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Hebert JD, Tang YJ, Szamecz M, Andrejka L, Lopez SS, Petrov DA, Boross G, Winslow MM. Combinatorial In Vivo Genome Editing Identifies Widespread Epistasis and an Accessible Fitness Landscape During Lung Tumorigenesis. Mol Biol Evol 2025; 42:msaf023. [PMID: 39907430 PMCID: PMC11824425 DOI: 10.1093/molbev/msaf023] [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: 05/28/2024] [Revised: 11/15/2024] [Accepted: 01/15/2025] [Indexed: 02/06/2025] Open
Abstract
Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the interactions that drive tumorigenesis in vivo.
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Affiliation(s)
- Jess D Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuning J Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Márton Szamecz
- Faculty of Informatics, Eötvös Loránd University, Budapest, Hungary
- National Laboratory for Health Security, Centre for Eco-Epidemiology, Budapest, Hungary
- Institute of Evolution, HUN-REN Centre for Ecological Research, Budapest, Hungary
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven S Lopez
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Gábor Boross
- National Laboratory for Health Security, Centre for Eco-Epidemiology, Budapest, Hungary
- Institute of Evolution, HUN-REN Centre for Ecological Research, Budapest, Hungary
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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Hebert JD, Tang YJ, Andrejka L, Lopez SS, Petrov DA, Boross G, Winslow MM. Combinatorial in vivo genome editing identifies widespread epistasis during lung tumorigenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583981. [PMID: 38496564 PMCID: PMC10942407 DOI: 10.1101/2024.03.07.583981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable tumorigenesis in vivo , largely due to a lack of methods for investigating genetic interactions in a high-throughput and multiplexed manner. Here, we employed a novel platform to generate tumors with all pairwise inactivation of ten tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including dramatically synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. This approach has the potential to expand the scope of genetic interactions that may be functionally characterized in vivo , which could lead to a better understanding of how complex tumor genotypes impact each step of carcinogenesis.
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Zhang Z, Zhang H, Liao X, Tsai HI. KRAS mutation: The booster of pancreatic ductal adenocarcinoma transformation and progression. Front Cell Dev Biol 2023; 11:1147676. [PMID: 37152291 PMCID: PMC10157181 DOI: 10.3389/fcell.2023.1147676] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer. It has a poor response to conventional therapy and has an extremely poor 5-year survival rate. PDAC is driven by multiple oncogene mutations, with the highest mutation frequency being observed in KRAS. The KRAS protein, which binds to GTP, has phosphokinase activity, which further activates downstream effectors. KRAS mutation contributes to cancer cell proliferation, metabolic reprogramming, immune escape, and therapy resistance in PDAC, acting as a critical driver of the disease. Thus, KRAS mutation is positively associated with poorer prognosis in pancreatic cancer patients. This review focus on the KRAS mutation patterns in PDAC, and further emphases its role in signal transduction, metabolic reprogramming, therapy resistance and prognosis, hoping to provide KRAS target therapy strategies for PDAC.
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Affiliation(s)
- Zining Zhang
- Institute of Medical Imaging and Artificial Intelligence, Jiangsu University, Zhenjiang, China
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Heng Zhang
- Institute of Medical Imaging and Artificial Intelligence, Jiangsu University, Zhenjiang, China
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiang Liao
- Institute of Medical Imaging and Artificial Intelligence, Jiangsu University, Zhenjiang, China
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Hsiang-i Tsai
- Institute of Medical Imaging and Artificial Intelligence, Jiangsu University, Zhenjiang, China
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
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Yamaguchi T, Ikehara S, Akimoto Y, Nakanishi H, Kume M, Yamamoto K, Ohara O, Ikehara Y. TGF-β signaling promotes tube-structure-forming growth in pancreatic duct adenocarcinoma. Sci Rep 2019; 9:11247. [PMID: 31375695 PMCID: PMC6677751 DOI: 10.1038/s41598-019-47101-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
Tube-forming growth is an essential histological feature of pancreatic duct adenocarcinoma (PDAC) and of the pancreatic duct epithelium; nevertheless, the nature of the signals that start to form the tubular structures remains unknown. Here, we showed the clonal growth of PDAC cell lines in a three-dimensional (3D) culture experiment that modeled the clonal growth of PDAC. At the beginning of this study, we isolated the sphere- and tube-forming clones from established mouse pancreatic cancer cell lines via limiting dilution culture using collagen gel. Compared with cells in spherical structures, the cells in the formed tubes exhibited a lower CK19 expression in 3D culture and in the tumor that grew in the abdominal cavity of nude mice. Conversely, the expression of the transforming growth factor β (TGF-β)-signaling target mRNAs was higher in the formed tube vs the spherical structures, suggesting that TGF-β signaling is more active in the tube-forming process than the sphere-forming process. Treatment of sphere-forming clones with TGF-β1 induced tube-forming growth, upregulated the TGF-β-signaling target mRNAs, and yielded electron microscopic findings of a fading epithelial phenotype. In contrast, the elimination of TGF-β-signaling activation by treatment with inhibitors diminished the tube-forming growth and suppressed the expression of the TGF-β-signaling target mRNAs. Moreover, upregulation of the Fn1, Mmp2, and Snai1 mRNAs, which are hallmarks of tube-forming growth in PDAC, was demonstrated in a mouse model of carcinogenesis showing rapid progression because of the aggressive invasion of tube-forming cancer. Our study suggests that the tube-forming growth of PDAC relies on the activation of TGF-β signaling and highlights the importance of the formation of tube structures.
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Affiliation(s)
- Takashi Yamaguchi
- Department of Molecular and Tumor Pathology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8565, Japan
| | - Sanae Ikehara
- Department of Molecular and Tumor Pathology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8565, Japan
| | - Yoshihiro Akimoto
- Department of Anatomy, Kyorin University School of Medicine, Mitaka, 181-8611, Japan
| | - Hayao Nakanishi
- Laboratory of Pathology and Clinical Research, Aichi Cancer Center Aichi Hospital, Okazaki, 444-0011, Japan
| | - Masahiko Kume
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Chiba, Japan
| | - Kazuo Yamamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Chiba, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Yuzuru Ikehara
- Department of Molecular and Tumor Pathology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan. .,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8565, Japan.
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Bai Z, Shi Y, Wang J, Qiu L, Monroe EJ, Teng G, Zhang F, Yang X. Intratumoral radiofrequency hyperthermia-enhanced direct chemotherapy of pancreatic cancer. Oncotarget 2018; 8:3591-3599. [PMID: 27690303 PMCID: PMC5356906 DOI: 10.18632/oncotarget.12295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/20/2016] [Indexed: 12/22/2022] Open
Abstract
Purpose To investigate the technical feasibility of using ultrasound-guided intratumoral radiofrequency hyperthermia (RFH) to enhance local chemotherapy of rat orthotopic pancreatic cancers. Materials and Methods Orthotopic pancreatic cancer masses were established by inoculating luciferase/mCherry labeled-pancreatic cancer cells into the pancreatic tails of Lewis model rats via a laparotomy approach. Twenty-four rats with pancreatic cancer and 24 mice with subcutaneous pancreatic cancer xenografts in four study groups (n = 6/group) received various treatments: i) combination therapy of intratumoral MR imaging-heating-guidewire-mediated RFH (42oC) plus local chemotherapy (gemcitabine); ii) intratumoral chemotherapy alone; iii) RFH alone; and (iv)phosphate-buffered saline (PBS). Transcutaneous ultrasound imaging was used to guide the treatment and subsequently follow changes in tumor sizes. Bioluminescence optical imaging was performed to follow photon signal changes. Sonographic and optical findings were correlated with histology at 14 days. Results Optical imaging demonstrated a significantly decreased bioluminescence signal in mice with combination therapy group, compared with the other control groups (0.51±0.18 VS 1.6±0.4 VS 3.18±0.9 VS 3.5±0.96, p < 0.05). Ultrasound imaging showed the smallest tumor volumes of both mice and rat group with the combination therapy, compared with other control groups (0.62±0.16 VS 1.25±0.19 VS 2.28±0.25 VS 2.64±0.26, p < 0.05) and (0.75±0.18 VS 1.31±0.30 VS 1.61±0.28 VS 1.72±0.28, p < 0.05). Both imaging findings were confirmed by histologic correlation. Conclusion Intratumoral RFH can augment the chemotherapeutic effect in an orthotopic pancreatic cancer model.
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Affiliation(s)
- Zhibin Bai
- Image-Guided Biomolecular Intervention Research, Section of Interventional Radiology, Department of Radiology, University of Washington School of Medicine, Seattle, WA, USA.,Department of Radiology, Zhongda Hospital, Southeastern University, Nanjing, China
| | - Yaoping Shi
- Image-Guided Biomolecular Intervention Research, Section of Interventional Radiology, Department of Radiology, University of Washington School of Medicine, Seattle, WA, USA.,Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jianfeng Wang
- Image-Guided Biomolecular Intervention Research, Section of Interventional Radiology, Department of Radiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Longhua Qiu
- Image-Guided Biomolecular Intervention Research, Section of Interventional Radiology, Department of Radiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Eric J Monroe
- Image-Guided Biomolecular Intervention Research, Section of Interventional Radiology, Department of Radiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Gaojun Teng
- Department of Radiology, Zhongda Hospital, Southeastern University, Nanjing, China
| | - Feng Zhang
- Image-Guided Biomolecular Intervention Research, Section of Interventional Radiology, Department of Radiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiaoming Yang
- Image-Guided Biomolecular Intervention Research, Section of Interventional Radiology, Department of Radiology, University of Washington School of Medicine, Seattle, WA, USA
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