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Huang J, Michaud E, Shinde-Jadhav S, Fehric S, Marcq G, Mansure JJ, Cury F, Brimo F, Piccirillo CA, Kassouf W. Effects of combined radiotherapy with immune checkpoint blockade on immunological memory in luminal-like subtype murine bladder cancer model. Cancer Biol Ther 2024; 25:2365452. [PMID: 38860746 PMCID: PMC11174127 DOI: 10.1080/15384047.2024.2365452] [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: 03/17/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024] Open
Abstract
MIBC is a highly lethal disease, and the patient survival rate has not improved significantly over the last decades. UPPL is a cell line that can be used to recapitulate the luminal-like molecular subtype of bladder cancer and to discover effective treatments to be translated in patients. Here, we investigate the effects of combinational treatments of radiotherapy and immunotherapy in this recently characterized UPPL tumor-bearing mice. We first characterized the baseline tumor microenvironment and the effect of radiation, anti-PD-L1, and combinatorial treatments. Then, the mice were re-challenged with a second tumor (rechallenged tumor) in the contralateral flank of the first tumor to assess the immunological memory. Radiation slowed down the tumor growth. All treatments also decreased the neutrophil population and increased the T cell population. Anti-PD-L1 therapy was not able to synergize with radiation to further delay tumor growth. Furthermore, none of the treatments were able to generate immune memory. The treatments were not sufficient to induce a significant and lasting pool of memory cells. We show here that anti-PD-L1 treatment added to radiotherapy was not enough to achieve T cell-mediated memory in UPPL tumors. Stronger T cell activation signals may be required to enhance radiation efficacy in luminal-like bladder cancer.
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Affiliation(s)
- JiaMin Huang
- Cancer Research Program, Research Institute of McGill University Health Center, Montréal, QC, Canada
| | - Eva Michaud
- Cancer Research Program, Research Institute of McGill University Health Center, Montréal, QC, Canada
| | - Surashri Shinde-Jadhav
- Cancer Research Program, Research Institute of McGill University Health Center, Montréal, QC, Canada
| | - Sabina Fehric
- Cancer Research Program, Research Institute of McGill University Health Center, Montréal, QC, Canada
| | - Gautier Marcq
- Division of Urology, Department of Surgery, McGill University Health Center, Montréal, QC, Canada
| | - Jose Joao Mansure
- Cancer Research Program, Research Institute of McGill University Health Center, Montréal, QC, Canada
| | - Fabio Cury
- Department of Radiation Oncology, McGill University Health Center, Montréal, QC, Canada
| | - Fadi Brimo
- Department of Pathology, McGill University Health Center, Montréal, QC, Canada
| | - Ciriaco A. Piccirillo
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunology in Global Health Program, The Research Institute of the McGill University Health Centre (RI-MUHC), Montréal, QC, Canada
- Centre of Excellence in Translational Immunology, Montréal, QC, Canada
| | - Wassim Kassouf
- Cancer Research Program, Research Institute of McGill University Health Center, Montréal, QC, Canada
- Division of Urology, Department of Surgery, McGill University Health Center, Montréal, QC, Canada
- Centre of Excellence in Translational Immunology, Montréal, QC, Canada
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2
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Yu S, Jiang Y, Li Q, Li M, Su J, Lai S, Gan Z, Ding Z, Yu Q. Nano-sensitizer with self-amplified drug release and hypoxia normalization properties potentiates efficient chemoradiotherapy of pancreatic cancer. Biomaterials 2024; 310:122634. [PMID: 38823195 DOI: 10.1016/j.biomaterials.2024.122634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/29/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024]
Abstract
The hypoxic nature of pancreatic cancer, one of the most lethal malignancies worldwide, significantly impedes the effectiveness of chemoradiotherapy. Although the development of oxygen carriers and hypoxic sensitizers has shown promise in overcoming tumor hypoxia. The heterogeneity of hypoxia-primarily caused by limited oxygen penetration-has posed challenges. In this study, we designed a hypoxia-responsive nano-sensitizer by co-loading tirapazamine (TPZ), KP372-1, and MK-2206 in a metronidazole-modified polymeric vesicle. This nano-sensitizer relies on efficient endogenous NAD(P)H quinone oxidoreductase 1-mediated redox cycling induced by KP372-1, continuously consuming periphery oxygen and achieving evenly distributed hypoxia. Consequently, the normalized tumor microenvironment facilitates the self-amplified release and activation of TPZ without requiring deep penetration. The activated TPZ and metronidazole further sensitize radiotherapy, significantly reducing the radiation dose needed for extensive cell damage. Additionally, the coloaded MK-2206 complements inhibition of therapeutic resistance caused by Akt activation, synergistically enhancing the hypoxic chemoradiotherapy. This successful hypoxia normalization strategy not only overcomes hypoxia resistance in pancreatic cancer but also provides a potential universal approach to sensitize hypoxic tumor chemoradiotherapy by reshaping the hypoxic distribution.
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Affiliation(s)
- Shuchen Yu
- Beijing Laboratory of Biomedical Materials, The State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Ministry of Education), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yitong Jiang
- Beijing Laboratory of Biomedical Materials, The State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Ministry of Education), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qian Li
- Beijing Laboratory of Biomedical Materials, The State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Ministry of Education), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Mengmeng Li
- Beijing Laboratory of Biomedical Materials, The State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Ministry of Education), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jiamin Su
- Beijing Laboratory of Biomedical Materials, The State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Ministry of Education), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shicong Lai
- Department of Urology, Peking University People's Hospital, Peking University, Beijing, 100044, China
| | - Zhihua Gan
- Beijing Laboratory of Biomedical Materials, The State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Ministry of Education), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhenshan Ding
- Department of Urology, China-Japan Friendship Hospitals, Beijing, 100029, China.
| | - Qingsong Yu
- Beijing Laboratory of Biomedical Materials, The State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Ministry of Education), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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3
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Gardner LL, Thompson SJ, O'Connor JD, McMahon SJ. Modelling radiobiology. Phys Med Biol 2024; 69:18TR01. [PMID: 39159658 DOI: 10.1088/1361-6560/ad70f0] [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: 04/25/2024] [Accepted: 08/19/2024] [Indexed: 08/21/2024]
Abstract
Radiotherapy has played an essential role in cancer treatment for over a century, and remains one of the best-studied methods of cancer treatment. Because of its close links with the physical sciences, it has been the subject of extensive quantitative mathematical modelling, but a complete understanding of the mechanisms of radiotherapy has remained elusive. In part this is because of the complexity and range of scales involved in radiotherapy-from physical radiation interactions occurring over nanometres to evolution of patient responses over months and years. This review presents the current status and ongoing research in modelling radiotherapy responses across these scales, including basic physical mechanisms of DNA damage, the immediate biological responses this triggers, and genetic- and patient-level determinants of response. Finally, some of the major challenges in this field and potential avenues for future improvements are also discussed.
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Affiliation(s)
- Lydia L Gardner
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - Shannon J Thompson
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - John D O'Connor
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
- Ulster University School of Engineering, York Street, Belfast BT15 1AP, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
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4
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van Goor IW, Raymakers L, Andel DS, Brosens LA, Kranenburg O, Leusen JH, Meijer GJ, Molenaar IQ, van Santvoort HC, de Vries JW, Wopereis AJ, Intven MP, Daamen LA. Radiation response assessment of organoids derived from patients with pancreatic cancer. Clin Transl Radiat Oncol 2024; 48:100829. [PMID: 39192878 PMCID: PMC11347840 DOI: 10.1016/j.ctro.2024.100829] [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: 06/19/2023] [Revised: 04/26/2024] [Accepted: 07/27/2024] [Indexed: 08/29/2024] Open
Abstract
Background The effectiveness of radiotherapy for pancreatic cancer is debated. Patient-derived organoids (PDOs) already mimicked clinical radiation response in other cancer types, which could be valuable in pancreatic cancer as well. This study aimed to investigate whether PDOs can be used to model RT response in pancreatic cancer and to explore the presence of a dose-response correlation. Methods PDOs derived from two pancreatic cancer patients (HUB-08-B2-022A and HUB-08-B2-026B) were irradiated with doses ranging from 0 to 40 Gray. Viability assessments were conducted after seven and 10 days by measuring ATP-levels. Results were normalized, defining the viability at 0 Gray as 100 % and an absolute viability of 0 as 0 %. The relative area under the curve (rAUC) was calculated (0 = total sensitivity, 1 = total resistance). Results With a readout time of seven days, both HUB-08-B2-022A and HUB-08-B2-026B exhibited viability above 50 % at the highest dose of 12 Gy (rAUC of 0.79 and 0.69, respectively). With a readout time of 10 days, both PDOs showed a dose-response relation although HUB-08-B2-022A was more sensitive than HUB-08-B2-026B (rAUC of 0.37 and 0.51, respectively). Increasing the radiation dose to 40 Gy did not further affect viability, but the dose-response relation remained present (rAUC of 0.13 and 0.26, respectively). In the final experiment with a readout time of 10 days and a maximum dose of 14 Gy, the dose-response correlation was paramount in both PDOs (rAUC 0.28 and 0.45, respectively), with HUB-08-B2-022A being most sensitive. Conclusions In this setup, both pancreatic cancer PDOs showed an irradiation dose-response correlation. These preliminary findings suggest that pancreatic cancer PDOs are suitable for assessing radiation response in vitro. Further experiments are needed to eventually simulate treatment responses to personalized treatment strategies.
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Affiliation(s)
- Iris W.J.M. van Goor
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Leon Raymakers
- Center for Translational Immunology, UMC Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Daan S.H. Andel
- Department of Surgical Oncology, Lab of Translational Oncology, UMC Utrecht Cancer Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lodewijk A.A. Brosens
- Department of Pathology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Onno Kranenburg
- Department of Surgical Oncology, Lab of Translational Oncology, UMC Utrecht Cancer Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jeanette H.W. Leusen
- Center for Translational Immunology, UMC Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gert J. Meijer
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - I. Quintus Molenaar
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Hjalmar C. van Santvoort
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - J.H. Wilfred de Vries
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Andre J.M. Wopereis
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Martijn P.W. Intven
- Department of Radiation Oncology, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
| | - Lois A. Daamen
- Department of Surgery, Regional Academic Cancer Center Utrecht, Utrecht University, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Utrecht, the Netherlands
- Imaging Division, University Medical Center Utrecht Cancer Center, Utrecht University, Utrecht, the Netherlands
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5
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Zhou Y, D'Andrea VD, Shanmugam SP, Stelter I, Stormoen DR, Chroneos R, Hanlon T, Epstein I, Bekele RT, Anderson WJ, Carvalho FFL, Bellmunt J, Mouw KW. Activity of Enfortumab Vedotin and Sacituzumab Govitecan with Radiation in Preclinical Models of Bladder Cancer. Eur Urol 2024; 86:69-71. [PMID: 38523005 DOI: 10.1016/j.eururo.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/23/2024] [Accepted: 03/07/2024] [Indexed: 03/26/2024]
Affiliation(s)
- Yuzhen Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vincent D D'Andrea
- Department of Urology, Brigham & Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Surish P Shanmugam
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Isabella Stelter
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dag R Stormoen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Rea Chroneos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Timothy Hanlon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ilana Epstein
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Raie T Bekele
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - William J Anderson
- Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
| | - Filipe F L Carvalho
- Department of Urology, Brigham & Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joaquim Bellmunt
- Harvard Medical School, Boston, MA, USA; Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Radiation Oncology, Brigham & Women's Hospital, Boston, MA, USA.
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6
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Wolfe AR, Feng H, Zuniga O, Rodrigues H, Eldridge DE, Yang L, Shen C, Williams TM. RAS-RAF-miR-296-3p signaling axis increases Rad18 expression to augment radioresistance in pancreatic and thyroid cancers. Cancer Lett 2024; 591:216873. [PMID: 38604313 PMCID: PMC11132429 DOI: 10.1016/j.canlet.2024.216873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/18/2024] [Accepted: 04/06/2024] [Indexed: 04/13/2024]
Abstract
Oncogenic RAS and RAF signaling has been implicated in contributing to radioresistance in pancreatic and thyroid cancers. In this study, we sought to better clarify molecular mechanisms contributing to this effect. We discovered that miRNA 296-3p (miR-296-3p) is significantly correlated with radiosensitivity in a panel of pancreatic cancer cells, and miR-296-3p is highly expressed in normal cells, but low in cancer cell lines. Elevated expression of miR-296-3p increases radiosensitization while decreasing the expression of the DNA repair enzyme RAD18 in both pancreatic and thyroid cancer cells. RAD18 is overexpressed in both pancreatic and thyroid tumors compared to matched normal controls, and high expression of RAD18 in tumors is associated with poor prognostic features. Modulating the expression of mutant KRAS in pancreatic cancer cells or mutant BRAF in thyroid cancer cells demonstrates a tight regulation of RAD18 expression in both cancer types. Depletion of RAD18 results in DNA damage and radiation-induced cell death. Importantly, RAD18 depletion in combination with radiotherapy results in marked and sustained tumor regression in KRAS mutant pancreatic cancer orthotopic tumors and BRAF mutant thyroid heterotopic tumors. Overall, our findings identify a novel coordinated RAS/RAF-miR-296-3p-RAD18 signaling network in pancreatic and thyroid cancer cells, which leads to enhanced radioresistance.
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Affiliation(s)
- Adam R Wolfe
- Department of Radiation Oncology, The University of Arkansas for Medical Sciences, The Winthrop P. Rockefeller Cancer Institute, Little Rock, AR, USA
| | - Haihua Feng
- Department of Radiation Oncology, City of Hope, Duarte, CA, USA
| | - Oscar Zuniga
- Department of Radiation Oncology, The University of Arkansas for Medical Sciences, The Winthrop P. Rockefeller Cancer Institute, Little Rock, AR, USA
| | - Henrique Rodrigues
- Department of Radiation Oncology, The University of Arkansas for Medical Sciences, The Winthrop P. Rockefeller Cancer Institute, Little Rock, AR, USA
| | - Daniel E Eldridge
- Department of Veterinary Medicine, The University of Arkansas for Medical Sciences, The Winthrop P. Rockefeller Cancer Institute, Little Rock, AR, USA
| | - Linlin Yang
- Department of Radiation Oncology, City of Hope, Duarte, CA, USA
| | - Changxian Shen
- Department of Radiation Oncology, City of Hope, Duarte, CA, USA
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7
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Sheva K, Roy Chowdhury S, Kravchenko-Balasha N, Meirovitz A. Molecular Changes in Breast Cancer Induced by Radiation Therapy. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)00435-8. [PMID: 38508467 DOI: 10.1016/j.ijrobp.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/29/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
PURPOSE Breast cancer treatments are based on prognostic clinicopathologic features that form the basis for therapeutic guidelines. Although the utilization of these guidelines has decreased breast cancer-associated mortality rates over the past three decades, they are not adequate for individualized therapy. Radiation therapy (RT) is the backbone of breast cancer treatment. Although a highly successful therapeutic modality clinically, from a biological perspective, preclinical studies have shown RT to have the potential to alter tumor cell phenotype, immunogenicity, and the surrounding microenvironment, potentially changing the behavior of cancer cells and resulting in a significant variation in RT response. This review presents the recent advances in revealing the complex molecular changes induced by RT in the treatment of breast cancer and highlights the complexities of translating this information into clinically relevant tools for improved prognostic insights and the revelation of novel approaches for optimizing RT. METHODS AND MATERIALS Current literature was reviewed with a focus on recent advances made in the elucidation of tumor-associated radiation-induced molecular changes across molecular, genetic, and proteomic bases. This review was structured with the aim of providing an up-to-date overview over the very broad and complex subject matter of radiation-induced molecular changes and radioresistance, familiarizing the reader with the broader issue at hand. RESULTS The subject of radiation-induced molecular changes in breast cancer has been broached from various physiological focal points including that of the immune system, immunogenicity and the abscopal effect, tumor hypoxia, breast cancer classification and subtyping, molecular heterogeneity, and molecular plasticity. It is becoming increasingly apparent that breast cancer clinical subtyping alone does not adequately account for variation in RT response or radioresistance. Multiple components of the tumor microenvironment and immune system, delivered RT dose and fractionation schedules, radiation-induced bystander effects, and intrinsic tumor physiology and heterogeneity all contribute to the resultant RT outcome. CONCLUSIONS Despite recent advances and improvements in anticancer therapies, tumor resistance remains a significant challenge. As new analytical techniques and technologies continue to provide crucial insight into the complex molecular mechanisms of breast cancer and its treatment responses, it is becoming more evident that personalized anticancer treatment regimens may be vital in overcoming radioresistance.
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Affiliation(s)
- Kim Sheva
- The Legacy Heritage Oncology Center & Dr Larry Norton Institute, Soroka University Medical Center, Ben Gurion University of the Negev, Faculty of Medicine, Be'er Sheva, Israel.
| | - Sangita Roy Chowdhury
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Amichay Meirovitz
- The Legacy Heritage Oncology Center & Dr Larry Norton Institute, Soroka University Medical Center, Ben Gurion University of the Negev, Faculty of Medicine, Be'er Sheva, Israel.
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8
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Andel D, Viergever BJ, Peters NA, Elisabeth Raats DA, Schenning-van Schelven SJ, Willem Intven MP, Zandvliet M, Hagendoorn J, Max Borel Rinkes IH, Kranenburg O. Pre-existing subclones determine radioresistance in rectal cancer organoids. Cell Rep 2024; 43:113735. [PMID: 38310513 DOI: 10.1016/j.celrep.2024.113735] [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: 09/28/2023] [Revised: 12/05/2023] [Accepted: 01/17/2024] [Indexed: 02/06/2024] Open
Abstract
More than half of all patients with cancer receive radiation therapy, but resistance is commonly observed. Currently, it is unknown whether resistance to radiation therapy is acquired or inherently present. Here, we employed organoids derived from rectal cancer and single-cell whole-genome sequencing to investigate the long-term evolution of subclones in response to radiation. Comparing single-cell whole-genome karyotypes between in-vitro-unirradiated and -irradiated organoids revealed three patterns of subclonal evolution: (1) subclonal persistence, (2) subclonal extinction, and (3) subclonal expansion. Organoids in which subclonal shifts occurred (i.e., expansion or extinction) became more resistant to radiation. Although radioresistant subclones did not share recurrent copy-number alterations that could explain their radioresistance, resistance was associated with reduced chromosomal instability, an association that was also observed in 529 human cancer cell lines. These data suggest that resistance to radiation is inherently present and associated with reduced chromosomal instability.
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Affiliation(s)
- Daan Andel
- Department of Surgical Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands; Laboratory for Translational Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands
| | - Bas Jeroen Viergever
- Laboratory for Translational Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands
| | - Niek Alexander Peters
- Department of Surgical Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands; Laboratory for Translational Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands
| | | | | | - Martijn Peter Willem Intven
- Department of Radiation Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands
| | - Maurice Zandvliet
- Department of Clinical Sciences - Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jeroen Hagendoorn
- Department of Surgical Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands; Laboratory for Translational Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands
| | - Inne Hilbrand Max Borel Rinkes
- Department of Surgical Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands; Laboratory for Translational Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands.
| | - Onno Kranenburg
- Department of Surgical Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands; Laboratory for Translational Oncology, University Medical Center Utrecht, Cancer Center, Utrecht, the Netherlands; Utrecht Platform for Organoid Technology, Utrecht University, Utrecht, the Netherlands.
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9
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Moura MLV, de Menezes AAPM, de Oliveira Filho JWG, do Nascimento MLLB, dos Reis AC, Ribeiro AB, da Silva FCC, Nunes AMV, Rolim HML, de Carvalho Melo Cavalcante AA, Sousa JMDCE. Advances in Antitumor Effects Using Liposomal Citrinin in Induced Breast Cancer Model. Pharmaceutics 2024; 16:174. [PMID: 38399235 PMCID: PMC10892831 DOI: 10.3390/pharmaceutics16020174] [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: 08/09/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 02/25/2024] Open
Abstract
The study aimed to evaluate the antitumor and toxicogenetic effects of liposomal nanoformulations containing citrinin in animal breast carcinoma induced by 7,12-dimethylbenzanthracene (DMBA). Mus musculus virgin females were divided into six groups treated with (1) olive oil (10 mL/kg); (2) 7,12-DMBA (6 mg/kg); (3) citrinin, CIT (2 mg/kg), (4) cyclophosphamide, CPA (25 mg/kg), (5) liposomal citrinin, LP-CIT (2 μg/kg), and (6) LP-CIT (6 µg/kg). Metabolic, behavioral, hematological, biochemical, histopathological, and toxicogenetic tests were performed. DMBA and cyclophosphamide induced behavioral changes, not observed for free and liposomal citrinin. No hematological or biochemical changes were observed for LP-CIT. However, free citrinin reduced monocytes and caused hepatotoxicity. During treatment, significant differences were observed regarding the weight of the right and left breasts treated with DMBA compared to negative controls. Treatment with CPA, CIT, and LP-CIT reduced the weight of both breasts, with better results for liposomal citrinin. Furthermore, CPA, CIT, and LP-CIT presented genotoxic effects for tumor, blood, bone marrow, and liver cells, although less DNA damage was observed for LP-CIT compared to CIT and CPA. Healthy cell damage induced by LP-CIT was repaired during treatment, unlike CPA, which caused clastogenic effects. Thus, LP-CIT showed advantages for its use as a model of nanosystems for antitumor studies.
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Affiliation(s)
- Michely Laiany Vieira Moura
- Laboratory of Toxicological Genetics—LAPGENIC, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil; (M.L.V.M.); (A.-A.P.M.d.M.); (J.W.G.d.O.F.); (M.L.L.B.d.N.); (A.C.d.R.); (F.C.C.d.S.); (A.A.d.C.M.C.); (J.M.d.C.e.S.)
| | - Ag-Anne Pereira Melo de Menezes
- Laboratory of Toxicological Genetics—LAPGENIC, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil; (M.L.V.M.); (A.-A.P.M.d.M.); (J.W.G.d.O.F.); (M.L.L.B.d.N.); (A.C.d.R.); (F.C.C.d.S.); (A.A.d.C.M.C.); (J.M.d.C.e.S.)
| | - José Williams Gomes de Oliveira Filho
- Laboratory of Toxicological Genetics—LAPGENIC, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil; (M.L.V.M.); (A.-A.P.M.d.M.); (J.W.G.d.O.F.); (M.L.L.B.d.N.); (A.C.d.R.); (F.C.C.d.S.); (A.A.d.C.M.C.); (J.M.d.C.e.S.)
| | - Maria Luiza Lima Barreto do Nascimento
- Laboratory of Toxicological Genetics—LAPGENIC, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil; (M.L.V.M.); (A.-A.P.M.d.M.); (J.W.G.d.O.F.); (M.L.L.B.d.N.); (A.C.d.R.); (F.C.C.d.S.); (A.A.d.C.M.C.); (J.M.d.C.e.S.)
| | - Antonielly Campinho dos Reis
- Laboratory of Toxicological Genetics—LAPGENIC, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil; (M.L.V.M.); (A.-A.P.M.d.M.); (J.W.G.d.O.F.); (M.L.L.B.d.N.); (A.C.d.R.); (F.C.C.d.S.); (A.A.d.C.M.C.); (J.M.d.C.e.S.)
| | - Alessandra Braga Ribeiro
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
| | - Felipe Cavalcanti Carneiro da Silva
- Laboratory of Toxicological Genetics—LAPGENIC, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil; (M.L.V.M.); (A.-A.P.M.d.M.); (J.W.G.d.O.F.); (M.L.L.B.d.N.); (A.C.d.R.); (F.C.C.d.S.); (A.A.d.C.M.C.); (J.M.d.C.e.S.)
| | | | - Hercília Maria Lins Rolim
- Laboratory of Pharmaceutical Nanosystems—NANOSFAR, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil
| | - Ana Amélia de Carvalho Melo Cavalcante
- Laboratory of Toxicological Genetics—LAPGENIC, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil; (M.L.V.M.); (A.-A.P.M.d.M.); (J.W.G.d.O.F.); (M.L.L.B.d.N.); (A.C.d.R.); (F.C.C.d.S.); (A.A.d.C.M.C.); (J.M.d.C.e.S.)
| | - João Marcelo de Castro e Sousa
- Laboratory of Toxicological Genetics—LAPGENIC, Graduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina 64049-550, Brazil; (M.L.V.M.); (A.-A.P.M.d.M.); (J.W.G.d.O.F.); (M.L.L.B.d.N.); (A.C.d.R.); (F.C.C.d.S.); (A.A.d.C.M.C.); (J.M.d.C.e.S.)
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10
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Kolnohuz A, Ebrahimpour L, Yolchuyeva S, Manem VSK. Gene expression signature predicts radiation sensitivity in cell lines using the integral of dose-response curve. BMC Cancer 2024; 24:2. [PMID: 38166789 PMCID: PMC10763485 DOI: 10.1186/s12885-023-11634-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Although substantial efforts have been made to build molecular biomarkers to predict radiation sensitivity, the ability to accurately stratify the patients is still limited. In this study, we aim to leverage large-scale radiogenomics datasets to build genomic predictors of radiation response using the integral of the radiation dose-response curve. METHODS Two radiogenomics datasets consisting of 511 and 60 cancer cell lines were utilized to develop genomic predictors of radiation sensitivity. The intrinsic radiation sensitivity, defined as the integral of the dose-response curve (AUC) was used as the radioresponse variable. The biological determinants driving AUC and SF2 were compared using pathway analysis. To build the predictive model, the largest and smallest datasets consisting of 511 and 60 cancer cell lines were used as the discovery and validation cohorts, respectively, with AUC as the response variable. RESULTS Utilizing a compendium of three pathway databases, we illustrated that integral of the radiobiological model provides a more comprehensive characterization of molecular processes underpinning radioresponse compared to SF2. Furthermore, more pathways were found to be unique to AUC than SF2-30, 288 and 38 in KEGG, REACTOME and WIKIPATHWAYS, respectively. Also, the leading-edge genes driving the biological pathways using AUC were unique and different compared to SF2. With regards to radiation sensitivity gene signature, we obtained a concordance index of 0.65 and 0.61 on the discovery and validation cohorts, respectively. CONCLUSION We developed an integrated framework that quantifies the impact of physical radiation dose and the biological effect of radiation therapy in interventional pre-clinical model systems. With the availability of more data in the future, the clinical potential of this signature can be assessed, which will eventually provide a framework to integrate genomics into biologically-driven precision radiation oncology.
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Affiliation(s)
- Alona Kolnohuz
- Quebec Heart & Lung Institute Research Center, Québec, Canada
- Department of Molecular Medicine, Laval University, Québec, Canada
| | - Leyla Ebrahimpour
- Quebec Heart & Lung Institute Research Center, Québec, Canada
- Department of Physics, Laval University, Québec, Canada
| | - Sevinj Yolchuyeva
- Department of Mathematics and Computer Science, Université du Québec à Trois Rivières, Trois Rivières, Canada
- Centre de Recherche du CHU de Québec - Université Laval, Québec, Canada
| | - Venkata S K Manem
- Quebec Heart & Lung Institute Research Center, Québec, Canada.
- Department of Mathematics and Computer Science, Université du Québec à Trois Rivières, Trois Rivières, Canada.
- Centre de Recherche du CHU de Québec - Université Laval, Québec, Canada.
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11
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Peters XQ, Elamin G, Aljoundi A, Alahmdi MI, Abo-Dya NE, Sidhom PA, Tawfeek AM, Ibrahim MAA, Soremekun O, Soliman MES. Therapeutic Path to Triple Knockout: Investigating the Pan-inhibitory Mechanisms of AKT, CDK9, and TNKS2 by a Novel 2-phenylquinazolinone Derivative in Cancer Therapy- An In-silico Investigation Therapy. Curr Pharm Biotechnol 2024; 25:1288-1303. [PMID: 37581526 DOI: 10.2174/1389201024666230815145001] [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: 02/27/2023] [Revised: 06/18/2023] [Accepted: 06/26/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND Blocking the oncogenic Wnt//β-catenin pathway has of late been investigated as a viable therapeutic approach in the treatment of cancer. This involves the multi-targeting of certain members of the tankyrase-kinase family; Tankyrase 2 (TNKS2), Protein Kinase B (AKT), and Cyclin- Dependent Kinase 9 (CDK9), which propagate the oncogenic Wnt/β-catenin signalling pathway. METHODS During a recent investigation, the pharmacological activity of 2-(4-aminophenyl)-7-chloro- 3H-quinazolin-4-one was repurposed to serve as a 'triple-target' inhibitor of TNKS2, AKT and CDK9. Yet, the molecular mechanism that surrounds its multi-targeting activity remains unanswered. As such, this study aims to explore the pan-inhibitory mechanism of 2-(4-aminophenyl)-7-chloro-3H-quinazolin- 4-one towards AKT, CDK9, and TNKS2, using in silico techniques. RESULTS Results revealed favourable binding affinities of -34.17 kcal/mol, -28.74 kcal/mol, and -27.30 kcal/mol for 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one towards TNKS2, CDK9, and AKT, respectively. Pan-inhibitory binding of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one is illustrated by close interaction with specific residues on tankyrase-kinase. Structurally, 2-(4-aminophenyl)-7-chloro- 3H-quinazolin-4-one had an impact on the flexibility, solvent-accessible surface area, and stability of all three proteins, which was illustrated by numerous modifications observed in the unbound as well as the bound states of the structures, which evidenced the disruption of their biological function. Prediction of the pharmacokinetics and physicochemical properties of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4- one further established its inhibitory potential, evidenced by the favourable absorption, metabolism, excretion, and minimal toxicity properties. CONCLUSION The following structural insights provide a starting point for understanding the paninhibitory activity of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one. Determining the criticality of the interactions that exist between the pyrimidine ring and catalytic residues could offer insight into the structure-based design of innovative tankyrase-kinase inhibitors with enhanced therapeutic effects.
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Affiliation(s)
- Xylia Q Peters
- Department of Pharmaceutical Science, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Ghazi Elamin
- Department of Pharmaceutical Science, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Aimen Aljoundi
- Department of Pharmaceutical Science, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mohamed Issa Alahmdi
- Department of Pharmaceutical Science, University of Tabuk, Tabuk, 7149, Saudi Arabia
| | - Nader E Abo-Dya
- Department of Pharmaceutical Science, University of Tabuk, Tabuk, 7149, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Peter A Sidhom
- Department of Pharmacy, Tanta University, Tanta, 31527, Egypt
| | - Ahmed M Tawfeek
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mahmoud A A Ibrahim
- Department of Pharmaceutical Science, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
- Chemistry Department, Computational Chemistry Laboratory, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Opeyemi Soremekun
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Mahmoud E S Soliman
- Department of Pharmaceutical Science, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
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12
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Pham TD, Sun X. Wavelet scattering networks in deep learning for discovering protein markers in a cohort of Swedish rectal cancer patients. Cancer Med 2023; 12:21502-21518. [PMID: 38014709 PMCID: PMC10726782 DOI: 10.1002/cam4.6672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/25/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Cancer biomarkers play a pivotal role in the diagnosis, prognosis, and treatment response prediction of the disease. In this study, we analyzed the expression levels of RhoB and DNp73 proteins in rectal cancer, as captured in immunohistochemical images, to predict the 5-year survival time of two patient groups: one with preoperative radiotherapy and one without. METHODS The utilization of deep convolutional neural networks in medical research, particularly in clinical cancer studies, has been gaining substantial attention. This success primarily stems from their ability to extract intricate image features that prove invaluable in machine learning. Another innovative method for extracting features at multiple levels is the wavelet-scattering network. Our study combines the strengths of these two convolution-based approaches to robustly extract image features related to protein expression. RESULTS The efficacy of our approach was evaluated across various tissue types, including tumor, biopsy, metastasis, and adjacent normal tissue. Statistical assessments demonstrated exceptional performance across a range of metrics, including prediction accuracy, classification accuracy, precision, and the area under the receiver operating characteristic curve. CONCLUSION These results underscore the potential of dual convolutional learning to assist clinical researchers in the timely validation and discovery of cancer biomarkers.
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Affiliation(s)
- Tuan D. Pham
- Barts and The London School of Medicine and Dentistry Queen MaryUniversity of London Turner StreetLondonUK
| | - Xiao‐Feng Sun
- Division of Oncology Department of Biomedical and Clinical SciencesLinkoping UniversityLinkopingSweden
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13
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Horeweg N, Nout RA, Jürgenliemk-Schulz IM, Lutgens LC, Jobsen JJ, Haverkort MA, Mens JWM, Slot A, Wortman BG, de Boer SM, Stelloo E, Verhoeven-Adema KW, Putter H, Smit VT, Bosse T, Creutzberg CL. Molecular Classification Predicts Response to Radiotherapy in the Randomized PORTEC-1 and PORTEC-2 Trials for Early-Stage Endometrioid Endometrial Cancer. J Clin Oncol 2023; 41:4369-4380. [PMID: 37487144 PMCID: PMC10522107 DOI: 10.1200/jco.23.00062] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/20/2023] [Accepted: 06/09/2023] [Indexed: 07/26/2023] Open
Abstract
PURPOSE The molecular classification of endometrial cancer (EC) has proven to have prognostic value and is predictive of response to adjuvant chemotherapy. Here, we investigate its predictive value for response to external beam radiotherapy (EBRT) and vaginal brachytherapy (VBT) in early-stage endometrioid EC (EEC). METHODS Data of the randomized PORTEC-1 trial (n = 714) comparing pelvic EBRT with no adjuvant therapy in early-stage intermediate-risk EC and the PORTEC-2 trial (n = 427) comparing VBT with EBRT in early-stage high-intermediate-risk EC were used. Locoregional (including vaginal and pelvic) recurrence-free survival was compared between treatment groups across the four molecular classes using Kaplan-Meier's methodology and log-rank tests. RESULTS A total of 880 molecularly classified ECs, 484 from PORTEC-1 and 396 from PORTEC-2, were included. The majority were FIGO-2009 stage I EEC (97.2%). The median follow-up was 11.3 years. No locoregional recurrences were observed in EC with a pathogenic mutation of DNA polymerase-ε (POLEmut EC). In mismatch repair-deficient (MMRd) EC, locoregional recurrence-free survival was similar after EBRT (94.2%), VBT (94.2%), and no adjuvant therapy (90.3%; P = .74). In EC with a p53 abnormality (p53abn EC), EBRT (96.9%) had a substantial benefit over VBT (64.3%) and no adjuvant therapy (72.2%; P = .048). In EC with no specific molecular profile (NSMP EC), both EBRT (98.3%) and VBT (96.2%) yielded better locoregional control than no adjuvant therapy (87.7%; P < .0001). CONCLUSION The molecular classification of EC predicts response to radiotherapy in stage I EEC and may guide adjuvant treatment decisions. Omitting radiotherapy seems to be safe in POLEmut EC. The benefit of radiotherapy seems to be limited in MMRd EC. EBRT yields a significantly better locoregional recurrence-free survival than VBT or no adjuvant therapy in p53abn EC. VBT is the treatment of choice for NSMP EC as it is as effective as EBRT and significantly better than no adjuvant therapy for locoregional tumor control.
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Affiliation(s)
- Nanda Horeweg
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Remi A. Nout
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Radiotherapy, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | | | - Jan J. Jobsen
- Department of Radiotherapy, Medisch Spectrum Twente, Enschede, the Netherlands
| | | | - Jan Willem M. Mens
- Department of Radiotherapy, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Annerie Slot
- Radiotherapeutic Institute Friesland, Leeuwarden, the Netherlands
| | - Bastiaan G. Wortman
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Radiotherapy, Catharina Ziekenhuis, Eindhoven, the Netherlands
| | - Stephanie M. de Boer
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ellen Stelloo
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Hein Putter
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Carien L. Creutzberg
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
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14
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Earland N, Chen K, Semenkovich NP, Chauhan PS, Zevallos JP, Chaudhuri AA. Emerging Roles of Circulating Tumor DNA for Increased Precision and Personalization in Radiation Oncology. Semin Radiat Oncol 2023; 33:262-278. [PMID: 37331781 DOI: 10.1016/j.semradonc.2023.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Recent breakthroughs in circulating tumor DNA (ctDNA) technologies present a compelling opportunity to combine this emerging liquid biopsy approach with the field of radiogenomics, the study of how tumor genomics correlate with radiotherapy response and radiotoxicity. Canonically, ctDNA levels reflect metastatic tumor burden, although newer ultrasensitive technologies can be used after curative-intent radiotherapy of localized disease to assess ctDNA for minimal residual disease (MRD) detection or for post-treatment surveillance. Furthermore, several studies have demonstrated the potential utility of ctDNA analysis across various cancer types managed with radiotherapy or chemoradiotherapy, including sarcoma and cancers of the head and neck, lung, colon, rectum, bladder, and prostate . Additionally, because peripheral blood mononuclear cells are routinely collected alongside ctDNA to filter out mutations associated with clonal hematopoiesis, these cells are also available for single nucleotide polymorphism analysis and could potentially be used to detect patients at high risk for radiotoxicity. Lastly, future ctDNA assays will be utilized to better assess locoregional MRD in order to more precisely guide adjuvant radiotherapy after surgery in cases of localized disease, and guide ablative radiotherapy in cases of oligometastatic disease.
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Affiliation(s)
- Noah Earland
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Kevin Chen
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Nicholas P Semenkovich
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Pradeep S Chauhan
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Jose P Zevallos
- Department of Otolaryngology, University of Pittsburgh Medical School, Pittsburgh, PA
| | - Aadel A Chaudhuri
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO; Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO; Department of Genetics, Washington University School of Medicine, St. Louis, MO; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO; Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO.
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15
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Rydzewski NR, Helzer KT, Bootsma M, Shi Y, Bakhtiar H, Sjöström M, Zhao SG. Machine Learning & Molecular Radiation Tumor Biomarkers. Semin Radiat Oncol 2023; 33:243-251. [PMID: 37331779 PMCID: PMC10287033 DOI: 10.1016/j.semradonc.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Developing radiation tumor biomarkers that can guide personalized radiotherapy clinical decision making is a critical goal in the effort towards precision cancer medicine. High-throughput molecular assays paired with modern computational techniques have the potential to identify individual tumor-specific signatures and create tools that can help understand heterogenous patient outcomes in response to radiotherapy, allowing clinicians to fully benefit from the technological advances in molecular profiling and computational biology including machine learning. However, the increasingly complex nature of the data generated from high-throughput and "omics" assays require careful selection of analytical strategies. Furthermore, the power of modern machine learning techniques to detect subtle data patterns comes with special considerations to ensure that the results are generalizable. Herein, we review the computational framework of tumor biomarker development and describe commonly used machine learning approaches and how they are applied for radiation biomarker development using molecular data, as well as challenges and emerging research trends.
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Affiliation(s)
- Nicholas R Rydzewski
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Matthew Bootsma
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Hamza Bakhtiar
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, WI; Carbone Cancer Center, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital, Madison, WI.
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16
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Wu Y, Song Y, Wang R, Wang T. Molecular mechanisms of tumor resistance to radiotherapy. Mol Cancer 2023; 22:96. [PMID: 37322433 PMCID: PMC10268375 DOI: 10.1186/s12943-023-01801-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Cancer is the most prevalent cause of death globally, and radiotherapy is considered the standard of care for most solid tumors, including lung, breast, esophageal, and colorectal cancers and glioblastoma. Resistance to radiation can lead to local treatment failure and even cancer recurrence. MAIN BODY In this review, we have extensively discussed several crucial aspects that cause resistance of cancer to radiation therapy, including radiation-induced DNA damage repair, cell cycle arrest, apoptosis escape, abundance of cancer stem cells, modification of cancer cells and their microenvironment, presence of exosomal and non-coding RNA, metabolic reprogramming, and ferroptosis. We aim to focus on the molecular mechanisms of cancer radiotherapy resistance in relation to these aspects and to discuss possible targets to improve treatment outcomes. CONCLUSIONS Studying the molecular mechanisms responsible for radiotherapy resistance and its interactions with the tumor environment will help improve cancer responses to radiotherapy. Our review provides a foundation to identify and overcome the obstacles to effective radiotherapy.
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Affiliation(s)
- Yu Wu
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042 Liaoning Province China
- School of Graduate, Dalian Medical University, Dalian, 116044 China
| | - Yingqiu Song
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042 Liaoning Province China
| | - Runze Wang
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042 Liaoning Province China
- School of Graduate, Dalian Medical University, Dalian, 116044 China
| | - Tianlu Wang
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042 Liaoning Province China
- Faculty of Medicine, Dalian University of Technology, Dalian, 116024 China
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17
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He YQ, Luo LT, Wang TM, Xue WQ, Yang DW, Li DH, Diao H, Xiao RW, Deng CM, Zhang WL, Liao Y, Wu YX, Wang QL, Zhou T, Li XZ, Zheng XH, Zhang PF, Zhang SD, Hu YZ, Sun Y, Jia WH. Clinical and genome-wide association analysis of chemoradiation-induced hearing loss in nasopharyngeal carcinoma. Hum Genet 2023; 142:759-772. [PMID: 37062025 PMCID: PMC10182145 DOI: 10.1007/s00439-023-02554-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023]
Abstract
Chemoradiation-induced hearing loss (CRIHL) is one of the most devasting side effects for nasopharyngeal carcinoma (NPC) patients, which seriously affects survivors' long-term quality of life. However, few studies have comprehensively characterized the risk factors for CRIHL. In this study, we found that age at diagnosis, tumor stage, and concurrent cisplatin dose were positively associated with chemoradiation-induced hearing loss. We performed a genome-wide association study (GWAS) in 777 NPC patients and identified rs1050851 (within the exon 2 of NFKBIA), a variant with a high deleteriousness score, to be significantly associated with hearing loss risk (HR = 5.46, 95% CI 2.93-10.18, P = 9.51 × 10-08). The risk genotype of rs1050851 was associated with higher NFKBIA expression, which was correlated with lower cellular tolerance to cisplatin. According to permutation-based enrichment analysis, the variants mapping to 149 hereditary deafness genes were significantly enriched among GWAS top signals, which indicated the genetic similarity between hereditary deafness and CRIHL. Pathway analysis suggested that synaptic signaling was involved in the development of CRIHL. Additionally, the risk score integrating genetic and clinical factors can predict the risk of hearing loss with a relatively good performance in the test set. Collectively, this study shed new light on the etiology of chemoradiation-induced hearing loss, which facilitates high-risk individuals' identification for personalized prevention and treatment.
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Affiliation(s)
- Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Lu-Ting Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Da-Wei Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Dan-Hua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Hua Diao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ruo-Wen Xiao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Qiao-Ling Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Shao-Dan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Ye-Zhu Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Ying Sun
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China.
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China.
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China.
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18
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Grandt CL, Brackmann LK, Foraita R, Schwarz H, Hummel-Bartenschlager W, Hankeln T, Kraemer C, Zahnreich S, Drees P, Mirsch J, Spix C, Blettner M, Schmidberger H, Binder H, Hess M, Galetzka D, Marini F, Poplawski A, Marron M. Gene expression variability in long-term survivors of childhood cancer and cancer-free controls in response to ionizing irradiation. Mol Med 2023; 29:41. [PMID: 36997855 PMCID: PMC10061869 DOI: 10.1186/s10020-023-00629-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/20/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Differential expression analysis is usually adjusted for variation. However, most studies that examined the expression variability (EV) have used computations affected by low expression levels and did not examine healthy tissue. This study aims to calculate and characterize an unbiased EV in primary fibroblasts of childhood cancer survivors and cancer-free controls (N0) in response to ionizing radiation. METHODS Human skin fibroblasts of 52 donors with a first primary neoplasm in childhood (N1), 52 donors with at least one second primary neoplasm (N2 +), as well as 52 N0 were obtained from the KiKme case-control study and exposed to a high (2 Gray) and a low dose (0.05 Gray) of X-rays and sham- irradiation (0 Gray). Genes were then classified as hypo-, non-, or hyper-variable per donor group and radiation treatment, and then examined for over-represented functional signatures. RESULTS We found 22 genes with considerable EV differences between donor groups, of which 11 genes were associated with response to ionizing radiation, stress, and DNA repair. The largest number of genes exclusive to one donor group and variability classification combination were all detected in N0: hypo-variable genes after 0 Gray (n = 49), 0.05 Gray (n = 41), and 2 Gray (n = 38), as well as hyper-variable genes after any dose (n = 43). While after 2 Gray positive regulation of cell cycle was hypo-variable in N0, (regulation of) fibroblast proliferation was over-represented in hyper-variable genes of N1 and N2+. In N2+, 30 genes were uniquely classified as hyper-variable after the low dose and were associated with the ERK1/ERK2 cascade. For N1, no exclusive gene sets with functions related to the radiation response were detected in our data. CONCLUSION N2+ showed high degrees of variability in pathways for the cell fate decision after genotoxic insults that may lead to the transfer and multiplication of DNA-damage via proliferation, where apoptosis and removal of the damaged genome would have been appropriate. Such a deficiency could potentially lead to a higher vulnerability towards side effects of exposure to high doses of ionizing radiation, but following low-dose applications employed in diagnostics, as well.
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Affiliation(s)
- Caine Lucas Grandt
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany.
- Faculty of Human and Health Sciences, University of Bremen, Bremen, Germany.
| | - Lara Kim Brackmann
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany
| | - Ronja Foraita
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany
| | - Heike Schwarz
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany
| | | | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christiane Kraemer
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Zahnreich
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Philipp Drees
- Department of Orthopaedics and Traumatology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Johanna Mirsch
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Claudia Spix
- Division of Childhood Cancer Epidemiology, German Childhood Cancer Registry, Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maria Blettner
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Center of the Johannes, University Medical, Gutenberg University, Mainz, Germany
| | - Heinz Schmidberger
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Harald Binder
- Institute of Medical Biometry and Statistics, University Medical Center, Freiburg, Germany
| | - Moritz Hess
- Institute of Medical Biometry and Statistics, University Medical Center, Freiburg, Germany
| | - Danuta Galetzka
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Center of the Johannes, University Medical, Gutenberg University, Mainz, Germany
| | - Alicia Poplawski
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Center of the Johannes, University Medical, Gutenberg University, Mainz, Germany
| | - Manuela Marron
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany
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19
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Guan L, Nambiar DK, Cao H, Viswanathan V, Kwok S, Hui AB, Hou Y, Hildebrand R, von Eyben R, Holmes BJ, Zhao J, Kong CS, Wamsley N, Zhang W, Major MB, Seol SW, Sunwoo JB, Hayes DN, Diehn M, Le QT. NFE2L2 Mutations Enhance Radioresistance in Head and Neck Cancer by Modulating Intratumoral Myeloid Cells. Cancer Res 2023; 83:861-874. [PMID: 36652552 PMCID: PMC10023320 DOI: 10.1158/0008-5472.can-22-1903] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/18/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
Radiotherapy (RT) is one of the primary treatments of head and neck squamous cell carcinoma (HNSCC), which has a high-risk of locoregional failure (LRF). Presently, there is no reliable predictive biomarker of radioresistance in HNSCC. Here, we found that mutations in NFE2L2, which encodes Nrf2, are associated with a significantly higher rate of LRF in patients with oral cavity cancer treated with surgery and adjuvant (chemo)radiotherapy but not in those treated with surgery alone. Somatic mutation of NFE2L2 led to Nrf2 activation and radioresistance in HNSCC cells. Tumors harboring mutant Nrf2E79Q were substantially more radioresistant than tumors with wild-type Nrf2 in immunocompetent mice, whereas the difference was diminished in immunocompromised mice. Nrf2E79Q enhanced radioresistance through increased recruitment of intratumoral polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) and reduction of M1-polarized macrophages. Treatment with the glutaminase inhibitor CB-839 overcame the radioresistance induced by Nrf2E79Q or Nrf2E79K. RT increased expression of PMN-MDSC-attracting chemokines, including CXCL1, CXLC3, and CSF3, in Nrf2E79Q-expressing tumors via the TLR4, which could be reversed by CB-839. This study provides insights into the impact of NFE2L2 mutations on radioresistance and suggests that CB-839 can increase radiosensitivity by switching intratumoral myeloid cells to an antitumor phenotype, supporting clinical testing of CB-839 with RT in HNSCC with NFE2L2 mutations. SIGNIFICANCE NFE2L2 mutations are predictive biomarkers of radioresistance in head and neck cancer and confer sensitivity to glutaminase inhibitors to overcome radioresistance.
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Affiliation(s)
- Li Guan
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Dhanya K. Nambiar
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Hongbin Cao
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Vignesh Viswanathan
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Shirley Kwok
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Angela B. Hui
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Rachel Hildebrand
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Rie von Eyben
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Brittany J. Holmes
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Junfei Zhao
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Christina S. Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Nathan Wamsley
- Washington University in St. Louis, Department of Cell Biology and Physiology, St. Louis, MO, USA
| | - Weiruo Zhang
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA
| | - Michael B. Major
- Washington University in St. Louis, Department of Cell Biology and Physiology, St. Louis, MO, USA
| | - Seung W. Seol
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John B. Sunwoo
- OHNS/Head &Neck Surgery Divisions, Stanford University School of Medicine, Stanford, California, USA
| | - D. Neil Hayes
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
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20
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Burkart S, Weusthof C, Khorani K, Steen S, Stögbauer F, Unger K, Hess J, Zitzelsberger H, Belka C, Kurth I, Hess J. A Novel Subgroup of UCHL1-Related Cancers Is Associated with Genomic Instability and Sensitivity to DNA-Damaging Treatment. Cancers (Basel) 2023; 15:cancers15061655. [PMID: 36980544 PMCID: PMC10099714 DOI: 10.3390/cancers15061655] [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: 01/30/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
PURPOSE Identification of molecularly-defined cancer subgroups and targeting tumor-specific vulnerabilities have a strong potential to improve treatment response and patient outcomes but remain an unmet challenge of high clinical relevance, especially in head and neck squamous cell carcinoma (HNSC). EXPERIMENTAL DESIGN We established a UCHL1-related gene set to identify and molecularly characterize a UCHL1-related subgroup within TCGA-HNSC by integrative analysis of multi-omics data. An extreme gradient boosting model was trained on TCGA-HNSC based on GSVA scores for gene sets of the MSigDB to robustly predict UCHL1-related cancers in other solid tumors and cancer cell lines derived thereof. Potential vulnerabilities of UCHL1-related cancer cells were elucidated by an in-silico drug screening approach. RESULTS We established a 497-gene set, which stratified the TCGA-HNSC cohort into distinct subgroups with a UCHL1-related or other phenotype. UCHL1-related HNSC were characterized by higher frequencies of genomic alterations, which was also evident for UCHL1-related cancers of other solid tumors predicted by the classification model. These data indicated an impaired maintenance of genomic integrity and vulnerability for DNA-damaging treatment, which was supported by a favorable prognosis of UCHL1-related tumors after radiotherapy, and a higher sensitivity of UCHL1-related cancer cells to irradiation or DNA-damaging compounds (e.g., Oxaliplatin). CONCLUSION Our study established UCHL1-related cancers as a novel subgroup across most solid tumor entities with a unique molecular phenotype and DNA-damaging treatment as a specific vulnerability, which requires further proof-of-concept in pre-clinical models and future clinical trials.
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Affiliation(s)
- Sebastian Burkart
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Christopher Weusthof
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Karam Khorani
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Sonja Steen
- Department of Oral and Maxillofacial Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Fabian Stögbauer
- Tissue Bank of the National Center for Tumor Diseases (NCT), Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Claus Belka
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, 81377 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 81377 Munich, Germany
| | - Ina Kurth
- Division of Radiooncology-Radiobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jochen Hess
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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21
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Lebow ES, Shepherd A, Eichholz JE, Offin M, Gelblum DY, Wu AJ, Simone CB, Schoenfeld AJ, Jones DR, Rimner A, Chaft JE, Riaz N, Gomez DR, Shaverdian N. Analysis of Tumor Mutational Burden, Progression-Free Survival, and Local-Regional Control in Patents with Locally Advanced Non-Small Cell Lung Cancer Treated With Chemoradiation and Durvalumab. JAMA Netw Open 2023; 6:e2249591. [PMID: 36602799 PMCID: PMC9856786 DOI: 10.1001/jamanetworkopen.2022.49591] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
IMPORTANCE The addition of consolidative durvalumab to chemoradiation has improved disease control and survival in locally advanced non-small cell lung cancer (NSCLC). However, there remains a need to identify biomarkers for response to this therapy to allow for risk adaptation and personalization. OBJECTIVES To evaluate whether TMB or other variants associated with radiation response are also associated with outcomes following definitive chemoradiation and adjuvant durvalumab among patients with locally advanced unresectable NSCLC. DESIGN, SETTING, AND PARTICIPANTS This cohort study included consecutive patients with unresectable locally advanced NSCLC treated with chemoradiation and adjuvant durvalumab between November 2013 and March 2020 who had prospective comprehensive genomic profiling. This study was completed at a multisite tertiary cancer center. The median (IQR) follow-up time was 26 (21-36) months. Statistical analysis was conducted from April to October 2022. EXPOSURES Patients were grouped into TMB-high (≥10 mutations/megabase [mt/Mb]) and TMB-low (<10 mt/Mb) groups and were additionally evaluated by the presence of somatic alterations associated with radiation resistance (KEAP1/NFE2L2) or radiation sensitivity (DNA damage repair pathway). MAIN OUTCOMES AND MEASURES The primary outcomes were 24-month local-regional failure (LRF) and progression-free survival (PFS). RESULTS In this cohort study of 81 patients (46 [57%] male patients; median [range] age, 67 [45-85] years), 36 patients (44%) had TMB-high tumors (≥10 mt/Mb). Patients with TMB-high vs TMB-low tumors had markedly lower 24-month LRF (9% [95% CI, 0%-46%] vs 51% [95% CI, 36%-71%]; P = .001) and improved 24-month PFS (66% [95% CI, 54%-84%] vs 27% [95% CI, 13%-40%]; P = .003). The 24-month LRF was 52% (95% CI, 25%-84%) among patients with KEAP1/NFE2L2-altered tumors compared with 27% (95% CI, 17%-42%) among patients with KEAP1/NFE2L2-wildtype tumors (P = .05). On Cox analysis, only TMB status was associated with LRF (hazard ratio [HR], 0.17; 95% CI, 0.03-0.64; P = .02) and PFS (HR, 0.45; 95% CI, 0.21-0.90; P = .03). Histology, disease stage, Eastern Cooperative Oncology Group status, programmed cell death ligand 1 expression, and pathogenic KEAP1/NFE2L2, KRAS, and DNA damage repair pathway alterations were not significantly associated with LRF or PFS. CONCLUSIONS AND RELEVANCE In this cohort study, TMB-high status was associated with improved local-regional control and PFS after definitive chemoradiation and adjuvant durvalumab. TMB status may facilitate risk-adaptive radiation strategies in unresectable locally advanced NSCLC.
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Affiliation(s)
- Emily S. Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Annemarie Shepherd
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jordan E. Eichholz
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daphna Y. Gelblum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Abraham J. Wu
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles B. Simone
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam J. Schoenfeld
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R. Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamie E. Chaft
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel R. Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Narek Shaverdian
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
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22
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Yuan Y, Long H, Zhou Z, Fu Y, Jiang B. PI3K-AKT-Targeting Breast Cancer Treatments: Natural Products and Synthetic Compounds. Biomolecules 2023; 13:biom13010093. [PMID: 36671478 PMCID: PMC9856042 DOI: 10.3390/biom13010093] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/16/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
Breast cancer is the most commonly diagnosed cancer in women. The high incidence of breast cancer, which is continuing to rise, makes treatment a significant challenge. The PI3K-AKT pathway and its downstream targets influence various cellular processes. In recent years, mounting evidence has shown that natural products and synthetic drugs targeting PI3K-AKT signaling have the potential to treat breast cancer. In this review, we discuss the role of the PI3K-AKT signaling pathway in the occurrence and development of breast cancer and highlight PI3K-AKT-targeting natural products and drugs in clinical trials for the treatment of breast cancer.
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Affiliation(s)
- Yeqin Yuan
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Huizhi Long
- School of Pharmacy, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Ziwei Zhou
- School of Pharmacy, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yuting Fu
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Binyuan Jiang
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Department of Clinical Laboratory, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Correspondence:
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23
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Randall J, Teo PT, Lou B, Shah J, Patel J, Kamen A, Abazeed ME. Image-Based Deep Neural Network for Individualizing Radiotherapy Dose Is Transportable Across Health Systems. JCO Clin Cancer Inform 2023; 7:e2200100. [PMID: 36652661 PMCID: PMC10166468 DOI: 10.1200/cci.22.00100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
PURPOSE We developed a deep neural network that queries the lung computed tomography-derived feature space to identify radiation sensitivity parameters that can predict treatment failures and hence guide the individualization of radiotherapy dose. In this article, we examine the transportability of this model across health systems. METHODS This multicenter cohort-based registry included 1,120 patients with cancer in the lung treated with stereotactic body radiotherapy. Pretherapy lung computed tomography images from the internal study cohort (n = 849) were input into a multitask deep neural network to generate an image fingerprint score that predicts time to local failure. Deep learning (DL) scores were input into a regression model to derive iGray, an individualized radiation dose estimate that projects a treatment failure probability of < 5% at 24 months. We validated our findings in an external, holdout cohort (n = 271). RESULTS There were substantive differences in the baseline patient characteristics of the two study populations, permitting an assessment of model transportability. In the external cohort, radiation treatments in patients with high DL scores failed at a significantly higher rate with 3-year cumulative incidences of local failure of 28.5% (95% CI, 19.8 to 37.8) versus 10.2% (95% CI, 5.9 to 16.2; hazard ratio, 3.3 [95% CI, 1.74 to 6.49]; P < .001). A model that included DL score alone predicted treatment failures with a concordance index of 0.68 (95% CI, 0.59 to 0.77), which had a similar performance to a nested model derived from within the internal cohort (0.70 [0.64 to 0.75]). External cohort patients with iGray values that exceeded the delivered doses had proportionately higher rates of local failure (P < .001). CONCLUSION Our results support the development and implementation of new DL-guided treatment guidance tools in the image-replete and highly standardized discipline of radiation oncology.
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Affiliation(s)
- James Randall
- Digital Technology and Innovation, Siemens Healthineers, Princeton, NJ
| | - P Troy Teo
- Digital Technology and Innovation, Siemens Healthineers, Princeton, NJ
| | - Bin Lou
- Digital Technology and Innovation, Siemens Healthineers, Princeton, NJ
| | - Jainil Shah
- Diagnostic Imaging Computed Tomography, Siemens Healthineers, Malvern, PA
| | - Jyoti Patel
- Division of Hematology/Oncology, Northwestern University, Chicago, IL
| | - Ali Kamen
- Digital Technology and Innovation, Siemens Healthineers, Princeton, NJ
| | - Mohamed E Abazeed
- Digital Technology and Innovation, Siemens Healthineers, Princeton, NJ.,Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL
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24
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Gopal P, Yard BD, Petty A, Lal JC, Bera TK, Hoang TQ, Buhimschi AD, Abazeed ME. The Mutational Landscape of Cancer's Vulnerability to Ionizing Radiation. Clin Cancer Res 2022; 28:5343-5358. [PMID: 36222846 PMCID: PMC9751780 DOI: 10.1158/1078-0432.ccr-22-1914] [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: 06/15/2022] [Revised: 08/24/2022] [Accepted: 10/10/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Large-scale sequencing efforts have established that cancer-associated genetic alterations are highly diverse, posing a challenge to the identification of variants that regulate complex phenotypes like radiation sensitivity. The impact of the vast majority of rare or common genetic variants on the sensitivity of cancers to radiotherapy remains largely unknown. EXPERIMENTAL DESIGN We developed a scalable gene editing and irradiation platform to assess the role of categories of variants in cells. Variants were prioritized on the basis of genotype-phenotype associations from a previously completed large-scale cancer cell line radiation profiling study. Altogether, 488 alleles (396 unique single-nucleotide variants) from 92 genes were generated and profiled in an immortalized lung cell line, BEAS-2B. We validated our results in other cell lines (TRT-HU1 and NCI-H520), in vivo via the use of both cell line and patient-derived murine xenografts, and in clinical cohorts. RESULTS We show that resistance to radiation is characterized by substantial inter- and intra-gene allelic variation. Some genes (e.g., KEAP1) demonstrated significant intragenic allelic variation in the magnitude of conferred resistance and other genes (e.g., CTNNB1) displayed both resistance and sensitivity in a protein domain-dependent manner. We combined results from our platform with gene expression and metabolite features and identified the upregulation of amino acid transporters that facilitate oxidative reductive capacity and cell-cycle deregulation as key regulators of radiation sensitivity. CONCLUSIONS Our results reveal new insights into the genetic determinants of tumor sensitivity to radiotherapy and nominate a multitude of cancer mutations that are predicted to impact treatment efficacy.
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Affiliation(s)
- Priyanka Gopal
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Brian D. Yard
- Department of Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio
| | - Aaron Petty
- Department of Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio
| | - Jessica C. Lal
- Department of Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio
| | - Titas K. Bera
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Trung Q. Hoang
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Alexandru D. Buhimschi
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Mohamed E. Abazeed
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.,Corresponding Author: Mohamed E. Abazeed, Feinberg School of Medicine, Northwestern University, 303 E. Superior St/Lurie 7-115, Chicago, IL 60611. Phone: 312-926-2520; Fax: 312-926-6524; E-mail:
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25
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Hong JA, Vikram B, Buchsbaum J, Capala J, Livinski A, Teicher B, Prasanna P, Ahmed MM, Obcemea C, Coleman CN, Espey MG. The State of Preclinical Modeling for Early Phase Cancer Trials Using Molecularly Targeted Agents with Radiation. Radiat Res 2022; 198:625-631. [PMID: 35976726 DOI: 10.1667/rade-22-00077.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/18/2022] [Indexed: 01/11/2023]
Abstract
Preclinical studies inform and guide the development of novel treatment combination strategies that bridge the laboratory with the clinic. We aimed to evaluate approaches cancer researchers used to justify advancing new combinations of molecularly targeted agents and radiation treatment into early-phase human clinical trials. Unsolicited early phase clinical trial proposals submitted to the National Cancer Institute's Cancer Therapy Evaluation Program between January 2016 and July 2020 were curated to quantify key characteristics and proportion of preclinical data provided by trialists seeking to conduct molecularly targeted agent-radiation combination studies in cancer patients. These data elucidate the current landscape for how the rationale for a molecularly targeted agent-radiation combination therapy is supported by preclinical research and illustrate unique challenges faced in translation at the intersection of precision medicine and radiation oncology.
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Affiliation(s)
- Julie A Hong
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
| | - Bhadrasian Vikram
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
| | - Jeffrey Buchsbaum
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
| | | | - Alicia Livinski
- National Institutes of Health Library, Office of Research Services, Office of the Director, National Institutes of Health, Bethesda, Maryland 20892
| | - Beverly Teicher
- Molecular Pharmacology Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
| | - Pataje Prasanna
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
| | - Mansoor M Ahmed
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
| | - Ceferino Obcemea
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
| | - C Norman Coleman
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
| | - Michael Graham Espey
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland 20892
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26
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Zhu S, Wang Y, Tang J, Cao M. Radiotherapy induced immunogenic cell death by remodeling tumor immune microenvironment. Front Immunol 2022; 13:1074477. [PMID: 36532071 PMCID: PMC9753984 DOI: 10.3389/fimmu.2022.1074477] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/15/2022] [Indexed: 12/04/2022] Open
Abstract
Emerging evidence indicates that the induction of radiotherapy(RT) on the immunogenic cell death (ICD) is not only dependent on its direct cytotoxic effect, changes in the tumor immune microenvironment also play an important role in it. Tumor immune microenvironment (TIME) refers to the immune microenvironment that tumor cells exist, including tumor cells, inflammatory cells, immune cells, various signaling molecules and extracellular matrix. TIME has a barrier effect on the anti-tumor function of immune cells, which can inhibit all stages of anti-tumor immune response. The remodeling of TIME caused by RT may affect the degree of immunogenicity, and make it change from immunosuppressive phenotype to immunostimulatory phenotype. It is of great significance to reveal the causes of immune escape of tumor cells, especially for the treatment of drug-resistant tumor. In this review, we focus on the effect of RT on the TIME, the mechanism of RT in reversing the TIME to suppress intrinsic immunity, and the sensitization effect of the remodeling of TIME caused by RT on the effectiveness of immunotherapy.
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27
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Zhang Y, Qiu L, Ren Y, Cheng Z, Li L, Yao S, Zhang C, Luo Z, Lu H. A meta-learning approach to improving radiation response prediction in cancers. Comput Biol Med 2022; 150:106163. [PMID: 37070625 DOI: 10.1016/j.compbiomed.2022.106163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/18/2022] [Accepted: 10/01/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE Predicting the efficacy of radiotherapy in individual patients has drawn widespread attention, but the limited sample size remains a bottleneck for utilizing high-dimensional multi-omics data to guide personalized radiotherapy. We hypothesize the recently developed meta-learning framework could address this limitation. METHODS AND MATERIALS By combining gene expression, DNA methylation, and clinical data of 806 patients who had received radiotherapy from The Cancer Genome Atlas (TCGA), we applied the Model-Agnostic Meta-Learning (MAML) framework to tasks consisting of pan-cancer data, to obtain the best initial parameters of a neural network for a specific cancer with smaller number of samples. The performance of meta-learning framework was compared with four traditional machine learning methods based on two training schemes, and tested on Cancer Cell Line Encyclopedia (CCLE) and Chinese Glioma Genome Atlas (CGGA) datasets. Moreover, biological significance of the models was investigated by survival analysis and feature interpretation. RESULTS The mean AUC (Area under the ROC Curve) [95% confidence interval] of our models across nine cancer types was 0.702 [0.691-0.713], which improved by 0.166 on average over other the four machine learning methods on two training schemes. Our models performed significantly better (p < 0.05) in seven cancer types and performed comparable to the other predictors in the rest of two cancer types. The more pan-cancer samples were used to transfer meta-knowledge, the greater the performance improved (p < 0.05). The predicted response scores that our models generated were negatively correlated with cell radiosensitivity index in four cancer types (p < 0.05), while not statistically significant in the other three cancer types. Moreover, the predicted response scores were shown to be prognostic factors in seven cancer types and eight potential radiosensitivity-related genes were identified. CONCLUSIONS For the first time, we established the meta-learning approach to improving individual radiation response prediction by transferring common knowledge from pan-cancer data with MAML framework. The results demonstrated the superiority, generalizability, and biological significance of our approach.
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28
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Michmerhuizen AR, Lerner LM, Ward C, Pesch AM, Zhang A, Schwartz R, Wilder-Romans K, Eisner JR, Rae JM, Pierce LJ, Speers CW. Androgen and oestrogen receptor co-expression determines the efficacy of hormone receptor-mediated radiosensitisation in breast cancer. Br J Cancer 2022; 127:927-936. [PMID: 35618789 PMCID: PMC9427858 DOI: 10.1038/s41416-022-01849-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Radiation therapy (RT) and hormone receptor (HR) inhibition are used for the treatment of HR-positive breast cancers; however, little is known about the interaction of the androgen receptor (AR) and estrogen receptor (ER) in response to RT in AR-positive, ER-positive (AR+/ER+) breast cancers. Here we assessed radiosensitisation of AR+/ER+ cell lines using pharmacologic or genetic inhibition/degradation of AR and/or ER. METHODS Radiosensitisation was assessed with AR antagonists (enzalutamide, apalutamide, darolutamide, seviteronel, ARD-61), ER antagonists (tamoxifen, fulvestrant) or using knockout of AR. RESULTS Treatment with AR antagonists or ER antagonists in combination with RT did not result in radiosensitisation changes (radiation enhancement ratios [rER]: 0.76-1.21). Fulvestrant treatment provided significant radiosensitisation of CAMA-1 and BT-474 cells (rER: 1.06-2.0) but not ZR-75-1 cells (rER: 0.9-1.11). Combining tamoxifen with enzalutamide did not alter radiosensitivity using a 1 h or 1-week pretreatment (rER: 0.95-1.14). Radiosensitivity was unchanged in AR knockout compared to Cas9 cells (rER: 1.07 ± 0.11), and no additional radiosensitisation was achieved with tamoxifen or fulvestrant compared to Cas9 cells (rER: 0.84-1.19). CONCLUSION While radiosensitising in AR + TNBC, AR inhibition does not modulate radiation sensitivity in AR+/ER+ breast cancer. The efficacy of ER antagonists in combination with RT may also be dependent on AR expression.
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Affiliation(s)
- Anna R Michmerhuizen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lynn M Lerner
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Connor Ward
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Andrea M Pesch
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Amanda Zhang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Rachel Schwartz
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Kari Wilder-Romans
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | | | - James M Rae
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lori J Pierce
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Corey W Speers
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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29
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Kleinendorst SC, Oosterwijk E, Bussink J, Westdorp H, Konijnenberg MW, Heskamp S. Combining Targeted Radionuclide Therapy and Immune Checkpoint Inhibition for Cancer Treatment. Clin Cancer Res 2022; 28:3652-3657. [PMID: 35471557 PMCID: PMC9433955 DOI: 10.1158/1078-0432.ccr-21-4332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/03/2022] [Accepted: 04/11/2022] [Indexed: 01/07/2023]
Abstract
The development of immunotherapy, in particular immune checkpoint inhibitors (ICI), has revolutionized cancer treatment in the past decades. However, its efficacy is still limited to subgroups of patients with cancer. Therefore, effective treatment combination strategies are needed. Here, radiotherapy is highly promising, as it can induce immunogenic cell death, triggering the release of pro-inflammatory cytokines, thereby creating an immunogenic phenotype and sensitizing tumors to ICI. Recently, targeted radionuclide therapy (TRT) has attained significant interest for cancer treatment. In this approach, a tumor-targeting radiopharmaceutical is used to specifically deliver a therapeutic radiation dose to all tumor cells, including distant metastatic lesions, while limiting radiation exposure to healthy tissue. However, fundamental differences between TRT and conventional radiotherapy make it impossible to directly extrapolate the biological effects from conventional radiotherapy to TRT. In this review, we present a comprehensive overview of studies investigating the immunomodulatory effects of TRT and the efficacy of combined TRT-ICI treatment. Preclinical studies have evaluated a variety of murine cancer models in which α- or β-emitting radionuclides were directed to a diverse set of targets. In addition, clinical trials are ongoing to assess safety and efficacy of combined TRT-ICI in patients with cancer. Taken together, research indicates that combining TRT and ICI might improve therapeutic response in patients with cancer. Future research has to disclose what the optimal conditions are in terms of dose and treatment schedule to maximize the efficacy of this combined approach.
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Affiliation(s)
- Simone C. Kleinendorst
- Department of Medical Imaging, Nuclear Medicine, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Egbert Oosterwijk
- Department of Urology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Johan Bussink
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Harm Westdorp
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mark W. Konijnenberg
- Department of Medical Imaging, Nuclear Medicine, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Sandra Heskamp
- Department of Medical Imaging, Nuclear Medicine, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Corresponding Author: Sandra Heskamp, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands. Phone: 243-614-511; E-mail:
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30
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Morin SM, Majhi PD, Crisi GM, Gregory KJ, Franca R, Schalet B, Mason H, Casaubon JT, Cao QJ, Haddad S, Makari-Judson G, Jerry DJ, Schneider SS. Interindividual variation contributes to differential PCB 126 induced gene expression in primary breast epithelial cells and tissues. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113722. [PMID: 35724515 DOI: 10.1016/j.ecoenv.2022.113722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
PCB 126 is a pervasive, dioxin-like chemical pollutant which can activate the aryl hydrocarbon receptor (AhR). Despite being banned from the market, PCB 126 can be detected in breast milk to this day. The extent to which interindividual variation impacts the adverse responses to this chemical in the breast tissue remains unclear. This study aimed to investigate the impact of 3 nM PCB 126 on gene expression in a panel of genetically diverse benign human breast epithelial cell (HBEC) cultures and patient derived breast tissues. Six patient derived HBEC cultures were treated with 3 nM PCB 126. RNAseq was used to interrogate the impact of exposure on differential gene expression. Gene expression changes from the top critical pathways were confirmed via qRT-PCR in a larger panel of benign patient derived HBEC cultures, as well as in patient-derived breast tissue explant cultures. RNAseq analysis of HBEC cultures revealed a signature of 144 genes significantly altered by 3 nM PCB 126 treatment. Confirmation of 8 targets using a panel of 12 HBEC cultures and commercially available breast cell lines demonstrated that while the induction of canonical downstream target gene, CYP1A1, was consistent across our primary HBECs, other genes including AREG, S100A8, IL1A, IL1B, MMP7, and CCL28 exhibited significant variability across individuals. The dependence on the activity of the aryl hydrocarbon receptor was confirmed using inhibitors. PCB 126 can induce significant and consistent changes in gene expression associated with xenobiotic metabolism in benign breast epithelial cells. Although the induction of most genes was reliant on the AhR, significant variability was noted between genes and individuals. These data suggest that there is a bifurcation of the pathway following AhR activation that contributes to the variation in interindividual responses.
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Affiliation(s)
- Stephanie M Morin
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, United States; Dept of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, United States
| | - Prabin Dhangada Majhi
- Dept of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, United States
| | - Giovanna M Crisi
- University of Massachusetts Chan Medical School-Baystate, Department of Pathology, Springfield, MA 01199, United States
| | - Kelly J Gregory
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, United States
| | - Renata Franca
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, United States
| | - Benjamin Schalet
- University of Massachusetts Chan Medical School-Baystate, Department of Surgery, Springfield, MA 01199, United States
| | - Holly Mason
- University of Massachusetts Chan Medical School-Baystate, Department of Surgery, Springfield, MA 01199, United States
| | - Jesse Thomas Casaubon
- University of Massachusetts Chan Medical School-Baystate, Department of Surgery, Springfield, MA 01199, United States
| | - Qing Jackie Cao
- University of Massachusetts Chan Medical School-Baystate, Department of Pathology, Springfield, MA 01199, United States
| | - Sandra Haddad
- Dept of Science, Bay Path University, Longmeadow, MA 01106, United States
| | - Grace Makari-Judson
- University of Massachusetts Chan Medical School-Baystate, Division of Hematology-Oncology, Springfield, MA, United States
| | - D Joseph Jerry
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, United States; Dept of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, United States
| | - Sallie S Schneider
- Pioneer Valley Life Sciences Institute, Springfield, MA 01199, United States; Dept of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, United States; University of Massachusetts Chan Medical School-Baystate, Department of Surgery, Springfield, MA 01199, United States.
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31
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Hong Z, Liu T, Wan L, Fa P, Kumar P, Cao Y, Prasad CB, Qiu Z, Joseph L, Hongbing W, Li Z, Wang QE, Guo P, Guo D, Yilmaz AS, Lu L, Papandreou I, Jacob NK, Yan C, Zhang X, She QB, Ma Z, Zhang J. Targeting Squalene Epoxidase Interrupts Homologous Recombination via the ER Stress Response and Promotes Radiotherapy Efficacy. Cancer Res 2022; 82:1298-1312. [PMID: 35045984 PMCID: PMC8983553 DOI: 10.1158/0008-5472.can-21-2229] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022]
Abstract
Over 50% of all patients with cancer are treated with radiotherapy. However, radiotherapy is often insufficient as a monotherapy and requires a nontoxic radiosensitizer. Squalene epoxidase (SQLE) controls cholesterol biosynthesis by converting squalene to 2,3-oxidosqualene. Given that SQLE is frequently overexpressed in human cancer, this study investigated the importance of SQLE in breast cancer and non-small cell lung cancer (NSCLC), two cancers often treated with radiotherapy. SQLE-positive IHC staining was observed in 68% of breast cancer and 56% of NSCLC specimens versus 15% and 25% in normal breast and lung tissue, respectively. Importantly, SQLE expression was an independent predictor of poor prognosis, and pharmacologic inhibition of SQLE enhanced breast and lung cancer cell radiosensitivity. In addition, SQLE inhibition enhanced sensitivity to PARP inhibition. Inhibition of SQLE interrupted homologous recombination by suppressing ataxia-telangiectasia mutated (ATM) activity via the translational upregulation of wild-type p53-induced phosphatase (WIP1), regardless of the p53 status. SQLE inhibition and subsequent squalene accumulation promoted this upregulation by triggering the endoplasmic reticulum (ER) stress response. Collectively, these results identify a novel tumor-specific radiosensitizer by revealing unrecognized cross-talk between squalene metabolites, ER stress, and the DNA damage response. Although SQLE inhibitors have been used as antifungal agents in the clinic, they have not yet been used as antitumor agents. Repurposing existing SQLE-inhibiting drugs may provide new cancer treatments. SIGNIFICANCE Squalene epoxidase inhibitors are novel tumor-specific radiosensitizers that promote ER stress and suppress homologous recombination, providing a new potential therapeutic approach to enhance radiotherapy efficacy.
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Affiliation(s)
- Zhipeng Hong
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian, 362000, P.R. China
| | - Tao Liu
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Lingfeng Wan
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Pengyan Fa
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Pankaj Kumar
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Yanan Cao
- Department of Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY, 40506, USA
| | - Chandra Bhushan Prasad
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Zhaojun Qiu
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Liu Joseph
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Wang Hongbing
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Zaibo Li
- Department of Pathology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Qi-En Wang
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Deliang Guo
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Ayse Selen Yilmaz
- Department of Biomedical Informatics, College of Medicine, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, USA
| | - Lanchun Lu
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Ioanna Papandreou
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Naduparambil K Jacob
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, USA
| | - Xiaoli Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, USA
| | - Qing-Bai She
- Department of Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY, 40506, USA
| | - Zhefu Ma
- Department Breast Surgery and Plastic Surgery, Cancer Hospital of China Medical University, 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, China
- Department Breast & Thyroid Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 of Zhongshan 2nd Road, Yuexiu District, Guangzhou, 510080, China
| | - Junran Zhang
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, OH, 43210, USA
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32
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Daniel Grass G, Alfonso JCL, Welsh E, Ahmed KA, Teer JK, Pilon-Thomas S, Harrison LB, Cleveland JL, Mulé JJ, Eschrich SA, Enderling H, Torres-Roca JF. The Radiosensitivity Index (RSI) Gene Signature Identifies Distinct Tumor Immune Microenvironment Characteristics Associated with Susceptibility to Radiotherapy. Int J Radiat Oncol Biol Phys 2022; 113:635-647. [PMID: 35289298 DOI: 10.1016/j.ijrobp.2022.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 12/09/2022]
Abstract
PURPOSE Radiotherapy (RT) is a mainstay of cancer care and accumulating evidence suggests the potential for synergism with components of the immune response. However, little data describes the tumor immune contexture in relation to RT-sensitivity. To address this challenge, we employed the radiation sensitivity index (RSI) gene signature to estimate the RT-sensitivity of >10,000 primary tumors and characterized their immune microenvironments in relation to the RSI. MATERIAL AND METHODS We analyzed gene expression profiles of 10,469 primary tumors (31 types) within a prospective tissue collection protocol. The RT-sensitivity of each tumor was estimated by the RSI and respective distributions were characterized. The tumor biology measured by the RSI was evaluated by differentially expressed genes (DEGs) combined with single sample gene set enrichment analysis (ssGSEA). Differences in the expression of immune regulatory molecules were assessed and deconvolution algorithms were used to estimate immune cell infiltrates in relation to the RSI. A subset (n=2,368) of tumors underwent DNA sequencing for mutational frequency characterization. RESULTS We identified a wide range of RSI values within and across various tumor types, with several demonstrating non-unimodal distributions (e.g. colon, renal, lung, prostate, esophagus, pancreas and PAM50 breast subtypes; p <0.05). Across all tumors types, stratifying RSI at a tumor type-specific median, identified 7,148 DEGs, of which 146 were coordinate in direction. Network topology analysis demonstrates RSI measures a coordinated STAT1, IRF1, and CCL4/MIP-1β transcriptional network. Tumors with an estimated high sensitivity to RT demonstrated distinct enrichment of interferon-associated signaling pathways and immune cell infiltrates (e.g. CD8+ T cells, activated natural killer cells, M1-macrophages; q < 0.05), which was in the context of diverse expression patterns of various immunoregulatory molecules. CONCLUSION This analysis describes the immune microenvironments of patient tumors in relation to the RSI gene expression signature.
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Affiliation(s)
- G Daniel Grass
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Juan C L Alfonso
- Departments of Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research
| | - Eric Welsh
- Departments of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Kamran A Ahmed
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Jamie K Teer
- Departments of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Shari Pilon-Thomas
- Departments of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Louis B Harrison
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - John L Cleveland
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - James J Mulé
- Departments of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Steven A Eschrich
- Departments of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA
| | - Heiko Enderling
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA; Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA.
| | - Javier F Torres-Roca
- Departments of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa FL, USA.
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33
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O’Connor JD, Overton IM, McMahon SJ. RadSigBench: a framework for benchmarking functional genomics signatures of cancer cell radiosensitivity. Brief Bioinform 2022; 23:bbab561. [PMID: 35066588 PMCID: PMC8921666 DOI: 10.1093/bib/bbab561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/20/2022] Open
Abstract
Multiple transcriptomic predictors of tumour cell radiosensitivity (RS) have been proposed, but they have not been benchmarked against one another or to control models. To address this, we present RadSigBench, a comprehensive benchmarking framework for RS signatures. The approach compares candidate models to those developed from randomly resampled control signatures and from cellular processes integral to the radiation response. Robust evaluation of signature accuracy, both overall and for individual tissues, is performed. The NCI60 and Cancer Cell Line Encyclopaedia datasets are integrated into our workflow. Prediction of two measures of RS is assessed: survival fraction after 2 Gy and mean inactivation dose. We apply the RadSigBench framework to seven prominent published signatures of radiation sensitivity and test for equivalence to control signatures. The mean out-of-sample R2 for the published models on test data was very poor at 0.01 (range: -0.05 to 0.09) for Cancer Cell Line Encyclopedia and 0.00 (range: -0.19 to 0.19) in the NCI60 data. The accuracy of both published and cellular process signatures investigated was equivalent to the resampled controls, suggesting that these signatures contain limited radiation-specific information. Enhanced modelling strategies are needed for effective prediction of intrinsic RS to inform clinical treatment regimes. We make recommendations for methodological improvements, for example the inclusion of perturbation data, multiomics, advanced machine learning and mechanistic modelling. Our validation framework provides for robust performance assessment of ongoing developments in intrinsic RS prediction.
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Affiliation(s)
- John D O’Connor
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, BT9 7AE, United Kingdom
| | - Ian M Overton
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, BT9 7AE, United Kingdom
| | - Stephen J McMahon
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, BT9 7AE, United Kingdom
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Estrogen receptor inhibition mediates radiosensitization of ER-positive breast cancer models. NPJ Breast Cancer 2022; 8:31. [PMID: 35273179 PMCID: PMC8913671 DOI: 10.1038/s41523-022-00397-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/03/2022] [Indexed: 11/28/2022] Open
Abstract
Endocrine therapy (ET) is an effective first-line therapy for women with estrogen receptor-positive (ER + ) breast cancers. While both ionizing radiation (RT) and ET are used for the treatment of women with ER+ breast cancer, the most effective sequencing of therapy and the effect of ET on tumor radiosensitization remains unclear. Here we sought to understand the effects of inhibiting estrogen receptor (ER) signaling in combination with RT in multiple preclinical ER+ breast cancer models. Clonogenic survival assays were performed using variable pre- and post-treatment conditions to assess radiosensitization with estradiol, estrogen deprivation, tamoxifen, fulvestrant, or AZD9496 in ER+ breast cancer cell lines. Estrogen stimulation was radioprotective (radiation enhancement ratios [rER]: 0.51–0.82). Conversely, when given one hour prior to RT, ER inhibition or estrogen depletion radiosensitized ER+ MCF-7 and T47D cells (tamoxifen rER: 1.50–1.60, fulvestrant rER: 1.76–2.81, AZD9496 rER: 1.33–1.48, estrogen depletion rER: 1.47–1.51). Combination treatment resulted in an increase in double-strand DNA (dsDNA) breaks as a result of inhibition of non-homologous end joining-mediated dsDNA break repair with no effect on homologous recombination. Treatment with tamoxifen or fulvestrant in combination with RT also increased the number of senescent cells but did not affect apoptosis or cell cycle distribution. Using an MCF-7 xenograft model, concurrent treatment with tamoxifen and RT was synergistic and resulted in a significant decrease in tumor volume and a delay in time to tumor doubling without significant toxicity. These findings provide preclinical evidence that concurrent treatment with ET and RT may be an effective radiosensitization strategy.
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35
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Du J, Kageyama SI, Yamashita R, Hirata H, Hakozaki Y, Okumura M, Motegi A, Hojo H, Nakamura M, Hirano Y, Sunakawa H, Minamide T, Kotani D, Tanaka K, Yano T, Kojima T, Ohashi A, Tsuchihara K, Akimoto T. Impacts of the STING-IFNAR1-STAT1-IRF1 pathway on the cellular immune reaction induced by fractionated irradiation. Cancer Sci 2022; 113:1352-1361. [PMID: 35133062 PMCID: PMC8990811 DOI: 10.1111/cas.15297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 11/27/2022] Open
Abstract
Radiotherapy (RT) combined with immune checkpoint inhibitors (ICIs) has recently produced outstanding results and is expected to be adaptable for various cancers. However, the precise molecular mechanism by which immune reactions are induced by fractionated RT is still controversial. We aimed to investigate the mechanism of the immune response regarding multifractionated, long-term radiation, which is most often combined with immunotherapy. Two human esophageal cancer cell lines, KYSE-450 and OE-21, were irradiated by fractionated irradiation (FIR) daily at a dose of 3 Gy in 5 days per week for 2 weeks. Western blotting (WB), and RNA sequencing identified type I interferon (IFN) and the STING pathway as candidates which regulate immune response by FIR. We inhibited STING, IFNAR1, STAT1 and IRF1 and investigated the effects on the immune response in cancer cells and the invasion of surrounding immune cells. We herein revealed type I IFN-dependent immune reactions and the positive feedback of STING, IRF1 and phosphorylated STAT1 induced by FIR. Knocking out STING, IFNAR1, STAT1 and IRF1 resulted in a poorer immunological response than that in wild-type cells. The STING-knockout KYSE-450 cell line exhibited significantly less invasion of peripheral blood mononuclear cells (PBMCs) than the wild-type cell line under FIR. In the analysis of STING-knockout cells and migrated PBMCs, we confirmed the occurrence of STING-dependent immune activation under FIR. In conclusion, we identified that the STING-IFNAR1-STAT1-IRF1 axis regulates immune reactions in cancer cells triggered by FIR and that the STING pathway also contributes to immune cell invasion of cancer cells.
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Affiliation(s)
- Junyan Du
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shun-Ichiro Kageyama
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan.,Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Riu Yamashita
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hidenari Hirata
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan.,Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Yumi Hakozaki
- Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Masayuki Okumura
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Atsushi Motegi
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hidehiro Hojo
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Masaki Nakamura
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Yasuhiro Hirano
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan
| | - Hironori Sunakawa
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Tatsunori Minamide
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Kosuke Tanaka
- Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Tomonori Yano
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Takashi Kojima
- Department of Gastroenterology and Gastrointestinal oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Akihiro Ohashi
- Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tetsuo Akimoto
- Division of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Chiba, Japan.,Department of Radiation Oncology, National Cancer Center Hospital East, Chiba, Japan
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36
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Abstract
Most of the transcribed human genome codes for noncoding RNAs (ncRNAs), and long noncoding RNAs (lncRNAs) make for the lion's share of the human ncRNA space. Despite growing interest in lncRNAs, because there are so many of them, and because of their tissue specialization and, often, lower abundance, their catalog remains incomplete and there are multiple ongoing efforts to improve it. Consequently, the number of human lncRNA genes may be lower than 10,000 or higher than 200,000. A key open challenge for lncRNA research, now that so many lncRNA species have been identified, is the characterization of lncRNA function and the interpretation of the roles of genetic and epigenetic alterations at their loci. After all, the most important human genes to catalog and study are those that contribute to important cellular functions-that affect development or cell differentiation and whose dysregulation may play a role in the genesis and progression of human diseases. Multiple efforts have used screens based on RNA-mediated interference (RNAi), antisense oligonucleotide (ASO), and CRISPR screens to identify the consequences of lncRNA dysregulation and predict lncRNA function in select contexts, but these approaches have unresolved scalability and accuracy challenges. Instead-as was the case for better-studied ncRNAs in the past-researchers often focus on characterizing lncRNA interactions and investigating their effects on genes and pathways with known functions. Here, we focus most of our review on computational methods to identify lncRNA interactions and to predict the effects of their alterations and dysregulation on human disease pathways.
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37
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Reddy AV, Hill CS, Sehgal S, Ding D, Hacker-Prietz A, He J, Zheng L, Herman JM, Meyer J, Narang AK. Impact of somatic mutations on clinical and pathologic outcomes in borderline resectable and locally advanced pancreatic cancer treated with neoadjuvant chemotherapy and stereotactic body radiotherapy followed by surgical resection. Radiat Oncol J 2021; 39:304-314. [PMID: 34986552 PMCID: PMC8743453 DOI: 10.3857/roj.2021.00815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/08/2021] [Accepted: 10/14/2021] [Indexed: 01/05/2023] Open
Abstract
PURPOSE The purpose of this study was to determine if somatic mutations are associated with clinical and pathologic outcomes in patients with borderline resectable pancreatic cancer (BRPC) or locally advanced pancreatic cancer (LAPC) who were treated with neoadjuvant chemotherapy and stereotactic body radiotherapy (SBRT). MATERIALS AND METHODS Patients treated with neoadjuvant chemotherapy and SBRT followed by surgical resection from August 2016 to January 2019 and who underwent next generation sequencing of their primary tumor were included in the study. Next-generation sequencing was performed either in-house with a Solid Tumor Panel or with FoundationOne CDx. Univariate (UVA) and multivariable analyses (MVA) were performed to determine associations between somatic mutations and pathologic and clinical outcomes. RESULTS Thirty-five patients were included in the study. Chemotherapy consisted of modified FOLFIRINOX, gemcitabine and nab-paclitaxel, or gemcitabine and capecitabine. Patients were treated with SBRT in 33 Gy in 5 fractions. On UVA and MVA, tumors with KRAS G12V mutation demonstrated better pathologic tumor regression grade (TRG) to neoadjuvant therapy when compared to tumors with other KRAS mutations (odds ratio = 0.087; 95% confidence interval [CI], 0.009-0.860; p = 0.036). On UVA and MVA, mutations in NOTCH1/2 were associated with worse overall survival (hazard ratio [HR] = 4.15; 95% CI, 1.57-10.95; p = 0.004) and progression-free survival (HR = 3.61; 95% CI, 1.41-9.28; p = 0.008). On UVA, only mutations in NOTCH1/2 were associated with inferior distant metastasis-free survival (HR = 3.38; 95% CI, 1.25-9.16; p = 0.017). CONCLUSION In BRPC and LAPC, the KRAS G12V mutation was associated with better TRG following chemotherapy and SBRT. Additionally, NOTCH1/2 mutations were associated with worse overall survival, distant metastasis-free survival, and progression-free survival.
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Affiliation(s)
- Abhinav V. Reddy
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin S. Hill
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shuchi Sehgal
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ding Ding
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy Hacker-Prietz
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jin He
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lei Zheng
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph M. Herman
- Department of Radiation Oncology, Northwell Health Cancer Institute, New Hyde Park, NY, USA
| | - Jeffrey Meyer
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amol K. Narang
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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38
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Yang L, Shen C, Estrada-Bernal A, Robb R, Chatterjee M, Sebastian N, Webb A, Mo X, Chen W, Krishnan S, Williams TM. Oncogenic KRAS drives radioresistance through upregulation of NRF2-53BP1-mediated non-homologous end-joining repair. Nucleic Acids Res 2021; 49:11067-11082. [PMID: 34606602 PMCID: PMC8565339 DOI: 10.1093/nar/gkab871] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/03/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
KRAS-activating mutations are oncogenic drivers and are correlated with radioresistance of multiple cancers, including colorectal cancer, but the underlying precise molecular mechanisms remain elusive. Herein we model the radiosensitivity of isogenic HCT116 and SW48 colorectal cancer cell lines bearing wild-type or various mutant KRAS isoforms. We demonstrate that KRAS mutations indeed lead to radioresistance accompanied by reduced radiotherapy-induced mitotic catastrophe and an accelerated release from G2/M arrest. Moreover, KRAS mutations result in increased DNA damage response and upregulation of 53BP1 with associated increased non-homologous end-joining (NHEJ) repair. Remarkably, KRAS mutations lead to activation of NRF2 antioxidant signaling to increase 53BP1 gene transcription. Furthermore, genetic silencing or pharmacological inhibition of KRAS, NRF2 or 53BP1 attenuates KRAS mutation-induced radioresistance, especially in G1 phase cells. These findings reveal an important role for a KRAS-induced NRF2-53BP1 axis in the DNA repair and survival of KRAS-mutant tumor cells after radiotherapy, and indicate that targeting NRF2, 53BP1 or NHEJ may represent novel strategies to selectively abrogate KRAS mutation-mediated radioresistance.
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Affiliation(s)
- Linlin Yang
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Changxian Shen
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Adriana Estrada-Bernal
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Ryan Robb
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Moumita Chatterjee
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Nikhil Sebastian
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Amy Webb
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Xiaokui Mo
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Wei Chen
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | | | - Terence M Williams
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
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Elbanna M, Chowdhury NN, Rhome R, Fishel ML. Clinical and Preclinical Outcomes of Combining Targeted Therapy With Radiotherapy. Front Oncol 2021; 11:749496. [PMID: 34733787 PMCID: PMC8558533 DOI: 10.3389/fonc.2021.749496] [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] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
In the era of precision medicine, radiation medicine is currently focused on the precise delivery of highly conformal radiation treatments. However, the tremendous developments in targeted therapy are yet to fulfill their full promise and arguably have the potential to dramatically enhance the radiation therapeutic ratio. The increased ability to molecularly profile tumors both at diagnosis and at relapse and the co-incident progress in the field of radiogenomics could potentially pave the way for a more personalized approach to radiation treatment in contrast to the current ‘‘one size fits all’’ paradigm. Few clinical trials to date have shown an improved clinical outcome when combining targeted agents with radiation therapy, however, most have failed to show benefit, which is arguably due to limited preclinical data. Several key molecular pathways could theoretically enhance therapeutic effect of radiation when rationally targeted either by directly enhancing tumor cell kill or indirectly through the abscopal effect of radiation when combined with novel immunotherapies. The timing of combining molecular targeted therapy with radiation is also important to determine and could greatly affect the outcome depending on which pathway is being inhibited.
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Affiliation(s)
- May Elbanna
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, United States.,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nayela N Chowdhury
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ryan Rhome
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, United States.,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Melissa L Fishel
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
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40
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Ghaderi N, Jung JH, Odde DJ, Peacock J. Clinically validated model predicts the effect of intratumoral heterogeneity on overall survival for non-small cell lung cancer (NSCLC) patients. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2021; 212:106455. [PMID: 34736167 DOI: 10.1016/j.cmpb.2021.106455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND OBJECTIVE Radiation therapy is used in nearly 50% of cancer treatments in the developed world. Currently, radiation treatments are homogenous and fail to take into consideration intratumoral heterogeneity. We demonstrate the importance of considering intratumoral heterogeneity and the development of resistance during fractionated radiotherapy when the same dose of radiation is delivered for all fractions (Fractional Equivalent Dosing FED). METHODS A mathematical model was developed with the following parameters: a starting population of 1011 non-small cell lung cancer (NSCLC) tumor cells, 48 h doubling time, and cell death per the linear-quadratic (LQ) model with α and β values derived from RSIα/β, in a previously described gene expression based model that estimates α and β. To incorporate both inter- and intratumor radiation sensitivity, RSIα/β output for each patient sample is assumed to represent an average value in a gamma distribution with the bounds set to -50% and +50% of RSIα/b. Therefore, we assume that within a given tumor there are subpopulations that have varying radiation sensitivity parameters that are distinct from other tumor samples with a different mean RSIα/β. A simulation cohort (SC) comprised of 100 lung cancer patients with available RSIα/β (patient specific α and β values) was used to investigate 60 Gy in 30 fractions with fractionally equivalent dosing (FED). A separate validation cohort (VC) of 57 lung cancer patients treated with radiation with available local control (LC), overall survival (OS), and tumor gene expression was used to clinically validate the model. Cox regression was used to test for significance to predict clinical outcomes as a continuous variable in multivariate analysis (MVA). Finally, the VC was used to compare FED schedules with various altered fractionation schema utilizing a Kruskal-Wallis test. This was examined using the end points of end of treatment log cell count (LCC) and by a parameter described as mean log kill efficiency (LKE) defined as: LCC = log10(tumorcellcount) [Formula: see text] RESULTS: Cox regression analysis on LCC for the VC demonstrates that, after incorporation of intratumoral heterogeneity, LCC has a linear correlation with local control (p = 0.002) and overall survival (p = < 0.001). Other suggested treatment schedules labeled as High Intensity Treatment (HIT) with a total 60 Gy delivered over 6 weeks have a lower mean LCC and an increased LKE compared to standard of care 60 Gy delivered in FED in the VC. CONCLUSION We find that LCC is a clinically relevant metric that is correlated with local control and overall survival in NSCLC. We conclude that 60 Gy delivered over 6 weeks with altered HIT fractionation leads to an enhancement in tumor control compared to FED when intratumoral heterogeneity is considered.
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Affiliation(s)
- Nima Ghaderi
- Department of Mechanical Engineering, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Joseph H Jung
- Department of Biomedical Engineering, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota Twin Cities, Minneapolis, MN, USA.
| | - Jeffrey Peacock
- Department of Radiation Oncology, University of Alabama Birmingham, Birmingham, AL, USA.
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41
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Orchestrating and sharing large multimodal data for transparent and reproducible research. Nat Commun 2021; 12:5797. [PMID: 34608132 PMCID: PMC8490371 DOI: 10.1038/s41467-021-25974-w] [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: 03/18/2021] [Accepted: 09/08/2021] [Indexed: 11/08/2022] Open
Abstract
Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial for scientists to describe their experiments in sufficient detail so they can be reproduced, scrutinized, challenged, and built upon. However, the intrinsic complexity and continuous growth of biomedical data makes it increasingly difficult to process, analyze, and share with the community in a FAIR (findable, accessible, interoperable, and reusable) manner. To overcome these issues, we created a cloud-based platform called ORCESTRA ( orcestra.ca ), which provides a flexible framework for the reproducible processing of multimodal biomedical data. It enables processing of clinical, genomic and perturbation profiles of cancer samples through automated processing pipelines that are user-customizable. ORCESTRA creates integrated and fully documented data objects with persistent identifiers (DOI) and manages multiple dataset versions, which can be shared for future studies.
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42
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Hirata H, Niida A, Kakiuchi N, Uchi R, Sugimachi K, Masuda T, Saito T, Kageyama SI, Motomura Y, Ito S, Yoshitake T, Tsurumaru D, Nishimuta Y, Yokoyama A, Hasegawa T, Chiba K, Shiraishi Y, Du J, Miura F, Morita M, Toh Y, Hirakawa M, Shioyama Y, Ito T, Akimoto T, Miyano S, Shibata T, Mori M, Suzuki Y, Ogawa S, Ishigami K, Mimori K. The Evolving Genomic Landscape of Esophageal Squamous Cell Carcinoma Under Chemoradiotherapy. Cancer Res 2021; 81:4926-4938. [PMID: 34413060 DOI: 10.1158/0008-5472.can-21-0653] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/22/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) often recurs after chemoradiotherapy, and the prognosis of ESCC after chemoradiotherapy has not improved over the past few decades. The mutation process in chemoradiotherapy-resistant clones and the functional relevance of genetic alterations remain unclear. To address these problems, we performed whole-exome sequencing of 52 tumor samples from 33 patients with ESCC who received radiotherapy combined with 5-fluorouracil/platinum. In multiregion analyses of pretreatment and locally recurrent lesions from five cases, most driver gene-altered clones remained under chemoradiotherapy selection pressure, while few driver gene alterations were acquired at recurrence. The mutation signatures of recurrent ESCC, including increased deletion frequency and platinum dose-dependent base substitution signatures, were substantially different from those of primary ESCC and reflected the iatrogenic impacts of chemoradiotherapy. Single-region analysis of 28 pretreatment tumors indicated that focal copy-number gain at the MYC locus was significantly associated with poor progression-free survival and overall survival after chemoradiotherapy. MYC gain remained throughout the chemoradiotherapy course and potentially contributes to intrinsic resistance to chemoradiotherapy. Consistent with these findings, MYC copy number and mRNA and protein levels in ESCC cell lines correlated positively with resistance to radiotherapy, and MYC knockdown improved sensitivity to radiotherapy. Overall, these data characterize the clonal evolution process induced by chemoradiotherapy and clinically relevant associations for genetic alterations in ESCC. These findings increase our understanding of therapeutic resistance and support the rationale for precision chemoradiotherapy. SIGNIFICANCE: Whole-exome sequencing reveals the genetic evolution of ESCC during chemoradiotherapy, highlighting MYC gain in pretreatment tumors as a potential marker of therapy resistance.
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Affiliation(s)
- Hidenari Hirata
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan.,Department of Radiation Oncology, National Cancer Center Hospital East, Kashiwa, Japan.,Division of Radiation Oncology and Particle Therapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Atsushi Niida
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Division of Health Medical Computational Science, Health Intelligence Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryutaro Uchi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Keishi Sugimachi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Tomoko Saito
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Shun-Ichiro Kageyama
- Department of Radiation Oncology, National Cancer Center Hospital East, Kashiwa, Japan.,Division of Radiation Oncology and Particle Therapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Yushi Motomura
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan.,Department of Radiology, Kyushu University Beppu Hospital, Beppu, Japan
| | - Shuhei Ito
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Tadamasa Yoshitake
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daisuke Tsurumaru
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yusuke Nishimuta
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akira Yokoyama
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takanori Hasegawa
- Division of Health Medical Computational Science, Health Intelligence Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Centre, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Section of Genome Analysis Platform, Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Centre, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Section of Genome Analysis Platform, Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Junyan Du
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Fumihito Miura
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaru Morita
- Department of Gastroenterological Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Yasushi Toh
- Department of Gastroenterological Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Masakazu Hirakawa
- Department of Radiology, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yoshiyuki Shioyama
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Ion Beam Therapy Center, SAGA HIMAT Foundation, Tosu, Japan
| | - Takashi Ito
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuo Akimoto
- Department of Radiation Oncology, National Cancer Center Hospital East, Kashiwa, Japan.,Division of Radiation Oncology and Particle Therapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Centre, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Masaki Mori
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kousei Ishigami
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan.
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Singh J, Hatcher S, Ku AA, Ding Z, Feng FY, Sharma RA, Pfister SX. Model Selection for the Preclinical Development of New Drug-Radiotherapy Combinations. Clin Oncol (R Coll Radiol) 2021; 33:694-704. [PMID: 34474951 DOI: 10.1016/j.clon.2021.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/13/2021] [Accepted: 08/11/2021] [Indexed: 12/12/2022]
Abstract
Radiotherapy plays an essential role in the treatment of more than half of all patients with cancer. In recent decades, advances in devices that deliver radiation and the development of treatment planning software have helped radiotherapy attain precise tumour targeting with minimal toxicity to surrounding tissues. Simultaneously, as more targeted drug therapies are being brought into the market, there has been significant interest in improving cure rates for cancer by adding drugs to radiotherapy to widen the therapeutic window, the difference between normal tissue toxicity and treatment efficacy. The development of new combination therapies will require judicious adaptation of preclinical models that are routinely used for traditional drug discovery. Here we highlight the strengths and weaknesses of each of these preclinical models and discuss how they can be used optimally to identify new and clinically beneficial drug-radiotherapy combinations.
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Affiliation(s)
- J Singh
- Global Translational Science, Varian, a Siemens Healthineers company, Palo Alto, California, USA
| | - S Hatcher
- Global Translational Science, Varian, a Siemens Healthineers company, Palo Alto, California, USA
| | - A A Ku
- Global Translational Science, Varian, a Siemens Healthineers company, Palo Alto, California, USA
| | - Z Ding
- Global Translational Science, Varian, a Siemens Healthineers company, Palo Alto, California, USA
| | - F Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, California, USA; Department of Radiation Oncology, University of California, San Francisco, California, USA; Department of Urology, University of California, San Francisco, California, USA
| | - R A Sharma
- Global Translational Science, Varian, a Siemens Healthineers company, Palo Alto, California, USA; UCL Cancer Institute, University College London, London, UK
| | - S X Pfister
- Global Translational Science, Varian, a Siemens Healthineers company, Palo Alto, California, USA.
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44
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Wong K, Ludwig L, Krijgsman O, Adams DJ, Wood GA, van der Weyden L. Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma. Dis Model Mech 2021; 14:dmm049044. [PMID: 34296746 PMCID: PMC8319545 DOI: 10.1242/dmm.049044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/15/2021] [Indexed: 01/03/2023] Open
Abstract
Angiosarcoma (AS) is a highly aggressive tumor of blood and lymphatic vessels in humans that shares many similarities with spontaneously occurring hemangiosarcoma (HSA) in dogs and cats. To investigate the genetic suitability of HSA as a model for AS, we sequenced ∼1000 cancer genes in 41 cases of HSA and matched germline tissue: 15 canine visceral HSAs, 13 canine skin HSAs and 13 feline skin HSAs. Analysis of visceral HSAs from dogs presenting with concurrent splenic and cardiac neoplasms showed that the tumors were not independent primaries, consistent with the highly metastatic nature of HSA. Comparison of HSA to AS revealed that several driver genes were recurrently mutated in both species, such as TP53, PIK3CA, ATRX, GRIN2A and LRP1B. Similar to AS, a UV mutational signature was found in a subset of canine cutaneous HSAs and both species show differing mutational profiles between tissue sites. Our characterization of canine and feline HSA demonstrates many important parallels to AS and provides hope that future studies on these cancers will benefit of all three species.
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Affiliation(s)
- Kim Wong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Latasha Ludwig
- Department of Pathobiology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
| | - Oscar Krijgsman
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - David J. Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Geoffrey A. Wood
- Department of Pathobiology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
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45
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McMahon SJ, Prise KM. A Mechanistic DNA Repair and Survival Model (Medras): Applications to Intrinsic Radiosensitivity, Relative Biological Effectiveness and Dose-Rate. Front Oncol 2021; 11:689112. [PMID: 34268120 PMCID: PMC8276175 DOI: 10.3389/fonc.2021.689112] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/31/2021] [Indexed: 01/04/2023] Open
Abstract
Variations in the intrinsic radiosensitivity of different cells to ionizing radiation is now widely believed to be a significant driver in differences in response to radiotherapy. While the mechanisms of radiosensitivity have been extensively studied in the laboratory, there are a lack of models which integrate this knowledge into a predictive framework. This paper presents an overview of the Medras model, which has been developed to provide a mechanistic framework in which different radiation responses can be modelled and individual responses predicted. This model simulates the repair of radiation-induced DNA damage, incorporating the overall kinetics of repair and its fidelity, to predict a range of biological endpoints including residual DNA damage, mutation, chromosome aberration, and cell death. Validation of this model against a range of exposure types is presented, including considerations of varying radiation qualities and dose-rates. This approach has the potential to inform new tools to deliver mechanistic predictions of radiation sensitivity, and support future developments in treatment personalization.
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Affiliation(s)
- Stephen Joseph McMahon
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, United Kingdom
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46
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Yu L, Wei J, Liu P. Attacking the PI3K/Akt/mTOR signaling pathway for targeted therapeutic treatment in human cancer. Semin Cancer Biol 2021; 85:69-94. [PMID: 34175443 DOI: 10.1016/j.semcancer.2021.06.019] [Citation(s) in RCA: 183] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/10/2021] [Accepted: 06/22/2021] [Indexed: 02/08/2023]
Abstract
Cancer is the second leading cause of human death globally. PI3K/Akt/mTOR signaling is one of the most frequently dysregulated signaling pathways observed in cancer patients that plays crucial roles in promoting tumor initiation, progression and therapy responses. This is largely due to that PI3K/Akt/mTOR signaling is indispensable for many cellular biological processes, including cell growth, metastasis, survival, metabolism, and others. As such, small molecule inhibitors targeting major kinase components of the PI3K/Akt/mTOR signaling pathway have drawn extensive attention and been developed and evaluated in preclinical models and clinical trials. Targeting a single kinase component within this signaling usually causes growth arrest rather than apoptosis associated with toxicity-induced adverse effects in patients. Combination therapies including PI3K/Akt/mTOR inhibitors show improved patient response and clinical outcome, albeit developed resistance has been reported. In this review, we focus on revealing the mechanisms leading to the hyperactivation of PI3K/Akt/mTOR signaling in cancer and summarizing efforts for developing PI3K/Akt/mTOR inhibitors as either mono-therapy or combination therapy in different cancer settings. We hope that this review will facilitate further understanding of the regulatory mechanisms governing dysregulation of PI3K/Akt/mTOR oncogenic signaling in cancer and provide insights into possible future directions for targeted therapeutic regimen for cancer treatment, by developing new agents, drug delivery systems, or combination regimen to target the PI3K/Akt/mTOR signaling pathway. This information will also provide effective patient stratification strategy to improve the patient response and clinical outcome for cancer patients with deregulated PI3K/Akt/mTOR signaling.
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Affiliation(s)
- Le Yu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Pengda Liu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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47
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Tan H, Cheung P, Louie AV, Myrehaug S, Niglas M, Atenafu EG, Chu W, Chung HT, Poon I, Sahgal A, Soliman H. Outcomes of extra-cranial stereotactic body radiotherapy for metastatic breast cancer: Treatment indication matters. Radiother Oncol 2021; 161:159-165. [PMID: 34119585 DOI: 10.1016/j.radonc.2021.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/29/2021] [Accepted: 06/06/2021] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND PURPOSE To summarize the clinical outcomes of stereotactic body radiotherapy (SBRT) for metastatic breast cancer (mBC) from a large institution. MATERIALS AND METHODS Patients with mBC who received extra-cranial SBRT to metastatic lesions from 2011 to 2017 were identified. Treatment indications were: oligometastases, oligoprogression, and local control of dominant tumor (CDT). Endpoints included overall survival (OS), progression-free survival (PFS), local control (LC) and cumulative incidence of starting/changing chemo or hormonal therapy (SCT). Univariate and multivariate analyses were used to identify predictive factors. RESULTS We analyzed 120 patients (193 treated metastatic lesions) with a median follow up of 15.25 months. 1-and 2-year LC rates were 89% and 86.6%, respectively. 1-and 2-year OS rates were 83.5% and 70%, respectively, with treatment indication and molecular subtype being the predictive factors on MVA. 1-year OS was 91.0%, 78.5% and 63.9% for oligometastases, oligoprogression and CDT, respectively (p = 0.003). The worst OS was seen in basal subtype with 1-and 2-year OS rates of 59.2% and 39.5% (p = 0.01). Treatment indication was found to be predictive for PFS and lower rates of SCT on MVA. 1-and 2-year PFS rates were 45% and 32%, respectively. The 1-year PFS for oligometastases, oligoprogression, and CDT was 66%, 19.6%, and 14.3%, respectively (p < 0.001). The cumulative incidence of SCT at 1-year was 12% for oligometastases, 39.7% for oligoprogression and 53.3% for CDT (p < 0.001). CONCLUSION Patients treated for oligometastases have better OS and PFS than those treated for oligoprogression or CDT. SBRT may delay SCT in mBC patients, particularly those with oligometastases. SBRT provided an excellent LC in mBC patients.
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Affiliation(s)
- Hendrick Tan
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Patrick Cheung
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Alexander V Louie
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Sten Myrehaug
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Mark Niglas
- Department of Radiation Oncology, RS Mclaughlin Durham Regional Cancer Centre, Toronto, Canada; Department of Oncology, Queen's University, Kingston, Canada
| | - Eshetu G Atenafu
- Department of Biostatistics, University Health Network, University of Toronto, Canada
| | - William Chu
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Hans T Chung
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Ian Poon
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Arjun Sahgal
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Hany Soliman
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Canada.
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48
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Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance. Nat Commun 2021; 12:2700. [PMID: 33976213 PMCID: PMC8113601 DOI: 10.1038/s41467-021-22989-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 04/09/2021] [Indexed: 02/07/2023] Open
Abstract
Resistance to ionizing radiation, a first-line therapy for many cancers, is a major clinical challenge. Personalized prediction of tumor radiosensitivity is not currently implemented clinically due to insufficient accuracy of existing machine learning classifiers. Despite the acknowledged role of tumor metabolism in radiation response, metabolomics data is rarely collected in large multi-omics initiatives such as The Cancer Genome Atlas (TCGA) and consequently omitted from algorithm development. In this study, we circumvent the paucity of personalized metabolomics information by characterizing 915 TCGA patient tumors with genome-scale metabolic Flux Balance Analysis models generated from transcriptomic and genomic datasets. Metabolic biomarkers differentiating radiation-sensitive and -resistant tumors are predicted and experimentally validated, enabling integration of metabolic features with other multi-omics datasets into ensemble-based machine learning classifiers for radiation response. These multi-omics classifiers show improved classification accuracy, identify clinical patient subgroups, and demonstrate the utility of personalized blood-based metabolic biomarkers for radiation sensitivity. The integration of machine learning with genome-scale metabolic modeling represents a significant methodological advancement for identifying prognostic metabolite biomarkers and predicting radiosensitivity for individual patients.
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49
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Flint DB, Bright SJ, McFadden CH, Konishi T, Ohsawa D, Turner B, Lin SH, Grosshans DR, Chiu HS, Sumazin P, Shaitelman SF, Sawakuchi GO. Cell lines of the same anatomic site and histologic type show large variability in intrinsic radiosensitivity and relative biological effectiveness to protons and carbon ions. Med Phys 2021; 48:3243-3261. [PMID: 33837540 DOI: 10.1002/mp.14878] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/27/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To show that intrinsic radiosensitivity varies greatly for protons and carbon (C) ions in addition to photons, and that DNA repair capacity remains important in governing this variability. METHODS We measured or obtained from the literature clonogenic survival data for a number of human cancer cell lines exposed to photons, protons (9.9 keV/μm), and C-ions (13.3-77.1 keV/μm). We characterized their intrinsic radiosensitivity by the dose for 10% or 50% survival (D10% or D50% ), and quantified the variability at each radiation quality by the coefficient of variation (COV) in D10% and D50% . We also treated cells with DNA repair inhibitors prior to irradiation to assess how DNA repair capacity affects their variability. RESULTS We found no statistically significant differences in the COVs of D10% or D50% between any of the radiation qualities investigated. The same was true regardless of whether the cells were treated with DNA repair inhibitors, or whether they were stratified into histologic subsets. Even within histologic subsets, we found remarkable differences in radiosensitivity for high LET C-ions that were often greater than the variations in RBE, with brain cancer cells varying in D10% (D50% ) up to 100% (131%) for 77.1 keV/μm C-ions, and non-small cell lung cancer and pancreatic cancer cell lines varying up to 55% (76%) and 51% (78%), respectively, for 60.5 keV/μm C-ions. The cell lines with modulated DNA repair capacity had greater variability in intrinsic radiosensitivity across all radiation qualities. CONCLUSIONS Even for cell lines of the same histologic type, there are remarkable variations in intrinsic radiosensitivity, and these variations do not differ significantly between photon, proton or C-ion radiation. The importance of DNA repair capacity in governing the variability in intrinsic radiosensitivity is not significantly diminished for higher LET radiation.
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Affiliation(s)
- David B Flint
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott J Bright
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Conor H McFadden
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Teruaki Konishi
- Single Cell Radiation Biology Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Daisuke Ohsawa
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
- Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Broderick Turner
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David R Grosshans
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hua-Sheng Chiu
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Pavel Sumazin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Simona F Shaitelman
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel O Sawakuchi
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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50
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Khan MT, Yang L, More E, Irlam-Jones JJ, Valentine HR, Hoskin P, Choudhury A, West CML. Developing Tumor Radiosensitivity Signatures Using LncRNAs. Radiat Res 2021; 195:324-333. [PMID: 33577642 DOI: 10.1667/rade-20-00157.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 01/11/2021] [Indexed: 11/03/2022]
Abstract
Long non-coding RNAs (lncRNAs) are involved in diverse biological processes, including DNA damage repair, and are of interest as potential biomarkers of radiosensitivity. We investigated whether lncRNA radiosensitivity signatures could be derived for use in cancer patients treated with radiotherapy. Signature development involved radiosensitivity measurements for cell lines and primary tumor samples, and patient outcome after radiotherapy. A 10-lncRNA signature trained on radiosensitivity measurements in bladder cell lines showed a trend towards independent validation. In multivariable analyses, patients with tumors classified as radioresistant by the lncRNA signature had poorer local relapse-free survival (P = 0.065) in 151 patients with muscle-invasive bladder cancer who underwent radiotherapy. An mRNA-based radiosensitivity index signature performed similarly to the lncRNA bladder signature for local relapse-free survival (P = 0.055). Pathway analysis showed the lncRNA signature associated with molecular processes involved in radiation responses. Knockdown of one of the lncRNAs in the signature showed a modest increase in radiosensitivity in one cell line. An alternative approach involved training on primary cervical tumor radiosensitivity or local control after radiotherapy. Both approaches failed to generate a cervix lncRNA radiosensitivity signature, which was attributed to the age of samples in our cohorts. Our work highlights challenges in validating lncRNA signatures as biomarkers in archival tissue from radiotherapy cohorts, but supports continued investigation of lncRNAs for a role in radiosensitivity.
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Affiliation(s)
- Mairah T Khan
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester M20 4BX, United Kingdom
| | - Lingjian Yang
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester M20 4BX, United Kingdom
| | - Elisabet More
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester M20 4BX, United Kingdom
| | - Joely J Irlam-Jones
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester M20 4BX, United Kingdom
| | - Helen R Valentine
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester M20 4BX, United Kingdom
| | - Peter Hoskin
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester M20 4BX, United Kingdom
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester M20 4BX, United Kingdom
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester M20 4BX, United Kingdom
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