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Ahmed J, Das B, Shin S, Chen A. Challenges and Future Directions in the Management of Tumor Mutational Burden-High (TMB-H) Advanced Solid Malignancies. Cancers (Basel) 2023; 15:5841. [PMID: 38136385 PMCID: PMC10741991 DOI: 10.3390/cancers15245841] [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: 11/06/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
A standardized assessment of Tumor Mutational Burden (TMB) poses challenges across diverse tumor histologies, treatment modalities, and testing platforms, requiring careful consideration to ensure consistency and reproducibility. Despite clinical trials demonstrating favorable responses to immune checkpoint inhibitors (ICIs), not all patients with elevated TMB exhibit benefits, and certain tumors with a normal TMB may respond to ICIs. Therefore, a comprehensive understanding of the intricate interplay between TMB and the tumor microenvironment, as well as genomic features, is crucial to refine its predictive value. Bioinformatics advancements hold potential to improve the precision and cost-effectiveness of TMB assessments, addressing existing challenges. Similarly, integrating TMB with other biomarkers and employing comprehensive, multiomics approaches could further enhance its predictive value. Ongoing collaborative endeavors in research, standardization, and clinical validation are pivotal in harnessing the full potential of TMB as a biomarker in the clinic settings.
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Affiliation(s)
- Jibran Ahmed
- Developmental Therapeutics Clinic (DTC), National Cancer Institute (NCI), National Institute of Health (NIH), Bethesda, MD 20892, USA
| | - Biswajit Das
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sarah Shin
- Developmental Therapeutics Clinic (DTC), National Cancer Institute (NCI), National Institute of Health (NIH), Bethesda, MD 20892, USA
| | - Alice Chen
- Developmental Therapeutics Clinic (DTC), National Cancer Institute (NCI), National Institute of Health (NIH), Bethesda, MD 20892, USA
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O'Connell GC, Wang J, Smothers C. Donor white blood cell differential is the single largest determinant of whole blood gene expression patterns. Genomics 2023; 115:110708. [PMID: 37730167 PMCID: PMC10872590 DOI: 10.1016/j.ygeno.2023.110708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/18/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
It has become widely accepted that sample cellular composition is a significant determinant of the gene expression patterns observed in any transcriptomic experiment performed with bulk tissue. Despite this, many investigations currently performed with whole blood do not experimentally account for possible inter-specimen differences in cellularity, and often assume that any observed gene expression differences are a result of true differences in nuclear transcription. In order to determine how confounding of an assumption this may be, in this study, we recruited a large cohort of human donors (n = 138) and used a combination of next generation sequencing and flow cytometry to quantify and compare the underlying contributions of variance in leukocyte counts versus variance in other biological factors to overall variance in whole blood transcript levels. Our results suggest that the combination of donor neutrophil and lymphocyte counts alone are the primary determinants of whole blood transcript levels for up to 75% of the protein-coding genes expressed in peripheral circulation, whereas the other factors such as age, sex, race, ethnicity, and common disease states have comparatively minimal influence. Broadly, this infers that a majority of gene expression differences observed in experiments performed with whole blood are driven by latent differences in leukocyte counts, and that cell count heterogeneity must be accounted for to meaningfully biologically interpret the results.
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Affiliation(s)
- Grant C O'Connell
- Molecular Biomarker Core, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, Case Western Reserve University, Cleveland, OH, USA.
| | - Jing Wang
- Molecular Biomarker Core, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, Case Western Reserve University, Cleveland, OH, USA
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Tanwar NA, Malhotra R, Satheesh AP, Khuntia SP, Sreekanthreddy P, Varghese L, Kolla S, Chandrani P, Choughule A, Pange P, Gupta V, Noronha V, Patil VM, Pramanik R, Kumar S, Nayak SP, Babu S, Shetty R, Kantharaju M, Chinder PS, Korlimarla A, Srinath BS, Prabhash K, Rishi KD, Goswami HM, Veldore VH. Understanding the Impact of Population and Cancer Type on Tumor Mutation Burden Scores: A Comprehensive Whole-Exome Study in Cancer Patients From India. JCO Glob Oncol 2023; 9:e2300047. [PMID: 38085046 PMCID: PMC10846780 DOI: 10.1200/go.23.00047] [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: 03/17/2023] [Revised: 07/12/2023] [Accepted: 07/22/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE The purpose of this study was to understand the impact of population diversity and geographic variation on tumor mutation burden (TMB) scores across cancers and its implication on stratification of patients for immune checkpoint inhibitor (ICI) therapy. MATERIALS AND METHODS This retrospective study used whole-exome sequencing (WES) to profile 1,233 Indian patients with cancer across 30 different cancer types and to estimate their TMB scores. A WES-based pipeline was adopted, along with an indigenously developed strategy for arriving at true somatic mutations. A robust unsupervised machine learning approach was used to understand the distribution of TMB scores across different populations and within the population. RESULTS The results of the study showed a biphasic distribution of TMB scores in most cancers, with different threshold scores across cancer types. Patients with cancer in India had higher TMB scores compared with the Caucasian patients. We also observed that the TMB score value at 90th percentile (predicting high efficacy to ICI) was high in four different cancer types (sarcoma, ovary, head and neck, and breast) in the Indian cohort as compared with The Cancer Genome Atlas or public cohort. However, in lung and colorectal cancers, the TMB score distribution was similar between the two population cohorts. CONCLUSION The findings of this study indicate that it is crucial to benchmark both cancer-specific and population-specific TMB distributions to establish a TMB threshold for each cancer in various populations. Additional prospective studies on much larger population across different cancers are warranted to validate this observation to become the standard of care.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Anuradha Choughule
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Priyanka Pange
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vinod Gupta
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | | | | | | | | | - Suresh Babu
- Fortis Cancer Research Centre, Bangalore, India
| | | | | | | | - Aruna Korlimarla
- Sri Shankara Cancer Hospital & Research Centre, Bangalore, India
| | - BS Srinath
- Sri Shankara Cancer Hospital & Research Centre, Bangalore, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
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Krekeler C, Wethmar K, Mikesch JH, Kerkhoff A, Menck K, Lenz G, Schildhaus HU, Wessolly M, Hoffmann MW, Pascher A, Asmus I, Wardelmann E, Bleckmann A. Complete Metabolic Response to Combined Immune Checkpoint Inhibition after Progression of Metastatic Colorectal Cancer on Pembrolizumab: A Case Report. Int J Mol Sci 2023; 24:12056. [PMID: 37569431 PMCID: PMC10418401 DOI: 10.3390/ijms241512056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
DNA mismatch repair deficient (dMMR) and microsatellite instable (MSI) metastatic colorectal cancer (mCRC) can be successfully treated with FDA- and EMA-approved immune checkpoint inhibitors (ICI) pembrolizumab and nivolumab (as single agents targeting the anti-programmed cell death protein-1 (PD-1)) or combinations of a PD-1 inhibitor with ipilimumab, a cytotoxic T-lymphocyte-associated protein 4 (CTLA-4)-targeting antibody. The best treatment strategy beyond progression on single-agent ICI therapy remains unclear. Here, we present the case of a 63-year-old male with Lynch-syndrome-associated, microsatellite instability-high (MSI-H) mCRC who achieved a rapid normalization of his tumor markers and a complete metabolic remission (CMR), currently lasting for ten months, on sequential ICI treatment with the combination of nivolumab and ipilimumab followed by nivolumab maintenance therapy after progression on single-agent anti-PD-1 ICI therapy. The therapy was well-tolerated, and no immune-related adverse events occurred. To the best of our knowledge, this is the first case of a sustained metabolic complete remission in an MSI-H mCRC patient initially progressing on single-agent anti-PD-1 therapy. Thus, dMMR mCRC patients might benefit from sequential immune checkpoint regimens even with long-term responses. However, further sophistication of clinical algorithms for treatment beyond progression on single-agent ICI therapy in MSI-mCRC is urgently needed.
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Affiliation(s)
- Carolin Krekeler
- Department for Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany (A.B.)
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Klaus Wethmar
- Department for Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany (A.B.)
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Jan-Henrik Mikesch
- Department for Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany (A.B.)
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Andrea Kerkhoff
- Department for Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany (A.B.)
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Kerstin Menck
- Department for Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany (A.B.)
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Georg Lenz
- Department for Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany (A.B.)
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Hans-Ulrich Schildhaus
- Institute of Pathology Nordhessen, 34119 Kassel, Germany
- Institute of Pathology, University Hospital Essen, 45147 Essen, Germany
- West German Cancer Center, University Hospital Essen, 45147 Essen, Germany
| | - Michael Wessolly
- Institute of Pathology, University Hospital Essen, 45147 Essen, Germany
- West German Cancer Center, University Hospital Essen, 45147 Essen, Germany
| | - Matthias W. Hoffmann
- Department of General and Visceral Surgery, Raphaelsklinik Muenster, 48143 Muenster, Germany
| | - Andreas Pascher
- Department of General, Visceral and Transplant Surgery, University Hospital Muenster, 48149 Muenster, Germany
| | - Inga Asmus
- Department of Nuclear Medicine, University Hospital Muenster, 48149 Muenster, Germany
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, 48149 Muenster, Germany
| | - Annalen Bleckmann
- Department for Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany (A.B.)
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
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Duraisamy P, Panicker VV, Jose WM. Characterization and Prognostic Significance of Cutaneous Immune-Related Adverse Events in Indian Patients on Immune Checkpoint Inhibitor Therapy. Dermatol Pract Concept 2023; 13:e2023127. [PMID: 37557151 PMCID: PMC10412045 DOI: 10.5826/dpc.1303a127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2022] [Indexed: 08/11/2023] Open
Abstract
INTRODUCTION Cutaneous immune-related adverse-events (cIRAEs), commonly seen in cancer patients receiving immune checkpoint inhibitors (ICI) are reported to be associated with better patient survival; however, they have seldom been studied in Indian population. Recent reports suggest racial differences in IRAEs and also in survival outcomes. OBJECTIVES To study the various cIRAEs in Indian patients on ICI therapy and to analyze the association between cIRAEs and patient survival outcomes. METHODS We conducted a retrospective cohort study of 86 cancer patients receiving immunotherapies in a tertiary care hospital in India and studied incidence, nature and grades of cutaneous immune-related adverse events and the association of cIRAEs with the patient survival outcomes. RESULTS Eighty-six patients were included, of whom 16 patients (18.6%) developed cIRAEs, with pruritus (12.8%) and maculopapular eruption (8.1%) being the most common. Kaplan-Meier plot with log-rank test showed that patients developing any type of cIRAE had longer progression-free survival than those without (P = 0.023) and a better objective-response-rate (50% versus 18.5%, P = 0.008). CONCLUSIONS Most common cIRAEs in our study were pruritus and maculopapular rash. The incidence of cIRAEs was lower in our Indian cohort compared to that reported in Caucasian cohorts. Development of cutaneous immune-related adverse event in cancer patients on ICI was associated with a longer progression-free-survival and a better objective-response-rate. Thus, cIRAEs may serve as a surrogate marker for better patient outcomes.
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Affiliation(s)
- Prasanna Duraisamy
- Department of Dermatology, Amrita Institute of Medical Sciences, Kochi, India
| | | | - Wesley Mannirathil Jose
- Department of Medical Oncology and Hematology, Amrita Institute of Medical Sciences, Kochi, India
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Stieg DC, Parris JLD, Yang THL, Mirji G, Reiser SK, Murali N, Werts M, Barnoud T, Lu DY, Shinde R, Murphy ME, Claiborne DT. The African-centric P47S Variant of TP53 Confers Immune Dysregulation and Impaired Response to Immune Checkpoint Inhibition. CANCER RESEARCH COMMUNICATIONS 2023; 3:1200-1211. [PMID: 37441266 PMCID: PMC10335007 DOI: 10.1158/2767-9764.crc-23-0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/18/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
The tumor suppressor TP53 is the most frequently mutated gene in cancer and is mutationally inactivated in 50% of sporadic tumors. Inactivating mutations in TP53 also occur in Li Fraumeni syndrome (LFS). In addition to germline mutations in TP53 in LFS that completely inactivate this protein, there are many more germline mutant forms of TP53 in human populations that partially inactivate this protein: we call these partially inactivating mutations "hypomorphs." One of these hypomorphs is a SNP that exists in 6%-10% of Africans and 1%-2% of African Americans, which changes proline at amino acid 47 to serine (Pro47Ser; P47S). We previously showed that the P47S variant of p53 is intrinsically impaired for tumor suppressor function, and that this SNP is associated with increased cancer risk in mice and humans. Here we show that this SNP also influences the tumor microenvironment, and the immune microenvironment profile in P47S mice is more protumorigenic. At basal levels, P47S mice show impaired memory T-cell formation and function, along with increased anti-inflammatory (so-called "M2") macrophages. We show that in tumor-bearing P47S mice, there is an increase in immunosuppressive myeloid-derived suppressor cells and decreased numbers of activated dendritic cells, macrophages, and B cells, along with evidence for increased T-cell exhaustion in the tumor microenvironment. Finally, we show that P47S mice demonstrate an incomplete response to anti-PD-L1 therapy. Our combined data suggest that the African-centric P47S variant leads to both intrinsic and extrinsic defects in tumor suppression. Significance Findings presented here show that the P47S variant of TP53 influences the immune microenvironment, and the immune response to cancer. This is the first time that a naturally occurring genetic variant of TP53 has been shown to negatively impact the immune microenvironment and the response to immunotherapy.
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Affiliation(s)
- David C. Stieg
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Joshua L. D. Parris
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Tyler Hong Loong Yang
- Program in Immunology, Microenvironment, and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Gauri Mirji
- Program in Immunology, Microenvironment, and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Sarah Kim Reiser
- Program in Immunology, Microenvironment, and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Nivitha Murali
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Madison Werts
- Program in Immunology, Microenvironment, and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Thibaut Barnoud
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina
| | - David Y. Lu
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Rahul Shinde
- Program in Immunology, Microenvironment, and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Maureen E. Murphy
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania
| | - Daniel T. Claiborne
- Program in Immunology, Microenvironment, and Metastasis, The Wistar Institute, Philadelphia, Pennsylvania
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania
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Olateju OA, Zeng Z, Adenaiye OO, Varisco TJ, Zakeri M, Sujit SS. Investigation of racial differences in survival from non-small cell lung cancer with immunotherapy use: A Texas study. Front Oncol 2023; 12:1092355. [PMID: 36698397 PMCID: PMC9869031 DOI: 10.3389/fonc.2022.1092355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
Background The use of immunotherapy is associated with improved survival among patients with Non-Small Cell Lung Cancer (NSCLC) and has gained widespread use in its management. However, there is limited information on whether the survival benefits associated with immunotherapy differ among races and ethnicities. Objective This study aimed to investigate racial differences in survival amongst patients with NSCLC who received immunotherapy as the first-line treatment in Texas. Methods Patients with NSCLC who received immunotherapy between October 2015 to December 2018 were identified from the Texas Cancer Registry (TCR). Disease-specific survival was evaluated and compared among patients across racial/ethnic categories using the Kaplan-Meier survival analysis, log-rank test, and a multivariable Cox proportional hazard regression model following an inverse probability treatment weighting (IPTW) propensity score analysis. Results A total of 1453 patients were included in the analysis. Median survival (in months) was longest among Asians (34, 95% CI: 15-Not Estimable), followed by African Americans (AAs) (23, 95% CI: 15-34), Hispanics (22, 95% CI: 16-26), and Whites (19, 95% CI: 17-22). The adjusted regression estimates had no statistically significant differences in survival among AAs (aHR = 0.97; 95% CI = 0.78-1.20; P =0.77) and Hispanics (aHR = 0.96; 95% CI = 0.77-1.19, P =0.73) when compared to White patients. Asians on the other hand, had 40% reduction in mortality risk compared to Whites (aHR = 0.60; 95% CI = 0.39-0.94, P = 0.03). Conclusions Our study indicated that African Americans and Hispanics do not have poorer survival compared to White patients when receiving immunotherapy as first-line treatment. Asians however had longer survival compared to Whites. Our findings suggest that existing racial disparity in NSCLC survival might be mitigated with the use of immunotherapy and should be considered in providing care to these minority groups.
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Affiliation(s)
- Olajumoke A. Olateju
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston College of Pharmacy, Houston, TX, United States
| | - Zhen Zeng
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston College of Pharmacy, Houston, TX, United States
| | - Oluwasanmi O. Adenaiye
- Department of Medicine and Rehabilitation Science, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Tyler J. Varisco
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston College of Pharmacy, Houston, TX, United States
| | - Marjan Zakeri
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston College of Pharmacy, Houston, TX, United States
| | - Sansgiry S. Sujit
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston College of Pharmacy, Houston, TX, United States,*Correspondence: Sansgiry S. Sujit,
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