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Nussbaum YI, Hossain KSMT, Kaifi J, Warren WC, Shyu CR, Mitchem JB. Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation. J Biomed Inform 2024:104644. [PMID: 38631462 DOI: 10.1016/j.jbi.2024.104644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/29/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
OBJECTIVE Gene expression analysis through single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of gene regulation in diverse cell types, tissues, and organisms. While existing methods primarily focus on identifying cell type-specific gene expression programs (GEPs), the characterization of GEPs associated with biological processes and stimuli responses remains limited. In this study, we aim to infer biologically meaningful GEPs that are associated with both cellular phenotypes and activity programs directly from scRNA-seq data. METHODS We applied linear CorEx, a machine-learning-based approach, to infer GEPs by grouping genes based on total correlation optimization function in simulated and real-world scRNA-seq datasets. Additionally, we utilized a transfer learning approach to project CorEx-inferred GEPs to other scRNA-seq datasets. RESULTS By leveraging total correlation optimization, linear CorEx groups genes and demonstrates superior performance in identifying cell types and activity programs compared to similar methods using simulated data. Furthermore, we apply this same approach to real-world scRNA-seq data from the mouse dentate gyrus and embryonic colon development, uncovering biologically relevant GEPs related to cell types, developmental ages, and cell cycle programs. We also demonstrate the potential for transfer learning by evaluating similar datasets, showcasing the cross-species sensitivity of linear CorEx. CONCLUSION Our findings validate linear CorEx as a valuable tool for comprehensively analyzing complex signals in scRNA-seq data, leading to deeper insights into gene expression dynamics, cellular heterogeneity, and regulatory mechanisms.
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Affiliation(s)
- Yulia I Nussbaum
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA
| | - K S M Tozammel Hossain
- Department of Information Science, University of North Texas, 3940 N Elm St, Denton, TX 76203, USA
| | - Jussuf Kaifi
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; Department of Surgery, University of Missouri Hospital, 1 Hospital Dr., Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, 800 Hospital Dr., Columbia, MO 65201, USA; Siteman Cancer Center, Washington University School of Medicine, 4921 Parkview Pl, St. Louis, MO 63110, USA
| | - Wesley C Warren
- Department of Surgery, University of Missouri Hospital, 1 Hospital Dr., Columbia, MO 65212, USA; Bond Life Sciences Center, University of Missouri, 1201 Rollin St., Columbia, MO 65211, USA
| | - Chi-Ren Shyu
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA
| | - Jonathan B Mitchem
- VA Northeast Ohio Healthcare System, 10701 East Boulevard, Cleveland, OH 44106, USA; Department of Colon and Rectal Surgery, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA; Department of Inflammation and Immunity, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
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Manjunath Y, Nagaraj SK, Nussbaum YI, Gadelkarim M, Staveley-O’Carroll KF, Kimchi ET, Li G, Warren W, Shyu CR, Ciorba M, Mitchem JB, Kaifi JT. Abstract 205: Patient-derived organoids from surgically treated, localized non-small cell lung cancer as high-throughput drug testing platforms for conventional and repurposed drugs. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Non-metastatic NSCLC treated with curative surgery has a five-year survival of ~50%, mostly due to development of recurrences. Despite being considered as potential drug screening platforms, patient-derived xenograft (PDX) models are inefficient due to low tumor engraftment rates and complex animal care. Patient-derived organoid (PDO) models overcome these limitations as potential clinically applicable drug testing platforms. Our objective was to develop PDO models from non-metastatic NSCLC patients to study epithelial cell type heterogeneity and drug sensitivities for precision medicine.
Hypothesis: PDO models reliably capitulate the patient primary tumor and serve as versatile platforms for high-throughput screening of standard-of-care and repurposed drugs.
Methods: Single cell suspensions prepared from resected lung tumor tissues from ten NSCLC patients (both adenocarcinoma and squamous cell carcinoma) were mixed with Matrigel (growth factor-reduced) and cultured in organoid growth medium. Organoids and matched primary tumors were compared by histopathology [H&E staining and immunohistochemistry for cytokeratin (CK) 5/6, CK7, Napsin A, Thyroid transcription factor-1 (TTF-1) and p40] and by bulk RNA sequencing. Upon passaging, PDOs were seeded in triplicates, treated with carboplatin/paclitaxel doublet chemotherapy, and drug responses were determined using bright-field 3D imaging (z-stack method). Tumor growth (%) was determined on day 3 and 6 of treatments. RNA sequencing analyses identified a potential drug targets and repurposed drug (aldoketoreductase inhibitor Epalrestat) was tested to overcome chemoresistance in PDOs.
Results: NSCLC PDO growth was established from 11/12 (91.7%) primary tumors with a median time of 11 days (range 4-18 days) to reach volume of 100 μm3. PDOs retained histopathological features and biomarker expression of the matched tumors. As determined by growth differences (p<0.05), 5/9 (55.6%) PDOs were chemosensitive and 4/9 (44.4%) PDOs were chemoresistant against carboplatin/paclitaxel. Whole transcriptome analysis confirmed conservation of the epithelial cell composition in all PDOs in comparison to the matched primary tumors. Potentially druggable genes associated with chemotherapy resistance were identified and the aldoketoreductase inhibitor Epalrestat was repurposed and shown to be effective in overcoming chemoresistance towards carboplatin/paclitaxel.
Conclusions: PDOs can be established from resectable NSCLC patients with high success rates, while preserving histopathological, cellular, and molecular characteristics of the matched primary tumors. Considering the time frames of growth and drug testing, PDOs can serve as clinically applicable drug response testing platforms to traditional and repurposed drugs.
Citation Format: Yariswamy Manjunath, Suvilesh Kanve Nagaraj, Yulia I. Nussbaum, Mohamed Gadelkarim, Kevin F. Staveley-O’Carroll, Eric T. Kimchi, Guangfu Li, Wesley Warren, Chi-Ren Shyu, Matthew Ciorba, Jonathan B. Mitchem, Jussuf T. Kaifi. Patient-derived organoids from surgically treated, localized non-small cell lung cancer as high-throughput drug testing platforms for conventional and repurposed drugs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 205.
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Affiliation(s)
| | | | | | | | | | | | - Guangfu Li
- 1University of Missouri - Columbia, Columbia, MO
| | | | - Chi-Ren Shyu
- 1University of Missouri - Columbia, Columbia, MO
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Nussbaum YI, Manjunath Y, Shumway E, Jussuf KT, Warren WC, Mitchem JB. Abstract B57: Studying the role of OPN-CD44 interaction in colorectal cancer antitumor immunity suppression using scRNA-seq data. Cancer Immunol Res 2022. [DOI: 10.1158/2326-6074.tumimm22-b57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Abstract
Colorectal cancer (CRC) remains one of the deadliest malignancies worldwide despite recent progress in screening and treatment strategies. Osteopontin (OPN) is a multifunctional protein expressed by multiple cells in the tumor microenvironment (TME) and is associated with immune suppression and poor prognosis in CRC. Tumor-associated macrophages (TAM), are also associated with immune suppression and poor prognosis in CRC, and may express OPN. While both TAM and OPN overlap in the TME, the role of OPN and OPN expressing TAM is poorly understood. In this study, we show the critical interaction and strategy for targeting this axis to overcome therapeutic resistance in CRC. Five publicly available CRC scRNA-seq data (571,818 cells total) from both untreated and treated patients were analyzed to determine the OPN expression and OPN-CD44 interaction in primary CRC and liver metastases using CellChat ligand-receptor interaction analysis. For experimental analyses, patient tissue was collected from the University of Missouri (MU) and the Harry S. Truman VA (HSTVA) on an approved IRB. OPN-positive TAMs were determined by immunofluorescence (IFC) and flow cytometry (FC). Analysis of FC data was completed using analyzed (FlowJo). Wilcoxon rank sum test was performed to find differentially expressed genes between the samples with and without OPN-CD44 interaction in each dataset. Data from scRNA-seq, IFC, and FC all demonstrated that TAMs were the predominant cells expressing OPN in the TME and the majority of TAM are OPN+. Most interestingly, in scRNA-seq data, we found minimal OPN+TAM in primary tumors from treated patients. These patients had a good response to therapy. Conversely, in FC data from our own patients, we found OPN+ TAM were preserved in primary tumors from patients’ post-therapy that had no response. Gene set enrichment analysis (GSEA) in treated patients with minimal OPN+TAM showed decreased exhaustion markers (logFC>0.5, FDR adjusted p-value<0.05). We then found that the strongest OPN-CD44 interactions were predicted between OPN+TAM and other TAM as well as T cells. Separating patients into high and low predicted OPN-CD44 interactors, GSEA demonstrated enrichment of cell death regulation and apoptosis pathways in CD8+ T cells in high interactors. To determine potential targets for modulation of OPN+TAM, we undertook trajectory analysis demonstrating that OPN+TAM were an intermediate phase, suggesting they are malleable. We then found that these OPN+TAM highly express TLR8 in both scRNAseq and FC, suggesting a potential target to modulate OPN+TAM. In this study, we demonstrate that OPN+TAM are the largest proportion of TAM in CRC tumors. Additionally, the presence of OPN+ TAM in treated samples is associated with response to systemic therapy. OPN+TAM appear to represent an intermediate phase of TAMs differentiation and highly express TLR8 suggesting a mechanism for modulation to improve patient response. Further ex vivo studies targeting these cells and their role in therapeutic response are critical.
Citation Format: Yulia I Nussbaum, Yariswamy Manjunath, Elizabeth Shumway, Kaifi T Jussuf, Wesley C Warren, Jonathan B Mitchem. Studying the role of OPN-CD44 interaction in colorectal cancer antitumor immunity suppression using scRNA-seq data [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr B57.
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Affiliation(s)
- Yulia I Nussbaum
- 1University of Missouri, Columbia, MO
- 1University of Missouri, Columbia, MO
| | | | - Elizabeth Shumway
- 1University of Missouri, Columbia, MO
- 1University of Missouri, Columbia, MO
| | - Kaifi T Jussuf
- 1University of Missouri, Columbia, MO
- 1University of Missouri, Columbia, MO
| | - Wesley C Warren
- 1University of Missouri, Columbia, MO
- 1University of Missouri, Columbia, MO
| | - Jonathan B Mitchem
- 1University of Missouri, Columbia, MO
- 1University of Missouri, Columbia, MO
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Mitchem JB, Miller A, Manjunath Y, Barbirou M, Raju M, Shen Y, Li G, Avella DM, Chaudhuri AA, Shyu CR, Warren WC, Tonellato PJ, Kaifi JT. Somatic mutation variant analysis in rural, resectable non-small cell lung carcinoma patients. Cancer Genet 2022; 268-269:75-82. [PMID: 36191390 DOI: 10.1016/j.cancergen.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/30/2022] [Accepted: 09/19/2022] [Indexed: 01/25/2023]
Abstract
Rural non-small cell lung cancer (NSCLC) patients do worse, largely related to lack of access to care. In this study, the mutational characteristics and potential for targeted therapy in rural, resectable NSCLC patients using whole exome sequencing (WES) were analyzed. WES was performed on tumor-adjacent normal pairs from rural patients undergoing resection for NSCLC. Sequencing alignment, variant-calling, annotation, and tumor mutational burden (TMB) calculations were performed using standard methods. cBioportal and OncoKB were used for comparisons of mutational frequencies and actionable targets. Thirty-four NSCLC patients underwent WES after surgical resection. The gene most frequently containing somatic variants was TP53. The median number of somatic variants was 188 (Range 11-1056), and median TMB was 3.30 (0.33-18.56) nonsynonymous mutations per Mb. Tumor stage and survival were not associated with number of variants, TMB or TP53 mutational status. Significant concordance among the most common mutations when cross-referenced to cBioportal (R = 0.78, p < 0.0001) was observed. 24% of patients had variants in actionable genes based on OncoKB annotation. In summary, we demonstrate baseline mutational frequency and establish foundations for targeted adjuvant trials in rural NSCLC patients with specific differences. Future studies must ensure to include rural patients to improve NSCLC patient outcomes.
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Affiliation(s)
- Jonathan B Mitchem
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA; Center for Biomedical Informatics, University of Missouri School of Medicine, Columbia, MO, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Amanda Miller
- Center for Biomedical Informatics, University of Missouri School of Medicine, Columbia, MO, USA
| | - Yariswamy Manjunath
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Mouadh Barbirou
- Center for Biomedical Informatics, University of Missouri School of Medicine, Columbia, MO, USA
| | - Murugesan Raju
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Yuanyuan Shen
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Guangfu Li
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Diego M Avella
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Chi-Ren Shyu
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Wesley C Warren
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA; Center for Biomedical Informatics, University of Missouri School of Medicine, Columbia, MO, USA
| | - Peter J Tonellato
- Center for Biomedical Informatics, University of Missouri School of Medicine, Columbia, MO, USA
| | - Jussuf T Kaifi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA; Center for Biomedical Informatics, University of Missouri School of Medicine, Columbia, MO, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Suvilesh KN, Nussbaum YI, Radhakrishnan V, Manjunath Y, Avella DM, Staveley-O’Carroll KF, Kimchi ET, Chaudhuri AA, Shyu CR, Li G, Pantel K, Warren WC, Mitchem JB, Kaifi JT. Abstract 267: Xenograft models of non-metastatic non-small cell lung cancer reveals micrometastasis-associated single cell composition. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Circulating tumor cells (CTCs) represent micrometastatic disease and may offer unique insights into future recurrences in lethal malignancies, including non-small cell lung cancer (NSCLC). Due to CTC rarity and limited stability, no CTC-derived xenograft (CDX) models have ever been generated from non-metastatic NSCLC patients directly. Alternative strategies are needed to molecularly characterize CTCs in this potentially curable patient group.
Methods: Surgically resected NSCLC primary tumor tissues were implanted in immunodeficient mice to establish ten patient-derived xenografts (PDXs). CTCs from 2/10 PDX models led to generation of two stable metastatic models that were studied by single cell sequencing.
Results: Single cell analysis revealed an additional alveolar epithelial type II (AT2) population in metastatic tumors, besides a common AT2 cluster in PDX/metastatic tumors. This was consistent with an external validation set analysis in primary and metastatic NSCLC patient tumors. Further, AT2 clusters of metastatic tumors expressed higher cancer stemness genes versus primary PDX tumor that was recapitulated in patients primary and metastatic tumors.
Conclusions: Stable metastatic models from early stage NSCLC patients can be generated with CTCs from PDX models. The distinct AT2 population identified in CDX tumors with cancer stemness features might be critical mediator of metastasis that deserves further study to discover personalized strategies against NSCLC micrometastases.
Citation Format: Kanve Nagaraj Suvilesh, Yulia I. Nussbaum, Vijay Radhakrishnan, Yariswamy Manjunath, Diego M. Avella, Kevin F. Staveley-O’Carroll, Eric T. Kimchi, Aadel A. Chaudhuri, Chi-Ren Shyu, Guangfu Li, Klaus Pantel, Wesley C. Warren, Jonathan B. Mitchem, Jussuf T. Kaifi. Xenograft models of non-metastatic non-small cell lung cancer reveals micrometastasis-associated single cell composition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 267.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Guangfu Li
- 1University of Missouri-Columbia, Columbia, MO
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Manjunath Y, Suvilesh KN, Mitchem JB, Avella Patino DM, Kimchi ET, Staveley-O'Carroll KF, Pantel K, Yi H, Li G, Harris PK, Chaudhuri AA, Kaifi JT. Circulating Tumor-Macrophage Fusion Cells and Circulating Tumor Cells Complement Non-Small-Cell Lung Cancer Screening in Patients With Suspicious Lung-RADS 4 Nodules. JCO Precis Oncol 2022; 6:e2100378. [PMID: 35417204 PMCID: PMC9012602 DOI: 10.1200/po.21.00378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Low-dose computed tomography (LDCT) screening of high-risk patients decreases lung cancer-related mortality. However, high false-positive rates associated with LDCT result in unnecessary interventions. To distinguish non-small-cell lung cancer (NSCLC) from benign nodules, in the present study, we integrated cellular liquid biomarkers in patients with suspicious lung nodules (lung cancer screening reporting and data system [Lung-RADS] 4). METHODS Prospectively, 7.5 mL of blood was collected from 221 individuals (training set: 90 nonscreened NSCLC patients, 74 high-risk screening patients with no/benign nodules [Lung-RADS 1-3], and 20 never smokers; validation set: 37 patients with suspicious nodules [Lung-RADS 4]). Circulating tumor cells (CTCs), CTC clusters, and tumor-macrophage fusion (TMF) cells were identified by blinded analyses. Screening patients underwent a median of two LDCTs (range, 1-4) with a median surveillance time of 30 (range, 11-50) months. RESULTS In the validation set of 37 Lung-RADS 4 patients, all circulating cellular biomarker counts (P < .005; Wilcoxon test) and positivity rates were significantly higher in 23 biopsy-proven NSCLC patients (CTCs: 23 of 23 [100%], CTC clusters: 6 of 23 [26.1%], and TMF cells: 15 of 23 [65.2%]) than in 14 patients with biopsy-proven benign nodules (6 of 14 [42.9%], 0 of 14 [0%], and 2 of 14 [14.3%]). On the basis of cutoff values from the training set, logistic regression with receiver operating characteristic and area under the curve analyses demonstrated that CTCs (sensitivity: 0.870, specificity: 1.0, and area under the curve: 0.989) and TMF cells (0.652; 0.880; 0.790) complement LDCT in diagnosing NSCLC in Lung-RADS 4 patients. CONCLUSION Cellular liquid biomarkers have a potential to complement LDCT interpretation of suspicious Lung-RADS 4 nodules to distinguish NSCLC from benign lung nodules. A future prospective, large-scale, multicenter clinical trial should validate the role of cellular liquid biomarkers in improving diagnostic accuracy in high-risk patients with Lung-RADS 4 nodules.
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Affiliation(s)
- Yariswamy Manjunath
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO
| | - Kanve Nagaraj Suvilesh
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO
| | - Jonathan B Mitchem
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Diego M Avella Patino
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO
| | - Eric T Kimchi
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Kevin F Staveley-O'Carroll
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
| | - Klaus Pantel
- Institute for Tumor Biology, University of Hamburg, Hamburg, Germany
| | - Huang Yi
- Departments of Radiation Oncology, Genetics, and Computer Science and Engineering, Washington University School of Medicine, St Louis, MO
| | - Guangfu Li
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO
| | - Peter K Harris
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO.,Departments of Radiation Oncology, Genetics, and Computer Science and Engineering, Washington University School of Medicine, St Louis, MO
| | - Aadel A Chaudhuri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO.,Departments of Radiation Oncology, Genetics, and Computer Science and Engineering, Washington University School of Medicine, St Louis, MO
| | - Jussuf T Kaifi
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri-Columbia, Columbia, MO.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO.,Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
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Suvilesh KN, Nussbaum YI, Radhakrishnan V, Manjunath Y, Avella DM, Staveley-O’Carroll KF, Kimchi ET, Chaudhuri AA, Shyu CR, Li G, Pantel K, Warren WC, Mitchem JB, Kaifi JT. Tumorigenic circulating tumor cells from xenograft mouse models of non-metastatic NSCLC patients reveal distinct single cell heterogeneity and drug responses. Mol Cancer 2022; 21:73. [PMID: 35279152 PMCID: PMC8917773 DOI: 10.1186/s12943-022-01553-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/26/2022] [Indexed: 12/22/2022] Open
Abstract
Background Circulating tumor cells (CTCs) are liquid biopsies that represent micrometastatic disease and may offer unique insights into future recurrences in non-small cell lung cancer (NSCLC). Due to CTC rarity and limited stability, no stable CTC-derived xenograft (CDX) models have ever been generated from non-metastatic NSCLC patients directly. Alternative strategies are needed to molecularly characterize CTCs and means of potential future metastases in this potentially curable patient group. Methods Surgically resected NSCLC primary tumor tissues from non-metastatic patients were implanted subcutaneously in immunodeficient mice to establish primary tumor patient-derived xenograft (ptPDX) models. CTCs were isolated as liquid biopsies from the blood of ptPDX mice and re-implanted subcutaneously into naïve immunodeficient mice to generate liquid biopsy CTC-derived xenograft (CDX) tumor models. Single cell RNA sequencing was performed and validated in an external dataset of non-xenografted human NSCLC primary tumor and metastases tissues. Drug response testing in CDX models was performed with standard of care chemotherapy (carboplatin/paclitaxel). Blockade of MYC, which has a known role in drug resistance, was performed with a MYC/MAX dimerization inhibitor (10058-F4). Results Out of ten ptPDX, two (20%) stable liquid biopsy CDX mouse models were generated. Single cell RNA sequencing analysis revealed an additional regenerative alveolar epithelial type II (AT2)-like cell population in CDX tumors that was also identified in non-xenografted NSCLC patients’ metastases tissues. Drug testing using these CDX models revealed different treatment responses to carboplatin/paclitaxel. MYC target genes and c-MYC protein were upregulated in the chemoresistant CDX model, while MYC/MAX dimerization blocking could overcome chemoresistance to carboplatin/paclitaxel. Conclusions To overcome the lack of liquid biopsy CDX models from non-metastatic NSCLC patients, CDX models can be generated with CTCs from ptPDX models that were originally established from patients’ primary tumors. Single cell analyses can identify distinct drug responses and cell heterogeneities in CDX tumors that can be validated in NSCLC metastases tissues. CDX models deserve further development and study to discover personalized strategies against micrometastases in non-metastatic NSCLC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01553-5.
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Barbirou M, Miller A, Manjunath Y, Ramirez AB, Ericson NG, Staveley-O’Carroll KF, Mitchem JB, Warren WC, Chaudhuri AA, Huang Y, Li G, Tonellato PJ, Kaifi JT. Single Circulating-Tumor-Cell-Targeted Sequencing to Identify Somatic Variants in Liquid Biopsies in Non-Small-Cell Lung Cancer Patients. Curr Issues Mol Biol 2022; 44:750-763. [PMID: 35723337 PMCID: PMC8928994 DOI: 10.3390/cimb44020052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) accounts for most cancer-related deaths worldwide. Liquid biopsy by a blood draw to detect circulating tumor cells (CTCs) is a tool for molecular profiling of cancer using single-cell and next-generation sequencing (NGS) technologies. The aim of the study was to identify somatic variants in single CTCs isolated from NSCLC patients by targeted NGS. Thirty-one subjects (20 NSCLC patients, 11 smokers without cancer) were enrolled for blood draws (7.5 mL). CTCs were identified by immunofluorescence, individually retrieved, and DNA-extracted. Targeted NGS was performed to detect somatic variants (single-nucleotide variants (SNVs) and insertions/deletions (Indels)) across 65 oncogenes and tumor suppressor genes. Cancer-associated variants were classified using OncoKB database. NSCLC patients had significantly higher CTC counts than control smokers (p = 0.0132; Mann–Whitney test). Analyzing 23 CTCs and 13 white blood cells across seven patients revealed a total of 644 somatic variants that occurred in all CTCs within the same subject, ranging from 1 to 137 per patient. The highest number of variants detected in ≥1 CTC within a patient was 441. A total of 18/65 (27.7%) genes were highly mutated. Mutations with oncogenic impact were identified in functional domains of seven oncogenes/tumor suppressor genes (NF1, PTCH1, TP53, SMARCB1, SMAD4, KRAS, and ERBB2). Single CTC-targeted NGS detects heterogeneous and shared mutational signatures within and between NSCLC patients. CTC single-cell genomics have potential for integration in NSCLC precision oncology.
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Affiliation(s)
- Mouadh Barbirou
- Center for Biomedical Informatics, Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA; (M.B.); (A.M.); (P.J.T.)
| | - Amanda Miller
- Center for Biomedical Informatics, Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA; (M.B.); (A.M.); (P.J.T.)
| | - Yariswamy Manjunath
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | | | | | - Kevin F. Staveley-O’Carroll
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
| | - Jonathan B. Mitchem
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
| | - Wesley C. Warren
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
- Department of Animal Sciences and Surgery, Informatics and Data Sciences Institute, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Aadel A. Chaudhuri
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yi Huang
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Guangfu Li
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
| | - Peter J. Tonellato
- Center for Biomedical Informatics, Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA; (M.B.); (A.M.); (P.J.T.)
| | - Jussuf T. Kaifi
- Center for Biomedical Informatics, Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA; (M.B.); (A.M.); (P.J.T.)
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA; (Y.M.); (K.F.S.-O.); (J.B.M.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA; (W.C.W.); (A.A.C.); (Y.H.)
- Correspondence:
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Nussbaum YI, Manjunath Y, Kaifi JT, Warren W, Mitchem JB. Analysis of tumor-associated macrophages' heterogeneity in colorectal cancer patients using single-cell RNA-seq data. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.4_suppl.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
146 Background: Colorectal cancer (CRC) is one of the deadliest malignancies worldwide. Though immune checkpoint inhibition has proven effective for a number of other tumors, it offers benefits in only a small group of CRC. In general, heterogenous cell groups in the tumor microenvironment (TME) are considered as the major barrier for unveiling the causes of low immune response. Therefore, deconvolution of cellular components in highly heterogeneous microenvironments is crucial for understanding those mechanisms. Single cell sequencing technology revolutionized TME research enabling profiling cells in high resolution. Methods: We have analyzed scRNA-seq data from 23 CRC patients with pre-treatment primary tumors using Seurat V3 pipeline. To investigate intercellular ligand-receptor interactions, we used CellPhoneDB and CellChat methods. The results of two independent analyses showed 4 CRC samples with no SPP1-CD44 interaction. It is known, that OPN which is the protein encoded by SPP1 gene, binds to CD44 and can cause cell survival, proliferation, and angiogenesis. Interestingly, analysis of the cellular composition of all 23 samples did not reveal differences in SPP1+ macrophages’ content for those 4 “no SPP1-CD44” samples. To investigate the mechanisms that could cause differences in SPP1-CD44 expression across the samples, we analyzed developmental trajectories of single cells using Slingshot trajectory inference method. Results: Ligand-receptor interactions analysis revealed 4 CRC samples that lacked SPP1-CD44 interaction that is known to be responsible for tumor progression in CRC. But the proportion of SPP1+ cells was not significantly different in those 4 samples compared to other samples. Trajectory inference analysis showed that the cells from “no SPP1-CD44” samples had high expression of anti-inflammatory macrophage markers in the end of the trajectory. While cells from “high SPP1-CD44” samples had high expression of pro-inflammatory macrophage markers at the same point. Conclusions: Based on our data-driven study, we suggest that SPP1+ macrophages’ heterogeneity may affect SPP1-CD44 interaction. Thus, targeting SPP1+ macrophages that have anti-inflammatory phenotype can potentially interrupt SPP1-CD44 interaction and therefore reduce tumor progression and immune suppression.
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11
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Mitchem JB. Getting involved in research in colorectal surgery. Seminars in Colon and Rectal Surgery 2021. [DOI: 10.1016/j.scrs.2021.100815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Otegbeye EE, Mitchem JB, Park H, Chaudhuri AA, Kim H, Mutch MG, Ciorba MA. Immunity, immunotherapy, and rectal cancer: A clinical and translational science review. Transl Res 2021; 231:124-138. [PMID: 33307273 PMCID: PMC8016725 DOI: 10.1016/j.trsl.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/28/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023]
Abstract
Rectal cancer remains a challenging disease to treat. Therapy for locally advanced rectal cancer (LARC), the most frequent presentation, has evolved to include a multimodal approach of radiation, chemotherapy, and surgery. While this approach improves local disease control, the distant recurrence rate is nearly 30% and treatment-related morbidity is substantial, thus underscoring the need for new therapeutic approaches with better efficacy and lower side effects. Immunotherapy could potentially fill this need, but its promise is not yet realized in rectal cancer. In this translational science review, we address what is known about how cytotoxic therapies shape rectal cancer immunity and potentially prime the tumor microenvironment for response to immune checkpoint inhibitors and other immunotherapies. We also address the role of current immunotherapies in colorectal cancer and highlight where novel immunotherapy approaches are currently being evaluated in LARC. Finally, we address important future directions in LARC immunotherapy including the need to define optimal therapeutic sequencing, predictive biomarkers, strategies to limit treatment-related side effects and the potential of gut microbiome manipulation to improve outcomes. In summary, this review provides a framework to guide future research and inform immunotherapy trial design so as to advance rectal cancer care.
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Affiliation(s)
- Ebunoluwa E Otegbeye
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Jonathan B Mitchem
- Department of Surgery, University of Missouri School of Medicine, Columbia, Missouri; Surgical Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, Missouri
| | - Haeseong Park
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Aadel A Chaudhuri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri; Department of Computer Science & Engineering, Washington University, St. Louis, Missouri
| | - Hyun Kim
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Matthew G Mutch
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri; Department of Surgery, Section of Colorectal Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Matthew A Ciorba
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri; Inflammatory Bowel Diseases Center and the Division of Gastroenterology, Washington University in Saint Louis School of Medicine, St. Louis, Missouri.
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13
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Nussbaum YI, Manjunath Y, Suvilesh KN, Warren WC, Shyu CR, Kaifi JT, Ciorba MA, Mitchem JB. Current and Prospective Methods for Assessing Anti-Tumor Immunity in Colorectal Cancer. Int J Mol Sci 2021; 22:4802. [PMID: 33946558 PMCID: PMC8125332 DOI: 10.3390/ijms22094802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) remains one of the deadliest malignancies worldwide despite recent progress in treatment strategies. Though immune checkpoint inhibition has proven effective for a number of other tumors, it offers benefits in only a small group of CRC patients with high microsatellite instability. In general, heterogenous cell groups in the tumor microenvironment are considered as the major barrier for unveiling the causes of low immune response. Therefore, deconvolution of cellular components in highly heterogeneous microenvironments is crucial for understanding the immune contexture of cancer. In this review, we assimilate current knowledge and recent studies examining anti-tumor immunity in CRC. We also discuss the utilization of novel immune contexture assessment methods that have not been used in CRC research to date.
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Affiliation(s)
- Yulia I. Nussbaum
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; (Y.I.N.); (C.-R.S.); (J.T.K.)
| | - Yariswamy Manjunath
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - Kanve N. Suvilesh
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
| | - Wesley C. Warren
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Chi-Ren Shyu
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; (Y.I.N.); (C.-R.S.); (J.T.K.)
| | - Jussuf T. Kaifi
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; (Y.I.N.); (C.-R.S.); (J.T.K.)
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Matthew A. Ciorba
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA;
- Division of Gastroenterology, Department of Medicine, Washington School of Medicine, St. Louis, MO 63110, USA
| | - Jonathan B. Mitchem
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; (Y.I.N.); (C.-R.S.); (J.T.K.)
- Department of Surgery, Columbia, MO 65212, USA; (Y.M.); (K.N.S.); (W.C.W.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA;
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14
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Al-Taie Z, Liu D, Mitchem JB, Papageorgiou C, Kaifi JT, Warren WC, Shyu CR. Explainable artificial intelligence in high-throughput drug repositioning for subgroup stratifications with interventionable potential. J Biomed Inform 2021; 118:103792. [PMID: 33915273 DOI: 10.1016/j.jbi.2021.103792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 03/26/2021] [Accepted: 04/21/2021] [Indexed: 01/02/2023]
Abstract
Enabling precision medicine requires developing robust patient stratification methods as well as drugs tailored to homogeneous subgroups of patients from a heterogeneous population. Developing de novo drugs is expensive and time consuming with an ultimately low FDA approval rate. These limitations make developing new drugs for a small portion of a disease population unfeasible. Therefore, drug repositioning is an essential alternative for developing new drugs for a disease subpopulation. This shows the importance of developing data-driven approaches that find druggable homogeneous subgroups within the disease population and reposition the drugs for these subgroups. In this study, we developed an explainable AI approach for patient stratification and drug repositioning. Contrast pattern mining and network analysis were used to discover homogeneous subgroups within a disease population. For each subgroup, a biomedical network analysis was done to find the drugs that are most relevant to a given subgroup of patients. The set of candidate drugs for each subgroup was ranked using an aggregated drug score assigned to each drug. The proposed method represents a human-in-the-loop framework, where medical experts use the data-driven results to generate hypotheses and obtain insights into potential therapeutic candidates for patients who belong to a subgroup. Colorectal cancer (CRC) was used as a case study. Patients' phenotypic and genotypic data was utilized with a heterogeneous knowledge base because it gives a multi-view perspective for finding new indications for drugs outside of their original use. Our analysis of the top candidate drugs for the subgroups identified by medical experts showed that most of these drugs are cancer-related, and most of them have the potential to be a CRC regimen based on studies in the literature.
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Affiliation(s)
- Zainab Al-Taie
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA; Department of Computer Science, College of Science for Women, University of Baghdad, Baghdad, Iraq
| | - Danlu Liu
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211, USA
| | - Jonathan B Mitchem
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA.
| | - Christos Papageorgiou
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Jussuf T Kaifi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA
| | - Wesley C Warren
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA; Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Chi-Ren Shyu
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA; Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211, USA; Department of Medicine, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
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15
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Avella DM, Manjunath Y, Singh A, Deroche CB, Kimchi ET, Staveley-O'Carroll KF, Mitchem JB, Kwon E, Li G, Kaifi JT. 18F-FDG PET/CT total lesion glycolysis is associated with circulating tumor cell counts in patients with stage I to IIIA non-small cell lung cancer. Transl Lung Cancer Res 2020; 9:515-521. [PMID: 32676315 PMCID: PMC7354116 DOI: 10.21037/tlcr.2020.04.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Background In non-small cell lung cancer (NSCLC), 18F-fluoro-2-deoxy-D-glucose (18F-FDG) uptake determined by PET and presence of circulating tumor cells (CTCs) in the peripheral blood independently predict outcomes. For 18F-FDG PET/CT staging interpretation, standardized uptake values (SUVmax/avg) are routinely used in clinical reporting. The goal was to investigate whether 18F-FDG uptake measured by SUVmax/avg, but also measures of metabolic tumor volume (MTV) and total lesion glycolysis (TLG) (MTV × SUVavg), are associated with CTCs. Methods Prospectively, 7.5 mL blood was drawn from NSCLC patients at the time of staging 18F-FDG PET/CT and from healthy control subjects. CTCs were identified by immunofluorescent staining (CK8/18/19pos/EpCAMpos/CD45neg/DAPIpos nucleus). 18F-FDG PET/CTs were analyzed for SUVmax, SUVavg, MTV, and TLG. Results In 16 NSCLC patients with stage I–IIIA, MTV and TLG, in contrast to SUVmax and SUVavg, were positively associated with CTCs (linear regression analysis). No CTCs were detectable in 20 healthy control subjects. Conclusions This pilot study demonstrates that 18F-FDG PET/CT TLG correlates with CTCs in NSCLC patients without distant metastases. TLG might be a more appropriate marker for hematogenous micrometastatic potential than SUVs.
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Affiliation(s)
- Diego M Avella
- Department of Surgery, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Yariswamy Manjunath
- Department of Surgery, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Amolak Singh
- Department of Nuclear Medicine, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA
| | - Chelsea B Deroche
- Biostatistics and Research Design Unit, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA
| | - Eric T Kimchi
- Department of Surgery, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Kevin F Staveley-O'Carroll
- Department of Surgery, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Jonathan B Mitchem
- Department of Surgery, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Eric Kwon
- Department of Surgery, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA
| | - Guangfu Li
- Department of Surgery, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA
| | - Jussuf T Kaifi
- Department of Surgery, Health Management and Medical Informatics, University of Missouri, Columbia, MO, USA.,Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
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Guan Y, Kraus SG, Quaney MJ, Daniels MA, Mitchem JB, Teixeiro E. FOLFOX Chemotherapy Ameliorates CD8 T Lymphocyte Exhaustion and Enhances Checkpoint Blockade Efficacy in Colorectal Cancer. Front Oncol 2020; 10:586. [PMID: 32391270 PMCID: PMC7190812 DOI: 10.3389/fonc.2020.00586] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Colorectal cancer (CRC) is the third most common malignancy worldwide. The presence of CD8 tumor-infiltrating T lymphocytes (TILs) is associated with improved prognosis and therapeutic response in CRC patients. FOLFOX chemotherapy is a standard first-line treatment for patients with CRC. Yet, the effect of FOLFOX on TILs is poorly understood. Specifically, it is unclear whether FOLFOX therapy impacts the phenotype and functionality of tumor antigen specific TILs. Immune checkpoint blockade (ICB) has significantly improved clinical outcome of cancer treatment but has shown limited efficacy in CRC patients. Recently, ICB efficiency has been linked to reinvigoration of T cells with a non-terminally dysfunctional phenotype. Here, we investigate the effect of FOLFOX on CD8 T cell tumor accumulation, phenotype and function and tested the combination of FOLFOX and ICB to improve tumor regression. Methods: A mouse model of CRC expressing a human tumor antigen was used to study the effect of FOLFOX on tumor growth and TILs phenotype and function. Tetramers were used to identify and monitor phenotype and function of tumor specific TILs. The phenotype and function of TILs were compared between FOLFOX and control treatment through flow cytometry, in vivo depletion and ex vivo stimulation. Furthermore, the anti-tumor effect of the single drug or combined therapy with anti-PD1 were also assessed. Results: We show that FOLFOX treatment effectively controlled tumor burden and this was dependent on CD8 T cells. FOLFOX enabled TILs to remain in a functional differentiation state characterized by lower levels of inhibitory receptors PD-1 and TIM-3 and a CD38loCD101loTIM-3-TCF-1hi phenotype. Consistent with this, TILs from FOLFOX treated tumors exhibited higher effector function. Importantly, while anti-PD-1 treatment alone had no significant effect on tumor burden, FOLFOX and PD-1 checkpoint blockade combination showed significant tumor control. Conclusions: FOLFOX treatment impacts the phenotype and function of TILs making them more responsive to checkpoint blockade. This study highlights the importance of combining chemotherapy and ICB to optimize treatment efficacy in patients with colorectal cancer.
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Affiliation(s)
- Yue Guan
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, United States.,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Sean G Kraus
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Michael J Quaney
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Mark A Daniels
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, United States.,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Jonathan B Mitchem
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States.,Informatics Institute, University of Missouri, Columbia, MO, United States.,Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, United States
| | - Emma Teixeiro
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, United States.,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
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Manjunath Y, Porciani D, Mitchem JB, Suvilesh KN, Avella DM, Kimchi ET, Staveley-O’Carroll KF, Burke DH, Li G, Kaifi JT. Tumor-Cell-Macrophage Fusion Cells as Liquid Biomarkers and Tumor Enhancers in Cancer. Int J Mol Sci 2020; 21:E1872. [PMID: 32182935 PMCID: PMC7084898 DOI: 10.3390/ijms21051872] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 02/06/2023] Open
Abstract
Although molecular mechanisms driving tumor progression have been extensively studied, the biological nature of the various populations of circulating tumor cells (CTCs) within the blood is still not well understood. Tumor cell fusion with immune cells is a longstanding hypothesis that has caught more attention in recent times. Specifically, fusion of tumor cells with macrophages might lead to the development of metastasis by acquiring features such as genetic and epigenetic heterogeneity, chemotherapeutic resistance, and immune tolerance. In addition to the traditional FDA-approved definition of a CTC (CD45-, EpCAM+, cytokeratins 8+, 18+ or 19+, with a DAPI+ nucleus), an additional circulating cell population has been identified as being potential fusions cells, characterized by distinct, large, polymorphonuclear cancer-associated cells with a dual epithelial and macrophage/myeloid phenotype. Artificial fusion of tumor cells with macrophages leads to migratory, invasive, and metastatic phenotypes. Further studies might investigate whether these have a potential impact on the immune response towards the cancer. In this review, the background, evidence, and potential relevance of tumor cell fusions with macrophages is discussed, along with the potential role of intercellular connections in their formation. Such fusion cells could be a key component in cancer metastasis, and therefore, evolve as a diagnostic and therapeutic target in cancer precision medicine.
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Affiliation(s)
- Yariswamy Manjunath
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65212, USA; (Y.M.); (J.B.M.); (K.N.S.); (D.M.A.); (E.T.K.); (K.F.S.-O.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - David Porciani
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65212, USA; (D.P.); (D.H.B.)
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA
| | - Jonathan B. Mitchem
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65212, USA; (Y.M.); (J.B.M.); (K.N.S.); (D.M.A.); (E.T.K.); (K.F.S.-O.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - Kanve N. Suvilesh
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65212, USA; (Y.M.); (J.B.M.); (K.N.S.); (D.M.A.); (E.T.K.); (K.F.S.-O.); (G.L.)
| | - Diego M. Avella
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65212, USA; (Y.M.); (J.B.M.); (K.N.S.); (D.M.A.); (E.T.K.); (K.F.S.-O.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - Eric T. Kimchi
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65212, USA; (Y.M.); (J.B.M.); (K.N.S.); (D.M.A.); (E.T.K.); (K.F.S.-O.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - Kevin F. Staveley-O’Carroll
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65212, USA; (Y.M.); (J.B.M.); (K.N.S.); (D.M.A.); (E.T.K.); (K.F.S.-O.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - Donald H. Burke
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65212, USA; (D.P.); (D.H.B.)
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65212, USA
| | - Guangfu Li
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65212, USA; (Y.M.); (J.B.M.); (K.N.S.); (D.M.A.); (E.T.K.); (K.F.S.-O.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65212, USA; (D.P.); (D.H.B.)
| | - Jussuf T. Kaifi
- Department of Surgery, Ellis Fischel Cancer Center, University of Missouri, Columbia, MO 65212, USA; (Y.M.); (J.B.M.); (K.N.S.); (D.M.A.); (E.T.K.); (K.F.S.-O.); (G.L.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
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Shen Y, Guan Y, Hummel JJ, Shyu CR, Mitchem JB. Immunogenomic pathways associated with cytotoxic lymphocyte infiltration and survival in colorectal cancer. BMC Cancer 2020; 20:124. [PMID: 32059711 PMCID: PMC7023815 DOI: 10.1186/s12885-020-6513-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/03/2020] [Indexed: 12/21/2022] Open
Abstract
Background Colorectal cancer (CRC) is the second leading cancer killer in the US today and patients with metastatic disease have only a 14% 5-year survival. One of the most impactful recent advances in cancer therapy, immune checkpoint inhibition, has not been shown to be effective for the majority of these patients. In this study, we use The Cancer Genome Atlas (TCGA) and recently developed informatic-based tools to identify targets for immune based therapy in colorectal cancer patients. Methods Open access, pre-processed (level 3) mRNA data and clinical data from colorectal patients from the TCGA was downloaded from FireCloud. Using the Microenvironment Cell Populations-Counter method (MCP-Counter), cytotoxic lymphocyte scores were calculated for all patients. Patients were then grouped by cytotoxic lymphocyte score (High vs Low), pathologic stage, and location to identify differentially expressed genes. Pathway enrichment analysis was performed using Reactome to determine differentially expressed genes associated with immune pathways. Survival analysis was performed with identified differentially expressed genes. Results In the TCGA dataset, there are 461 colon and 172 rectal cancer patients. After stratifying patients by cytotoxic lymphocyte score, anatomical location, and stage, we found a significant number of differentially expressed genes. We identified one pathway, “immunoregulatory interactions between a lymphoid and non-lymphoid cell”, that was highly enriched and included in all tumor locations and stages. Survival analysis performed with differentially expressed genes in this pathway identified 21 different genes associated with survival and cytotoxic lymphocyte infiltration, with ~ 70% of these genes occurring in the metastatic right-sided CRC group. Specifically, all genes associated with survival in the metastatic right-sided colorectal cancer group with low cytotoxic lymphocyte scores positively impacted survival. Conclusions Utilizing the TCGA, a publicly available dataset, and informatics-based analyses, we identified potential targets to improve immune based therapy in colorectal cancer. Additionally, we note the most targets in metastatic right-sided CRC patients, the patient group with the worst predicted survival. The results from this study demonstrate the ability of informatics-based analytic techniques to identify new therapeutic targets as well as improve patient selection for intervention, helping us to achieve the goals of precision-based oncology.
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Affiliation(s)
- Yuanyuan Shen
- Institute for Data Science and Informatics, University of Missouri, 238 Naka Hall, Columbia, MO, 65211-2060, USA
| | - Yue Guan
- Department of Surgery, University of Missouri School of Medicine, 1 Hospital Dr., Columbia, MO, 65212, USA
| | - Justin J Hummel
- Institute for Data Science and Informatics, University of Missouri, 238 Naka Hall, Columbia, MO, 65211-2060, USA
| | - Chi-Ren Shyu
- Institute for Data Science and Informatics, University of Missouri, 238 Naka Hall, Columbia, MO, 65211-2060, USA
| | - Jonathan B Mitchem
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA. .,Institute for Data Science and Informatics, University of Missouri, 238 Naka Hall, Columbia, MO, 65211-2060, USA. .,Department of Surgery, University of Missouri School of Medicine, 1 Hospital Dr., Columbia, MO, 65212, USA.
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Shen Y, Hummel J, Trindade IC, Papageorgiou C, Shyu CR, Mitchem JB. Regulation of gene expression by DNA methylation with cytotoxic T lymphocytes evaluation in consensus molecular subtypes of colorectal cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.5_suppl.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
25 Background: Low cytotoxic T lymphocyte (CTLs) infiltration in colorectal cancer (CRC) tumors is a challenge to treatment with immune checkpoint inhibitors. Consensus molecular subtypes (CMS) classify patients based on tumor attributes, and CMS1 patients include the majority of patients with high CTL infiltration and “inflamed” tumors. Epigenetic modification plays a critical role in gene expression and therapy resistance. Therefore, in this study we compared DNA methylation, gene expression, and CTL infiltration of CMS1 patients to other CMS groups to determine targets for improving immunotherapy in CRC. Methods: RNA-seq (n = 511) and DNA methylation (n = 316) from The Cancer Genome Atlas databases were used to determine gene expression and methylation profiles based on CMSs. CMS1 was used as a reference and compared to other subtypes (CMS2-4). Microenvironment Cell Populations- counter (MCPcounter) was used to determine tumor CTL infiltration. Genes with significantly different expression (p < 0.01, LogFC≥|1.5|) and difference of mean methylation β value ≥|0.25| were integrated for Pearson correlation coefficient analysis with MCPcounter score (r > |0.7|). Results: Comparing CMS1 and CMS2, ARHGAP9, TBX21, and LAG3 were differentially methylated and correlated with CTL scores. ARHGAP9 and TBX21 were decreased and hypomethylated in CMS2. Comparing CMS1 and CMS3, ARHGAP9, TBX21, FMNL1, HLA-DPB1, and STX11 were downregulated in CMS3 and highly correlated with CTL scores. ARHGAP9, FMNL1, HLA-DPB1, and STX11 were hypomethylated in CMS3 and TBX21 was methylated in both, but had a higher methylation ratio in CMS1. Comparing CMS1 and CMS4, TBX21 was the only gene downregulated, hypomethylated, and highly correlated with CTL scores in CMS4 patients. Conclusions: We found six genes differentially expressed, differentially methylated, and highly correlated with CTL infiltration when comparing CMS1 to other CMS groups. Specifically, TBX21 was the only gene highly correlated with CTL scores with differential gene expression and methylation in CMS2-4 when compared to CMS1. Thus, T-bet may be a critical regulator of T cell responses in CRC.
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Affiliation(s)
- Yuanyuan Shen
- University of Missouri-Columbia, Institute for Data Science & Informatics, Columbia, MO
| | - Justin Hummel
- University of Missouri-Columbia, Institute for Data Science & Informatics, Columbia, MO
| | | | | | - Chi-Ren Shyu
- University of Missouri-Columbia, Institute for Data Science & Informatics, Columbia, MO
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Hummel J, Shen Y, Innokenteva I, Papageorgiou C, Shyu CR, Mitchem JB. Network analysis to reveal BTK as a link between myeloid and T cells in TLR signaling in colorectal cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.5_suppl.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
30 Background: Colorectal cancer (CRC) is the second-leading cause of cancer mortality in the US today. Recent advances in immunotherapy have only been shown to benefit a limited subgroup of patients with CRC. In other malignancies, activation of Toll-like receptors (TLRs) has been shown to overcome resistance to immunotherapy, such as immune checkpoint inhibition (ICI). In this study, using publicly available data and informatics-based analysis, we identified BTK as a critical link between TLR signaling and T cells in the CRC tumor microenvironment. Methods: Using RNA-seq data from The Cancer Genome Atlas (TCGA) and the Microenvironment Cell Populations (MCP)-Counter, abundance scores were generated for the tumor microenvironment of each patient. A curated TLR gene panel was generated using Reactome and GO. Pearson analysis was used to evaluate each pairwise combination of genes and cell-types. Significance was determined by the correlation coefficient, r ≥ | 0.7 | with a p-value < 0.05. Network analysis was performed using the Girvan–Newman algorithm to establish critical connections across these features. Results: After establishing a 453 gene TLR panel and creating MCP-Counter scores, correlation analysis demonstrated strong correlations between 54 different genes and 7 cell-types. As expected the most genes were associated with monocytic lineage cells' (30) and 'myeloid dendritic cells' (7). Only 5 genes were significantly associated with 'T cells'. Genes and cell-types that were highly correlated were then further analyzed for network association. From this analysis, BTK was identified as a critical edge acting as the primary link between ‘myeloid cells’ and ‘T cells’. Conclusions: Developing novel strategies for the treatment of CRC is critical and immunotherapy represents an area ripe for advancement. Informatics based analysis combined with publicly available data provides us with an opportunity to shape pre-clinical and translational studies. Using this approach, we have identified BTK as a critical link between myeloid cells and T cells in the tumor microenvironment in CRC. Further studies in our laboratory will focus confirming these findings for translation into patients.
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Affiliation(s)
- Justin Hummel
- University of Missouri-Columbia, Institute for Data Science & Informatics, Columbia, MO
| | - Yuanyuan Shen
- University of Missouri-Columbia, Institute for Data Science & Informatics, Columbia, MO
| | - Iiulia Innokenteva
- University of Missouri-Columbia, Institute for Data Science & Informatics, Columbia, MO
| | | | - Chi-Ren Shyu
- University of Missouri-Columbia, Institute for Data Science & Informatics, Columbia, MO
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Shen Y, Shyu CR, Mitchem JB, Ding F, Shajahan-Haq AN. Abstract P2-09-14: Immunogenomic pathway and survival analysis in breast cancers based on tumor location and molecular subtypes. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p2-09-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Most breast tumors respond poorly to immunotherapy. Triple-negative breast cancer (TNBC) breast tumors are thought to be more immunogenic than other breast cancer subtypes (luminal A/B or HER2+). Increased immune response in TNBC are characterized by high levels of tumor infiltrating T lymphocyte (TIL) composition that would predict excellent response to immune checkpoint blockade. For all breast cancers, tumors appear more commonly in the upper outer quadrant. However, it is not clear whether expression of immune response genes vary with tumor location among the subtypes. Here, we hypothesized that by analyzing differential gene expression associated with immune response pathways among molecular subtypes of breast cancer such as luminal A/B, HER2+ or TNBC, we can identify targetable pathways to improve therapy with breast cancer.
Methods: Using the Cancer Genome Atlas (TCGA) dataset, we have identified 918 breast cancer tumor samples and compared RNAseq gene expression based on molecular subtypes and anatomic locations of biopsies (i.e., right, left, lower inner quadrant, lower outer quadrant, upper inner quadrant or upper outer quadrant). Genes with significantly different expression (p<0.01) were selected for survival analysis. R, Reactome Pathway Browser were used to retrieve and analyze data.
Results: In TNBC, tumors from lower outer quadrant, lower inner quadrant demonstrated significantly higher CD8B mRNA expression compared with luminalA/B and HER2 (p=2.93E-04, 2.73E-04) from same locations. CD8B mRNA was not significantly higher in TNBC tumors of other sites compared with luminalA/B and HER2. However, pathway/genes associated with CTL function remained significantly different between the different sites for TNBC compared with other subtypes. The metastasis suppressor gene, CD82, was significantly higher in TNBC samples from the right side (p=4.83E-05), lower outer quadrant (p=4.33E-05), lower inner quadrant (p=3.32E-03) and upper inner quadrant (p=4.51E-07), but this gene was not significantly expressed in the upper outer region, where tumors are prevalent.
From immune pathway analysis, genes involved in the antigen activates B cell receptor pathway (p<0.05) were associated with overall survival (OS) in right and left sided Luminal A/B and HER2 tumors and right sided TNBC tumors. Finally, genes from pathway involved in immune-regulatory interactions between a lymphoid and a non-lymphoid cells were associated with OS in lower outer quadrant, upper outer quadrant tumors in luminal A/B and HER2 cases and right sided tumors in TNBC (p<0.05).
Conclusion: While previous studies have reported that tumor infiltrating lymphocytes and lymphoid aggregates in tumors are associated with survival, following more complex analysis, we reveal novel genes and immune pathways that demonstrate improved survival prediction in the TCGA dataset for breast cancers. Furthermore, as expected, we confirm that different immune pathways are associated with survival in luminalA/B, HER2 and TNBC tumors. Our findings demonstrate the importance of a patient-centered approach to the treatment of patients with breast cancer.
Citation Format: Shen Y, Shyu C-R, Mitchem JB, Ding F, Shajahan-Haq AN. Immunogenomic pathway and survival analysis in breast cancers based on tumor location and molecular subtypes [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-09-14.
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Affiliation(s)
- Y Shen
- Informatics Institute, University of Missouri, Columbia, MO; Hamden Hall Country Day School, Hamden, CT; Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - C-R Shyu
- Informatics Institute, University of Missouri, Columbia, MO; Hamden Hall Country Day School, Hamden, CT; Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - JB Mitchem
- Informatics Institute, University of Missouri, Columbia, MO; Hamden Hall Country Day School, Hamden, CT; Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - F Ding
- Informatics Institute, University of Missouri, Columbia, MO; Hamden Hall Country Day School, Hamden, CT; Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - AN Shajahan-Haq
- Informatics Institute, University of Missouri, Columbia, MO; Hamden Hall Country Day School, Hamden, CT; Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
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22
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Jones JE, Busi SB, Mitchem JB, Amos-Landgraf JM, Lewis MR. Evaluation of a Tumor-Targeting, Near-Infrared Fluorescent Peptide for Early Detection and Endoscopic Resection of Polyps in a Rat Model of Colorectal Cancer. Mol Imaging 2018; 17:1536012118790065. [PMID: 30064304 PMCID: PMC6071153 DOI: 10.1177/1536012118790065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The goal of these studies was to use a tumor-targeting, near-infrared (NIR) fluorescent
peptide to evaluate early detection and to guide surgical removal of polyps in a
genetically engineered rat model of spontaneous colorectal cancer. This peptide, LS301,
was conjugated to Cy7.5 and applied topically to the colon of adenoma-bearing Pirc rats.
Ten minutes after administration, rats underwent targeted NIR laser colonoscopy. Rats were
also evaluated by white light colonoscopy and narrow-band imaging, for comparison to the
NIR technique. Unlike white light and narrow-band colonoscopy, NIR imaging detected
unexpected flat lesions in young Pirc rats. NIR imaging was also used to assess resection
margins after electrocauterization of polyps. Tumor margins remained negative at 5 weeks
postsurgery, demonstrating successful polypectomy. The present studies show that
NIR-targeted colonoscopy is an attractive strategy to improve screening for and resection
of colorectal neoplasia.
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Affiliation(s)
- Jade E Jones
- 1 Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA.,2 Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Susheel Bhanu Busi
- 3 Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | | | | | - Michael R Lewis
- 1 Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA.,2 Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
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23
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Mitchem JB, Stafford C, Francone TD, Roberts PL, Schoetz DJ, Marcello PW, Ricciardi R. What is the optimal management of an intra-operative air leak in a colorectal anastomosis? Colorectal Dis 2018; 20:O39-O45. [PMID: 29172236 DOI: 10.1111/codi.13971] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/07/2017] [Indexed: 01/26/2023]
Abstract
AIM An airtight anastomosis on intra-operative leak testing has been previously demonstrated to be associated with a lower risk of clinically significant postoperative anastomotic leak following left-sided colorectal anastomosis. However, to date, there is no consistently agreed upon method for management of an intra-operative anastomotic leak. Therefore, we powered a noninferiority study to determine whether suture repair alone was an appropriate strategy for the management of an intra-operative air leak. METHOD This is a retrospective cohort analysis of prospectively collected data from a tertiary care referral centre. We included all consecutive patients with left-sided colorectal or ileorectal anastomoses and evidence of air leak during intra-operative leak testing. Patients were excluded if proximal diversion was planned preoperatively, a pre-existing proximal diversion was present at the time of surgery or an anastomosis was ultimately unable to be completed. The primary outcome measure was clinically significant anastomotic leak, as defined by the Surgical Infection Study Group at 30 days. RESULTS From a sample of 2360 patients, 119 had an intra-operative air leak during leak testing. Sixty-eight patients underwent suture repair alone and 51 underwent proximal diversion or anastomotic reconstruction. The clinically significant leak rate was 9% (6/68; 95% CI: 2-15%) in the suture repair alone arm and 0% (0/51) in the diversion or reconstruction arm. CONCLUSION Suture repair alone does not meet the criteria for noninferiority for the management of intra-operative air leak during left-sided colorectal anastomosis. Further repair of intra-operative air leak by suture repair alone should be reconsidered given these findings.
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Affiliation(s)
- J B Mitchem
- Department of Surgery, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - C Stafford
- Section of Colon and Rectal Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - T D Francone
- Section of Colon and Rectal Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - P L Roberts
- Department of Surgery, University of Missouri School of Medicine, Columbia, Missouri, USA.,Department of Colon and Rectal Surgery, The Lahey Clinic, Burlington, Massachusetts, USA
| | - D J Schoetz
- Department of Surgery, University of Missouri School of Medicine, Columbia, Missouri, USA.,Department of Colon and Rectal Surgery, The Lahey Clinic, Burlington, Massachusetts, USA
| | - P W Marcello
- Department of Surgery, University of Missouri School of Medicine, Columbia, Missouri, USA.,Department of Colon and Rectal Surgery, The Lahey Clinic, Burlington, Massachusetts, USA
| | - R Ricciardi
- Section of Colon and Rectal Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
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Abstract
Familial adenomatous polyposis (FAP) syndromes make up fewer than 1% of patients diagnosed with colorectal cancer each year. Patients with familial polyposis syndromes including FAP, attenuated FAP, and MYH-associated polyposis (MAP), are an important group often cared for by colorectal surgeons. Registry and screening programs have been shown to improve survival in patients with adenomatous polyposis, as it allows patients to undergo surgical intervention prior to the development of colorectal cancer. There are several surgical options for the treatment of colorectal polyps in patients with adenomatous polyposis, so it is important to choose the appropriate procedure for each patient after discussing the risk of cancer in the rectal remnant, as well as bowel and sexual function in a predominantly young patient group. Regardless of procedure choice, long-term follow-up is important with yearly endoscopic evaluation of the pouch or remnant rectum, as well as appropriate screening for extracolonic malignancy. Adenomatous polyposis patients require an intense care regimen, but can have a normal lifespan with good quality when cared for appropriately.
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Affiliation(s)
- Jonathan B Mitchem
- Department of Colon and Rectal Surgery, Lahey Hospital and Medical Center, Burlington, Massachusetts
| | - Jason F Hall
- Department of Colon and Rectal Surgery, Lahey Hospital and Medical Center, Burlington, Massachusetts
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25
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Sanford DE, Belt BA, Panni RZ, Mayer A, Deshpande AD, Carpenter D, Mitchem JB, Plambeck-Suess SM, Worley LA, Goetz BD, Wang-Gillam A, Eberlein TJ, Denardo DG, Goedegebuure SP, Linehan DC. Inflammatory monocyte mobilization decreases patient survival in pancreatic cancer: a role for targeting the CCL2/CCR2 axis. Clin Cancer Res 2013; 19:3404-15. [PMID: 23653148 DOI: 10.1158/1078-0432.ccr-13-0525] [Citation(s) in RCA: 410] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE To determine the role of the CCL2/CCR2 axis and inflammatory monocytes (CCR2(+)/CD14(+)) as immunotherapeutic targets in the treatment of pancreatic cancer. EXPERIMENTAL DESIGN Survival analysis was conducted to determine if the prevalence of preoperative blood monocytes correlates with survival in patients with pancreatic cancer following tumor resection. Inflammatory monocyte prevalence in the blood and bone marrow of patients with pancreatic cancer and controls was compared. The immunosuppressive properties of inflammatory monocytes and macrophages in the blood and tumors, respectively, of patients with pancreatic cancer were assessed. CCL2 expression by human pancreatic cancer tumors was compared with normal pancreas. A novel CCR2 inhibitor (PF-04136309) was tested in an orthotopic model of murine pancreatic cancer. RESULTS Monocyte prevalence in the peripheral blood correlates inversely with survival, and low monocyte prevalence is an independent predictor of increased survival in patients with pancreatic cancer with resected tumors. Inflammatory monocytes are increased in the blood and decreased in the bone marrow of patients with pancreatic cancer compared with controls. An increased ratio of inflammatory monocytes in the blood versus the bone marrow is a novel predictor of decreased patient survival following tumor resection. Human pancreatic cancer produces CCL2, and immunosuppressive CCR2(+) macrophages infiltrate these tumors. Patients with tumors that exhibit high CCL2 expression/low CD8 T-cell infiltrate have significantly decreased survival. In mice, CCR2 blockade depletes inflammatory monocytes and macrophages from the primary tumor and premetastatic liver resulting in enhanced antitumor immunity, decreased tumor growth, and reduced metastasis. CONCLUSIONS Inflammatory monocyte recruitment is critical to pancreatic cancer progression, and targeting CCR2 may be an effective immunotherapeutic strategy in this disease.
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Affiliation(s)
- Dominic E Sanford
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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Sanford DE, Belt BA, Panni RZ, Mitchem JB, Denardo DG, Goedegebuure SP, Linehan DC. Abstract A64: Peripheral blood monocytes predict survival in pancreatic cancer. Cancer Res 2013. [DOI: 10.1158/1538-7445.tumimm2012-a64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy with a 5-year survival of < 5%, and a mortality rate nearly equal to its incidence. Characteristic of this tumor is a microenvironment in which monocytes/macrophages are abundant. Human monocytes are divided into two major subsets: inflammatory (IM) and resident (RM) monocytes. IM make up 85%-90% of human peripheral blood monocytes, and are identified by the expression of CD14 and CCR2. The CCL2-CCR2 chemokine axis is a crucial signaling pathway in physiologic IM recruitment from the bone marrow under inflammatory conditions. Within the tumor microenvironment, IM can differentiate into tumor associated-macrophages (TAM) which are immunosuppressive, and directly promote tumor progression by enhancing angiogenesis, growth, and invasion. We present evidence that IM are recruited from the bone marrow to the peripheral blood and tumors of PDAC patients. Furthermore, we hypothesize that that peripheral blood monocyte count is predictive of patient survival in PDAC.
Methods: PDAC tumor specimens (n=11) and normal pancreas (n=10) were subjected to flow cytometry and RT-PCR. Flow cytometry was performed on the peripheral blood mononuclear cells (PBMC) and bone marrow mononuclear cells (BMMC) of PDAC patients (n=13) and compared to healthy controls (n=11). For the survival analysis, 483 patients with PDAC underwent pancreaticoduodenectomy between 1997 and 2011 at a single institution. We excluded 110 patients with pre-operative leukocytosis (WBC>11,000 cell/ul) or who died within 30 days of surgery. We stratified the remaining 373 patients into 3 groups based on the prevalence of monocytes in peripheral blood leukocytes using their pre-operative CBC: low(<6%)[n=47], mid(≥6% to <11%)[n=271], and high(≥11%)[n=55] %monocyte groups. We used standard Kaplan-Meier survival statistics to compare overall survival between the three groups.
Results: PDAC tumors are infiltrated by CCR2+ cells of monocyte lineage (CD45+, CD11b+, HLA-DR+, CD115+, CD14+) [37.9% ±1.6% of CD45+ cells], and these tumors expressed significantly more CCL2 relative to normal pancreas[p<0.01]. IM (CD45+, CD11b+, HLA-DR+, CD14+, CCR2+, CD16-, CX3CR1 low) were significantly more prevalent in the PBMC of PDAC patients compared to controls [10.8%±1.1% vs 5.7%±1.1% of CD45+ cells; p<0.005]; whereas, resident monocytes (CD45+, CD11b+, HLA-DR+, CD16+, CX3CR1 high, CD14 low, CCR2-) were not significantly different [0.67% ±0.1% vs 0.72% ±0.1%; p=0.76]. However, IM were significantly decreased in the bone marrow of PDAC patients compared to healthy controls [10.4% ±1.1 vs 14.9 ±1.2%; p<0.01]. This suggests that the mechanism of increased IM in the peripheral blood of PDAC patients is mobilization from the bone marrow. Survival analysis of PDAC patients revealed that patients in the low %monocyte group survived significantly longer than patients in the high %monocyte group (27.8 months vs 18.2 months; p=0.02 on log-rank test). Also, there was a statistically significant incremental decrease in survival from the low to mid to high %monocyte groups (p=0.01 on log-rank test for trend).
Conclusion: IM are recruited from the bone marrow to the tumor microenvironment in PDAC through the CCL2/CCR2 chemokine axis, and the prevalence of peripheral blood monocytes correlates with decreased patient survival. Developing effective intervention strategies to thwart monocyte recruitment may hold significant promise in this disease.
Citation Format: Dominic E. Sanford, Brian A. Belt, Roheena Z. Panni, Jonathan B. Mitchem, David G. Denardo, S. Peter Goedegebuure, David C. Linehan. Peripheral blood monocytes predict survival in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology: Multidisciplinary Science Driving Basic and Clinical Advances; Dec 2-5, 2012; Miami, FL. Philadelphia (PA): AACR; Cancer Res 2013;73(1 Suppl):Abstract nr A64.
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Mitchem JB, Brennan DJ, Sanford DE, Knolhoff BL, Zhu Y, Brian B, Wang-Gillam A, Goedegebuure P, Linehan DC, DeNardo DG. Abstract B83: Targeting tumor-infiltrating macrophages decreases pancreatic tumor-initiating cells and improves chemotherapeutic responses by relieving immune suppression. Cancer Res 2013. [DOI: 10.1158/1538-7445.tumimm2012-b83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tumor-infiltrating immune cells can promote chemoresistance and metastatic spread in aggressive tumors. Consequently, the type and quality of immune responses present in the neoplastic stroma are highly predictive of patient outcome in several cancer types. In addition to host immune responses, intrinsic tumor cell activities that mimic stem cell properties have been linked to chemoresistance, metastatic dissemination, and the induction of immune suppression. Far from being a static cell population, the presence of cancer stem cells appears to be controlled by highly dynamic processes that are dependent on cues from the tumor stroma. However, the impact that immune responses have on the differentiation or expansion of tumor stem cells is not well understood. In this study, we demonstrate that targeting tumor-infiltrating macrophages and inflammatory monocytes by either inhibition of colony stimulating factor-1 receptor (CSF1R) or chemokine (C-C motif) receptor 2 (CCR2) decreases the number of tumor-initiating cells in pancreatic tumors. Targeting CCR2 or CSF1R improves chemotherapeutic efficacy, inhibits metastasis, and increases antitumor T-cell responses. We also found that tumor-educated macrophages could directly enhance the tumor-initiating capacity of pancreatic tumor cells through the activation of signal transducer and activator of transcription 3 (STAT3). In turn, these STAT3-activated tumor-initiating cells facilitate macrophage-mediated suppression of CD8+ T lymphocytes. These data suggest that targeting tumor-infiltrating macrophages is an effective strategy for overcoming therapeutic resistance due to the presence of tumor-initiating cells.
Citation Format: Jonathan B. Mitchem, Donal J. Brennan, Dominic E. Sanford, Brett L. Knolhoff, Yu Zhu, Belt Brian, Andrea Wang-Gillam, Peter Goedegebuure, David C. Linehan, David G. DeNardo. Targeting tumor-infiltrating macrophages decreases pancreatic tumor-initiating cells and improves chemotherapeutic responses by relieving immune suppression. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology: Multidisciplinary Science Driving Basic and Clinical Advances; Dec 2-5, 2012; Miami, FL. Philadelphia (PA): AACR; Cancer Res 2013;73(1 Suppl):Abstract nr B83.
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Affiliation(s)
| | - Donal J. Brennan
- 2Queensland Centre for Gynaecological Cancer, Brisbane, Australia
| | | | - Brett L. Knolhoff
- 1Washington University, St. Louis, School of Medicine, St. Louis, MO,
| | - Yu Zhu
- 1Washington University, St. Louis, School of Medicine, St. Louis, MO,
| | - Belt Brian
- 1Washington University, St. Louis, School of Medicine, St. Louis, MO,
| | | | | | - David C. Linehan
- 1Washington University, St. Louis, School of Medicine, St. Louis, MO,
| | - David G. DeNardo
- 1Washington University, St. Louis, School of Medicine, St. Louis, MO,
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Sanford DE, Porembka MR, Panni RZ, Mitchem JB, Belt BA, Plambeck-Suess SM, Lin G, Denardo DG, Fields RC, Hawkins WG, Strasberg SM, Lockhart AC, Wang-Gillam A, Goedegebuure SP, Linehan DC. A Study of Zoledronic Acid as Neo-Adjuvant, Perioperative Therapy in Patients with Resectable Pancreatic Ductal Adenocarcinoma. ACTA ACUST UNITED AC 2013; 4:797-803. [PMID: 24089656 DOI: 10.4236/jct.2013.43096] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by abundant granulocytic myeloid-derived suppressor cells (G-MDSC = CD45+/Lin-/CD33+/CD11b+/CD15+), which infiltrate tumors and suppress anti-tumor immunity. We have previously demonstrated in a murine model of PDAC that zoledronic acid (ZA) depletes G-MDSC resulting in decreased tumor growth and improved survival. We report here the results of a phase 1 clinical trial (NCT00892242) using ZA as neo-adjuvant, perioperative therapy in patients with non-metastatic, resectable pancreatic adenocarcinoma. METHODS Eligible PDAC patients received ZA (4mg) IV 2 weeks prior to surgery. Patients then received 2 additional doses of ZA 4 weeks apart. Blood and bone marrow were obtained from patients prior to treatment with ZA and 3 months after surgery for analysis of G-MDSC by flow cytometry. RESULTS Twenty-three patients received pre-operative ZA with at least 6 months of follow-up Only 15 PDAC patients had non-metastatic PDAC, which was amenable to resection. ZA was well tolerated, and all adverse events were grade 1 or 2. The most common adverse events were fatigue, abdominal pain/discomfort, anorexia, and arthralgia. Of resected PDAC patients treated with ZA, 1- and 2-year overall survival (OS) was 85.7% and 33.3%, respectively, with a median OS of 18 months. This group had a 1- and 2-year progression-free survival (PFS) of 26.9% and 8.9%, respectively, with a median PFS of 12 months. The prevalence of G-MDSC was unchanged in the blood and bone marrow of PDAC patients pre- and post-treatment with ZA. CONCLUSION ZA is safe and well tolerated as neo-adjuvant, peri-operative therapy in PDAC patients. In this small study, we did not observe a difference in OS or PFS compared to historical controls. Also, there was no difference in the prevalence of G-MDSC in the blood and bone marrow of PDAC patients pre- and post-treatment with ZA.
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Mitchem JB, Brennan DJ, Knolhoff BL, Belt BA, Zhu Y, Sanford DE, Belaygorod L, Carpenter D, Collins L, Piwnica-Worms D, Hewitt S, Udupi GM, Gallagher WM, Wegner C, West BL, Wang-Gillam A, Goedegebuure P, Linehan DC, DeNardo DG. Targeting tumor-infiltrating macrophages decreases tumor-initiating cells, relieves immunosuppression, and improves chemotherapeutic responses. Cancer Res 2012; 73:1128-41. [PMID: 23221383 DOI: 10.1158/0008-5472.can-12-2731] [Citation(s) in RCA: 711] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tumor-infiltrating immune cells can promote chemoresistance and metastatic spread in aggressive tumors. Consequently, the type and quality of immune responses present in the neoplastic stroma are highly predictive of patient outcome in several cancer types. In addition to host immune responses, intrinsic tumor cell activities that mimic stem cell properties have been linked to chemoresistance, metastatic dissemination, and the induction of immune suppression. Cancer stem cells are far from a static cell population; rather, their presence seems to be controlled by highly dynamic processes that are dependent on cues from the tumor stroma. However, the impact immune responses have on tumor stem cell differentiation or expansion is not well understood. In this study, we show that targeting tumor-infiltrating macrophages (TAM) and inflammatory monocytes by inhibiting either the myeloid cell receptors colony-stimulating factor-1 receptor (CSF1R) or chemokine (C-C motif) receptor 2 (CCR2) decreases the number of tumor-initiating cells (TIC) in pancreatic tumors. Targeting CCR2 or CSF1R improves chemotherapeutic efficacy, inhibits metastasis, and increases antitumor T-cell responses. Tumor-educated macrophages also directly enhanced the tumor-initiating capacity of pancreatic tumor cells by activating the transcription factor STAT3, thereby facilitating macrophage-mediated suppression of CD8(+) T lymphocytes. Together, our findings show how targeting TAMs can effectively overcome therapeutic resistance mediated by TICs.
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Affiliation(s)
- Jonathan B Mitchem
- Department of Surgery, Washington University School of Medicine, St Louis, MO 63110, USA
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Abstract
Tumor-derived factors, such as proinflammatory cytokines, can increase the hospitality of metastatic sites by recruiting and activating leukocytes to perform supporting roles during metastatic dissemination. These same cytokines, however, are natural danger signals for the immune system and as such can induce anti-tumor immune responses by both adaptive and innate immune cells. The outcome of tumor-derived inflammatory cytokines is probably closely related to the exact repertoire of factors produced by each tumor. Several recent studies have investigated these seemingly contradictory roles of tumor-derived CCL2 with significant clinical implications.
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Hornick JR, Johnston FM, Simon PO, Younkin M, Chamberlin M, Mitchem JB, Azar RR, Linehan DC, Strasberg SM, Edmundowicz SA, Hawkins WG. A single-institution review of 157 patients presenting with benign and malignant tumors of the ampulla of Vater: management and outcomes. Surgery 2011; 150:169-76. [PMID: 21801957 DOI: 10.1016/j.surg.2011.05.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 05/13/2011] [Indexed: 12/13/2022]
Abstract
BACKGROUND Although benign ampullary tumors are removed endoscopically, due to their potential to progress to malignant disease, the favored treatment for adenocarcinoma is pancreaticoduodenectomy. We reviewed our institution's experience in order to identify which patients were at highest risk of disease progression following surgical resection, as well as evaluate whether localized T1 tumors are best treated by pancreaticoduodenectomy. METHODS We retrospectively reviewed 157 patients who presented with an ampullary mass, from 2001 to 2010, and identified 51 with benign adenoma and 106 with adenocarcinoma. RESULTS Patients with malignant tumors most often presented with larger tumors and jaundice, which alone was predictive of survival (OR = 67). Forty-five percent of patients with pathologically confirmed T1 tumors had positive lymph nodes and median survival was modest at 60 months. Lymph node involvement was predictive of recurrence and decreased survival. CONCLUSION Patients with malignant tumors often present with jaundice and larger tumors. These findings should warrant suspicion for cancer and expedited preoperative workup. Based on our finding that nearly half the patients with T1 tumors had positive lymph nodes, we recommend pancreaticoduodenectomy for any patient with biopsy proven adenocarcinoma who is a suitable candidate for surgery.
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Affiliation(s)
- John R Hornick
- Division of Hepatobiliary, Pancreatic, and Gastrointestinal Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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Goedegebuure P, Mitchem JB, Porembka MR, Tan MCB, Belt BA, Wang-Gillam A, Gillanders WE, Hawkins WG, Linehan DC. Myeloid-derived suppressor cells: general characteristics and relevance to clinical management of pancreatic cancer. Curr Cancer Drug Targets 2011; 11:734-51. [PMID: 21599634 PMCID: PMC3670669 DOI: 10.2174/156800911796191024] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 12/30/2010] [Indexed: 02/08/2023]
Abstract
Recent studies describe a heterogeneous population of cells of the myeloid lineage, termed myeloid derived suppressor cells (MDSC), which are observed with increased prevalence in the peripheral blood and tumor microenvironment of cancer patients, including pancreatic cancer. Accumulation of MDSC in the peripheral circulation has been related to extent of disease, and correlates with stage. MDSC have primarily been implicated in promoting tumor growth by suppressing antitumor immunity. There is also compelling evidence MDSC are also involved in angiogenesis and metastatic spread. Two main subsets of MDSC have been identified in cancer patients: a monocytic subset, characterized by expression of CD14, and a granulocytic subset characterized by expression of CD15. Both subsets of MDSC actively suppress host immunity through a variety of mechanisms including production of reactive oxygen species and arginase. Just as in humans, accumulation of monocytic and granulocytic MDSC has been noted in the bone marrow, spleen, peripheral circulation, and tumors of tumor bearing mice. Successful targeting of MDSC in mice is associated with improved immune responses, delayed tumor growth, improved survival, and increased efficacy of vaccine therapy. By further elucidating mechanisms of MDSC recruitment and maintenance in the tumor environment, strategies could be developed to reverse immune tolerance to tumor. We discuss here what is currently known about MDSC as well as some potential strategies targeting MDSC in the context of our work on pancreatic cancer and recent literature. Due to the number of new reports on MDSC, the most pertinent ones have been selected.
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Affiliation(s)
- P Goedegebuure
- Department of Surgery and Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Hornick JR, Xu J, Vangveravong S, Tu Z, Mitchem JB, Spitzer D, Goedegebuure P, Mach RH, Hawkins WG. The novel sigma-2 receptor ligand SW43 stabilizes pancreas cancer progression in combination with gemcitabine. Mol Cancer 2010; 9:298. [PMID: 21092190 PMCID: PMC3106998 DOI: 10.1186/1476-4598-9-298] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 11/22/2010] [Indexed: 11/25/2022] Open
Abstract
Background Sigma-2 receptors are over-expressed in proliferating cancer cells, making an attractive target for the targeted treatment of pancreatic cancer. In this study, we investigated the role of the novel sigma-2 receptor ligand SW43 to induce apoptosis and augment standard chemotherapy. Results The binding affinity for sigma-2 ligands is high in pancreas cancer, and they induce apoptosis with a rank order of SV119 < SW43 < SRM in vitro. Combining these compounds with gemcitabine further increased apoptosis and decreased viability. Our in vivo model showed that sigma-2 ligand treatment decreased tumor volume to the same extent as gemcitabine. However, SW43 combination treatment with gemcitabine was superior to the other compounds and resulted in stabilization of tumor volume during treatment, with minimal toxicities. Conclusions This study shows that the sigma-2 ligand SW43 has the greatest capacity to augment gemcitabine in a pre-clinical model of pancreas cancer and has provided us with the rationale to move this compound forward with clinical investigations for patients with pancreatic cancer.
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Affiliation(s)
- John R Hornick
- Department of Surgery, Washington University School of Medicine, S, Euclid Avenue, St. Louis, MO, USA
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Gnerlich JL, Mitchem JB, Weir JS, Sankpal NV, Kashiwagi H, Belt BA, Porembka MR, Herndon JM, Eberlein TJ, Goedegebuure P, Linehan DC. Induction of Th17 cells in the tumor microenvironment improves survival in a murine model of pancreatic cancer. J Immunol 2010; 185:4063-71. [PMID: 20805420 DOI: 10.4049/jimmunol.0902609] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An important mechanism by which pancreatic cancer avoids antitumor immunity is by recruiting regulatory T cells (Tregs) to the tumor microenvironment. Recent studies suggest that suppressor Tregs and effector Th17 cells share a common lineage and differentiate based on the presence of certain cytokines in the microenvironment. Because IL-6 in the presence of TGF-β has been shown to inhibit Treg development and induce Th17 cells, we hypothesized that altering the tumor cytokine environment could induce Th17 and reverse tumor-associated immune suppression. Pan02 murine pancreatic tumor cells that secrete TGF-β were transduced with the gene encoding IL-6. C57BL/6 mice were injected s.c. with wild-type (WT), empty vector (EV), or IL-6-transduced Pan02 cells (IL-6 Pan02) to investigate the impact of IL-6 secretion in the tumor microenvironment. Mice bearing IL-6 Pan02 tumors demonstrated significant delay in tumor growth and better overall median survival compared with mice bearing WT or EV Pan02 tumors. Immunohistochemical analysis demonstrated an increase in Th17 cells (CD4(+)IL-23R(+) cells and CD4(+)IL-17(+) cells) in tumors of the IL-6 Pan02 group compared with WT or EV Pan02 tumors. The upregulation of IL-17-secreting CD4(+) tumor-infiltrating lymphocytes was substantiated at the cellular level by flow cytometry and ELISPOT assay and mRNA level for retinoic acid-related orphan receptor γt and IL-23R by RT-PCR. Thus, the addition of IL-6 to the tumor microenvironment skews the balance toward Th17 cells in a murine model of pancreatic cancer. The delayed tumor growth and improved survival suggests that induction of Th17 in the tumor microenvironment produces an antitumor effect.
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Affiliation(s)
- Jennifer L Gnerlich
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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Sieg SF, Mitchem JB, Bazdar DA, Lederman MM. Close link between CD4+ and CD8+ T cell proliferation defects in patients with human immunodeficiency virus disease and relationship to extended periods of CD4+ lymphopenia. J Infect Dis 2002; 185:1401-16. [PMID: 11992274 DOI: 10.1086/340509] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2001] [Revised: 01/14/2002] [Indexed: 11/03/2022] Open
Abstract
T cell proliferation failure is commonly associated with human immunodeficiency virus (HIV) infection. By examining T cell function on a single-cell basis, we found that CD4(+) T cell proliferation failure was often accompanied by CD8(+) T cell proliferation defects in patients with HIV disease. The defects are characterized by a proportional failure and reduced efficiency of precursor T cell proliferation after stimulation. In this study, patients who historically had low levels of circulating CD4(+) T cells were most likely to demonstrate cellular proliferation failure, regardless of current CD4(+) T cell counts. In contrast, neither historical nor current plasma HIV RNA levels were predictive of proliferation failure. These results suggest that mechanisms of T cell proliferation failure are more complex than can be explained by the direct effects of HIV replication and that therapeutic intervention to avoid prolonged periods of CD4(+) lymphopenia may be desirable for the preservation of immune function in patients with HIV disease.
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Affiliation(s)
- Scott F Sieg
- Center for AIDS Research, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, Ohio 44106, USA.
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