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Yu L, Zhang Y, Wang D, Li L, Zhang R, Li J. Harmonizing tumor mutational burden analysis: Insights from a multicenter study using in silico reference data sets in clinical whole-exome sequencing (WES). Am J Clin Pathol 2024:aqae056. [PMID: 38733635 DOI: 10.1093/ajcp/aqae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/13/2024] [Indexed: 05/13/2024] Open
Abstract
OBJECTIVES Tumor mutational burden (TMB) is a significant biomarker for predicting immune checkpoint inhibitor response, but the clinical performance of whole-exome sequencing (WES)-based TMB estimation has received less attention compared to panel-based methods. This study aimed to assess the reliability and comparability of WES-based TMB analysis among laboratories under routine testing conditions. METHODS A multicenter study was conducted involving 24 laboratories in China using in silico reference data sets. The accuracy and comparability of TMB estimation were evaluated using matched tumor-normal data sets. Factors such as accuracy of variant calls, limit of detection (LOD) of WES test, size of regions of interest (ROIs) used for TMB calculation, and TMB cutoff points were analyzed. RESULTS The laboratories consistently underestimated the expected TMB scores in matched tumor-normal samples, with only 50% falling within the ±30% TMB interval. Samples with low TMB score (<2.5) received the consensus interpretation. Accuracy of variant calls, LOD of the WES test, ROI, and TMB cutoff points were important factors causing interlaboratory deviations. CONCLUSIONS This study highlights real-world challenges in WES-based TMB analysis that need to be improved and optimized. This research will aid in the selection of more reasonable analytical procedures to minimize potential methodologic biases in estimating TMB in clinical exome sequencing tests. Harmonizing TMB estimation in clinical testing conditions is crucial for accurately evaluating patients' response to immunotherapy.
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Affiliation(s)
- Lijia Yu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Lin Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
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Marques A, Cavaco P, Torre C, Sepodes B, Rocha J. Tumor mutational burden in colorectal cancer: Implications for treatment. Crit Rev Oncol Hematol 2024; 197:104342. [PMID: 38614266 DOI: 10.1016/j.critrevonc.2024.104342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/15/2024] Open
Abstract
Although immune checkpoint inhibitors have revolutionized the treatment of several advanced solid cancers, in colorectal cancer, the transformative benefit of these innovative medicines is currently limited to those with deficient mismatch repair or high microsatellite instability. Tumor mutational burden (TMB) has emerged as a potential predictor of immunotherapy benefit, but the lack of standardization in its assessment and reporting has hindered the introduction of this biomarker in routine clinical practice. Here, we compiled 45 colorectal cancer studies utilizing numerical thresholds for high-TMB. In this group of studies, TMB cut-offs ranged from 6.88 to 41 mut/Mb and were most often set at 10, 17, or 20 mut/Mb. Additionally, we observed divergent TMB definitions and inconsistent disclosure of specific methodological details, which collectively emphasize the substantial lack of harmonization within the field. Ongoing efforts to harmonize TMB assessment will be critical to validate TMB as a predictive marker of immunotherapy response.
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Affiliation(s)
- Adriana Marques
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Patrícia Cavaco
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal; Pharmacy Department, Centro Hospitalar de Lisboa Ocidental, Lisboa 1449-005, Portugal
| | - Carla Torre
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Bruno Sepodes
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - João Rocha
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal.
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Ma C, Zhao H, Sun Y, Ding W, Wang H, Li Y, Gu Z. Deciphering disulfidptosis: Uncovering a lncRNA-based signature for prognostic assessment, personalized immunotherapy, and therapeutic agent selection in lung adenocarcinoma patients. Cell Signal 2024; 117:111105. [PMID: 38369264 DOI: 10.1016/j.cellsig.2024.111105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/30/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND Disulfidptosis, a recently identified type of regulated cell death, plays critical roles in various biological processes of cancer; however, whether they can impact the prognosis of lung adenocarcinoma (LUAD) remains to be fully elucidated. We aimed to adopt this concept to develop and validate a lncRNA signature for LUAD prognostic prediction. METHODS For this study, the TCGA-LUAD dataset was used as the training cohort, and multiple datasets from the GEO database were pooled as the validation cohort. Disulfidptosis regulated genes were obtained from published studies, and various statistical methods, including Kaplan-Meier (KM), Cox, and LASSO, were used to train our gene signature DISULncSig. We utilized KM analysis, COX analysis, receiver operating characteristic analysis, time-dependent AUC analysis, principal component analysis, nomogram predictor analysis, and functional assays in our validation process. We also compared DISULncSig with previous studies. We performed analyses to evaluate DISULncSig's immunotherapeutic ability, focusing on eight immune algorithms, TMB, and TIDE. Additionally, we investigated potential drugs that could be effective in treating patients with high-risk scores. Additionally qRT-PCR examined the expression patterns of DISULncSig lncRNAs, and the ability of DISULncSig in pan-cancer was also assessed. RESULTS DISULncSig containing twelve lncRNAs was trained and showed strong predictive ability in the validation cohort. Compared with previous similar studies, DISULncSig had more prognostic ability advantages. DISULncSig was closely related to the immune status of LUAD, and its tight relationship with checkpoints KIR2DL3, IL10, IL2, CD40LG, SELP, BTLA, and CD28 may be the key to its potential immunotherapeutic ability. For the high DISULncSig score population, we found ten drug candidates, among which epothilone-b may have the most potential. The pan-cancer analysis found that DISULncSig was a risk factor in multiple cancers. Additionally, we discovered that some of the DISULncSig lncRNAs could play crucial roles in specific cancer types. CONCLUSION The current study established a powerful prognostic DISULncSig signature for LUAD that was also valid for most pan-cancers. This signature could serve as a potential target for immunotherapy and might help the more efficient application of drugs to specific populations.
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Affiliation(s)
- Chao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, PR China
| | - Huan Zhao
- Department of Clinical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, PR China
| | - Yang Sun
- Department of Cardiothoracic Surgery, Zibo First Hospital, Weifang Medical University, Zibo, Shandong, PR China
| | - Weizheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, PR China
| | - Hui Wang
- Department of Clinical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, PR China
| | - Yixin Li
- Department of Clinical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, PR China.
| | - Zhuoyu Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, PR China.
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Popescu I, Dudău AM, Dima S, Herlea V, Croitoru VM, Dinu IM, Miron M, Lupescu I, Croitoru-Cazacu IM, Dumitru R, Croitoru AE. Multimodal Treatment of Metastatic Rectal Cancer in a Young Patient: Case Report and Literature Review. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:696. [PMID: 38792879 PMCID: PMC11123219 DOI: 10.3390/medicina60050696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024]
Abstract
Metastatic colorectal cancer requires a multidisciplinary and individualized approach. Herein, we reported the case of a young woman diagnosed with metastatic rectal cancer who received an individualized multimodal treatment strategy that resulted in a remarkable survival. There were several particular aspects of this case, such as the early onset of the disease, the successful use of conversion therapy, the application of liquid biopsy to guide treatment, and the specific nature of the bone metastasis. To offer more insights for navigating such challenges in patients with metastatic colorectal cancer, we have conducted a literature review to find more data related to the particularities of this case. The incidence of early onset colorectal cancer is on the rise. Data suggests that it differs from older-onset colorectal cancer in terms of its pathological, epidemiological, anatomical, metabolic, and biological characteristics. Conversion therapy and surgical intervention provide an opportunity for cure and improve outcomes in metastatic colorectal cancer. It is important to approach each case individually, as every patient with limited liver disease should be considered as a candidate for secondary resection. Moreover, liquid biopsy has an important role in the individualized management of metastatic colorectal cancer patients, as it offers additional information for treatment decisions.
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Affiliation(s)
- Ionuț Popescu
- Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania; (I.P.); (V.M.C.)
| | - Ana-Maria Dudău
- Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania; (I.P.); (V.M.C.)
- Medical Oncology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania; (I.M.D.); (M.M.); (I.M.C.-C.); (A.E.C.)
| | - Simona Dima
- Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 020021 Bucharest, Romania; (S.D.); (V.H.); (I.L.); (R.D.)
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Vlad Herlea
- Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 020021 Bucharest, Romania; (S.D.); (V.H.); (I.L.); (R.D.)
- Pathology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Vlad M. Croitoru
- Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania; (I.P.); (V.M.C.)
- Medical Oncology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania; (I.M.D.); (M.M.); (I.M.C.-C.); (A.E.C.)
| | - Ioana Mihaela Dinu
- Medical Oncology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania; (I.M.D.); (M.M.); (I.M.C.-C.); (A.E.C.)
| | - Monica Miron
- Medical Oncology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania; (I.M.D.); (M.M.); (I.M.C.-C.); (A.E.C.)
| | - Ioana Lupescu
- Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 020021 Bucharest, Romania; (S.D.); (V.H.); (I.L.); (R.D.)
- Radiology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Irina M. Croitoru-Cazacu
- Medical Oncology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania; (I.M.D.); (M.M.); (I.M.C.-C.); (A.E.C.)
- Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 020021 Bucharest, Romania; (S.D.); (V.H.); (I.L.); (R.D.)
| | - Radu Dumitru
- Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 020021 Bucharest, Romania; (S.D.); (V.H.); (I.L.); (R.D.)
- Radiology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Adina Emilia Croitoru
- Medical Oncology Department, Fundeni Clinical Institute, 022328 Bucharest, Romania; (I.M.D.); (M.M.); (I.M.C.-C.); (A.E.C.)
- Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 020021 Bucharest, Romania; (S.D.); (V.H.); (I.L.); (R.D.)
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Privitera GF, Alaimo S, Caruso A, Ferro A, Forte S, Pulvirenti A. TMBcalc: a computational pipeline for identifying pan-cancer Tumor Mutational Burden gene signatures. Front Genet 2024; 15:1285305. [PMID: 38645485 PMCID: PMC11026579 DOI: 10.3389/fgene.2024.1285305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
Background In the precision medicine era, identifying predictive factors to select patients most likely to benefit from treatment with immunological agents is a crucial and open challenge in oncology. Methods This paper presents a pan-cancer analysis of Tumor Mutational Burden (TMB). We developed a novel computational pipeline, TMBcalc, to calculate the TMB. Our methodology can identify small and reliable gene signatures to estimate TMB from custom targeted-sequencing panels. For this purpose, our pipeline has been trained on top of 17 cancer types data obtained from TCGA. Results Our results show that TMB, computed through the identified signature, strongly correlates with TMB obtained from whole-exome sequencing (WES). Conclusion We have rigorously analyzed the effectiveness of our methodology on top of several independent datasets. In particular we conducted a comprehensive testing on: (i) 126 samples sourced from the TCGA database; few independent whole-exome sequencing (WES) datasets linked to colon, breast, and liver cancers, all acquired from the EGA and the ICGC Data Portal. This rigorous evaluation clearly highlights the robustness and practicality of our approach, positioning it as a promising avenue for driving substantial progress within the realm of clinical practice.
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Affiliation(s)
- Grete Francesca Privitera
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Anna Caruso
- Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Stefano Forte
- Istituto Oncologico del Mediterraneo (IOM) Ricerca, Viagrande, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
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Ma C, Gu Z, Yang Y. Development of m6A/m5C/m1A regulated lncRNA signature for prognostic prediction, personalized immune intervention and drug selection in LUAD. J Cell Mol Med 2024; 28:e18282. [PMID: 38647237 PMCID: PMC11034373 DOI: 10.1111/jcmm.18282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
Research indicates that there are links between m6A, m5C and m1A modifications and the development of different types of tumours. However, it is not yet clear if these modifications are involved in the prognosis of LUAD. The TCGA-LUAD dataset was used as for signature training, while the validation cohort was created by amalgamating publicly accessible GEO datasets including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081. The study focused on 33 genes that are regulated by m6A, m5C or m1A (mRG), which were used to form mRGs clusters and clusters of mRG differentially expressed genes clusters (mRG-DEG clusters). Our subsequent LASSO regression analysis trained the signature of m6A/m5C/m1A-related lncRNA (mRLncSig) using lncRNAs that exhibited differential expression among mRG-DEG clusters and had prognostic value. The model's accuracy underwent validation via Kaplan-Meier analysis, Cox regression, ROC analysis, tAUC evaluation, PCA examination and nomogram predictor validation. In evaluating the immunotherapeutic potential of the signature, we employed multiple bioinformatics algorithms and concepts through various analyses. These included seven newly developed immunoinformatic algorithms, as well as evaluations of TMB, TIDE and immune checkpoints. Additionally, we identified and validated promising agents that target the high-risk mRLncSig in LUAD. To validate the real-world expression pattern of mRLncSig, real-time PCR was carried out on human LUAD tissues. The signature's ability to perform in pan-cancer settings was also evaluated. The study created a 10-lncRNA signature, mRLncSig, which was validated to have prognostic power in the validation cohort. Real-time PCR was applied to verify the actual manifestation of each gene in the signature in the real world. Our immunotherapy analysis revealed an association between mRLncSig and immune status. mRLncSig was found to be closely linked to several checkpoints, such as IL10, IL2, CD40LG, SELP, BTLA and CD28, which could be appropriate immunotherapy targets for LUAD. Among the high-risk patients, our study identified 12 candidate drugs and verified gemcitabine as the most significant one that could target our signature and be effective in treating LUAD. Additionally, we discovered that some of the lncRNAs in mRLncSig could play a crucial role in certain cancer types, and thus, may require further attention in future studies. According to the findings of this study, the use of mRLncSig has the potential to aid in forecasting the prognosis of LUAD and could serve as a potential target for immunotherapy. Moreover, our signature may assist in identifying targets and therapeutic agents more effectively.
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Affiliation(s)
- Chao Ma
- Department of Thoracic SurgeryFirst Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Zhuoyu Gu
- Department of Thoracic SurgeryFirst Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yang Yang
- Department of Thoracic SurgeryFirst Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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Ahluwalia MS, Khosla AA, Ozair A, Gouda MA, Subbiah V. Impact of tissue-agnostic approvals on management of primary brain tumors. Trends Cancer 2024; 10:256-274. [PMID: 38245379 DOI: 10.1016/j.trecan.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 01/22/2024]
Abstract
Novel tissue-agnostic therapeutics targeting driver mutations in tumor cells have been recently approved by FDA, driven by basket trials that have demonstrated their efficacy and safety across diverse tumor histology. However, the relative rarity of primary brain tumors (PBTs) has limited their representation in early trials of tissue-agnostic medications. Thus, consensus continues to evolve regarding utility of tissue-agnostic medications in routine practice for PBTs, a diverse group of neoplasms characterized by limited treatment options and unfavorable prognoses. We describe current and potential impact of tissue-agnostic approvals on management of PBTs. We discuss data from clinical trials for PBTs regarding tissue-agnostic targets, including BRAFV600E, neurotrophic tyrosine receptor kinase (NTRK) fusions, microsatellite instability-high (MSI-High), mismatch repair deficiency (dMMR), and high tumor mutational burden (TMB-H), in context of challenges in managing PBTs. Described are additional tissue-agnostic targets that hold promise for benefiting patients with PBTs, including RET fusion, fibroblast growth factor receptor (FGFR), ERBB2/HER2, and KRASG12C, and TP53Y220C.
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Affiliation(s)
- Manmeet S Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA; Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Atulya A Khosla
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA; Department of Internal Medicine, William Beaumont University Hospital, Royal Oak, MI, USA
| | - Ahmad Ozair
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mohamed A Gouda
- Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivek Subbiah
- Early Phase Drug Development Program, Sarah Cannon Research Institute, Nashville, TN, USA.
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Dupain C, Gutman T, Girard E, Kamoun C, Marret G, Castel-Ajgal Z, Sablin MP, Neuzillet C, Borcoman E, Hescot S, Callens C, Trabelsi-Grati O, Melaabi S, Vibert R, Antonio S, Franck C, Galut M, Guillou I, Halladjian M, Allory Y, Cyrta J, Romejon J, Frouin E, Stoppa-Lyonnet D, Wong J, Le Tourneau C, Bièche I, Servant N, Kamal M, Masliah-Planchon J. Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine. BMC Biol 2024; 22:43. [PMID: 38378561 PMCID: PMC10880437 DOI: 10.1186/s12915-024-01839-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND High tumor mutational burden (TMB) was reported to predict the efficacy of immune checkpoint inhibitors (ICIs). Pembrolizumab, an anti-PD-1, received FDA-approval for the treatment of unresectable/metastatic tumors with high TMB as determined by the FoundationOne®CDx test. It remains to be determined how TMB can also be calculated using other tests. RESULTS FFPE/frozen tumor samples from various origins were sequenced in the frame of the Institut Curie (IC) Molecular Tumor Board using an in-house next-generation sequencing (NGS) panel. A TMB calculation method was developed at IC (IC algorithm) and compared to the FoundationOne® (FO) algorithm. Using IC algorithm, an optimal 10% variant allele frequency (VAF) cut-off was established for TMB evaluation on FFPE samples, compared to 5% on frozen samples. The median TMB score for MSS/POLE WT tumors was 8.8 mut/Mb versus 45 mut/Mb for MSI/POLE-mutated tumors. When focusing on MSS/POLE WT tumor samples, the highest median TMB scores were observed in lymphoma, lung, endometrial, and cervical cancers. After biological manual curation of these cases, 21% of them could be reclassified as MSI/POLE tumors and considered as "true TMB high." Higher TMB values were obtained using FO algorithm on FFPE samples compared to IC algorithm (40 mut/Mb [10-3927] versus 8.2 mut/Mb [2.5-897], p < 0.001). CONCLUSIONS We herein propose a TMB calculation method and a bioinformatics tool that is customizable to different NGS panels and sample types. We were not able to retrieve TMB values from FO algorithm using our own algorithm and NGS panel.
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Affiliation(s)
- Célia Dupain
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Tom Gutman
- Bioinformatics Core Facility, INSERM U900, Mines Paris Tech, Institut Curie, Paris, France
| | - Elodie Girard
- Bioinformatics Core Facility, INSERM U900, Mines Paris Tech, Institut Curie, Paris, France
| | - Choumouss Kamoun
- Bioinformatics Core Facility, INSERM U900, Mines Paris Tech, Institut Curie, Paris, France
| | - Grégoire Marret
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Zahra Castel-Ajgal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Marie-Paule Sablin
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Cindy Neuzillet
- Department of Medical Oncology, Institut Curie, Paris & Saint Cloud, France
| | - Edith Borcoman
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Ségolène Hescot
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | | | | | - Samia Melaabi
- Department of Genetics, Institut Curie, Paris, France
| | | | | | | | - Michèle Galut
- Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - Isabelle Guillou
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Maral Halladjian
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Yves Allory
- Department of Pathology, Université Paris-Saclay, UVSQ, Institut Curie, Saint-Cloud, France
| | - Joanna Cyrta
- Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - Julien Romejon
- Bioinformatics Core Facility, INSERM U900, Mines Paris Tech, Institut Curie, Paris, France
| | | | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France
- Paris-Cité University, Paris, France
- INSERM U830, Paris, France
| | - Jennifer Wong
- Department of Genetics, Institut Curie, Paris, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
- Inserm U900 Research Unit, Saint Cloud, France
- Paris-Saclay University, Paris, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie, Paris, France
- Paris-Cité University, Paris, France
- Faculty of Pharmaceutical and Biological Sciences, INSERM U1016, Paris Descartes University, Paris, France
| | - Nicolas Servant
- Bioinformatics Core Facility, INSERM U900, Mines Paris Tech, Institut Curie, Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
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Paz-Ares L, Garassino MC, Chen Y, Reinmuth N, Hotta K, Poltoratskiy A, Trukhin D, Hochmair MJ, Özgüroğlu M, Ji JH, Statsenko G, Conev N, Bondarenko I, Havel L, Losonczy G, Xie M, Lai Z, Godin-Heymann N, Mann H, Jiang H, Shrestha Y, Goldman JW. Durvalumab ± Tremelimumab + Platinum-Etoposide in Extensive-Stage Small Cell Lung Cancer (CASPIAN): Outcomes by PD-L1 Expression and Tissue Tumor Mutational Burden. Clin Cancer Res 2024; 30:824-835. [PMID: 37801329 PMCID: PMC10870117 DOI: 10.1158/1078-0432.ccr-23-1689] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
PURPOSE In the CASPIAN trial, first-line durvalumab plus platinum-etoposide (EP) significantly improved overall survival (OS) versus EP alone in extensive-stage small cell lung cancer (ES-SCLC). We report exploratory analyses of CASPIAN outcomes by programmed cell death ligand-1 (PD-L1) expression and tissue tumor mutational burden (tTMB). EXPERIMENTAL DESIGN Patients were randomized (1:1:1) to durvalumab (1,500 mg) plus EP, durvalumab plus tremelimumab (75 mg) plus EP, or EP alone. Treatment effects in PD-L1 and tTMB subgroups were estimated using an unstratified Cox proportional hazards model. RESULTS The PD-L1 and tTMB biomarker-evaluable populations (BEP) comprised 54.4% (438/805) and 35.2% (283/805) of the intention-to-treat population, respectively. PD-L1 prevalence was low: 5.7%, 25.8%, and 28.3% had PD-L1 expression on ≥1% tumor cells (TC), ≥1% immune cells (IC), and ≥1% TCs or ICs, respectively. OS benefit with durvalumab plus EP versus EP was similar across PD-L1 subgroups, with HRs all falling within the 95% confidence interval (CI) for the PD-L1 BEP (0.47‒0.79). OS benefit with durvalumab plus tremelimumab plus EP versus EP was greater in PD-L1 ≥1% versus <1% subgroups, although CIs overlapped. There was no evidence of an interaction between tTMB and treatment effect on OS (durvalumab plus EP vs. EP, P = 0.916; durvalumab plus tremelimumab plus EP vs. EP, P = 0.672). CONCLUSIONS OS benefit with first-line durvalumab plus EP in patients with ES-SCLC was observed regardless of PD-L1 or tTMB status. PD-L1 expression may prove to be a useful biomarker for combined treatment with PD-(L)1 and CTLA-4 inhibition, although this requires confirmation with an independent dataset. See related commentary by Rolfo and Russo, p. 652.
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Affiliation(s)
- Luis Paz-Ares
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Lung Cancer Unit CNIO-H120, Complutense University and Ciberonc, Madrid, Spain
| | - Marina Chiara Garassino
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Medicine, Section of Hematology/Oncology, Thoracic Oncology Unit, University of Chicago, Chicago, Illinois
| | - Yuanbin Chen
- Cancer and Hematology Centers of Western Michigan, Grand Rapids, Michigan
| | - Niels Reinmuth
- Asklepios Lung Clinic, Member of the German Center for Lung Research (DZL), Munich-Gauting, Germany
| | | | - Artem Poltoratskiy
- Petrov Research Institute of Oncology, St. Petersburg, Russian Federation
| | | | - Maximilian J. Hochmair
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Mustafa Özgüroğlu
- Istanbul University−Cerrahpaşa, Cerrahpaşa School of Medicine, Istanbul, Turkey
| | - Jun Ho Ji
- Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of South Korea
| | | | - Nikolay Conev
- Clinic of Medical Oncology, UMHAT St Marina, Varna, Bulgaria
| | | | - Libor Havel
- Thomayer Hospital, First Faculty of Medicine, Charles University, Prague, Czech Republic
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Fielding D, Lakis V, Dalley AJ, Chittoory H, Newell F, Koufariotis LT, Patch AM, Kazakoff S, Bashirzadeh F, Son JH, Ryan K, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Pattison A, Fairbairn D, Gune S, Christie J, Holmes O, Leonard C, Wood S, Pearson JV, Lakhani SR, Waddell N, Simpson PT, Nones K. Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing. Cancers (Basel) 2024; 16:785. [PMID: 38398180 PMCID: PMC10887389 DOI: 10.3390/cancers16040785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from 220 EBUS-TBNA aspirates to evaluate their suitability for whole genome (WGS), whole exome (WES), and comprehensive panel sequencing. For a subset of 40 cases, the same nucleic acid extraction was sequenced using WGS, WES, and the TruSight Oncology 500 assay. Genomic features were compared between sequencing platforms and compared with those reported by clinical testing. A total of 204 aspirates (92.7%) had sufficient DNA (100 ng) for comprehensive panel sequencing, and 109 aspirates (49.5%) had sufficient material for WGS. Comprehensive sequencing platforms detected all seven clinically reported tier 1 actionable mutations, an additional three (7%) tier 1 mutations, six (15%) tier 2-3 mutations, and biomarkers of potential immunotherapy benefit (tumor mutation burden and microsatellite instability). As expected, WGS was more suited for the detection and discovery of emerging novel biomarkers of treatment response. WGS could be performed in half of all EBUS-TBNA aspirates, which points to the enormous potential of EBUS-TBNA as source material for large, well-curated discovery-based studies for novel and more effective predictors of treatment response. Comprehensive panel sequencing is possible in the vast majority of fresh EBUS-TBNA aspirates and enhances the detection of actionable mutations over current clinical testing.
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Affiliation(s)
- David Fielding
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Andrew J. Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Haarika Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Lambros T. Koufariotis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Jung Hwa Son
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Kimberley Ryan
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Daniel Steinfort
- Department of Respiratory and Sleep Medicine, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia; (D.S.); (J.C.)
| | - Jonathan P. Williamson
- Department of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, NSW 2170, Australia;
| | - Michael Bint
- Department of Respiratory and Sleep Medicine, Sunshine Coast University Hospital, Birtinya, QLD 4575, Australia; (M.B.); (A.P.)
| | - Carl Pahoff
- Department of Thoracic Medicine, Gold Coast University Hospital, Southport, QLD 4215, Australia;
| | - Phan Tien Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia;
| | - Scott Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - David Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - Christopher Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - Andrew Pattison
- Department of Respiratory and Sleep Medicine, Sunshine Coast University Hospital, Birtinya, QLD 4575, Australia; (M.B.); (A.P.)
| | - David Fairbairn
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia;
| | - Shailendra Gune
- NSW Health Pathology South, Liverpool Hospital, Sydney, NSW 2170, Australia;
| | - Jemma Christie
- Department of Respiratory and Sleep Medicine, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia; (D.S.); (J.C.)
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia;
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4067, Australia
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Esposito Abate R, Pasquale R, Sacco A, Simeon V, Maiello MR, Frezzetti D, Chiodini P, Normanno N. Harmonization of tumor mutation burden testing with comprehensive genomic profiling assays: an IQN Path initiative. J Immunother Cancer 2024; 12:e007800. [PMID: 38309725 PMCID: PMC10840060 DOI: 10.1136/jitc-2023-007800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2023] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Although conflicting results emerged from different studies, the tumor mutational burden (TMB) appears as one of most reliable biomarkers of sensitivity to immune checkpoint inhibitors. Several laboratories are reporting TMB values when performing comprehensive genomic profiling (CGP) without providing a clinical interpretation, due to the lack of validated cut-off values. The International Quality Network for Pathology launched an initiative to harmonize TMB testing with CGP assay and favor the clinical implementation of this biomarker. METHODS TMB evaluation was performed with three commercially available CGP panels, TruSight Oncology 500 (TSO500), Oncomine Comprehensive Plus Assay (OCA) and QIAseq Multimodal Panel (QIA), versus the reference assay FoundationOne CDx (F1CDx). Archived clinical samples derived from 60 patients with non-small cell lung cancer were used for TMB assessment. Adjusted cut-off values for each panel were calculated. RESULTS Testing was successful for 91.7%, 100%, 96.7% and 100% of cases using F1CDx, TSO500, OCA and QIA, respectively. The matrix comparison analysis, between the F1CDx and CGP assays, showed a linear correlation for all three panels, with a higher correlation between F1CDx and TSO500 (rho=0.88) than in the other two comparisons (rho=0.77 for QIA; 0.72 for OCA). The TSO500 showed the best area under the curve (AUC, value 0.96), with a statistically significant difference when compared with the AUC of OCA (0.83, p value=0.01) and QIA (0.88, p value=0.028). The Youden Index calculation allowed us to extrapolate TMB cut-offs of the different panels corresponding to the 10 mutations/megabase (muts/Mb) cut-off of F1CDx: 10.19, 10.4 and 12.37 muts/Mb for TSO500, OCA and QIA, respectively. Using these values, we calculated the relative accuracy measures for the three panels. TSO500 showed 86% specificity and 96% sensitivity, while OCA and QIA had lower yet similar values of specificity and sensitivity (73% and 88%, respectively). CONCLUSION This study estimated TMB cut-off values for commercially available CGP panels. The results showed a good performance of all panels on clinical samples and the calculated cut-offs support better accuracy measures for TSO500. The validated cut-off values can drive clinical interpretation of TMB testing in clinical research and clinical practice.
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Affiliation(s)
- Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
| | | | - Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
| | - Vittorio Simeon
- Medical Statistics Unit, Department of Mental Health and Public Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Monica Rosaria Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
| | - Daniela Frezzetti
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
| | - Paolo Chiodini
- Medical Statistics Unit, Department of Mental Health and Public Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
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12
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Soliman N, Saharia A, Abdelrahim M, Connor AA. Molecular profiling in the management of hepatocellular carcinoma. Curr Opin Organ Transplant 2024; 29:10-22. [PMID: 38038621 DOI: 10.1097/mot.0000000000001124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to both summarize the current knowledge of hepatocellular carcinoma molecular biology and to suggest a framework in which to prospectively translate this knowledge into patient care. This is timely as recent guidelines recommend increased use of these technologies to advance personalized liver cancer care. RECENT FINDINGS The main themes covered here address germline and somatic genetic alterations recently discovered in hepatocellular carcinoma, largely owing to next generation sequencing technologies, and nascent efforts to translate these into contemporary practice. SUMMARY Early efforts of translating molecular profiling to hepatocellular carcinoma care demonstrate a growing number of potentially actionable alterations. Still lacking are a consensus on what biomarkers and technologies to adopt, at what scale and cost, and how to integrate them most effectively into care.
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13
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Zhang Y, Wang D, Zhao Z, Peng R, Han Y, Li J, Zhang R. Enhancing the quality of panel-based tumor mutation burden assessment: a comprehensive study of real-world and in-silico outcomes. NPJ Precis Oncol 2024; 8:18. [PMID: 38263314 PMCID: PMC10805867 DOI: 10.1038/s41698-024-00504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
Targeted panel-based tumor mutation burden (TMB) assays are widely employed to guide immunotherapy for patients with solid tumors. However, the accuracy and consistency of this method can be compromised due to the variability in technical details across different laboratories, particularly in terms of panel size, somatic mutation detection and TMB calculation rules. Currently, systematic evaluations of the impact of these technical factors on existing assays and best practice recommendations remain lacking. We assessed the performance of 50 participating panel-based TMB assays involving 38 unique methods using cell line samples. In silico experiments utilizing TCGA MC3 datasets were performed to further dissect the impact of technical factors. Here we show that the panel sizes beyond 1.04 Mb and 389 genes are necessary for the basic discrete accuracy, as determined by over 40,000 synthetic panels. The somatic mutation detection should maintain a reciprocal gap of recall and precision less than 0.179 for reliable psTMB calculation results. The inclusion of synonymous, nonsense and hotspot mutations could enhance the accuracy of panel-based TMB assay. A 5% variant allele frequency cut-off is suitable for TMB assays using tumor samples with at least 20% tumor purity. In conclusion, this multicenter study elucidates the major technical factors as sources of variability in panel-based TMB assays and proposed comprehensive recommendations for the enhancement of accuracy and consistency. These findings will assist clinical laboratories in optimizing the methodological details through bioinformatic experiments to enhance the reliability of panel-based methods.
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Affiliation(s)
- Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Zihong Zhao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
- Peking University Fifth School of Clinical Medicine, Beijing, PR China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China.
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China.
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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14
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Zhao W, Ding C, Zhao M, Li Y, Huang H, Li X, Cheng Q, Shi Z, Gao W, Liu H, Chen J. Identification and Validation of a Hypoxia and Glycolysis Prognostic Signatures in Lung Adenocarcinoma. J Cancer 2024; 15:1568-1582. [PMID: 38370379 PMCID: PMC10869968 DOI: 10.7150/jca.91504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/29/2023] [Indexed: 02/20/2024] Open
Abstract
Background: Lung adenocarcinoma (LUAD) represents a prevalent subtype of non-small cell lung cancer with a complex molecular landscape. Dysregulated cellular energetics, notably the interplay between hypoxia and glycolysis, has emerged as a hallmark feature of LUAD tumorigenesis and progression. In this study, we aimed to identify hypoxia and glycolysis related gene signatures and construct a prognostic model to enhance the clinical management of LUAD. Methods: A gene signature associated with hypoxia and glycolysis was established within the The Cancer Genome Atlas (TCGA) cohort and subsequently validated in the GSE31210 cohort. Additionally, a nomogram was formulated to aid in predictive modeling. Subsequently, an evaluation of the tumor microenvironment and immune checkpoints expression levels was conducted to discern disparities between low risk and high risk groups. Lastly, an exploration for drugs with potential effectiveness was carried out. Results: Our analyses revealed a distinct hypoxia and glycolysis related gene signature consisting of 6 genes significantly associated with LUAD patient survival. Integration of these genes into the prognostic model demonstrated superior predictive accuracy for patient outcomes. Furthermore, we developed a user-friendly nomogram that effectively translates the model's prognostic information into a practical tool for clinical decision-making. Conclusion: This study elucidates the critical role of hypoxia and glycolysis related genes in LUAD and offers a novel prognostic model with promising clinical utility. This model has the potential to refine risk stratification and guide personalized therapeutic interventions, ultimately improving the prognosis of LUAD patients.
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Affiliation(s)
- Wenhao Zhao
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Chen Ding
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Meiru Zhao
- Department of Dermatovenereology, Tianjin Medical University General Hospital/ Tianjin Institute of Sexually Transmitted Disease, Tianjin, China
| | - Yongwen Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Hua Huang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xuanguang Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Qian Cheng
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zijian Shi
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Weining Gao
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongyu Liu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Jun Chen
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
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Makker V, Taylor MH, Aghajanian C, Cohn AL, Brose MS, Simone CD, Cao ZA, Suttner L, Loboda A, Cristescu R, Jelinic P, Orlowski R, Dutta L, Matsui J, Dutcus CE, Minoshima Y, Messing MJ. Evaluation of potential biomarkers for lenvatinib plus pembrolizumab among patients with advanced endometrial cancer: results from Study 111/KEYNOTE-146. J Immunother Cancer 2024; 12:e007929. [PMID: 38242717 PMCID: PMC10806562 DOI: 10.1136/jitc-2023-007929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Lenvatinib plus pembrolizumab demonstrated clinically meaningful benefit in patients with previously treated advanced endometrial carcinoma in Study 111/KEYNOTE-146 (NCT02501096). In these exploratory analyses from this study, we evaluated the associations between clinical outcomes and gene expression signature scores and descriptively summarized response in biomarker subpopulations defined by tumor mutational burden (TMB) and DNA variants for individual genes of interest. METHODS Patients with histologically confirmed metastatic endometrial carcinoma received oral lenvatinib 20 mg once daily plus intravenous pembrolizumab 200 mg every 3 weeks for 35 cycles. Archived formalin-fixed paraffin-embedded tissue was obtained from all patients. T-cell-inflamed gene expression profile (TcellinfGEP) and 11 other gene signatures were evaluated by RNA sequencing. TMB, hotspot mutations in PIK3CA (oncogene), and deleterious mutations in PTEN and TP53 (tumor suppressor genes) were evaluated by whole-exome sequencing (WES). RESULTS 93 and 79 patients were included in the RNA-sequencing-evaluable and WES-evaluable populations, respectively. No statistically significant associations were observed between any of the RNA-sequencing signature scores and objective response rate or progression-free survival. Area under the receiver operating characteristic curve values for response ranged from 0.39 to 0.54; all 95% CIs included 0.50. Responses were seen regardless of TMB (≥175 or <175 mutations/exome) and mutation status. There were no correlations between TcellinfGEP and TMB, TcellinfGEP and microvessel density (MVD), or MVD and TMB. CONCLUSIONS This analysis demonstrated efficacy for lenvatinib plus pembrolizumab regardless of biomarker status. Results from this study do not support clinical utility of the evaluated biomarkers. Further investigation of biomarkers for this regimen is warranted. TRIAL REGISTRATION NUMBER NCT02501096.
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Affiliation(s)
- Vicky Makker
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew H Taylor
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | | | - Allen L Cohn
- Rocky Mountain Cancer Center, Denver, Colorado, USA
| | - Marcia S Brose
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
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Faghfuri E. Recent advances in personalized cancer immunotherapy with immune checkpoint inhibitors, T cells and vaccines. Per Med 2024; 21:45-57. [PMID: 38088165 DOI: 10.2217/pme-2023-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The results of genomic and molecular profiling of cancer patients can be effectively applied to immunotherapy agents, including immune checkpoint inhibitors, to select the most appropriate treatment. In addition, accurate prediction of neoantigens facilitates the development of individualized cancer vaccines and T-cell therapy. This review summarizes the biomarker(s) predicting responses to immune checkpoint inhibitors and focuses on current strategies to identify and isolate neoantigen-reactive T cells as well as the clinical development of neoantigen-based therapeutics. The results suggest that maximal T-cell stimulation and expansion can be achieved with combination therapies that enhance antigen-presenting cells' function and optimal T-cell priming in lymph nodes.
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Affiliation(s)
- Elnaz Faghfuri
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, 5613658115, Iran
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17
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Xia M, Tong S, Gao L. Identification of MDK as a Hypoxia- and Epithelial-Mesenchymal Transition-Related Gene Biomarker of Glioblastoma Based on a Novel Risk Model and In Vitro Experiments. Biomedicines 2024; 12:92. [PMID: 38255198 PMCID: PMC10813330 DOI: 10.3390/biomedicines12010092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/23/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Tumor cells are commonly exposed to a hypoxic environment, which can easily induce the epithelial-mesenchymal transition (EMT) of tumor cells, further affecting tumor proliferation, invasion, metastasis, and drug resistance. However, the predictive role of hypoxia and EMT-related genes in glioblastoma (GBM) has not been investigated. METHODS Intersection genes were identified by weighted correlation network analysis (WGCNA) and differential expression analyses, and a risk model was further constructed by LASSO and Cox analyses. Clinical, immune infiltration, tumor mutation, drug treatment, and enrichment profiles were analyzed based on the risk model. The expression level of the MDK gene was tested using RT-PCR, immunohistochemistry, and immunofluorescence. CCK8 and EdU were employed to determine the GBM cells' capacity for proliferation while the migration and invasion ability were detected by a wound healing assay and transwell assay, respectively. RESULTS Based on the GBM data of the TCGA and GTEx databases, 58 intersection genes were identified, and a risk model was constructed. The model was verified in the CGGA cohort, and its accuracy was confirmed by the ROC curve (AUC = 0.807). After combining clinical subgroups, univariate and multivariate Cox regression analyses showed that risk score and age were independent risk factors for GBM patients. Furthermore, our subsequent analysis of immune infiltration, tumor mutation, and drug treatment showed that risk score and high- and low-risk groups were associated with multiple immune cells, mutated genes, and drugs. Enrichment analysis indicated that the differences between high- and low-risk groups were manifested in tumor-related pathways, including the PI3K-AKT and JAK-STAT pathways. Finally, in vivo experiments proved that the hypoxia environment promoted the expression of MDK, and MDK knockdown reduced the proliferation, migration, and EMT of GBM cells induced by hypoxia. CONCLUSIONS Our novel prognostic correlation model provided more potential treatment strategies for GBM patients.
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Affiliation(s)
- Minqi Xia
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Shiao Tong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ling Gao
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Wuhan 430060, China
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18
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Yu Y, Chen G, Jiang C, Guo T, Tang H, Yuan Z, Wang Y, Tan X, Chen J, Zhang E, Wang X. USP31 serves as a potential biomarker for predicting prognosis and immune responses for clear cell renal cell carcinoma via single-cell and bulk RNA-sequencing. J Gene Med 2024; 26:e3594. [PMID: 37699648 DOI: 10.1002/jgm.3594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Currently, there is no research available on the prognosis, potential effect and therapeutic value of USP31 in clear cell renal cell carcinoma (ccRCC). To address this gap, the present study aimed to shed light on its potential roles and possible mechanisms in ccRCC. METHODS R software was utilized to conduct bioinformatics analyses with the data derived from The Cancer Genome Atlas (i.e. KIRC) and Gene Expression Omnibus datasets. The expression of USP31 in ccRCC was validated by a PCR. The independent prognostic ability of USP31 was evaluated by Cox regression analysis. We conducted gene set enrichment analysis (GSEA) to explore the potential USP31-related pathways. We also discussed the relationships between USP31 and immunity, by predicting its possible upstream transcription factors (TFs) by ChEA3. RESULTS In ccRCC, USP31 demonstrated a high level of expression and this increased expression was correlated with a poor prognosis (p < 0.05). Through univariate and multivariate Cox regression analysis, USP31 was identified as an independent prognostic factor for ccRCC (p < 0.05). Furthermore, eight USP31-related pathways were identified by GSEA (p < 0.05). Moreover, USP31 was found to be associated with microsatellite instability, tumor microenvironment, a variety of immune cells and immune checkpoints and immune infiltration (p < 0.05). Additionally, Patients with high USP31 expression in ccRCC were shown to have better curative effects after immunotherapy (p < 0.05). Finally, we found that AR, USF1, MXI1 and CLOCK could be the potential upstream TFs of USP31. CONCLUSIONS USP31 could serve as a potential biomarker for predicting both prognosis and immune responses, revealing its potential mechanisms of TF-USP31 mRNA networks in ccRCC.
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Affiliation(s)
- Yaoyu Yu
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guihua Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Jiang
- Laoximen Street Community Health Service Center, Huangpu District, Shanghai, China
| | - Tuanjie Guo
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Heting Tang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihao Yuan
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangyin Tan
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyuan Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Encheng Zhang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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19
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Ma C, Gu Z, Ding W, Li F, Yang Y. Crosstalk between copper homeostasis and cuproptosis reveals a lncRNA signature to prognosis prediction, immunotherapy personalization, and agent selection for patients with lung adenocarcinoma. Aging (Albany NY) 2023; 15:13504-13541. [PMID: 38011277 DOI: 10.18632/aging.205281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/26/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Copper homeostasis and cuproptosis play critical roles in various biological processes of cancer; however, whether they can impact the prognosis of lung adenocarcinoma (LUAD) remain to be fully elucidated. We aimed to adopt these concepts to create and validate a lncRNA signature for LUAD prognostic prediction. METHODS For this study, the TCGA-LUAD dataset was used as the training cohort, and multiple datasets from the GEO database were pooled as the validation cohort. Copper homeostasis and cuproptosis regulated genes were obtained from published studies, and various statistical methods, including Kaplan-Meier (KM), Cox, and LASSO, were used to train our gene signature CoCuLncSig. We utilized KM analysis, COX analysis, receiver operating characteristic analysis, time-dependent AUC analysis, principal component analysis, and nomogram predictor analysis in our validation process. We also compared CoCuLncSig with previous studies. We performed analyses using R software to evaluate CoCuLncSig's immunotherapeutic ability, focusing on eight immune algorithms, TMB, and TIDE. Additionally, we investigated potential drugs that could be effective in treating patients with high-risk scores. Additionally qRT-PCR examined the expression patterns of CoCuLncSig lncRNAs, and the ability of CoCuLncSig in pan-cancer was also assessed. RESULTS CoCuLncSig containing eight lncRNAs was trained and showed strong predictive ability in the validation cohort. Compared with previous similar studies, CoCuLncSig had more prognostic ability advantages. CoCuLncSig was closely related to the immune status of LUAD, and its tight relationship with checkpoints IL10, IL2, CD40LG, SELP, BTLA, and CD28 may be the key to its potential immunotherapeutic ability. For the high CoCuLncSig score population, we found 16 drug candidates, among which epothilone-b and gemcitabine may have the most potential. The pan-cancer analysis found that CoCuLncSig was a risk factor in multiple cancers. Additionally, we discovered that some of the CoCuLncSig lncRNAs could play crucial roles in specific cancer types. CONCLUSION The current study established a powerful prognostic CoCuLncSig signature for LUAD that was also valid for most pan-cancers. This signature could serve as a potential target for immunotherapy and might help the more efficient application of drugs to specific populations.
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Affiliation(s)
- Chao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhuoyu Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weizheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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20
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Yao S, Han Y, Yang M, Jin K, Lan H. Integration of liquid biopsy and immunotherapy: opening a new era in colorectal cancer treatment. Front Immunol 2023; 14:1292861. [PMID: 38077354 PMCID: PMC10702507 DOI: 10.3389/fimmu.2023.1292861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
Immunotherapy has revolutionized the conventional treatment approaches for colorectal cancer (CRC), offering new therapeutic prospects for patients. Liquid biopsy has shown significant potential in early screening, diagnosis, and postoperative monitoring by analyzing circulating tumor cells (CTC) and circulating tumor DNA (ctDNA). In the era of immunotherapy, liquid biopsy provides additional possibilities for guiding immune-based treatments. Emerging technologies such as mass spectrometry-based detection of neoantigens and flow cytometry-based T cell sorting offer new tools for liquid biopsy, aiming to optimize immune therapy strategies. The integration of liquid biopsy with immunotherapy holds promise for improving treatment outcomes in colorectal cancer patients, enabling breakthroughs in early diagnosis and treatment, and providing patients with more personalized, precise, and effective treatment strategies.
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Affiliation(s)
- Shiya Yao
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yuejun Han
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Mengxiang Yang
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Ketao Jin
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Huanrong Lan
- Department of Surgical Oncology, Hangzhou Cancer Hospital, Hangzhou, Zhejiang, China
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21
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Patelli G, Mauri G, Tosi F, Amatu A, Bencardino K, Bonazzina E, Pizzutilo EG, Villa F, Calvanese G, Agostara AG, Stabile S, Ghezzi S, Crisafulli G, Di Nicolantonio F, Marsoni S, Bardelli A, Siena S, Sartore-Bianchi A. Circulating Tumor DNA to Drive Treatment in Metastatic Colorectal Cancer. Clin Cancer Res 2023; 29:4530-4539. [PMID: 37436743 PMCID: PMC10643999 DOI: 10.1158/1078-0432.ccr-23-0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/28/2023] [Accepted: 06/23/2023] [Indexed: 07/13/2023]
Abstract
In the evolving molecular treatment landscape of metastatic colorectal cancer (mCRC), the identification of druggable alterations is pivotal to achieve the best therapeutic opportunity for each patient. Because the number of actionable targets is expanding, there is the need to timely detect their presence or emergence to guide the choice of different available treatment options. Liquid biopsy, through the analysis of circulating tumor DNA (ctDNA), has proven safe and effective as a complementary method to address cancer evolution while overcoming the limitations of tissue biopsy. Even though data are accumulating regarding the potential for ctDNA-guided treatments applied to targeted agents, still major gaps in knowledge exist as for their application to different areas of the continuum of care. In this review, we recapitulate how ctDNA information could be exploited to drive different targeted treatment strategies in mCRC patients, by refining molecular selection before treatment by addressing tumor heterogeneity beyond tumor tissue biopsy; longitudinally monitoring early-tumor response and resistance mechanisms to targeted agents, potentially leading to tailored, molecular-driven, therapeutic options; guiding the molecular triage towards rechallenge strategies with anti-EGFR agents, suggesting the best time for retreatment; and providing opportunities for an "enhanced rechallenge" through additional treatments or combos aimed at overcoming acquired resistance. Besides, we discuss future perspectives concerning the potential role of ctDNA to fine-tune investigational strategies such as immuno-oncology.
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Affiliation(s)
- Giorgio Patelli
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- IFOM ETS – The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Gianluca Mauri
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- IFOM ETS – The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Federica Tosi
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Alessio Amatu
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Katia Bencardino
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Erica Bonazzina
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Elio Gregory Pizzutilo
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Federica Villa
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Gabriele Calvanese
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Alberto Giuseppe Agostara
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Stefano Stabile
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Silvia Ghezzi
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Federica Di Nicolantonio
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia-IRCCS, Candiolo, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Silvia Marsoni
- IFOM ETS – The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, Fondazione del Piemonte per l'Oncologia-IRCCS, Candiolo, Italy
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Salvatore Siena
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Andrea Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Division of Clinical Research and Innovation, Grande Ospedale Metropolitano Niguarda, Milan, Italy
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22
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Zhang Q, Tao X, Yuan P, Zhang Z, Ying J, Guo L, Li N, Wang S, Li J, Liu Y, Guo W, Zhao S, Wu N. Predictive value of 18 F-FDG PET/CT and serum tumor markers for tumor mutational burden in patients with non-small cell lung cancer. Cancer Med 2023; 12:20864-20877. [PMID: 37965789 PMCID: PMC10709729 DOI: 10.1002/cam4.6665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/16/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023] Open
Abstract
PURPOSE To investigate the correlations between metabolic parameters (MPs) of 18 F-fluorodeoxyglucose (FDG) uptake on positron emission tomography/computed tomography (PET/CT), serum tumor markers (STMs), and tumor mutational burden (TMB) in patients with non-small cell lung cancer (NSCLC). MATERIALS AND METHODS In this retrospective study, we enrolled 129 patients with NSCLC (males, 78; females, 51) who underwent baseline TMB and STM tests and 18 F-FDG PET/CT scans before treatment between March 2018 and September 2022. Patients were categorized into TMB-high (TMB ≥10 mutations/Mb; n = 27 [20.9%]) and non-TMB-high (TMB <10 mutations/Mb; n = 102 [79.1%]) groups. Binary logistic regression analyses were performed to determine independent predictors of TMB-high. Univariate and multivariate linear regression analyses were performed to determine independent predictors of TMB level on a log scale. Subgroup analyses for adenocarcinoma (ADC), ADC with EGFR+, ADC with EGFR-, and squamous cell carcinoma (SCC) were performed. RESULTS For ADC, all MPs (SULpeak , SULmax , SULmean , MTV, and TLG) were significantly higher in the TMB-high group than the non-TMB-high group; smoker (odds ratio [OR] = 27.08, p = 0.018), EGFR+ (OR = 0.03, p = 0.033), KRAS+ (OR = 7.98, p = 0.083), high CEA (OR = 33.56, p = 0.029), and high CA125 (OR = 13.68, p = 0.030) were independent predictors of TMB-high; and all MPs showed significant positive linear correlations with TMB on a log scale, with SULpeak as an independent predictor. However, no significant correlation was observed for SCC. CONCLUSION MPs and STMs can predict the TMB level for patients with ADC, and may serve as potential substitutes for TMB with increased value and easy implementation in guiding immunotherapy through noninvasive methods.
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Affiliation(s)
- Qian Zhang
- Department of Diagnostic Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xiuli Tao
- Department of Nuclear Medicine (PET‐CT Center)National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Pei Yuan
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zewei Zhang
- Department of Nuclear Medicine (PET‐CT Center)National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ning Li
- Department of Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Shuhang Wang
- Department of Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jing Li
- Department of Diagnostic Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of Nuclear Medicine (PET‐CT Center)National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ying Liu
- Department of Nuclear Medicine (PET‐CT Center)National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Shijun Zhao
- Department of Diagnostic Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ning Wu
- Department of Diagnostic Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Department of Nuclear Medicine (PET‐CT Center)National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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23
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孟 祥, 俞 纯, 杨 啸, 杨 子, 刘 邓. [Multi-classification prediction model of lung cancer tumor mutation burden based on residual network]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2023; 40:867-875. [PMID: 37879915 PMCID: PMC10600436 DOI: 10.7507/1001-5515.202304055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/28/2023] [Indexed: 10/27/2023]
Abstract
Medical studies have found that tumor mutation burden (TMB) is positively correlated with the efficacy of immunotherapy for non-small cell lung cancer (NSCLC), and TMB value can be used to predict the efficacy of targeted therapy and chemotherapy. However, the calculation of TMB value mainly depends on the whole exon sequencing (WES) technology, which usually costs too much time and expenses. To deal with above problem, this paper studies the correlation between TMB and slice images by taking advantage of digital pathological slices commonly used in clinic and then predicts the patient TMB level accordingly. This paper proposes a deep learning model (RCA-MSAG) based on residual coordinate attention (RCA) structure and combined with multi-scale attention guidance (MSAG) module. The model takes ResNet-50 as the basic model and integrates coordinate attention (CA) into bottleneck module to capture the direction-aware and position-sensitive information, which makes the model able to locate and identify the interesting positions more accurately. And then, MSAG module is embedded into the network, which makes the model able to extract the deep features of lung cancer pathological sections and the interactive information between channels. The cancer genome map (TCGA) open dataset is adopted in the experiment, which consists of 200 pathological sections of lung adenocarcinoma, including 80 data samples with high TMB value, 77 data samples with medium TMB value and 43 data samples with low TMB value. Experimental results demonstrate that the accuracy, precision, recall and F1 score of the proposed model are 96.2%, 96.4%, 96.2% and 96.3%, respectively, which are superior to the existing mainstream deep learning models. The model proposed in this paper can promote clinical auxiliary diagnosis and has certain theoretical guiding significance for TMB prediction.
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Affiliation(s)
- 祥福 孟
- 辽宁工程技术大学 电子与信息工程学院 (辽宁葫芦岛 125000)School of Electronics and Information Engineering, Liaoning Technical University, Huludao, Liaoning 125000, P. R. China
| | - 纯林 俞
- 辽宁工程技术大学 电子与信息工程学院 (辽宁葫芦岛 125000)School of Electronics and Information Engineering, Liaoning Technical University, Huludao, Liaoning 125000, P. R. China
| | - 啸林 杨
- 辽宁工程技术大学 电子与信息工程学院 (辽宁葫芦岛 125000)School of Electronics and Information Engineering, Liaoning Technical University, Huludao, Liaoning 125000, P. R. China
| | - 子毅 杨
- 辽宁工程技术大学 电子与信息工程学院 (辽宁葫芦岛 125000)School of Electronics and Information Engineering, Liaoning Technical University, Huludao, Liaoning 125000, P. R. China
| | - 邓 刘
- 辽宁工程技术大学 电子与信息工程学院 (辽宁葫芦岛 125000)School of Electronics and Information Engineering, Liaoning Technical University, Huludao, Liaoning 125000, P. R. China
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24
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Ding W, Zhang M, Zhang P, Zhang X, Sun J, Lin B. Identification of anoikis-related subtypes and immune landscape in kidney renal clear cell carcinoma. Sci Rep 2023; 13:18069. [PMID: 37872217 PMCID: PMC10593771 DOI: 10.1038/s41598-023-45069-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/15/2023] [Indexed: 10/25/2023] Open
Abstract
Anoikis is a specific form of programmed cell death induced by the loss of cell contact with the extracellular matrix and other cells, and plays an important role in organism development, tissue homeostasis, disease development and tumor metastasis. We comprehensively investigated the expression patterns of anoikis-related genes (ARGs) in kidney renal clear cell carcinoma (KIRC) from public databases. Anoikis-related prognostic signatures were established based on four ARGs expression, in which KIRC patients were assigned different risk scores and divided into two different risk groups. In addition, four ARGs expression was validated by qRT-PCR. A better prognosis was observed in the low-risk group, but with lower immune activity (including immune cells and immune-related functions) in the tumor microenvironment. Combined with the relevant clinical characteristics, a nomogram for clinical application was established. Receiver operating characteristics (ROC) and calibration curves were constructed to demonstrate the predictive power of this risk signature. In addition, higher risk scores were significantly and positively correlated with higher gene expression of tumor mutation load (TMB), immune checkpoints (ICPs) and mismatch repair (MMR)-related proteins in general. The results also suggested that the high-risk group was more sensitive to immunotherapy and certain chemotherapeutic agents. Anoikis-related prognostic signatures may provide a better understanding of the roles of ARGs and offer new perspectives for clinical prognosis and individualized treatment.
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Affiliation(s)
- Wencong Ding
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Min Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Ping Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Xianghong Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Junwei Sun
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Biying Lin
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China.
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Yu Z, Qin L, Yu G. The progresses of relevant factors on the efficacy of immune checkpoint inhibitors in the non-small cell lung cancer patients. Cancer Treat Res Commun 2023; 37:100758. [PMID: 37776694 DOI: 10.1016/j.ctarc.2023.100758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/29/2023] [Accepted: 09/02/2023] [Indexed: 10/02/2023]
Abstract
Lung cancer has the highest mortality rate of all cancers worldwide. Although immune checkpoint inhibitor (ICI)-based therapy can improve the survival of patients with lung cancer, its efficacy is affected by many factors. Therefore, it is necessary to identify factors that affect the efficacy of ICI-based treatment and establish a model for predicting drug response and resistance before and during treatment for individualized and accurate treatment of patients. This review summarizes the clinical and biological factors related to ICI-based treatment of non-small cell lung cancer (NSCLC) and the recent research progress of predictive models for assessing ICI efficacy.
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Affiliation(s)
- Zhaoqing Yu
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Li Qin
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Guifang Yu
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, PR China.
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Wankhede D, Grover S, Hofman P. The prognostic value of TMB in early-stage non-small cell lung cancer: a systematic review and meta-analysis. Ther Adv Med Oncol 2023; 15:17588359231195199. [PMID: 37667779 PMCID: PMC10475237 DOI: 10.1177/17588359231195199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/31/2023] [Indexed: 09/06/2023] Open
Abstract
Background Tumor mutation burden (TMB) has been validated as a predictive biomarker for immunotherapy response and survival in numerous cancer types. Limited data is available on the inherent prognostic role of TMB in early-stage tumors. Objective To evaluate the prognostic role of TMB in early-stage, resected non-small cell lung cancer (NSCLC). Design Systematic review and meta-analysis of pertinent prospective and retrospective studies. Data sources and methods Publication search was performed in PubMed, Embase, Cochrane Library, and Web of Science databases. Based on the level of heterogeneity, a random- or fixed-effects model was used to calculate pooled effects of hazard ratio (HR) for overall survival (OS) and disease-free survival (DFS). The source of heterogeneity was investigated using sensitivity analysis, subgroup analysis, and publication bias assessment. Results Ten studies comprising 2520 patients were included in this analysis. There was no statistically significant difference in OS (HR, 1.18, 95% CI, 0.70, 1.33; p 0.53, I2 = 80%; phet < 0.0001) and DFS (HR, 1.18, 95% CI, 0.91, 1.52; p = 0.53, I2 = 75%; phet = 0.0001) between the high-TMB and low-TMB group. Subgroup analyses indicated that East Asian ethnicity, and TMB detected using whole exome sequencing, and studies with <100 patients had poor DFS in the high-TMB group. Conclusion The inherent prognostic role of TMB is limited in early-stage NSCLC. Ethnic differences in mutation burden must be considered while designing future trials on neoadjuvant immunotherapy. Further research in the harmonization and standardization of panel-based TMB is essential for its widespread clinical utility.Registration: CRD42023392846.
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Affiliation(s)
- Durgesh Wankhede
- German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Sandeep Grover
- Center for Human Genetics, Universitatsklinikum Giessen und Marburg – Standort Marburg, Marburg, Germany
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, University Côte d’Azur, Nice, France
- Institute for Research on Cancer and Ageing, Nice (IRCAN), INSERM U1081 and UMR CNRS 7284, Team 4, Nice, France
- Hospital-Integrated Biobank BB-0033-00025, Pasteur Hospital, Nice, France
- University Hospital Institute RespirERA, Nice, France
- University Hospital Federation OncoAge, CHU de Nice, University Côte d’Azur, Nice, France
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Ma C, Li F, Gu Z, Yang Y, Qi Y. A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinoma. Front Pharmacol 2023; 14:1146840. [PMID: 37670938 PMCID: PMC10475834 DOI: 10.3389/fphar.2023.1146840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023] Open
Abstract
Background: Cuproptosis is a newly discovered non-apoptotic form of cell death that may be related to the development of tumors. Nonetheless, the potential role of cuproptosis-related lncRNAs in tumor immunity formation and patient-tailored treatment optimization of lung adenocarcinoma (LUAD) is still unclear. Methods: RNA sequencing and survival data of LUAD patients were downloaded from The Cancer Genome Atlas (TCGA) database for model training. The patients with LUAD in GSE29013, GSE30219, GSE31210, GSE37745, and GSE50081 were used for validation. The proofed cuproptosis-related genes were extracted from the previous studies. The Pearson correlation was applied to select cuproptosis-related lncRNAs. We chose differentially expressed cuproptosis-related lncRNAs in the tumor and normal tissues and allowed them to go to a Cox regression and a LASSO regression for a lncRNA signature that predicts the LUAD prognosis. Kaplan-Meier estimator, Cox model, ROC, tAUC, PCA, nomogram predictor, decision curve analysis, and real-time PCR were further deployed to confirm the model's accuracy. We examined this model's link to other regulated cell death forms. Applying TMB, immune-related signatures, and TIDE demonstrated the immunotherapeutic capabilities of signatures. We evaluated the relationship of our signature to anticancer drug sensitivity. GSEA, immune infiltration analysis, and function experiments further investigated the functional mechanisms of the signature and the role of immune cells in the prognostic power of the signature. Results: An eight-lncRNA signature (TSPOAP1-AS1, AC107464.3, AC006449.7, LINC00324, COLCA1, HAGLR, MIR4435-2HG, and NKILA) was built and demonstrated owning prognostic power by applied to the validation cohort. Each signature gene was confirmed differentially expressed in the real world by real-time PCR. The eight-lncRNA signature correlated with 2321/3681 (63.05%) apoptosis-related genes, 11/20 (55.00%) necroptosis-related genes, 34/50 (68.00%) pyroptosis-related genes, and 222/380 (58.42%) ferroptosis-related genes. Immunotherapy analysis suggested that our signature may have utility in predicting immunotherapy efficacy in patients with LUAD. Mast cells were identified as key players that support the predicting capacity of the eight-lncRNA signature through the immune infiltrating analysis. Conclusion: In this study, an eight-lncRNA signature linked to cuproptosis was identified, which may improve LUAD management strategies. This signature may possess the ability to predict the effect of LUAD immunotherapy. In addition, infiltrating mast cells may affect the signature's prognostic power.
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Affiliation(s)
| | | | | | - Yang Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Tong L, Wang S, Yang J, Zhang Q, Gu X, Mo T, Luo Y, Zhang C, Zhang J, Liu Y. Combined ARHGEF6 and Tumor Mutational Burden may serve as a potential biomarker for immunotherapy of lung adenocarcinoma. Heliyon 2023; 9:e18501. [PMID: 37600416 PMCID: PMC10432614 DOI: 10.1016/j.heliyon.2023.e18501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
ARHGEF6, a member of the Dbl-related guanylate exchanger (GEF) family, is highly expressed in gastric cancer and glioma. However, scientists still do not know whether it plays a pivotal role in the pathogenesis of lung adenocarcinoma(LUAD). The prognostic significance of ARHGEF6 expression was assessed by TCGA data. This paper focuses on the level of immune infiltration associated with ARHGEF6 and explored the relationship of this gene with the tumor mutational burden (TMB), immune checkpoints, and drug sensitivity. The results showed that the high expression of ARHGEF6 was associated with a good prognosis in LUAD patients, and positively correlated with a variety of immune cells and drugs. Meanwhile, ARHGEF6 was found to be negatively correlated with TMB. In conclusion, the results of this study suggest that ARHGEF6 is a protective gene in LUAD patients. A combination of ARHGEF6 and TMB could be used as a potential biomarker in the screening of immunotherapy regimens, which are provided to patients with LUAD.
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Affiliation(s)
- Li Tong
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- Dalian Medical University, Dalian, China
| | - Sichu Wang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- Dalian Medical University, Dalian, China
| | - Juanjuan Yang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Qing Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xue Gu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Taoming Mo
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Yang Luo
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | | | - Jianguo Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
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29
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Venetis K, Sajjadi E, Ivanova M, Peccatori FA, Fusco N, Guerini-Rocco E. Characterization of the immune environment in pregnancy-associated breast cancer. Future Oncol 2023. [PMID: 37376974 DOI: 10.2217/fon-2022-1321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023] Open
Abstract
Pregnancy-associated breast cancer (PrBC) is a rare and clinically challenging condition. Specific immune mechanisms and pathways are involved in maternal-fetal tolerance and tumor-host immunoediting. The comprehension of the molecular processes underpinning this immune synergy in PrBC is needed to improve patients' clinical management. Only a few studies focused on the immune biology of PrBC and attempted to identify bona fide biomarkers. Therefore, clinically actionable information remains extremely puzzling for these patients. In this review article, we discuss the current knowledge on the immune environment of PrBC, in comparison with pregnancy-unrelated breast cancer and in the context of maternal immune changes during pregnancy. A particular emphasis is given to the actual role of potential immune-related biomarkers for PrBC clinical management.
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Affiliation(s)
- Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Fedro Alessandro Peccatori
- Fertility & Procreation Unit, Division of Gynecologic Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
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Geng T, Zheng M, Wang Y, Reseland JE, Samara A. An artificial intelligence prediction model based on extracellular matrix proteins for the prognostic prediction and immunotherapeutic evaluation of ovarian serous adenocarcinoma. Front Mol Biosci 2023; 10:1200354. [PMID: 37388244 PMCID: PMC10301747 DOI: 10.3389/fmolb.2023.1200354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Background: Ovarian Serous Adenocarcinoma is a malignant tumor originating from epithelial cells and one of the most common causes of death from gynecological cancers. The objective of this study was to develop a prediction model based on extracellular matrix proteins, using artificial intelligence techniques. The model aimed to aid healthcare professionals to predict the overall survival of patients with ovarian cancer (OC) and determine the efficacy of immunotherapy. Methods: The Cancer Genome Atlas Ovarian Cancer (TCGA-OV) data collection was used as the study dataset, whereas the TCGA-Pancancer dataset was used for validation. The prognostic importance of 1068 known extracellular matrix proteins for OC were determined by the Random Forest algorithm and the Lasso algorithm establishing the ECM risk score. Based on the gene expression data, the differences in mRNA abundance, tumour mutation burden (TMB) and tumour microenvironment (TME) between the high- and low-risk groups were assessed. Results: Combining multiple artificial intelligence algorithms we were able to identify 15 key extracellular matrix genes, namely, AMBN, CXCL11, PI3, CSPG5, TGFBI, TLL1, HMCN2, ESM1, IL12A, MMP17, CLEC5A, FREM2, ANGPTL4, PRSS1, FGF23, and confirm the validity of this ECM risk score for overall survival prediction. Several other parameters were identified as independent prognostic factors for OC by multivariate COX analysis. The analysis showed that thyroglobulin (TG) targeted immunotherapy was more effective in the high ECM risk score group, while the low ECM risk score group was more sensitive to the RYR2 gene-related immunotherapy. Additionally, the patients with low ECM risk scores had higher immune checkpoint gene expression and immunophenoscore levels and responded better to immunotherapy. Conclusion: The ECM risk score is an accurate tool to assess the patient's sensitivity to immunotherapy and forecast OC prognosis.
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Affiliation(s)
- Tianxiang Geng
- Department of Biomaterials, FUTURE, Center for Functional Tissue Reconstruction, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Mengxue Zheng
- Laboratory of Reproductive Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yongfeng Wang
- Department of Obstetrics and Gynecology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Janne Elin Reseland
- Department of Biomaterials, FUTURE, Center for Functional Tissue Reconstruction, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Athina Samara
- Department of Biomaterials, FUTURE, Center for Functional Tissue Reconstruction, Faculty of Dentistry, University of Oslo, Oslo, Norway
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31
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Yang W, Qiang Y, Wu W, Xin J. Graph-ETMB: A graph neural network-based model for tumour mutation burden estimation. Comput Biol Chem 2023; 105:107900. [PMID: 37285654 DOI: 10.1016/j.compbiolchem.2023.107900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/06/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
As a critical indicator of how easily the human immune system recognizes tumour cells, tumour mutational burden (TMB) is widely used to identify the potential effectiveness of immune checkpoint inhibitor therapy. However, the difficulties associated with the whole exome sequencing (WES) process, such as high tissue sampling requirements, high costs, and long turnaround times, have hindered the widespread clinical use of WES. Furthermore, the mutation landscape varies across cancer types, and the distribution of TMBs varies across cancer subtypes. Therefore, there is an urgent clinical need to develop a small cancer-specific panel to estimate TMB accurately, predict immunotherapy response cost-effectively and assist physicians in precise decision-making. This paper uses a graph neural network framework (Graph-ETMB) to address the cancer specificity problem in TMB. The correlation and tractability between mutated genes are described through message-passing and aggregation algorithms between graph networks. Then the graph neural network is trained in the lung adenocarcinoma data through a semi-supervised approach, resulting in a mutation panel containing 20 genes with a length of only 0.16 Mb. The number of genes to be detected is smaller than most commercial panels currently in clinical use. In addition, the efficacy of the designed panel in predicting immunotherapy response was further determined in an independent validation dataset, exploring the association between TMB and immunotherapy efficacy.
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Affiliation(s)
- Wanting Yang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, Shanxi 030000, China
| | - Yan Qiang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, Shanxi 030000, China.
| | - Wei Wu
- Department of Clinical Laboratory, Affiliated People's Hospital of Shanxi Medical University, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China
| | - Jialong Xin
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, Shanxi 030000, China
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32
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Alessi JV, Elkrief A, Ricciuti B, Wang X, Cortellini A, Vaz VR, Lamberti G, Frias RL, Venkatraman D, Fulgenzi CAM, Pecci F, Recondo G, Di Federico A, Barrichello A, Park H, Nishino M, Hambelton GM, Egger JV, Ladanyi M, Digumarthy S, Johnson BE, Christiani DC, Lin X, Gainor JF, Lin JJ, Pinato DJ, Schoenfeld AJ, Awad MM. Clinicopathologic and Genomic Factors Impacting Efficacy of First-Line Chemoimmunotherapy in Advanced NSCLC. J Thorac Oncol 2023; 18:731-743. [PMID: 36775193 PMCID: PMC10500613 DOI: 10.1016/j.jtho.2023.01.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/17/2023] [Accepted: 01/29/2023] [Indexed: 02/12/2023]
Abstract
INTRODUCTION Although programmed cell death protein 1 and programmed death-ligand 1 (PD-L1) blockade in combination with platinum-doublet chemotherapy has become a mainstay of first-line treatment for advanced NSCLC, factors associated with efficacy of chemoimmunotherapy (CIT) are not well characterized. METHODS In this multicenter retrospective analysis, clinicopathologic and genomic data were collected from patients with advanced NSCLC (lacking sensitizing genomic alterations in EGFR and ALK) and evaluated with clinical outcomes to first-line CIT. RESULTS Among 1285 patients treated with CIT, a worsening performance status and increasing derived neutrophil-to-lymphocyte ratio in the blood were associated with a significantly reduced objective response rate (ORR), median progression-free survival (mPFS), and median overall survival (mOS). With increasing PD-L1 tumor proportion scores of less than 1%, 1% to 49%, 50% to 89%, and greater than or equal to 90%, there was a progressive improvement in ORR (32.7% versus 37.5% versus 51.6% versus 61.7%, p < 0.001), mPFS (5.0 versus 6.1 versus 6.8 versus 13.0 mo, p < 0.001), and generally mOS (12.9 versus 14.6 versus 34.7 versus 23.1 mo, p = 0.009), respectively. Of 789 NSCLCs with comprehensive genomic data, NSCLCs with a tumor mutational burden (TMB) greater than or equal to the 90th percentile had an improved ORR (53.5% versus 36.4%, p = 0.004), mPFS (10.8 versus 5.5 mo, p < 0.001), and mOS (29.2 versus 13.1 mo, p < 0.001), compared with those with a TMB less than the 90th percentile. In all-comers with nonsquamous NSCLC, the presence of an STK11, KEAP1, or SMARCA4 mutation was associated with significantly worse ORR, mPFS, and mOS to CIT (all p < 0.05); this was also observed in the KRAS-mutant subgroup of NSCLCs with co-occurring mutations in STK11, KEAP1, or SMARCA4 (all p < 0.05). In KRAS wild-type NSCLC, KEAP1 and SMARCA4 mutations were associated with a significantly shorter mPFS and mOS to CIT (all p < 0.05), but STK11 mutation status had no significant impact on mPFS (p = 0.16) or mOS (p = 0.38). CONCLUSIONS In advanced NSCLC, better patient performance status, low derived neutrophil-to-lymphocyte ratio, increasing PD-L1 expression, a very high TMB, and STK11/KEAP1/SMARCA4 wild-type status are associated with improved clinical outcomes to first-line CIT.
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Affiliation(s)
- Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Arielle Elkrief
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xinan Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Alessio Cortellini
- Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Imperial College London, London, United Kingdom; Department of Medical Oncology, University Campus Bio-Medico of Rome, Italy
| | - Victor R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Rosa L Frias
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Deepti Venkatraman
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Claudia A M Fulgenzi
- Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Imperial College London, London, United Kingdom; Department of Medical Oncology, University Campus Bio-Medico of Rome, Italy
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gonzalo Recondo
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Adriana Barrichello
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hyesun Park
- Department of Radiology, Lahey Hospital and Medical Center, Burlington, Massachusetts; Department of Radiology, Brigham and Women's Hospital and Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital and Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Grace M Hambelton
- Center for Thoracic Cancers, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jacklynn V Egger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Subba Digumarthy
- Department of Radiology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Bruce E Johnson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Justin F Gainor
- Center for Thoracic Cancers, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jessica J Lin
- Center for Thoracic Cancers, Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - David J Pinato
- Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Imperial College London, London, United Kingdom
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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Pang J, Xia H, Mi S, Zhang W, Pendrick D, Freeman C, Fernandes H, Mansukhani M, Hsiao SJ. Benchmarking bioinformatics approaches for tumour mutational burden evaluation from a large cancer panel against whole-exome sequencing. J Clin Pathol 2023; 76:276-280. [PMID: 35906043 DOI: 10.1136/jcp-2022-208385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/22/2022] [Indexed: 11/03/2022]
Abstract
Tumour mutational burden (TMB) is used to predict response to immunotherapies. Although several groups have proposed calculation methods for TMB, a clear consensus has not yet emerged. In this study, we explored TMB calculation approaches with a 586-gene cancer panel (1.75 Mb) benchmarked to TMB measured by whole-exome sequencing (WES), using 30 samples across a range of tumour types. We explored variant allelic fraction (VAF) cut-offs of 5% and 10%, population database filtering at 0.001, 0.0001 and 0.000025, as well as different combinations of synonymous, insertion/deletion and intronic (splice site) variants, as well as exclusion of hotspot mutations, and examined the effect on TMB correlation. Good correlation (Spearman, range 0.66-0.78) between WES and panel TMB was seen across all methods evaluated. Each method of TMB calculation evaluated showed good positive per cent agreement and negative per cent agreement using 10 mutations/Mb as a cut-off, suggesting that multiple TMB calculation approaches may yield comparable results.
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Affiliation(s)
- Jiuhong Pang
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Hongai Xia
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Shijun Mi
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Wen Zhang
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Danielle Pendrick
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Christopher Freeman
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Helen Fernandes
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Mahesh Mansukhani
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
| | - Susan J Hsiao
- Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, New York, USA
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Bazhenova L. Exploring the role of accessory biomarkers TMB, STK11, KEAP1, and KRAS in non-small-cell lung cancer: confused, but on a much higher level. Ann Oncol 2023; 34:327-332. [PMID: 37061249 DOI: 10.1016/j.annonc.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 04/17/2023] Open
Affiliation(s)
- L Bazhenova
- University of California San Diego Moores Cancer Center, La Jolla, USA.
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Shimozaki K, Nakayama I, Hirota T, Yamaguchi K. Current Strategy to Treat Immunogenic Gastrointestinal Cancers: Perspectives for a New Era. Cells 2023; 12:1049. [PMID: 37048122 PMCID: PMC10093684 DOI: 10.3390/cells12071049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/15/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023] Open
Abstract
Since pembrolizumab, an anti-programmed death-1 (PD-1) antibody, showed a dramatic response to immunogenic cancers with microsatellite instability-high (MSI-H) and/or deficient mismatch repair (dMMR) in the pilot clinical trial KEYNOTE-016, subsequent studies have confirmed durable responses of anti-PD-1 inhibitors for MSI-H/dMMR solid tumors. As immunotherapy is described as a "game changer," the therapeutic landscape for MSI-H/dMMR solid tumors including gastrointestinal cancers has changed considerably in the last decade. An MSI/MMR status has been established as the predictive biomarker for immune checkpoint blockades, playing an indispensable role in the clinical practice of patients with MSI-H/dMMR tumors. Immunotherapy is also now investigated for locally advanced MSI-H/dMMR gastrointestinal cancers. Despite this great success, a few populations with MSI-H/dMMR gastrointestinal cancers do not respond to immunotherapy, possibly due to the existence of intrinsic or acquired resistance mechanisms. Clarifying the underlying mechanisms of resistance remains a future task, whereas attempts to overcome resistance and improve the efficacy of immunotherapy are currently ongoing. Herein, we review recent clinical trials with special attention to MSI-H/dMMR gastrointestinal cancers together with basic/translational findings, which provide their rationale, and discuss perspectives for the further therapeutic development of treatment in this field.
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Affiliation(s)
- Keitaro Shimozaki
- Department of Gastrointestinal Oncology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
- Department of Gastroenterology and Hepatology, Division of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Izuma Nakayama
- Department of Gastrointestinal Oncology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
| | - Toru Hirota
- Department of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Kensei Yamaguchi
- Department of Gastrointestinal Oncology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
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Zhang G, Tai P, Fang J, Chen A, Chen X, Cao K. Molecular subtypes based on centrosome-related genes can predict prognosis and therapeutic responsiveness in patients with low-grade gliomas. Front Oncol 2023; 13:1157115. [PMID: 37051542 PMCID: PMC10083401 DOI: 10.3389/fonc.2023.1157115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
BackgroundAbnormalities in centrosome regulatory genes can induce chromosome instability, cell differentiation errors, and tumorigenesis. However, a limited number of comprehensive analyses of centrosome-related genes have been performed in low-grade gliomas (LGG).MethodsLGG data were extracted from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. The ConsensusClusterPlus” R package was used for unsupervised clustering. We constructed a centrosome-related genes (CRGs) signature using a random forest model, lasso Cox model, and multivariate Cox model, and quantified the centrosome-related risk score (centS). The prognostic prediction efficacy of centS was evaluated using a Receiver Operating Characteristic (ROC) curve. Immune cell infiltration and genomic mutational landscapes were evaluated using the ESTIMATE algorithm, single-sample Gene Set Enrichment Analysis (ssGSEA) algorithm, and “maftools” R package, respectively. Differences in clinical features, isocitrate dehydrogenase (IDH) mutation, 1p19q codeletion, O6-methylguanine-DNA methyltransferase promoter (MGMTp) methylation, and response to antitumor therapy between the high- and low-centS groups were explored. “pRRophetic” R packages were used for temozolomide (TMZ) sensitivity analysis. qRT-PCR verified the differential expression of the centrosomal gene team, the core of which is CEP135, between LGG cells and normal cells.ResultsTwo distinct CRG-based clusters were identified using consensus unsupervised clustering analysis. The prognosis, biological characteristics, and immune cell infiltration of the two clusters differed significantly. A well-performing centS signature was developed to predict the prognosis of patients with LGG based on 12 potential CRGs. We found that patients in the high-centS group showed poorer prognosis and lower proportion of IDH mutation and 1p19q codeletion compared to those in the low-centS group. Furthermore, patients in the high-centS group showed higher sensitivity to TMZ, higher tumor mutation burden, and immune cell infiltration. Finally, we identified a centrosomal gene team whose core was CEP135, and verified their differential expression between LGG cells and normal glial cells.ConclusionOur findings reveal a novel centrosome-related signature for predicting the prognosis and therapeutic responsiveness of patients with LGG. This may be helpful for the accurate clinical treatment of LGG.
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Raiber-Moreau EA, Portella G, Butler MG, Clement O, Konigshofer Y, Hadfield J. Development and validation of blood tumor mutational burden reference standards. Genes Chromosomes Cancer 2023; 62:121-130. [PMID: 36326821 PMCID: PMC10107199 DOI: 10.1002/gcc.23100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/19/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Tumor mutational burden (TMB), measured by exome or panel sequencing of tumor tissue or blood (bTMB), is a potential predictive biomarker for treatment benefit in patients with various cancer types receiving immunotherapy targeting checkpoint pathways. However, significant variability in TMB measurement has been observed. We developed contrived bTMB reference materials using DNA from tumor cell lines and donor-matched lymphoblastoid cell lines to support calibration and alignment across laboratories and platforms. Contrived bTMB reference materials were developed using genomic DNA from lung tumor cell lines blended into donor-matched lymphoblastoid cell lines at 0.5% and 2% tumor content, fragmented and size-selected to mirror the size profile of circulating cell-free tumor DNA with TMB scores of 7, 9, 20, and 26 mut/Mb. Variant allele frequency (VAF) and bTMB scores were assessed using PredicineATLAS and GuardantOMNI next-generation sequencing assays. DNA fragment sizes in the contrived reference samples were similar to those found within patient plasma-derived cell-free DNA, and mutational patterns aligned with those in the parental tumor lines. For the 7, 20, and 26 mut/Mb contrived reference samples with 2% tumor content, bTMB scores estimated using either assay aligned with expected scores from the parental tumor cell lines and showed good reproducibility. A bioinformatic filtration step was required to account for low-VAF artifact variants. We demonstrate the feasibility and challenges of producing and using bTMB reference standards across a range of bTMB levels, and how such standards could support the calibration and validation of bTMB platforms and help harmonization between panels and laboratories.
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Affiliation(s)
- Eun-Ang Raiber-Moreau
- Precision Medicine and Biosamples, Diagnostic Development Unit, AstraZeneca, Cambridge, UK
| | - Guillem Portella
- Precision Medicine and Biosamples, Diagnostic Science Unit, AstraZeneca, Cambridge, UK
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Parisi R, Patel RR, Rood G, Bowden A, Turco G, Korones DN, Andolina JR, Comito M, Barth M, Weintraub L. Multi-institution analysis of tumor mutational burden and outcomes in pediatric central nervous system tumor patients. Pediatr Blood Cancer 2023; 70:e30139. [PMID: 36573296 DOI: 10.1002/pbc.30139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Pediatric central nervous system (CNS) tumors are the leading cause of pediatric cancer mortality. Research addressing genomic biomarkers and clinical outcomes is needed to inform therapeutic decision-making. METHODS We conducted a retrospective analysis of pediatric patients (age <21) diagnosed with a primary CNS tumor at four upstate New York hospitals from 2008 to 2021. Clinical and histopathologic data were identified from each patient, including genomic analysis of somatic mutations and tumor mutational burden (TMB) where available. These variables were each compared with overall survival using Cox regression analyses. Multivariable analysis was conducted to identify patient characteristics that may independently predict survival. RESULTS We identified 119 patients. Common tumor types included low-grade glioma (N = 51), high-grade glioma (N = 29), and medulloblastoma (N = 11). Common driver mutations included TP53 inactivation (N = 16), BRAF-KIAA1549 fusion (N = 16), FGFR1 amplification (N = 12), BRAF V600E mutation (N = 12), NF1 loss (N = 12), and H3F3A K28M mutation (N = 6). Median TMB was one mutation/megabase (mut/Mb, range = 0-132). Overall survival was 79.9%. Variables associated with poorer survival on univariable analysis were higher TMB (p = .002, HR 4.97), high-grade tumors (p = .009, HR 84.3), and high-grade glioma histology (p = .021, HR 3.14). Multivariable analyses further identified TMB (p = .011, HR 4.46) and high-grade histology (p = .015, HR 5.28) as independently predictive of worse survival. Tumor progression was more common in high-TMB (N = 15, 44%) than in low-TMB tumors (N = 19, 35%). CONCLUSIONS High TMB is correlated with higher rates of progression and death as compared to low-TMB tumors. These findings may help identify patients who may benefit from alternative treatments, such as immunotherapies.
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Affiliation(s)
- Rose Parisi
- Albany Medical College, Albany, New York, USA
| | - Roshal R Patel
- Albany Medical College, Albany, New York, USA.,Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gavrielle Rood
- Upstate Medical University College of Medicine, Syracuse, New York, USA
| | - Acacia Bowden
- University of Rochester School of Medicine, Rochester, New York, USA
| | - George Turco
- Pediatric Hematology/Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - David N Korones
- Pediatric Hematology/Oncology, University of Rochester Medical Center, Rochester, New York, USA
| | - Jeffrey R Andolina
- Pediatric Hematology/Oncology, University of Rochester Medical Center, Rochester, New York, USA
| | - Melanie Comito
- Pediatric Hematology/Oncology, Upstate University Hospital, Syracuse, New York, USA
| | - Matthew Barth
- Pediatric Hematology/Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Lauren Weintraub
- Pediatric Hematology/Oncology, Albany Medical Center, Albany, New York, USA
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Abboud K, Umoru G, Esmail A, Abudayyeh A, Murakami N, Al-Shamsi HO, Javle M, Saharia A, Connor AA, Kodali S, Ghobrial RM, Abdelrahim M. Immune Checkpoint Inhibitors for Solid Tumors in the Adjuvant Setting: Current Progress, Future Directions, and Role in Transplant Oncology. Cancers (Basel) 2023; 15:cancers15051433. [PMID: 36900226 PMCID: PMC10000896 DOI: 10.3390/cancers15051433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
The rationale for administering immune checkpoint inhibitors (ICIs) in the adjuvant setting is to eradicate micro-metastases and, ultimately, prolong survival. Thus far, clinical trials have demonstrated that 1-year adjuvant courses of ICIs reduce the risk of recurrence in melanoma, urothelial cancer, renal cell carcinoma, non-small cell lung cancer, and esophageal and gastroesophageal junction cancers. Overall survival benefit has been shown in melanoma while survival data are still not mature in other malignancies. Emerging data also show the feasibility of utilizing ICIs in the peri-transplant setting for hepatobiliary malignancies. While ICIs are generally well-tolerated, the development of chronic immune-related adverse events, typically endocrinopathies or neurotoxicities, as well as delayed immune-related adverse events, warrants further scrutiny regarding the optimal duration of adjuvant therapy and requires a thorough risk-benefit determination. The advent of blood-based, dynamic biomarkers such as circulating tumor DNA (ctDNA) can help detect minimal residual disease and identify the subset of patients who would likely benefit from adjuvant treatment. In addition, the characterization of tumor-infiltrating lymphocytes, neutrophil-to-lymphocyte ratio, and ctDNA-adjusted blood tumor mutation burden (bTMB) has also shown promise in predicting response to immunotherapy. Until additional, prospective studies delineate the magnitude of overall survival benefit and validate the use of predictive biomarkers, a tailored, patient-centered approach to adjuvant ICIs that includes extensive patient counseling on potentially irreversible adverse effects should be routinely incorporated into clinical practice.
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Affiliation(s)
- Karen Abboud
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Godsfavour Umoru
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Abdullah Esmail
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA
- Correspondence: (A.E.); (M.A.)
| | - Ala Abudayyeh
- Section of Nephrology, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Naoka Murakami
- Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Humaid O. Al-Shamsi
- Department of Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ashish Saharia
- JC Walter Jr Center for Transplantation and Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA
| | - Ashton A. Connor
- JC Walter Jr Center for Transplantation and Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA
| | - Sudha Kodali
- JC Walter Jr Center for Transplantation and Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA
| | - Rafik M. Ghobrial
- JC Walter Jr Center for Transplantation and Sherrie and Alan Conover Center for Liver Disease and Transplantation, Houston, TX 77030, USA
| | - Maen Abdelrahim
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA
- Cockrell Center of Advanced Therapeutics Phase I Program, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Internal Medicine, Weill Cornell Medical College, New York, NY 14853, USA
- Correspondence: (A.E.); (M.A.)
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Meri-Abad M, Moreno-Manuel A, García SG, Calabuig-Fariñas S, Pérez RS, Herrero CC, Jantus-Lewintre E. Clinical and technical insights of tumour mutational burden in non-small cell lung cancer. Crit Rev Oncol Hematol 2023; 182:103891. [PMID: 36565893 DOI: 10.1016/j.critrevonc.2022.103891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Despite the durable responses provided by the introduction of checkpoint inhibitors in advanced Non-Small Cell Lung Cancer (NSCLC) without actionable targets in a subset of patients, a large proportion of them will progress after immunotherapy. Programmed Death Ligand 1 (PD-L1) was the first biomarker approved for immunotherapy, although it has multiple limitations, thus the development of novel biomarkers is an urgent need. Tumour Mutational Burden (TMB) is an emerging biomarker defined as the total number of mutations per coding area of tumour genome. Targeted gene panels have emerged as a cost-effective approach to estimate TMB. However, there is still an unmet need to fully standardize sample requirements, panel size, and bioinformatic pipelines to ensure that TMB is calculated appropriately. In addition, researchers are also evaluating TMB calculation in liquid biopsy. In this work, we summarize the relevant advances and the clinical utility of TMB in NSCLC.
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Affiliation(s)
- Marina Meri-Abad
- Medical Oncology Department, General University Hospital of Valencia, Valencia, Spain
| | - Andrea Moreno-Manuel
- Mixed Unit TRIAL (Príncipe Felipe Research Centre & Fundación para la Investigación del Hospital General Universitario de Valencia), Valencia, Spain; CIBERONC, Valencia, Spain
| | - Sandra Gallach García
- Mixed Unit TRIAL (Príncipe Felipe Research Centre & Fundación para la Investigación del Hospital General Universitario de Valencia), Valencia, Spain; CIBERONC, Valencia, Spain
| | - Silvia Calabuig-Fariñas
- Mixed Unit TRIAL (Príncipe Felipe Research Centre & Fundación para la Investigación del Hospital General Universitario de Valencia), Valencia, Spain; CIBERONC, Valencia, Spain; Pathology Department, Universitat de València, Valencia, Spain
| | - Rafael Sirera Pérez
- CIBERONC, Valencia, Spain; Biotechnology Department, Universitat Politècnica de València, Valencia, Spain; Mixed Unit Nanomedicine, Centro Investigación Príncipe Felipe-Universitat Politècnica de Valencia, 46022 Valencia, Spain
| | - Carlos Camps Herrero
- Medical Oncology Department, General University Hospital of Valencia, Valencia, Spain; Mixed Unit TRIAL (Príncipe Felipe Research Centre & Fundación para la Investigación del Hospital General Universitario de Valencia), Valencia, Spain; CIBERONC, Valencia, Spain; Department of Medicine, Universitat de València, Valencia, Spain
| | - Eloisa Jantus-Lewintre
- Mixed Unit TRIAL (Príncipe Felipe Research Centre & Fundación para la Investigación del Hospital General Universitario de Valencia), Valencia, Spain; CIBERONC, Valencia, Spain; Biotechnology Department, Universitat Politècnica de València, Valencia, Spain; Mixed Unit Nanomedicine, Centro Investigación Príncipe Felipe-Universitat Politècnica de Valencia, 46022 Valencia, Spain.
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Esposito Abate R, Cheetham MH, Fairley JA, Pasquale R, Sacco A, Nicola W, Deans ZC, Patton SJ, Normanno N. External quality assessment (EQA) for tumor mutational burden: results of an international IQN path feasibility pilot scheme. Virchows Arch 2023; 482:347-355. [PMID: 36355212 PMCID: PMC9931778 DOI: 10.1007/s00428-022-03444-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022]
Abstract
Tumor mutational burden (TMB) has recently been approved as an agnostic biomarker for immune checkpoint inhibitors. However, methods for TMB testing have not yet been standardized. The International Quality Network for Pathology (IQNPath) organized a pilot external quality assessment (EQA) scheme for TMB testing. The aim of this program was the validation of the materials and the procedures for the EQA of this complex biomarker. Five formalin-fixed paraffin-embedded (FFPE) cell lines were selected to mimic the various TMB values observed in clinical practice. The FFPE samples were tested with the FoundationOne CDx (F1CDx) assay as the reference test and three commercially available targeted sequencing panels. Following this internal validation, the five cell lines were sent to 29 laboratories selected on the basis of a previous survey. Nineteen of the 23 laboratories that submitted results (82.6%) used targeted sequencing for TMB estimation. Only two laboratories performed whole exome sequencing (WES) and two assessed TMB by clinical exome. A high variability in the reported TMB values was observed. The variability was higher for samples with the highest TMB value according to the F1CDx test. However, good reproducibility of the TMB score was shown by laboratories using the same panel. The majority of laboratories did not indicate a TMB cut-off value for clinical interpretation. In conclusion, this pilot EQA scheme suggests that it is feasible to run such an EQA program for TMB assessment. However, the results of our pilot highlight the numerous challenges for the standardization of this test.
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Affiliation(s)
- Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Melanie H Cheetham
- European Molecular Genetics Quality Network (EMQN), Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Jennifer A Fairley
- GenQA, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Raffaella Pasquale
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Wolstenholme Nicola
- European Molecular Genetics Quality Network (EMQN), Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Zandra C Deans
- GenQA, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Simon J Patton
- European Molecular Genetics Quality Network (EMQN), Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy.
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Mok TSK, Lopes G, Cho BC, Kowalski DM, Kasahara K, Wu YL, de Castro G, Turna HZ, Cristescu R, Aurora-Garg D, Loboda A, Lunceford J, Kobie J, Ayers M, Pietanza MC, Piperdi B, Herbst RS. Associations of tissue tumor mutational burden and mutational status with clinical outcomes in KEYNOTE-042: pembrolizumab versus chemotherapy for advanced PD-L1-positive NSCLC. Ann Oncol 2023; 34:377-388. [PMID: 36709038 DOI: 10.1016/j.annonc.2023.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND We evaluated whether tissue tumor mutational burden (tTMB) and STK11, KEAP1, and KRAS mutations have clinical utility as biomarkers for pembrolizumab monotherapy versus platinum-based chemotherapy in patients with programmed death ligand- 1 (PD-L1)-positive (tumor proportion score ≥1%) advanced/metastatic non-small-cell lung cancer (NSCLC) without EGFR/ALK alterations in the phase III KEYNOTE-042 trial. PATIENTS AND METHODS This retrospective exploratory analysis assessed prevalence of tTMB and STK11, KEAP1, and KRAS mutations determined by whole-exome sequencing of tumor tissue and matched normal DNA and their associations with outcomes in KEYNOTE-042. Clinical utility of tTMB was assessed using a prespecified cut point of 175 mutations/exome. RESULTS Of 793 patients, 345 (43.5%) had tTMB ≥175 mutations/exome and 448 patients (56.5%) had tTMB <175 mutations/exome. No association was observed between PD-L1 expression and tTMB. Continuous tTMB score was associated with improved overall survival (OS) and progression-free survival among patients receiving pembrolizumab (Wald test, one-sided P < 0.001) but not those receiving chemotherapy (Wald test, two-sided P > 0.05). tTMB ≥175 mutations/exome was associated with improved outcomes for pembrolizumab versus chemotherapy, whereas tTMB <175 mutations/exome was not {OS: hazard ratio, 0.62 [95% confidence interval (CI) 0.48-0.80] and 1.09 (95% CI 0.88-1.36); progression-free survival: 0.75 (0.59-0.95) and 1.27 (1.04-1.55), respectively}. Improved OS [hazard ratio (95% CI)] for pembrolizumab versus chemotherapy was observed regardless of STK11 [STK11 mutant (n = 33): 0.37 (0.16-0.86), STK11 wild-type (n = 396): 0.83 (0.65-1.05)]; KEAP1 [KEAP1 mutant (n = 64): 0.75 (0.42-1.35), KEAP1 wild-type (n = 365): 0.78 (0.61-0.99)], or KRAS [KRAS mutant (n = 69): 0.42 (0.22-0.81); KRAS wild-type (n = 232): 0.86 (0.63-1.18)] mutation status. CONCLUSION tTMB with a cut point of ≥175 mutations/exome is a potential predictive biomarker for pembrolizumab monotherapy for advanced/metastatic PD-L1 tumor proportion score ≥1% NSCLC. Pembrolizumab is a standard first-line treatment in this setting regardless of STK11, KEAP1, or KRAS mutation status.
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Affiliation(s)
- T S K Mok
- State Key Laboratory of Translational Oncology, Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
| | - G Lopes
- Sylvester Comprehensive Cancer Center at the University of Miami, Miami, FL, USA
| | - B C Cho
- Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - D M Kowalski
- Maria Sklodowska-Curie National Research Institute of Oncology, Department of Lung Cancer and Thoracic Tumours, Warsaw, Poland
| | - K Kasahara
- Kanazawa University Hospital, Kanazawa, Japan
| | - Y-L Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - G de Castro
- Instituto do Cancer do Estado de Sao Paulo, Sao Paulo, Brazil
| | - H Z Turna
- Istanbul University Cerrahpasa Medical Faculty, Istanbul, Turkey
| | | | | | - A Loboda
- Merck & Co., Inc., Rahway, NJ, USA
| | | | - J Kobie
- Merck & Co., Inc., Rahway, NJ, USA
| | - M Ayers
- Merck & Co., Inc., Rahway, NJ, USA
| | | | | | - R S Herbst
- Yale University School of Medicine, Yale Cancer Center, New Haven, CT, USA
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Garassino MC, Gadgeel S, Novello S, Halmos B, Felip E, Speranza G, Hui R, Garon EB, Horinouchi H, Sugawara S, Rodriguez-Abreu D, Reck M, Cristescu R, Aurora-Garg D, Loboda A, Lunceford J, Kobie J, Ayers M, Piperdi B, Pietanza MC, Paz-Ares L. Associations of Tissue Tumor Mutational Burden and Mutational Status With Clinical Outcomes With Pembrolizumab Plus Chemotherapy Versus Chemotherapy For Metastatic NSCLC. JTO Clin Res Rep 2023; 4:100431. [PMID: 36793385 PMCID: PMC9923193 DOI: 10.1016/j.jtocrr.2022.100431] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
Abstract
Introduction We evaluated tissue tumor mutational burden (tTMB) and mutations in STK11, KEAP1, and KRAS as biomarkers for outcomes with pembrolizumab plus platinum-based chemotherapy (pembrolizumab-combination) for NSCLC among patients in the phase 3 KEYNOTE-189 (ClinicalTrials.gov, NCT02578680; nonsquamous) and KEYNOTE-407 (ClinicalTrials.gov, NCT02775435; squamous) trials. Methods This retrospective exploratory analysis evaluated prevalence of high tTMB and STK11, KEAP1, and KRAS mutations in patients enrolled in KEYNOTE-189 and KEYNOTE-407 and the relationship between these potential biomarkers and clinical outcomes. tTMB and STK11, KEAP1, and KRAS mutation status was assessed using whole-exome sequencing in patients with available tumor and matched normal DNA. The clinical utility of tTMB was assessed using a prespecified cutpoint of 175 mutations/exome. Results Among patients with evaluable data from whole-exome sequencing for evaluation of tTMB (KEYNOTE-189, n = 293; KEYNOTE-407, n = 312) and matched normal DNA, no association was found between continuous tTMB score and overall survival (OS) or progression-free survival for pembrolizumab-combination (Wald test, one-sided p > 0.05) or placebo-combination (Wald test, two-sided p > 0.05) in patients with squamous or nonsquamous histology. Pembrolizumab-combination improved outcomes for patients with tTMB greater than or equal to 175 compared with tTMB less than 175 mutations/exome in KEYNOTE-189 (OS, hazard ratio = 0.64 [95% confidence interval (CI): 0.38‒1.07] and 0.64 [95% CI: 0.42‒0.97], respectively) and KEYNOTE-407 (OS, hazard ratio = 0.74 [95% CI: 0.50‒1.08 and 0.86 [95% CI: 0.57‒1.28], respectively) versus placebo-combination. Treatment outcomes were similar regardless of KEAP1, STK11, or KRAS mutation status. Conclusions These findings support pembrolizumab-combination as first-line treatment in patients with metastatic NSCLC and do not suggest the utility of tTMB, STK11, KEAP1, or KRAS mutation status as a biomarker for this regimen.
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Affiliation(s)
- Marina C. Garassino
- Section of Hematology/Oncology, Thoracic Oncology program, University of Chicago, Chicago, Illinois, and IRCCS Istituto Nazionale dei Tumori, Milano
| | - Shirish Gadgeel
- Division of Hematology/Oncology, Department of Internal Medicine, Henry Ford Cancer Institute/Henry Ford Health System, Detroit, Michigan
| | - Silvia Novello
- Department of Oncology, University of Turin, Orbassano, Italy
| | - Balazs Halmos
- Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
| | - Enriqueta Felip
- Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron University, Barcelona, Spain
| | - Giovanna Speranza
- Centre integré de cancérologie de la Montérégie, Université de Sherbrooke, Greenfield Park, Quebec, Canada
| | - Rina Hui
- Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia
| | - Edward B. Garon
- David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California
| | - Hidehito Horinouchi
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Shunichi Sugawara
- Department of Pulmonary Medicine, Sendai Kousei Hospital, Miyagi, Japan
| | - Delvys Rodriguez-Abreu
- Complejo Hospitalario Universitario Insular Materno-Infantil de Gran Canaria, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Martin Reck
- LungenClinic, Airway Research Center North, German Center for Lung Research, Grosshansdorf, Germany
| | | | | | | | | | | | | | | | | | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center, Universidad Complutense and Ciberonc, Madrid, Spain
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Ma C, Li F, He Z, Zhao S, Yang Y, Gu Z. Prognosis and personalized treatment prediction in lung adenocarcinoma: An in silico and in vitro strategy adopting cuproptosis related lncRNA towards precision oncology. Front Pharmacol 2023; 14:1113808. [PMID: 36874011 PMCID: PMC9975170 DOI: 10.3389/fphar.2023.1113808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Background: There is a rapid increase in lung adenocarcinomas (LUAD), and studies suggest associations between cuproptosis and the occurrence of various types of tumors. However, it remains unclear whether cuproptosis plays a role in LUAD prognosis. Methods: Dataset of the TCGA-LUAD was treated as training cohort, while validation cohort consisted of the merged datasets of the GSE29013, GSE30219, GSE31210, GSE37745, and GSE50081. Ten studied cuproptosis-related genes (CRG) were used to generated CRG clusters and CRG cluster-related differential expressed gene (CRG-DEG) clusters. The differently expressed lncRNA that with prognosis ability between the CRG-DEG clusters were put into a LASSO regression for cuproptosis-related lncRNA signature (CRLncSig). Kaplan-Meier estimator, Cox model, receiver operating characteristic (ROC), time-dependent AUC (tAUC), principal component analysis (PCA), and nomogram predictor were further deployed to confirm the model's accuracy. We examined the model's connections with other forms of regulated cell death, including apoptosis, necroptosis, pyroptosis, and ferroptosis. The immunotherapy ability of the signature was demonstrated by applying eight mainstream immunoinformatic algorithms, TMB, TIDE, and immune checkpoints. We evaluated the potential drugs for high risk CRLncSig LUADs. Real-time PCR in human LUAD tissues were performed to verify the CRLncSig expression pattern, and the signature's pan-cancer's ability was also assessed. Results: A nine-lncRNA signature, CRLncSig, was built and demonstrated owning prognostic power by applied to the validation cohort. Each of the signature genes was confirmed differentially expressed in the real world by real-time PCR. The CRLncSig correlated with 2,469/3,681 (67.07%) apoptosis-related genes, 13/20 (65.00%) necroptosis-related genes, 35/50 (70.00%) pyroptosis-related genes, and 238/380 (62.63%) ferroptosis-related genes. Immunotherapy analysis suggested that CRLncSig correlated with immune status, and checkpoints, KIR2DL3, IL10, IL2, CD40LG, SELP, BTLA, and CD28, were linked closely to our signature and were potentially suitable for LUAD immunotherapy targets. For those high-risk patients, we found three agents, gemcitabine, daunorubicin, and nobiletin. Finally, we found some of the CRLncSig lncRNAs potentially play a vital role in some types of cancer and need more attention in further studies. Conclusion: The results of this study suggest our cuproptosis-related CRLncSig can help to determine the outcome of LUAD and the effectiveness of immunotherapy, as well as help to better select targets and therapeutic agents.
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Affiliation(s)
- Chao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhanfeng He
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Song Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhuoyu Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Zhang W, Zhang Y, Wan Y, Liu Q, Zhu X. A bile acid-related prognostic signature in hepatocellular carcinoma. Sci Rep 2022; 12:22355. [PMID: 36572736 PMCID: PMC9792463 DOI: 10.1038/s41598-022-26795-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Due to the high mortality of hepatocellular carcinoma (HCC), its prognostic models are urgently needed. Bile acid (BA) metabolic disturbance participates in hepatocarcinogenesis. We aim to develop a BA-related gene signature for HCC patients. Research data of HCC were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) online databases. After least absolute shrinkage and selection operator (LASSO) regression analysis, we developed a BA-related prognostic signature in TCGA cohort based on differentially expressed prognostic BA-related genes. Then, the predictive performance of the signature was evaluated and verified in TCGA and ICGC cohort respectively. We obtained the risk score of each HCC patient according to the model. The differences of immune status and drug sensitivity were compared in patients that were stratified based on risk score. The protein and mRNA levels of the modeling genes were validated in the Human Protein Atlas database and our cell lines, respectively. In TCGA cohort, we selected 4 BA-related genes to construct the first BA-related prognostic signature. The risk signature exhibited good discrimination and predictive ability, which was verified in ICGC cohort. Patients were classified into high- and low-risk groups according to their median scores. The occurrence of death increased with increasing risk score. Low-risk patients owned favorable overall survival. High-risk patients possessed high immune checkpoint expression and low IC50 values for sorafenib, cisplatin and doxorubicin. Real-time quantitative PCR and immunohistochemical results validate expression of modeling genes in the signature. We constructed the first BA-related gene signature, which might help to identify HCC patients with poor prognosis and guide individualized treatment.
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Affiliation(s)
- Wang Zhang
- grid.412604.50000 0004 1758 4073Department of Gastroenterology, Jiangxi Clinical Research Center for Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yue Zhang
- grid.412604.50000 0004 1758 4073Department of Gastroenterology, Jiangxi Clinical Research Center for Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yipeng Wan
- grid.412604.50000 0004 1758 4073Department of Gastroenterology, Jiangxi Clinical Research Center for Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qi Liu
- grid.412604.50000 0004 1758 4073Department of Gastroenterology, Jiangxi Clinical Research Center for Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xuan Zhu
- grid.412604.50000 0004 1758 4073Department of Gastroenterology, Jiangxi Clinical Research Center for Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
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He R, Yuan X, Chen Z, Zheng Y. Combined immunotherapy for metastatic triple-negative breast cancer based on PD-1/PD-L1 immune checkpoint blocking. Int Immunopharmacol 2022; 113:109444. [DOI: 10.1016/j.intimp.2022.109444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022]
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Bubendorf L, Zoche M, Dafni U, Rüschoff JH, Prince SS, Marti N, Stavrou A, Kammler R, Finn SP, Moch H, Peters S, Stahel RA. Prognostic impact of tumour mutational burden in resected stage I and II lung adenocarcinomas from a European Thoracic Oncology Platform Lungscape cohort. Lung Cancer 2022; 174:27-35. [PMID: 36283211 DOI: 10.1016/j.lungcan.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The primary objective of this study is to evaluate tumor mutational burden (TMB), its associations with selected clinicopathological and molecular characteristics as well as its clinical significance, in a retrospective cohort of surgically resected stage I-II lung adenocarcinomas, subset of the ETOP Lungscape cohort. METHODS TMB was evaluated on tumor DNA extracted from resected primary lung adenocarcinomas, based on FoundationOne®CDx (F1CDx) genomic profiling, centrally performed at the University Hospital Zurich. The F1CDx test sequences the complete exons of 324 cancer-related genes and detects substitutions, insertions and deletions (indels), copy number alterations and gene rearrangements. In addition, the genomic biomarkers TMB and microsatellite instability (MSI) are analyzed. RESULTS In the Lungscape cohort, TMB was assessed in 78 surgically resected lung adenocarcinomas from two Swiss centers (62 % males, 55 %/45 % stage I/II). Median TMB was 7.6 Muts/Mb, with TMB high (≥10 Muts/Mb) in 40 % of cases (95 %CI:29 %-52 %). The most frequently mutated genes were TP53/KRAS/EGFR/MLL2 detected in 58 %/38 %/33 %/30 % of samples, respectively. TMB was significantly higher among males (TMB high: 50 % vs 23 % in females, p = 0.032), as well as among current/former smokers (TMB high: 44 % vs 8 % in never smokers, p = 0.023). Furthermore, TMB was significantly higher in TP53 mutated than in non-mutated patients (TMB high: 60 % vs 12 %, p < 0.001), while it was higher in EGFR non-mutated patients compared to EGFR mutated (TMB high: 48 % vs 23 %, p = 0.049). At a median follow-up time of 56.1 months (IQR:38.8-72.0), none of the three outcome variables (OS, RFS, TTR) differed significantly by TMB status (all p-values > 5 %). This was also true when adjusting for clinicopathological characteristics. CONCLUSIONS While presence of TP53 mutations and absence of EGFR mutations are associated with high TMB, increased TMB had no significant prognostic impact in patients with resected stage I/II lung adenocarcinoma beyond T and N classification, in both unadjusted and adjusted analyses.
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Affiliation(s)
- Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Martin Zoche
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Urania Dafni
- ETOP IBCSG Partners Foundation Statistical Center, Frontier Science Foundation-Hellas & National and Kapodistrian University of Athens, Athens, Greece
| | - Jan Hendrik Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Spasenija Savic Prince
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Nesa Marti
- Translational Research Coordination, ETOP IBCSG Partners Foundation, Coordinating Center Bern, Switzerland
| | - Androniki Stavrou
- ETOP IBCSG Partners Foundation Statistical Center, Frontier Science Foundation-Hellas, Athens, Greece
| | - Roswitha Kammler
- Translational Research Coordination, ETOP IBCSG Partners Foundation, Coordinating Center Bern, Switzerland
| | - Stephen P Finn
- Cancer Molecular Diagnostics and Histopathology, St. James's Hospital and Trinity College Dublin, Ireland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Rolf A Stahel
- ETOP IBCSG Partners Foundation, Coordinating Center, Bern, Switzerland.
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Xie T, Fan G, Huang L, Lou N, Han X, Xing P, Shi Y. Analysis on methylation and expression of PSMB8 and its correlation with immunity and immunotherapy in lung adenocarcinoma. Epigenomics 2022; 14:1427-1448. [PMID: 36683462 DOI: 10.2217/epi-2022-0282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Aim: To find biomarkers for immunity and immunotherapy in lung adenocarcinoma (LUAD) through multiomics analysis. Materials & methods: The multiomics data of patients with LUAD were downloaded from the TCGA and GEO databases. CIBERSORT, quanTIseq, ESTIMATEScore, k-means clustering, gene set enrichment analysis, gene set variation analysis, immunophenoscore and logistic regression were used in this study. Results: PSMB8 HypoMet-HighExp group patients have more active immune-related pathways, more antitumor immune cells, less protumor immune cells, higher immunophenoscore and longer progression-free survival of immune checkpoint inhibitor therapy than HyperMet-LowExp group. In multivariate analysis, PSMB8 showed an independent value. Conclusion: The combination of DNA methylation and mRNA expression of PSMB8 could independently distinguish types of tumor immune microenvironment and predict programmed cell death protein 1/programmed cell death-ligand 1 inhibitors' effects in patients with LUAD.
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Affiliation(s)
- Tongji Xie
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Guangyu Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Liling Huang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Ning Lou
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe & Rare Diseases, NMPA Key Laboratory for Clinical Research & Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Puyuan Xing
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
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Liu X, Liu J, Xu J, Zhang B, Wei M, Li J, Xu H, Yu X, Wang W, Shi S. Intra-tumoral infiltration of adipocyte facilitates the activation of antitumor immune response in pancreatic ductal adenocarcinoma. Transl Oncol 2022; 27:101561. [PMID: 36257208 PMCID: PMC9576545 DOI: 10.1016/j.tranon.2022.101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 10/03/2022] [Indexed: 12/15/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal malignancy that is characterized by an immunosuppressive microenvironment. The immune suppression in PDAC is largely driven by heterogeneous stromal and tumor cells. However, how adipocyte in the tumor microenvironment (TME) is related to the immune cell infiltration in PDAC has rarely been published. We identified adipocytes by performing bioinformatics analyses, and explored the clinical outcomes and TME characters in PDAC with different levels of adipocyte infiltration. Interestingly, in contrast to adiposity, high adipocyte infiltration in the TME was related to significantly increased median overall survival and a lower total tumor mutational burden. Functionally, high adipocyte infiltration was associated with the immune response, particularly with the abundant cytokine infiltration in PDAC samples. Moreover, adipocyte infiltration in the TME was positively associated with anticancer signatures in the immune microenvironment. Immunohistochemistry and RT-PCR were performed with PDAC tissue samples from our center to study the expression of adipocytes in PDAC. The mature adipocytes were strongly associated with the immune composition and prognosis of patients with PDAC. Primary adipocytes were isolated from mice to construct a PDAC transplantation tumor model. In vivo experiments showed that adipocytes elicited increased CD8+ T cell infiltration and potent antitumor activity in tumor-bearing mice. Overall, we innovatively found that adipocytes facilitated the antitumor immune response in the TME by performing mouse experiments and analyzing PDAC samples. This study provides a new perspective on the activation of the immune microenvironment in PDAC.
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Affiliation(s)
- Xiaomeng Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Jiang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Miaoyan Wei
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Jialin Li
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Hang Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China,Corresponding authors at: Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China,Shanghai Pancreatic Cancer Institute, Shanghai 200032, China,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China,Corresponding authors at: Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
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Titmuss E, Corbett RD, Davidson S, Abbasi S, Williamson LM, Pleasance ED, Shlien A, Renouf DJ, Jones SJM, Laskin J, Marra MA. TMBur: a distributable tumor mutation burden approach for whole genome sequencing. BMC Med Genomics 2022; 15:190. [PMID: 36071521 PMCID: PMC9450342 DOI: 10.1186/s12920-022-01348-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
Background Tumor mutation burden (TMB) is a key characteristic used in a tumor-type agnostic context to inform the use of immune checkpoint inhibitors (ICI). Accurate and consistent measurement of TMB is crucial as it can significantly impact patient selection for therapy and clinical trials, with a threshold of 10 mutations/Mb commonly used as an inclusion criterion. Studies have shown that the most significant contributor to variability in mutation counts in whole genome sequence (WGS) data is differences in analysis methods, even more than differences in extraction or library construction methods. Therefore, tools for improving consistency in whole genome TMB estimation are of clinical importance.
Methods We developed a distributable TMB analysis suite, TMBur, to address the need for genomic TMB estimate consistency in projects that span jurisdictions. TMBur is implemented in Nextflow and performs all analysis steps to generate TMB estimates directly from fastq files, incorporating somatic variant calling with Manta, Strelka2, and Mutect2, and microsatellite instability profiling with MSISensor. These tools are provided in a Singularity container downloaded by the workflow at runtime, allowing the entire workflow to be run identically on most computing platforms. To test the reproducibility of TMBur TMB estimates, we performed replicate runs on WGS data derived from the COLO829 and COLO829BL cell lines at multiple research centres. The clinical value of derived TMB estimates was then evaluated using a cohort of 90 patients with advanced, metastatic cancer that received ICIs following WGS analysis. Patients were split into groups based on a threshold of 10/Mb, and time to progression from initiation of ICIs was examined using Kaplan–Meier and cox-proportional hazards analyses. Results TMBur produced identical TMB estimates across replicates and at multiple analysis centres. The clinical utility of TMBur-derived TMB estimates were validated, with a genomic TMB ≥ 10/Mb demonstrating improved time to progression, even after correcting for differences in tumor type (HR = 0.39, p = 0.012). Conclusions TMBur, a shareable workflow, generates consistent whole genome derived TMB estimates predictive of response to ICIs across multiple analysis centres. Reproducible TMB estimates from this approach can improve collaboration and ensure equitable treatment and clinical trial access spanning jurisdictions. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01348-z.
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Affiliation(s)
- Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Scott Davidson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
| | - Sanna Abbasi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Erin D Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Adam Shlien
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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