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Mai Z, Kongjia L, Wang X, Xie X, Pang L, Yang H, Wen J, Fu J. Impaired TGF-β signaling via AHNAK family mutations elicits an esophageal cancer subtype with sensitivities to genotoxic therapy and immunotherapy. Cancer Immunol Immunother 2024; 73:225. [PMID: 39235488 PMCID: PMC11377381 DOI: 10.1007/s00262-024-03798-z] [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: 03/22/2024] [Accepted: 08/01/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Genome instability (GI) is a hallmark of esophageal squamous cell carcinoma (ESCC) while factors affecting GI remain unclear. METHODS Here, we aimed to characterize genomic events representing specific mechanisms of GI based on 201 ESCC samples and validated our findings at the patient, single-cell and cancer cell-line levels, including a newly generated multi-omics dataset of the trial NCT04006041. RESULTS A two-gene (AHNAK and AHNAK2) mutation signature was identified to define the "AHNAK1/2-mutant" cancer subtype. Single-cell-assisted multi-omics analysis showed that this subtype had a higher neoantigen load, active antigen presentation, and proficient CD8 + T cell infiltrations, which were validated at pan-cancer levels. Mechanistically, AHNAK1/2-mutant ESCC was characterized by impaired response of TGF-β and the inefficient alternative end-join repair (Alt-EJ) that might promote GI. Knockdown of AHNAK in ESCC cell lines resulted in more Alt-EJ events and increased sensitivities to cisplatin. Furthermore, this two-gene signature accurately predicted better responses to DNA-damaging therapy in various clinical settings (HR ≈ 0.25). The two-gene signature predicted higher pCR rates in ESCCs receiving neoadjuvant immunotherapy-involved treatment. Finally, a molecular classification scheme was built and outperformed established molecular typing models in the prognosis stratification of ESCC patients. CONCLUSION Our study extended our understanding of the AHNAK family in promoting GI and selecting treatment responders of ESCC.
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Affiliation(s)
- Zihang Mai
- Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, Guangdong Province, China
| | - Luo Kongjia
- Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, Guangdong Province, China
| | - Xinye Wang
- Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, Guangdong Province, China
| | - Xiuying Xie
- Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, Guangdong Province, China
| | - Lanlan Pang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China
| | - Hong Yang
- Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, Guangdong Province, China.
| | - Jing Wen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, Guangdong Province, China.
| | - Jianhua Fu
- Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, Guangdong Province, China.
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2
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Nam C, Li LY, Yang Q, Ziman B, Zhao H, Hu B, Collet C, Jing P, Lei Q, Xu LY, Li EM, Koeffler HP, Sinha UK, Lin DC. A druggable cascade links methionine metabolism to epigenomic reprogramming in squamous cell carcinoma. Proc Natl Acad Sci U S A 2024; 121:e2320835121. [PMID: 38900797 PMCID: PMC11214090 DOI: 10.1073/pnas.2320835121] [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: 12/04/2023] [Accepted: 05/20/2024] [Indexed: 06/22/2024] Open
Abstract
Upper aerodigestive squamous cell carcinoma (UASCC) is a common and aggressive malignancy with few effective therapeutic options. Here, we investigate amino acid metabolism in this cancer, surprisingly noting that UASCC exhibits the highest methionine level across all human cancers, driven by its transporter LAT1. We show that LAT1 is also expressed at the highest level in UASCC, transcriptionally activated by UASCC-specific promoter and enhancers, which are directly coregulated by SCC master regulators TP63/KLF5/SREBF1. Unexpectedly, unbiased bioinformatic screen identifies EZH2 as the most significant target downstream of the LAT1-methionine pathway, directly linking methionine metabolism to epigenomic reprogramming. Importantly, this cascade is indispensable for the survival and proliferation of UASCC patient-derived tumor organoids. In addition, LAT1 expression is closely associated with cellular sensitivity to inhibition of the LAT1-methionine-EZH2 axis. Notably, this unique LAT1-methionine-EZH2 cascade can be targeted effectively by either pharmacological approaches or dietary intervention in vivo. In summary, this work maps a unique mechanistic cross talk between epigenomic reprogramming with methionine metabolism, establishes its biological significance in the biology of UASCC, and identifies a unique tumor-specific vulnerability which can be exploited both pharmacologically and dietarily.
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Affiliation(s)
- Chehyun Nam
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90033
| | - Li-Yan Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, Guangdong, China
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA90048
| | - Qian Yang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA90048
| | - Benjamin Ziman
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90033
| | - Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90033
| | - Boyan Hu
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90033
| | - Casey Collet
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90033
| | - Pei Jing
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, Guangdong, China
| | - Qifang Lei
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen, Guangdong518116, China
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, Guangdong, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, Guangdong, China
| | | | - Uttam K. Sinha
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA90033
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA90048
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3
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Takahashi J, Suzuki T, Sato M, Nitta S, Yaguchi N, Muta T, Tsuchida K, Suda H, Morita M, Hamada S, Masamune A, Takahashi S, Kamei T, Yamamoto M. Differential squamous cell fates elicited by NRF2 gain of function versus KEAP1 loss of function. Cell Rep 2024; 43:114104. [PMID: 38602872 DOI: 10.1016/j.celrep.2024.114104] [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: 10/16/2023] [Revised: 02/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Clinical evidence has revealed that high-level activation of NRF2 caused by somatic mutations in NRF2 (NFE2L2) is frequently detected in esophageal squamous cell carcinoma (ESCC), whereas that caused by somatic mutations in KEAP1, a negative regulator of NRF2, is not. Here, we aspire to generate a mouse model of NRF2-activated ESCC using the cancer-derived NRF2L30F mutation and cancer driver mutant TRP53R172H. Concomitant expression of NRF2L30F and TRP53R172H results in formation of NRF2-activated ESCC-like lesions. In contrast, while squamous-cell-specific deletion of KEAP1 induces similar NRF2 hyperactivation, the loss of KEAP1 combined with expression of TRP53R172H does not elicit the formation of ESCC-like lesions. Instead, KEAP1-deleted cells disappear from the esophageal epithelium over time. These findings demonstrate that, while cellular NRF2 levels are similarly induced, NRF2 gain of function and KEAP1 loss of function elicits distinct fates of squamous cells. The NRF2L30F mutant mouse model developed here will be instrumental in elucidating the mechanistic basis leading to NRF2-activated ESCC.
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Affiliation(s)
- Jun Takahashi
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan; Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takafumi Suzuki
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.
| | - Miu Sato
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Shuji Nitta
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Nahoko Yaguchi
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Tatsuki Muta
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Kouhei Tsuchida
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Hiromi Suda
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Masanobu Morita
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center in Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
| | - Takashi Kamei
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.
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4
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Li X, Cong J, Zhou X, Gao W, Li W, Yang Q, Li X, Liu Z, Luo A. JunD-miR494-CUL3 axis promotes radioresistance and metastasis by facilitating EMT and restraining PD-L1 degradation in esophageal squamous cell carcinoma. Cancer Lett 2024; 587:216731. [PMID: 38369005 DOI: 10.1016/j.canlet.2024.216731] [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: 11/14/2023] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024]
Abstract
Therapy resistance and metastatic progression jointly determine the fatal outcome of cancer, therefore, elucidating their crosstalk may provide new opportunities to improve therapeutic efficacy and prevent recurrence and metastasis in esophageal squamous cell carcinoma (ESCC). Here, we have established radioresistant ESCC cells with the remarkable metastatic capacity, and identified miR-494-3p (miR494) as a radioresistant activator. Mechanistically, we demonstrated that cullin 3 (CUL3) is a direct target of miR494, which is transcriptionally regulated by JunD, and highlighted that JunD-miR494-CUL3 axis promotes radioresistance and metastasis by facilitating epithelial-mesenchymal transition (EMT) and restraining programmed cell death 1 ligand 1 (PD-L1) degradation. In clinical specimens, miR494 is significantly up-regulated and positively associated with T stage and lymph node metastasis in ESCC tissues and serum. Notably, patients with higher serum miR494 expression have poor prognosis, and patients with higher CUL3 expression have more conventional dendritic cells (cDCs) and plasmacytoid DCs (pDCs), less cancer-associated fibroblasts (CAF2/4), and tumor endothelial cells (TEC2/3) infiltration than patients with lower CUL3 expression, suggesting that CUL3 may be involved in tumor microenvironment (TME). Overall, miR494 may serve as a potential prognostic predictor and therapeutic target, providing a promising strategy for ESCC treatment.
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Affiliation(s)
- Xin Li
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Ji Cong
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xuantong Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Wenyan Gao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wenxin Li
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qi Yang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xinyue Li
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhihua Liu
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Aiping Luo
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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5
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Huang Y, Huo Y, Huang L, Zhang L, Zheng Y, Zhang N, Yang M. Super-enhancers: Implications in gastric cancer. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108489. [PMID: 38355091 DOI: 10.1016/j.mrrev.2024.108489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Gastric cancer (GC) is the fifth most prevalent malignancy and the third leading cause of cancer-related mortality globally. Despite intensive efforts to enhance the efficiencies of various therapeutics (chemotherapy, surgical interventions, molecular-targeted therapies, immunotherapies), the prognosis for patients with GC remains poor. This might be predominantly due to the limited understanding of the complicated etiology of GC. Importantly, epigenetic modifications and alterations are crucial during GC development. Super-enhancers (SEs) are a large cluster of adjacent enhancers that greatly activate transcription. SEs sustain cell-specific identity by enhancing the transcription of specific oncogenes. In this review, we systematically summarize how SEs are involved in GC development, including the SE landscape in GC, the SE target genes in GC, and the interventions related to SE functions for treating GC.
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Affiliation(s)
- Yizhou Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Yanfei Huo
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Linying Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Long Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Yanxiu Zheng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China.
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China.
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6
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Jin Y, Xia Y, Du H, Xiang T, Lan B, Wei S, Li H, Huang H. Super-enhancer-associated EEPD1 facilitates EMT-mediated metastasis by regulating the PI3K/AKT/mTOR pathway in gastric cancer. Biochem Biophys Res Commun 2023; 689:149188. [PMID: 37976838 DOI: 10.1016/j.bbrc.2023.149188] [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: 10/08/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
This study focused on exploring the mechanism of the EMT mediated by endonuclease/exonuclease/phosphatase family domain-containing 1 (EEPD1) in gastric cancer metastasis. Through bioinformatics analysis, EEPD1 was found to be a target gene of super enhancers (SEs) in gastric cancer tissues. EEPD1 exhibited higher expression levels in tumor tissues and was associated with poor prognosis. In vitro and in vivo studies have demonstrated that silencing EEPD1 significantly suppressed the proliferation, metastasis, and invasion of gastric cancer cells. Furthermore, EEPD1 knockdown was involved in the regulation of the EMT and suppressed expression of AKT, a downstream component of the PI3K pathway, leading to a reduction in the phosphorylation levels of AKT and its downstream molecule, mTOR. These results showed the potential of EEPD1 as a prognostic indicator and therapeutic target in gastric cancer.
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Affiliation(s)
- Yong Jin
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China; Department of Laboratory Medicine, The Second People's Hospital of Guizhou Province, Guiyang, 550004, China
| | - Ying Xia
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China; Department of Clinical Laboratory, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550001, China; Division of Gastroenterology and Hepatology, Department of Medicine and Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Hong Du
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China
| | - Tingting Xiang
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China
| | - Bingxue Lan
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China
| | - Sixi Wei
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Hongyu Li
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China
| | - Hai Huang
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China; School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China.
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Zhao J, Faryabi RB. Spatial promoter-enhancer hubs in cancer: organization, regulation, and function. Trends Cancer 2023; 9:1069-1084. [PMID: 37599153 PMCID: PMC10840977 DOI: 10.1016/j.trecan.2023.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/14/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
Transcriptional dysregulation is a hallmark of cancer and can be driven by altered enhancer landscapes. Recent studies in genome organization have revealed that multiple enhancers and promoters can spatially coalesce to form dynamic topological assemblies, known as promoter-enhancer hubs, which strongly correlate with elevated gene expression. In this review, we discuss the structure and complexity of promoter-enhancer hubs recently identified in multiple cancer types. We further discuss underlying mechanisms driving dysregulation of promoter-enhancer hubs and speculate on their functional role in pathogenesis. Understanding the role of promoter-enhancer hubs in transcriptional dysregulation can provide insight into new therapeutic approaches to target these complex features of genome organization.
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Affiliation(s)
- Jingru Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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8
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Ding J, Su Y, Liu Y, Xu Y, Yang D, Wang X, Hao S, Zhou H, Li H. The role of CSTF2 in cancer: from technology to clinical application. Cell Cycle 2023; 22:2622-2636. [PMID: 38166492 PMCID: PMC10936678 DOI: 10.1080/15384101.2023.2299624] [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: 03/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024] Open
Abstract
A protein called cleavage-stimulating factor subunit 2 (CSTF2, additionally called CSTF-64) binds RNA and is needed for the cleavage and polyadenylation of mRNA. CSTF2 is an important component subunit of the cleavage stimulating factor (CSTF), which is located on the X chromosome and encodes 557 amino acids. There is compelling evidence linking elevated CSTF2 expression to the pathological advancement of cancer and on its impact on the clinical aspects of the disease. The progression of cancers, including hepatocellular carcinoma, melanoma, prostate cancer, breast cancer, and pancreatic cancer, is correlated with the upregulation of CSTF2 expression. This review provides a fresh perspective on the investigation of the associations between CSTF2 and various malignancies and highlights current studies on the regulation of CSTF2. In particular, the mechanism of action and potential clinical applications of CSTF2 in cancer suggest that CSTF2 can serve as a new biomarker and individualized treatment target for a variety of cancer types.
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Affiliation(s)
- Jiaxiang Ding
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical University, Bengbu, Anhui, China
| | - Yue Su
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical University, Bengbu, Anhui, China
| | - Youru Liu
- The People’s Hospital of Bozhou, Bozhou, Anhui, China
| | - Yuanyuan Xu
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical University, Bengbu, Anhui, China
| | - Dashuai Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province; School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Xuefeng Wang
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical University, Bengbu, Anhui, China
| | - Shuli Hao
- The People’s Hospital of Bozhou, Bozhou, Anhui, China
| | - Huan Zhou
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical University, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical University, Bengbu, Anhui, China
| | - Hongtao Li
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
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9
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Li S, Hoefnagel SJM, Krishnadath KK. Molecular Biology and Clinical Management of Esophageal Adenocarcinoma. Cancers (Basel) 2023; 15:5410. [PMID: 38001670 PMCID: PMC10670638 DOI: 10.3390/cancers15225410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) is a highly lethal malignancy. Due to its rising incidence, EAC has become a severe health challenge in Western countries. Current treatment strategies are mainly chosen based on disease stage and clinical features, whereas the biological background is hardly considered. In this study, we performed a comprehensive review of existing studies and discussed how etiology, genetics and epigenetic characteristics, together with the tumor microenvironment, contribute to the malignant behavior and dismal prognosis of EAC. During the development of EAC, several intestinal-type proteins and signaling cascades are induced. The anti-inflammatory and immunosuppressive microenvironment is associated with poor survival. The accumulation of somatic mutations at the early phase and chromosomal structural rearrangements at relatively later time points contribute to the dynamic and heterogeneous genetic landscape of EAC. EAC is also characterized by frequent DNA methylation and dysregulation of microRNAs. We summarize the findings of dysregulations of specific cytokines, chemokines and immune cells in the tumor microenvironment and conclude that DNA methylation and microRNAs vary with each different phase of BE, LGD, HGD, early EAC and invasive EAC. Furthermore, we discuss the suitability of the currently employed therapies in the clinic and possible new therapies in the future. The development of targeted and immune therapies has been hampered by the heterogeneous genetic characteristics of EAC. In view of this, the up-to-date knowledge revealed by this work is absolutely important for future EAC studies and the discovery of new therapeutics.
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Affiliation(s)
- Shulin Li
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | | | - Kausilia Krishnawatie Krishnadath
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, 2000 Antwerpen, Belgium
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10
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Zhang L, Zheng Y, Chien W, Ziman B, Billet S, Koeffler HP, Lin DC, Bhowmick NA. ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma. Cancers (Basel) 2023; 15:5377. [PMID: 38001638 PMCID: PMC10670331 DOI: 10.3390/cancers15225377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
ARID1A, a member of the chromatin remodeling SWI/SNF complex, is frequently lost in many cancer types, including esophageal adenocarcinoma (EAC). Here, we study the impact of ARID1A deficiency on the anti-tumor immune response in EAC. We find that EAC tumors with ARID1A mutations are associated with enhanced tumor-infiltrating CD8+ T cell levels. ARID1A-deficient EAC cells exhibit heightened IFN response signaling and promote CD8+ T cell recruitment and cytolytic activity. Moreover, we demonstrate that ARID1A regulates fatty acid metabolism genes in EAC, showing that fatty acid metabolism could also regulate CD8+ T cell recruitment and CD8+ T cell cytolytic activity in EAC cells. These results suggest that ARID1A deficiency shapes both tumor immunity and lipid metabolism in EAC, with significant implications for immune checkpoint blockade therapy in EAC.
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Affiliation(s)
- Le Zhang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Wenwen Chien
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - Benjamin Ziman
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
- Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Sandrine Billet
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - H. Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
- Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Neil A. Bhowmick
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (L.Z.); (Y.Z.); (W.C.); (B.Z.); (S.B.); (H.P.K.)
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11
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Gao A, Bai P, Zhang M, Yao Y, Herman JG, Guo M. RASSF1A promotes ATM signaling and RASSF1A methylation is a synthetic lethal marker for ATR inhibitors. Epigenomics 2023; 15:1205-1220. [PMID: 38093706 DOI: 10.2217/epi-2023-0306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
Aim: The mechanism of RASSF1A in DNA damage repair remains to be further clarified for applying to synthetic lethal strategy. Materials & methods: Eight esophageal cancer cell lines, 181 cases of esophageal dysplasia and 1066 cases of primary esophageal squamous cell carcinoma (ESCC) were employed. Methylation-specific PCR, the CRISPR/Cas9 technique, immunoprecipitation assay and a xenograft mouse model were used. Results: RASSF1A was methylated in 2.21% of esophageal dysplasia and 11.73% of ESCC. RASSF1A was also involved in DNA damage repair through activating Hippo signaling. Loss of RASSF1A expression sensitized esophageal cancer cell lines to ataxia telangiectasia mutated and rad3-related (ATR) inhibitor (VE-822) both in vitro and in vivo. Conclusion: RASSF1A methylation is a synthetic lethal marker for ATR inhibitors.
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Affiliation(s)
- Aiai Gao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Panpan Bai
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- Henan Advanced Technology Research Institute, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Meiying Zhang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yuanxin Yao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- National Key Laboratory of Kidney Diseases, Beijing, 100853, China
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12
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Arora M, Kumari S, Kadian L, Anupa G, Singh J, Kumar A, Verma D, Pramanik R, Kumar S, Yadav R, Chopra A, Chauhan S. Involvement of DPP3 in modulating oncological features and oxidative stress response in esophageal squamous cell carcinoma. Biosci Rep 2023; 43:BSR20222472. [PMID: 37531267 PMCID: PMC10500228 DOI: 10.1042/bsr20222472] [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: 12/07/2022] [Revised: 07/13/2023] [Accepted: 08/02/2023] [Indexed: 08/04/2023] Open
Abstract
Resistance to therapy in esophageal squamous cell carcinoma (ESCC) is a critical clinical problem and identification of novel therapeutic targets is highly warranted. Dipeptidyl peptidase III (DPP3) is a zinc-dependent aminopeptidase and functions in the terminal stages of the protein turnover. Several studies have reported overexpression and oncogenic functions of DPP3 in numerous malignancies. The present study aimed to determine the expression pattern and functional role of DPP3 in ESCC. DPP3 expression was assessed in normal and tumor tissues using quantitative real-time (qRT)-PCR and corroborated with ESCC gene expression datasets from Gene Expression Omnibus (GEO) and The cancer genome atlas (TCGA). DPP3 stable knockdown was performed in ESCC cells by shRNA and its effect on cell proliferation, migration, cell cycle, apoptosis, and activation of nuclear factor erythroid 2-related factor 2 (NRF2) pathway was assessed. The results suggested that DPP3 is overexpressed in ESCC and its knockdown leads to reduced proliferation, increased apoptosis, and inhibited migration of ESCC cells. Additionally, DPP3 knockdown leads to down-regulation of the NRF2 pathway proteins, such as NRF2, G6PD, and NQO1 along with increased sensitivity toward oxidative stress-induced cell death and chemotherapy. Conclusively, these results demonstrate critical role of DPP3 in ESCC and DPP3/NRF2 axis may serve as an attractive therapeutic target against chemoresistance in this malignancy.
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Affiliation(s)
- Mohit Arora
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sarita Kumari
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Lokesh Kadian
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Geethadevi Anupa
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Jay Singh
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Anurag Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Deepika Verma
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Raja Pramanik
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Kumar
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajni Yadav
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Anita Chopra
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Shyam S. Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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13
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Liu Z, Liu M, Liu Y, Zhou R, Abliz A, Yuan W, Guo C, Zhang L, He W, Zheng H, Huang Y, Pan Y, Liu F, Hu Z, Chen H, Cai H, He Z, Ke Y. Absence of Lugol staining indicates initiation of esophageal squamous cell carcinoma: A combined genomic and epidemiologic study. Cell Rep Med 2023; 4:101168. [PMID: 37625408 PMCID: PMC10518598 DOI: 10.1016/j.xcrm.2023.101168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023]
Abstract
The genomic characteristics during the carcinogenic process of esophageal squamous cell carcinoma (ESCC) remain largely unknown. We report here the genomic characteristics of 106 esophageal tissues of various stages from a population-based screening cohort in China ("Endoscopic Screening for Esophageal Cancer in China" trial) and 57 ESCC tissues from a local hospital. A significant increase in somatic mutation and copy number alterations is observed in the non-dysplastic Lugol unstaining lesions (ND-LULs). Extensive clonal expansion has emerged in the ND-LULs to an extent similar to that in higher-stage lesions. The burden of genomic alterations correlates with the size of LULs in the ND-LULs. 8-year follow-up shows that ND-LULs harbor an increased risk of progression to ESCC (adjusted IRR6-10 mm vs. none = 4.66, adjusted IRR>10 mm vs. none = 40.70), and the risk is correlated with LUL size for both non-dysplastic and dysplastic lesions. Lugol unstaining can be the initial stage in the carcinogenic process of ESCC.
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Affiliation(s)
- Zhen Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Mengfei Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ren Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Amir Abliz
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China; Department of Biochemistry and Molecular Biology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Wenqing Yuan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China; Department of Education, Peking University Third Hospital, Beijing, China
| | - Chuanhai Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lixin Zhang
- Anyang Cancer Hospital, Anyang, Henan, China
| | - Wei He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hongchen Zheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yi Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yaqi Pan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Fangfang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhe Hu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Huanyu Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hong Cai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhonghu He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China.
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China.
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14
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Li X, Wang Y, Min Q, Zhang W, Teng H, Li C, Zhang K, Shi L, Wang B, Zhan Q. Comparative transcriptome characterization of esophageal squamous cell carcinoma and adenocarcinoma. Comput Struct Biotechnol J 2023; 21:3841-3853. [PMID: 37564101 PMCID: PMC10410469 DOI: 10.1016/j.csbj.2023.07.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/12/2023] Open
Abstract
Background Esophageal cancers are primarily categorized as esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). While various (epi) genomic alterations associated with tumor development in ESCC and EAC have been documented, a comprehensive comparison of the transcriptomes in these two cancer subtypes remains lacking. Methods We collected 551 gene expression profiles from publicly available sources, including normal, ESCC, and EAC tissues or cell lines. Subsequently, we conducted a systematic analysis to compare the transcriptomes of these samples at various levels, including gene expression, promoter activity, alternative splicing (AS), alternative polyadenylation (APA), and gene fusion. Results Seven distinct cluster gene expression patterns were identified among the differentially expressed genes in normal, ESCC, and EAC tissues. These patterns were enriched in the PI3K-Akt signaling pathway and the activation of extracellular matrix organization and exhibited repression of epidermal development. Notably, we observed additional genes or unique expression levels enriched in these shared pathways and biological processes related to tumor development and immune activation. In addition to the differentially expressed genes, there was an enrichment of lncRNA co-expression networks and downregulation of promoter activity associated with the repression of epidermal development in both ESCC and EAC. This indicates a common feature between these two cancer subtypes. Furthermore, differential AS and APA patterns in ESCC and EAC appear to partially affect the expression of host genes associated with bacterial or viral infections in these subtypes. No gene fusions were observed between ESCC and EAC, thus highlighting the distinct molecular mechanisms underlying these two cancer subtypes. Conclusions We conducted a comprehensive comparison of ESCC and EAC transcriptomes and uncovered shared and distinct transcriptomic signatures at multiple levels. These findings suggest that ESCC and EAC may exhibit common and unique mechanisms involved in tumorigenesis.
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Affiliation(s)
- Xianfeng Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
- Department of Gastroenterology and Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10# Changjiang Branch Road, Yuzhong District, Chongqing 400042, People's Republic of China
- Institute of Pathology and Southwest Cancer Center, Key Laboratory of Tumor Immunopathology of Ministry of Education of China, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, People's Republic of China
- Jinfeng Laboratory, Chongqing 401329, People's Republic of China
| | - Yan Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Qingjie Min
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Weimin Zhang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Huajing Teng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Chao Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Leisheng Shi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Wang
- Department of Gastroenterology and Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10# Changjiang Branch Road, Yuzhong District, Chongqing 400042, People's Republic of China
- Institute of Pathology and Southwest Cancer Center, Key Laboratory of Tumor Immunopathology of Ministry of Education of China, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, People's Republic of China
- Jinfeng Laboratory, Chongqing 401329, People's Republic of China
| | - Qimin Zhan
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
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15
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Lu J, Yang J, Ma C, Wang X, Luo J, Ma X, Fu X, Zheng S. Model construction and risk analysis of the lncRNA genes associated with the prognosis of esophageal adenocarcinoma with immune infiltration. J Gastrointest Oncol 2023; 14:22-28. [PMID: 36915426 PMCID: PMC10007919 DOI: 10.21037/jgo-22-1279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
Background Our study analyzed the immune infiltration of esophageal adenocarcinoma (EAC) tumor cells and identified long non-coding ribonucleic acid (lncRNA) genes to construct a prognostic model of EAC to evaluate the survival prognosis of patients and explore potential therapeutic targets. Methods The data of 89 patients with EAC, including 11 normal tissue samples and 78 EAC of tumor tissue samples, were downloaded from The Cancer Genome Atlas public database. Perl script and R software were used to run the code, conduct the statistical analysis, calculate the risk coefficients of the patients, and conduct the Cox regression analysis, immune-related lncRNA survival analysis, risk analysis, principal component analysis (PCA), and receiver operating characteristic (ROC) curve analysis. Results We screened and identified 19 prognostic biomarkers, including LINC01612, AC008443.2, and LINC02582, allocated the patients into high- and low-risk groups, and found significant differences in the prognosis between the high- and low-risk groups using the Kaplan-Meier survival analysis (P<0.001). A ROC curve was used to evaluate the feasibility of the prognostic model for EAC, and we found that the model had high predictability (area under the curve =0.964). A PCA analysis was performed of the complex transcriptome sequencing data and other cubes to transform the data into a 3-dimensional space constructed by feature vectors. Conclusions Our study effectively screened and identified the lncRNA genes related to the immune infiltration of EAC and successfully constructed a prognostic model. In total, 19 potential diagnostic and therapeutic target genes, including LINC01612, AC008443.2, and LINC02582, were identified that have certain significance in guiding the clinical treatment of EAC patients.
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Affiliation(s)
- Jun Lu
- Intensive Care Unit, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Juan Yang
- Department of Gastroenterology, The Third People's Hospital of Yunnan Province, Kunming, China
| | - Chi Ma
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Xinxin Wang
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Jiangyan Luo
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Xiaoying Ma
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Xinnian Fu
- Graduate School of Clinical Medicine, Dali University, Dali, China
| | - Sheng Zheng
- Department of Gastroenterology, The Third People's Hospital of Yunnan Province, Kunming, China
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16
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Wang S, Yang M, Li R, Bai J. Current advances in noninvasive methods for the diagnosis of oral squamous cell carcinoma: a review. Eur J Med Res 2023; 28:53. [PMID: 36707844 PMCID: PMC9880940 DOI: 10.1186/s40001-022-00916-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC), one of the most common types of cancers worldwide, is diagnosed mainly through tissue biopsy. However, owing to the tumor heterogeneity and other drawbacks, such as the invasiveness of the biopsy procedure and high cost and limited usefulness of longitudinal surveillance, there has been a focus on adopting more rapid, economical, and noninvasive screening methods. Examples of these include liquid biopsy, optical detection systems, oral brush cytology, microfluidic detection, and artificial intelligence auxiliary diagnosis, which have their own strengths and weaknesses. Extensive research is being performed on various liquid biopsy biomarkers, including novel microbiome components, noncoding RNAs, extracellular vesicles, and circulating tumor DNA. The majority of these elements have demonstrated encouraging clinical outcomes in early OSCC detection. This review summarizes the screening methods for OSCC with a focus on providing new guiding strategies for the diagnosis of the disease.
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Affiliation(s)
- Shan Wang
- grid.443397.e0000 0004 0368 7493Department of Oral Pathology, School of Stomatology, Hainan Medical College, Haikou, 571199 People’s Republic of China ,grid.443397.e0000 0004 0368 7493Department of Stomatology, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216 People’s Republic of China
| | - Mao Yang
- grid.13291.380000 0001 0807 1581West China School of Stomatology, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Ruiying Li
- grid.443397.e0000 0004 0368 7493Department of Oral Pathology, School of Stomatology, Hainan Medical College, Haikou, 571199 People’s Republic of China
| | - Jie Bai
- grid.13402.340000 0004 1759 700XDepartment of Ophthalmology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000 People’s Republic of China
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17
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Ooki A, Osumi H, Chin K, Watanabe M, Yamaguchi K. Potent molecular-targeted therapies for advanced esophageal squamous cell carcinoma. Ther Adv Med Oncol 2023; 15:17588359221138377. [PMID: 36872946 PMCID: PMC9978325 DOI: 10.1177/17588359221138377] [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: 05/01/2022] [Accepted: 10/21/2022] [Indexed: 01/15/2023] Open
Abstract
Esophageal cancer (EC) remains a public health concern with a high mortality and disease burden worldwide. Esophageal squamous cell carcinoma (ESCC) is a predominant histological subtype of EC that has unique etiology, molecular profiles, and clinicopathological features. Although systemic chemotherapy, including cytotoxic agents and immune checkpoint inhibitors, is the main therapeutic option for recurrent or metastatic ESCC patients, the clinical benefits are limited with poor prognosis. Personalized molecular-targeted therapies have been hampered due to the lack of robust treatment efficacy in clinical trials. Therefore, there is an urgent need to develop effective therapeutic strategies. In this review, we summarize the molecular profiles of ESCC based on the findings of pivotal comprehensive molecular analyses, highlighting potent therapeutic targets for establishing future precision medicine for ESCC patients, with the most recent results of clinical trials.
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Affiliation(s)
- Akira Ooki
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Hiroki Osumi
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Keisho Chin
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
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18
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Li XP, Qu J, Teng XQ, Zhuang HH, Dai YH, Yang Z, Qu Q. The Emerging Role of Super-enhancers as Therapeutic Targets in The Digestive System Tumors. Int J Biol Sci 2023; 19:1036-1048. [PMID: 36923930 PMCID: PMC10008685 DOI: 10.7150/ijbs.78535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/09/2022] [Indexed: 02/05/2023] Open
Abstract
Digestive system tumors include malignancies of the stomach, pancreas, colon, rectum, and the esophagus, and are associated with high morbidity and mortality. Aberrant epigenetic modifications play a vital role in the progression of digestive system tumors. The aberrant transcription of key oncogenes is driven by super-enhancers (SEs), which are characterized by large clusters of enhancers with significantly high density of transcription factors, cofactors, and epigenetic modulatory proteins. The SEs consist of critical epigenetic regulatory elements, which modulate the biological characteristics of digestive system tumors including tumor cell identity and differentiation, tumorigenesis, environmental response, immune response, and chemotherapeutic resistance. The core transcription regulatory loop of the digestive system tumors is complex and a high density of transcription regulatory complexes in the SEs and the crosstalk between SEs and the noncoding RNAs. In this review, we summarized the known characteristics and functions of the SEs in the digestive system tumors. Furthermore, we discuss the oncogenic roles and regulatory mechanisms of SEs in the digestive system tumors. We highlight the role of SE-driven genes, enhancer RNAs (eRNAs), lncRNAs, and miRNAs in the digestive system tumor growth and progression. Finally, we discuss clinical significance of the CRISPR-Cas9 gene editing system and inhibitors of SE-related proteins such as BET and CDK7 as potential cancer therapeutics.
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Affiliation(s)
- Xiang-Ping Li
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410007, PR China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410007, PR China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, Changsha 410011, PR China.,Hunan key laboratory of the research and development of novel pharmaceutical preparations, Changsha Medical University, Changsha, 410219, PR China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, Changsha 410011, PR China
| | - Hai-Hui Zhuang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, Changsha 410011, PR China
| | - Ying-Huan Dai
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha 410011, PR China
| | - Zhi Yang
- Department of Colorectal and Anal Surgery, Hepatobiliary and Enteric Surgery Research Center, Xiangya Hospital, Central South University, Changsha 410007, PR China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410007, PR China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410007, PR China.,Hunan key laboratory of the research and development of novel pharmaceutical preparations, Changsha Medical University, Changsha, 410219, PR China
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19
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Zhao H, Cheng Y, Kalra A, Ma K, Zheng Y, Ziman B, Tressler C, Glunde K, Shin EJ, Ngamruengphong S, Khashab M, Singh V, Anders RA, Jit S, Wyhs N, Chen W, Li X, Lin DC, Meltzer SJ. Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model. Sci Transl Med 2022; 14:eabq6146. [PMID: 36449602 PMCID: PMC10026384 DOI: 10.1126/scitranslmed.abq6146] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Inactivation of the tumor suppressor genes tumor protein p53 (TP53) and cyclin-dependent kinase inhibitor 2A (CDKN2A) occurs early during gastroesophageal junction (GEJ) tumorigenesis. However, because of a paucity of GEJ-specific disease models, cancer-promoting consequences of TP53 and CDKN2A inactivation at the GEJ have not been characterized. Here, we report the development of a wild-type primary human GEJ organoid model and a CRISPR-edited transformed GEJ organoid model. CRISPR-Cas9-mediated TP53 and CDKN2A knockout (TP53/CDKN2AKO) in GEJ organoids induced morphologic dysplasia and proneoplastic features in vitro and tumor formation in vivo. Lipidomic profiling identified several platelet-activating factors (PTAFs) among the most up-regulated lipids in CRISPR-edited organoids. PTAF/PTAF receptor (PTAFR) abrogation by siRNA knockdown or a pharmacologic inhibitor (WEB2086) reduced proliferation and other proneoplastic features of TP53/CDKN2AKO GEJ organoids in vitro and tumor formation in vivo. In addition, murine xenografts of Eso26, an established human esophageal adenocarcinoma cell line, were suppressed by WEB2086. Mechanistically, TP53/CDKN2A dual inactivation disrupted both the transcriptome and the DNA methylome, likely mediated by key transcription factors, particularly forkhead box M1 (FOXM1). FOXM1 activated PTAFR transcription by binding to the PTAFR promoter, further amplifying the PTAF-PTAFR pathway. Together, these studies established a robust model system for investigating early GEJ neoplastic events, identified crucial metabolic and epigenomic changes occurring during GEJ model tumorigenesis, and revealed a potential cancer therapeutic strategy. This work provides insights into proneoplastic mechanisms associated with TP53/CDKN2A inactivation in early GEJ neoplasia, which may facilitate early diagnosis and prevention of GEJ neoplasms.
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Affiliation(s)
- Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an 710061, Shaanxi, China
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Andrew Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ke Ma
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Einstein Healthcare Network, Philadelphia, PA 19136, USA
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Benjamin Ziman
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Caitlin Tressler
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kristine Glunde
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eun Ji Shin
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Saowanee Ngamruengphong
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mouen Khashab
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vikesh Singh
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Robert A. Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Simran Jit
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nicolas Wyhs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Wei Chen
- Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an 710061, Shaanxi, China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, China
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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20
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Zhang Q, Lin X, Jiang K, Deng J, Ke L, Wu Z, Xia P, Li Q, Yu L, Ni P, Lv W, Hu J. PD0166285 sensitizes esophageal squamous cell carcinoma to radiotherapy by dual inhibition of WEE1 and PKMYT1. Front Oncol 2022. [DOI: 10.3389/fonc.2022.1061988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BackgroundEsophageal squamous cell carcinoma (ESCC) is an aggressive tumor with a 5-year survival rate of only 20%. More than 80% of ESCC patients possess TP53 mutation, which abolishes the G1/S checkpoint and accelerates the cell cycle. Thus, WEE1 and PKMYT1, regulators of G2/M phase in cell cycle, play essential roles in TP53-mutated cancer cells. PD0166285(PD) is a pyridopyrimidine compound that can inhibit WEE1 and PKMYT1 simultaneously, however, the effects of PD on ESCC, either as monotherapy or in combination therapy with radiotherapy, remain unclear.MethodsTo measure the anti-tumor efficacy of PD in ESCC cells, cell viability, cell cycle and cell apoptosis assays were examined in KYSE150 and TE1 cells with PD treatment. The combination therapy of PD and irradiation was also performed in ESCC cells to find whether PD can sensitize ESCC cells to irradiation. Vivo assays were also performed to investigate the efficacy of PD.ResultsWe found that the IC50 values of PD among ESCC cells ranged from 234 to 694 nM, PD can regulate cell cycle and induce cell apoptosis in ESCC cells in a dose-dependent manner. When combined with irradiation, PD sensitized ESCC cells to irradiation by abolishing G2/M phase arrest, inducing a high ratio of mitosis catastrophe, eventually leading to cell death. We also demonstrated that PD can attenuate DNA damage repair by inhibiting Rad51, further research also found the interaction of WEE1 and Rad51. In vivo assays, PD inhibited the tumor growth in mice, combination therapy showed better therapeutic efficacy.ConclusionPD0166285 can exert antitumor effect by inhibiting the function of WEE1 and PKMYT1 in ESCC cells, and also sensitize ESCC cells to irradiation not only by abolishing G2/M arrest but also attenuating DNA repair directly. We believe PD0166285 can be a potent treatment option for ESCC in the future.
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21
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Jajosky A, Fels Elliott DR. Esophageal Cancer Genetics and Clinical Translation. Thorac Surg Clin 2022; 32:425-435. [DOI: 10.1016/j.thorsurg.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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22
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Zhao H, Collet C, Peng D, Sinha UK, Lin DC. Investigation of early neoplastic transformation and premalignant biology using genetically engineered organoid models. Comput Struct Biotechnol J 2022; 20:5309-5315. [PMID: 36212534 PMCID: PMC9513696 DOI: 10.1016/j.csbj.2022.09.026] [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: 07/08/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Organoid modeling is a powerful, robust and efficient technology faithfully preserving physiological and pathological characteristics of tissues of origin. Recently, substantial advances have been made in applying genetically engineered organoid models to study early tumorigenesis and premalignant biology. These efforts promise to identify novel avenues for early cancer detection, intervention and prevention. Here, we highlight significant advancements in the functional characterization of early genomic and epigenomic events during neoplastic evolution using organoid modeling, discuss the application of the lineage-tracing methodology in organoids to study cancer cells-of-origin, and review future opportunities for further development and improvement of organoid modeling of cancer precursors.
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Affiliation(s)
- Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Casey Collet
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Dongzi Peng
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Uttam K. Sinha
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
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23
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Rooper LM, Thompson LDR, Gagan J, Hwang JSG, London NR, Mikula MW, Stevens TM, Bishop JA. Low-grade non-intestinal-type sinonasal adenocarcinoma: a histologically distinctive but molecularly heterogeneous entity. Mod Pathol 2022; 35:1160-1167. [PMID: 35322195 DOI: 10.1038/s41379-022-01068-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 11/10/2022]
Abstract
Although low-grade non-intestinal-type sinonasal adenocarcinoma (SNAC) is formally a diagnosis of exclusion defined by the absence of salivary or intestinal differentiation, most tumors in this category comprise a distinctive histologic group that are increasingly thought to derive from seromucinous glands. However, the molecular underpinnings of SNAC remain poorly understood, and it is unclear if diverse genetic alterations recently reported in isolated cases should delineate separate subgroups. This study aims to perform comprehensive evaluation of gene fusions and mutations and their histologic correlates in low-grade SNAC to clarify its pathogenesis and classification. We identified 18 non-intestinal-type SNAC that all displayed characteristic tubulopapillary architecture and low-grade cytology, although several cases had other unique histologic features and 3 showed intermixed high-grade areas. Among tumors stained with S100 protein, SOX10, and DOG1, 86% expressed at least one of these seromucinous markers. Of 17 cases with sufficient RNA or DNA available for analysis, likely oncogenic molecular alterations were identified in 76% of cases, most notably including CTNNB1 p.S33F mutations in 2 cases, concomitant BRAF p.V600E and AKT1 p.E17K mutations in 2 cases, and ETV6::NTRK3, PRKAR1A::MET, FN1::NRG1, and DNAJB1::PRKACA fusions in 1 case each. While tumors with most genetic alterations were histologically indistinguishable, cases with CTNNB1 mutations had intermixed squamoid morules and cases with BRAF and AKT1 mutations showed a myoepithelial cell population and prominent papillary to micropapillary architecture. Overall, these findings confirm previous reports of frequent seromucinous differentiation in low-grade SNAC. However, these tumors display striking molecular diversity with involvement of multiple kinase fusions, leading to frequent activation of signaling cascades including the MAPK pathway. While most genetic alterations are not associated with sufficiently distinctive histologic features to suggest separate classification, biphasic tumors with BRAF p.V600E mutations are more unique and may represent a distinctive subgroup.
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Affiliation(s)
- Lisa M Rooper
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Nyall R London
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael W Mikula
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Todd M Stevens
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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24
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Song D, Wei Y, Hu Y, Sun Y, Liu M, Ren Q, Hu Z, Guo Q, Wang Y, Zhou Y. Identification of immunophenotypes in esophageal squamous cell carcinoma based on immune gene sets. Clin Transl Oncol 2022; 24:1100-1114. [PMID: 35098447 DOI: 10.1007/s12094-021-02749-9] [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: 10/13/2021] [Accepted: 12/06/2021] [Indexed: 02/05/2023]
Abstract
PURPOSE Esophageal squamous cell carcinoma (ESCC) is a malignant tumor with high heterogeneity. Research on molecular mechanisms involved in the process of tumor origination and progression is extremely limited to investigating mechanisms of molecular typing for ESCC. METHODS After comprehensively analyzing the gene expression profiles in The Cancer Genome Atlas and Gene Expression Omnibus databases, we identified four immunotypes of ESCC (referred to as C1-C4) based on the gene sets of 28 immune cell subpopulations. The discrepancies in prognostic value, clinical features, drug sensitivity, and tumor components between the immunotypes were individually analyzed. RESULTS The ranking of immune infiltration is C1 > C4 > C3 > C2. These subtypes are characterized by high and low expression of immune checkpoint proteins, enrichment and insufficiency of immune-related pathways, and differential distribution of immune cell subgroups. Poorer survival was observed in the C1 subtype, which we hypothesized could be caused by an immunosuppressive cell population. Fortunately, C1's susceptibility to anti-PD-1 therapy offers hope for patients with poor prognosis in advanced stages. On the other hand, C4 is sensitive to docetaxel, which may offer novel treatment strategies for ESCC in the future. It is worth noting that immunophenotyping is tightly bound to the abundance of stromal components and stem cells, which could explain the tumor immune escape to some extent. Ultimately, determination of hub genes based on the C1 subtypes provides a reference for the discovery of immunotarget drugs against ESCC. CONCLUSION The identification of immunophenotypes in our study provides new therapeutic strategies for patients with ESCC.
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Affiliation(s)
- Danlei Song
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Yongjian Wei
- The First Department of Hepatobiliary and Pancreatic Surgery, Cangzhou Central Hospital, Cangzhou, China
| | - Yuping Hu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Hospital of Reproductive Medicine, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yueting Sun
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Min Liu
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Qian Ren
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Zenan Hu
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Qinghong Guo
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Yuping Wang
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Yongning Zhou
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China.
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25
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Kadian LK, Arora M, Prasad CP, Pramanik R, Chauhan SS. Signaling pathways and their potential therapeutic utility in esophageal squamous cell carcinoma. Clin Transl Oncol 2022; 24:1014-1032. [PMID: 34990001 DOI: 10.1007/s12094-021-02763-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
Esophageal cancer is a complex gastrointestinal malignancy with an extremely poor outcome. Approximately 80% of cases of this malignancy in Asian countries including India are of squamous cell origin, termed Esophageal Squamous Cell Carcinoma (ESCC).The five-year survival rate in ESCC patients is less than 20%. Neo-adjuvant chemo-radiotherapy (NACRT) followed by surgical resection remains the major therapeutic strategy for patients with operable ESCC. However, resistance to NACRT and local recurrence after initial treatment are the leading cause of dismal outcomes in these patients. Therefore, an alternative strategy to promote response to the therapy and reduce the post-operative disease recurrence is highly needed. At the molecular level, wide variations have been observed in tumor characteristics among different populations, nevertheless, several common molecular features have been identified which orchestrate disease progression and clinical outcome in the malignancy. Therefore, determination of candidate molecular pathways for targeted therapy remains the mainstream idea of focus in ESCC research. In this review, we have discussed the key signaling pathways associated with ESCC, i.e., Notch, Wnt, and Nrf2 pathways, and their crosstalk during disease progression. We further discuss the recent developments of novel agents to target these pathways in the context of targeted cancer therapy. In-depth research of the signaling pathways, gene signatures, and a combinatorial approach may help in discovering targeted therapy for ESCC.
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Affiliation(s)
- L K Kadian
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - M Arora
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - C P Prasad
- Department of Medical Oncology (Lab), Dr. B. R. Ambedkar-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - R Pramanik
- Department of Medical Oncology, Dr. B. R. Ambedkar-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - S S Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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26
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Liu M, Liu Y, Zhou R, Liu Z, Guo C, Xu R, Li F, Liu A, Yang H, Zhang S, Shen L, Duan L, Wu Q, Zhao M, Su H, Liu F, Pan Y, Cai H, He Z, Ke Y. Absence of NOTCH1 mutation and presence of CDKN2A deletion predict progression of esophageal lesions. J Pathol 2022; 258:38-48. [PMID: 35612571 DOI: 10.1002/path.5970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/14/2022] [Accepted: 05/22/2022] [Indexed: 12/24/2022]
Abstract
Currently surveillance for esophageal squamous cell carcinoma (ESCC) runs a risk of under-estimation of early lesions which show absence of iodine staining, with no or only mild histologic changes. Development of molecular markers which indicate risk of progression is thus warranted. We performed whole exome sequencing (WES) on biopsies from two sequential endoscopies of a single esophageal lesion and matching blood samples. There were 27 pairs of age, gender, pathologic stage and sampling interval matched progressors and non-progressors identified in a prospective community-based ESCC screening trial. Putative molecular progression markers for ESCC were first evaluated by comparing somatic mutation, copy number alteration (CNA) and mutational signature information among progressors and non-progressors. These markers were then validated with another 24 pairs of matched progressors and non-progressors from the same population using gene alteration status identified by target sequencing and quantitative PCR. Progressors had more somatic mutation and CNA burden, as well as apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) and age-related signature weights as compared with non-progressors. A gene score consisting of somatic NOTCH1 mutation and CDKN2A deletion is predictive of risk of progression in lesions which show absence of iodine staining under endoscopy but have no or only mild dysplasia. This gene score was also validated in an external cohort of matched progressors and non-progressors. Absence of NOTCH1 mutation and presence of CDKN2A deletion are markers of progression in squamous lesions of the esophagus. The gene score established in this study would be ideal for assisting the pathologist identifying high-risk individuals who are potentially "missed" or subject to a risk under-estimation by histologic analysis and might improve the performance of ESCC surveillance. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mengfei Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Ying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Ren Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Zhen Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Chuanhai Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Ruiping Xu
- Anyang Cancer Hospital, Anyang, Henan Province, PR China
| | - Fenglei Li
- Hua County People's Hospital, Henan Province, PR China
| | - Anxiang Liu
- Endoscopy Center, Anyang Cancer Hospital, Anyang, Henan Province, PR China
| | - Haijun Yang
- Department of Pathology, Anyang Cancer Hospital, Anyang, Henan Province, PR China
| | - Sanshen Zhang
- Department of Pathology, Anyang Cancer Hospital, Anyang, Henan Province, PR China
| | - Lin Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Liping Duan
- Department of Gastroenterology, Peking University Third Hospital, Beijing, PR China
| | - Qi Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Endoscopy Center, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Meng Zhao
- Novogene Bioinformatics Technology Co., Ltd, Beijing, PR China
| | - Hong Su
- Novogene Bioinformatics Technology Co., Ltd, Beijing, PR China
| | - Fangfang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Yaqi Pan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Hong Cai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Zhonghu He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, PR China
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27
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Li Z, Liang H, Zhang S, Luo W. A practical framework RNMF for exploring the association between mutational signatures and genes using gene cumulative contribution abundance. Cancer Med 2022; 11:4053-4069. [PMID: 35575002 PMCID: PMC9636515 DOI: 10.1002/cam4.4717] [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: 11/27/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background Mutational signatures are somatic mutation patterns enriching operational mutational processes, which can provide abundant information about the mechanism of cancer. However, understanding of the pathogenic biological processes is still limited, such as the association between mutational signatures and genes. Methods We developed a simple and practical R package called RNMF (https://github.com/zhenzhang‐li/RNMF) for mutational signature analysis, including a key model of cumulative contribution abundance (CCA), which was designed to highlight the association between mutational signatures and genes and then applying it to a meta‐analysis of 1073 individuals with esophageal squamous cell carcinoma (ESCC). Results We revealed a number of known and previously undescribed SBS or ID signatures, and we found that APOBEC signatures (SBS2* and SBS13*) were closely associated with PIK3CA mutation, especially the E545k mutation. Furthermore, we found that age signature is closely related to the frequent mutation of TP53, of which R342* is highlighted due to strongly linked to age signature. In addition, the CCA matrix image data of genes in the signatures New, SBS3*, and SBS17b* were helpful for the preliminary evaluation of shortened survival outcome. These results can be extended to estimate the distribution of mutations or features, and study the potential impact of clinical factors. Conclusions In a word, RNMF can successfully achieve the correlation analysis of mutational signatures and genes, proving a strong theoretical basis for the study of mutational processes during tumor development.
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Affiliation(s)
- Zhenzhang Li
- College of Mathematics and Systems Science, Guangdong Polytechnic Normal University, Guangzhou, China.,School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.,Cloud and Gene AI Research Institute, Guangzhou, China
| | - Haihua Liang
- College of Mathematics and Systems Science, Guangdong Polytechnic Normal University, Guangzhou, China
| | - Shaoan Zhang
- College of Mathematics and Systems Science, Guangdong Polytechnic Normal University, Guangzhou, China.,School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Wen Luo
- College of Mathematics and Systems Science, Guangdong Polytechnic Normal University, Guangzhou, China
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28
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Bregni G, Beck B. Toward Targeted Therapies in Oesophageal Cancers: An Overview. Cancers (Basel) 2022; 14:1522. [PMID: 35326673 PMCID: PMC8946490 DOI: 10.3390/cancers14061522] [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: 02/25/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Oesophageal cancer is one of the leading causes of cancer-related death worldwide. Oesophageal cancer occurs as squamous cell carcinoma (ESCC) or adenocarcinoma (EAC). Prognosis for patients with either ESCC or EAC is poor, with less than 20% of patients surviving more than 5 years after diagnosis. A major progress has been made in the development of biomarker-driven targeted therapies against breast and lung cancers, as well as melanoma. However, precision oncology for patients with oesophageal cancer is still virtually non-existent. In this review, we outline the recent advances in oesophageal cancer profiling and clinical trials based on targeted therapies in this disease.
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Affiliation(s)
- Giacomo Bregni
- Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium;
| | - Benjamin Beck
- Welbio and FNRS Investigator at IRIBHM, Faculty of Medicine, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
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29
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Jiang W, de Jong JM, van Hillegersberg R, Read M. Predicting Response to Neoadjuvant Therapy in Oesophageal Adenocarcinoma. Cancers (Basel) 2022; 14:cancers14040996. [PMID: 35205743 PMCID: PMC8869950 DOI: 10.3390/cancers14040996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/07/2022] [Accepted: 02/12/2022] [Indexed: 12/20/2022] Open
Abstract
(1) Background: Oesophageal cancers are often late-presenting and have a poor 5-year survival rate. The standard treatment of oesophageal adenocarcinomas involves neoadjuvant chemotherapy with or without radiotherapy followed by surgery. However, less than one third of patients respond to neoadjuvant therapy, thereby unnecessarily exposing patients to toxicity and deconditioning. Hence, there is an urgent need for biomarkers to predict response to neoadjuvant therapy. This review explores the current biomarker landscape. (2) Methods: MEDLINE, EMBASE and ClinicalTrial databases were searched with key words relating to “predictive biomarker”, “neoadjuvant therapy” and “oesophageal adenocarcinoma” and screened as per the inclusion and exclusion criteria. All peer-reviewed full-text articles and conference abstracts were included. (3) Results: The search yielded 548 results of which 71 full-texts, conference abstracts and clinical trials were eligible for review. A total of 242 duplicates were removed, 191 articles were screened out, and 44 articles were excluded. (4) Discussion: Biomarkers were discussed in seven categories including imaging, epigenetic, genetic, protein, immunologic, blood and serum-based with remaining studies grouped in a miscellaneous category. (5) Conclusion: Although promising markers and novel methods have emerged, current biomarkers lack sufficient evidence to support clinical application. Novel approaches have been recommended to assess predictive potential more efficiently.
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Affiliation(s)
- William Jiang
- Upper Gastrointestinal Surgery Department, St Vincent’s Hospital Melbourne, 41 Victoria Parade, Fitzroy, VIC 3065, Australia
- Correspondence: (W.J.); (M.R.)
| | - Jelske M. de Jong
- Gastrointestinal Oncology Department, The University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands; (J.M.d.J.); (R.v.H.)
| | - Richard van Hillegersberg
- Gastrointestinal Oncology Department, The University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands; (J.M.d.J.); (R.v.H.)
| | - Matthew Read
- Upper Gastrointestinal Surgery Department, St Vincent’s Hospital Melbourne, 41 Victoria Parade, Fitzroy, VIC 3065, Australia
- Correspondence: (W.J.); (M.R.)
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30
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The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Fan N, Wang Z, Zhou C, Bludau M, Contino G, Zhao Y, Bruns C. Comparison of outcomes between neoadjuvant chemoradiotherapy and neoadjuvant chemotherapy in patients with locally advanced esophageal cancer: A network meta-analysis. EClinicalMedicine 2021; 42:101183. [PMID: 34805809 PMCID: PMC8585620 DOI: 10.1016/j.eclinm.2021.101183] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/07/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Neoadjuvant chemoradiotherapy (NCRT) or neoadjuvant chemotherapy (NCT) followed by surgery are two standard strategies in treating locally advanced esophageal cancer (EC). We aim to compare NCRT and NCT in the management of locally advanced EC patients. METHODS MEDLINE, Embase, CENTRAL, and conferences were systematically searched for clinical trials published up to September 2021. Pairwise comparisons and Bayesian network meta-analyses were conducted to compare overall survival (OS) and disease-free survival (DFS) by reporting the hazard ratio (HR) and 95% credible intervals (CrIs). The study was registered at PROSPERO (CRD42020170619). FINDINGS 25 trials with 4563 EC patients met inclusion criteria. NCRT improved OS (HR: 0·72, 95%CrI: 0·63-0·82) and DFS (HR: 0·72, 95%CrI: 0·63-0·81) compared to surgery alone. NCRT improved OS (HR: 0·83, 95%CrI: 0·69-0·99) and DFS (HR: 0·83, 95%CI: 0·69-0·99) compared to NCT. Subgroup analysis demonstrated that both NCRT (HR: 0·77, 95%CrI: 0·65-0·90) and NCT (HR: 0·81, 95%CrI: 0·67-0·99) improved OS than surgery in esophageal squamous cell carcinoma (ESCC) patients. No significant differences were observed between NCRT and NCT regarding OS (HR: 0·95, 95%CrI: 0·75-1·19) and DFS (HR: 0·90, 95%CrI: 0·50-1·62) in ESCC. The short-term outcomes were similar between NCRT and NCT. The three treatment strategies were comparable in esophageal adenocarcinoma (EAC) subpopulations. INTERPRETATION The study corroborated current guidelines in addressing the importance of analysing EC according to histopathological types. The analysis suggested that in locally advanced ESCC patients, both NCRT and NCT improved OS as compared to surgery alone, whereas no clear evidence supported the optimal strategies between NCRT and NCT. More RCTs comparing different therapeutic strategies in EAC patients are warranted. FUNDING Köln Fortune Program, University of Cologne.
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Affiliation(s)
- Ningbo Fan
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Zhefang Wang
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Chenghui Zhou
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Marc Bludau
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Gianmarco Contino
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Von Hügel Institute, St Edmund College, University of Cambridge, Cambridge, CB3 0BN, United Kingdom
- Queen Elizabeth Hospital, University of Birmingham Hospital Trust, Edgbaston, Birmingham, B15 2GW, United Kingdom
| | - Yue Zhao
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, 50937 Cologne, Germany
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32
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Lin A, Ji P, Niu X, Zhao X, Chen Y, Liu W, Liu Y, Fan W, Sun Y, Miao C, Zhang S, Tan W, Lin D, Wagner EJ, Wu C. CstF64-Induced Shortening of the BID 3'UTR Promotes Esophageal Squamous Cell Carcinoma Progression by Disrupting ceRNA Cross-talk with ZFP36L2. Cancer Res 2021; 81:5638-5651. [PMID: 34607841 DOI: 10.1158/0008-5472.can-21-1201] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/20/2021] [Accepted: 09/30/2021] [Indexed: 12/09/2022]
Abstract
The majority of human genes have multiple polyadenylation sites, which are differentially used through the process of alternative polyadenylation (APA). Dysregulation of APA contributes to numerous diseases, including cancer. However, specific genes subject to APA that impact oncogenesis have not been well characterized, and many cancer APA landscapes remain underexplored. Here, we used dynamic analyses of APA from RNA-seq (DaPars) to define both the 3'UTR APA profile in esophageal squamous cell carcinoma (ESCC) and to identify 3'UTR shortening events that may drive tumor progression. In four distinct squamous cell carcinoma datasets, BID 3'UTRs were recurrently shortened and BID mRNA levels were significantly upregulated. Moreover, system correlation analysis revealed that CstF64 is a candidate upstream regulator of BID 3'UTR length. Mechanistically, a shortened BID 3'UTR promoted proliferation of ESCC cells by disrupting competing endogenous RNA (ceRNA) cross-talk, resulting in downregulation of the tumor suppressor gene ZFP36L2. These in vitro and in vivo results were supported by human patient data whereby 3'UTR shortening of BID and low expression of ZFP36L2 are prognostic factors of survival in ESCC. Collectively, these findings demonstrate that a key ceRNA network is disrupted through APA and promotes ESCC tumor progression.Significance: High-throughput analysis of alternative polyadenylation in esophageal squamous cell carcinoma identifies recurrent shortening of the BID 3'UTR as a driver of disease progression.
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Affiliation(s)
- Ai Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas.,Fulgent Genetics, Houston, Texas
| | - Xiangjie Niu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuan Zhao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yamei Chen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiling Liu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yachen Liu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenyi Fan
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanxia Sun
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chuanwang Miao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen Tan
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,CAMS Key Laboratory of Genetics and Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas. .,Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York.,Center for RNA Biology, University of Rochester, Rochester, New York.,Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,CAMS Key Laboratory of Genetics and Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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33
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Hao D, He S, Harada K, Pizzi MP, Lu Y, Guan P, Chen L, Wang R, Zhang S, Sewastjanow-Silva M, Abdelhakeem A, Shanbhag N, Bhutani M, Han G, Lee JH, Zhao S, Weston B, Blum Murphy M, Waters R, Estrella JS, Roy-Chowdhuri S, Gan Q, Lee JS, Peng G, Hanash SM, Calin GA, Song X, Zhang J, Song S, Wang L, Ajani JA. Integrated genomic profiling and modelling for risk stratification in patients with advanced oesophagogastric adenocarcinoma. Gut 2021; 70:2055-2065. [PMID: 33334899 PMCID: PMC10643023 DOI: 10.1136/gutjnl-2020-322707] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Prognosis of patients with advanced oesophagogastric adenocarcinoma (mEGAC) is poor and molecular determinants of shorter or longer overall survivors are lacking. Our objective was to identify molecular features and develop a prognostic model by profiling the genomic features of patients with mEGAC with widely varying outcomes. DESIGN We profiled 40 untreated mEGACs (20 shorter survivors <13 months and 20 longer survivors >36 months) with whole-exome sequencing (WES) and RNA sequencing and performed an integrated analysis of exome, transcriptome, immune profile and pathological phenotypes to identify the molecular determinants, developing an integrated model for prognosis and comparison with The Cancer Genome Atlas (TCGA) cohorts. RESULTS KMT2C alterations were exclusively observed in shorter survivors together with high level of intratumour heterogeneity and complex clonal architectures, whereas the APOBEC mutational signatures were significantly enriched in longer survivors. Notably, the loss of heterozygosity in chromosome 4 (Chr4) was associated with shorter survival and 'cold' immune phenotype characterised by decreased B, CD8, natural killer cells and interferon-gamma responses. Unsupervised transcriptomic clustering revealed a shorter survivor subtype with distinct expression features (eg, upregulated druggable targets JAK2, MAP3K13 and MECOM). An integrated model was then built based on clinical variables and the identified molecular determinants, which significantly segregated shorter and longer survivors. All the above features and the integrated model have been validated independently in multiple TCGA cohorts. CONCLUSION This study discovered novel molecular features prognosticating overall survival in patients with mEGAC and identified potential novel targets in shorter survivors.
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Affiliation(s)
- Dapeng Hao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Siyuan He
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kazuto Harada
- Gastroenterological Surgery, Kumamoto University, Kumamoto, Kumamoto, Japan
| | - Melissa Pool Pizzi
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Pujun Guan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lu Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Matheus Sewastjanow-Silva
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ahmed Abdelhakeem
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Namita Shanbhag
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Manoop Bhutani
- Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jeffrey H Lee
- Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shuangtao Zhao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brian Weston
- Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mariela Blum Murphy
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rebecca Waters
- Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | - Qiong Gan
- Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ju-Seog Lee
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guang Peng
- Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samir M Hanash
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - George Adrian Calin
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xingzhi Song
- Computational Genomics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianhua Zhang
- Computational Genomics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Magistri M, Happ LE, Ramdial J, Lu X, Stathias V, Kunkalla K, Agarwal N, Jiang X, Schürer SC, Dubovy SR, Chapman JR, Vega F, Dave S, Lossos IS. The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways. CANCER RESEARCH COMMUNICATIONS 2021; 1:1-16. [PMID: 35528192 PMCID: PMC9075502 DOI: 10.1158/2767-9764.crc-21-0022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/03/2021] [Indexed: 12/31/2022]
Abstract
A comprehensive constellation of somatic non-silent mutations and copy number (CN) variations in ocular adnexa marginal zone lymphoma (OAMZL) is unknown. By utilizing whole-exome sequencing in 69 tumors we define the genetic landscape of OAMZL. Mutations and CN changes in CABIN1 (30%), RHOA (26%), TBL1XR1 (22%), and CREBBP (17%) and inactivation of TNFAIP3 (26%) were among the most common aberrations. Candidate cancer driver genes cluster in the B-cell receptor (BCR), NFkB, NOTCH and NFAT signaling pathways. One of the most commonly altered genes is CABIN1, a calcineurin inhibitor acting as a negative regulator of the NFAT and MEF2B transcriptional activity. CABIN1 deletions enhance BCR-stimulated NFAT and MEF2B transcriptional activity, while CABIN1 mutations enhance only MEF2B transcriptional activity by impairing binding of mSin3a to CABIN1. Our data provide an unbiased identification of genetically altered genes that may play a role in the molecular pathogenesis of OAMZL and serve as therapeutic targets.
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Affiliation(s)
- Marco Magistri
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Lanie E. Happ
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Jeremy Ramdial
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - XiaoQing Lu
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
- Center for Computational Science, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Kranthi Kunkalla
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Nitin Agarwal
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Xiaoyu Jiang
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Stephan C. Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
- Center for Computational Science, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Sander R. Dubovy
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Jennifer R. Chapman
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Francisco Vega
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Sandeep Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Izidore S. Lossos
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
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35
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He F, Sha Y, Wang B. Relationship between alcohol consumption and the risks of liver cancer, esophageal cancer, and gastric cancer in China: Meta-analysis based on case-control studies. Medicine (Baltimore) 2021; 100:e26982. [PMID: 34414976 PMCID: PMC8376346 DOI: 10.1097/md.0000000000026982] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 06/25/2021] [Accepted: 07/27/2021] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE : To study the correlation between alcohol consumption and the risks of liver, esophageal squamous cell carcinoma (ESCC), and gastric cancers in China mainland by meta-analysis. METHODS : We systematically searched electronic databases to identify the case-control studies that reported the association between alcohol consumption and the risks of liver, ESCC, and gastric cancers from January 1, 2010 to April 1, 2020. The Newcastle-Ottawa Scale (NOS) was used to evaluate literature quality, and I2 analyzes were used to evaluate the heterogeneity. RESULTS : A total of 2855-related studies were retrieved. After conditional screening, we included 26 case-control studies for meta-analysis. Meta-analysis showed that alcohol consumption was associated with increased risks of liver, ESCC, and gastric cancers (total pooled odds ratio [OR], 1.83; 95% confidence interval [CI], 1.58-2.11; liver cancer OR, 1.83; 95% CI, 1.39-2.40; ESCC OR, 2.00; 95% CI, 1.66-2.40; gastric-cancer OR, 1.54; 95% CI, 1.10-2.15). Subgroup analysis results showed that the pooled ORs of volume of alcohol consumed, years of drinking, age of starting drinking, and drinking status were 1.71 (95% CI, 1.36-2.15), 1.65 (95% CI, 1.33-2.06), 1.38 (95% CI, 0.98-1.94), and 2.00 (95% CI, 1.42-2.81), respectively. Regression analysis showed that geographical region was a source of heterogeneity. CONCLUSION : Alcohol consumption increased the risks of liver cancer, ESCC, and gastric cancers in China. Volume of alcohol consumed, years of drinking, age of starting drinking, and drinking status were all significant factors for these risks.
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Huang Y, Yang Q, Zheng Y, Lin L, Xu X, Xu XE, Silva TC, Hazawa M, Peng L, Cao H, Ding Y, Lu D, Berman BP, Xu LY, Li EM, Yin D. Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma. Nucleic Acids Res 2021; 49:9246-9263. [PMID: 34370013 PMCID: PMC8450110 DOI: 10.1093/nar/gkab679] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 12/31/2022] Open
Abstract
To reconstruct systematically hyperactive transcription factor (TF)-dependent transcription networks in squamous cell carcinomas (SCCs), a computational method (ELMER) was applied to 1293 pan-SCC patient samples, and 44 hyperactive SCC TFs were identified. As a top candidate, DLX5 exhibits a notable bifurcate re-configuration of its bivalent promoter in cancer. Specifically, DLX5 maintains a bivalent state in normal tissues; its promoter is hypermethylation, leading to DLX5 transcriptional silencing in esophageal adenocarcinoma (EAC). In stark contrast, DLX5 promoter gains active histone marks and becomes transcriptionally activated in ESCC, which is directly mediated by SOX2. Functionally, silencing of DLX5 substantially inhibits SCC viability both in vitro and in vivo. Mechanistically, DLX5 cooperates with TP63 in regulating ∼2000 enhancers and promoters, which converge on activating cancer-promoting pathways. Together, our data establish a novel and strong SCC-promoting factor and elucidate a new epigenomic mechanism - bifurcate chromatin re-configuration - during cancer development.
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Affiliation(s)
- Yongsheng Huang
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Qian Yang
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou, China
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lehang Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xin Xu
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou, China
| | - Xiu-E Xu
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou, China
| | - Tiago C Silva
- Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, 920-1192 Ishikawa, Japan
| | - Li Peng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Haotian Cao
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yanbing Ding
- Department of Gastroenterology, Affiliated Hospital of Yangzhou University, Yangzhou University, Jiangsu, China
| | - Daning Lu
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou, China
| | - En-Min Li
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou, China
| | - Dong Yin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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Erkizan HV, Sukhadia S, Natarajan TG, Marino G, Notario V, Lichy JH, Wadleigh RG. Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma. Sci Rep 2021; 11:14814. [PMID: 34285259 PMCID: PMC8292420 DOI: 10.1038/s41598-021-94064-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Esophageal cancer has a strikingly low survival rate mainly due to the lack of diagnostic markers for early detection and effective therapies. In the U.S., 75% of individuals diagnosed with esophageal squamous cell carcinoma (ESCC) are of African descent. African American ESCC (AA ESCC) is particularly aggressive, and its biological underpinnings remain poorly understood. We sought to identify the genomic abnormalities by conducting whole exome sequencing of 10 pairs of matched AA esophageal squamous cell tumor and control tissues. Genomic analysis revealed diverse somatic mutations, copy number alterations (SCNAs), and potential cancer driver genes. Exome variants created two subgroups carrying either a high or low tumor mutation burden. Somatic mutational analysis based on the Catalog of Somatic Mutations in Cancer (COSMIC) detected SBS16 as the prominent signature in the high mutation rate group suggesting increased DNA damage. SBS26 was also detected, suggesting possible defects in mismatch repair and microsatellite instability. We found SCNAs in multiple chromosome segments, encoding MYC on 8q24.21, PIK3CA and SOX2 on 3q26, CCND1, SHANK2, CTTN on 11q13.3, and KRAS on 12p12. Amplifications of EGFRvIII and EGFRvIVa mutants were observed in two patients, representing a novel finding in ESCC that has potential clinical relevance. This present exome sequencing, which to our knowledge, represents the first comprehensive exome analysis exclusively in AA ESCC, and highlights novel mutated loci that might explain the aggressive nature of AA ESCC and lead to the development of diagnostic and prognostic markers as well as therapeutic targets.
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Affiliation(s)
- Hayriye Verda Erkizan
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington, DC, USA.
| | | | | | - Gustavo Marino
- Hepatology and Gastroenterology, Veterans Affairs Medical Center, Washington, DC, USA
| | - Vicente Notario
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Jack H Lichy
- Pathology and Laboratory Service, Veterans Affairs Medical Center, Washington, DC, USA
| | - Robert G Wadleigh
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington, DC, USA.,Hematology and Medical Oncology, Veterans Affairs Medical Center, Washington, DC, USA
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Li LY, Yang Q, Jiang YY, Yang W, Jiang Y, Li X, Hazawa M, Zhou B, Huang GW, Xu XE, Gery S, Zhang Y, Ding LW, Ho AS, Zumsteg ZS, Wang MR, Fullwood MJ, Freedland SJ, Meltzer SJ, Xu LY, Li EM, Koeffler HP, Lin DC. Interplay and cooperation between SREBF1 and master transcription factors regulate lipid metabolism and tumor-promoting pathways in squamous cancer. Nat Commun 2021; 12:4362. [PMID: 34272396 PMCID: PMC8285542 DOI: 10.1038/s41467-021-24656-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/29/2021] [Indexed: 02/05/2023] Open
Abstract
Squamous cell carcinomas (SCCs) comprise one of the most common histologic types of human cancer. Transcriptional dysregulation of SCC cells is orchestrated by tumor protein p63 (TP63), a master transcription factor (TF) and a well-researched SCC-specific oncogene. In the present study, both Gene Set Enrichment Analysis (GSEA) of SCC patient samples and in vitro loss-of-function assays establish fatty-acid metabolism as a key pathway downstream of TP63. Further studies identify sterol regulatory element binding transcription factor 1 (SREBF1) as a central mediator linking TP63 with fatty-acid metabolism, which regulates the biosynthesis of fatty-acids, sphingolipids (SL), and glycerophospholipids (GPL), as revealed by liquid chromatography tandem mass spectrometry (LC-MS/MS)-based lipidomics. Moreover, a feedback co-regulatory loop consisting of SREBF1/TP63/Kruppel like factor 5 (KLF5) is identified, which promotes overexpression of all three TFs in SCCs. Downstream of SREBF1, a non-canonical, SCC-specific function is elucidated: SREBF1 cooperates with TP63/KLF5 to regulate hundreds of cis-regulatory elements across the SCC epigenome, which converge on activating cancer-promoting pathways. Indeed, SREBF1 is essential for SCC viability and migration, and its overexpression is associated with poor survival in SCC patients. Taken together, these data shed light on mechanisms of transcriptional dysregulation in cancer, identify specific epigenetic regulators of lipid metabolism, and uncover SREBF1 as a potential therapeutic target and prognostic marker in SCC.
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Affiliation(s)
- Li-Yan Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Qian Yang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yan-Yi Jiang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yuan Jiang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiang Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Bo Zhou
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Guo-Wei Huang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiu-E Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Sigal Gery
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ying Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Allen S Ho
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zachary S Zumsteg
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Stephen J Freedland
- Division of Urology, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, USA and the Durham VA Medical Center, Durham, NC, USA
| | - Stephen J Meltzer
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - De-Chen Lin
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Su R, Qing Y, Chen J. Targeting differentiation blockade in AML: New hope from cell-surface-based CRISPR screens. Cell Stem Cell 2021; 28:585-587. [PMID: 33798415 DOI: 10.1016/j.stem.2021.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Accumulation of undifferentiated myeloid progenitors is a hallmark of AML, and targeting differentiation blockade represents a promising therapeutic strategy for AML. In this issue of Cell Stem Cell, Wang et al. (2021) conducted surface antigen-guided CRISPR screening and identified ZFP36L2 as a myeloid leukemia differentiation regulator and new therapeutic target.
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Affiliation(s)
- Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA; Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA.
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Wang E, Zhou H, Nadorp B, Cayanan G, Chen X, Yeaton AH, Nomikou S, Witkowski MT, Narang S, Kloetgen A, Thandapani P, Ravn-Boess N, Tsirigos A, Aifantis I. Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation. Cell Stem Cell 2021; 28:718-731.e6. [PMID: 33450187 PMCID: PMC8145876 DOI: 10.1016/j.stem.2020.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/19/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022]
Abstract
Lack of cellular differentiation is a hallmark of many human cancers, including acute myeloid leukemia (AML). Strategies to overcome such a differentiation blockade are an approach for treating AML. To identify targets for differentiation-based therapies, we applied an integrated cell surface-based CRISPR platform to assess genes involved in maintaining the undifferentiated state of leukemia cells. Here we identify the RNA-binding protein ZFP36L2 as a critical regulator of AML maintenance and differentiation. Mechanistically, ZFP36L2 interacts with the 3' untranslated region of key myeloid maturation genes, including the ZFP36 paralogs, to promote their mRNA degradation and suppress terminal myeloid cell differentiation. Genetic inhibition of ZFP36L2 restores the mRNA stability of these targeted transcripts and ultimately triggers myeloid differentiation in leukemia cells. Epigenome profiling of several individuals with primary AML revealed enhancer modules near ZFP36L2 that associated with distinct AML cell states, establishing a coordinated epigenetic and post-transcriptional mechanism that shapes leukemic differentiation.
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Affiliation(s)
- Eric Wang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| | - Hua Zhou
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Bettina Nadorp
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Geraldine Cayanan
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Xufeng Chen
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Anna H Yeaton
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Sofia Nomikou
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Matthew T Witkowski
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Sonali Narang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Andreas Kloetgen
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Palaniraja Thandapani
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Niklas Ravn-Boess
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA; Institute for Computational Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
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Fei Z, Xie R, Chen Z, Xie J, Gu Y, Zhou Y, Xu T. Establishment of a Novel Risk Score System of Immune Genes Associated With Prognosis in Esophageal Carcinoma. Front Oncol 2021; 11:625271. [PMID: 33859939 PMCID: PMC8042266 DOI: 10.3389/fonc.2021.625271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/15/2021] [Indexed: 01/19/2023] Open
Abstract
Background Few studies have addressed the role of immune-related genes in the survival and prognosis of different esophageal cancer (EC) sub-types. We established two new prognostic model indexes by bioinformatics analysis to select patients with esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) who may benefit from immunotherapy. Methods Based on TCGA and ImmPort data sets, we screened immune genes differentially expressed between tumor and normal tissues in ESCC and EAC and analyzed the relationship between these genes and patient survival outcomes. We established the risk score models of immune-related genes in ESCC and EAC by multivariate COX regression analysis. Results We identified 12 and 11 immune-related differentially expressed genes associated with the clinical prognosis of ESCC and EAC respectively, based on which two prognostic risk score models of the two EC sub-types were constructed. It was found that the survival probability of patients with high scores was significantly lower than that of patients with low scores (p < 0.001). BMP1, EGFR, S100A12, HLA-B, TNFSF18, IL1B, MAPT and OXTR were significantly related to sex, TNM stage or survival outcomes of ESCC or EAC patients (p < 0.05). In addition, the risk score of ESCC was significantly correlated with the level of B cell infiltration in immune cells (p < 0.05). Conclusions The prognosis-related immune gene model indexes described herein prove to be useful prognostic biomarkers of the two EC sub-types in that they may provide a reference direction for looking for the beneficiaries of immunotherapy for EC patients.
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Affiliation(s)
- Zhenghua Fei
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongrong Xie
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhi Chen
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Junhui Xie
- Department of Head and Neck Surgery, Tumor Hospital of Ganzhou, Ganzhou, China
| | - Yuyang Gu
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yue Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tongpeng Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Gotovac JR, Kader T, Milne JV, Fujihara KM, Lara-Gonzalez LE, Gorringe KL, Kalimuthu SN, Jayawardana MW, Duong CP, Phillips WA, Clemons NJ. Loss of SMAD4 Is Sufficient to Promote Tumorigenesis in a Model of Dysplastic Barrett's Esophagus. Cell Mol Gastroenterol Hepatol 2021; 12:689-713. [PMID: 33774196 PMCID: PMC8267443 DOI: 10.1016/j.jcmgh.2021.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Esophageal adenocarcinoma (EAC) develops from its precursor Barrett's esophagus through intermediate stages of low- and high-grade dysplasia. However, knowledge of genetic drivers and molecular mechanisms implicated in disease progression is limited. Herein, we investigated the effect of Mothers against decapentaplegic homolog 4 (SMAD4) loss on transforming growth factor β (TGF-β) signaling functionality and in vivo tumorigenicity in high-grade dysplastic Barrett's cells. METHODS An in vivo xenograft model was used to test tumorigenicity of SMAD4 knockdown or knockout in CP-B high-grade dysplastic Barrett's cells. RT2 polymerase chain reaction arrays were used to analyze TGF-β signaling functionality, and low-coverage whole-genome sequencing was performed to detect copy number alterations upon SMAD4 loss. RESULTS We found that SMAD4 knockout significantly alters the TGF-β pathway target gene expression profile. SMAD4 knockout positively regulates potential oncogenes such as CRYAB, ACTA2, and CDC6, whereas the CDKN2A/B tumor-suppressor locus was regulated negatively. We verified that SMAD4 in combination with CDC6-CDKN2A/B or CRYAB genetic alterations in patient tumors have significant predictive value for poor prognosis. Importantly, we investigated the effect of SMAD4 inactivation in Barrett's tumorigenesis. We found that genetic knockdown or knockout of SMAD4 was sufficient to promote tumorigenesis in dysplastic Barrett's esophagus cells in vivo. Progression to invasive EAC was accompanied by distinctive and consistent copy number alterations in SMAD4 knockdown or knockout xenografts. CONCLUSIONS Altogether, up-regulation of oncogenes, down-regulation of tumor-suppressor genes, and chromosomal instability within the tumors after SMAD4 loss implicates SMAD4 as a protector of genome integrity in EAC development and progression. Foremost, SMAD4 loss promotes tumorigenesis from dysplastic Barrett's toward EAC.
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Affiliation(s)
- Jovana R Gotovac
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Tanjina Kader
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Julia V Milne
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Kenji M Fujihara
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Luis E Lara-Gonzalez
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Kylie L Gorringe
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Sangeetha N Kalimuthu
- Anatomical Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Madawa W Jayawardana
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Cuong P Duong
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Wayne A Phillips
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia; Department of Surgery, St Vincent's Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia.
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Wang L, Jia YM, Zuo J, Wang YD, Fan ZS, Feng L, Zhang X, Han J, Lyu WJ, Ni ZY. Gene mutations of esophageal squamous cell carcinoma based on next-generation sequencing. Chin Med J (Engl) 2021; 134:708-715. [PMID: 33725708 PMCID: PMC7990006 DOI: 10.1097/cm9.0000000000001411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancers without effective therapy. To explore potential molecular targets in ESCC, we quantified the mutation spectrum and explored the relationship between gene mutation and clinicopathological characteristics and programmed death-ligand 1 (PD-L1) expression. METHODS Between 2015 and 2019, 29 surgically resected ESCC tissues and adjacent normal tissues from the Fourth Hospital of Hebei Medical University were subjected to targeted next-generation sequencing. The expression levels of PD-L1 were detected by immunohistochemistry. Mutational signatures were extracted from the mutation count matrix by using non-negative matrix factorization. The relationship between detected genomic alterations and clinicopathological characteristics and PD-L1 expression was estimated by Spearman rank correlation analysis. RESULTS The most frequently mutated gene was TP53 (96.6%, 28/29), followed by NOTCH1 (27.6%, 8/29), EP300 (17.2%, 5/29), and KMT2C (17.2%, 5/29). The most frequently copy number amplified and deleted genes were CCND1/FGF3/FGF4/FGF19 (41.4%, 12/29) and CDKN2A/2B (10.3%, 3/29). By quantifying the contribution of the mutational signatures to the mutation spectrum, we found that the contribution of signature 1, signature 2, signature 10, signature 12, signature 13, and signature 17 was relatively high. Further analysis revealed genetic variants associated with cell cycle, chromatin modification, Notch, and Janus kinase-signal transducer and activator of transcription signaling pathways, which may be key pathways in the development and progression of ESCC. Evaluation of PD-L1 expression in samples showed that 13.8% (4/29) of samples had tumor proportion score ≥1%. 17.2% (5/29) of patients had tumor mutation burden (TMB) above 10 mut/Mb. All samples exhibited microsatellite stability. TMB was significantly associated with lymph node metastasis (r = 0.468, P = 0.010), but not significantly associated with PD-L1 expression (r = 0.246, P = 0.198). There was no significant correlation between PD-L1 expression and detected gene mutations (all P > 0.05). CONCLUSION Our research initially constructed gene mutation profile related to surgically resected ESCC in high-incidence areas to explore the mechanism underlying ESCC development and potential therapeutic targets.
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Affiliation(s)
- Long Wang
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Yi-Meng Jia
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Jing Zuo
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Yu-Dong Wang
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Zhi-Song Fan
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Li Feng
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Xue Zhang
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Jing Han
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Wen-Jing Lyu
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Zhi-Yu Ni
- The Affiliated Hospital of Hebei University, Baoding, Hebei 071000, China
- School of Basic Medical Science, Hebei University, Baoding, Hebei 071000, China
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Bányai L, Trexler M, Kerekes K, Csuka O, Patthy L. Use of signals of positive and negative selection to distinguish cancer genes and passenger genes. eLife 2021; 10:e59629. [PMID: 33427197 PMCID: PMC7877913 DOI: 10.7554/elife.59629] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022] Open
Abstract
A major goal of cancer genomics is to identify all genes that play critical roles in carcinogenesis. Most approaches focused on genes positively selected for mutations that drive carcinogenesis and neglected the role of negative selection. Some studies have actually concluded that negative selection has no role in cancer evolution. We have re-examined the role of negative selection in tumor evolution through the analysis of the patterns of somatic mutations affecting the coding sequences of human genes. Our analyses have confirmed that tumor suppressor genes are positively selected for inactivating mutations, oncogenes, however, were found to display signals of both negative selection for inactivating mutations and positive selection for activating mutations. Significantly, we have identified numerous human genes that show signs of strong negative selection during tumor evolution, suggesting that their functional integrity is essential for the growth and survival of tumor cells.
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Affiliation(s)
- László Bányai
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Maria Trexler
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Krisztina Kerekes
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Orsolya Csuka
- Department of Pathogenetics, National Institute of OncologyBudapestHungary
| | - László Patthy
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
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45
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Zhang C, Luo Y, Zhang Z, Zhang Z, Zhang G, Wang F, Che Y, Fang L, Zhang Y, Sun N, He J. Identification of a Prognostic Immune Signature for Esophageal Squamous Cell Carcinoma to Predict Survival and Inflammatory Landscapes. Front Cell Dev Biol 2020; 8:580005. [PMID: 33392181 PMCID: PMC7773787 DOI: 10.3389/fcell.2020.580005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/03/2020] [Indexed: 01/06/2023] Open
Abstract
Immunotherapy has achieved success in the treatment of esophageal squamous cell carcinoma (ESCC). However, studies concerning immune phenotypes within the ESCC microenvironment and their relationship with prognostic outcomes are limited. We constructed and validated an individual immune-related risk signature for patients with ESCC. We collected 196 ESCC cases, including 119 samples from our previous public data (GSE53624) to use as a training set and an independent cohort with 77 quantitative real-time polymerase chain reaction (qRT-PCR) data, which we used for validation. Head and neck squamous cell carcinoma (HNSCC) and lung squamous cell carcinoma (LUSC) cohorts were also collected for validation. A least absolute shrinkage and selection operator (LASSO) model and a stepwise Cox proportional hazards regression model were used to construct the immune-specific signature. The potential mechanism and inflammatory landscapes of the signature were explored using bioinformatics and immunofluorescence assay methods. This signature predicted different prognoses in clinical subgroups and the independent cohort, as well as in patients with HNSCC and LUSC. Further exploration revealed that the signature was associated with specific inflammatory activities (activation of macrophages and T-cell signaling transduction). Additionally, high-risk patients exhibited distinctive immune checkpoints panel and higher regulatory T cell and fibroblast infiltration. This signature served as an independent prognostic factor in ESCC. This was the first applicable immune-related risk signature for ESCC. Our results furnished new hints of immune profiling of ESCC, which may provide some clues to further optimize associated cancer immunotherapies.
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Affiliation(s)
- Chaoqi Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yuejun Luo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhen Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhihui Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Guochao Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Feng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yun Che
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lingling Fang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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46
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Shi X, Zheng Y, Jiang L, Zhou B, Yang W, Li L, Ding L, Huang M, Gery S, Lin DC, Koeffler HP. EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma. Nucleic Acids Res 2020; 48:11434-11451. [PMID: 33080033 PMCID: PMC7672457 DOI: 10.1093/nar/gkaa901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/22/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Core regulatory circuitry (CRC)-dependent transcriptional network is critical for developmental tumors in children and adolescents carrying few gene mutations. However, whether and how CRC contributes to transcription regulation in Ewing sarcoma is unknown. Here, we identify and functionally validate a CRC 'trio' constituted by three transcription factors (TFs): KLF15, TCF4 and NKX2-2, in Ewing sarcoma cells. Epigenomic analyses demonstrate that EWS-FLI1, the primary fusion driver for this cancer, directly establishes super-enhancers of each of these three TFs to activate their transcription. In turn, KLF15, TCF4 and NKX2-2 co-bind to their own and each other's super-enhancers and promoters, forming an inter-connected auto-regulatory loop. Functionally, CRC factors contribute significantly to cell proliferation of Ewing sarcoma both in vitro and in vivo. Mechanistically, CRC factors exhibit prominent capacity of co-regulating the epigenome in cooperation with EWS-FLI1, occupying 77.2% of promoters and 55.6% of enhancers genome-wide. Downstream, CRC TFs coordinately regulate gene expression networks in Ewing sarcoma, controlling important signaling pathways for cancer, such as lipid metabolism pathway, PI3K/AKT and MAPK signaling pathways. Together, molecular characterization of the oncogenic CRC model advances our understanding of the biology of Ewing sarcoma. Moreover, CRC-downstream genes and signaling pathways may contain potential therapeutic targets for this malignancy.
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Affiliation(s)
- Xianping Shi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation; State Key Laboratory of Respiratory Disease; Affiliated Cancer Hospital of Guangzhou Medical University; Sino-French Hoffmann institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 510120, P.R. China
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Liling Jiang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation; State Key Laboratory of Respiratory Disease; Affiliated Cancer Hospital of Guangzhou Medical University; Sino-French Hoffmann institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 510120, P.R. China
| | - Bo Zhou
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Liyan Li
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Lingwen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117600, Singapore
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, P.R. China
| | - Sigal Gery
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117600, Singapore
- National University Cancer Institute, National University Hospital Singapore, Singapore 119074, Singapore
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47
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Smolková K, Mikó E, Kovács T, Leguina-Ruzzi A, Sipos A, Bai P. Nuclear Factor Erythroid 2-Related Factor 2 in Regulating Cancer Metabolism. Antioxid Redox Signal 2020; 33:966-997. [PMID: 31989830 PMCID: PMC7533893 DOI: 10.1089/ars.2020.8024] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Nuclear factor erythroid 2 (NFE2)-related factor 2 (NFE2L2, or NRF2) is a transcription factor predominantly affecting the expression of antioxidant genes. NRF2 plays a significant role in the control of redox balance, which is crucial in cancer cells. NRF2 activation regulates numerous cancer hallmarks, including metabolism, cancer stem cell characteristics, tumor aggressiveness, invasion, and metastasis formation. We review the molecular characteristics of the NRF2 pathway and discuss its interactions with the cancer hallmarks previously listed. Recent Advances: The noncanonical activation of NRF2 was recently discovered, and members of this pathway are involved in carcinogenesis. Further, cancer-related changes (e.g., metabolic flexibility) that support cancer progression were found to be redox- and NRF2 dependent. Critical Issues: NRF2 undergoes Janus-faced behavior in cancers. The pro- or antineoplastic effects of NRF2 are context dependent and essentially based on the specific molecular characteristics of the cancer in question. Therefore, systematic investigation of NRF2 signaling is necessary to clarify its role in cancer etiology. The biggest challenge in the NRF2 field is to determine which cancers can be targeted for better clinical outcomes. Further, large-scale genomic and transcriptomic studies are missing to correlate the clinical outcome with the activity of the NRF2 system. Future Directions: To exploit NRF2 in a clinical setting in the future, the druggable members of the NRF2 pathway should be identified. In addition, it will be important to study how the modulation of the NRF2 system interferes with cytostatic drugs and their combinations.
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Affiliation(s)
- Katarína Smolková
- Department of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences (IPHYS CAS), Prague, Czech Republic
| | - Edit Mikó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, Hungary
| | - Tünde Kovács
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Alberto Leguina-Ruzzi
- Department of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences (IPHYS CAS), Prague, Czech Republic
| | - Adrienn Sipos
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, Hungary.,Faculty of Medicine, Research Center for Molecular Medicine, University of Debrecen, Debrecen, Hungary
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48
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[Mutation signatures in head and neck squamous cell carcinoma : Pathogenesis and therapeutic potential]. HNO 2020; 68:922-926. [PMID: 33044581 DOI: 10.1007/s00106-020-00954-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND The pathogenesis of head and neck squamous cell carcinoma (HNSCC) is a complex and multistage process which results from the interaction of exogenous and endogenous cellular processes. Each of these processes leaves a characteristic pattern of mutations on the tumor genome, a so-called mutational signature. STATE OF THE ART The subject of current studies is to decipher specific signatures of mutational processes operating during HNSCC pathogenesis and to address their prognostic value. Computational analysis of genomic sequencing data by The Cancer Genome Atlas (TCGA) revealed mutational signatures 1, 2, 4, 5, 7, and 13 as the main players in HNSCC pathogenesis. Signature 16 was first discovered in human papillomavirus (HPV)-negative oral and oropharyngeal tumors. In many studies, an association of signature 16 with alcohol and tobacco consumption as well as with an unfavorable prognosis was described.
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49
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Geng Q, Lao J, Zuo X, Chen S, Bei JX, Xu D. Identification of the distinct genomic features in gastroesophageal junction adenocarcinoma and its Siewert subtypes. J Pathol 2020; 252:263-273. [PMID: 32715475 DOI: 10.1002/path.5516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/15/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022]
Abstract
Rates of gastroesophageal junction adenocarcinomas (GEJAs) have shown an alarming increase; however, the genetic background of GEJA and its Siewert classification have yet to be uncovered. Here, 60 paired tumor and normal DNA samples from GEJA patients were analyzed by whole-exome sequencing. Among them, 13 were Siewert type I, 14 were type II, and 33 were type III. A predominance of C/G>T/A substitutions was discovered in GEJA, followed by C/G>A/T substitutions. Notably, Siewert type I and type II/III display distinct sets of driver genes, mutational spectrum, and recurrently disrupted pathways. Siewert type I showed similarity to esophageal adenocarcinomas (EACs) and the chromosomal instability subtype of stomach adenocarcinomas, while Siewert type II/III showed similarity to the genomic stable subtype of stomach adenocarcinoma. We also found that mutation of FBXW7, a driver gene of GEJA, was enriched in Siewert type I. Our data identify differences between GEJA and stomach/EACs at the genomic level and provide evidence for differential treatment based on Siewert classification of GEJA. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Qirong Geng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Dongan Road, Shanghai, PR China
| | - Jiawen Lao
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Xiaoyu Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Shangxiang Chen
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Jin-Xin Bei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Dazhi Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Dongan Road, Shanghai, PR China.,Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China
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50
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Plath M, Gass J, Hlevnjak M, Li Q, Feng B, Hostench XP, Bieg M, Schroeder L, Holzinger D, Zapatka M, Freier K, Weichert W, Hess J, Zaoui K. Unraveling most abundant mutational signatures in head and neck cancer. Int J Cancer 2020; 148:115-127. [PMID: 32930393 DOI: 10.1002/ijc.33297] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022]
Abstract
Genomic alterations are a driving force in the multistep process of head and neck cancer (HNC) and result from the interaction of exogenous environmental exposures and endogenous cellular processes. Each of these processes leaves a characteristic pattern of mutations on the tumor genome providing the unique opportunity to decipher specific signatures of mutational processes operative during HNC pathogenesis and to address their prognostic value. Computational analysis of whole exome sequencing data of the HIPO-HNC (Heidelberg Center for Personalized Oncology-head and neck cancer) (n = 83) and TCGA-HNSC (The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma) (n = 506) cohorts revealed five common mutational signatures (Catalogue of Somatic Mutations in Cancer [COSMIC] Signatures 1, 2, 3, 13 and 16) and demonstrated their significant association with etiological risk factors (tobacco, alcohol and HPV16). Unsupervised hierarchical clustering identified four clusters (A, B, C1 and C2) of which Subcluster C2 was enriched for cases with a higher frequency of signature 16 mutations. Tumors of Subcluster C2 had significantly lower p16INK4A expression accompanied by homozygous CDKN2A deletion in almost one half of cases. Survival analysis revealed an unfavorable prognosis for patients with tumors characterized by a higher mutation burden attributed to signature 16 as well as cases in Subcluster C2. Finally, a LASSO-Cox regression model was applied to prioritize clinically relevant signatures and to establish a prognostic risk score for head and neck squamous cell carcinoma patients. In conclusion, our study provides a proof of concept that computational analysis of somatic mutational signatures is not only a powerful tool to decipher environmental and intrinsic processes in the pathogenesis of HNC, but could also pave the way to establish reliable prognostic patterns.
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Affiliation(s)
- Michaela Plath
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Johanna Gass
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Mario Hlevnjak
- Division Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Qiaoli Li
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Bohai Feng
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Xavier Pastor Hostench
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology, DKFZ-HIPO, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology, DKFZ-HIPO, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lea Schroeder
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dana Holzinger
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Zapatka
- Division Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kolja Freier
- Department of Oral and Cranio-Maxillofacial Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Jochen Hess
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karim Zaoui
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
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