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Puchalski M, Tretiakow D, Skorek A, Szydłowski K, Stodulski D, Mikaszewski B, Odroniec A, Musiał N, Thiel M, Czaplewska P, Ołdziej S. Comparison of Peptidomes Extracted from Healthy Tissue and Tumor Tissue of the Parotid Glands and Saliva Samples. Int J Mol Sci 2024; 25:8799. [PMID: 39201484 PMCID: PMC11354857 DOI: 10.3390/ijms25168799] [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: 06/21/2024] [Revised: 08/04/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Salivary gland tumors are highly variable in clinical presentation and histology. The World Health Organization (WHO) classifies 22 types of malignant and 11 types of benign tumors of the salivary glands. Diagnosis of salivary gland tumors is based on imaging (ultrasound, magnetic resonance imaging) and fine-needle aspiration biopsy, but the final diagnosis is based on histopathological examination of the removed tumor tissue. In this pilot study, we are testing a new approach to identifying peptide biomarkers in saliva that can be used to diagnose salivary gland tumors. The research material for the peptidomic studies was extracts from washings of neoplastic tissues and healthy tissues (control samples). At the same time, saliva samples from patients and healthy individuals were analyzed. The comparison of the peptidome composition of tissue extracts and saliva samples may allow the identification of potential peptide markers of salivary gland tumors in patients' saliva. The peptidome compositions extracted from 18 tumor and 18 healthy tissue samples, patients' saliva samples (11 samples), and healthy saliva samples (8 samples) were analyzed by LC-MS tandem mass spectrometry. A group of 109 peptides was identified that were present only in the tumor tissue extracts and in the patients' saliva samples. Some of the identified peptides were derived from proteins previously suggested as potential biomarkers of salivary gland tumors (ANXA1, BPIFA2, FGB, GAPDH, HSPB1, IGHG1, VIM) or tumors of other tissues or organs (SERPINA1, APOA2, CSTB, GSTP1, S100A8, S100A9, TPI1). Unfortunately, none of the identified peptides were present in all samples analyzed. This may be due to the high heterogeneity of this type of cancer. The surprising result was that extracts from tumor tissue did not contain peptides derived from salivary gland-specific proteins (STATH, SMR3B, HTN1, HTN3). These results could suggest that the developing tumor suppresses the production of proteins that are essential components of saliva.
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Affiliation(s)
- Michał Puchalski
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (M.P.); (A.O.); (N.M.); (M.T.); (P.C.)
| | - Dmitry Tretiakow
- Department of Otolaryngology, the Nicolaus Copernicus Hospital in Gdansk, Copernicus Healthcare Entity, Powstańców Warszawskich 1/2, 80-152 Gdansk, Poland; (A.S.); (K.S.)
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdansk, Smoluchowskiego 17, 80-214 Gdansk, Poland; (D.S.); (B.M.)
| | - Andrzej Skorek
- Department of Otolaryngology, the Nicolaus Copernicus Hospital in Gdansk, Copernicus Healthcare Entity, Powstańców Warszawskich 1/2, 80-152 Gdansk, Poland; (A.S.); (K.S.)
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdansk, Smoluchowskiego 17, 80-214 Gdansk, Poland; (D.S.); (B.M.)
| | - Konrad Szydłowski
- Department of Otolaryngology, the Nicolaus Copernicus Hospital in Gdansk, Copernicus Healthcare Entity, Powstańców Warszawskich 1/2, 80-152 Gdansk, Poland; (A.S.); (K.S.)
| | - Dominik Stodulski
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdansk, Smoluchowskiego 17, 80-214 Gdansk, Poland; (D.S.); (B.M.)
| | - Bogusław Mikaszewski
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdansk, Smoluchowskiego 17, 80-214 Gdansk, Poland; (D.S.); (B.M.)
| | - Amadeusz Odroniec
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (M.P.); (A.O.); (N.M.); (M.T.); (P.C.)
| | - Natalia Musiał
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (M.P.); (A.O.); (N.M.); (M.T.); (P.C.)
| | - Marcel Thiel
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (M.P.); (A.O.); (N.M.); (M.T.); (P.C.)
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (M.P.); (A.O.); (N.M.); (M.T.); (P.C.)
| | - Stanisław Ołdziej
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (M.P.); (A.O.); (N.M.); (M.T.); (P.C.)
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Cao L, Ba Y, Chen F, Zhang S, Zhang H. Exploration of bacterial lipopolysaccharide-related genes signature based on T cells for predicting prognosis in colorectal cancer. Aging (Albany NY) 2024; 16:11606-11625. [PMID: 39115879 PMCID: PMC11346792 DOI: 10.18632/aging.206041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/19/2024] [Indexed: 08/22/2024]
Abstract
PURPOSE The intratumoral microorganisms participates in the progression and immunotherapy of colorectal cancer (CRC). However, due to technical limitations, the impact of microorganisms on CRC has not been fully understood. Therefore, we conducted a systematic analysis of relationship between bacterial lipopolysaccharide (LPS)-associated genes and immune cells to explore new biomarkers for predicting the prognosis of CRC. METHODS The single-cell RNA sequencing data and the Comparative Toxicogenomics Database were used to screen T cells-associated LPS-related genes (TALRGs). Then, we established and validated the TALRGs risk signature in The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) cohort and GSE39582 cohort. Besides, we compared the differences in tumor-infiltrating immune cell types, immunotherapeutic response, somatic mutation profiles, and tumor mutation burden (TMB) between high-risk group and low-risk group. In addition, the immunotherapeutic cohort (Imvigor210) treated with an anti-PD-L1 agent was performed to explore the potential value of the TALRGs signature on immunotherapy. RESULTS Five prognostic TALRGs were identified and selected to build the prognostic model. The high-risk group had poor prognosis in both TCGA-COAD cohort (P < 0.0001) and GSE39582 cohort (P = 0.00019). The areas under the curves (AUCs) of TALRGs signature were calculated (TCGA-COAD cohort: 0.624 at 1 years, 0.639 at 3 years, 0.648 at 5 years; anti-PD-L1 cohort was 0.59). The high-risk group had advanced pathological stages and higher TMN stages in both TCGA-COAD cohort and GSE39582 cohort. The high-risk group had the higher infiltration of immunosuppressive cells, the expressions of immune checkpoint molecules, the IC50 values of chemotherapy drugs, and TP53 mutation rate (P < 0.05). In addition, patients with high TMB had worse prognosis (P < 0.05). Furthermore, the Imvigor210 also showed patients with high-risk scores had poor prognosis (platinum-treated cohort: P = 0.0032; non-platinum-treated cohort: P = 0.00017). CONCLUSIONS Microorganisms are closely related to the tumor microenvironment to influence the progression and immune response of CRC via stimulating T cells through LPS-related genes. The TALRGs signature contributed to predict the prognosis and immunotherapy of CRC, and became new therapeutic targets and biomarkers of CRC.
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Affiliation(s)
- Lichao Cao
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Ying Ba
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Fang Chen
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Shenrui Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
| | - Hezi Zhang
- Shenzhen Nucleus Gene Technology Co., Ltd., Shenzhen, Guangdong, China
- Shenzhen Nucleus Huaxi Medical Laboratory, Shenzhen, Guangdong, China
- Shanghai Nucleus Biotechnology Co., Ltd., Shanghai, China
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Nielsen BS, Madsen NH, Larsen J, Skandorff I, Gad M, Holmstrøm K. Architectural organization and molecular profiling of 3D cancer heterospheroids and their application in drug testing. Front Oncol 2024; 14:1386097. [PMID: 39011470 PMCID: PMC11246882 DOI: 10.3389/fonc.2024.1386097] [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: 02/14/2024] [Accepted: 05/31/2024] [Indexed: 07/17/2024] Open
Abstract
3D cancer cell cultures have enabled new opportunities for replacing compound testing in experimental animals. However, most solid tumors are composed of multiple cell types, including fibroblasts. In this study we developed multicellular tumor heterospheroids composed of cancer and fibroblasts cell lines. We developed heterospheroids by combining HT-29, MCF-7, PANC-1 or SW480 with 1BR.3.G fibroblasts, which we have previously reported support spheroid formation. We also tested fibroblast cell lines, MRC-5, GM00498 and HIF, but 1BR.3.G was found to best form heterospheroids with morphological similarity to in vivo tumor tissue. The architectural organization of heterospheroids was based on histological examination using immunohistochemistry. We found that HT-29 and MCF-7 cells developed spheroids with the cancer cells surrounding the fibroblasts, whereas PANC-1 cells interspersed with the fibroblasts and SW480 cells were surrounded by fibroblasts. The fibroblasts also expressed collagen-1 and FAP-α, and whole transcriptomic analysis (WTA) showed abundant ECM- and EMT-related expression in heterospheroids, thus reflecting a representative tumor-like microenvironment. The WTA showed that PANC-1 heterospheroids possess a strong EMT profile with abundant Vimentin and CDH2 expression. Drug testing was evaluated by measuring cytotoxicity of 5FU and cisplatin using cell viability and apoptosis assays. We found no major impact on the cytotoxicity when fibroblasts were added to the spheroids. We conclude that the cancer cell lines together with fibroblasts shape the architectural organization of heterospheroids to form tumor-like morphology, and we propose that the various 3D tumor structures can be used for drug testing directed against the cancer cells as well as the fibroblasts.
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Affiliation(s)
- Boye Schnack Nielsen
- Department of Cellular Engineering & Disease Modeling, Bioneer A/S, Hørsholm, Denmark
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Ma Y, Chen Y, Zhan L, Dong Q, Wang Y, Li X, He L, Zhang J. CEBPB-mediated upregulation of SERPINA1 promotes colorectal cancer progression by enhancing STAT3 signaling. Cell Death Discov 2024; 10:219. [PMID: 38710698 DOI: 10.1038/s41420-024-01990-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Colorectal cancer (CRC) is a highly malignant carcinoma associated with poor prognosis, and metastasis is one of the most common causes of death in CRC. Serpin Family A Member 1 (SERPINA1) is a serine protease inhibitor from the Serpin family. Till now, the function and mechanism of SERPINA1 in CRC progression have not been fully illustrated. We established highly metastatic colorectal cancer cells named as RKO-H and Caco2-H by mice liver metastasis model. By integrative bioinformatic approaches, we analyzed the prognostic value and clinical significance of SERPINA1 in CRC, and predicted potential transcription factors. Colony formation, EDU, MTS, Transwell and wound healing assay were performed to evaluate the biological functions of SERPINA1 in CRC in vitro. Experiments in vivo were conducted to explore the effects of SERPINA1 on liver metastasis of CRC. ChIP and luciferase reporter gene assays were performed to identify the transcriptional regulatory mechanism of SERPINA1 by CEBPB. Our results show that SERPINA1 is highly expressed in CRC and correlated with poor clinical outcomes. SERPINA1 promotes the proliferation, migration by activating STAT3 pathway. Mechanistically, CEBPB binds SERPINA1 gene promoter sequence and promotes the transcription of SERPINA1. SERPINA1 drives CEBPB-induced tumor cell growth and migration via augmenting STAT3 signaling. Our results suggest that SERPINA1 is a potential prognostic marker and may serve as a novel treatment target for CRC.
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Affiliation(s)
- Yiming Ma
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
| | - Ying Chen
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Lei Zhan
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
| | - Qian Dong
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
| | - Yuanhe Wang
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
| | - Xiaoyan Li
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China
- Department of Pathology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
| | - Lian He
- Department of Pathology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China
| | - Jingdong Zhang
- Department of Medical Oncology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, China.
- Liaoning Key Laboratory of Gastrointestinal Cancer Translational Research, Shenyang, Liaoning Province, China.
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Buijs JT, van Beijnum R, Anijs RJS, Laghmani EH, Sensuk L, Minderhoud C, Ünlü B, Klok FA, Kuppen PJK, Cannegieter SC, Versteeg HH. The association of tumor-expressed REG4, SPINK4 and alpha-1 antitrypsin with cancer-associated thrombosis in colorectal cancer. J Thromb Thrombolysis 2024; 57:370-380. [PMID: 38066386 PMCID: PMC10961291 DOI: 10.1007/s11239-023-02907-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 03/26/2024]
Abstract
Novel biomarkers are needed to improve current imperfect risk prediction models for cancer-associated thrombosis (CAT). We recently identified an RNA-sequencing profile that associates with CAT in colorectal cancer (CRC) patients, with REG4, SPINK4, and SERPINA1 as the top-3 upregulated genes at mRNA level. In the current study, we investigated whether protein expression of REG4, SPINK4 and alpha-1 antitrypsin (A1AT, encoded by SERPINA1) in the tumor associated with CAT in an independent cohort of CRC patients. From 418 patients with resected CRC, 18 patients who developed CAT were age, sex, and tumor stage-matched to 18 CRC patients without CAT. Protein expression was detected by immunohistochemical staining and scored blindly by assessing the H-score (percentage positive cells*scoring intensity). The association with CAT was assessed by means of logistic regression, using patients with an H-score below 33 as reference group. The odds ratios (ORs) for developing CAT for patients with A1AThigh, REG4high, SPINK4high tumors were 3.5 (95%CI 0.8-14.5), 2.0 (95%CI 0.5-7.6) and 2.0 (95%CI 0.5-7.4) when compared to A1ATlow, REG4low, SPINK4low, respectively. The OR was increased to 24.0 (95%CI 1.1-505.1) when two proteins were combined (A1AThigh/REG4high). This nested case-control study shows that combined protein expression of A1AT and REG4 associate with CAT in patients with colorectal cancer. Therefore, REG4/A1AT are potential biomarkers to improve the identification of patients with CRC who may benefit from thromboprophylaxis.
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Affiliation(s)
- Jeroen T Buijs
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands.
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
| | - Robin van Beijnum
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Rayna J S Anijs
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - El Houari Laghmani
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Lily Sensuk
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Cas Minderhoud
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Betül Ünlü
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Frederikus A Klok
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Suzanne C Cannegieter
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Epidemiology, LUMC, Leiden, The Netherlands
| | - Henri H Versteeg
- Einthoven Laboratory for Vascular and Regenerative Medicine, Division of Thrombosis and Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
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Jeon Y, Lee G, Jeong H, Gong G, Kim J, Kim K, Jeong JH, Lee HJ. Proteomic analysis of breast cancer based on immune subtypes. Clin Proteomics 2024; 21:17. [PMID: 38424522 PMCID: PMC10905797 DOI: 10.1186/s12014-024-09463-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Immunotherapy is applied to breast cancer to resolve the limitations of survival gain in existing treatment modalities. With immunotherapy, a tumor can be classified into immune-inflamed, excluded and desert based on the distribution of immune cells. We assessed the clinicopathological features, each subtype's prognostic value and differentially expressed proteins between immune subtypes. METHODS Immune subtyping and proteomic analysis were performed on 56 breast cancer cases with neoadjuvant chemotherapy. The immune subtyping was based on the level of tumor-infiltrating lymphocytes (TILs) and Klintrup criteria. If the level of TILs was ≥ 10%, it was classified as immune-inflamed type without consideration of the Klintrup criteria. In cases of 1-9% TIL, Klintrup criteria 1-3 were classified as the immune-excluded subtype and Klintrup criteria not available (NA) was classified as NA. Cases of 1% TILs and Klintrup 0 were classified as the immune-desert subtype. Mass spectrometry was used to identify differentially expressed proteins in formalin-fixed paraffin-embedded biopsy tissues. RESULTS Of the 56 cases, 31 (55%) were immune-inflamed, 21 (38%) were immune-excluded, 2 (4%) were immune-desert and 2 (4%) were NA. Welch's t-test revealed two differentially expressed proteins between immune-inflamed and immune-excluded/desert subtypes. Coronin-1A was upregulated in immune-inflamed tumors (adjusted p = 0.008) and α-1-antitrypsin was upregulated in immune-excluded/desert tumors (adjusted p = 0.008). Titin was upregulated in pathologic complete response (pCR) than non-pCR among immune-inflamed tumors (adjusted p = 0.036). CONCLUSIONS Coronin-1A and α-1-antitrypsin were upregulated in immune-inflamed and immune-excluded/desert subtypes, respectively. Titin's elevated expression in pCR within the immune-inflamed subtype may indicate a favorable prognosis. Further studies involving large representative cohorts are necessary to validate these findings.
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Affiliation(s)
- Yeonjin Jeon
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - GunHee Lee
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hwangkyo Jeong
- Prometabio Research Institute, Prometabio co., ltd, Hanam-Si, Gyeonggi-Do, Republic of Korea
| | - Gyungyub Gong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - JiSun Kim
- Division of Breast Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyunggon Kim
- Department of Digital Medicine, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
- Biomedical Sciences, Asan Medical Institute of Convergence Science and Technology (AMIST), Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
- NeogenTC Corp, Seoul, Korea.
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Mirian C, Thastrup M, Mathiasen R, Schmiegelow K, Olsen JV, Østergaard O. Mass spectrometry-based proteomics of cerebrospinal fluid in pediatric central nervous system malignancies: a systematic review with meta-analysis of individual patient data. Fluids Barriers CNS 2024; 21:14. [PMID: 38350915 PMCID: PMC10863112 DOI: 10.1186/s12987-024-00515-x] [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: 09/21/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The cerebrospinal fluid (CSF) proteome could offer important insights into central nervous system (CNS) malignancies. To advance proteomic research in pediatric CNS cancer, the current study aims to (1) evaluate past mass spectrometry-based workflows and (2) synthesize previous CSF proteomic data, focusing on both qualitative summaries and quantitative re-analysis. MAIN: In our analysis of 11 studies investigating the CSF proteome in pediatric patients with acute lymphoblastic leukemia (ALL) or primary brain tumors, we observed significant methodological variability. This variability negatively affects comparative analysis of the included studies, as per GRADE criteria for quality of evidence. The qualitative summaries covered 161 patients and 134 non-tumor controls, while the application of validation cohort varied among the studies. The quantitative re-analysis comprised 15 B-ALL vs 6 "healthy" controls and 15 medulloblastoma patients vs 22 non-tumor controls. Certain CSF proteins were identified as potential indicators of specific malignancies or stages of neurotoxicity during chemotherapy, yet definitive conclusions were impeded by inconsistent data. There were no proteins with statistically significant differences when comparing cases versus controls that were corroborated across studies where quantitative reanalysis was feasible. From a gene ontology enrichment, we observed that age disparities between unmatched case and controls may mislead to protein correlations more indicative of age-related CNS developmental stages rather than neuro-oncological disease. Despite efforts to batch correct (HarmonizR) and impute missing values, merging of dataset proved unfeasible and thereby limited meaningful data integration across different studies. CONCLUSION Infrequent publications on rare pediatric cancer entities, which often involve small sample sizes, are inherently prone to result in heterogeneous studies-particularly when conducted within a rapidly evolving field like proteomics. As a result, obtaining clear evidence, such as CSF proteome biomarkers for CNS dissemination or early-stage neurotoxicity, is currently impractical. Our general recommendations comprise the need for standardized methodologies, collaborative efforts, and improved data sharing in pediatric CNS malignancy research. We specifically emphasize the possible importance of considering natural age-related variations in CSF due to different CNS development stages when matching cases and controls in future studies.
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Affiliation(s)
- Christian Mirian
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Maria Thastrup
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - René Mathiasen
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Velgaard Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Østergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Attachaipanich T, Chattipakorn SC, Chattipakorn N. Current evidence regarding the cellular mechanisms associated with cancer progression due to cardiovascular diseases. J Transl Med 2024; 22:105. [PMID: 38279150 PMCID: PMC10811855 DOI: 10.1186/s12967-023-04803-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/13/2023] [Indexed: 01/28/2024] Open
Abstract
Several large cohort studies in cardiovascular disease (CVD) patients have shown an increased incidence of cancer. Previous studies in a myocardial infarction (MI) mouse model reported increased colon, breast, and lung cancer growth. The potential mechanisms could be due to secreted cardiokines and micro-RNAs from pathological hearts and immune cell reprogramming. A study in a MI-induced heart failure (HF) mouse demonstrated an increase in cardiac expression of SerpinA3, resulting in an enhanced proliferation of colon cancer cells. In MI-induced HF mice with lung cancer, the attenuation of tumor sensitivity to ferroptosis via the secretion of miR-22-3p from cardiomyocytes was demonstrated. In MI mice with breast cancer, immune cell reprogramming toward the immunosuppressive state was shown. However, a study in mice with renal cancer reported no impact of MI on tumor growth. In addition to MI, cardiac hypertrophy was shown to promote the growth of breast and lung cancer. The cardiokine potentially involved, periostin, was increased in the cardiac tissue and serum of a cardiac hypertrophy model, and was reported to increase breast cancer cell proliferation. Since the concept that CVD could influence the initiation and progression of several types of cancer is quite new and challenging regarding future therapeutic and preventive strategies, further studies are needed to elucidate the potential underlying mechanisms which will enable more effective risk stratification and development of potential therapeutic interventions to prevent cancer in CVD patients.
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Affiliation(s)
- Tanawat Attachaipanich
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Siriporn C Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nipon Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Cardiac Electrophysiology Research Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
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9
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Everest‐Dass A, Nersisyan S, Maar H, Novosad V, Schröder‐Schwarz J, Freytag V, Stuke JL, Beine MC, Schiecke A, Haider M, Kriegs M, Elakad O, Bohnenberger H, Conradi L, Raygorodskaya M, Krause L, von Itzstein M, Tonevitsky A, Schumacher U, Maltseva D, Wicklein D, Lange T. Spontaneous metastasis xenograft models link CD44 isoform 4 to angiogenesis, hypoxia, EMT and mitochondria-related pathways in colorectal cancer. Mol Oncol 2024; 18:62-90. [PMID: 37849446 PMCID: PMC10766209 DOI: 10.1002/1878-0261.13535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/10/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Hematogenous metastasis limits the survival of colorectal cancer (CRC) patients. Here, we illuminated the roles of CD44 isoforms in this process. Isoforms 3 and 4 were predominantly expressed in CRC patients. CD44 isoform 4 indicated poor outcome and correlated with epithelial-mesenchymal transition (EMT) and decreased oxidative phosphorylation (OxPhos) in patients; opposite associations were found for isoform 3. Pan-CD44 knockdown (kd) independently impaired primary tumor formation and abrogated distant metastasis in CRC xenografts. The xenograft tumors mainly expressed the clinically relevant CD44 isoforms 3 and 4. Both isoforms were enhanced in the paranecrotic, hypoxic tumor regions but were generally absent in lung metastases. Upon CD44 kd, tumor angiogenesis was increased in the paranecrotic areas, accompanied by reduced hypoxia-inducible factor-1α and CEACAM5 but increased E-cadherin expression. Mitochondrial genes and proteins were induced upon pan-CD44 kd, as were OxPhos genes. Hypoxia increased VEGF release from tumor spheres, particularly upon CD44 kd. Genes affected upon CD44 kd in xenografts specifically overlapped concordantly with genes correlating with CD44 isoform 4 (but not isoform 3) in patients, validating the clinical relevance of the used model and highlighting the metastasis-promoting role of CD44 isoform 4.
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Affiliation(s)
- Arun Everest‐Dass
- Institute for GlycomicsGriffith University, Gold Coast CampusAustralia
| | - Stepan Nersisyan
- Faculty of Biology and BiotechnologyHSE UniversityMoscowRussia
- Institute of Molecular BiologyThe National Academy of Sciences of the Republic of ArmeniaYerevanArmenia
- Armenian Bioinformatics Institute (ABI)YerevanArmenia
- Present address:
Computational Medicine CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Hanna Maar
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Victor Novosad
- Faculty of Biology and BiotechnologyHSE UniversityMoscowRussia
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
| | | | - Vera Freytag
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Johanna L. Stuke
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Mia C. Beine
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Alina Schiecke
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Marie‐Therese Haider
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Malte Kriegs
- Department of Radiobiology and Radiation OncologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Omar Elakad
- Institute of PathologyUniversity Medical Center GöttingenGermany
| | | | - Lena‐Christin Conradi
- Clinic for General, Visceral and Pediatric SurgeryUniversity Medical Center GöttingenGermany
| | | | - Linda Krause
- Institute of Medical Biometry and EpidemiologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Mark von Itzstein
- Institute for GlycomicsGriffith University, Gold Coast CampusAustralia
| | - Alexander Tonevitsky
- Faculty of Biology and BiotechnologyHSE UniversityMoscowRussia
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
- Art Photonics GmbHBerlinGermany
| | - Udo Schumacher
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
- Medical School BerlinGermany
| | - Diana Maltseva
- Faculty of Biology and BiotechnologyHSE UniversityMoscowRussia
| | - Daniel Wicklein
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
- Department of Anatomy and Cell BiologyUniversity of MarburgGermany
| | - Tobias Lange
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
- Institute of Anatomy IJena University HospitalGermany
- Comprehensive Cancer Center Central Germany (CCCG)Jena and LeipzigGermany
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10
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Lee EJ, Noh SJ, Choi H, Kim MW, Kim SJ, Seo YA, Jeong JE, Shin I, Kim JS, Choi JK, Cho DY, Chang S. Comparative RNA-Seq Analysis Revealed Tissue-Specific Splicing Variations during the Generation of the PDX Model. Int J Mol Sci 2023; 24:17001. [PMID: 38069324 PMCID: PMC10707456 DOI: 10.3390/ijms242317001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Tissue-specific gene expression generates fundamental differences in the function of each tissue and affects the characteristics of the tumors that are created as a result. However, it is unclear how much the tissue specificity is conserved during grafting of the primary tumor into an immune-compromised mouse model. Here, we performed a comparative RNA-seq analysis of four different primary-patient derived xenograft (PDX) tumors. The analysis revealed a conserved RNA biotype distribution of primary-PDX pairs, as revealed by previous works. Interestingly, we detected significant changes in the splicing pattern of PDX, which was mainly comprised of skipped exons. This was confirmed by splicing variant-specific RT-PCR analysis. On the other hand, the correlation analysis for the tissue-specific genes indicated overall strong positive correlations between the primary and PDX tumor pairs, with the exception of gastric cancer cases, which showed an inverse correlation. These data propose a tissue-specific change in splicing events during PDX formation as a variable factor that affects primary-PDX integrity.
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Affiliation(s)
- Eun Ji Lee
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Seung-Jae Noh
- PentaMedix Co., Ltd., Seongnam 13449, Republic of Korea; (S.-J.N.); (H.C.); (D.-Y.C.)
| | - Huiseon Choi
- PentaMedix Co., Ltd., Seongnam 13449, Republic of Korea; (S.-J.N.); (H.C.); (D.-Y.C.)
| | - Min Woo Kim
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Su Jin Kim
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Yeon Ah Seo
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Ji Eun Jeong
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Inkyung Shin
- PentaMedix Co., Ltd., Seongnam 13449, Republic of Korea; (S.-J.N.); (H.C.); (D.-Y.C.)
| | - Jong-Seok Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea; (J.-S.K.); (J.-K.C.)
| | - Jong-Kwon Choi
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea; (J.-S.K.); (J.-K.C.)
| | - Dae-Yeon Cho
- PentaMedix Co., Ltd., Seongnam 13449, Republic of Korea; (S.-J.N.); (H.C.); (D.-Y.C.)
| | - Suhwan Chang
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
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11
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Li H, Pan L, Guo J, Lao J, Wei M, Huang F. Integration of single-cell and bulk RNA sequencing to establish a prognostic signature based on tumor-associated macrophages in colorectal cancer. BMC Gastroenterol 2023; 23:385. [PMID: 37950156 PMCID: PMC10638776 DOI: 10.1186/s12876-023-03035-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Several studies have shown significant involvement of tumor-associated macrophages (TAMs) in the tumor microenvironment and cancer progression. However, no data on reliable TAM-related biomarkers are available for predicting the prognosis of patients with colorectal cancer (CRC). We analyzed the clinical data and gene expression profiles of patients with CRC from databases. The single-cell transcriptomic data was applied to identify M2-like TAM-related differentially expressed genes. Univariate Cox and least absolute shrinkage and selection operator regression analyses were used to determine the prognostic signature genes. Then, seven key genes were screened to develop the prognostic signature. In the training and external validation cohorts, the overall survival (OS) of patients in the high-risk group was significantly shorter compared to the low-risk group. Consequently, we created a nomogram that could accurately and reliably predict the prognosis of patient with CRC. A significant correlation was observed between the patient's prognosis, clinical features, sensitivity to anticancer drugs, TME, and risk scores. Moreover, risk score was strongly related to the response to immunotherapy in patients from GSE91061, GSE78220, and GSE60331 cohorts. Finally, high expression of HSPA1A, SERPINA1, CXCL1, and low expression of DNASE1L3 were found in human CRC tissue and normal tissue by using qRT-PCR. In conclusion, the M2-like TAM-related prognostic signature could predict the survival, prognosis, and response of patients with CRC to immunotherapy, which sheds light on the role of TAMs in CRCs and enhances our understanding of TAMs.
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Affiliation(s)
- Hua Li
- Department of Anorectal Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Province, China
| | - Lujuan Pan
- Gastroenterology Department, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Province, China
| | - Junyu Guo
- Department of Anorectal Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Province, China
| | - JianLe Lao
- Department of Cardiothoracic Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Province, China
| | - Mingwei Wei
- Department of Anorectal Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Province, China
| | - Fuda Huang
- Department of Anorectal Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Province, China.
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12
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Kuai X, Lv J, Zhang J, Xu M, Ji J. Serpin Family A Member 1 Is Prognostic and Involved in Immunological Regulation in Human Cancers. Int J Mol Sci 2023; 24:11566. [PMID: 37511325 PMCID: PMC10380780 DOI: 10.3390/ijms241411566] [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: 05/16/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Serpin family A member 1 (SERPINA1) encodes a protease inhibitor participating in many human diseases, but its value in immunoregulation and prognosis of human cancers remains unclear. In this study, through comprehensive analysis of data from The Cancer Genome Atlas (TCGA) datasets, we found that SERPINA1 was dysregulated in many cancers compared with normal tissues. SERPINA1 expression was significantly associated with prognosis, immune subtype, molecular subtype, immune checkpoint (ICP) genes, tumor mutational burden (TMB), microsatellite instability (MSI), and the estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE) score. There was a strong connection between SERPINA1 expression and tumor-infiltrating lymphocytes, and SERPINA1 showed significant relation to gene markers of immune cells in digestive tumors. Fluorescence-based multiplex immunohistochemistry confirmed that SERPINA1 protein expression was related to clinicopathologic features and immune infiltrates in hepatic cancer. This study suggests that SERPINA can potentially serve as a novel biomarker for cancer prognosis and immunotherapy.
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Affiliation(s)
- Xingwang Kuai
- Department of Pathology, Department of Clinical Biobank, Medical School of Nantong University, Nantong 226001, China; (X.K.); (J.L.); (J.Z.)
| | - Jiaying Lv
- Department of Pathology, Department of Clinical Biobank, Medical School of Nantong University, Nantong 226001, China; (X.K.); (J.L.); (J.Z.)
| | - Junyu Zhang
- Department of Pathology, Department of Clinical Biobank, Medical School of Nantong University, Nantong 226001, China; (X.K.); (J.L.); (J.Z.)
| | - Manyu Xu
- Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong 226001, China;
| | - Juling Ji
- Department of Pathology, Department of Clinical Biobank, Medical School of Nantong University, Nantong 226001, China; (X.K.); (J.L.); (J.Z.)
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13
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Lesur A, Bernardin F, Koncina E, Letellier E, Kruppa G, Schmit PO, Dittmar G. Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics. J Proteome Res 2023. [PMID: 37011904 DOI: 10.1021/acs.jproteome.2c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Blood analysis is one of the foundations of clinical diagnostics. In recent years, the analysis of proteins in blood samples by mass spectrometry has taken a jump forward in terms of sensitivity and the number of identified proteins. The recent development of parallel reaction monitoring with parallel accumulation and serial fragmentation (prm-PASEF) combines ion mobility as an additional separation dimension. This increases the proteome coverage while allowing the use of shorter chromatographic gradients. To demonstrate the method's full potential, we used an isotope-labeled synthetic peptide mix of 782 peptides, derived from 579 plasma proteins, spiked into blood plasma samples with a prm-PASEF measurement allowing the quantification of 565 plasma proteins by targeted proteomics. As a less time-consuming alternative to the prm-PASEF method, we describe guided data independent acquisition (dia)-PASEF (g-dia-PASEF) and compare its application to prm-PASEF for measuring blood plasma. To demonstrate both methods' performance in clinical samples, 20 patient plasma samples from a colorectal cancer (CRC) cohort were analyzed. The analysis identified 14 differentially regulated proteins between the CRC patient and control individual plasma samples. This shows the technique's potential for the rapid and unbiased screening of blood proteins, abolishing the need for the preselection of potential biomarker proteins.
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Affiliation(s)
- Antoine Lesur
- Luxembourg Institute of Health, Strassen L-1445, Luxembourg
| | | | - Eric Koncina
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
| | - Elisabeth Letellier
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
| | - Gary Kruppa
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | | | - Gunnar Dittmar
- Luxembourg Institute of Health, Strassen L-1445, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
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14
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Sun R, Yang Y, Lü W, Yang Y, Li Y, Liu Z, Diao D, Wang Y, Chang S, Lu M, Jiang Q, Dai B, Ma X, Zhao C, Lü M, Zhang J, Ding C, Li N, Zhang J, Xiao Z, Zhou D, Huang C. Single-cell transcriptomic analysis of normal and pathological tissues from the same patient uncovers colon cancer progression. Cell Biosci 2023; 13:62. [PMID: 36944972 PMCID: PMC10031920 DOI: 10.1186/s13578-023-01002-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
The aim of the present study was to elucidate the evolutionary trajectory of colon cells from normal colon mucosa, to adenoma, then to carcinoma in the same microenvironment. Normal colon, adenoma and carcinoma tissues from the same patient were analyzed by single-cell sequencing, which perfectly simulated the process of time-dependent colon cancer due to the same microenvironment. A total of 22 cell types were identified. Results suggest the presence of dominant clones of same cells including C2 goblet cell, epithelial cell subtype 1 (Epi1), enterocyte cell subset 0 (Entero0), and Entero5 in carcinoma. Epi1 and Entero0 were Co-enriched in antibacterial and IL-17 signaling, Entero5 was enriched in immune response and mucin-type O-glycan biosynthesis. We discovered new colon cancer related genes including AC007952.4, NEK8, CHRM3, ANO7, B3GNT6, NEURL1, ODC1 and KCNMA1. The function of TBC1D4, LTB, C2CD4A, AND GBP4/5 in T cells needs to be clarified. We used colon samples from the same person, which provide new information for colon cancer therapy.
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Affiliation(s)
- Ruifang Sun
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yang Yang
- School of Public Health, Shaanxi University of Chinese Medicine, Middle Section of Century Avenue, Xianyang, Shaanxi, People's Republic of China.
| | - Weidong Lü
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yanqi Yang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yulong Li
- Department of Gastroenterology, Shaanxi Provincial People's Hospital, 256 Youyi West Road, Xi'an, Shaanxi, People's Republic of China
| | - Zhigang Liu
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Dongmei Diao
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yang Wang
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Su'e Chang
- Department of Orthopedics, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Qiuyu Jiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Bingling Dai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Chang'an Zhao
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Moqi Lü
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Juan Zhang
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Caixia Ding
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Na Li
- School of Pharmacy, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang, Henan, People's Republic of China
| | - Jian Zhang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Zhengtao Xiao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Dangxia Zhou
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
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15
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Atanasova VS, de Jesus Cardona C, Hejret V, Tiefenbacher A, Mair T, Tran L, Pfneissl J, Draganić K, Binder C, Kabiljo J, Clement J, Woeran K, Neudert B, Wohlhaupter S, Haase A, Domazet S, Hengstschläger M, Mitterhauser M, Müllauer L, Tichý B, Bergmann M, Schweikert G, Hartl M, Dolznig H, Egger G. Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model. Cell Mol Gastroenterol Hepatol 2023; 15:1391-1419. [PMID: 36868311 PMCID: PMC10141529 DOI: 10.1016/j.jcmgh.2023.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023]
Abstract
BACKGROUND & AIMS Patient-derived organoid cancer models are generated from epithelial tumor cells and reflect tumor characteristics. However, they lack the complexity of the tumor microenvironment, which is a key driver of tumorigenesis and therapy response. Here, we developed a colorectal cancer organoid model that incorporates matched epithelial cells and stromal fibroblasts. METHODS Primary fibroblasts and tumor cells were isolated from colorectal cancer specimens. Fibroblasts were characterized for their proteome, secretome, and gene expression signatures. Fibroblast/organoid co-cultures were analyzed by immunohistochemistry and compared with their tissue of origin, as well as on gene expression levels compared with standard organoid models. Bioinformatics deconvolution was used to calculate cellular proportions of cell subsets in organoids based on single-cell RNA sequencing data. RESULTS Normal primary fibroblasts, isolated from tumor adjacent tissue, and cancer associated fibroblasts retained their molecular characteristics in vitro, including higher motility of cancer associated compared with normal fibroblasts. Importantly, both cancer-associated fibroblasts and normal fibroblasts supported cancer cell proliferation in 3D co-cultures, without the addition of classical niche factors. Organoids grown together with fibroblasts displayed a larger cellular heterogeneity of tumor cells compared with mono-cultures and closely resembled the in vivo tumor morphology. Additionally, we observed a mutual crosstalk between tumor cells and fibroblasts in the co-cultures. This was manifested by considerably deregulated pathways such as cell-cell communication and extracellular matrix remodeling in the organoids. Thrombospondin-1 was identified as a critical factor for fibroblast invasiveness. CONCLUSION We developed a physiological tumor/stroma model, which will be vital as a personalized tumor model to study disease mechanisms and therapy response in colorectal cancer.
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Affiliation(s)
- Velina S Atanasova
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria; Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | | | - Václav Hejret
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andreas Tiefenbacher
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria; Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Theresia Mair
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Loan Tran
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria; Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Janette Pfneissl
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Kristina Draganić
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Carina Binder
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Julijan Kabiljo
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria; Clinic of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Janik Clement
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Katharina Woeran
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Barbara Neudert
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | | | - Astrid Haase
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Sandra Domazet
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria
| | | | | | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Boris Tichý
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Bergmann
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria; Clinic of General Surgery, Medical University of Vienna, Vienna, Austria; Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Gabriele Schweikert
- Max Planck Institute for Intelligent Systems, Tübingen, Germany; Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Markus Hartl
- Department of Biochemistry and Cell Biology, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria; Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, University of Vienna, Vienna, Austria
| | - Helmut Dolznig
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria.
| | - Gerda Egger
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria; Department of Pathology, Medical University of Vienna, Vienna, Austria; Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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16
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Differential Plasma Proteins Identified via iTRAQ-Based Analysis Serve as Diagnostic Markers of Pancreatic Ductal Adenocarcinoma. DISEASE MARKERS 2023; 2023:5145152. [PMID: 36712921 PMCID: PMC9883097 DOI: 10.1155/2023/5145152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023]
Abstract
Objective We aimed to identify differentially expressed proteins in the plasma of patients with pancreatic cancer and control subjects, which could serve as potential tumor biomarkers. Methods Differentially expressed proteins were determined via isostatic labeling and absolute quantification (iTRAQ). Potential protein biomarkers were identified via enzyme-linked immunosorbent assay (ELISA) in 40 patients and 40 control subjects, and those eventually selected were further validated in 40 pancreatic cancer and normal pancreatic tissues. Results In total, 30 proteins displayed significant differences in expression among which 21 were downregulated and 9 were upregulated compared with the control group. ELISA revealed downregulation of peroxiredoxin-2 (PRDX2) and upregulation of alpha-1-antitrypsin (AAT), Ras-related protein Rab-2B (RAB2B), insulin-like growth factor-binding protein 2 (IGFBP2), Rho-related GTP-binding protein RhoC (RHOC), and prelamin-A/C (LMNA) proteins in 40 other samples of pancreatic cancer. Notably, only AAT, RAB2B, and IGFBP2 levels were consistent with expression patterns obtained with iTRAQ. Moreover, all three proteins displayed a marked increase in pancreatic cancer tissues. Data from ROC curve analysis indicated that the diagnostic ability of AAT, RAB2B, and IGFBP2 combined with carbohydrate antigen 19-9 (CA19-9) for pancreatic cancer was significantly greater than that of the single indexes (area under the curve (AUC): 90% vs. 75% (CA19-9), 76% (AAT), 71% (RAB2B), and 71% (IGFBP2), all P < 0.01). Conclusion AAT, RAB2B, and IGFBP2 could serve as effective biomarkers to facilitate the early diagnosis of pancreatic cancer.
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Alpha-1 antitrypsin expression is upregulated in multidrug-resistant cancer cells. Histochem Cell Biol 2022; 159:431-437. [PMID: 36536187 DOI: 10.1007/s00418-022-02172-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
Identification of the signature molecular profiles involved in therapy resistance is of vital importance in developing new strategies for treatments and disease monitoring. Protein alpha-1 antitrypsin (AAT, encoded by SERPINA1 gene) is an acute-phase protein, and its high expression has been linked with unfavorable clinical outcome in different types of cancer; however, data on its involvement in therapy resistance are still insufficient. We analyzed SERPINA1 mRNA expression in three different multidrug-resistant (MDR) cell lines-U87-TxR, NCI-H460/R, and DLD1-TxR-and in U87 cells grown in alginate microfibers as a 3D cellular model of glioblastoma. Expression of IL-6 as a major modulator of SERPINA1 was also analyzed. Additionally, AAT protein expression in MDR cells was analyzed by immunofluorescence. SERPINA1 gene expression and AAT protein expression were significantly upregulated in all the tested MDR cell lines compared with their sensitive counterparts. Moreover, SERPINA1 was significantly upregulated in 3D models of glioblastoma, previously found to have upregulated drug-resistance-related gene expression compared with 2D cells. With the exception of NCI-H460/R, in all cell lines as well as in a 3D model of U87 cells, increase in SERPINA1 expression correlated with the increase in IL-6 expression. Our results indicate that AAT could be utilized as a biomarker of therapy resistance in cancer; however, further studies are needed to elucidate the mechanisms driving AAT upregulation in therapy resistance and its biological significance in this process.
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Pakalniškytė D, Schönberger T, Strobel B, Stierstorfer B, Lamla T, Schuler M, Lenter M. Rosa26-LSL-dCas9-VPR: a versatile mouse model for tissue specific and simultaneous activation of multiple genes for drug discovery. Sci Rep 2022; 12:19268. [PMID: 36357523 PMCID: PMC9649745 DOI: 10.1038/s41598-022-23127-7] [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: 06/29/2022] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
Transgenic animals with increased or abrogated target gene expression are powerful tools for drug discovery research. Here, we developed a CRISPR-based Rosa26-LSL-dCas9-VPR mouse model for targeted induction of endogenous gene expression using different Adeno-associated virus (AAV) capsid variants for tissue-specific gRNAs delivery. To show applicability of the model, we targeted low-density lipoprotein receptor (LDLR) and proprotein convertase subtilisin/kexin type 9 (PCSK9), either individually or together. We induced up to ninefold higher expression of hepatocellular proteins. In consequence of LDLR upregulation, plasma LDL levels almost abolished, whereas upregulation of PCSK9 led to increased plasma LDL and cholesterol levels. Strikingly, simultaneous upregulation of both LDLR and PCSK9 resulted in almost unaltered LDL levels. Additionally, we used our model to achieve expression of all α1-Antitrypsin (AAT) gene paralogues simultaneously. These results show the potential of our model as a versatile tool for optimized targeted gene expression, alone or in combination.
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Affiliation(s)
- Dalia Pakalniškytė
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Tanja Schönberger
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Benjamin Strobel
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Birgit Stierstorfer
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Nonclinical Drug Safety Germany, 88400 Biberach an der Riß, Germany
| | - Thorsten Lamla
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Discovery Research Coordination, 88400 Biberach an der Riß, Germany
| | - Michael Schuler
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Martin Lenter
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
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Liu W, Du M, Wan H, Yang H, Deng X, Chen Y, Zhang Q. Serpin family A member 1 is an oncogene in glioma and its translation is enhanced by NAD(P)H quinone dehydrogenase 1 through RNA-binding activity. Open Med (Wars) 2022; 17:1645-1654. [PMID: 36349191 PMCID: PMC9587530 DOI: 10.1515/med-2022-0572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/06/2022] Open
Abstract
Serpin family A member 1 (SERPINA1) is expressed abundantly in gliomas and can predict unfavorable prognosis of patients with glioma. Studies have shown that nicotinamide adenine dinucleotide phosphate quinone dehydrogenase 1 (NQO1) can promote the proliferation of glioblastoma multiforme cells and enhance the expression of SERPINA1, but its effects on glioma cells remain unknown. In this study, we explored the functions of SERPINA1 in glioma tumorigenesis in vitro and then investigated whether NQO1 affects the protein expression of SERPINA1 and its mRNA level. The results showed that the translation of SERPINA1 was suppressed while its mRNA level had no significant changes under the condition of NQO1 silencing. Luciferase reporter assay and biotin pull-down assay further indicated that NQO1 bond with SERPINA1 3′ untranslated region. miR-1321 was also identified to target SERPINA1, repressing its mRNA and protein levels. SERPINA1 and NQO1 promoted glioma cell proliferation and suppressed cell apoptosis. Moreover, SERPINA1 rescued the effects of sh-NQO1 in glioma cell malignant phenotypes. In conclusion, our findings showed that oncogene NQO1 and antioncogene miR-1321 bind to oncogene SERPINA1 to affect proliferation and apoptosis of glioma cells, which can bring new solution of antitumor treatments for glioma in the future.
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Affiliation(s)
- Wenjun Liu
- Department of Neurology, Hubei No. 3 People’s Hospital of Jianghan University , Wuhan , Hubei , China
| | - Min Du
- Department of Neurology, Hubei No. 3 People’s Hospital of Jianghan University , Wuhan , Hubei , China
| | - Hongping Wan
- Department of Neurology, Hubei No. 3 People’s Hospital of Jianghan University , Wuhan , Hubei , China
| | - Hao Yang
- Department of Neurology, Hubei No. 3 People’s Hospital of Jianghan University , No. 26 Zhongshan Avenue, Qiaokou District , Wuhan , Hubei , China
| | - Xiaorong Deng
- Department of Neurology, Hubei No. 3 People’s Hospital of Jianghan University , No. 26 Zhongshan Avenue, Qiaokou District , Wuhan , Hubei , China
| | - Yu Chen
- Department of Neurology, Hubei No. 3 People’s Hospital of Jianghan University , Wuhan , Hubei , China
| | - Qian Zhang
- Department of Neurology, Hubei No. 3 People’s Hospital of Jianghan University , Wuhan , Hubei , China
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Rodriguez A, Corchete LA, Alcazar JA, Montero JC, Rodriguez M, Chinchilla-Tábora LM, Vidal Tocino R, Moyano C, Muñoz-Bravo S, Sayagués JM, Abad M. Dysregulated Expression of Three Genes in Colorectal Cancer Stratifies Patients into Three Risk Groups. Cancers (Basel) 2022; 14:cancers14174076. [PMID: 36077612 PMCID: PMC9454483 DOI: 10.3390/cancers14174076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Despite advances in recent years in the study of the molecular profile of sporadic colorectal cancer (sCRC), the specific genetic events that lead to increased aggressiveness or the development of the metastatic process of tumours are not yet clear. In previous studies of the gene expression profile (GEP) using a high-density array (50,000 genes and 6000 miRNAs in a single assay) in sCRC tumours, we identified a 28-gene signature that was found to be associated with an adverse prognostic value for predicting patient survival. Here, we analyse the differential expression of these 28 genes for their possible association with tumour local aggressiveness and metastatic processes in 66 consecutive sCRC patients, followed for >5 years, using the NanoString nCounter platform. The global transcription profile (expression levels of the 28 genes studied simultaneously) allowed us to discriminate between sCRC tumours and nontumoral colonic tissues. Analysis of the biological and functional significance of the dysregulated GEPs observed in our sCRC tumours revealed 31 significantly altered canonical pathways. Among the most commonly altered pathways, we observed the increased expression of genes involved in signalling pathways and cellular processes, such as the PI3K-Akt pathway, the interaction with the extracellular matrix (ECM), and other functions related to cell signalling processes (SRPX2). From a prognostic viewpoint, the altered expression of BST2 and SRPX2 genes were the only independent variables predicting for disease-free survival (DFS). In addition to the pT stage at diagnosis, dysregulated transcripts of ADH1B, BST2, and FER1L4 genes showed a prognostic impact on OS in the multivariate analysis. Based on the altered expression of these three genes, a scoring system was built to stratify patients into low-, intermediate-, and high-risk groups with significantly different 5-year OS rates: 91%, 83%, and 52%, respectively. The prognostic impact was validated in two independent series of sCRC patients from the public GEO database (n = 562 patients). In summary, we show a strong association between the altered expression of three genes and the clinical outcome of sCRC patients, making them potential markers of suitability for adjuvant therapy after complete tumour resection. Additional prospective studies in larger series of patients are required to confirm the clinical utility of the newly identified biomarkers because the number of patients analysed remains small.
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Affiliation(s)
- Alba Rodriguez
- Department of Pathology and IBSAL, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Luís Antonio Corchete
- Cancer Research Center and Hematology Service, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - José Antonio Alcazar
- General and Gastrointestinal Surgery Service, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Juan Carlos Montero
- Department of Pathology and IBSAL, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Marta Rodriguez
- Department of Pathology and IBSAL, University Hospital of Salamanca, 37007 Salamanca, Spain
| | | | - Rosario Vidal Tocino
- Medical Oncology Service and IBSAL, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Carlos Moyano
- Clinical Biochemistry Service, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Saray Muñoz-Bravo
- Department of Pathology and IBSAL, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - José María Sayagués
- Department of Pathology and IBSAL, University Hospital of Salamanca, 37007 Salamanca, Spain
- Correspondence: (J.M.S.); (M.A.)
| | - Mar Abad
- Department of Pathology and IBSAL, University Hospital of Salamanca, 37007 Salamanca, Spain
- Correspondence: (J.M.S.); (M.A.)
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Simó-Riudalbas L, Offner S, Planet E, Duc J, Abrami L, Dind S, Coudray A, Coto-Llerena M, Ercan C, Piscuoglio S, Andersen CL, Bramsen JB, Trono D. Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis. Nat Commun 2022; 13:4913. [PMID: 35987910 PMCID: PMC9392749 DOI: 10.1038/s41467-022-32649-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThe treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we find that expression of the hominid-restricted retrogene POU5F1B through aberrant activation of a primate-specific endogenous retroviral promoter is a strong negative prognostic biomarker. Correlating this observation, we demonstrate that POU5F1B fosters the proliferation and metastatic potential of CRC cells. We further determine that POU5F1B, in spite of its phylogenetic relationship with the POU5F1/OCT4 transcription factor, is a membrane-enriched protein that associates with protein kinases and known targets or interactors as well as with cytoskeleton-related molecules, and induces intracellular signaling events and the release of trans-acting factors involved in cell growth and cell adhesion. As POU5F1B is an apparently non-essential gene only lowly expressed in normal tissues, and as POU5F1B-containing TcGTs are detected in other tumors besides CRC, our data provide interesting leads for the development of cancer therapies.
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22
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Celsi F, Monasta L, Arrigoni G, Battisti I, Licastro D, Aloisio M, Di Lorenzo G, Romano F, Ricci G, Ura B. Gel-Based Proteomic Identification of Suprabasin as a Potential New Candidate Biomarker in Endometrial Cancer. Int J Mol Sci 2022; 23:ijms23042076. [PMID: 35216190 PMCID: PMC8880426 DOI: 10.3390/ijms23042076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
Endometrial cancer (EC) is the most frequent gynaecologic cancer in postmenopausal women. We used 2D-DIGE and mass spectrometry to identify candidate biomarkers in endometrial cancer, analysing the serum protein contents of 10 patients versus 10 control subjects. Using gel-based proteomics, we identified 24 candidate biomarkers, considering only spots with a fold change in volume percentage ≥ 1.5 or intensity change ≤ 0.6, which were significantly different between cases and controls (p < 0.05). We used Western blotting analysis both in the serum and tissue of 43 patients for data validation. Among the identified proteins, we selected Suprabasin (SBSN), an oncogene previously associated with poor prognosis in different cancers. SBSN principal isoforms were subjected to Western blotting analysis in serum and surgery-excised tissue: both isoforms were downregulated in the tissue. However, in serum, isoform 1 was upregulated, while isoform 2 was downregulated. Data-mining on the TCGA and GTEx projects, using the GEPIA2.0 interface, indicated a diminished SBSN expression in the Uterine Corpus Endometrial Cancer (UCEC) database compared to normal tissue, confirming proteomic results. These results suggest that SBSN, specifically isoform 2, in tissue or serum, could be a potential novel biomarker in endometrial cancer.
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Affiliation(s)
- Fulvio Celsi
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Lorenzo Monasta
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy;
- Proteomics Centre, University of Padova and Azienda Ospedaliera di Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- Correspondence: (G.A.); (B.U.)
| | - Ilaria Battisti
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy;
- Proteomics Centre, University of Padova and Azienda Ospedaliera di Padova, 35131 Padova, Italy
| | - Danilo Licastro
- ARGO Laboratorio Genomica ed Epigenomica, AREA Science Park, Basovizza, 34149 Trieste, Italy;
| | - Michelangelo Aloisio
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Giovanni Di Lorenzo
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Federico Romano
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
| | - Giuseppe Ricci
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34129 Trieste, Italy
| | - Blendi Ura
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 65/1 Via dell’Istria, 34137 Trieste, Italy; (F.C.); (L.M.); (M.A.); (G.D.L.); (F.R.); (G.R.)
- Correspondence: (G.A.); (B.U.)
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Definition of an Inflammatory Biomarker Signature in Plasma-Derived Extracellular Vesicles of Glioblastoma Patients. Biomedicines 2022; 10:biomedicines10010125. [PMID: 35052804 PMCID: PMC8773644 DOI: 10.3390/biomedicines10010125] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GB) is an aggressive type of tumour for which therapeutic options and biomarkers are limited. GB diagnosis mostly relies on symptomatic presentation of the tumour and, in turn, brain imaging and invasive biopsy that can delay its diagnosis. Description of easily accessible and effective biomarkers present in biofluids would thus prove invaluable in GB diagnosis. Extracellular vesicles (EVs) derived from both GB and stromal cells are essential to intercellular crosstalk in the tumour bulk, and circulating EVs have been described as a potential reservoir of GB biomarkers. Therefore, EV-based liquid biopsies have been suggested as a promising tool for GB diagnosis and follow up. To identify GB specific proteins, sEVs were isolated from plasma samples of GB patients as well as healthy volunteers using differential ultracentrifugation, and their content was characterised through mass spectrometry. Our data indicate the presence of an inflammatory biomarker signature comprising members of the complement and regulators of inflammation and coagulation including VWF, FCGBP, C3, PROS1, and SERPINA1. Overall, this study is a step forward in the development of a non-invasive liquid biopsy approach for the identification of valuable biomarkers that could significantly improve GB diagnosis and, consequently, patients’ prognosis and quality of life.
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Tang X, Sui X, Weng L, Liu Y. SNAIL1: Linking Tumor Metastasis to Immune Evasion. Front Immunol 2021; 12:724200. [PMID: 34917071 PMCID: PMC8669501 DOI: 10.3389/fimmu.2021.724200] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
The transcription factor Snail1, a key inducer of epithelial-mesenchymal transition (EMT), plays a critical role in tumor metastasis. Its stability is strictly controlled by multiple intracellular signal transduction pathways and the ubiquitin-proteasome system (UPS). Increasing evidence indicates that methylation and acetylation of Snail1 also affects tumor metastasis. More importantly, Snail1 is involved in tumor immunosuppression by inducing chemokines and immunosuppressive cells into the tumor microenvironment (TME). In addition, some immune checkpoints potentiate Snail1 expression, such as programmed death ligand 1 (PD-L1) and T cell immunoglobulin 3 (TIM-3). This mini review highlights the pathways and molecules involved in maintenance of Snail1 level and the significance of Snail1 in tumor immune evasion. Due to the crucial role of EMT in tumor metastasis and tumor immunosuppression, comprehensive understanding of Snail1 function may contribute to the development of novel therapeutics for cancer.
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Affiliation(s)
- Xiaolong Tang
- Department of Laboratory Medicine, Binzhou Medical University, Binzhou, China
| | - Xue Sui
- Department of Laboratory Medicine, Binzhou Medical University, Binzhou, China
| | - Liang Weng
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Xiangya Hospital, Central South University, Changsha, China.,Hunan Provincial Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Institute of Gerontological Cancer Research, National Clinical Research Center for Gerontology, Changsha, China.,Center for Molecular Imaging of Central South University, Xiangya Hospital, Changsha, China
| | - Yongshuo Liu
- Department of Clinical Laboratory, Binzhou Medical University Hospital, Binzhou, China.,Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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25
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Li Y, Deng Y, He J. Monocyte-related gene biomarkers for latent and active tuberculosis. Bioengineered 2021; 12:10799-10811. [PMID: 34751089 PMCID: PMC8809927 DOI: 10.1080/21655979.2021.2003931] [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] [Indexed: 11/01/2022] Open
Abstract
Monocytes are closely associated with tuberculosis (TB). Latent tuberculosis in some patients gradually develops into its active state. This study aimed to investigate the role of hub monocyte-associated genes in distinguishing latent TB infection (LTBI) from active TB. The gene expression profiles of 15 peripheral blood mononuclear cells (PBMCs) samples were downloaded from the gene expression omnibus (GEO) database, GSE54992. The monocyte abundance was high in active TB as evaluated by the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm. The limma test and correlation analysis documented 165 differentially expressed monocyte-related genes (DEMonRGs) between latent TB and active TB. Functional annotation and enrichment analyses of the DEMonRGs using the database for annotation, visualization, and integration discovery (DAVID) tools showed enrichment of inflammatory response mechanisms and immune-related pathways. A protein-protein interaction network was constructed with a node degree ≥10. The expression levels of these hub DEMonRGs (SERPINA1, FUCA2, and HP) were evaluated and verified using several independent datasets and clinical settings. Finally, a single sample scoring method was used to establish a gene signature for the three DEMonRGs, distinguishing active TB from latent TB. The findings of the present study provide a better understanding of monocyte-related molecular fundamentals in TB progression and contribute to the identification of new potential biomarkers for the diagnosis of active TB.
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Affiliation(s)
- Yu Li
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning Guangxi, China
| | - Yaju Deng
- Emergency Department, Guangxi District Maternal and Child Health Hospital, Nanning, Guangxi, China
| | - Jie He
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China.,Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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26
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Rocconi RP, Wilhite AM, Schambeau L, Scalici J, Pannell L, Finan MA. A novel proteomic-based screening method for ovarian cancer using cervicovaginal fluids: A window into the abdomen. Gynecol Oncol 2021; 164:181-186. [PMID: 34756750 DOI: 10.1016/j.ygyno.2021.10.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Our objective is to develop a site-specific proteomic-based screening test for ovarian cancer(OC) using the mucus of the cervix and vagina and evaluate a potential means for home testing. METHODS Cervicovaginal fluid samples were obtained from ovarian cancer and normal control patients for LC-mass spectrometry(MS) proteomic evaluation. Statistical modeling determined the protein panel with the highest penetrance across ovarian cancer samples. A subcohort of patients consented to provide self-collected vaginal samples at home with questionnaire on feasibility. Cohen's kappa methodology was utilized to determine agreement between physician-collected and patient-collected samples. RESULTS A total of 83 consecutive patient samples were collected prospectively (33 ovarian cancer & 50 controls). Thirty patients consented for self-collection. Using LC-MS, 30 peptides demonstrated independent statistical significance for detecting ovarian cancer. Using statistical modeling, the protein panel that determined the best predictor for detecting OC formed a "fingerprint" consisting of 5 proteins: serine proteinase inhibitor A1; periplakin; profilin1; apolipoprotein A1; and thymosin beta4-like protein. These peptides demonstrated a significant increase probability of detecting ovarian cancer with the ROC curve having an AUC of 0.86 (p = 0.00001). Physician-collected and patient-collected specimens demonstrated moderate agreement with kappa average of 0.6 with upper bound of 0.75. CONCLUSIONS Using novel site-specific collection methods, we identified an OC "fingerprint" with adequate sensitivity and specificity to warrant further evaluation in a larger cohort. Agreement of physician-collected and patient-collected samples were encouraging and could improve access to screening with a home self-collection if this screening test is validated in future studies.
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Affiliation(s)
- Rodney P Rocconi
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, United States of America.
| | - Annelise M Wilhite
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, United States of America
| | - Lindsay Schambeau
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, United States of America
| | - Jennifer Scalici
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, United States of America
| | - Lewis Pannell
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, United States of America
| | - Michael A Finan
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, United States of America
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Chen S, Wang Y, Wang B, Zhang L, Su Y, Xu M, Zhang M. A signature based on 11 autophagy genes for prognosis prediction of colorectal cancer. PLoS One 2021; 16:e0258741. [PMID: 34699544 PMCID: PMC8547631 DOI: 10.1371/journal.pone.0258741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/04/2021] [Indexed: 01/26/2023] Open
Abstract
Aim To develop an autophagy-gene-based signature that could help to anticipate the therapeutic effects of Colorectal Cancer (CRC). Methods We downloaded the gene expression profiles of CRC samples from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) datasets. Genes with significant prognostic value in CRC were screened through univariate Cox regression analysis, while the LASSO Cox regression method was applied to screen optimal genes to construct the autophagy‐related prognostic signature. Results 11 autophagy genes were identified and selected for the establishment of prognosis prediction model for CRC patients. The CRC patients were classified into the low- and high-risk groups according to the optimal cutoff value. The time-dependent ROC curves indicated the good performance of this model in prognosis prediction, with AUC values of 0.66, 0.66, and 0.67 at 1, 3 and 5 years for TCGA samples, as well as AUC values of 0.63, 0.65 and 0.64 for GEO samples, respectively. The multivariate Cox regression analysis results confirmed risk score as the independent marker for prognosis prediction in CRC. Besides, the constructed nomogram also had high predictive value. The results analysis on the tumor infiltrating immune cells (TIICs) relative ratios and mRNA levels of key immune checkpoint receptors indicated the signature was closely related to immune microenvironment of CRC in the context of TIICs and immune checkpoint receptors’ mRNA level. The proportion of MSI-L + MSI-H in the high-risk group was higher than that in the low-risk group. Moreover, the tumor purity was evaluated by estimate function package suggested that lower tumor purity in CRC might lead to a poorer prognosis. Conclusion The autophagy-related features obtained in this study were able to divide the CRC patients into low- and high-risk groups, which should be contribute to the decision-making of CRC treatment.
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Affiliation(s)
- Shuo Chen
- Department of colorectal Surgery, Tianjin Union Medical Center, Tianjin, P.R. China
- Tianjin Institute of Coloproctology, Tianjin, P.R. China
- * E-mail:
| | - Yan Wang
- Department of Traditional Chinese Medicine, Shanghai Pudong New Area People’s Hospital, Shanghai, P.R. China
| | - Boxue Wang
- Department of colorectal Surgery, Tianjin Union Medical Center, Tianjin, P.R. China
- Tianjin Institute of Coloproctology, Tianjin, P.R. China
| | - Lin Zhang
- Department of colorectal Surgery, Tianjin Union Medical Center, Tianjin, P.R. China
- Tianjin Institute of Coloproctology, Tianjin, P.R. China
| | - Yinan Su
- Department of colorectal Surgery, Tianjin Union Medical Center, Tianjin, P.R. China
- Tianjin Institute of Coloproctology, Tianjin, P.R. China
| | - Mingyue Xu
- Department of colorectal Surgery, Tianjin Union Medical Center, Tianjin, P.R. China
- Tianjin Institute of Coloproctology, Tianjin, P.R. China
| | - Mingqing Zhang
- Department of colorectal Surgery, Tianjin Union Medical Center, Tianjin, P.R. China
- Tianjin Institute of Coloproctology, Tianjin, P.R. China
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Meng K, Cao J, Dong Y, Zhang M, Ji C, Wang X. Application of Bioinformatics Analysis to Identify Important Pathways and Hub Genes in Ovarian Cancer Affected by WT1. Front Bioeng Biotechnol 2021; 9:741051. [PMID: 34692659 PMCID: PMC8526536 DOI: 10.3389/fbioe.2021.741051] [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: 07/14/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022] Open
Abstract
Wilms tumor gene (WT1) is used as a marker for the diagnosis and prognosis of ovarian cancer. However, the molecular mechanisms involving WT1 in ovarian cancer require further study. Herein, we used bioinformatics and other methods to identify important pathways and hub genes in ovarian cancer affected by WT1. The results showed that WT1 is highly expressed in ovarian cancer and is closely related to the overall survival and progression-free survival (PFS) of ovarian cancer. In ovarian cancer cell line SKOV3, WT1 downregulation increased the mRNA expression of 638 genes and decreased the mRNA expression of 512 genes, which were enriched in the FoxO, AMPK, and the Hippo signaling pathways. The STRING online tool and Cytoscape software were used to construct a Protein-protein interaction (PPI) network and for Module analysis, and 18 differentially expressed genes (DEGs) were selected. Kaplan-Meier plotter analysis revealed that 16 of 18 genes were related to prognosis. Analysis of GEPIA datasets indicated that 7 of 16 genes were differentially expressed in ovarian cancer tissues and in normal tissues. The expression of IGFBP1 and FBN1 genes increased significantly after WT1 interference, while the expression of the SERPINA1 gene decreased significantly. The correlation between WT1 expression and that of these three genes was consistent with that of ovarian cancer tissues and normal tissues. According to the GeneMANIA online website analysis, there were complex interactions between WT1, IGFBP1, FBN1, SERPINA1, and 20 other genes. In conclusion, we have identified important signaling pathways involving WT1 that affect ovarian cancer, and distinguished three differentially expressed genes regulated by WT1 associated with the prognosis of ovarian cancer. Our findings provide evidence outlining mechanisms involving WT1 gene expression in ovarian cancer and provides a rational for novel treatment of ovarian cancer.
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Affiliation(s)
- Kai Meng
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Jinghe Cao
- Affiliated Hospital of Jining Medical University, Jining, China
| | - Yehao Dong
- Affiliated Hospital of Jining Medical University, Jining, China
| | - Mengchen Zhang
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Chunfeng Ji
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Xiaomei Wang
- College of Basic Medicine, Jining Medical University, Jining, China
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Li J, Du J, Wang Y, Jia H. A Coagulation-Related Gene-Based Prognostic Model for Invasive Ductal Carcinoma. Front Genet 2021; 12:722992. [PMID: 34621293 PMCID: PMC8490773 DOI: 10.3389/fgene.2021.722992] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022] Open
Abstract
Background: Invasive ductal carcinoma (IDC) is the most common type of metastatic breast cancer. Due to the lack of valuable molecular biomarkers, the diagnosis and prognosis of IDC remain a challenge. A large number of studies have confirmed that coagulation is positively correlated with angiogenesis-related factors in metastatic breast cancer. Therefore, the purpose of this study was to construct a COAGULATION-related genes signature for IDC using the bioinformatics approaches. Methods: The 50 hallmark gene sets were obtained from the molecular signature database (MsigDB) to conduct Gene Set Variation Analysis (GSVA). Gene Set Enrichment Analysis (GSEA) was applied to analyze the enrichment of HALLMARK_COAGULATION. The COAGULATION-related genes were extracted from the gene set. Then, Limma Package was used to identify the differentially expressed COAGULATION-related genes (DECGs) between ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) samples in GSE26340 data set. A total of 740 IDC samples from The Cancer Genome Atlas (TCGA) database were divided into a training set and a validation set (7:3). The univariate and multivariate Cox regression analyses were performed to construct a risk signature, which divided the IDC samples into the high- and low-risk groups. The overall survival (OS) curve and receiver operating characteristic (ROC) curve were drawn in both training set and validation set. Finally, a nomogram was constructed to predict the 1-, 2-, 3-, 4-, and 5-year survival rates of IDC patients. Quantitative real-time fluorescence PCR (qRT-PCR) was performed to verify the expression levels of the prognostic genes. Results: The "HALLMARK_COAGULATION" was significantly activated in IDC. There was a significant difference in the clinicopathological parameters between the DCIS and IDC patients. Twenty-four DECGs were identified, of which five genes (SERPINA1, CAPN2, HMGCS2, MMP7, and PLAT) were screened to construct the prognostic model. The high-risk group showed a significantly lower survival rate than the low-risk group both in the training set and validation set (p=3.5943e-06 and p=0.014243). The risk score was demonstrated to be an independent predictor of IDC prognosis. A nomogram including risk score, pathological_stage, and pathological_N provided a quantitative method to predict the survival probability of 1-, 2-, 3-, 4-, and 5-year in IDC patients. The results of decision curve analysis (DCA) further demonstrated that the nomogram had a high potential for clinical utility. Conclusion: This study established a COAGULATION-related gene signature and showed its prognostic value in IDC through a comprehensive bioinformatics analysis, which may provide a potential new prognostic mean for patients with IDC.
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Affiliation(s)
- Jing Li
- Department of Breast Surgery, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Jiajia Du
- Department of Breast Surgery, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yanhong Wang
- Department of Microbiology and Immunology, Shanxi Medical University, Taiyuan, China
| | - Hongyan Jia
- Department of Breast Surgery, First Hospital of Shanxi Medical University, Taiyuan, China
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Snail Upregulates Transcription of FN, LEF, COX2, and COL1A1 in Hepatocellular Carcinoma: A General Model Established for Snail to Transactivate Mesenchymal Genes. Cells 2021; 10:cells10092202. [PMID: 34571852 PMCID: PMC8467536 DOI: 10.3390/cells10092202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/14/2021] [Accepted: 08/22/2021] [Indexed: 12/21/2022] Open
Abstract
SNA is one of the essential EMT transcriptional factors capable of suppressing epithelial maker while upregulating mesenchymal markers. However, the mechanisms for SNA to transactivate mesenchymal markers was not well elucidated. Recently, we demonstrated that SNA collaborates with EGR1 and SP1 to directly upregulate MMP9 and ZEB1. Remarkably, a SNA-binding motif (TCACA) upstream of EGR/SP1 overlapping region on promoters was identified. Herein, we examined whether four other mesenchymal markers, lymphoid enhancer-binding factor (LEF), fibronectin (FN), cyclooxygenase 2 (COX2), and collagen type alpha I (COL1A1) are upregulated by SNA in a similar fashion. Expectedly, SNA is essential for expression of these mesenchymal genes. By deletion mapping and site directed mutagenesis coupled with dual luciferase promoter assay, SNA-binding motif and EGR1/SP1 overlapping region are required for TPA-induced transcription of LEF, FN, COX2 and COL1A1. Consistently, TPA induced binding of SNA and EGR1/SP1 on relevant promoter regions of these mesenchymal genes using ChIP and EMSA. Thus far, we found six of the mesenchymal genes are transcriptionally upregulated by SNA in the same fashion. Moreover, comprehensive screening revealed similar sequence architectures on promoter regions of other SNA-upregulated mesenchymal markers, suggesting that a general model for SNA-upregulated mesenchymal genes can be established.
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Madka V, Kumar G, Pathuri G, Panneerselvam J, Zhang Y, Ganta V, Lightfoot S, Lubet RA, Suen CS, Steele VE, Janakiram NB, Mohammed A, Rao CV. Proton pump inhibitor omeprazole suppresses carcinogen induced colonic adenoma progression to adenocarcinoma in F344 rat. Cancer Prev Res (Phila) 2021; 14:1009-1020. [PMID: 34341012 DOI: 10.1158/1940-6207.capr-21-0057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/25/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022]
Abstract
Colorectal cancer (CRC) causes over 53,000 deaths annually in the United States. Its rising incidences worldwide and particularly in young adults is a major concern. Here, we evaluated the efficacy of omeprazole (OME) that is clinically approved for treating acid-reflux, to enable its repurposing for CRC prevention. In the azoxymethane (AOM)-induced rat CRC model, dietary OME (250 and 500 ppm) was administered at early adenoma stage (8 weeks after AOM) to assess the progression of early lesions to adenocarcinoma. Administration of OME at 250 ppm or 500 ppm doses led to suppression of total colon adenocarcinoma incidence by 15.7% and 32% (p<0.01), respectively. Importantly, invasive carcinoma incidence was reduced by 59% (p<0.0005) and 90% (p<0.0001) in OME administered rats in a dose-dependent manner. There was also a strong and dose-dependent inhibition in the adenocarcinoma multiplicity in rats exposed to OME. Administration of 250 and 500 ppm OME inhibited total colon adenocarcinoma multiplicity by ~49% and ~65% (p<0.0001), respectively. While non-invasive adenocarcinomas multiplicity was suppressed by ~34% to ~48% (p<0.02), the invasive carcinomas multiplicity was reduced by ~74% to ~94% (p<0.0001) in OME exposed rats in comparison to the untreated rats. Biomarker analysis results showed a decrease in cell proliferation and anti-apoptotic/pro-survival proteins with an increase in apoptosis. Transcriptome analysis of treated tumors revealed a significant increase in adenocarcinoma inhibitory genes (Olmf4; Spink4) expression and down regulation of progression promoting genes (SerpinA1, MMP21, IL6). In summary, OME showed significant protection against the progression of adenoma to adenocarcinoma.
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Affiliation(s)
- Venkateshwar Madka
- Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section, University of Oklahoma Health Sciences Center
| | - Gaurav Kumar
- Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section, University of Oklahoma Health Sciences Center
| | - Gopal Pathuri
- Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section, University of Oklahoma Health Sciences Center
| | - Janani Panneerselvam
- Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section, University of Oklahoma Health Sciences Center
| | - Yuting Zhang
- Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section, University of Oklahoma Health Sciences Center
| | - Vishal Ganta
- Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section, University of Oklahoma Health Sciences Center
| | - Stanley Lightfoot
- Pathology-Retired, Center for Cancer Prevention and Drug Development
| | - Ronald A Lubet
- Division of Cancer Prevention, National Cancer Institute
| | - Chen S Suen
- Cancer Prevention, National Cancer Institute
| | | | | | - Altaf Mohammed
- Division of Cancer Prevention, National Cancer Institute
| | - Chinthalapally V Rao
- Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section, University of Oklahoma Health Sciences Center
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Wang Y, Lin K, Xu T, Wang L, Fu L, Zhang G, Ai J, Jiao Y, Zhu R, Han X, Cai H. Development and validation of prognostic model based on the analysis of autophagy-related genes in colon cancer. Aging (Albany NY) 2021; 13:19028-19047. [PMID: 34315829 PMCID: PMC8351728 DOI: 10.18632/aging.203352] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/08/2021] [Indexed: 04/12/2023]
Abstract
BACKGROUND Autophagy, a process of self-digestion, is closely related to multiple biological processes of colon cancer. This study aimed to construct and evaluate prognostic signature of autophagy-related genes (ARGs) to predict overall survival (OS) in colon cancer patients. MATERIALS AND METHODS First, a total of 234 ARGs were downloaded via The Cancer Genome Atlas (TCGA) database. Based on the TCGA dataset, differentially expressed ARGs were identified in colon cancer. The univariate and multivariate Cox regression analysis was performed to screen prognostic ARGs to construct the prognostic model. The feasibility of the prognostic model was evaluated using receiver operating characteristic curves and Kaplan-Meier curves. A prognostic model integrating the gene signature with clinical parameters was established with a nomogram. RESULTS We developed an autophagy risk signature based on the 6 ARGs (ULK3, ATG101, MAP1LC3C, TSC1, DAPK1, and SERPINA1). The risk score was positively correlated with poor outcome and could independently predict prognosis. Furthermore, the autophagy-related signature could effectively reflect the levels of immune cell type fractions and indicate an immunosuppressive microenvironment. CONCLUSION We innovatively identified and validated 6 autophagy-related gene signature that can independently predict prognosis and reflect overall immune response intensity in the colon cancer microenvironment.
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Affiliation(s)
- Yongfeng Wang
- The First Clinical Medical College of Gansu University of Chinese Medicine, Lanzhou 730000, Gansu, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou 730000, Gansu, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, Gansu, China
| | - Kaili Lin
- Graduate School, Ning Xia Medical University, Yinchuan 750004, Ning Xia, China
| | - Tianchun Xu
- Intelligent Medical Laboratory, Gansu Provincial Hospital, Lanzhou 730000, Gansu, China
| | - Liuli Wang
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou 730000, Gansu, China
- First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Liangyin Fu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Lanzhou 730000, Gansu, China
| | - Guangming Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine, Lanzhou 730000, Gansu, China
| | - Jing Ai
- The First Clinical Medical College of Gansu University of Chinese Medicine, Lanzhou 730000, Gansu, China
| | - Yajun Jiao
- Graduate School, Ning Xia Medical University, Yinchuan 750004, Ning Xia, China
| | - Rongrong Zhu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Lanzhou 730000, Gansu, China
| | - Xiaoyong Han
- Graduate School, Ning Xia Medical University, Yinchuan 750004, Ning Xia, China
| | - Hui Cai
- The First Clinical Medical College of Gansu University of Chinese Medicine, Lanzhou 730000, Gansu, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou 730000, Gansu, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, Gansu, China
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Fu C, Yu Z, He Y, Ding J, Wei M. Down-Regulation of an Autophagy-Related Gene SERPINA1 as a Superior Prognosis Biomarker Associates with Relapse and Distant Metastasis in Colon Adenocarcinoma. Onco Targets Ther 2021; 14:3861-3872. [PMID: 34188492 PMCID: PMC8235941 DOI: 10.2147/ott.s306405] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
Background The relapse and distant metastasis in colon adenocarcinoma (COAD) patients with a poor prognosis. Autophagy has gained increasing attention recently. Methods This study utilized univariate Cox analysis from the TCGA database to obtain 10 prognostic autophagy-related genes (ARGs). GO and KEGG functional annotation analysis suggested that the ARGs were significantly enriched in tumor metabolic processes. We verified the autophagy-related genes screened by TCGA clinical data. Then, we compared the expression of SERPINA1 in primary and metastatic tumor cells in the GEO database, and finally verified the relationship between SERPINA1 protein expression and prognosis with the CPTAC database. Results The ROC curves showed SERPINA1 had robust prediction capability in judging the prognosis and disease process compared with the other 4 ARGs and risk score in COAD. Clinical relationship analysis further indicated SERPINA1 was related to TMN stage, clinical-stage, OS, RFS, and DMFS in COAD. Besides, survival analysis presented that higher expression of SERPINA1 was significantly associated with the longer OS, RFS, or DMFS. Moreover, SERPINA1 protein was validated to be associated with OS, RFS, and DMFS through our own IHC and CPTAC database. Finally, we exploratoryly combined the SERPINA1 mRNA and SERPINA1 protein as a new index for prognostics. Conclusion This new combined index showed the highest prognostic value for OS, RFS, and DMFS, and had the potential to become a practical biomarker for prognosis.
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Affiliation(s)
- Chen Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, China Medical University, Shenyang, 110122, People's Republic of China
| | - Zhaojin Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, China Medical University, Shenyang, 110122, People's Republic of China
| | - Ying He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Department of Oncology, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, People's Republic of China
| | - Jian Ding
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Department of Pharmacology, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Medical Diagnosis and Treatment Center, Shenyang, 110000, People's Republic of China
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Cai R, Lu Q, Wang D. Construction and prognostic analysis of miRNA-mRNA regulatory network in liver metastasis from colorectal cancer. World J Surg Oncol 2021; 19:7. [PMID: 33397428 PMCID: PMC7784011 DOI: 10.1186/s12957-020-02107-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/03/2020] [Indexed: 02/08/2023] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common cancers in the world, and liver metastasis is the leading cause of colorectal cancer-related deaths. However, the mechanism of liver metastasis in CRC has not been clearly elucidated. Methods Three datasets from the Gene Expression Omnibus (GEO) database were analyzed to obtain differentially expressed genes (DEGs), which were subjected to functional enrichment analysis and protein-protein interaction analysis. Subsequently, mRNA-miRNA network was constructed, and the associated DEGs and DEMs were performed for prognostic analysis. Finally, we did infiltration analysis of growth arrest specific 1 (GAS1)-associated immune cells. Results We obtained 325 DEGs and 9 differentially expressed miRNAs (DEMs) between primary CRC and liver metastases. Enrichment analysis and protein-protein interactions (PPI) further revealed the involvement of DEGs in the formation of the inflammatory microenvironment and epithelial-mesenchymal transition (EMT) during the liver metastases process in CRC. Survival analysis demonstrated that low-expressed GAS1 as well as low-expressed hsa-miR-33b-5p was a favorable prognostic indicator of overall survival. Further exploration of GAS1 revealed that its expression was interrelated with the infiltration of immune cells in tumor tissues. Conclusions In summary, DEGs, DEMs, and their interactions found in liver metastasis of CRC may provide a basis for further understanding of the mechanism of CRC metastasis.
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Affiliation(s)
- Ruyun Cai
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
| | - Qian Lu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
| | - Da Wang
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
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Chen X, Sun J, Wang X, Yuan Y, Cai L, Xie Y, Fan Z, Liu K, Jiao X. A Meta-Analysis of Proteomic Blood Markers of Colorectal Cancer. Curr Med Chem 2021; 28:1176-1196. [PMID: 32338203 DOI: 10.2174/0929867327666200427094054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/23/2020] [Accepted: 03/24/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Early diagnosis will significantly improve the survival rate of colorectal cancer (CRC); however, the existing methods for CRC screening were either invasive or inefficient. There is an emergency need for novel markers in CRC's early diagnosis. Serum proteomics has gained great potential in discovering novel markers, providing markers that reflect the early stage of cancer and prognosis prediction of CRC. In this paper, the results of proteomics of CRC studies were summarized through a meta-analysis in order to obtain the diagnostic efficiency of novel markers. METHODS A systematic search on bibliographic databases was performed to collect the studies that explore blood-based markers for CRC applying proteomics. The detection and validation methods, as well as the specificity and sensitivity of the biomarkers in these studies, were evaluated. Newcastle- Ottawa Scale (NOS) case-control studies version was used for quality assessment of included studies. RESULTS Thirty-four studies were selected from 751 studies, in which markers detected by proteomics were summarized. In total, fifty-nine proteins were classified according to their biological function. The sensitivity, specificity, or AUC varied among these markers. Among them, Mammalian STE20-like protein kinase 1/ Serine threonine kinase 4 (MST1/STK4), S100 calcium-binding protein A9 (S100A9), and Tissue inhibitor of metalloproteinases 1 (TIMP1) were suitable for effect sizes merging, and their diagnostic efficiencies were recalculated after merging. MST1/STK4 obtained a sensitivity of 68% and a specificity of 78%. S100A9 achieved a sensitivity of 72%, a specificity of 83%, and an AUC of 0.88. TIMP1 obtained a sensitivity of 42%, a specificity of 88%, and an AUC of 0.71. CONCLUSION MST1/STK4, S100A9, and TIMP1 showed excellent performance for CRC detection. Several other markers also presented optimized diagnostic efficacy for CRC early detection, but further verification is still needed before they are suitable for clinical use. The discovering of more efficient markers will benefit CRC treatment.
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Affiliation(s)
- Xiang Chen
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Jiayu Sun
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xue Wang
- Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Leshan Cai
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yanxuan Xie
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Zhiqiang Fan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Kaixi Liu
- Shantou Central Hospital, Shantou, Guangdong 515041, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
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Jiang L, Hu LG. Serpin peptidase inhibitor clade A member 1-overexpression in gastric cancer promotes tumor progression in vitro and is associated with poor prognosis. Oncol Lett 2020; 20:278. [PMID: 33014156 PMCID: PMC7520747 DOI: 10.3892/ol.2020.12141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is the second most common cause of cancer-associated death in Asia. The incidence and mortality rates of gastric cancer have markedly increased in the past few decades. Therefore, the identification of novel gastric cancer biomarkers are needed to determine prognosis. The role of serpin peptidase inhibitor clade A member 1 (SERPINA1) has been studied in several types of cancer; however, little is known about its mechanism in gastric cancer. The present study aimed to evaluate SERPINA1 as a potential prognostic biomarker in gastric cancer and to identify the possible mechanisms underlying its action. The expression levels of SERPINA1 in several gastric cancer datasets were assessed, and it was identified that high expression of SERPINA1 was associated to poor clinical outcomes. Furthermore, using histochemical analysis, western blotting, apoptotic analysis, gap closure and invasion assays in cell lines, it was reported that silencing of SERPINA1 inhibited the formation of cellular pseudopodia and did not affect apoptosis, but promoted cell cycle S-phase entry. In addition, overexpression of SERPINA1 increased the migration and invasion of gastric cancer cells, whereas knockdown of SERPINA1 decreased these functions. Moreover, SERPINA1 overexpression increased the protein levels of SMAD4, which is a key regulator of the transforming growth factor (TGF)-β signaling pathway. Taken together, the present data demonstrated that SERPINA1 promotes gastric cancer progression through TGF-β signaling, and suggested that SERPINA1 may be a novel prognostic biomarker from tumor tissue biopsy in gastric cancer.
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Affiliation(s)
- Longchang Jiang
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Asia Research and Development Center, Shanghai 201210, P.R. China
| | - Liangbiao George Hu
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Asia Research and Development Center, Shanghai 201210, P.R. China
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Wang X, Xu Y, Li T, Chen B, Yang W. Development of prognosis model for colon cancer based on autophagy-related genes. World J Surg Oncol 2020; 18:285. [PMID: 33126898 PMCID: PMC7602324 DOI: 10.1186/s12957-020-02061-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/21/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Autophagy is an orderly catabolic process for degrading and removing unnecessary or dysfunctional cellular components such as proteins and organelles. Although autophagy is known to play an important role in various types of cancer, the effects of autophagy-related genes (ARGs) on colon cancer have not been well studied. METHODS Expression profiles from ARGs in 457 colon cancer patients were retrieved from the TCGA database ( https://portal.gdc.cancer.gov ). Differentially expressed ARGs and ARGs related to overall patient survival were identified. Cox proportional-hazard models were used to investigate the association between ARG expression profiles and patient prognosis. RESULTS Twenty ARGs were significantly associated with the overall survival of colon cancer patients. Five of these ARGs had a mutation rate ≥ 3%. Patients were divided into high-risk and low-risk groups based on Cox regression analysis of 8 ARGs. Low-risk patients had a significantly longer survival time than high-risk patients (p < 0.001). Univariate and multivariate Cox regression analysis showed that the resulting risk score, which was associated with infiltration depth and metastasis, could be an independent predictor of patient survival. A nomogram was established to predict 1-, 3-, and 5-year survival of colon cancer patients based on 5 independent prognosis factors, including the risk score. The prognostic nomogram with online webserver was more effective and convenient to provide information for researchers and clinicians. CONCLUSION The 8 ARGs can be used to predict the prognosis of patients and provide information for their individualized treatment.
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Affiliation(s)
- Xu Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yuanmin Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Ting Li
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Bo Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Wenqi Yang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China.
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Tutanov O, Proskura K, Kamyshinsky R, Shtam T, Tsentalovich Y, Tamkovich S. Proteomic Profiling of Plasma and Total Blood Exosomes in Breast Cancer: A Potential Role in Tumor Progression, Diagnosis, and Prognosis. Front Oncol 2020. [DOI: 10.3389/fonc.2020.580891] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Behera A, Ashraf R, Srivastava AK, Kumar S. Bioinformatics analysis and verification of molecular targets in ovarian cancer stem-like cells. Heliyon 2020; 6:e04820. [PMID: 32984578 PMCID: PMC7492822 DOI: 10.1016/j.heliyon.2020.e04820] [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: 06/13/2020] [Revised: 08/01/2020] [Accepted: 08/26/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Epithelial ovarian cancer (EOC) is a lethal and aggressive gynecological malignancy. Despite recent advances, existing therapies are challenged by a high relapse rate, eventually resulting in disease recurrence and chemoresistance. Emerging evidence indicates that a subpopulation of cells known as cancer stem-like cells (CSLCs) exists with non-tumorigenic cancer cells (non-CSCs) within a bulk tumor and is thought to be responsible for tumor recurrence and drug-resistance. Therefore, identifying the molecular drivers for cancer stem cells (CSCs) is critical for the development of novel therapeutic strategies for the treatment of EOC. METHODS Two gene datasets were downloaded from the Gene Expression Omnibus (GEO) database based on our search criteria. Differentially expressed genes (DEGs) in both datasets were obtained by the GEO2R web tool. Based on log2 (fold change) >2, the top thirteen up-regulated genes and log2 (fold change) < -1.5 top thirteen down-regulated genes were selected, and the association between their expressions and overall survival was analyzed by OncoLnc web tool. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathways analysis, and protein-protein interaction (PPI) networks were performed for all the common DEGs found in both datasets. SK-OV-3 cells were cultured in an adherent culture medium and spheroids were generated in suspension culture with CSCs specific medium. RNA from both cell population was extracted to validate the selected DEGs expression by q-PCR. Growth inhibition assay was performed in SK-OV-3 cells after carboplatin treatment. RESULTS A total of 200 DEGs, 117 up-regulated and 83 down-regulated genes were commonly identified in both datasets. Analysis of pathways and enrichment tests indicated that the extracellular matrix part, cell proliferation, tissue development, and molecular function regulation were enriched in CSCs. Biological pathways such as interferon-alpha/beta signaling, molecules associated with elastic fibers, and synthesis of bile acids and bile salts were significantly enriched in CSCs. Among the top 13 up-regulated and down-regulated genes, MMP1 and PPFIBP1 expression were associated with overall survival. Higher expression of ADM, CXCR4, LGR5, and PTGS2 in carboplatin treated SK-OV-3 cells indicate a potential role in drug resistance. CONCLUSIONS The molecular signature and signaling pathways enriched in ovarian CSCs were identified by bioinformatics analysis. This analysis could provide further research ideas to find the new mechanism and novel potential therapeutic targets for ovarian CSCs.
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Affiliation(s)
- Abhijeet Behera
- Division of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India
| | - Rahail Ashraf
- Division of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India
| | - Amit Kumar Srivastava
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, WB, India
| | - Sanjay Kumar
- Division of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India
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Niu J, Yan T, Guo W, Wang W, Zhao Z, Ren T, Huang Y, Zhang H, Yu Y, Liang X. Identification of Potential Therapeutic Targets and Immune Cell Infiltration Characteristics in Osteosarcoma Using Bioinformatics Strategy. Front Oncol 2020; 10:1628. [PMID: 32974202 PMCID: PMC7471873 DOI: 10.3389/fonc.2020.01628] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
Osteosarcoma is one of the most aggressive malignant bone tumors worldwide. Although great advancements have been made in its treatment owing to the advent of neoadjuvant chemotherapy, the problem of lung metastasis is a major obstacle in the improvement of survival outcomes. Thus, the aim of the present study is to screen novel and key biomarkers, which may act as potential prognostic markers and therapeutic targets in osteosarcoma. We utilized the robust rank aggregation (RRA) method to integrate three osteosarcoma microarray datasets downloaded from the Gene Expression Omnibus (GEO) database, and we identified the robust differentially expressed genes (DEGs) between primary and metastatic osteosarcoma tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the functions of robust DEGs. The results of enrichment analysis showed that the robust DEGs were closely associated with osteosarcoma development and progression. Immune cell infiltration analysis was also conducted by CIBERSORT algorithm, and we found that macrophages are the most principal infiltrating immune cells in osteosarcoma, especially macrophages M0 and M2. Then, the protein–protein interaction network and key modules were constructed by Cytoscape, and 10 hub genes were selected by plugin cytoHubba from the whole network. The survival analysis of hub genes was also carried out based on the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. The integrated bioinformatics analysis was utilized to provide new insight into osteosarcoma development and metastasis and identified EGR1, CXCL10, MYC, and CXCR4 as potential biomarkers for prognosis of osteosarcoma.
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Affiliation(s)
- Jianfang Niu
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Taiqiang Yan
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Wei Guo
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Wei Wang
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Zhiqing Zhao
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Tingting Ren
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Yi Huang
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Hongliang Zhang
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Yiyang Yu
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Xin Liang
- Musculoskeletal Tumor Center, Peking University People's Hospital, Peking University, Beijing, China.,Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
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Wang X, Li Z, Fu J, Xu W, Li Z. Diagnostic value and prognostic significance of LI-cadherin and miR-378e in colorectal cancer. Oncol Lett 2020; 20:2456-2464. [PMID: 32782563 PMCID: PMC7400983 DOI: 10.3892/ol.2020.11755] [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: 12/14/2018] [Accepted: 12/03/2019] [Indexed: 11/25/2022] Open
Abstract
Expression levels of LI-cadherin and miR-378e in the serum of patients with colorectal cancer, and the diagnostic value and prognostic significance in colorectal cancer were investigated. A total of 110 patients who were diagnosed with colorectal cancer in Weihai Central Hospital, from January 2012 to November 2014, were selected and enrolled in the experimental group, and 90 healthy subjects who underwent physical examination were enrolled in the control group. The expression level of miR-378e in serum was detected by reverse transcription-quantitative PCR and the expression of LI-cadherin in serum was detected by ELISA. ROC curves of LI-cadherin and miR-378e were drawn and the sensitivity and specificity of the diagnosis were estimated. The association of the expression levels of LI-cadherin and miR-378e with the survival of the patients was analyzed. LI-cadherin and miR-378e expression levels were significantly higher in the control group than those in the experimental group (P<0.001). LI-cadherin was significantly associated with the pathogenic site, the lymphatic metastasis, depth of infiltration, degree of differentiation and clinical stage (P<0.05). The sensitivity and specificity of the LI-cadherin combined with miR-378e detection were respectively 86 and 94%; the sensitivity of miR-378e detection was the highest, as well as the specificity of the combined detection. At the end of the follow-up period, the survival rates of the patients in the LI-cadherin high-expression group and miR-378e high-expression group were significantly higher than those in the low-expression groups (P<0.05). There was a significant positive correlation between the LI-cadherin and miR-378e expression levels in both the experimental and control group (r=0.5845 and 0.6356, respectively; P<0.05). In conclusion, LI-cadherin and miR-378e are expressed at low levels in colorectal cancer, suggesting that they have a good diagnostic value for colorectal cancer and can be used as biomarkers for colorectal cancer prognosis.
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Affiliation(s)
- Xujie Wang
- Department I of Gastrointestinal Surgery, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
| | - Zhihua Li
- Department III of Oncology, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
| | - Jixin Fu
- Department II of Gastrointestinal Surgery, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
| | - Weiwei Xu
- Department I of Gastrointestinal Surgery, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
| | - Zongxian Li
- Department III of Oncology, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
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42
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Ahmadiankia N, Khosravi A. Significance of epithelial-to-mesenchymal transition inducing transcription factors in predicting distance metastasis and survival in patients with colorectal cancer: A systematic review and meta-analysis. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2020; 25:60. [PMID: 33088297 PMCID: PMC7554549 DOI: 10.4103/jrms.jrms_174_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/25/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022]
Abstract
Background: The clinical relevance of epithelial-to-mesenchymal transition (EMT) in colorectal cancer (CRC) progression has been highlighted over the last decade. Several EMT-inducing transcription factors (EMT-TFs) have been implicated in the regulation of EMT, including Twist, Snail1, Slug, ZEB1, and ZEB2. Here, this meta-analysis aimed to predict the risk of distance metastasis and overall survival in CRC patients with high expression of EMT-TFs. Materials and Methods: All eligible studies were searched in PubMed, Scopus, and Web of Science databases. The search was carried out to include literatures published as late as September 1, 2018. In overall, 16 studies that investigated the relationship between EMT-TFs with distance metastasis and survival in CRC patients were included. In meta-analysis, a pooled hazard ratio (HR) and odds ratio (OR) were estimated for associations. Results: The results of this review indicated that expressions of all EMT-TFs are significantly correlated with poor overall survival in CRC. Moreover, there are a significant association between Twist (OR, 1.46; 95% confidence interval [CI], 1.03–2.09), Slug (OR, 3.43; 95% CI, 1.98–5.93), and ZEB2 (OR, 2.42; 95% CI, 1.09–5.40) expression with distance metastatic in CRC patients. Conclusion: These findings suggest that the overexpression of EMT-TFs plays a key role in increasing the risk of distance metastasis as well as decreasing overall survival in CRC patients.
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Affiliation(s)
- Naghmeh Ahmadiankia
- Cancer Prevention Research Center, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Ahmad Khosravi
- Center for Health Related Social and Behavioral Sciences Research, Shahroud University of Medical Sciences, Shahroud, Iran
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Lian H, Wang A, Shen Y, Wang Q, Zhou Z, Zhang R, Li K, Liu C, Jia H. Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer. BMC Gastroenterol 2020; 20:171. [PMID: 32503434 PMCID: PMC7275609 DOI: 10.1186/s12876-020-01288-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 04/30/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an important mechanism of regulating eukaryotic gene expression. Understanding the most common AS events in colorectal cancer (CRC) will help developing diagnostic, prognostic or therapeutic tools in CRC. METHODS Publicly available RNA-seq data of 28 pairs of CRC and normal tissues and 18 pairs of metastatic and normal tissues were used to identify AS events using PSI and DEXSeq methods. RESULT The highly significant splicing events were used to search a database of The Cancer Genome Atlas (TCGA). We identified AS events in 9 genes in CRC (more inclusion of CLK1-E4, COL6A3-E6, CD44v8-10, alternative first exon regulation of ARHGEF9, CHEK1, HKDC1 and HNF4A) or metastasis (decrease of SERPINA1-E1a, CALD-E5b, E6). Except for CHEK1, all other 8 splicing events were confirmed by TCGA data with 382 CRC tumors and 51 normal controls. The combination of three splicing events was used to build a logistic regression model that can predict sample type (CRC or normal) with near perfect performance (AUC = 1). Two splicing events (COL6A3 and HKDC1) were found to be significantly associated with patient overall survival. The AS features of the 9 genes are highly consistent with previous reports and/or relevant to cancer biology. CONCLUSIONS The significant association of higher expression of the COL6A3 E5-E6 junction and HKDC1 E1-E2 with better overall survival was firstly reported. This study might be of significant value in the future biomarker, prognosis marker and therapeutics development of CRC.
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Affiliation(s)
- Haifeng Lian
- Department of Gastroenterology, Binzhou Medical University Hospital (BMUH), No. 662 Huanghe 2nd Road, Binzhou City, Shandong Province, People's Republic of China
| | - Aili Wang
- Department of Gastroenterology, Binzhou Medical University Hospital (BMUH), No. 662 Huanghe 2nd Road, Binzhou City, Shandong Province, People's Republic of China
| | - Yuanyuan Shen
- Department of Gastroenterology, Binzhou Medical University Hospital (BMUH), No. 662 Huanghe 2nd Road, Binzhou City, Shandong Province, People's Republic of China
| | - Qian Wang
- Tianjia Genomes Tech CO., LTD., Anhui Chaohu Economic Develop Zone, No. 6 Longquan Road, Hefei, 238014, People's Republic of China
| | - Zhenru Zhou
- Tianjia Genomes Tech CO., LTD., Anhui Chaohu Economic Develop Zone, No. 6 Longquan Road, Hefei, 238014, People's Republic of China
| | - Ranran Zhang
- Department of Gastroenterology, Binzhou Medical University Hospital (BMUH), No. 662 Huanghe 2nd Road, Binzhou City, Shandong Province, People's Republic of China
| | - Kun Li
- Department of Gastroenterology, Binzhou Medical University Hospital (BMUH), No. 662 Huanghe 2nd Road, Binzhou City, Shandong Province, People's Republic of China
| | - Chengxia Liu
- Department of Gastroenterology, Binzhou Medical University Hospital (BMUH), No. 662 Huanghe 2nd Road, Binzhou City, Shandong Province, People's Republic of China.
| | - Hongtao Jia
- Tianjia Genomes Tech CO., LTD., Anhui Chaohu Economic Develop Zone, No. 6 Longquan Road, Hefei, 238014, People's Republic of China.
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Zeng Q, Zhang Y, Zhang W, Guo Q. Baicalein suppresses the proliferation and invasiveness of colorectal cancer cells by inhibiting Snail‑induced epithelial‑mesenchymal transition. Mol Med Rep 2020; 21:2544-2552. [PMID: 32323825 PMCID: PMC7185271 DOI: 10.3892/mmr.2020.11051] [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: 06/07/2019] [Accepted: 03/06/2020] [Indexed: 12/18/2022] Open
Abstract
Scutellaria baicalensis (S. baicalensis) is a plant that is widely used for medicinal purposes. Baicalein, one of the primary bioactive compounds found in S. baicalensis, is thought to possess antitumor activity, although the specific mechanisms remain unclear. Therefore, the present study aimed to evaluate the ability of baicalein to disrupt the proliferation and metastatic potential of colorectal cancer (CRC) cells; a rapid and sensitive ultra-high performance liquid chromatography-tandem mass spectrometric method was employed for the identification of baicalein in an S. baicalensis aqueous extract and in rat plasma. To investigate the effects of baicalein, Cell Counting Kit-8 (CCK-8), western blotting, wound-healing and Transwell assays were performed. The data indicated that baicalein was absorbed into the blood and was able to effectively disrupt the proliferation, migration and invasion abilities of CRC cells in a dose- and time-dependent manner. Baicalein treatment was also revealed to decrease the expression of epithelial-mesenchymal transition (EMT)-promoting factors including vimentin, Twist1, and Snail, but to upregulate the expression of E-cadherin in CRC cells. The expression levels of cell cycle inhibitory proteins p53 and p21 also increased following baicalein treatment. In addition, Snail-induced vimentin and Twist1 upregulation, as well as E-cadherin downregulation, were reversed following treatment with baicalein. In conclusion, the results of the present study indicate that baicalein may suppress EMT, at least in part, by decreasing Snail activity.
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Affiliation(s)
- Qiongyao Zeng
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Yu Zhang
- Department of Gastroenterology, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, P.R. China
| | - Wenjing Zhang
- Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Qiang Guo
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
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Sarquis M, Moraes DC, Bastos-Rodrigues L, Azevedo PG, Ramos AV, Reis FV, Dande PV, Paim I, Friedman E, De Marco L. Germline Mutations in Familial Papillary Thyroid Cancer. Endocr Pathol 2020; 31:14-20. [PMID: 32034658 DOI: 10.1007/s12022-020-09607-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Thyroid cancer, predominantly of papillary histology (PTC), is a common cancer mostly diagnosed sporadically. Hereditary PTC is encountered in ~ 5% of cases and may present at an earlier age, with greater risks of metastasis and recurrence, compared with sporadic cases. The molecular basis of hereditary PTC is unknown in most cases. In this study, the genetic basis of hereditary PTC in three Brazilian families was investigated. Whole exome sequencing (WES) was carried out for probands in each family, and validated, pathogenic/likely pathogenic sequence variants (P/LPSVs) were genotyped in additional family members to establish their putative pathogenic role. Overall, seven P/LPSVs in seven novel genes were detected: p.D283N*ANXA3, p.Y157S*NTN4, p.G172W*SERPINA1, p.G188S*FKBP10, p.R937C*PLEKHG5, p.L32Q*P2RX5, and p.Q76*SAPCD1. These results indicate that these novel genes are seemingly associated with hereditary PTC, but extension and validation in other PTC families are required.
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Affiliation(s)
- Marta Sarquis
- Department of Medicine, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debora C Moraes
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luciana Bastos-Rodrigues
- Department of Nutrition, Faculdade de Enfermagem, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Pedro G Azevedo
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Fabiana Versiani Reis
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula V Dande
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Isabela Paim
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eitan Friedman
- The Suzanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Chaim Sheba Medical Center, Tel-Hashomer, Israel
- The Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Luiz De Marco
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Pavlakis E, Stiewe T. p53's Extended Reach: The Mutant p53 Secretome. Biomolecules 2020; 10:biom10020307. [PMID: 32075247 PMCID: PMC7072272 DOI: 10.3390/biom10020307] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 02/08/2023] Open
Abstract
p53 suppresses tumorigenesis by activating a plethora of effector pathways. While most of these operate primarily inside of cells to limit proliferation and survival of incipient cancer cells, many extend to the extracellular space. In particular, p53 controls expression and secretion of numerous extracellular factors that are either soluble or contained within extracellular vesicles such as exosomes. As part of the cellular secretome, they execute key roles in cell-cell communication and extracellular matrix remodeling. Mutations in the p53-encoding TP53 gene are the most frequent genetic alterations in cancer cells, and therefore, have profound impact on the composition of the tumor cell secretome. In this review, we discuss how the loss or dominant-negative inhibition of wild-type p53 in concert with a gain of neomorphic properties observed for many mutant p53 proteins, shapes a tumor cell secretome that creates a supportive microenvironment at the primary tumor site and primes niches in distant organs for future metastatic colonization.
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47
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López-Sánchez LM, Jiménez-Izquierdo R, Peñarando J, Mena R, Guil-Luna S, Toledano M, Conde F, Villar C, Díaz C, Ortea I, De la Haba-Rodríguez JR, Aranda E, Rodríguez-Ariza A. SWATH-based proteomics reveals processes associated with immune evasion and metastasis in poor prognosis colorectal tumours. J Cell Mol Med 2019; 23:8219-8232. [PMID: 31560832 PMCID: PMC6850959 DOI: 10.1111/jcmm.14693] [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: 05/10/2019] [Revised: 07/25/2019] [Accepted: 08/25/2019] [Indexed: 01/02/2023] Open
Abstract
Newly emerged proteomic methodologies, particularly data‐independent acquisition (DIA) analysis–related approaches, would improve current gene expression–based classifications of colorectal cancer (CRC). Therefore, this study was aimed to identify protein expression signatures using SWATH‐MS DIA and targeted data extraction, to aid in the classification of molecular subtypes of CRC and advance in the diagnosis and development of new drugs. For this purpose, 40 human CRC samples and 7 samples of healthy tissue were subjected to proteomic and bioinformatic analysis. The proteomic analysis identified three different molecular CRC subtypes: P1, P2 and P3. Significantly, P3 subtype showed high agreement with the mesenchymal/stem‐like subtype defined by gene expression signatures and characterized by poor prognosis and survival. The P3 subtype was characterized by decreased expression of ribosomal proteins, the spliceosome, and histone deacetylase 2, as well as increased expression of osteopontin, SERPINA 1 and SERPINA 3, and proteins involved in wound healing, acute inflammation and complement pathway. This was also confirmed by immunodetection and gene expression analyses. Our results show that these tumours are characterized by altered expression of proteins involved in biological processes associated with immune evasion and metastasis, suggesting new therapeutic options in the treatment of this aggressive type of CRC.
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Affiliation(s)
- Laura M López-Sánchez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Jon Peñarando
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Rafael Mena
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Silvia Guil-Luna
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Marta Toledano
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Francisco Conde
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Carlos Villar
- Unidad de Gestión Clínica de Anatomía Patológica, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - César Díaz
- Unidad de Gestión Clínica de Cirugía General y del Aparato Digestivo, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Ignacio Ortea
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Juan R De la Haba-Rodríguez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| | - Enrique Aranda
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
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48
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Vishnubalaji R, Sasidharan Nair V, Ouararhni K, Elkord E, Alajez NM. Integrated Transcriptome and Pathway Analyses Revealed Multiple Activated Pathways in Breast Cancer. Front Oncol 2019; 9:910. [PMID: 31620367 PMCID: PMC6759650 DOI: 10.3389/fonc.2019.00910] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/02/2019] [Indexed: 12/27/2022] Open
Abstract
Breast cancer (BC) is the leading cause of cancer-related death in women. Therefore, a better understanding of BC biology and signaling pathways might lead to the development of novel biomarkers and targeted therapies. Although a number of transcriptomic studies have been performed on breast cancer patients from various geographic regions, there are almost no such comprehensive studies performed on breast cancer from patients in the gulf region. This study aimed to provide a better understanding of the altered molecular networks in BC from the gulf region. Herein, we compared the transcriptome of BC to adjacent normal tissue from six BC patients and identified 1,108 upregulated and 518 downregulated transcripts. A selected number of genes from the RNA-Seq analysis were subsequently validated using qRT-PCR. Differentially expressed (2.0-fold change, adj. p < 0.05) transcripts were subjected to ingenuity pathway analysis, which revealed a myriad of affected signaling pathways and functional categories. Activation of ERBB2, FOXM1, ESR1, and IGFBP2 mechanistic networks was most prominent in BC tissue. Additionally, BC tissue exhibited marked enrichment in genes promoting cellular proliferation, migration, survival, and DNA replication and repair. The presence of genes indicative of immune cell infiltration and activation was also observed in BC tissue. We observed high concordance [43.5% (upregulated) and 62.1% (downregulated)] between differentially expressed genes in our study group and those reported for the TCGA BC cohort. Our data provide novel insight on BC biology and suggest common altered molecular networks in BC in this geographic region. Our data suggest future development of therapeutic interventions targeting those common signaling pathways.
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Affiliation(s)
- Radhakrishnan Vishnubalaji
- Cancer Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Varun Sasidharan Nair
- Cancer Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Khalid Ouararhni
- Cancer Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Eyad Elkord
- Cancer Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Nehad M Alajez
- Cancer Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
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49
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Ercetin E, Richtmann S, Delgado BM, Gomez-Mariano G, Wrenger S, Korenbaum E, Liu B, DeLuca D, Kühnel MP, Jonigk D, Yuskaeva K, Warth A, Muley T, Winter H, Meister M, Welte T, Janciauskiene S, Schneider MA. Clinical Significance of SERPINA1 Gene and Its Encoded Alpha1-antitrypsin Protein in NSCLC. Cancers (Basel) 2019; 11:cancers11091306. [PMID: 31487965 PMCID: PMC6770941 DOI: 10.3390/cancers11091306] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 12/20/2022] Open
Abstract
High expression of SERPINA1 gene encoding acute phase protein, alpha1-antitrypsin (AAT), is associated with various tumors. We sought to examine the significance of SERPINA1 and AAT protein in non-small-cell lung cancer (NSCLC) patients and NSCLC cell lines. Tumor and adjacent non-tumor lung tissues and serum samples from 351 NSCLC patients were analyzed for SERPINA1 expression and AAT protein levels. We also studied the impact of SERPINA1 expression and AAT protein on H1975 and H661 cell behavior, in vitro. Lower SERPINA1 expression in tumor but higher in adjacent non-tumor lung tissues (n = 351, p = 0.016) as well as higher serum levels of AAT protein (n = 170, p = 0.033) were associated with worse survival rates. Specifically, in NSCLC stage III patients, higher blood AAT levels (>2.66 mg/mL) correlated with a poor survival (p = 0.002). Intriguingly, levels of serum AAT do not correlate with levels of C-reactive protein, neutrophils-to-leukocyte ratio, and do not correlate with SERPINA1 expression or AAT staining in the tumor tissue. Additional experiments in vitro revealed that external AAT and/or overexpressed SERPINA1 gene significantly improve cancer cell migration, colony formation and resistance to apoptosis. SERPINA1 gene and AAT protein play an active role in the pathogenesis of lung cancer and not just reflect inflammatory reaction related to cancer development.
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Affiliation(s)
- Evrim Ercetin
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
| | - Sarah Richtmann
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany.
- Translational Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany.
| | - Beatriz Martinez Delgado
- Department of Molecular Genetics. Institute of Health Carlos III. Center for Biomedical Research in the Network of Rare Diseases (CIBERER), 28220 Majadahonda (Madrid), Spain.
| | - Gema Gomez-Mariano
- Department of Molecular Genetics. Institute of Health Carlos III. Center for Biomedical Research in the Network of Rare Diseases (CIBERER), 28220 Majadahonda (Madrid), Spain.
| | - Sabine Wrenger
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
| | - Elena Korenbaum
- Institute of Biophysical Chemistry and Anatomy, Hannover Medical School, 30625 Hannover, Germany.
| | - Bin Liu
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
| | - David DeLuca
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
| | - Mark P Kühnel
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany.
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany.
| | - Kadriya Yuskaeva
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany.
| | - Arne Warth
- Institute of Pathology, Heidelberg University Hospital, D-69120 Heidelberg, Germany.
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany.
- Translational Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany.
| | - Hauke Winter
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany.
- Department of Surgery, Thoraxklinik at Heidelberg University Hospital, D-69126 Heidelberg, Germany.
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany.
- Translational Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany.
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
| | - Sabina Janciauskiene
- Department of Respiratory Medicine, Hannover Medical School, 30625 Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany.
- Translational Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany.
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50
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Chakroborty D, Emani MR, Klén R, Böckelman C, Hagström J, Haglund C, Ristimäki A, Lahesmaa R, Elo LL. L1TD1 - a prognostic marker for colon cancer. BMC Cancer 2019; 19:727. [PMID: 31337362 PMCID: PMC6651905 DOI: 10.1186/s12885-019-5952-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Prognostic markers specific to a particular cancer type can assist in the evaluation of survival probability of patients and help clinicians to assess the available treatment modalities. METHODS Gene expression data was analyzed from three independent colon cancer microarray gene expression data sets (N = 1052). Survival analysis was performed for the three data sets, stratified by the expression level of the LINE-1 type transposase domain containing 1 (L1TD1). Correlation analysis was performed to investigate the role of the interactome of L1TD1 in colon cancer patients. RESULTS We found L1TD1 as a novel positive prognostic marker for colon cancer. Increased expression of L1TD1 associated with longer disease-free survival in all the three data sets. Our results were in contrast to a previous study on medulloblastoma, where high expression of L1TD1 was linked with poor prognosis. Notably, in medulloblastoma L1TD1 was co-expressed with its interaction partners, whereas our analysis revealed lack of co-expression of L1TD1 with its interaction partners in colon cancer. CONCLUSIONS Our results identify increased expression of L1TD1 as a prognostic marker predicting longer disease-free survival in colon cancer patients.
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Affiliation(s)
- Deepankar Chakroborty
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Maheswara Reddy Emani
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riku Klén
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Camilla Böckelman
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jaana Hagström
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland
- Department of Pathology and Oral Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Caj Haglund
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ari Ristimäki
- Department of Pathology, HUSLAB, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research program, University of Helsinki, 00290 Helsinki, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
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