Comprehensive Genomic Profiling and Therapeutic Implications for Patients with Advanced Cancers: The Experience of an Academic Hospital

Teuwen, Laure-Anne; Roets, Evelyne; D'Hoore, P; Pauwels, Patrick; Prenen, Hans

doi:10.3390/diagnostics13091619

Cited by 3 publications

(4 citation statements)

References 48 publications

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“…The median age of the patients included in our study was 60.5 (range 27-82) years, which is similar to the median age of the population reported in different studies that analysed solid tumour samples with the Foundation Medicine ® platform [17][18][19][20]. A total of 72 samples were processed for the identification of genomic alterations, and data were obtained for 67 samples, corresponding to a success rate of 93.1%.…”

Section: Discussionsupporting

confidence: 54%

“…Despite the presented data and the potential benefits that patients can gain following the development of precision oncology, most of the genomic alterations identified in this study have no direct match with currently approved drugs, as reported in other large series using the same test [17][18][19]. One such example in this study is the cancers of unknown primary, which presented KRAS alterations.…”

Section: Discussionmentioning

confidence: 57%

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A Real-World Study Reporting the Use of Foundation Medicine® Testing in Portugal

Pinto

Schmitt

2023

JMP

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Foundation Medicine® testing is a next-generation sequence (NGS)-based platform that allows clinicians to obtain the comprehensive genomic profiling (CGP) of several cancers. By using NGS approaches, relevant genomic alterations can be identified in a short timeframe, providing guidance to diagnostic and therapeutic decisions. This study reports the implementation of three commercially available Foundation Medicine® tests in a Portuguese institution and explores the genomic alterations identified. Data obtained from 72 patients tested with Foundation Medicine® between July 2017 and December 2020 were analysed retrospectively. A total of 290 gene alterations were identified, and TP53 was the gene most frequently altered. Among the 67 successfully profiled samples, 37.3% presented a potentially actionable variation. Breast carcinoma represented the most frequent tumour-carrying variation that can be targeted using currently approved drugs. A limited number of potentially actionable variants using approved drugs was found in this study; however, the genomic information provided by Foundation Medicine® may help clinicians in directing cancer patients into clinical trials or to off-label treatments.

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Section: Discussionsupporting

confidence: 54%

Section: Discussionmentioning

confidence: 57%

A Real-World Study Reporting the Use of Foundation Medicine® Testing in Portugal

Pinto

Schmitt

2023

JMP

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“…No significant differences in IPS were observed in PD1, ALT4, and PD1+ALT4 between the two groups ( Figure 9A )., indicating that patients with high TRIB3 expression cannot benefit from PD1 and ALT4 ICP inhibitor treatments. However, the TMB analysis indicated that the high TRIB3 expression group was significantly higher than the low expression group ( Figure 9B ), implying that high TRIB3 expression patients have better immune responses ( 34 ). Therefore, to explore potential immune targets, a correlation analysis between TRIB3 and 47 well-known ICP genes was carried out ( 12 ).…”

Section: Resultsmentioning

confidence: 98%

TRIB3, as a robust prognostic biomarker for HNSC, is associated with poor immune infiltration and cancer cell immune evasion

Wu,

Fu,

et al. 2024

Front. Immunol.

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ObjectiveAs a pseudokinase, Tribbles Pseudokinase 3 (TRIB3) is implicated in a wide array of biological processes, including cell signal transduction, metabolic regulation, stress responses, and immune regulation. While its significant role in the immune regulation of certain cancers is well-established, the specific functions and impact of TRIB3 in head and neck squamous cell carcinoma (HNSC) remain unclear.MethodsThe data of RNA-sequence was acquired from the TCGA database to analyze the expression patterns of TRIB3 and elucidate its prognostic value in HNSC patients. Furthermore, the correlation between TRIB3 and tumor mutation burden, clinical data, immune checkpoint genes, and immune cell infiltration was explored. Moreover, the TRIB3 location in tumor tissues and subcellular structures was identified via Tisch in the HPA database, and the potential protein interaction molecules for TRIB3 were elucidated in the STRING database. The potential TRIB3 gene function was assessed using gene set enrichment analysis (GSEA), whereas the TRIB3 expression levels in clinical HNSC samples were verified by RT-qPCR and immunohistochemistry. the role of TRIB3 in enhancing the malignant behavior of HNSC cells was validated in vitro through a series of methods including RT-qPCR, CCK8 assay, wound healing assay, and transwell assay.ResultsIt was revealed that TRIB3 was significantly overexpressed in the nucleus and cytoplasm of HNSC. Furthermore, this overexpression markedly enhanced the migration ability of tumor cells. As an independent prognostic factor, TRIB3 was associated with advanced tumor T stage and was significantly involved with tumor mutation burden and immune cell infiltration in HNSC. Moreover, it was observed that TRIB3 was not a predicted factor for PD1/PDL1 and ATL4 inhibitor treatment; however, it was substantially correlated with various immune evasion-related genes in HNSC.ConclusionTRIB3 could serve as a potential prognostic marker for HNSC and might be a key gene mediating HNSC immune evasion.

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“…), has been reported at various frequencies between 10% and 20% in all patients in Japan (5-7). Conversely, these cases have higher frequency overseas than that in Japan; however, the usefulness of multi-CGP testing remained not fully clarified (8,9) in Japan. In this study, we analyzed clinical data from multi-CGP testing in various solid cancers to clarify the significance of multi-CGP testing at our Hospital.…”

mentioning

confidence: 98%

Clinical Significance of Multi-Cancer Genome Profiling: Data from a Single Hospital in Japan

AOYAMA,

NISHIKUBO,

KAWABATA

et al. 2023

Cancer Genomics Proteomics

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Background/Aim: Multi-cancer genome profiling (multi-CGP) testing intends to predict the therapeutic efficacy of anticancer medication treatments for eligible patients as part of "precision cancer care." The number of cases in which a new treatment was applied based on multi-CGP testing has been reported to be between 10% and 20% for all patients in Japan. This study aimed to determine the significance of multi-CGP testing in Japan by analyzing clinical data from multi-CGP testing in various solid cancers at our Hospital. Patients and Methods: A total of 230 patients examined by one of three tests for multi-CGP including NCC Oncopanel, FoundationOne CDx, and FoundationOne Liquid were retrospectively enrolled. Adequate treatment for each patient was discussed at the expert panel meeting according to the results from the genome profiling tests. Results: The most frequent cancer types enrolled in this study were pancreas cancer, bowel cancer, and biliary cancer. Of the 230 cases, 106 (46%) were druggable cases, and 21 (9.1%) were administered medication. Partial response (PR) effect was found in 7 (33.3%) of the 21 cases, of which 3 were biliary cancer and 3 had a BRCA2 mutation. Of all the 21 cases, 7 (33.3%) had the maximum treatment benefit of PR. Three cases of biliary tumors were found in the 7 PR cases within the 21 cases. Conclusion: Of 230 patients, 21 were administered medication following multi-CGP testing data, especially frequent in biliary tumor patients. Multi-CGP testing might be particularly beneficial to patients with biliary tumors in Japan. Patients and MethodsPatients. A total of 237 patients were enrolled between December 2019 and January 2023 at the Osaka Metropolitan University Hospital. Since 7 patients died before results were reported, we 79

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Comprehensive Genomic Profiling and Therapeutic Implications for Patients with Advanced Cancers: The Experience of an Academic Hospital

Cited by 3 publications

References 48 publications

A Real-World Study Reporting the Use of Foundation Medicine® Testing in Portugal

A Real-World Study Reporting the Use of Foundation Medicine® Testing in Portugal

TRIB3, as a robust prognostic biomarker for HNSC, is associated with poor immune infiltration and cancer cell immune evasion

Clinical Significance of Multi-Cancer Genome Profiling: Data from a Single Hospital in Japan

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