adverse in localized CUP treated with surgery and/or radiotherapy, but not in disseminated poor-risk CUP treated with palliative chemotherapy. CNV loss also worsened the prognosis in squamous cell CUP. Chromothripsis was detected in 18/59 (30.5%) patients without prognostic effect. TMB was highest in cases with MSI, squamous cell histology, and with lung, anal or cervical putative primaries. Overall, CNV, chromothripsis, TMB, and MSI profiles in CUP are reminiscent of biological characteristics known from other cancer entities without a unifying CUP-specific signature. Markedly, high-level CNV loss is an adverse predictive biomarker in localized but not disseminated chemotherapy-treated CUP. This implies that chromosomal losses drive CUP progression, but also increase susceptibility to chemotherapy, with both effects apparently leveling out in disseminated CUP.

Due to the diversity of histopathologic types in salivary gland carcinoma, genomic analysis of large cohorts with next-generation sequencing by histologic type has not been adequately performed. We analysed data from 93 patients with salivary duct carcinoma and 243 patients with adenoid cystic carcinoma who underwent comprehensive genomic profiling testing in the Center for Cancer Genomics and Advanced Therapeutics database, a Japanese national genome profiling database. We visualised gene mutation profiles using the OncoPrinter platform. Fisher's exact test, Kaplan-Meier analysis, log-rank test and Cox regression models were used for statistical analysis. In salivary duct carcinoma, a population with CDK12 and ERBB2 co-amplification was detected in 20 of 37 (54.1%) patients with ERBB2 amplification. We identified five loss-of-function variants in genes related to homologous recombination deficiency, such as BRCA2 and CDK12. Cox survival analysis showed that CDK12 and ERBB2 co-amplification is associated with overall survival (hazard ratio, 3.597; P=0.045). In salivary duct carcinoma, NOTCH1 mutations were the most common, followed by mutations in chromatin modification genes such as KMT2D, BCOR, KDM6A, ARID1A, EP300 and CREBBP. In the multivariate Cox analysis, activating NOTCH1 mutations (hazard ratio, 3.569; P=0.009) and ARID1A mutations (hazard ratio, 4.029; P=0.034) were significantly associated with overall survival. CDK12 and ERBB2 co-amplification is associated with a poor prognosis in salivary duct carcinoma. Chromatin remodelling genes are deeply involved in tumour progression in adenoid cystic carcinoma. One such gene, ARID1A, was an independent prognostic factor. In salivary duct carcinoma and adenoid cystic carcinoma, there might be minor populations with mutations that could be targeted for treatment with the synthetic lethality approach.

Carcinoma of unknown primary (CUP) is a rare malignancy characterized by metastatic disease without an identifiable primary tumor, even after extensive diagnostic evaluation. This case report described a 70-year-old female patient with squamous cell CUP (SCCUP) who initially presented with elevated carbohydrate antigen 19–9 and a diaphragmatic mass. Despite comprehensive workup, including 18F-fluorodeoxyglucose positron emission tomography–computed tomography and a 90-gene expression assay, the primary site remained unclear. The patient underwent surgical resection followed by two cycles of systematic therapy and achieved a disease-free survival of 14 months. This case underscores the limitations of the current diagnostic tools and the potential role of multimodal therapy in the management of CUP. The discordance between molecular testing and the clinical findings further emphasizes the perplexing nature of CUP. This report also reviews the literature on diagnosis and therapeutic options. Due to the absence of standardized regimens, future international collaboration and comprehensive genomic profiling are warranted to advance the understanding of this heterogeneous disease.

7 Background: Nodal metastases from SCC are a clinical challenge in urologic and gynecologic oncology. Strategies employing CGP to identify targeted therapies for CUPs have shown potential; however, the molecular landscape of SCCUP remains poorly defined. We report the results of CGP testing in patients with SCCUPs identified in the Foundation Medicine, Inc. database, with a focus on those with I/P/RP involvement. Methods: SCCUP cases with FoundationOneCDx (F1CDx) assay results were identified based on a reported diagnosis of CUP and the presence of SCC histology. After central pathologist review, cases were excluded if a known primary site could be determined based on histology and disease location. Cases with I/P/RP involvement were selected based on the site of tissue biopsy. Genomic alterations (GAs) were assessed using the FoundationCORE database. Results: Ninety-seven cases of SCCUP presenting with I/P/RP involvement were identified. GAs were observed in 140 of 324 genes evaluated by the F1CDx assay. The most frequently altered genes were PIK3CA (38.1%) , TP53 (37.1%) , KMT2D (23.7%) , PTEN (21.6%) , and CDKN2A (19.6%). The most frequently altered potentially actionable GAs were in PIK3CA, PTEN, FGFR3 (9.1%), MTAP (7.2%), BRCA1 (5.2%) and BRCA2 (5.2%). One patient had microsatellite instability high disease, while 27 (27.8%) had a tumor mutational burden ≥ 10 mut/Mb. Of 54 evaluable patients, 18 (33.3%) had high-positive PD-L1 expression. Two patients (2.1%) had TMPRSS2-ERG fusions supporting occult prostate cancer, while 13 (13.4%) had UV light exposure signatures suggesting unrecognized cutaneous origin. No significant differences in GAs were observed between 64 patients with inguinal disease and 33 patients with pelvic and retroperitoneal disease. An additional 346 cases of SCCUP were identified with involvement outside of the I/P/RP. Compared to these patients, those with I/P/RP involvement were more likely to be female (64% vs 42%,odds ratio [OR] 2.46, p=0.001), and were less likely to have mutations in CDKN2A (19.6% vs 41.9%, OR 0.34, p=0.002), TP53 (37.1% vs 69.7%, OR 0.26, p<0.001), and KRAS (2% vs 12.7%, OR 0.14, p=0.02). Patients with I/P/RP disease were also more likely to have evidence of HPV infection (54.6% vs 14.4%, OR 7.1, p<0.001) and APOBEC mutation signatures (70% vs 18.7%, OR 10.1, p<0.001), which have been associated with viral infection. Conclusions: Fifty-three of 97 (54.6%) patients with SCCUPs presenting with I/P/RP involvement had at least one GA that could potentially guide targeted treatment decisions including entry into biomarker-driven clinical trials. I/P/RP SCCUP patients frequently demonstrated HPV infection and APOBEC mutation signatures. To our knowledge, this is the first report that describes the genomic landscape of SCCUPs presenting with I/P/RP metastases.

Variable Response to ALK Inhibitors in NSCLC with a Novel MYT1L-ALK Fusion

Cancer driver mutations often display mutual exclusion or co-occurrence, underscoring the key role of epistasis in carcinogenesis. However, estimating the magnitude of epistasis and quantifying its effect on tumor evolution remains a challenge. We develop a method (Coselens) to quantify conditional selection on the excess of nonsynonymous substitutions in cancer genes. Coselens infers the number of drivers per gene in different partitions of a cancer genomics dataset using covariance-based mutation models and determines whether coding mutations in a gene affect selection for drivers in any other gene. Using Coselens, we identify 296 conditionally selected gene pairs across 16 cancer types in the TCGA dataset. Conditional selection affects 25%-50% of driver substitutions in tumors with >2 drivers. Conditionally co-selected genes form modular networks, whose structures challenge the traditional interpretation of within-pathway mutual exclusivity and across-pathway synergy, suggesting a more complex scenario where gene-specific across-pathway epistasis shapes differentiated cancer subtypes.

To examine the effect of centralized surgery on overall survival in patients with ovarian cancer and, in particular, patients with advanced disease (stage III/IV). In a historical prospective study design, patients referred from community hospitals to a teaching hospital for primary surgery during the 2-year period, 1995-1997, were included as cases. For each referred case, two controls, matched for International Federation of Gynecology and Obstetrics (FIGO) stage and age, were selected among patients who had had primary surgery at the referral hospitals (nonteaching) in the years, 1992-1995. Kaplan-Meier survival curves were computed and tested statistically by the log rank test. Cox proportional hazard model was applied for estimation of prognostic factors of survival. There was no difference in postoperative mortality for stage I/II patients by level of care (community hospitals versus teaching hospital). However, for advanced stage disease (III + IV), the controls had significantly shorter crude survival than patients who had been operated on at the teaching hospital (5-year survival: 4% versus 26%; median survival: 12 months versus 21 months) (P=.01). Multivariable analyses showed that completed chemotherapy and size of residual tumor after primary surgery were independent prognostic factors of survival. Patients optimally operated on at the teaching hospital had significantly lower risk of death compared with all other groups, independently of chemotherapy. This indicates that the extent of cytoreductive surgery and the overall management undertaken in the teaching hospital are significant predictors of improved survival. Centralization of primary ovarian cancer surgery in one health region in Norway has improved survival for patients with advanced disease. Patients with apparent advanced ovarian cancer should be referred to a subspecialty unit for primary surgery, and every effort should be made to attain as complete cytoreduction as possible.

Objective To examine the effect of centralized surgery on overall survival in patients with ovarian cancer and, in particular, patients with advanced disease (stage III/IV). Methods In a historical prospective study design, patients referred from community hospitals to a teaching hospital for primary surgery during the 2-year period, 1995–1997, were included as cases. For each referred case, two controls, matched for International Federation of Gynecology and Obstetrics (FIGO) stage and age, were selected among patients who had had primary surgery at the referral hospitals (nonteaching) in the years, 1992–1995. Kaplan–Meier survival curves were computed and tested statistically by the log rank test. Cox proportional hazard model was applied for estimation of prognostic factors of survival. Results There was no difference in postoperative mortality for stage I/II patients by level of care (community hospitals versus teaching hospital). However, for advanced stage disease (III + IV), the controls had significantly shorter crude survival than patients who had been operated on at the teaching hospital (5-year survival: 4% versus 26%; median survival: 12 months versus 21 months) (P = .01). Multivariable analyses showed that completed chemotherapy and size of residual tumor after primary surgery were independent prognostic factors of survival. Patients optimally operated on at the teaching hospital had significantly lower risk of death compared with all other groups, independently of chemotherapy. This indicates that the extent of cytoreductive surgery and the overall management undertaken in the teaching hospital are significant predictors of improved survival. Conclusion Centralization of primary ovarian cancer surgery in one health region in Norway has improved survival for patients with advanced disease. Patients with apparent advanced ovarian cancer should be referred to a subspecialty unit for primary surgery, and every effort should be made to attain as complete cytoreduction as possible.

Cancer genomic profile (CGP) testing, which is covered by the national health insurance system in Japan, has been introduced as a routine clinical practice. However, the effects of CGP testing on prognoses remain unclear. Drug accessibility rates and prognoses after CGP testing were retrospectively investigated in 713 patients who underwent CGP testing examined by our molecular tumor board between November 2019 and October 2022,. Overall survival (OS) was examined using the log-rank test and the Kaplan-Meier method. The median age of patients (326 males and 387 females) was 58 years (12-85 years). CGP testing revealed one or more gene mutations in 681 cases (95.5%), among which actionable gene mutations were detected in 439 (61.6%). Although treatment options were recommended for 285 cases (40.0%) by the molecular tumor board, only 45 received treatment based on their gene mutations. During the median observation period of 8.6 months, 351 (49.2%) patients died of the exacerbation of existing diseases. No significant differences were observed in OS between patients treated with and without genomically matched therapy (p = 0.285). According to clinical responses to treatment based on gene mutations, median OS was significantly longer in patients who achieved partial response and stable disease (26.5 months; 95% CI 14.4-38.6) than in those with progressive disease and not evaluated (9.8 months; 95% CI 5.8-13.8, p = 0.013). Responses to treatment based on gene mutations may improve prognoses, and it is important to increase the drug accessibility rate after CGP testing.

Systematic Analysis of Cell-of-Origin, Sequencing and Genomic Imbalances Identifies a Distinct Subset of Rituximab Treated Diffuse Large B-Cell Lymphoma with an Inferior Survival

Molecular Genetics and Prognosis in Younger Patients with Chronic Lymphocytic Leukemia (CLL)

Background of the studyBreast cancer is the most common cancer among women in both developed and developing nations. The survival of breast cancer is increasing in developed countries with improved treatment modalities, while still very poor in developing countries. In Nigeria, few breast cancer survival data are available.Research designThis is a retrospective cross-sectional study.ObjectivesTo determine the survival of breast cancer patients and possible factors influencing it.MethodologySocio-demographic and clinical variables from treatment records and case notes of breast cancer patients treated from 1 January 2004 to 31 December 2008 at the Department of Radiation Oncology, University College Hospital, Ibadan. The status of patients was determined at 2 and 5 years after diagnosis. The survival of patients with breast cancer was compared using Log Rank test according to socio-demographic and clinical variables. The median survival times were obtained from the Kaplan–Meier survival curve. Cox’s proportional hazard model was fitted for those that were statistically significant in the Log Rank test. Missing data were reported as unknown, not documented or missing.ResultsA total of 378 patients were analysed. Age ranged between 22.0 and 87.0 years with mean of 47.6 (standard deviation (SD) = 11.2) years. Almost all patients were females (98.4%). More than half (55.3%) presented at stage III, 28.0% had metastasis and the stage was unknown in about 6.6% of the patients. Invasive ductal carcinoma was the most prevalent histology (89.2%). Only 124 (32.8%) patients had their histological grade stated and most of the patients had no immunohistochemistry done. All the patients had radiotherapy, chemotherapy and surgery. About 25.1% of the patients were lost to follow up. The 2- and 5-year survival rates were 56.4% and 37.6%, respectively. The 2- and 5-year survival rates according to stage were stage I (80.0% and 66.7%), stage II (67.7% and 57.6%), stage III (51.4% and 27.9%) and stage IV (37.9% and 13.8%). Median survival time was 41 months (95%CI = 35.0–44.0). The disease-free survival at 2 and 5 years was 66.6% and 60.3%, respectively. Median time for recurrence was 8.0 months. Level of education, height, tumour unilaterality, clinical tumour size, stage at presentation, presence of distant metastases, clinical axillary lymph node metastasis, supraclavicular node metastasis, mode of surgery and axillary clearance were found to have statistically significant association with survival.ConclusionA large number of the patients in our study presented at a young age, late with advanced stage disease which results in poor survival outcome.