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Shan H, Wang X, Yin F, Zhou Y, Mao L, Zhu X, Liu C. Combination of transcriptome and Mendelian inheritance reveals novel prognostic biomarker of CTLA-4-related lncRNAs and protective role of nitrogen metabolism pathway in lung adenocarcinoma development. BMC Cancer 2024; 24:1009. [PMID: 39143529 PMCID: PMC11323378 DOI: 10.1186/s12885-024-12777-7] [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: 04/12/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
OBJECTIVE Since in the cancer setting, tumor cells may use cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) to evade the immune system. This study aimed to identify CTLA-4-related long non-coding RNAs (lncRNAs) and assess their roles in lung adenocarcinoma (LUAD) development. METHODS Clinical and genomic data were obtained from The Cancer Genome Atlas (TCGA), MSigDB and Gene Weaver. CTLA-4-related lncRNA-based gene signatures (CTLA4LncSigs) were identified using Cox regression, establishing a risk score model and an independent prognostic model. Enrichment analysis (GO/KEGG) was performed. Mendelian randomization (MR) analysis investigated the nitrogen metabolism and lung cancer relationship, with Bayesian weighted MR (BWMR) addressing uncertainties. Correlations with tumor microenvironment and drug sensitivity were explored. RESULTS Nineteen CTLA4LncSigs significantly influenced LUAD prognosis. The risk score demonstrated independence as a prognostic factor. Functional analysis revealed lncRNAs' impact on nitrogen metabolism. MR and BWMR confirmed the protective role of the nitrogen metabolism pathway in lung cancer. CONCLUSION Our study identifies CTLA-4-related lncRNAs associated with LUAD prognosis and uncovers a previously undiscovered protective role of the nitrogen metabolism pathway in combating LUAD development, providing new insights into potential therapeutic targets and prognostic biomarkers for this aggressive cancer subtype.
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Affiliation(s)
- Huisi Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Department of Radiation Oncology, Guangdong Second People's Hospital, Jinan University, Guangzhou, China
| | - Xiaocong Wang
- Department of Pathology, Qingdao Municipal Hospital Group, Qingdao, China
| | - Fei Yin
- Department of Clinical Laboratory, Qingdao Sixth People's Hospital, Qingdao, China
| | - Yiting Zhou
- The Second Affiliated Hospital, Guangdong Medical University, Zhanjiang, China
- Department of Internal Medicine, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Liuhan Mao
- The Second Affiliated Hospital, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- The Second Affiliated Hospital, Guangdong Medical University, Zhanjiang, China.
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China.
| | - Caixin Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China.
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Werner R, Crosbie R, Dorney M, Connolly A, Collins D, Hand CK, Burke L. Implementation of an ISO 15189 accredited next generation sequencing service for cell-free total nucleic acid (cfTNA) analysis to facilitate driver mutation reporting in blood: the experience of a clinical diagnostic laboratory. J Clin Pathol 2024:jcp-2024-209514. [PMID: 38914446 DOI: 10.1136/jcp-2024-209514] [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: 03/04/2024] [Accepted: 06/11/2024] [Indexed: 06/26/2024]
Abstract
AIMS Next generation sequencing (NGS) on tumour tissue is integral to the delivery of personalised medicine and targeted therapy. NGS on liquid biopsy, a much less invasive technology, is an emerging clinical tool that has rapidly expanded clinical utility. Gene mutations in cell-free total nucleic acids (cfTNA) circulating in the blood are representative of whole tumour biology and can reveal different mutations from different tumour sites, thus addressing tumour heterogeneity challenges. METHODS The novel Ion Torrent Genexus NGS system with automated sample preparation, onboard library preparation, templating, sequencing, data analysis and Oncomine Reporter software was used. cfTNA extracted from plasma was verified with the targeted pan-cancer (~50 genes) Oncomine Precision Assay (OPA). Assessment criteria included analytical sensitivity, specificity, limits of detection (LOD), accuracy, repeatability, reproducibility and the establishment of performance metrics. RESULTS An ISO 15189 accredited, minimally invasive cfTNA NGS diagnostic service has been implemented. High sensitivity (>83%) and specificity between plasma and tissue were observed. A sequencing LOD of 1.2% was achieved when the depth of coverage was >22 000×. A reduction (>68%) in turnaround time (TAT) of liquid biopsy results was achieved: 5 days TAT for in-house analysis from sample receipt to a final report issued to oncologists as compared with >15 days from reference laboratories. CONCLUSION Tumour-derived somatic variants can now be reliably assessed from plasma to provide minimally invasive tumour profiling. Successful implementation of this accredited service resulted in:Appropriate molecular profiling of patients where tumour tissue is unavailable or inaccessible.Rapid TAT of plasma NGS results.
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Affiliation(s)
- Reiltin Werner
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
| | - Ruth Crosbie
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Mairead Dorney
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Amy Connolly
- Pathology Department, Cork University Hospital, Cork, Ireland
| | | | - Collette K Hand
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
| | - Louise Burke
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
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Tang H, Li YX, Lian JJ, Ng HY, Wang SSY. Personalized treatment using predictive biomarkers in solid organ malignancies: A review. TUMORI JOURNAL 2024:3008916241261484. [PMID: 39091157 DOI: 10.1177/03008916241261484] [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: 08/04/2024]
Abstract
In recent years, the influence of specific biomarkers in the diagnosis and prognosis of solid organ malignancies has been increasingly prominent. The relevance of the use of predictive biomarkers, which predict cancer response to specific forms of treatment provided, is playing a more significant role than ever before, as it affects diagnosis and initiation of treatment, monitoring for efficacy and side effects of treatment, and adjustment in treatment regimen in the long term. In the current review, we explored the use of predictive biomarkers in the treatment of solid organ malignancies, including common cancers such as colorectal cancer, breast cancer, lung cancer, prostate cancer, and cancers associated with high mortalities, such as pancreatic cancer, liver cancer, kidney cancer and cancers of the central nervous system. We additionally analyzed the goals and types of personalized treatment using predictive biomarkers, and the management of various types of solid organ malignancies using predictive biomarkers and their relative efficacies so far in the clinical settings.
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Dahiya R, Sutariya VB, Gupta SV, Pant K, Ali H, Alhadrawi M, Kaur K, Sharma A, Rajput P, Gupta G, Almujri SS, Chinni SV. Harnessing pyroptosis for lung cancer therapy: The impact of NLRP3 inflammasome activation. Pathol Res Pract 2024; 260:155444. [PMID: 38986361 DOI: 10.1016/j.prp.2024.155444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/22/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024]
Abstract
Lung cancer is still a global health challenge in terms of high incidence, morbidity, and mortality. Recent scientific studies have determined that pyroptosis, a highly inflammatory form of programmed cell death, can be identified as a potential lung cancer therapeutic target. The NLRP3 inflammasome acts as a critical mediator in this process and, upon activation, activates multiprotein complex formation as well as caspase-1 activation. This process, triggered by a release of pro-inflammatory cytokines, results in pyroptotic cell death. Also, the relationship between the NLRP3 inflammasome and lung cancer was justified by its influence on tumour growth or metastasis. The molecular pathways produce progenitive mediators and remake the tissue. Finally, targeting NLRP3 inflammasome for pyroptosis induction and inhibition of its activation appears to be a promising lung cancer treatment approach. This technique makes cancer treatment more promising and personalized. This review explores the role of NLRP3 inflammasome activation and its possibilities in lung cancer treatment.
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Affiliation(s)
- Rajiv Dahiya
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad & Tobago, West Indies
| | - Vijaykumar B Sutariya
- USF Health Taneja College of Pharmacy, University of South Florida, Tampa, FL 33612, USA
| | - Sheeba Varghese Gupta
- USF Health Taneja College of Pharmacy, University of South Florida, Tampa, FL 33612, USA
| | - Kumud Pant
- Graphic Era (Deemed to be University) Clement Town Dehradun, 248002, India; Graphic Era Hill University Clement Town Dehradun, 248002, India.
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Merwa Alhadrawi
- College of Technical Engineering, The Islamic University, Najaf, Iraq; College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
| | - Kiranjeet Kaur
- Chandigarh Pharmacy College, Chandigarh Group of Colleges, Jhanjeri, Mohali, Punjab 140307, India
| | - Abhishek Sharma
- Department of Medicine, National Institute of Medical Sciences, NIMS University Rajasthan, Jaipur, India
| | - Pranchal Rajput
- School of Applied and Life Sciences, Division of Research and Innovation, Uttaranchal University, Dehradun, India
| | - Gaurav Gupta
- Centre for Research Impact & Outcome-Chitkara College of Pharmacy, Chitkara University, Punjab
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Asir 61421, Saudi Arabia
| | - Suresh V Chinni
- Department of Biochemistry, Faculty of Medicine, Bioscience, and Nursing, MAHSA University, Jenjarom, Selangor 42610, Malaysia
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Huang H, Chen G, Zhang Z, Wu G, Zhang Z, Yu A, Wang J, Quan C, Li Y, Zhou M. Deciphering the role of cuproptosis-related lncRNAs in shaping the lung cancer immune microenvironment: A comprehensive prognostic model. J Cell Mol Med 2024; 28:e18519. [PMID: 38973477 PMCID: PMC11228428 DOI: 10.1111/jcmm.18519] [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: 12/19/2023] [Revised: 05/21/2024] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Cuproptosis plays an important role in cancer, but its role in lung cancer remains unknown. Transcriptional profiles, clinical details and mutation data were acquired from the Cancer Genome Atlas database through a variety of methods. The analysis of this publicly available data was comprehensively performed using R software along with its relevant packages, ensuring a thorough examination of the information. In this study, we conducted a detailed analysis of cuproptosis-related genes and lncRNA co-expression, identifying 129 relevant lncRNAs and establishing a prognostic model with four key lncRNAs (LINC00996, RPARP-AS1, SND1-IT1, TMPO-AS1). Utilizing data from TCGA and GEO databases, the model effectively categorized patients into high- and low-risk groups, showing significant survival differences. Correlation analysis highlighted specific relationships between individual lncRNAs and cuproptosis genes. Our survival analysis indicated a higher survival rate in the low-risk group across various cohorts. Additionally, the model's predictive accuracy was confirmed through independent prognostic analysis and ROC curve evaluations. Functional enrichment analysis revealed distinct biological pathways and immune functions between risk groups. Tumour mutation load analysis differentiated high- and low-risk groups by their mutation profiles. Drug sensitivity analysis and immune infiltration studies using the CIBERSORT algorithm further elucidated the potential treatment responses in different risk groups. This comprehensive evaluation underscores the significance of lncRNAs in cuproptosis and their potential as biomarkers for lung cancer prognosis and immune microenvironment.
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Affiliation(s)
- Hai Huang
- Tuberculosis ward No.2, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, Hubei, China
| | - Guoxi Chen
- Tuberculosis ward No.2, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, Hubei, China
| | - Zongqi Zhang
- Tuberculosis ward No.2, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, Hubei, China
| | - Gang Wu
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Zhengbin Zhang
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Aiping Yu
- Infectious disease prevention and control department, Dongxihu Centers for Disease Prevention and Control, Wuhan, Hubei, China
| | - Jianjie Wang
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Chao Quan
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Yuehua Li
- Department of Tuberculosis control, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
| | - Meilan Zhou
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Affiliated to Jianghan University, Wuhan, Hubei, China
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Malapelle U, Leighl N, Addeo A, Hershkovitz D, Hochmair MJ, Khorshid O, Länger F, de Marinis F, Peled N, Sheffield BS, Smit EF, Viteri S, Wolf J, Venturini F, O'Hara RM, Rolfo C. Recommendations for reporting tissue and circulating tumour (ct)DNA next-generation sequencing results in non-small cell lung cancer. Br J Cancer 2024; 131:212-219. [PMID: 38750115 PMCID: PMC11263606 DOI: 10.1038/s41416-024-02709-4] [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: 01/04/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 07/24/2024] Open
Abstract
Non-small cell lung cancer is a heterogeneous disease and molecular characterisation plays an important role in its clinical management. Next-generation sequencing-based panel testing enables many molecular alterations to be interrogated simultaneously, allowing for comprehensive identification of actionable oncogenic drivers (and co-mutations) and appropriate matching of patients with targeted therapies. Despite consensus in international guidelines on the importance of broad molecular profiling, adoption of next-generation sequencing varies globally. One of the barriers to its successful implementation is a lack of accepted standards and guidelines specifically for the reporting and clinical annotation of next-generation sequencing results. Based on roundtable discussions between pathologists and oncologists, we provide best practice recommendations for the reporting of next-generation sequencing results in non-small cell lung cancer to facilitate its use and enable easy interpretation for physicians. These are intended to complement existing guidelines related to the use of next-generation sequencing (solid and liquid). Here, we discuss next-generation sequencing workflows, the structure of next-generation sequencing reports, and our recommendations for best practice thereof. The aim of these recommendations and considerations is ultimately to ensure that reports are fully interpretable, and that the most appropriate treatment options are selected based on robust molecular profiles in well-defined reports.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Natasha Leighl
- Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Alfredo Addeo
- Oncology Unit, Geneva University Hospital, Geneva, Switzerland
| | | | - Maximilian J Hochmair
- Department of Respiratory & Critical Care Medicine, Karl Landsteiner Institute of Lung Research & Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Ola Khorshid
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Florian Länger
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Filippo de Marinis
- Division of Thoracic Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Nir Peled
- Helmesely Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Brandon S Sheffield
- Division of Advanced Diagnostics, William Osler Health System, Brampton, ON, Canada
| | - Egbert F Smit
- Department of Pulmonary Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - Santiago Viteri
- UOMI Cancer Center, Clínica Mi Tres Torres, Barcelona, Spain
| | - Jürgen Wolf
- Lung Cancer Group Cologne, Center for Integrated Oncology, University Hospital of Cologne, Cologne, Germany
| | | | | | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA.
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Gueye A, Maroun B, Zimur A, Berkovits T, Tan SM. The future of collaborative precision oncology approaches in sub-Saharan Africa: learnings from around the globe. Front Oncol 2024; 14:1426558. [PMID: 38974239 PMCID: PMC11224929 DOI: 10.3389/fonc.2024.1426558] [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: 05/01/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024] Open
Abstract
As the projected incidence and mortality of cancer in Sub-Saharan Africa (SSA) rises to epidemic proportions, it is imperative that more is done to identify the genomic differences and commonalities between patients of African and European ancestry to fulfil the promise of precision oncology. Here, we summarize the utility of precision oncology approaches, with a focus on comprehensive genomic profiling (CGP) and consolidate examples of national and international consortia that are driving the field forward. We describe the importance of genomic diversity and its relevance in cancer, and propose recommendations, success factors and desired outcomes for precision oncology consortia to adopt in SSA. Through this, we hope to catalyze the initiation of such projects and to contribute to improving cancer patient outcomes in the region.
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Meernik C, Raveendran Y, Kolarova M, Rahman F, Olunuga E, Hammond E, Shivaramakrishnan A, Hendren S, Bosworth HB, Check DK, Green M, Strickler JH, Akinyemiju T. Racial and ethnic disparities in genomic testing among lung cancer patients: a systematic review. J Natl Cancer Inst 2024; 116:812-828. [PMID: 38321254 PMCID: PMC11160502 DOI: 10.1093/jnci/djae026] [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: 08/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Racial and ethnic disparities in genomic testing could exacerbate disparities in access to precision cancer therapies and survival-particularly in the context of lung cancer where genomic testing has been recommended for the past decade. However, prior studies assessing disparities in genomic testing have yielded mixed results. METHODS We conducted a systemic review to examine racial and ethnic disparities in the use of genomic testing among lung cancer patients in the United States. Two comprehensive searches in PubMed, Embase, and Scopus were conducted (September 2022, May 2023). Original studies that assessed rates of genomic testing by race or ethnicity were included. Findings were narratively synthesized by outcome. RESULTS The search yielded 2739 unique records, resulting in 18 included studies. All but 1 study were limited to patients diagnosed with non-small cell lung cancer. Diagnosis years ranged from 2007 to 2022. Of the 18 studies, 11 found statistically significant differences in the likelihood of genomic testing by race or ethnicity; in 7 of these studies, testing was lower among Black patients compared with White or Asian patients. However, many studies lacked adjustment for key covariates and included patients with unclear eligibility for testing. CONCLUSIONS A majority of studies, though not all, observed racial and ethnic disparities in the use of genomic testing among patients with lung cancer. Heterogeneity of study results throughout a period of changing clinical guidelines suggests that minoritized populations-Black patients in particular-have faced additional barriers to genomic testing, even if not universally observed at all institutions.
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Affiliation(s)
- Clare Meernik
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | | | - Michaela Kolarova
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Fariha Rahman
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | | | - Emmery Hammond
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | | | - Steph Hendren
- Medical Center Library and Archives, Duke University School of Medicine, Durham, NC, USA
| | - Hayden B Bosworth
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
- Center of Innovation to Accelerate Discovery and Practice Transformation, Durham Veterans Affairs Medical Center, Durham, NC, USA
- Department of Medicine, Division of General Internal Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
- Duke University School of Nursing, Duke University School of Medicine, Durham, NC, USA
| | - Devon K Check
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Michelle Green
- Duke Pathology, Duke University School of Medicine, Durham, NC, USA
| | - John H Strickler
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tomi Akinyemiju
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
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Wang H, Li W. Prognostic significance of SIRI in patients with late-stage lung adenocarcinoma receiving EGFR-TKI treatment. Curr Probl Cancer 2024; 50:101099. [PMID: 38723294 DOI: 10.1016/j.currproblcancer.2024.101099] [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: 11/08/2023] [Revised: 03/10/2024] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
Abstract
OBJECTIVE In this study, we examined the relationship between the Systemic Inflammatory Response Index (SIRI) and the overall prognosis of patients with late-stage lung adenocarcinoma who harbor epidermal growth factor receptor (EGFR) mutations and are undergoing first-line treatment with EGFR-tyrosine kinase inhibitors (EGFR-TKIs). METHODS A cohort comprising 52 patients with late-stage lung adenocarcinoma, who received treatment at Jinzhou Central Hospital between January 2018 and December 2022, were carefully selected. Patient data spanning from pre-treatment assessments through follow-up periods were meticulously collected from electronic medical records and subsequently subjected to a comprehensive retrospective analysis. The collected data was subjected to in-depth processing and analyzed using SPSS 27.0 statistical software. To determine the optimal cut-off value of the pre-treatment SIRI, a receiver operating characteristic (ROC) curve was employed. Survival analysis was performed using the Kaplan-Meier method, and both univariate and multivariate prognostic analyses were conducted using Cox regression. RESULTS The optimal SIRI cut-off value was determined to be 1.659 (with a specificity of 0.964 and sensitivity of 0.652, P = 0.000). Based on this value, patients were categorized into high and low SIRI groups. Chi-squared tests demonstrated that SIRI exhibited statistically significant correlations with patient age and smoking history (P < 0.05). Survival analysis revealed that the group with a lower SIRI had a significantly extended progression-free survival (PFS) (P < 0.001). Cox univariate analysis identified hypertension, pleural metastasis, liver metastasis, and SIRI as factors associated with PFS (P < 0.05). In the subsequent multivariate analysis, liver metastasis and SIRI ≥ 1.659 (P < 0.001) were identified as independent risk factors for patients. CONCLUSION Pre-treatment SIRI holds predictive significance for the prognosis of patients with late-stage lung adenocarcinoma with EGFR mutations undergoing first-line treatment EGFR-TKI treatment.
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Affiliation(s)
- Herong Wang
- Graduate Student Training Base of Jinzhou Medical University (Central Hospital of Jinzhou), Jinzhou 121000, China
| | - Wei Li
- Department of Oncology, Central Hospital of Jinzhou, Jinzhou 121000, China.
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10
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Tomic K, Krpina K, Baticic L, Samarzija M, Vranic S. Comprehensive molecular and clinical insights into non-small cell lung cancer transformation to small cell lung cancer with an illustrative case report. J Drug Target 2024; 32:499-509. [PMID: 38506620 DOI: 10.1080/1061186x.2024.2332733] [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: 01/24/2024] [Accepted: 03/10/2024] [Indexed: 03/21/2024]
Abstract
Histologic transformation to small cell lung cancer (tSCLC) is a rare but increasingly recognised mechanism of acquired resistance to tyrosine kinase inhibitors (TKI) in patients with epidermal growth factor receptor (EGFR)-positive non-small cell lung cancer (NSCLC). Beyond its acknowledged role in TKI resistance, histologic transformation to SCLC might be an important, yet under-recognised, mechanism of resistance in NSCLC treated with immunotherapy. Our review identified 32 studies that investigated tSCLC development in patients with EGFR-mutated NSCLC treated with TKI therapy and 16 case reports of patients treated with immunotherapy. It revealed the rarity of tSCLC, with a predominance of EGFR exon 19 mutations and limited therapeutic options and outcomes. Across all analysed studies in EGFR-mutated NSCLC treated with TKI therapy, the median time to tSCLC development was ∼17 months, with a median overall survival of 10 months. Histologic transformation of EGFR-mutated NSCLC to SCLC is a rare, but challenging clinical problem with a poor prognosis. A small number of documented cases of tSCLC after immunotherapy highlight the need for rebiopsies at progression to diagnose this potential resistance mechanism. Further research is needed to better understand the mechanisms underlying this phenomenon and to develop more effective treatment strategies for patients with tSCLC.
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Affiliation(s)
- Kresimir Tomic
- Department of Oncology, University Clinical Hospital Mostar, Mostar, Bosnia and Herzegovina
| | - Kristina Krpina
- Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Lara Baticic
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Miroslav Samarzija
- Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
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11
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Dwyer LL, Vadagam P, Vanderpoel J, Cohen C, Lewing B, Tkacz J. Disparities in Lung Cancer: A Targeted Literature Review Examining Lung Cancer Screening, Diagnosis, Treatment, and Survival Outcomes in the United States. J Racial Ethn Health Disparities 2024; 11:1489-1500. [PMID: 37204663 PMCID: PMC11101514 DOI: 10.1007/s40615-023-01625-2] [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: 12/16/2022] [Revised: 03/31/2023] [Accepted: 04/30/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although incidence and mortality of lung cancer have been decreasing, health disparities persist among historically marginalized Black, Hispanic, and Asian populations. A targeted literature review was performed to collate the evidence of health disparities among these historically marginalized patients with lung cancer in the U.S. METHODS Articles eligible for review included 1) indexed in PubMed®, 2) English language, 3) U.S. patients only, 4) real-world evidence studies, and 5) publications between January 1, 2018, and November 8, 2021. RESULTS Of 94 articles meeting selection criteria, 49 publications were selected, encompassing patient data predominantly between 2004 and 2016. Black patients were shown to develop lung cancer at an earlier age and were more likely to present with advanced-stage disease compared to White patients. Black patients were less likely to be eligible for/receive lung cancer screening, genetic testing for mutations, high-cost and systemic treatments, and surgical intervention compared to White patients. Disparities were also detected in survival, where Hispanic and Asian patients had lower mortality risks compared to White patients. Literature on survival outcomes between Black and White patients was inconclusive. Disparities related to sex, rurality, social support, socioeconomic status, education level, and insurance type were observed. CONCLUSIONS Health disparities within the lung cancer population begin with initial screening and continue through survival outcomes, with reports persisting well into the latter portion of the past decade. These findings should serve as a call to action, raising awareness of persistent and ongoing inequities, particularly for marginalized populations.
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Affiliation(s)
- Lisa L Dwyer
- Real World Value & Evidence, Janssen Scientific Affairs, LLC, 1125 Trenton-Harbourton Road, Titusville, NJ, 08560, USA.
| | - Pratyusha Vadagam
- Real World Value & Evidence, Janssen Scientific Affairs, LLC, 1125 Trenton-Harbourton Road, Titusville, NJ, 08560, USA
| | - Julie Vanderpoel
- Real World Value & Evidence, Janssen Scientific Affairs, LLC, 1125 Trenton-Harbourton Road, Titusville, NJ, 08560, USA
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12
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Hirsch FR, Kim C. The Importance of Biomarker Testing in the Treatment of Advanced Non-Small Cell Lung Cancer: A Podcast. Oncol Ther 2024; 12:223-231. [PMID: 38536631 PMCID: PMC11187040 DOI: 10.1007/s40487-024-00271-w] [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: 08/23/2023] [Accepted: 03/06/2024] [Indexed: 06/20/2024] Open
Abstract
The identification of actionable biomarkers and development of targeted therapies have revolutionized the field of lung cancer treatment. In patients with advanced non-small cell lung cancer (NSCLC), biomarker testing can inform selection of effective targeted therapies as well as avoid therapies that are less likely to be effective in certain populations. A growing number of actionable targets, including those involving EGFR, ALK, ROS1, BRAF, MET, KRAS, NTRK, RET, HER2, and PD-L1, can be identified with biomarker testing. More than half of patients with advanced NSCLC have tumors that harbor genetic alterations that can be targeted. When these patients are treated with targeted therapy, survival and quality of life may be significantly improved. In addition, broad-based molecular testing may detect alterations identifying patients who are potentially eligible for current or future clinical trials. Comprehensive biomarker testing rates in communities are often low, and turnaround times for results can be unacceptably long. There is an unmet need for widespread, efficient, and routine testing of all biomarkers recommended by clinical guidelines. New testing techniques and technologies can make this an attainable goal. Panel-based sequencing platforms are becoming more accessible, and molecular biomarker analysis of circulating tumor DNA is becoming more common. In this podcast, we discuss the importance of biomarker testing in advanced NSCLC and explore topics such as testing methodologies, effect of biomarker testing on patient outcomes, emerging technologies, and strategies for improving testing rates in the United States. Supplementary file1 (MP4 121301 KB).
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Affiliation(s)
- Fred R Hirsch
- Icahn School of Medicine, Center for Thoracic Oncology, Tisch Cancer Center, Mount Sinai, New York, NY, USA.
| | - Chul Kim
- Georgetown University, Washington, DC, USA
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Sun Z, Sun J, Hu H, Han S, Ma P, Zuo B, Wang Z, Liu Z. A novel microRNA miR-4433a-3p as a potential diagnostic biomarker for lung adenocarcinoma. Heliyon 2024; 10:e30646. [PMID: 38765119 PMCID: PMC11101798 DOI: 10.1016/j.heliyon.2024.e30646] [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: 06/28/2023] [Revised: 05/01/2024] [Accepted: 05/01/2024] [Indexed: 05/21/2024] Open
Abstract
Background Lung adenocarcinoma is one of the leading causes of cancer-related deaths because of the lack of early specific clinical indicators. MicroRNAs (miRNAs) have become the focus in lung cancer diagnosis. Further studies are required to explore miRNA expression in the serum of lung adenocarcinoma patients and their correlation with therapy and analyse specific messenger RNA targets to improve the specificity and sensitivity of early diagnosis. Methods The Toray 3D-Gene miRNA array was used to compare the expression levels of various miRNAs in the sera of patients with lung adenocarcinoma and healthy volunteers. Highly expressed miRNAs were selected for further analysis. To verify the screening results, serum and pleural fluid samples were analysed using qRT-PCR. Serum levels of the miRNAs and their correlation with the clinical information of patients with lung adenocarcinoma were analysed. The functions of miRNAs were further analysed using the Kyoto Encyclopedia of Gene and Genomes and Gene Ontology databases. Results Microarray analysis identified 60 and 50 miRNAs with upregulated and downregulated expressions, respectively, in the serum of patients with lung adenocarcinoma compared to those in healthy individuals. Using qRT-qPCR to detection of miRNAs expression in the serum or pleural effusion of patients with early and advanced lung adenocarcinoma, we found that miR-4433a-3p could be used as a diagnostic marker and therapeutic evaluation indicator for lung adenocarcinoma. Serum of miR-4433a-3p levels significantly correlated with the clinical stage. miR-4433a-3p may be more suitable than other tumour markers for the early diagnosis and evaluation of therapeutic effects in lung adenocarcinoma. miR-4433a-3p may affect tumour growth and metastasis by acting on target genes (PIK3CD, UBE2J2, ICMT, PRDM16 and others) and regulating tumour-related signalling pathways (MAPK signal pathway, Ras signalling pathway and others). Conclusion miR-4433a-3p may serve as a biomarker for the early diagnosis of lung adenocarcinoma and monitoring of therapeutic effects.
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Affiliation(s)
- Zhixiao Sun
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
- Department of Central Laboratory, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Jian Sun
- Department of Cardiothoracic Surgery, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Hang Hu
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Shuhua Han
- Department of Pulmonary and Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, China
| | - Panpan Ma
- Department of Clinical Laboratory, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Bingqing Zuo
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Zheng Wang
- Department of Chronic Disease Medical Center, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Zhongxiang Liu
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
- Department of Central Laboratory, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
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Hu M, Zhong C, Wang J, Chen J, Zhou T. Current status and breakthroughs in treating advanced non-small cell lung cancer with EGFR exon 20 insertion mutations. Front Immunol 2024; 15:1399975. [PMID: 38774882 PMCID: PMC11106363 DOI: 10.3389/fimmu.2024.1399975] [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: 03/12/2024] [Accepted: 04/23/2024] [Indexed: 05/24/2024] Open
Abstract
Recently, targeted therapy and immunotherapy have emerged as effective treatment options for non-small cell lung cancer (NSCLC). This progress has been facilitated by the rapid development of diagnostic and therapeutic technologies and the continuous research and development of new drugs, leading to a new era in precision medicine for NSCLC. This is a breakthrough for patients with common mutations in the human epidermal growth factor receptor (EGFR) gene in NSCLC. Consequently, the use of targeted drugs has significantly improved survival. Nevertheless, certain rare genetic mutations are referred to as EGFR exon 20 insertion (ex20ins) mutations, which differ in structure from conventional EGFR gene mutations, namely, exon 19 deletion mutations (19-Del) and exon 21 point mutations. Owing to their distinct structural characteristics, patients harboring these EGFR ex20ins mutations are unresponsive to traditional tyrosine kinase inhibitor (TKI) therapy. This particular group of patients did not fall within the scope of their applicability. However, the activating A763_Y764insFQEA mutation elicits a more pronounced response than mutations in the near and far regions of the C-helix immediately following it and should, therefore, be treated differently. Currently, there is a lack of effective treatments for EGFR ex20ins mutations NSCLC. The efficacy of chemotherapy has been relatively favorable, whereas the effectiveness of immunotherapy remains ambiguous owing to inadequate clinical data. In addition, the efficacy of the first- and second-generation targeted drugs remains limited. However, third-generation and novel targeted drugs have proven to be effective. Although novel EGFR-TKIs are expected to treat EGFR ex20ins mutations in patients with NSCLC, they face many challenges. The main focus of this review is on emerging therapies that target NSCLC with EGFR ex20ins and highlight major ongoing clinical trials while also providing an overview of the associated challenges and research advancements in this area.
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Affiliation(s)
- Meng Hu
- Department of Oncology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Congying Zhong
- Department of Oncology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Jiabing Wang
- Department of Oncology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - JinQin Chen
- Department of Oncology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Tao Zhou
- Department of Chinese and Western Medicine Oncology, Jiangxi Provincial People’s Hospital, Nanchang, China
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Ramos R, Moura CS, Costa M, Lamas NJ, Correia R, Garcez D, Pereira JM, Sousa C, Vale N. Enhancing Lung Cancer Care in Portugal: Bridging Gaps for Improved Patient Outcomes. J Pers Med 2024; 14:446. [PMID: 38793028 PMCID: PMC11121920 DOI: 10.3390/jpm14050446] [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: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Lung cancer has the highest incidence and cancer-related mortality worldwide. In Portugal, it ranks as the fourth most common cancer, with nearly 6000 new cases being diagnosed every year. Lung cancer is the main cause of cancer-related death among males and the third cause of cancer-related death in females. Despite the globally accepted guidelines and recommendations for what would be the ideal path for a lung cancer patient, several challenges occur in real clinical management across the world. The recommendations emphasize the importance of adequate screening of high-risk individuals, a precise tumour biopsy, and an accurate final diagnosis to confirm the neoplastic nature of the nodule. A detailed histological classification of the lung tumour type and a comprehensive molecular characterization are of utmost importance for the selection of an efficacious and patient-directed therapeutic approach. However, in the context of the Portuguese clinical organization and the national healthcare system, there are still several gaps in the ideal pathway for a lung cancer patient, involving aspects ranging from the absence of a national lung cancer screening programme through difficulties in histological diagnosis and molecular characterization to challenges in therapeutic approaches. In this manuscript, we address the most relevant weaknesses, presenting several proposals for potential solutions to improve the management of lung cancer patients, helping to decisively improve their overall survival and quality of life.
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Affiliation(s)
- Raquel Ramos
- PerMed Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal; (R.R.); (C.S.)
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Molecular Diagnostics Laboratory, Unilabs Portugal, Centro Empresarial Lionesa Porto, Rua Lionesa, 4465-671 Leça do Balio, Portugal; (M.C.); (N.J.L.)
| | - Conceição Souto Moura
- Pathology Laboratory, Unilabs Portugal, Rua Manuel Pinto de Azevedo 173, 4100-321 Porto, Portugal;
| | - Mariana Costa
- Molecular Diagnostics Laboratory, Unilabs Portugal, Centro Empresarial Lionesa Porto, Rua Lionesa, 4465-671 Leça do Balio, Portugal; (M.C.); (N.J.L.)
| | - Nuno Jorge Lamas
- Molecular Diagnostics Laboratory, Unilabs Portugal, Centro Empresarial Lionesa Porto, Rua Lionesa, 4465-671 Leça do Balio, Portugal; (M.C.); (N.J.L.)
- Anatomic Pathology Service, Pathology Department, Centro Hospitalar Universitário de Santo António (CHUdSA), Largo Professor Abel Salazar, 4099-001 Porto, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Campus de Gualtar, University of Minho, Rua da Universidade, 4710-057 Braga, Portugal
| | - Renato Correia
- Technology & Innovation Department, Unilabs Portugal, Rua Manuel Pinto de Azevedo 173, 4100-321 Porto, Portugal; (R.C.); (D.G.)
| | - Diogo Garcez
- Technology & Innovation Department, Unilabs Portugal, Rua Manuel Pinto de Azevedo 173, 4100-321 Porto, Portugal; (R.C.); (D.G.)
| | - José Miguel Pereira
- Radiology Department, Unilabs Portugal, Rua de Diogo Botelho 485, 4150-255 Porto, Portugal;
| | - Carlos Sousa
- PerMed Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal; (R.R.); (C.S.)
- Molecular Diagnostics Laboratory, Unilabs Portugal, Centro Empresarial Lionesa Porto, Rua Lionesa, 4465-671 Leça do Balio, Portugal; (M.C.); (N.J.L.)
| | - Nuno Vale
- PerMed Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal; (R.R.); (C.S.)
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Health Information and Decision (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
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Zhang Q, Liang XY, Wang ZS, Sun A, Cao TB, Zhang YP, Li N, Yi TY, Qu KP. Immune checkpoint inhibitor for different age patients with NSCLC in efficacy: A systematic review and meta-analysis. Asian J Surg 2024:S1015-9584(24)00572-4. [PMID: 38641539 DOI: 10.1016/j.asjsur.2024.03.145] [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: 11/29/2023] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/21/2024] Open
Abstract
OBJECTIVE This article is a Meta-analysis aiming to systematically evaluate the difference in efficacy of immune checkpoint inhibitor in patients with non-small cell lung cancer (NSCLC) by age. METHODS We performed a Meta-analysis of published randomized controlled trials concerning for patients with NSCLC by age. We compared overall survival among three groups (age <65 years, age 65-75 years, age ≥75 years). Hazard ratios (HRs) and 95% confidence intervals (CIs) were collected and pooled. RESULTS A total of 10,291 patients from 17 RCTs were included. In the group under age 65 years, immune checkpoint inhibitor can significantly prolong the overall survival of patients with NSCLC (HR = 0.73, 95% CI: 0.66∼0.81, P < 0.00001). In the age 65-75 years group, immune checkpoint inhibitors prolonged overall survival in patients with NSCLC (HR = 0.78, 95% CI:0.71∼0.84, P < 0.00001). However, it has no significant effect on the overall survival of NSCLC patients (HR = 0.88, 95% CI:0.72∼1.08, P > 0.05) in the group older than 75 years. CONCLUSIONS Immune checkpoint inhibitors prolonged the overall survival of NSCLC patients in the age <65 years group and the age 65-75 years group, but in the age ≥75 years group, there was no significant effect on overall survival. This may be related to innate immune and adaptive immune dysregulation due to "immunosenescence" in older patients.
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Affiliation(s)
- Qi Zhang
- Gansu Provincial Central Hospital, Lanzhou, China
| | | | | | - An Sun
- Gansu Provincial Central Hospital, Lanzhou, China
| | - Tin-Bao Cao
- Gansu Provincial Central Hospital, Lanzhou, China
| | | | - Nan Li
- Gansu Provincial Central Hospital, Lanzhou, China
| | - Tong-Ying Yi
- Gansu Provincial Central Hospital, Lanzhou, China
| | - Kun-Peng Qu
- Gansu Provincial Central Hospital, Lanzhou, China.
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Conde E, Hernandez S, Rodriguez Carrillo JL, Martinez R, Alonso M, Curto D, Jimenez B, Caminoa A, Benito A, Garrido P, Clave S, Arriola E, Esteban-Rodriguez I, De Castro J, Sansano I, Felip E, Rojo F, Dómine M, Abdulkader I, Garcia-Gonzalez J, Teixido C, Reguart N, Compañ D, Insa A, Mancheño N, Palanca S, Juan-Vidal O, Baixeras N, Nadal E, Cebollero M, Calles A, Martin P, Salas C, Provencio M, Aranda I, Massuti B, Lopez-Vilaro L, Majem M, Paz-Ares L, Lopez-Rios F. RET Fusion Testing in Patients With NSCLC: The RETING Study. JTO Clin Res Rep 2024; 5:100653. [PMID: 38525319 PMCID: PMC10957499 DOI: 10.1016/j.jtocrr.2024.100653] [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: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction RET inhibitors with impressive overall response rates are now available for patients with NSCLC, yet the identification of RET fusions remains a difficult challenge. Most guidelines encourage the upfront use of next-generation sequencing (NGS), or alternatively, fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction (RT-PCR) when NGS is not possible or available. Taken together, the suboptimal performance of single-analyte assays to detect RET fusions, although consistent with the notion of encouraging universal NGS, is currently widening some of the clinical practice gaps in the implementation of predictive biomarkers in patients with advanced NSCLC. Methods This situation prompted us to evaluate several RET assays in a large multicenter cohort of RET fusion-positive NSCLC (n = 38) to obtain real-world data. In addition to RNA-based NGS (the criterion standard method), all positive specimens underwent break-apart RET FISH with two different assays and were also tested by an RT-PCR assay. Results The most common RET partners were KIF5B (78.9%), followed by CCDC6 (15.8%). The two RET NGS-positive but FISH-negative samples contained a KIF5B(15)-RET(12) fusion. The three RET fusions not identified with RT-PCR were AKAP13(35)-RET(12), KIF5B(24)-RET(9) and KIF5B(24)-RET(11). All three false-negative RT-PCR cases were FISH-positive, exhibited a typical break-apart pattern, and contained a very high number of positive tumor cells with both FISH assays. Signet ring cells, psammoma bodies, and pleomorphic features were frequently observed (in 34.2%, 39.5%, and 39.5% of tumors, respectively). Conclusions In-depth knowledge of the advantages and disadvantages of the different RET testing methodologies could help clinical and molecular tumor boards implement and maintain sensible algorithms for the rapid and effective detection of RET fusions in patients with NSCLC. The likelihood of RET false-negative results with both FISH and RT-PCR reinforces the need for upfront NGS in patients with NSCLC.
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Affiliation(s)
- Esther Conde
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Susana Hernandez
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | | | | | - Marta Alonso
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Daniel Curto
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | | | - Pilar Garrido
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Sergi Clave
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital del Mar, Barcelona, Spain
| | - Edurne Arriola
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital del Mar, Barcelona, Spain
| | | | - Javier De Castro
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital Universitario La Paz, Madrid, Spain
- Instituto de Investigacion Sanitaria del Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | - Irene Sansano
- Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | | | - Federico Rojo
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
| | - Manuel Dómine
- Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Ihab Abdulkader
- Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | | | - Cristina Teixido
- Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Noemi Reguart
- Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | | | - Amelia Insa
- Hospital Clinico Universitario, Valencia, Spain
| | - Nuria Mancheño
- Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Sarai Palanca
- Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | | | - Nuria Baixeras
- Hospital Universitari de Bellvitge, L’Hospitalet, Barcelona, Spain
| | - Ernest Nadal
- Catalan Institute of Oncology, L’Hospitalet, Barcelona, Spain
| | - Maria Cebollero
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Antonio Calles
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Paloma Martin
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Clara Salas
- Hospital Universitario Puerta de Hierro, Madrid, Spain
| | | | - Ignacio Aranda
- Hospital General Universitario Dr. Balmis – Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Bartomeu Massuti
- Hospital General Universitario Dr. Balmis – Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | | | | | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Fernando Lopez-Rios
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
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Prasad R, Sharma K, Bhutani K, Prasad S, Manhas S, Kishan J. Identification of Genetic Variants in Exon 4 of TP53 in Lung Carcinoma and in Silico Prediction of Their Significance. Indian J Clin Biochem 2024; 39:276-282. [PMID: 38577139 PMCID: PMC10987423 DOI: 10.1007/s12291-022-01099-9] [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: 03/09/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022]
Abstract
Lung cancer is a severe and the leading cause of cancer related deaths in men and women all over the world. Tumor suppressor protein (TP53) encoded by the TP53 gene which plays a pivotal role in various cellular tumor suppression processes viz cell cycle arrest and apoptosis. Henceforth, the present study was aimed to TP53 exon4 variants from lung carcinoma. Histopathologic and clinically proven 20 patients of lung cancer were enrolled in this study the average age of patients was 45 ± 8 years which categorized as early onset of lung cancer. Genomic DNA was isolated from the blood specimen of patients. Extracted DNA was subjected to PCR amplification for exon 4 of TP53 using appropriate primers and subsequently amplified products were applied to nucleotide alterations via using the DNA sanger sequencing. The genetic analysis documented five variants in exon4 of TP53 which include viz. 4 substitutions [c.215 > C at codon 72, C. 358-359AA > GG at codon 120] were highly prevalent, occurring in 63% and 25% frequency in patients. Other two variants viz. C. 358 A > C at codon 120, C. 365T > G at codon 122 were present at frequency of 15% whilst one deletion variant [152 del C] was found with 5% frequency. Furthermore, alterations on codon 72, 120,122 and 51 were characterized as possibly damaging by Poly Phen-2 and decreased stability using stability bioinformatic tool. Taken together all these findings infer that TP53 gene involved in modulation and susceptibility to lung cancer.
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Affiliation(s)
- Rajendra Prasad
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Kirti Sharma
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Karanpreet Bhutani
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Suvarna Prasad
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
- Department of Biochemistry, AIIMS, Deoghar, India
| | - Sunita Manhas
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Jai Kishan
- Department of Respiratory Medicine, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
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Chen B, Cheng Y, Wu H, Yao J. XAF1 overexpression inhibits the malignant progression and cisplatin resistance of NSCLC by activating endoplasmic reticulum stress. Mol Biol Rep 2024; 51:435. [PMID: 38520543 DOI: 10.1007/s11033-024-09347-2] [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: 11/21/2023] [Accepted: 02/13/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND XIAP-associated factor 1 (XAF1) has been found to participate in the progression of multiple human cancers. Nevertheless, its role as well as the reaction mechanism in non-small cell lung cancer (NSCLC) still remains obscure. METHODS In this study, the protein expression of XAF1 in NSCLC cell lines was evaluated using western blot. With the employment of CCK-8 assay, EdU staining, wound healing and transwell, capabilities of NSCLC cells to proliferate, migrate and invade were assessed. Cell apoptotic level and cell cycle were resolved utilizing flow cytometry. Western blot was applied for the estimation of apoptosis- and endoplasmic reticulum (ER) stress-related proteins. RESULTS It was discovered that XAF1 expression was conspicuously reduced in NSCLC cell lines. XAF1 overexpression suppressed H1299 cell proliferative, invasive and migrative capabilities, but exhibited promotive effects on cell cycle arrest. Meanwhile, XAF1 overexpression inhibited cisplatin resistance in H1299 and H1299/DDP cells by promoting cell apoptosis and enhanced the expression levels of ER stress-related proteins CHOP, GRP78 and ATF4. What's more, 4-PBA treatment reversed the impacts of XAF1 overexpression on the proliferative, invasive, migrative and apoptotic capabilities of H1299 cells, as well as cell cycle and cisplatin resistance. CONCLUSION In conclusion, XAF1 overexpression impeded the advancement of NSCLC and repressed cisplatin resistance of NSCLC cells through inducing ER stress, which indicated that XAF1 might be a novel targeted-therapy for NSCLC.
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Affiliation(s)
- Bin Chen
- Department of Cardiothoracic Surgery, People's Hospital of Chizhou, Chizhou, 247000, China.
| | - Yuanjun Cheng
- Department of Cardiothoracic Surgery, People's Hospital of Chizhou, Chizhou, 247000, China
| | - Hanqing Wu
- Department of Cardiothoracic Surgery, People's Hospital of Chizhou, Chizhou, 247000, China
| | - Jie Yao
- Department of Cardiothoracic Surgery, People's Hospital of Chizhou, Chizhou, 247000, China.
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Werner R, Connolly A, Bennett M, Hand CK, Burke L. Implementation of an ISO15189 accredited next-generation sequencing service with the fully automated Ion Torrent Genexus: the experience of a clinical diagnostic laboratory. J Clin Pathol 2024; 77:278-283. [PMID: 36522176 PMCID: PMC10958377 DOI: 10.1136/jcp-2022-208625] [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: 10/11/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022]
Abstract
AIMS Next-generation sequencing (NGS) is integral to the delivery of personalised medicine for targeted cancer therapy. Average turnaround times (TAT) from reference laboratories with advanced expertise in sequencing are typically 2-3 weeks. Prolonged TAT for biomarker analysis can adversely affect patient outcomes. The project aim was to establish an accredited NGS service integrated within a routine clinical diagnostic laboratory, in a designated tertiary cancer centre with no previous experience in NGS or bioinformatics. METHODS Platform selected was the novel Ion Torrent Genexus Sequencer with automated onboard library preparation, templating, sequencing and data analysis, with subsequent reporting using Oncomine Reporter software.Entire workflow validation was performed with a targeted panel, the Oncomine Precision Assay, on formalin-fixed paraffin embedded clinical tumour samples. Oncomine Reporter software was used to report on variants including mutations, copy number variations and fusions across 50 key genes.Samples included surgical resections, biopsies, cytology and commercial reference material. Assessment of criteria included analytical sensitivity, specificity, limit of detection, accuracy, repeatability and reproducibility, with the establishment of performance metrics and quality parameters. RESULTS High sensitivity, specificity and reproducibility were achieved. DNA/RNA input requirements optimised to >10 ng, and sequencing performance established with a limit of detection of 5% when depth of coverage of 2500X was reached. This NGS service attained ISO15189 accreditation with no non-conformances and >56% reduction in TAT. CONCLUSION Successful implementation, clinical validation and accreditation of a novel NGS technology was achieved in this institution, with a significantly improved TAT of results to oncologists.
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Affiliation(s)
- Réiltín Werner
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork, Cork, Ireland
| | - Amy Connolly
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Michael Bennett
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Collette K Hand
- Department of Pathology, School of Medicine, University College Cork, Cork, Ireland
| | - Louise Burke
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork, Cork, Ireland
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21
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Fleming KE, Hupel A, Mithoowani H, Lulic-Kuryllo T, Valdes M. Biomarker Turnaround Times and Impact on Treatment Decisions in Patients with Advanced Non-Small Cell Lung Carcinoma at a Large Canadian Community Hospital with an Affiliated Regional Cancer Centre. Curr Oncol 2024; 31:1515-1528. [PMID: 38534948 PMCID: PMC10969576 DOI: 10.3390/curroncol31030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 05/26/2024] Open
Abstract
Background: Timely reporting of molecular biomarkers is critical in guiding optimal treatment decisions in patients with advanced non-small cell lung carcinoma (NSCLC). Any delays along the tissue or treatment pathway may be associated with suboptimal treatment/outcomes and a reduced quality of life. For many centres, biomarkers are tested off-site. Methods: A retrospective chart review of 123 patients with advanced NSCLC seen between 1 June 2021 and 30 June 2022 was conducted. With a focus on core biomarkers (PD L1, EGFR, and ALK), the outcome variables were as follows: total turnaround time (total TAT), divided into pre-laboratory, laboratory, and post-laboratory time intervals, as well as time to treatment decision (TOTD) and time to optimal systemic therapy decision (TOTSD). Results: At first consult, only 20.3% of patients had all core biomarker results available. The median total TAT was significantly longer for non-squamous (non-SCC) than squamous cell carcinoma (SCC) specimens (36.5 versus 22 days, p < 0.001). The median pre-laboratory time for the entire cohort was 5 calendar days. The median laboratory testing time was greater for non-SCC compared to the SCC specimens (23 versus 12 days, p < 0.001). The median time from consult to TOTD was 19 calendar days for the entire cohort. Conclusions: This study emphasizes the need for the expansion of regional resources to meet the clinical needs of advanced NSCLC patients treated at a regional cancer centre which uses an off-site molecular laboratory.
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Affiliation(s)
- Katelyn E. Fleming
- Office of Innovation & Research, Grand River Hospital, Kitchener, ON N2G 1G3, Canada
| | - Ava Hupel
- Office of Innovation & Research, Grand River Hospital, Kitchener, ON N2G 1G3, Canada
| | - Hamid Mithoowani
- Department of Oncology, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Tea Lulic-Kuryllo
- Office of Innovation & Research, Grand River Hospital, Kitchener, ON N2G 1G3, Canada
| | - Mario Valdes
- Department of Oncology, Grand River Regional Cancer Centre, Kitchener, ON N2G 1G3, Canada
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22
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Christopoulos P, Harel M, McGregor K, Brody Y, Puzanov I, Bar J, Elon Y, Sela I, Yellin B, Lahav C, Raveh S, Reiner-Benaim A, Reinmuth N, Nechushtan H, Farrugia D, Bustinza-Linares E, Lou Y, Leibowitz R, Kamer I, Zer Kuch A, Moskovitz M, Levy-Barda A, Koch I, Lotem M, Katzenelson R, Agbarya A, Price G, Cheley H, Abu-Amna M, Geldart T, Gottfried M, Tepper E, Polychronis A, Wolf I, Dicker AP, Carbone DP, Gandara DR. Plasma Proteome-Based Test for First-Line Treatment Selection in Metastatic Non-Small Cell Lung Cancer. JCO Precis Oncol 2024; 8:e2300555. [PMID: 38513170 PMCID: PMC10965206 DOI: 10.1200/po.23.00555] [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: 10/09/2023] [Revised: 12/15/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
PURPOSE Current guidelines for the management of metastatic non-small cell lung cancer (NSCLC) without driver mutations recommend checkpoint immunotherapy with PD-1/PD-L1 inhibitors, either alone or in combination with chemotherapy. This approach fails to account for individual patient variability and host immune factors and often results in less-than-ideal outcomes. To address the limitations of the current guidelines, we developed and subsequently blindly validated a machine learning algorithm using pretreatment plasma proteomic profiles for personalized treatment decisions. PATIENTS AND METHODS We conducted a multicenter observational trial (ClinicalTrials.gov identifier: NCT04056247) of patients undergoing PD-1/PD-L1 inhibitor-based therapy (n = 540) and an additional patient cohort receiving chemotherapy (n = 85) who consented to pretreatment plasma and clinical data collection. Plasma proteome profiling was performed using SomaScan Assay v4.1. RESULTS Our test demonstrates a strong association between model output and clinical benefit (CB) from PD-1/PD-L1 inhibitor-based treatments, evidenced by high concordance between predicted and observed CB (R2 = 0.98, P < .001). The test categorizes patients as either PROphet-positive or PROphet-negative and further stratifies patient outcomes beyond PD-L1 expression levels. The test successfully differentiates between PROphet-negative patients exhibiting high tumor PD-L1 levels (≥50%) who have enhanced overall survival when treated with a combination of immunotherapy and chemotherapy compared with immunotherapy alone (hazard ratio [HR], 0.23 [95% CI, 0.1 to 0.51], P = .0003). By contrast, PROphet-positive patients show comparable outcomes when treated with immunotherapy alone or in combination with chemotherapy (HR, 0.78 [95% CI, 0.42 to 1.44], P = .424). CONCLUSION Plasma proteome-based testing of individual patients, in combination with standard PD-L1 testing, distinguishes patient subsets with distinct differences in outcomes from PD-1/PD-L1 inhibitor-based therapies. These data suggest that this approach can improve the precision of first-line treatment for metastatic NSCLC.
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Affiliation(s)
- Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital and National Center for Tumor Diseases, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | | | | | | | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY
- The Roswell Park Comprehensive Cancer Center Data Bank and BioRepository
| | - Jair Bar
- Institute of Oncology, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | | | | | | | | | | | - Anat Reiner-Benaim
- Department of Epidemiology, Biostatistics and Community Health Sciences, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Niels Reinmuth
- Asklepios Kliniken GmbH, Asklepios Fachkliniken Muenchen, Gauting, Germany
- The German Center for Lung Research (DZL), Munich-Gauting, Germany
| | - Hovav Nechushtan
- Oncology Laboratory, Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | | | - Yanyan Lou
- Division of Hematology and Oncology, Mayo Clinic School of Medicine, Jacksonville, FL
| | - Raya Leibowitz
- Shamir Medical Center, Oncology Institute, Zerifin, Israel
| | - Iris Kamer
- Institute of Oncology, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Alona Zer Kuch
- Department of Oncology, Rambam Medical Center, Haifa, Israel
| | - Mor Moskovitz
- Thoracic Cancer Service, Davidoff Cancer Center, Beilinson, Petah Tikva, Israel
| | - Adva Levy-Barda
- Biobank, Department of Pathology, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Ina Koch
- Asklepios Kliniken GmbH, Asklepios Fachkliniken Muenchen, Gauting, Germany
| | - Michal Lotem
- Center for Melanoma and Cancer Immunotherapy, Hadassah Hebrew University Medical Center, Sharett Institute of Oncology, Jerusalem, Israel
| | | | - Abed Agbarya
- Institute of Oncology, Bnai Zion Medical Center, Haifa, Israel
| | - Gillian Price
- Department of Medical Oncology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, United Kingdom
| | | | - Mahmoud Abu-Amna
- Oncology & Hematology Division, Cancer Center, Emek Medical Center, Afula, Israel
| | | | - Maya Gottfried
- Department of Oncology, Meir Medical Center, Kfar-Saba, Israel
| | - Ella Tepper
- Department of Oncology, Assuta Hospital, Tel Aviv, Israel
| | | | - Ido Wolf
- Division of Oncology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | - David P. Carbone
- Comprehensive Cancer Center, Ohio State University, Columbus, OH
| | - David R. Gandara
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, CA
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Díaz Del Arco C, Fernández Aceñero MJ, Ortega Medina L. Molecular Classifications in Gastric Cancer: A Call for Interdisciplinary Collaboration. Int J Mol Sci 2024; 25:2649. [PMID: 38473896 DOI: 10.3390/ijms25052649] [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: 01/11/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Gastric cancer (GC) is a heterogeneous disease, often diagnosed at advanced stages, with a 5-year survival rate of approximately 20%. Despite notable technological advancements in cancer research over the past decades, their impact on GC management and outcomes has been limited. Numerous molecular alterations have been identified in GC, leading to various molecular classifications, such as those developed by The Cancer Genome Atlas (TCGA) and the Asian Cancer Research Group (ACRG). Other authors have proposed alternative perspectives, including immune, proteomic, or epigenetic-based classifications. However, molecular stratification has not yet transitioned into clinical practice for GC, and little attention has been paid to alternative molecular classifications. In this review, we explore diverse molecular classifications in GC from a practical point of view, emphasizing their relationships with clinicopathological factors, prognosis, and therapeutic approaches. We have focused on classifications beyond those of TCGA and the ACRG, which have been less extensively reviewed previously. Additionally, we discuss the challenges that must be overcome to ensure their impact on patient treatment and prognosis. This review aims to serve as a practical framework to understand the molecular landscape of GC, facilitate the development of consensus molecular categories, and guide the design of innovative molecular studies in the field.
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Affiliation(s)
- Cristina Díaz Del Arco
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
| | - María Jesús Fernández Aceñero
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
| | - Luis Ortega Medina
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
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24
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Nguyen Hoang TP, Nguyen TA, Tran NHB, Nguyen Hoang VA, Thi Dao HT, Tran VU, Nguyen YN, Nguyen AT, Nguyen Thi CT, Do Thi TT, Nguyen DS, Nguyen HN, Giang H, Tu LN. Analytical validation and clinical utilization of K-4CARE™: a comprehensive genomic profiling assay with personalized MRD detection. Front Mol Biosci 2024; 11:1334808. [PMID: 38404964 PMCID: PMC10886136 DOI: 10.3389/fmolb.2024.1334808] [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: 11/07/2023] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
Background: Biomarker testing has gradually become standard of care in precision oncology to help physicians select optimal treatment for patients. Compared to single-gene or small gene panel testing, comprehensive genomic profiling (CGP) has emerged as a more time- and tissue-efficient method. This study demonstrated in-depth analytical validation of K-4CARE, a CGP assay that integrates circulating tumor DNA (ctDNA) tracking for residual cancer surveillance. Methods: The assay utilized a panel of 473 cancer-relevant genes with a total length of 1.7 Mb. Reference standards were used to evaluate limit of detection (LOD), concordance, sensitivity, specificity and precision of the assay to detect single nucleotide variants (SNVs), small insertion/deletions (Indels), gene amplification and fusion, microsatellite instability (MSI) and tumor mutational burden (TMB). The assay was then benchmarked against orthogonal methods using 155 clinical samples from 10 cancer types. In selected cancers, top tumor-derived somatic mutations, as ranked by our proprietary algorithm, were used to detect ctDNA in the plasma. Results: For detection of somatic SNVs and Indels, gene fusion and amplification, the assay had sensitivity of >99%, 94% and >99% respectively, and specificity of >99%. Detection of germline variants also achieved sensitivity and specificity of >99%. For TMB measurement, the correlation coefficient between whole-exome sequencing and our targeted panel was 97%. MSI analysis when benchmarked against polymerase chain reaction method showed sensitivity of 94% and specificity of >99%. The concordance between our assay and the TruSight Oncology 500 assay for detection of somatic variants, TMB and MSI measurement was 100%, 89%, and 98% respectively. When CGP-informed mutations were used to personalize ctDNA tracking, the detection rate of ctDNA in liquid biopsy was 79%, and clinical utility in cancer surveillance was demonstrated in 2 case studies. Conclusion: K-4CARE™ assay provides comprehensive and reliable genomic information that fulfills all guideline-based biomarker testing for both targeted therapy and immunotherapy. Integration of ctDNA tracking helps clinicians to further monitor treatment response and ultimately provide well-rounded care to cancer patients.
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Affiliation(s)
- Thien-Phuc Nguyen Hoang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Tien Anh Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Nam H. B. Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Van-Anh Nguyen Hoang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hong Thuy Thi Dao
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Vu-Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Yen Nhi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Anh Tuan Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Cam Tu Nguyen Thi
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | | | - Duy Sinh Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoai-Nghia Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Lan N. Tu
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
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25
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Grafham GK, Craddock KJ, Huang W, Louie AV, Zhang L, Hwang DM, Parmar A. Referred molecular testing as a barrier to optimal treatment decision making in metastatic non-small cell lung cancer: Experience at a tertiary academic institution in Canada. Cancer Med 2024; 13:e6886. [PMID: 38317584 PMCID: PMC10905241 DOI: 10.1002/cam4.6886] [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: 07/03/2023] [Revised: 11/08/2023] [Accepted: 12/16/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Molecular testing is critical to guiding treatment approaches in patients with metastatic non-small cell lung cancer (mNSCLC), with testing delays adversely impacting the timeliness of treatment decisions. Here, we aimed to evaluate the time from initial mNSCLC diagnosis to treatment decision (TTD) following implementation of in-house EGFR, ALK, and PD-L1 testing at our institution. METHODS We conducted a retrospective chart review of 165 patients (send-out testing, n = 92; in-house testing, n = 73) with newly diagnosed mNSCLC treated at our institution. Data were compared during the send-out (March 2017-May 2019) and in-house (July 2019-March 2021) testing periods. We performed a detailed workflow analysis to provide insight on the pre-analytic, analytic, and post-analytic intervals that constituted the total TTD. RESULTS TTD was significantly shorter with in-house testing (10 days vs. 18 days, p < 0.0001), driven largely by decreased internal handling and specimen transit times (2 days vs. 3 days, p < 0.0001) and laboratory turnaround times (TAT, 3 days vs. 8 days, p < 0.0001), with 96% of in-house cases meeting the international guideline of a ≤ 10-day intra-laboratory TAT (vs. 74% send-out, p < 0.001). Eighty-eight percent of patients with in-house testing had results available at their first oncology consultation (vs. 52% send-out, p < 0.0001), and all patients with in-house testing had results available at the time of treatment decision (vs. 86% send-out, p = 0.57). CONCLUSION Our results demonstrate the advantages of in-house biomarker testing for mNSCLC at a tertiary oncology center. Incorporation of in-house testing may reduce barriers to offering personalized medicine by improving the time to optimal systemic therapy decision.
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Affiliation(s)
- Grace K. Grafham
- Temerty Faculty of MedicineUniversity of TorontoTorontoOntarioCanada
| | - Kenneth J. Craddock
- Department of Laboratory Medicine and Molecular DiagnosticsSunnybrook Health Sciences CentreTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Weei‐Yuarn Huang
- Department of Laboratory Medicine and Molecular DiagnosticsSunnybrook Health Sciences CentreTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Alexander V. Louie
- Temerty Faculty of MedicineUniversity of TorontoTorontoOntarioCanada
- Department of Radiation OncologySunnybrook Health Sciences CentreTorontoOntarioCanada
| | | | - David M. Hwang
- Department of Laboratory Medicine and Molecular DiagnosticsSunnybrook Health Sciences CentreTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Ambica Parmar
- Temerty Faculty of MedicineUniversity of TorontoTorontoOntarioCanada
- Division of Hematology and Medical Oncology, Department of MedicineSunnybrook Health Sciences CentreTorontoOntarioCanada
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Lai WA, Huang YS, Chang KC, Yang SF, Yang CJ, Liu YW, Chen HD. Next-Generation Sequencing in Lung Cancers-A Single-Center Experience in Taiwan. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:236. [PMID: 38399524 PMCID: PMC10890140 DOI: 10.3390/medicina60020236] [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: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
Background and Objectives: Lung cancer is a leading cause of cancer mortality in Taiwan. With rapid advancement of targeted therapeutics in non-small cell lung cancers, next-generation sequencing (NGS) is becoming an important tool for biomarker testing. In this study, we describe institutional experience of NGS analysis in non-small cell carcinoma (NSCLC). Materials and Methods: A cohort of 73 cases was identified from the institutional pathology archive in the period between November 2020 and December 2022. Results: Adenocarcinoma was the most common histologic type (91.8%). Most patients presented with stage IIIB and beyond (87.7%). Twenty-nine patients (39.7%) were evaluated at the time of initial diagnosis, while the others had received prior chemotherapy or targeted therapy. The most frequently mutated gene was EGFR (63%), and this was followed by TP53 (50.7%), KRAS (13.7%), RB1 (13.7%), and CDKN2A (13.7%). Clinically actionable mutations associated with a guideline-suggested targeted therapy were identified in 55 cases (75.3%) overall, and in 47.1% of cases excluding EGFR TKI-sensitizing mutation. Biomarkers other than EGFR TKI-sensitizing mutations were compared. Cases without TKI-sensitizing EGFR mutation had more level 1 or 2 biomarkers (excluding EGFR TKI-sensitizing mutations) than cases with TKI-sensitizing EGFR mutations (47.1% versus 20.1%, p = 0.016). Progressive disease was associated with co-occurrence of clinically actionable mutations (20.5% versus 0%, p < 0.05). Eight of the nine cases with co-occurring actionable genetic alternations had an EGFR mutation. After an NGS test, 46.1% of actionable or potentially actionable genetic alternations led to patients receiving a matched therapy. Conclusions: Our study demonstrated that NGS analysis identifies therapeutic targets and may guide treatment strategies in NSCLC. NGS tests may be advantageous over multiple single-gene tests for optimization of treatment plans, especially for those with non-EGFR mutations or those with progressive disease.
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Affiliation(s)
- Wei-An Lai
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-S.H.)
| | - Yen-Shuo Huang
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-S.H.)
| | - Kung-Chao Chang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Pathology, Kaohsiung Medical University Hospital, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Sheau-Fang Yang
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-S.H.)
- Department of Pathology, Kaohsiung Medical University Hospital, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chih-Jen Yang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yu-Wei Liu
- Division of Thoracic Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Huan-Da Chen
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (Y.-S.H.)
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Gosney JR, Peake MD, Kerr KM. Improving practice in PD-L1 testing of non-small cell lung cancer in the UK: current problems and potential solutions. J Clin Pathol 2024; 77:135-139. [PMID: 36604178 PMCID: PMC10850646 DOI: 10.1136/jcp-2022-208643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023]
Abstract
AIMS Programmed cell death ligand 1 (PD-L1) expression, used universally to predict response of non-small cell lung cancer (NSCLC) to immune-modulating drugs, is a fragile biomarker due to biological heterogeneity and challenges in interpretation. The aim of this study was to assess current PD-L1 testing practices in the UK, which may help to define strategies to improve its reliability and consistency. METHODS A questionnaire covering NSCLC PD-L1 testing practice was devised and members of the Association of Pulmonary Pathologists were invited to complete this online. RESULTS Of 44 pathologists identified as involved in PD-L1 testing, 32 (73%) responded. There was good consistency in practice and approach, but there was wide variability in the distribution of PD-L1 scoring. Although the proportions of scores falling into the three groups (negative, low and high) defined by the 1% and 50% 'cut-offs' (38%, 33% and 27%, respectively) reflect the general experience, the range within each group was wide at 23-70%, 10-60% and 15-36%, respectively. CONCLUSIONS There is inconsistency in the crucial endpoint of PD-L1 testing of NSCLC, the expression score that guides management. Addressing this requires formal networking of individuals and laboratories to devise a strategy for its reduction.
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Affiliation(s)
- John R Gosney
- Cellular Pathology, Royal Liverpool and Broadgreen Hospitals NHS Trust, Liverpool, UK
| | - Michael D Peake
- Center for Cancer Outcomes, North Central and North East London Cancer Alliances, UCLH, London, UK
- Groby Road Hospital, University of Leicester, Leicester, UK
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28
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Ren J, Zhao S, Lai J. Triptolide restrains the growth, invasion, stemness, and glycolysis of non-small cell lung cancer cells by PFKFB2-mediated PI3K/AKT pathway. Chem Biol Drug Des 2024; 103:e14450. [PMID: 38230789 DOI: 10.1111/cbdd.14450] [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: 10/27/2023] [Revised: 12/14/2023] [Accepted: 12/31/2023] [Indexed: 01/18/2024]
Abstract
Triptolide (TP) has been found to have anti-tumor effects. However, more potential molecular mechanisms of TP in the progression of non-small cell lung cancer (NSCLC) deserve further investigation. Cell proliferation, apoptosis, invasion, and stemness were detected by cell counting kit 8 assay, EdU assay, flow cytometry, transwell assay, and sphere formation assay. Cell glycolysis was evaluated by corresponding assay kits. 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (PFKFB2) expression was measured by western blot (WB), qRT-PCR and immunohistochemical staining. PI3K/AKT pathway-related markers were determined by WB. Besides, xenograft tumor model was conducted to evaluate the anti-tumor effect of TP in NSCLC. Our results revealed that TP treatment suppressed NSCLC cell proliferation, invasion, stemness, glycolysis, and enhanced apoptosis. PFKFB2 was upregulated in NSCLC tissues and cells, and its expression was decreased by TP. PFKFB2 knockdown restrained NSCLC cell functions, and its overexpression also eliminated TP-mediated NSCLC cell functions inhibition. TP decreased PFKFB2 expression to inactivate PI3K/AKT pathway. Moreover, PI3K/AKT pathway inhibitor LY294002 also could reverse the promoting effect of PFKFB2 on NSCLC cell functions. In addition, TP suppressed NSCLC tumorigenesis by inhibiting PFKFB2/PI3K/AKT pathway. In conclusion, TP exerted anti-tumor role in NSCLC, which was achieved by reducing PFKFB2 expression to inactivate PI3K/AKT pathway.
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Affiliation(s)
- Jiankun Ren
- Nursing School, Hebi Polytechnic, Hebi, Henan, China
| | - Songwei Zhao
- Nursing School, Hebi Polytechnic, Hebi, Henan, China
| | - Junyu Lai
- Department of Cardiology, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, China
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Scott JA, Lennerz J, Johnson ML, Gordan LN, Dumanois RH, Quagliata L, Ritterhouse LL, Cappuzzo F, Wang B, Xue M, Vasudevan A, Varughese P, Vaidya V, Gart M, Dorrow N, Gierman HJ, Choksi RJ. Compromised Outcomes in Stage IV Non-Small-Cell Lung Cancer With Actionable Mutations Initially Treated Without Tyrosine Kinase Inhibitors: A Retrospective Analysis of Real-World Data. JCO Oncol Pract 2024; 20:145-153. [PMID: 37556776 PMCID: PMC10827288 DOI: 10.1200/op.22.00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 05/24/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023] Open
Abstract
PURPOSE Identification and targeting of actionable oncogenic drivers (AODs) in advanced non-small-cell lung cancer (NSCLC) has dramatically improved outcomes. However, genomic testing uptake is variable and hampered by factors including slow turnaround time, frequently resulting in initial non-tyrosine kinase inhibitor (TKI) treatment. We investigate how this behavior affects outcomes. METHODS This retrospective analysis of real-world, deidentified data from the Integra Connect Database included adults with stage IV NSCLC newly diagnosed from January 1, 2018, to December 31, 2020, with mutations of EGFR, ALK, ROS1, BRAF, MET, RET, ERBB2, or NTRK. Outcomes were reported as time to next treatment or death (TTNT) and overall survival (OS). RESULTS Five hundred ten patients harboring AODs were identified and grouped as follows: group A (n = 379) were treated after the AOD was reported and served as the comparator. One hundred thirty-one patients treated before their AOD report were divided into group B (n = 47) who were initially started on chemotherapy and/or checkpoint inhibitor but switched to appropriate TKI within 35 days and group C (n = 84) who were also started empirically on non-TKI and did not switch within 35 days. Survival (OS) was significantly superior in group A compared with group C; TTNT was significantly superior in group A compared with groups B and C. CONCLUSION For patients harboring AODs in advanced NSCLC, initial treatment before receipt of genomic test results yields significantly inferior outcomes and should be avoided. Molecular profiling panels with rapid turnaround times are essential to optimize patient outcomes and should be standard of care.
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Affiliation(s)
| | - Jochen Lennerz
- Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | | | - Lucio N. Gordan
- Research Institute, Florida Cancer Specialists, Fort Myers, FL
| | | | | | | | - Federico Cappuzzo
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Roma, Italy
| | | | - Mei Xue
- Integra Connect, West Palm Beach, FL
| | | | | | - Varun Vaidya
- Department of Pharmacy Practice, The University of Toledo, Toledo, OH
| | - Mike Gart
- Integra Connect, West Palm Beach, FL
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Diks J, Tang Z, Altan M, Anderson S, Chen H, Rashid A, Yang RK, Routbort MJ, Patel KP, Toruner GA, Medeiros LJ, Tang G, Luthra R, Roy-Chowdhuri S. Detection of clinically actionable gene fusions by next-generation sequencing-based RNA sequencing of non-small cell lung cancer cytology specimens: A single-center experience with comparison to fluorescence in situ hybridization. Cancer Cytopathol 2024; 132:41-49. [PMID: 37747438 DOI: 10.1002/cncy.22766] [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: 07/18/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Genomic profiling is needed to identify actionable alterations in non-small cell lung cancer (NSCLC). Panel-based testing such as next-generation sequencing (NGS) is often preferred to interrogate multiple alterations simultaneously. In this study, we evaluate the utility of an RNA-based NGS assay to detect genomic alterations in NSCLC cytology specimens and compare these results to fluorescence in situ hybridization (FISH) testing. METHODS A retrospective review was performed of 264 NSCLC cytology specimens that were concurrently tested for gene fusions by RNA-based NGS and ALK, RET, and/or ROS1 by FISH. RESULTS Genomic alterations were detected in 29 cases by NGS, including ALK, RET, ROS1, NTRK, NUTM1, and FGFR3 fusions and MET exon 14 skipping alterations. Of the 20 cases with ALK, RET, and ROS1 fusions detected by NGS, 16 (80%) were concordant with the corresponding FISH results. Three cases showed discordance, where EML4::ALK (n = 2) and SLC34A2::ROS1 (n = 1) fusions were not detected by the corresponding FISH assay; one case with EZR::ROS1 was inadequate for FISH. No gene fusions were detected in 181 cases by NGS and 54 cases failed testing. The concordance rates for detecting ALK, RET, and ROS1 fusions using NGS and FISH were 97%, 100%, and 99.5%, respectively. CONCLUSION RNA-based NGS can be used to detect gene fusions in NSCLC cytology cases with high concordance with FISH results. However, RNA-based NGS may have high failure rates and therefore a low threshold for reflexing inadequate cases to an orthogonal testing method is essential for comprehensive genomic profiling.
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Affiliation(s)
- John Diks
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah Anderson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hui Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Kenneth Yang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Bestvina CM, Waters D, Morrison L, Emond B, Lafeuille MH, Hilts A, Lefebvre P, He A, Vanderpoel J. Cost of genetic testing, delayed care, and suboptimal treatment associated with polymerase chain reaction versus next-generation sequencing biomarker testing for genomic alterations in metastatic non-small cell lung cancer. J Med Econ 2024; 27:292-303. [PMID: 38391239 DOI: 10.1080/13696998.2024.2314430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
AIMS To assess US payers' per-patient cost of testing associated with next-generation sequencing (NGS) versus polymerase chain reaction (PCR) biomarker testing strategies among patients with metastatic non-small cell lung cancer (mNSCLC), including costs of testing, delayed care, and suboptimal treatment initiation. METHODS A decision tree model considered biomarker testing for genomic alterations using either NGS, sequential PCR testing, or hotspot panel PCR testing. Literature-based model inputs included time-to-test results, costs for testing/medical care, costs of delaying care, costs of immunotherapy [IO]/chemotherapy [CTX] initiation prior to receiving test results, and costs of suboptimal treatment initiation after test results (i.e. costs of first-line IO/CTX in patients with actionable mutations that were undetected by PCR that would have been identified with NGS). The proportion of patients testing positive for a targetable alteration, time to appropriate therapy initiation, and per-patient costs were estimated for NGS and PCR strategies combined. RESULTS In a modeled cohort of 1,000,000 members (25% Medicare, 75% commercial), an estimated 1,119 had mNSCLC and received testing. The proportion of patients testing positive for a targetable alteration was 45.9% for NGS and 40.0% for PCR testing. Mean per-patient costs were lowest for NGS ($8,866) compared to PCR ($18,246), with lower delayed care costs of $1,301 for NGS compared to $3,228 for PCR, and lower costs of IO/CTX initiation prior to receiving test results (NGS: $2,298; PCR:$5,991). Cost savings, reaching $10,496,220 at the 1,000,000-member plan level, were driven by more rapid treatment with appropriate therapy for patients tested with NGS (2.1 weeks) compared to PCR strategies (5.2 weeks). LIMITATIONS Model inputs/assumptions were based on published literature or expert opinion. CONCLUSIONS NGS testing was associated with greater cost savings versus PCR, driven by more rapid results, shorter time to appropriate therapy initiation, and minimized use of inappropriate therapies while awaiting and after test results.
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Affiliation(s)
- Christine M Bestvina
- University of Chicago Comprehensive Cancer Center; Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Dexter Waters
- Janssen Scientific Affairs, LLC, a Johnson & Johnson company, Horsham, PA, USA
| | | | | | | | | | | | - Andy He
- Janssen Scientific Affairs, LLC, a Johnson & Johnson company, Horsham, PA, USA
| | - Julie Vanderpoel
- Janssen Scientific Affairs, LLC, a Johnson & Johnson company, Horsham, PA, USA
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Russo A, Lee JK, Pasquina LW, Del Re M, Dilks HH, Murugesan K, Madison RW, Lee Y, Schrock AB, Comment L, Dietrich M, Oxnard GR, Rolfo C. Liquid Biopsy of Lung Cancer Before Pathological Diagnosis Is Associated With Shorter Time to Treatment. JCO Precis Oncol 2024; 8:e2300535. [PMID: 38295321 PMCID: PMC10843270 DOI: 10.1200/po.23.00535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024] Open
Abstract
PURPOSE Studies have investigated the early use of liquid biopsy (LBx) during the diagnostic workup of patients presenting with clinical evidence of advanced lung cancer, but real-world adoption and impact has not been characterized. The aim of this study was to determine whether the use of LBx before diagnosis (Dx; LBx-Dx) enables timely comprehensive genomic profiling (CGP) and shortens time until treatment initiation for advanced non-small-cell lung cancer (aNSCLC). MATERIALS AND METHODS This study used the Flatiron Health-Foundation Medicine electronic health record-derived deidentified clinicogenomic database of patients with aNSCLC from approximately 280 US cancer clinics. RESULTS Of 1,076 patients with LBx CGP ordered within 30 days prediagnosis/postdiagnosis, we focused on 56 (5.2%) patients who ordered LBx before diagnosis date (median 8 days between order and diagnosis, range, 1-28). Compared with 1,020 patients who ordered LBx after diagnosis (Dx-LBx), LBx-Dx patients had similar stage and ctDNA tumor fraction (TF). LBx-Dx patients received CGP results a median of 1 day after Dx versus 25 days for Dx-LBx patients. Forty-three percent of LBx-Dx were positive for an National Comprehensive Cancer Network driver, and 32% had ctDNA TF >1% but were driver negative (presumed true negatives). In 748 patients with previously untreated aNSCLC, median time from Dx to therapy was shorter in the LBx-Dx versus Dx-LBx group (21 v 35 days; P < .001). CONCLUSION Early LBx in anticipation of pathologic diagnosis of aNSCLC was uncommon in this real-world cohort, yet this emerging paradigm was associated with an abbreviated time to CGP results and faster therapy initiation. Forthcoming prospective studies will clarify the utility of LBx in parallel with biopsy for diagnostic confirmation for patients presenting with suspected advanced lung cancer.
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Affiliation(s)
- Alessandro Russo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Onco-hematology, Papardo Hospital, Messina, Italy
| | | | | | - Marzia Del Re
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | | | | | - Yi Lee
- Trinity Health Oakland, Pontiac, MI
- Wayne State University School of Medicine, Detroit, MI
| | | | | | - Martin Dietrich
- Florida Cancer Specialists & Research Institute, Lake Mary, FL
| | | | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
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Iams WT, Konduri K. Biomarker Testing for Actionable Alterations in NSCLC-Perspectives from US-Based Academic and Community Oncologists: A Podcast. Adv Ther 2023; 40:5567-5578. [PMID: 37779172 PMCID: PMC10611827 DOI: 10.1007/s12325-023-02664-1] [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: 04/25/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
The identification of actionable oncogenic driver mutations in patients with non-small cell lung cancer impacts therapy selection, and appropriate therapy administration results in improvements in clinical outcomes. Although biomarker testing for actionable oncogenic driver mutations is recommended in national and international guidelines, there are still unmet needs in the real world. Through this podcast we provide, from a US perspective, an overview and discuss challenges in biomarker testing from both an academic and a community oncologist viewpoint. We describe the importance of comprehensive testing, actionable biomarkers as recommended by guidelines such as National Comprehensive Cancer Network® (NCCN®) and European Society for Medical Oncology, types of tests and assessment techniques for detection of actionable biomarkers, and challenges in testing. These challenges include the lack of awareness of the biomarker testing guidelines among physicians, inconsistent reimbursement, longer turnaround time resulting in delays in therapy initiation, and nihilism associated with particular patient characteristics. To tackle these challenges, we offer recommendations from the perspective of our own clinical settings.
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Affiliation(s)
- Wade T Iams
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, 2220 Pierce Ave, 780 PRB, Nashville, TN, 37232, USA.
| | - Kartik Konduri
- Baylor Charles A. Sammons Cancer Center, Texas Oncology PA, Dallas, TX, USA
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Batra U, Prabhash K, Agarwal JP, Darlong L, Munshi A, Penumadu P, Thangakunam B, Bansal A. Clinical management of stage III non-small cell lung cancer in India: An expert consensus statement. Asia Pac J Clin Oncol 2023; 19:606-617. [PMID: 36815621 DOI: 10.1111/ajco.13938] [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: 06/08/2022] [Revised: 11/17/2022] [Accepted: 01/07/2023] [Indexed: 02/24/2023]
Abstract
Non-small cell lung cancer (NSCLC) is considered the most common type of lung cancer (>80% of all lung cancers); patients are often diagnosed at advanced stages of the disease. The management of NSCLC is considered challenging owing to variations in size, an extension of the tumors, involvement patterns, and classification. Although adequate literature and guidelines are available on the management of NSCLC in several countries, an Indian perspective on stage III NSCLC management is lacking. We used the modified Delphi approach to form consensus statements. A thorough literature search was done. The authors then convened and deliberated over published literature, available guidelines, and clinical judgment. Recommendation statements were formed for different clinical scenarios. These statements were sent as a form of survey to other oncologists, and their responses were recorded and mentioned. Evidence-based statements were formed for diagnosing and managing stage III NSCLC. These recommendation statements cover various aspects-surgical, radiation, and medical treatment in various clinical scenarios including adjuvant, neoadjuvant, and consolidation therapies.
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Affiliation(s)
- Ullas Batra
- Department of Medical Oncology, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi, Delhi, India
| | - Kumar Prabhash
- Department of Medical Oncology, TATA Memorial Hospital, Parel, Mumbai, Maharashtra, India
| | - Jai Prakash Agarwal
- Department of Radiation Oncology, TATA Memorial Hospital, Parel, Mumbai, Maharashtra, India
| | - Laleng Darlong
- Department of Oncosurgery, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi, Delhi, India
| | - Anusheel Munshi
- Department of Radiation Oncology, Manipal Hospitals, Dwarka, Delhi, India
| | | | | | - Abhishek Bansal
- Department of Radiology, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi, Delhi, India
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Pan B, Liang J, Shi H, Rao K, Guo W, Zhan C. Epidemiological characteristics and therapeutic advances of EGFR exon 20 insertion mutations in non-small cell lung cancer. Thorac Cancer 2023; 14:3247-3258. [PMID: 37795778 PMCID: PMC10665789 DOI: 10.1111/1759-7714.15127] [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: 08/15/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
The third most prevalent type of epidermal growth factor receptor (EGFR) mutation, EGFR exon 20 insertions (EGFRex20ins), involves 2%-12% of all cases of EGFR-positive non-small cell lung cancer (NSCLC). Approximately 90% of the mutations occur within the loop structure region, and the most frequently reported subtypes are A767_V769dup and S768_D770dup, which together account for almost 50% of instances. Apart from the unique subtype of A763_Y764insFQEA, NSCLCs with EGFRex20ins are resistant to approved EGFR tyrosine kinase inhibitors (TKIs) and are also insensitive to chemotherapy or immunotherapy. A new modality of treatment for NSCLC patients with EGFRx20ins has been established with the approval of mobocertinib and amivantamab. There are also numerous novel targeted treatments for NSCLC with EGFRex20ins in development, which are anticipated to improve this patient population's survival even further. This review provides a reference for the clinical management of these patients by summarizing the most recent epidemiological, and clinicopathological characteristics, diagnostic techniques, and therapeutic advances of EGFRex20ins in NSCLC.
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Affiliation(s)
- Binyang Pan
- Department of Thoracic Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Haochun Shi
- Department of Thoracic Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Kungeng Rao
- Department of Thoracic Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Weigang Guo
- Department of Thoracic Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of Thoracic Surgery and UrologyShigatse People's HospitalShigatseChina
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
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Kobayashi N, Miura K, Kaneko A, Matsumoto H, Somekawa K, Hirose T, Kajita Y, Tanaka A, Teranishi S, Sairenji Y, Kawashima H, Yumoto K, Tsukahara T, Fukuda N, Nishihira R, Kudo M, Miyazawa N, Kaneko T. Tailoring Therapeutic Strategies in Non-Small-Cell Lung Cancer: The Role of Genetic Mutations and Programmed Death Ligand-1 Expression in Survival Outcomes. Cancers (Basel) 2023; 15:5248. [PMID: 37958421 PMCID: PMC10648983 DOI: 10.3390/cancers15215248] [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: 09/24/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND This study aims to assess the real-world impact of advancements in first-line systemic therapies for non-small-cell lung cancer (NSCLC), focusing on the role of driver gene mutations and programmed death-ligand 1 (PD-L1) expression levels. METHODS Conducted across eight medical facilities in Japan, this multicenter, retrospective observational research included 863 patients diagnosed with NSCLC and treated between January 2015 and December 2022. The patients were categorized based on the type of systemic therapy received: cytotoxic agents, molecular targeting agents, immune checkpoint inhibitors, and combination therapies. Comprehensive molecular and immunohistochemical analyses were conducted, and statistical evaluations were performed. RESULTS The median overall survival (OS) shows significant variations among treatment groups, with targeted therapies demonstrating the longest OS. This study also revealed that high PD-L1 expression was common in the group treated with immune checkpoint inhibitors. Multivariate analysis was used to identify the type of anticancer drug and the expression of PD-L1 at diagnosis as the impactful variables affecting 5-year OS. CONCLUSIONS This study underscores the efficacy of targeted therapies and the critical role of comprehensive molecular diagnostics and PD-L1 expression in affecting OS in NSCLC patients, advocating for their integration into routine clinical practice.
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Affiliation(s)
- Nobuaki Kobayashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kenji Miura
- Department of Respiratory Medicine, Yokohama Sakae Kyosai Hospital, Yokohama 247-8581, Japan
| | - Ayami Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hiromi Matsumoto
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kohei Somekawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Tomofumi Hirose
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Yukihito Kajita
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Anna Tanaka
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Shuhei Teranishi
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Yu Sairenji
- Department of Respiratory Medicine, Yokohama Sakae Kyosai Hospital, Yokohama 247-8581, Japan
| | - Hidetoshi Kawashima
- Department of Respiratory Medicine, Kanto Rosai Hospital, Kawasaki 211-8510, Japan
| | - Kentaro Yumoto
- Department of Respiratory Medicine, Yokohama Minami Kyosai Hospital, Yokohama 236-0037, Japan
| | - Toshinori Tsukahara
- Department of Respiratory Medicine, Chigasaki Municipal Hospital, Chigasaki 253-0042, Japan
| | - Nobuhiko Fukuda
- Department of Respiratory Medicine, Fujisawa Municipal Hospital, Fujisawa 251-8550, Japan
| | - Ryuichi Nishihira
- Department of Respiratory Medicine, Kanto Rosai Hospital, Kawasaki 211-8510, Japan
| | - Makoto Kudo
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Naoki Miyazawa
- Department of Respiratory Medicine, Yokohama Nanbu Hospital, Yokohama 234-0054, Japan
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
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Babu B, Stoltz SA, Mittal A, Pawar S, Kolanthai E, Coathup M, Seal S. Inorganic Nanoparticles as Radiosensitizers for Cancer Treatment. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2873. [PMID: 37947718 PMCID: PMC10647410 DOI: 10.3390/nano13212873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
Nanotechnology has expanded what can be achieved in our approach to cancer treatment. The ability to produce and engineer functional nanoparticle formulations to elicit higher incidences of tumor cell radiolysis has resulted in substantial improvements in cancer cell eradication while also permitting multi-modal biomedical functionalities. These radiosensitive nanomaterials utilize material characteristics, such as radio-blocking/absorbing high-Z atomic number elements, to mediate localized effects from therapeutic irradiation. These materials thereby allow subsequent scattered or emitted radiation to produce direct (e.g., damage to genetic materials) or indirect (e.g., protein oxidation, reactive oxygen species formation) damage to tumor cells. Using nanomaterials that activate under certain physiologic conditions, such as the tumor microenvironment, can selectively target tumor cells. These characteristics, combined with biological interactions that can target the tumor environment, allow for localized radio-sensitization while mitigating damage to healthy cells. This review explores the various nanomaterial formulations utilized in cancer radiosensitivity research. Emphasis on inorganic nanomaterials showcases the specific material characteristics that enable higher incidences of radiation while ensuring localized cancer targeting based on tumor microenvironment activation. The aim of this review is to guide future research in cancer radiosensitization using nanomaterial formulations and to detail common approaches to its treatment, as well as their relations to commonly implemented radiotherapy techniques.
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Affiliation(s)
- Balaashwin Babu
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (B.B.); (S.A.S.); (A.M.); (S.P.); (E.K.)
| | - Samantha Archer Stoltz
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (B.B.); (S.A.S.); (A.M.); (S.P.); (E.K.)
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Agastya Mittal
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (B.B.); (S.A.S.); (A.M.); (S.P.); (E.K.)
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Shreya Pawar
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (B.B.); (S.A.S.); (A.M.); (S.P.); (E.K.)
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (B.B.); (S.A.S.); (A.M.); (S.P.); (E.K.)
| | - Melanie Coathup
- Biionix Cluster, University of Central Florida, Orlando, FL 32827, USA;
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Sudipta Seal
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32826, USA; (B.B.); (S.A.S.); (A.M.); (S.P.); (E.K.)
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA
- Nanoscience Technology Center, University of Central Florida, Orlando, FL, USA
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Cabrera K, Gole J, Leatham B, Springer MJ, Smith M, Herdt L, Jacky L, Brown BA. Analytical Performance and Concordance with Next-Generation Sequencing of a Rapid, Multiplexed dPCR Panel for the Detection of DNA and RNA Biomarkers in Non-Small-Cell Lung Cancer. Diagnostics (Basel) 2023; 13:3299. [PMID: 37958195 PMCID: PMC10650055 DOI: 10.3390/diagnostics13213299] [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: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
FDA approval of targeted therapies for lung cancer has significantly improved patient survival rates. Despite these improvements, barriers to timely access to biomarker information, such as nucleic acid input, still exist. Here, we report the analytical performance and concordance with next-generation sequencing (NGS) of a highly multiplexed research-use-only (RUO) panel using digital PCR (dPCR). The panel's analytical sensitivity and reactivity were determined using contrived DNA and RNA mixes. The limit of blank was established by testing FFPE curls classified as negative by pathology. Concordance was established on 77 FFPE samples previously characterized using the Oncomine Precision Assay®, and any discordant results were resolved with Archer Fusionplex® and Variantplex® panels. The analytical sensitivity, reported as the estimated mutant allele fraction (MAF), for DNA targets ranged from 0.1 to 0.9%. For RNA targets (ALK, RET, ROS, NTRK 1/2/3 Fusions, and MET Exon 14 skipping alteration), the analytical sensitivity ranged from 23 to 101 detected counts with 5 ng of total RNA input. The population prevalence-based coverage ranged from 89.2% to 100.0% across targets and exceeded 99.0% in aggregate. The assay demonstrated >97% concordance with respect to the comparator method.
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Affiliation(s)
- Kerri Cabrera
- ChromaCode Inc., 2330 Faraday Ave., Carlsbad, CA 92008, USA; (J.G.); (M.J.S.); (M.S.); (L.H.); (L.J.)
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Clavé S, Jackson JB, Salido M, Kames J, Gerding KMR, Verner EL, Kong EF, Weingartner E, Gibert J, Hardy-Werbin M, Rocha P, Riera X, Torres E, Hernandez J, Cerqueira G, Nichol D, Simmons J, Taus Á, Pijuan L, Bellosillo B, Arriola E. Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer. Front Oncol 2023; 13:1225646. [PMID: 37927472 PMCID: PMC10623306 DOI: 10.3389/fonc.2023.1225646] [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: 05/19/2023] [Accepted: 08/28/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor's molecular landscape. However, further evaluation of technical aspects related to the detection of gene rearrangements and copy number alterations is warranted. Methods There were 12 ALK rearrangement-positive tumor specimens from patients with non-small cell lung cancer (NSCLC) previously detected via fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and an RNA-based NGS assay, and 26 MET high gene copy number (GCN) cases detected by FISH, selected for this retrospective study. All 38 pre-characterized cases were reassessed utilizing the PGDx™ elio™ tissue complete assay, a 505 gene targeted NGS panel, to evaluate concordance with these conventional diagnostic techniques. Results The detection of ALK rearrangements using the DNA-based NGS assay demonstrated excellent sensitivity with the added benefit of characterizing gene fusion partners and genomic breakpoints. MET copy number alterations were also detected; however, some discordances were observed likely attributed to differences in algorithm, reporting thresholds and gene copy number state. TMB was also assessed by the assay and correlated to the presence of NSCLC driver alterations and was found to be significantly lower in cases with NGS-confirmed canonical driver mutations compared with those without (p=0.0019). Discussion Overall, this study validates NGS as an accurate approach for detecting structural variants while also highlighting the need for further optimization to enable harmonization across methodologies for amplifications.
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Affiliation(s)
- Sergi Clavé
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Marta Salido
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Jacob Kames
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | | | - Ellen L. Verner
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Eric F. Kong
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | | | - Joan Gibert
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Max Hardy-Werbin
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Pedro Rocha
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Xènia Riera
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Erica Torres
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - James Hernandez
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Gustavo Cerqueira
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Donna Nichol
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - John Simmons
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Álvaro Taus
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Lara Pijuan
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Edurne Arriola
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
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Kim H, Lee JK, Oh AC, Kim HR, Hong YJ. The Usefulness of the Ratio of Antigen-Autoantibody Immune Complexes to Their Free Antigens in the Diagnosis of Non-Small Cell Lung Cancer. Diagnostics (Basel) 2023; 13:2999. [PMID: 37761366 PMCID: PMC10529727 DOI: 10.3390/diagnostics13182999] [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: 06/19/2023] [Revised: 08/21/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Autoantibodies against specific lung cancer-associated antigens have been suggested for the performance of lung cancer diagnosis. This study aimed to evaluate the diagnostic performance of the antigen-autoantibody immune complex (AIC) against its free antigens for CYFRA21-1, ProGRP, neutrophil gelatinase-associated lipocalin (NGAL), and neuron-specific enolase (NSE) in non-small cell lung cancer (NSCLC). In total, 85 patients with NSCLC and 120 healthy controls (HCs) were examined using a 9-guanine DNA chip method. The ratios of AICs to their antigens and the combinations of ratios consisting of two to four markers were calculated. The levels of AICs for CYFRA21-1, ProGRP, NGAL, and NSE were higher than those for their free antigens in all participants. The levels of each free antigens distinguished patients with NSCLC from the HCs. The ratios of the AIC to its antigen and seven combinations of two to four ratios were significantly higher in patients with NSCLC than in the HCs. Excellent diagnostic performance was observed for all combination ratios (C4-1), with 85.9% sensitivity and 86.7% specificity at a 3.51 cut-off. Higher sensitivity was observed in the early stages (0-I) and adenocarcinoma than in stages II-IV and other pathological types. Combining all ratios of AICs and their antigens for all four markers was useful when diagnosing NSCLC.
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Affiliation(s)
- Heyjin Kim
- Department of Laboratory Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea; (H.K.); (J.K.L.)
| | - Jin Kyung Lee
- Department of Laboratory Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea; (H.K.); (J.K.L.)
| | - Ae-Chin Oh
- Department of Laboratory Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea; (H.K.); (J.K.L.)
| | - Hye-Ryoun Kim
- Division of Pulmonology, Department of Internal Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea;
| | - Young Jun Hong
- Department of Laboratory Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea; (H.K.); (J.K.L.)
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Wang Y, Liu H, Yu N, Xiang X. Concordance of Abundance for Mutational EGFR and Co-Mutational TP53 with Efficacy of EGFR-TKI Treatment in Metastatic Patients with Non-Small-Cell Lung Cancer. Curr Oncol 2023; 30:8464-8476. [PMID: 37754531 PMCID: PMC10528559 DOI: 10.3390/curroncol30090616] [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: 08/11/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023] Open
Abstract
The present study aimed to investigate the influence of the mutation abundance of the epidermal growth factor receptor (EGFR) and its co-mutation with TP53 on the therapeutic efficacy of tyrosine kinase inhibitor (TKI) treatment in patients with metastatic lung adenocarcinoma (LUAD). In total, 130 patients (January 2018-September 2022) with metastatic LUAD from the Second Affiliated Hospital of Zhejiang University were included. Kaplan-Meier analysis was performed to measure the duration of drug application (DDA) and the log-rank test was used to compare differences. Univariate and multivariate analyses of Cox proportional hazard regression models were used to evaluate the association between the relevant clinicopathological factors and DDA. Hazard ratios with 95% confidence intervals were also calculated. Among the 130 patients who were treated with first-generation EGFR-TKIs, 86 showed high-EGFR mutation abundance (>22.0%) and 44 showed low-EGFR mutation abundance (≤22.0%). Patients in the high-EGFR group had a greater DDA than those in the low-EGFR group (p < 0.05). The results of the subgroup analysis were consistent with those of the total mutation population (exon19: >18.5% vs. ≤18.5%, 14 months vs. 10 months, p = 0.049; exon21: >22.0% vs. ≤22.0%, 15 months vs. 9 months, p = 0.005). In addition, the mutation abundance of TP53 was negatively correlated with the DDA (p < 0.05). Patients in the combination group had a better DDA than those in the monotherapy group (p < 0.05). Subgroup analysis showed that, among the low mutation abundance of the EGFR exon 21 or 19 cohort, the combination group had a better DDA than the monotherapy group (p < 0.05). An EGFR mutation abundance greater than 22.0% was a positive predictor of DDA in patients with metastatic LUAD. However, a TP53 mutation abundance higher than 32.5% could reverse this situation. Finally, first-line treatment with EGFR-TKIs plus chemotherapy is a potential treatment strategy for patients with low-abundance EGFR mutations.
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Affiliation(s)
- Youping Wang
- Department of Medical Oncology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;
| | - Hong Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China;
| | - Ningjuan Yu
- Department of Medical Oncology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;
| | - Xueping Xiang
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;
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Yaghoubi Naei V, Bordhan P, Mirakhorli F, Khorrami M, Shrestha J, Nazari H, Kulasinghe A, Ebrahimi Warkiani M. Advances in novel strategies for isolation, characterization, and analysis of CTCs and ctDNA. Ther Adv Med Oncol 2023; 15:17588359231192401. [PMID: 37692363 PMCID: PMC10486235 DOI: 10.1177/17588359231192401] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Over the past decade, the detection and analysis of liquid biopsy biomarkers such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have advanced significantly. They have received recognition for their clinical usefulness in detecting cancer at an early stage, monitoring disease, and evaluating treatment response. The emergence of liquid biopsy has been a helpful development, as it offers a minimally invasive, rapid, real-time monitoring, and possible alternative to traditional tissue biopsies. In resource-limited settings, the ideal platform for liquid biopsy should not only extract more CTCs or ctDNA from a minimal sample volume but also accurately represent the molecular heterogeneity of the patient's disease. This review covers novel strategies and advancements in CTC and ctDNA-based liquid biopsy platforms, including microfluidic applications and comprehensive analysis of molecular complexity. We discuss these systems' operational principles and performance efficiencies, as well as future opportunities and challenges for their implementation in clinical settings. In addition, we emphasize the importance of integrated platforms that incorporate machine learning and artificial intelligence in accurate liquid biopsy detection systems, which can greatly improve cancer management and enable precision diagnostics.
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Affiliation(s)
- Vahid Yaghoubi Naei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Science, Institute for Biomedical Materials & Devices, University of Technology Sydney, Australia
| | - Fatemeh Mirakhorli
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Arutha Kulasinghe
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, 1, Broadway, Ultimo New South Wales 2007, Australia
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Yan JT, Jin Y, Lo E, Chen Y, Hanlon Newell AE, Kong Y, Inge LJ. Real-World Biomarker Test Utilization and Subsequent Treatment in Patients with Early-Stage Non-small Cell Lung Cancer in the United States, 2011-2021. Oncol Ther 2023; 11:343-360. [PMID: 37330972 PMCID: PMC10447355 DOI: 10.1007/s40487-023-00234-7] [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: 03/13/2023] [Accepted: 05/11/2023] [Indexed: 06/20/2023] Open
Abstract
INTRODUCTION Biomarker testing is increasingly crucial for patients with early-stage non-small cell lung cancer (eNSCLC). We explored biomarker test utilization and subsequent treatment in eNSCLC patients in the real-world setting. METHODS Using COTA's oncology database, this retrospective observational study included adult patients ≥ 18 years old diagnosed with eNSCLC (disease stage 0-IIIA) between January 1, 2011 and December 31, 2021. Date of first eNSCLC diagnosis was the study index date. We reported testing rates by index year for patients who received any biomarker test within 6 months of eNSCLC diagnosis and by each molecular marker. We also evaluated treatments received among patients receiving the five most common biomarker tests. RESULTS Among the 1031 eNSCLC patients included in the analysis, 764 (74.1%) received ≥ 1 biomarker test within 6 months of eNSCLC diagnosis. Overall, epidermal growth factor receptor (EGFR; 64%), anaplastic lymphoma kinase (ALK; 60%), programmed death receptor ligand 1 (PD-L1; 48%), ROS proto-oncogene 1 (ROS1; 46%), B-Raf proto-oncogene (40%), mesenchymal epithelial transition factor receptor (35%), Kirsten rat sarcoma viral oncogene (29%), RET proto-oncogene (22%), human epidermal growth factor receptor 2 (21%), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (20%) were the 10 most frequently tested biomarkers. The proportion of patients undergoing biomarker testing rose from 55.3% in 2011 to 88.1% in 2021. The most common testing methods were Sanger sequencing for EGFR (244, 37%), FISH (fluorescence in situ hybridization) for ALK (464, 75%) and ROS1 (357, 76%), immunohistochemical assay for PD-L1 (450, 90%), and next-generation sequencing testing for other biomarkers. Almost all the 763 patients who received the five most common biomarker tests had a test before the initiation of a systemic treatment. CONCLUSION This study suggests a high biomarker testing rate among patients with eNSCLC in the US, with testing rates for various biomarkers increasing over the past decade, indicating a continuous trend towards the personalization of treatment decisions.
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Affiliation(s)
- Jessie T Yan
- Roche Information Solutions, Roche Diagnostics, Santa Clara, CA, USA.
| | - Yue Jin
- Roche Information Solutions, Roche Diagnostics, Santa Clara, CA, USA
| | - Ernest Lo
- Roche Information Solutions, Roche Diagnostics, Santa Clara, CA, USA
| | - Yilin Chen
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Amy E Hanlon Newell
- Clinical Development/Medical Affairs, Global, Roche Diagnostics Solutions, Tucson, AZ, USA
| | - Ying Kong
- Clinical Development/Medical Affairs, Global, Roche Diagnostics Solutions, Tucson, AZ, USA
| | - Landon J Inge
- Clinical Development/Medical Affairs, Global, Roche Diagnostics Solutions, Tucson, AZ, USA
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Pack A, Russell A, Kircher S, Weldon C, Bailey SC, Lockwood K, Marquart T, Afonso AS, Payakachat N, Wolf M. Current communication practices for biomarker testing in non-small cell lung cancer: Exploring patient and clinician perspectives. PATIENT EDUCATION AND COUNSELING 2023; 114:107839. [PMID: 37321114 PMCID: PMC10528088 DOI: 10.1016/j.pec.2023.107839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/13/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
OBJECTIVES We qualitatively explored patient and clinician experiences with biomarker testing in one academic health system to identify current communication practices and unmet testing information needs. METHODS We conducted 1:1 in-depth interviews with 15 clinicians (i.e., nurses, oncologists, pathologists) and 12 patients diagnosed with non-small cell lung cancer between January and May 2022. Participants described experiences with biomarker testing as well as associated communication practices and needs. Interviews were audio-recorded and transcribed. Analysis was informed by the Framework Method. RESULTS Patients described challenges retaining information early in their patient journey. While patients were generally aware of biomarkers and their effect on treatment options, they expressed limited knowledge of expected time delays between testing and receiving results. Additionally, many did not know their testing results. Clinicians and patients both noted no standard education material on biomarker testing is currently available. They suggested such materials could support patient knowledge and decision-making. CONCLUSIONS Communication between patients and clinicians about biomarker testing is largely delivered through verbal counseling at a time when patients may be cognitively compromised. All participants supported the idea of delivering standard, tangible education materials on biomarker testing to patients. PRACTICE IMPLICATIONS Education materials may enhance counseling efforts and patient knowledge.
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Affiliation(s)
- Allison Pack
- The Center for Applied Health Research on Aging and The Division of General Internal Medicine, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA.
| | - Andrea Russell
- The Center for Applied Health Research on Aging and The Division of General Internal Medicine, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Sheetal Kircher
- The Center for Applied Health Research on Aging and The Division of General Internal Medicine, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Christine Weldon
- The Center for Applied Health Research on Aging and The Division of General Internal Medicine, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA; Division of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA; The Center for Business Models in Healthcare, Glencoe, IL, USA
| | - Stacy C Bailey
- The Center for Applied Health Research on Aging and The Division of General Internal Medicine, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | | | | | | | | | - Michael Wolf
- The Center for Applied Health Research on Aging and The Division of General Internal Medicine, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
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Saldivar JS, Harris J, Ayash E, Hong M, Tandon P, Sinha S, Hebron PM, Houghton EE, Thorne K, Goodman LJ, Li C, Marfatia TR, Anderson J, Morra M, Lyle J, Bartha G, Chen R. Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay. Oncotarget 2023; 14:789-806. [PMID: 37646774 PMCID: PMC10467627 DOI: 10.18632/oncotarget.28490] [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: 05/31/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen. This provides highly accurate somatic variant calls as well as the incidental reporting of pathogenic and likely pathogenic germline alterations. Fusion detection via RNA sequencing provides more extensive and accurate fusion calling compared to DNA-based tests. NeXT Dx features the proprietary Accuracy and Content Enhanced technology, developed to optimize sequencing and provide more uniform coverage across the exome. The exome was validated at a median sequencing depth of >500x. While variants from 401 cancer-associated genes are currently reported from the assay, the exome/transcriptome assay is broadly validated to enable reporting of additional variants as they become clinically relevant. NeXT Dx demonstrated analytic sensitivities as follows: SNVs (99.4%), indels (98.2%), CNAs (98.0%), and fusions (95.8%). The overall analytic specificity was >99.0%.
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Affiliation(s)
| | - Jason Harris
- Personalis, Inc., Fremont, CA 94555, USA
- These authors contributed equally to this work
| | - Erin Ayash
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | | | | | | | | | - Conan Li
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | - John Lyle
- Personalis, Inc., Fremont, CA 94555, USA
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Chen W, Chen J, Zhang L, Cheng S, Yu J. Network meta-analysis of first-line immune checkpoint inhibitor therapy in advanced non-squamous non-small cell lung cancer patients with PD-L1 expression ≥ 50. BMC Cancer 2023; 23:791. [PMID: 37612622 PMCID: PMC10464425 DOI: 10.1186/s12885-023-11285-4] [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: 04/20/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
INTRODUCTION The optimal first-line immunotherapy regimen for advanced non-squamous non-small cell lung cancer (NS-NSCLC) patients with programmed cell death ligand 1 (PD-L1) expression ≥ 50% remains unclear. Our aim is to determine the most effective treatment regimen through a network meta-analysis (NMA) comparing these treatments. METHODS A systematic search was performed in PubMed, Cochrane Library, Web of Science, and Embase databases, and a Bayesian network meta-analysis was conducted. To ensure transparency, the study was registered in the International Prospective Register of Systematic Reviews (CRD42022349712). RESULTS The analysis included 11 randomized controlled trials (RCTs) with 2037 patients and 12 immunotherapy combinations. ICI-ICI, ICI alone, and chemotherapy-ICI showed significant advantages over chemotherapy in terms of overall survival (OS) and progression-free survival (PFS). Pembrolizumab plus chemotherapy showed the best OS results compared to chemotherapy. Tislelizumab plus chemotherapy and sintilimab plus chemotherapy provided the best PFS results. CONCLUSIONS For NS-NSCLC patients with PD-L1 ≥ 50%, pembrolizumab plus chemotherapy, tislelizumab plus chemotherapy, and sintilimab plus chemotherapy are recommended as good treatment options based on the results of this Network meta-analysis (NMA).
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Affiliation(s)
- Wei Chen
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jiayi Chen
- School of Nursing, Capital Medical University, Beijing, China
| | - Lin Zhang
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Sheng Cheng
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Junxian Yu
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
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Grolleau E, Candiracci J, Lescuyer G, Barthelemy D, Benzerdjeb N, Haon C, Geiguer F, Raffin M, Hardat N, Balandier J, Rabeuf R, Chalabreysse L, Wozny AS, Rommelaere G, Rodriguez-Lafrasse C, Subtil F, Couraud S, Herzog M, Payen-Gay L. Circulating H3K27 Methylated Nucleosome Plasma Concentration: Synergistic Information with Circulating Tumor DNA Molecular Profiling. Biomolecules 2023; 13:1255. [PMID: 37627320 PMCID: PMC10452235 DOI: 10.3390/biom13081255] [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: 07/05/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The molecular profiling of circulating tumor DNA (ctDNA) is a helpful tool not only in cancer treatment, but also in the early detection of relapse. However, the clinical interpretation of a ctDNA negative result remains challenging. The characterization of circulating nucleosomes (carrying cell-free DNA) and associated epigenetic modifications (playing a key role in the tumorigenesis of different cancers) may provide useful information for patient management, by supporting the contributive value of ctDNA molecular profiling. Significantly elevated concentrations of H3K27Me3 nucleosomes were found in plasmas at the diagnosis, and during the follow-up, of NSCLC patients, compared to healthy donors (p-value < 0.0001). By combining the H3K27Me3 level and the ctDNA molecular profile, we found that 25.5% of the patients had H3K27Me3 levels above the cut off, and no somatic alteration was detected at diagnosis. This strongly supports the presence of non-mutated ctDNA in the corresponding plasma. During the patient follow-up, a high H3K27Me3-nucleosome level was found in 15.1% of the sample, despite no somatic mutations being detected, allowing the identification of disease progression from 43.1% to 58.2% over molecular profiling alone. Measuring H3K27Me3-nucleosome levels in combination with ctDNA molecular profiling may improve confidence in the negative molecular result for cfDNA in lung cancer at diagnosis, and may also be a promising biomarker for molecular residual disease (MRD) monitoring, during and/or after treatment.
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Affiliation(s)
- Emmanuel Grolleau
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Pulmonology Department, Lyon Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Julie Candiracci
- Belgian Volition SRL, Parc Scientifique Créalys, 5032 Isnes, Belgium
| | - Gaelle Lescuyer
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - David Barthelemy
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Nazim Benzerdjeb
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Pathology Department, Claude Bernard University Lyon I, Hospices Civils de Lyon, 69677 Bron, France
| | - Christine Haon
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Florence Geiguer
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Margaux Raffin
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Nathalie Hardat
- Belgian Volition SRL, Parc Scientifique Créalys, 5032 Isnes, Belgium
| | - Julie Balandier
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
| | - Rémi Rabeuf
- Belgian Volition SRL, Parc Scientifique Créalys, 5032 Isnes, Belgium
| | - Lara Chalabreysse
- Pathology Department, Claude Bernard University Lyon I, Hospices Civils de Lyon, 69677 Bron, France
| | - Anne-Sophie Wozny
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
- Cellular and Molecular Radiobiology Laboratory UMR CNRS5822/IP2I, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
| | | | - Claire Rodriguez-Lafrasse
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
- Cellular and Molecular Radiobiology Laboratory UMR CNRS5822/IP2I, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
| | - Fabien Subtil
- Statistic Department, Hospices Civils de Lyon, 69008 Lyon, France
- LBBE, Claude Bernard University Lyon I, UMR 5558, CNRS, 69100 Villeurbanne, France
| | - Sébastien Couraud
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Pulmonology Department, Lyon Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Marielle Herzog
- Belgian Volition SRL, Parc Scientifique Créalys, 5032 Isnes, Belgium
| | - Lea Payen-Gay
- Center for Innovation in Cancerology of Lyon (CICLY) EA 3738, Faculty of Medicine and Maieutic Lyon Sud, Claude Bernard University Lyon I, 69921 Oullins, France
- Institute of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard University Lyon I, 69373 Lyon, France
- Department of Biochemistry and Molecular Biology, Lyon-Sud Hospital, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
- Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon, Cancer Institute, 69495 Pierre-Bénite, France
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Liu T, Yu S, Hu T, Ji W, Cheng X, Lv L, Shi Z. Comprehensive analyses of genome-wide methylation and RNA epigenetics identify prognostic biomarkers, regulating the tumor immune microenvironment in lung adenocarcinoma. Pathol Res Pract 2023; 248:154621. [PMID: 37336075 DOI: 10.1016/j.prp.2023.154621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
The aim of our study was to identify a signature of immune-regulated molecules and reveal its prognostic role in lung adenocarcinoma (LUAD). We downloaded RNA-Sequencing data and DNA methylation data from the Gene Expression Omnibus (GEO) database. GEO2R was used to analyze differentially expressed mRNAs (DEmRNAs). we used "factoextra" R package to do the principal component analysis (PCA) of DEmRNAs. "Limma" R package was used to identify DEmRNAs, differentially expressed miRNAs (DEmiRNAs), differentially expressed lncRNAs (DElncRNAs) from The Cancer Genome Atlas (TCGA) database. Three R packages "org.Hs.eg.db", "clusterProfiler", "ggplot2″ were used to show enrichment results. Considering about methylation and mutation data, TEK and SOX17 mediated cancer signaling pathways. Through tumor-immune system interactions database (TISIDB) and Tumor Immune Estimation Resource (TIMER), higher methylated and lower expressed TEK may act as a prognostic marker, regulating the tumor immunity in LUAD. Through four databases (MEXPRESS, DNMIVD, MethSurv, Firehose), we further verified the methylation (P = 2.33e-23) and mutation about TEK. A signature of immune-associated TEK to predict survival of LUAD patients was validated. Prognostic, methylation, immune microenvironment analysis showed new light on potential novel therapeutic targets in LUAD.
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Affiliation(s)
- Tingting Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuo Yu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.; Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong, University, Xi'an, Shaanxi 710000, China
| | - Tinghua Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wen Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xue Cheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lin Lv
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhihong Shi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China..
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49
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Gosney JR, Paz-Ares L, Jänne P, Kerr KM, Leighl NB, Lozano MD, Malapelle U, Mok T, Sheffield BS, Tufman A, Wistuba II, Peters S. Pathologist-initiated reflex testing for biomarkers in non-small-cell lung cancer: expert consensus on the rationale and considerations for implementation. ESMO Open 2023; 8:101587. [PMID: 37356358 PMCID: PMC10485396 DOI: 10.1016/j.esmoop.2023.101587] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/18/2023] [Accepted: 05/18/2023] [Indexed: 06/27/2023] Open
Abstract
Biomarker tests in lung cancer have been traditionally ordered by the treating oncologist upon confirmation of an appropriate pathological diagnosis. The delay this introduces prolongs yet further what is already a complex, multi-stage, pre-treatment pathway and delays the start of first-line systemic treatment, which is crucially informed by the results of such analysis. Reflex testing, in which the responsibility for testing for an agreed range of biomarkers lies with the pathologist, has been shown to standardise and expedite the process. Twelve experts discussed the rationale and considerations for implementing reflex testing as standard clinical practice.
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Affiliation(s)
- J R Gosney
- Department of Cellular Pathology, Royal Liverpool University Hospital, Liverpool, UK
| | - L Paz-Ares
- Hospital Universitario 12 de Octubre, H12O-CNIO Lung Cancer Unit, Ciberonc and Complutense University, Madrid, Spain
| | - P Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - K M Kerr
- School of Medicine and Dentistry, University of Aberdeen, Aberdeen, UK
| | - N B Leighl
- Princess Margaret Cancer Centre, Toronto, Canada
| | - M D Lozano
- Pathology, Universidad de Navarra-Clínica Universidad de Navarra, Pamplona, Spain
| | - U Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - T Mok
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - B S Sheffield
- Department of Pathology and Laboratory Medicine, William Osler Health System, Brampton, Canada
| | - A Tufman
- Department of Internal Medicine V, Thoracic Oncology Centre Munich, Ludwig Maximilian University, Munich; Comprehensive Pneumology Center Munich (CPC-M), Munich; German Center for Lung Research (DZL), Munich, Germany
| | - I I Wistuba
- Departments of Thoracic/Head and Neck Medical Oncology; Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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50
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Restrepo JC, Dueñas D, Corredor Z, Liscano Y. Advances in Genomic Data and Biomarkers: Revolutionizing NSCLC Diagnosis and Treatment. Cancers (Basel) 2023; 15:3474. [PMID: 37444584 DOI: 10.3390/cancers15133474] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is a significant public health concern with high mortality rates. Recent advancements in genomic data, bioinformatics tools, and the utilization of biomarkers have improved the possibilities for early diagnosis, effective treatment, and follow-up in NSCLC. Biomarkers play a crucial role in precision medicine by providing measurable indicators of disease characteristics, enabling tailored treatment strategies. The integration of big data and artificial intelligence (AI) further enhances the potential for personalized medicine through advanced biomarker analysis. However, challenges remain in the impact of new biomarkers on mortality and treatment efficacy due to limited evidence. Data analysis, interpretation, and the adoption of precision medicine approaches in clinical practice pose additional challenges and emphasize the integration of biomarkers with advanced technologies such as genomic data analysis and artificial intelligence (AI), which enhance the potential of precision medicine in NSCLC. Despite these obstacles, the integration of biomarkers into precision medicine has shown promising results in NSCLC, improving patient outcomes and enabling targeted therapies. Continued research and advancements in biomarker discovery, utilization, and evidence generation are necessary to overcome these challenges and further enhance the efficacy of precision medicine. Addressing these obstacles will contribute to the continued improvement of patient outcomes in non-small cell lung cancer.
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Affiliation(s)
- Juan Carlos Restrepo
- Grupo de Investigación en Salud Integral (GISI), Departamento Facultad de Salud, Universidad Santiago de Cali, Cali 760035, Colombia
| | - Diana Dueñas
- Grupo de Investigación en Salud Integral (GISI), Departamento Facultad de Salud, Universidad Santiago de Cali, Cali 760035, Colombia
| | - Zuray Corredor
- Grupo de Investigaciones en Odontología (GIOD), Facultad de Odontología, Universidad Cooperativa de Colombia, Pasto 520002, Colombia
- Facultad de Salud, Departamento de Ciencias Básicas, Universidad Libre, Cali 760026, Colombia
| | - Yamil Liscano
- Grupo de Investigación en Salud Integral (GISI), Departamento Facultad de Salud, Universidad Santiago de Cali, Cali 760035, Colombia
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