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Almeida M, Ferreira CL, Tomé RM, Fonseca-Moutinho J, Polónia A, Ramalhinho AC, Breitenfeld L. Somatic Mutations in KEAP1-NRF2 Complex in Breast Cancer. Cancers (Basel) 2024; 16:2411. [PMID: 39001473 PMCID: PMC11240725 DOI: 10.3390/cancers16132411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Breast cancer remains the leading cause of cancer deaths for women. Long-term estrogen exposure is considered carcinogenic due to semiquinone production and to compromised detoxification. Metabolic regulator polymorphisms, such as KEAP1 (rs1048290) and NRF2 (rs35652124, rs6721961, rs6706649), can be valuable in understanding the individual cytoprotection profile. Thus, we aim to genotype these polymorphisms in blood, tumours and surrounding tissue, to identify somatic mutations and correlate it to prognoses. A total of 23 controls and 69 women with histological confirmed breast cancer were recruited, and DNA from blood/surrounding/tumour tissue was genotyped. Genotyping and clinicopathological data were correlated. We verified that rs35652124 presents different genotype distribution between the blood/surrounding tissue (p-value = 0.023) and tumour/surrounding tissues (p-value = 0.041). Apart from rs35652124 and considering the histological grade, the other four polymorphisms have different distributions among different tissues. There is a tendency towards the loss of heterozygosity in the surrounding tissue when compared to blood and tumour tissues, and higher genotype variability in histologic grade 2. These somatic mutations and different distribution patterns may indicate a heterogeneous and active microenvironment, influencing breast cancer outcome. Additionally, it would be pertinent to evaluate the predictive value of the histologic grade 2 considering somatic mutation profiles and distributions.
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Affiliation(s)
- Micaela Almeida
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI), Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (C.L.F.); (J.F.-M.); (L.B.)
- Clinical Academic Centre of Beiras (CACB), Edifício UBImedical, Estrada Municipal 506, 6200 Covilhã, Portugal;
- Department of Pathology, Ipatimup Diagnostics, Rua Júlio Amaral de Carvalho, 45, 4200-135 Porto, Portugal;
| | - Catarina L. Ferreira
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI), Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (C.L.F.); (J.F.-M.); (L.B.)
- Clinical Academic Centre of Beiras (CACB), Edifício UBImedical, Estrada Municipal 506, 6200 Covilhã, Portugal;
| | - Rosa Maria Tomé
- Clinical Academic Centre of Beiras (CACB), Edifício UBImedical, Estrada Municipal 506, 6200 Covilhã, Portugal;
- Cova da Beira Local Health Unit, Alameda Pêro da Covilhã, 6200-251 Covilhã, Portugal
| | - José Fonseca-Moutinho
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI), Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (C.L.F.); (J.F.-M.); (L.B.)
- Clinical Academic Centre of Beiras (CACB), Edifício UBImedical, Estrada Municipal 506, 6200 Covilhã, Portugal;
- Cova da Beira Local Health Unit, Alameda Pêro da Covilhã, 6200-251 Covilhã, Portugal
| | - António Polónia
- Department of Pathology, Ipatimup Diagnostics, Rua Júlio Amaral de Carvalho, 45, 4200-135 Porto, Portugal;
- Escola de Medicina e Ciências Biomédicas, Instituto de Investigação, Inovação e Desenvolvimento, Fundação Fernando Pessoa (FP-I3ID), Avenida Fernando Pessoa, 150, 4420-096 Gondomar, Portugal
| | - Ana Cristina Ramalhinho
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI), Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (C.L.F.); (J.F.-M.); (L.B.)
- Clinical Academic Centre of Beiras (CACB), Edifício UBImedical, Estrada Municipal 506, 6200 Covilhã, Portugal;
- Cova da Beira Local Health Unit, Alameda Pêro da Covilhã, 6200-251 Covilhã, Portugal
| | - Luiza Breitenfeld
- Health Sciences Research Centre (CICS), Faculty of Health Sciences, University of Beira Interior (UBI), Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal; (C.L.F.); (J.F.-M.); (L.B.)
- Clinical Academic Centre of Beiras (CACB), Edifício UBImedical, Estrada Municipal 506, 6200 Covilhã, Portugal;
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2
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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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3
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Bhartiya D, Raouf S, Pansare K, Tripathi A, Tripathi A. Initiation of Cancer: The Journey From Mutations in Somatic Cells to Epigenetic Changes in Tissue-resident VSELs. Stem Cell Rev Rep 2024; 20:857-880. [PMID: 38457060 DOI: 10.1007/s12015-024-10694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2024] [Indexed: 03/09/2024]
Abstract
Multiple theories exist to explain cancer initiation, although a consensus on this is crucial for developing effective therapies. 'Somatic mutation theory' suggests that mutations in somatic cells during DNA repair initiates cancer but this concept has several attached paradoxes. Research efforts to identify quiescent cancer stem cells (CSCs) that survive therapy and result in metastasis and recurrence have remained futile. In solid cancers, CSCs are suggested to appear during epithelial-mesenchymal transition by the dedifferentiation and reprogramming of epithelial cells. Pluripotent and quiescent very small embryonic-like stem cells (VSELs) exist in multiple tissues but remain elusive owing to their small size and scarce nature. VSELs are developmentally connected to primordial germ cells, undergo rare, asymmetrical cell divisions and are responsible for the regular turnover of cells to maintain tissue homeostasis throughout life. VSELs are directly vulnerable to extrinsic endocrine insults because they express gonadal and gonadotropin hormone receptors. VSELs undergo epigenetic changes due to endocrine insults and transform into CSCs. CSCs exhibit genomic instability and develop mutations due to errors during DNA replication while undergoing excessive proliferation and clonal expansion to form spheroids. Thus tissue-resident VSELs offer a connection between extrinsic insults and variations in cancer incidence reported in various body tissues. To conclude, cancer is indeed a stem cell disease with mutations occurring as a consequence. In addition to immunotherapy, targeting mutations, and Lgr5 + organoids for developing new therapeutics, targeting CSCs (epigenetically altered VSELs) by improving their niche and epigenetic status could serve as a promising strategy to treat cancer.
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Affiliation(s)
- Deepa Bhartiya
- Epigeneres Biotech Pvt Ltd, Todi Mill Compound, Senapati Bapat Marg, Lower Parel, 400013, Mumbai, India.
| | | | - Kshama Pansare
- Epigeneres Biotech Pvt Ltd, Todi Mill Compound, Senapati Bapat Marg, Lower Parel, 400013, Mumbai, India
| | - Anish Tripathi
- Epigeneres Biotech Pvt Ltd, Todi Mill Compound, Senapati Bapat Marg, Lower Parel, 400013, Mumbai, India
| | - Ashish Tripathi
- Epigeneres Biotech Pvt Ltd, Todi Mill Compound, Senapati Bapat Marg, Lower Parel, 400013, Mumbai, India
- 23Ikigai Pte Ltd, 30 Cecil Street, #21-08 Prudentsial Tower, Singapore, 049712, Singapore
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4
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Stańkowska W, Sarkisyan D, Bruhn-Olszewska B, Duzowska K, Bieńkowski M, Jąkalski M, Wójcik-Zalewska M, Davies H, Drężek-Chyła K, Pęksa R, Harazin-Lechowska A, Ambicka A, Przewoźnik M, Adamczyk A, Sasim K, Makarewicz W, Matuszewski M, Biernat W, Järhult JD, Lipcsey M, Hultström M, Frithiof R, Jaszczyński J, Ryś J, Genovese G, Piotrowski A, Filipowicz N, Dumanski JP. Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium. Cancers (Basel) 2024; 16:961. [PMID: 38473323 DOI: 10.3390/cancers16050961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/15/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Bladder urothelial carcinoma (BLCA) is the 10th most common cancer with a low survival rate and strong male bias. We studied the field cancerization in BLCA using multi-sample- and multi-tissue-per-patient protocol for sensitive detection of autosomal post-zygotic chromosomal alterations and loss of chromosome Y (LOY). We analysed 277 samples of histologically normal urothelium, 145 tumors and 63 blood samples from 52 males and 15 females, using the in-house adapted Mosaic Chromosomal Alterations (MoChA) pipeline. This approach allows identification of the early aberrations in urothelium from BLCA patients. Overall, 45% of patients exhibited at least one alteration in at least one normal urothelium sample. Recurrence analysis resulted in 16 hotspots composed of either gains and copy number neutral loss of heterozygosity (CN-LOH) or deletions and CN-LOH, encompassing well-known and new BLCA cancer driver genes. Conservative assessment of LOY showed 29%, 27% and 18% of LOY-cells in tumors, blood and normal urothelium, respectively. We provide a proof of principle that our approach can characterize the earliest alterations preconditioning normal urothelium to BLCA development. Frequent LOY in blood and urothelium-derived tissues suggest its involvement in BLCA.
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Affiliation(s)
- Wiktoria Stańkowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Daniil Sarkisyan
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Katarzyna Duzowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Marcin Jąkalski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Magdalena Wójcik-Zalewska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Kinga Drężek-Chyła
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Karol Sasim
- Clinic of Urology and Oncological Urology, Specialist Hospital of Kościerzyna, Piechowskiego 36, 83-400 Kościerzyna, Poland
| | - Wojciech Makarewicz
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Piechowskiego 36, 83-400 Kościerzyna, Poland
| | - Marcin Matuszewski
- Department and Clinic of Urology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Miklós Lipcsey
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
- Hedenstierna Laboratory, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Michael Hultström
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Robert Frithiof
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Janusz Jaszczyński
- Department of Urology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Giulio Genovese
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
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Kholodenko BN, Kolch W, Rukhlenko OS. Reversing pathological cell states: the road less travelled can extend the therapeutic horizon. Trends Cell Biol 2023; 33:913-923. [PMID: 37263821 PMCID: PMC10593090 DOI: 10.1016/j.tcb.2023.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 06/03/2023]
Abstract
Acquisition of omics data advances at a formidable pace. Yet, our ability to utilize these data to control cell phenotypes and design interventions that reverse pathological states lags behind. Here, we posit that cell states are determined by core networks that control cell-wide networks. To steer cell fate decisions, core networks connecting genotype to phenotype must be reconstructed and understood. A recent method, cell state transition assessment and regulation (cSTAR), applies perturbation biology to quantify causal connections and mechanistically models how core networks influence cell phenotypes. cSTAR models are akin to digital cell twins enabling us to purposefully convert pathological states back to physiologically normal states. While this capability has a range of applications, here we discuss reverting oncogenic transformation.
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Affiliation(s)
- Boris N Kholodenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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6
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Chatanaka MK, Sohaei D, Diamandis EP, Prassas I. Beyond the amyloid hypothesis: how current research implicates autoimmunity in Alzheimer's disease pathogenesis. Crit Rev Clin Lab Sci 2023; 60:398-426. [PMID: 36941789 DOI: 10.1080/10408363.2023.2187342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023]
Abstract
The amyloid hypothesis has so far been at the forefront of explaining the pathogenesis of Alzheimer's Disease (AD), a progressive neurodegenerative disorder that leads to cognitive decline and eventual death. Recent evidence, however, points to additional factors that contribute to the pathogenesis of this disease. These include the neurovascular hypothesis, the mitochondrial cascade hypothesis, the inflammatory hypothesis, the prion hypothesis, the mutational accumulation hypothesis, and the autoimmunity hypothesis. The purpose of this review was to briefly discuss the factors that are associated with autoimmunity in humans, including sex, the gut and lung microbiomes, age, genetics, and environmental factors. Subsequently, it was to examine the rise of autoimmune phenomena in AD, which can be instigated by a blood-brain barrier breakdown, pathogen infections, and dysfunction of the glymphatic system. Lastly, it was to discuss the various ways by which immune system dysregulation leads to AD, immunomodulating therapies, and future directions in the field of autoimmunity and neurodegeneration. A comprehensive account of the recent research done in the field was extracted from PubMed on 31 January 2022, with the keywords "Alzheimer's disease" and "autoantibodies" for the first search input, and "Alzheimer's disease" with "IgG" for the second. From the first search, 19 papers were selected, because they contained recent research on the autoantibodies found in the biofluids of patients with AD. From the second search, four papers were selected. The analysis of the literature has led to support the autoimmune hypothesis in AD. Autoantibodies were found in biofluids (serum/plasma, cerebrospinal fluid) of patients with AD with multiple methods, including ELISA, Mass Spectrometry, and microarray analysis. Through continuous research, the understanding of the synergistic effects of the various components that lead to AD will pave the way for better therapeutic methods and a deeper understanding of the disease.
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Affiliation(s)
- Miyo K Chatanaka
- Department of Laboratory and Medicine Pathobiology, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Dorsa Sohaei
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory and Medicine Pathobiology, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Ioannis Prassas
- Laboratory Medicine Program, University Health Network, Toronto, Canada
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7
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Ho TLF, Lee MY, Goh HC, Ng GYN, Lee JJH, Kannan S, Lim YT, Zhao T, Lim EKH, Phua CZJ, Lee YF, Lim RYX, Ng PJH, Yuan J, Chan DKH, Lieske B, Chong CS, Lee KC, Lum J, Cheong WK, Yeoh KG, Tan KK, Sobota RM, Verma CS, Lane DP, Tam WL, Venkitaraman AR. Domain-specific p53 mutants activate EGFR by distinct mechanisms exposing tissue-independent therapeutic vulnerabilities. Nat Commun 2023; 14:1726. [PMID: 36977662 PMCID: PMC10050071 DOI: 10.1038/s41467-023-37223-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Mis-sense mutations affecting TP53 promote carcinogenesis both by inactivating tumor suppression, and by conferring pro-carcinogenic activities. We report here that p53 DNA-binding domain (DBD) and transactivation domain (TAD) mis-sense mutants unexpectedly activate pro-carcinogenic epidermal growth factor receptor (EGFR) signaling via distinct, previously unrecognized molecular mechanisms. DBD- and TAD-specific TP53 mutants exhibited different cellular localization and induced distinct gene expression profiles. In multiple tissues, EGFR is stabilized by TAD and DBD mutants in the cytosolic and nuclear compartments respectively. TAD mutants promote EGFR-mediated signaling by enhancing EGFR interaction with AKT via DDX31 in the cytosol. Conversely, DBD mutants maintain EGFR activity in the nucleus, by blocking EGFR interaction with the phosphatase SHP1, triggering c-Myc and Cyclin D1 upregulation. Our findings suggest that p53 mutants carrying gain-of-function, mis-sense mutations affecting two different domains form new protein complexes that promote carcinogenesis by enhancing EGFR signaling via distinctive mechanisms, exposing clinically relevant therapeutic vulnerabilities.
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Affiliation(s)
- Teresa Lai Fong Ho
- Disease Intervention Technology Lab (DITL), Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - May Yin Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hui Chin Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Jane Jia Hui Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Tianyun Zhao
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Edwin Kok Hao Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yi Fei Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Rebecca Yi Xuan Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Perry Jun Hao Ng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ju Yuan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dedrick Kok Hong Chan
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Bettina Lieske
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Choon Seng Chong
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kuok Chung Lee
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Jeffrey Lum
- Department of Pathology, National University Health System, Singapore, Singapore
| | - Wai Kit Cheong
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Khay Guan Yeoh
- University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Ker Kan Tan
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - David P Lane
- Disease Intervention Technology Lab (DITL), Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Wai Leong Tam
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ashok R Venkitaraman
- Disease Intervention Technology Lab (DITL), Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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8
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Lee SS, Paliouras M, Trifiro MA. Functionalized Carbon Nanoparticles as Theranostic Agents and Their Future Clinical Utility in Oncology. BIOENGINEERING (BASEL, SWITZERLAND) 2023; 10:bioengineering10010108. [PMID: 36671680 PMCID: PMC9854994 DOI: 10.3390/bioengineering10010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
Over the years, research of nanoparticle applications in pre-clinical and clinical applications has greatly advanced our therapeutic and imaging approaches to many diseases, most notably neoplastic disorders. In particular, the innate properties of inorganic nanomaterials, such as gold and iron oxide, as well as carbon-based nanoparticles, have provided the greatest opportunities in cancer theranostics. Carbon nanoparticles can be used as carriers of biological agents to enhance the therapeutic index at a tumor site. Alternatively, they can also be combined with external stimuli, such as light, to induce irreversible physical damaging effects on cells. In this review, the recent advances in carbon nanoparticles and their use in cancer theranostics will be discussed. In addition, the set of evaluations that will be required during their transition from laboratory investigations toward clinical trials will be addressed.
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Affiliation(s)
- Seung S. Lee
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Lady Davis Institute for Medical Research—Jewish General Hospital, Montreal, QC H4A 3J1, Canada
| | - Miltiadis Paliouras
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Lady Davis Institute for Medical Research—Jewish General Hospital, Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Department of Oncology, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence:
| | - Mark A. Trifiro
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Lady Davis Institute for Medical Research—Jewish General Hospital, Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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9
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Rahal Z, Sinjab A, Wistuba II, Kadara H. Game of clones: Battles in the field of carcinogenesis. Pharmacol Ther 2022; 237:108251. [PMID: 35850404 PMCID: PMC10249058 DOI: 10.1016/j.pharmthera.2022.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 11/22/2022]
Abstract
Recent advances in bulk sequencing approaches as well as genomic decoding at the single-cell level have revealed surprisingly high somatic mutational burdens in normal tissues, as well as increased our understanding of the landscape of "field cancerization", that is, molecular and immune alterations in mutagen-exposed normal-appearing tissues that recapitulated those present in tumors. Charting the somatic mutational landscapes in normal tissues can have strong implications on our understanding of how tumors arise from mutagenized epithelium. Making sense of those mutations to understand the progression along the pathologic continuum of normal epithelia, preneoplasias, up to malignant tissues will help pave way for identification of ideal targets that can guide new strategies for preventing or eliminating cancers at their earliest stages of development. In this review, we will provide a brief history of field cancerization and its implications on understanding early stages of cancer pathogenesis and deviation from the pathologically "normal" state. The review will provide an overview of how mutations accumulating in normal tissues can lead to a patchwork of mutated cell clones that compete while maintaining an overall state of functional homeostasis. The review also explores the role of clonal competition in directing the fate of normal tissues and summarizes multiple mechanisms elicited in this phenomenon and which have been linked to cancer development. Finally, we highlight the importance of understanding mutations in normal tissues, as well as clonal competition dynamics (in both the epithelium and the microenvironment) and their significance in exploring new approaches to combatting cancer.
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Affiliation(s)
- Zahraa Rahal
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, USA.
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10
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Matas J, Kohrn B, Fredrickson J, Carter K, Yu M, Wang T, Gui X, Soussi T, Moreno V, Grady WM, Peinado MA, Risques RA. Colorectal Cancer Is Associated with the Presence of Cancer Driver Mutations in Normal Colon. Cancer Res 2022; 82:1492-1502. [PMID: 35425963 PMCID: PMC9022358 DOI: 10.1158/0008-5472.can-21-3607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/20/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022]
Abstract
Although somatic mutations in colorectal cancer are well characterized, little is known about the accumulation of cancer mutations in the normal colon before cancer. Here, we have developed and applied an ultrasensitive, single-molecule mutational test based on CRISPR-DS technology, which enables mutation detection at extremely low frequency (<0.001) in normal colon from patients with and without colorectal cancer. This testing platform revealed that normal colon from patients with and without colorectal cancer carries mutations in common colorectal cancer genes, but these mutations are more abundant in patients with cancer. Oncogenic KRAS mutations were observed in the normal colon of about one third of patients with colorectal cancer but in none of the patients without colorectal cancer. Patients with colorectal cancer also carried more TP53 mutations than patients without cancer and these mutations were more pathogenic and formed larger clones, especially in patients with early-onset colorectal cancer. Most mutations in the normal colon were different from the driver mutations in tumors, suggesting that the occurrence of independent clones with pathogenic KRAS and TP53 mutations is a common event in the colon of individuals who develop colorectal cancer. These results indicate that somatic evolution contributes to clonal expansions in the normal colon and that this process is enhanced in individuals with cancer, particularly in those with early-onset colorectal cancer. SIGNIFICANCE This work suggests prevalent somatic evolution in the normal colon of patients with colorectal cancer, highlighting the potential of using ultrasensitive gene sequencing to predict disease risk.
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Affiliation(s)
- Julia Matas
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
- Institut Germans Trias i Pujol, Badalona, Spain
| | - Brendan Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Kelly Carter
- Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Ming Yu
- Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Ting Wang
- Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Xianyong Gui
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Thierry Soussi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Sorbonne Université, UPMC Univ Paris 06, F- 75005 Paris, France
- INSERM, U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | | | | | - Rosa Ana Risques
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
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11
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Birkou M, Raptis V, Marousis KD, Tsevis A, Bourikas K, Bentrop D, Episkopou V, Spyroulias GA. Impact of a Single Nucleotide Polymorphism on the 3D Protein Structure and Ubiquitination Activity of E3 Ubiquitin Ligase Arkadia. Front Mol Biosci 2022; 9:844129. [PMID: 35281275 PMCID: PMC8905620 DOI: 10.3389/fmolb.2022.844129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are genetic variations which can play a vital role in the study of human health. SNP studies are often used to identify point mutations that are associated with diseases. Arkadia (RNF111) is an E3 ubiquitin ligase that enhances transforming growth factor-beta (TGF-β) signaling by targeting negative regulators for degradation. Dysregulation of the TGF-β pathway is implicated in cancer because it exhibits tumor suppressive activity in normal cells while in tumor cells it promotes invasiveness and metastasis. Τhe SNP CGT > TGT generated an amino-acid (aa) substitution of Arginine 957 to Cysteine on the enzymatic RING domain of Arkadia. This was more prevalent in a tumor than in a normal tissue sample of a patient with colorectal cancer. This prompted us to investigate the effect of this mutation in the structure and activity of Arkadia RING. We used nuclear magnetic resonance (NMR) to analyze at an atomic-level the structural and dynamic properties of the R957C Arkadia RING domain, while ubiquitination and luciferase assays provided information about its enzymatic functionality. Our study showed that the R957C mutation changed the electrostatic properties of the RING domain however, without significant effects on the structure of its core region. However, the functional studies revealed that the R957C Arkadia exhibits significantly increased enzymatic activity supporting literature data that Arkadia within tumor cells promotes aggressive and metastatic behavior.
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Affiliation(s)
- Maria Birkou
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Vasilios Raptis
- Department of Pharmacy, University of Patras, Patras, Greece
| | | | - Athanasios Tsevis
- School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Kyriakos Bourikas
- School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Detlef Bentrop
- Institute of Physiology II, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vasso Episkopou
- Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Burlington Danes, London, United Kingdom
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12
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Nguyen HT, Luong BA, Tran DH, Nguyen TH, Ngo QD, Le LGH, Ho QC, Nguyen HHT, Nguyen CM, Tran VU, Pham TVN, Le MT, Le NAT, Le TK, Nguyen TL, Pham HAT, Le HT, Duong HDT, Hoang AV, Nguyen HB, Truong Dinh K, Phan MD, Nguyen HN, Do TTT, Giang H, Tran LS, Tran DT. Ultra-Deep Sequencing of Plasma-Circulating DNA for the Detection of Tumor- Derived Mutations in Patients with Nonmetastatic Colorectal Cancer. Cancer Invest 2021; 40:354-365. [PMID: 34894952 DOI: 10.1080/07357907.2021.2017951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Identification of tumor-derived mutation (TDM) in liquid biopsies (LB), especially in early-stage patients, faces several challenges, including low variant-allele frequencies, interference by white blood cell (WBC)-derived mutations (WDM), benign somatic mutations and tumor heterogeneity. Here, we addressed the above-mentioned challenges in a cohort of 50 nonmetastatic colorectal cancer patients, via a workflow involving parallel sequencing of paired WBC- and tumor-gDNA. After excluding potential false positive mutations, we detected at least one TDM in LB of 56% (28/50) of patients, with the majority showing low-patient coverage, except for one TDM mapped to KMT2D that recurred in 30% (15/30) of patients.
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Affiliation(s)
| | - Bac An Luong
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Duc-Huy Tran
- University Medical Center, Ho Chi Minh City, Vietnam
| | | | - Quoc Dat Ngo
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Quoc Chuong Ho
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | | | - Vu Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Minh Triet Le
- University Medical Center, Ho Chi Minh City, Vietnam
| | | | - Trung Kien Le
- University Medical Center, Ho Chi Minh City, Vietnam
| | | | | | - Hong Thuy Le
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Anh Vu Hoang
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | | | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | | | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Diep Tuan Tran
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
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13
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Can Circulating Tumor DNA Support a Successful Screening Test for Early Cancer Detection? The Grail Paradigm. Diagnostics (Basel) 2021; 11:diagnostics11122171. [PMID: 34943407 PMCID: PMC8700281 DOI: 10.3390/diagnostics11122171] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 01/02/2023] Open
Abstract
Circulating tumor DNA (ctDNA) is a new pan-cancer tumor marker with important applications for patient prognosis, monitoring progression, and assessing the success of the therapeutic response. Another important goal is an early cancer diagnosis. There is currently a debate if ctDNA can be used for early cancer detection due to the small tumor burden and low mutant allele fraction (MAF). We compare our previous calculations on the size of detectable cancers by ctDNA analysis with the latest experimental data from Grail’s clinical trial. Current ctDNA-based diagnostic methods could predictably detect tumors of sizes greater than 10–15 mm in diameter. When tumors are of this size or smaller, their MAF is about 0.01% (one tumor DNA molecule admixed with 10,000 normal DNA molecules). The use of 10 mL of blood (4 mL of plasma) will likely contain less than a complete cancer genome, thus rendering the diagnosis of cancer impossible. Grail’s new data confirm the low sensitivity for early cancer detection (<30% for Stage I–II tumors, <20% for Stage I tumors), but specificity was high at 99.5%. According to these latest data, the sensitivity of the Grail test is less than 20% in Stage I disease, casting doubt if this test could become a viable pan-cancer clinical screening tool.
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14
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Aging and Cancer: The Waning of Community Bonds. Cells 2021; 10:cells10092269. [PMID: 34571918 PMCID: PMC8468626 DOI: 10.3390/cells10092269] [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: 06/21/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer often arises in the context of an altered tissue landscape. We argue that a major contribution of aging towards increasing the risk of neoplastic disease is conveyed through effects on the microenvironment. It is now firmly established that aged tissues are prone to develop clones of altered cells, most of which are compatible with a normal histological appearance. Such increased clonogenic potential results in part from a generalized decrease in proliferative fitness, favoring the emergence of more competitive variant clones. However, specific cellular genotypes can emerge with reduced cooperative and integrative capacity, leading to disruption of tissue architecture and paving the way towards progression to overt neoplastic phenotypes.
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15
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Foley JF, Elgart B, Alex Merrick B, Phadke DP, Cook ME, Malphurs JA, Solomon GG, Shah RR, Fessler MB, Miller FW, Gerrish KE. Whole genome sequencing of low input circulating cell-free DNA obtained from normal human subjects. Physiol Rep 2021; 9:e14993. [PMID: 34350716 PMCID: PMC8339531 DOI: 10.14814/phy2.14993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/29/2022] Open
Abstract
Cell-free DNA circulates in plasma at low levels as a normal by-product of cellular apoptosis. Multiple clinical pathologies, as well as environmental stressors can lead to increased circulating cell-free DNA (ccfDNA) levels. Plasma DNA studies frequently employ targeted amplicon deep sequencing platforms due to limited concentrations (ng/ml) of ccfDNA in the blood. Here, we report whole genome sequencing (WGS) and read distribution across chromosomes of ccfDNA extracted from two human plasma samples from normal, healthy subjects, representative of limited clinical samples at <1 ml. Amplification was sufficiently robust with ~90% of the reference genome (GRCh38.p2) exhibiting 10X coverage. Chromosome read coverage was uniform and directly proportional to the number of reads for each chromosome across both samples. Almost 99% of the identified genomic sequence variants were known annotated dbSNP variants in the hg38 reference genome. A high prevalence of C>T and T>C mutations was present along with a strong concordance of variants shared between the germline genome databases; gnomAD (81.1%) and the 1000 Genome Project (93.6%). This study demonstrates isolation and amplification procedures from low input ccfDNA samples that can detect sequence variants across the whole genome from amplified human plasma ccfDNA that can translate to multiple clinical research disciplines.
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Affiliation(s)
- Julie F. Foley
- Division of National Toxicology ProgramNIEHSDurhamNorth CarolinaUSA
| | | | - B. Alex Merrick
- Division of National Toxicology ProgramNIEHSDurhamNorth CarolinaUSA
| | | | - Molly E. Cook
- Division of Intramural ResearchNIEHSDurhamNorth CarolinaUSA
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16
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Baker SG. The case for a cancer paradox initiative. Carcinogenesis 2021; 42:1023-1025. [PMID: 34128969 DOI: 10.1093/carcin/bgab052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- Stuart G Baker
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
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17
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Duffy MJ, Diamandis EP, Crown J. Circulating tumor DNA (ctDNA) as a pan-cancer screening test: is it finally on the horizon? Clin Chem Lab Med 2021; 59:1353-1361. [PMID: 33856748 DOI: 10.1515/cclm-2021-0171] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/29/2021] [Indexed: 11/15/2022]
Abstract
The detection of cancer at an early stage while it is curable by surgical resection is widely believed to be one of the most effective strategies for reducing cancer mortality. Hence, the intense interests in the development of a simple pan-cancer screening test. Lack of sensitivity and specificity when combined with the low prevalence of most types of cancer types in the general population limit the use of most of the existing protein biomarkers for this purpose. Like proteins, tumor DNA also can be released into the circulation. Such circulating tumor DNA (ctDNA) can be differentiated from normal cell DNA by the presence of specific genetic alteration such as mutations, copy number changes, altered methylation patterns or being present in different sized fragments. Emerging results with test such as CancerSEEK or GRAIL suggest that the use of ctDNA can detect cancer with specificities >99%. Sensitivity however, is cancer type and stage-dependent, varying from approximately 40% in stage I disease to approximately 80% in stage III disease. It is important to stress however, that most of the studies published to date have used patients with an established diagnosis of cancer while the control population were healthy individuals. Although the emerging results are promising, evidence of clinical utility will require demonstration of reduced mortality following evaluation in a prospective randomized screening trial.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
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18
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Ohnishi I, Iwashita Y, Matsushita Y, Ohtsuka S, Yamashita T, Inaba K, Fukazawa A, Ochiai H, Matsumoto K, Kurono N, Matsushima Y, Mori H, Suzuki S, Suzuki S, Tanioka F, Sugimura H. Mass spectrometric profiling of DNA adducts in the human stomach associated with damage from environmental factors. Genes Environ 2021; 43:12. [PMID: 33836837 PMCID: PMC8034090 DOI: 10.1186/s41021-021-00186-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/27/2021] [Indexed: 02/07/2023] Open
Abstract
Background A comprehensive understanding of DNA adducts, one of the most plausible origins of cancer mutations, is still elusive, especially in human tissues in clinical settings. Recent technological developments have facilitated the identification of multiple DNA adducts in a single experiment. Only a few attempts toward this “DNA adductome approach” in human tissues have been reported. Geospatial information on DNA adducts in human organs has been scarce. Aim Mass spectrometry of human gastric mucosal DNA was performed to identify DNA adducts associated with environmental factors. Materials and methods From 59 subjects who had received gastrectomy for gastric cancer, 306 samples of nontumor tissues and 15 samples of tumors (14 cases) were taken for DNA adductome analysis. Gastric nontumor tissue from autopsies of 7 subjects without gastric cancer (urothelial cancer, hepatocellular carcinoma, lung cancer each; the other four cases were without any cancers) was also investigated. Briefly, DNA was extracted from each sample with antioxidants, digested into nucleosides, separated by liquid chromatography, and then electrospray-ionized. Specific DNA adducts were identified by mass/charge number and column retention time compared to standards. Information on lifestyle factors such as tobacco smoking and alcohol drinking was taken from the clinical records of each subject. Results Seven DNA adducts, including modified bases, C5-methyl-2′-deoxycytidine, 2′-deoxyinosine, C5-hydroxymethyl-2′-deoxycytidine, N6-methyl-2′-deoxyadenosine, 1,N6-etheno-2′-deoxyadenosine, N6-hydroxymethyl-2′-deoxyadenosine, and C8-oxo-2′-deoxyguanosine, were identified in the human stomach and characterized. Intraindividual differences according to the multiple sites of these adducts were noted but were less substantial than interindividual differences. N6-hydroxymethyl-2′-deoxyadenosine was identified in the human stomach for the first time. The amount of C5-hydroxymethyl-2′-deoxycytidine was higher in the stomachs of subjects without gastric cancer than in the nontumor and tumor portions of the stomach in gastric cancer patients. Higher levels of 1,N6-etheno-2′-deoxyadenosine were detected in the subjects who reported both smoking and drinking than in those without these habits. These DNA adducts showed considerable correlations with each other. Conclusions We characterized 7 DNA adducts in the nontumor portion of the human stomach in both gastric cancer subjects and nongastric cancer subjects. A reduction in C5-hydroxymethyl-dC even in the nontumor mucosa of patients with gastric cancer was observed. Smoking and drinking habits significantly influenced the quantity of one of the lipid peroxidation-derived adducts, etheno-dA. A more expansive DNA adductome profile would provide a comprehensive understanding of the origin of human cancer in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s41021-021-00186-2.
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Affiliation(s)
- Ippei Ohnishi
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Pathology Division, Iwata City Hospital, 512-3 Ohkubo, Iwata, Shizuoka, 438-8550, Japan
| | - Yuji Iwashita
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
| | - Yuto Matsushita
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Department of Urology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Shunsuke Ohtsuka
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Hamamatsu Medical Center, 328 Tomitsuka-cho, Naka-ku, Hamamatsu, Shizuoka, 432-8580, Japan
| | - Takashi Yamashita
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,First Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Keisuke Inaba
- Surgery Division, Iwata City Hospital, 512-3 Ohkubo, Iwata, Shizuoka, 438-8550, Japan
| | - Atsuko Fukazawa
- Surgery Division, Iwata City Hospital, 512-3 Ohkubo, Iwata, Shizuoka, 438-8550, Japan
| | - Hideto Ochiai
- Surgery Division, Iwata City Hospital, 512-3 Ohkubo, Iwata, Shizuoka, 438-8550, Japan
| | - Keigo Matsumoto
- Surgery Division, Iwata City Hospital, 512-3 Ohkubo, Iwata, Shizuoka, 438-8550, Japan
| | - Nobuhito Kurono
- Department of Chemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Yoshitaka Matsushima
- Department of Agricultural Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Hiroki Mori
- Hamamatsu Medical Center, 328 Tomitsuka-cho, Naka-ku, Hamamatsu, Shizuoka, 432-8580, Japan
| | - Shioto Suzuki
- Pathology Division, Iwata City Hospital, 512-3 Ohkubo, Iwata, Shizuoka, 438-8550, Japan
| | - Shohachi Suzuki
- Surgery Division, Iwata City Hospital, 512-3 Ohkubo, Iwata, Shizuoka, 438-8550, Japan
| | - Fumihiko Tanioka
- Pathology Division, Iwata City Hospital, 512-3 Ohkubo, Iwata, Shizuoka, 438-8550, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
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Yousef M, Kumar A, Bakir-Gungor B. Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data. ENTROPY (BASEL, SWITZERLAND) 2020; 23:E2. [PMID: 33374969 PMCID: PMC7821996 DOI: 10.3390/e23010002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022]
Abstract
In the last two decades, there have been massive advancements in high throughput technologies, which resulted in the exponential growth of public repositories of gene expression datasets for various phenotypes. It is possible to unravel biomarkers by comparing the gene expression levels under different conditions, such as disease vs. control, treated vs. not treated, drug A vs. drug B, etc. This problem refers to a well-studied problem in the machine learning domain, i.e., the feature selection problem. In biological data analysis, most of the computational feature selection methodologies were taken from other fields, without considering the nature of the biological data. Thus, integrative approaches that utilize the biological knowledge while performing feature selection are necessary for this kind of data. The main idea behind the integrative gene selection process is to generate a ranked list of genes considering both the statistical metrics that are applied to the gene expression data, and the biological background information which is provided as external datasets. One of the main goals of this review is to explore the existing methods that integrate different types of information in order to improve the identification of the biomolecular signatures of diseases and the discovery of new potential targets for treatment. These integrative approaches are expected to aid the prediction, diagnosis, and treatment of diseases, as well as to enlighten us on disease state dynamics, mechanisms of their onset and progression. The integration of various types of biological information will necessitate the development of novel techniques for integration and data analysis. Another aim of this review is to boost the bioinformatics community to develop new approaches for searching and determining significant groups/clusters of features based on one or more biological grouping functions.
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Affiliation(s)
- Malik Yousef
- Department of Information Systems, Zefat Academic College, Zefat 13206, Israel
- Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat 13206, Israel
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Burcu Bakir-Gungor
- Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri 38080, Turkey;
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