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Huang Y, Liu H, Liu B, Chen X, Li D, Xue J, Li N, Zhu L, Yang L, Xiao J, Liu C. Quantified pathway mutations associate epithelial-mesenchymal transition and immune escape with poor prognosis and immunotherapy resistance of head and neck squamous cell carcinoma. BMC Med Genomics 2024; 17:49. [PMID: 38331768 PMCID: PMC10854145 DOI: 10.1186/s12920-024-01818-6] [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: 06/14/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Pathway mutations have been calculated to predict the poor prognosis and immunotherapy resistance in head and neck squamous cell carcinoma (HNSCC). To uncover the unique markers predicting prognosis and immune therapy response, the accurate quantification of pathway mutations are required to evaluate epithelial-mesenchymal transition (EMT) and immune escape. Yet, there is a lack of score to accurately quantify pathway mutations. MATERIAL AND METHODS Firstly, we proposed Individualized Weighted Hallmark Gene Set Mutation Burden (IWHMB, https://github.com/YuHongHuang-lab/IWHMB ) which integrated pathway structure information and eliminated the interference of global Tumor Mutation Burden to accurately quantify pathway mutations. Subsequently, to further elucidate the association of IWHMB with EMT and immune escape, support vector machine regression model was used to identify IWHMB-related transcriptomic features (IRG), while Adversarially Regularized Graph Autoencoder (ARVGA) was used to further resolve IRG network features. Finally, Random walk with restart algorithm was used to identify biomarkers for predicting ICI response. RESULTS We quantified the HNSCC pathway mutation signatures and identified pathway mutation subtypes using IWHMB. The IWHMB-related transcriptomic features (IRG) identified by support vector machine regression were divided into 5 communities by ARVGA, among which the Community 1 enriching malignant mesenchymal components promoted EMT dynamically and regulated immune patterns associated with ICI responses. Bridge Hub Gene (BHG) identified by random walk with restart was key to IWHMB in EMT and immune escape, thus, more predictive for ICI response than other 70 public signatures. CONCLUSION In summary, the novel pathway mutation scoring-IWHMB suggested that the elevated malignancy mediated by pathway mutations is a major cause of poor prognosis and immunotherapy failure in HNSCC, and is capable of identifying novel biomarkers to predict immunotherapy response.
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Affiliation(s)
- Yuhong Huang
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China
| | - Han Liu
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China
| | - Bo Liu
- Institute for Genome Engineered Animal Models of Human Diseases, Dalian Medical University, Dalian, China
| | - Xiaoyan Chen
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
| | - Danya Li
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
| | - Junyuan Xue
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
| | - Nan Li
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China
| | - Lei Zhu
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China
| | - Liu Yang
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
| | - Jing Xiao
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China.
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China.
| | - Chao Liu
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China.
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China.
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Martini A, Prasai K, Zemla TJ, Ahmed FY, Elnagar MB, Giama NH, Guzzardo V, Biasiolo A, Fassan M, Yin J, Pontisso P, Roberts LR. SerpinB3/4 Expression Is Associated with Poor Prognosis in Patients with Cholangiocarcinoma. Cancers (Basel) 2024; 16:225. [PMID: 38201652 PMCID: PMC10778206 DOI: 10.3390/cancers16010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/30/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Cholangiocarcinoma (CCA), the second most common primary liver tumor, is associated with a dismal outcome, and useful prognostic markers are not currently available in clinical practice. SerpinB3, a serine protease inhibitor, was recently found to play a relevant role in malignant transformation in different cancers. The aim of the present study was to determine the expression of SerpinB3/4 in tissue and serum samples of patients with CCA in relation to clinical outcomes. SerpinB3/4 was assessed in the tissue microarrays (TMAs) of 123 surgically resected CCAs. ELISA assays were carried out in 188 patients with CCA to detect the free and IgM-linked forms of SerpinB3/4. Overall survival was analyzed in relation to SerpinB3/4 expression, and Cox models were used to identify the variables associated with survival. High levels of SerpinB3/4 (TMA score 2+/3+) were detected in 15 tumors (12.2%), characterized by a more advanced TNM stage (III/IV: 64.3% vs. 31.3%; p = 0.031) and lower overall patient survival, independently of CCA subclass (intrahepatic CCA: median 1.1 (0.8-Not Estimable, NE) vs. 2.4 (1.8-3.4) years; p = 0.0007; extrahepatic CCA: median 0.8 (0.2-NE) vs. 2.2 (1.5-5.4) years; p = 0.011). Vascular invasion (p = 0.027) and SerpinB3/4 scores (p = 0.0016) were independently associated with mortality in multivariate analysis. Patients who had detectable free or IgM-linked SerpinB3/4 in their serum showed poorer survival (1 vs. 2.4 years, p = 0.015, for free SerpinB3/4, and 1 vs. 2.6 years, p = 0.0026, for SerpinB3/4-IgM). In conclusion, high levels of SerpinB3/4 in tissue and serum in CCA are associated with poor outcomes after surgery, regardless of tumor subclass.
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Affiliation(s)
- Andrea Martini
- Department of Medicine, University of Padua, via Giustiniani 2, 35128 Padua, Italy; (A.M.); (V.G.); (A.B.); (M.F.)
| | - Kritika Prasai
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN 55905, USA; (K.P.); (F.Y.A.); (M.B.E.); (N.H.G.); (L.R.R.)
| | - Tyler J. Zemla
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN 55905, USA; (T.J.Z.); (J.Y.)
| | - Fowsiyo Y. Ahmed
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN 55905, USA; (K.P.); (F.Y.A.); (M.B.E.); (N.H.G.); (L.R.R.)
| | - Mamoun B. Elnagar
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN 55905, USA; (K.P.); (F.Y.A.); (M.B.E.); (N.H.G.); (L.R.R.)
| | - Nasra H. Giama
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN 55905, USA; (K.P.); (F.Y.A.); (M.B.E.); (N.H.G.); (L.R.R.)
| | - Vincenza Guzzardo
- Department of Medicine, University of Padua, via Giustiniani 2, 35128 Padua, Italy; (A.M.); (V.G.); (A.B.); (M.F.)
| | - Alessandra Biasiolo
- Department of Medicine, University of Padua, via Giustiniani 2, 35128 Padua, Italy; (A.M.); (V.G.); (A.B.); (M.F.)
| | - Matteo Fassan
- Department of Medicine, University of Padua, via Giustiniani 2, 35128 Padua, Italy; (A.M.); (V.G.); (A.B.); (M.F.)
- Veneto Institute of Oncology, (IOV-IRCCS), via Gattamelata 64, 35128 Padua, Italy
| | - Jun Yin
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN 55905, USA; (T.J.Z.); (J.Y.)
| | - Patrizia Pontisso
- Department of Medicine, University of Padua, via Giustiniani 2, 35128 Padua, Italy; (A.M.); (V.G.); (A.B.); (M.F.)
- European Reference Network—ERN RARE-LIVER, 72076 Tübingen, Germany
| | - Lewis R. Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN 55905, USA; (K.P.); (F.Y.A.); (M.B.E.); (N.H.G.); (L.R.R.)
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Debets DO, Stecker KE, Piskopou A, Liefaard MC, Wesseling J, Sonke GS, Lips EH, Altelaar M. Deep (phospho)proteomics profiling of pre- treatment needle biopsies identifies signatures of treatment resistance in HER2 + breast cancer. Cell Rep Med 2023; 4:101203. [PMID: 37794585 PMCID: PMC10591042 DOI: 10.1016/j.xcrm.2023.101203] [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: 12/21/2022] [Revised: 07/06/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Patients with early-stage HER2-overexpressing breast cancer struggle with treatment resistance in 20%-40% of cases. More information is needed to predict HER2 therapy response and resistance in vivo. In this study, we perform (phospho)proteomics analysis of pre-treatment HER2+ needle biopsies of early-stage invasive breast cancer to identify molecular signatures predictive of treatment response to trastuzumab, pertuzumab, and chemotherapy. Our data show that accurate quantification of the estrogen receptor (ER) and HER2 biomarkers, combined with the assessment of associated biological features, has the potential to enable better treatment outcome prediction. In addition, we identify cellular mechanisms that potentially precondition tumors to resist therapy. We find proteins with expression changes that correlate with resistance and constitute to a strong predictive signature for treatment success in our patient cohort. Our results highlight the multifactorial nature of drug resistance in vivo and demonstrate the necessity of deep tumor profiling.
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Affiliation(s)
- Donna O Debets
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 Utrecht, the Netherlands
| | - Kelly E Stecker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 Utrecht, the Netherlands
| | - Anastasia Piskopou
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 Utrecht, the Netherlands
| | - Marte C Liefaard
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jelle Wesseling
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, University of Amsterdam, Amsterdam, the Netherlands
| | - Esther H Lips
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 Utrecht, the Netherlands.
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Campos Segura AV, Velásquez Sotomayor MB, Gutiérrez Román AIF, Ortiz Rojas CA, Murillo Carrasco AG. Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers. PeerJ 2023; 11:e15410. [PMID: 37214090 PMCID: PMC10198153 DOI: 10.7717/peerj.15410] [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: 12/14/2022] [Accepted: 04/23/2023] [Indexed: 05/24/2023] Open
Abstract
Background Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, and its development is associated with the gains and/or losses of genetic material, which leads to the emergence of main driver genes with higher mutational frequency. In addition, there are other genes with mutations that have weak tumor-promoting effects, known as mini-drivers, which could aggravate the development of oncogenesis when they occur together. The aim of our work was to use computer analysis to explore the survival impact, frequency, and incidence of mutations of possible mini-driver genes to be used for the prognosis of CRC. Methods We retrieved data from three sources of CRC samples using the cBioPortal platform and analyzed the mutational frequency to exclude genes with driver features and those mutated in less than 5% of the original cohort. We also observed that the mutational profile of these mini-driver candidates is associated with variations in the expression levels. The candidate genes obtained were subjected to Kaplan-Meier curve analysis, making a comparison between mutated and wild-type samples for each gene using a p-value threshold of 0.01. Results After gene filtering by mutational frequency, we obtained 159 genes of which 60 were associated with a high accumulation of total somatic mutations with Log2 (fold change) > 2 and p values < 10-5. In addition, these genes were enriched to oncogenic pathways such as epithelium-mesenchymal transition, hsa-miR-218-5p downregulation, and extracellular matrix organization. Our analysis identified five genes with possible implications as mini-drivers: DOCK3, FN1, PAPPA2, DNAH11, and FBN2. Furthermore, we evaluated a combined classification where CRC patients with at least one mutation in any of these genes were separated from the main cohort obtaining a p-value < 0.001 in the evaluation of CRC prognosis. Conclusion Our study suggests that the identification and incorporation of mini-driver genes in addition to known driver genes could enhance the accuracy of prognostic biomarkers for CRC.
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Affiliation(s)
- Anthony Vladimir Campos Segura
- Biochemistry and Molecular Biology Research Laboratory. Faculty of Natural Sciences and Mathematics, Universidad Nacional Federico Villarreal, Lima, Peru
- Research Group in Biochemistry and Synthetic Biology (GIBBS-UNFV), Lima, Peru
- Research Group in Immunology and Cancer (IMMUCA), Lima, Peru
| | - Mariana Belén Velásquez Sotomayor
- Research Group in Immunology and Cancer (IMMUCA), Lima, Peru
- School of Human Medicine, Faculty of Health Sciences, Universidad Cientifica del Sur, Lima, Peru
| | - Ana Isabel Flor Gutiérrez Román
- Biochemistry and Molecular Biology Research Laboratory. Faculty of Natural Sciences and Mathematics, Universidad Nacional Federico Villarreal, Lima, Peru
- Research Group in Biochemistry and Synthetic Biology (GIBBS-UNFV), Lima, Peru
| | - César Alexander Ortiz Rojas
- Research Group in Immunology and Cancer (IMMUCA), Lima, Peru
- Hematology Division, LIM31, Medical School, Universidade de São Paulo, Sao Paulo, Brazil
| | - Alexis Germán Murillo Carrasco
- Research Group in Immunology and Cancer (IMMUCA), Lima, Peru
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
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