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Furtado LV, Bifulco C, Dolderer D, Hsiao SJ, Kipp BR, Lindeman NI, Ritterhouse LL, Temple-Smolkin RL, Zehir A, Nowak JA. Recommendations for Tumor Mutational Burden Assay Validation and Reporting: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, and Society for Immunotherapy of Cancer. J Mol Diagn 2024; 26:653-668. [PMID: 38851389 DOI: 10.1016/j.jmoldx.2024.05.002] [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: 12/01/2023] [Revised: 04/05/2024] [Accepted: 05/07/2024] [Indexed: 06/10/2024] Open
Abstract
Tumor mutational burden (TMB) has been recognized as a predictive biomarker for immunotherapy response in several tumor types. Several laboratories offer TMB testing, but there is significant variation in how TMB is calculated, reported, and interpreted among laboratories. TMB standardization efforts are underway, but no published guidance for TMB validation and reporting is currently available. Recognizing the current challenges of clinical TMB testing, the Association for Molecular Pathology convened a multidisciplinary collaborative working group with representation from the American Society of Clinical Oncology, the College of American Pathologists, and the Society for the Immunotherapy of Cancer to review the laboratory practices surrounding TMB and develop recommendations for the analytical validation and reporting of TMB testing based on survey data, literature review, and expert consensus. These recommendations encompass pre-analytical, analytical, and postanalytical factors of TMB analysis, and they emphasize the relevance of comprehensive methodological descriptions to allow comparability between assays.
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Affiliation(s)
- Larissa V Furtado
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Carlo Bifulco
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Providence Portland Medical Center, Portland, Oregon
| | - Daniel Dolderer
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Jupiter Medical Center, Jupiter, Florida
| | - Susan J Hsiao
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Benjamin R Kipp
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Neal I Lindeman
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Weill Cornell Medicine, New York, New York
| | - Lauren L Ritterhouse
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Ahmet Zehir
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan A Nowak
- The Tumor Mutational Burden Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
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Pan M, Zhou MY, Jiang C, Zhang Z, Bui NQ, Bien J, Siy A, Achacoso N, Solorzano AV, Tse P, Chung E, Thomas S, Habel LA, Ganjoo KN. Sex-dependent Prognosis of Patients with Advanced Soft Tissue Sarcoma. Clin Cancer Res 2024; 30:413-419. [PMID: 37831066 PMCID: PMC10792361 DOI: 10.1158/1078-0432.ccr-23-1990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE To examine whether overall survival (OS) differs for male and female patients with advanced soft-tissue sarcoma (STS). EXPERIMENTAL DESIGN The study included patients from Kaiser Permanente Northern California and Stanford Cancer Center with grade 2 and 3 locally advanced or metastatic STS whose tumor underwent next-generation sequencing. We used Cox regression modeling to examine association of sex and OS adjusting for other important factors. RESULTS Among 388 eligible patients, 174 had leiomyosarcoma (LMS), 136 had undifferentiated pleomorphic sarcoma (UPS), and 78 had liposarcoma. OS for male versus female patients appeared to be slightly better among the full cohort [HR = 0.89; 95% confidence interval (CI), 0.66-1.20]; this association appeared to be stronger among the subsets of patients with LMS (HR = 0.76; 95% CI, 0.39-1.49) or liposarcoma (HR = 0.74; 95% CI, 0.32-1.70). Better OS for male versus female patients was also observed among all molecular subgroups except mutRB1 and mutATRX, especially among patients whose tumor retained wtTP53 (HR = 0.73; 95% CI, 0.44-1.18), wtCDKN2A (HR = 0.85; 95% CI, 0.59-1.23), wtRB1 (HR = 0.73; 95% CI, 0.51-1.04), and among patients whose tumor had mutPTEN (HR = 0.37; 95% CI, 0.09-1.62). OS also appeared to be better for males in the MSK-IMPACT and TCGA datasets. CONCLUSIONS A fairly consistent pattern of apparent better OS for males across histologic and molecular subgroups of STS was observed. If confirmed, our results could have implications for clinical practice for prognostic stratification and possibly treatment tailoring as well as for future clinical trials design.
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Affiliation(s)
- Minggui Pan
- Sarcoma Program, Division of Oncology, Stanford University School of Medicine, Stanford, California
- Division of Research, Kaiser Permanente, Oakland, California
| | - Maggie Yuxi Zhou
- Sarcoma Program, Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Chen Jiang
- Division of Research, Kaiser Permanente, Oakland, California
| | - Zheyang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University; and National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, China
| | - Nam Q. Bui
- Sarcoma Program, Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Jeffrey Bien
- Sarcoma Program, Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Amanda Siy
- Sarcoma Program, Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Ninah Achacoso
- Division of Research, Kaiser Permanente, Oakland, California
| | | | - Pamela Tse
- Division of Research, Kaiser Permanente, Oakland, California
| | - Elaine Chung
- Division of Research, Kaiser Permanente, Oakland, California
| | - Sachdev Thomas
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, California
| | - Laurel A. Habel
- Division of Research, Kaiser Permanente, Oakland, California
| | - Kristen N. Ganjoo
- Sarcoma Program, Division of Oncology, Stanford University School of Medicine, Stanford, California
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Lozar T, Laklouk I, Golfinos AE, Gavrielatou N, Xu J, Flynn C, Keske A, Yu M, Bruce JY, Wang W, Grasic Kuhar C, Bailey HH, Harari PM, Dinh HQ, Rimm DL, Hu R, Lambert PF, Fitzpatrick MB. Stress Keratin 17 Is a Predictive Biomarker Inversely Associated with Response to Immune Check-Point Blockade in Head and Neck Squamous Cell Carcinomas and Beyond. Cancers (Basel) 2023; 15:4905. [PMID: 37835599 PMCID: PMC10571921 DOI: 10.3390/cancers15194905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Low response rates in immune check-point blockade (ICB)-treated head and neck squamous cell carcinoma (HNSCC) drive a critical need for robust, clinically validated predictive biomarkers. Our group previously showed that stress keratin 17 (CK17) suppresses macrophage-mediated CXCL9/CXCL10 chemokine signaling involved in attracting activated CD8+ T cells into tumors, correlating with decreased response rate to pembrolizumab-based therapy in a pilot cohort of ICB-treated HNSCC (n = 26). Here, we performed an expanded analysis of the predictive value of CK17 in ICB-treated HNSCC according to the REMARK criteria and investigated the gene expression profiles associated with high CK17 expression. Pretreatment samples from pembrolizumab-treated HNSCC patients were stained via immunohistochemistry using a CK17 monoclonal antibody (n = 48) and subjected to spatial transcriptomic profiling (n = 8). Our findings were validated in an independent retrospective cohort (n = 22). CK17 RNA expression in pembrolizumab-treated patients with various cancer types was investigated for predictive significance. Of the 48 patients (60% male, median age of 61.5 years), 21 (44%) were CK17 high, and 27 (56%) were CK17 low. A total of 17 patients (35%, 77% CK17 low) had disease control, while 31 patients (65%, 45% CK17 low) had progressive disease. High CK17 expression was associated with a lack of disease control (p = 0.037), shorter time to treatment failure (p = 0.025), and progression-free survival (PFS, p = 0.004), but not overall survival (OS, p = 0.06). A high CK17 expression was associated with lack of disease control in an independent validation cohort (p = 0.011). PD-L1 expression did not correlate with CK17 expression or clinical outcome. CK17 RNA expression was predictive of PFS and OS in 552 pembrolizumab-treated cancer patients. Our findings indicate that high CK17 expression may predict resistance to ICB in HNSCC patients and beyond.
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Affiliation(s)
- Taja Lozar
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
- University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Israa Laklouk
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Athena E Golfinos
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
| | - Niki Gavrielatou
- Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Jin Xu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Christopher Flynn
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Aysenur Keske
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Justine Y Bruce
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Wei Wang
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
| | - Cvetka Grasic Kuhar
- University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia
| | - Howard H Bailey
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Paul M Harari
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - David L Rimm
- Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Rong Hu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
| | - Megan B Fitzpatrick
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
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Ferreiro-Pantín M, Anido-Herranz U, Betancor YZ, Cebey-López V, León-Mateos L, García-González J, García-Acuña SM, Fernández-Díaz N, Tubio JMC, López-López R, Ruiz-Bañobre J. Clinical, molecular, and immune correlates of the Immunotherapy Response Score in patients with advanced urothelial carcinoma under atezolizumab monotherapy: analysis of the phase II IMvigor210 trial. ESMO Open 2023; 8:101611. [PMID: 37516059 PMCID: PMC10485401 DOI: 10.1016/j.esmoop.2023.101611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/22/2023] [Accepted: 06/22/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND In the advanced urothelial carcinoma (aUC) scenario there are no consistent immune checkpoint blockade predictive biomarkers. Recently a novel pan-tumor molecular tissue-based biomarker, the Immunotherapy Response Score (IRS), has been proposed. We conducted a retrospective study to validate the prognostic/predictive utility of the IRS in patients with aUC under atezolizumab monotherapy and to characterize its underlying molecular/immune features in the context of the IMvigor210 phase II trial. PATIENTS AND METHODS This is a post hoc pooled analysis of 261 patients with available clinical, molecular, and immune tumor data treated with atezolizumab monotherapy in the IMvigor210 phase II clinical trial. Efficacy endpoints were overall survival (OS), disease control rate (DCR), and overall response rate (ORR). Survival estimates were calculated by the Kaplan-Meier method, and groups were compared with the log-rank test. The Cox proportional hazards regression model was used to evaluate factors independently associated with OS. Factors associated with disease control (DC) and response were tested with logistic regression in univariable and multivariable analyses. Comparisons between patient and disease characteristics were carried out using chi-square or Fisher's exact tests. All P values were two-sided, and those <0.05 were considered statistically significant. RESULTS High IRS was significantly associated with a better OS in univariable [hazard ratio (HR) = 0.49, P < 0.001] and multivariable (HR = 0.60, P = 0.018) analyses. DCR and ORR were significantly higher among high IRS patients (DCR for high IRS versus low IRS patients: 57% versus 32%, P < 0.001; ORR: 42% versus 10%, P < 0.001). High IRS patients presented a higher probability of DC and response in univariable [DC: odds ratio (OR) = 2.72, P < 0.001; response: OR = 3.92, P < 0.001] and multivariable (DC: OR = 2.72, P < 0.001; response: OR = 3.92, P < 0.001) analyses. CONCLUSIONS This study validates IRS as a strong independent prognostic and predictive biomarker for OS and DC/response in patients with aUC treated with atezolizumab monotherapy in the IMvigor210 phase II clinical trial.
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Affiliation(s)
- M Ferreiro-Pantín
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), Santiago de Compostela
| | - U Anido-Herranz
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), Santiago de Compostela
| | - Y Z Betancor
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), Santiago de Compostela
| | - V Cebey-López
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), Santiago de Compostela
| | - L León-Mateos
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), Santiago de Compostela; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid
| | - J García-González
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), Santiago de Compostela; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid
| | - S M García-Acuña
- Department of Pathology, University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - N Fernández-Díaz
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), Santiago de Compostela
| | - J M C Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), Santiago de Compostela
| | - R López-López
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), Santiago de Compostela; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid
| | - J Ruiz-Bañobre
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela, University of Santiago de Compostela (USC), Santiago de Compostela; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), University of Santiago de Compostela (USC), Santiago de Compostela; Department of Medical Oncology, University Clinical Hospital of Santiago de Compostela (SERGAS), University of Santiago de Compostela (USC), Santiago de Compostela; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid.
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Bulen BJ, Khazanov NA, Hovelson DH, Lamb LE, Matrana M, Burkard ME, Yang ESH, Edenfield WJ, Claire Dees E, Onitilo AA, Buchschacher GL, Miller AM, Parsons BM, Wassenaar TR, Suga JM, Siegel RD, Irvin W, Nair S, Slim JN, Misleh J, Khatri J, Masters GA, Thomas S, Safa MM, Anderson DM, Mowers J, Dusenbery AC, Drewery S, Plouffe K, Reeder T, Vakil H, Patrias L, Falzetta A, Hamilton R, Kwiatkowski K, Johnson DB, Rhodes DR, Tomlins SA. Validation of Immunotherapy Response Score as Predictive of Pan-solid Tumor Anti-PD-1/PD-L1 Benefit. CANCER RESEARCH COMMUNICATIONS 2023; 3:1335-1349. [PMID: 37497337 PMCID: PMC10367935 DOI: 10.1158/2767-9764.crc-23-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/16/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023]
Abstract
Immunotherapy response score (IRS) integrates tumor mutation burden (TMB) and quantitative expression biomarkers to predict anti-PD-1/PD-L1 [PD-(L)1] monotherapy benefit. Here, we evaluated IRS in additional cohorts. Patients from an observational trial (NCT03061305) treated with anti-PD-(L)1 monotherapy were included and assigned to IRS-High (-H) versus -Low (-L) groups. Associations with real-world progression-free survival (rwPFS) and overall survival (OS) were determined by Cox proportional hazards (CPH) modeling. Those with available PD-L1 IHC treated with anti-PD-(L)1 with or without chemotherapy were separately assessed. Patients treated with PD-(L)1 and/or chemotherapy (five relevant tumor types) were assigned to three IRS groups [IRS-L divided into IRS-Ultra-Low (-UL) and Intermediate-Low (-IL), and similarly assessed]. In the 352 patient anti-PD-(L)1 monotherapy validation cohort (31 tumor types), IRS-H versus IRS-L patients had significantly longer rwPFS and OS. IRS significantly improved CPH associations with rwPFS and OS beyond microsatellite instability (MSI)/TMB alone. In a 189 patient (10 tumor types) PD-L1 IHC comparison cohort, IRS, but not PD-L1 IHC nor TMB, was significantly associated with anti-PD-L1 rwPFS. In a 1,103-patient cohort (from five relevant tumor types), rwPFS did not significantly differ in IRS-UL patients treated with chemotherapy versus chemotherapy plus anti-PD-(L)1, nor in IRS-H patients treated with anti-PD-(L)1 versus anti-PD-(L)1 + chemotherapy. IRS associations were consistent across subgroups, including both Europeans and non-Europeans. These results confirm the utility of IRS utility for predicting pan-solid tumor PD-(L)1 monotherapy benefit beyond available biomarkers and demonstrate utility for informing on anti-PD-(L)1 and/or chemotherapy treatment. Significance This study confirms the utility of the integrative IRS biomarker for predicting anti-PD-L1/PD-1 benefit. IRS significantly improved upon currently available biomarkers, including PD-L1 IHC, TMB, and MSI status. Additional utility for informing on chemotherapy, anti-PD-L1/PD-1, and anti-PD-L1/PD-1 plus chemotherapy treatments decisions is shown.
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Affiliation(s)
| | | | | | | | - Marc Matrana
- Ochsner Cancer Institute, New Orleans, Louisiana
| | - Mark E. Burkard
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| | - Eddy Shih-Hsin Yang
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | | | | | - Adedayo A. Onitilo
- Cancer Care and Research Center, Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | | | | | | | | | | | | | | | - Suresh Nair
- Lehigh Valley Topper Cancer Institute, Allentown, Pennsylvania
| | | | | | - Jamil Khatri
- ChristianaCare Oncology Hematology, Newark, Delaware
| | - Gregory A. Masters
- Medical Oncology Hematology Consultants, Helen F Graham Cancer Center and Research Institute, Newark, Delaware
| | - Sachdev Thomas
- Kaiser Permanente Northern California, Oakland, California
| | | | - Daniel M. Anderson
- Metro-Minnesota Community Oncology Research Consortium, St. Louis Park, Minnesota
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Pan M, Jiang C, Zhang Z, Achacoso N, Solorzano-Pinto AV, Tse P, Chung E, Suga JM, Thomas S, Habel LA. Sex- and Co-Mutation-Dependent Prognosis in Patients with SMARCA4-Mutated Malignancies. Cancers (Basel) 2023; 15:2665. [PMID: 37345003 DOI: 10.3390/cancers15102665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/12/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Whether sex and co-mutations impact prognosis of patients with SMARCA4-mutated (mutSMARCA4) malignancies is not clear. METHODS This cohort included patients from Northern California Kaiser Permanente with next-generation sequencing (NGS) performed from August 2020 to October 2022. We used Cox regression modeling to examine the association between sex and overall survival (OS), adjusting for demographics, performance status, Charlson comorbidity index, receipt of treatment, tumor mutation burden (TMB), and TP53, KRAS, CDKN2A, STK11, and Keap1 co-mutations. RESULTS Out of 9221 cases with NGS performed, 125 cases (1.4%) had a mutSMARCA4. The most common malignancies with a mutSMARCA4 were non-small cell lung cancer (NSCLC, 35.2%), esophageal and stomach adenocarcinoma (12.8%), and cancer of unknown primary (11.2%). The most common co-mutations were p53 (mutp53, 59.2%), KRAS (mutKRAS, 28.8%), CDKN2A (mutCDKN2A, 31.2%), STK11 (mutSTK11, 12.8%), and Keap1 (mutKeap1, 8.8%) mutations. Male patients had substantially worse OS than female patients both among the entire mutSMARCA4 cohort (HR = 1.71, [95% CI 0.92-3.18]) with a median OS of 3.0 versus 43.3 months (p < 0.001), and among the NSCLC subgroup (HR = 14.2, [95% CI 2.76-73.4]) with a median OS of 2.75 months versus un-estimable (p = 0.02). Among all patients with mutSMARCA4, mutp53 versus wtp53 (HR = 2.12, [95% CI 1.04-4.29]) and mutSTK11 versus wtSTK11 (HR = 2.59, [95% CI 0.87-7.73]) were associated with worse OS. Among the NSCLC subgroup, mutp53 versus wtp53 (HR = 0.35, [0.06-1.97]) and mutKRAS versus wtKRAS (HR = 0.04, [0.003-.45]) were associated with better OS, while mutCDKN2A versus wtCDKN2A (HR = 5.04, [1.12-22.32]), mutSTK11 versus wtSTK11 (HR = 13.10, [95% CI 1.16-148.26]), and mutKeap1 versus wtKeap1 (HR = 5.06, [95% CI 0.89-26.61}) were associated with worse OS. CONCLUSION In our cohort of patients with mutSMARCA4, males had substantially worse prognosis than females, while mutTP53, mutKRAS, mutCDKN2A, mutSTK11 and mutKeap1were differentially associated with prognosis among all patients and among the NSCLC subgroup. Our results, if confirmed, could suggest potentially unidentified mechanisms that underly this sex and co-mutation-dependent prognostic disparity among patients whose tumor bears a mutSMARCA4.
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Affiliation(s)
- Minggui Pan
- Department of Oncology and Hematology, Kaiser Permanente, Santa Clara, CA 94051, USA
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Chen Jiang
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Zheyang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, and National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
| | - Ninah Achacoso
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | | | - Pam Tse
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Elaine Chung
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Jennifer Marie Suga
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Sachdev Thomas
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
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Hoffman TL, Kershberg H, Goff J, Holmquist KJ, Haque R, Alvarado M. Next-generation universal hereditary cancer screening: implementation of an automated hereditary cancer screening program for patients with advanced cancer undergoing tumor sequencing in a large HMO. Fam Cancer 2023; 22:225-235. [PMID: 36261688 PMCID: PMC10020326 DOI: 10.1007/s10689-022-00317-w] [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: 01/14/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022]
Abstract
Variants in hereditary cancer risk genes are frequently identified following tumor-based DNA sequencing and represent an opportunity to diagnose hereditary cancer. We implemented an automated hereditary cancer screening program in a large HMO for all patients who underwent tumor-based DNA sequencing to identify patients with hereditary cancer and determine if this approach augmented existing genetic counseling approaches driven by personal/family history criteria. Regular automated searches of a centralized tumor DNA variant database were performed for ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6, PALB2, and/or PMS2 variants, and germline hereditary cancer gene panel testing was offered to patients with tumor variants who had never undergone germline testing. Patients completing germline testing due to their tumor DNA test results were considered part of the tumor DNA safety net. Patients previously completing germline testing via traditional genetic counseling and tumor DNA safety net were compared for demographics, tumor type, presence of germline pathogenic/likely pathogenic (P/LP) variant, and whether NCCN criteria were met for hereditary cancer genetic testing. Germline P/LP variants were common in both groups. Patients who received germline testing through traditional genetic counseling were more likely to have cardinal hereditary tumors than the tumor DNA safety net group. Patients identified with hereditary cancer through traditional genetic counseling were more likely to meet NCCN personal/family history criteria for germline testing than the tumor DNA safety net group (99% versus 34%). A universal tumor DNA safety net screen is an important diagnostic strategy which augments traditional genetic counseling approaches based on personal/family history.
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Affiliation(s)
- Trevor L Hoffman
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA.
| | - Hilary Kershberg
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - John Goff
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - Kimberly J Holmquist
- Department of Research & Evaluation, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - Reina Haque
- Department of Research & Evaluation, Southern California Permanente Medical Group, Pasadena, CA, USA
- Dept. of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, 91101, Pasadena, CA, USA
| | - Monica Alvarado
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
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Development and validation of an integrative pan-solid tumor predictor of PD-1/PD-L1 blockade benefit. COMMUNICATIONS MEDICINE 2023; 3:14. [PMID: 36750617 PMCID: PMC9905474 DOI: 10.1038/s43856-023-00243-7] [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: 01/25/2022] [Accepted: 01/12/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Anti-PD-1 and PD-L1 (collectively PD-[L]1) therapies are approved for many advanced solid tumors. Biomarkers beyond PD-L1 immunohistochemistry, microsatellite instability, and tumor mutation burden (TMB) may improve benefit prediction. METHODS Using treatment data and genomic and transcriptomic tumor tissue profiling from an observational trial (NCT03061305), we developed Immunotherapy Response Score (IRS), a pan-tumor predictive model of PD-(L)1 benefit. IRS real-world progression free survival (rwPFS) and overall survival (OS) prediction was validated in an independent cohort of trial patients. RESULTS Here, by Cox modeling, we develop IRS-which combines TMB with CD274, PDCD1, ADAM12 and TOP2A quantitative expression-to predict pembrolizumab rwPFS (648 patients; 26 tumor types; IRS-High or -Low groups). In the 248 patient validation cohort (248 patients; 24 tumor types; non-pembrolizumab PD-[L]1 monotherapy treatment), median rwPFS and OS are significantly longer in IRS-High vs. IRS-Low patients (rwPFS adjusted hazard ratio [aHR] 0.52, p = 0.003; OS aHR 0.49, p = 0.005); TMB alone does not significantly predict PD-(L)1 rwPFS nor OS. In 146 patients treated with systemic therapy prior to pembrolizumab monotherapy, pembrolizumab rwPFS is only significantly longer than immediately preceding therapy rwPFS in IRS-High patients (interaction test p = 0.001). In propensity matched lung cancer patients treated with first-line pembrolizumab monotherapy or pembrolizumab+chemotherapy, monotherapy rwPFS is significantly shorter in IRS-Low patients, but is not significantly different in IRS-High patients. Across 24,463 molecularly-evaluable trial patients, 7.6% of patients outside of monotherapy PD-(L)1 approved tumor types are IRS-High/TMB-Low. CONCLUSIONS The validated, predictive, pan-tumor IRS model can expand PD-(L)1 monotherapy benefit outside currently approved indications.
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Wang D, Zhang Y, li R, Li J, Zhang R. Consistency and reproducibility of large panel next-generation sequencing: Multi-laboratory assessment of somatic mutation detection on reference materials with mismatch repair and proofreading deficiency. J Adv Res 2022; 44:161-172. [PMID: 36725187 PMCID: PMC9937796 DOI: 10.1016/j.jare.2022.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Clinical precision oncology increasingly relies on accurate genome-wide profiling using large panel next generation sequencing; however, difficulties in accurate and consistent detection of somatic mutation from individual platforms and pipelines remain an open question. OBJECTIVES To obtain paired tumor-normal reference materials that can be effectively constructed and interchangeable with clinical samples, and evaluate the performance of 56 panels under routine testing conditions based on the reference samples. METHODS Genes involved in mismatch repair and DNA proofreading were knocked down using the CRISPR-Cas9 technology to accumulate somatic mutations in a defined GM12878 cell line. They were used as reference materials to comprehensively evaluate the reproducibility and accuracy of detection results of oncopanels and explore the potential influencing factors. RESULTS In total, 14 paired tumor-normal reference DNA samples from engineered cell lines were prepared, and a reference dataset comprising 168 somatic mutations in a high-confidence region of 1.8 Mb were generated. For mutations with an allele frequency (AF) of more than 5% in reference samples, 56 panels collectively reported 1306 errors, including 729 false negatives (FNs), 179 false positives (FPs) and 398 reproducibility errors. The performance metric varied among panels with precision and recall ranging from 0.773 to 1 and 0.683 to 1, respectively. Incorrect and inadequate filtering accounted for a large proportion of false discovery (including FNs and FPs), while low-quality detection, cross-contamination and other sequencing errors during the wet bench process were other sources of FNs and FPs. In addition, low AF (<5%) considerably influenced the reproducibility and comparability among panels. CONCLUSIONS This study provided an integrated practice for developing reference standard to assess oncopanels in detecting somatic mutations and quantitatively revealed the source of detection errors. It will promote optimization, validation, and quality control among laboratories with potential applicability in clinical use.
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Affiliation(s)
- Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Rui li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
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