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Zaman S, Gorelick FS, Chrobrutskiy A, Chobrutskiy BI, Desir GV, Blanck G. Chemical complementarity of tumor resident, T-cell receptor CDR3s and renalase-1 correlates with increased melanoma survival. Oncotarget 2024; 15:550-561. [PMID: 39102218 PMCID: PMC11299663 DOI: 10.18632/oncotarget.28633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/02/2024] [Indexed: 08/06/2024] Open
Abstract
Overexpression of the secretory protein renalase-1 negatively impacts the survival of melanoma and pancreatic cancer patients, while inhibition of renalase-1 signaling drives tumor rejection by promoting T-cell activation. Thus, we investigated the chemical complementarity between melanoma-resident, T-cell receptor (TCR) complementarity-determining region 3 (CDR3) amino acid sequences (AAs) and the renalase-1 protein. Increasing complementarity of TCR CDR3s to renalase-1 AAs, as assessed by a chemical complementarity scoring algorithm, was associated with improved overall survival (OS) in melanoma patients. The expression levels of several immune signature genes were significantly, positively correlated with increasing TCR CDR3-renalase-1 complementarity scores. Additionally, the survival association observed with high complementarity of TCR CDR3s to renalase-1 AAs was more robust in cases with low renalase-1 gene expression levels. Mapping of TCR CDR3-renalase-1 in silico interaction sites identified major epitope candidates including RP220, the signaling module of the renalase-1 protein, consistent with the fact that a monoclonal antibody to RP220 is a potent inhibitor of melanoma growth. These findings indicate that renalase-1 is a potential antigen for TCR recognition in melanoma and could be considered as a target for immunotherapy.
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Affiliation(s)
- Saif Zaman
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Fred S. Gorelick
- Veteran’s Administration Healthcare System, CT 06516, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Andrea Chrobrutskiy
- 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
| | - Gary V. Desir
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Veteran’s Administration Healthcare System, CT 06516, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, FL 33612, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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Hudock TR, Song JJ, Chobrutskiy A, Chobrutskiy BI, Blanck G. IGH Complementarity Determining Region-3-Cytomegalovirus Protein Chemical Complementarity Linked to Better Overall Survival Probabilities for Glioblastoma. Viral Immunol 2024; 37:259-265. [PMID: 38848306 DOI: 10.1089/vim.2024.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024] Open
Abstract
Cytomegalovirus (CMV) has long been thought to have an association with glioblastoma multiforme (GBM), although the exact role of CMV and any subsequent implications for treatment have yet to be fully understood. This study addressed whether IGH complementarity determining region-3 (CDR3)-CMV protein chemical complementarity, with IGH CDR3s representing both tumor resident and blood-sourced IGH recombinations, was associated with overall survival (OS) distinctions. IGH recombination sequencing reads were obtained from (a) the Clinical Proteomic Tumor Analysis Consortium, tumor RNAseq files; and (b) the cancer genome atlas, blood exome-derived files. The Adaptive Match web tool was used to calculate chemical complementarity scores (CSs) based on hydrophobic interactions, and those scores were used to group GBM cases and assess survival probabilities. We found a higher OS probability for cases whose hydrophobic IGH CDR3-CMV protein chemical complementarity scores (Hydro CSs) were in the upper 50th percentile for several CMV proteins, including UL99 and UL123, as well as for CSs based on known B cell epitopes representing these proteins. We also identified multiple immune signature genes, including CD79A and TNFRSF17, for which higher RNA expression was associated with higher Hydro CSs. Results were consistent with the idea that stronger immunoglobulin responses to CMV are associated with better OS probabilities for GBM.
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Affiliation(s)
- Tabitha R Hudock
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - 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
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Department of Immunology, Moffitt Cancer Center and Research Institute, Tampa, Florida, 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] [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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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] [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] [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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Dabkowski TR, Varkhedi M, Song JJ, Gozlan EC, Blanck G. Neuroblastoma and Glioblastoma Cases With Amplified Oncogenes Have Reduced Numbers of Tumor-Resident Adaptive Immune Receptor Recombinations. JCO Precis Oncol 2023; 7:e2300057. [PMID: 38085056 DOI: 10.1200/po.23.00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/11/2023] [Accepted: 08/24/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE In certain cancers, oncogene amplification is correlated with an immunologically cold or noninflamed, tumor immune microenvironment (TIME) and a worse prognosis, for example, in the case of MYCN-amplified neuroblastoma (NBL). However, for other cancer types, the relationship between oncogene amplification and immune response is more complicated or unresolved. One such cancer is glioblastoma multiforme (GBM), in which the epidermal growth factor receptor (EGFR) oncogene is commonly amplified. Unlike MYCN-amplified NBL, EGFR-amplified GBM has not been shown to correlate with a distinct survival probability. METHODS Given this contrasting state for NBL and GBM, we sought to apply a genomics approach to evaluating the immune response for cases with gene amplification. RESULTS Our results confirmed and added further specificity to the cold TIME of MYCN-amplified NBL. Moreover, we demonstrated a novel state of immunologically cold EGFR-amplified GBM tumors. CONCLUSION This approach to using copy number variation and immune receptor recombination read recovery levels to assess gene amplification and TIME, respectively, may be particularly efficient for the rapid evaluation of many other cancer types.
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Affiliation(s)
- Toriana R Dabkowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Mallika Varkhedi
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Joanna J Song
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
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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] [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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Mwangi KW, Kamita MK, Waweru JW, Sayed S, Figueroa JD, Ambs S, Cios KJ, Blanck G, Makokha FW. Adaptive immune receptor features related to breast cancer tissue in Kenyan patients: high immunoglobulin gene expression and high levels of gamma-delta T-cells. Breast Cancer Res Treat 2023; 199:207-214. [PMID: 36882607 PMCID: PMC10687744 DOI: 10.1007/s10549-023-06897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
BACKGROUND Characterization of the breast cancer (BC) immune response may provide information for a point of intervention, such as application of immunotherapeutic treatments. In this study, we sought to recover and characterize the adaptive immune receptor (IR) recombination reads from genomics files representing Kenyan patients, to better understand the immune response specifically related to those patients. METHODS We used a previously applied algorithm and software to obtain productive IR recombination reads from cancer and adjacent normal tissue samples representing 22 Kenyan BC patients. RESULTS From both the RNAseq and exome files, there were significantly more T-cell receptor (TCR) recombination reads recovered from tumor samples compared to marginal tissue samples. Also, the immunoglobulin (IG) genes were expressed at a much higher level than the TCR genes (p-value = 0.0183) in the tumor samples. And, the tumor IG CDR3s consistently represented more positively charged amino acid R-groups, in comparison to the marginal tissue, IG CDR3s. CONCLUSION For Kenyan patients, a high level of IG expression, representing specific CDR3 chemistries, was associated with BC. These results lay the foundation for studies that could support specific immunotherapeutic interventions for Kenyan BC patients.
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Affiliation(s)
- Kennedy W Mwangi
- Directorate of Research & Innovation, Mount Kenya University, Thika, Kenya
| | - Moses K Kamita
- Directorate of Research & Innovation, Mount Kenya University, Thika, Kenya
| | | | - Shahin Sayed
- Department of Pathology, Aga Khan University Hospital Nairobi, Nairobi, Kenya
| | - Jonine D Figueroa
- Usher Institute and the Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Stefan Ambs
- National Cancer Institute, National Institutes of Health, Bethesda, MD, 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
| | - 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.
| | - Francis W Makokha
- Directorate of Research & Innovation, Mount Kenya University, Thika, Kenya
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Angelakakis G, Serraneau KS, Barker VR, Callahan BM, Tong WL, Zaman S, Huda TI, Blanck G. TCR gene segment usage and HLA alleles that are associated with cancer survival rates also represent racial disparities. Int J Immunogenet 2023; 50:41-47. [PMID: 36585798 DOI: 10.1111/iji.12610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023]
Abstract
Understanding racial disparities in cancer outcomes continues to be a challenge, with likely many factors at play, including socioeconomic factors and genetic polymorphisms impacting basic cellular and molecular functions. Additionally, it is possible that specific combinations of environment and genetics have specific impacts. T-cell receptor (TCR) gene segment usage, HLA allele combinations have been associated with autoimmune and infectious disease courses, and more recently, TCR gene segment usage, HLA allele combinations have been associated with distinct survival outcomes in cancer as well. We examined several such, previously reported cancer-related TCR gene segment usage, HLA allele combinations for evidence of racial disparities, with regard to the prevalence of the combination in different racial groups. Results indicated that TCR gene segment usage, potentially reflecting environmental factors related to previous pathogen exposure, in combination with certain HLA alleles or independently, may represent a novel explanation for racial disparities in cancer outcomes. Overall, at this point, a genetic connection to racial disparities in cancer outcomes is detectable but remains modest, suggesting that other factors, such as socioeconomic factors, remain as important considerations.
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Affiliation(s)
- George Angelakakis
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Karisa S Serraneau
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Vayda R Barker
- 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
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Saif Zaman
- 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
| | - 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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10
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Tumor resident, TRA anti-viral CDR3 chemical sequence motifs are associated with a better breast cancer outcome. Genes Immun 2023; 24:92-98. [PMID: 36805542 DOI: 10.1038/s41435-023-00201-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/20/2023]
Abstract
While for certain cancers, such as cervical cancer, the link to viral infections is very strong and very clear, other cancers represent a history of links to viral infections that are either co-morbidities or drive the cancer in ways that are not yet fully understood, for example the "hit and run" possibility. To further understand the connection of viral infections and the progress of breast cancer, we identified the chemical features of known anti-viral, T-cell receptor alpha chain (TRA) complementarity determining region-3 (CDR3) amino acid sequences among the CDR3s of breast cancer patient TRA recombinations and assessed the association of those features with patient outcomes. The application of this novel paradigm indicated consistent associations of tumor-derived, anti-CMV CDR3 chemical sequence motifs with better breast cancer patient outcomes but did not indicate an opportunity to establish risk stratifications for other cancer types. Interestingly, breast cancer samples with no detectable TRA recombinations represented a better outcome than samples with the non-anti-CMV CDR3s, further adding to a rapidly developing series of results allowing a distinction between positive and possibly harmful cancer immune responses.
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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] [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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Delineation of a T-cell receptor CDR3-cancer mutanome aromaticity factor, assessable via blood samples, that facilitates the establishment of survival distinctions in bladder cancer. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04339-w. [PMID: 36098856 DOI: 10.1007/s00432-022-04339-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 10/14/2022]
Abstract
PURPOSE A very large and still expanding collection of adaptive immune receptor (IR) recombination reads, representing many diseases, is becoming available for downstream analyses. Among the most productive approaches has been to establish risk stratification parameters via the chemical features of the IR complementarity determining region-3 (CDR3) amino acid (AA) sequences, particularly for large datasets where clinical information is available. Because the IR CDR3 AA sequences often play a large role in antigen binding, the chemistry of these AAs has the likelihood of representing a disease-related fingerprint as well as providing pre-screening information for candidate antigens. To approach this issue in a novel manner, we developed a bladder cancer, case evaluation approach based on CDR3 aromaticity. METHODS We developed and applied a simple and efficient algorithm for assessing aromatic, chemical complementarity between T-cell receptor (TCR) CDR3 AA sequences and the cancer specimen mutanome. RESULTS Results indicated a survival distinction for aromatic CDR3-aromatic mutanome complementary, versus non-complementary, bladder cancer case sets. This result applied to both tumor resident and blood TCR CDR3 AA sequences and was supported by CDR3 AA sequences represented by both exome and RNAseq files. CONCLUSION The described aromaticity factor algorithm has the potential of assisting in prognostic assessments and guiding immunotherapies for bladder cancer.
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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] [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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Mcbreairty B, Chobrutskiy B, Chobrutskiy A, Gozlan E, Diaz M, Blanck G. Immune receptor CDR3 chemical features that preserve sequence information are highly efficient in reflecting survival distinctions: A pan‑cancer analysis. Biomed Rep 2022; 17:68. [DOI: 10.3892/br.2022.1551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Brooke Mcbreairty
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Boris Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Andrea Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Etienne Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Michael Diaz
- 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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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] [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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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] [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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