1
|
Um JH, Zheng Y, Mao Q, Nam C, Zhao H, Koh YW, Shin SJ, Park YM, Lin DC. Genomic and single-cell characterization of patient-derived tumor organoid models of head and neck squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601068. [PMID: 39005427 PMCID: PMC11244938 DOI: 10.1101/2024.06.28.601068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) remains a significant health burden due to tumor heterogeneity and treatment resistance, emphasizing the need for improved biological understanding and tailored therapies. This study enrolled 31 HNSCC patients for the establishment of patient-derived tumor organoids (PDOs), which faithfully maintained genomic features and histopathological traits of primary tumors. Long-term culture preserved key characteristics, affirming PDOs as robust representative models. PDOs demonstrated predictive capability for cisplatin treatment responses, correlating ex vivo drug sensitivity with patient outcomes. Bulk and single-cell RNA sequencing unveiled molecular subtypes and intratumor heterogeneity (ITH) in PDOs, paralleling patient tumors. Notably, a hybrid epithelial-mesenchymal transition (hEMT)-like ITH program is associated with cisplatin resistance and poor patient survival. Functional analyses identified amphiregulin (AREG) as a potential regulator of the hybrid epithelial/mesenchymal state. Moreover, AREG contributes to cisplatin resistance via EGFR pathway activation, corroborated by clinical samples. In summary, HNSCC PDOs serve as reliable and versatile models, offer predictive insights into ITH programs and treatment responses, and uncover potential therapeutic targets for personalized medicine.
Collapse
Affiliation(s)
- Jung Hyun Um
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Yueyuan Zheng
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Qiong Mao
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou, 510120, P.R. China
| | - Chehyun Nam
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| | - Yoon Woo Koh
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Su-Jin Shin
- Department of Pathology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Young Min Park
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, USA
| |
Collapse
|
2
|
de Leeuw ALMP, Giralt J, Tao Y, Benavente S, France Nguyen TV, Hoebers FJP, Hoeben A, Terhaard CHJ, Wai Lee L, Friesland S, Steenbakkers RJHM, Tans L, Heukelom J, Kayembe MT, van Kranen SR, Bartelink H, Rasch CRN, Sonke JJ, Hamming-Vrieze O. A multicentric randomized controlled phase III trial of adaptive and 18F-FDG-PET-guided dose-redistribution in locally advanced head and neck squamous cell carcinoma (ARTFORCE). Radiother Oncol 2024; 196:110281. [PMID: 38636708 DOI: 10.1016/j.radonc.2024.110281] [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: 10/04/2023] [Revised: 03/16/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND AND PURPOSE This multicenter randomized phase III trial evaluated whether locoregional control of patients with LAHNSCC could be improved by fluorodeoxyglucose-positron emission tomography (FDG-PET)-guided dose-escalation while minimizing the risk of increasing toxicity using a dose-redistribution and scheduled adaptation strategy. MATERIALS AND METHODS Patients with T3-4-N0-3-M0 LAHNSCC were randomly assigned (1:1) to either receive a dose distribution ranging from 64-84 Gy/35 fractions with adaptation at the 10thfraction (rRT) or conventional 70 Gy/35 fractions (cRT). Both arms received concurrent three-cycle 100 mg/m2cisplatin. Primary endpoints were 2-year locoregional control (LRC) and toxicity. Primary analysis was based on the intention-to-treat principle. RESULTS Due to slow accrual, the study was prematurely closed (at 84 %) after randomizing 221 eligible patients between 2012 and 2019 to receive rRT (N = 109) or cRT (N = 112). The 2-year LRC estimate difference of 81 % (95 %CI 74-89 %) vs. 74 % (66-83 %) in the rRT and cRT arm, respectively, was not found statistically significant (HR 0.75, 95 %CI 0.43-1.31,P=.31). Toxicity prevalence and incidence rates were similar between trial arms, with exception for a significant increased grade ≥ 3 pharyngolaryngeal stenoses incidence rate in the rRT arm (0 versus 4 %,P=.05). In post-hoc subgroup analyses, rRT improved LRC for patients with N0-1 disease (HR 0.21, 95 %CI 0.05-0.93) and oropharyngeal cancer (0.31, 0.10-0.95), regardless of HPV. CONCLUSION Adaptive and dose redistributed radiotherapy enabled dose-escalation with similar toxicity rates compared to conventional radiotherapy. While FDG-PET-guided dose-escalation did overall not lead to significant tumor control or survival improvements, post-hoc results showed improved locoregional control for patients with N0-1 disease or oropharyngeal cancer treated with rRT.
Collapse
Affiliation(s)
- Anna Liza M P de Leeuw
- Department of Radiation Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
| | - Jordi Giralt
- Department of Radiation Oncology, Hospital General Vall d'Hebron, Barcelona, Spain; Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Yungan Tao
- Department of Radiation Oncology, Institut Gustave Roussy, Villejuif, France
| | - Sergi Benavente
- Department of Radiation Oncology, Hospital General Vall d'Hebron, Barcelona, Spain; Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Frank J P Hoebers
- Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ann Hoeben
- Division of Medical Oncology, Department of Internal Medicine, GROW-School of Oncology and Developmental Biology Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Chris H J Terhaard
- Department of Radiation Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lip Wai Lee
- Department of Radiation Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Signe Friesland
- Department of Radiation Oncology, Karolinska Institute, Stockholm, Sweden
| | - Roel J H M Steenbakkers
- Department of Radiation Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Lisa Tans
- Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jolien Heukelom
- Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Mutamba T Kayembe
- Department of Bioinformatics and Statistics, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Simon R van Kranen
- Department of Radiation Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Harry Bartelink
- Department of Radiation Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Coen R N Rasch
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan-Jakob Sonke
- Department of Radiation Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Olga Hamming-Vrieze
- Department of Radiation Oncology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
| |
Collapse
|
3
|
Murakami K, Kamiakito T, Kawata H, Kosami K, Nakaya T, Noguchi T, Mori Y, Tanaka A. Basal differentiation and expression status of SOX2 and KLF4 in basal layers are prognostic factors for disease-specific survival in oral squamous cell carcinoma. J Oral Pathol Med 2024; 53:303-309. [PMID: 38659289 DOI: 10.1111/jop.13535] [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: 01/10/2024] [Revised: 03/15/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Basal differentiation in oral squamous cell carcinoma is usually detected at invasive sites. However, its significance as a prognostic value has been poorly investigated. METHODS COL17 was selected as a basal differentiation marker because of its stable expression in the basal-like cells of oral squamous cell carcinoma. Sixty-five cases of oral squamous cell carcinoma were subclassified into COL17-high (30 cases) and -low (35 cases) types, and the prognostic value was analyzed by Cox regression analysis. In addition, the stem cell markers such as SOX2, KLF4, MYC as well as the stem cell-related markers BMI1, EZH2, and YAP and its paralog TAZ, were immunohistochemically analyzed. Their prognostic values were investigated along with their COL17 status by Cox regression analysis. RESULTS No significant difference was observed between the COL17-high and -low groups in the disease-specific survival and recurrence-free survival in oral squamous cell carcinoma. When the COL17-high and -low categories were combined with the SOX2, KLF4, EZH2, or YAP/TAZ status in the basal layers, together with gender and age as covariates, the hazard ratios reached 3.3, 3.7, 2.8, and 3.1, respectively. In addition, multivariate analysis, including COL17, SOX2, and KLF4, with gender and age as covariates, showed a significantly poor prognosis for disease-specific survival. CONCLUSION Based on the relatively high hazard ratios, it is indicated that basal differentiation and the expression status of SOX2 and KLF4 in the basal layers are prognostic factors for oral squamous cell carcinoma.
Collapse
Affiliation(s)
- Kazuhiro Murakami
- Division of Human Pathology, Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi, Japan
- Department of Oral and Maxillofacial Surgery, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Tomoko Kamiakito
- Division of Human Pathology, Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hirotoshi Kawata
- Division of Human Pathology, Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Koki Kosami
- Division of Public Health, Center for Communities, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Takeo Nakaya
- Division of Human Pathology, Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Tadahide Noguchi
- Department of Oral and Maxillofacial Surgery, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Yoshiyuki Mori
- Department of Oral and Maxillofacial Surgery, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Akira Tanaka
- Division of Human Pathology, Department of Pathology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| |
Collapse
|
4
|
Hu X, Dong H, Qin W, Bin Y, Huang W, Kang M, Wang R. Machine learning-based identification of a consensus immune-derived gene signature to improve head and neck squamous cell carcinoma therapy and outcome. Front Pharmacol 2024; 15:1341346. [PMID: 38666027 PMCID: PMC11044683 DOI: 10.3389/fphar.2024.1341346] [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: 11/20/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSCC), an extremely aggressive tumor, is often associated with poor outcomes. The standard anatomy-based tumor-node-metastasis staging system does not satisfy the requirements for screening treatment-sensitive patients. Thus, an ideal biomarker leading to precise screening and treatment of HNSCC is urgently needed. Methods Ten machine learning algorithms-Lasso, Ridge, stepwise Cox, CoxBoost, elastic network (Enet), partial least squares regression for Cox (plsRcox), random survival forest (RSF), generalized boosted regression modelling (GBM), supervised principal components (SuperPC), and survival support vector machine (survival-SVM)-as well as 85 algorithm combinations were applied to construct and identify a consensus immune-derived gene signature (CIDGS). Results Based on the expression profiles of three cohorts comprising 719 patients with HNSCC, we identified 236 consensus prognostic genes, which were then filtered into a CIDGS, using the 10 machine learning algorithms and 85 algorithm combinations. The results of a study involving a training cohort, two testing cohorts, and a meta-cohort consistently demonstrated that CIDGS was capable of accurately predicting prognoses for HNSCC. Incorporation of several core clinical features and 51 previously reported signatures, enhanced the predictive capacity of the CIDGS to a level which was markedly superior to that of other signatures. Notably, patients with low CIDGS displayed fewer genomic alterations and higher immune cell infiltrate levels, as well as increased sensitivity to immunotherapy and other therapeutic agents, in addition to receiving better prognoses. The survival times of HNSCC patients with high CIDGS, in particular, were shorter. Moreover, CIDGS enabled accurate stratification of the response to immunotherapy and prognoses for bladder cancer. Niclosamide and ruxolitinib showed potential as therapeutic agents in HNSCC patients with high CIDGS. Conclusion CIDGS may be used for stratifying risks as well as for predicting the outcome of patients with HNSCC in a clinical setting.
Collapse
Affiliation(s)
- Xueying Hu
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi, China
| | - Haiqun Dong
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi, China
| | - Wen Qin
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi, China
| | - Ying Bin
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi, China
| | - Wenhua Huang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi, China
| | - Min Kang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi, China
| | - Rensheng Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning, Guangxi, China
| |
Collapse
|
5
|
Sosa J, Glathar A, Sinha S. Architecture of head and neck squamous cell carcinoma tumor microenvironment revealed: can tertiary lymphoid structures predict post-surgery recurrence? Transl Cancer Res 2024; 13:484-489. [PMID: 38482424 PMCID: PMC10928623 DOI: 10.21037/tcr-23-2098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/24/2024] [Indexed: 05/30/2024]
Affiliation(s)
- Jennifer Sosa
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Alexandra Glathar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| |
Collapse
|
6
|
Cheng Y, Song Z, Chen J, Tang Z, Wang B. Molecular basis, potential biomarkers, and future prospects of OSCC and PD-1/PD-L1 related immunotherapy methods. Heliyon 2024; 10:e25895. [PMID: 38380036 PMCID: PMC10877294 DOI: 10.1016/j.heliyon.2024.e25895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) affects a large number of individuals worldwide. Despite advancements in surgery, radiation, and chemotherapy, satisfactory outcomes have not been achieved. In recent years, the success of drugs targeting programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) has led to breakthroughs in cancer treatment, but systematic summaries on their effectiveness against OSCC are lacking. This article reviews the latest research on the PD-1/PD-L1 pathway and the potential of combination therapy based on this pathway in OSCC. Further, it explores the mechanisms involved in the interaction of this pathway with exosomes and protein-protein interactions, and concludes with potential future OSCC therapeutic strategies.
Collapse
Affiliation(s)
- Yuxi Cheng
- Xiangya Stomatological Hospital, Central South University, Changsha, 410008, China
- Xiangya School of Stomatology, Central South University, Changsha, 410008, China
- Clinical Research Center of Oral Major Diseases and Oral Health, 410008, Hunan, China
| | - Zhengzheng Song
- Xiangya Stomatological Hospital, Central South University, Changsha, 410008, China
- Xiangya School of Stomatology, Central South University, Changsha, 410008, China
- Clinical Research Center of Oral Major Diseases and Oral Health, 410008, Hunan, China
| | - Juan Chen
- Xiangya Stomatological Hospital, Central South University, Changsha, 410008, China
- Xiangya School of Stomatology, Central South University, Changsha, 410008, China
- Clinical Research Center of Oral Major Diseases and Oral Health, 410008, Hunan, China
| | - Zhangui Tang
- Xiangya Stomatological Hospital, Central South University, Changsha, 410008, China
- Xiangya School of Stomatology, Central South University, Changsha, 410008, China
- Clinical Research Center of Oral Major Diseases and Oral Health, 410008, Hunan, China
| | - Baisheng Wang
- Xiangya Stomatological Hospital, Central South University, Changsha, 410008, China
- Xiangya School of Stomatology, Central South University, Changsha, 410008, China
- Clinical Research Center of Oral Major Diseases and Oral Health, 410008, Hunan, China
| |
Collapse
|
7
|
Kreis J, Aybey B, Geist F, Brors B, Staub E. Stromal Signals Dominate Gene Expression Signature Scores That Aim to Describe Cancer Cell-intrinsic Stemness or Mesenchymality Characteristics. CANCER RESEARCH COMMUNICATIONS 2024; 4:516-529. [PMID: 38349551 PMCID: PMC10885853 DOI: 10.1158/2767-9764.crc-23-0383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/14/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Epithelial-to-mesenchymal transition (EMT) in cancer cells confers migratory abilities, a crucial aspect in the metastasis of tumors that frequently leads to death. In multiple studies, authors proposed gene expression signatures for EMT, stemness, or mesenchymality of tumors based on bulk tumor expression profiling. However, recent studies suggested that noncancerous cells from the microenvironment or macroenvironment heavily influence such signature profiles. Here, we strengthen these findings by investigating 11 published and frequently referenced gene expression signatures that were proposed to describe EMT-related (EMT, mesenchymal, or stemness) characteristics in various cancer types. By analyses of bulk, single-cell, and pseudobulk expression data, we show that the cell type composition of a tumor sample frequently dominates scores of these EMT-related signatures. A comprehensive, integrated analysis of bulk RNA sequencing (RNA-seq) and single-cell RNA-seq data shows that stromal cells, most often fibroblasts, are the main drivers of EMT-related signature scores. We call attention to the risk of false conclusions about tumor properties when interpreting EMT-related signatures, especially in a clinical setting: high patient scores of EMT-related signatures or calls of "stemness subtypes" often result from low cancer cell content in tumor biopsies rather than cancer cell-specific stemness or mesenchymal/EMT characteristics. SIGNIFICANCE Cancer self-renewal and migratory abilities are often characterized via gene module expression profiles, also called EMT or stemness gene expression signatures. Using published clinical tumor samples, cancer cell lines, and single cancer cells, we highlight the dominating influence of noncancer cells in low cancer cell content biopsies on their scores. We caution on their application for low cancer cell content clinical cancer samples with the intent to assign such characteristics or subtypes.
Collapse
Affiliation(s)
- Julian Kreis
- The healthcare business of Merck KGaA, Darmstadt, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Bogac Aybey
- The healthcare business of Merck KGaA, Darmstadt, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Felix Geist
- The healthcare business of Merck KGaA, Darmstadt, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
- Medical Faculty Heidelberg and Faculty of Biosciences, Heidelberg University, and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Eike Staub
- The healthcare business of Merck KGaA, Darmstadt, Germany
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Stögbauer F, Otto R, Jöhrens K, Tinhofer I, Keilholz U, Poremba C, Keller U, Leser U, Weichert W, Boxberg M, Klinghammer K. Molecular subtyping of head and neck cancer - Clinical applicability and correlations with morphological characteristics. Oral Oncol 2024; 149:106678. [PMID: 38219707 DOI: 10.1016/j.oraloncology.2023.106678] [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: 05/17/2023] [Revised: 11/27/2023] [Accepted: 12/23/2023] [Indexed: 01/16/2024]
Abstract
AIM We aimed to evaluate the applicability of a customized NanoString panel for molecular subtyping of recurrent or metastatic head and neck squamous cell carcinoma (R/M-HNSCC). Additionally, histological analyses were conducted, correlated with the molecular subtypes and tested for their prognostic value. MATERIAL AND METHODS We conducted molecular subtyping of R/M-HNSCC according to the molecular subtypes defined by Keck et al. For molecular analyses a 231 gene customized NanoString panel (the most accurately subtype defining genes, based on previous analyses) was applied to tumor samples from R/M-HNSCC patients that were treated in the CeFCiD trial (AIO/IAG-KHT trial 1108). A total of 130 samples from 95 patients were available for sequencing, of which 80 samples from 67 patients passed quality controls and were included in histological analyses. H&E stained slides were evaluated regarding distinct morphological patterns (e.g. tumor budding, nuclear size, stroma content). RESULTS Determination of molecular subtypes led to classification of tumor samples as basal (n = 46, 45 %), inflamed/mesenchymal (n = 31, 30 %) and classical (n = 26, 25 %). Expression levels of Amphiregulin (AREG) were significantly higher for the basal and classical subtypes compared to the mesenchymal subtype. While molecular subtypes did not have an impact on survival, high levels of tumor budding were associated with poor outcomes. No correlation was found between molecular subtypes and histological characteristics. CONCLUSIONS Utilizing the 231-gene NanoString panel we were able to determine the molecular subtype of R/M-HNSCC samples by the use of FFPE material. The value to stratify for different treatment options remains to be explored in the future. The prognostic value of tumor budding was underscored in this clinically well annotated cohort.
Collapse
Affiliation(s)
- Fabian Stögbauer
- Technical University of Munich, Germany; TUM School of Medicine and Health, Institute of General and Surgical Pathology, Germany
| | - Raik Otto
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Korinna Jöhrens
- Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstr. 74, 01307 Dresden, TU, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK), Partner Site Berlin, Germany; Department of Radiooncology and Radiotherapy, Charité-Universitätsmedizin Berlin, Germany
| | - Ulrich Keilholz
- German Cancer Consortium (DKTK), Partner Site Berlin, Germany; Berlin Institute of Health, Berlin, Germany; Charité Comprehensive Cancer Center, Berlin, Germany
| | | | - Ulrich Keller
- German Cancer Consortium (DKTK), Partner Site Berlin, Germany; Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine, Berlin, Germany; German Center for Translational Cancer Research (DKTK), DKFZ, Heidelberg, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Wilko Weichert
- Technical University of Munich, Germany; TUM School of Medicine and Health, Institute of General and Surgical Pathology, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Institute of Pathology, Munich, Germany
| | - Melanie Boxberg
- Technical University of Munich, Germany; TUM School of Medicine and Health, Institute of General and Surgical Pathology, Germany; Charité Comprehensive Cancer Center, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Institute of Pathology, Munich, Germany
| | - Konrad Klinghammer
- German Cancer Consortium (DKTK), Partner Site Berlin, Germany; Charité Comprehensive Cancer Center, Berlin, Germany; Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| |
Collapse
|
10
|
Zhu Y, Peng B, Luo X, Sun W, Liu D, Li N, Qiu P, Long G. High-Resolution Profiling of Head and Neck Squamous Cells Carcinoma Identifies Specific Biomarkers and Expression Subtypes of Clinically Relevant Vulnerabilities. Curr Med Chem 2024; 31:2431-2448. [PMID: 37936459 DOI: 10.2174/0109298673276128231031112655] [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: 08/07/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSC) is the seventh most common cancer worldwide. Although there are several options for the treatment of HNSC, there is still a lack of better biomarkers to accurately predict the response to treatment and thus be more able to correctly treat the therapeutic modality. METHODS First, we typed cases from the TCGA-HNSC cohort into subtypes by a Bayesian non-negative matrix factorization (BayesNMF)-based consensus clustering approach. Subsequently, genomic and proteomic data from HNSC cell lines were integrated to identify biomarkers of response to targeted therapies and immunotherapies. Finally, associations between HNSC subtypes and CD8 T-cell-associated effector molecules, common immune checkpoint genes, were compared to assess the potential of HNSC subtypes as clinically predictive immune checkpoint blockade therapy. RESULTS The 500 HNSC cases from TCGA were put through a consensus clustering approach to identify six HNSC expression subtypes. In addition, subtypes with unique proteomics and dependency profiles were defined based on HNSC cell line histology and proteomics data. Subtype 4 (S4) exhibits hyperproliferative and hyperimmune properties, and S4-associated cell lines show specific vulnerability to ADAT2, EIF5AL1, and PAK2. PD-L1 and CASP1 inhibitors have therapeutic potential in S4, and we have also demonstrated that S4 is more responsive to immune checkpoint blockade therapy. CONCLUSION Overall, our HNSC typing approach identified robust tumor-expressing subtypes, and data from multiple screens also revealed subtype-specific biology and vulnerabilities. These HNSC expression subtypes and their biomarkers will help develop more effective therapeutic strategies.
Collapse
Affiliation(s)
- Yingying Zhu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bi Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoxiao Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Sun
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dongbo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Na Li
- Department of Medical, Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen, 518038, China
| | - Ping Qiu
- Department of Medical, Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen, 518038, China
| | - Guoxian Long
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| |
Collapse
|
11
|
Xie M, Chaudhary R, Slebos RJ, Lee K, Song F, Poole MI, Hoening DS, Noel LC, Hernandez-Prera JC, Conejo-Garcia JR, Chung CH, Tan AC. Immune landscape in molecular subtypes of human papillomavirus-negative head and neck cancer. Mol Carcinog 2024; 63:120-135. [PMID: 37750589 PMCID: PMC10841270 DOI: 10.1002/mc.23640] [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: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
Head and neck squamous cell carcinomas (HNSCC) remain a poorly understood disease clinically and immunologically. HPV is a known risk factor of HNSCC associated with better outcome, whereas HPV-negative HNSCC are more heterogeneous in outcome. Gene expression signatures have been developed to classify HNSCC into four molecular subtypes (classical, basal, mesenchymal, and atypical). However, the molecular underpinnings of treatment response and the immune landscape for these molecular subtypes are largely unknown. Herein, we described a comprehensive immune landscape analysis in three independent HNSCC cohorts (>700 patients) using transcriptomics data. We assigned the HPV- HNSCC patients into these four molecular subtypes and characterized the tumor microenvironment using deconvolution method. We determined that atypical and mesenchymal subtypes have greater immune enrichment and exhibit a T-cell exhaustion phenotype, compared to classical and basal subtypes. Further analyses revealed different B cell maturation and antibody isotypes enrichment patterns, and distinct immune microenvironment crosstalk in the atypical and mesenchymal subtypes. Taken together, our study suggests that treatments that enhances B cell activity may benefit patients with HNSCC of the atypical subtypes. The rationale can be utilized in the design of future precision immunotherapy trials based on the molecular subtypes of HPV- HNSCC.
Collapse
Affiliation(s)
- Mengyu Xie
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Ritu Chaudhary
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Robbert J.C. Slebos
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Kyubum Lee
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Feifei Song
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Maria I. Poole
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Dirk S. Hoening
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Leenil C. Noel
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Juan C. Hernandez-Prera
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jose R. Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Christine H. Chung
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Aik Choon Tan
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Huntsman Cancer Institute, Department of Oncological Sciences and Biomedical Informatics, University of Utah, Salt Lake City, UT, 84112 USA
| |
Collapse
|
12
|
Lee YC, Nam Y, Kim M, Kim SI, Lee JW, Eun YG, Kim D. Prognostic significance of senescence-related tumor microenvironment genes in head and neck squamous cell carcinoma. Aging (Albany NY) 2023; 16:985-1001. [PMID: 38154113 PMCID: PMC10866405 DOI: 10.18632/aging.205346] [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: 08/24/2023] [Accepted: 11/06/2023] [Indexed: 12/30/2023]
Abstract
The impact of the senescence related microenvironment on cancer prognosis and therapeutic response remains poorly understood. In this study, we investigated the prognostic significance of senescence related tumor microenvironment genes (PSTGs) and their potential implications for immunotherapy response. Using the Cancer Genome Atlas- head and neck squamous cell carcinoma (HNSC) data, we identified two subtypes based on the expression of PSTGs, acquired from tumor-associated senescence genes, tumor microenvironment (TME)-related genes, and immune-related genes, using consensus clustering. Using the LASSO, we constructed a risk model consisting of senescence related TME core genes (STCGs). The two subtypes exhibited significant differences in prognosis, genetic alterations, methylation patterns, and enriched pathways, and immune infiltration. Our risk model stratified patients into high-risk and low-risk groups and validated in independent cohorts. The high-risk group showed poorer prognosis and immune inactivation, suggesting reduced responsiveness to immunotherapy. Additionally, we observed a significant enrichment of STCGs in stromal cells using single-cell RNA transcriptome data. Our findings highlight the importance of the senescence related TME in HNSC prognosis and response to immunotherapy. This study contributes to a deeper understanding of the complex interplay between senescence and the TME, with potential implications for precision medicine and personalized treatment approaches in HNSC.
Collapse
Affiliation(s)
- Young Chan Lee
- Department of Otolaryngology-Head and Neck Surgery, Kyung Hee University School of Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea
- Department of Medicine (AgeTech-Service Convergence Major) College of Medicine, Kyung Hee University, Seoul, Republic of Korea
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yonghyun Nam
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Minjeong Kim
- Department of Medicine (AgeTech-Service Convergence Major) College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Su Il Kim
- Department of Otolaryngology-Head and Neck Surgery, Kyung Hee University School of Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea
| | - Jung-Woo Lee
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Kyung Hee University, Seoul, Republic of Korea
| | - Young-Gyu Eun
- Department of Otolaryngology-Head and Neck Surgery, Kyung Hee University School of Medicine, Kyung Hee University Medical Center, Seoul, Republic of Korea
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
13
|
Brennan K, Espín-Pérez A, Chang S, Bedi N, Saumyaa S, Shin JH, Plevritis SK, Gevaert O, Sunwoo JB, Gentles AJ. Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer. Genome Med 2023; 15:98. [PMID: 37978395 PMCID: PMC10656821 DOI: 10.1186/s13073-023-01236-w] [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: 01/14/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The prognosis for patients with head and neck cancer (HNC) is poor and has improved little in recent decades, partially due to lack of therapeutic options. To identify effective therapeutic targets, we sought to identify molecular pathways that drive metastasis and HNC progression, through large-scale systematic analyses of transcriptomic data. METHODS We performed meta-analysis across 29 gene expression studies including 2074 primary HNC biopsies to identify genes and transcriptional pathways associated with survival and lymph node metastasis (LNM). To understand the biological roles of these genes in HNC, we identified their associated cancer pathways, as well as the cell types that express them within HNC tumor microenvironments, by integrating single-cell RNA-seq and bulk RNA-seq from sorted cell populations. RESULTS Patient survival-associated genes were heterogenous and included drivers of diverse tumor biological processes: these included tumor-intrinsic processes such as epithelial dedifferentiation and epithelial to mesenchymal transition, as well as tumor microenvironmental factors such as T cell-mediated immunity and cancer-associated fibroblast activity. Unexpectedly, LNM-associated genes were almost universally associated with epithelial dedifferentiation within malignant cells. Genes negatively associated with LNM consisted of regulators of squamous epithelial differentiation that are expressed within well-differentiated malignant cells, while those positively associated with LNM represented cell cycle regulators that are normally repressed by the p53-DREAM pathway. These pro-LNM genes are overexpressed in proliferating malignant cells of TP53 mutated and HPV + ve HNCs and are strongly associated with stemness, suggesting that they represent markers of pre-metastatic cancer stem-like cells. LNM-associated genes are deregulated in high-grade oral precancerous lesions, and deregulated further in primary HNCs with advancing tumor grade and deregulated further still in lymph node metastases. CONCLUSIONS In HNC, patient survival is affected by multiple biological processes and is strongly influenced by the tumor immune and stromal microenvironments. In contrast, LNM appears to be driven primarily by malignant cell plasticity, characterized by epithelial dedifferentiation coupled with EMT-independent proliferation and stemness. Our findings postulate that LNM is initially caused by loss of p53-DREAM-mediated repression of cell cycle genes during early tumorigenesis.
Collapse
Affiliation(s)
- Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Almudena Espín-Pérez
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Serena Chang
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Nikita Bedi
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Saumyaa Saumyaa
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - June Ho Shin
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - John B Sunwoo
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
14
|
Gu H, Li T, Beeraka NM, Zheng Y, Zhang X, Song R, Zhou R, Wang X, Sukocheva O, Fan R, Liu J. Molecular classification of human papilloma virus-negative head and neck squamous cell carcinomas: Cell cycle-based classifier and prognostic signature. PLoS One 2023; 18:e0286414. [PMID: 37903125 PMCID: PMC10615317 DOI: 10.1371/journal.pone.0286414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/15/2023] [Indexed: 11/01/2023] Open
Abstract
The molecular classification of human papillomavirus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs) remains questionable. Differentially expressed genes were detected between tumor and normal tissues and GSEA showed they are associated with cell cycle pathways. This study aimed to classify HPV-negative HNSCCs based on cell cycle-related genes. The established gene pattern was correlated with tumor progression, clinical prognosis, and drug treatment efficacy. Biological analysis was performed using HNSCC patient sample data obtained from the Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Gene Expression Omnibus (GEO) databases. All samples included in this study contained survival information. RNA sequencing data from 740 samples were used for the analysis. Previously characterized cell cycle-related genes were included for unsupervised consensus clustering. Two subtypes of HPV-negative HNSCCs (C1, C2) were identified. Subtype C1 displayed low cell cycle activity, 'hot' tumor microenvironment (TME), earlier N stage, lower pathological grade, better prognosis, and higher response rate to the immunotherapy and targeted therapy. Subtype C2 was associated with higher cell cycle activity, 'cold' TME, later N stage, higher pathological grade, worse prognosis, and lower response rate to the treatment. According to the nearest template prediction method, classification rules were established and verified. Our work explored the molecular mechanism of HPV-negative HNSCCs in the view of cell cycle and might provide new sights for personalized anti-cancer treatment.
Collapse
Affiliation(s)
- Hao Gu
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tingxuan Li
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Narasimha M. Beeraka
- Raghavendra Institute of Pharmaceutical Education and Research (RIPER), Anantapuramu, Andhra Pradesh, India
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Yufei Zheng
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xintan Zhang
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruixia Song
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Runze Zhou
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoyan Wang
- Endocrinology Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Olga Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, Australia
- Department of Hepatology, Royal Adelaide Hospital, SA Health, Adelaide, SA, Australia
| | - Ruitai Fan
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junqi Liu
- Department of Radiation Oncology & Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
15
|
Reed ER, Jankowski SA, Spinella AJ, Noonan V, Haddad R, Nomoto K, Matsui J, Bais MV, Varelas X, Kukuruzinska MA, Monti S. β-catenin/CBP activation of mTORC1 signaling promotes partial epithelial-mesenchymal states in head and neck cancer. Transl Res 2023; 260:46-60. [PMID: 37353110 PMCID: PMC10527608 DOI: 10.1016/j.trsl.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/27/2023] [Accepted: 05/20/2023] [Indexed: 06/25/2023]
Abstract
Head and neck cancers, which include oral squamous cell carcinoma (OSCC) as a major subsite, exhibit cellular plasticity that includes features of an epithelial-mesenchymal transition (EMT), referred to as partial-EMT (p-EMT). To identify molecular mechanisms contributing to OSCC plasticity, we performed a multiphase analysis of single cell RNA sequencing (scRNAseq) data from human OSCC. This included a multiresolution characterization of cancer cell subgroups to identify pathways and cell states that are heterogeneously represented, followed by casual inference analysis to elucidate activating and inhibitory relationships between these pathways and cell states. This approach revealed signaling networks associated with hierarchical cell state transitions, which notably included an association between β-catenin-driven CREB-binding protein (CBP) activity and mTORC1 signaling. This network was associated with subpopulations of cancer cells that were enriched for markers of the p-EMT state and poor patient survival. Functional analyses revealed that β-catenin/CBP induced mTORC1 activity in part through the transcriptional regulation of a raptor-interacting protein, chaperonin containing TCP1 subunit 5 (CCT5). Inhibition of β-catenin-CBP activity through the use of the orally active small molecule, E7386, reduced the expression of CCT5 and mTORC1 activity in vitro, and inhibited p-EMT-associated markers and tumor development in a murine model of OSCC. Our study highlights the use of multiresolution network analyses of scRNAseq data to identify targetable signals for therapeutic benefit, thus defining an underappreciated association between β-catenin/CBP and mTORC1 signaling in head and neck cancer plasticity.
Collapse
Affiliation(s)
- Eric R Reed
- Data Intensive Studies Center, Tufts University, Medford, Massachusetts; Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts; Bioinformatics Program, Boston University, Boston, Massachusetts.
| | - Stacy A Jankowski
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, Massachusetts; Molecular and Translational Medicine Program, Boston University School of Medicine, Boston, Massachusetts
| | - Anthony J Spinella
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts
| | - Vikki Noonan
- Division of Oral Pathology, Boston University School of Dental Medicine, Boston, Massachusetts
| | - Robert Haddad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Junji Matsui
- Eisai Inc, 200 Metro Blvd, Nutley, NJ, 07110, USA
| | - Manish V Bais
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, Massachusetts
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts.
| | - Maria A Kukuruzinska
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, Massachusetts.
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts; Bioinformatics Program, Boston University, Boston, Massachusetts; Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.
| |
Collapse
|
16
|
Long Y, Wu Y, Peng J, Song J, Li N. Pyroptosis-related gene signatures are associated with prognosis and tumor microenvironment infiltration in head and neck cancer. Health Sci Rep 2023; 6:e1622. [PMID: 37841942 PMCID: PMC10568974 DOI: 10.1002/hsr2.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
Background and Aims Recent studies have highlighted the biological significance of pyroptosis in cancer development. Nevertheless, it is still uncertain if pyroptosis also plays a part in immune modulation and the creation of the tumor microenvironment (TME). Methods The pyroptosis regulatory genes (PRGs) were comprehensively assessed in 1938 head and neck cancer samples, and systematically correlated these modification patterns with the infiltration characteristics of TME cells. The unsupervised consensus analysis method was used to identify specific pyroptosis clusters. The single-sample gene set enrichment analysis and CIBERSOFT algorithms were used to evaluate the infiltration levels of various immune cell subsets. A principal component analysis algorithm was used to construct the pyrolysis potential index (PPI) to quantify the pyrolysis regulation patterns in head and neck squamous cell carcinoma (HNSC). Results Pyrophosphate regulatory genes (PRGs) are often upregulated in tumors due to mutations. PRGs relate to various clinical outcomes and pathways. Molecular subtyping identified pyroptosis patterns, which align with three tumor immunophenotypes: immune-inflamed, immune-excluded, and immune-desert. The PPI measures pyrolysis roles, showing higher PPI in tumor samples linked to subtypes and clinical characteristics. Lower PPI correlates with longer survival, increased immune activity, more tumor mutations, high PD-L1 expression, and mutations in significant genes like PIK3CA. Such patients also experience enhanced immune responses in immunotherapy trials. Conclusion We conducted a comprehensive examination of pyroptosis in HNSC and developed a PPI indicator that shows a strong correlation with the variety and intricacy of the TME.
Collapse
Affiliation(s)
- Yan Long
- Department of Medical CosmetologyGuizhou Provincial People's HospitalGuiyangGuizhouChina
| | - Yadong Wu
- Department of Oral and Maxillofacial SurgeryThe Affiliated Stomatological Hospital of Guizhou Medical UniversityGuiyangChina
| | - Juxiang Peng
- Department of OrthodonticsGuiyang Stomatological HospitalGuiyangGuizhouChina
| | - Jukun Song
- Department of Oral and Maxillofacial SurgeryThe Affiliated Stomatological Hospital of Guizhou Medical UniversityGuiyangChina
| | - Na Li
- The Obstetrics and Gynecology DepartmentThe Second Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| |
Collapse
|
17
|
Bill R, Wirapati P, Messemaker M, Roh W, Zitti B, Duval F, Kiss M, Park JC, Saal TM, Hoelzl J, Tarussio D, Benedetti F, Tissot S, Kandalaft L, Varrone M, Ciriello G, McKee TA, Monnier Y, Mermod M, Blaum EM, Gushterova I, Gonye ALK, Hacohen N, Getz G, Mempel TR, Klein AM, Weissleder R, Faquin WC, Sadow PM, Lin D, Pai SI, Sade-Feldman M, Pittet MJ. CXCL9:SPP1 macrophage polarity identifies a network of cellular programs that control human cancers. Science 2023; 381:515-524. [PMID: 37535729 PMCID: PMC10755760 DOI: 10.1126/science.ade2292] [Citation(s) in RCA: 75] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/22/2023] [Indexed: 08/05/2023]
Abstract
Tumor microenvironments (TMEs) influence cancer progression but are complex and often differ between patients. Considering that microenvironment variations may reveal rules governing intratumoral cellular programs and disease outcome, we focused on tumor-to-tumor variation to examine 52 head and neck squamous cell carcinomas. We found that macrophage polarity-defined by CXCL9 and SPP1 (CS) expression but not by conventional M1 and M2 markers-had a noticeably strong prognostic association. CS macrophage polarity also identified a highly coordinated network of either pro- or antitumor variables, which involved each tumor-associated cell type and was spatially organized. We extended these findings to other cancer indications. Overall, these results suggest that, despite their complexity, TMEs coordinate coherent responses that control human cancers and for which CS macrophage polarity is a relevant yet simple variable.
Collapse
Affiliation(s)
- Ruben Bill
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pratyaksha Wirapati
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Marius Messemaker
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Whijae Roh
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Beatrice Zitti
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Florent Duval
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Máté Kiss
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Jong Chul Park
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Talia M Saal
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Jan Hoelzl
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Tarussio
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Oncology, Center for Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Department of Oncology, Center for Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Stéphanie Tissot
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Oncology, Center for Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Lana Kandalaft
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Oncology, Center for Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Marco Varrone
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Giovanni Ciriello
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Thomas A McKee
- Division of Clinical Pathology, Diagnostic Department, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Yan Monnier
- Department of Otorhinolaryngology-Head and Neck Surgery, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Maxime Mermod
- Department of Otorhinolaryngology-Head and Neck Surgery, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Emily M Blaum
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Irena Gushterova
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Anna L K Gonye
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Nir Hacohen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thorsten R Mempel
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Derrick Lin
- Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Sara I Pai
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Moshe Sade-Feldman
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Mikael J Pittet
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Department of Oncology, Geneva University Hospitals (HUG), Geneva, Switzerland
| |
Collapse
|
18
|
Yang Z, Liu F, Li Z, Liu N, Yao X, Zhou Y, Zhang L, Jiang P, Liu H, Kong L, Lang C, Xu X, Jia J, Nakajima T, Gu W, Zheng L, Zhang Z. Histone lysine methyltransferase SMYD3 promotes oral squamous cell carcinoma tumorigenesis via H3K4me3-mediated HMGA2 transcription. Clin Epigenetics 2023; 15:92. [PMID: 37237385 DOI: 10.1186/s13148-023-01506-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Epigenetic dysregulation is essential to the tumorigenesis of oral squamous cell carcinoma (OSCC). SET and MYND domain-containing protein 3 (SMYD3), a histone lysine methyltransferase, is implicated in gene transcription regulation and tumor development. However, the roles of SMYD3 in OSCC initiation are not fully understood. The present study investigated the biological functions and mechanisms involved in the SMYD3-mediated tumorigenesis of OSCC utilizing bioinformatic approaches and validation assays with the aim of informing the development of targeted therapies for OSCC. RESULTS 429 chromatin regulators were screened by a machine learning approach and aberrant expression of SMYD3 was found to be closely associated with OSCC formation and poor prognosis. Data profiling of single-cell and tissue demonstrated that upregulated SMYD3 significantly correlated with aggressive clinicopathological features of OSCC. Alterations in copy number and DNA methylation patterns may contribute to SMYD3 overexpression. Functional experimental results suggested that SMYD3 enhanced cancer cell stemness and proliferation in vitro and tumor growth in vivo. SMYD3 was observed to bind to the High Mobility Group AT-Hook 2 (HMGA2) promoter and elevated tri-methylation of histone H3 lysine 4 at the corresponding site was responsible for transactivating HMGA2. SMYD3 also was positively linked to HMGA2 expression in OSCC samples. Furthermore, treatment with the SMYD3 chemical inhibitor BCI-121 exerted anti-tumor effects. CONCLUSIONS Histone methyltransferase activity and transcription-potentiating function of SMYD3 were found to be essential for tumorigenesis and the SMYD3-HMGA2 is a potential therapeutic target in OSCC.
Collapse
Affiliation(s)
- Zongcheng Yang
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Fen Liu
- Department of Clinical Laboratory, Linyi Central Hospital, Linyi, Shandong, People's Republic of China
| | - Zongkai Li
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Nianping Liu
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Xinfeng Yao
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Yu Zhou
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Liyu Zhang
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Pan Jiang
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Honghong Liu
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Lingming Kong
- Department of General Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Chuandong Lang
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Xin Xu
- Department of Implantology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Oral Tissue Regeneration, Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, People's Republic of China
| | - Jihui Jia
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Takahito Nakajima
- Department of Diagnostic and Interventional Radiology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Wenchao Gu
- Department of Diagnostic and Interventional Radiology, University of Tsukuba, Tsukuba, Ibaraki, Japan.
- Department of Diagnostic Radiology and Nuclear Medicine, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan.
| | - Lixin Zheng
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China.
| | - Zhihong Zhang
- Department of Stomatology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
| |
Collapse
|
19
|
Chaudhary R, Slebos RJ, Noel LC, Song F, Poole MI, Hoening DS, Hernandez-Prera JC, Conejo-Garcia JR, Guevara-Patino JA, Wang X, Xie M, Tan AC, Chung CH. EGFR Inhibition by Cetuximab Modulates Hypoxia and IFN Response Genes in Head and Neck Squamous Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:896-907. [PMID: 37377902 PMCID: PMC10202124 DOI: 10.1158/2767-9764.crc-22-0443] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/01/2023] [Accepted: 05/02/2023] [Indexed: 06/29/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) has one of the most hypoxic and immunosuppressive tumor microenvironments (TME) among solid tumors. However, there is no proven therapeutic strategy to remodel the TME to be less hypoxic and proinflammatory. In this study, we classified tumors according to a Hypoxia-Immune signature, characterized the immune cells in each subgroup, and analyzed the signaling pathways to identify a potential therapeutic target that can remodel the TME. We confirmed that hypoxic tumors had significantly higher numbers of immunosuppressive cells, as evidenced by a lower ratio of CD8+ T cells to FOXP3+ regulatory T cells, compared with nonhypoxic tumors. Patients with hypoxic tumors had worse outcomes after treatment with pembrolizumab or nivolumab, anti-programmed cell death-1 inhibitors. Our expression analysis also indicated that hypoxic tumors predominantly increased the expression of the EGFR and TGFβ pathway genes. Cetuximab, an anti-EGFR inhibitor, decreased the expression of hypoxia signature genes, suggesting that it may alleviate the effects of hypoxia and remodel the TME to become more proinflammatory. Our study provides a rationale for treatment strategies combining EGFR-targeted agents and immunotherapy in the management of hypoxic HNSCC. Significance While the hypoxic and immunosuppressive TME of HNSCC has been well described, comprehensive evaluation of the immune cell components and signaling pathways contributing to immunotherapy resistance has been poorly characterized. We further identified additional molecular determinants and potential therapeutic targets of the hypoxic TME to fully leverage currently available targeted therapies that can be administered with immunotherapy.
Collapse
Affiliation(s)
- Ritu Chaudhary
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Robbert J.C. Slebos
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Leenil C. Noel
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Feifei Song
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Maria I. Poole
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Dirk S. Hoening
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida
| | | | | | | | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Mengyu Xie
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Aik Choon Tan
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Christine H. Chung
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida
| |
Collapse
|
20
|
Boudra R, Patenall BL, King S, Wang D, Best SA, Ko JY, Xu S, Padilla MG, Schmults CD, Barthel SR, Lian CG, Ramsey MR. PRMT1 Inhibition Selectively Targets BNC1-Dependent Proliferation, but not Migration in Squamous Cell Carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.533164. [PMID: 37034732 PMCID: PMC10081292 DOI: 10.1101/2023.03.27.533164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Squamous Cell Carcinoma (SCC) develops in stratified epithelial tissues and demonstrates frequent alterations in transcriptional regulators. We sought to discover SCC-specific transcriptional programs and identified the transcription factor Basonuclin 1 (BNC1) as highly expressed in SCC compared to other tumor types. RNA-seq and ChIP-seq analysis identified pro-proliferative genes activated by BNC1 in SCC cells and keratinocytes. Inhibition of BNC1 in SCC cells suppressed proliferation and increased migration via FRA1. In contrast, BNC1 reduction in keratinocytes caused differentiation, which was abrogated by IRF6 knockdown, leading to increased migration. Protein interactome analysis identified PRMT1 as a co-activator of BNC1-dependent proliferative genes. Inhibition of PRMT1 resulted in a dose-dependent reduction in SCC cell proliferation without increasing migration. Importantly, therapeutic inhibition of PRMT1 in SCC xenografts significantly reduced tumor size, resembling functional effects of BNC1 knockdown. Together, we identify BNC1-PRMT1 as an SCC-lineage specific transcriptional axis that promotes cancer growth, which can be therapeutically targeted to inhibit SCC tumorigenesis.
Collapse
|
21
|
Bai Y, Gotz C, Chincarini G, Zhao Z, Slaney C, Boath J, Furic L, Angel C, Jane SM, Phillips WA, Stacker SA, Farah CS, Darido C. YBX1 integration of oncogenic PI3K/mTOR signalling regulates the fitness of malignant epithelial cells. Nat Commun 2023; 14:1591. [PMID: 36949044 PMCID: PMC10033729 DOI: 10.1038/s41467-023-37161-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
In heterogeneous head and neck cancer (HNC), subtype-specific treatment regimens are currently missing. An integrated analysis of patient HNC subtypes using single-cell sequencing and proteome profiles reveals an epithelial-mesenchymal transition (EMT) signature within the epithelial cancer-cell population. The EMT signature coincides with PI3K/mTOR inactivation in the mesenchymal subtype. Conversely, the signature is suppressed in epithelial cells of the basal subtype which exhibits hyperactive PI3K/mTOR signalling. We further identify YBX1 phosphorylation, downstream of the PI3K/mTOR pathway, restraining basal-like cancer cell proliferation. In contrast, YBX1 acts as a safeguard against the proliferation-to-invasion switch in mesenchymal-like epithelial cancer cells, and its loss accentuates partial-EMT and in vivo invasion. Interestingly, phospho-YBX1 that is mutually exclusive to partial-EMT, emerges as a prognostic marker for overall patient outcomes. These findings create a unique opportunity to sensitise mesenchymal cancer cells to PI3K/mTOR inhibitors by shifting them towards a basal-like subtype as a promising therapeutic approach against HNC.
Collapse
Affiliation(s)
- Yuchen Bai
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Carolin Gotz
- Department of Oral and Maxillofacial Surgery, Technische Universität München, Fakultät für Medizin, Klinikum rechts der Isar, Ismaningerstraße 22, 81675, Munich, Germany
- Department of Oral and Maxillofacial Surgery, Medizinische Universität Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - Ginevra Chincarini
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Zixuan Zhao
- Sun Yat-sen University Cancer Center, Yuexiu District, Guangzhou, Guangdong Province, China
| | - Clare Slaney
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jarryd Boath
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Luc Furic
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Christopher Angel
- Department of Histopathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Stephen M Jane
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Wayne A Phillips
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Steven A Stacker
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Camile S Farah
- Australian Centre for Oral Oncology Research & Education; Fiona Stanley Hospital; Hollywood Private Hospital; Australian Clinical Labs, CQ University, Perth, WA, 6009, Australia
| | - Charbel Darido
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
22
|
Lee RH, Roy R, Li H, Hechmer A, Zhu TR, Izgutdina A, Olshen AB, Johnson DE, Grandis JR. Therapeutic implications of transcriptomics in head and neck cancer patient-derived xenografts. PLoS One 2023; 18:e0282177. [PMID: 36857322 PMCID: PMC9977000 DOI: 10.1371/journal.pone.0282177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/08/2023] [Indexed: 03/02/2023] Open
Abstract
There are currently no clinical strategies utilizing tumor gene expression to inform therapeutic selection for patients with head and neck squamous cell carcinoma (HNSCC). One of the challenges in developing predictive biomarkers is the limited characterization of preclinical HNSCC models. Patient-derived xenografts (PDXs) are increasingly recognized as translationally relevant preclinical avatars for human tumors; however, the overall transcriptomic concordance of HNSCC PDXs with primary human HNSCC is understudied, especially in human papillomavirus-associated (HPV+) disease. Here, we characterized 64 HNSCC PDXs (16 HPV+ and 48 HPV-) at the transcriptomic level using RNA-sequencing. The range of human-specific reads per PDX varied from 64.6%-96.5%, with a comparison of the most differentially expressed genes before and after removal of mouse transcripts revealing no significant benefit to filtering out mouse mRNA reads in this cohort. We demonstrate that four previously established HNSCC molecular subtypes found in The Cancer Genome Atlas (TCGA) are also clearly recapitulated in HNSCC PDXs. Unsupervised hierarchical clustering yielded a striking natural division of HNSCC PDXs by HPV status, with C19orf57 (BRME1), a gene previously correlated with positive response to cisplatin in cervical cancer, among the most significantly differentially expressed genes between HPV+ and HPV- PDXs. In vivo experiments demonstrated a possible relationship between increased C19orf57 expression and superior anti-tumor responses of PDXs to cisplatin, which should be investigated further. These findings highlight the value of PDXs as models for HPV+ and HPV- HNSCC, providing a resource for future discovery of predictive biomarkers to guide treatment selection in HNSCC.
Collapse
Affiliation(s)
- Rex H. Lee
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Hua Li
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Aaron Hechmer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Tian Ran Zhu
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Adila Izgutdina
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Adam B. Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Daniel E. Johnson
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Jennifer R. Grandis
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
23
|
Zhou Z, Tang J, Lu Y, Jia J, Luo T, Su K, Dai X, Zhang H, Liu O. Prognosis-related molecular subtyping in head and neck squamous cell carcinoma patients based on glycolytic/cholesterogenic gene data. Cancer Cell Int 2023; 23:37. [PMID: 36841765 PMCID: PMC9960414 DOI: 10.1186/s12935-023-02880-3] [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: 07/29/2022] [Accepted: 02/19/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) remains an unmet medical challenge. Metabolic reprogramming is a hallmark of diverse cancers, including HNSCC. METHODS We investigated the metabolic profile in HNSCC by using The Cancer Genome Atlas (TCGA) (n = 481) and Gene Expression Omnibus (GEO) (n = 97) databases. The metabolic stratification of HNSCC samples was identified by using unsupervised k-means clustering. We analyzed the correlations of the metabolic subtypes in HNSCC with featured genomic alterations and known HNSCC subtypes. We further validated the metabolism-related subtypes based on features of ENO1, PFKFB3, NSDHL and SQLE expression in HNSCC by Immunohistochemistry. In addition, genomic characteristics of tumor metabolism that varied among different cancer types were confirmed. RESULTS Based on the median expression of coexpressed cholesterogenic and glycolytic genes, HNSCC subtypes were identified, including glycolytic, cholesterogenic, quiescent and mixed subtypes. The quiescent subtype was associated with the longest survival and was distributed in stage I and G1 HNSCC. Mutation analysis of HNSCC genes indicated that TP53 has the highest mutation frequency. The CDKN2A mutation frequency has the most significant differences amongst these four subtypes. There is good overlap between our metabolic subtypes and the HNSCC subtype. CONCLUSION The four metabolic subtypes were successfully determined in HNSCC. Compared to the quiescent subtype, glycolytic, cholesterogenic and mixed subtypes had significantly worse outcome, which might offer guidelines for developing a novel treatment strategy for HNSCC.
Collapse
Affiliation(s)
- Zekun Zhou
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, 410008 Hunan China
| | - Jianfei Tang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, 410008 Hunan China
| | - Yixuan Lu
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, 410008 Hunan China
| | - Jia Jia
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, 410008 Hunan China
| | - Tiao Luo
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, 410008 Hunan China
| | - Kaixin Su
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, 410008 Hunan China
| | - Xiaohan Dai
- Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, 410008, Hunan, China.
| | - Haixia Zhang
- The Oncology Department of Xiangya Second Hospital, Central South University, Changsha, 410011, Hunan, China.
| | - Ousheng Liu
- Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha, 410008, Hunan, China.
| |
Collapse
|
24
|
Zhang T, Kutler D, Scognamiglio T, Gudas LJ, Tang XH. Transcriptomic analysis predicts the risk of progression of premalignant lesions in human tongue. Discov Oncol 2023; 14:24. [PMID: 36820942 PMCID: PMC9950315 DOI: 10.1007/s12672-023-00629-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/12/2023] [Indexed: 02/24/2023] Open
Abstract
The 5-year survival rate for patients with oral squamous cell carcinomas (SCC), including tongue SCC, has not significantly improved over the last several decades. Oral potentially malignant disorders (OPMD), including oral dysplasias, are oral epithelial disorders that can develop into oral SCCs. To identify molecular characteristics that might predict conversion of OPMDs to SCCs and guide treatment plans, we performed global transcriptomic analysis of human tongue OPMD (n = 9) and tongue SCC (n = 11) samples with paired normal margin tissue from patients treated at Weill Cornell Medicine. Compared to margin tissue, SCCs showed more transcript changes than OPMDs. OPMDs and SCCs shared some altered transcripts, but these changes were generally greater in SCCs than OPMDs. Both OPMDs and SCCs showed altered signaling pathways related to cell migration, basement membrane disruption, and metastasis. We suggest that OPMDs are on the path toward malignant transformation. Based on patterns of gene expression, both OPMD and tongue SCC samples can be categorized into subclasses (mesenchymal, classical, basal, and atypical) similar to those seen in human head and neck SCC (HNSCC). These subclasses of OPMDs have the potential to be used to stratify patient prognoses and therapeutic options for tongue OPMDs. Lastly, we identified a gene set (ELF5; RPTN; IGSF10; CRMP1; HTR3A) whose transcript changes have the power to classify OPMDs and SCCs and developed a Firth logistic regression model using the changes in these transcripts relative to paired normal tissue to validate pathological diagnosis and potentially predict the likelihood of an OPMD developing into SCC, as data sets become available.
Collapse
Affiliation(s)
- Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - David Kutler
- Division of Head and Neck Surgery in the Department of Otolaryngology at New York Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, 10065, USA
| | - Theresa Scognamiglio
- Division of Anatomic Pathology, New York Presbyterian Hospital, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY, 10065, USA.
| | - Xiao-Han Tang
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY, 10065, USA.
| |
Collapse
|
25
|
Dhara V, Shetty SS, de Arruda JAA, Silva TA, Russo RC, Shetty NJ, Pidaparthi M, Wollenberg B, Rao VUS, Gopinath TPS. Decoding the influence of the immune system and immunotherapy targets on carcinomas: A hidden prism in oral cancer therapy. Dis Mon 2023; 69:101353. [PMID: 35311656 DOI: 10.1016/j.disamonth.2022.101353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In recent decades, understanding tumorigenesis and the complex interaction between the host and the immune system has been the pillar for significant advances in anticancer therapy. Conventional anticancer therapy (e.g., cut, burn, and cytotoxic drugs) involves multiple targeting of tumor cells. However, the tumor tissue microenvironment can present a dysregulated, stimulating, or subverted immune response which, in turn, reveals pro-tumor activities favoring tumor expansion and progression. Recently, new potential targets have been identified based on immunomodulatory therapies, which are crafted to re-establish the host anti-tumoral immune response. Clinicians should fully understand the intricate interactions between carcinogens, the tumor milieu, the immune system, and traditional anticancer therapies in order to progress and to overcome the refractory/recurrent challenges and morbidity of the disease. Thus, in this article, we highlight the complex milieu of the oral cancer immune response, pointing out potential therapeutic immunotargets for oral squamous cell carcinomas. The impact of traditional anticancer therapy on the immune system is also outlined.
Collapse
Affiliation(s)
- Vasantha Dhara
- Consultant Maxillofacial Surgeon, Hyderabad, Telangana, India
| | - Sameep S Shetty
- Department of Oral and Maxillofacial Surgery, Manipal College of Dental Sciences, Mangalore, Manipal Academy of Higher Education, A constituent of MAHE, Manipal, Karnataka, India.
| | - José Alcides Almeida de Arruda
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Tarcília Aparecida Silva
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Remo Castro Russo
- Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Neetha J Shetty
- Department of Periodontology, Manipal College of Dental Sciences, Mangalore, Manipal Academy of Higher Education, A constituent of MAHE, Mangalore, Karnataka, India
| | | | - Barbara Wollenberg
- Klinik für Hals-, Nasen- und Ohrenheilkunde, Klinikum rechts der Isar der TU München, Ismaningerstraße 22, 81675 München, Germany
| | - Vishal U S Rao
- Department of Head and Neck Surgical Oncology, HealthCare Global Enterprises Ltd., Bangalore, Karnataka, India
| | - Thilak P S Gopinath
- Nitte (Deemed to be University) , AB Shetty Memorial Institute of Dental Sciences (ABSMIDS) , Department of Oral and Maxillofacial Surgery, Mangalore, India
| |
Collapse
|
26
|
Gopal P, Petty A, Rogacki K, Bera T, Bareja R, Peacock CD, Abazeed ME. Multivalent state transitions shape the intratumoral composition of small cell lung carcinoma. SCIENCE ADVANCES 2022; 8:eabp8674. [PMID: 36516249 PMCID: PMC9750150 DOI: 10.1126/sciadv.abp8674] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Studies to date have not resolved how diverse transcriptional programs contribute to the intratumoral heterogeneity of small cell lung carcinoma (SCLC), an aggressive tumor associated with a dismal prognosis. Here, we identify distinct and commutable transcriptional states that confer discrete functional attributes in individual SCLC tumors. We combine an integrative approach comprising the transcriptomes of 52,975 single cells, high-resolution measurement of cell state dynamics at the single-cell level, and functional and correlative studies using treatment naïve xenografts with associated clinical outcomes. We show that individual SCLC tumors contain distinctive proportions of stable cellular states that are governed by bidirectional cell state transitions. Using drugs that target the epigenome, we reconfigure tumor state composition in part by altering individual state transition rates. Our results reveal new insights into how single-cell transition behaviors promote cell state equilibrium in SCLC and suggest that facile plasticity underlies its resistance to therapy and lethality.
Collapse
Affiliation(s)
- Priyanka Gopal
- Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, 251 E. Huron St., Galter Pavilion LC-178, Chicago, IL 60611, USA
| | - Aaron Petty
- Department of Translational Hematology Oncology Research, Cleveland Clinic, 2111 East 96th St./NE-6, Cleveland, OH 44195, USA
| | - Kevin Rogacki
- Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, 251 E. Huron St., Galter Pavilion LC-178, Chicago, IL 60611, USA
| | - Titas Bera
- Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, 251 E. Huron St., Galter Pavilion LC-178, Chicago, IL 60611, USA
| | - Rohan Bareja
- Institute for Computational Biomedicine, Weill Cornell Medicine, 1305 York Ave., New York, NY 10021, USA
| | - Craig D. Peacock
- Department of Genetics and Genome Sciences, Case Western Reserve University, 2109 Adelbert Road, Biomedical Research Building 647B, Cleveland, OH 44106, USA
| | - Mohamed E. Abazeed
- Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, 251 E. Huron St., Galter Pavilion LC-178, Chicago, IL 60611, USA
- Robert H. Lurie Cancer Center, Northwestern University, 303 E. Superior St./Lurie 7, Chicago, IL 60611, USA
| |
Collapse
|
27
|
Chen X, Chen L, Kürten CHL, Jabbari F, Vujanovic L, Ding Y, Lu B, Lu K, Kulkarni A, Tabib T, Lafyatis R, Cooper GF, Ferris R, Lu X. An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors. PLoS Comput Biol 2022; 18:e1010761. [PMID: 36548438 PMCID: PMC9822106 DOI: 10.1371/journal.pcbi.1010761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 01/06/2023] [Accepted: 11/26/2022] [Indexed: 12/24/2022] Open
Abstract
Cells within a tumor microenvironment (TME) dynamically communicate and influence each other's cellular states through an intercellular communication network (ICN). In cancers, intercellular communications underlie immune evasion mechanisms of individual tumors. We developed an individualized causal analysis framework for discovering tumor specific ICNs. Using head and neck squamous cell carcinoma (HNSCC) tumors as a testbed, we first mined single-cell RNA-sequencing data to discover gene expression modules (GEMs) that reflect the states of transcriptomic processes within tumor and stromal single cells. By deconvoluting bulk transcriptomes of HNSCC tumors profiled by The Cancer Genome Atlas (TCGA), we estimated the activation states of these transcriptomic processes in individual tumors. Finally, we applied individualized causal network learning to discover an ICN within each tumor. Our results show that cellular states of cells in TMEs are coordinated through ICNs that enable multi-way communications among epithelial, fibroblast, endothelial, and immune cells. Further analyses of individual ICNs revealed structural patterns that were shared across subsets of tumors, leading to the discovery of 4 different subtypes of networks that underlie disparate TMEs of HNSCC. Patients with distinct TMEs exhibited significantly different clinical outcomes. Our results show that the capability of estimating individual ICNs reveals heterogeneity of ICNs and sheds light on the importance of intercellular communication in impacting disease development and progression.
Collapse
Affiliation(s)
- Xueer Chen
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Causal Discovery, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
| | - Lujia Chen
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Causal Discovery, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
| | - Cornelius H. L. Kürten
- Department of Otolaryngology, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
- University of Pittsburgh Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, University Duisburg-Essen, Duisburg, Germany
| | - Fattaneh Jabbari
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Causal Discovery, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
| | - Lazar Vujanovic
- Department of Otolaryngology, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
- University of Pittsburgh Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
| | - Binfeng Lu
- Department of Immunology, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
| | - Kevin Lu
- Williamsville North High School, Williamsville, New York, United States of America
| | - Aditi Kulkarni
- Department of Otolaryngology, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
| | - Tracy Tabib
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, University Duisburg-Essen, Duisburg, Germany
| | - Robert Lafyatis
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, University Duisburg-Essen, Duisburg, Germany
| | - Gregory F. Cooper
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Causal Discovery, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
- University of Pittsburgh Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robert Ferris
- Department of Otolaryngology, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
- University of Pittsburgh Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Causal Discovery, University of Pittsburgh, Pennsylvania, Pittsburgh, United States of America
- University of Pittsburgh Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| |
Collapse
|
28
|
Mezi S, Pomati G, Zizzari IG, Di Filippo A, Cerbelli B, Cirillo A, Fiscon G, Amirhassankhani S, Valentini V, De Vincentiis M, Corsi A, Di Gioia C, Tombolini V, Della Rocca C, Polimeni A, Nuti M, Marchetti P, Botticelli A. Genomic and Immune Approach in Platinum Refractory HPV-Negative Head and Neck Squamous Cell Carcinoma Patients Treated with Immunotherapy: A Novel Combined Profile. Biomedicines 2022; 10:biomedicines10112732. [PMID: 36359251 PMCID: PMC9687656 DOI: 10.3390/biomedicines10112732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 12/05/2022] Open
Abstract
Introduction: Only a minority of patients with platinum refractory head and neck squamous cell carcinoma (PR/HNSCC) gain some lasting benefit from immunotherapy. Methods: The combined role of the comprehensive genomic (through the FoundationOne Cdx test) and immune profiles of 10 PR/HNSCC patients treated with the anti-PD-1 nivolumab was evaluated. The immune profiles were studied both at baseline and at the second cycle of immunotherapy, weighing 20 circulating cytokines/chemokines, adhesion molecules, and 14 soluble immune checkpoints dosed through a multiplex assay. A connectivity map was obtained by calculating the Spearman correlation between the expression profiles of circulating molecules. Results: Early progression occurred in five patients, each of them showing TP53 alteration and three of them showing a mutation/loss/amplification of genes involved in the cyclin-dependent kinase pathway. In addition, ERB2 amplification (1 patient), BRCA1 mutation (1 patient), and NOTCH1 genes alteration (3 patients) occurred. Five patients achieved either stable disease or partial response. Four of them carried mutations in PI3K/AKT/PTEN pathways. In the only two patients, with a long response to immunotherapy, the tumor mutational burden (TMB) was high. Moreover, a distinct signature, in terms of network connectivity of the circulating soluble molecules, characterizing responder and non-responder patients, was evidenced. Moreover, a strong negative and statistically significant (p-value ≤ 0.05) correlation with alive status was evidenced for sE-selectin at T1. Conclusions: Our results highlighted the complexity and heterogeneity of HNSCCs, even though it was in a small cohort. Molecular and immune approaches, combined in a single profile, could represent a promising strategy, in the context of precision immunotherapy.
Collapse
Affiliation(s)
- Silvia Mezi
- Department of Radiological, Oncological and Pathological Science, “Sapienza” University of Rome, 00161 Rome, Italy
- Correspondence: (S.M.); (G.P.)
| | - Giulia Pomati
- Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy
- Correspondence: (S.M.); (G.P.)
| | - Ilaria Grazia Zizzari
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Alessandra Di Filippo
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Bruna Cerbelli
- Department of Radiological, Oncological and Pathological Science, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Alessio Cirillo
- Department of Radiological, Oncological and Pathological Science, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Giulia Fiscon
- Department of Computer, Control, and Management Engineering “Antonio Ruberti”, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Sasan Amirhassankhani
- Department of Urology, S. Orsola-Malpighi Hospital University of Bologna, Via Palagi 9, 40138 Bologna, Italy
| | - Valentino Valentini
- Department of Oral and Maxillo-Facial Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Marco De Vincentiis
- Department of Oral and Maxillo-Facial Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Alessandro Corsi
- Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Cira Di Gioia
- Department of Radiological, Oncological and Pathological Science, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Vincenzo Tombolini
- Department of Radiological, Oncological and Pathological Science, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Carlo Della Rocca
- Department of Medico-Surgical Sciences and Biotechnology, Polo Pontino, “Sapienza” University of Rome, 04100 Latina, Italy
| | - Antonella Polimeni
- Department of Oral and Maxillo-Facial Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Marianna Nuti
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Paolo Marchetti
- IDI-IRCCS Istituto Dermopatico Dell’Immacolata, 00167 Rome, Italy
| | - Andrea Botticelli
- Department of Radiological, Oncological and Pathological Science, “Sapienza” University of Rome, 00161 Rome, Italy
| |
Collapse
|
29
|
Schinke H, Shi E, Lin Z, Quadt T, Kranz G, Zhou J, Wang H, Hess J, Heuer S, Belka C, Zitzelsberger H, Schumacher U, Genduso S, Riecken K, Gao Y, Wu Z, Reichel CA, Walz C, Canis M, Unger K, Baumeister P, Pan M, Gires O. A transcriptomic map of EGFR-induced epithelial-to-mesenchymal transition identifies prognostic and therapeutic targets for head and neck cancer. Mol Cancer 2022; 21:178. [PMID: 36076232 PMCID: PMC9454230 DOI: 10.1186/s12943-022-01646-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/24/2022] [Indexed: 01/05/2023] Open
Abstract
Background Epidermal growth factor receptor (EGFR) is both a driver oncogene and a therapeutic target in advanced head and neck squamous cell carcinoma (HNSCC). However, response to EGFR treatment is inconsistent and lacks markers for treatment prediction. This study investigated EGFR-induced epithelial-to-mesenchymal transition (EMT) as a central parameter in tumor progression and identified novel prognostic and therapeutic targets, and a candidate predictive marker for EGFR therapy response. Methods Transcriptomic profiles were analyzed by RNA sequencing (RNA-seq) following EGFR-mediated EMT in responsive human HNSCC cell lines. Exclusive genes were extracted via differentially expressed genes (DEGs) and a risk score was determined through forward feature selection and Cox regression models in HNSCC cohorts. Functional characterization of selected prognostic genes was conducted in 2D and 3D cellular models, and findings were validated by immunohistochemistry in primary HNSCC. Results An EGFR-mediated EMT gene signature composed of n = 171 genes was identified in responsive cell lines and transferred to the TCGA-HNSCC cohort. A 5-gene risk score comprising DDIT4, FADD, ITGB4, NCEH1, and TIMP1 prognosticated overall survival (OS) in TCGA and was confirmed in independent HNSCC cohorts. The EGFR-mediated EMT signature was distinct from EMT hallmark and partial EMT (pEMT) meta-programs with a differing enrichment pattern in single malignant cells. Molecular characterization showed that ITGB4 was upregulated in primary tumors and metastases compared to normal mucosa and correlated with EGFR/MAPK activity in tumor bulk and single malignant cells. Preferential localization of ITGB4 together with its ligand laminin 5 at tumor-stroma interfaces correlated with increased tumor budding in primary HNSCC tissue sections. In vitro, ITGB4 knock-down reduced EGFR-mediated migration and invasion and ITGB4-antagonizing antibody ASC8 impaired 2D and 3D invasion. Furthermore, a logistic regression model defined ITGB4 as a predictive marker of progression-free survival in response to Cetuximab in recurrent metastatic HNSCC patients. Conclusions EGFR-mediated EMT conveyed through MAPK activation contributes to HNSCC progression upon induction of migration and invasion. A 5-gene risk score based on a novel EGFR-mediated EMT signature prognosticated survival of HNSCC patients and determined ITGB4 as potential therapeutic and predictive target in patients with strong EGFR-mediated EMT. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01646-1.
Collapse
Affiliation(s)
- Henrik Schinke
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Enxian Shi
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Zhongyang Lin
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Tanja Quadt
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Gisela Kranz
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Jiefu Zhou
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Hongxia Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, China
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Steffen Heuer
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Claus Belka
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Sandra Genduso
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Yujing Gao
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Zhengquan Wu
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Christoph A Reichel
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Philipp Baumeister
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Min Pan
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany. .,Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China.
| | - Olivier Gires
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University, Munich, Marchioninistr. 15, 81377, Munich, Germany. .,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.
| |
Collapse
|
30
|
Gu Z, Yao Y, Yang G, Zhu G, Tian Z, Wang R, Wu Q, Wang Y, Wu Y, Chen L, Wang C, Gao J, Kang X, Zhang J, Wang L, Duan S, Zhao Z, Zhang Z, Sun S. Pharmacogenomic landscape of head and neck squamous cell carcinoma informs precision oncology therapy. Sci Transl Med 2022; 14:eabo5987. [PMID: 36070368 DOI: 10.1126/scitranslmed.abo5987] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common and frequently lethal cancer with few therapeutic options. In particular, there are few effective targeted therapies. Development of highly effective therapeutic strategies tailored to patients with HNSCC remains a pressing challenge. To address this, we present a pharmacogenomic study to facilitate precision treatments for patients with HNSCC. We established a large collection of 56 HNSCC patient-derived cells (PDCs), which recapitulated the molecular features of the original tumors. Pharmacological assessment of HNSCCs was conducted using a three-tiered high-throughput drug screening using 2248 compounds across these PDC models and an additional 18 immortalized cell lines. We integrated genomic, transcriptomic, and pharmacological analysis to predict biomarkers, gene-drug associations, and validated biomarkers. These results supported drug repurposing for multiple HNSCC subtypes, including the JAK2 inhibitor fedratinib, for low KRT18-expressing HNSCC cases, and the topoisomerase inhibitor mitoxantrone, for IL6R-activated HNSCC cases. Our results demonstrated concordance between susceptibility predictions from the PDCs and the matched patients' responses to standard clinical medication. Moreover, we identified and experimentally confirmed that high expression of ITGB1 elicited therapeutic resistance to docetaxel and high SOD1 expression conferred resistance to afatinib. We further validated ITGB1 as a predictive biomarker for the efficacy of docetaxel therapy in a phase 2 clinical trial. In summary, our study shows that this HNSCC cell resource, as well as the resulting pharmacogenomic profiles, is effective for biomarker discovery and for guiding precision oncology therapies in HNSCCs.
Collapse
Affiliation(s)
- Ziyue Gu
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Yanli Yao
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Guizhu Yang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Guopei Zhu
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.,Department of Oral and Maxillofacial-Head Neck Oncology, Division of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Zhen Tian
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.,Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Rui Wang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Qi Wu
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Yujue Wang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Yaping Wu
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Lan Chen
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Chong Wang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Jiamin Gao
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Xindan Kang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Jie Zhang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Lizhen Wang
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.,Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Shengzhong Duan
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.,Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics and School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Zhiyuan Zhang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Shuyang Sun
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| |
Collapse
|
31
|
Mayhew GM, Uronis JM, Hayes DN, Zevallos JP. Mesenchymal gene expression subtyping analysis for early-stage human papillomavirus-negative head and neck squamous cell carcinoma reveals prognostic and predictive applications. Front Oncol 2022; 12:954037. [PMID: 36147910 PMCID: PMC9486405 DOI: 10.3389/fonc.2022.954037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with oral cavity squamous cell carcinoma (OCSCC) are predominantly human papillomavirus (HPV)(−), and treatment typically involves surgical resection ± neck dissection, followed by radiation ± chemotherapy. We previously described four mRNA expression patterns (classical, atypical, basal, and mesenchymal), each with unique genomic features and prognosis. Here, we examine the clinical utility of gene expression subtyping in head and neck squamous cell carcinoma (HNSCC) and introduce potentially predictive applications in HPV(−) OCSCC. A retrospective genomic database analysis was performed including 562 HNSCC patients from MD Anderson (MDA-GSE41116) and The Cancer Genome Atlas (TCGA). Samples were assigned molecular subtypes (classical, atypical, basal, and mesenchymal) using an 88-gene classifier. HPV status was determined by gene expression. The clinical endpoint was overall survival censured at 36 months. The Kaplan–Meier plots and log-rank tests were used to investigate associations between clinical variables and survival. Of the 418 TCGA training patients who met analysis criteria, nearly 20% presented as stage I/II. Among node(−) OCSCC patients, the mesenchymal subtype is associated with worse survival (hazard ratio (HR) = 2.4, p = 0.021), offering a potentially actionable biomarker in otherwise early-stage, low-risk disease. This was confirmed in the MDA validation cohort. Node(−) non-mesenchymal OCSCC patients had far better survival compared to node(−) mesenchymal, and all node(+) patients had similarly poor survival. These findings suggest that the mesenchymal subtype is associated with poor survival in surgically resected, early-stage, node(−) OCSCC otherwise expected to have favorable outcomes. These findings highlight the potential value of gene expression subtyping as a pathology adjunct for prognostication and treatment decision-making in OCSCC patients.
Collapse
Affiliation(s)
- Gregory M. Mayhew
- Department of Bioinformatics and Biostatstics, GeneCentric Therapeutics Inc., Durham, NC, United States
| | - Joshua M. Uronis
- Department of Genomics Sequencing Operations, GeneCentric Therapeutics Inc., Durham, NC, United States
| | - David Neil Hayes
- Department of Medical Oncology, University of Tennessee Health Sciences West Cancer Center, Memphis, TN, United States
| | - Jose P. Zevallos
- Department of Otolaryngology-Head and Neck Surgery , Washington University School of Medicine in St. Louis, MO, United States
- *Correspondence: Jose P. Zevallos,
| |
Collapse
|
32
|
Jing L, Du Y, Fu D. Characterization of tumor immune microenvironment and cancer therapy for head and neck squamous cell carcinoma through identification of a genomic instability-related lncRNA prognostic signature. Front Genet 2022; 13:979575. [PMID: 36105083 PMCID: PMC9465021 DOI: 10.3389/fgene.2022.979575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) represents one of the most prevalent and malignant tumors of epithelial origins with unfavorable outcomes. Increasing evidence has shown that dysregulated long non-coding RNAs (lncRNAs) correlate with tumorigenesis and genomic instability (GI), while the roles of GI-related lncRNAs in the tumor immune microenvironment (TIME) and predicting cancer therapy are still yet to be clarified. In this study, transcriptome and somatic mutation profiles with clinical parameters were obtained from the TCGA database. Patients were classified into GI-like and genomic stable (GS)-like groups according to the top 25% and bottom 25% cumulative counts of somatic mutations. Differentially expressed lncRNAs (DElncRNAs) between GI- and GS-like groups were identified as GI-related lncRNAs. These lncRNA-related coding genes were enriched in cancer-related KEGG pathways. Patients totaling 499 with clinical information were randomly divided into the training and validation sets. A total of 18 DElncRNAs screened by univariate Cox regression analysis were associated with overall survival (OS) in the training set. A GI-related lncRNA signature that comprised 10 DElncRNAs was generated through least absolute shrinkage and selection operator (Lasso)-Cox regression analysis. Patients in the high-risk group have significantly decreased OS vs. patients in the low-risk group, which was verified in internal validation and entire HNSCC sets. Integrated HNSCC sets from GEO confirmed the notable survival stratification of the signature. The time-dependent receiver operating characteristic curve demonstrated that the signature was reliable. In addition, the signature retained a strong performance of OS prediction for patients with various clinicopathological features. Cell composition analysis showed high anti-tumor immunity in the low-risk group which was evidenced by increased infiltrating CD8+ T cells and natural killer cells and reduced cancer-associated fibroblasts, which was convinced by immune signatures analysis via ssGSEA algorithm. T helper/IFNγ signaling, co-stimulatory, and co-inhibitory signatures showed increased expression in the low-risk group. Low-risk patients were predicted to be beneficial to immunotherapy, which was confirmed by patients with progressive disease who had high risk scores vs. complete remission patients. Furthermore, the drugs that might be sensitive to HNSCC were identified. In summary, the novel prognostic GILncRNA signature provided a promising approach for characterizing the TIME and predicting therapeutic strategies for HNSCC patients.
Collapse
Affiliation(s)
- Lijun Jing
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Denggang Fu,
| | - Yabing Du
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Denggang Fu,
| | - Denggang Fu
- School of Medicine, Indiana University, Indianapolis, IN, United States
- *Correspondence: Denggang Fu,
| |
Collapse
|
33
|
Callahan SC, Kochat V, Liu Z, Raman AT, Divenko M, Schulz J, Terranova CJ, Ghosh AK, Tang M, Johnson FM, Wang J, Skinner HD, Pickering CR, Myers JN, Rai K. High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma. Front Cell Dev Biol 2022; 10:936168. [PMID: 35927986 PMCID: PMC9343809 DOI: 10.3389/fcell.2022.936168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with significant mortality and frequent recurrence. Prior efforts to transcriptionally classify HNSCC into groups of varying prognoses have identified four accepted molecular subtypes of the disease: Atypical (AT), Basal (BA), Classical (CL), and Mesenchymal (MS). Here, we investigate the active enhancer landscapes of these subtypes using representative HNSCC cell lines and identify samples belonging to the AT subtype as having increased enhancer activity compared to the other 3 HNSCC subtypes. Cell lines belonging to the AT subtype are more resistant to enhancer-blocking bromodomain inhibitors (BETi). Examination of nascent transcripts reveals that both AT TCGA tumors and cell lines express higher levels of enhancer RNA (eRNA) transcripts for enhancers controlling BETi resistance pathways, such as lipid metabolism and MAPK signaling. Additionally, investigation of higher-order chromatin structure suggests more enhancer-promoter (E-P) contacts in the AT subtype, including on genes identified in the eRNA analysis. Consistently, known BETi resistance pathways are upregulated upon exposure to these inhibitors. Together, our results identify that the AT subtype of HNSCC is associated with higher enhancer activity, resistance to enhancer blockade, and increased signaling through pathways that could serve as future targets for sensitizing HNSCC to BET inhibition.
Collapse
Affiliation(s)
- S. Carson Callahan
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Veena Kochat
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Zhiyi Liu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ayush T. Raman
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Graduate Program in Quantitative Sciences, Baylor College of Medicine, Houston, TX, United States
- Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Margarita Divenko
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jonathan Schulz
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Christopher J. Terranova
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Archit K. Ghosh
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ming Tang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Faye M. Johnson
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jing Wang
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Heath D Skinner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | - Curtis R. Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Jeffrey N. Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
| |
Collapse
|
34
|
Bard JE, Nowak NJ, Buck MJ, Sinha S. Multimodal Dimension Reduction and Subtype Classification of Head and Neck Squamous Cell Tumors. Front Oncol 2022; 12:892207. [PMID: 35912202 PMCID: PMC9326399 DOI: 10.3389/fonc.2022.892207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/09/2022] [Indexed: 01/18/2023] Open
Abstract
Traditional analysis of genomic data from bulk sequencing experiments seek to group and compare sample cohorts into biologically meaningful groups. To accomplish this task, large scale databases of patient-derived samples, like that of TCGA, have been established, giving the ability to interrogate multiple data modalities per tumor. We have developed a computational strategy employing multimodal integration paired with spectral clustering and modern dimension reduction techniques such as PHATE to provide a more robust method for cancer sub-type classification. Using this integrated approach, we have examined 514 Head and Neck Squamous Carcinoma (HNSC) tumor samples from TCGA across gene-expression, DNA-methylation, and microbiome data modalities. We show that these approaches, primarily developed for single-cell sequencing can be efficiently applied to bulk tumor sequencing data. Our multimodal analysis captures the dynamic heterogeneity, identifies new and refines subtypes of HNSC, and orders tumor samples along well-defined cellular trajectories. Collectively, these results showcase the inherent molecular complexity of tumors and offer insights into carcinogenesis and importance of targeted therapy. Computational techniques as highlighted in our study provide an organic and powerful approach to identify granular patterns in large and noisy datasets that may otherwise be overlooked.
Collapse
Affiliation(s)
- Jonathan E. Bard
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States,Genomics and Bioinformatics Core, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Norma J. Nowak
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States,Genomics and Bioinformatics Core, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Michael J. Buck
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States,Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States,*Correspondence: Michael J. Buck, ; Satrajit Sinha,
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States,*Correspondence: Michael J. Buck, ; Satrajit Sinha,
| |
Collapse
|
35
|
Ni Y, Low JT, Silke J, O’Reilly LA. Digesting the Role of JAK-STAT and Cytokine Signaling in Oral and Gastric Cancers. Front Immunol 2022; 13:835997. [PMID: 35844493 PMCID: PMC9277720 DOI: 10.3389/fimmu.2022.835997] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/16/2022] [Indexed: 12/12/2022] Open
Abstract
When small proteins such as cytokines bind to their associated receptors on the plasma membrane, they can activate multiple internal signaling cascades allowing information from one cell to affect another. Frequently the signaling cascade leads to a change in gene expression that can affect cell functions such as proliferation, differentiation and homeostasis. The Janus kinase-signal transducer and activator of transcription (JAK-STAT) and the tumor necrosis factor receptor (TNFR) are the pivotal mechanisms employed for such communication. When deregulated, the JAK-STAT and the TNF receptor signaling pathways can induce chronic inflammatory phenotypes by promoting more cytokine production. Furthermore, these signaling pathways can promote replication, survival and metastasis of cancer cells. This review will summarize the essentials of the JAK/STAT and TNF signaling pathways and their regulation and the molecular mechanisms that lead to the dysregulation of the JAK-STAT pathway. The consequences of dysregulation, as ascertained from founding work in haematopoietic malignancies to more recent research in solid oral-gastrointestinal cancers, will also be discussed. Finally, this review will highlight the development and future of therapeutic applications which modulate the JAK-STAT or the TNF signaling pathways in cancers.
Collapse
Affiliation(s)
- Yanhong Ni
- Central Laboratory, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jun T. Low
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - John Silke
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lorraine A. O’Reilly
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
36
|
Glathar AR, Oyelakin A, Gluck C, Bard J, Sinha S. p63 Directs Subtype-Specific Gene Expression in HPV+ Head and Neck Squamous Cell Carcinoma. Front Oncol 2022; 12:879054. [PMID: 35712470 PMCID: PMC9192977 DOI: 10.3389/fonc.2022.879054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/19/2022] [Indexed: 11/22/2022] Open
Abstract
The complex heterogeneity of head and neck squamous cell carcinoma (HNSCC) reflects a diverse underlying etiology. This heterogeneity is also apparent within Human Papillomavirus-positive (HPV+) HNSCC subtypes, which have distinct gene expression profiles and patient outcomes. One aggressive HPV+ HNSCC subtype is characterized by elevated expression of genes involved in keratinization, a process regulated by the oncogenic transcription factor ΔNp63. Furthermore, the human TP63 gene locus is a frequent HPV integration site and HPV oncoproteins drive ΔNp63 expression, suggesting an unexplored functional link between ΔNp63 and HPV+ HNSCC. Here we show that HPV+ HNSCCs can be molecularly stratified according to ΔNp63 expression levels and derive a ΔNp63-associated gene signature profile for such tumors. We leveraged RNA-seq data from p63 knockdown cells and ChIP-seq data for p63 and histone marks from two ΔNp63high HPV+ HNSCC cell lines to identify an epigenetically refined ΔNp63 cistrome. Our integrated analyses reveal crucial ΔNp63-bound super-enhancers likely to mediate HPV+ HNSCC subtype-specific gene expression that is anchored, in part, by the PI3K-mTOR pathway. These findings implicate ΔNp63 as a key regulator of essential oncogenic pathways in a subtype of HPV+ HNSCC that can be exploited as a biomarker for patient stratification and treatment choices.
Collapse
|
37
|
Huang Y, Liu H, Liu X, Li N, Bai H, Guo C, Xu T, Zhu L, Liu C, Xiao J. The Chemokines Initiating and Maintaining Immune Hot Phenotype Are Prognostic in ICB of HNSCC. Front Genet 2022; 13:820065. [PMID: 35692828 PMCID: PMC9186378 DOI: 10.3389/fgene.2022.820065] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The immune checkpoint blockade (ICB) with anti-programmed cell death protein 1(PD-1) on HNSCC is not as effective as on other tumors. In this study, we try to find out the key factors in the heterogeneous tumor-associated monocyte/macrophage (TAMM) that could regulate immune responses and predict the validity of ICB on HNSCC.Experimental Design: To explore the correlation of the TAMM heterogeneity with the immune properties and prognosis of HNSCC, we established the differentiation trajectory of TAMM by analyzing the single-cell RNA-seq data of HNSCC, by which the HNSCC patients were divided into different sub-populations. Then, we exploited the topology of the network to screen out the genes critical for immune hot phenotype of HNSCC, as well as their roles in TAMM differentiation, tumor immune cycle, and progression. Finally, these key genes were used to construct a neural net model via deep-learning framework to predict the validity of treatment with anti-PD-1/PDL-1Results: According to the differentiation trajectory, the genes involved in TAMM differentiation were categorized into early and later groups. Then, the early group genes divided the HNSCC patients into sub-populations with more detailed immune properties. Through network topology, CXCL9, 10, 11, and CLL5 related to TAMM differentiation in the TME were identified as the key genes initiating and maintaining the immune hot phenotype in HNSCC by remarkably strengthening immune responses and infiltration. Genome wide, CASP8 mutations were found to be key to triggering immune responses in the immune hot phenotype. On the other hand, in the immune cold phenotype, the evident changes in CNV resulted in immune evasion by disrupting immune balance. Finally, based on the framework of CXCL9-11, CLL5, CD8+, CD4+ T cells, and Macrophage M1, the neural network model could predict the validity of PD-1/PDL-1 therapy with 75% of AUC in the test cohort.Conclusion: We concluded that the CXCL9, 10,11, and CCL5 mediated TAMM differentiation and constructed immune hot phenotype of HNSCC. Since they positively regulated immune cells and immune cycle in HNSCC, the CXCL9-11 and CCL5 could be used to predict the effects of anti-PD-1/PDL-1 therapy on HNSCC.
Collapse
Affiliation(s)
- Yuhong Huang
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
| | - Han Liu
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
- Dalian Key Laboratory of Basic Research in Oral Medicine, School of Stomatology, Dalian Medical University, Dalian, China
| | - Xuena Liu
- Department of Nuclear Medicine, The 2nd Hospital Affiliated to Dalian Medical University, Dalian, China
| | - Nan Li
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
- Dalian Key Laboratory of Basic Research in Oral Medicine, School of Stomatology, Dalian Medical University, Dalian, China
| | - Han Bai
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
| | - Chenyang Guo
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
| | - Tian Xu
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
| | - Lei Zhu
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
- Dalian Key Laboratory of Basic Research in Oral Medicine, School of Stomatology, Dalian Medical University, Dalian, China
| | - Chao Liu
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
- Dalian Key Laboratory of Basic Research in Oral Medicine, School of Stomatology, Dalian Medical University, Dalian, China
- *Correspondence: Chao Liu, ; Jing Xiao,
| | - Jing Xiao
- Department of Oral Pathology, School of Stomatology, Dalian Medical University, Dalian, China
- Dalian Key Laboratory of Basic Research in Oral Medicine, School of Stomatology, Dalian Medical University, Dalian, China
- *Correspondence: Chao Liu, ; Jing Xiao,
| |
Collapse
|
38
|
Zhu G, Yang K, Xu C, Feng R, Li W, Ma J. Development of a prediction model for radiotherapy response among patients with head and neck squamous cell carcinoma based on the tumor immune microenvironment and hypoxia signature. Cancer Med 2022; 11:4673-4687. [PMID: 35505641 PMCID: PMC9741991 DOI: 10.1002/cam4.4791] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION The immune system and hypoxia are major factors influencing radiosensitivity in patients with different cancer types. This study aimed at developing a model to predict radiotherapy response in patients with head and neck squamous cell carcinoma (HNSCC) based on the tumor immune microenvironment and hypoxia signature. MATERIALS AND METHODS We first evaluated the hypoxia status and tumor immune microenvironment in the Cancer Genome Atlas (TCGA) cohort by using transcriptomic data. Differentially expressed genes (DEGs) were identified between the "high immunity and low hypoxia" and "low immunity and high hypoxia" groups and those DEGs significantly associated with disease-specific survival in the univariate Cox regression analysis were selected as the prognostic DEGs. We selected the immune hypoxia-related genes (IHRGs) by intersecting prognostic DEGs with immune and hypoxia gene sets. We used the IHRGs to train a multivariate Cox regression model in the TCGA cohort, based on which we calculated the IHRG prognostic index (IHRGPI) for each patient and validated its efficacy in predicting radiotherapy response in the Gene Expression Omnibus cohorts. Furthermore, we explored potential mechanisms and effective combinational treatment strategies for different IHRGPI groups. RESULTS Five IHRGs were used to construct the IHRGPI, which was used to dichotomize the cohorts. The patients with lower IHRGPI showed a better radiotherapy response across different cohorts and endpoints, including overall survival, progression-free survival, and recurrence-free survival (p < 0.05). Patients with higher IHRGPI showed greater hypoxia and lesser immune cell infiltration. A lower IHRGPI indicated a better immunotherapy response, while a higher IHRGPI indicated a better chemotherapy response. CONCLUSIONS IHRGPI is promising for predicting radiotherapy response and guiding combinational treatment strategies in patients with HNSCC.
Collapse
Affiliation(s)
- Guang‐Li Zhu
- Department of Radiation OncologySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhouP. R. China
| | - Kai‐Bin Yang
- Department of Radiation OncologySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhouP. R. China
| | - Cheng Xu
- Department of Radiation OncologySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhouP. R. China
| | - Rui‐Jia Feng
- Department of Radiation OncologySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhouP. R. China
| | - Wen‐Fei Li
- Department of Radiation OncologySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhouP. R. China
| | - Jun Ma
- Department of Radiation OncologySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhouP. R. China
| |
Collapse
|
39
|
Yang Q, Xu F, Jian A, Yu H, Ye T, Hu W. m6A Regulator-Mediated Methylation Modification Patterns and Tumor Microenvironment Cell-Infiltration Characterization in Head and Neck Cancer. Front Cell Dev Biol 2022; 9:803141. [PMID: 35198565 PMCID: PMC8859267 DOI: 10.3389/fcell.2021.803141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Recently, RNA modifications have emerged as essential epigenetic regulators of gene expression. However, the mechanism of how RNA N6-methyladenosine (m6A) modification interacts with tumor microenvironment (TME) infiltration remains obscure. Methods: A total of 876 head and neck cancer samples considering 21 m6A regulators were included and analyzed to determine the m6A modification patterns. These modification patterns were then correlated with TME immune cell-infiltrating characteristics. A scoring system, the m6Ascore, was constructed using principal component analysis algorithms to quantify m6A modification of tumors. Results: Three m6A modification patterns were identified, with TME infiltrating characteristics highly consistent with tumors with three distinct immune phenotypes, including immune-inflamed, immune-exclude, and immune-desert phenotypes. It was demonstrated that the identification of the m6A modification patterns via m6Ascore could predict tumor progression, subtypes, TME stromal activity, variation of relevant genes, and patient prognosis. Low m6Ascore, identified to be an inflamed phenotype, is found to be associated with low stroma activity and tumor mutation burden, high survival probability, increased tumor neoantigen burden, and enhanced response to anti-PD-1/L1 immunotherapy. The therapeutic advantages and clinical benefits of patients with low m6Ascore were further verified in two immunotherapy cohorts. Conclusion: This study identified the significant role that the m6A modification played in the formation of TME characteristics. A more comprehensive understanding of the m6A modification patterns and their correlation with TME infiltration will contribute to the discovery of immunotherapy strategies with better efficacy.
Collapse
Affiliation(s)
- Qinghui Yang
- Department of Oncology, Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, China
| | - Feng Xu
- Department of Nuclear Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aiwen Jian
- School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Hongmei Yu
- Department of Oncology, Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, China
| | - Tao Ye
- Department of Oncology, Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, China
| | - Weiqi Hu
- Department of Otolaryngology, Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
40
|
Blise KE, Sivagnanam S, Banik GL, Coussens LM, Goecks J. Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma. NPJ Precis Oncol 2022; 6:10. [PMID: 35217711 PMCID: PMC8881577 DOI: 10.1038/s41698-022-00253-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 01/07/2022] [Indexed: 01/10/2023] Open
Abstract
There is increasing evidence that the spatial organization of cells within the tumor-immune microenvironment (TiME) of solid tumors influences survival and response to therapy in numerous cancer types. Here, we report results and demonstrate the applicability of quantitative single-cell spatial proteomics analyses in the TiME of primary and recurrent human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) tumors. Single-cell compositions of a nine patient, primary and recurrent (n = 18), HNSCC cohort is presented, followed by deeper investigation into the spatial architecture of the TiME and its relationship with clinical variables and progression free survival (PFS). Multiple spatial algorithms were used to quantify the spatial landscapes of immune cells within TiMEs and demonstrate that neoplastic tumor-immune cell spatial compartmentalization, rather than mixing, is associated with longer PFS. Mesenchymal (αSMA+) cellular neighborhoods describe distinct immune landscapes associated with neoplastic tumor-immune compartmentalization and improved patient outcomes. Results from this investigation are concordant with studies in other tumor types, suggesting that trends in TiME cellular heterogeneity and spatial organization may be shared across cancers and may provide prognostic value in multiple cancer types.
Collapse
Affiliation(s)
- Katie E Blise
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.,The Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Shamilene Sivagnanam
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Grace L Banik
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA.,Otolaryngology-Head & Neck Surgery, Oregon Health & Science University, Portland, OR, USA.,Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lisa M Coussens
- The Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Jeremy Goecks
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA. .,The Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| |
Collapse
|
41
|
Pokorna Z, Vyslouzil J, Vojtesek B, Coates PJ. Identifying pathways regulating the oncogenic p53 family member ΔNp63 provides therapeutic avenues for squamous cell carcinoma. Cell Mol Biol Lett 2022; 27:18. [PMID: 35196980 PMCID: PMC8903560 DOI: 10.1186/s11658-022-00323-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/15/2022] [Indexed: 12/17/2022] Open
Abstract
Background ΔNp63 overexpression is a common event in squamous cell carcinoma (SCC) that contributes to tumorigenesis, making ΔNp63 a potential target for therapy. Methods We created inducible TP63-shRNA cells to study the effects of p63-depletion in SCC cell lines and non-malignant HaCaT keratinocytes. DNA damaging agents, growth factors, signaling pathway inhibitors, histone deacetylase inhibitors, and metabolism-modifying drugs were also investigated for their ability to influence ΔNp63 protein and mRNA levels. Results HaCaT keratinocytes, FaDu and SCC-25 cells express high levels of ΔNp63. HaCaT and FaDu inducible TP63-shRNA cells showed reduced proliferation after p63 depletion, with greater effects on FaDu than HaCaT cells, compatible with oncogene addiction in SCC. Genotoxic insults and histone deacetylase inhibitors variably reduced ΔNp63 levels in keratinocytes and SCC cells. Growth factors that regulate proliferation/survival of squamous cells (IGF-1, EGF, amphiregulin, KGF, and HGF) and PI3K, mTOR, MAPK/ERK or EGFR inhibitors showed lesser and inconsistent effects, with dual inhibition of PI3K and mTOR or EGFR inhibition selectively reducing ΔNp63 levels in HaCaT cells. In contrast, the antihyperlipidemic drug lovastatin selectively increased ΔNp63 in HaCaT cells. Conclusions These data confirm that ΔNp63-positive SCC cells require p63 for continued growth and provide proof of concept that p63 reduction is a therapeutic option for these tumors. Investigations of ΔNp63 regulation identified agent-specific and cell-specific pathways. In particular, dual inhibition of the PI3K and mTOR pathways reduced ΔNp63 more effectively than single pathway inhibition, and broad-spectrum histone deacetylase inhibitors showed a time-dependent biphasic response, with high level downregulation at the transcriptional level within 24 h. In addition to furthering our understanding of ΔNp63 regulation in squamous cells, these data identify novel drug combinations that may be useful for p63-based therapy of SCC. Supplementary Information The online version contains supplementary material available at 10.1186/s11658-022-00323-x.
Collapse
Affiliation(s)
- Zuzana Pokorna
- Research Center of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Jan Vyslouzil
- Research Center of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Center of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Philip J Coates
- Research Center of Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic.
| |
Collapse
|
42
|
Truchard E, Bertolus C, Martinez P, Thomas E, Saintigny P, Foy JP. Identification of a Gene-Expression-Based Surrogate of Genomic Instability during Oral Carcinogenesis. Cancers (Basel) 2022; 14:834. [PMID: 35159101 PMCID: PMC8834046 DOI: 10.3390/cancers14030834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Our goal was to identify a gene-expression-based surrogate of genomic instability (GI) associated with the transformation of oral potentially malignant disorder (OPMD) into oral squamous cell carcinoma (OSCC). METHODS GI was defined as the fraction of genome altered (FGA). Training sets included the CCLE and TCGA databases. The relevance of the enrichment score of the top correlated genes, referred to as the GIN score, was evaluated in eight independent public datasets from the GEO repository, including a cohort of patients with OPMD with available outcome. RESULTS A set of 20 genes correlated with FGA in head and neck SCC were identified. A significant correlation was found between the 20-gene based GIN score and FGA in 95 esophagus SCC (r = 0.59) and 501 lung SCC (r = 0.63), and in 33 OPMD/OSCC (r = 0.38). A significantly increased GIN score was observed at different stages of oral carcinogenesis (normal-dysplasia -OSCC) in five independent datasets. The GIN score was higher in 10 OPMD that transformed into oral cancer compared to 10 nontransforming OPMD (p = 0.0288), and was associated with oral-cancer-free survival in 86 patients with OPMD (p = 0.0081). CONCLUSIONS The GIN score is a gene-expression surrogate of GI, and is associated with oral carcinogenesis and OPMD malignant transformation.
Collapse
Affiliation(s)
- Eléonore Truchard
- Sorbonne Université, Department of Maxillo-Facial Surgery, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France; (E.T.); (C.B.)
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
- Department of Translational Medicine, Centre Léon Bérard, 69008 Lyon, France
| | - Chloé Bertolus
- Sorbonne Université, Department of Maxillo-Facial Surgery, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France; (E.T.); (C.B.)
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
- Department of Translational Medicine, Centre Léon Bérard, 69008 Lyon, France
| | - Pierre Martinez
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
| | - Emilie Thomas
- Synergie Lyon Cancer-Platform of Bioinformatics Gilles Thomas, 69008 Lyon, France;
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
- Department of Translational Medicine, Centre Léon Bérard, 69008 Lyon, France
- Department of Medical Oncology, Centre Léon Bérard, 69008 Lyon, France
| | - Jean-Philippe Foy
- Sorbonne Université, Department of Maxillo-Facial Surgery, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France; (E.T.); (C.B.)
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France; (P.M.); (P.S.)
- Department of Translational Medicine, Centre Léon Bérard, 69008 Lyon, France
| |
Collapse
|
43
|
Huang C, He J, Dong Y, Huang L, Chen Y, Peng A, Huang H. Identification of Novel Prognostic Markers Associated With Laryngeal Squamous Cell Carcinoma Using Comprehensive Analysis. Front Oncol 2022; 11:779153. [PMID: 35087752 PMCID: PMC8787159 DOI: 10.3389/fonc.2021.779153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/13/2021] [Indexed: 01/02/2023] Open
Abstract
Background Laryngeal squamous cell carcinoma (LSCC) is a leading malignant cancer of the head and neck. Patients with LSCC, in which the cancer has infiltrated and metastasized, have a poor prognosis. Therefore, there is an urgent need to identify more potential targets for drugs and biomarkers for early diagnosis. Methods RNA sequence data from LSCC and patients’ clinical traits were obtained from the Gene Expression Omnibus (GEO) (GSE142083) and The Cancer Genome Atlas (TCGA) database. Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify hub genes. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, prognostic value analysis, receiver operating characteristic (ROC) curve analysis, gene mutation analysis, tumor-infiltrating immune cell abundance profile estimation, gene set variation analysis (GSVA), and gene set enrichment analysis (GSEA) were performed. Single-gene RNA sequencing data were obtained from the GSE150321 dataset. Cell proliferation and viability were confirmed by the CCK-8 assay and real-time PCR. Results A total of 701 DEGs, including 329 upregulated and 372 downregulated genes, were screened in the GSE142083 dataset. Using WGCNA, three modules were identified to be closely related to LSCC. After intersecting the DEGs and performing univariate and multivariate Cox analyses, a novel prognostic model based on three genes (SLC35C1, HOXB7, and TEDC2) for LSCC was established. Interfering TEDC2 expression inhibited tumor cell proliferation and migration. Conclusions Our results show that SLC35C1, HOXB7, and TEDC2 have the potential to become new therapeutic targets and prognostic biomarkers for LSCC.
Collapse
Affiliation(s)
- Chao Huang
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Jun He
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Yi Dong
- Department of Nephrology, Xiangya Hospital Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
| | - Li Huang
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Yichao Chen
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Anquan Peng
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Hao Huang
- Department of Nephrology, Xiangya Hospital Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, China
| |
Collapse
|
44
|
den bossche VV, Zaryouh H, Vara-Messler M, Vignau J, Machiels JP, Wouters A, Schmitz S, Corbet C. Microenvironment-driven intratumoral heterogeneity in head and neck cancers: clinical challenges and opportunities for precision medicine. Drug Resist Updat 2022; 60:100806. [DOI: 10.1016/j.drup.2022.100806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023]
|
45
|
Zhang Y, Liu Y, Huang J, Hu Z, Miao Y. Identification of new head and neck squamous cell carcinoma subtypes and development of a novel score system (PGSscore) based on variations in pathway activity between tumor and adjacent non-tumor samples. Comput Struct Biotechnol J 2022; 20:4786-4805. [PMID: 36147682 PMCID: PMC9464652 DOI: 10.1016/j.csbj.2022.08.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/20/2022] [Accepted: 08/27/2022] [Indexed: 12/24/2022] Open
|
46
|
Identification of Novel Biomarkers for Predicting Prognosis and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma Based on ceRNA Network and Immune Infiltration Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4532438. [PMID: 34917682 PMCID: PMC8670464 DOI: 10.1155/2021/4532438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/23/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
Objectives Patients with head and neck squamous cell carcinoma (HNSCC) have poor prognosis and show poor responses to immune checkpoint (IC) inhibitor (ICI) therapy. Competing endogenous RNA (ceRNA) networks, tumor-infiltrating immune cells (TIICs), and ICIs may influence tumor prognosis and response rates to ICI therapy. This study is aimed at identifying prognostic and IC-related biomarkers and key TIIC signatures to improve prognosis and ICI therapy response in HNSCC patients. Methods and Results Ninety-five long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and 1746 mRNAs were identified using three independent methods. We constructed a ceRNA network and estimated the proportions of 22 immune cell subtypes. Ten ceRNAs were related to prognosis according to Kaplan–Meier analysis. Two risk signatures based, respectively, on nine ceRNAs (ANLN, CFL2, ITGA5, KDELC1, KIF23, NFIA, PTX3, RELT, and TMC7) and three immune cell types (naïve B cells, neutrophils, and regulatory T cells) via univariate Cox regression, least absolute shrinkage and selection operator, and multivariate Cox regression analyses could accurately and independently predict the prognosis of HNSCC patients. Key mRNAs in the ceRNA network were significantly correlated with naïve B cells and regulatory T cells and with stage, grade, and immune and molecular subtype. Eight IC genes exhibited higher expression in tumor tissues and were correlated with eight key mRNAs in the ceRNA network in HNSCC patients with different HPV statuses according to coexpression and TIMER 2.0 analyses. Most drugs were effective in association with expression of these key signatures (ANLN, CFL2, ITGA5, KIF23, NFIA, PTX3, RELT, and TMC7) based on GSCALite analysis. The prognostic value of key biomarkers and associations between key ceRNAs and IC genes were validated using online databases. Eight key ceRNAs were confirmed to predict response to ICI in other cancers based on TIDE analysis. Conclusions We constructed two risk signatures to accurately predict prognosis in HNSCC. Key IC-related signatures may be associated with response to ICI therapy. Combinations of ICIs with inhibitors of eight key mRNAs may improve survival outcomes of HNSCC patients.
Collapse
|
47
|
Prevalence of HPV in Mexican Patients with Head and Neck Squamous Carcinoma and Identification of Potential Prognostic Biomarkers. Cancers (Basel) 2021; 13:cancers13225602. [PMID: 34830760 PMCID: PMC8616077 DOI: 10.3390/cancers13225602] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Head and neck squamous cell carcinomas (HNSCC) are a heterogeneous group of neoplasms that show diverse clinical and biological characteristics associated with human papillomavirus (HPV). Biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. The biological features of HNSCC may change according to geography and population characteristics. Studies on the molecular biology of HNSCC in Mexico are scarce. In the present study, we analyzed 414 Mexican patients with HNSCC and determined the presence and genotype of HPV, p16 expression, and global gene expression profiles. Twenty-two percent of total cases were HPV+, and 32% were p16+. We identified genes associated with survival, such as SLIRP, KLF10, AREG, ACT1, and LIMA. In addition, CSF1R, MYC, and SRC genes were identified as potential therapeutic targets. This study offers information that may be relevant for our understanding of the biology of HNSCC and the development of therapeutic strategies. Abstract Head and neck squamous cell carcinomas (HNSCC) show a variety of biological and clinical characteristics that could depend on the association with the human papillomavirus (HPV). Biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. Reports on HNSCC are scarce in Mexico. Herein, we analyzed 414 Mexican patients with HNSCC, including oropharynx (OPSCC), larynx (LASCC), and oral cavity (OCSCC), and identified HPV DNA and p16 expression. Global gene expression profiles were analyzed in 25 HPV+/p16+ vs. HPV−/p16− cases. We found 32.3% p16+ and 22.3% HPV+ samples, HPV 16, 18, 39, 52, and 31 being the most frequent genotypes. For OPSCC, LASCC and OCSCC, 39.2, 14.7, and 9.6% were HPV+/p16+, respectively. High expression of SLIRP, KLF10, AREG, and LIMA was associated with poor survival; in contrast, high expression of MYB and SYCP2 correlated with better survival. In HPV+ cases, high expression of SLC25A39 and GJB2 was associated with poor survival. Likewise, EGFR, IL-1, IL-6, JAK-STAT, WNT, NOTCH, and ESR1 signaling pathways were downregulated in HPV+ cases. CSF1R, MYC, and SRC genes were identified as key hubs and therapeutic targets. Our study offers information regarding the molecular and clinical characteristics of HNSCC in Mexican patients.
Collapse
|
48
|
de Sousa LG, Ferrarotto R. Pembrolizumab in the first-line treatment of advanced head and neck cancer. Expert Rev Anticancer Ther 2021; 21:1321-1331. [PMID: 34689660 DOI: 10.1080/14737140.2021.1996228] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Recurrent or metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) is associated with dismal prognosis and has limited therapeutic options. PD-1/PD-L1 axis blockade was initially shown to improve outcomes in platinum-refractory HNSCC. More recently, pembrolizumab monotherapy or pembrolizumab combined with chemotherapy resulted in better overall survival than platinum, 5-fluorouracil, and cetuximab (EXTREME regimen) as first-line therapy for R/M HNSCC, establishing a new standard-of-care therapy for this disease. AREAS COVERED We review pembrolizumab in the first-line treatment of R/M HNSCC and summarize the impact of PD-L1 expression, tumor and symptom burden, and patient's performance status on treatment decisions. Future perspectives are summarized. EXPERT OPINION The standard-of-care first-line therapy for R/M HNSCC is pembrolizumab monotherapy for patients with a PD-L1 combined positive score (CPS)≥1 or pembrolizumab combined with platinum and 5-fluorouracil for patients with any PD-L1 status. Addition of chemotherapy to pembrolizumab increases the response rate but also toxicity and is preferred for patients with good performance status and significant tumor and symptom burden. For patients with a PD-L1 CPS <1, the EXTREME regimen should be considered. New strategies combining pembrolizumab with targeted therapies and immune checkpoints inhibitors are being explored to synergize or overcome resistance to anti-PD-1.
Collapse
Affiliation(s)
- Luana Guimaraes de Sousa
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas Md Anderson Cancer Center, Houston, Texas, USA
| | - Renata Ferrarotto
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas Md Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
49
|
Sun J, Fang G, Zuo Z, Yu X, Xue L, Li C, Li S. Identification of Immune Subtypes for Predicting the Prognosis of Patients in Head and Neck Squamous Cell Carcinoma. Technol Cancer Res Treat 2021; 20:15330338211045823. [PMID: 34657509 PMCID: PMC8521413 DOI: 10.1177/15330338211045823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common malignancy with poor prognosis and immune response, which plays an important role in tumor progression. Recently, immunotherapies have revolutionized the therapeutic means of malignancies including HNSCC. However, the relationship between immunophenotypes of HNSCC and its clinical response to immune-checkpoint inhibitors remains unclear. We aim to identify molecular subtyping related to distinct immunophenotypes in HNSCC. Consensus clustering algorithm was conducted for subtyping. Immunophenotypes between subtypes were compared according to infiltrating immunocytes, immune reactions, major histocompatibility complex (MHC) family, immunoinhibitory, immunostimulatory and immune scores. The relationship between immunophenotype and genotype was investigated from gene mutation and tumor mutation burden. The potential response of Immune-checkpoint blockade (ICB) therapy was estimated with TIDE and ImmuCellAI algorithms, and immune-checkpoint genes. The immune characteristics were also investigated. Biological functions were annotated by the gene-set enrichment analysis (GSEA) algorithm. Two distinct immune subtypes of HNSCC with different survival outcomes, biological characteristics, immunophenotype, and ICB response were identified. The subtype-1 was featured with better prognosis, more infiltrated immunocytes, stronger immune reaction, higher immune-related gene expression, higher immune-checkpoint gene expression (PD-1, PD-L1, and CTLA-4), and better ICB response. A higher immune response in subtype-1 was also revealed by GSEA. Subtype-1 possessed a higher immune response and more sensitivity to ICB therapy leading to a better prognosis. These findings may shed promising light on the immunotherapy strategy in HNSCC
Collapse
Affiliation(s)
- Jing Sun
- Department of Periodontology, Jinan Stomatological Hospital, Jinan, China
- Jing Sun, No.101 Jingliu Road, Jinan, Shandong 250001, People's Republic of China.
| | - Guiqing Fang
- Department of Periodontology, Jinan Stomatological Hospital, Jinan, China
- Jing Sun, No.101 Jingliu Road, Jinan, Shandong 250001, People's Republic of China.
| | - Zhibin Zuo
- Department of Periodontology, Jinan Stomatological Hospital, Jinan, China
| | - Xijiao Yu
- Department of Periodontology, Jinan Stomatological Hospital, Jinan, China
| | - Lande Xue
- Department of Periodontology, Jinan Stomatological Hospital, Jinan, China
| | - Chong Li
- Department of Periodontology, Jinan Stomatological Hospital, Jinan, China
- Chong Li, No.44 to 1 Wenhua Road West, 250012, Jinan, Shandong, China.
| | - Shu Li
- Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, China
- Shu Li, Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China.
| |
Collapse
|
50
|
Evaluation of the Targeting and Therapeutic Efficiency of Anti-EGFR Functionalised Nanoparticles in Head and Neck Cancer Cells for Use in NIR-II Optical Window. Pharmaceutics 2021; 13:pharmaceutics13101651. [PMID: 34683944 PMCID: PMC8537270 DOI: 10.3390/pharmaceutics13101651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/16/2022] Open
Abstract
Gold nanoparticles have been indicated for use in a diagnostic and/or therapeutic role in several cancer types. The use of gold nanorods (AuNRs) with a surface plasmon resonance (SPR) in the second near-infrared II (NIR-II) optical window promises deeper anatomical penetration through increased maximum permissible exposure and lower optical attenuation. In this study, the targeting and therapeutic efficiency of anti-epidermal growth factor receptor (EGFR)-antibody-functionalised AuNRs with an SPR at 1064 nm was evaluated in vitro. Four cell lines, KYSE-30, CAL-27, Hep-G2 and MCF-7, which either over- or under-expressed EGFR, were used once confirmed by flow cytometry and immunofluorescence. Optical microscopy demonstrated a significant difference (p < 0.0001) between targeted AuNRs (tAuNRs) and untargeted AuNRs (uAuNRs) in all four cancer cell lines. This study demonstrated that anti-EGFR functionalisation significantly increased the association of tAuNRs with each EGFR-positive cancer cell. Considering this, the MTT assay showed that photothermal therapy (PTT) significantly increased cancer cell death (>97%) in head and neck cancer cell line CAL-27 using tAuNRs but not uAuNRs, apoptosis being the major mechanism of cell death. This successful targeting and therapeutic outcome highlight the future use of tAuNRs for molecular photoacoustic imaging or tumour treatment through plasmonic photothermal therapy.
Collapse
|