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Xie L, Kong Q, Ai M, He A, Yao B, Zhang L, Zhang K, Zhu C, Li Y, Xia L, Tian R, Xu R. Spatial Proteomic Profiling of Colorectal Cancer Revealed Its Tumor Microenvironment Heterogeneity. J Proteome Res 2024; 23:3342-3352. [PMID: 39026393 DOI: 10.1021/acs.jproteome.3c00719] [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] [Indexed: 07/20/2024]
Abstract
Colorectal cancer is a predominant malignancy with a second mortality worldwide. Despite its prevalence, therapeutic options remain constrained and surgical operation is still the most useful therapy. In this regard, a comprehensive spatially resolved quantitative proteome atlas was constructed to explore the functional proteomic landscape of colorectal cancer. This strategy integrates histopathological analysis, laser capture microdissection, and proteomics. Spatial proteome profiling of 200 tissue section samples facilitated by the fully integrated sample preparation technology SISPROT enabled the identification of more than 4000 proteins on the Orbitrap Exploris 240 from 2 mm2 × 10 μm tissue sections. Compared with normal adjacent tissues, we identified a spectrum of cancer-associated proteins and dysregulated pathways across various regions of colorectal cancer including ascending colon, transverse colon, descending colon, sigmoid colon, and rectum. Additionally, we conducted proteomic analysis on tumoral epithelial cells and paracancerous epithelium from early to advanced stages in hallmark rectum cancer and sigmoid colon cancer. Bioinformatics analysis revealed functional proteins and cell-type signatures associated with different regions of colorectal tumors, suggesting potential clinical implications. Overall, this study provides a comprehensive spatially resolved functional proteome landscape of colorectal cancer, serving as a valuable resource for exploring potential biomarkers and therapeutic targets.
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Affiliation(s)
- Lifen Xie
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), 1017 Dongmen North Road, Shenzhen 518020, China
- The First Affiliated Hospital, Jinan University, 613 Huangpu Avenue West Road, Guangzhou 510632, China
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Qian Kong
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Meiling Ai
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), 1017 Dongmen North Road, Shenzhen 518020, China
- The First Affiliated Hospital, Jinan University, 613 Huangpu Avenue West Road, Guangzhou 510632, China
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - An He
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Bin Yao
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Luobin Zhang
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), 1017 Dongmen North Road, Shenzhen 518020, China
| | - Keren Zhang
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Chaowei Zhu
- Department of Gastrointestinal Surgery, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), 1017 Dongmen North Road, Shenzhen 518020, China
| | - Yangqiu Li
- Department of Hematology, First Affiliated Hospital, Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, 613 Huangpu Avenue West Road, Guangzhou 510632, China
| | - Ligang Xia
- Department of Gastrointestinal Surgery, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), 1017 Dongmen North Road, Shenzhen 518020, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Ruilian Xu
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), 1017 Dongmen North Road, Shenzhen 518020, China
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2
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Tan YC, Low TY, Lee PY, Lim LC. Single-cell proteomics by mass spectrometry: Advances and implications in cancer research. Proteomics 2024; 24:e2300210. [PMID: 38727198 DOI: 10.1002/pmic.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 02/22/2024] [Accepted: 04/29/2024] [Indexed: 06/16/2024]
Abstract
Cancer harbours extensive proteomic heterogeneity. Inspired by the prior success of single-cell RNA sequencing (scRNA-seq) in characterizing minute transcriptomics heterogeneity in cancer, researchers are now actively searching for information regarding the proteomics counterpart. Therefore recently, single-cell proteomics by mass spectrometry (SCP) has rapidly developed into state-of-the-art technology to cater the need. This review aims to summarize application of SCP in cancer research, while revealing current development progress of SCP technology. The review also aims to contribute ideas into research gaps and future directions, ultimately promoting the application of SCP in cancer research.
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Affiliation(s)
- Yong Chiang Tan
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Lay Cheng Lim
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
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3
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López-Cortés R, Muinelo-Romay L, Fernández-Briera A, Gil Martín E. High-Throughput Mass Spectrometry Analysis of N-Glycans and Protein Markers after FUT8 Knockdown in the Syngeneic SW480/SW620 Colorectal Cancer Cell Model. J Proteome Res 2024; 23:1379-1398. [PMID: 38507902 PMCID: PMC11002942 DOI: 10.1021/acs.jproteome.3c00833] [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: 12/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Disruption of the glycosylation machinery is a common feature in many types of cancer, and colorectal cancer (CRC) is no exception. Core fucosylation is mediated by the enzyme fucosyltransferase 8 (FucT-8), which catalyzes the addition of α1,6-l-fucose to the innermost GlcNAc residue of N-glycans. We and others have documented the involvement of FucT-8 and core-fucosylated proteins in CRC progression, in which we addressed core fucosylation in the syngeneic CRC model formed by SW480 and SW620 tumor cell lines from the perspective of alterations in their N-glycosylation profile and protein expression as an effect of the knockdown of the FUT8 gene that encodes FucT-8. Using label-free, semiquantitative mass spectrometry (MS) analysis, we found noticeable differences in N-glycosylation patterns in FUT8-knockdown cells, affecting core fucosylation and sialylation, the Hex/HexNAc ratio, and antennarity. Furthermore, stable isotopic labeling of amino acids in cell culture (SILAC)-based proteomic screening detected the alteration of species involved in protein folding, endoplasmic reticulum (ER) and Golgi post-translational stabilization, epithelial polarity, and cellular response to damage and therapy. This data is available via ProteomeXchange with identifier PXD050012. Overall, the results obtained merit further investigation to validate their feasibility as biomarkers of progression and malignization in CRC, as well as their potential usefulness in clinical practice.
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Affiliation(s)
- Rubén López-Cortés
- Doctoral
Program in Methods and Applications in Life Sciences, Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Laura Muinelo-Romay
- Liquid
Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela
(IDIS), CIBERONC, Travesía da Choupana, 15706 Santiago de Compostela, A Coruña
(Galicia), Spain
| | - Almudena Fernández-Briera
- Molecular
Biomarkers, Biomedical Research Centre (CINBIO), Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Emilio Gil Martín
- Nutrition
and Food Science Group, Department of Biochemistry, Genetics and Immunology,
Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
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4
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El-Sheikh NM, Abulsoud AI, Fawzy A, Wasfey EF, Hamdy NM. LncRNA NNT-AS1/hsa-miR-485-5p/HSP90 axis in-silico and clinical prospect correlated-to histologic grades-based CRC stratification: A step toward ncRNA Precision. Pathol Res Pract 2023; 247:154570. [PMID: 37244051 DOI: 10.1016/j.prp.2023.154570] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
The oncogenic effects of long non-coding RNA (lncRNA) Nicotinamide Nucleotide Transhydrogenase-antisense RNA1 (NNT-AS1) role in colorectal cancer (CRC) hasn't been sufficiently inspected in relation to the Homo sapiens (hsa)-microRNA (miR)- 485-5p/ heat shock protein 90 (HSP90) axis, clinically. qRT-PCR was performed to detect lncRNA NNT-AS1 and hsa-miR-485-5p expression levels in 60 Egyptian patients' sera. HSP90 serum level was quantified using Enzyme-linked immunosorbent assay (ELISA). The relative expression level of the studied non-coding RNAs as well as the HSP90 ELISA concentration were correlated with patients clinicopathological characteristics and correlated to each other. The axis diagnostic utility in comparison with carbohydrate antigen 19-9 (CA19-9) and carcinoembryonic antigen (CEA) tumor markers (TMs) was studied by receiver operating characteristic (ROC) curve analysis. The relative lncRNA NNT-AS1 expression level fold change 56.7 (13.5-112) and HSP90 protein ELISA level 6.68 (5.14-8.77) (ng/mL) were elevated, while, for hsa-miR-485-5p 0.0474 (0.0236-0.135) expression fold change was repressed in CRC Egyptian patients' cohort sera, being compared to 28 apparently healthy control subjects. LncRNA NNT-AS1 specificity is 96.4% and a sensitivity of 91.7%, hsa-miR-485-5p showed 96.4% specificity, 90% sensitivity, and for HSP90 89.3%, 70% specificity and sensitivity, respectively. Those specificities and sensitivities were superior to the classical CRC TMs. A significant negative correlation was found between hsa-miR-485-5p with lncRNA NNT-AS1 (r = -0.933) expression fold change or with HSP90 protein blood level (r = -0.997), but, significant positive correlation was there between lncRNA NNT-AS1 and HSP90 (r = 0.927). LncRNA NNT-AS1/hsa-miR-485-5p/HSP90 axis could be a prospect for CRC development as well as diagnosis. Being correlated and related to CRC histologic grades 1-3, therefore, lncRNA NNT-AS1/hsa-miR-485-5p/HSP90 axis (not individually) expression approved clinically and in silico, could aid treatment precision.
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Affiliation(s)
- Nada M El-Sheikh
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, 11785 Cairo, Egypt
| | - Ahmed I Abulsoud
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, 11785 Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy (Boy's Branch), Al-Azhar University, Nasr City, 11884 Cairo, Egypt
| | - Amal Fawzy
- Department of Clinical and Chemical Pathology, National Cancer Institute, Cairo University, 11796 Cairo, Egypt
| | - Eman F Wasfey
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, 11566 Cairo, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, 11566 Cairo, Egypt.
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5
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From the Catastrophic Objective Irreproducibility of Cancer Research and Unavoidable Failures of Molecular Targeted Therapies to the Sparkling Hope of Supramolecular Targeted Strategies. Int J Mol Sci 2023; 24:ijms24032796. [PMID: 36769134 PMCID: PMC9917659 DOI: 10.3390/ijms24032796] [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: 11/30/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The unprecedented non-reproducibility of the results published in the field of cancer research has recently come under the spotlight. In this short review, we try to highlight some general principles in the organization and evolution of cancerous tumors, which objectively lead to their enormous variability and, consequently, the irreproducibility of the results of their investigation. This heterogeneity is also extremely unfavorable for the effective use of molecularly targeted medicine. Against the seemingly comprehensive background of this heterogeneity, we single out two supramolecular characteristics common to all tumors: the clustered nature of tumor interactions with their microenvironment and the formation of biomolecular condensates with tumor-specific distinctive features. We suggest that these features can form the basis of strategies for tumor-specific supramolecular targeted therapies.
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6
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Heck KA, Lindholm HT, Niederdorfer B, Tsirvouli E, Kuiper M, Flobak Å, Lægreid A, Thommesen L. Characterisation of Colorectal Cancer Cell Lines through Proteomic Profiling of Their Extracellular Vesicles. Proteomes 2023; 11:proteomes11010003. [PMID: 36648961 PMCID: PMC9844407 DOI: 10.3390/proteomes11010003] [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: 10/24/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers, driven by several factors including deregulations in intracellular signalling pathways. Small extracellular vesicles (sEVs) are nanosized protein-packaged particles released from cells, which are present in liquid biopsies. Here, we characterised the proteome landscape of sEVs and their cells of origin in three CRC cell lines HCT116, HT29 and SW620 to explore molecular traits that could be exploited as cancer biomarker candidates and how intracellular signalling can be assessed by sEV analysis instead of directly obtaining the cell of origin itself. Our findings revealed that sEV cargo clearly reflects its cell of origin with proteins of the PI3K-AKT pathway highly represented in sEVs. Proteins known to be involved in CRC were detected in both cells and sEVs including KRAS, ARAF, mTOR, PDPK1 and MAPK1, while TGFB1 and TGFBR2, known to be key players in epithelial cancer carcinogenesis, were found to be enriched in sEVs. Furthermore, the phosphopeptide-enriched profiling of cell lysates demonstrated a distinct pattern between cell lines and highlighted potential phosphoproteomic targets to be investigated in sEVs. The total proteomic and phosphoproteomics profiles described in the current work can serve as a source to identify candidates for cancer biomarkers that can potentially be assessed from liquid biopsies.
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Affiliation(s)
- Kathleen A. Heck
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Håvard T. Lindholm
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Barbara Niederdorfer
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eirini Tsirvouli
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Åsmund Flobak
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- The Cancer Clinic, St. Olav’s University Hospital, 7030 Trondheim, Norway
| | - Astrid Lægreid
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Liv Thommesen
- Department of Biomedical Laboratory Science, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Correspondence:
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7
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Song H, Ruan C, Xu Y, Xu T, Fan R, Jiang T, Cao M, Song J. Survival stratification for colorectal cancer via multi-omics integration using an autoencoder-based model. Exp Biol Med (Maywood) 2021; 247:898-909. [PMID: 34904882 DOI: 10.1177/15353702211065010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Prognosis stratification in colorectal cancer helps to address cancer heterogeneity and contributes to the improvement of tailored treatments for colorectal cancer patients. In this study, an autoencoder-based model was implemented to predict the prognosis of colorectal cancer via the integration of multi-omics data. DNA methylation, RNA-seq, and miRNA-seq data from The Cancer Genome Atlas (TCGA) database were integrated as input for the autoencoder, and 175 transformed features were produced. The survival-related features were used to cluster the samples using k-means clustering. The autoencoder-based strategy was compared to the principal component analysis (PCA)-, t-distributed random neighbor embedded (t-SNE)-, non-negative matrix factorization (NMF)-, or individual Cox proportional hazards (Cox-PH)-based strategies. Using the 175 transformed features, tumor samples were clustered into two groups (G1 and G2) with significantly different survival rates. The autoencoder-based strategy performed better at identifying survival-related features than the other transformation strategies. Further, the two survival groups were robustly validated using "hold-out" validation and five validation cohorts. Gene expression profiles, miRNA profiles, DNA methylation, and signaling pathway profiles varied from the poor prognosis group (G2) to the good prognosis group (G1). miRNA-mRNA networks were constructed using six differentially expressed miRNAs (let-7c, mir-34c, mir-133b, let-7e, mir-144, and mir-106a) and 19 predicted target genes. The autoencoder-based computational framework could distinguish good prognosis samples from bad prognosis samples and facilitate a better understanding of the molecular biology of colorectal cancer.
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Affiliation(s)
- Hu Song
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Chengwei Ruan
- Department of Anorectal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Yixin Xu
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Teng Xu
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Ruizhi Fan
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Tao Jiang
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Meng Cao
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Jun Song
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
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8
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Jung Y, Son M, Nam YR, Choi J, Heath JR, Yang S. Microfluidic Single-Cell Proteomics Assay Chip: Lung Cancer Cell Line Case Study. MICROMACHINES 2021; 12:mi12101147. [PMID: 34683198 PMCID: PMC8541572 DOI: 10.3390/mi12101147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/22/2022]
Abstract
Cancer is a dynamic disease involving constant changes. With these changes, cancer cells become heterogeneous, resulting in varying sensitivity to chemotherapy. The heterogeneity of cancer cells plays a key role in chemotherapy resistance and cancer recurrence. Therefore, for effective treatment, cancer cells need to be analyzed at the single-cell level by monitoring various proteins and investigating their heterogeneity. We propose a microfluidic chip for a single-cell proteomics assay that is capable of analyzing complex cellular signaling systems to reveal the heterogeneity of cancer cells. The single-cell assay chip comprises (i) microchambers (n = 1376) for manipulating single cancer cells, (ii) micropumps for rapid single-cell lysis, and (iii) barcode immunosensors for detecting nine different secretory and intracellular proteins to reveal the correlation among cancer-related proteins. Using this chip, the single-cell proteomics of a lung cancer cell line, which may be easily masked in bulk analysis, were evaluated. By comparing changes in the level of protein secretion and heterogeneity in response to combinations of four anti-cancer drugs, this study suggests a new method for selecting the best combination of anti-cancer drugs. Subsequent preclinical and clinical trials should enable this platform to become applicable for patient-customized therapies.
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Affiliation(s)
- Yugyung Jung
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
| | - Minkook Son
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
| | - Yu Ri Nam
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jongchan Choi
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea;
- Institute for Systems Biology, Seattle, WA 98109, USA;
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA 98109, USA;
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Sung Yang
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea;
- Correspondence:
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Proteomic Characterization of Colorectal Cancer Tissue from Patients Identifies Novel Putative Protein Biomarkers. Curr Issues Mol Biol 2021; 43:1043-1056. [PMID: 34563043 PMCID: PMC8929084 DOI: 10.3390/cimb43020074] [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: 08/21/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related death over the world. There is a great need for biomarkers capable of early detection and as targets for treatment. Differential protein expression was investigated with two-dimensional gel electrophoresis (2D-PAGE) followed by identification with liquid chromatography–tandem mass spectrometry (LC-MS/MS) in CRC patient tissue from (i) the peripheral part of the tumor, (ii) the central part of the tumor as well as from (iii) a non-involved part of the colorectal tissue. The expression patterns of six identified proteins were further evaluated by one-dimensional Western blot (1D-WB) analysis of the CRC tissue. Proteins that were perturbed in expression level in the peripheral or in the central part of the tumor as compared with the non-involved part included S100A11, HNRNPF, HNRNPH1 or HNRNPH2, GSTP1, PKM and FABP1. These identified markers may have future diagnostic potential or may be novel treatment targets after further evaluation in larger patient cohorts.
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10
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Lindhorst PH, Hummon AB. Proteomics of Colorectal Cancer: Tumors, Organoids, and Cell Cultures-A Minireview. Front Mol Biosci 2020; 7:604492. [PMID: 33363210 PMCID: PMC7758474 DOI: 10.3389/fmolb.2020.604492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Proteomics, the study of the complete protein composition of a sample, is an important field for cancer research. Changes in the proteome can serve as a biomarker of cancer or lead to the development of a targeted therapy. This minireview will focus on mass spectrometry-based proteomics studies applied specifically to colorectal cancer, particularly the variety of cancer model systems used, including tumor samples, two-dimensional (2D) and three-dimensional (3D) cell cultures such as spheroids and organoids. A thorough discussion of the application of these systems will accompany the review of the literature, as each provides distinct advantages and disadvantages for colorectal cancer research. Finally, we provide conclusions and future perspectives for the application of these model systems to cancer research as a whole.
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Affiliation(s)
- Philip H Lindhorst
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States.,The Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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11
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N-glycomic profiling of colorectal cancer according to tumor stage and location. PLoS One 2020; 15:e0234989. [PMID: 32598367 PMCID: PMC7323945 DOI: 10.1371/journal.pone.0234989] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/06/2020] [Indexed: 12/24/2022] Open
Abstract
Alterations in glycosylation are seen in many types of cancer, including colorectal cancer (CRC). Glycans, the sugar moieties of glycoconjugates, are involved in many important functions relevant to cancer and can be of value as biomarkers. In this study, we have used mass spectrometry to analyze the N-glycan profiles of 35 CRC tissue samples and 10 healthy tissue samples from non-CRC patients who underwent operations for other reasons. The tumor samples were divided into groups depending on tumor location (right or left colon) and stage (II or III), while the healthy samples were divided into right or left colon. The levels of neutral and acidic N-glycan compositions and glycan classes were analyzed in a total of ten different groups. Surprisingly, there were no significant differences in glycan levels when all right- and left-sided CRC samples were compared, and few differences (such as in the abundance of the neutral N-glycan H3N5) were seen when the samples were divided according to both location and stage. Multiple significant differences were found in the levels of glycans and glycan classes when stage II and III samples were compared, and these glycans could be of value as candidates for new markers of cancer progression. In order to validate our findings, we analyzed healthy tissue samples from the right and left colon and found no significant differences in the levels of any of the glycans analyzed, confirming that our findings when comparing CRC samples from the right and left colon are not due to normal variations in the levels of glycans between the healthy right and left colon. Additionally, the levels of the acidic glycans H4N3F1P1, H5N4F1P1, and S1H5N4F1 were found to change in a cancer-specific but colon location-nonspecific manner, indicating that CRC affects glycan levels in similar ways regardless of tumor location.
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12
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Holm M, Joenväärä S, Saraswat M, Tohmola T, Ristimäki A, Renkonen R, Haglund C. Plasma protein expression differs between colorectal cancer patients depending on primary tumor location. Cancer Med 2020; 9:5221-5234. [PMID: 32452655 PMCID: PMC7367633 DOI: 10.1002/cam4.3178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer (CRC) includes tumors in the right colon, left colon, and rectum, although they differ significantly from each other in aspects such as prognosis and treatment. Few previous mass spectrometry-based studies have analyzed differences in protein expression depending on the tumor location. In this study, we have used mass spectrometry-based proteomics to analyze plasma samples from 83 CRC patients to study if differences in plasma protein expression can be seen depending on primary tumor location (right colon, left colon, or rectum). Differences were studied between the groups both regardless of and according to tumor stage (II or III). Large differences in plasma protein expression were seen, and we found that plasma samples from patients with rectal cancer separated from samples from patients with colon cancer when analyzed by principal component analysis and hierarchical clustering. Samples from patients with cancer in the right and left colon also tended to separate from each other. Pathway analysis discovered canonical pathways involved in lipid metabolism and inflammation to be enriched. This study will help to further define CRC as distinct entities depending on tumor location, as shown by the widespread differences in plasma protein profile and dysregulated pathways.
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Affiliation(s)
- Matilda Holm
- Department of Surgery, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Department of Pathology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sakari Joenväärä
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland.,HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Tiialotta Tohmola
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland.,HUSLAB, Helsinki University Hospital, Helsinki, Finland.,Department of Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Department of Pathology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Risto Renkonen
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland.,HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Caj Haglund
- Department of Surgery, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,HUSLAB, Helsinki University Hospital, Helsinki, Finland
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13
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de Oliveira G, Paccielli Freire P, Santiloni Cury S, de Moraes D, Santos Oliveira J, Dal-Pai-Silva M, do Reis PP, Francisco Carvalho R. An Integrated Meta-Analysis of Secretome and Proteome Identify Potential Biomarkers of Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2020; 12:E716. [PMID: 32197468 PMCID: PMC7140071 DOI: 10.3390/cancers12030716] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is extremely aggressive, has an unfavorable prognosis, and there are no biomarkers for early detection of the disease or identification of individuals at high risk for morbidity or mortality. The cellular and molecular complexity of PDAC leads to inconsistences in clinical validations of many proteins that have been evaluated as prognostic biomarkers of the disease. The tumor secretome, a potential source of biomarkers in PDAC, plays a crucial role in cell proliferation and metastasis, as well as in resistance to treatments, which together contribute to a worse clinical outcome. The massive amount of proteomic data from pancreatic cancer that has been generated from previous studies can be integrated and explored to uncover secreted proteins relevant to the diagnosis and prognosis of the disease. The present study aimed to perform an integrated meta-analysis of PDAC proteome and secretome public data to identify potential biomarkers of the disease. Our meta-analysis combined mass spectrometry data obtained from two systematic reviews of the pancreatic cancer literature, which independently selected 20 studies of the secretome and 35 of the proteome. Next, we predicted the secreted proteins using seven in silico tools or databases, which identified 39 secreted proteins shared between the secretome and proteome data. Notably, the expression of 31 genes of these secretome-related proteins was upregulated in PDAC samples from The Cancer Genome Atlas (TCGA) when compared to control samples from TCGA and The Genotype-Tissue Expression (GTEx). The prognostic value of these 39 secreted proteins in predicting survival outcome was confirmed using gene expression data from four PDAC datasets (validation set). The gene expression of these secreted proteins was able to distinguish high- and low-survival patients in nine additional tumor types from TCGA, demonstrating that deregulation of these secreted proteins may also contribute to the prognosis in multiple cancers types. Finally, we compared the prognostic value of the identified secreted proteins in PDAC biomarkers studies from the literature. This analysis revealed that our gene signature performed equally well or better than the signatures from these previous studies. In conclusion, our integrated meta-analysis of PDAC proteome and secretome identified 39 secreted proteins as potential biomarkers, and the tumor gene expression profile of these proteins in patients with PDAC is associated with worse overall survival.
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Affiliation(s)
- Grasieli de Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Paula Paccielli Freire
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Diogo de Moraes
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Jakeline Santos Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Maeli Dal-Pai-Silva
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Patrícia Pintor do Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, São Paulo, Brazil;
- Experimental Research Unity, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-970, São Paulo, Brazil
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
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14
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Zheng YF, Luo J, Gan GL, Li W. Overexpression of microRNA-98 inhibits cell proliferation and promotes cell apoptosis via claudin-1 in human colorectal carcinoma. J Cell Biochem 2019; 120:6090-6105. [PMID: 30506722 DOI: 10.1002/jcb.27895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/24/2018] [Indexed: 02/05/2023]
Abstract
Colorectal carcinoma (CRC) is a major cause of cancer-related deaths worldwide, and investigations on novel targets are imperative. MiR-98 has been reported to act as a tumor suppressor in several cancers. To evaluate miR-98 as a novel anticancer molecule for CRC, examinations to validate whether miR-98 conferred an inhibiting effect on proliferation, migration, and invasion were performed. The microarray-based gene expression profiling involving CRC was used to identify the differentially expressed genes. The potential relationship between miR-98 and CLDN1 was analyzed by cell experimentation. Then, the CRC cells were transfected with miR-98 mimic or miR-98 inhibitor to investigate the potential effect of miR-98 overexpression and depletion on CRC cell proliferation, migration, invasion, and apoptosis. The expressions of CLDN1, Bcl-2 associated protein x (Bax), runt-related transcription factor 3 (RUNX3), B-cell lymphoma 2 (Bcl-2), C-myc, and proliferating cell nuclear antigen (PCNA) were determined. The downregulated miR-98 along with an upregulated CLDN1 was observed in CRC, in which miR-98 could target to regulate CLDN1. The overexpression of miR-98 or silencing of CLDN1 was shown to increase the expression of Bax and RUNX3 along with promoted cell apoptosis and arrested cells in G1 phase, while decreasing the expression of CLDN1, Bcl-2, C-myc, and PCNA with suppressed proliferation, migration, and invasion. Collectively, the current study supports the notion that miR-98 plays an inhibitory role in human CRC cell proliferation, migration, and invasion and act as a contributor for cell apoptosis by downregulating CLDN1. The current study highlights a potential future strategy to help prevent the development of CRC.
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Affiliation(s)
- Yi-Feng Zheng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jie Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Guo-Lian Gan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Wei Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
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15
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Kawaguchi N, Tashiro K, Taniguchi K, Kawai M, Tanaka K, Okuda J, Hayashi M, Uchiyama K. Nogo-B (Reticulon-4B) functions as a negative regulator of the apoptotic pathway through the interaction with c-FLIP in colorectal cancer cells. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2600-2609. [PMID: 29684585 DOI: 10.1016/j.bbadis.2018.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/10/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022]
Abstract
Nogo-B is a member of the Nogo/Reticulon-4 family and has been reported to be an inducer of apoptosis in certain types of cancer cells. However, the role of Nogo-B in human cancer remains less understood. Here, we demonstrated the functions of Nogo-B in colorectal cancer cells. In clinical colorectal cancer specimens, Nogo-B was obviously overexpressed, as determined by immunohistochemistry; and Western blot analysis showed its expression level to be significantly up-regulated. Furthermore, knockdown of Nogo-B in two colorectal cancer cell lines, SW480 and DLD-1, by transfection with si-RNA (siR) resulted in significantly reduced cell viability and a dramatic increase in apoptosis with insistent overexpression of cleaved caspase-8 and cleaved PARP. The transfection with Nogo-B plasmid cancelled that apoptosis induced by siRNogoB in SW480 cells. Besides, combinatory treatment with siR-Nogo-B/staurosporine (STS) or siR-Nogo-B/Fas ligand (FasL) synergistically reduced cell viability and increased the expression of apoptotic signaling proteins in colorectal cancer cells. These results strongly support our contention that Nogo-B most likely played an oncogenic role in colorectal cancer cells, mainly by negatively regulating the extrinsic apoptotic pathway in them. Finally, we revealed that suppression of Nogo-B caused down-regulation of c-FLIP, known as a major anti-apoptotic protein, and activation of caspase-8 in the death receptor pathway. Interaction between Nogo-B and c-FLIP was shown by immunoprecipitation and immunofluorescence studies. In conclusion, Nogo-B was shown to play an important negative role in apoptotic signaling through its interaction with c-FLIP in colorectal cancer cells, and may thus become a novel therapeutic target for colorectal cancer.
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Affiliation(s)
- Nao Kawaguchi
- Department of General and Gastroenterological Surgery, Osaka Medical College, Osaka, Japan
| | - Keitaro Tashiro
- Department of General and Gastroenterological Surgery, Osaka Medical College, Osaka, Japan.
| | - Kohei Taniguchi
- Department of General and Gastroenterological Surgery, Osaka Medical College, Osaka, Japan
| | - Masaru Kawai
- Department of General and Gastroenterological Surgery, Osaka Medical College, Osaka, Japan
| | - Keitaro Tanaka
- Department of General and Gastroenterological Surgery, Osaka Medical College, Osaka, Japan
| | - Junji Okuda
- Osaka Medical College Hospital Cancer Center, Osaka, Japan
| | - Michihiro Hayashi
- Department of General and Gastroenterological Surgery, Osaka Medical College, Osaka, Japan
| | - Kazuhisa Uchiyama
- Department of General and Gastroenterological Surgery, Osaka Medical College, Osaka, Japan
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