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Xue Y, Zhang Y, Su Y, Zhao J, Yu D, Jo Y, Joo J, Lee HJ, Ryu D, Wei S. The implicated role of GDF15 in gastrointestinal cancer. Eur J Clin Invest 2024:e14290. [PMID: 39044314 DOI: 10.1111/eci.14290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Growth differentiation factor 15 (GDF15), a stress-responsive cytokine from transforming growth factor superfamily, is highly expressed in mammalian tissues, including pancreas, stomach and intestine under pathological conditions. In particular, elevated levels of GDF15 might play an important role in the development and progression of various gastrointestinal cancers (GCs), suggesting its potential as a promising target for disease prediction and treatment. METHODS In this review, systematic reviews addressing the role of GDF15 in GCs were updated, along with the latest clinical trials focussing on the GDF15-associated digestive malignancies. RESULTS The multiple cellular pathways through which GDF15 is involved in the regulation of physiological and pathological conditions were first summarized. Then, GDF15 was also established as a valuable clinical index, functioning as a predictive marker in diverse GCs. Notably, latest clinical treatments targeting GDF15 were also highlighted, demonstrating its promising potential in mitigating and curing digestive malignancies. CONCLUSIONS This review unveils the pivotal roles of GDF15 and its potential as a promising target in the pathogenesis of GCs, which may provide insightful directions for future investigations.
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Affiliation(s)
- Yingqi Xue
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Yan Zhang
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Yale Su
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Jiangqi Zhao
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Daoquan Yu
- Department of Hepatological Surgery, Shuangliao Center Hospital, Shuangliao, China
| | - Yunju Jo
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Jongkil Joo
- Department of Obstetrics and Gynecology, Pusan National University Hospital, Busan, Korea
| | - Hyun Joo Lee
- Department of Obstetrics and Gynecology, Pusan National University Hospital, Busan, Korea
| | - Dongryeol Ryu
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Shibo Wei
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
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2
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Omran TA, Tunsjø HS, Jahanlu D, Brackmann SA, Bemanian V, Sæther PC. Decoding immune-related gene-signatures in colorectal neoplasia. Front Immunol 2024; 15:1407995. [PMID: 38979413 PMCID: PMC11229009 DOI: 10.3389/fimmu.2024.1407995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
Background Colorectal cancer (CRC) is a significant health issue, with notable incidence rates in Norway. The immune response plays a dual role in CRC, offering both protective effects and promoting tumor growth. This research aims to provide a detailed screening of immune-related genes and identify specific genes in CRC and adenomatous polyps within the Norwegian population, potentially serving as detection biomarkers. Methods The study involved 69 patients (228 biopsies) undergoing colonoscopy, divided into CRC, adenomatous polyps, and control groups. We examined the expression of 579 immune genes through nCounter analysis emphasizing differential expression in tumor versus adjacent non-tumorous tissue and performed quantitative reverse transcription polymerase chain reaction (RT-qPCR) across patient categories. Results Key findings include the elevated expression of CXCL1, CXCL2, IL1B, IL6, CXCL8 (IL8), PTGS2, and SPP1 in CRC tissues. Additionally, CXCL1, CXCL2, IL6, CXCL8, and PTGS2 showed significant expression changes in adenomatous polyps, suggesting their early involvement in carcinogenesis. Conclusions This study uncovers a distinctive immunological signature in colorectal neoplasia among Norwegians, highlighting CXCL1, CXCL2, IL1B, IL6, CXCL8, PTGS2, and SPP1 as potential CRC biomarkers. These findings warrant further research to confirm their role and explore their utility in non-invasive screening strategies.
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Affiliation(s)
- Thura Akrem Omran
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - Hege Smith Tunsjø
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - David Jahanlu
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - Stephan Andreas Brackmann
- Division of Medicine, Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vahid Bemanian
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
| | - Per Christian Sæther
- Department of Immunology and Transfusion Medicine, Akershus University Hospital, Lørenskog, Norway
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3
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Urbiola-Salvador V, Jabłońska A, Miroszewska D, Kamysz W, Duzowska K, Drężek-Chyła K, Baber R, Thieme R, Gockel I, Zdrenka M, Śrutek E, Szylberg Ł, Jankowski M, Bała D, Zegarski W, Nowikiewicz T, Makarewicz W, Adamczyk A, Ambicka A, Przewoźnik M, Harazin-Lechowska A, Ryś J, Macur K, Czaplewska P, Filipowicz N, Piotrowski A, Dumanski JP, Chen Z. Mass Spectrometry Proteomics Characterization of Plasma Biomarkers for Colorectal Cancer Associated With Inflammation. Biomark Insights 2024; 19:11772719241257739. [PMID: 38911905 PMCID: PMC11191626 DOI: 10.1177/11772719241257739] [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: 01/16/2024] [Accepted: 05/07/2024] [Indexed: 06/25/2024] Open
Abstract
Background Colorectal cancer (CRC) prognosis is determined by the disease stage with low survival rates for advanced stages. Current CRC screening programs are mainly using colonoscopy, limited by its invasiveness and high cost. Therefore, non-invasive, cost-effective, and accurate alternatives are urgently needed. Objective and design This retrospective multi-center plasma proteomics study was performed to identify potential blood-based biomarkers in 36 CRC patients and 26 healthy volunteers by high-resolution mass spectrometry proteomics followed by the validation in an independent CRC cohort (60 CRC patients and 44 healthy subjects) of identified selected biomarkers. Results Among the 322 identified plasma proteins, 37 were changed between CRC patients and healthy volunteers and were associated with the complement cascade, cholesterol metabolism, and SERPIN family members. Increased levels in CRC patients of the complement proteins C1QB, C4B, and C5 as well as pro-inflammatory proteins, lipopolysaccharide-binding protein (LBP) and serum amyloid A4, constitutive (SAA4) were revealed for first time. Importantly, increased level of C5 was verified in an independent validation CRC cohort. Increased C4B and C8A levels were correlated with cancer-associated inflammation and CRC progression, while cancer-associated inflammation was linked to the acute-phase reactant leucine-rich alpha-2-glycoprotein 1 (LRG1) and ceruloplasmin. Moreover, a 4-protein signature including C4B, C8A, apolipoprotein C2 (APO) C2, and immunoglobulin heavy constant gamma 2 was changed between early and late CRC stages. Conclusion Our results suggest that C5 could be a potential biomarker for CRC diagnosis. Further validation studies will aid the application of these new potential biomarkers to improve CRC diagnosis and patient care.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Agnieszka Jabłońska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Weronika Kamysz
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Katarzyna Duzowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Kinga Drężek-Chyła
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Ronny Baber
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Universitätsklinikum Leipzig, Leipzig University, Leipzig, Saxony, Germany
- Leipzig Medical Biobank, Leipzig University, Leipzig, Saxony, Germany
| | - René Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Saxony, Germany
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Saxony, Germany
| | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Ewa Śrutek
- Department of Tumor Pathology and Pathomorphology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Obstetrics, Gynaecology and Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Michał Jankowski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Surgical Oncology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Dariusz Bała
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Surgical Oncology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Wojciech Zegarski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Surgical Oncology, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Tomasz Nowikiewicz
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Kuyavian-Pomeranian, Poland
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center‒Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Kuyavian-Pomeranian, Poland
| | - Wojciech Makarewicz
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Kościerzyna, Pomeranian, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Lesser Poland, Poland
| | - Katarzyna Macur
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Uppland, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Pomeranian, Poland
| | - Zhi Chen
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Pomeranian, Poland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, North Ostrobothnia, Finland
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4
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Li CMY, Briggs MT, Lee YR, Tin T, Young C, Pierides J, Kaur G, Drew P, Maddern GJ, Hoffmann P, Klingler-Hoffmann M, Fenix K. Use of tryptic peptide MALDI mass spectrometry imaging to identify the spatial proteomic landscape of colorectal cancer liver metastases. Clin Exp Med 2024; 24:53. [PMID: 38492056 PMCID: PMC10944452 DOI: 10.1007/s10238-024-01311-5] [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: 01/29/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide. CRC liver metastases (CRLM) are often resistant to conventional treatments, with high rates of recurrence. Therefore, it is crucial to identify biomarkers for CRLM patients that predict cancer progression. This study utilised matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to spatially map the CRLM tumour proteome. CRLM tissue microarrays (TMAs) of 84 patients were analysed using tryptic peptide MALDI-MSI to spatially monitor peptide abundances across CRLM tissues. Abundance of peptides was compared between tumour vs stroma, male vs female and across three groups of patients based on overall survival (0-3 years, 4-6 years, and 7+ years). Peptides were then characterised and matched using LC-MS/MS. A total of 471 potential peptides were identified by MALDI-MSI. Our results show that two unidentified m/z values (1589.876 and 1092.727) had significantly higher intensities in tumours compared to stroma. Ten m/z values were identified to have correlation with biological sex. Survival analysis identified three peptides (Histone H4, Haemoglobin subunit alpha, and Inosine-5'-monophosphate dehydrogenase 2) and two unidentified m/z values (1305.840 and 1661.060) that were significantly higher in patients with shorter survival (0-3 years relative to 4-6 years and 7+ years). This is the first study using MALDI-MSI, combined with LC-MS/MS, on a large cohort of CRLM patients to identify the spatial proteome in this malignancy. Further, we identify several protein candidates that may be suitable for drug targeting or for future prognostic biomarker development.
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Affiliation(s)
- Celine Man Ying Li
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- The Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Adelaide, SA, 5011, Australia
| | - Matthew T Briggs
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Yea-Rin Lee
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Teresa Tin
- The Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Adelaide, SA, 5011, Australia
| | - Clifford Young
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - John Pierides
- SA Pathology, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Gurjeet Kaur
- Institute for Research in Molecular Medicine, University Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Paul Drew
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- The Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Adelaide, SA, 5011, Australia
| | - Guy J Maddern
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- The Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Adelaide, SA, 5011, Australia
| | - Peter Hoffmann
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | | | - Kevin Fenix
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia.
- The Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Adelaide, SA, 5011, Australia.
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5
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Martín-García D, García-Aranda M, Redondo M. Biomarker Identification through Proteomics in Colorectal Cancer. Int J Mol Sci 2024; 25:2283. [PMID: 38396959 PMCID: PMC10888664 DOI: 10.3390/ijms25042283] [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: 01/26/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Colorectal cancer (CRC) is a devastating disease that ranks third in diagnosis and as the second leading cause of cancer-related deaths. The early detection of CRC has been shown to be the most effective strategy to improve treatment outcomes and patient survival. Therefore, current lines of research focus on the development of reliable diagnostic tools. Targeted therapies, in combination with standard chemotherapy and immune checkpoint inhibitors, have emerged as promising treatment protocols in CRC. However, their effectiveness is linked to the molecular characteristics of each patient. The importance of discovering biomarkers that help predict response to therapies and assess prognosis is evident as they allow for a fundamental step towards personalized care and successful treatments. Among the ongoing efforts to identify them, mass spectrometry-based translational proteomics presents itself as a unique opportunity as it enables the discovery and application of protein biomarkers that may revolutionize the early detection and treatment of CRC. Our objective is to show the most recent studies focused on the identification of CRC-related protein markers, as well as to provide an updated view of advances in the field of proteomics and cancer.
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Affiliation(s)
- Desirée Martín-García
- Surgical Specialties, Biochemistry and Immunology Department, Faculty of Medicine, University of Málaga, 29010 Málaga, Spain;
- Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), 29590 Málaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Málaga, Spain
- Research and Innovation Unit, Hospital Universitario Costa del Sol, 29602 Marbella, Spain
| | - Marilina García-Aranda
- Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), 29590 Málaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Málaga, Spain
- Research and Innovation Unit, Hospital Universitario Costa del Sol, 29602 Marbella, Spain
| | - Maximino Redondo
- Surgical Specialties, Biochemistry and Immunology Department, Faculty of Medicine, University of Málaga, 29010 Málaga, Spain;
- Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), 29590 Málaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Málaga, Spain
- Research and Innovation Unit, Hospital Universitario Costa del Sol, 29602 Marbella, Spain
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6
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Amalric A, Attina A, Bastide A, Buffard M, Mateus S, Planque C, Rivals E, Hirtz C, David A. Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation. Anal Chem 2024; 96:1825-1833. [PMID: 38275837 PMCID: PMC10851184 DOI: 10.1021/acs.analchem.3c02635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024]
Abstract
Cancer onset and progression are known to be regulated by genetic and epigenetic events, including RNA modifications (a.k.a. epitranscriptomics). So far, more than 150 chemical modifications have been described in all RNA subtypes, including messenger, ribosomal, and transfer RNAs. RNA modifications and their regulators are known to be implicated in all steps of post-transcriptional regulation. The dysregulation of this complex yet delicate balance can contribute to disease evolution, particularly in the context of carcinogenesis, where cells are subjected to various stresses. We sought to discover RNA modifications involved in cancer cell adaptation to inhospitable environments, a peculiar feature of cancer stem cells (CSCs). We were particularly interested in the RNA marks that help the adaptation of cancer cells to suspension culture, which is often used as a surrogate to evaluate the tumorigenic potential. For this purpose, we designed an experimental pipeline consisting of four steps: (1) cell culture in different growth conditions to favor CSC survival; (2) simultaneous RNA subtype (mRNA, rRNA, tRNA) enrichment and RNA hydrolysis; (3) the multiplex analysis of nucleosides by LC-MS/MS followed by statistical/bioinformatic analysis; and (4) the functional validation of identified RNA marks. This study demonstrates that the RNA modification landscape evolves along with the cancer cell phenotype under growth constraints. Remarkably, we discovered a short epitranscriptomic signature, conserved across colorectal cancer cell lines and associated with enrichment in CSCs. Functional tests confirmed the importance of selected marks in the process of adaptation to suspension culture, confirming the validity of our approach and opening up interesting prospects in the field.
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Affiliation(s)
- Amandine Amalric
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Aurore Attina
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Amandine Bastide
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Marion Buffard
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- LIRMM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Stéphanie Mateus
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Chris Planque
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Eric Rivals
- LIRMM, Université de Montpellier,
CNRS, 34090 Montpellier, France
| | - Christophe Hirtz
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
| | - Alexandre David
- IGF,
INSERM, Université de Montpellier,
CNRS, 34090 Montpellier, France
- IRMB-PPC,
INM, CHU Montpellier, INSERM, Université
de Montpellier, CNRS, 34090 Montpellier, France
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7
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Luz IS, Takaya R, Ribeiro DG, Castro MS, Fontes W. Proteomics: Unraveling the Cross Talk Between Innate Immunity and Disease Pathophysiology, Diagnostics, and Treatment Options. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:221-242. [PMID: 38409424 DOI: 10.1007/978-3-031-50624-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Inflammation is crucial in diseases, and proteins play a key role in the interplay between innate immunity and pathology. This review explores how proteomics helps understanding this relationship, focusing on diagnosis and treatment. We explore the dynamic innate response and the significance of proteomic techniques in deciphering the complex network of proteins involved in prevalent diseases, including infections, cancer, autoimmune and neurodegenerative disorders. Proteomics identifies key proteins in host-pathogen interactions, shedding light on infection mechanisms and inflammation. These discoveries hold promise for diagnostic tools, therapies, and vaccines. In cancer research, proteomics reveals innate signatures associated with tumor development, immune evasion, and therapeutic response. Additionally, proteomic analysis has unveiled autoantigens and dysregulation of the innate immune system in autoimmunity, offering opportunities for early diagnosis, disease monitoring, and new therapeutic targets. Moreover, proteomic analysis has identified altered protein expression patterns in neurodegenerative diseases like Alzheimer's and Parkinson's, providing insights into potential therapeutic strategies. Proteomics of the innate immune system provides a comprehensive understanding of disease mechanisms, identifies biomarkers, and enables effective interventions in various diseases. Despite still in its early stages, this approach holds great promise to revolutionize innate immunity research and significantly improve patient outcomes across a wide range of diseases.
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Affiliation(s)
- Isabelle Souza Luz
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Raquel Takaya
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Daiane Gonzaga Ribeiro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Mariana S Castro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil.
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8
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Kotnala S, Dhasmana A, Dhasmana S, Haque S, Yallapu MM, Tripathi MK, Jaggi M, Chauhan SC. A Systems Biology Approach Unveils a Critical Role of DPP4 in Upper Gastrointestinal Cancer Patient Outcomes. J Environ Pathol Toxicol Oncol 2024; 43:43-55. [PMID: 38505912 DOI: 10.1615/jenvironpatholtoxicoloncol.2023048056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Gastrointestinal (GI) cancers comprise of cancers that affect the digestive system and its accessory organs. The late detection and poor prognosis of GI cancer emphasizes the importance of identifying reliable and precise biomarkers for early diagnosis and prediction of prognosis. The membrane-bound glycoprotein dipeptidyl-peptidase 4 (DPP4), also known as CD26, is ubiquitously expressed and has a wide spectrum of biological roles. The role of DPP4/CD26 in tumor progression in different types of cancers remains elusive. However, the link between DPP4 and tumor-infiltrating cells, as well as its prognostic significance in malignancies, still require further investigation. This study was intended to elucidate the correlation of DPP4 expression and survival along with prognosis, followed by its associated enriched molecular pathways and immune cell marker levels in upper GI cancers. Results demonstrated a strong correlation between increased DPP4 expression and a worse prognosis in esophageal and gastric cancer and the co-expressed common genes with DPP4 were associated with crucial molecular pathways involved in tumorigenesis. Additionally, DPP4 was shown to be significantly linked to several immune infiltrating cell marker genes, including Macrophages (M1, M2 and Tumor Associated Macrophages), neutrophils, Treg, T-cell exhaustion, Th1 and Th2. Overall, our findings suggest that DPP4 may serve as a substantial prognostic biomarker, a possible therapeutic target, as well as it can play a critical role in the regulation of immune cell invasion in patients with gastroesophageal (esophageal, gastroesophageal junction and gastric) cancer. KEY WORDS: DPP4, integrated analysis, GI cancer, gastroesophageal cancer, gastroesophageal junction, prognosis.
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Affiliation(s)
- Sudhir Kotnala
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Anupam Dhasmana
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA; Department of Biosciences and Cancer Research Institute, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun, India
| | - Swati Dhasmana
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon; Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Murali M Yallapu
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Manish K Tripathi
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Meena Jaggi
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C Chauhan
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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9
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Yang L, Atakhanova N, Arellano MTC, Mohamed MY, Hani T, Fahdil AA, Castillo-Acobo RY, Juyal A, Hussein AK, Amin AH, Pecho RDC, Akhavan-Sigari R. Translational research of new developments in targeted therapy of colorectal cancer. Pathol Res Pract 2023; 252:154888. [PMID: 37948996 DOI: 10.1016/j.prp.2023.154888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 11/12/2023]
Abstract
A severe global health concern is the rising incidence and mortality rate of colorectal cancer (CRC). Chemotherapy, which is typically used to treat CRC, is known to have limited specificity and can have noticeable side effects. A paradigm shift in cancer treatment has been brought about by the development of targeted therapies, which has led to the appearance of pharmacological agents with improved efficacy and decreased toxicity. Epidermal growth factor receptor (EGFR), vascular endothelial growth factor (VEGF), human epidermal growth factor receptor 2 (HER2), and BRAF are among the molecular targets covered in this review that are used in targeted therapy for CRC. The current discussion also covers advancements in targeted therapeutic approaches, such as antibody-drug conjugates, immune checkpoint inhibitors, and chimeric antigen receptor (CAR) T-cell therapy. A review of the clinical trials and application of these particular therapies in treating CRC is also done. Despite the improvements in targeted therapy for CRC, problems such as drug resistance and patient selection remain to be solved. Despite this, targeted therapies have offered fresh possibilities for identifying and treating CRC, paving the way for the development of personalized medicine and extending the life expectancy and general well-being of CRC patients.
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Affiliation(s)
- Lei Yang
- Department of Clinical Laboratory, People's Hospital of Chongqing Liangjiang New Area, Chongqing 401121, China
| | - Nigora Atakhanova
- Head of the Department of Oncology, Tashkent Medical Academy, Tashkent 100109, Uzbekistan
| | | | | | - Thamer Hani
- Dentistry Department, Al-Turath University College, Baghdad, Iraq
| | - Ali A Fahdil
- Medical technical college, Al-Farahidi University, Iraq
| | | | - Ashima Juyal
- Uttaranchal Institute of Technology, Uttaranchal University, Dehradun 248007, India
| | | | - Ali H Amin
- Deanship of Scientific Research, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center Tuebingen, Germany; Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Poland
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10
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Gowda BHJ, Ahmed MG, Alshehri SA, Wahab S, Vora LK, Singh Thakur RR, Kesharwani P. The cubosome-based nanoplatforms in cancer therapy: Seeking new paradigms for cancer theranostics. ENVIRONMENTAL RESEARCH 2023; 237:116894. [PMID: 37586450 DOI: 10.1016/j.envres.2023.116894] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
Lyotropic liquid crystals are self-assembled, non-lamellar, and mesophase nanostructured materials that have garnered significant attention as drug carriers. Cubosomes, a subtype of lyotropic liquid crystalline nanoparticles, possess three-dimensional structures that display bicontinuous cubic liquid-crystalline patterns. These patterns are formed through the self-organization of unsaturated monoglycerides (amphphilic lipids such as glyceryl monooleate or phytantriol), followed by stabilization using steric polymers (poloxamers). Owing to their bicontinuous structure and steric polymer-based stabilization, cubosomes have been demonstrated to possess greater entrapment efficiency for hydrophobic drugs compared to liposomes, while also exhibiting high stability. In the past decade, there has been significant interest in cubosomes due to their ability to deliver therapeutic and contrast agents for cancer treatment and imaging with minimal side effects, establishing them as a safe and effective approach. Concerning these advantages, the present review elaborates on the general aspects, composition, and preparation techniques of cubosomes, followed by explanations of their mechanisms of drug loading and release patterns. Furthermore, the review provides meticulous discussions on the use of cubosomes in the treatment and imaging of various types of cancer, culminating in the enumeration of patents related to cubosome-based drug delivery systems.
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Affiliation(s)
- B H Jaswanth Gowda
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India
| | - Mohammed Gulzar Ahmed
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India
| | - Saad Ali Alshehri
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, 62529, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, 62529, Saudi Arabia
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, United Kingdom
| | - Raghu Raj Singh Thakur
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, United Kingdom
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India; Center for Global health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India.
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11
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Islam MS, Gopalan V, Lam AK, Shiddiky MJA. Current advances in detecting genetic and epigenetic biomarkers of colorectal cancer. Biosens Bioelectron 2023; 239:115611. [PMID: 37619478 DOI: 10.1016/j.bios.2023.115611] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Colorectal carcinoma (CRC) is the third most common cancer in terms of diagnosis and the second in terms of mortality. Recent studies have shown that various proteins, extracellular vesicles (i.e., exosomes), specific genetic variants, gene transcripts, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and altered epigenetic patterns, can be used to detect, and assess the prognosis of CRC. Over the last decade, a plethora of conventional methodologies (e.g., polymerase chain reaction [PCR], direct sequencing, enzyme-linked immunosorbent assay [ELISA], microarray, in situ hybridization) as well as advanced analytical methodologies (e.g., microfluidics, electrochemical biosensors, surface-enhanced Raman spectroscopy [SERS]) have been developed for analyzing genetic and epigenetic biomarkers using both optical and non-optical tools. Despite these methodologies, no gold standard detection method has yet been implemented that can analyze CRC with high specificity and sensitivity in an inexpensive, simple, and time-efficient manner. Moreover, until now, no study has critically reviewed the advantages and limitations of these methodologies. Here, an overview of the most used genetic and epigenetic biomarkers for CRC and their detection methods are discussed. Furthermore, a summary of the major biological, technical, and clinical challenges and advantages/limitations of existing techniques is also presented.
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Affiliation(s)
- Md Sajedul Islam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia.
| | - Alfred K Lam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia; Pathology Queensland, Gold Coast University Hospital, Southport, QLD, 4215, Australia
| | - Muhammad J A Shiddiky
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
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12
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Shaygannejad A, Sohrabi B, Rad SR, Yousefisadr F, Darvish H, Soosanabadi M. Promoter methylation of matrix metallopeptidase 9 in peripheral blood mononuclear cells: A novel biomarker in a promising source for noninvasive colorectal cancer diagnosis. J Cancer Res Ther 2023; 19:1797-1802. [PMID: 38376281 DOI: 10.4103/jcrt.jcrt_2188_21] [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: 12/05/2021] [Accepted: 01/03/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Colorectal cancer (CRC) has been described as a "silent disease," which can be readily treated in most patients when discovered in its early stages. Considering the limitations of the current conventional tests for the diagnosis of CRC, researchers strive to find noninvasive and more valid biomarkers for the early detection of CRC. It has been shown that tumor-specific methylation patterns can also be identified in peripheral blood mononuclear cells (PBMCs) and are reliable sources of methylation analysis for CRC screening. MATERIALS AND METHODS We carried out a quantitative methylation analysis on matrix metallopeptidase 9 (MMP9) promoter using methylation quantification endonuclease-resistant DNA (MethyQESD) method. A total of 70 patients with CRC and 70 normal controls were enrolled in this study for methylation analysis in the PBMCs. RESULTS Our findings discovered a considerable hypermethylation of MMP9 promoter in CRC patients compared with healthy controls (mean: 47.30% and 20.31%, respectively; P > 0.001). The sensitivity and specificity of the MMP9 gene for the diagnosis of CRC were 88% and 78%, respectively. In addition, on the basis of area under the curve values, the diagnostic power of the MMP9 gene was 0.976 (P < 0.001). Moreover, our analysis established that MMP9 methylation was significantly different between the different stages of CRC (P: 0.034). CONCLUSIONS Our results showed that MMP9 promoter methylation in PBMCs can be used as an outstanding biomarker for CRC diagnosis. Besides, we confirmed that PBMCs are reliable sources of methylation analysis for CRC screening and MethyQESD is an accurate and fast method for quantitative methylation analyses.
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Affiliation(s)
- Alireza Shaygannejad
- Department of Internal Medicine, Division of Gastrointestinal, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Behnoush Sohrabi
- Department of Biology, Faculty of Sciences, Arak University, Arak, Iran
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
| | - Shima Rahimi Rad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzaneh Yousefisadr
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
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13
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Bonilla CE, Montenegro P, O’Connor JM, Hernando-Requejo O, Aranda E, Pinto Llerena J, Llontop A, Gallardo Escobar J, Díaz Romero MDC, Bautista Hernández Y, Graña Suárez B, Batagelj EJ, Wali Mushtaq A, García-Foncillas J. Ibero-American Consensus Review and Incorporation of New Biomarkers for Clinical Practice in Colorectal Cancer. Cancers (Basel) 2023; 15:4373. [PMID: 37686649 PMCID: PMC10487247 DOI: 10.3390/cancers15174373] [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: 05/16/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Advances in genomic technologies have significantly improved the management of colorectal cancer (CRC). Several biomarkers have been identified in CRC that enable personalization in the use of biologic agents that have shown to enhance the clinical outcomes of patients. However, technologies used for their determination generate massive amounts of information that can be difficult for the clinician to interpret and use adequately. Through several discussion meetings, a group of oncology experts from Spain and several Latin American countries reviewed the latest literature to provide practical recommendations on the determination of biomarkers in CRC based on their clinical experience. The article also describes the importance of looking for additional prognostic biomarkers and the use of histopathology to establish an adequate molecular classification. Present and future of immunotherapy biomarkers in CRC patients are also discussed, together with several techniques for marker determination, including liquid biopsy, next-generation sequencing (NGS), polymerase chain reaction (PCR), and fecal immunohistochemical tests. Finally, the role of Molecular Tumor Boards in the diagnosis and treatment of CRC is described. All of this information will allow us to highlight the importance of biomarker determination in CRC.
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Affiliation(s)
- Carlos Eduardo Bonilla
- Fundación CTIC—Centro de Tratamiento e Investigación sobre Cáncer, Bogotá 1681442, Colombia
| | - Paola Montenegro
- Institución AUNA OncoSalud e Instituto Nacional de Enfermedades Neoplásicas, Lima 15023, Peru
| | | | | | - Enrique Aranda
- Departamento de Oncología Médica, Hospital Reina Sofía, IMIBIC, UCO, CIBERONC, 14004 Cordoba, Spain;
| | | | - Alejandra Llontop
- Instituto de Oncología Ángel H. Roffo, Ciudad Autónoma de Buenos Aires C1437FBG, Argentina
| | | | | | | | - Begoña Graña Suárez
- Servicio de Oncología Médica, Hospital Universitario de A Coruña, Servicio Galego de Saúde (SERGAS), 15006 A Coruña, Spain;
| | | | | | - Jesús García-Foncillas
- Hospital Universitario Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain
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14
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Minh Cuong H, Hong Thang V, Thu Huong BT, Thuan Loi N, Minh Duc N. KRAS mutations and their associations with clinicopathological features and survival in Vietnamese non‑polyp colon cancer patients. Mol Clin Oncol 2023; 19:63. [PMID: 37456800 PMCID: PMC10345899 DOI: 10.3892/mco.2023.2659] [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: 04/24/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
The aim of the present study was to determine Kirsten Ras sarcoma virus (KRAS) mutations and the associations of KRAS mutations with clinicopathological features and treatment outcomes in Vietnamese non-polyp colon cancer (NPCC) patients. The data in the present study covered 194 patients with non-polyp colon cancers at stages II or III, according to the 8th edition of the American Joint Committee on Cancer staging system, in northern Vietnam from January 2016 to August 2020. All patients underwent radical surgery and adjuvant therapy with FOLFOX4 or XELOX. Subsequently, the recruited patients were followed-up with scheduled hospital exams for diagnosing recurrence. Genomic DNA samples were prepared from dissected tumors and specific sequences of the KRAS gene were amplified by polymerase chain reactions (PCR). The mutations at codons 12, 13, 59, 60, 61, 117 and 146 of the gene were determined. Possible associations of the KRAS mutations with clinicopathological properties and the survival of patients were analysed. The KRAS mutation rate was 47.9% in Vietnamese patients with NPCC, of those, mutations in exon 2 accounted for 91.4% of all detected mutations. The mutated-KRAS patients exhibited a significantly higher rate of anemia. Moreover, the KRAS mutation rate was higher in females (57.1%) than in males (39.8%). The KRAS mutation rate was also higher in patients with right colon cancers. Furthermore, KRAS mutations were an independent prognosis for poor disease-free survival (DFS) and overall survival (OS) in stage II patients. Among left-sided colon patients, mutated KRAS was a significant predictive factor for poor DFS but not for OS. The present study revealed a very high mutation rate of KRAS in Vietnamese patients with NPCC. The data of the present study indicated that the mutation status was associated with female patients and right-sided tumors. The KRAS mutations were a negative factor for the survival of patients with stage II NPCC and patients with left-sided colon cancer.
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Affiliation(s)
- Hoang Minh Cuong
- Department of Oncology, Hanoi Medical University, Hanoi 100000, Vietnam
| | - Vu Hong Thang
- Department of Oncology, Hanoi Medical University, Hanoi 100000, Vietnam
| | - Bui-Thi Thu Huong
- Department of Biochemistry, Thai Nguyen University of Medicine and Pharmacy, Thai Nguyen 250000, Vietnam
| | - Nguyen Thuan Loi
- Nuclear Medicine and Oncology Center, Bach Mai Hospital, Hanoi 100000, Vietnam
| | - Nguyen Minh Duc
- Department of Radiology, Pham Ngoc Thach University of Medicine, Ho Chi Minh City 700000, Vietnam
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15
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Jolugbo P, Willott T, Lin WH, Maisey T, O'Callaghan D, Green MA, Jayne DG, Khot MI. Fluorescent imaging using novel conjugated polymeric nanoparticles-affimer probes in complex in vitro models of colorectal cancer. NANOSCALE 2023. [PMID: 37466243 DOI: 10.1039/d3nr02160b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
We developed a carcinoembryonic antigen (CEA) conjugated polymer nanoparticle (CPN510-CEA-Af) probe to target CEA-expressing CRC cells in vitro. Its efficacy was evaluated in 2D and 3D cultures of LS174T, LoVo, and HT29 CRC cell lines. CPN510-CEA-Af produced greater fluorescent signal intensity than unconjugated particles in both 2D cells and 3D spheriods, indicating its potential as a probe for image-guided colorectal cancer surgery.
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Affiliation(s)
- Precious Jolugbo
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
| | - Thomas Willott
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
| | - Wei-Hsiang Lin
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Thomas Maisey
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
| | | | - Mark A Green
- Stream Bio Ltd, Alderley Park, Nether Alderley, Cheshire, SK10 4TG, UK
- Department of Physics, Faculty of Natural, Mathematical & Engineering Sciences, King's College London, Strand, London, WC2R 2LS, UK
| | - David G Jayne
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
| | - M Ibrahim Khot
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
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16
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Giannopoulou N, Constantinou C. Recent Developments in Diagnostic and Prognostic Biomarkers for Colorectal Cancer: A Narrative Review. Oncology 2023; 101:675-684. [PMID: 37364542 DOI: 10.1159/000531474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Colorectal cancer was reported as the second most common cause of cancer death worldwide, in the year 2020. This disease is an important public health problem considering its high incidence and mortality rates. SUMMARY The molecular events that lead to colorectal cancer include genetic and epigenetic abnormalities. Some of the most important molecular mechanisms involved include the APC/β-catenin pathway, the microsatellite pathway, and the CpG island hypermethylation. Evidence in the literature supports a role for the microbiota in the development of colon carcinogenesis, and specific microbes may contribute to or prevent carcinogenesis. Progress in prevention, screening, and management has improved the overall prognosis of the disease when diagnosed at an early stage; yet metastatic disease continues to have a poor long-term prognosis due to late-stage diagnosis and treatment failure. Biomarkers are a key tool for early detection and prognosis and aim to reduce morbidity and mortality associated with colorectal cancer. The main focus of this narrative review is to provide an update on the recent development of diagnostic and prognostic biomarkers in stool, blood, and tumor tissue samples. KEY MESSAGES The review focuses on recent investigations in microRNAs, cadherins, Piwi-interacting RNAs, circulating cell-free DNA, and microbiome biomarkers which can be applied for the diagnosis and prognosis of colorectal cancer.
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Affiliation(s)
- Nefeli Giannopoulou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus
| | - Constantina Constantinou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus
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17
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Liu Q, Ran D, Wang L, Feng J, Deng W, Mei D, Peng Y, Du C. Association between Ki67 expression and therapeutic outcome in colon cancer. Oncol Lett 2023; 25:272. [PMID: 37216165 PMCID: PMC10193363 DOI: 10.3892/ol.2023.13858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/14/2023] [Indexed: 05/24/2023] Open
Abstract
Ki67 is a commonly used proliferation marker in pathological diagnosis of tumors; however, its prognostic value in colon cancer is controversial. A total of 312 consecutive patients with stage I-III colon cancer who underwent radical surgery with or without adjuvant chemotherapy were included in the present study. Ki67 expression was assessed using immunohistochemistry and was classified according to 25% intervals. The association between Ki67 expression and clinicopathological features was analyzed. Long-term postoperative survival, including disease-free survival (DFS) and overall survival, was calculated, and its association with Ki67 was analyzed. High Ki67 expression (>50%) was associated with improved DFS in patients treated with adjuvant chemotherapy postoperatively, but not in patients who received surgery alone (P=0.138). Ki67 expression was significantly associated with histological differentiation of the tumor (P=0.01), while it was not associated with other clinicopathological factors. Multivariate analysis demonstrated that pathological T and N stage were independent prognostic factors. In conclusion, high Ki67 expression was associated with a good therapeutic outcome in patients receiving adjuvant chemotherapy in colon cancer.
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Affiliation(s)
- Qi Liu
- Key University Laboratory of Metabolism and Health of Guangdong, Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P.R. China
| | - Dongmei Ran
- Department of Pathology, Southern University of Science and Technology Hospital, Shenzhen, Guangdong 518055, P.R. China
- Digestive Tumor Center, Southern University of Science and Technology Hospital, Shenzhen, Guangdong 518055, P.R. China
| | - Liping Wang
- Digestive Tumor Center, Southern University of Science and Technology Hospital, Shenzhen, Guangdong 518055, P.R. China
- Department of Medical Oncology, Southern University of Science and Technology Hospital, Shenzhen, Guangdong 518055, P.R. China
| | - Jiajun Feng
- Department of General Surgery, Southern University of Science and Technology Hospital, Shenzhen, Guangdong 518055, P.R. China
| | - Wei Deng
- Department of Pathology, Southern University of Science and Technology Hospital, Shenzhen, Guangdong 518055, P.R. China
| | - Dongdong Mei
- Department of Pathology, Southern University of Science and Technology Hospital, Shenzhen, Guangdong 518055, P.R. China
| | - Yifan Peng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, P.R. China
| | - Changzheng Du
- Key University Laboratory of Metabolism and Health of Guangdong, Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P.R. China
- Digestive Tumor Center, Southern University of Science and Technology Hospital, Shenzhen, Guangdong 518055, P.R. China
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18
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Barpanda A, Biswas D, Verma A, Parihari S, Singh A, Kapoor S, Kantharia C, Srivastava S. Integrative Proteomic and Pharmacological Analysis of Colon Cancer Reveals the Classical Lipogenic Pathway with Prognostic and Therapeutic Opportunities. J Proteome Res 2023; 22:871-884. [PMID: 36731020 DOI: 10.1021/acs.jproteome.2c00646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Despite recent advancements, the high mortality rate remains a concern in colon cancer (CAC). Identification of therapeutic markers could prove to be a great asset in CAC management. Multiple studies have reported hyperactivation of de novo lipogenesis (DNL), but its association with the pathology is unclear. This study aims to establish the importance as well as the prognostic and therapeutic potential of DNL in CAC. The key lipogenic enzymes fatty acid synthase along with ATP citrate lyase were quantified using an LC-MS/MS-based targeted proteomics approach in the samples along with the matched controls. The potential capacity of the proteins to distinguish between the tumor and controls was demonstrated using random forest-based class prediction analysis using the peptide intensities. Furthermore, in-depth proteomics of DNL inhibition in the CAC cell line revealed the significance of the pathway in proliferation and metastasis. DNL inhibition affected the major signaling pathways, including DNA repair, PI3K-AKT-mTOR pathway, membrane trafficking, proteasome, etc. The study revealed the upregulation of 26S proteasome machinery as a result of the treatment with subsequent induction of apoptosis. Again, in silico molecular docking-based drug repurposing was performed to find potential drug candidates. Furthermore, we have demonstrated that blocking DNL could be explored as a therapeutic option in CAC treatment.
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Affiliation(s)
- Abhilash Barpanda
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India.,Centre for Research in Nanotechnology and Science, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Deeptarup Biswas
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Ayushi Verma
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Shashwati Parihari
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Avinash Singh
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Shobhna Kapoor
- Department of Chemistry, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Chetan Kantharia
- Department of Surgical Gastroenterology, Seth G.S. Medical College and KEM Hospital, Mumbai 400076 Maharashtra, India
| | - Sanjeeva Srivastava
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India.,Centre for Research in Nanotechnology and Science, IIT Bombay, Mumbai 400076 Maharashtra, India
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Barpanda A, Tuckley C, Ray A, Banerjee A, Duttagupta SP, Kantharia C, Srivastava S. A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer. Proteomics Clin Appl 2023; 17:e2200062. [PMID: 36408811 DOI: 10.1002/prca.202200062] [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: 08/08/2022] [Revised: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
PURPOSE Colorectal cancer (CRC) has been reported as the second leading cause of cancer death worldwide. The 5-year annual survival is around 50%, mainly due to late diagnosis, striking necessity for early detection. This study aims to identify autoantibody in patients' sera for early screening of cancer. EXPERIMENTAL DESIGN The study used a high-density human proteome array with approximately 17,000 recombinant proteins. Screening of sera from healthy individuals, CRC from Indian origin, and CRC from middle-east Asia origin were performed. Bio-statistical analysis was performed to identify significant autoantibodies altered. Pathway analysis was performed to explore the underlying mechanism of the disease. RESULTS The comprehensive proteomic analysis revealed dysregulation of 15 panels of proteins including CORO7, KCNAB1, WRAP53, NDUFS6, KRT30, and COLGALT2. Further biological pathway analysis for the top dysregulated autoantigenic proteins revealed perturbation in important biological pathways such as ECM degradation and cytoskeletal remodeling etc. CONCLUSIONS AND CLINICAL RELEVANCE: The generation of an autoimmune response against cancer-linked pathways could be linked to the screening of the disease. The process of immune surveillance can be detected at an early stage of cancer. Moreover, AAbs can be easily extracted from blood serum through the least invasive test for disease screening.
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Affiliation(s)
- Abhilash Barpanda
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Arka Ray
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Siddhartha P Duttagupta
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Chetan Kantharia
- Department of surgical gastroenterology at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Sanjeeva Srivastava
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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20
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Fang Y, Skog S, Ou Q, Chen Z, Liu S, Hei A, Li J, Zhou J, He E, Wan D. Is serum thymidine kinase 1 a prognostic biomarker in primary tumor location of colorectal carcinomas? Discov Oncol 2023; 14:21. [PMID: 36800051 PMCID: PMC9938097 DOI: 10.1007/s12672-023-00614-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/11/2023] [Indexed: 04/17/2023] Open
Abstract
AIM To assess whether serum thymidine kinase 1 (STK1p), CEA and CA19.9 can be used as prognostic biomarkers in the primary tumor location (PTL) of colorectal carcinoma (CRC). Additional clinical factors of TNM stage, pathological grade, age and sex were also included. METHODS STK1p was determined by an ECL-dot-blot assay, and CEA/CA19.9 was determined by an automatic electrochemiluminescence analyzer in a retrospective presurgery of right-colon carcinoma (R-CC, n = 90), left-colon carcinoma (L-CC, n = 128) and rectal carcinoma (RC, n = 270). Prognostic factors were evaluated by COX and overall survival (OS). RESULTS The multivariate-COX and OS in relation to the prognostic factors of PTL in CRC were different and complex. An elevated STK1p value was significantly associated with poor OS in RC (P = 0.002) and L-CC (P = 0.037) but not in R-CC (P > 0.05). Elevated CEA (P≈.000) and CA19.9 (P≈.000) were significantly associated with poor OS in RC but not in L-CC and R-CC. Multivariate-COX showed that STK1p (P = 0.02, HR = 1.779, 95%CI 1.30-7.582), CEA (P = 0.001, HR = 2.052, 95%CI 1.320-3.189), CA19.9 (P≈.000, HR = 2.574, 95%CI 1.592-4.162) and TNM-stage (P≈.000, HR = 2.368, 95%CI 1.518-3.694) were independent prognostic factors in RC, while TNM-stage was an independent prognostic factor only in R-CC (P = 0.011, HR = 3.139, 95% CI 1.30-7.582) and L-CC (P≈.000, HR = 4.168, 95%CI 1.980-8.852). Moreover, elevated STK1p was significantly more sensitive (P < .001) for predicting mortality than CEA and CA19.9. No correlation was found between STK1p, CEA or AFP. CONCLUSION Combining TNM stage and suitable biomarkers, STK1p provides further reliable information on the survival of PTL of CRC.
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Affiliation(s)
- Yujing Fang
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yassin University Cancer Centre, Guangzhou, Guangdong 510060 People’s Republic of China
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yassin University Cancer Centre, Guangzhou, 510060 Guangdong People’s Republic of China
| | - Sven Skog
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, 3rd Floor, Building 1, Guanlan Street, Longhua District, Shenzhen, 518110 Guangdong People’s Republic of China
| | - Qingjian Ou
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yassin University Cancer Centre, Guangzhou, Guangdong 510060 People’s Republic of China
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yassin University Cancer Centre, Guangzhou, 510060 Guangdong People’s Republic of China
| | - Zhiheng Chen
- Management Centre, Third Xiangyan Hospital, Central South University, Changsha, 410013 People’s Republic of China
| | - Senbo Liu
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, 3rd Floor, Building 1, Guanlan Street, Longhua District, Shenzhen, 518110 Guangdong People’s Republic of China
| | - Ailian Hei
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, 3rd Floor, Building 1, Guanlan Street, Longhua District, Shenzhen, 518110 Guangdong People’s Republic of China
| | - Jin Li
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, 3rd Floor, Building 1, Guanlan Street, Longhua District, Shenzhen, 518110 Guangdong People’s Republic of China
| | - Ji Zhou
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, 3rd Floor, Building 1, Guanlan Street, Longhua District, Shenzhen, 518110 Guangdong People’s Republic of China
| | - Ellen He
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, 3rd Floor, Building 1, Guanlan Street, Longhua District, Shenzhen, 518110 Guangdong People’s Republic of China
| | - Desen Wan
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yassin University Cancer Centre, Guangzhou, Guangdong 510060 People’s Republic of China
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yassin University Cancer Centre, Guangzhou, 510060 Guangdong People’s Republic of China
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21
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Sundararaman N, Bhat A, Venkatraman V, Binek A, Dwight Z, Ariyasinghe NR, Escopete S, Joung SY, Cheng S, Parker SJ, Fert-Bober J, Van Eyk JE. BIRCH: An Automated Workflow for Evaluation, Correction, and Visualization of Batch Effect in Bottom-Up Mass Spectrometry-Based Proteomics Data. J Proteome Res 2023; 22:471-481. [PMID: 36695565 DOI: 10.1021/acs.jproteome.2c00671] [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: 01/26/2023]
Abstract
Recent surges in large-scale mass spectrometry (MS)-based proteomics studies demand a concurrent rise in methods to facilitate reliable and reproducible data analysis. Quantification of proteins in MS analysis can be affected by variations in technical factors such as sample preparation and data acquisition conditions leading to batch effects, which adds to noise in the data set. This may in turn affect the effectiveness of any biological conclusions derived from the data. Here we present Batch-effect Identification, Representation, and Correction of Heterogeneous data (BIRCH), a workflow for analysis and correction of batch effect through an automated, versatile, and easy to use web-based tool with the goal of eliminating technical variation. BIRCH also supports diagnosis of the data to check for the presence of batch effects, feasibility of batch correction, and imputation to deal with missing values in the data set. To illustrate the relevance of the tool, we explore two case studies, including an iPSC-derived cell study and a Covid vaccine study to show different context-specific use cases. Ultimately this tool can be used as an extremely powerful approach for eliminating technical bias while retaining biological bias, toward understanding disease mechanisms and potential therapeutics.
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Affiliation(s)
- Niveda Sundararaman
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Archana Bhat
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Vidya Venkatraman
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandra Binek
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Zachary Dwight
- Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Nethika R Ariyasinghe
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Sean Escopete
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Sandy Y Joung
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Susan Cheng
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Sarah J Parker
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Justyna Fert-Bober
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
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22
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Kaya IH, Al-Harazi O, Colak D. Transcriptomic data analysis coupled with copy number aberrations reveals a blood-based 17-gene signature for diagnosis and prognosis of patients with colorectal cancer. Front Genet 2023; 13:1031086. [PMID: 36685857 PMCID: PMC9854115 DOI: 10.3389/fgene.2022.1031086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/01/2022] [Indexed: 01/07/2023] Open
Abstract
Background: Colorectal cancer (CRC) is the third most common cancer and third leading cause of cancer-associated deaths worldwide. Diagnosing CRC patients reliably at an early and curable stage is of utmost importance to reduce the risk of mortality. Methods: We identified global differentially expressed genes with copy number alterations in patients with CRC. We then identified genes that are also expressed in blood, which resulted in a blood-based gene signature. We validated the gene signature's diagnostic and prognostic potential using independent datasets of gene expression profiling from over 800 CRC patients with detailed clinical data. Functional enrichment, gene interaction networks and pathway analyses were also performed. Results: The analysis revealed a 17-gene signature that is expressed in blood and demonstrated that it has diagnostic potential. The 17-gene SVM classifier displayed 99 percent accuracy in predicting the patients with CRC. Moreover, we developed a prognostic model and defined a risk-score using 17-gene and validated that high risk score is strongly associated with poor disease outcome. The 17-gene signature predicted disease outcome independent of other clinical factors in the multivariate analysis (HR = 2.7, 95% CI = 1.3-5.3, p = 0.005). In addition, our gene network and pathway analyses revealed alterations in oxidative stress, STAT3, ERK/MAPK, interleukin and cytokine signaling pathways as well as potentially important hub genes, including BCL2, MS4A1, SLC7A11, AURKA, IL6R, TP53, NUPR1, DICER1, DUSP5, SMAD3, and CCND1. Conclusion: Our results revealed alterations in various genes and cancer-related pathways that may be essential for CRC transformation. Moreover, our study highlights diagnostic and prognostic value of our gene signature as well as its potential use as a blood biomarker as a non-invasive diagnostic method. Integrated analysis transcriptomic data coupled with copy number aberrations may provide a reliable method to identify key biological programs associated with CRC and lead to improved diagnosis and therapeutic options.
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Affiliation(s)
- Ibrahim H. Kaya
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Olfat Al-Harazi
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Dilek Colak
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia,*Correspondence: Dilek Colak,
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23
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Pham TD, Ravi V, Luo B, Fan C, Sun XF. Artificial intelligence fusion for predicting survival of rectal cancer patients using immunohistochemical expression of Ras homolog family member B in biopsy. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1-16. [PMID: 36937315 PMCID: PMC10017185 DOI: 10.37349/etat.2023.00119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/31/2022] [Indexed: 02/10/2023] Open
Abstract
Aim The process of biomarker discovery is being accelerated with the application of artificial intelligence (AI), including machine learning. Biomarkers of diseases are useful because they are indicators of pathogenesis or measures of responses to therapeutic treatments, and therefore, play a key role in new drug development. Proteins are among the candidates for biomarkers of rectal cancer, which need to be explored using state-of-the-art AI to be utilized for prediction, prognosis, and therapeutic treatment. This paper aims to investigate the predictive power of Ras homolog family member B (RhoB) protein in rectal cancer. Methods This study introduces the integration of pretrained convolutional neural networks and support vector machines (SVMs) for classifying biopsy samples of immunohistochemical expression of protein RhoB in rectal-cancer patients to validate its biologic measure in biopsy. Features of the immunohistochemical expression images were extracted by the pretrained networks and used for binary classification by the SVMs into two groups of less and more than 5-year survival rates. Results The fusion of neural search architecture network (NASNet)-Large for deep-layer feature extraction and classifier using SVMs provided the best average classification performance with a total accuracy = 85%, prediction of survival rate of more than 5 years = 90%, and prediction of survival rate of less than 5 years = 75%. Conclusions The finding obtained from the use of AI reported in this study suggest that RhoB expression on rectal-cancer biopsy can be potentially used as a biomarker for predicting survival outcomes in rectal-cancer patients, which can be informative for clinical decision making if the patient would be recommended for preoperative therapy.
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Affiliation(s)
- Tuan D. Pham
- Center for Artificial Intelligence, Prince Mohammad Bin Fahd University, Khobar 34754, Saudi Arabia
- Correspondence: Tuan D. Pham, Center for Artificial Intelligence, Prince Mohammad Bin Fahd University, Khobar 34754, Saudi Arabia. ;
| | - Vinayakumar Ravi
- Center for Artificial Intelligence, Prince Mohammad Bin Fahd University, Khobar 34754, Saudi Arabia
| | - Bin Luo
- Department of Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden
- Department of Gastrointestinal Surgery, Sichuan Provincial People’s Hospital, Chengdu 610032, Sichuan, China
| | - Chuanwen Fan
- Department of Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden
| | - Xiao-Feng Sun
- Department of Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden
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24
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Babic T, Lygirou V, Rosic J, Miladinov M, Rom AD, Baira E, Stroggilos R, Pappa E, Zoidakis J, Krivokapic Z, Nikolic A. Pilot proteomic study of locally advanced rectal cancer before and after neoadjuvant chemoradiotherapy indicates high metabolic activity in non-responders' tumor tissue. Proteomics Clin Appl 2023; 17:e2100116. [PMID: 35997210 DOI: 10.1002/prca.202100116] [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: 11/22/2021] [Revised: 05/28/2022] [Accepted: 08/03/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE In the search for candidate predictive biomarkers to evaluate response to neoadjuvant chemoradiotherapy (nCRT) in rectal cancer, only a few studies report proteomic profiles of tumor tissue before and after nCRT. The aim of our study was to determine differentially expressed proteins between responders and non-responders before and after the therapy in order to identify candidate molecules for prediction and follow-up of response to nCRT. EXPERIMENTAL DESIGN The study has included tissue sections of rectal tumor and non-tumor mucosa from five responders and five non-responders taken before and after nCRT from patients with locally advanced rectal cancer. Extracted proteins were analyzed by LC-MS/MS analysis followed by a set of bioinformatics analyses. RESULT Proteomics analysis provided a mean of approximately 1050 protein identifications per sample. A comparison of proteomic profiles between responders and non-responders has identified 18 differentially expressed proteins. Pathway analysis demonstrated high metabolic activity in non-responders' tumors before nCRT, indicating the presence of intrinsic chemoradioresistance in these subjects. Two proteins associated with poor prognosis in colorectal cancer, ADAM10 and CAD, were identified as candidate predictive biomarkers as they were present in non-responders only. CONCLUSIONS AND CLINICAL RELEVANCE Shortlisted proteins from our study should be further validated as candidate biomarkers for response to routinely applied nCRT protocols.
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Affiliation(s)
- Tamara Babic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Vasiliki Lygirou
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of The Academy of Athens (BRFAA), Athens, Greece
| | - Jovana Rosic
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marko Miladinov
- Clinic for Digestive Surgery - First Surgical Clinic, Clinical Center of Serbia, Belgrade, Serbia
| | - Aleksandra Djikic Rom
- Clinic for Digestive Surgery - First Surgical Clinic, Clinical Center of Serbia, Belgrade, Serbia
| | - Eirini Baira
- Laboratory of Toxicological Assessment of pesticides, Scientific Directorate of Pesticides Assessment and Phytopharmacy, Benaki Phytopathological Institute, Athens, Greece
| | - Rafael Stroggilos
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of The Academy of Athens (BRFAA), Athens, Greece
| | - Eftychia Pappa
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of The Academy of Athens (BRFAA), Athens, Greece
| | - Jerome Zoidakis
- Biotechnology Division, Centre of Basic Research, Biomedical Research Foundation of The Academy of Athens (BRFAA), Athens, Greece
| | - Zoran Krivokapic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic for Digestive Surgery - First Surgical Clinic, Clinical Center of Serbia, Belgrade, Serbia.,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Aleksandra Nikolic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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Studies on 1,4-Quinone Derivatives Exhibiting Anti-Leukemic Activity along with Anti-Colorectal and Anti-Breast Cancer Effects. Molecules 2022; 28:molecules28010077. [PMID: 36615273 PMCID: PMC9822417 DOI: 10.3390/molecules28010077] [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: 11/13/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC), breast cancer, and chronic myeloid leukemia (CML) are life-threatening malignancies worldwide. Although potent therapeutic and screening strategies have been developed so far, these cancer types are still major public health problems. Therefore, the exploration of more potent and selective new agents is urgently required for the treatment of these cancers. Quinones represent one of the most important structures in anticancer drug discovery. We have previously identified a series of quinone-based compounds (ABQ-1-17) as anti-CML agents. In the current work, ABQ-3 was taken to the National Cancer Institute (NCI) for screening to determine its in vitro antiproliferative effects against a large panel of human tumor cell lines at five doses. ABQ-3 revealed significant growth inhibition against HCT-116 CRC and MCF-7 breast cancer cells with 2.00 µM and 2.35 µM GI50 values, respectively. The MTT test also showed that ABQ-3 possessed anticancer effects towards HCT-116 and MCF-7 cells with IC50 values of 5.22 ± 2.41 μM and 7.46 ± 2.76 μM, respectively. Further experiments indicated that ABQ-3 induced apoptosis in both cell lines, and molecular docking studies explicitly suggested that ABQ-3 exhibited DNA binding in a similar fashion to previously reported compounds. Based on in silico pharmacokinetic prediction, ABQ-3 might display drug-like features enabling this compound to become a lead molecule for future studies.
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26
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Colorectal Cancer and the Role of the Gut Microbiota-Do Medical Students Know More Than Other Young People?-Cross-Sectional Study. Nutrients 2022; 14:nu14194185. [PMID: 36235836 PMCID: PMC9572037 DOI: 10.3390/nu14194185] [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: 09/17/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Malignant neoplasms account for an increasing share of the disease burden of the world population and are an increasingly common cause of death. In the aspect of colorectal cancer, increasing attention is paid to the microbiota. According to current knowledge, the composition of gut microbiota in patients diagnosed with colorectal cancer significantly differs from the composition of microorganisms in the intestines of healthy individuals. (2) Material and methods: The survey included 571 students from the three universities located in Silesia. The research tool was an original, anonymous questionnaire created for the study. The ratio of correct answers to the total number of points possible to obtain was evaluated according to the adopted criteria (≤25%—very low level of knowledge; >75%—high level of knowledge). (3) Results: From the questions about the gut microbiota, the subjects scored an average of six points (SD ± 1.31) out of nine possible points. Statistical analysis showed differences between the number of correct answers among students of the Medical University of Silesia and the University of Silesia (p = 0.04, p < 0.05). On the other hand, in the field of colorectal cancer, the respondents scored on average four points (SD ± 2.07) out of eight possible. Statistical analysis showed significant differences between the ratio of correct answers and the respondent’s university affiliation (p < 0.05). Both age and place of residence did not positively correlate with knowledge level (p = 0.08 NS). In contrast, chronic diseases were found to have a significant effect on the amount of information held by the students surveyed (p < 0.05). (4) Conclusions: The level of knowledge of the surveyed students of the Silesia Province is unsatisfactory. The higher awareness among the students of medical universities results from the presence of issues related to microbiota and CRC in the medical educational content. Therefore, there is a need to consider the introduction of educational activities in the field of cancer prevention, including CRC, especially among non-medical university students.
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27
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Bayo Calero J, Castaño López MA, Casado Monge PG, Díaz Portillo J, Bejarano García A, Navarro Roldán F. Analysis of blood markers for early colorectal cancer diagnosis. J Gastrointest Oncol 2022; 13:2259-2268. [PMID: 36388660 PMCID: PMC9660082 DOI: 10.21037/jgo-21-747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/20/2022] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a very common tumor worldwide. Its mortality can be limited by early diagnosis through screening programs. These programs are based on fecal occult blood testing and colonoscopy. Our objective was to find a model based on the determination of blood biomarkers that was efficacious enough to become part of the early diagnosis of CRC. METHODS In a total of 221 patients who underwent a colonoscopy, two types of markers were identified (I) classic: carcinoembryonic antigen (CEA), CA19.9, α-fetoprotein, CA125, CA72.4, and ferritin; and (II) experimental: neutrophil gelatinase-associated lipocalin (NGAL), estimated glomerular filtration rate (EGFR), 8-hydroxydeoxyguanosine (8OHdG), calprotectin, and cysteine-rich 61 (Cyr61). We divided the patients into four groups according to colonoscopy results: a control group (n=83) with normal colonoscopy, a polyp group (n=56), a CRC group (n=45), and an inflammatory disease group (n=37). We built an algorithm based on multivariate logistic regression analysis. RESULTS A total of 51.6% were males, and the median age was 63 years. We designed an algorithm based on the combination of several markers that discriminated CRC patients from the rest of the patients with a performance of 94%, a sensitivity of 95.6%, and a specificity of 80.6%. Discriminating by sex also resulted in two powerful algorithms, although it performed better in males (97% vs. 91%). CONCLUSIONS Our study has devised a predictive model with high efficacy based on the determination of several biomarkers. We think that it could be incorporated into the set of methods used in CRC screening.
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Affiliation(s)
- Juan Bayo Calero
- Medical Oncology Service, Hospital “Juan Ramón Jiménez”, Huelva, Spain
| | | | | | | | | | - Francisco Navarro Roldán
- Department of Integrated Sciences, Cell Biology, Faculty of Experimental Sciences, University of Huelva, Huelva, Spain
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28
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Leng X, Yang J, Liu T, Zhao C, Cao Z, Li C, Sun J, Zheng S. A bioinformatics framework to identify the biomarkers and potential drugs for the treatment of colorectal cancer. Front Genet 2022; 13:1017539. [PMID: 36238159 PMCID: PMC9551025 DOI: 10.3389/fgene.2022.1017539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer (CRC), a common malignant tumor, is one of the main causes of death in cancer patients in the world. Therefore, it is critical to understand the molecular mechanism of CRC and identify its diagnostic and prognostic biomarkers. The purpose of this study is to reveal the genes involved in the development of CRC and to predict drug candidates that may help treat CRC through bioinformatics analyses. Two independent CRC gene expression datasets including The Cancer Genome Atlas (TCGA) database and GSE104836 were used in this study. Differentially expressed genes (DEGs) were analyzed separately on the two datasets, and intersected for further analyses. 249 drug candidates for CRC were identified according to the intersected DEGs and the Crowd Extracted Expression of Differential Signatures (CREEDS) database. In addition, hub genes were analyzed using Cytoscape according to the DEGs, and survival analysis results showed that one of the hub genes, TIMP1 was related to the prognosis of CRC patients. Thus, we further focused on drugs that could reverse the expression level of TIMP1. Eight potential drugs with documentary evidence and two new drugs that could reverse the expression of TIMP1 were found among the 249 drugs. In conclusion, we successfully identified potential biomarkers for CRC and achieved drug repurposing using bioinformatics methods. Further exploration is needed to understand the molecular mechanisms of these identified genes and drugs/small molecules in the occurrence, development and treatment of CRC.
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Urbiola-Salvador V, Miroszewska D, Jabłońska A, Qureshi T, Chen Z. Proteomics approaches to characterize the immune responses in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119266. [PMID: 35390423 DOI: 10.1016/j.bbamcr.2022.119266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/01/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Despite the dynamic development of cancer research, annually millions of people die of cancer. The human immune system is the major 'guard' against tumor development. Unfortunately, cancer cells have the ability to evade the immune system and continue to grow. The proper understanding of the intricate immune response in tumorigenesis remains the holy grail of cancer immunology and designing effective immunotherapy. To decode the immune responses in cancer, in recent years, proteomics studies have received considerable attention. Proteomics studies focus on the detection and quantification of proteins, which are the effectors of biological functions, and as such, are proven to reflect the cell state more accurately, in comparison to genomic or transcriptomic studies. In this review, we discuss the proteomics studies applied to characterize the immune responses in cancer and tumor immune microenvironment heterogeneity. Further, we describe emerging single-cell proteomics approaches that have the potential to be applied in cancer immunity studies.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Agnieszka Jabłońska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Talha Qureshi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
| | - Zhi Chen
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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Sattar RSA, Verma R, Nimisha, Kumar A, Dar GM, Apurva, Sharma AK, Kumari I, Ahmad E, Ali A, Mahajan B, Saluja SS. Diagnostic and prognostic biomarkers in colorectal cancer and the potential role of exosomes in drug delivery. Cell Signal 2022; 99:110413. [PMID: 35907519 DOI: 10.1016/j.cellsig.2022.110413] [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: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/03/2022]
Abstract
Colorectal cancer (CRC) is third most common cancer with second most common cause of death worldwide. One fourth to one fifth of the CRC cases are detected at advance stage. Early detection of colorectal cancer might help in decreasing mortality and morbidity worldwide. CRC being a heterogeneous disease, new non-invasive approaches are needed to complement and improve the screening and management of CRC. Reliable and early detectable biomarkers would improve diagnosis, prognosis, therapeutic responses, and will enable the prediction of drug response and recurrence risk. Over the past decades molecular research has demonstrated the potentials of CTCs, ctDNAs, circulating mRNA, ncRNAs, and exosomes as tumor biomarkers. Non-invasive screening approaches using fecal samples for identification of altered gut microbes in CRC is also gaining attention. Exosomes can be potential candidates that can be employed in the drug delivery system. Further, the integration of in vitro, in vivo and in silico models that involve CRC biomarkers will help to understand the interactions occurring at the cellular level. This review summarizes recent update on CRC biomarkers and their application along with the nanoparticles followed by the application of organoid culture in CRC.
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Affiliation(s)
- Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Renu Verma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ghulam Mehdi Dar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Indu Kumari
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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31
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Munro MJ, Wickremesekera SK, Tan ST, Peng L. Proteomic analysis of low- and high-grade human colon adenocarcinoma tissues and tissue-derived primary cell lines reveals unique biological functions of tumours and new protein biomarker candidates. Clin Proteomics 2022; 19:27. [PMID: 35842572 PMCID: PMC9287856 DOI: 10.1186/s12014-022-09364-y] [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: 03/04/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background Colon cancer is the third most common cancer and second highest cause of cancer deaths worldwide. The aim of the study was to find new biomarkers for diagnosis, prognosis and therapeutic drug targets for this disease. Methods Four low-grade and four high-grade human colon adenocarcinoma tumours with patient-matched normal colon tissues were analysed. Additionally, tissue-derived primary cell lines were established from each tumour tissue. The cell lines were validated using DNA sequencing to confirm that they are a suitable in vitro model for colon adenocarcinoma based on conserved gene mutations. Label-free quantitation proteomics was performed to compare the proteomes of colon adenocarcinoma samples to normal colon samples, and of colon adenocarcinoma tissues to tissue-derived cell lines to find significantly differentially abundant proteins. The functions enriched within the differentially expressed proteins were assessed using STRING. Proteomics data was validated by Western blotting. Results A total of 4767 proteins were identified across all tissues, and 4711 across primary tissue-derived cell lines. Of these, 3302 proteins were detected in both the tissues and the cell lines. On average, primary cell lines shared about 70% of proteins with their parent tissue, and they retained mutations to key colon adenocarcinoma-related genes and did not diverge far genetically from their parent tissues. Colon adenocarcinoma tissues displayed upregulation of RNA processing, steroid biosynthesis and detoxification, and downregulation of cytoskeletal organisation and loss of normal muscle function. Tissue-derived cell lines exhibited increased interferon-gamma signalling and aberrant ferroptosis. Overall, 318 proteins were significantly up-regulated and 362 proteins significantly down-regulated by comparisons of high-grade with low-grade tumours and low-grade tumour with normal colon tissues from both sample types. Conclusions The differences exhibited between tissues and cell lines highlight the additional information that can be obtained from patient-derived primary cell lines. DNA sequencing and proteomics confirmed that these cell lines can be considered suitable in vitro models of the parent tumours. Various potential biomarkers for colon adenocarcinoma initiation and progression and drug targets were identified and discussed, including seven novel markers: ACSL4, ANK2, AMER3, EXOSC1, EXOSC6, GCLM, and TFRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09364-y.
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Affiliation(s)
- Matthew J Munro
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.,Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand
| | - Susrutha K Wickremesekera
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand.,Upper Gastrointestinal, Hepatobiliary & Pancreatic Section, Department of General Surgery, Wellington Regional Hospital, Wellington, 6021, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand. .,Wellington Regional Plastic, Maxillofacial & Burns Unit, Hutt Hospital, Lower Hutt, 5040, New Zealand. .,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, 3050, Australia.
| | - Lifeng Peng
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.
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Li M, Guo D, Chen X, Lu X, Huang X, Wu Y. Transcriptome profiling and co-expression network analysis of lncRNAs and mRNAs in colorectal cancer by RNA sequencing. BMC Cancer 2022; 22:780. [PMID: 35842644 PMCID: PMC9288709 DOI: 10.1186/s12885-022-09878-6] [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: 01/02/2022] [Accepted: 06/27/2022] [Indexed: 12/24/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are widely involved in the pathogenesis of cancers. However, biological roles of lncRNAs in occurrence and progression of colorectal cancer (CRC) remain unclear. The current study aimed to evaluate the expression pattern of lncRNAs and messenger RNAs (mRNAs). Methods RNA sequencing (RNA-Seq) in CRC tissues and adjacent normal tissues from 6 CRC patients was performed and functional lncRNA-mRNA co-expression network was constructed afterwards. Gene enrichment analysis was demonstrated using DAVID 6.8 tool. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to validate the expression pattern of differentially expressed lncRNAs. Pearson correlation analysis was applied to evaluate the relationships between selected lncRNAs and mRNAs. Results One thousand seven hundred and sixteenth differentially expressed mRNAs and 311 differentially expressed lncRNAs were screened out. Among these, 568 mRNAs were up-regulated while 1148 mRNAs down-regulated, similarly 125 lncRNAs were up-regulated and 186 lncRNAs down-regulated. In addition, 1448 lncRNA–mRNA co-expression pairs were screened out from 940,905 candidate lncRNA-mRNA pairs. Gene enrichment analysis revealed that these lncRNA-related mRNAs are associated with cell adhesion, collagen adhesion, cell differentiation, and mainly enriched in ECM-receptor interaction and PI3K-Akt signaling pathways. Finally, RT-qPCR results verified the expression pattern of lncRNAs, as well as the relationships between lncRNAs and mRNAs in 60 pairs of CRC tissues. Conclusions In conclusion, these results of the RNA-seq and bioinformatic analysis strongly suggested that the dysregulation of lncRNA is involved in the complicated process of CRC development, and providing important insight regarding the lncRNAs involved in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09878-6.
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Affiliation(s)
- Mingjie Li
- Department of Clinical Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, China.,Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, 350001, China
| | - Dandan Guo
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, 350001, China
| | - Xijun Chen
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, 350001, China
| | - Xinxin Lu
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, 350001, China
| | - Xiaoli Huang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, 350001, China
| | - Yan'an Wu
- Department of Clinical Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, China. .,Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, 350001, China.
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Characterizing the Antitumor Effect of Coptis chinensis and Mume Fructus against Colorectal Cancer Based on Pharmacological Analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:9061752. [PMID: 35783510 PMCID: PMC9246580 DOI: 10.1155/2022/9061752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/14/2022] [Indexed: 11/24/2022]
Abstract
Colorectal cancer (CRC) is the third most diagnosed cancer worldwide and is a significant cause of cancer-related deaths. Previous studies have observed that Coptis chinensis (CC) and Mume Fructus (MF) are effective against CRC, enteritis, and intestinal dysbiosis, but the chemical and pharmacological mechanisms remain poorly understood. In this study, we employed pharmacological network analysis to reveal mechanisms underlying the therapeutic effect of CC and MF against CRC. All compounds and targeted genes were obtained from the traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP). Differentially expressed genes (DEGs) were identified based on GSE146587, GSE156720, and GSE184093 datasets. A protein-protein interaction (PPI) network was constructed to identify putative target genes of CC and MF. Ten key targeted genes were identified, including CCND1, ICAM1, IL1B, IL-6, MMP1, MMP3, MMP9, MYC, SERPINE1, and VEGFA. Among these genes, six (ICAM1, IL1B, IL-6, MMP1, MMP3, MMP9, and SERPINE1) were positively correlated with levels of effector memory CD4 T cells and natural killer T cells, and three (CCND1, MYC, and VEGFA) were negatively correlated with type 17 T helper cells and CD56dim natural killer cells. Molecular docking analysis showed that four compounds of CC and MF (kaempferol, oleanolic acid, quercetin, and ursolic acid) could affect CRC by interacting with target genes. Our study proved that pharmacological analysis could reliably assess the mechanism of traditional Chinese medicines for treating cancer.
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Bottom-Up Approach to the Discovery of Clinically Relevant Biomarker Genes: The Case of Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14112654. [PMID: 35681633 PMCID: PMC9179423 DOI: 10.3390/cancers14112654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 12/07/2022] Open
Abstract
Traditional approaches to genome-wide marker discovery often follow a common top-down strategy, where a large scale ‘omics’ investigation is followed by the analysis of functional pathways involved, to narrow down the list of identified putative biomarkers, and to deconvolute gene expression networks, or to obtain an insight into genetic alterations observed in cancer. We set out to investigate whether a reverse approach would allow full or partial reconstruction of the transcriptional programs and biological pathways specific to a given cancer and whether the full or substantially expanded list of putative markers could thus be identified by starting with the partial knowledge of a few disease-specific markers. To this end, we used 10 well-documented differentially expressed markers of colorectal cancer (CRC), analyzed their transcription factor networks and biological pathways, and predicted the existence of 193 new putative markers. Incredibly, the use of a validation marker set of 10 other completely different known CRC markers and the same procedure resulted in a very similar set of 143 predicted markers. Of these, 138 were identical to those found using the training set, confirming our main hypothesis that a much-expanded set of disease markers can be predicted by starting with just a small subset of validated markers. Further to this, we validated the expression of 42 out of 138 top-ranked predicted markers experimentally using qPCR in surgically removed CRC tissues. We showed that 41 out of 42 mRNAs tested have significantly altered levels of mRNA expression in surgically excised CRC tissues. Of the markers tested, 36 have been reported to be associated with aspects of CRC in the past, whilst only limited published evidence exists for another three genes (BCL2, PDGFRB and TSC2), and no published evidence directly linking genes to CRC was found for CCNA1, SHC1 and TGFB3. Whilst we used CRC to test and validate our marker discovery strategy, the reported procedures apply more generally to cancer marker discovery.
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Rajczewski AT, Han Q, Mehta S, Kumar P, Jagtap PD, Knutson CG, Fox JG, Tretyakova NY, Griffin TJ. Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow. Proteomes 2022; 10:proteomes10020011. [PMID: 35466239 PMCID: PMC9036229 DOI: 10.3390/proteomes10020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/27/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Chronic inflammation of the colon causes genomic and/or transcriptomic events, which can lead to expression of non-canonical protein sequences contributing to oncogenesis. To better understand these mechanisms, Rag2−/−Il10−/− mice were infected with Helicobacter hepaticus to induce chronic inflammation of the cecum and the colon. Transcriptomic data from harvested proximal colon samples were used to generate a customized FASTA database containing non-canonical protein sequences. Using a proteogenomic approach, mass spectrometry data for proximal colon proteins were searched against this custom FASTA database using the Galaxy for Proteomics (Galaxy-P) platform. In addition to the increased abundance in inflammatory response proteins, we also discovered several non-canonical peptide sequences derived from unique proteoforms. We confirmed the veracity of these novel sequences using an automated bioinformatics verification workflow with targeted MS-based assays for peptide validation. Our bioinformatics discovery workflow identified 235 putative non-canonical peptide sequences, of which 58 were verified with high confidence and 39 were validated in targeted proteomics assays. This study provides insights into challenges faced when identifying non-canonical peptides using a proteogenomics approach and demonstrates an integrated workflow addressing these challenges. Our bioinformatic discovery and verification workflow is publicly available and accessible via the Galaxy platform and should be valuable in non-canonical peptide identification using proteogenomics.
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Affiliation(s)
- Andrew T. Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
| | - Charles G. Knutson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.)
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.)
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, the Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (A.T.R.); (Q.H.); (S.M.); (P.K.); (P.D.J.)
- Correspondence:
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Wang J, Liu J, Wang J, Wang S, Li F, Li R, Liu P, Li M, Wang C. Identification of proteomic markers for prediction of the response to 5-Fluorouracil based neoadjuvant chemoradiotherapy in locally advanced rectal cancer patients. Cancer Cell Int 2022; 22:117. [PMID: 35292026 PMCID: PMC8922748 DOI: 10.1186/s12935-022-02530-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Neoadjuvant chemoradiotherapy (nCRT) prior to surgery is the standard treatment for patients with locally advanced rectal cancer (LARC), while parts of them show poor therapeutic response accompanied by therapy adverse effects. Predictive biomarkers for nCRT response could facilitate the guidance on treatment decisions but are still insufficient until now, which limits the clinical applications of nCRT in LARC patients. Methods In our study, 37 formalin-fixed paraffin-embedded tumor biopsies were obtained from patients with LARC before receiving 5-fluorouracil based nCRT. Proteomics analyses were conducted to identify the differentially expressed proteins (DEPs) between total responders (TR) and poor responders (PR). The DEPs were validated via ROC plotter web tool and their predictive performance was evaluated by receiver operating characteristic analysis. Functional enrichment analyses were performed to further explore the potential mechanisms underlying nCRT response. Results Among 3,998 total proteins, 91 DEPs between TR and PR were screened out. HSPA4, NIPSNAP1, and SPTB all with areas under the curve (AUC) ~ 0.8 in the internal discovery cohort were independently validated by the external mRNA datasets (AUC ~ 0.7), and their protein levels were linearly correlated with the graded responses to nCRT in the internal cohort. The combination of HSPA4 and SPTB could distinctly discriminate the TR and PR groups (AUC = 0.980, p < 0.0001). Moreover, multiple combinations of the three proteins realized increased specificity and/or sensitivity, while achieving favorable predictive value when moderate responders were introduced into the ROC analysis. Pathways including DNA damage repair, cell cycle, and epithelial mesenchymal transition were involved in nCRT response according to the enrichment analysis results. Conclusions HSPA4, SPTB and NIPSNAP1 in tumor biopsies and/or their optional combinations might be potential predictive markers for nCRT response in patients with LARC. The DEPs and their related functions have implications for the potential mechanisms of treatment response to nCRT in patients with LARC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02530-0.
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Affiliation(s)
- Jianan Wang
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China.,Medical School of Chinese PLA, Beijing, 100853, China
| | - Jiayu Liu
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jinyang Wang
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China.,School of Laboratory Medicine, Weifang Medical College, Weifang, 261053, Shandong, China
| | - Shijian Wang
- Nankai University School of Medicine, Nankai University, Tianjin, 300071, China
| | - Feifei Li
- Department of Pathology, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China
| | - Ruibing Li
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China
| | - Peng Liu
- Department of Pathology, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China
| | - Mianyang Li
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China.
| | - Chengbin Wang
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China.
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Luo L, Ma Y, Zheng Y, Su J, Huang G. Application Progress of Organoids in Colorectal Cancer. Front Cell Dev Biol 2022; 10:815067. [PMID: 35273961 PMCID: PMC8902504 DOI: 10.3389/fcell.2022.815067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
Currently, colorectal cancer is still the third leading cause of cancer-related mortality, and the incidence is rising. It is a long time since the researchers used cancer cell lines and animals as the study subject. However, these models possess various limitations to reflect the cancer progression in the human body. Organoids have more clinical significance than cell lines, and they also bridge the gap between animal models and humans. Patient-derived organoids are three-dimensional cultures that simulate the tumor characteristics in vivo and recapitulate tumor cell heterogeneity. Therefore, the emergence of colorectal cancer organoids provides an unprecedented opportunity for colorectal cancer research. It retains the molecular and cellular composition of the original tumor and has a high degree of homology and complexity with patient tissues. Patient-derived colorectal cancer organoids, as personalized tumor organoids, can more accurately simulate colorectal cancer patients’ occurrence, development, metastasis, and predict drug response in colorectal cancer patients. Colorectal cancer organoids show great potential for application, especially preclinical drug screening and prediction of patient response to selected treatment options. Here, we reviewed the application of colorectal cancer organoids in disease model construction, basic biological research, organoid biobank construction, drug screening and personalized medicine, drug development, drug toxicity and safety, and regenerative medicine. In addition, we also displayed the current limitations and challenges of organoids and discussed the future development direction of organoids in combination with other technologies. Finally, we summarized and analyzed the current clinical trial research of organoids, especially the clinical trials of colorectal cancer organoids. We hoped to lay a solid foundation for organoids used in colorectal cancer research.
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Affiliation(s)
- Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China.,The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Yucui Ma
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Yilin Zheng
- Clinical Research Center, Shantou Central Hospital, Shantou, China
| | - Jiating Su
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Guoxin Huang
- Clinical Research Center, Shantou Central Hospital, Shantou, China
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Advances in High Throughput Proteomics Profiling in Establishing Potential Biomarkers for Gastrointestinal Cancer. Cells 2022; 11:cells11060973. [PMID: 35326424 PMCID: PMC8946849 DOI: 10.3390/cells11060973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/24/2022] Open
Abstract
Gastrointestinal cancers (GICs) remain the most diagnosed cancers and accounted for the highest cancer-related death globally. The prognosis and treatment outcomes of many GICs are poor because most of the cases are diagnosed in advanced metastatic stages. This is primarily attributed to the deficiency of effective and reliable early diagnostic biomarkers. The existing biomarkers for GICs diagnosis exhibited inadequate specificity and sensitivity. To improve the early diagnosis of GICs, biomarkers with higher specificity and sensitivity are warranted. Proteomics study and its functional analysis focus on elucidating physiological and biological functions of unknown or annotated proteins and deciphering cellular mechanisms at molecular levels. In addition, quantitative analysis of translational proteomics is a promising approach in enhancing the early identification and proper management of GICs. In this review, we focus on the advances in mass spectrometry along with the quantitative and functional analysis of proteomics data that contributes to the establishment of biomarkers for GICs including, colorectal, gastric, hepatocellular, pancreatic, and esophageal cancer. We also discuss the future challenges in the validation of proteomics-based biomarkers for their translation into clinics.
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Expression of Spermine Oxidase Is Associated with Colorectal Carcinogenesis and Prognosis of Patients. Biomedicines 2022; 10:biomedicines10030626. [PMID: 35327428 PMCID: PMC8944969 DOI: 10.3390/biomedicines10030626] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/25/2022] [Accepted: 03/06/2022] [Indexed: 12/11/2022] Open
Abstract
Uncovering tumor markers of colorectal cancer is important for the early detection and prognosis of the patients. Spermine oxidase (SMOX) is upregulated in various cancers. The present study aims to explore the biologic function and expression patterns of SMOX in colorectal cancer (CRC), the third most common type of cancer worldwide. We used quantitative real-time PCR, Western blot, and in vitro functional studies in four CRC cell lines knocked down by SMOX siRNA and immunohistochemistry in 350 cases of CRC tissues. The results showed that SMOX was overexpressed in CRC cell lines and clinical samples. SMOX overexpression in tumor tissues was an independent prognostic factor, worsening overall survival (p = 0.001). The knock-down of SMOX inhibited CRC cell proliferation, invasion, and soft agar colony formation, uncovering its carcinogenic functions. This study indicated that SMOX overexpression could be an important oncogene in CRC and might serve as a valuable prognostic marker and potential therapeutic target for CRC.
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Kaufmann Y, Byrum SD, Acott AA, Siegel ER, Washam CL, Mancino AT. Proteomic profiling of tear fluid as a promising non-invasive screening test for colon cancer. Am J Surg 2022; 224:19-24. [DOI: 10.1016/j.amjsurg.2022.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 11/19/2021] [Accepted: 03/22/2022] [Indexed: 01/03/2023]
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de Assis JV, Coutinho LA, Oyeyemi IT, Oyeyemi OT, Grenfell RFEQ. Diagnostic and therapeutic biomarkers in colorectal cancer: a review. Am J Cancer Res 2022; 12:661-680. [PMID: 35261794 PMCID: PMC8900002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023] Open
Abstract
Colorectal cancer (CRC) is a public health concern and the second most common type of cancer among men and women causing a significant mortality. Biomarkers closely linked to the disease morbidity could holds potential as diagnostic and/or prognostic biomarker for the disease. This review provides an overview of recent advances in the search for colorectal cancer biomarkers through genomics and proteomics according to clinical function and application. Specifically, a number of biomarkers were identified and discussed. Emphasis was placed on their clinical applications relative to the diagnosis and prognosis of CRC. The discovery of more sensitive and specific markers for CRC is an urgent need, and the study of molecular targets is extremely important in this process, as they will allow for a better understanding of colorectal carcinogenesis, identification and validation of potential genetic signatures.
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Affiliation(s)
- Jéssica Vieira de Assis
- Diagnosis and Therapy of Infectious Diseases and Cancer, René Rachou Institute, Oswaldo Cruz Foundation (Fiocruz)Belo Horizonte, Minas Gerais, Brazil
| | - Lucélia Antunes Coutinho
- Diagnosis and Therapy of Infectious Diseases and Cancer, René Rachou Institute, Oswaldo Cruz Foundation (Fiocruz)Belo Horizonte, Minas Gerais, Brazil
| | | | - Oyetunde Timothy Oyeyemi
- Diagnosis and Therapy of Infectious Diseases and Cancer, René Rachou Institute, Oswaldo Cruz Foundation (Fiocruz)Belo Horizonte, Minas Gerais, Brazil
- Department of Biological Sciences, University of Medical SciencesOndo, Ondo State, Nigeria
| | - Rafaella Fortini e Queiroz Grenfell
- Diagnosis and Therapy of Infectious Diseases and Cancer, René Rachou Institute, Oswaldo Cruz Foundation (Fiocruz)Belo Horizonte, Minas Gerais, Brazil
- Department of Infectious Diseases, College of Veterinary Medicine, University of GeorgiaAthens, Georgia, United States of America
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Sun Y, Lin Y, Deng Y, Wu X, Zhong J, Huang Y, Jiang W, Chi P. Identification of proteins associated with treatment response of neoadjuvant chemoradiotherapy in rectal mucinous adenocarcinoma by co-expression network analysis based on proteomic analysis. J Proteomics 2022; 254:104472. [PMID: 34990823 DOI: 10.1016/j.jprot.2021.104472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/17/2021] [Accepted: 12/29/2021] [Indexed: 11/19/2022]
Abstract
For rectal mucinous adenocarcinoma (MAC), identifying biomarkers of neoadjuvant chemoradiotherapy (NCRT) response has become imperative. This study applied label-free mass spectrometry and weighted gene co-expression network analysis to identify hub proteins in association with the NCRT response in 20 rectal MAC patients. We identified 131 differentially abundant proteins and 7 candidate proteins associated with the NCRT response. The immunostaining expressions of six proteins (ENOA, ILEU, MDHM, RM11, PTGDS, and RL3) were significantly associated with the NCRT response. Logistic regression analysis revealed that ENOA (OR = 6.275, P = 0.006) was independent risk hub protein for the NCRT response. Tow hub proteins (ENOA and PTGDS) were identified as significant risk factors by Cox regression analysis. A prognostic risk score system was constructed: risk score = (0.910 × EXPENOA) + (-1.519 × EXPPTGDS), and found to be an independent predictor of DFS in rectal MAC patients (HR = 10.308, P < 0.001). Our study suggested that ENOA may be a novel biomarker for the NCRT response and prognosis in rectal MAC patients. A two-hub-protein-based risk score system might be used for predicting tumor recurrence in rectal MAC patients. SIGNIFICANCE: NCRT resistance is a major problem in the treatment of rectal MAC patients. Identifying robust predictive biomarkers for NCRT resistance is beneficial to the stratified treatment of rectal MAC patients. In this study, label-free mass spectrometry and weighted gene co-expression network analysis identified ENOA as a potential novel biomarker for the NCRT response and prognosis. ENOA may be involved in the process of the NCRT resistance and tumor recurrence through the carbon metabolism pathway.
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Affiliation(s)
- Yanwu Sun
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Minimal Invasive Center, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Fujian Medical University, Fuzhou, Fujian, PR China
| | - Yu Lin
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Minimal Invasive Center, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Fujian Medical University, Fuzhou, Fujian, PR China
| | - Yu Deng
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Fujian Medical University, Fuzhou, Fujian, PR China
| | - Xuejing Wu
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China
| | | | - Ying Huang
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Minimal Invasive Center, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Fujian Medical University, Fuzhou, Fujian, PR China
| | - Weizhong Jiang
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Minimal Invasive Center, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Fujian Medical University, Fuzhou, Fujian, PR China.
| | - Pan Chi
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Minimal Invasive Center, Fujian Medical University Union Hospital, Fuzhou, Fujian, PR China; Fujian Medical University, Fuzhou, Fujian, PR China.
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Huang Z, Yang M. Molecular Network of Colorectal Cancer and Current Therapeutic Options. Front Oncol 2022; 12:852927. [PMID: 35463300 PMCID: PMC9018988 DOI: 10.3389/fonc.2022.852927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC), a leading cause of cancer-related mortalities globally, results from the accumulation of multiple genetic and epigenetic alterations in the normal colonic and rectum epithelium, leading to the progression from colorectal adenomas to invasive carcinomas. Almost half of CRC patients will develop metastases in the course of the disease and most patients with metastatic CRC are incurable. Particularly, the 5-year survival rate of patients with stage 4 CRC at diagnosis is less than 10%. Although genetic understanding of these CRC tumors and paired metastases has led to major advances in elucidating early driver genes responsible for carcinogenesis and metastasis, the pathophysiological contribution of transcriptional and epigenetic aberrations in this malignancy which influence many central signaling pathways have attracted attention recently. Therefore, treatments that could affect several different molecular pathways may have pivotal implications for their efficacy. In this review, we summarize our current knowledge on the molecular network of CRC, including cellular signaling pathways, CRC microenvironment modulation, epigenetic changes, and CRC biomarkers for diagnosis and predictive/prognostic use. We also provide an overview of opportunities for the treatment and prevention strategies in this field.
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Affiliation(s)
- Zhe Huang
- The Department of 11 General Surgery, Minimally Invasive Colorectal Hernia Unit, Shengjing Hospital of China Medical University, Shenyang, China
| | - Mingli Yang
- The Department of 3Oncology, Gastrointestinal Cancer Unit, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Mingli Yang,
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Cruz A, Carvalho CM, Cunha A, Crespo A, Iglesias Á, García-Nimo L, Freitas PP, Cubiella J. Faecal Diagnostic Biomarkers for Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13215568. [PMID: 34771730 PMCID: PMC8582677 DOI: 10.3390/cancers13215568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is a significant public health problem, being a major cause of cancer death worldwide. Hence, the identification of biomarkers able to support CRC detection is crucial. This work analyses a panel of six biomarkers, namely interleukin-6 (IL-6), tumour necrosis factor-alpha (TNF-α), matrix metalloproteinase (MMP)-2, MMP-9, haemoglobin (Hb) and M2-pyruvate kinase (M2-PK), in stool samples from patients with CRC, advanced adenomas, other lesions and healthy individuals. Our results indicate that the levels of Hb and M2-PK were increased in CRC patients in comparison to the controls. Moreover, the combination of these biomarkers increased the specificity or sensitivity for CRC detection and thus present potential for diagnosis of CRC. Abstract Background: Colorectal cancer (CRC) is a major cause of cancer-related death worldwide. Cancer progression, including invasion and metastasis, is a major cause of death among CRC patients. Current methods for CRC screening commonly consist of a combination of faecal immunochemical test (FIT) for stool occult blood detection and invasive procedures such as colonoscopy. Considering the slow progression of CRC, and that symptoms usually emerge at advanced stages, its early diagnostic can limit cancer’s spread and provide a successful treatment. Biomarkers have a high potential for the diagnosis of CRC in either blood or stool samples. Methods: In this study, we analysed the diagnostic value of six different biomarkers in stool samples of patients with CRC, advanced adenomas, other lesions and healthy individuals. We have also assessed the overall performance of the combination of these biomarkers for CRC detection. Results: The results indicate that haemoglobin (Hb) and M2-pyruvate kinase (M2-PK) levels were increased in CRC patients in comparison to the controls. Conversely, the concentrations of matrix metalloproteinase (MMP)-2, MMP-9, and tumour necrosis factor-alpha (TNF-α) were not significantly different between the tested groups. Conclusion: The combination of FIT-Hb with the M2-PK levels increased the specificity or sensitivity for CRC detection and thus present potential as faecal diagnostic biomarkers for CRC.
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Affiliation(s)
- Andrea Cruz
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal; (A.C.); (P.P.F.)
- Correspondence: (A.C.); (C.M.C.)
| | - Carla M. Carvalho
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal; (A.C.); (P.P.F.)
- Correspondence: (A.C.); (C.M.C.)
| | - Alexandra Cunha
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal; (A.C.); (P.P.F.)
| | - Anais Crespo
- Servicio de Aparato Digestivo, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, CIBEREHD, 32005 Ourense, Spain; (A.C.); (Á.I.); (J.C.)
| | - Águeda Iglesias
- Servicio de Aparato Digestivo, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, CIBEREHD, 32005 Ourense, Spain; (A.C.); (Á.I.); (J.C.)
| | - Laura García-Nimo
- Servicio de Análisis Clínicos, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, 32005 Ourense, Spain;
| | - Paulo P. Freitas
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal; (A.C.); (P.P.F.)
| | - Joaquín Cubiella
- Servicio de Aparato Digestivo, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, CIBEREHD, 32005 Ourense, Spain; (A.C.); (Á.I.); (J.C.)
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Louie AD, Huntington K, Carlsen L, Zhou L, El-Deiry WS. Integrating Molecular Biomarker Inputs Into Development and Use of Clinical Cancer Therapeutics. Front Pharmacol 2021; 12:747194. [PMID: 34737704 PMCID: PMC8560682 DOI: 10.3389/fphar.2021.747194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
Biomarkers can contribute to clinical cancer therapeutics at multiple points along the patient’s diagnostic and treatment course. Diagnostic biomarkers can screen or classify patients, while prognostic biomarkers predict their survival. Biomarkers can also predict treatment efficacy or toxicity and are increasingly important in development of novel cancer therapeutics. Strategies for biomarker identification have involved large-scale genomic and proteomic analyses. Pathway-specific biomarkers are already in use to assess the potential efficacy of immunotherapy and targeted cancer therapies. Judicious application of machine learning techniques can identify disease-relevant features from large data sets and improve predictive models. The future of biomarkers likely involves increasing utilization of liquid biopsy and multiple samplings to better understand tumor heterogeneity and identify drug resistance.
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Affiliation(s)
- Anna D Louie
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Department of Surgery, Lifespan Health System and Brown University, Providence, RI, United States
| | - Kelsey Huntington
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Pathobiology Graduate Program, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Lindsey Carlsen
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Pathobiology Graduate Program, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Lanlan Zhou
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI, United States.,Cancer Center at Brown University, Providence, RI, United States
| | - Wafik S El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Pathobiology Graduate Program, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States.,Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI, United States.,Cancer Center at Brown University, Providence, RI, United States.,Hematology/Oncology Division, Department of Medicine, Lifespan Health System and Brown University, Providence, RI, United States
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Mostafa AM, Barton SJ, Wren SP, Barker J. Review on molecularly imprinted polymers with a focus on their application to the analysis of protein biomarkers. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Core Circadian Clock Proteins as Biomarkers of Progression in Colorectal Cancer. Biomedicines 2021; 9:biomedicines9080967. [PMID: 34440171 PMCID: PMC8391187 DOI: 10.3390/biomedicines9080967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/31/2021] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common tumours in developed countries. Although its incidence and mortality rates have decreased, its prognosis has not changed, and a high percentage of patients with CRC develop relapse (metachronous metastasis, MM, or local recurrence, LR) during their disease. The identification of these patients is very important for their correct management, but the lack of prognostic markers makes it difficult. Given the connection between circadian disruption and cancer development and progression, we aimed to analyse the prognostic significance of core circadian proteins in CRC. We measured the expression of PER1-3, CRY1-2, BMAL1 and NR1D2 in a cohort of CRC patients by immunohistochemistry (IHC) and analysed their prognostic potential in this disease. A low expression of PER2 and BMAL1 was significantly associated with metastasis at the moment of disease diagnosis, whereas a high expression of CRY1 appeared as an independent prognostic factor of MM development. A high expression of NR1D2 appeared as an independent prognostic factor of LR development after disease diagnosis. Moreover, patients with a low expression of BMAL1 and a high expression of CRY1 showed lower OS and DFS at five years. Although these markers need to be validated in larger and different ethnic cohorts, the simplicity of IHC makes these proteins candidates for personalizing CRC treatment.
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Soluble SIGLEC5: A New Prognosis Marker in Colorectal Cancer Patients. Cancers (Basel) 2021; 13:cancers13153896. [PMID: 34359797 PMCID: PMC8345516 DOI: 10.3390/cancers13153896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Amongst colorectal cancers, there is significant heterogeneity, which hinders the search for a single disease detection approach. Clinical prognostic markers are urgently needed. The aim of our prospective study was to analyse the possible role of pre-operative soluble SIGLEC5 plasma levels in patient prognosis and evolution. In a cohort of 114 patients with colorectal cancer, our data confirmed the relevance of soluble SIGLEC5 levels as a prognosis marker and exitus predictor. Altogether, our data indicate that levels of this protein could be a novel and promising biomarker for patients with colorectal cancer. Abstract Colorectal cancer (CRC) is the second most deadly and third most commonly diagnosed cancer worldwide. There is significant heterogeneity among patients with CRC, which hinders the search for a standard approach for the detection of this disease. Therefore, the identification of robust prognostic markers for patients with CRC represents an urgent clinical need. In search of such biomarkers, a total of 114 patients with colorectal cancer and 67 healthy participants were studied. Soluble SIGLEC5 (sSIGLEC5) levels were higher in plasma from patients with CRC compared with healthy volunteers. Additionally, sSIGLEC5 levels were higher in exitus than in survivors, and the receiver operating characteristic curve analysis revealed sSIGLEC5 to be an exitus predictor (area under the curve 0.853; cut-off > 412.6 ng/mL) in these patients. A Kaplan–Meier analysis showed that patients with high levels of sSIGLEC5 had significantly shorter overall survival (hazard ratio 15.68; 95% CI 4.571–53.81; p ≤ 0.0001) than those with lower sSIGLEC5 levels. Our study suggests that sSIGLEC5 is a soluble prognosis marker and exitus predictor in CRC.
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Beklen H, Yildirim E, Kori M, Turanli B, Arga KY. Systems-level biomarkers identification and drug repositioning in colorectal cancer. World J Gastrointest Oncol 2021. [DOI: 10.4251/wjgo.v13.i7.463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Beklen H, Yildirim E, Kori M, Turanli B, Arga KY. Systems-level biomarkers identification and drug repositioning in colorectal cancer. World J Gastrointest Oncol 2021; 13:638-661. [PMID: 34322194 PMCID: PMC8299930 DOI: 10.4251/wjgo.v13.i7.638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the most commonly diagnosed fatal cancer in both women and men worldwide. CRC ranked second in mortality and third in incidence in 2020. It is difficult to diagnose CRC at an early stage as there are no clinical symptoms. Despite advances in molecular biology, only a limited number of biomarkers have been translated into routine clinical practice to predict risk, prognosis and response to treatment. In the last decades, systems biology approaches at the omics level have gained importance. Over the years, several biomarkers for CRC have been discovered in terms of disease diagnosis and prognosis. On the other hand, a few drugs are being developed and used in clinics for the treatment of CRC. However, the development of new drugs is very costly and time-consuming as the research and development takes about 10 years and more than $1 billion. Therefore, drug repositioning (DR) could save time and money by establishing new indications for existing drugs. In this review, we aim to provide an overview of biomarkers for the diagnosis and prognosis of CRC from the systems biology perspective and insights into DR approaches for the prevention or treatment of CRC.
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Affiliation(s)
- Hande Beklen
- Department of Bioengineering, Marmara University, Istanbul 34722, Turkey
| | - Esra Yildirim
- Department of Bioengineering, Marmara University, Istanbul 34722, Turkey
| | - Medi Kori
- Department of Bioengineering, Marmara University, Istanbul 34722, Turkey
| | - Beste Turanli
- Department of Bioengineering, Marmara University, Istanbul 34722, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Istanbul 34722, Turkey
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