1
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Amodio V, Vitiello PP, Bardelli A, Germano G. DNA repair-dependent immunogenic liabilities in colorectal cancer: opportunities from errors. Br J Cancer 2024:10.1038/s41416-024-02848-8. [PMID: 39271762 DOI: 10.1038/s41416-024-02848-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/26/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Colorectal cancer (CRC) remains one of the major causes of cancer death worldwide. Chemotherapy continues to serve as the primary treatment modality, while immunotherapy is largely ineffective for the majority of CRC patients. Seminal discoveries have emphasized that modifying DNA damage response (DDR) mechanisms confers both cell-autonomous and immune-related vulnerabilities across various cancers. In CRC, approximately 15% of tumours exhibit alterations in the mismatch repair (MMR) machinery, resulting in a high number of neoantigens and the activation of the type I interferon response. These factors, in conjunction with immune checkpoint blockades, collectively stimulate anticancer immunity. Furthermore, although less frequently, somatic alterations in the homologous recombination (HR) pathway are observed in CRC; these defects lead to genome instability and telomere alterations, supporting the use of poly (ADP-ribose) polymerase (PARP) inhibitors in HR-deficient CRC patients. Additionally, other DDR inhibitors, such as Ataxia Telangiectasia and Rad3-related protein (ATR) inhibitors, have shown some efficacy both in preclinical models and in the clinical setting, irrespective of MMR proficiency. The aim of this review is to elucidate how preexisting or induced vulnerabilities in DNA repair pathways represent an opportunity to increase tumour sensitivity to immune-based therapies in CRC.
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Affiliation(s)
- V Amodio
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
- Department of Oncology, Molecular Biotechnology Center, University of Torino, 10126, Turin, Italy
| | - P P Vitiello
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
- Department of Oncology, Molecular Biotechnology Center, University of Torino, 10126, Turin, Italy
| | - A Bardelli
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
- Department of Oncology, Molecular Biotechnology Center, University of Torino, 10126, Turin, Italy.
| | - G Germano
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
- Department of Medical Biotechnologies and Translational Medicine, University of Milano, 20133, Milan, Italy.
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2
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Barreto SG, Moy C, Pandol SJ, Kow L. Fecundity and Nutrient Deficiency Following Obesity Treatment: Implications for Young-Onset Cancer Risk in Offspring. Cancers (Basel) 2024; 16:3099. [PMID: 39272957 PMCID: PMC11394245 DOI: 10.3390/cancers16173099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 09/03/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
Young-onset adult cancers have been an emerging problem over the last three decades in Australia [...].
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Affiliation(s)
- Savio George Barreto
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia
- Flinders Medical Center, Division of Surgery and Perioperative Medicine, Flinders University, Adelaide, SA 5042, Australia
| | - Chris Moy
- Arkaba Medical Centre, Adelaide, SA 5063, Australia
| | - Stephen J Pandol
- Cedars-Sinai Medical Center, Division of Digestive and Liver Diseases, Los Angeles, CA 90048, USA
| | - Lilian Kow
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia
- Flinders Medical Center, Division of Surgery and Perioperative Medicine, Flinders University, Adelaide, SA 5042, Australia
- Adelaide Bariatric Centre, Flinders Private Hospital, Bedford Park, Adelaide, SA 5042, Australia
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3
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Mauri G, Patelli G, Sartore-Bianchi A, Abrignani S, Bodega B, Marsoni S, Costanzo V, Bachi A, Siena S, Bardelli A. Early-onset cancers: Biological bases and clinical implications. Cell Rep Med 2024:101737. [PMID: 39260369 DOI: 10.1016/j.xcrm.2024.101737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/02/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024]
Abstract
Since the nineties, the incidence of sporadic early-onset (EO) cancers has been rising worldwide. The underlying reasons are still unknown. However, identifying them is vital for advancing both prevention and intervention. Here, we exploit available knowledge derived from clinical observations to formulate testable hypotheses aimed at defining the causal factors of this epidemic and discuss how to experimentally test them. We explore the potential impact of exposome changes from the millennials to contemporary young generations, considering both environmental exposures and enhanced susceptibilities to EO-cancer development. We emphasize how establishing the time required for an EO cancer to develop is relevant to defining future screening strategies. Finally, we discuss the importance of integrating multi-dimensional data from international collaborations to generate comprehensive knowledge and translate these findings back into clinical practice.
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Affiliation(s)
- Gianluca Mauri
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Giorgio Patelli
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Andrea Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Beatrice Bodega
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy; Department of Biosciences, University of Milan, Milan, Italy
| | - Silvia Marsoni
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Vincenzo Costanzo
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Angela Bachi
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Salvatore Siena
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy; Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Alberto Bardelli
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology, Molecular Biotechnology Center, University of Torino, Torino, Italy.
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4
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Shuai A, Ullah S, Yu Y, Pandol SJ, Barreto SG. Perinatal Famine Exposure and Young-Onset Cancer-Lessons from China Health and Nutrition Survey. Cancers (Basel) 2024; 16:2537. [PMID: 39061177 PMCID: PMC11275197 DOI: 10.3390/cancers16142537] [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: 06/21/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Background/Objectives: Perinatal exposure to malnutrition has been hypothesised to influence the development of young-onset cancer (≤50 years of age). This study aimed to determine if perinatal malnutrition in individuals exposed to the Great Famine of China increased their risk of developing young-onset cancer compared to other individuals born prior to the famine. Subjects/Methods: This cross-sectional study involved 7272 participants from the China Health and Nutrition Survey who were classified into four groups based on birth year: participants born between 1953 and 1955 (before the famine) were designated as the pre-famine group (unexposed); the remainder formed perinatal exposure groups comprised of those exposed during the famine (1959-1961), those exposed in the early post-famine period (1962-1964), and those exposed in the late post-famine period (1965-1967). Multivariable adjusted log-binomial regression models were used to calculate the RR and 95% CI of young-onset cancer (including genitourinary cancer) across four groups. Results: Perinatal exposure to early post-famine (RR 2.08; 95%CI 1.04, 4.34; p = 0.043) and the female sex (RR 15.6, 95%CI 4.54, 60.3; p < 0.001) were noted to have a significantly increased risk of young-onset cancer. In addition, the early (RR 13.8; 95%CI 2.68, 253; p = 0.012) and late post-famine (RR 12.3; 95%CI 2.16, 231; p = 0.020) cohorts demonstrated a significantly increased risk of young-onset genitourinary cancer. The latter was accompanied by an increased risk of hypertension (RR 3.30; 95%CI 1.28, 7.87; p = 0.009). Conclusions: Perinatal exposure to famine, especially in females, was associated with a higher risk of young-onset cancer. This was particularly evident for young-onset genitourinary cancers. These findings highlight the potential long-term impact of perinatal malnutrition on young-onset carcinogenesis.
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Affiliation(s)
- Aidi Shuai
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia;
| | - Shahid Ullah
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia;
| | - Yongfu Yu
- School of Public Health, Shanghai Medical College, Fudan University, Shanghai 200031, China;
| | - Stephen J. Pandol
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA;
| | - Savio George Barreto
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia;
- Division of Surgery and Perioperative Medicine, Flinders Medical Centre, Bedford Park, Adelaide, SA 5042, Australia
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5
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Derényi I, Demeter MC, Pérez-Jiménez M, Grajzel D, Szöllősi GJ. How mutation accumulation depends on the structure of the cell lineage tree. Phys Rev E 2024; 109:044407. [PMID: 38755817 DOI: 10.1103/physreve.109.044407] [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: 03/15/2023] [Accepted: 03/08/2024] [Indexed: 05/18/2024]
Abstract
All the cells of a multicellular organism are the product of cell divisions that trace out a single binary tree, the so-called cell lineage tree. Because cell divisions are accompanied by replication errors, the shape of the cell lineage tree is a key determinant of how somatic evolution, which can potentially lead to cancer, proceeds. Carcinogenesis requires the accumulation of a certain number of driver mutations. By mapping the accumulation of mutations into a graph theoretical problem, we present an exact numerical method to calculate the probability of collecting a given number of mutations and show that for low mutation rates it can be approximated with a simple analytical formula, which depends only on the distribution of the lineage lengths, and is dominated by the longest lineages. Our results are crucial in understanding how natural selection can shape the cell lineage trees of multicellular organisms and curtail somatic evolution.
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Affiliation(s)
- Imre Derényi
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary and MTA-ELTE Statistical and Biological Physics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary
| | - Márton C Demeter
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary and MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary
| | - Mario Pérez-Jiménez
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary and MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary
| | - Dániel Grajzel
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary and MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary
| | - Gergely J Szöllősi
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary; MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary; HUN-REN Centre for Ecological Research, Institute of Evolution, H-1113 Budapest, Hungary; and Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0412 Okinawa, Japan
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6
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Nicholson MD, Cheek D, Antal T. Sequential mutations in exponentially growing populations. PLoS Comput Biol 2023; 19:e1011289. [PMID: 37428805 PMCID: PMC10359018 DOI: 10.1371/journal.pcbi.1011289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 07/20/2023] [Accepted: 06/21/2023] [Indexed: 07/12/2023] Open
Abstract
Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with n alterations, and how long will it take for these cells to appear. For exponentially growing populations, these questions have been tackled only in special cases so far. Here, within a multitype branching process framework, we consider a general mutational path where mutations may be advantageous, neutral or deleterious. In the biologically relevant limiting regimes of large times and small mutation rates, we derive probability distributions for the number, and arrival time, of cells with n mutations. Surprisingly, the two quantities respectively follow Mittag-Leffler and logistic distributions regardless of n or the mutations' selective effects. Our results provide a rapid method to assess how altering the fundamental division, death, and mutation rates impacts the arrival time, and number, of mutant cells. We highlight consequences for mutation rate inference in fluctuation assays.
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Affiliation(s)
- Michael D. Nicholson
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David Cheek
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tibor Antal
- School of Mathematics and Maxwell Institute for Mathematical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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7
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Phua TJ. Understanding human aging and the fundamental cell signaling link in age-related diseases: the middle-aging hypovascularity hypoxia hypothesis. FRONTIERS IN AGING 2023; 4:1196648. [PMID: 37384143 PMCID: PMC10293850 DOI: 10.3389/fragi.2023.1196648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Aging-related hypoxia, oxidative stress, and inflammation pathophysiology are closely associated with human age-related carcinogenesis and chronic diseases. However, the connection between hypoxia and hormonal cell signaling pathways is unclear, but such human age-related comorbid diseases do coincide with the middle-aging period of declining sex hormonal signaling. This scoping review evaluates the relevant interdisciplinary evidence to assess the systems biology of function, regulation, and homeostasis in order to discern and decipher the etiology of the connection between hypoxia and hormonal signaling in human age-related comorbid diseases. The hypothesis charts the accumulating evidence to support the development of a hypoxic milieu and oxidative stress-inflammation pathophysiology in middle-aged individuals, as well as the induction of amyloidosis, autophagy, and epithelial-to-mesenchymal transition in aging-related degeneration. Taken together, this new approach and strategy can provide the clarity of concepts and patterns to determine the causes of declining vascularity hemodynamics (blood flow) and physiological oxygenation perfusion (oxygen bioavailability) in relation to oxygen homeostasis and vascularity that cause hypoxia (hypovascularity hypoxia). The middle-aging hypovascularity hypoxia hypothesis could provide the mechanistic interface connecting the endocrine, nitric oxide, and oxygen homeostasis signaling that is closely linked to the progressive conditions of degenerative hypertrophy, atrophy, fibrosis, and neoplasm. An in-depth understanding of these intrinsic biological processes of the developing middle-aged hypoxia could provide potential new strategies for time-dependent therapies in maintaining healthspan for healthy lifestyle aging, medical cost savings, and health system sustainability.
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Affiliation(s)
- Teow J. Phua
- Molecular Medicine, NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
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8
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Zhang S, Hur J, Song R, Wang P, Cao Y, Wu K, Giovannucci E. Adherence to the World Cancer Research Fund/American Institute for Cancer Research cancer prevention recommendations throughout the life course and risk of colorectal cancer precursors. Br J Cancer 2023; 128:2243-2252. [PMID: 37029199 PMCID: PMC10241897 DOI: 10.1038/s41416-023-02255-5] [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: 07/10/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND Despite the increasing incidence in colorectal cancer (CRC) among the young population, the involvement of modifiable early-life exposures is understudied. METHODS We prospectively investigated the association of lifestyle score, which measures adherence to the 2018 World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) cancer prevention recommendations, in adolescence and adulthood with risk of CRC precursors in 34,509 women enrolled in the Nurses' Health Study II. Participants reported adolescent diet in 1998 and subsequently underwent at least one lower gastrointestinal endoscopy between 1999 and 2015. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using multivariable logistic regression for clustered data. RESULTS During follow-up (1998-2015), 3036 women had at least one adenoma, and 2660 had at least one serrated lesion. In multivariable analysis, per unit increase in adolescent WCRF/AICR lifestyle score was not associated with risk of total adenoma or serrated lesions, in contrast to adult WCRF/AICR lifestyle score (OR = 0.92, 95% CI: 0.87-0.97, Ptrend = 0.002 for total adenoma; and OR = 0.86, 95% CI: 0.81-0.92, Ptrend < 0.001 for total serrated lesions). CONCLUSION Adherence to the 2018 WCRF/AICR recommendations during adulthood but not during adolescence was associated with a lower risk of CRC precursors.
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Affiliation(s)
- Shuqi Zhang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jinhee Hur
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Gyeonggi, South Korea.
- Food Clinical Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi, South Korea.
| | - Rui Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Peilu Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yin Cao
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kana Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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9
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Evaluating cancer etiology and risk with a mathematical model of tumor evolution. Nat Commun 2022; 13:7224. [PMID: 36433937 PMCID: PMC9700699 DOI: 10.1038/s41467-022-34760-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
Recent evidence arising from DNA sequencing of healthy human tissues has clearly indicated that our organs accumulate a relevant number of somatic mutations due to normal endogenous mutational processes, in addition to those caused by environmental factors. A deeper understanding of the evolution of this endogenous mutational load is critical for understanding what causes cancer. Here we present a mathematical model of tumor evolution that is able to predict the expected number of endogenous somatic mutations present in various tissue types of a patient at a given age. These predictions are then compared to those observed in patients. We also obtain an improved fitting of the variation in cancer incidence across cancer types, showing that the endogenous mutational processes can explain 4/5 of the variation in cancer risk. Overall, these results offer key insights into cancer etiology, by providing further evidence for the major role these endogenous processes play in cancer.
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10
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Nakamura JL. Considerations for carcinogenesis countermeasure development using mouse models. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:158-162. [PMID: 36336361 DOI: 10.1016/j.lssr.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
Activities in space will expose humans to profoundly new environments, challenging human performance and will require innovative supportive technologies. Among these environmental variables, exposure to ionizing radiation is a major concern for astronauts, as the long-term effects of exposure on diverse tissues are poorly understood. This need however creates opportunities for novel approaches, particularly in the development of countermeasures against the effects of ionizing radiation exposure. Carcinogenesis presents a unique challenge as a disease process, due to the inherent complexities of the process and the challenges of obtaining a large volume of clinical evidence. Thus, developing the countermeasures to address potential effects of ionizing radiation exposure will require understanding biological underpinnings to design countermeasures effectively in conjunction with highly robust modeling approaches to test and examine in vivo. This review will highlight specific considerations for accelerated development of space radiation countermeasures against carcinogenesis.
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Affiliation(s)
- Jean L Nakamura
- University of California, San Francisco, Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, United States.
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11
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Lee ND, Bozic I. Inferring parameters of cancer evolution in chronic lymphocytic leukemia. PLoS Comput Biol 2022; 18:e1010677. [PMID: 36331987 PMCID: PMC9668150 DOI: 10.1371/journal.pcbi.1010677] [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: 05/26/2022] [Revised: 11/16/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
As a cancer develops, its cells accrue new mutations, resulting in a heterogeneous, complex genomic profile. We make use of this heterogeneity to derive simple, analytic estimates of parameters driving carcinogenesis and reconstruct the timeline of selective events following initiation of an individual cancer, where two longitudinal samples are available for sequencing. Using stochastic computer simulations of cancer growth, we show that we can accurately estimate mutation rate, time before and after a driver event occurred, and growth rates of both initiated cancer cells and subsequently appearing subclones. We demonstrate that in order to obtain accurate estimates of mutation rate and timing of events, observed mutation counts should be corrected to account for clonal mutations that occurred after the founding of the tumor, as well as sequencing coverage. Chronic lymphocytic leukemia (CLL), which often does not require treatment for years after diagnosis, presents an optimal system to study the untreated, natural evolution of cancer cell populations. When we apply our methodology to reconstruct the individual evolutionary histories of CLL patients, we find that the parental leukemic clone typically appears within the first fifteen years of life.
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Affiliation(s)
- Nathan D. Lee
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Ivana Bozic
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
- Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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12
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Teimouri H, Spaulding C, Kolomeisky AB. Optimal pathways control fixation of multiple mutations during cancer initiation. Biophys J 2022; 121:3698-3705. [PMID: 35568975 PMCID: PMC9617135 DOI: 10.1016/j.bpj.2022.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 11/02/2022] Open
Abstract
Cancer starts after initially healthy tissue cells accumulate several specific mutations or other genetic alterations. The dynamics of tumor formation is a very complex phenomenon due to multiple involved biochemical and biophysical processes. It leads to a very large number of possible pathways on the road to final fixation of all mutations that marks the beginning of the cancer, complicating the understanding of microscopic mechanisms of tumor formation. We present a new theoretical framework of analyzing the cancer initiation dynamics by exploring the properties of effective free-energy landscape of the process. It is argued that although there are many possible pathways for the fixation of all mutations in the system, there are only a few dominating pathways on the road to tumor formation. The theoretical approach is explicitly tested in the system with only two mutations using analytical calculations and Monte Carlo computer simulations. Excellent agreement with theoretical predictions is found for a large range of parameters, supporting our hypothesis and allowing us to better understand the mechanisms of cancer initiation. Our theoretical approach clarifies some important aspects of microscopic processes that lead to tumor formation.
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Affiliation(s)
- Hamid Teimouri
- Department of Chemistry, Rice University, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas
| | - Cade Spaulding
- Department of Chemistry, Rice University, Houston, Texas
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas; Department of Physics and Astronomy, Rice University, Houston, Texas.
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13
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The timing of adiposity and changes in the life course on the risk of cancer. Cancer Metastasis Rev 2022; 41:471-489. [PMID: 35908000 DOI: 10.1007/s10555-022-10054-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
Excess body weight has been established as a risk factor for at least twelve cancer sites, though questions remain as to the timing of associations for adiposity and cancer risk throughout the life course. We conducted a narrative review summarizing existing evidence to provide insights into the complex timing relationship between adiposity and risk of seven common obesity-related cancers. We considered five types of studies, including traditional epidemiologic studies examining adiposity at different time points, studies examining weight gain in specific life phases, studies examining weight loss over a period including from bariatric surgery, life course trajectory analysis, and Mendelian randomization studies. The results showed that lifetime excess body weight is associated with increased risk of cancers of endometrium, colorectum, liver, kidney, and pancreas. Early life obesity is one of the strongest risk factors for pancreatic cancer but less directly important than adult obesity for endometrial and kidney cancer. Interestingly, heavy weight during childhood, adolescence, and early adulthood is protective against pre- and postmenopausal breast cancer and possibly advanced prostate cancer. It is apparent that preventing weight gain later in adulthood would likely reduce risk of many cancers, including postmenopausal breast cancer, endometrial cancer, colorectal cancer (especially in men), liver cancer, kidney cancer, and probably advanced prostate cancer. Furthermore, weight loss even late in life may confer benefits for cancers of breast, endometrium, colorectum, and liver among patients with obesity, as mostly demonstrated by studies of bariatric surgery. Overall, maintaining a healthy weight throughout the life course will help prevent a large number of cancers.
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14
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Demeter M, Derényi I, Szöllősi GJ. Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization. Nat Commun 2022; 13:1666. [PMID: 35351889 PMCID: PMC8964737 DOI: 10.1038/s41467-022-29004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/23/2022] [Indexed: 11/09/2022] Open
Abstract
Species-specific differences control cancer risk across orders of magnitude variation in body size and lifespan, e.g., by varying the copy numbers of tumor suppressor genes. It is unclear, however, how different tissues within an organism can control somatic evolution despite being subject to markedly different constraints, but sharing the same genome. Hierarchical differentiation, characteristic of self-renewing tissues, can restrain somatic evolution both by limiting divisional load, thereby reducing mutation accumulation, and by increasing cells' commitment to differentiation, which can "wash out" mutants. Here, we explore the organization of hierarchical tissues that have evolved to limit their lifetime incidence of cancer. Estimating the likelihood of cancer in the presence of mutations that enhance self-proliferation, we demonstrate that a trade-off exists between mutation accumulation and the strength of washing out. Our results explain differences in the organization of widely different hierarchical tissues, such as colon and blood.
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Affiliation(s)
- Márton Demeter
- Dept. Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- ELTE-MTA "Lendület" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Imre Derényi
- Dept. Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary.
- ELTE-MTA Statistical and Biological Physics Research Group, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary.
| | - Gergely J Szöllősi
- Dept. Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary.
- ELTE-MTA "Lendület" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary.
- Institute of Evolution, Centre for Ecological Research, Konkoly-Thege M. u 29-33, Budapest, Hungary.
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15
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Simulating the Dynamic Intra-Tumor Heterogeneity and Therapeutic Responses. Cancers (Basel) 2022; 14:cancers14071645. [PMID: 35406417 PMCID: PMC8996855 DOI: 10.3390/cancers14071645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
A tumor is a complex tissue comprised of heterogeneous cell subpopulations which exhibit substantial diversity at morphological, genetic and epigenetic levels. Under the selective pressure of cancer therapies, a minor treatment-resistant subpopulation could survive and repopulate. Therefore, the intra-tumor heterogeneity is recognized as a major obstacle to effective treatment. In this paper, we propose a stochastic clonal expansion model to simulate the dynamic evolution of tumor subpopulations and the therapeutic effect at different times during tumor progression. The model is incorporated in the CES webserver, for the convenience of simulation according to initial user input. Based on this model, we investigate the influence of various factors on tumor progression and treatment consequences and present conclusions drawn from observations, highlighting the importance of treatment timing. The model provides an intuitive illustration to deepen the understanding of temporal intra-tumor heterogeneity dynamics and treatment responses, thus helping the improvement of personalized diagnostic and therapeutic strategies.
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16
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Pol J, Paillet J, Plantureux C, Kroemer G. Beneficial autoimmunity and maladaptive inflammation shape epidemiological links between cancer and immune-inflammatory diseases. Oncoimmunology 2022; 11:2029299. [PMID: 35070497 PMCID: PMC8773133 DOI: 10.1080/2162402x.2022.2029299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Jonathan Pol
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Juliette Paillet
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Céleste Plantureux
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine, Kremlin-Bicêtre, France
| | - Guido Kroemer
- Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Inserm U1138, Université de Paris, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Institut Universitaire de France, Paris, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, Ap-hp, Paris, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
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17
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Schell D, Ullah S, Brooke-Smith ME, Hollington P, Yeow M, Karapetis CS, Watson DI, Pandol SJ, Roberts CT, Barreto SG. Gastrointestinal Adenocarcinoma Incidence and Survival Trends in South Australia, 1990-2017. Cancers (Basel) 2022; 14:cancers14020275. [PMID: 35053439 PMCID: PMC8773524 DOI: 10.3390/cancers14020275] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary This study from South Australia using the state’s Cancer Registry data provides compelling evidence for a significant increase in the incidence of young-onset (18–50 years) gastrointestinal (oesophageal, stomach, colon and rectum, and pancreas) adenocarcinomas over the last three decades. The trend observed in the young cohort was not mirrored in older individuals >50 years. This increased incidence, though noted in both sexes, was more pronounced in males compared to females. Survival in the young-onset adenocarcinoma cohort was only seen in patients with colorectal cancers, but not oesophagus, stomach and pancreas. This study calls for a concerted effort aimed at determining the sociodemographic factors underlying this disturbing trend with the aim of developing preventative strategies. Abstract Background & Aims: Globally, there has been a concerning rise in the incidence of young-onset cancers. The aim of this study was to provide trends in the incidence and survival of gastrointestinal adenocarcinomas (oesophagus, stomach, pancreas, and colorectal) in South Australia over a 27-year period. Methods: This is a cross-sectional analysis of a prospective longitudinal database including all cases of gastrointestinal adenocarcinomas prospectively reported to the South Australian (State) Cancer Registry from 1990 to 2017. Results: A total of 28,566 patients diagnosed with oesophageal, stomach, pancreatic, or colorectal adenocarcinoma between 1990 and 2017 were included in the study. While the overall incidence for gastrointestinal adenocarcinomas in individuals >50 years has decreased since 2000 (IRR of 0.97 (95% CI 0.94–1.00; p = 0.06)) compared to 1990–1999, the rate amongst individuals aged 18–50 has significantly increased (IRR 1.41 (95% CI 1.27–1.57; p < 0.001)) during the same reference time period. Although noted in both sexes, the rate of increase in incidence was significantly greater in males (11.5 to 19.7/100,000; p < 0.001). The overall survival from adenocarcinomas across all subsites improved in the >50-year cohort in the last decade (HR 0.89 (95% CI 0.86–0.93; p < 0.001)) compared to 1990–1999. In individuals aged 18–50 years, there has only been a significant improvement in survival for colorectal cancer (HR 0.82 (95% CI 0.68–0.99; p < 0.04)), but not the other subsites. A lower overall survival was noted for males in both age cohorts (18–50 years—HR 1.24 (95% CI 1.09–1.13; p < 0.01) and >50 years—HR 1.13 (95% CI 1.10–1.16; p < 0.001), respectively) compared to females. Conclusions: This study from South Australia demonstrates a significant increase in young-onset gastrointestinal adenocarcinomas over the last 28 years, with a greater increase in the male sex. The only significant improvement in survival in this cohort has been noted in colorectal cancer patients.
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Affiliation(s)
- Dominique Schell
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.S.); (S.U.); (P.H.); (C.S.K.); (D.I.W.)
| | - Shahid Ullah
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.S.); (S.U.); (P.H.); (C.S.K.); (D.I.W.)
| | - Mark E. Brooke-Smith
- Flinders Medical Center, Division of Surgery and Perioperative Medicine, Flinders University, Adelaide, SA 5042, Australia; (M.E.B.-S.); (M.Y.)
| | - Paul Hollington
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.S.); (S.U.); (P.H.); (C.S.K.); (D.I.W.)
- Flinders Medical Center, Division of Surgery and Perioperative Medicine, Flinders University, Adelaide, SA 5042, Australia; (M.E.B.-S.); (M.Y.)
| | - Marina Yeow
- Flinders Medical Center, Division of Surgery and Perioperative Medicine, Flinders University, Adelaide, SA 5042, Australia; (M.E.B.-S.); (M.Y.)
| | - Christos S. Karapetis
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.S.); (S.U.); (P.H.); (C.S.K.); (D.I.W.)
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, SA 5042, Australia
- Department of Medical Oncology, Flinders Medical Centre, Flinders University, Adelaide, SA 5042, Australia
| | - David I. Watson
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.S.); (S.U.); (P.H.); (C.S.K.); (D.I.W.)
- Flinders Medical Center, Division of Surgery and Perioperative Medicine, Flinders University, Adelaide, SA 5042, Australia; (M.E.B.-S.); (M.Y.)
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, SA 5042, Australia
| | - Stephen J. Pandol
- Cedars-Sinai Medical Center, Division of Digestive and Liver Diseases, Los Angeles, CA 90048, USA;
| | - Claire T. Roberts
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.S.); (S.U.); (P.H.); (C.S.K.); (D.I.W.)
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, SA 5042, Australia
- Correspondence: (C.T.R.); (S.G.B.)
| | - Savio G. Barreto
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.S.); (S.U.); (P.H.); (C.S.K.); (D.I.W.)
- Flinders Medical Center, Division of Surgery and Perioperative Medicine, Flinders University, Adelaide, SA 5042, Australia; (M.E.B.-S.); (M.Y.)
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, SA 5042, Australia
- Correspondence: (C.T.R.); (S.G.B.)
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Bozic I. Quantification of the Selective Advantage of Driver Mutations Is Dependent on the Underlying Model and Stage of Tumor Evolution. Cancer Res 2022; 82:21-24. [PMID: 34983781 DOI: 10.1158/0008-5472.can-21-1064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/11/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022]
Abstract
Measuring the selective fitness advantages provided by driver mutations has the potential to facilitate a precise quantitative understanding of cancer evolution. However, accurately measuring the selective advantage of driver mutations has remained a challenge in the field. Early studies reported small selective advantages of drivers, on the order of 1%, whereas newer studies report much larger selective advantages, as high as 1,200%. In this article, we argue that the calculated selective advantages of cancer drivers are dependent on the underlying mathematical model and stage of cancer evolution and that comparisons of numerical values of selective advantage without regard for the underlying model and stage can lead to spurious conclusions.
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Affiliation(s)
- Ivana Bozic
- Department of Applied Mathematics, University of Washington, Seattle, Washington. .,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington
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19
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Lin Y, Pan X, Chen Z, Lin S, Shen Z, Chen S. Prognostic value and immune infiltration of novel signatures in colon cancer microenvironment. Cancer Cell Int 2021; 21:679. [PMID: 34922547 PMCID: PMC8684099 DOI: 10.1186/s12935-021-02342-8] [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: 02/14/2020] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
Background Growing evidence has shown that the prognosis for colon cancer depends on changes in microenvironment. The purpose of this study was to elucidate the prognostic value of long noncoding RNAs (lncRNAs) related to immune microenvironment (IM) in colon cancer. Methods Single sample gene set enrichment analysis (ssGSEA) was used to identify the subtypes of colon cancer based on the immune genomes of 29 immune signatures. Cox regression analysis identified a lncRNA signatures associated with immune infiltration. The Tumor Immune Estimation Resource database was used to analyze immune cell content. Results Colon cancer samples were divided into three subtypes by unsupervised cluster analysis. Cox regression analysis identified an immune infiltration-related 5-lncRNA signature. This signature combined with clinical factors can effectively improve the predictive ability for the overall survival (OS) of colon cancer. At the same time, we found that the expression of H19 affects the content of B cells and macrophages in the microenvironment of colon cancer and affects the prognosis of colon cancer. Finally, we constructed the H19 regulatory network and further analyzed the possible mechanisms. We found that knocking down the expression of H19 can significantly inhibit the expression of CCND1 and VEGFA. At the same time, the immunohistochemical assay found that the expression of CCND1 and VEGFA protein was significantly positively correlated with the infiltration of M2 type macrophages. Conclusion The findings may help to formulate clinical strategies and understand the underlying mechanisms of H19 regulation. H19 may be a biomarker for targeted treatment of colon cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02342-8.
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Affiliation(s)
- Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Xicheng, Beijing, China
| | - Xiaoxian Pan
- Department of Radiotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Zhihua Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China
| | - Suyong Lin
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Xicheng, Beijing, China.
| | - Shaoqin Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China.
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20
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Conte E. Targeting monocytes/macrophages in fibrosis and cancer diseases: Therapeutic approaches. Pharmacol Ther 2021; 234:108031. [PMID: 34774879 DOI: 10.1016/j.pharmthera.2021.108031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/19/2021] [Accepted: 11/02/2021] [Indexed: 02/08/2023]
Abstract
Over almost 140 years since their identification, the knowledge about macrophages has unbelievably evolved. The 'big eaters' from being thought of as simple phagocytic cells have been recognized as master regulators in immunity, homeostasis, healing/repair and organ development. Long considered to originate exclusively from bone marrow-derived circulating monocytes, macrophages have been also demonstrated to be the first immune cells colonizing tissues in the developing embryo and persisting in adult life by self-renewal, as long-lived tissue resident macrophages. Therefore, heterogeneous populations of macrophages with different ontogeny and functions co-exist in tissues. Macrophages act as sentinels of homeostasis and are intrinsically programmed to lead the wound healing and repair processes that occur after injury. However, in certain pathological circumstances macrophages get dysfunctional, and impaired or aberrant macrophage activities become key features of diseases. For instance, in both fibrosis and cancer, that have been defined 'wounds that do not heal', dysfunctional monocyte-derived macrophages overall play a key detrimental role. On the other hand, due to their plasticity these cells can be 're-educated' and exert anti-fibrotic and anti-cancer functions. Therefore macrophages represent an important therapeutic target in both fibrosis and cancer diseases. The current review will illustrate new insights into the role of monocytes/macrophages in these devastating diseases and summarize new therapeutic strategies and applications of macrophage-targeted drug development in their clinical setting.
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21
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Is this the evidence for perinatal and early life events impacting on cancer outcomes? Support Care Cancer 2021; 30:1895-1896. [PMID: 34694497 DOI: 10.1007/s00520-021-06645-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/18/2021] [Indexed: 12/30/2022]
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22
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Ta HDK, Wang WJ, Phan NN, An Ton NT, Anuraga G, Ku SC, Wu YF, Wang CY, Lee KH. Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer. Cancers (Basel) 2021; 13:4902. [PMID: 34638387 PMCID: PMC8508234 DOI: 10.3390/cancers13194902] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 12/26/2022] Open
Abstract
In recent decades, breast cancer (BRCA) has become one of the most common diseases worldwide. Understanding crucial genes and their signaling pathways remain an enormous challenge in evaluating the prognosis and possible therapeutics. The "Like-Smith" (LSM) family is known as protein-coding genes, and its member play pivotal roles in the progression of several malignancies, although their roles in BRCA are less clear. To discover biological processes associated with LSM family genes in BRCA development, high-throughput techniques were applied to clarify expression levels of LSMs in The Cancer Genome Atlas (TCGA)-BRCA dataset, which was integrated with the cBioPortal database. Furthermore, we investigated prognostic values of LSM family genes in BCRA patients using the Kaplan-Meier database. Among genes of this family, LSM4 expression levels were highly associated with poor prognostic outcomes with a hazard ratio of 1.35 (95% confidence interval 1.21-1.51, p for trend = 3.4 × 10-7). MetaCore and GlueGo analyses were also conducted to examine transcript expression signatures of LSM family members and their coexpressed genes, together with their associated signaling pathways, such as "Cell cycle role of APC in cell cycle regulation" and "Immune response IL-15 signaling via MAPK and PI3K cascade" in BRCA. Results showed that LSM family members, specifically LSM4, were significantly correlated with oncogenesis in BRCA patients. In summary, our results suggested that LSM4 could be a prospective prognosticator of BRCA.
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Affiliation(s)
- Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Wei-Jan Wang
- Department of Biological Science and Technology, Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan;
| | - Nam Nhut Phan
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam;
| | - Nu Thuy An Ton
- NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam;
| | - Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Yung-Fu Wu
- National Defense Medical Center, Department of Medical Research, School of Medicine, Tri-Service General Hospital, Taipei 11490, Taiwan;
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Kuen-Haur Lee
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
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Rachakonda S, Hoheisel JD, Kumar R. Occurrence, functionality and abundance of the TERT promoter mutations. Int J Cancer 2021; 149:1852-1862. [PMID: 34313327 DOI: 10.1002/ijc.33750] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/14/2021] [Accepted: 07/16/2021] [Indexed: 12/18/2022]
Abstract
Telomere shortening at chromosomal ends due to the constraints of the DNA replication process acts as a tumor suppressor by restricting the replicative potential in primary cells. Cancers evade that limitation primarily through the reactivation of telomerase via different mechanisms. Mutations within the promoter of the telomerase reverse transcriptase (TERT) gene represent a definite mechanism for the ribonucleic enzyme regeneration predominantly in cancers that arise from tissues with low rates of self-renewal. The promoter mutations cause a moderate increase in TERT transcription and consequent telomerase upregulation to the levels sufficient to delay replicative senescence but not prevent bulk telomere shortening and genomic instability. Since the discovery, a staggering number of studies have resolved the discrete aspects, effects and clinical relevance of the TERT promoter mutations. The promoter mutations link transcription of TERT with oncogenic pathways, associate with markers of poor outcome and define patients with reduced survivals in several cancers. In this review, we discuss the occurrence and impact of the promoter mutations and highlight the mechanism of TERT activation. We further deliberate on the foundational question of the abundance of the TERT promoter mutations and a general dearth of functional mutations within noncoding sequences, as evident from pan-cancer analysis of the whole-genomes. We posit that the favorable genomic constellation within the TERT promoter may be less than a common occurrence in other noncoding functional elements. Besides, the evolutionary constraints limit the functional fraction within the human genome, hence the lack of abundant mutations outside the coding sequences.
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Affiliation(s)
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rajiv Kumar
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
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Abstract
Pancreatic cancer is a genetic disease, and the recurrent genetic alterations characteristic of pancreatic cancer indicate the cellular processes that are targeted for malignant transformation. In addition to somatic alterations in the most common driver genes (KRAS, CDKN2A, TP53 and SMAD4), large-scale studies have revealed major roles for genetic alterations of the SWI/SNF and COMPASS complexes, copy number alterations in GATA6 and MYC that partially define phenotypes of pancreatic cancer, and the role(s) of polyploidy and chromothripsis as factors contributing to pancreatic cancer biology and progression. Germline variants that increase the risk of pancreatic cancer continue to be discovered along with a greater appreciation of the features of pancreatic cancers with mismatch repair deficiencies and homologous recombination deficiencies that confer sensitivity to therapeutic targeting. Wild-type KRAS pancreatic cancers, some of which are driven by alternative oncogenic events affecting NRG1 or NTRK1 - for which targeted therapies exist - further underscore that pancreatic cancer is formally entering the era of precision medicine. Given the vast developments within this field, here we review the wide-ranging and most current information related to pancreatic cancer genomics with the goal of integrating this information into a unifying description of the life history of pancreatic cancer.
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25
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Li J, Huang G, Ren C, Wang N, Sui S, Zhao Z, Li M. Identification of differentially expressed genes-related prognostic risk model for survival prediction in breast carcinoma patients. Aging (Albany NY) 2021; 13:16577-16599. [PMID: 34175839 PMCID: PMC8266316 DOI: 10.18632/aging.203178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/31/2021] [Indexed: 11/25/2022]
Abstract
Since the imbalance of gene expression has been demonstrated to tightly related to breast cancer (BRCA) genesis and growth, common genes expressed of BRCA were screened to explore the essence in-between. In current work, most common differentially expressed genes (DEGs) in various subtypes of BRCA were identified. Functional enrichment analysis illustrated the driving factor of deactivation of the cell cycle and the oocyte meiosis, which critically triggers the development of BRCA. Herein, we constructed a 12-gene prognostic risk model relative to differential gene expression. Subsequently, the K-M curves, analysis on time-ROC curve and Cox regression were performed to assess this risk model by determining the respective prognostic value, and the prediction performance were ascertained for both training and validation cohorts. In addition, multivariate Cox regression was analysed to reveal the independence between risk score and prognostic stage, and the accuracy and sensitivity of prognosis are particularly improved after clinical indicators are included into the analysis. In summary, this study offers novel insights into the imbalance of gene expression within BRCA, and highlights 12 selected genes associated with patient prognosis. The risk model can help individualize treatment for patients at different risks, and propose precise strategies and treatments for BRCA therapy.
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Affiliation(s)
- Jinyu Li
- Department of Breast Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
| | - Gena Huang
- Department of Breast Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
| | - Caixia Ren
- Department of Respiratory Medicine, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
| | - Ning Wang
- Institute for Genome Engineered Animal Models of Human Diseases, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Silei Sui
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Zuowei Zhao
- Department of Breast Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China.,Department of Breast Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
| | - Man Li
- Department of Breast Oncology, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, China
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Exploration of the Key Proteins in the Normal-Adenoma-Carcinoma Sequence of Colorectal Cancer Evolution Using In-Depth Quantitative Proteomics. JOURNAL OF ONCOLOGY 2021; 2021:5570058. [PMID: 34194496 PMCID: PMC8214504 DOI: 10.1155/2021/5570058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 12/30/2022]
Abstract
Purpose In most cases, the carcinogenesis of colorectal cancer (CRC) follows the normal-adenoma-carcinoma (N-A-C) sequence. In this study, we aimed to identify the key proteins in the N-A-C sequence. Methods Differentially expressed proteins (DEPs) in normal, adenoma, and carcinoma tissues were identified using the Tandem Mass Tag- (TMT-) based quantitative proteomics approach. The landscape of proteomic variation in the N-A-C sequence was explored using gene set enrichment analysis (GSEA) and Proteomaps. Key proteins in the N-A-C sequence were identified, verified, and validated based on our proteomic data, external proteomic data, and external transcriptomic data in the ProteomeXchange, CPTAC, GEO, and TCGA databases. The prognostic value of the key proteins in our database was evaluated by univariate and multivariate Cox regression analysis. The effects of the key proteins on adenoma organoids and colorectal cancer cells were explored in functional studies. Results Based on our proteomic profiles, we identified 1,294 DEPs between the carcinoma (CG) and normal (NG) groups, 919 DEPs between the adenoma group (AG) and NG, and 1,030 DEPs between the CG and AG. Ribosome- and spliceosome-related pathways were mainly enriched in the N-A process. Extracellular matrix- and epithelial-mesenchymal transition- (EMT-) related pathways were mainly enriched in the A-C process. RRP12 and SERPINH1 were identified, verified, and validated as candidate key proteins in the N-A and A-C processes, respectively. Furthermore, RRP12 and SERPINH1 knockdown impeded the viability and proliferation of adenoma organoids. SERPINH1 was validated as a risk factor for disease-free survival (DFS) based on the TCGA and our database, whereas RRP12 did not show prognostic value. SERPINH1 knockdown was accompanied by EMT-related protein variation, increased apoptosis, and reduced proliferation, invasion, and migration of CRC cells in vitro. Conclusions RRP12 and SERPINH1 may play an important role in the N-A and A-C processes, respectively. Furthermore, SERPINH1 showed favorable prognostic value for DFS in CRC patients. We speculate that SERPINH1 might promote not only the A-C process but also the development of CRC.
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Phua TJ. The Etiology and Pathophysiology Genesis of Benign Prostatic Hyperplasia and Prostate Cancer: A New Perspective. MEDICINES 2021; 8:medicines8060030. [PMID: 34208086 PMCID: PMC8230771 DOI: 10.3390/medicines8060030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022]
Abstract
Background: The etiology of benign prostatic hyperplasia and prostate cancer are unknown, with ageing being the greatness risk factor. Methods: This new perspective evaluates the available interdisciplinary evidence regarding prostate ageing in terms of the cell biology of regulation and homeostasis, which could explain the timeline of evolutionary cancer biology as degenerative, inflammatory and neoplasm progressions in these multifactorial and heterogeneous prostatic diseases. Results: This prostate ageing degeneration hypothesis encompasses the testosterone-vascular-inflamm-ageing triad, along with the cell biology regulation of amyloidosis and autophagy within an evolutionary tumorigenesis microenvironment. Conclusions: An understanding of these biological processes of prostate ageing can provide potential strategies for early prevention and could contribute to maintaining quality of life for the ageing individual along with substantial medical cost savings.
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Affiliation(s)
- Teow J Phua
- Molecular Medicine, NSW Health Pathology, John Hunter Hospital, Newcastle, NSW 2305, Australia
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Barreto SG, Pandol SJ. Young-Onset Carcinogenesis - The Potential Impact of Perinatal and Early Life Metabolic Influences on the Epigenome. Front Oncol 2021; 11:653289. [PMID: 33996575 PMCID: PMC8116793 DOI: 10.3389/fonc.2021.653289] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
The last decade has witnessed a significant rise in cancers in young adults. This spectrum of solid organ cancers occurring in individuals under the age of 40 years (some reports extending the age-group to <50 years) in whom aetiology of cancer cannot be traced back to pre-existing familial cancer syndromes, is referred to as termed young-, or early- onset cancers. The underlying causes for young-onset carcinogenesis have remained speculative. We recently proposed a hypothesis to explain the causation of this entity. We propose that the risk for young-onset cancer begins in the perinatal period as a result of the exposure of the foetus to stressors, including maternal malnutrition, smoking or alcohol, with the consequent epigenomic events triggered to help the foetus cope/adapt. Exposure to the same stressors, early in the life of that individual, facilitates a re-activation of these 'responses designed to be protective' but ultimately resulting in a loss of regulation at a metabolic and/or genetic level culminating in the evolution of the neoplastic process. In this manuscript, we will provide a rationale for this hypothesis and present evidence to further support it by clarifying the pathways involved, including elucidating a role for Acetyl-CoA and its effect on the epigenome. We present strategies and experimental models that can be used to test the hypothesis. We believe that a concerted effort by experts in different, but complementary fields, such as epidemiology, genetics, and epigenetics united towards the common goal of deciphering the underlying cause for young-onset cancers is the urgent need. Such efforts might serve to prove, or disprove, the presented hypothesis. However, the more important aim is to develop strategies to reverse the disturbing trend of the rise in young-onset cancers.
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Affiliation(s)
- Savio George Barreto
- Division of Surgery and Perioperative Medicine, Flinders Medical Center, Adelaide, SA, Australia
- College of Medicine and Public Health, Flinders University, Los Angeles, SA, Australia
| | - Stephen J. Pandol
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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Gonzalez A, Nieves J, Leon DA, Bringas Vega ML, Sosa PV. Gene expression rearrangements denoting changes in the biological state. Sci Rep 2021; 11:8470. [PMID: 33875699 PMCID: PMC8055689 DOI: 10.1038/s41598-021-87764-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/30/2021] [Indexed: 11/30/2022] Open
Abstract
In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may be the result of a selective pressure, as in the Long Term Evolution Experiment with E. Coli populations, or the progression to Alzheimer disease in aged brains, or the progression from a normal tissue to the cancer state. The first two cases seem to belong to a class of transitions, where the initial and final states are relatively close to each other, and the distribution function for the differential expressions is short ranged, with a tail of only a few dozens of strongly varying genes. In the latter case, cancer, the initial and final states are far apart and separated by a low-fitness barrier. The distribution function shows a very heavy tail, with thousands of silenced and over-expressed genes. We characterize the biological states by means of their principal component representations, and the expression distribution functions by their maximal and minimal differential expression values and the exponents of the Pareto laws describing the tails.
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Affiliation(s)
- Augusto Gonzalez
- University of Electronic Science and Technology, 610051, Chengdu, People's Republic of China
- Institute of Cybernetics, Mathematics and Physics, 10400, Havana, Cuba
| | - Joan Nieves
- Faculty of Physics, University of Havana, 10400, Havana, Cuba
| | - Dario A Leon
- Institute of Cybernetics, Mathematics and Physics, 10400, Havana, Cuba
- University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Maria Luisa Bringas Vega
- University of Electronic Science and Technology, 610051, Chengdu, People's Republic of China
- Cuban Neurosciences Center, 11600, Havana, Cuba
| | - Pedro Valdes Sosa
- University of Electronic Science and Technology, 610051, Chengdu, People's Republic of China.
- Cuban Neurosciences Center, 11600, Havana, Cuba.
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Gmeiner WH. Recent Advances in Our Knowledge of mCRC Tumor Biology and Genetics: A Focus on Targeted Therapy Development. Onco Targets Ther 2021; 14:2121-2130. [PMID: 33790575 PMCID: PMC8007558 DOI: 10.2147/ott.s242224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/11/2021] [Indexed: 12/20/2022] Open
Abstract
Metastatic colorectal cancer (mCRC) remains a highly lethal malignancy although considerable progress has resulted from characterizing molecular alterations such as RAS mutation status and extent of microsatellite instability (MSI) to guide optimal use of available therapies. The availability of gene expression profiling, next generation sequencing technologies, proteomics analysis and other technologies provides high resolution information on individual tumors, including metastatic lesions to better define intra-tumor and inter-tumor heterogeneity. Recent literature applying this information to further customize personalized therapies is reviewed. Current biomarker-based stratification used to select optimal therapy that is personalized to the mutation profile of individual tumors is described. Recent literature using whole exome sequencing of metastatic lesions and primary CRC tumors and other advanced technologies to more fully elucidate the tumor biology specific to mCRC sub-types and to develop more precise therapies that improve outcomes is also reviewed.
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Affiliation(s)
- William H Gmeiner
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
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Noë M, Hong SM, Wood LD, Thompson ED, Roberts NJ, Goggins MG, Klein AP, Eshleman JR, Kern SE, Hruban RH. Pancreatic cancer pathology viewed in the light of evolution. Cancer Metastasis Rev 2021; 40:661-674. [PMID: 33555482 PMCID: PMC8556193 DOI: 10.1007/s10555-020-09953-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022]
Abstract
One way to understand ductal adenocarcinoma of the pancreas (pancreatic cancer) is to view it as unimaginably large numbers of evolving living organisms interacting with their environment. This “evolutionary view” creates both expected and surprising perspectives in all stages of neoplastic progression. Advances in the field will require greater attention to this critical evolutionary prospective.
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Affiliation(s)
- Michaël Noë
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Laura D Wood
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Elizabeth D Thompson
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
| | - Nicholas J Roberts
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Michael G Goggins
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Alison P Klein
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - James R Eshleman
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Scott E Kern
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Ralph H Hruban
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA.
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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Hori SS, Tong L, Swaminathan S, Liebersbach M, Wang J, Gambhir SS, Felsher DW. A mathematical model of tumor regression and recurrence after therapeutic oncogene inactivation. Sci Rep 2021; 11:1341. [PMID: 33446671 PMCID: PMC7809285 DOI: 10.1038/s41598-020-78947-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
The targeted inactivation of individual oncogenes can elicit regression of cancers through a phenomenon called oncogene addiction. Oncogene addiction is mediated by cell-autonomous and immune-dependent mechanisms. Therapeutic resistance to oncogene inactivation leads to recurrence but can be counteracted by immune surveillance. Predicting the timing of resistance will provide valuable insights in developing effective cancer treatments. To provide a quantitative understanding of cancer response to oncogene inactivation, we developed a new 3-compartment mathematical model of oncogene-driven tumor growth, regression and recurrence, and validated the model using a MYC-driven transgenic mouse model of T-cell acute lymphoblastic leukemia. Our mathematical model uses imaging-based measurements of tumor burden to predict the relative number of drug-sensitive and drug-resistant cancer cells in MYC-dependent states. We show natural killer (NK) cell adoptive therapy can delay cancer recurrence by reducing the net-growth rate of drug-resistant cells. Our studies provide a novel way to evaluate combination therapy for personalized cancer treatment.
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Affiliation(s)
- Sharon S Hori
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.
- Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA.
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA.
| | - Ling Tong
- Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Srividya Swaminathan
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, CA, USA
| | - Mariola Liebersbach
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jingjing Wang
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, People's Republic of China
| | - Sanjiv S Gambhir
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
- Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Dean W Felsher
- Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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Curtius K, Dewanji A, Hazelton WD, Rubenstein JH, Luebeck GE. Optimal Timing for Cancer Screening and Adaptive Surveillance Using Mathematical Modeling. Cancer Res 2020; 81:1123-1134. [PMID: 33293425 DOI: 10.1158/0008-5472.can-20-0335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/08/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Cancer screening and early detection efforts have been partially successful in reducing incidence and mortality, but many improvements are needed. Although current medical practice is informed by epidemiologic studies and experts, the decisions for guidelines are ultimately ad hoc. We propose here that quantitative optimization of protocols can potentially increase screening success and reduce overdiagnosis. Mathematical modeling of the stochastic process of cancer evolution can be used to derive and optimize the timing of clinical screens so that the probability is maximal that a patient is screened within a certain "window of opportunity" for intervention when early cancer development may be observable. Alternative to a strictly empirical approach or microsimulations of a multitude of possible scenarios, biologically based mechanistic modeling can be used for predicting when best to screen and begin adaptive surveillance. We introduce a methodology for optimizing screening, assessing potential risks, and quantifying associated costs to healthcare using multiscale models. As a case study in Barrett's esophagus, these methods were applied for a model of esophageal adenocarcinoma that was previously calibrated to U.S. cancer registry data. Optimal screening ages for patients with symptomatic gastroesophageal reflux disease were older (58 for men and 64 for women) than what is currently recommended (age > 50 years). These ages are in a cost-effective range to start screening and were independently validated by data used in current guidelines. Collectively, our framework captures critical aspects of cancer evolution within patients with Barrett's esophagus for a more personalized screening design. SIGNIFICANCE: This study demonstrates how mathematical modeling of cancer evolution can be used to optimize screening regimes, with the added potential to improve surveillance regimes. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/4/1123/F1.large.jpg.
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Affiliation(s)
- Kit Curtius
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom. .,Division of Biomedical Informatics, Department of Medicine, University of California, San Diego, San Diego, California
| | - Anup Dewanji
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, India
| | - William D Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Joel H Rubenstein
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan.,Center for Clinical Management Research, Ann Arbor Veterans Affairs Medical Center, Ann Arbor, Michigan
| | - Georg E Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
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Halaburkova A, Cahais V, Novoloaca A, Araujo MGDS, Khoueiry R, Ghantous A, Herceg Z. Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes. Genome Res 2020; 30:1517-1532. [PMID: 32963031 PMCID: PMC7605261 DOI: 10.1101/gr.268292.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
The recent identification of recurrently mutated epigenetic regulator genes (ERGs) supports their critical role in tumorigenesis. We conducted a pan-cancer analysis integrating (epi)genome, transcriptome, and DNA methylome alterations in a curated list of 426 ERGs across 33 cancer types, comprising 10,845 tumor and 730 normal tissues. We found that, in addition to mutations, copy number alterations in ERGs were more frequent than previously anticipated and tightly linked to expression aberrations. Novel bioinformatics approaches, integrating the strengths of various driver prediction and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far; it is also the first experimental effort to specifically identify ERG drivers (epidrivers) and characterize their deregulation and functional impact in oncogenic processes.
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Affiliation(s)
- Andrea Halaburkova
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Rita Khoueiry
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
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35
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Dingli D. Computational and systems biology of cancer. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2020. [DOI: 10.1002/cso2.1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- David Dingli
- Division of Hematology, Department of Molecular Medicine Mayo Clinic Rochester Minnesota USA
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Liu X, Zou H, Zhao Y, Chen H, Liu T, Wu Z, Yang C, Li Q, Li Y. Tanshinone Inhibits NSCLC by Downregulating AURKA Through Let-7a-5p. Front Genet 2020; 11:838. [PMID: 32849824 PMCID: PMC7427477 DOI: 10.3389/fgene.2020.00838] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is the most deadly malignancy in the last decade, accounting for about 1.6 million deaths every year globally. Tanshinone is the constituent of Salvia miltiorrhiza; it has been found that they influence tumorigenesis. However, the role of tanshinones on lung cancer is still not clear. Let-7a-5p, a short non-coding RNA, is regarded as a suppressor gene in tumorigenesis. Herein, we verified that let-7a-5p is significantly downregulated in non-small-cell lung cancer (NSCLC) tissues and cell lines. Tanshinone suppressed the expression of aurora kinase A (AURKA), inhibited cell proliferation, and arrested cell cycle progression. Our results showed that tanshinones suppressed NSCLC by upregulating the expressions of let-7a-5p via directly targeting AURKA. Besides, the data reveal that the knockdown of AURKA can also inhibit cell proliferation, arrest cell cycle, and promote cell apoptosis. Furthermore, this study demonstrates that AURKA was negatively correlated with let-7a-5p in NSCLC patient tissues. Taken together, our findings suggest that tanshinone inhibits NSCLC by downregulating AURKA through let-7a-5p. Tanshinones and let-7a-5p have the potential to be candidates for drug development of NSCLC. In conclusion, this study revealed that tanshinones with miRNA linking lead to partial mechanism in NSCLC.
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Affiliation(s)
- Xiaomin Liu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Heng Zou
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Yiqi Zhao
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Hang Chen
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Tanglin Liu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Zong Wu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Chenghao Yang
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Qian Li
- School of Life Sciences and Technology, China Pharmaceutical University, Nanjing, China
| | - Yanli Li
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
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Abstract
Patient-derived tumor organoids (PDOs) currently represent important modeling tools in pre-clinical investigation of malignancies. Organoid cultures conserve the genetic and phenotypic characteristics of the original tumor and maintain its heterogeneity, allowing their application in many research fields. PDOs derived from colorectal cancer (CRC) have been used for genetic modeling to investigate the function of driver genes. Some researchers have been exploring the value of CRC PDOs in chemotherapy, targeted therapy, and radiotherapy response prediction. The successful generation of PDOs derived from CRC could deepen our understanding of CRC biology and provide novel tools for cancer modeling, for realizing precision medicine by assessing specimens from individual patients ex vivo. The present review discusses recently reported advances in CRC PDOs and the challenges they face as pre-clinical models in CRC research.
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Affiliation(s)
- Deng-Bo Ji
- Department of Gastrointestinal Surgery III, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing 100142, China
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We Asked the Experts: Providing the Road Map to Uncovering the Pathophysiology of Young-Onset Cancer to Guide Treatment and Preventive Strategies. World J Surg 2020; 44:3212-3213. [DOI: 10.1007/s00268-020-05642-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Hammarlund EU, Amend SR, Pienta KJ. The issues with tissues: the wide range of cell fate separation enables the evolution of multicellularity and cancer. Med Oncol 2020; 37:62. [PMID: 32535731 PMCID: PMC7293661 DOI: 10.1007/s12032-020-01387-5] [Citation(s) in RCA: 2] [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: 04/23/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
Abstract
Our understanding of the rises of animal and cancer multicellularity face the same conceptual hurdles: what makes the clade originate and what makes it diversify. Between the events of origination and diversification lies complex tissue organization that gave rise to novel functionality for organisms and, unfortunately, for malignant transformation in cells. Tissue specialization with distinctly separated cell fates allowed novel functionality at organism level, such as for vertebrate animals, but also involved trade-offs at the cellular level that are potentially disruptive. These trade-offs are under-appreciated and here we discuss how the wide separation of cell phenotypes may contribute to cancer evolution by (a) how factors can reverse differentiated cells into a window of phenotypic plasticity, (b) the reversal to phenotypic plasticity coupled with asexual reproduction occurs in a way that the host cannot adapt, and (c) the power of the transformation factor correlates to the power needed to reverse tissue specialization. The role of reversed cell fate separation for cancer evolution is strengthened by how some tissues and organisms maintain high cell proliferation and plasticity without developing tumours at a corresponding rate. This demonstrates a potential proliferation paradox that requires further explanation. These insights from the cancer field, which observes tissue evolution in real time and closer than any other field, allow inferences to be made on evolutionary events in animal history. If a sweet spot of phenotypic and reproductive versatility is key to transformation, factors stimulating cell fate separation may have promoted also animal diversification on Earth.
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Affiliation(s)
- Emma U Hammarlund
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, DK, Denmark.
| | - Sarah R Amend
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Kenneth J Pienta
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
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