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Wallenta Law J, Bapat B, Sweetnam C, Mohammed H, McBratney A, Izano MA, Scannell Bryan M, Spencer S, Schroeder B, Hostin D, Simon GR, Berry AB. Real-World Impact of Comprehensive Genomic Profiling on Biomarker Detection, Receipt of Therapy, and Clinical Outcomes in Advanced Non-Small Cell Lung Cancer. JCO Precis Oncol 2024; 8:e2400075. [PMID: 38754057 DOI: 10.1200/po.24.00075] [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: 01/30/2024] [Revised: 03/13/2024] [Accepted: 03/29/2024] [Indexed: 05/18/2024] Open
Abstract
PURPOSE Therapeutic decision making for patients with advanced non-small cell lung cancer (aNSCLC) includes a growing number of options for genomic, biomarker-guided, targeted therapies. We compared actionable biomarker detection, targeted therapy receipt, and real-world overall survival (rwOS) in patients with aNSCLC tested with comprehensive genomic profiling (CGP) versus small panel testing (SP) in real-world community health systems. METHODS Patients older than 18 years diagnosed with aNSCLC between January 1, 2015, and December 31, 2020, who received biomarker testing were followed until death or study end (September 30, 2021), and categorized by most comprehensive testing during follow-up: SP (≤52 genes) or CGP (>52 genes). RESULTS Among 3,884 patients (median age, 68 years; 50% female; 73% non-Hispanic White), 20% received CGP and 80% SP. The proportion of patients with ≥one actionable biomarker (actionability) was significantly higher in CGP than in SP (32% v 14%; P < .001). Of patients with actionability, 43% (CGP) and 38% (SP) received matched therapies (P = .20). Among treated patients, CGP before first-line treatment was associated with higher likelihood of matched therapy in any line (odds ratio, 3.2 [95% CI, 1.84 to 5.53]). CGP testing (hazard ratio [HR], 0.80 [95% CI, 0.72 to 0.89]) and actionability (HR, 0.84 [95% CI, 0.77 to 0.91]) were associated with reduced risk of mortality. Among treated patients with actionability, matched therapy receipt showed improved median rwOS in months in CGP (34 [95% CI, 21 to 49] matched v 14 [95% CI, 10 to 18] unmatched) and SP (27 [95% CI, 21 to 43] matched v 10 [95% CI, 8 to 14] unmatched). CONCLUSION Patients who received CGP had improved detection of actionable biomarkers and greater use of matched therapies, both of which were associated with significant increases in survival.
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Anderson EC, DiPalazzo J, Lucas FL, Hall MJ, Antov A, Helbig P, Bourne J, Graham L, Gaitor L, Lu-Emerson C, Bradford LS, Inhorn R, Sinclair SJ, Brooks PL, Thomas CA, Rasmussen K, Han PKJ, Liu ET, Rueter J. Genome-matched treatments and patient outcomes in the Maine Cancer Genomics Initiative (MCGI). NPJ Precis Oncol 2024; 8:67. [PMID: 38461318 PMCID: PMC10924947 DOI: 10.1038/s41698-024-00547-4] [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: 06/11/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024] Open
Abstract
Genomic tumor testing (GTT) is an emerging technology aimed at identifying variants in tumors that can be targeted with genomically matched drugs. Due to limited resources, rural patients receiving care in community oncology settings may be less likely to benefit from GTT. We analyzed GTT results and observational clinical outcomes data from patients enrolled in the Maine Cancer Genomics Initiative (MCGI), which provided access to GTTs; clinician educational resources; and genomic tumor boards in community practices in a predominantly rural state. 1603 adult cancer patients completed enrollment; 1258 had at least one potentially actionable variant identified. 206 (16.4%) patients received a total of 240 genome matched treatments, of those treatments, 64% were FDA-approved in the tumor type, 27% FDA-approved in a different tumor type and 9% were given on a clinical trial. Using Inverse Probability of Treatment Weighting to adjust for baseline characteristics, a Cox proportional hazards model demonstrated that patients who received genome matched treatment were 31% less likely to die within 1 year compared to those who did not receive genome matched treatment (HR: 0.69; 95% CI: 0.52-0.90; p-value: 0.006). Overall, GTT through this initiative resulted in levels of genome matched treatment that were similar to other initiatives, however, clinical trials represented a smaller share of treatments than previously reported, and "off-label" treatments represented a greater share. Although this was an observational study, we found evidence for a potential 1-year survival benefit for patients who received genome matched treatments. These findings suggest that when disseminated and implemented with a supportive infrastructure, GTT may benefit cancer patients in rural community oncology settings, with further work remaining on providing genome-matched clinical trials.
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Affiliation(s)
- Eric C Anderson
- Center for Interdisciplinary Population and Health Research, MaineHealth Institute for Research, Portland, ME, USA
- Tufts University School of Medicine, Boston, MA, USA
| | - John DiPalazzo
- Center for Interdisciplinary Population and Health Research, MaineHealth Institute for Research, Portland, ME, USA
| | - F Lee Lucas
- Center for Interdisciplinary Population and Health Research, MaineHealth Institute for Research, Portland, ME, USA
| | | | | | | | | | | | | | | | - Leslie S Bradford
- Maine Medical Partners Women's Health, Gynecologic Oncology, Scarborough, ME, USA
| | - Roger Inhorn
- PenBay Medical Center Oncology, Rockport, ME, USA
| | | | | | | | | | - Paul K J Han
- Center for Interdisciplinary Population and Health Research, MaineHealth Institute for Research, Portland, ME, USA
- National Cancer Institute, Bethesda, MD, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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Gezelius H, Enblad AP, Lundmark A, Åberg M, Blom K, Rudfeldt J, Raine A, Harila A, Rendo V, Heinäniemi M, Andersson C, Nordlund J. Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening. NAR Genom Bioinform 2024; 6:lqae001. [PMID: 38288374 PMCID: PMC10823582 DOI: 10.1093/nargab/lqae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024] Open
Abstract
Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.
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Affiliation(s)
- Henrik Gezelius
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Anna Pia Enblad
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Women's and Children's Health, Uppsala University, Uppsala 751 85, Sweden
| | - Anders Lundmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Martin Åberg
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Clinical Chemistry and Pharmacology, Uppsala University Hospital, Uppsala 751 85, Sweden
| | - Kristin Blom
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Clinical Chemistry and Pharmacology, Uppsala University Hospital, Uppsala 751 85, Sweden
| | - Jakob Rudfeldt
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Clinical Chemistry and Pharmacology, Uppsala University Hospital, Uppsala 751 85, Sweden
| | - Amanda Raine
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Arja Harila
- Department of Women's and Children's Health, Uppsala University, Uppsala 751 85, Sweden
| | - Verónica Rendo
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 751 85, Sweden
| | - Merja Heinäniemi
- School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Claes Andersson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Clinical Chemistry and Pharmacology, Uppsala University Hospital, Uppsala 751 85, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
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Bottosso M, Mosele F, Michiels S, Cournède PH, Dogan S, Labaki C, André F. Moving toward precision medicine to predict drug sensitivity in patients with metastatic breast cancer. ESMO Open 2024; 9:102247. [PMID: 38401248 PMCID: PMC10982863 DOI: 10.1016/j.esmoop.2024.102247] [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: 07/29/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/26/2024] Open
Abstract
Tumor heterogeneity represents a major challenge in breast cancer, being associated with disease progression and treatment resistance. Precision medicine has been extensively applied to dissect tumor heterogeneity and, through a deeper molecular understanding of the disease, to personalize therapeutic strategies. In the last years, technological advances have widely improved the understanding of breast cancer biology and several trials have been developed to translate these new insights into clinical practice, with the ultimate aim of improving patients' outcomes. In the era of molecular oncology, genomics analyses and other methodologies are shaping a new treatment algorithm in breast cancer care. In this manuscript, we review the main steps of precision medicine to predict drug sensitivity in breast cancer from a translational point of view. Genomic developments and their clinical implications are discussed, along with technological advancements that could broaden precision medicine applications. Current achievements are put into perspective to provide an overview of the state-of-art of breast cancer precision oncology as well as to identify future research directions.
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Affiliation(s)
- M Bottosso
- INSERM Unit U981, Gustave Roussy Cancer Campus, Villejuif, France; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - F Mosele
- INSERM Unit U981, Gustave Roussy Cancer Campus, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif
| | - S Michiels
- Gustave Roussy, Department of Biostatistics and Epidemiology, Villejuif; Oncostat U1018, Inserm, Université Paris-Saclay, Ligue Contre le Cancer, Villejuif
| | - P-H Cournède
- Université Paris-Saclay, Centrale Supélec, Laboratory of Mathematics and Computer Science (MICS), Gif-Sur-Yvette, France
| | - S Dogan
- INSERM Unit U981, Gustave Roussy Cancer Campus, Villejuif, France
| | - C Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, USA
| | - F André
- INSERM Unit U981, Gustave Roussy Cancer Campus, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif; Paris Saclay University, Gif Sur-Yvette, France.
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Callegari AJ, Tsang J, Park S, Swartzfager D, Kapoor S, Choy K, Lim S. Multimodal machine learning models identify chemotherapy drugs with prospective clinical efficacy in dogs with relapsed B-cell lymphoma. Front Oncol 2024; 14:1304144. [PMID: 38390257 PMCID: PMC10881812 DOI: 10.3389/fonc.2024.1304144] [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: 09/29/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
Dogs with B-cell lymphoma typically respond well to first-line CHOP-based chemotherapy, but there is no standard of care for relapsed patients. To help veterinary oncologists select effective drugs for dogs with lymphoid malignancies such as B-cell lymphoma, we have developed multimodal machine learning models that integrate data from multiple tumor profiling modalities and predict the likelihood of a positive clinical response for 10 commonly used chemotherapy drugs. Here we report on clinical outcomes that occurred after oncologists received a prediction report generated by our models. Remarkably, we found that dogs that received drugs predicted to be effective by the models experienced better clinical outcomes by every metric we analyzed (overall response rate, complete response rate, duration of complete response, patient survival times) relative to other dogs in the study and relative to historical controls.
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Affiliation(s)
| | | | | | | | | | - Kevin Choy
- Department of Oncology, Blue Pearl Seattle Veterinary Specialist, Kirkland, WA, United States
| | - Sungwon Lim
- ImpriMed Inc., Mountain View, CA, United States
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Schmidt VF, Öcal O, Walther V, Fabritius MP, Dietrich O, Kazmierczak PM, Weiss L, Deniz S, Ümütlü MR, Puhr-Westerheide D, Wildgruber M, Ricke J, Seidensticker M. Clinical benefits of MRI-guided freehand biopsy of small focal liver lesions in comparison to CT guidance. Eur Radiol 2024:10.1007/s00330-024-10623-9. [PMID: 38319427 DOI: 10.1007/s00330-024-10623-9] [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: 08/24/2023] [Revised: 01/02/2024] [Accepted: 01/14/2024] [Indexed: 02/07/2024]
Abstract
OBJECTIVES To compare clinical success, procedure time, and complication rates between MRI-guided and CT-guided real-time biopsies of small focal liver lesions (FLL) < 20 mm. METHODS A comparison of a prospectively collected MRI-guided cohort (n = 30) to a retrospectively collected CT-guided cohort (n = 147) was performed, in which patients underwent real-time biopsies of small FLL < 20 mm in a freehand technique. In both groups, clinical and periprocedural data, including clinical success, procedure time, and complication rates (classified according to CIRSE guidelines), were analyzed. Wilcoxon rank sum test, Pearson's chi-squared test, and Fisher's exact test were used for statistical analysis. Additionally, propensity score matching (PSM) was performed using the following criteria for direct matching: age, gender, presence of liver cirrhosis, liver lobe, lesion diameter, and skin-to-target distance. RESULTS The median FLL diameter in the MRI-guided cohort was significantly smaller compared to CT guidance (p < 0.001; 11.0 mm vs. 16.3 mm), while the skin-to-target distance was significantly longer (p < 0.001; 90.0 mm vs. 74.0 mm). MRI-guided procedures revealed significantly higher clinical success compared to CT guidance (p = 0.021; 97% vs. 79%) as well as lower complication rates (p = 0.047; 0% vs. 13%). Total procedure time was significantly longer in the MRI-guided cohort (p < 0.001; 38 min vs. 28 min). After PSM (n = 24/n = 38), MRI-guided procedures still revealed significantly higher clinical success compared to CT guidance (p = 0.039; 96% vs. 74%). CONCLUSION Despite the longer procedure time, freehand biopsy of small FLL < 20 mm under MR guidance can be considered superior to CT guidance because of its high clinical success and low complication rates. CLINICAL RELEVANCE STATEMENT Biopsy of small liver lesions is challenging due to the size and conspicuity of the lesions on native images. MRI offers higher soft tissue contrast, which translates into a higher success of obtaining enough tissue material with MRI compared to CT-guided biopsies. KEY POINTS • Image-guided biopsy of small focal liver lesions (FLL) is challenging due to inadequate visualization, leading to sampling errors and false-negative biopsies. • MRI-guided real-time biopsy of FLL < 20 mm revealed significantly higher clinical success (p = 0.021; 97% vs. 79%) and lower complication rates (p = 0.047; 0% vs. 13%) compared to CT guidance. • Although the procedure time is longer, MRI-guided biopsy can be considered superior for small FLL < 20 mm.
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Affiliation(s)
- Vanessa F Schmidt
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany.
| | - Osman Öcal
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Viktoria Walther
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | | | - Olaf Dietrich
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | | | - Lena Weiss
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Sinan Deniz
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Muzzafer R Ümütlü
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | | | - Moritz Wildgruber
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Jens Ricke
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Max Seidensticker
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
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Popa AM, Stejeroiu MA, Iaciu C, Olaru M, Orlov Slavu C, Parosanu A, Stanciu IM, Pirlog C, Pavel S, Nitipir C. Role of Tumor Molecular Profiling With FoundationOne®CDx in Advanced Solid Tumors: A Single-Centre Experience From Romania. Cureus 2023; 15:e50709. [PMID: 38111812 PMCID: PMC10726298 DOI: 10.7759/cureus.50709] [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] [Accepted: 12/18/2023] [Indexed: 12/20/2023] Open
Abstract
Background In the field of precision oncology, comprehensive genomic profiling tests play a very important role by providing a complex understanding of the molecular characteristics of malignant tumors. Therefore, next-generation sequencing (NGS) has become a valuable tool in various aspects of cancer care from diagnosis and monitoring to treatment selection and personalized cancer treatment. Our aim was to evaluate the role of tumor molecular profiling in tailored treatment selection. Methods In our study, we conducted a retrospective analysis to assess the practicality of utilizing NGS testing in patients with metastatic solid tumors. The genomic testing was performed on blood or tissue samples from a fresh biopsy, less than six months old, and the expression of programmed death-ligand 1 was evaluated by immunohistochemistry. Results A total of 75 tests were performed on 66 patients between 2019 and 2022, with a success rate of 80%. The most common pathologies were gastro-intestinal tract cancer (26%), breast cancer (14%), non-small cell lung cancer (11%), and pancreatic cancer (11%). There were 9% liquid biopsies and 91% tissue biopsies. From all 66 patients tested, 55 had at least one genetic alteration. The most frequent genetic alteration found was TP53 (n=32) followed by KRAS (n=15) and BRCA1/2 (n=12) mutations. There were nine patients tested (14%) that presented a high tumor mutational burden, and only one patient presented high microsatellite instability. There were 37 patients (56%) with actionable alterations found from which 14 received matched therapy and four patients were enrolled in clinical trials. The NGS testing played a significant role in determining the next therapeutic strategy in 20 out of 66 patients (30.3%). Conclusion From all the patients included in our analysis, 83% had at least one mutation that is known to be of pathogenic significance but only 23% received treatment selected by the analysis of the tumor's genome, and only 6% were included in a clinical trial. This moderate success of personalized medicine using NGS testing highlights the importance of evaluating the factors that could lead to further improvement.
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Affiliation(s)
- Ana Maria Popa
- Medical Oncology, Elias Emergency University Hospital, Bucharest, ROU
| | | | - Cristian Iaciu
- Medical Oncology, Elias Emergency University Hospital, Bucharest, ROU
| | - Mihaela Olaru
- Medical Oncology, Elias Emergency University Hospital, Bucharest, ROU
| | | | - Andreea Parosanu
- Medical Oncology, Elias Emergency University Hospital, Bucharest, ROU
| | | | - Cristina Pirlog
- Medical Oncology, Elias Emergency University Hospital, Bucharest, ROU
| | - Simina Pavel
- Medical Oncology, Elias Emergency University Hospital, Bucharest, ROU
| | - Cornelia Nitipir
- Medical Oncology, Elias Emergency University Hospital, Bucharest, ROU
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Aldea M, Friboulet L, Apcher S, Jaulin F, Mosele F, Sourisseau T, Soria JC, Nikolaev S, André F. Precision medicine in the era of multi-omics: can the data tsunami guide rational treatment decision? ESMO Open 2023; 8:101642. [PMID: 37769400 PMCID: PMC10539962 DOI: 10.1016/j.esmoop.2023.101642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/30/2023] Open
Abstract
Precision medicine for cancer is rapidly moving to an approach that integrates multiple dimensions of the biology in order to model mechanisms of cancer progression in each patient. The discovery of multiple drivers per tumor challenges medical decision that faces several treatment options. Drug sensitivity depends on the actionability of the target, its clonal or subclonal origin and coexisting genomic alterations. Sequencing has revealed a large diversity of drivers emerging at treatment failure, which are potential targets for clinical trials or drug repurposing. To effectively prioritize therapies, it is essential to rank genomic alterations based on their proven actionability. Moving beyond primary drivers, the future of precision medicine necessitates acknowledging the intricate spatial and temporal heterogeneity inherent in cancer. The advent of abundant complex biological data will make artificial intelligence algorithms indispensable for thorough analysis. Here, we will discuss the advancements brought by the use of high-throughput genomics, the advantages and limitations of precision medicine studies and future perspectives in this field.
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Affiliation(s)
- M Aldea
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif.
| | | | - S Apcher
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Jaulin
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Mosele
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif
| | | | - J-C Soria
- Paris Saclay University, Orsay; Drug Development Department, Gustave Roussy, Villejuif, France
| | - S Nikolaev
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F André
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif; Paris Saclay University, Orsay
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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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Lam TC, Cho WCS, Au JSK, Ma ESK, Lam STS, Loong HHF, Wong JWH, Wong SM, Lee VHF, Leung RCY, Lau JKS, Kam MTY, Mok FST, Lim FMY, Nyaw JSF, Tin WWY, Cheung KM, Chan OSH, Kwong PWK, Cheung FY, Poon DM, Chik JYK, Lam MHC, Chan LWC, Wong SCC, Cao YB, Hui CV, Chen JZJ, Chang JH, Kong SFM, El Helali A. Consensus Statements on Precision Oncology in the China Greater Bay Area. JCO Precis Oncol 2023; 7:e2200649. [PMID: 37315266 PMCID: PMC10309548 DOI: 10.1200/po.22.00649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Next-generation sequencing comprehensive genomic panels (NGS CGPs) have enabled the delivery of tailor-made therapeutic approaches to improve survival outcomes in patients with cancer. Within the China Greater Bay Area (GBA), territorial differences in clinical practices and health care systems and strengthening collaboration warrant a regional consensus to consolidate the development and integration of precision oncology (PO). Therefore, the Precision Oncology Working Group (POWG) formulated standardized principles for the clinical application of molecular profiling, interpretation of genomic alterations, and alignment of actionable mutations with sequence-directed therapy to deliver clinical services of excellence and evidence-based care to patients with cancer in the China GBA. METHODS Thirty experts used a modified Delphi method. The evidence extracted to support the statements was graded according to the GRADE system and reported according to the Revised Standards for Quality Improvement Reporting Excellence guidelines, version 2.0. RESULTS The POWG reached consensus in six key statements: harmonization of reporting and quality assurance of NGS; molecular tumor board and clinical decision support systems for PO; education and training; research and real-world data collection, patient engagement, regulations, and financial reimbursement of PO treatment strategies; and clinical recommendations and implementation of PO in clinical practice. CONCLUSION POWG consensus statements standardize the clinical application of NGS CGPs, streamline the interpretation of clinically significant genomic alterations, and align actionable mutations with sequence-directed therapies. The POWG consensus statements may harmonize the utility and delivery of PO in China's GBA.
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Affiliation(s)
- Tai-Chung Lam
- Department of Clinical Oncology, Queen Mary Hospital/Hong Kong University-Shenzhen Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Joseph Siu-Kie Au
- Adventist Oncology Centre, Hong Kong Adventist Hospital, Hong Kong SAR, China
| | - Edmond Shiu-Kwan Ma
- Clinical and Molecular Pathology and Cancer Genetics Centre, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Stephen Tak-Sum Lam
- Clinical Genetic Service Centre, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Herbert Ho-Fung Loong
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jason Wing Hon Wong
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - S.N. Michael Wong
- Department of Clinical Oncology, Queen Mary Hospital/Hong Kong University-Shenzhen Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Victor Ho-Fun Lee
- Department of Clinical Oncology, Queen Mary Hospital/Hong Kong University-Shenzhen Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | | | - Michael Tsz-Yeung Kam
- Department of Clinical Oncology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR, China
| | | | - Fiona Mei-Ying Lim
- Department of Clinical Oncology, Princess Margaret Hospital, Hong Kong SAR, China
| | | | | | - Ka-Man Cheung
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | | | | | - Foon-Yiu Cheung
- Hong Kong International Oncology Centre, Hong Kong SAR, China
| | - Darren M.C. Poon
- Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | | | | | - Lawrence Wing-Chi Chan
- Department of Health Technology & Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Sze-Chuen Cesar Wong
- Department of Health Technology & Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Ya-Bing Cao
- Department of Radiology & Oncology, Kiang Wu Hospital, Macao SAR, China
| | - Cheng-Vai Hui
- Department of Clinical Oncology, Centro Hospitalar Conde de São Januário, Macao SAR, China
| | - Jack Zhi-Jian Chen
- Department of Radiation Oncology, Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen Center, Shenzhen, China
| | - Jian-Hua Chang
- Department of Medical Oncology, Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen Center, Shenzhen, China
| | - Spring Feng-Ming Kong
- Department of Clinical Oncology, Queen Mary Hospital/Hong Kong University-Shenzhen Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Aya El Helali
- Department of Clinical Oncology, Queen Mary Hospital/Hong Kong University-Shenzhen Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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11
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Shareef ZA, Hachim MY, Talaat IM, Bhamidimarri PM, Ershaid MNA, Ilce BY, Venkatachalam T, Eltayeb A, Hamoudi R, Hachim IY. DKK3's protective role in prostate cancer is partly due to the modulation of immune-related pathways. Front Immunol 2023; 14:978236. [PMID: 36845147 PMCID: PMC9947504 DOI: 10.3389/fimmu.2023.978236] [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: 06/25/2022] [Accepted: 01/03/2023] [Indexed: 02/11/2023] Open
Abstract
While it is considered one of the most common cancers and the leading cause of death in men worldwide, prognostic stratification and treatment modalities are still limited for patients with prostate cancer (PCa). Recently, the introduction of genomic profiling and the use of new techniques like next-generation sequencing (NGS) in many cancers provide novel tools for the discovery of new molecular targets that might improve our understanding of the genomic aberrations in PCa and the discovery of novel prognostic and therapeutic targets. In this study, we investigated the possible mechanisms through which Dickkopf-3 (DKK3) produces its possible protective role in PCa using NGS in both the DKK3 overexpression PCa cell line (PC3) model and our patient cohort consisting of nine PCa and five benign prostatic hyperplasia. Interestingly, our results have shown that DKK3 transfection-modulated genes are involved in the regulation of cell motility, senescence-associated secretory phenotype (SASP), and cytokine signaling in the immune system, as well as in the regulation of adaptive immune response. Further analysis of our NGS using our in vitro model revealed the presence of 36 differentially expressed genes (DEGs) between DKK3 transfected cells and PC3 empty vector. In addition, both CP and ACE2 genes were differentially expressed not only between the transfected and empty groups but also between the transfected and Mock cells. The top common DEGs between the DKK3 overexpression cell line and our patient cohort are the following: IL32, IRAK1, RIOK1, HIST1H2BB, SNORA31, AKR1B1, ACE2, and CP. The upregulated genes including IL32, HIST1H2BB, and SNORA31 showed tumor suppressor functions in various cancers including PCa. On the other hand, both IRAK1 and RIOK1 were downregulated and involved in tumor initiation, tumor progression, poor outcome, and radiotherapy resistance. Together, our results highlighted the possible role of the DKK3-related genes in protecting against PCa initiation and progression.
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Affiliation(s)
- Zainab Al Shareef
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Mahmood Y. Hachim
- College of Medicine, Mohammed bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Iman M. Talaat
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | | | - Mai Nidal Asad Ershaid
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Burcu Yener Ilce
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Thenmozhi Venkatachalam
- Department of Physiology and Immunology, College of Medicine and Health Science, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Abdulla Eltayeb
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Ibrahim Y. Hachim
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
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12
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Bayle A, Belcaid L, Aldea M, Vasseur D, Peyraud F, Nicotra C, Geraud A, Sakkal M, Seknazi L, Cerbone L, Blanc-Durand F, Hadoux J, Mosele F, Tagliamento M, Bernard-Tessier A, Verret B, Smolenschi C, Clodion R, Auger N, Romano PM, Gazzah A, Camus MN, Micol J, Caron O, Hollebecque A, Loriot Y, Besse B, Lacroix L, Rouleau E, Ponce S, Soria JC, Barlesi F, Andre F, Italiano A. Clinical utility of circulating tumor DNA sequencing with a large panel: a National Center for Precision Medicine (PRISM) study. Ann Oncol 2023; 34:389-396. [PMID: 36709039 DOI: 10.1016/j.annonc.2023.01.008] [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: 10/31/2022] [Revised: 12/10/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) sequencing is a promising approach for tailoring therapy in patients with cancer. We report hereby the results from a prospective study where we investigated the impact of comprehensive molecular profiling of ctDNA in patients with advanced solid tumors. PATIENTS AND METHODS Genomic analysis was performed using the FoundationOne Liquid CDx Assay [324 genes, tumor mutational burden (TMB), microsatellite instability status]. Each individual genomic report was reviewed and discussed weekly by a multidisciplinary tumor board (MTB). Actionable targets were classified by ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT) tier leading to molecular-based treatment suggestions wherever it was possible. RESULTS Between December 2020 and November 2021, 1772 patients with metastatic solid tumors underwent molecular profiling. Median time to assay results was 12 days. Results were contributive for 1658 patients (94%). At least one actionable target was detected in 1059 patients (64%) with a total of 1825 actionable alterations including alteration of the DNA damage repair response pathway (n = 336, 18%), high TMB (>16 mutations/Mb; n = 243, 13%), PIK3CA mutations (n = 150, 8%), ERBB family pathway alterations (n = 127, 7%), PTEN alterations (n = 95, 5%), FGFR alterations (n = 67, 4%) and MET activations (n = 13, 0.7%). The MTB recommended a matched therapy for 597 patients (56%) with a total of 819 therapeutic orientations: clinical trials (n = 639, 78%), off-label/compassionate use (n = 81, 10%), approved drug (n = 51, 6%), and early access program (n = 48, 6%). In total, 122 patients (21%) were treated. Among the assessable patients (n = 107), 4 (4%) had complete response, 35 (33%) had partial response, 27 (25%) had stable disease, and 41 (38%) a progressive disease as best response. The median progression-free survival and median overall survival were 4.7 months (95% confidence interval 2.7-6.7 months) and 8.3 months (95% confidence interval 4.7-11.9 months) respectively. CONCLUSIONS ctDNA sequencing with a large panel is an efficient approach to match patients with advanced cancer with targeted therapies.
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Affiliation(s)
- A Bayle
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif; Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Oncostat U1018, Inserm, Paris-Saclay University, labeled Ligue Contre le Cancer, Villejuif, France
| | - L Belcaid
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif; Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - M Aldea
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - D Vasseur
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - F Peyraud
- Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux
| | - C Nicotra
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - A Geraud
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - M Sakkal
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - L Seknazi
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - L Cerbone
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - F Blanc-Durand
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - J Hadoux
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - F Mosele
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - M Tagliamento
- Department of Cancer Medicine, Gustave Roussy, Villejuif
| | | | - B Verret
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - C Smolenschi
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - R Clodion
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - N Auger
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - P M Romano
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - A Gazzah
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - M N Camus
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - J Micol
- Department of Hematology, Gustave Roussy, Villejuif
| | - O Caron
- Department of Genetics, Gustave Roussy, Villejuif
| | - A Hollebecque
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - Y Loriot
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - B Besse
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - L Lacroix
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - E Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - S Ponce
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - J C Soria
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - F Barlesi
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - F Andre
- Université Paris-Saclay, Faculté de médecine, Le Kremlin Bicêtre, Paris; Department of Cancer Medicine, Gustave Roussy, Villejuif
| | - A Italiano
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif; Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux; Faculty of Medicine, University of Bordeaux, Bordeaux, France.
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13
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Personalized matched targeted therapy in advanced pancreatic cancer: a pilot cohort analysis. NPJ Genom Med 2023; 8:1. [PMID: 36670111 PMCID: PMC9860045 DOI: 10.1038/s41525-022-00346-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/07/2022] [Indexed: 01/21/2023] Open
Abstract
Despite progress, 2-year pancreatic cancer survival remains dismal. We evaluated a biomarker-driven, combination/N-of-one strategy in 18 patients (advanced/metastatic pancreatic cancer) (from Molecular Tumor Board). Targeted agents administered/patient = 2.5 (median) (range, 1-4); first-line therapy (N = 5); second line, (N = 13). Comparing patients (high versus low degrees of matching) (matching score ≥50% versus <50%; reflecting number of alterations matched to targeted agents divided by number of pathogenic alterations), survival was significantly longer (hazard ratio [HR] 0.24 (95% confidence interval [CI], 0.078-0.76, P = 0.016); clinical benefit rates (CBR) (stable disease ≥6 months/partial/complete response) trended higher (45.5 vs 0.0%, P = 0.10); progression-free survival, HR, 95% CI, 0.36 (0.12-1.10) (p = 0.075). First versus ≥2nd-line therapy had higher CBRs (80.0 vs 7.7%, P = 0.008). No grade 3-4 toxicities occurred. The longest responder achieved partial remission (17.5 months) by co-targeting MEK and CDK4/6 alterations (chemotherapy-free). Therefore, genomically matched targeted agent combinations were active in these advanced pancreatic cancers. Larger prospective trials are warranted.
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14
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Cifuentes C, Lombana M, Vargas H, Laguado P, Ruiz-Patiño A, Rojas L, Navarro U, Vargas C, Ricaurte L, Arrieta O, Zatarain-Barron L, Zapata L, González G, Ortiz C, Bernal L, Restrepo JG, Viola L, Grosso F, Zapata R, Mantilla W, Carranza H, Bustillo I, Llinas N, Duarte R, Rodríguez J, Archila P, Ávila J, Bermúdez M, Gámez T, Sotelo C, Otero J, Forero E, Lema M, Limpias C, Ordóñez-Reyes C, Mejía S, Rolfo C, Rosell R, Cardona AF. Application of Comprehensive Genomic Profiling-Based Next-Generation Sequencing Assay to Improve Cancer Care in a Developing Country. Cancer Control 2023; 30:10732748231175256. [PMID: 37148308 PMCID: PMC10164853 DOI: 10.1177/10732748231175256] [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: 05/08/2023] Open
Abstract
PURPOSE Identifying actionable oncogenic mutations have changed the therapeutic landscape in different types of tumors. This study investigated the utility of comprehensive genomic profiling (CGP), a hybrid capture-based next-generation sequencing (NGS) assay, in clinical practice in a developing country. METHODS In this retrospective cohort study, CGP was performed on clinical samples from patients with different solid tumors recruited between December 2016 and November 2020, using hybrid capture-based genomic profiling, at the individual treating physicians' request in the clinical care for therapy decisions. Kaplan-Meier survival curves were estimated to characterize the time-to-event variables. RESULTS Patients median age was 61 years (range: 14-87 years), and 64.7% were female. The most common histological diagnosis was lung primary tumors, with 90 patients corresponding to 52.9% of the samples (95% CI 45.4-60.4%). Actionable mutations with FDA-approved medications for specific alterations correspondent to tumoral histology were identified in 58 cases (46.4%), whereas other alterations were detected in 47 different samples (37.6%). The median overall survival was 15.5 months (95% CI 11.7 months-NR). Patients who were subjected to genomic evaluation at diagnosis reached a median overall survival of 18.3 months (95% CI 14.9 months-NR) compared to 14.1 months (95% CI 11.1 months-NR) in patients who obtained genomic evaluation after tumor progression and during standard treatment (P = .7). CONCLUSION CGP of different types of tumors identifies clinically relevant genomic alterations that have benefited from targeted therapy and improve cancer care in a developing country to guide personalized treatment to beneficial outcomes of cancer patients.
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Affiliation(s)
- Claudia Cifuentes
- Clinical Oncology Department, Hospital Universitario Mayor de Mederi, Bogotá, Colombia
| | - Milton Lombana
- Hematology and Oncology Department, Clínica de Occidente, Cali, Colombia
| | - Henry Vargas
- Oncology Department, Clínica Colsanitas, Bogotá, Colombia
| | - Paola Laguado
- Clinical Research Institute, Clínica del Country, Bogotá Colombia
| | - Alejandro Ruiz-Patiño
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Leonardo Rojas
- Oncology Department, Clínica Colsanitas, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Clinical Oncology Department, Clínica del Country, Bogotá, Colombia
| | - Uriel Navarro
- Clinical Oncology Department, Clínica General del Norte, Barranquilla, Colombia
| | - Carlos Vargas
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Clinical Oncology Department, Clínica del Country, Bogotá, Colombia
| | | | - Oscar Arrieta
- Thoracic Oncology Unit, National Cancer Institute (INCan), México City, México
| | | | - Leandro Zapata
- Oncology Department, San Vicente Fundación, Medellín, Colombia
| | - Guido González
- Centro Integral del Cáncer, Clínica de Occidente, Cali, Colombia
| | - Carlos Ortiz
- Clinical Oncology Department, Clínica del Country, Bogotá, Colombia
| | - Laura Bernal
- Oncology Department, Clínica Colsanitas, Bogotá, Colombia
- Clinical Oncology Department, Clínica Marly, Bogotá, Colombia
| | - Juan G Restrepo
- Oncology Department, Fundación Valle de Lili, Cali, Colombia
| | - Lucia Viola
- Thoracic Oncology Unit, Fundación Neumológica Colombiana, Bogotá, Colombia
| | - Fabio Grosso
- Oncology Department, Medical Plus, Bogotá, Colombia
| | - Ricardo Zapata
- Oncology Department, Clínica Cardio-VID, Medellín, Colombia
| | - William Mantilla
- Hematology and Oncology Department, Fundación Cardio Infantil, Bogotá, Colombia
| | - Hernán Carranza
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Clinical Oncology Department, Clínica del Country, Bogotá, Colombia
| | - Iván Bustillo
- Oncology Department, Clínica Porto Azul, Barranquilla, Colombia
| | - Néstor Llinas
- Oncology Department, Clínica Vida, Medellín, Colombia
| | - Ricardo Duarte
- Oncology Department, Clínica Colsanitas, Bogotá, Colombia
| | - July Rodríguez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Pilar Archila
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Jenny Ávila
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Maritza Bermúdez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Tatiana Gámez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Carolina Sotelo
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Jorge Otero
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Elkin Forero
- Clinical Oncology Department, Hospital Universitario Mayor de Mederi, Bogotá, Colombia
| | - Mauricio Lema
- Hematology and Oncology Department, Clínica Astorga, Medellín, Colombia
| | | | - Camila Ordóñez-Reyes
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Sergio Mejía
- Clinical Oncology Department, San Vicente Fundación, Medellín, Colombia
| | - Christian Rolfo
- Thoracic Oncology Center, Icahn School of Medicine at Mount Sinai Tisch Cáncer Center, Mount Sinai Hospital System, New York, NY, US
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Direction of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
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15
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Pinet S, Durand S, Perani A, Darnaud L, Amadjikpe F, Yon M, Darbas T, Vergnenegre A, Egenod T, Simonneau Y, Le Brun-Ly V, Pestre J, Venat L, Thuillier F, Chaunavel A, Duchesne M, Fermeaux V, Guyot A, Lacorre S, Bessette B, Lalloué F, Durand K, Deluche E. Clinical management of molecular alterations identified by high throughput sequencing in patients with advanced solid tumors in treatment failure: Real-world data from a French hospital. Front Oncol 2023; 13:1104659. [PMID: 36923436 PMCID: PMC10009270 DOI: 10.3389/fonc.2023.1104659] [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: 11/21/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
Background In the context of personalized medicine, screening patients to identify targetable molecular alterations is essential for therapeutic decisions such as inclusion in clinical trials, early access to therapies, or compassionate treatment. The objective of this study was to determine the real-world impact of routine incorporation of FoundationOne analysis in cancers with a poor prognosis and limited treatment options, or in those progressing after at least one course of standard therapy. Methods A FoundationOneCDx panel for solid tumor or liquid biopsy samples was offered to 204 eligible patients. Results Samples from 150 patients were processed for genomic testing, with a data acquisition success rate of 93%. The analysis identified 2419 gene alterations, with a median of 11 alterations per tumor (range, 0-86). The most common or likely pathogenic variants were on TP53, TERT, PI3KCA, CDKN2A/B, KRAS, CCDN1, FGF19, FGF3, and SMAD4. The median tumor mutation burden was three mutations/Mb (range, 0-117) in 143 patients with available data. Of 150 patients with known or likely pathogenic actionable alterations, 13 (8.6%) received matched targeted therapy. Sixty-nine patients underwent Molecular Tumor Board, which resulted in recommendations in 60 cases. Treatment with genotype-directed therapy had no impact on overall survival (13 months vs. 14 months; p = 0.95; hazard ratio = 1.04 (95% confidence interval, 0.48-2.26)]. Conclusions This study highlights that an organized center with a Multidisciplinary Molecular Tumor Board and an NGS screening system can obtain satisfactory results comparable with those of large centers for including patients in clinical trials.
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Affiliation(s)
- Sandra Pinet
- Medical Oncology Department, Dupuytren University Hospital, Limoges, France
| | - Stéphanie Durand
- The National Institute for Health and Medical Research (INSERM) U1308 - CAPTuR "Control Of Cell Activation, Tumor Progression and Therapeutic Resistance", Faculty of Medicine, University of Limoges, Limoges, France
| | - Alexandre Perani
- Cytogenetic, Medical Genetic and Reproductive Biology, Dupuytren University Hospital, Limoges, France
| | - Léa Darnaud
- Department of Pathology, Dupuytren University Hospital, Limoges, France
| | - Fifame Amadjikpe
- Department of Pathology, Dupuytren University Hospital, Limoges, France
| | - Mathieu Yon
- Department of Pathology, Dupuytren University Hospital, Limoges, France
| | - Tiffany Darbas
- Medical Oncology Department, Dupuytren University Hospital, Limoges, France
| | | | - Thomas Egenod
- Chest Department, Dupuytren University Hospital, Limoges, France
| | | | - Valérie Le Brun-Ly
- Medical Oncology Department, Dupuytren University Hospital, Limoges, France
| | - Julia Pestre
- Medical Oncology Department, Dupuytren University Hospital, Limoges, France
| | - Laurence Venat
- Medical Oncology Department, Dupuytren University Hospital, Limoges, France
| | - Frédéric Thuillier
- Medical Oncology Department, Dupuytren University Hospital, Limoges, France
| | - Alain Chaunavel
- The National Institute for Health and Medical Research (INSERM) U1308 - CAPTuR "Control Of Cell Activation, Tumor Progression and Therapeutic Resistance", Faculty of Medicine, University of Limoges, Limoges, France.,Department of Pathology, Dupuytren University Hospital, Limoges, France
| | - Mathilde Duchesne
- Department of Pathology, Dupuytren University Hospital, Limoges, France.,Research Unit (UR) 20218 - NEURIT "Neuropathies et Innovations Thérapeutiques", Faculty of Medicine, University of Limoges, Limoges, France
| | | | - Anne Guyot
- Department of Pathology, Dupuytren University Hospital, Limoges, France
| | - Sylvain Lacorre
- Department of Pathology, Dupuytren University Hospital, Limoges, France
| | - Barbara Bessette
- The National Institute for Health and Medical Research (INSERM) U1308 - CAPTuR "Control Of Cell Activation, Tumor Progression and Therapeutic Resistance", Faculty of Medicine, University of Limoges, Limoges, France
| | - Fabrice Lalloué
- The National Institute for Health and Medical Research (INSERM) U1308 - CAPTuR "Control Of Cell Activation, Tumor Progression and Therapeutic Resistance", Faculty of Medicine, University of Limoges, Limoges, France
| | - Karine Durand
- The National Institute for Health and Medical Research (INSERM) U1308 - CAPTuR "Control Of Cell Activation, Tumor Progression and Therapeutic Resistance", Faculty of Medicine, University of Limoges, Limoges, France.,Department of Pathology, Dupuytren University Hospital, Limoges, France
| | - Elise Deluche
- Medical Oncology Department, Dupuytren University Hospital, Limoges, France.,The National Institute for Health and Medical Research (INSERM) U1308 - CAPTuR "Control Of Cell Activation, Tumor Progression and Therapeutic Resistance", Faculty of Medicine, University of Limoges, Limoges, France
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16
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Implementation of Comprehensive Genomic Profiling in Ovarian Cancer Patients: A Retrospective Analysis. Cancers (Basel) 2022; 15:cancers15010218. [PMID: 36612212 PMCID: PMC9818378 DOI: 10.3390/cancers15010218] [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: 09/21/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Comprehensive genomic profiling (CGP) allows for the detection of driver alterations at high resolution, but the limited number of approved targeted therapies and their high costs have contributed to its limited clinical utilization. We retrospectively compared data of 946 women with ovarian cancer (11.4% were referred to CGP, and 88.6% served as control) to examine whether CGP provides a prognosis benefit. Patient baseline parameters were similar between the groups. Cox regression analysis adjusted for age, disease stage at diagnosis, and recurrence status showed statistically significantly longer median overall survival (mOS) in the CGP group versus the control (73.4 versus 54.5 months, p < 0.001). Fifty-four patients (52.9%) had actionable mutations with potential treatments; twenty-six (48.2%) were treated with matched targeted therapy, showing a trend for longer mOS than the eighty-six women in the CGP group who were not given a suggested treatment (105.5 versus 63.6 months, p = 0.066). None of the genomic alterations predicted metastasis location. CCNE1 amplification and KRAS mutations were associated with shorter mOS. Patients with tumor mutation burden ≥4 mutations/megabase had longer mOS. High loss of heterozygosity was associated with longer mOS (99.0 versus 48.2 months, p = 0.004). CGP testing may provide both prognostic and predictive insights for treatment of patients with ovarian cancer. Prospective studies of larger cohorts are warranted.
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17
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Tarawneh TS, Rodepeter FR, Teply-Szymanski J, Ross P, Koch V, Thölken C, Schäfer JA, Gremke N, Mack HID, Gold J, Riera-Knorrenschild J, Wilhelm C, Rinke A, Middeke M, Klemmer A, Romey M, Hattesohl A, Jesinghaus M, Görg C, Figiel J, Chung HR, Wündisch T, Neubauer A, Denkert C, Mack EKM. Combined Focused Next-Generation Sequencing Assays to Guide Precision Oncology in Solid Tumors: A Retrospective Analysis from an Institutional Molecular Tumor Board. Cancers (Basel) 2022; 14:4430. [PMID: 36139590 PMCID: PMC9496918 DOI: 10.3390/cancers14184430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Increasing knowledge of cancer biology and an expanding spectrum of molecularly targeted therapies provide the basis for precision oncology. Despite extensive gene diagnostics, previous reports indicate that less than 10% of patients benefit from this concept. METHODS We retrospectively analyzed all patients referred to our center's Molecular Tumor Board (MTB) from 2018 to 2021. Molecular testing by next-generation sequencing (NGS) included a 67-gene panel for the detection of short-sequence variants and copy-number alterations, a 53- or 137-gene fusion panel and an ultra-low-coverage whole-genome sequencing for the detection of additional copy-number alterations outside the panel's target regions. Immunohistochemistry for microsatellite instability and PD-L1 expression complemented NGS. RESULTS A total of 109 patients were referred to the MTB. In all, 78 patients received therapeutic proposals (70 based on NGS) and 33 were treated accordingly. Evaluable patients treated with MTB-recommended therapy (n = 30) had significantly longer progression-free survival than patients treated with other therapies (n = 17) (4.3 vs. 1.9 months, p = 0.0094). Seven patients treated with off-label regimens experienced major clinical benefits. CONCLUSION The combined focused sequencing assays detected targetable alterations in the majority of patients. Patient benefits appeared to lie in the same range as with large-scale sequencing approaches.
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Affiliation(s)
- Thomas S. Tarawneh
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Fiona R. Rodepeter
- Institute of Pathology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Julia Teply-Szymanski
- Institute of Pathology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Petra Ross
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Vera Koch
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
- Institute of Medical Bioinformatics and Biostatistics, Philipps-University Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
| | - Clemens Thölken
- Institute of Medical Bioinformatics and Biostatistics, Philipps-University Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
| | - Jonas A. Schäfer
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Niklas Gremke
- Department of Gynecology, Gynecologic Endocrinology and Oncology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Hildegard I. D. Mack
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Judith Gold
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Jorge Riera-Knorrenschild
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Christian Wilhelm
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Anja Rinke
- Department of Gastroenterology and Endocrinology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Martin Middeke
- Comprehensive Cancer Center Marburg, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Andreas Klemmer
- Department of Pulmonary and Critical Care Medicine, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Marcel Romey
- Institute of Pathology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Akira Hattesohl
- Institute of Pathology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Christian Görg
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
- Department of Gastroenterology and Endocrinology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Jens Figiel
- Department of Diagnostic and Interventional Radiology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Ho-Ryun Chung
- Institute of Medical Bioinformatics and Biostatistics, Philipps-University Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
| | - Thomas Wündisch
- Comprehensive Cancer Center Marburg, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Andreas Neubauer
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Carsten Denkert
- Institute of Pathology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
| | - Elisabeth K. M. Mack
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg, Baldingerstraße, 35043 Marburg, Germany
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18
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Molecular oncology: what is needed to speed access to innovative therapies in clinical research? Curr Opin Oncol 2022; 34:575-578. [PMID: 35855513 DOI: 10.1097/cco.0000000000000880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW A better understanding of the biology of cancer cells has led in the past 20 years to more and more molecular and immunological driven treatment strategies impacting both clinical trials and day-to-day practice. The aim of this review is to describe new approaches to conduct clinical trials in this area to speed up drug development and increase access to innovation for cancer patients. RECENT FINDINGS The design of an early phase trial has an impact on its clinical benefit. Trials deriving from a specific biomarker or histologic characteristic (also known as enrichment design) are more likely to demonstrate benefit than trials based on a more conventional design. However, the increase of low incidence cancer molecular subtypes poses a major hurdle in the clinical management and drug development research for cancer patients. SUMMARY With the identification of news targets and the subsequent introduction of precision medicine, new strategies and tools are needed to provide access to biomarker identification and target-oriented clinical trials to all cancer patients. We propose to set up a new patient-centered model to conduct clinical trials allowing simply to 'bring the trial to the patient'.
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Crimini E, Repetto M, Tarantino P, Ascione L, Antonarelli G, Rocco EG, Barberis M, Mazzarella L, Curigliano G. Challenges and Obstacles in Applying Therapeutical Indications Formulated in Molecular Tumor Boards. Cancers (Basel) 2022; 14:3193. [PMID: 35804968 PMCID: PMC9264928 DOI: 10.3390/cancers14133193] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Considering the rapid improvement of cancer drugs' efficacy and the discovery of new molecular targets, the formulation of therapeutical indications based on the multidisciplinary approach of MTB is becoming increasingly important for attributing the correct salience to the targets identified in a single patient. Nevertheless, one of the biggest stumbling blocks faced by MTBs is not the bare indication, but its implementation in the clinical practice. Indeed, administering the drug suggested by MTB deals with some relevant difficulties: the economical affordability and geographical accessibility represent some of the major limits in the patient's view, while bureaucracy and regulatory procedures are often a disincentive for the physicians. In this review, we explore the current literature reporting MTB experiences and precision medicine clinical trials, focusing on the challenges that authors face in applying their therapeutical indications. Furthermore, we analyze and discuss some of the solutions devised to overcome these difficulties to support the MTBs in finding the most suitable solution for their specific situation. In conclusion, we strongly encourage regulatory agencies and pharmaceutical companies to develop effective strategies with medical centers implementing MTBs to facilitate access to innovative drugs and thereby allow broader therapeutical opportunities to patients.
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Affiliation(s)
- Edoardo Crimini
- Division of Early Drug Development, European Institute of Oncology, IRCCS, 20141 Milan, Italy
- Department of Oncology and Hematology (DIPO), University of Milan, 20122 Milan, Italy
| | - Matteo Repetto
- Division of Early Drug Development, European Institute of Oncology, IRCCS, 20141 Milan, Italy
- Department of Oncology and Hematology (DIPO), University of Milan, 20122 Milan, Italy
| | - Paolo Tarantino
- Division of Early Drug Development, European Institute of Oncology, IRCCS, 20141 Milan, Italy
- Department of Oncology and Hematology (DIPO), University of Milan, 20122 Milan, Italy
| | - Liliana Ascione
- Division of Early Drug Development, European Institute of Oncology, IRCCS, 20141 Milan, Italy
- Department of Oncology and Hematology (DIPO), University of Milan, 20122 Milan, Italy
| | - Gabriele Antonarelli
- Division of Early Drug Development, European Institute of Oncology, IRCCS, 20141 Milan, Italy
- Department of Oncology and Hematology (DIPO), University of Milan, 20122 Milan, Italy
| | - Elena Guerini Rocco
- Department of Oncology and Hematology (DIPO), University of Milan, 20122 Milan, Italy
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Massimo Barberis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Luca Mazzarella
- Division of Early Drug Development, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Giuseppe Curigliano
- Division of Early Drug Development, European Institute of Oncology, IRCCS, 20141 Milan, Italy
- Department of Oncology and Hematology (DIPO), University of Milan, 20122 Milan, Italy
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20
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HER2 G776S mutation promotes oncogenic potential in colorectal cancer cells when accompanied by loss of APC function. Sci Rep 2022; 12:9213. [PMID: 35654814 PMCID: PMC9163061 DOI: 10.1038/s41598-022-13189-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 05/04/2022] [Indexed: 12/03/2022] Open
Abstract
Clinical cancer genome sequencing detects oncogenic variants that are potential targets for cancer treatment, but it also detects variants of unknown significance. These variants may interact with each other to influence tumor pathophysiology, however, such interactions have not been fully elucidated. Additionally, the effect of target therapy for those variants also unclarified. In this study, we investigated the biological functions of a HER2 mutation (G776S mutation) of unknown pathological significance, which was detected together with APC mutation by cancer genome sequencing of samples from a colorectal cancer (CRC) patient. Transfection of the HER2 G776S mutation alone slightly increased the kinase activity and phosphorylation of HER2 protein, but did not activate HER2 downstream signaling or alter the cell phenotype. On the other hand, the HER2 G776S mutation was shown to have strong oncogenic potential when loss of APC function was accompanied. We revealed that loss of APC function increased Wnt pathway activity but also increased RAS–GTP, which increased ERK phosphorylation triggered by HER2 G776S transfection. In addition, afatinib, a pan-HER tyrosine kinase inhibitor, suppressed tumor growth in xenografts derived from HER2 G776S-transfected CRC cells. These findings suggest that this HER2 mutation in CRC may be a potential therapeutic target.
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21
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Boichard A, Kurzrock R. Variable mutation expression in human cancers: A 'hide-and-seek' mechanism linked to differential MHC-I presentation dynamics. Mol Cancer Ther 2022; 21:1219-1226. [PMID: 35545005 DOI: 10.1158/1535-7163.mct-21-0831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022]
Abstract
Not all genomic mutations are expressed at the transcript/protein level, which may explain variation in cancer development, prognosis, and treatment response/resistance. In this study, our aim was to describe the prevalence of somatic mutation loss of expression ('variant silencing') in a large collection of human samples, and the potential impact of such variant silencing on tumor immunogenicity. Whole-exome mutation description and tumor-normal paired mRNA expression data originating from 636 unique patients diagnosed with 21 distinct tumor types (all solid tumors) were retrieved from The Cancer Genome Atlas (TCGA). Antigenicity and immunogenicity of neo-peptides originating from mutated proteins within a same tumor sample were predicted using the tools available from the Immune Epitope Database (IEDB). A total of 65,072 missense mutations were studied. We demonstrated that 9.06% (N=10,604 silenced/117,505 total variants) somatic variants were silenced in human tumors. Transciptomic silencing is significantly associated with proteins presenting better peptide processing, MHC-I binding, and T-cell recognition; and is more likely observed in lymphocyte-depleted tumors. Silencing may participate in tumor resistance by clonal selection and immune evasion. In the era of precision medicine, we suggest that therapeutic choices should be informed by both the presence of a genomic mutation and its actual transcript expression.
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Affiliation(s)
| | - Razelle Kurzrock
- Worldwide Innovative Network (WIN) for Personalized Cancer Therapy, Villejuif, France
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22
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Caputo V, De Falco V, Ventriglia A, Famiglietti V, Martinelli E, Morgillo F, Martini G, Corte CMD, Ciardiello D, Poliero L, De Vita F, Orditura M, Fasano M, Franco R, Caraglia M, Avitabile A, Scalamogna R, Marchi B, Ciardiello F, Troiani T, Napolitano S. Comprehensive genome profiling by next generation sequencing of circulating tumor DNA in solid tumors: a single academic institution experience. Ther Adv Med Oncol 2022; 14:17588359221096878. [PMID: 35547096 PMCID: PMC9082754 DOI: 10.1177/17588359221096878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 04/07/2022] [Indexed: 01/18/2023] Open
Abstract
Background: Recently, new evidence of the next-generation sequencing (NGS) liquid biopsy utility in clinical practice has been developed. This assay is emerging as a new promising tool to use as a noninvasive biomarker for cancer mutation profiling. Additional data supporting the clinical validity of cell free DNA (cfDNA) based testing is necessary to inform optimal use of these assays in the clinic. Materials and methods: A total of 398 cancer patients were analyzed by FoundationOne Liquid Analysis (F1LA), a genomic profiling assay and by standard NGS diagnostic ThermoFisher platform. The association between diagnostic technique was evaluated using a Poisson regression model. FoundationOne Liquid (F1L) and FoundationOne Liquid CDx (F1LCDx) detect 70 and 324 cancer-related genes alterations, respectively, including genomic signatures tumor fraction, blood tumor mutational burden (only for the 324 genes version), and microsatellite instability high status. Both assays used a single DNA extraction method to obtain cfDNA. The real-life clinical impact and feasibility of F1L and F1LCDx were evaluated across different solid tumors in our department. Results: Between 1 January 2019 and 28 February 2021, 398 samples of different tumor types from 398 patients were analyzed (overall success rate: 92%, in FoundationOne Liquid CDx Analysis success rate: 97%). Most frequent molecular alterations were TP53 (74), APC (40), DNMT3A (39), KRAS (23). The comprehensive clinical impact of F1LA compared with standard diagnostic was 64.7% versus 22.1% [risk ratio (RR) = 2.94; p < 0.001] and the potential clinical impact was 58.6% versus 11.0% (RR = 5.32; p < 0.001), respectively. Furthermore, some clinical cases were selected, in which F1LA detected actionable alterations offering an unexpected therapeutic choice. Conclusions: Although additional studies are needed to better select patients and setting, NGS F1LA is a useful, noninvasive, and repeatable assay to guide therapeutic choice in oncology. It provides a snapshot of cancer heterogeneity profile that could be incorporated in routinely clinical practice.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Vincenzo De Falco
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Anna Ventriglia
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Vincenzo Famiglietti
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Erika Martinelli
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Floriana Morgillo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Davide Ciardiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
- Oncology Unit, Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Luca Poliero
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Ferdinando De Vita
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Michele Orditura
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Morena Fasano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Michele Caraglia
- Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | | | | | | | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Napoli, Italy
| | - Teresa Troiani
- Full Professor, Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Via S. Pansini 5, Napoli 80131, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, Via S. Pansini 5, Napoli 80131, Italy
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23
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Milbury CA, Creeden J, Yip WK, Smith DL, Pattani V, Maxwell K, Sawchyn B, Gjoerup O, Meng W, Skoletsky J, Concepcion AD, Tang Y, Bai X, Dewal N, Ma P, Bailey ST, Thornton J, Pavlick DC, Frampton GM, Lieber D, White J, Burns C, Vietz C. Clinical and analytical validation of FoundationOne®CDx, a comprehensive genomic profiling assay for solid tumors. PLoS One 2022; 17:e0264138. [PMID: 35294956 PMCID: PMC8926248 DOI: 10.1371/journal.pone.0264138] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
FoundationOne®CDx (F1CDx) is a United States (US) Food and Drug Administration (FDA)-approved companion diagnostic test to identify patients who may benefit from treatment in accordance with the approved therapeutic product labeling for 28 drug therapies. F1CDx utilizes next-generation sequencing (NGS)-based comprehensive genomic profiling (CGP) technology to examine 324 cancer genes in solid tumors. F1CDx reports known and likely pathogenic short variants (SVs), copy number alterations (CNAs), and select rearrangements, as well as complex biomarkers including tumor mutational burden (TMB) and microsatellite instability (MSI), in addition to genomic loss of heterozygosity (gLOH) in ovarian cancer. CGP services can reduce the complexity of biomarker testing, enabling precision medicine to improve treatment decision-making and outcomes for cancer patients, but only if test results are reliable, accurate, and validated clinically and analytically to the highest standard available. The analyses presented herein demonstrate the extensive analytical and clinical validation supporting the F1CDx initial and subsequent FDA approvals to ensure high sensitivity, specificity, and reliability of the data reported. The analytical validation included several in-depth evaluations of F1CDx assay performance including limit of detection (LoD), limit of blank (LoB), precision, and orthogonal concordance for SVs (including base substitutions [SUBs] and insertions/deletions [INDELs]), CNAs (including amplifications and homozygous deletions), genomic rearrangements, and select complex biomarkers. The assay validation of >30,000 test results comprises a considerable and increasing body of evidence that supports the clinical utility of F1CDx to match patients with solid tumors to targeted therapies or immunotherapies based on their tumor’s genomic alterations and biomarkers. F1CDx meets the clinical needs of providers and patients to receive guideline-based biomarker testing, helping them keep pace with a rapidly evolving field of medicine.
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Affiliation(s)
- Coren A. Milbury
- Department Product Development, Cambridge, MA, United States of America
| | - James Creeden
- Global Medical Affairs, Basel, MA, United States of America
- * E-mail:
| | - Wai-Ki Yip
- Department Product Development, Cambridge, MA, United States of America
| | - David L. Smith
- Department of Franchise Development, Cambridge, MA, United States of America
| | - Varun Pattani
- Department Product Development, Cambridge, MA, United States of America
| | - Kristi Maxwell
- Department of Health Economic and Outcomes Research & Payer Policy, Reimbursement, Cambridge, MA, United States of America
| | - Bethany Sawchyn
- Department of Scientific and Medical Publications, Clinical Operations, Cambridge, MA, United States of America
| | - Ole Gjoerup
- Department of Scientific and Medical Publications, Clinical Operations, Cambridge, MA, United States of America
| | - Wei Meng
- Department Product Development, Cambridge, MA, United States of America
| | - Joel Skoletsky
- Department Product Development, Cambridge, MA, United States of America
| | | | - Yanhua Tang
- Department Product Development, Cambridge, MA, United States of America
| | - Xiaobo Bai
- Department Product Development, Cambridge, MA, United States of America
| | - Ninad Dewal
- Department Product Development, Cambridge, MA, United States of America
| | - Pei Ma
- Department Product Development, Cambridge, MA, United States of America
| | - Shannon T. Bailey
- Department Product Development, Cambridge, MA, United States of America
| | - James Thornton
- Department Product Development, Cambridge, MA, United States of America
| | - Dean C. Pavlick
- Department of Cancer Genomics, Cambridge, MA, United States of America
| | | | - Daniel Lieber
- Department of Computational Biology, Cambridge, MA, United States of America
| | - Jared White
- Department of Computational Biology, Cambridge, MA, United States of America
| | - Christine Burns
- Department Product Development, Cambridge, MA, United States of America
| | - Christine Vietz
- Department Product Development, Cambridge, MA, United States of America
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24
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Mathew A, Joseph S, Boby J, Benny S, Veedu J, Rajappa S, Rohatgi N, Sirohi B, Jain R, Agarwala V, Shukla DK, Mehta A, Pramanik R, Talwar V, Maka V, Raut N. Clinical Benefit of Comprehensive Genomic Profiling for Advanced Cancers in India. JCO Glob Oncol 2022; 8:e2100421. [PMID: 35404667 PMCID: PMC9200397 DOI: 10.1200/go.21.00421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Comprehensive genomic profiling (CGP) assay is increasingly used in low-middle–income countries to detect clinically relevant genomic alterations despite its clinical benefits not being well known. Here, we describe the proportion of patients with advanced cancer in India who received targeted therapy for an actionable genetic alteration identified on CGP assays. Genomic profiling assay study from India showcases both the promise and limitations of testing in advanced cancers. 10% of patients who were tested got a targeted drug. 4% took it for at least 6 months.![]()
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Affiliation(s)
- Aju Mathew
- MOSC Medical College, Kolenchery, Ernakulam, Ernakulam, India
| | - Serena Joseph
- MOSC Medical College, Kolenchery, Ernakulam, Ernakulam, India
| | | | | | | | - Senthil Rajappa
- Indo American Cancer Hospital and Research Institute, Hyderabad, India
| | | | | | | | | | | | - Anurag Mehta
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Raja Pramanik
- All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Talwar
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | | | - Nirmal Raut
- Bhaktivedanta Hospital and Research Centre, Mumbai, India
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25
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Gupta D, Kurzrock R, Lee S, Okamura R, Lim HJ, Kim KH, Sicklick JK, Kato S. Case series of outcomes in advanced cancer patients with single pathway alterations receiving N-of-One therapies. NPJ Precis Oncol 2022; 6:18. [PMID: 35347205 PMCID: PMC8960821 DOI: 10.1038/s41698-022-00259-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/11/2022] [Indexed: 12/11/2022] Open
Abstract
Though advanced cancers generally display complex molecular portfolios, there is a subset of patients whose malignancies possess only one genomic alteration or alterations in one oncogenic pathway. We assess how N-of-One therapeutic strategies impact outcomes in these patients. From 12/2012 to 9/2018, 429 therapy-evaluable patients with diverse treatment-refractory cancers were presented at Molecular Tumor Boards at Moores Cancer Center at UC San Diego. The clinical benefit rate, defined by RECIST1.1, was assessed for patients with solid tumors who underwent next-generation sequencing (NGS) profiling revealing one genomic or pathway alteration, subsequently managed with N-of-One therapies. Nine of 429 patients (2.1%) met evaluation criteria. Using matched therapy indicated by NGS, the clinical benefit rate (stable disease ≥ 6 months/partial/complete response) was 66.7%. Median progression-free survival was 11.3 months (95% CI: 3.4–not evaluable). Thus, a small subset of diverse cancers has single pathway alterations on NGS testing. These patients may benefit from customized therapeutic matching.
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Affiliation(s)
- Diviya Gupta
- School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Razelle Kurzrock
- School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Center for Personalized Cancer Therapy, UC San Diego Moores Cancer Center, La Jolla, CA, USA. .,Division of Hematology/Oncology, UC San Diego, San Diego, CA, USA.
| | - Suzanna Lee
- Center for Personalized Cancer Therapy, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy, UC San Diego Moores Cancer Center, La Jolla, CA, USA.,Division of Hematology/Oncology, UC San Diego, San Diego, CA, USA
| | - Hyo Jeong Lim
- Department of Internal Medicine, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Ki Hwan Kim
- Division of Hematology and Medical Oncology, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Jason K Sicklick
- School of Medicine, University of California San Diego, La Jolla, CA, USA.,Center for Personalized Cancer Therapy, UC San Diego Moores Cancer Center, La Jolla, CA, USA.,Department of Surgery, Division of Surgical Oncology, UC San Diego, San Diego, CA, USA
| | - Shumei Kato
- School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Center for Personalized Cancer Therapy, UC San Diego Moores Cancer Center, La Jolla, CA, USA. .,Division of Hematology/Oncology, UC San Diego, San Diego, CA, USA.
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Assessment of a cancer genomic profile test for patients with metastatic breast cancer. Sci Rep 2022; 12:4813. [PMID: 35315838 PMCID: PMC8938506 DOI: 10.1038/s41598-022-08925-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
Comprehensive cancer genomic profile (CGP) tests are being implemented under Japanese universal health insurance system. However, the clinical usefulness of CGP test for breast cancer patients has not been evaluated. Of the 310 patients who underwent CGP testing at our institution between November 2019 and April 2021, 35 patients with metastatic breast cancer whose treatment strategy was discussed by our molecular tumor board within the study period were investigated after exclusion of 2 cases that could not be analyzed. The turn-around time, drug accessibility, and germline identification detection were evaluated. The subtype was luminal in 20 patients (57.1%), triple-negative in 12 patients (34.3%), and luminal-HER2 in 3 patients (8.6%). Actionable gene mutations were detected in 30 patients (85.7%), and 7 patients (20.0%) were recommended for clinical trial participation, with the drug administered to 2 patients (5.7%). Three patients (8.6%) died due to disease progression before the test results were disclosed. We report the results of an initial assessment of the utility of CGP testing for patients with metastatic breast cancer under Japanese universal health insurance system. Conducting CGP tests at a more appropriate time could provide patients with greater benefit from treatments based on their specific gene mutations.
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Clinical Impact of High Throughput Sequencing on Liquid Biopsy in Advanced Solid Cancer. Curr Oncol 2022; 29:1902-1918. [PMID: 35323355 PMCID: PMC8947301 DOI: 10.3390/curroncol29030155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/31/2022] Open
Abstract
Background: Cancer therapies targeting actionable molecular alterations (AMA) have developed, but the clinical routine impact of high-throughput molecular profiling remains unclear. We present a monocentric experience of molecular profiling based on liquid biopsy in patients with cancer. Methods: Patients included had solid cancer and underwent cfDNA genomic profiling with FoudationOne Liquid CDx (F1LCDx) test, analyzing 324 genes. Primary endpoint was to describe patients with an AMA for whom clinical decisions were impacted by F1LCDx test results. Results: 191 patients were included, mostly with lung cancer (46%). An AMA was found in 52%. The most common molecular alterations were: TP53 (52%), KRAS (14%) and DNMT3 (11%). The most common AMA were: CHEK2 (10%), PIK3CA (9%), ATM (7%). There was no difference in progression-free survival (2.66 months vs. 3.81 months, p = 0.17), overall survival (5.3 months vs. 7.1 months, p = 0.64), or PFS2/PFS1 ratio ≥ 1.3 (20% vs. 24%, p = 0.72) between patients receiving a molecularly matched therapy (MMT) or a non-MMT, respectively. Patients with a MMT had an overall response rate of 19% and a disease control of 32%. Conclusions: Routine cfDNA molecular profiling is feasible and can lead to the access of targeted therapies. However, no notable benefit in patient’s outcomes was shown in this unselected pan-cancer study.
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Kornauth C, Pemovska T, Vladimer GI, Bayer G, Bergmann M, Eder S, Eichner R, Erl M, Esterbauer H, Exner R, Felsleitner-Hauer V, Forte M, Gaiger A, Geissler K, Greinix HT, Gstöttner W, Hacker M, Hartmann BL, Hauswirth AW, Heinemann T, Heintel D, Hoda MA, Hopfinger G, Jaeger U, Kazianka L, Kenner L, Kiesewetter B, Krall N, Krajnik G, Kubicek S, Le T, Lubowitzki S, Mayerhoefer ME, Menschel E, Merkel O, Miura K, Müllauer L, Neumeister P, Noesslinger T, Ocko K, Öhler L, Panny M, Pichler A, Porpaczy E, Prager GW, Raderer M, Ristl R, Ruckser R, Salamon J, Schiefer AI, Schmolke AS, Schwarzinger I, Selzer E, Sillaber C, Skrabs C, Sperr WR, Srndic I, Thalhammer R, Valent P, van der Kouwe E, Vanura K, Vogt S, Waldstein C, Wolf D, Zielinski CC, Zojer N, Simonitsch-Klupp I, Superti-Furga G, Snijder B, Staber PB. Functional Precision Medicine Provides Clinical Benefit in Advanced Aggressive Hematologic Cancers and Identifies Exceptional Responders. Cancer Discov 2022; 12:372-387. [PMID: 34635570 PMCID: PMC9762339 DOI: 10.1158/2159-8290.cd-21-0538] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/22/2021] [Accepted: 09/24/2021] [Indexed: 01/07/2023]
Abstract
Personalized medicine aims to match the right drug with the right patient by using specific features of the individual patient's tumor. However, current strategies of personalized therapy matching provide treatment opportunities for less than 10% of patients with cancer. A promising method may be drug profiling of patient biopsy specimens with single-cell resolution to directly quantify drug effects. We prospectively tested an image-based single-cell functional precision medicine (scFPM) approach to guide treatments in 143 patients with advanced aggressive hematologic cancers. Fifty-six patients (39%) were treated according to scFPM results. At a median follow-up of 23.9 months, 30 patients (54%) demonstrated a clinical benefit of more than 1.3-fold enhanced progression-free survival compared with their previous therapy. Twelve patients (40% of responders) experienced exceptional responses lasting three times longer than expected for their respective disease. We conclude that therapy matching by scFPM is clinically feasible and effective in advanced aggressive hematologic cancers. SIGNIFICANCE: This is the first precision medicine trial using a functional assay to instruct n-of-one therapies in oncology. It illustrates that for patients lacking standard therapies, high-content assay-based scFPM can have a significant value in clinical therapy guidance based on functional dependencies of each patient's cancer.See related commentary by Letai, p. 290.This article is highlighted in the In This Issue feature, p. 275.
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Affiliation(s)
- Christoph Kornauth
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center Vienna, Medical University of Vienna and Vienna General Hospital, Vienna, Austria
| | - Tea Pemovska
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gregory I Vladimer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Exscientia GmbH, Vienna, Austria
| | - Günther Bayer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Michael Bergmann
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Sandra Eder
- Department of Internal Medicine and Hematology/Oncology, Klinikum Klagenfurt, Klagenfurt, Austria
| | - Ruth Eichner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Martin Erl
- Abteilung für Innere Medizin, Krankenhaus der Barmherzigen Brüder Salzburg, Salzburg, Austria
| | - Harald Esterbauer
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Ruth Exner
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | | | - Maurizio Forte
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Alexander Gaiger
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center Vienna, Medical University of Vienna and Vienna General Hospital, Vienna, Austria
| | - Klaus Geissler
- Medical School, Sigmund Freud University, Vienna, Austria
| | - Hildegard T Greinix
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Wolfgang Gstöttner
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Marcus Hacker
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | | | - Alexander W Hauswirth
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Tim Heinemann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Heintel
- Division of Medicine I, Klinik Ottakring, Vienna, Austria
| | - Mir Alireza Hoda
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Georg Hopfinger
- Third Medical Department, Centre for Oncology and Haematology, Klinik Favoriten, Vienna, Austria
| | - Ulrich Jaeger
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center Vienna, Medical University of Vienna and Vienna General Hospital, Vienna, Austria
| | - Lukas Kazianka
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Barbara Kiesewetter
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Nikolaus Krall
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Exscientia GmbH, Vienna, Austria
| | - Gerhard Krajnik
- Department of Medicine I, Universitätsklinikum St. Pölten, St. Pölten, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Trang Le
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Simone Lubowitzki
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Marius E Mayerhoefer
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisabeth Menschel
- Third Medical Department, Hematology & Oncology, Hanusch Hospital, Vienna, Austria
| | - Olaf Merkel
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Katsuhiro Miura
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Peter Neumeister
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Thomas Noesslinger
- Third Medical Department, Hematology & Oncology, Hanusch Hospital, Vienna, Austria
| | - Katharina Ocko
- Pharmacy Department, Vienna General Hospital, Vienna, Austria
| | - Leopold Öhler
- Internal Medicine I, Department of Oncology, St. Josef Hospital, Vienna, Austria
| | - Michael Panny
- Third Medical Department, Hematology & Oncology, Hanusch Hospital, Vienna, Austria
| | - Alexander Pichler
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Edit Porpaczy
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Gerald W Prager
- Comprehensive Cancer Center Vienna, Medical University of Vienna and Vienna General Hospital, Vienna, Austria
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Markus Raderer
- Comprehensive Cancer Center Vienna, Medical University of Vienna and Vienna General Hospital, Vienna, Austria
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Robin Ristl
- Section for Medical Statistics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | | | - Julius Salamon
- Department of Medicine, Landesklinikum Waidhofen a.d. Ybbs, Waidhofen-Ybbs, Austria
| | - Ana-Iris Schiefer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Ann-Sofie Schmolke
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Ilse Schwarzinger
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Edgar Selzer
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
| | - Christian Sillaber
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Cathrin Skrabs
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang R Sperr
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Ismet Srndic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Renate Thalhammer
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Peter Valent
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Emiel van der Kouwe
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Katrina Vanura
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Stefan Vogt
- Department of Medicine and Oncology, LKH Wiener Neustadt, Wiener Neustadt, Austria
| | - Cora Waldstein
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
| | - Dominik Wolf
- Department of Internal Medicine V, Department of Hematology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Niklas Zojer
- Division of Medicine I, Klinik Ottakring, Vienna, Austria
| | | | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Berend Snijder
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Philipp B Staber
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center Vienna, Medical University of Vienna and Vienna General Hospital, Vienna, Austria
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Szeto C, Kurzrock R, Kato S, Goloubev A, Veerapaneni S, Preble A, Reddy S, Adashek J. Association of differential expression of immunoregulatory molecules and presence of targetable mutations may inform rational design of clinical trials. ESMO Open 2022; 7:100396. [PMID: 35158206 PMCID: PMC8850727 DOI: 10.1016/j.esmoop.2022.100396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/07/2021] [Accepted: 01/03/2022] [Indexed: 12/31/2022] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) and genomic biomarker-driven targeted therapies have revolutionized the modern oncologic treatment arsenal. The next step has been to combine targeted agents and ICIs. In doing so, some combination regimens may be more logical than others. Patients and methods Whole-exome and whole-transcriptome sequencing were performed on 2739 unselected later-stage clinical cases from 24 solid tumor subtypes in the NantHealth database, and data were also curated from 5746 similarly sequenced patients across 28 solid tumor subtypes in The Cancer Genome Atlas (TCGA). Significant differential expression of 10 immunoregulatory molecules [IRMs (genes)] was analyzed for association with mutant versus wild-type genes. Results Twenty-three significant associations between currently actionable variants and RNA-expressed checkpoint genes were identified in the TCGA cases; 10 were validated in the external cohort of 2739 clinical cases from NantHealth (P values were adjusted using Benjamini–Hochberg multiple hypothesis correction to reduce false-discovery rate). Within the same 5746 TCGA profiles, 2740 TCGA patients were identified as having one or more potentially oncogenic single-nucleotide variant (SNV) mutation within an established 50-gene hotspot panel. Of the 50 genes, SNVs within 15 were found to be significantly associated with differential expression of at least one IRM after adjusting for tissue enrichment; six were confirmed significant associations in an independent set of 2739 clinical cases from NantHealth. Conclusions Logically combining ICIs with targeted therapies may offer unique treatment strategies for patients with cancer. The presence of specific mutations impacts the expression of IRMs, an observation of potential importance for selecting combinations of gene- and immune-targeted therapeutics. Altered actionable genes correlated with specific checkpoint transcripts. Associations between IRMs and altered genes were validated in independent datasets. Combining immune- and gene-targeted drugs based on IRM/gene correlations merits study.
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Choucair K, Mattar BI, Van Truong Q, Koeneke T, Van Truong P, Dakhil C, Cannon MW, Page SJ, Deutsch JM, Carlson E, Moore DF, Nabbout NH, Kallail KJ, Dakhil SR, Reddy PS. OUP accepted manuscript. Oncologist 2022; 27:183-190. [PMID: 35274713 PMCID: PMC8914479 DOI: 10.1093/oncolo/oyac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/16/2021] [Indexed: 11/14/2022] Open
Abstract
Background Liquid biopsy testing offers a significant potential in selecting signal-matched therapies for advanced solid malignancies. The feasibility of liquid biopsy testing in a community-based oncology practice, and its actual impact on selecting signal-matched therapies, and subsequent survival effects have not previously been reported. Patients and Methods A retrospective chart review was conducted on adult patients with advanced solid cancer tested with a liquid-biopsy assay between December 2018 and 2019, in a community oncology practice. The impact of testing on treatment assignment and survival was assessed at 1-year follow-up. Results A total of 178 patients underwent testing. A positive test was reported in 140/178 patients (78.7%), of whom 75% had an actionable mutation. The actual overall signal-based matching rate was 17.8%. While 85.7% of patients with no actionable mutation had a signal-based clinical trial opportunity, only 10% were referred to a trial. Survival analysis of lung, breast, and colorectal cancer patients with actionable mutations who received any therapy (n = 66) revealed a survival advantage for target-matched (n = 22) compared to unmatched therapy (n = 44): patients who received matched therapy had significantly longer progression-free survival (PFS) (mPFS: 12 months; 95%CI, 10.6-13.4 vs. 5.0 months; 95%CI, 3.4-6.6; P = .029), with a tendency towards longer overall survival (OS) (mOS: 15 months; 95%CI, 13.5-16.5 vs. 13 months; 95%CI: 11.3-14.7; P = .087). Conclusions Implementation of liquid biopsy testing is feasible in a US community practice and impacts therapeutic choices in patients with advanced malignancies. Receipt of liquid biopsy-generated signal-matched therapies conferred added survival benefits.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Pavan S Reddy
- Corresponding author: Pavan S. Reddy, MD, 818 Emporia St. Unit #300 Wichita, KS 67208, USA. Tel: +1 316 262 4467;
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Ring A, Campo D, Porras TB, Kaur P, Forte VA, Tripathy D, Lu J, Kang I, Press MF, Jeong YJ, Snow A, Zhu Y, Zada G, Wagle N, Lang JE. Circulating Tumor Cell Transcriptomics as Biopsy Surrogates in Metastatic Breast Cancer. Ann Surg Oncol 2022; 29:2882-2894. [PMID: 35000083 PMCID: PMC8989945 DOI: 10.1245/s10434-021-11135-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/11/2021] [Indexed: 01/28/2023]
Abstract
BACKGROUND Metastatic breast cancer (MBC) and the circulating tumor cells (CTCs) leading to macrometastases are inherently different than primary breast cancer. We evaluated whether whole transcriptome RNA-Seq of CTCs isolated via an epitope-independent approach may serve as a surrogate for biopsies of macrometastases. METHODS We performed RNA-Seq on fresh metastatic tumor biopsies, CTCs, and peripheral blood (PB) from 19 newly diagnosed MBC patients. CTCs were harvested using the ANGLE Parsortix microfluidics system to isolate cells based on size and deformability, independent of a priori knowledge of cell surface marker expression. RESULTS Gene expression separated CTCs, metastatic biopsies, and PB into distinct groups despite heterogeneity between patients and sample types. CTCs showed higher expression of immune oncology targets compared with corresponding metastases and PB. Predictive biomarker (n = 64) expression was highly concordant for CTCs and metastases. Repeat observation data post-treatment demonstrated changes in the activation of different biological pathways. Somatic single nucleotide variant analysis showed increasing mutational complexity over time. CONCLUSION We demonstrate that RNA-Seq of CTCs could serve as a surrogate biomarker for breast cancer macrometastasis and yield clinically relevant insights into disease biology and clinically actionable targets.
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Affiliation(s)
- Alexander Ring
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA ,Present Address: Department of Hematology and Medical Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Daniel Campo
- Department of Biological Sciences, University of Southern California, Los Angeles, CA USA
| | - Tania B. Porras
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Pushpinder Kaur
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Victoria A. Forte
- Division of Medical Oncology, Department of Medicine, SUNY Downstate Medical Center, New York, NY USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX USA
| | - Janice Lu
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Irene Kang
- Department of Pathology and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Michael F. Press
- Department of Pathology and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Young Ju Jeong
- Department of Surgery, Catholic University of Daegu School of Medicine, Daegu, Republic of Korea
| | - Anson Snow
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Yue Zhu
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Gabriel Zada
- Department of Neurosurgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Naveed Wagle
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Julie E. Lang
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA ,Present Address: Division of Breast Services, Department of General Surgery, Cleveland Clinic Breast Cancer Program, Cleveland, Ohio USA
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Frank MS, Bodtger U, Gehl J, Ahlborn LB. Actionable Molecular Alterations Are Revealed in Majority of Advanced Non-Small Cell Lung Cancer Patients by Genomic Tumor Profiling at Progression after First Line Treatment. Cancers (Basel) 2021; 14:cancers14010132. [PMID: 35008297 PMCID: PMC8749927 DOI: 10.3390/cancers14010132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Genomic profiling in advanced Non-Small Cell Lung cancer (NSCLC) can reveal Actionable Molecular Alterations (AMAs). Our study aims to investigate clinical relevance of re-biopsy after first line treatment, by reporting on acquired and persistent AMAs and potential targeted treatments in a real-time cohort of NSCLC patients. Methods: Patients with advanced NSCLC receiving first-line treatment were prospectively included in an observational study (NCT03512847). Genomic profiling was performed by TruSight Oncology 500 HT gene panel on tumor tissue collected at diagnosis and at time of progression. Results: The 92 patients re-biopsied at progression had received immunotherapy (n = 44), chemotherapy (n = 44), or combination treatment (n = 4). In 87 of these patients (95%), successful genomic profiling was performed at both the diagnostic biopsy and the re-biopsy. In 74 patients (85%), ≥1 AMA were found. The AMAs were acquired in 28%. The most frequent AMAs were observed in TP53 (45%), KRAS (24%), PIK3CA (6%), and FGFR1 (6%). Only five patients (5%) received targeted treatment mainly due to deterioration in performance status. Conclusions: Re-biopsy at progression revealed acquired AMAs in approximately one third of patients, and 85% had at least one AMA with the potential of receiving targeted treatment, thus strengthening the clinical relevance of re-biopsy.
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Affiliation(s)
- Malene Støchkel Frank
- Department of Clinical Oncology and Palliative Care, Zealand University Hospital, 4000 Roskilde, Denmark;
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence: ; Tel.: +45-28-574-392
| | - Uffe Bodtger
- Department of Respiratory Medicine, Zealand University Hospital, 4700 Naestved, Denmark;
- Institute for Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Julie Gehl
- Department of Clinical Oncology and Palliative Care, Zealand University Hospital, 4000 Roskilde, Denmark;
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lise Barlebo Ahlborn
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark;
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Kehl KL, Xu W, Gusev A, Bakouny Z, Choueiri TK, Riaz IB, Elmarakeby H, Van Allen EM, Schrag D. Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset. Nat Commun 2021; 12:7304. [PMID: 34911934 PMCID: PMC8674229 DOI: 10.1038/s41467-021-27358-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/16/2021] [Indexed: 02/08/2023] Open
Abstract
To accelerate cancer research that correlates biomarkers with clinical endpoints, methods are needed to ascertain outcomes from electronic health records at scale. Here, we train deep natural language processing (NLP) models to extract outcomes for participants with any of 7 solid tumors in a precision oncology study. Outcomes are extracted from 305,151 imaging reports for 13,130 patients and 233,517 oncologist notes for 13,511 patients, including patients with 6 additional cancer types. NLP models recapitulate outcome annotation from these documents, including the presence of cancer, progression/worsening, response/improvement, and metastases, with excellent discrimination (AUROC > 0.90). Models generalize to cancers excluded from training and yield outcomes correlated with survival. Among patients receiving checkpoint inhibitors, we confirm that high tumor mutation burden is associated with superior progression-free survival ascertained using NLP. Here, we show that deep NLP can accelerate annotation of molecular cancer datasets with clinically meaningful endpoints to facilitate discovery. To accelerate cancer research that correlates biomarkers with clinical endpoints, methods are needed to ascertain outcomes from electronic health records at scale. Here, the authors train natural language processing to extract outcomes for participants in a precision oncology study.
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Affiliation(s)
- Kenneth L Kehl
- From Dana-Farber Cancer Institute, Boston, MA, USA. .,Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Wenxin Xu
- From Dana-Farber Cancer Institute, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Alexander Gusev
- From Dana-Farber Cancer Institute, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Ziad Bakouny
- From Dana-Farber Cancer Institute, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Toni K Choueiri
- From Dana-Farber Cancer Institute, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Haitham Elmarakeby
- From Dana-Farber Cancer Institute, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,The Broad Institute, Rochester, USA
| | - Eliezer M Van Allen
- From Dana-Farber Cancer Institute, Boston, MA, USA.,Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,The Broad Institute, Rochester, USA
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Conroy JM, Pabla S, Glenn ST, Seager RJ, Van Roey E, Gao S, Burgher B, Andreas J, Giamo V, Mallon M, Lee YH, DePietro P, Nesline M, Wang Y, Lenzo FL, Klein R, Zhang S. A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors. PLoS One 2021; 16:e0260089. [PMID: 34855780 PMCID: PMC8639101 DOI: 10.1371/journal.pone.0260089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
Timely and accurate identification of molecular alterations in solid tumors is essential for proper management of patients with advanced cancers. This has created a need for rapid, scalable comprehensive genomic profiling (CGP) systems that detect an increasing number of therapeutically-relevant variant types and molecular signatures. In this study, we assessed the analytical performance of the TruSight Oncology 500 High-Throughput assay for detection of somatic alterations from formalin-fixed paraffin-embedded tissue specimens. In parallel, we developed supporting software and automated sample preparation systems designed to process up to 70 clinical samples in a single NovaSeq 6000TM sequencing run with a turnaround time of <7 days from specimen receipt to report. The results demonstrate that the scalable assay accurately and reproducibly detects small variants, copy number alterations, microsatellite instability (MSI) and tumor mutational burden (TMB) from 40ng DNA, and multiple gene fusions, including known and unknown partners and splice variants from 20ng RNA. 717 tumor samples and reference materials with previously known alterations in 96 cancer-related genes were sequenced to evaluate assay performance. All variant classes were reliably detected at consistent and reportable variant allele percentages with >99% overall accuracy and precision. Our results demonstrate that the high-throughput CGP assay is a reliable method for accurate detection of molecular alterations in support of precision therapeutics in oncology. The supporting systems and scalable workflow allow for efficient interpretation and prompt reporting of hundreds of patient cancer genomes per week with excellent analytical performance.
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Affiliation(s)
- Jeffrey M. Conroy
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
- Research Support Services, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Sarabjot Pabla
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Sean T. Glenn
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
- Laboratory Operations, OmniSeq Inc., Buffalo, New York, United States of America
- HemePath Molecular, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - R. J. Seager
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Erik Van Roey
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Shuang Gao
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Blake Burgher
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Jonathan Andreas
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Vincent Giamo
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Melissa Mallon
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Yong Hee Lee
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Paul DePietro
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Mary Nesline
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Yirong Wang
- Information Technology, OmniSeq Inc., Buffalo, New York, United States of America
| | - Felicia L. Lenzo
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Roger Klein
- Medical Affairs, OmniSeq Inc., Buffalo, New York, United States of America
| | - Shengle Zhang
- Laboratory Operations, OmniSeq Inc., Buffalo, New York, United States of America
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Kato S, Weipert C, Gumas S, Okamura R, Lee S, Sicklick JK, Saam J, Kurzrock R. Therapeutic Actionability of Circulating Cell-Free DNA Alterations in Carcinoma of Unknown Primary. JCO Precis Oncol 2021; 5:PO.21.00011. [PMID: 34778692 PMCID: PMC8585281 DOI: 10.1200/po.21.00011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/09/2021] [Accepted: 08/18/2021] [Indexed: 12/22/2022] Open
Abstract
Cancer of unknown primary (CUP) is a metastatic disease with unidentifiable primary tumor. Somatic alterations can be assessed noninvasively via liquid biopsies interrogating cell-free DNA (cfDNA). METHODS We evaluated 1,931 patients with CUP with a cfDNA next-generation sequencing panel (73-74 genes). RESULTS Overall, 1,739 patients (90%) had ≥ 1 cfDNA alteration. We then explored alteration actionability (per the levels of evidence from the OncoKB database); 825 patients (47.4% of 1,739) had level 1, level 2, or resistance/R1 alterations. Among 40 clinically annotated patients with CUP who had cfDNA evaluated, higher degrees of matching treatment to alterations (Matching Score > 50% v ≤ 50%) was the only variable predicting improved outcome: longer median progression-free survival (10.4 v 2.5 months; P = .002), overall survival (13.4 v 5.7 months; P = .07, trend), and higher clinical benefit rate (stable disease ≥ 6 months/partial response/complete response; 83% v 25%; P = .003). CONCLUSION In summary, cfDNA frequently reveals strong level-of-evidence actionable alterations in CUP, and high degrees of matching to therapy correlates with better outcomes.
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Affiliation(s)
- Shumei Kato
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, La Jolla, CA
| | | | - Sophia Gumas
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, La Jolla, CA
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, La Jolla, CA.,Department of Surgery, Kyoto University Hospital, Kyoto, Japan
| | - Suzanna Lee
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, La Jolla, CA
| | - Jason K Sicklick
- Center for Personalized Cancer Therapy, University of California San Diego Moores Cancer Center, La Jolla, CA.,Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA
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Hamilton JG, Banerjee SC, Carlsson SV, Vera J, Lynch KA, Sar-Graycar L, Martin CM, Parker PA, Hay JL. Clinician perspectives on communication and implementation challenges in precision oncology. Per Med 2021; 18:559-572. [PMID: 34674550 DOI: 10.2217/pme-2021-0048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To describe patient communication challenges encountered by oncology clinicians, which represent a fundamental barrier to implementing precision oncology. Materials & methods: We conducted three focus groups including breast, melanoma and thoracic oncology clinicians regarding their precision oncology communication experiences. Transcripts were reviewed and coded using inductive thematic text analysis. Results: We identified four themes: varied definitions of precision oncology exist, clinicians and patients face unique challenges to precision oncology implementation, patient communication challenges engendered or heightened by precision oncology implementation and clinician communication solutions and training needs. Conclusion: This study elucidated clinicians' perspectives on implementing precision oncology and related communication challenges. Understanding these challenges and developing strategies to help clinicians navigate these discussions are critical for ensuring that patients reap the full benefits of precision oncology.
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Affiliation(s)
- Jada G Hamilton
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Medical College, New York, NY 10065, USA
| | - Smita C Banerjee
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA.,Weill Cornell Medical College, New York, NY 10065, USA
| | - Sigrid V Carlsson
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10017, USA.,Department of Urology, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - Jacqueline Vera
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA
| | - Kathleen A Lynch
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA
| | - Lili Sar-Graycar
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA
| | - Chloé M Martin
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA
| | - Patricia A Parker
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA.,Weill Cornell Medical College, New York, NY 10065, USA
| | - Jennifer L Hay
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA.,Weill Cornell Medical College, New York, NY 10065, USA
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Sawada K, Nakayama K, Nakamura K, Yoshimura Y, Razia S, Ishikawa M, Yamashita H, Ishibashi T, Sato S, Kyo S. Clinical Outcomes of Genotype-Matched Therapy for Recurrent Gynecological Cancers: A Single Institutional Experience. Healthcare (Basel) 2021; 9:healthcare9101395. [PMID: 34683075 PMCID: PMC8535840 DOI: 10.3390/healthcare9101395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Recent advances in next-generation sequencing and genome medicine have contributed to treatment decisions in patients with cancer. Most advanced gynecological cancers develop resistance to chemotherapy and have a poor prognosis. Therefore, we conducted genomic tests in gynecological tumors to examine the efficacy and clinical feasibility of genotype-matched therapy. Target sequencing was performed in 20 cases of gynecological cancers (cervical cancer, 6; endometrial cancer, 6; and ovarian cancer, 6). Both actionable and druggable genes were identified in 95% (19/20) of the cases. Among them, seven patients (35%) received genotype-matched therapy, which was effective in three patients. Of the three patients, one patient with a PTEN mutation received everolimus, another patient with a TSC2 mutation received everolimus and letrozole, and the patient with a BRIP1 mutation received olaparib. Subsequently, disease control in these three patients lasted for more than half a year. However, all patients relapsed between 9 and 13 months after the initiation of genotype-matched therapy. In this study, the response rate of genotype-matched therapy was 43% (3/7), which may have contributed to improved prognoses. Therefore, genotype-matched therapies may help patients with refractory gynecological cancers achieve better outcomes.
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Personalization of medical treatments in oncology: time for rethinking the disease concept to improve individual outcomes. EPMA J 2021; 12:545-558. [PMID: 34642594 PMCID: PMC8495186 DOI: 10.1007/s13167-021-00254-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
The agenda of pharmacology discovery in the field of personalized oncology was dictated by the search of molecular targets assumed to deterministically drive tumor development. In this perspective, genes play a fundamental "causal" role while cells simply act as causal proxies, i.e., an intermediate between the molecular input and the organismal output. However, the ceaseless genomic change occurring across time within the same primary and metastatic tumor has broken the hope of a personalized treatment based only upon genomic fingerprint. Indeed, current models are unable in capturing the unfathomable complexity behind the outbreak of a disease, as they discard the contribution of non-genetic factors, environment constraints, and the interplay among different tiers of organization. Herein, we posit that a comprehensive personalized model should view at the disease as a "historical" process, in which different spatially and timely distributed factors interact with each other across multiple levels of organization, which collectively interact with a dynamic gene-expression pattern. Given that a disease is a dynamic, non-linear process - and not a static-stable condition - treatments should be tailored according to the "timing-frame" of each condition. This approach can help in detecting those critical transitions through which the system can access different attractors leading ultimately to diverse outcomes - from a pre-disease state to an overt illness or, alternatively, to recovery. Identification of such tipping points can substantiate the predictive and the preventive ambition of the Predictive, Preventive and Personalized Medicine (PPPM/3PM). However, an unusual effort is required to conjugate multi-omics approaches, data collection, and network analysis reconstruction (eventually involving innovative Artificial Intelligent tools) to recognize the critical phases and the relevant targets, which could help in patient stratification and therapy personalization.
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Sicklick JK, Kato S, Okamura R, Patel H, Nikanjam M, Fanta PT, Hahn ME, De P, Williams C, Guido J, Solomon BM, McKay RR, Krie A, Boles SG, Ross JS, Lee JJ, Leyland-Jones B, Lippman SM, Kurzrock R. Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study. Genome Med 2021; 13:155. [PMID: 34607609 PMCID: PMC8491393 DOI: 10.1186/s13073-021-00969-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/15/2021] [Indexed: 01/07/2023] Open
Abstract
Background Malignancies are molecularly complex and become more resistant with each line of therapy. We hypothesized that offering matched, individualized combination therapies to patients with treatment-naïve, advanced cancers would be feasible and efficacious. Patients with newly diagnosed unresectable/metastatic, poor-prognosis cancers were enrolled in a cross-institutional prospective study. Methods A total of 145 patients were included in the study. Genomic profiling (tissue and/or circulating tumor DNA) was performed in all patients, and PD-L1 immunohistochemistry, tumor mutational burden, and microsatellite status assessment were performed in a subset of patients. We evaluated safety and outcomes: disease-control rate (stable disease for ≥ 6 months or partial or complete response), progression-free survival (PFS), and overall survival (OS). Results Seventy-six of 145 patients (52%) were treated, most commonly for non-colorectal gastrointestinal cancers, carcinomas of unknown primary, and hepatobiliary malignancies (53% women; median age, 63 years). The median number of deleterious genomic alterations per patient was 5 (range, 0–15). Fifty-four treated patients (71%) received ≥ 1 molecularly matched therapy, demonstrating the feasibility of administering molecularly matched therapy. The Matching Score, which reflects the percentage of targeted alterations, correlated linearly with progression-free survival (R2 = 0.92; P = 0.01), and high (≥ 60%) Matching Score was an independent predictor of improved disease control rate [OR 3.31 (95% CI 1.01–10.83), P = 0.048], PFS [HR 0.55 (0.28–1.07), P = 0.08], and OS [HR 0.42 (0.21–0.85), P = 0.02]. Serious adverse event rates were similar in the unmatched and matched groups. Conclusions Personalized combination therapies targeting a majority of a patient’s molecular alterations have antitumor activity as first-line treatment. These findings underscore the feasibility and importance of using tailored N-of-1 combination therapies early in the course of lethal malignancies. Trial registration I-PREDICT (NCT02534675) was registered on August 25, 2015. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00969-w.
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Affiliation(s)
- Jason K Sicklick
- Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA, USA. .,Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.
| | - Shumei Kato
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Hitendra Patel
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Mina Nikanjam
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Paul T Fanta
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Michael E Hahn
- Department of Radiology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Pradip De
- Avera Cancer Institute, Sioux Falls, SD, USA
| | | | - Jessica Guido
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA
| | | | - Rana R McKay
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Amy Krie
- Avera Cancer Institute, Sioux Falls, SD, USA
| | - Sarah G Boles
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA.,Departments of Pathology and Urology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - J Jack Lee
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Scott M Lippman
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA.,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, Moores Cancer Center, UC San Diego Health, 3855 Health Sciences Drive, Mail Code 0658, La Jolla, CA, 92093-0658, USA. .,Department of Medicine, Division of Hematology Oncology, UC San Diego School of Medicine, San Diego, CA, USA.
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Niogret J, Dalens L, Truntzer C, Chevrier S, Favier L, Lagrange A, Coudert B, Fraisse C, Foucher P, Zouak A, Westeel V, Goussot V, Dérangère V, Albuisson J, Arnould L, Boidot R, Kaderbhai CG, Ghiringhelli F. Does large NGS panel analysed using exome tumour sequencing improve the management of advanced non-small-cell lung cancers? Lung Cancer 2021; 161:98-107. [PMID: 34560426 DOI: 10.1016/j.lungcan.2021.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/02/2021] [Accepted: 08/24/2021] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Non-small-cell lung cancer (NSCLC) is one of the most common and deadly cancers. Several molecular drivers of oncogene addiction are now known to be strong predictive biomarkers for target therapies. Advances in large Next Generation Sequencing (LNGS) have improved the ability to detect potentially targetable mutations. However, the integration of LNGS into clinical management in an individualized manner remains challenging. METHODS In this single-center observational study we included all patients with advanced NSCLC who underwent LNGS. Somatic and germline exome analysis was performed with a restriction on 323 cancer related genes. Variants were classified and Molecular Tumour Board (MTB) made therapeutic propositions. RESULTS We performed LNGS analysis in 281 patients with advanced NSCLC between March 2015 and January 2018. Technical failure occurred in only 3% of cases. Three hundred and fifty-six targetable mutations were detected. At least one targetable mutation was found in 209 patients. For all these patients, the MTB was able to recommend treatment with a targeted agent based on the evaluation of the tumour's genetic profile and treatment history. Twenty-nine patients (13.9%) were subsequently treated with an MTB-recommended targeted therapy. We did not observe any improvement in terms of clinical benefit for these patients. CONCLUSIONS In this case series, we show that including LNGS into routine clinical management was feasible but does not appear to provide clinical benefit in the management of patients with advanced NSCLC.
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Affiliation(s)
- Julie Niogret
- Department of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; University of Burgundy-Franche Comté, Maison de l'université Esplanade Erasme, 21000 Dijon, France
| | - Lorraine Dalens
- Department of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; University of Burgundy-Franche Comté, Maison de l'université Esplanade Erasme, 21000 Dijon, France
| | - Caroline Truntzer
- Platform of Transfert in Biological Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; Genomic and Immunotherapy Medical Institute, Dijon University Hospital, 14 rue Paul Gaffarel 21000 Dijon, France
| | - Sandy Chevrier
- Platform of Transfert in Biological Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; Department of Tumour Biology and Pathology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - Laure Favier
- Department of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - Aurélie Lagrange
- Department of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - Bruno Coudert
- Department of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - Cléa Fraisse
- Department of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - Pascal Foucher
- Department of Thoracic Oncology, Dijon University Hospital, 14 rue Paul Gaffarel, 21000 Dijon, France
| | - Ayoub Zouak
- Department of Thoracic Oncology, Dijon University Hospital, 14 rue Paul Gaffarel, 21000 Dijon, France
| | - Virginie Westeel
- Department of Pneumology, Besançon University Hospital, 3 Boulevard Alexandre Fleming, 25000 Besançon, France
| | - Vincent Goussot
- Department of Tumour Biology and Pathology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - Valentin Dérangère
- University of Burgundy-Franche Comté, Maison de l'université Esplanade Erasme, 21000 Dijon, France; Platform of Transfert in Biological Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; Department of Tumour Biology and Pathology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; UMR INSERM 1231, 7 Boulevard Jeanne d'Arc, 21000 Dijon, France
| | - Juliette Albuisson
- Platform of Transfert in Biological Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; Genomic and Immunotherapy Medical Institute, Dijon University Hospital, 14 rue Paul Gaffarel 21000 Dijon, France; Department of Tumour Biology and Pathology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - Laurent Arnould
- Department of Tumour Biology and Pathology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - Romain Boidot
- University of Burgundy-Franche Comté, Maison de l'université Esplanade Erasme, 21000 Dijon, France; Platform of Transfert in Biological Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; Genomic and Immunotherapy Medical Institute, Dijon University Hospital, 14 rue Paul Gaffarel 21000 Dijon, France; Department of Tumour Biology and Pathology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; UMR INSERM 1231, 7 Boulevard Jeanne d'Arc, 21000 Dijon, France
| | - Courèche-Guillaume Kaderbhai
- Department of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France
| | - François Ghiringhelli
- Department of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; University of Burgundy-Franche Comté, Maison de l'université Esplanade Erasme, 21000 Dijon, France; Platform of Transfert in Biological Oncology, Georges François Leclerc Cancer Center - UNICANCER, 1 rue du Professeur Marion, Dijon 21000, France; Genomic and Immunotherapy Medical Institute, Dijon University Hospital, 14 rue Paul Gaffarel 21000 Dijon, France; UMR INSERM 1231, 7 Boulevard Jeanne d'Arc, 21000 Dijon, France.
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Moazzendizaji S, Sevbitov A, Ezzatifar F, Jalili HR, Aalii M, Hemmatzadeh M, Aslani S, Gholizadeh Navashenaq J, Safari R, Hosseinzadeh R, Rahmany MR, Mohammadi H. microRNAs: Small molecules with a large impact on colorectal cancer. Biotechnol Appl Biochem 2021; 69:1893-1908. [PMID: 34550619 DOI: 10.1002/bab.2255] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) accounts for one of the main cancer-related mortality and morbidity worldwide. The molecular mechanisms of CRC development have been broadly investigated and, over the last decade, it has become evident that aberrant transcription of microRNAs (miRNAs), a class of small, noncoding RNA molecules, has a significant role in the inception and promotion of CRC. In the involved tissues of CRC, the transcription profile of miRNAs is modulated, and their expression templates are related with prognosis, diagnosis, and treatment outcomes. Here, in the current review, we attempted to discuss the latest information regarding the aberrantly expressed miRNAs in CRC and the advantages of utilizing miRNAs as biomarkers for early diagnosis and prognosis of CRC as well as potential therapeutic application. The effect of miRNAs involved in various signaling pathways, primarily p53, EGFR, Wnt, and TGF-β pathways, was clarified.
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Affiliation(s)
- Sahand Moazzendizaji
- Department of Immunology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Andrey Sevbitov
- Head of Department of Propaedeutics of Dental Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Fatemeh Ezzatifar
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hamid Reza Jalili
- Department of Immunology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Morteza Aalii
- Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Maryam Hemmatzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Aslani
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Roghaiyeh Safari
- Molecular and Cellular Epigenetics (GIGA), University of Liege, Sart-Tilman Liège, Belgium.,13. Molecular and Cellular Biology (TERRA), Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Ramin Hosseinzadeh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rahmany
- Department of Immunology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Hamed Mohammadi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
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Stadler ZK, Maio A, Chakravarty D, Kemel Y, Sheehan M, Salo-Mullen E, Tkachuk K, Fong CJ, Nguyen B, Erakky A, Cadoo K, Liu Y, Carlo MI, Latham A, Zhang H, Kundra R, Smith S, Galle J, Aghajanian C, Abu-Rustum N, Varghese A, O'Reilly EM, Morris M, Abida W, Walsh M, Drilon A, Jayakumaran G, Zehir A, Ladanyi M, Ceyhan-Birsoy O, Solit DB, Schultz N, Berger MF, Mandelker D, Diaz LA, Offit K, Robson ME. Therapeutic Implications of Germline Testing in Patients With Advanced Cancers. J Clin Oncol 2021; 39:2698-2709. [PMID: 34133209 PMCID: PMC8376329 DOI: 10.1200/jco.20.03661] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Tumor mutational profiling is increasingly performed in patients with advanced cancer. We determined the extent to which germline mutation profiling guides therapy selection in patients with advanced cancer. METHODS Patients with cancer undergoing tumor genomic profiling were prospectively consented for germline cancer predisposition gene analysis (2015-2019). In patients harboring germline likely pathogenic or pathogenic (LP/P) alterations, therapeutic actionability was classified using a precision oncology knowledge base. Patients with metastatic or recurrent cancer receiving germline genotype-directed therapy were determined. RESULTS Among 11,947 patients across > 50 malignancies, 17% (n = 2,037) harbored a germline LP/P variant. By oncology knowledge base classification, 9% (n = 1042) had an LP/P variant in a gene with therapeutic implications (4% level 1; 4% level 3B; < 1% level 4). BRCA1/2 variants accounted for 42% of therapeutically actionable findings, followed by CHEK2 (13%), ATM (12%), mismatch repair genes (11%), and PALB2 (5%). When limited to the 9,079 patients with metastatic or recurrent cancer, 8% (n = 710) harbored level 1 or 3B genetic findings and 3.2% (n = 289) received germline genotype-directed therapy. Germline genotype-directed therapy was received by 61% and 18% of metastatic cancer patients with level 1 and level 3B findings, respectively, and by 54% of BRCA1/2, 75% of mismatch repair, 43% of PALB2, 35% of RAD51C/D, 24% of BRIP1, and 19% of ATM carriers. Of BRCA1/2 patients receiving a poly(ADP-ribose) polymerase inhibitor, 45% (84 of 188) had tumors other than breast or ovarian cancer, wherein the drug, at time of delivery, was delivered in an investigational setting. CONCLUSION In a pan-cancer analysis, 8% of patients with advanced cancer harbored a germline variant with therapeutic actionability with 40% of these patients receiving germline genotype-directed treatment. Germline sequence analysis is additive to tumor sequence analysis for therapy selection and should be considered for all patients with advanced cancer.
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Affiliation(s)
- Zsofia K. Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Debyani Chakravarty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yelena Kemel
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christopher J. Fong
- Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bastien Nguyen
- Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amanda Erakky
- David M. Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karen Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria I. Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shaleigh Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jesse Galle
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nadeem Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eileen M. O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- David M. Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B. Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikolaus Schultz
- Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luis A. Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Treatment Experience and Predictive Factors Associated with Response in Platinum-Resistant Recurrent Ovarian Cancer: A Retrospective Single-Institution Study. J Clin Med 2021; 10:jcm10163596. [PMID: 34441892 PMCID: PMC8397105 DOI: 10.3390/jcm10163596] [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: 07/21/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022] Open
Abstract
Ovarian cancer (OC) represents the most common and lethal gynecologic malignancy, due to its increased incidence and mortality rate. It is usually diagnosed in advanced stages and, even though surgery and platinum-based treatments are initially efficient, recurrences emerge in over 70% of cases. Although there are multiple options of chemotherapy drugs from which to choose, little is known regarding the best strategy for prolonged survival. Thus, this study aimed to assess the effect that most frequently used chemotherapeutic regimens have upon time-to-treatment-failure (TTF) from the first line and beyond, considering clinical and biological factors which influence the treatment outcome of platinum-resistant recurrent OC. We retrospectively analyzed data from 78 patients diagnosed with platinum-resistant OC, who underwent chemotherapy-based treatment with or without anti-angiogenic therapy at OncoHelp Oncology Center, Romania (January 2016–February 2021). Our study identified positive predictive factors for TTF related to histology (serous carcinoma subtype), anthropometry (age over 60 for patients treated with topotecan with or without bevacizumab), renal function (creatinine levels between 0.65 and 1 mg/dL for patients treated with regimens containing bevacizumab and pegylated liposomal doxorubicin) and treatment choice (bevacizumab in combination with pegylated liposomal doxorubicin or topotecan used from the first line and beyond).
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44
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Terraf P, Sholl LM, Davids MS, Awad MM, Garcia EP, MacConaill LE, Dal Cin P, Kim A, Lindeman NI, Stachler M, Hwang DH, Dubuc AM. Twists and turns from "tumor in tumor" profiling: surveillance of chronic lymphocytic leukemia (CLL) leads to detection of a lung adenocarcinoma, whose genomic characterization alters the original hematologic diagnosis. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006089. [PMID: 34074652 PMCID: PMC8327883 DOI: 10.1101/mcs.a006089] [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: 02/22/2021] [Accepted: 05/03/2021] [Indexed: 11/25/2022] Open
Abstract
Comprehensive characterization of somatic genomic alterations has led to fundamental shifts in our understanding of tumor biology. In clinical practice, these studies can lead to modifications of diagnosis and/or specific treatment implications, fulfilling the promise of personalized medicine. Herein, we describe a 78-yr-old woman under surveillance for long-standing untreated chronic lymphocytic leukemia (CLL). Molecular studies from a peripheral blood specimen revealed a TP53 p.V157F mutation, whereas karyotype and fluorescence in situ hybridization (FISH) identified a 17p deletion, trisomy 12, and no evidence of IGH-CCND1 rearrangement. Positron emission tomography-computed tomography scan identified multistation intra-abdominal lymphadenopathy and a pulmonary nodule, and subsequent pulmonary wedge resection confirmed the presence of a concurrent lung adenocarcinoma. Targeted next-generation sequencing of the lung tumor identified an EGFR in-frame exon 19 deletion, two TP53 mutations (p.P152Q, p.V157F), and, unexpectedly, a IGH-CCND1 rearrangement. Follow-up immunohistochemistry (IHC) studies demonstrated a cyclin D1–positive lymphoid aggregate within the lung adenocarcinoma. The presence of the TP53 p.V157F mutation in the lung resection, detection of an IGH-CCND1 rearrangement, and cyclin D1 positivity by IHC led to revision of the patient's hematologic diagnosis and confirmed the extranodal presence of mantle cell lymphoma within the lung mass, thus representing a “tumor in tumor.” Manual review of the sequencing data suggested the IGH-CCND1 rearrangement occurred via an insertional event, whose size precluded detection by original FISH studies. Thus, routine imaging for this patient's known hematologic malignancy led to detection of an unexpected solid tumor, whose subsequent precision medicine studies in the solid tumor redefined the original hematological diagnosis.
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Affiliation(s)
- Panieh Terraf
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Mark M Awad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Elizabeth P Garcia
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Annette Kim
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthew Stachler
- Department of Pathology, University of California San Francisco, San Francisco, California 94143, USA
| | - David H Hwang
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Adrian M Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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Sharifi-Rad J, Quispe C, Imran M, Rauf A, Nadeem M, Gondal TA, Ahmad B, Atif M, Mubarak MS, Sytar O, Zhilina OM, Garsiya ER, Smeriglio A, Trombetta D, Pons DG, Martorell M, Cardoso SM, Razis AFA, Sunusi U, Kamal RM, Rotariu LS, Butnariu M, Docea AO, Calina D. Genistein: An Integrative Overview of Its Mode of Action, Pharmacological Properties, and Health Benefits. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:3268136. [PMID: 34336089 PMCID: PMC8315847 DOI: 10.1155/2021/3268136] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/11/2021] [Accepted: 06/28/2021] [Indexed: 12/15/2022]
Abstract
Genistein is an isoflavone first isolated from the brooming plant Dyer's Genista tinctoria L. and is widely distributed in the Fabaceae family. As an isoflavone, mammalian genistein exerts estrogen-like functions. Several biological effects of genistein have been reported in preclinical studies, such as the antioxidant, anti-inflammatory, antibacterial, and antiviral activities, the effects of angiogenesis and estrogen, and the pharmacological activities on diabetes and lipid metabolism. The purpose of this review is to provide up-to-date evidence of preclinical pharmacological activities with mechanisms of action, bioavailability, and clinical evidence of genistein. The literature was researched using the most important keyword "genistein" from the PubMed, Science, and Google Scholar databases, and the taxonomy was validated using The Plant List. Data were also collected from specialized books and other online resources. The main positive effects of genistein refer to the protection against cardiovascular diseases and to the decrease of the incidence of some types of cancer, especially breast cancer. Although the mechanism of protection against cancer involves several aspects of genistein metabolism, the researchers attribute this effect to the similarity between the structure of soy genistein and that of estrogen. This structural similarity allows genistein to displace estrogen from cellular receptors, thus blocking their hormonal activity. The pharmacological activities resulting from the experimental studies of this review support the traditional uses of genistein, but in the future, further investigations are needed on the efficacy, safety, and use of nanotechnologies to increase bioavailability and therapeutic efficacy.
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Affiliation(s)
- Javad Sharifi-Rad
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Cristina Quispe
- Facultad de Ciencias de la Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique 1110939, Chile
| | - Muhammad Imran
- University Institute of Diet and Nutritional Sciences, Faculty of Allied Health Sciences, The University of Lahore, Lahore, Pakistan
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar-, 23561 Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Nadeem
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari-, Pakistan
| | | | - Bashir Ahmad
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar-, 25120 KPK, Pakistan
| | - Muhammad Atif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72341, Saudi Arabia
| | | | - Oksana Sytar
- Department of Plant Biology Department, Institute of Biology, Taras Shevchenko National University of Kyiv, Volodymyrska Str., 64, Kyiv 01033, Ukraine
- Department of Plant Physiology, Slovak University of Agriculture, A. Hlinku 2, 94976 Nitra, Slovakia
| | - Oxana Mihailovna Zhilina
- Department of Organic Chemistry, Pyatigorsk Medical-Pharmaceutical Institute (PMPI), Branch of Volgograd State Medical University, Ministry of Health of Russia, Pyatigorsk 357532, Russia
| | - Ekaterina Robertovna Garsiya
- Department of Pharmacognosy, Botany and Technology of Phytopreparations, Pyatigorsk Medical-Pharmaceutical Institute (PMPI), Branch of Volgograd State Medical University, Ministry of Health of Russia, Pyatigorsk 357532, Russia
| | - Antonella Smeriglio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
| | - Domenico Trombetta
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
| | - Daniel Gabriel Pons
- Grupo Multidisciplinar de Oncología Traslacional (GMOT), Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears (UIB), Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma 07122, Spain
| | - Miquel Martorell
- Department of Nutrition and Dietetics, Faculty of Pharmacy, University of Concepción, Concepción 4070386, Chile
- Unidad de Desarrollo Tecnológico, Universidad de Concepción UDT, Concepción 4070386, Chile
| | - Susana M Cardoso
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ahmad Faizal Abdull Razis
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Usman Sunusi
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Bayero University Kano, PMB 3011 Kano, Nigeria
| | - Ramla Muhammad Kamal
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Pharmacology, Federal University Dutse, PMB 7156 Dutse Jigawa State, Nigeria
| | - Lia Sanda Rotariu
- Banat's University of Agricultural Sciences and Veterinary Medicine "King Michael I of Romania" from Timisoara, Romania
| | - Monica Butnariu
- Banat's University of Agricultural Sciences and Veterinary Medicine "King Michael I of Romania" from Timisoara, Romania
| | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
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De Falco V, Poliero L, Vitello PP, Ciardiello D, Vitale P, Zanaletti N, Giunta EF, Terminiello M, Caputo V, Carlino F, Di Liello R, Ventriglia A, Famiglietti V, Martinelli E, Morgillo F, Orditura M, De Vita F, Fasano M, Napolitano S, Martini G, Della Corte CM, Franco R, Altucci L, Ciardiello F, Troiani T. Feasibility of next-generation sequencing in clinical practice: results of a pilot study in the Department of Precision Medicine at the University of Campania 'Luigi Vanvitelli'. ESMO Open 2021; 5:S2059-7029(20)30067-3. [PMID: 32234730 PMCID: PMC7174013 DOI: 10.1136/esmoopen-2020-000675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/28/2022] Open
Abstract
Background The emerging role of next-generation sequencing (NGS) targeted panels is revolutionising our approach to cancer patients, providing information on gene alterations helpful for diagnosis and clinical decision, in a short time and with acceptable costs. Materials and methods In this work, we evaluated the clinical application of FoundationOne CDx test, a hybrid capture-based NGS. This test identifies alterations in 324 genes, tumour mutational burden and genomic signatures as microsatellite instability. The decision to obtain the NGS assay for a particular patient was done according to investigator’s choice. Results Overall, 122 tumour specimens were analysed, of which 84 (68.85%) succeeded. The success rate was influenced by type of specimen formalin-fixed paraffin embedded (FFPE block vs FFPE slides), by origin of the sample (surgery vs biopsy) and by time of fixation (<5 years vs ≥5 years). The most frequent subgroups of effective reports derived from colorectal cancer (25 samples), non-small-cell lung cancer (16 samples), ovarian cancer (10 samples), biliary tract cancer (9 samples), breast cancer (7 samples), gastric cancer (7 samples). The most frequent alterations found in whole population referred to TP53 (45.9%), KRAS (19.6%) and APC (13.9%). Furthermore, we performed an analysis of patients in whom this comprehensive genomic profiling (CGP) had a relevance for the patient’s disease. Conclusions On our opinion, CGP could be proposed in clinical practice in order to select patients that could most benefit from the analysis proposed, like patients with good performance status without any available treatments or with unexpected resistance to a therapy.
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Affiliation(s)
- Vincenzo De Falco
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Luca Poliero
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Pietro Paolo Vitello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Davide Ciardiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Pasquale Vitale
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Nicoletta Zanaletti
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Emilio Francesco Giunta
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Marinella Terminiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Francesca Carlino
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Raimondo Di Liello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Anna Ventriglia
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Vincenzo Famiglietti
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Erika Martinelli
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Floriana Morgillo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Michele Orditura
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Ferdinando De Vita
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Morena Fasano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Renato Franco
- Department of Mental, Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Lucia Altucci
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
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Affiliation(s)
- Jennifer Y Wang
- Department of Dermatology, Stanford University School of Medicine, Stanford, California
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, California
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Yam C, Ma BBY, Yap TA. Global Implementation of Precision Oncology. JCO Precis Oncol 2021; 5:PO.21.00001. [PMID: 34250385 PMCID: PMC8232074 DOI: 10.1200/po.21.00001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 01/17/2021] [Indexed: 01/12/2023] Open
Affiliation(s)
- Clinton Yam
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Brigette B Y Ma
- Department of Clinical Oncology, Phase I Clinical Trial Center, Kingboard Precision Oncology Program, The Chinese University of Hong Kong, Hong Kong, China
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX.,Khalifa Institute of Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.,The Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX
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49
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Bertucci F, Gonçalves A, Guille A, Adelaïde J, Garnier S, Carbuccia N, Billon E, Finetti P, Sfumato P, Monneur A, Pécheux C, Khran M, Brunelle S, Mescam L, Thomassin-Piana J, Poizat F, Charafe-Jauffret E, Turrini O, Lambaudie E, Provansal M, Extra JM, Madroszyk A, Gilabert M, Sabatier R, Vicier C, Mamessier E, Chabannon C, Pakradouni J, Viens P, André F, Gravis G, Popovici C, Birnbaum D, Chaffanet M. Prospective high-throughput genome profiling of advanced cancers: results of the PERMED-01 clinical trial. Genome Med 2021; 13:87. [PMID: 34006291 PMCID: PMC8132379 DOI: 10.1186/s13073-021-00897-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The benefit of precision medicine based on relatively limited gene sets and often-archived samples remains unproven. PERMED-01 (NCT02342158) was a prospective monocentric clinical trial assessing, in adults with advanced solid cancer, the feasibility and impact of extensive molecular profiling applied to newly biopsied tumor sample and based on targeted NGS (t-NGS) of the largest gene panel to date and whole-genome array-comparative genomic hybridization (aCGH) with assessment of single-gene alterations and clinically relevant genomic scores. METHODS Eligible patients with refractory cancer had one tumor lesion accessible to biopsy. Extracted tumor DNA was profiled by t-NGS and aCGH. We assessed alterations of 802 "candidate cancer" genes and global genomic scores, such as homologous recombination deficiency (HRD) score and tumor mutational burden. The primary endpoint was the number of patients with actionable genetic alterations (AGAs). Secondary endpoints herein reported included a description of patients with AGA who received a "matched therapy" and their clinical outcome, and a comparison of AGA identification with t-NGS and aCGH versus whole-exome sequencing (WES). RESULTS Between November 2014 and September 2019, we enrolled 550 patients heavily pretreated. An exploitable complete molecular profile was obtained in 441/550 patients (80%). At least one AGA, defined in real time by our molecular tumor board, was found in 393/550 patients (71%, two-sided 90%CI 68-75%). Only 94/550 patients (17%, 95%CI 14-21) received an "AGA-matched therapy" on progression. The most frequent AGAs leading to "matched therapy" included PIK3CA mutations, KRAS mutations/amplifications, PTEN deletions/mutations, ERBB2 amplifications/mutations, and BRCA1/2 mutations. Such "matched therapy" improved by at least 1.3-fold the progression-free survival on matched therapy (PFS2) compared to PFS on prior therapy (PFS1) in 36% of cases, representing 6% of the enrolled patients. Within patients with AGA treated on progression, the use of "matched therapy" was the sole variable associated with an improved PFS2/PFS1 ratio. Objective responses were observed in 19% of patients treated with "matched therapy," and 6-month overall survival (OS) was 62% (95%CI 52-73). In a subset of 112 metastatic breast cancers, WES did not provide benefit in term of AGA identification when compared with t-NGS/aCGH. CONCLUSIONS Extensive molecular profiling of a newly biopsied tumor sample identified AGA in most of cases, leading to delivery of a "matched therapy" in 17% of screened patients, of which 36% derived clinical benefit. WES did not seem to improve these results. TRIAL REGISTRATION ID-RCB identifier: 2014-A00966-41; ClinicalTrials.gov identifier: NCT02342158 .
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Affiliation(s)
- François Bertucci
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France.
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.
| | - Anthony Gonçalves
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Arnaud Guille
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - José Adelaïde
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Séverine Garnier
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Nadine Carbuccia
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Emilien Billon
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Patrick Sfumato
- Biostatistics Unit, Institut Paoli-Calmettes, Marseille, France
| | - Audrey Monneur
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Christophe Pécheux
- Department of Medical genetics, Hôpital Timone Enfants, AP-HM, Marseille, France
| | - Martin Khran
- Department of Medical genetics, Hôpital Timone Enfants, AP-HM, Marseille, France
- Aix-Marseille University, Inserm, U1251-MMG, Marseille Medical Genetics, Marseille, France
| | - Serge Brunelle
- Department of Imaging, Institut Paoli-Calmettes, Marseille, France
| | - Lenaïg Mescam
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | | | - Flora Poizat
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | | | - Olivier Turrini
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Eric Lambaudie
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Magali Provansal
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Jean-Marc Extra
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Anne Madroszyk
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Marine Gilabert
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Renaud Sabatier
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Cécile Vicier
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Emilie Mamessier
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Christian Chabannon
- Biobank, Department of Hematology, Institut Paoli-Calmettes, Marseille, France
| | - Jihane Pakradouni
- Department of Clinical Research and Innovation, Institut Paoli-Calmettes, Marseille, France
| | - Patrice Viens
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Fabrice André
- Department of Medical Oncology, Gustave Roussy Cancer Campus, UMR981 Inserm, Villejuif, France
- Paris Sud University, Orsay, France
| | - Gwenaelle Gravis
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Cornel Popovici
- Department of Oncogenetics, Institut Paoli-Calmettes, Marseille, France
| | - Daniel Birnbaum
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Max Chaffanet
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
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Chan KKW, Tannock IF. Should Basket Trials Be Pathways to Drug Registration for Biomarker-Defined Subgroups of Advanced Cancers? J Clin Oncol 2021; 39:2426-2429. [PMID: 33979191 DOI: 10.1200/jco.21.00552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Kelvin K-W Chan
- Sunnybrook Research Institute & Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Ian F Tannock
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
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