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Kaur P, Ring A, Porras TB, Zhou G, Lu J, Kang I, Lang JE. Integrated Proteogenomic Analysis Reveals Distinct Potentially Actionable Therapeutic Vulnerabilities in Triple-Negative Breast Cancer Subtypes. Cancers (Basel) 2024; 16:516. [PMID: 38339267 PMCID: PMC10854633 DOI: 10.3390/cancers16030516] [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: 09/27/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is characterized by an aggressive clinical presentation and a paucity of clinically actionable genomic alterations. Here, we utilized the Cancer Genome Atlas (TCGA) to explore the proteogenomic landscape of TNBC subtypes to see whether genomic alterations can be inferred from proteomic data. We found only 4% of the protein level changes are explained by mutations, while 21% of the protein and 35% of the transcriptomics changes were determined by copy number alterations (CNAs). We found tighter coupling between proteome and genome in some genes that are predicted to be the targets of drug inhibitors, including CDKs, PI3K, tyrosine kinase (TKI), and mTOR. The validation of our proteogenomic workflow using mass spectrometry Clinical Proteomic Tumor Analysis Consortium (MS-CPTAC) data also demonstrated the highest correlation between protein-RNA-CNA. The integrated proteogenomic approach helps to prioritize potentially actionable targets and may enable the acceleration of personalized cancer treatment.
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Affiliation(s)
- Pushpinder Kaur
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Alexander Ring
- Department of Medical Oncology and Hematology, University Hospital Zürich, 8091 Zurich, Switzerland
| | - Tania B. Porras
- Cancer and Blood Disease Institute, Children Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA
| | - Guang Zhou
- Division of Breast Services, Department of General Surgery, Digestive Disease and Surgery Institute, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Janice Lu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Medical Oncology, Department of Medicine, University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Irene Kang
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Medical Oncology, Department of Medicine, University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Julie E. Lang
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Breast Services, Department of General Surgery, Digestive Disease and Surgery Institute, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Welter L, Zheng S, Setayesh SM, Morikado M, Agrawal A, Nevarez R, Naghdloo A, Pore M, Higa N, Kolatkar A, Thiele JA, Sharma P, Moore HCF, Richer JK, Elias A, Pienta KJ, Zurita AJ, Gross ME, Shishido SN, Hicks J, Velasco CR, Kuhn P. Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics. Cancers (Basel) 2023; 15:3949. [PMID: 37568766 PMCID: PMC10417732 DOI: 10.3390/cancers15153949] [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: 06/13/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Bi-directional crosstalk between the tumor and the tumor microenvironment (TME) has been shown to increase the rate of tumor evolution and to play a key role in neoplastic progression, therapeutic resistance, and a patient's overall survival. Here, we set out to use a comprehensive liquid-biopsy analysis to study cancer and specific TME cells in circulation and their association with disease status. Cytokeratin+, CD45- circulating rare cells (CRCs) from nine breast and four prostate cancer patients were characterized through morphometrics, single-cell copy number analysis, and targeted multiplexed proteomics to delineate cancer cell lineage from other rare cells originating in the TME. We show that we can detect epithelial circulating tumor cells (EPI.CTC), CTCs undergoing epithelial-to-mesenchymal transition (EMT.CTC) and circulating endothelial cells (CECs) using a universal rare event detection platform (HDSCA). Longitudinal analysis of an index patient finds that CTCs are present at the time of disease progression, while CECs are predominately present at the time of stable disease. In a small cohort of prostate and breast cancer patients, we find high inter-patient and temporal intra-patient variability in the expression of tissue specific markers such as ER, HER2, AR, PSA and PSMA and EpCAM. Our study stresses the importance of the multi-omic characterization of circulating rare cells in patients with breast and prostate carcinomas, specifically highlighting overlapping and cell type defining proteo-genomic characteristics of CTCs and CECs.
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Affiliation(s)
- Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Serena Zheng
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Sonia Maryam Setayesh
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael Morikado
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Arushi Agrawal
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Amin Naghdloo
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Milind Pore
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Nikki Higa
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Jana-Aletta Thiele
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Priyanka Sharma
- University of Kansas Medical Center, Westwood, KS 66205, USA;
| | - Halle C. F. Moore
- Cleveland Clinic Taussig Cancer Institute, Cleveland, OH 44195, USA;
| | - Jennifer K. Richer
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (J.K.R.); (A.E.)
| | - Anthony Elias
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (J.K.R.); (A.E.)
| | - Kenneth J. Pienta
- The Cancer Ecology Center, Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA;
| | - Amado J. Zurita
- Department of Genitourinary Medical Oncology, MD Anderson, Houston, TX 77230, USA;
| | - Mitchell E. Gross
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA 90064, USA;
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carmen Ruiz Velasco
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Brewer T, Yehia L, Bazeley P, Eng C. Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome. NPJ Genom Med 2023; 8:14. [PMID: 37407629 DOI: 10.1038/s41525-023-00361-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Women with germline PTEN variants (PTEN hamartoma tumor syndrome, PHTS) have up to 85% lifetime risk of female breast cancer (BC). We previously showed that PHTS-derived BCs are distinct from sporadic BCs both at the clinical and genomic levels. In this study, we examined somatic copy number variations (CNV) and transcriptome data to further characterize the somatic landscape of PHTS-derived BCs. We analyzed exome sequencing data from 44 BCs from women with PHTS for CNV. The control group comprised of 558 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset. Here, we found that PHTS-derived BCs have several distinct CNV peaks compared to TCGA. Furthermore, RNA sequencing data revealed that PHTS-derived BCs have a distinct immunologic cell type signature, which points toward cancer immune evasion. Transcriptomic data also revealed PHTS-derived BCs with pathogenic germline PTEN variants appear to have vitamin E degradation as a key pathway associated with tumorigenesis. In conclusion, our study revealed distinct CNV x transcript features in PHTS-derived BCs, which further facilitate understanding of BC biology arising in the setting of germline PTEN mutations.
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Affiliation(s)
- Takae Brewer
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA.
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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Classification with 2-D convolutional neural networks for breast cancer diagnosis. Sci Rep 2022; 12:21857. [PMID: 36528717 PMCID: PMC9759564 DOI: 10.1038/s41598-022-26378-6] [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: 04/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is the most common cancer in women. Classification of cancer/non-cancer patients with clinical records requires high sensitivity and specificity for an acceptable diagnosis test. The state-of-the-art classification model-convolutional neural network (CNN), however, cannot be used with such kind of tabular clinical data that are represented in 1-D format. CNN has been designed to work on a set of 2-D matrices whose elements show some correlation with neighboring elements such as in image data. Conversely, the data examples represented as a set of 1-D vectors-apart from the time series data-cannot be used with CNN, but with other classification models such as Recurrent Neural Networks for tabular data or Random Forest. We have proposed three novel preprocessing methods of data wrangling that transform a 1-D data vector, to a 2-D graphical image with appropriate correlations among the fields to be processed on CNN. We tested our methods on Wisconsin Original Breast Cancer (WBC) and Wisconsin Diagnostic Breast Cancer (WDBC) datasets. To our knowledge, this work is novel on non-image tabular data to image data transformation for the non-time series data. The transformed data processed with CNN using VGGnet-16 shows competitive results for the WBC dataset and outperforms other known methods for the WDBC dataset.
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Shi H, Seegobin K, Heng F, Zhou K, Chen R, Qin H, Manochakian R, Zhao Y, Lou Y. Genomic landscape of lung adenocarcinomas in different races. Front Oncol 2022; 12:946625. [PMID: 36248982 PMCID: PMC9557241 DOI: 10.3389/fonc.2022.946625] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022] Open
Abstract
Background Lung adenocarcinoma is a molecularly heterogeneous disease. Several studies, including The Cancer Genome Atlas Research Network (TCGA) and Lung Cancer Mutation Consortium (LCMC), explored the genetic alterations among different ethnic groups. However, minority groups are often under-represented in these relevant studies and the genomic alterations among racial groups are not fully understood. Methods We analyze genomic characteristics among racial groups to understand the diversities and their impact on clinical outcomes. Results Native Americans had significantly higher rates of insertions and deletions than other races (P<0.001). Among patients with lung adenocarcinomas, EGFR and KRAS were the highest discrepancy genes in the different racial groups (P<0.001). The EGFR exon 21 L858R point mutation was three times higher in Asians than in all other races (P<0.001). Asians, Whites, and Blacks had 4.7%, 3.1%, and 1.8% ALK rearrangement, respectively (P<0.001). White patients had the highest rates of reported KRAS G12C (15.51%) than other races (P<0.001). Whites (17.2%), Blacks (15.1%), and Other (15.7%) had higher rates of STK11 mutation than Asians (3.94%) (P<0.001). RET rearrangement and ERBB2 amplification were more common in Asian patients than in Other racial groups. Apart from point mutations, structural variations, and fusion genes, we identified a significant amount of copy number alterations in each race. Conclusions The tumor genomic landscape is significantly distinct in different races. This data would shed light on the understanding of molecular alterations and their impacts on clinical management in different lung cancer patients.
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Affiliation(s)
- Huashan Shi
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, United States
| | - Karan Seegobin
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Fei Heng
- Department of Mathematics and Statistics, University of North Florida, Jacksonville, FL, United States
| | - Kexun Zhou
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, United States
| | - Ruqin Chen
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Hong Qin
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Rami Manochakian
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Yujie Zhao
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Yanyan Lou
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
- *Correspondence: Yanyan Lou,
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Shen Y, Nussbaum YI, Manjunath Y, Hummel JJ, Ciorba MA, Warren WC, Kaifi JT, Papageorgiou C, Cortese R, Shyu CR, Mitchem JB. TBX21 Methylation as a Potential Regulator of Immune Suppression in CMS1 Subtype Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14194594. [PMID: 36230517 PMCID: PMC9558549 DOI: 10.3390/cancers14194594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL) infiltration is associated with survival, recurrence, and therapeutic response in colorectal cancer (CRC). Immune checkpoint inhibitor (ICI) therapy, which requires CTLs for response, does not work for most CRC patients. Therefore, it is critical to improve our understanding of immune resistance in this disease. We utilized 2391 CRC patients and 7 omics datasets, integrating clinical and genomic data to determine how DNA methylation may impact survival and CTL function in CRC. Using comprehensive molecular subtype (CMS) 1 patients as reference, we found TBX21 to be the only gene with altered expression and methylation that was associated with CTL infiltration. We found that CMS1 patients with high TBX21 expression and low methylation had a significant survival advantage. To confirm the role of Tbx21 in CTL function, we utilized scRNAseq data, demonstrating the association of TBX21 with markers of enhanced CTL function. Further analysis using pathway enrichment found that the genes TBX21, MX1, and SP140 had altered expression and methylation, suggesting that the TP53/P53 pathway may modify TBX21 methylation to upregulate TBX21 expression. Together, this suggests that targeting epigenetic modification more specifically for therapy and patient stratification may provide improved outcomes in CRC.
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Affiliation(s)
- Yuanyuan Shen
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Yulia I. Nussbaum
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Yariswamy Manjunath
- Harry S. Truman Memorial Veterans’ Hospital, University of Missouri, Columbia, MO 65211, USA
| | - Justin J. Hummel
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Matthew A. Ciorba
- School of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wesley C. Warren
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jussuf T. Kaifi
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
- Harry S. Truman Memorial Veterans’ Hospital, University of Missouri, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Columbia, MO 65211, USA
- School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Christos Papageorgiou
- School of Medicine, University of Missouri, Columbia, MO 65211, USA
- Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65211, USA
| | - Rene Cortese
- School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Chi-Ren Shyu
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
- College of Engineering, University of Missouri, Columbia, MO 65211, USA
| | - Jonathan B. Mitchem
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
- Harry S. Truman Memorial Veterans’ Hospital, University of Missouri, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Columbia, MO 65211, USA
- School of Medicine, University of Missouri, Columbia, MO 65211, USA
- Correspondence:
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Left sided breast cancer is associated with aggressive biology and worse outcomes than right sided breast cancer. Sci Rep 2022; 12:13377. [PMID: 35927418 PMCID: PMC9352772 DOI: 10.1038/s41598-022-16749-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022] Open
Abstract
Breast cancer is more common on the left side than the right side. We aim to evaluate differences in clinicopathological and genomic characteristics based on laterality. We analyzed survival outcomes and clinical characteristics of 881,320 patients recorded by the Surveillance, Epidemiology, and End Results (SEER) program. The Cancer Genome Atlas (TCGA) was used to explore genomic and clinical features from 1,062 patients. Gene expression data was used to quantitate cytolytic activity and hallmark gene-sets were used for gene set enrichment analysis. An institutional retrospective review was conducted on 155 patients treated with neoadjuvant chemotherapy (NACT). Patient characteristics were summarized by pathological complete response (pCR). Left sided tumors were found to be more prevalent than right sided tumors. No major clinicopathological differences were noted by laterality. Left sided breast cancer demonstrated poorer outcomes versus right sided tumors (HR 1.05, 95% CI 1.01–1.08; p = 0.011). Cell proliferation gene sets, including E2F Targets, G2M Checkpoint, Mitotic spindle, and MYC Targets, were enriched on the left side compared to the right. Left sided tumors had lower pCR rates versus right sided tumors (15.4% versus 29.9%, p = 0.036). Our findings suggest that left sided breast cancer is associated with aggressive biology and worse outcomes compared to right sided breast cancer.
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Brewer T, Yehia L, Bazeley P, Eng C. Exome sequencing reveals a distinct somatic genomic landscape in breast cancer from women with germline PTEN variants. Am J Hum Genet 2022; 109:1520-1533. [PMID: 35931053 PMCID: PMC9388380 DOI: 10.1016/j.ajhg.2022.07.005] [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: 03/25/2022] [Accepted: 07/01/2022] [Indexed: 02/06/2023] Open
Abstract
Germline PTEN variants (PTEN hamartoma tumor syndrome [PHTS]) confer up to 85% lifetime risk of female breast cancer (BC). BCs arising in PHTS are clinically distinct from sporadic BCs, including younger age of onset, multifocality, and an increased risk of second primary BCs. Yet, there is no previous investigation into the underlying genomic landscape of this entity. We sought to address the hypothesis that BCs arising in PHTS have a distinct genomic landscape compared to sporadic counterparts. We performed and analyzed exome sequencing data from 44 women with germline PTEN variants who developed BCs. The control cohort comprised of 497 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset. We demonstrate that PHTS-derived BCs have a distinct somatic mutational landscape compared to the sporadic counterparts, namely second somatic hits in PTEN, distinct mutational signatures, and increased genomic instability. The PHTS group had a significantly higher frequency of somatic PTEN variants compared to TCGA (22.7% versus 5.6%; odds ratio [OR] 4.93; 95% confidence interval [CI] 2.21 to 10.98; p < 0.001) and a lower mutational frequency in PIK3CA (22.7% versus 33.4%; OR 0.59; 95% CI 0.28 to 1.22; p = 0.15). Somatic variants in PTEN and PIK3CA were mutually exclusive in PHTS (p = 0.01) but not in TCGA. Our findings have important implications for the personalized management of PTEN-related BCs, especially in the context of more accessible genetic testing.
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Affiliation(s)
- Takae Brewer
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA,Corresponding author
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You D, Zhang S, Yan S, Ding Y, Li C, Cheng X, Wu L, Wang W, Zhang T, Li Z, He Y. SAMHD1 as a prognostic and predictive biomarker in stage II colorectal cancer: A multicenter cohort study. Front Oncol 2022; 12:939982. [PMID: 35978833 PMCID: PMC9376296 DOI: 10.3389/fonc.2022.939982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
Background The identification of high-risk population patients is key to the personalized treatment options for the stage II colorectal cancers. The use of proteomics in the prognosis of patients with stage II colorectal cancer remains unclear. Methods Using quantitative proteomics, we analyzed proteins that are differentially expressed in the tumor and adjacent normal tissues of 11 paired colorectal cancer patients with and without recurrence selected by a nested case-control design. Of the 21 identified proteins, we selected one candidate protein. The association of the corresponding gene of the selected protein with overall survival (OS) and adjuvant chemotherapy was analyzed using two independent cohorts of patients with stages II colorectal cancer. Results Sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) was selected as the candidate biomarker. A group of 124 patients (12.5%) were stratified into SAMHD1-high subgroup. The 5-year OS rate of SAMHD1-high patients was lower than that of SAMHD1-low patients with stage II colorectal cancer (discovery cohort: hazard ratio [HR] = 2.89, 95% confidence interval [CI], 1.17-7.18, P = 0.016; validation cohort: HR = 2.25, 95% CI, 1.17-4.34, P = 0.013). The Cox multivariate analysis yielded similar results. In a pooled database, the 5-year OS rate was significantly different between patients with and without adjuvant chemotherapy among stage II SAMHD1-low tumors than in patients with stage II SAMHD1-high tumors (88% vs. 77%, P = 0.032). Conclusions SAMHD1-high expression could help in identifying patients with stage II colorectal cancer with poor prognosis and less benefit from adjuvant chemotherapy.
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Affiliation(s)
- Dingyun You
- Department of Dental Research, The Affiliated Stomatological Hospital of Kunming Medical University, Kunming, China
- Yunnan Key Laboratory of Stomatology, Kunming Medical University, Kunming, China
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming, China
| | - Shuai Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shan Yan
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming, China
| | - Yingying Ding
- Department of Radiology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Chunxia Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xianshuo Cheng
- Department of Colorectal Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Lin Wu
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Weizhou Wang
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Tao Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhenhui Li
- Department of Radiology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Yongwen He
- Department of Dental Research, The Affiliated Stomatological Hospital of Kunming Medical University, Kunming, China
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10
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Shishido SN, Masson R, Xu L, Welter L, Prabakar RK, D' Souza A, Spicer D, Kang I, Jayachandran P, Hicks J, Lu J, Kuhn P. Disease characterization in liquid biopsy from HER2-mutated, non-amplified metastatic breast cancer patients treated with neratinib. NPJ Breast Cancer 2022; 8:22. [PMID: 35181666 PMCID: PMC8857263 DOI: 10.1038/s41523-022-00390-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
Metastatic breast cancer (mBC) patients have a high risk of progression and face poor prognosis overall, with about one third (34%) surviving five years or more. In rare instances (2-4% of cases) patients with mBC have ERBB2 (HER2) activating mutations but are ERBB2 non-amplified. Neratinib is a potent, irreversible inhibitor that binds HER2 and inhibits downstream signaling. We used the previously validated high-definition single cell assay (HDSCA) workflow to investigate the clinical significance of the liquid biopsy in ERBB2 mutant, non-amplified, post-menopausal mBC patients starting neratinib and fulvestrant combination therapy. Characterization with a comprehensive liquid biopsy methodology (HDSCA) included genomic analysis of both the cell-free DNA (cfDNA) and single circulating tumor cells (CTCs) to monitor tumor evolution and identify potential mutational variants unique to the patient's clinical response. A limited series of five sequentially enrolled patients presented here were from the MutHER ( https://www.clinicaltrials.gov , NCT01670877) or SUMMIT ( https://www.clinicaltrials.gov , NCT01953926) trials. Patients had an average of 5.4 lines of therapy before enrollment, variable hormone receptor status, and ERBB2 mutations at diagnosis and during treatment. CTC enumeration alone was not sufficient to predict clinical response. Treatment pressure was shown to lead to an observable change in CTC morphology and genomic instability (GI), suggesting these parameters may inform prognosis. Single cell copy number alteration (CNA) analysis indicated that the persistence or development of a clonal population of CTCs during treatment was associated with a worse response. Hierarchical clustering analysis of the single cells across all patients and timepoints identified distinct aberrant regions shared among patients, comprised of 26 genes that are similarly affected and may be related to drug resistance. Additionally, the genomic analysis of the cfDNA, identified new mutations in ERBB2, PIK3CA, and TP53 that arose likely due to treatment pressure in a patient with poor response, further providing insights on the dynamics of the cancer genome over the course of therapy. The data presented in this small cohort study demonstrates the feasibility of real-time molecular profiling of the cellular and acellular fractions of the liquid biopsy using the HDSCA methodology. Additional studies are necessary to determine the potential use of morphometric and genomic analysis as a prognostic tool to advance personalized oncology.
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Affiliation(s)
- Stephanie N Shishido
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Rahul Masson
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Liya Xu
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Lisa Welter
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Rishvanth Kaliappan Prabakar
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Anishka D' Souza
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Darcy Spicer
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Irene Kang
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Priya Jayachandran
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - James Hicks
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Janice Lu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA.
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11
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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: 18] [Impact Index Per Article: 9.0] [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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12
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Kaur P, Porras TB, Colombo A, Ring A, Lu J, Kang I, Lang JE. Identification of putative actionable alterations in clinically relevant genes in breast cancer. Br J Cancer 2021; 125:1270-1284. [PMID: 34455425 PMCID: PMC8548334 DOI: 10.1038/s41416-021-01522-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 06/27/2021] [Accepted: 07/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Individualising treatment in breast cancer requires effective predictive biomarkers. While relatively few genomic aberrations are clinically relevant, there is a need for characterising patients across different subtypes to identify actionable alterations. METHODS We identified genomic alterations in 49 potentially actionable genes for which drugs are available either clinically or via clinical trials. We explored the landscape of mutations and copy number alterations (CNAs) in actionable genes in seven breast cancer subtypes utilising The Cancer Genome Atlas. To dissect the genomic complexity, we analysed the patterns of co-occurrence and mutual exclusivity in actionable genes. RESULTS We found that >30% of tumours harboured putative actionable events that are targetable by currently available drugs. We identified genes that had multiple targetable alterations, representing candidate targets for combination therapy. Genes predicted to be drivers in primary breast tumours fell into five categories: mTOR pathway, immune checkpoints, oestrogen signalling, tumour suppression and DNA damage repair. Our analysis also revealed that CNAs in 34/49 (69%) and mutations in 13/49 (26%) genes were significantly associated with gene expression, validating copy number events as a dominant oncogenic mechanism in breast cancer. CONCLUSION These results may enable the acceleration of personalised therapy and improve clinical outcomes in breast cancer.
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Affiliation(s)
- Pushpinder Kaur
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Tania B Porras
- Cancer and Blood Disease Institute, Children Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Anthony Colombo
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alexander Ring
- Department of Medical Oncology and Hematology, University Hospital Zürich, Zurich, Switzerland
| | - Janice Lu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- 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
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- 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
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
- Division of Breast Services, Department of General Surgery, Digestive Disease and Surgery Institute, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
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13
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Addeo A, Friedlaender A, Banna GL, Weiss GJ. TMB or not TMB as a biomarker: That is the question. Crit Rev Oncol Hematol 2021; 163:103374. [PMID: 34087341 DOI: 10.1016/j.critrevonc.2021.103374] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/10/2021] [Accepted: 05/29/2021] [Indexed: 12/11/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized the landscape of therapeutic options for many cancers. These treatments have demonstrated improved efficacy and often a more favourable toxicity profile compared to standard cytotoxic chemotherapy. There are considerable differences among responders, with some patients experiencing durable long-term disease control and even remission. Given this variability, determining a proper biomarker to select patients for ICI therapy has become increasingly important. The only biomarker proven to be predictive of overall survival benefit with ICI therapy is PD-L1 expression level measured by immunohistochemistry. Several attempts have been made to identify different predictive biomarkers. One of the most intriguing and divisive is tumor mutational burden (TMB). TMB represents the number of mutations per megabase (Mut/Mb) of DNA that were sequenced in a specific cancer. With a higher number of mutations detected, and consequentially an increase in the number neo-epitopes, then it is more likely that one or more of those neo-antigens could be immunogenic and trigger a T cell response. Initially, TMB was identified as a biomarker for ICIs in melanoma and subsequent studies suggested a possible clinical role for TMB in non-small cell lung cancer. The initial data were not confirmed in a prospective study assessing OS as the primary endpoint. Recently, the FDA has approved pembrolizumab in all cancers with a TMB > 10Mut/Mb[12] based on findings from the phase 2 KEYNOTE-158. Much criticism has emerged about this pan-cancer approval, in particular about the use of TMB as biomarker to select patients. Here we review the data about the importance and role of TMB as possible pan-cancer one-size-fits-all biomarker. We highlight the strengths and intrinsic limitations of such a complex biomarker and its adoption in the daily practice.
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Affiliation(s)
- Alfredo Addeo
- Oncology Department, University Hospital of Geneva, Switzerland.
| | - Alex Friedlaender
- Oncology Department, University Hospital of Geneva, Switzerland; Clinique Générale Beaulieu, Geneva, Switzerland
| | | | - Glen J Weiss
- MiRanostics Consulting, Oro Valley, AZ, United States
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14
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Wang Y, Yin C, Geng L, Cai W. Immune Infiltration Landscape in Clear Cell Renal Cell Carcinoma Implications. Front Oncol 2021; 10:491621. [PMID: 33665156 PMCID: PMC7923891 DOI: 10.3389/fonc.2020.491621] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/21/2020] [Indexed: 01/02/2023] Open
Abstract
The malignant phenotypes of cancer are defined not only by its intrinsic tumor cells but also by the tumor infiltrating immune cells (TIICs) recruited to the cancer microenvironment. Clear cell renal cell carcinoma (ccRCC) immune microenvironment plays an important role in the tumorigenesis. This research investigated the characteristics of immune cell invasion of renal cell carcinoma and provided clues for future clinical implementation. Retrospectively, ccRCC gene expression was analyzed with appropriate clinicopathological data from the Cancer Genome Atlas (TCGA) and GEO database up to December 2019. The CIBERSORT algorithm, meta-analysis, principal component analysis (PCA), Single-Sample Gene Set Enrichment Analysis (ssGSEA) and hierarchical agglomerative clustering were used to measure and evaluate the respective proportions of 22 cell types of immune infiltration using normalized gene expression data. We also focused on evaluating the association with TIICs subpopulations and clinical features and molecular subtypes. TIICs subpopulation, especially Macrophages subgroup, T follicular helper (Tfh) cells and CD8 T cells, all contribute to tumorigenesis. Unsupervised clustering analysis revealed that there existed two distinct TIICs subgroups with different survival patterns. TIICs are extensively involved in the pathogenesis and development of the ccRCC. Characterizing the composition of TIICs influences the metabolism of tumors, activity, level, stage, and survival of patients. Collectively, the TIIC analysis has the potential to assist in the assessment and selection of ccRCC prognosis and treatment.
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Affiliation(s)
- Yongfeng Wang
- Department of Gynecology and Obstetrics, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ci Yin
- Department of Neonatology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Lele Geng
- Department of Plastic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Weiyang Cai
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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15
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Lu J, Wilfred P, Korbie D, Trau M. Regulation of Canonical Oncogenic Signaling Pathways in Cancer via DNA Methylation. Cancers (Basel) 2020; 12:E3199. [PMID: 33143142 PMCID: PMC7692324 DOI: 10.3390/cancers12113199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
Disruption of signaling pathways that plays a role in the normal development and cellular homeostasis may lead to the dysregulation of cellular signaling and bring about the onset of different diseases, including cancer. In addition to genetic aberrations, DNA methylation also acts as an epigenetic modifier to drive the onset and progression of cancer by mediating the reversible transcription of related genes. Although the role of DNA methylation as an alternative driver of carcinogenesis has been well-established, the global effects of DNA methylation on oncogenic signaling pathways and the presentation of cancer is only emerging. In this article, we introduced a differential methylation parsing pipeline (MethylMine) which mined for epigenetic biomarkers based on feature selection. This pipeline was used to mine for biomarkers, which presented a substantial difference in methylation between the tumor and the matching normal tissue samples. Combined with the Data Integration Analysis for Biomarker discovery (DIABLO) framework for machine learning and multi-omic analysis, we revisited the TCGA DNA methylation and RNA-Seq datasets for breast, colorectal, lung, and prostate cancer, and identified differentially methylated genes within the NRF2-KEAP1/PI3K oncogenic pathway, which regulates the expression of cytoprotective genes, that serve as potential therapeutic targets to treat different cancers.
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Affiliation(s)
- Jennifer Lu
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; (J.L.); (P.W.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Premila Wilfred
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; (J.L.); (P.W.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; (J.L.); (P.W.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; (J.L.); (P.W.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
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16
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Kaur P, Campo D, Porras TB, Ring A, Lu J, Chairez Y, Su Y, Kang I, Lang JE. A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer. Int J Mol Sci 2020; 21:ijms21144826. [PMID: 32650480 PMCID: PMC7402350 DOI: 10.3390/ijms21144826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022] Open
Abstract
The comparison of the landscape of somatic alterations in circulating tumor cells (CTCs) versus metastases is challenging. Here, we comprehensively characterized the somatic landscape in bulk (amplified and non-amplified), spike-in breast cancer cells, CTCs, and metastases from breast cancer patients using whole-exome sequencing (WES). We determined the level of genomic concordance for somatic nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs). The variant allele fractions (VAFs) of somatic variants were remarkably similar between amplified and non-amplified cell line samples as technical replicates. In clinical samples, a significant fraction of somatic variants had low VAFs in CTCs compared to metastases. The most frequently recurrent gene mutations in clinical samples were associated with an elevated C > T mutational signature. We found complex rearrangement patterns including intra- and inter-chromosomal rearrangements, singleton, and recurrent gene fusions, and tandem duplications. We observed high molecular discordance for somatic alterations between paired samples consistent with marked heterogeneity of the somatic landscape. The most prevalent copy number calls were focal deletion events in CTCs and metastases. Our results demonstrate the feasibility of an integrated workflow for the identification of a complete repertoire of somatic alterations and highlight the intrapatient genomic differences that occur between CTCs and metastases.
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Affiliation(s)
- Pushpinder Kaur
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
| | - Daniel Campo
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Tania B. Porras
- Cancer and Blood Disease Institute, Children Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA;
| | - Alexander Ring
- Department of Oncology and Hematology, UniversitätsSpital Zürich, Rämistrasse 100, 8091 Zürich, Switzerland;
| | - Janice Lu
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Yvonne Chairez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Yunyun Su
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
| | - Irene Kang
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Julie E. Lang
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Correspondence: ; Tel.: +1-(323)-442-8140
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17
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Snow A, Chen D, Lang JE. The current status of the clinical utility of liquid biopsies in cancer. Expert Rev Mol Diagn 2019; 19:1031-1041. [PMID: 31482746 DOI: 10.1080/14737159.2019.1664290] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Liquid biopsies have attracted considerable attention as potential diagnostic, prognostic, predictive, and screening assays in oncology. The term liquid biopsies include circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) in the blood. While many liquid biopsy technologies are under active investigation, relatively few liquid biopsy assays have been proven to serve as a diagnostic surrogate for biopsies of metastatic disease as predictive biomarkers to guide the selection of therapy in the clinic. Areas covered: The objective of this review is to highlight the status of liquid biopsies in solid tumors in the oncology literature with attention to proven utility as diagnostic surrogates for macrometastases. Expert opinion: Carefully designed clinical-translational studies are needed to establish the diagnostic accuracy and clinical utility of liquid biopsy biomarkers in oncology. Investigators must fully consider relevant pre-analytical variables, assay sensitivity, bioinformatics considerations as well as the clinical utility of rare event profiling in the context of the normal blood background. Future liquid biopsy research should address the concern that not all DNA mutations are expressed and should provide the means to discover potential therapeutic targets in metastatic patients via a minimally invasive blood draw.
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Affiliation(s)
- Anson Snow
- Department of Surgery, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
| | - Denaly Chen
- Department of Medicine, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
| | - Julie E Lang
- Department of Surgery, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
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18
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Abstract
With rapid advances in genetics and genomics, the commercialization and access to new applications has become more widespread and omnipresent throughout biomedical research. Thus, increasingly, more patients will have personal genomic information they may share with primary care providers (PCPs) to better understand the clinical significance of the data. To be able to respond to patient inquiries about genomic data, variant interpretation, disease risk, and other issues, PCPs will need to be able to increase or refresh their awareness about genetics and genomics, and identify reliable resources to use or refer patients. While provider educational efforts have increased, with the rapid advances in the field, ongoing efforts will be needed to prepare PCPs to manage patient needs, integrate results into care, and refer as indicated.
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Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA.
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Baer C, Walter W, Hutter S, Twardziok S, Meggendorfer M, Kern W, Haferlach T, Haferlach C. "Somatic" and "pathogenic" - is the classification strategy applicable in times of large-scale sequencing? Haematologica 2019; 104:1515-1520. [PMID: 31273095 PMCID: PMC6669162 DOI: 10.3324/haematol.2019.218917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022] Open
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