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Kohs TCL, Weeder BR, Chobrutskiy BI, Kartika T, Moore KK, McCarty OJT, Zonies D, Zakhary B, Shatzel JJ. Predictors of thrombosis during VV ECMO: an analysis of 9809 patients from the ELSO registry. J Thromb Thrombolysis 2024; 57:345-351. [PMID: 38095743 DOI: 10.1007/s11239-023-02909-4] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/22/2023] [Indexed: 03/26/2024]
Abstract
Venovenous extracorporeal membrane oxygenation (VV-ECMO) is a life-saving therapy for critically ill patients, but it carries an increased risk of thrombosis due to blood interacting with non-physiological surfaces. While the relationship between clinical variables and thrombosis remains unclear, our study aimed to identify which factors are most predictive of thrombosis. The Extracorporeal Life Support Organization Registry was queried to obtain a cohort of VV-ECMO patients aged 18 years and older from 2015 to 2019. Patients who were over 80-years-old, at the extremes of weight, who received less than 24 h of ECMO, multiple rounds of ECMO, or had missing data were excluded. Multivariate logistic regression modeling was used to assess predictors of thrombosis and mortality. A total of 9809 patients were included in the analysis, with a mean age of 47.1 ± 15.1 years and an average ECMO run time of 305 ± 353 h. Thrombosis occurred in 19.9% of the cohort, with circuit thrombosis (8.6%) and membrane lung failure (6.1%) being the most common. Multivariate analysis showed that ECMO runs over 14 days (OR: 2.62, P < 0.001) and pregnancy-related complications (OR: 1.79, P = 0.004) were associated with an increased risk of thrombosis. Risk factors for circuit thrombosis included incremental unit increases in the pump flow rate at 24 h (OR: 1.07 [1.00-1.14], P = 0.044) and specific cannulation sites. Increased body weight (OR: 1.02 [1.00-1.04], P = 0.026) and increased duration on ECMO (OR: 3.82 [3.12-4.71], P < 0.001) were predictive of membrane lung failure. Additionally, patients with thrombosis were at increased likelihood of in-hospital mortality (OR: 1.52, P < 0.001). This study identified multiple thrombotic risk factors in VV-ECMO, suggesting that future studies investigating the impact of pregnancy associated complications and ECMO flow rate on hemostasis would be illuminating.
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Affiliation(s)
- Tia C L Kohs
- Department of Biomedical Engineering, Oregon Health & Science University, 3303 S. Bond Avenue, Portland, OR, 97239, USA.
| | - Benjamin R Weeder
- Program in Molecular and Cellular Biology, Oregon Health & Science University, Portland, OR, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Thomas Kartika
- Department of Internal Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kerry K Moore
- Department of Pharmacy, Oregon Health & Science University, Portland, OR, USA
| | - Owen J T McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, 3303 S. Bond Avenue, Portland, OR, 97239, USA
| | - David Zonies
- Department of Surgery, Division of Trauma, Critical Care and Acute Care Surgery, Oregon Health & Science University, Portland, OR, USA
| | - Bishoy Zakhary
- Department of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Joseph J Shatzel
- Department of Biomedical Engineering, Oregon Health & Science University, 3303 S. Bond Avenue, Portland, OR, 97239, USA
- Division of Hematology and Oncology, Oregon Health & Science University, Portland, OR, USA
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Charkowick SV, Huda TI, Patel DN, Yeagley M, Arturo JF, Cios KJ, Gozlan EC, Chobrutskiy A, Chobrutskiy BI, Blanck G. IGL CDR3 Hydropathy and Antigen Chemical Complementarity Associated with Greater Disease-Free Survival in Lung Adenocarcinoma: Implications for Gender Disparities. Biochem Genet 2024; 62:530-546. [PMID: 37392243 DOI: 10.1007/s10528-023-10437-2] [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: 01/16/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023]
Abstract
With lung cancer remaining a challenging disease, new approaches to biomarker discovery and therapy development are needed. Recent immunogenomics, adaptive immune receptor approaches have indicated that it is very likely that B cells play an important role in mediating better overall outcomes. As such, we assessed physicochemical features of lung adenocarcinoma resident IGL complementarity determining region-3 (CDR3) amino acid (AA) sequences and determined that hydrophobic CDR3 AA sequences were associated with a better disease-free survival (DFS) probability. Further, using a recently developed chemical complementarity scoring algorithm particularly suitable for the evaluation of large patient datasets, we determined that IGL CDR3 chemical complementarity with certain cancer testis antigens was associated with better DFS. Chemical complementarity scores for IGL CDR3-MAGEC1 represented a gender bias, with an overrepresentation of males among the higher IGL-CDR3-CTA complementarity scores that were in turn associated with better DFS (logrank p < 0.065). Overall, this study pointed towards potential biomarkers for prognoses that, in some cases are likely gender-specific; and towards biomarkers for guiding therapy, e.g., IGL-based opportunities for antigen targeting in the lung cancer setting.
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Affiliation(s)
- Shaun V Charkowick
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Juan F Arturo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Konrad J Cios
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, Oregon, 97239, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, Oregon, 97239, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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Zaman S, Chobrutskiy BI, Quach JU, Blanck G. Specific Intratumor Bacteria Genera and TRG Recombinations Associated with Greater Survival Probability in Alimentary Tract Cancers. J Gastrointest Cancer 2023; 54:1300-1307. [PMID: 37103748 DOI: 10.1007/s12029-023-00935-2] [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] [Accepted: 04/03/2023] [Indexed: 04/28/2023]
Abstract
INTRODUCTION There remains a lack of knowledge regarding the effects of the intratumor microbiome on the tumor immune milieu. We aimed to investigate whether intratumoral bacterial RNA sequence abundance in gastric and esophageal cancers is associated with T-cell infiltrate features. METHODS We assessed cases representing the stomach adenocarcinoma (STAD) and esophageal cancer (ESCA) databases of The Cancer Genome Atlas. RNA-seq data estimating intratumoral bacterial abundance was obtained from publicly available sources. TCR recombination reads were mined from exome files. Survival models were generated using the lifelines python package. RESULTS Increasing levels of the Klebsiella genus were associated with a better OS probability (hazard ratio, 0.5), via a Cox proportional hazards model. The higher Klebsiella abundance was associated with a significantly increased overall (p = 0.0001) and disease-specific survival (p = 0.0289) probability for the STAD dataset. Cases representing the upper 50th percentile of Klebsiella abundance also represented a significantly increased recovery of TRG and TRD recombination reads (p = 0.00192). Analogous results were found for the Aquincola genus in ESCA. CONCLUSIONS This is the first report of associations between low biomass bacterial samples from primary tumor samples with patient survival and with an increased gamma-delta T cell infiltrate. Results indicate that the gamma-delta T cells potentially play a role in the dynamics of the bacterial infiltration of primary tumors of the alimentary tract.
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Affiliation(s)
- Saif Zaman
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, 97239, USA
| | - Jessica U Quach
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa Florida, 33612, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa Florida, 33612, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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Song JJ, Chobrutskiy A, Chobrutskiy BI, Cios KJ, Huda TI, Eakins RA, Diaz MJ, Blanck G. Chemical Complementarity of Tumor Resident, Adaptive Immune Receptor CDR3s and Previously Defined Hepatitis C Virus Epitopes Correlates with Improved Outcomes in Hepatocellular Carcinoma. Viral Immunol 2023; 36:669-677. [PMID: 38052065 DOI: 10.1089/vim.2023.0078] [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] [Indexed: 12/07/2023] Open
Abstract
To better understand how adaptive immune receptors (IRs) in hepatocellular carcinoma (HCC) microenvironments are related to disease outcomes, we employed a chemical complementarity scoring algorithm to quantify electrostatic complementarity between HCC tumor TRB or IGH complementarity-determining region 3 (CDR3) amino acid (AA) sequences and previously characterized hepatitis C virus (HCV) epitopes. High electrostatic complementarity between HCC-resident CDR3s and 12 HCV epitopes was associated with greater survival probabilities, as indicated by two distinct HCC IR CDR3 datasets. Two of the HCV epitopes, HCV*71871 (TRB) and HCV*13458 (IGH), were also determined to represent significantly larger electrostatic CDR3-HCV epitope complementarity in HCV-positive HCC cases, compared with HCV-negative HCC cases, with the CDR3s representing yet a third, independent HCC dataset. Overall, the results indicated the utility of CDR3 AA sequences as biomarkers for HCC patient stratification and as potential guides for the development of therapeutic reagents.
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Affiliation(s)
- Joanna J Song
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, Oregon, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, Oregon, USA
| | - Konrad J Cios
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Rachel A Eakins
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Michael J Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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Cheng P, Cios KJ, Varkhedi M, Barker VR, Yeagley M, Chobrutskiy A, Chobrutskiy BI, Blanck G. An immunoinformatics assessment of the cancer testis antigen, DDX53, as a potential early esophageal cancer antigen. Oncoscience 2023; 10:59-66. [PMID: 37953875 PMCID: PMC10637345 DOI: 10.18632/oncoscience.590] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
T-lymphocytes have been implicated in facilitating a pro-inflammatory, pro-tumorigenic microenvironment that worsens prognosis for esophageal carcinoma (ESCA). In this study, we identified tumor resident, T-cell receptor (TCR) complementarity determining region-3 (CDR3) amino acid sequences and employed an algorithm particularly suited to the big data setting to evaluate TCR CDR3-cancer testis antigen (CTA) chemical complementarities. Chemical complementarity of the ESCA TCR CDR3s and the cancer testis antigen DDX53 represented a disease-free survival (DFS) distinction, whereby the upper fiftieth percentile complementarity group correlated with worse DFS. The high TCR CDR3-DDX53 complementarity group also represented a greater proportion of tumor samples lacking DDX53 expression. These data and analyses raise the question of whether the TCR CDR3-DDX53 chemical complementarity assessment detected an ESCA immune response that selected for DDX53-negative cells?
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Affiliation(s)
- Peter Cheng
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA
| | - Konrad J. Cios
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA
| | - Mallika Varkhedi
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA
| | - Vayda R. Barker
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, Oregon (OR) 97239, USA
| | - Boris I. Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, Oregon (OR) 97239, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida (FL) 33612, USA
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Kacsoh DB, Diaz MJ, Gozlan EC, Sahoo A, Song JJ, Yeagley M, Chobrutskiy A, Chobrutskiy BI, Blanck G. Blood-based T cell receptor anti-viral CDR3s are associated with worse overall survival for neuroblastoma. J Cancer Res Clin Oncol 2023; 149:12047-12056. [PMID: 37421457 DOI: 10.1007/s00432-023-05059-5] [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: 05/24/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
With the advent of large collections of adaptive immune receptor recombination reads representing cancer, there is the opportunity to further investigate the adaptive immune response to viruses in the cancer setting. This is a particularly important goal due to longstanding but still not well-resolved questions about viral etiologies in cancer and viral infections as comorbidities. In this report, we assessed the T cell receptor complementarity determining region-3 (CDR3) amino acid (AA) sequences, for blood-sourced TCRs from neuroblastoma (NBL) cases, for exact AA sequence matches to previously identified anti-viral TCR CDR3 AA sequences. Results indicated the presence of anti-viral TCR CDR3 AA sequences in the NBL blood samples highly significantly correlated with worse overall survival. Furthermore, the TCR CDR3 AA sequences demonstrating chemical complementarity to many cytomegalovirus antigens represented cases with a worse outcome, including cases where such CDR3s were obtained from tumor samples. Overall, these results indicate a significant need for, and provide a novel strategy for assessing viral infection complications in NBL patients.
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Affiliation(s)
- Dorottya B Kacsoh
- College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Michael J Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Arpan Sahoo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Joanna J Song
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Michelle Yeagley
- University of Pittsburgh Medical Center, Pittsburgh, PA, 15261, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, 97239, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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7
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Kinskey JC, Huda TI, Gozlan EC, Quach JU, Arturo JF, Chobrutskiy A, Chobrutskiy BI, Blanck G. The presence of intratumoral Porphyromonas gingivalis correlates with a previously defined pancreatic adenocarcinoma, immune cell expression phenotype and with tumor resident, adaptive immune receptor features. Carcinogenesis 2023; 44:411-417. [PMID: 37195907 DOI: 10.1093/carcin/bgad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/20/2023] [Accepted: 05/15/2023] [Indexed: 05/19/2023] Open
Abstract
The association between pancreatic adenocarcinoma (PAAD) and the pancreatic microbiome is not fully understood, although bacteria may decrease the effectiveness of chemotherapy and lead to anti-apoptotic, pro-inflammatory microenvironments. To better understand the relationship between the PAAD microbiome and the microenvironment, we identified Porphyromonas gingivalis-positive PAAD samples and found a strong association between intratumoral P. gingivalis and: (i) an immune cell gene expression phenotype previously defined by others as gene program 7; and (ii) recovery of immunoglobulin recombination, sequencing reads. We applied a novel chemical complementarity scoring algorithm, suitable for a big data setting, and determined that the previously established P. gingivalis antigen, rpgB had a reduced chemical complementarity with T-cell receptor (TCR) complementarity-determining region-3 amino acid sequences recovered from PAAD samples with P. gingivalis in comparison to TCR-rpgB chemical complementarity represented by the PAAD samples that lacked P. gingivalis. This finding strengthens the existing body of evidence correlating P. gingivalis with PAAD, which may have implications for the treatment and prognosis of patients. Furthermore, demonstrating the correlation of P. gingivalis and gene program 7 raises the question of whether P. gingivalis infection is responsible for the gene program 7 subdivision of PAAD?
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Affiliation(s)
- Jacob C Kinskey
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Jessica U Quach
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Juan F Arturo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University, Portland, OR 97239, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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8
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Song JJ, Chobrutskiy A, Chobrutskiy BI, Cios KJ, Huda TI, Eakins RA, Diaz MJ, Blanck G. TRB CDR3 chemical complementarity with HBV epitopes correlates with increased hepatocellular carcinoma, disease-free survival. J Med Virol 2023; 95:e29043. [PMID: 37621059 DOI: 10.1002/jmv.29043] [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: 05/01/2023] [Revised: 07/06/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
The liver is a site of immune privilege, compared with the bladder and skin, for example. To study this attenuation of the immune response in the cancer setting, we compared quantities and features of adaptive immune receptor (IR) recombination reads obtained from hepatocellular carcinoma (HCC) and six other cancers. Of these cancers, HCC had the lowest numbers of IR recombination reads and was the only cancer with a greater number immunoglobulin rather than T-cell receptor recombination reads. To better understand the role of adaptive IRs obtained from the tumor microenvironment in shaping the outcome of HCC cases, we quantified the chemical complementarity between HCC tumor TRB and IGH complementarity determining region-3 (CDR3) amino acid (AA) sequences, and known hepatitis B virus (HBV) epitopes. High chemical complementarity between HCC-resident CDR3s and three HBV epitopes correlated with increased survival probabilities, for two sources of CDR3s representing different CDR3 recovery algorithms. These results suggest the potential of CDR3 AA sequences as biomarkers for HCC patient stratification and as guides for future development of therapeutics.
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Affiliation(s)
- Joanna J Song
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, Oregon, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, Oregon, USA
| | - Konrad J Cios
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Rachel A Eakins
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Michael J Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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9
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Wolmarans HJ, Barker VR, Chobrutskiy A, Chobrutskiy BI, Huda TI, Blanck G. Exploiting big data survival information to unify risk-stratification related, adaptive immune receptor parameters for multiple myeloma. Genes Immun 2023; 24:194-199. [PMID: 37443300 DOI: 10.1038/s41435-023-00212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023]
Abstract
With the improvement of treatment options, multiple myeloma related life expectancy has been prolonged, but the disease remains largely incurable. Immunotherapy is a growing field that shows promise in advancements for treatment, and recent work has demonstrated an opportunity to use immune receptor, complementarity determining region-3 (CDR3)-candidate antigen chemical complementarity scores to identify survival distinctions among subgroups of patients. Here, we have applied the complementarity scoring algorithm to identify multiple myeloma related, CDR3-cancer testis antigen (CTA) relationships associated with survival distinctions. Furthermore, we have overlapped these immune receptor features with a previous study that showed a dramatic survival distinction based on T-cell receptor, V- and J-gene segment usage, HLA allele combinations, whereby 100% of the patients in certain combination groups had no mortality related to multiple myeloma, during the study period. This overlap evaluation was consistent with the idea that there are likely considerable constraints on productive TRB-antigen-HLA combinations but more flexibility, and unpredictability, for the TRA-antigen-HLA combinations. Also, the approaches in this reported indicated the potential importance of the CTA, IGSF11, as a multiple myeloma antigen, an antigen previously, independently considered as a vaccine candidate in other settings.
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Affiliation(s)
- Hope J Wolmarans
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Vayda R Barker
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR, 97239, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, 97239, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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10
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Agnila DRL, Huda TI, Eakins RA, Patel DN, Hsiang M, Chobrutskiy A, Chobrutskiy BI, Blanck G. Chemical features of melanoma tumor resident TRG CDR3s associated with better survival probabilities. Melanoma Res 2023; 33:275-282. [PMID: 37222076 DOI: 10.1097/cmr.0000000000000899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We assessed the T-cell receptor gamma (TRG) recombination reads from the cancer genome atlas melanoma tumor exome files and the TRG recombination reads from an independent, melanoma exome file dataset, from the Moffitt Cancer Center. TRG complementarity determining region-3 (CDR3) amino acid (AA) sequences were assessed for chemical complementarity to cancer testis antigens, with such complementarity for FAM133A and CRISP2 associated with better survival probabilities for both datasets. These results, along with related TRG CDR3 AA chemical feature assessments provided in this report, have indicated opportunities for melanoma patient stratifications based on the recovery of TRG recombination reads from both tumor and blood samples, and the results may point towards novel, effective melanoma antigens.
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Affiliation(s)
- Deo Rei L Agnila
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, Departments of
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, Departments of
| | - Rachel A Eakins
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, Departments of
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, Departments of
| | - Monica Hsiang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, Departments of
| | | | - Boris I Chobrutskiy
- Internal Medicine, Oregon Health and Science University Hospital, Portland, Oregon
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, Departments of
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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Pakasticali N, Chobrutskiy A, Patel DN, Hsiang M, Zaman S, Cios KJ, Blanck G, Chobrutskiy BI. Chemical Complementarity of Breast Cancer Resident, T-Cell Receptor CDR3 Domains and the Cancer Antigen, ARMC3, is Associated With Higher Levels of Survival and Granzyme Expression. Cancer Inform 2023; 22:11769351231177269. [PMID: 37313373 PMCID: PMC10259117 DOI: 10.1177/11769351231177269] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/03/2023] [Indexed: 06/15/2023] Open
Abstract
Introduction One of the most pressing goals for cancer immunotherapy at this time is the identification of actionable antigens. Methods This study relies on the following considerations and approaches to identify potential breast cancer antigens: (i) the significant role of the adaptive immune receptor, complementarity determining region-3 (CDR3) in antigen binding, and the existence cancer testis antigens (CTAs); (ii) chemical attractiveness; and (iii) informing the relevance of the integration of items (i) and (ii) with patient outcome and tumor gene expression data. Results We have assessed CTAs for associations with survival, based on their chemical complementarity with tumor resident T-cell receptor (TCR), CDR3s. Also, we have established gene expression correlations with the high TCR CDR3-CTA chemical complementarities, for Granzyme B, and other immune biomarkers. Conclusions Overall, for several independent TCR CDR3 breast cancer datasets, the CTA, ARMC3, stood out as a completely novel, candidate antigen based on multiple algorithms with highly consistent approaches. This conclusion was facilitated by use of the recently constructed Adaptive Match web tool.
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Affiliation(s)
- Nagehan Pakasticali
- Department of Pathology, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR, USA
| | - Dhruv N. Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Monica Hsiang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Konrad J. Cios
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Boris I. Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, USA
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12
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Mandala SR, Thomson AJ, Gozlan EC, Patel DN, Chobrutskiy A, Chobrutskiy BI, Blanck G. A Bioinformatics Assessment Indicating Better Outcomes With Breast Cancer Resident, Immunoglobulin CDR3-MMP2 Binding. Cancer Genomics Proteomics 2023; 20:239-246. [PMID: 37093687 PMCID: PMC10148069 DOI: 10.21873/cgp.20378] [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: 01/30/2023] [Revised: 03/04/2023] [Accepted: 03/16/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND/AIM The recombination of V, D, and J immunoglobulin (IG) gene segments leads to many variations in the amino acids (AAs) encoded at that site, the complementarity determining region-3 (CDR3). Thus, cancer patients may have varying degrees of CDR3 AA binding specificity for cancer proteases, for example, matrix metalloproteinase 2 (MMP2). MMP2 in breast cancer has been found to contribute to metastasis and is used as a marker for tumor staging. Thus, this report evaluated the tumor resident, patient specific IG CDR3 binding affinities to cancer proteases to test the hypothesis that greater binding affinities would be associated with a better outcome. MATERIALS AND METHODS Using two independent bioinformatics tools, we evaluated the IG CDR3-MMP2 binding affinities throughout the cancer genome atlas breast cancer (TCGA-BRCA) dataset. RESULTS Results indicated that the better the CDR3-MMP2 binding, the better the survival probability. An analogous evaluation for four other proteases, including calpain-1 and thermolysin, displayed no such associations with survival probabilities. CONCLUSION This study is consistent with the possibility that patient IG-cancer protease interactions could impact outcomes and raises the question of whether therapeutic antibody targeting of MMP2 would reduce breast cancer mediated tissue destruction and breast cancer mortality rates.
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Affiliation(s)
- Suhaas R Mandala
- Department of Molecular Medicine, Morsani College of Medicine, University of South Tampa, Tampa, FL, U.S.A
| | - Alexis J Thomson
- Department of Molecular Medicine, Morsani College of Medicine, University of South Tampa, Tampa, FL, U.S.A
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Tampa, Tampa, FL, U.S.A
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Tampa, Tampa, FL, U.S.A
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR, U.S.A
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, U.S.A
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Tampa, Tampa, FL, U.S.A.;
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A
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13
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Arias MA, Cios KJ, Kacsoh DB, Montgomery BE, Song JJ, Patel AR, Chobrutskiy A, Chobrutskiy BI, Blanck G. Electrostatic Complementarities of Glioblastoma-Resident T-Cell Receptors and Cancer Testis Antigens Linked to Poor Outcomes and High Levels of Sphingosine Kinase-2 Expression. Biology (Basel) 2023; 12:biology12040575. [PMID: 37106775 PMCID: PMC10135705 DOI: 10.3390/biology12040575] [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] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
Abstract
INTRODUCTION Glioblastoma (GBM) is the most aggressive primary brain tumor in adults. Despite a growing understanding of glioblastoma pathology, the prognosis remains poor. METHODS In this study, we used a previously extensively benchmarked algorithm to retrieve immune receptor (IR) recombination reads from GBM exome files available from the cancer genome atlas. The T-cell receptor complementarity determining region-3 (CDR3) amino acid sequences that represent the IR recombination reads were assessed and used for the generation of chemical complementarity scores (CSs) that represent potential binding interactions with cancer testis antigens (CTAs), which is an approach particularly suited to a big data setting. RESULTS The electrostatic CSs representing the TRA and TRB CDR3s and the CTAs, SPAG9, GAGE12E, and GAGE12F, indicated that an increased electrostatic CS was associated with worse disease-free survival (DFS). We also assessed the RNA expression of immune marker genes, which indicated that a high-level expression of SPHK2 and CIITA genes also correlated with high CSs and worse DFS. Furthermore, apoptosis-related gene expression was revealed to be lower when the TCR CDR3-CTA electrostatic CSs were high. CONCLUSION Adaptive IR recombination reads from exome files have the potential to aid in GBM prognoses and may provide opportunities to detect unproductive immune responses.
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Affiliation(s)
- Miguel A Arias
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Konrad J Cios
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Dorottya B Kacsoh
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Bailey E Montgomery
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Joanna J Song
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Anishaa R Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR 97239, USA
| | - Boris I Chobrutskiy
- Internal Medicine, Oregon Health and Science University Hospital, Portland, OR 97239, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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14
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Barker VR, Varkhedi M, Patel DN, Hsiang M, Chobrutskiy A, Chobrutskiy BI, Blanck G. TCR CDR3-antigen chemical complementarity associated with poor ovarian cancer outcomes: A vestigial immune response to early cancer antigens? Am J Reprod Immunol 2023; 89:e13639. [PMID: 36317868 DOI: 10.1111/aji.13639] [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: 05/31/2022] [Revised: 09/05/2022] [Accepted: 10/14/2022] [Indexed: 11/15/2022] Open
Abstract
Ovarian cancer continues to present significant challenges for early detection and treatment, indicating a need for novel approaches to improve disease outcomes. In this report, we applied a previously described algorithm for detecting chemical complementarity between candidate cancer antigens and complementarity determining region-3 (CDR3) amino acid sequences from tumor resident T-cell receptors. Current literature indicates an association between high CDR3-cancer antigen complementarity and improved survival outcomes. For example, high CDR3-BRAF electrostatic complementarity is associated with a better melanoma outcome. However, such CDR3-cancer antigen chemical complementarity in ovarian cancer was largely associated with worse outcomes. Specifically, high CDR3-MAGEB4 and CDR3-TDRD1 electrostatic complementarity was associated with lower ovarian cancer disease free survival (DFS). Additionally, high CDR3-MAGEB4 and CDR3-TDRD1 electrostatic complementarity was associated with decreased MAGEB4/TDRD1 gene expression and gene copy numbers, consistent with a selection against ovarian cancer cells expressing these antigens. However, when TDRD1 was split into fragments, high CDR3-TDRD1 hydrophobicity complementarity, for a specific TDRD1 fragment, was associated with increased DFS and higher immune marker expression levels. This dichotomy highlights the myriad of opportunities to establish risk stratifications and to identify potential, actionable cancer antigens using immunogenomic parameters.
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Affiliation(s)
- Vayda R Barker
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Mallika Varkhedi
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Monica Hsiang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, Oregon, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, Oregon, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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15
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Hudock TR, Barker VR, Manley BJ, Chobrutskiy A, Chobrutskiy BI, Diaz MJ, Song JJ, Blanck G. TRB CDR3-cancer testis antigen chemical complementarity scoring for identifying productive immune responses in renal cell carcinoma. Cancer Biomark 2023; 38:103-110. [PMID: 37545223 DOI: 10.3233/cbm-230047] [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] [Indexed: 08/08/2023]
Abstract
BACKGROUND Immunogenomics approaches to the characterization of renal cell carcinoma (RCC) have helped to better our understanding of the features of RCC immune dysfunction. However, much is still unknown with regard to specific immune interactions and their impact in the tumor microenvironment. OBJECTIVE This study applied chemical complementarity scoring for the TRB complementarity determining region-3 (CDR3) amino acid sequences and cancer testis antigens (CTAs) to determine whether such complementarity correlated with survival and the expression of immune marker genes. METHODS TRB recombination reads from RCC tumor samples from RNAseq files obtained from two separate databases, Moffitt Cancer Center and The Cancer Genome Atlas (TCGA), were evaluated. Chemical complementarity scores (CSs) were calculated for TRB CDR3-CTA pairs and survival assessments based on those CSs were performed. RESULTS Moffitt Cancer Center and TCGA cases representing the upper 50th percentile of chemical CSs for TRB CDR3 amino acid sequences and the CTA POTEA were found to be associated with a better overall survival (OS) Also, greater tumor RNA expression of multiple immune signature genes, including granzyme A, granzyme B, and interferon-gamma were correlated with the higher chemical CSs. CONCLUSIONS These results indicate that TRB CDR3-CTA chemical complementarity scoring may be useful in distinguishing RCC cases with a productive, anti-tumor immune response from cases where basic immune parameter assessments are inconsistent with a productive immune response.
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Affiliation(s)
- Tabitha R Hudock
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Vayda R Barker
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Brandon J Manley
- Department of Genitourinary Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, USA
| | - Michael J Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Joanna J Song
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Department of Immunology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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16
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Eakins RA, Chobrutskiy A, Teer JK, Patel DN, Hsiang M, Huda TI, Zaman S, Sexton WJ, Coppola D, Falasiri S, Blanck G, Chobrutskiy BI. Chemical complementarity between tumor resident, T-cell receptor CDR3s and MAGEA3/6 correlates with increased melanoma survival: Potential relevance to MAGE vaccine auto-reactivity. Mol Immunol 2022; 150:58-66. [PMID: 35987136 DOI: 10.1016/j.molimm.2022.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 03/24/2022] [Revised: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022]
Abstract
Cancer testis antigens have been of interest as possible targets for cancer immunotherapies. To better understand the opportunities for the use of such immunotherapy targets, we used a chemical complementarity scoring algorithm and an original web tool to establish aspects of electrostatic complementarity of the CTAs, MAGEA3 and MAGEA6, with melanoma specimen resident, T-cell receptor (TCR) complementarity determining region 3 (CDR3) amino acid sequences. Greater electrostatic complementarity between T-cell receptor CDR3 and tumor CTAs MAGEA3/6 was associated with a greater probability of overall survival, for both the cancer genome atlas and Moffitt Cancer Center samples; and was associated with high levels of T-cell cytotoxicity-related gene expression. Most importantly, this approach allowed for the highly efficient screening of specific segments of the MAGEA3/6 antigens which indicated that certain MAGE segments would have either more or less risk of auto-reactivity. In sum, the chemical complementarity algorithm, and its efficient application via the web tool, adaptivematch.com, offers a convenient opportunity to identify likely parameters important for immunotherapy considerations and melanoma patient risk stratifications.
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Affiliation(s)
- Rachel A Eakins
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 33612, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR 97239, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 33612, USA
| | - Monica Hsiang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 33612, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 33612, USA
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 33612, USA
| | - Wade J Sexton
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Domenico Coppola
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Shayan Falasiri
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 33612, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 33612, USA; Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR 97239, USA
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17
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Kacsoh DB, Patel DN, Hsiang M, Gozlan EC, Chobrutskiy A, Chobrutskiy BI, Blanck G. Tumor Resident, B-Cell Receptor Chemical Characteristics Associated with Better Overall Survival for Neuroblastoma. J Mol Neurosci 2022; 72:2011-2019. [PMID: 35896862 DOI: 10.1007/s12031-022-02050-6] [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: 03/26/2022] [Accepted: 07/12/2022] [Indexed: 10/16/2022]
Abstract
Pediatric neuroblastoma (NBL) is one of the most common pediatric cancers, and it can often be aggressive. Genetic and demographic factors can correlate with the severity of NBL, but the variations in the B-cell receptors (BCRs) or immunoglobulin proteins present in the NBL tumors, and their relationships to survival, are not well understood. BCRs contain variations in their complementary determining region-3 (CDR3s) amino acid sequences, due to variable recombinations of the V- and J-gene segments. Accordingly, these variations in CDR3s may represent different antigen interactions and thereby different survival probabilities. Thus, we mined the TARGET project, NBL tumor RNAseq files for BCR recombination reads. Evaluations of the physicochemical properties of IGK, IGL, and IGH CDR3s from these tumors pointed to properties of IGK and IGL in particular as associated with survival distinctions, based on several independent bioinformatics approaches, including a novel homology grouping approach facilitated by a recently developed web tool, adaptivematch.com. In conclusion, tumor resident BCR chemical features are likely useful for better risk stratification and for guiding therapy, and the availability of a user-friendly web tool will likely facilitate using BCR chemical features to meet those goals.
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Affiliation(s)
- Dorottya B Kacsoh
- College of Medicine, University of Central Florida, Orlando, FL, 32827, USA
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, USA
| | - Monica Hsiang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR, 97239, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, 97239, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, USA. .,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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18
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Huda TI, Diaz MJ, Gozlan EC, Chobrutskiy A, Chobrutskiy BI, Blanck G. Immunogenomics Parameters for Patient Stratification in Alzheimer's Disease. J Alzheimers Dis 2022; 88:619-629. [PMID: 35662120 DOI: 10.3233/jad-220119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Despite the fact that only modest adaptive immune system related approaches to treating Alzheimer's disease (AD) are available, an immunogenomics approach to the study of AD has not yet substantially advanced. OBJECTIVE Thus, we sought to better understand adaptive immune receptor chemical features in the AD setting. METHODS We characterized T-cell receptor alpha (TRA) complementarity determining region-3 (CDR3) physicochemical features and identified TRA CDR3 homology groups, represented by TRA recombination reads extracted from 2,665 AD-related, blood- and brain-derived exome files. RESULTS We found that a higher isoelectric value for the brain TRA CDR3s was associated with a higher (clinically worse) Braak stage and that a number of TRA CDR3 chemical homology groups, in particular representing bloodborne TRA CDR3s, were associated with higher or lower Braak stages. Lastly, greater chemical complementarity of both blood- and brain-derived TRA CDR3s and tau, based on a recently described CDR3-candidate antigen chemical complementarity scoring process (https://adaptivematch.com), was associated with higher Braak stages. CONCLUSION Overall, the data reported here raise the questions of (a) whether progression of AD is facilitated by the adaptive immune response to tau; and (b) whether assessment of such an anti-tau immune response could potentially serve as a basis for adaptive immune receptor related, AD risk stratification?
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Affiliation(s)
- Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Michael J Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Patel AR, Patel DN, Tu YN, Yeagley M, Chobrutskiy A, Chobrutskiy BI, Blanck G. Chemical complementarity between immune receptor CDR3s and candidate cancer antigens correlating with reduced survival: evidence for outcome mitigation with corticosteroid treatments. J Biomol Struct Dyn 2022:1-9. [PMID: 35538689 DOI: 10.1080/07391102.2022.2070546] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The evaluation of physicochemical characteristics of extensive adaptive immune receptor (IR) recombination sequence collections has led to the discovery of many correlations of those sequences and a variety of diseases, including cancer. In the cancer setting, these evaluations have recently focused on the adaptive IR, complementarity determining region-3 (CDR3) amino acid (AA) sequences, which play a major role in antigen binding. For example, the chemical complementarities of the tumor resident, CDR3 AA sequences and the BRAFV600E mutant, common in melanoma, have proved informative with regard to outcomes. Many of these evaluations led to the conclusion that a high affinity match, efficiently, algorithmically designated as a high chemical complementarity score (CS) for the patient specific, IR CDR3 AA sequences and the cancer antigens, correlated with improved survival outcomes. In this report, the complementarity scoring algorithms were used to investigate the opposite phenomenon, high complementarity chemistry between CRD3 AAs and cancer antigens that correlated with a worse survival, an approach that revealed potential risk stratification biomarkers for lung adenocarcinoma, lung squamous carcinoma, and likely other cancer types. Most importantly, analyses suggested that high IR CDR3 AA-candidate antigen CS, low overall survival results for low grade glioma were mitigated by neoadjuvant corticosteroid treatments. Overall, the analyses of this report, coupled with earlier work establishing the CS approach for identifying likely good outcomes, have the potential to distinguish patients who will benefit from (i) immune activating or (ii) immune augmenting or (iii) even immunosuppressive treatment strategies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anishaa R Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, USA
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, USA
| | - Yaping N Tu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, USA
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, USA
| | - Andrea Chobrutskiy
- Department of Pediatrics, Oregon Health and Science University Hospital, Portland, OR, USA
| | - Boris I Chobrutskiy
- Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, OR, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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20
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Gozlan EC, Chobrutskiy BI, Blanck G. Exploiting adaptive immune receptor recombination read recoveries from exome files to identify subsets of
ALL
and to establish
TCR
features that correlate with better outcomes. Int J Lab Hematol 2022; 44:883-891. [DOI: 10.1111/ijlh.13862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
Affiliation(s)
- Etienne C. Gozlan
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida Tampa Florida USA
| | - Boris I. Chobrutskiy
- Department of Internal Medicine Oregon Health and Science University Hospital Portland Oregon USA
| | - George Blanck
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida Tampa Florida USA
- Department of Immunology H. Lee Moffitt Cancer Center and Research Institute Tampa Florida USA
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21
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Ferrall-Fairbanks MC, Chakiryan N, Chobrutskiy BI, Kim Y, Teer JK, Berglund A, Mulé JJ, Fournier M, Siegel EM, Dhillon J, Falasiri SSA, Arturo JF, Katende EN, Blanck G, Manley BJ, Altrock PM. Quantification of T- and B-cell immune receptor distribution diversity characterizes immune cell infiltration and lymphocyte heterogeneity in clear cell renal cell carcinoma. Cancer Res 2022; 82:929-942. [DOI: 10.1158/0008-5472.can-21-1747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/02/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022]
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Patel DN, Yeagley M, Arturo JF, Falasiri S, Chobrutskiy BI, Gozlan EC, Blanck G. A comparison of immune receptor recombination databases sourced from tumour exome or RNAseq files: Verifications of immunological distinctions between primary and metastatic melanoma. Int J Immunogenet 2021; 48:409-418. [PMID: 34298587 DOI: 10.1111/iji.12550] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 06/23/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023]
Abstract
It became apparent several years ago that RNAseq and exome files prepared from tissue could be mined for adaptive immune receptor (IR) recombinations, which has given extra value to datasets originally intended for gene expression or mutation studies. For example, recovery of IR recombination reads from tumour specimen genomics files can correlate with survival rates. In particular, many benchmarking processes have been applied to the two sets of the IR recombination reads obtained from the cancer genome atlas files, but these two sets have never been directly compared. Here we show that both sets largely agree regarding several parameters. For example, recovery of TRB recombination reads from both WXS and RNAseq files representing metastatic melanoma was associated with a better outcome (p < .0004 in both cases); and T-cell receptor recombination read recovery, for both genomics file types, associated very strongly with T-cell gene expression markers. However, the use of CDR3 chemical features for survival distinctions was not consistent. This topic, and the surprising result that both datasets indicated that primary melanoma with recovery of IR recombination reads, in stark contrast to metastatic melanoma, represents a worse outcome, are discussed.
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Affiliation(s)
- Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Juan F Arturo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Shayan Falasiri
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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23
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Chobrutskiy BI, Chobrutskiy A, Zaman S, Yeagley M, Huda TI, Blanck G. High-throughput, sliding-window algorithm for assessing chemical complementarity between immune receptor CDR3 domains and cancer mutant peptides: TRG-PIK3CA interactions and breast cancer. Mol Immunol 2021; 135:247-253. [PMID: 33933816 DOI: 10.1016/j.molimm.2021.02.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/03/2021] [Accepted: 02/24/2021] [Indexed: 01/25/2023]
Abstract
Physicochemical assessments of a vast accumulation of adaptive immune receptor (IR) recombinations have led to correlations of those properties with sub-divisions of various diseases. In the cancer setting, such assessments, particularly for the complementarity determining region-3 (CDR3) immune receptor domain, have been used to establish chemical complementarity matches to mutant amino acids (AA). These matches, in some cases, over very large numbers of tumor samples, have correlated with survival and gene expression distinctions. For example, in melanoma, electrostatic charge based, T-cell receptor CDR3-DNAH9 mutant AA complementarity represents better survival over multiple datasets that represent tumor tissue, T-cell receptor CDR3s. In this report, the complementarity approach has been expanded to include a more comprehensive representation of the interaction of T-cell receptor CDR3s and mutant AAs by incorporating the impact of the wild-type AAs surrounding the mutant AA. This "sliding window" approach was benchmarked against two large datasets of empirically determined CDR3-epitope pairs; showed more significant patient subdivisions; revealed a novel, TRG CDR3-mutant PIK3CA linkage in breast cancer; and was particularly suited to use with big data collections using only modest and widely-available processors. Thus, the algorithm should support more rapid and convenient indications (or prescreens) of CDR3-mutant peptide interactions for more focused studies and more efficient development of patient immunology-related prognostic tools and therapies.
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Affiliation(s)
- Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, United States
| | - Andrea Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, United States
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, United States
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, United States
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, United States
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL, United States; Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, United States.
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Yeagley M, Chobrutskiy BI, Gozlan EC, Medikonda N, Patel DN, Falasiri S, Callahan BM, Huda T, Blanck G. Electrostatic Complementarity of T-Cell Receptor-Alpha CDR3 Domains and Mutant Amino Acids Is Associated with Better Survival Rates for Sarcomas. Pediatr Hematol Oncol 2021; 38:251-264. [PMID: 33616477 DOI: 10.1080/08880018.2020.1843576] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
While sarcoma immunology has advanced with regard to basic, and even some applied topics, this disease has not been subject to more recent immunogenomics approaches. Thus, we assessed the immune receptor recombinations available from the cancer genome atlas (TCGA) sarcoma database via tumor sample exome and RNASeq files. Results indicated that recovery of T-cell receptor-alpha recombination reads (TRA) correlated with a better survival rate, with the expression of T-cell biomarkers, and with tumor sample apoptosis signatures consistent with the longer patient survival times. Furthermore, samples representing TRA complementarity determining region-3 (CDR3) net charge per residue (NCPR) based complementarity with the corresponding sarcoma mutanome had a better survival rate, and more granzyme expression, than samples lacking such complementarity. By specifically using RNASeq-recovered TRA CDR3s and related NCPR assessments, three genes, TP53, ATRX, and RB1, were identified as being key components of the mutanome-based complementarity. Thus, these genes may represent key immune system targets for soft tissue sarcomas. Also, several key results from above were reproduced with a pediatric osteosarcoma dataset, work that led to identification of MUC6 mutations as potentially linked to a strong immune response. In sum, TRA CDR3s are likely to be important prognostic indicators, and possibly a beginning tool for immunotherapy development strategies, for adult and pediatric sarcomas.
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Affiliation(s)
- Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Nikhila Medikonda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Shayan Falasiri
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Blake M Callahan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Taha Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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25
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Gozlan EC, Chobrutskiy BI, Zaman S, Yeagley M, Blanck G. Systemic Adaptive Immune Parameters Associated with Neuroblastoma Outcomes: the Significance of Gamma-Delta T Cells. J Mol Neurosci 2021; 71:2393-2404. [DOI: 10.1007/s12031-021-01813-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/08/2021] [Indexed: 12/17/2022]
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26
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Huda TI, Mihyu M, Gozlan EC, Arndt MF, Diaz MJ, Zaman S, Chobrutskiy BI, Blanck G. Specific HLA alleles, paired with TCR V- and J-gene segment usage, link to distinct multiple myeloma survival rates. Leuk Lymphoma 2021; 62:1711-1720. [PMID: 33622167 DOI: 10.1080/10428194.2021.1885655] [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] [Indexed: 01/05/2023]
Abstract
Multiple myeloma (MM) immunogenomics studies related to T-cell characterizations and involving large patient sets have been lacking, particularly in comparison to solid tumor types. Thus, we evaluated (i) HLA alleles, and (ii) T-Cell Receptor (TCR) V- and J-gene segment, HLA allele combinations, based on TCR recombinations in blood samples, for their potential associations with overall survival distinctions among an MM cohort. Two HLA alleles, and seven TCR V- or J-gene segment, HLA allele combinations were found to be associated with distinct overall survival rates. For examples, HLA-C*08:02, and the TRAV19, HLA-C*07:01 combination, were found to be associated with negative outcomes. In addition, anti-cytomegalovirus immune receptor sequences, from blood samples, were found to be associated with a positive outcome (p = 0.012, n = 278). These data, and other related immunogenomics data, indicate a potential opportunity to use personal immunogenetics parameters as guides to prognosis and therapies.
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Affiliation(s)
- Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Moody Mihyu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Mary F Arndt
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Michael J Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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27
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Chobrutskiy A, Chobrutskiy BI, Zaman S, Hsiang M, Blanck G. Chemical features of blood-borne TRG CDR3s associated with an increased overall survival in breast cancer. Breast Cancer Res Treat 2020; 185:591-600. [PMID: 33180235 DOI: 10.1007/s10549-020-05996-6] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022]
Abstract
PURPOSE Immunogenomics and earlier, pioneering studies, particularly by Whiteside and colleagues, have indicated a positive role for B-cells in breast cancer, as well as a positive role for gamma-delta T-cells. However, these studies have been completely limited to assessing breast cancer tumor tissue. METHODS AND RESULTS Our analyses here has shown that blood-borne T-cell receptor gamma (TRG) chain sequences were associated with greater overall survival, of particular note due to the comparative longevity of primary breast cancer patients, whereby assessments of disease-free, but rarely overall survival parameters are possible. Additional immunogenomics approaches narrowed the overall survival correlations to specific, TRG complementarity determining region-3, amino acid (AA) sequence chemical features, independently of many common, confounding variables in the breast cancer setting, such as estrogen or progesterone receptor status. CONCLUSIONS These results are discussed in the context of patient age and with regard to potential antigenic targets, based on the chemistry of the TRG CDR3 AA sequences associated with the higher survival rates.
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Affiliation(s)
- Andrea Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South, Florida, Tampa, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South, Florida, Tampa, USA
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South, Florida, Tampa, USA
| | - Monica Hsiang
- Department of Molecular Medicine, Morsani College of Medicine, University of South, Florida, Tampa, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South, Florida, Tampa, USA. .,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA.
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28
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Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Mihyu M, Diviney A, Tong WL, Blanck G. Abstract B12: Potential neoantigen release and increased lymphocyte activity is facilitated by matrix metalloproteinase-dependent cleavage of mutant matrisome peptides in cutaneous melanoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-b12] [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: Proteases in the cancer microenvironment have been studied for decades, with a general conclusion that such proteases facilitate the spread of cancer, although there is some controversy regrading that conclusion in later stages of cancer development. More recently, a very large collection of data regarding mutant amino acids in the potential substrates of the cancer microenvironment has become available.
Methods: To better understand the potential impact of these mutant amino acids on protease function and cancer progression, we established a bioinformatics approach to assessing the impact of melanoma mutants, among a previously defined set of ECM structural proteins, on MMP2, a protease extensively associated with melanoma in terms of both protease sensitivity and MHC class I binding using original software. Additionally, T-cell receptor TRα and TRβ recombinations were bioinformatically obtained using whole-exome sequencing data from 479 melanoma tumor samples.
Results: Tumor samples with mutant amino acids adjacent to ECM structural protein, MMP2-cleavage sites represented a better survival rate and a larger proportion of mutant peptides with high HLA class I binding affinities, particularly in comparison to melanoma samples lacking a T-cell infiltrate. Furthermore, even better MHC class I binders, as a group, were identified among the sample representing ECM structural proteins mutants not adjacent to MMP2 sensitive sites and evincing a relatively poor survival rate.
Conclusion: Overall, this analysis suggested that MMP2 has the capacity of freeing mutant peptides that could facilitate an antitumor response and a better survival rate, and this analysis has the potential of resolving some of the controversy surrounding the role of cancer proteases in cancer progression.
Citation Format: Saif Zaman, Boris I. Chobrutskiy, Jay S. Patel, Blake M. Callahan, Moody Mihyu, Andrea Diviney, Wei Lue Tong, George Blanck. Potential neoantigen release and increased lymphocyte activity is facilitated by matrix metalloproteinase-dependent cleavage of mutant matrisome peptides in cutaneous melanoma [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr B12.
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Affiliation(s)
- Saif Zaman
- University of South Florida Morsani College of Medicine, Tampa, FL
| | | | - Jay S. Patel
- University of South Florida Morsani College of Medicine, Tampa, FL
| | | | - Moody Mihyu
- University of South Florida Morsani College of Medicine, Tampa, FL
| | - Andrea Diviney
- University of South Florida Morsani College of Medicine, Tampa, FL
| | - Wei Lue Tong
- University of South Florida Morsani College of Medicine, Tampa, FL
| | - George Blanck
- University of South Florida Morsani College of Medicine, Tampa, FL
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29
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Arndt MF, Koohestani DM, Chobrutskiy BI, Mihyu MM, Diaz M, Gozlan EC, Yeagley M, Zaman S, Roca AM, Blanck G. TRBV and TRBJ usage, when paired with specific HLA alleles, associates with distinct head and neck cancer survival rates. Hum Immunol 2020; 81:692-696. [PMID: 32950267 DOI: 10.1016/j.humimm.2020.08.007] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 10/23/2022]
Abstract
Common or dominant, T-cell receptor (TCR), V and J usage, in combination with particular human leukocyte antigen (HLA) alleles, has been associated with differing outcomes in viral infections, autoimmunity, and more recently, in cancer. Cervical cancer in particular represents the most dramatic series of distinctions of outcomes associated with differing combinations of dominant V or J usage and HLA alleles, possibly because of the strong association of cervical cancer with human papilloma virus (HPV), in turn leading to a likely molecular consistency in the mechanism of HPV antigen presentation. Thus, we considered assessing TRB V and J usage, HLA allele combinations, for their associations with survival rates and related data, in the cancer genome atlas head and neck cancer dataset. We obtained the TRB VDJ recombination reads from both the blood and tumor exome files and determined the V and J identities. We then established case ID (patient) subsets of V or J usage, HLA alleles, and determined, for example, that the TRBJ2-7, HLA-B*40:01 combination was associated with a better disease free survival rate than were either the TRBJ1-3, HLA-DPB1*03:01 or the TRBJ2-1, HLA-DPB1*02:01 combinations. Furthermore, these analyses led to the conclusion that TRBJ1-5 usage, and the HLA-C*08:02 and HLA-DRB1*03:01 alleles, had independent associations with distinct overall survival rates. In sum, the results suggest that dominant V or J usage, HLA allele combinations, and in certain cases, dominant V or J usage independently of HLA, could be useful in prognosis and in guiding immunotherapies.
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Affiliation(s)
- Mary F Arndt
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Darush M Koohestani
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Moody M Mihyu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Michael Diaz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - Andrea M Roca
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States; Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States.
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30
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Zaman S, Chobrutskiy BI, Patel JS, Diviney A, Tu YN, Tong WL, Gill T, Blanck G. Antiviral T Cell Receptor Complementarity Determining Region-3 Sequences Are Associated with a Worse Cancer Outcome: A Pancancer Analysis. Viral Immunol 2020; 33:404-412. [PMID: 32315578 DOI: 10.1089/vim.2019.0156] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human papilloma virus has a clearly demonstrated role in cervical and head and neck cancers, but viral etiology for other solid tumors is less well understood. To expand this area of research, we obtained and analyzed the immune receptor recombinations available from both blood and tumor samples, through mining of exome files produced from those sources, for 32 cancer types represented by the cancer genome atlas (TCGA). Among TCGA data sets, the recovery frequency for antiviral complementarity determining region-3 sequences (CDR3s), for T cell receptor-alpha and T cell receptor-beta, ranged from 0% to 21% of the patients, for the different cancer types, with breast, lung, pancreatic, and thymus cancers representing the highest of that range, particularly for tumor tissue resident T cells. In several cases, recovery of the antiviral CDR3s associated with distinct survival rates, and in all of these cases, the recovery of an antiviral CDR3 associated with a worse survival rate.
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Affiliation(s)
- Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Jay S Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Andrea Diviney
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Yaping N Tu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Tommy Gill
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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31
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Tu YN, Tong WL, Callahan BM, Chobrutskiy BI, Blanck G. B-cell Receptor Recombinations in Lung Adenocarcinoma Exome Files Correlate With a Higher Overall Survival Rate. Anticancer Res 2020; 40:2043-2051. [PMID: 32234895 DOI: 10.21873/anticanres.14161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 01/27/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM While there has been a rapid development in genomic data mining approaches for T-cell receptor recombinations (TcR), less emphasis has been placed on B-cell receptor (BcR) recombinations. MATERIALS AND METHODS We obtained lung cancer exome files from the cancer genome atlas (TCGA) and mined the files for TcR and BcR recombination reads. RESULTS There was a robust detection of BcR light chain recombination reads in lung adenocarcinoma (TCGA-LUAD) samples, and there was a correlation between the detection of light chain recombination reads and a more favorable outcome. This result was supported by analyses of the expression of B-cell markers as indicated by LUAD RNASeq files. CONCLUSION BcR and TcR recombination reads recovered from LUAD WXS files, either alone or in combination with the human leukocyte antigen (HLA) type, are likely to have prognostic value.
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Affiliation(s)
- Yaping N Tu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, U.S.A
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, U.S.A
| | - Blake M Callahan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, U.S.A
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, U.S.A
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, U.S.A. .,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A
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32
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Chobrutskiy BI, Yeagley M, Diviney A, Zaman S, Gozlan EC, Tipping P, Koohestani DM, Roca AM, Blanck G. A scoring system for the electrostatic complementarities of T-cell receptors and cancer-mutant amino acids: multi-cancer analyses of associated survival rates. Immunology 2020; 159:373-383. [PMID: 31821535 DOI: 10.1111/imm.13165] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 06/11/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 12/21/2022] Open
Abstract
The anti-tumor immune response is considered to be due to the T-cell receptor (TCR) binding to tumor antigens, which can be either wild-type, early stem cell proteins, presumably foreign to a developed immune system; or mutant peptides, foreign to the immune system because of a mutant amino acid (aa) or otherwise somatically altered aa sequence. Recently, very large numbers of TCR complementarity-determining region-3 (CDR3) aa sequences obtained from tumor specimens have become available. We developed a novel algorithm for assessing the complementarity of tumor mutant peptides and TCR CDR3s, based on the retrieval of TCR CDR3 aa sequences from both tumor specimen and patient blood exomes and by using an automated process of assessing CDR3 and mutant aa electrical charges. Results indicated many instances where high electrostatic complementarity was associated with a higher survival rate. In particular, our approach led to the identification of specific genes contributing significantly to the complementary, TCR CDR3-mutant aa. These results suggest a novel approach to tumor immunoscoring and may lead to the identification of high-priority neo-antigen, peptide vaccines; or to the identification of ex vivo stimulants of tumor-infiltrating lymphocytes.
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Affiliation(s)
- Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Andrea Diviney
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Price Tipping
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Darush M Koohestani
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Andrea M Roca
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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33
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Zaman S, Hajiran A, Coba GA, Robinson T, Madanayake TW, Segarra DT, Chobrutskiy BI, Boyle TA, Zhou JM, Kim Y, Mulé JJ, Teer JK, Manley BJ. Aberrant Epidermal Growth Factor Receptor RNA Splice Products Are Among the Most Frequent Somatic Alterations in Clear Cell Renal Cell Carcinoma and Are Associated with a Poor Response to Immunotherapy. Eur Urol Focus 2019; 7:373-380. [PMID: 31901438 DOI: 10.1016/j.euf.2019.12.001] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/14/2019] [Accepted: 12/10/2019] [Indexed: 12/01/2022]
Abstract
BACKGROUND Accumulating evidence suggests that alternative RNA splicing has an important role in cancer development and progression by driving the expression of a diverse array of RNA and protein isoforms from a handful of genes. However, our understanding of the clinical significance of cancer-specific RNA splicing in renal cell carcinoma (RCC) is limited. OBJECTIVE To characterize and validate a novel oncogene RNA splicing event discovered in patients with RCC and to correlate expression with clinical outcomes. DESIGN, SETTING, AND PARTICIPANTS Using DNA and RNA sequencing, we identified a novel epidermal growth factor receptor (EGFR) splicing alteration (EGFR_pr20CTF) in RCC tumor tissue. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We confirmed the frequency and specificity of the EGFR_pr20CTF variant by analyzing cohorts of patients from our institution (n = 699) and The Cancer Genome Atlas (TCGA; n = 832). Furthermore, we analyzed its expression in tumor tissue and a human kidney cancer cell line using reverse transcriptase-polymerase chain reaction. Variant expression was also correlated with survival and response to systemic therapy. RESULTS AND LIMITATIONS EGFR_pr20CTF expression was identified in 71.7% (n = 71/99) of patients with RCC in our institutional cohort and in 56.7% (n = 279/492) of patients in the TCGA cohort. EGFR_pr20CTF was found to be specific to clear cell renal cell carcinoma (ccRCC), occurring in <0.2% of non-RCC tumors (n = 2/1091). High levels of EGFR_pr20CTF correlated with lower survival at 48 mo following immunotherapy (p = 0.036). The average survival in patients with high EGFR_pr20CTF expression was <16 mo. CONCLUSIONS The EGFR_pr20CTF RNA splice variant occurs frequently, is specific to patients with advanced ccRCC, and is associated with a poor response to immunotherapy. PATIENT SUMMARY Cancer-specific RNA alternative splicing may portend a poor prognosis in patients with advanced clear cell renal cell carcinoma. Further investigation will help clarify whether EGFR_pr20CTF can be used as a biomarker for this patient population.
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Affiliation(s)
- Saif Zaman
- Department of Genitourinary Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ali Hajiran
- Department of Genitourinary Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
| | - George A Coba
- Department of Genitourinary Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Timothy Robinson
- Department of Radiation Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Thushara W Madanayake
- Department of Radiation Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Daniel T Segarra
- Department of Genitourinary Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Boris I Chobrutskiy
- Department of Genitourinary Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Theresa A Boyle
- Department of Pathology, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Jun-Min Zhou
- Department of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - James J Mulé
- Immunology Department, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Brandon J Manley
- Department of Genitourinary Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA; Integrated Mathematical Oncology Department, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Arturo JF, Chobrutskiy BI, Yeagley M, Patel DN, Falasiri S, Patel JS, Blanck G. Electrostatic complementarity of B-cell receptor CDR3s and TP53-mutant amino acids in breast cancer is associated with increased disease-free survival rates. Cell Mol Immunol 2019; 17:776-778. [PMID: 31729463 DOI: 10.1038/s41423-019-0328-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022] Open
Affiliation(s)
- Juan F Arturo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Shayan Falasiri
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Jay S Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States. .,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, United States.
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Pakasticali N, Gill T, Chobrutskiy BI, Tong WL, Ramsamooj M, Blanck G. TRAV gene segments further away from the TRAJ gene segment cluster appear more commonly in human tumor and blood samples. Mol Immunol 2019; 116:174-179. [PMID: 31704500 DOI: 10.1016/j.molimm.2019.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 06/25/2019] [Revised: 09/17/2019] [Accepted: 10/13/2019] [Indexed: 10/25/2022]
Abstract
We considered the possibility that the greater the distance between an immune receptor V and J, the more likely the V usage. Such a hypothesis is supported by results from mouse experiments. And, such a hypothesis is consistent with the fundamental nature of recombination and genomic distance: the further the distance, the greater the chance of a DNA break. Thus, we exploited the vast dataset of V and J recombination reads available for the human TRA gene, particularly from cancer and blood specimens, to assess the frequency of TRAV usage with respect to distance from the TRAJ cluster. Results indicated that, indeed, over the entire TRAV cluster, there is a greater chance of V usage the further the distance from the J cluster. These results do not address causation, and are not consistent for certain individual V gene segments, but the results do indicate that overall, the larger the distance between the V and J gene segment cluster, the more likely the appearance of at least a subset of TRAV segments, particularly among tumor infiltrating lymphocytes. With a similar approach, the distal TRAV gene segments were also found to be more commonly associated with a subset of distal TRAJ segments. These results have implications for restrictions on the apparent TRA repertoire in disease settings.
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Affiliation(s)
- Nagehan Pakasticali
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States; Department of Basic Sciences, National University of Health Sciences, Pinellas Park, Florida, 33781, United States
| | - Tommy Gill
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States
| | - Michael Ramsamooj
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States; Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, 33612, United States.
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Koohestani D, Chobrutskiy BI, Janjua HC, Velanovich V. Stability of the Modified Frailty Index for Postoperative Mortality and Readmissions over Multiple Calendar Year Cohorts. J Am Coll Surg 2019. [DOI: 10.1016/j.jamcollsurg.2019.08.273] [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: 11/29/2022]
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Roca AM, Chobrutskiy BI, Callahan BM, Blanck G. T-cell receptor V and J usage paired with specific HLA alleles associates with distinct cervical cancer survival rates. Hum Immunol 2019; 80:237-242. [DOI: 10.1016/j.humimm.2019.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 11/29/2022]
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Diviney A, Chobrutskiy BI, Zaman S, Blanck G. An age-based, RNA expression paradigm for survival biomarker identification for pediatric neuroblastoma and acute lymphoblastic leukemia. Cancer Cell Int 2019; 19:73. [PMID: 30962767 PMCID: PMC6438000 DOI: 10.1186/s12935-019-0790-5] [Citation(s) in RCA: 4] [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] [Received: 11/06/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023] Open
Abstract
Background Pediatric cancer survival rates overall have been improving, but neuroblastoma (NBL) and acute lymphoblastic leukemia (ALL), two of the more prevalent pediatric cancers, remain particularly challenging. One issue not yet fully addressed is distinctions attributable to age of diagnosis. Methods In this report, we verified a survival difference based on diagnostic age for both pediatric NBL and pediatric ALL datasets, with younger patients surviving longer for both diseases. We identified several gene expression markers that correlated with age, along a continuum, and then used a series of age-independent survival metrics to filter these initial correlations. Results For pediatric NBL, we identified 2 genes that are expressed at a higher level in lower surviving patients with an older diagnostic age; and 4 genes that are expressed at a higher level in longer surviving patients with a younger diagnostic age. For pediatric ALL, we identified 3 genes expressed at a higher level in lower surviving patients with an older diagnostic age; and 17 genes expressed at a higher level in longer surviving patients with a younger diagnostic age. Conclusions This process implicated pan-chromosome effects for chromosomes 11 and 17 in NBL; and for the X chromosome in ALL. Electronic supplementary material The online version of this article (10.1186/s12935-019-0790-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Diviney
- 1Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, USA
| | - Boris I Chobrutskiy
- 1Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, USA
| | - Saif Zaman
- 1Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, USA
| | - George Blanck
- 1Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, USA.,2Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612 USA
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Patel JS, Callahan BM, Chobrutskiy BI, Blanck G. Matrix-Metalloprotease Resistant Mucin-16 (MUC16) Peptide Mutants Represent a Worse Lung Adenocarcinoma Outcome. Proteomics Clin Appl 2019; 13:e1800155. [PMID: 30790454 DOI: 10.1002/prca.201800155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 09/19/2018] [Revised: 02/06/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE The relationship of lung adenocarcinoma (LUAD)-specific proteases and the mutant profile of cytoskeletal and extracellular matrix proteins (CECMPs) are examined. EXPERIMENTAL DESIGN Mutant CECMPs are assessed with an automated application of a protease binding, amino acid-based, scoring database. RESULTS MUC16 (Human Genome Organization symbol for mucin-16 gene) mutants in particular are, more often than not, resistant to matrix-metalloproteases (MMPs) commonly secreted by LUAD cells, and LUAD cases representing the MUC16, MMP resistant mutants have a worse outcome. Similar results are obtained for MUC16 mutants resistant to cathepsins, also commonly secreted by LUAD cells. Analyses also show that MUC16, MMP resistant peptide mutants have greater binding affinities to HLA-A and HLA-B when compared to MUC16, MMP nonresistant peptide mutants. CONCLUSION These results provide a potential, novel biomarker for lung cancer progression, in particular, protease resistant MUC16 peptides; and suggest a possible mechanism of immune escape entailing the reduction of mutant peptides available for HLA class I binding.
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Affiliation(s)
- Jay S Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, 33612, FL, USA
| | - Blake M Callahan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, 33612, FL, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, 33612, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, 33612, FL, USA.,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, 33612, FL, USA
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Zaman S, Chobrutskiy BI, Sikaria D, Blanck G. MAPT (Tau) expression is a biomarker for an increased rate of survival for low‑grade glioma. Oncol Rep 2019; 41:1359-1366. [PMID: 30535461 DOI: 10.3892/or.2018.6896] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/08/2018] [Indexed: 11/06/2022] Open
Abstract
The association of MAPT (Tau) with various tauopathies and other neurological disorders has long been established. However, the role of microtubule‑associated protein Tau (MAPT) expression in brain cancer is largely unknown. To determine whether MAPT expression is related to low‑grade glioma (LGG) survival rates, RNASeq data representing samples from the Cancer Genome Atlas (TCGA) were assessed. Results revealed that high expression of the MAPT gene is very strongly associated with increased overall and disease‑free survival in LGG but not in breast cancer or melanoma. No such association was apparent for either amyloid precursor protein or α‑synuclein gene expression. The expression levels of particular apoptosis‑ and pro‑proliferative‑effector genes were consistent with the Tau‑associated increased survival rates. It has been well established that the Tau protein plays a neurodegenerative role, and in this study we identified, for the first time, a potential cell apoptosis function that Tau may play in cancers of the central nervous system.
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Affiliation(s)
- Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Dhiraj Sikaria
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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Chobrutskiy BI, Zaman S, Diviney A, Mihyu MM, Blanck G. T-cell receptor-α CDR3 domain chemical features correlate with survival rates in bladder cancer. J Cancer Res Clin Oncol 2018; 145:615-623. [DOI: 10.1007/s00432-018-2815-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/04/2018] [Indexed: 01/04/2023]
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Abstract
Although the impact of MAPT (Tau) expression has been well documented for neuronal cells in the context of tauopathies and neurodegenerative diseases, the impact and role of Tau expression in cancer, and specifically cancers of neuronal origin, is in its infancy. To determine the correlation between MAPT expression and survival in pediatric neuroblastoma, MAPT gene expression for samples from the TARGET pediatric neuroblastoma dataset was assessed. Initial analyses indicated that increased MAPT expression correlated with increased overall survival in neuroblastoma but not in ovarian cancer. Expression of apoptosis- and proliferation-effector genes in the neuroblastoma samples was consistent with the MAPT related survival result. Furthermore, we determined that higher neuroblastoma expression of APP also associated with neurodegeneration, correlated with better neuroblastoma survival rates. In sum, Gene expression associated with neuronal degenerative diseases was associated with a better neuroblastoma outcome. Abbreviations: ALS: Amyotrophic Lateral Sclerosis; APP: Amyloid Precursor Protein gene; CASP3: Caspase 3 gene; CASP9: Caspase 9 gene; H2AFX: H2A histone family, member X gene; HIST1H2AL: Histone H2A type 1 gene; HIST1H2BK: Histone H2B type 1-K gene; HIST1H3J: Histone H3J gene; HIST1H4B: Histone H4B gene; HIST2H2BE: Histone H2B type 2-E gene; HUGO: human genome organization; KM: Kaplan-Meier survival curve; MAPT: Tau gene; OV: Ovarian cancer; SNCA: alpha-syneculin gene; TARDBP: Transactive response DNA binding protein 43 kDa; TCGA: the cancer genome atlas.
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Affiliation(s)
- Saif Zaman
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA
| | - Boris I Chobrutskiy
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA
| | - George Blanck
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA.,b Immunology Program, H. Lee Moffitt Cancer Center and Research Institute , Tampa , FL , USA
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Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Blanck G. P081 ST14 protease resistant peptides, from glioblastoma multiforme mutant proteins, represent higher binding affinities as potential HLA class I epitopes. Hum Immunol 2018. [DOI: 10.1016/j.humimm.2018.07.140] [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: 10/28/2022]
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Tong WL, Callahan BM, Tu YN, Zaman S, Chobrutskiy BI, Blanck G. Immune receptor recombinations from breast cancer exome files, independently and in combination with specific HLA alleles, correlate with better survival rates. Breast Cancer Res Treat 2018; 173:167-177. [DOI: 10.1007/s10549-018-4961-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022]
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Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Tong WL, Blanck G. Mutant cytoskeletal and ECM peptides sensitive to the ST14 protease are associated with a worse outcome for glioblastoma multiforme. Biochem Biophys Res Commun 2018; 503:2218-2225. [PMID: 29953855 DOI: 10.1016/j.bbrc.2018.06.141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 06/04/2018] [Accepted: 06/25/2018] [Indexed: 11/19/2022]
Abstract
We previously identified a set of the most frequently mutated cytoskeleton- and extracellular matrix-related proteins (CECMPs) in numerous cancer datasets. In this report, we used a bioinformatics approach to assess the impact of amino acid (AA) substitutions on the sensitivity of CECMPs to the ST14 protease (matriptase I), a transmembrane serine protease previously implicated in cancer development. Results indicated that AA substitutions in glioblastoma multiforme (GBM) CECMPs are skewed toward increased resistance to the ST14 protease, in comparison to the wild-type peptide sequence. Furthermore, the protease resistant AA substitutions represent relatively high binding affinities to HLA class I proteins, when assessing the binding specificities using HLA class I alleles matched to the source of the mutant AA. Moreover, samples representing AA substitutions that increased protease sensitivity also represented reduced overall and disease-free survival periods for patients with glioblastoma. To assess tumor specimen immunogenicity, we identified T-cell receptor (TCR) V(D)J recombinations in GBM exome files. The overlap between ST14 protease sensitive mutant barcodes and the TCR V(D)J recombination read positive barcodes represented significantly reduced survival.
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Affiliation(s)
- Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jay S Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Blake M Callahan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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