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Xiong E, Liu P, Deng R, Zhang K, Yang R, Li J. Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assay in vitro. Natl Sci Rev 2024; 11:nwae118. [PMID: 38742234 PMCID: PMC11089818 DOI: 10.1093/nsr/nwae118] [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: 08/28/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 05/16/2024] Open
Abstract
Single-nucleotide variants (SNVs) are the most common type variation of sequence alterations at a specific location in the genome, thus involving significant clinical and biological information. The assay of SNVs has engaged great awareness, because many genome-wide association studies demonstrated that SNVs are highly associated with serious human diseases. Moreover, the investigation of SNV expression levels in single cells are capable of visualizing genetic information and revealing the complexity and heterogeneity of single-nucleotide mutation-related diseases. Thus, developing SNV assay approaches in vitro, particularly in single cells, is becoming increasingly in demand. In this review, we summarized recent progress in the enzyme-free and enzyme-mediated strategies enabling SNV assay transition from sensing interface to the test tube and single cells, which will potentially delve deeper into the knowledge of SNV functions and disease associations, as well as discovering new pathways to diagnose and treat diseases based on individual genetic profiles. The leap of SNV assay achievements will motivate observation and measurement genetic variations in single cells, even within living organisms, delve into the knowledge of SNV functions and disease associations, as well as open up entirely new avenues in the diagnosis and treatment of diseases based on individual genetic profiles.
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Affiliation(s)
- Erhu Xiong
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Pengfei Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, China
| | - Ronghua Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Jinghong Li
- Department of Chemistry, Center for Bioanalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Beijing Institute of Life Science and Technology, Beijing 102206, China
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2
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Scarini JF, Gonçalves MWA, de Lima-Souza RA, Lavareze L, de Carvalho Kimura T, Yang CC, Altemani A, Mariano FV, Soares HP, Fillmore GC, Egal ESA. Potential role of the Eph/ephrin system in colorectal cancer: emerging druggable molecular targets. Front Oncol 2024; 14:1275330. [PMID: 38651144 PMCID: PMC11033724 DOI: 10.3389/fonc.2024.1275330] [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: 08/16/2023] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
The Eph/ephrin system regulates many developmental processes and adult tissue homeostasis. In colorectal cancer (CRC), it is involved in different processes including tumorigenesis, tumor angiogenesis, metastasis development, and cancer stem cell regeneration. However, conflicting data regarding Eph receptors in CRC, especially in its putative role as an oncogene or a suppressor gene, make the precise role of Eph-ephrin interaction confusing in CRC development. In this review, we provide an overview of the literature and highlight evidence that collaborates with these ambiguous roles of the Eph/ephrin system in CRC, as well as the molecular findings that represent promising therapeutic targets.
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Affiliation(s)
- João Figueira Scarini
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
| | - Moisés Willian Aparecido Gonçalves
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
| | - Reydson Alcides de Lima-Souza
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
| | - Luccas Lavareze
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
| | - Talita de Carvalho Kimura
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
| | - Ching-Chu Yang
- Department of Pathology, School of Medicine, University of Utah (UU), Salt Lake City, UT, United States
| | - Albina Altemani
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fernanda Viviane Mariano
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Heloisa Prado Soares
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah (UU), Salt Lake City, UT, United States
| | - Gary Chris Fillmore
- Biorepository and Molecular Pathology, Huntsman Cancer Institute, University of Utah (UU), Salt Lake City, UT, United States
| | - Erika Said Abu Egal
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Biorepository and Molecular Pathology, Huntsman Cancer Institute, University of Utah (UU), Salt Lake City, UT, United States
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3
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Desai S, Ahmad S, Bawaskar B, Rashmi S, Mishra R, Lakhwani D, Dutt A. Singleton mutations in large-scale cancer genome studies: uncovering the tail of cancer genome. NAR Cancer 2024; 6:zcae010. [PMID: 38487301 PMCID: PMC10939354 DOI: 10.1093/narcan/zcae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Singleton or low-frequency driver mutations are challenging to identify. We present a domain driver mutation estimator (DOME) to identify rare candidate driver mutations. DOME analyzes positions analogous to known statistical hotspots and resistant mutations in combination with their functional and biochemical residue context as determined by protein structures and somatic mutation propensity within conserved PFAM domains, integrating the CADD scoring scheme. Benchmarked against seven other tools, DOME exhibited superior or comparable accuracy compared to all evaluated tools in the prediction of functional cancer drivers, with the exception of one tool. DOME identified a unique set of 32 917 high-confidence predicted driver mutations from the analysis of whole proteome missense variants within domain boundaries across 1331 genes, including 1192 noncancer gene census genes, emphasizing its unique place in cancer genome analysis. Additionally, analysis of 8799 TCGA (The Cancer Genome Atlas) and in-house tumor samples revealed 847 potential driver mutations, with mutations in tyrosine kinase members forming the dominant burden, underscoring its higher significance in cancer. Overall, DOME complements current approaches for identifying novel, low-frequency drivers and resistant mutations in personalized therapy.
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Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Suhail Ahmad
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Bhargavi Bawaskar
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Sonal Rashmi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Deepika Lakhwani
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
- Department of Genetics, University of Delhi, South Campus, New Delhi 110021, India
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4
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Osterlund E, Ristimäki A, Mäkinen MJ, Kytölä S, Kononen J, Pfeiffer P, Soveri LM, Keinänen M, Sorbye H, Nunes L, Salminen T, Nieminen L, Uutela A, Halonen P, Ålgars A, Sundström J, Kallio R, Ristamäki R, Lamminmäki A, Stedt H, Heervä E, Kuopio T, Sjöblom T, Isoniemi H, Glimelius B, Osterlund P. Atypical (non-V600E) BRAF mutations in metastatic colorectal cancer in population and real-world cohorts. Int J Cancer 2024; 154:488-503. [PMID: 37724848 DOI: 10.1002/ijc.34733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 09/21/2023]
Abstract
BRAF-V600E mutation (mt) is a strong negative prognostic and predictive biomarker in metastatic colorectal cancer (mCRC). Non-V600Emt, designated atypical BRAFmt (aBRAFmt) are rare, and little is known about their frequency, co-mutations and prognostic and predictive role. These were compared between mutational groups of mCRC patients collected from three Nordic population-based or real-world cohorts. Pathology of aBRAFmt was studied. The study included 1449 mCRC patients with 51 (3%) aBRAFmt, 182 (13%) BRAF-V600Emt, 456 (31%) RAS&BRAF wild-type (wt) and 760 (52%) RASmt tumours. aBRAFmt were seen in 2% of real-world and 4% of population-based cohorts. Twenty-six different aBRAFmt were detected, 11 (22%) class 2 (serrated adenocarcinoma in 2/9 tested), 32 (64%) class 3 (serrated in 15/25) and 4 (8%) unclassified. aBRAFmt patients were predominantly male, had more rectal primaries, less peritoneal metastases, deficient mismatch repair in one (2%), and better survival after metastasectomy (89% 5-year overall survival [OS]-rate) compared with BRAF-V600Emt. aBRAFmt and BRAF-V600Emt had poorer performance status and received fewer treatment lines than RAS&BRAFwt and RASmt. OS among aBRAFmt (median 14.4 months) was longer than for BRAF-V600Emt (11.2 months), but shorter than for RAS&BRAFwt (30.5 months) and RASmt (23.4 months). Addition of bevacizumab trended for better OS for the aBRAFmt. Nine patients with aBRAFmt received cetuximab/panitumumab without response. aBRAFmt represents a distinct subgroup differing from other RAS/BRAF groups, with serrated adenocarcinoma in only half. OS for patients with aBRAFmt tumours was slightly better than for BRAF-V600Emt, but worse than for RASmt and RAS&BRAFwt. aBRAFmt should not be a contraindication for metastasectomy.
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Affiliation(s)
- Emerik Osterlund
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Transplantation and Liver Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Ari Ristimäki
- Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- Faculty of Medicine, Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Markus J Mäkinen
- Department of Pathology, Oulu University Hospital, Oulu, Finland
- Translational Medicine Research Unit, Department of Pathology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu, Finland
| | - Soili Kytölä
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- Department of Genetics, University of Helsinki, Helsinki, Finland
| | - Juha Kononen
- Departemnt of Oncology, Central hospital of Central Finland, Jyväskylä, Finland
- Docrates hospital, Helsinki, Finland
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Leena-Maija Soveri
- Home Care, Geriatric Clinic and Palliative Care, Joint Municipal Authority for Health Care and Social Services in Keski-Uusimaa, Hyvinkää, Finland
- Department of Oncology, Helsinki University Hospital, Helsinki, Finland
| | - Mauri Keinänen
- Department of Genetics, Fimlab Laboratories, Tampere, Finland
| | - Halfdan Sorbye
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Luís Nunes
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tapio Salminen
- Department of Oncology, Tampere University Hospital, Tampere, Finland
- Department of Oncology, University of Tampere, Tampere, Finland
| | - Lasse Nieminen
- Department of Pathology, Tampere University Hospital, Tampere, Finland
- Department of Pathology, University of Tampere, Tampere, Finland
| | - Aki Uutela
- Department of Transplantation and Liver Surgery, Helsinki University Hospital, Helsinki, Finland
- Department of Surgery, University of Helsinki, Helsinki, Finland
- Department of Transplant and HPB Surgery, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Päivi Halonen
- Department of Oncology, Helsinki University Hospital, Helsinki, Finland
- Department of Oncology, University of Helsinki, Helsinki, Finland
| | - Annika Ålgars
- Department of Oncology, Turku University Hospital, Turku, Finland
- Department of Oncology, University of Turku, Turku, Finland
| | - Jari Sundström
- Department of Pathology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Raija Kallio
- Department of Oncology, Oulu University Hospital, Oulu, Finland
- Department of Oncology, University of Oulu, Oulu, Finland
| | - Raija Ristamäki
- Department of Oncology, Turku University Hospital, Turku, Finland
- Department of Oncology, University of Turku, Turku, Finland
| | - Annamarja Lamminmäki
- Department of Oncology, Kuopio University Hospital, Kuopio, Finland
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Hanna Stedt
- Department of Oncology, Kuopio University Hospital, Kuopio, Finland
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Eetu Heervä
- Department of Oncology, Turku University Hospital, Turku, Finland
- Department of Oncology, University of Turku, Turku, Finland
| | - Teijo Kuopio
- Department of Pathology, Central Finland Hospital Nova, Jyväskylä, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Helena Isoniemi
- Department of Transplantation and Liver Surgery, Helsinki University Hospital, Helsinki, Finland
- Department of Surgery, University of Helsinki, Helsinki, Finland
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pia Osterlund
- Department of Oncology, Tampere University Hospital, Tampere, Finland
- Department of Oncology, University of Tampere, Tampere, Finland
- Department of Surgery, University of Helsinki, Helsinki, Finland
- Department of Transplant and HPB Surgery, Royal Infirmary of Edinburgh, Edinburgh, UK
- Department of Gastrointestinal Oncology, Karolinska Universitetssjukhuset, Stockholm, Sweden
- Department of Oncology/Pathology, Karolinska Institutet, Stockholm, Sweden
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5
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Kim Y, Miller WT. Contrasting Effects of Cancer-Associated Mutations in EphA3 and EphB2 Kinases. Biochemistry 2024:10.1021/acs.biochem.3c00674. [PMID: 38252844 PMCID: PMC11265570 DOI: 10.1021/acs.biochem.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors are a family of tyrosine kinases that can act as tumor promoters or tumor suppressors, depending on the receptor and cancer cell type. Cancer-associated somatic mutations have been identified in all Eph receptors, but in most cases, the functional effects of the mutations are unknown. In this study, we expressed and purified the kinase domains of wild-type (WT) EphA3 and EphB2 along with 16 cancer-associated mutants. We identified mutations that decrease EphA3 activity and both activating and inhibitory mutations in EphB2. To shed light on the mechanisms by which the mutations altered kinase activity, we measured the thermal stabilities of the enzymes and performed steady-state kinetic experiments. We also expressed the full-length receptors in HEK293T cells to determine the cellular effects. WT EphB2 promoted downstream ERK signaling, while a kinase-inactive mutant (S706F) was similar to the control cells. In contrast, WT EphA3 (but not loss-of-function mutants) inhibited ERK signaling. The reciprocal effects of EphB2 and EphA3 on ERK phosphorylation in HEK293T cells were also evident in Ras-GTP loading. Thus, consistent with the dual roles of Eph receptors as tumor promoters and tumor suppressors, somatic mutations have the potential to increase or decrease Eph function, resulting in changes in the downstream signaling transduction.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Veterans Affairs Medical Center, Northport, New York 11768, United States
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Pasquale EB. Eph receptors and ephrins in cancer progression. Nat Rev Cancer 2024; 24:5-27. [PMID: 37996538 PMCID: PMC11015936 DOI: 10.1038/s41568-023-00634-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/25/2023]
Abstract
Evidence implicating Eph receptor tyrosine kinases and their ephrin ligands (that together make up the 'Eph system') in cancer development and progression has been accumulating since the discovery of the first Eph receptor approximately 35 years ago. Advances in the past decade and a half have considerably increased the understanding of Eph receptor-ephrin signalling mechanisms in cancer and have uncovered intriguing new roles in cancer progression and drug resistance. This Review focuses mainly on these more recent developments. I provide an update on the different mechanisms of Eph receptor-ephrin-mediated cell-cell communication and cell autonomous signalling, as well as on the interplay of the Eph system with other signalling systems. I further discuss recent advances in elucidating how the Eph system controls tumour expansion, invasiveness and metastasis, supports cancer stem cells, and drives therapy resistance. In addition to functioning within cancer cells, the Eph system also mediates the reciprocal communication between cancer cells and cells of the tumour microenvironment. The involvement of the Eph system in tumour angiogenesis is well established, but recent findings also demonstrate roles in immune cells, cancer-associated fibroblasts and the extracellular matrix. Lastly, I discuss strategies under evaluation for therapeutic targeting of Eph receptors-ephrins in cancer and conclude with an outlook on promising future research directions.
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Affiliation(s)
- Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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7
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Kundu S, Nunes L, Adler J, Mathot L, Stoimenov I, Sjöblom T. Recurring EPHB1 mutations in human cancers alter receptor signalling and compartmentalisation of colorectal cancer cells. Cell Commun Signal 2023; 21:354. [PMID: 38102712 PMCID: PMC10722860 DOI: 10.1186/s12964-023-01378-9] [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: 08/25/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Ephrin (EPH) receptors have been implicated in tumorigenesis and metastasis, but the functional understanding of mutations observed in human cancers is limited. We previously demonstrated reduced cell compartmentalisation for somatic EPHB1 mutations found in metastatic colorectal cancer cases. We therefore integrated pan-cancer and pan-EPH mutational data to prioritise recurrent EPHB1 mutations for functional studies to understand their contribution to cancer development and metastasis. METHODS Here, 79,151 somatic mutations in 9,898 samples of 33 different tumour types were analysed with a bioinformatic pipeline to find 3D-mutated cluster pairs and hotspot mutations in EPH receptors. From these, 15 recurring EPHB1 mutations were stably expressed in colorectal cancer followed by confocal microscopy based in vitro compartmentalisation assays and phospho-proteome analysis. RESULTS The 3D-protein structure-based bioinformatics analysis resulted in 63% EPHB1 mutants with compartmentalisation phenotypes vs 43% for hotspot mutations. Whereas the ligand-binding domain mutations C61Y, R90C, and R170W, the fibronectin domain mutation R351L, and the kinase domain mutation D762N displayed reduced to strongly compromised cell compartmentalisation, the kinase domain mutations R743W and G821R enhanced this phenotype. While mutants with reduced compartmentalisation also had reduced ligand induced receptor phosphorylation, the enhanced compartmentalisation was not linked to receptor phosphorylation level. Phosphoproteome mapping pinpointed the PI3K pathway and PIK3C2B phosphorylation in cells harbouring mutants with reduced compartmentalisation. CONCLUSIONS This is the first integrative study of pan-cancer EPH receptor mutations followed by in vitro validation, a robust way to identify cancer-causing mutations, uncovering EPHB1 mutation phenotypes and demonstrating the utility of protein structure-based mutation analysis in characterization of novel cancer genes. Video Abstract.
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Affiliation(s)
- Snehangshu Kundu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Luís Nunes
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jeremy Adler
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ivaylo Stoimenov
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Kim Y, Ahmed S, Miller WT. Colorectal cancer-associated mutations impair EphB1 kinase function. J Biol Chem 2023; 299:105115. [PMID: 37527777 PMCID: PMC10463257 DOI: 10.1016/j.jbc.2023.105115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Erythropoietin-producing hepatoma (Eph) receptor tyrosine kinases regulate the migration and adhesion of cells that are required for many developmental processes and adult tissue homeostasis. In the intestinal epithelium, Eph signaling controls the positioning of cell types along the crypt-villus axis. Eph activity can suppress the progression of colorectal cancer (CRC). The most frequently mutated Eph receptor in metastatic CRC is EphB1. However, the functional effects of EphB1 mutations are mostly unknown. We expressed and purified the kinase domains of WT and five cancer-associated mutant EphB1 and developed assays to assess the functional effects of the mutations. Using purified proteins, we determined that CRC-associated mutations reduce the activity and stability of the folded structure of EphB1. By mammalian cell expression, we determined that CRC-associated mutant EphB1 receptors inhibit signal transducer and activator of transcription 3 and extracellular signal-regulated kinases 1 and 2 signaling. In contrast to the WT, the mutant EphB1 receptors are unable to suppress the migration of human CRC cells. The CRC-associated mutations also impair cell compartmentalization in an assay in which EphB1-expressing cells are cocultured with ligand (ephrin B1)-expressing cells. These results suggest that somatic mutations impair the kinase-dependent tumor suppressor function of EphB1 in CRC.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA; Department of Veterans Affairs Medical Center, Northport, New York, USA.
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9
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Venkitachalam S, Babu D, Ravillah D, Katabathula RM, Joseph P, Singh S, Udhayakumar B, Miao Y, Martinez-Uribe O, Hogue JA, Kresak AM, Dawson D, LaFramboise T, Willis JE, Chak A, Garman KS, Blum AE, Varadan V, Guda K. The Ephrin B2 Receptor Tyrosine Kinase Is a Regulator of Proto-oncogene MYC and Molecular Programs Central to Barrett's Neoplasia. Gastroenterology 2022; 163:1228-1241. [PMID: 35870513 PMCID: PMC9613614 DOI: 10.1053/j.gastro.2022.07.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 06/20/2022] [Accepted: 07/12/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND & AIMS Mechanisms contributing to the onset and progression of Barrett's (BE)-associated esophageal adenocarcinoma (EAC) remain elusive. Here, we interrogated the major signaling pathways deregulated early in the development of Barrett's neoplasia. METHODS Whole-transcriptome RNA sequencing analysis was performed in primary BE, EAC, normal esophageal squamous, and gastric biopsy tissues (n = 89). Select pathway components were confirmed by quantitative polymerase chain reaction in an independent cohort of premalignant and malignant biopsy tissues (n = 885). Functional impact of selected pathway was interrogated using transcriptomic, proteomic, and pharmacogenetic analyses in mammalian esophageal organotypic and patient-derived BE/EAC cell line models, in vitro and/or in vivo. RESULTS The vast majority of primary BE/EAC tissues and cell line models showed hyperactivation of EphB2 signaling. Transcriptomic/proteomic analyses identified EphB2 as an endogenous binding partner of MYC binding protein 2, and an upstream regulator of c-MYC. Knockdown of EphB2 significantly impeded the viability/proliferation of EAC and BE cells in vitro/in vivo. Activation of EphB2 in normal esophageal squamous 3-dimensional organotypes disrupted epithelial maturation and promoted columnar differentiation programs, notably including MYC. EphB2 and MYC showed selective induction in esophageal submucosal glands with acinar ductal metaplasia, and in a porcine model of BE-like esophageal submucosal gland spheroids. Clinically approved inhibitors of MEK, a protein kinase that regulates MYC, effectively suppressed EAC tumor growth in vivo. CONCLUSIONS The EphB2 signaling is frequently hyperactivated across the BE-EAC continuum. EphB2 is an upstream regulator of MYC, and activation of EphB2-MYC axis likely precedes BE development. Targeting EphB2/MYC could be a promising therapeutic strategy for this often refractory and aggressive cancer.
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Affiliation(s)
- Srividya Venkitachalam
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Deepak Babu
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Durgadevi Ravillah
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Ramachandra M Katabathula
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Peronne Joseph
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Salendra Singh
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Bhavatharini Udhayakumar
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Yanling Miao
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Omar Martinez-Uribe
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Joyce A Hogue
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Adam M Kresak
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Dawn Dawson
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Thomas LaFramboise
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Joseph E Willis
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Amitabh Chak
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio; Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Katherine S Garman
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Andrew E Blum
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio; Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio; Division of Gastroenterology, Northeast Ohio Veteran Affairs Healthcare System, Cleveland, Ohio
| | - Vinay Varadan
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio.
| | - Kishore Guda
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio; Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio.
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10
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Chandrasekera P, Perfetto M, Lu C, Zhuo M, Bahudhanapati H, Li J, Chen WC, Kulkarni P, Christian L, Liu J, Yien YY, Yu C, Wei S. Metalloprotease ADAM9 cleaves ephrin-B ligands and differentially regulates Wnt and mTOR signaling downstream of Akt kinase in colorectal cancer cells. J Biol Chem 2022; 298:102225. [PMID: 35780836 PMCID: PMC9358476 DOI: 10.1016/j.jbc.2022.102225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 12/02/2022] Open
Abstract
Ephrin-B signaling has been implicated in many normal and pathological processes, including neural crest development and tumor metastasis. We showed previously that proteolysis of ephrin-B ligands by the disintegrin metalloprotease ADAM13 is necessary for canonical Wnt signal activation and neural crest induction in Xenopus, but it was unclear if these mechanisms are conserved in mammals. Here, we report that mammalian ADAM9 cleaves ephrin-B1 and ephrin-B2 and can substitute for Xenopus ADAM13 to induce the neural crest. We found that ADAM9 expression is elevated in human colorectal cancer (CRC) tissues and that knockdown (KD) of ADAM9 inhibits the migration and invasion of SW620 and HCT116 CRC cells by reducing the activity of Akt kinase, which is antagonized by ephrin-Bs. Akt is a signaling node that activates multiple downstream pathways, including the Wnt and mTOR pathways, both of which can promote CRC cell migration/invasion. Surprisingly, we also found that KD of ADAM9 downregulates Wnt signaling but has negligible effects on mTOR signaling in SW620 cells; in contrast, mTOR activity is suppressed while Wnt signaling remains unaffected by ADAM9 KD in HCT116 cells. These results suggest that mammalian ADAM9 cleaves ephrin-Bs to derepress Akt and promote CRC migration and invasion; however, the signaling pathways downstream of Akt are differentially regulated by ADAM9 in different CRC cell lines, reflecting the heterogeneity of CRC cells in responding to manipulations of upstream Akt regulators.
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Affiliation(s)
| | - Mark Perfetto
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Biology, West Virginia University, Morgantown, West Virginia, USA; Pittsburgh Heart, Lung and Blood Vascular Medicine Institute and Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Congyu Lu
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Minghui Zhuo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | | | - Jiejing Li
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA; Department of Clinical Laboratory, The Affiliated Hospital of KMUST, Medical School, Kunming University of Science and Technology, Kunming, China
| | - Wei-Chih Chen
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Pallavi Kulkarni
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Laura Christian
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Jun Liu
- Department of Biochemistry and Cancer Institute, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Yvette Y Yien
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Pittsburgh Heart, Lung and Blood Vascular Medicine Institute and Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chundong Yu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA.
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11
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Dahpy MA, Salama RHM, Kamal AA, El-Deek HE, AbdelMotaleb AA, Abd-El-Rehim AS, Hassan EA, Alsanory AA, Saad MM, Ali M. Evaluation of tripartite motif 59 and its diagnostic utility in benign bowel diseases and colorectal cancer. J Biochem Mol Toxicol 2022; 36:e23065. [PMID: 35377964 DOI: 10.1002/jbt.23065] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 10/31/2021] [Accepted: 03/23/2022] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related mortality in developing countries. Tripartite motif-59 (TRIM59) a member of the TRIM ubiquitin ligase family, is a surface molecule that regulates biological processes such as cell proliferation, apoptosis, and tumorigenesis. Previous studies reported that TRIM59 expression was upregulated in human CRC, however, the expression pattern and role of TRIM59 in benign colorectal lesions remain unclear. Sixty patients diagnosed with CRC and 60 patients with benign lesions (Crohn's disease, ulcerative colitis, adenoma, and familial adenomatous polyposis) were recruited to the present study. TRIM59 gene expression was assessed by real-time quantitative polymerase chain reaction. Expression of TRIM59 protein and p-AKT were determined using, enzyme-linked immunoassay while p53 expression was detected by immunohistochemistry. Antioxidant/oxidant role of glutathione (GSH)/malondialdehyde (MDA) were evaluated by colorimetric methods in all of the studied groups. Our results showed upregulated expressions of TRIM59 gene and protein levels in CRC tissues and benign colonic lesions compared to nontumor tissues. Their levels were higher in inflammatory compared to noninflammatory bowel lesions. There were significant interrelations among TRIM59 gene expression, protein levels, tumor, node, metastasis staging, and the presence of metastasis (p < 0.0001). Receiver-operator characteristic curve analyses showed that at the cutoff point of 2.5 TRIM59 mRNA expression can discriminate between CRC cases and benign bowel group (area under the curve [AUC]: 0.639, sensitivity: 86.7%, specificity: 41.7%), and between CRC and controls (AUC: 0.962, sensitivity: 90%, specificity: 91.7%). TRIM59 could be a potential biomarker in the early detection, diagnosis, and treatment of benign colonic lesions and CRC.
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Affiliation(s)
- Marwa A Dahpy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Assiut University, Assiut, Egypt.,Department of Medical Biochemistry and Molecular Biology, Armed forces collage of Medicine (AFCM), Cairo, Egypt
| | - Ragaa H M Salama
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Asmaa A Kamal
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Heba E El-Deek
- Department of Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Ali A AbdelMotaleb
- Department of Surgery, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Abeer S Abd-El-Rehim
- Department of Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Elham A Hassan
- Department of Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Aya A Alsanory
- House Officer, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mahmoud M Saad
- House Officer, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Maha Ali
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Assiut University, Assiut, Egypt
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12
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Papadakos SP, Petrogiannopoulos L, Pergaris A, Theocharis S. The EPH/Ephrin System in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23052761. [PMID: 35269901 PMCID: PMC8910949 DOI: 10.3390/ijms23052761] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 01/27/2023] Open
Abstract
The EPH/ephrin system constitutes a bidirectional signaling pathway comprised of a family of tyrosine kinase receptors in tandem with their plasma membrane-bound ligand (ephrins). Its significance in a wide variety of physiologic and pathologic processes has been recognized during the past decades. In carcinogenesis, EPH/ephrins coordinate a wide spectrum of pathologic processes, such as angiogenesis, vessel infiltration, and metastasis. Despite the recent advances in colorectal cancer (CRC) diagnosis and treatment, it remains a leading cause of death globally, accounting for 9.2% of all cancer deaths. A growing body of literature has been published lately revitalizing our scientific interest towards the role of EPH/ephrins in pathogenesis and the treatment of CRC. The aim of the present review is to present the recent CRC data which might lead to clinical practice changes in the future.
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Affiliation(s)
- Stavros P Papadakos
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | - Leonidas Petrogiannopoulos
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | - Alexandros Pergaris
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
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13
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Lee J, Choi S, Jung D, Jung Y, Kim JH, Jung S, Lee WS. Mutational Characterization of Colorectal Cancer from Korean Patients with Targeted Sequencing. J Cancer 2022; 12:7300-7310. [PMID: 35003350 PMCID: PMC8734410 DOI: 10.7150/jca.61324] [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: 04/06/2021] [Accepted: 10/09/2021] [Indexed: 11/11/2022] Open
Abstract
Purpose: Effective treatment of colorectal cancer could benefit from understanding molecular characteristics including mutation profiles of important genes. This study aimed to explore the molecular characteristics of colorectal cancer based on next generation sequencing. Methods: The mutational characteristics by targeted next generation sequencing in 172 colorectal tumor samples from Korean patients were evaluated to explore their associations with clinical features. Targeted sequencing of 375 genes was performed with an average target-depth of 800X. Results: TP53 and APC showed higher mutation frequencies from the left-sided tumors, while CTNNB1 were more frequent from the right-sided tumors. The tumor suppressor NOTCH1 and the DNA strand break repair gene PALB2 were more frequently mutated in early onset tumors. KRAS and PTEN mutations were more frequent from patients with advanced cancers by cancer antigen markers. TP53 and BRAF mutations were more frequent from patients of T3 and T4 stages, where their variant allele fractions were generally higher in T4 tumors, implying that advanced tumors have higher fraction of cancer cells with TP53 and BRAF mutations. Mutational profiles of these patients were also assessed with other clinical features. Comparison of mutational characteristics with the Caucasian subjects from independent data showed that the identified mutational characteristics are largely Korean-specific except for a few key colorectal cancer genes. Conclusion: Next generation sequencing-based targeted sequencing can provide valuable information on molecular characterization of colorectal cancer patients, and its clinically relevant information can provide benefits to better understand colorectal cancer.
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Affiliation(s)
- Jongmin Lee
- Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, Republic of Korea.,Gachon Advanced Institute for Health Science and Technology, Gachon University, Incheon, Republic of Korea
| | - Sangtae Choi
- Department of Surgery, Gachon University College of Medicine Gil Medical Center, Incheon, Republic of Korea
| | - Donghae Jung
- Department of Pathology, Gachon University College of Medicine Gil Medical Center, Incheon, Republic of Korea
| | - YunJae Jung
- Gachon Advanced Institute for Health Science and Technology, Gachon University, Incheon, Republic of Korea.,Department of Microbiology, Gachon University College of Medicine, Incheon, Republic of Korea
| | - Jung Ho Kim
- Department of Internal Medicine, Gachon University College of Medicine Gil Medical Center, Incheon, Republic of Korea
| | - Sungwon Jung
- Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, Republic of Korea.,Gachon Advanced Institute for Health Science and Technology, Gachon University, Incheon, Republic of Korea.,Department of Genome Medicine and Science, Gachon University College of Medicine, Incheon, Republic of Korea
| | - Won-Suk Lee
- Department of Surgery, Gachon University College of Medicine Gil Medical Center, Incheon, Republic of Korea
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14
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Wang GH, Ni K, Gu C, Huang J, Chen J, Wang XD, Ni Q. EphA8 inhibits cell apoptosis via AKT signaling and is associated with poor prognosis in breast cancer. Oncol Rep 2021; 46:183. [PMID: 34278497 DOI: 10.3892/or.2021.8134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/11/2021] [Indexed: 11/06/2022] Open
Abstract
Erythropoietin‑producing hepatocellular receptors (Ephs) comprise the largest subfamily of receptor tyrosine kinases and have been reported to be involved in a variety of biological cellular processes, including tumorigenesis and cancer progression. The present study aimed to determine the expression levels and clinicopathological significance of EphA8 in breast cancer (BC) using immunohistochemistry analysis of tissue microarrays. The results of the present study revealed that EphA8 expression levels were upregulated in BC tissue and were associated with tumor size and TNM stage. In addition, upregulated expression levels of EphA8 were identified to be a poor prognostic biomarker for patients with BC. The knockdown of EphA8 expression using short hairpin RNA resulted in increased levels of apoptosis as well as decreased proliferation, migration and invasion of BC cells both in vivo and in vitro. The knockdown of EphA8 also decreased the phosphorylation of AKT, which was accompanied by downregulation of Bcl‑2 expression levels and upregulation of p53, Caspase‑3 and Bax expression levels. Moreover, knockdown of EphA8 expression increased the chemosensitivity of BC cells to paclitaxel. In conclusion, the results of the present study indicated that EphA8 may be a useful prognostic marker in BC and that knockdown of EphA8 may represent a novel strategy in adjuvant chemotherapy for the treatment of BC.
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Affiliation(s)
- Gui-Hua Wang
- Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Kan Ni
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Changjiang Gu
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jianfei Huang
- Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jing Chen
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xu-Dong Wang
- Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Qichao Ni
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
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15
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Zhang K, Deng R, Gao H, Teng X, Li J. Lighting up single-nucleotide variation in situ in single cells and tissues. Chem Soc Rev 2020; 49:1932-1954. [PMID: 32108196 DOI: 10.1039/c9cs00438f] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to 'see' genetic information directly in single cells can provide invaluable insights into complex biological systems. In this review, we discuss recent advances of in situ imaging technologies for visualizing the subtlest sequence alteration, single-nucleotide variation (SNV), at single-cell level. The mechanism of recently developed methods for SNV discrimination are summarized in detail. With recent developments, single-cell SNV imaging methods have opened a new door for studying the heterogenous and stochastic genetic information in individual cells. Furthermore, SNV imaging can be used on morphologically preserved tissue, which can provide information on histological context for gene expression profiling in basic research and genetic diagnosis. Moreover, the ability to visualize SNVs in situ can be further developed into in situ sequencing technology. We expect this review to inspire more research work into in situ SNV imaging technologies for investigating cellular phenotypes and gene regulation at single-nucleotide resolution, and developing new clinical and biomedical applications.
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Affiliation(s)
- Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Hua Gao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and Department of Pathogeny Biology, Medical College, Zhengzhou University, Zhengzhou 450001, China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
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16
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Abstract
GOALS The goal of this study was to quantify the association between demographic factors and advanced colorectal cancer (CRC) in patients under age 50. BACKGROUND CRC incidence in the United States has declined in older individuals but increased in those under age 50 (early-onset). More than 60% of early-onset CRC patients present with advanced disease (stage III/IV), but predictors of stage in this population are poorly defined. STUDY We analyzed CRC cases diagnosed between age 20 and 49 in the United States Surveillance, Epidemiology, and End Results (SEER) 18 database during 2004 to 2015. Logistic regression models were fit to assess the impact of age, sex, race, ethnicity, marital status, and cancer site on the probability of advanced disease. RESULTS The analysis included 37,044 cases. On multivariable regression, age was inversely associated with advanced disease. Relative to 45 to 49-year-olds, 40 to 44-year-olds had 8% greater odds of having advanced CRC, and 20 to 24-year-olds had 53% greater odds. Asians, blacks, and Pacific Islanders had 10%, 12%, and 45% greater odds of advanced disease compared with whites. Compared with nonpartnered individuals, those with partners had 11% lower odds of advanced CRC. Both right-sided and left-sided colon cancer were more likely to be diagnosed at stage IV compared with rectal cancer. CONCLUSIONS Among individuals with early-onset CRC, younger age, Asian, black, or Pacific Islander race, and being nonpartnered were predictors of advanced disease at presentation. Colon cancer was more likely to be diagnosed at stage IV than rectal cancer. Patient characteristics associated with advanced CRC may indicate both differences in tumor biology and disparities in health care access.
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17
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Cakiroglu E, Senturk S. Genomics and Functional Genomics of Malignant Pleural Mesothelioma. Int J Mol Sci 2020; 21:ijms21176342. [PMID: 32882916 PMCID: PMC7504302 DOI: 10.3390/ijms21176342] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare, aggressive cancer of the mesothelial cells lining the pleural surface of the chest wall and lung. The etiology of MPM is strongly associated with prior exposure to asbestos fibers, and the median survival rate of the diagnosed patients is approximately one year. Despite the latest advancements in surgical techniques and systemic therapies, currently available treatment modalities of MPM fail to provide long-term survival. The increasing incidence of MPM highlights the need for finding effective treatments. Targeted therapies offer personalized treatments in many cancers. However, targeted therapy in MPM is not recommended by clinical guidelines mainly because of poor target definition. A better understanding of the molecular and cellular mechanisms and the predictors of poor clinical outcomes of MPM is required to identify novel targets and develop precise and effective treatments. Recent advances in the genomics and functional genomics fields have provided groundbreaking insights into the genomic and molecular profiles of MPM and enabled the functional characterization of the genetic alterations. This review provides a comprehensive overview of the relevant literature and highlights the potential of state-of-the-art genomics and functional genomics research to facilitate the development of novel diagnostics and therapeutic modalities in MPM.
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Affiliation(s)
- Ece Cakiroglu
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey;
- Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Serif Senturk
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey;
- Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
- Correspondence:
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18
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Teves JM, Won KJ. Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology. Mol Cells 2020; 43:591-599. [PMID: 32507771 PMCID: PMC7398793 DOI: 10.14348/molcells.2020.0020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/22/2020] [Accepted: 05/10/2020] [Indexed: 12/13/2022] Open
Abstract
Complex cell-to-cell communication underlies the basic processes essential for homeostasis in the given tissue architecture. Obtaining quantitative gene-expression of cells in their native context has significantly advanced through single-cell RNA sequencing technologies along with mechanical and enzymatic tissue manipulation. This approach, however, is largely reliant on the physical dissociation of individual cells from the tissue, thus, resulting in a library with unaccounted positional information. To overcome this, positional information can be obtained by integrating imaging and positional barcoding. Collectively, spatial transcriptomics strategies provide tissue architecture-dependent as well as position-dependent cellular functions. This review discusses the current technologies for spatial transcriptomics ranging from the methods combining mechanical dissociation and single-cell RNA sequencing to computational spatial re-mapping.
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Affiliation(s)
- Joji Marie Teves
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-00 Copenhagen, Denmark
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-00 Copenhagen, Denmark
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19
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DiPrima M, Wang D, Tröster A, Maric D, Terrades-Garcia N, Ha T, Kwak H, Sanchez-Martin D, Kudlinzki D, Schwalbe H, Tosato G. Identification of Eph receptor signaling as a regulator of autophagy and a therapeutic target in colorectal carcinoma. Mol Oncol 2019; 13:2441-2459. [PMID: 31545551 PMCID: PMC6822245 DOI: 10.1002/1878-0261.12576] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/02/2019] [Accepted: 09/20/2019] [Indexed: 01/07/2023] Open
Abstract
Advanced colorectal carcinoma is currently incurable, and new therapies are urgently needed. We report that phosphotyrosine‐dependent Eph receptor signaling sustains colorectal carcinoma cell survival, thereby uncovering a survival pathway active in colorectal carcinoma cells. We find that genetic and biochemical inhibition of Eph tyrosine kinase activity or depletion of the Eph ligand EphrinB2 reproducibly induces colorectal carcinoma cell death by autophagy. Spautin and 3‐methyladenine, inhibitors of early steps in the autophagic pathway, significantly reduce autophagy‐mediated cell death that follows inhibition of phosphotyrosine‐dependent Eph signaling in colorectal cancer cells. A small‐molecule inhibitor of the Eph kinase, NVP‐BHG712 or its regioisomer NVP‐Iso, reduces human colorectal cancer cell growth in vitro and tumor growth in mice. Colorectal cancers express the EphrinB ligand and its Eph receptors at significantly higher levels than numerous other cancer types, supporting Eph signaling inhibition as a potential new strategy for the broad treatment of colorectal carcinoma.
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Affiliation(s)
- Michael DiPrima
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD, USA
| | - Dunrui Wang
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD, USA
| | - Alix Tröster
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Dragan Maric
- National Institutes of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nekane Terrades-Garcia
- Vasculitis Research Unit, Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Spain
| | - Taekyu Ha
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD, USA
| | - Hyeongil Kwak
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD, USA
| | - David Sanchez-Martin
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD, USA
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Giovanna Tosato
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), Bethesda, MD, USA
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20
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Park SH, Jo MJ, Kim BR, Jeong YA, Na YJ, Kim JL, Jeong S, Yun HK, Kim DY, Kim BG, Kang SH, Oh SC, Lee DH. Sonic hedgehog pathway activation is associated with cetuximab resistance and EPHB3 receptor induction in colorectal cancer. Am J Cancer Res 2019; 9:2235-2251. [PMID: 31149041 PMCID: PMC6531304 DOI: 10.7150/thno.30678] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/17/2019] [Indexed: 02/06/2023] Open
Abstract
A major problem of colorectal cancer (CRC) targeted therapies is relapse caused by drug resistance. In most cases of CRC, patients develop resistance to anticancer drugs. Cetuximab does not show many of the side effects of other anticancer drugs and improves the survival of patients with metastatic CRC. However, the molecular mechanism of cetuximab resistance is not fully understood. Methods: EPHB3-mediated cetuximab resistance was confirmed by in vitro western blotting, colony-forming assays, WST-1 colorimetric assay, and in vivo xenograft models (n = 7 per group). RNA-seq analysis and receptor tyrosine kinase assays were performed to identify the cetuximab resistance mechanism of EPHB3. All statistical tests were two-sided. Results: The expression of EFNB3, which upregulates the EPHB3 receptor, was shown to be increased via microarray analysis. When resistance to cetuximab was acquired, EPHB3 protein levels increased. Hedgehog signaling, cancer stemness, and epithelial-mesenchymal transition signaling proteins were also increased in the cetuximab-resistant human colon cancer cell line SW48R. Despite cells acquiring resistance to cetuximab, STAT3 was still responsive to EGF and cetuximab treatment. Moreover, inhibition of EPHB3 was associated with decreased STAT3 activity. Co-immunoprecipitation confirmed that EGFR and EPHB3 bind to each other and this binding increases upon resistance acquisition, suggesting that STAT3 is activated by the binding between EGFR and EPHB3. Protein levels of GLI-1, SOX2, and Vimentin, which are affected by STAT3, also increased. Similar results were obtained in samples from patients with CRC. Conclusion: EPHB3 expression is associated with anticancer drug resistance.
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Wu W, He K, Guo Q, Chen J, Zhang M, Huang K, Yang D, Wu L, Deng Y, Luo X, Yu H, Ding Q, Xiang G. SSRP1 promotes colorectal cancer progression and is negatively regulated by miR-28-5p. J Cell Mol Med 2019; 23:3118-3129. [PMID: 30762286 PMCID: PMC6484412 DOI: 10.1111/jcmm.14134] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/13/2018] [Accepted: 12/12/2018] [Indexed: 12/15/2022] Open
Abstract
In this study, microarray data analysis, real‐time quantitative PCR and immunohistochemistry were used to detect the expression levels of SSRP1 in colorectal cancer (CRC) tissue and in corresponding normal tissue. The association between structure‐specific recognition protein 1 (SSRP1) expression and patient prognosis was examined by Kaplan‐Meier analysis. SSRP1 was knocked down and overexpressed in CRC cell lines, and its effects on proliferation, cell cycling, migration, invasion, cellular energy metabolism, apoptosis, chemotherapeutic drug sensitivity and cell phenotype‐related molecules were assessed. The growth of xenograft tumours in nude mice was also assessed. MiRNAs that potentially targeted SSRP1 were determined by bioinformatic analysis, Western blotting and luciferase reporter assays. We showed that SSRP1 mRNA levels were significantly increased in CRC tissue. We also confirmed that this upregulation was related to the terminal tumour stage in CRC patients, and high expression levels of SSRP1 predicted shorter disease‐free survival and faster relapse. We also found that SSRP1 modulated proliferation, metastasis, cellular energy metabolism and the epithelial‐mesenchymal transition in CRC. Furthermore, SSRP1 induced apoptosis and SSRP1 knockdown augmented the sensitivity of CRC cells to 5‐fluorouracil and cisplatin. Moreover, we explored the molecular mechanisms accounting for the dysregulation of SSRP1 in CRC and identified microRNA‐28‐5p (miR‐28‐5p) as a direct upstream regulator of SSRP1. We concluded that SSRP1 promotes CRC progression and is negatively regulated by miR‐28‐5p.
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Affiliation(s)
- Wei Wu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,Hubei Key laboratory of Digestive System, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Ke He
- Department of General Surgery, The Second People's Hospital of Guangdong Province, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Qian Guo
- Hepatic Disease Institute, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei, P.R. China
| | - Jingdi Chen
- Department of orthopedics, The Airborne Military Hospital, Wuhan, Hubei, P.R. China
| | - Mengjiao Zhang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,Hubei Key laboratory of Digestive System, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Kai Huang
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Dongmei Yang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,Hubei Key laboratory of Digestive System, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Lu Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,Hubei Key laboratory of Digestive System, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Yunchao Deng
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,Hubei Key laboratory of Digestive System, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Xu Luo
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Honggang Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,Hubei Key laboratory of Digestive System, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Qianshan Ding
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,Hubei Key laboratory of Digestive System, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China.,School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore
| | - Guoan Xiang
- Department of General Surgery, The Second People's Hospital of Guangdong Province, Southern Medical University, Guangzhou, Guangdong, P.R.China
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22
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Birgisson H, Tsimogiannis K, Freyhult E, Kamali-Moghaddam M. Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer. Transl Oncol 2018; 11:1034-1043. [PMID: 29982101 PMCID: PMC6037900 DOI: 10.1016/j.tranon.2018.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/18/2018] [Accepted: 05/23/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND: Due to difficulties in predicting recurrences in colorectal cancer stages II and III, reliable prognostic biomarkers could be a breakthrough for individualized treatment and follow-up. OBJECTIVE: To find potential prognostic protein biomarkers in colorectal cancer, using the proximity extension assays. METHODS: A panel of 92 oncology-related proteins was analyzed with proximity extension assays, in plasma from a cohort of 261 colorectal cancer patients with stage II-IV. The survival analyses were corrected for disease stage and age, and the recurrence analyses were corrected for disease stage. The significance threshold was adjusted for multiple comparisons. RESULTS: The plasma proteins expression levels had a greater prognostic relevance in disease stage III colorectal cancer than in disease stage II, and for overall survival than for time to recurrence. Osteoprotegerin was the only biomarker candidate in the protein panel that had a statistical significant association with overall survival (P = .00029). None of the proteins were statistically significantly associated with time to recurrence. CONCLUSIONS: Of the 92 analyzed plasma proteins, osteoprotegerin showed the strongest prognostic impact in patients with colorectal cancer, and therefore osteoprotegerin is a potential predictive marker, and it also could be a target for treatments.
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Affiliation(s)
- Helgi Birgisson
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.
| | | | - Eva Freyhult
- Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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23
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Strell C, Hilscher MM, Laxman N, Svedlund J, Wu C, Yokota C, Nilsson M. Placing RNA in context and space - methods for spatially resolved transcriptomics. FEBS J 2018. [PMID: 29542254 DOI: 10.1111/febs.14435] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Single-cell transcriptomics provides us with completely new insights into the molecular diversity of different cell types and the different states they can adopt. The technique generates inventories of cells that constitute the building blocks of multicellular organisms. However, since the method requires isolation of discrete cells, information about the original location within tissue is lost. Therefore, it is not possible to draw detailed cellular maps of tissue architecture and their positioning in relation to other cells. In order to better understand the cellular and tissue function of multicellular organisms, we need to map the cells within their physiological, morphological, and anatomical context and space. In this review, we will summarize and compare the different methods of in situ RNA analysis and the most recent developments leading to more comprehensive and highly multiplexed spatially resolved transcriptomic approaches. We will discuss their highlights and advantages as well as their limitations and challenges and give an outlook on promising future applications and directions both within basic research as well as clinical integration.
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Affiliation(s)
- Carina Strell
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Markus M Hilscher
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Navya Laxman
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Jessica Svedlund
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Chenglin Wu
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Chika Yokota
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
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24
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Kou CTJ, Kandpal RP. Differential Expression Patterns of Eph Receptors and Ephrin Ligands in Human Cancers. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7390104. [PMID: 29682554 PMCID: PMC5851329 DOI: 10.1155/2018/7390104] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/11/2018] [Accepted: 01/22/2018] [Indexed: 12/20/2022]
Abstract
Eph receptors constitute the largest family of receptor tyrosine kinases, which are activated by ephrin ligands that either are anchored to the membrane or contain a transmembrane domain. These molecules play important roles in the development of multicellular organisms, and the physiological functions of these receptor-ligand pairs have been extensively documented in axon guidance, neuronal development, vascular patterning, and inflammation during tissue injury. The recognition that aberrant regulation and expression of these molecules lead to alterations in proliferative, migratory, and invasive potential of a variety of human cancers has made them potential targets for cancer therapeutics. We present here the involvement of Eph receptors and ephrin ligands in lung carcinoma, breast carcinoma, prostate carcinoma, colorectal carcinoma, glioblastoma, and medulloblastoma. The aberrations in their abundances are described in the context of multiple signaling pathways, and differential expression is suggested as the mechanism underlying tumorigenesis.
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Affiliation(s)
- Chung-Ting Jimmy Kou
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Raj P. Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
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25
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Wu W, Chen J, Wu J, Lin J, Yang S, Yu H. Knockdown of tripartite motif-59 inhibits the malignant processes in human colorectal cancer cells. Oncol Rep 2017; 38:2480-2488. [PMID: 28849218 DOI: 10.3892/or.2017.5896] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/01/2017] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to clarify the clinical implication and functional role of tripartite motif-59 (TRIM59) in colorectal carcinoma (CRC) and explore the underlying mechanism of aberrant high expression of TRIM59 in cancer. We validated that TRIM59 was upregulated in CRC samples, and also demonstrated that its upregulation was associated with advanced tumor stage of CRC patients; and its high expression indicated shorter overall survival and faster recurrence. Knockdown of TRIM59 significantly inhibited cell proliferation, migration and invasion. Cell cycle analysis showed that TRIM59-depleted cells accumulated in S-phase. In addition, the cell cycle regulators CDC25C, cyclin B1 and cyclin D1 were decreased by TRIM59 siRNA mediated knockdown. Furthermore, the depletion of TRIM59 promoted apoptosis in cell culture as indicated by the cleavage of caspase-3 and PARP when TRIM59 was depleted. These results suggested that TRIM59 is upregulated in human colorectal tumors compared with non-tumor tissues. The level of TRIM59 is correlated with malignant features of CRC and may serve as potential therapeutic and preventive strategies for CRC.
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Affiliation(s)
- Wei Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jingdi Chen
- 73th Contingent, 95969 Troops, The Airborne Force of Chinese PLA, Wuhan, Hubei 430300, P.R. China
| | - Jicheng Wu
- Tumor Basic and Translational Laboratory, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
| | - Jun Lin
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Sheng Yang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Honggang Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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