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Swain IX, Kresak AM. Proteins Involved in Focal Cell Adhesion and Podosome Formation Are Differentially Expressed during Colorectal Tumorigenesis in AOM-Treated Rats. Cancers (Basel) 2024; 16:1678. [PMID: 38730628 PMCID: PMC11083089 DOI: 10.3390/cancers16091678] [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: 04/10/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Colorectal tumorigenesis involves the development of aberrant crypt foci (ACF) or preneoplastic lesions, representing the earliest morphological lesion visible in colon cancer. The purpose of this study was to determine changes in protein expression in carcinogen-induced ACF as they mature and transform into adenomas. Protein expression profiles of azoxymethane (AOM)-induced F344 rat colon ACF and adenomas were compared at four time points, 4 (control), 8, 16, and 24 weeks post AOM administration (n = 9/group), with time points correlating with induction and transformation events. At each time point, micro-dissected ACF and/or adenoma tissues were analyzed across multiple quantitative two-dimensional (2D-DIGE) gels using a Cy-dye labeling technique and a pooled internal standard to quantify expression changes with statistical confidence. Western blot and subsequent network pathway mapping were used to confirm and elucidate differentially expressed (p ≤ 0.05) proteins, including changes in vinculin (Vcl; p = 0.007), scinderin (Scin; p = 0.02), and profilin (Pfn1; p = 0.01), By determining protein expression changes in ACF as they mature and transform into adenomas, a "baseline" of altered regulatory proteins associated with adenocarcinoma development in this model has been elucidated. These data will enable future studies aimed at biomarker identification and understanding the molecular biology of intestinal tumorigenesis and adenocarcinoma maturation under varying intestinal conditions.
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Affiliation(s)
- Ian X. Swain
- Department of Pathology, School of Medicine, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA;
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Flesken-Nikitin A, Pirtz MG, Ashe CS, Ellenson LH, Cosgrove BD, Nikitin AY. Dysregulation of cell state dynamics during early stages of serous endometrial carcinogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585274. [PMID: 38562813 PMCID: PMC10983873 DOI: 10.1101/2024.03.15.585274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Serous endometrial carcinoma (SEC) constitutes about 10% of endometrial carcinomas and is one of the most aggressive and lethal types of uterine cancer. Due to the rapid progression of SEC, early detection of this disease is of utmost importance. However, molecular and cellular dynamics during the pre-dysplastic stage of this disease remain largely unknown. Here, we provide a comprehensive census of cell types and their states for normal, pre-dysplastic, and dysplastic endometrium in a mouse model of SEC. This model is associated with inactivation of tumor suppressor genes Trp53 and Rb1 , whose pathways are altered frequently in SEC. We report that pre-dysplastic changes are characterized by an expanded and increasingly diverse immature luminal epithelial cell populations. Consistent with transcriptome changes, cells expressing the luminal epithelial marker TROP2 begin to substitute FOXA2+ cells in the glandular epithelium. These changes are associated with a reduction in number and strength of predicted interactions between epithelial and stromal endometrial cells. By using a multi-level approach combining single-cell and spatial transcriptomics paired with screening for clinically relevant genes in human endometrial carcinoma, we identified a panel of 44 genes suitable for further testing of their validity as early diagnostic and prognostic markers. Among these genes are known markers of human SEC, such as C DKN2A, and novel markers, such as OAS2 and OASL, members of 2-5A synthetase family that is essential for the innate immune response. In summary, our results suggest an important role of the luminal epithelium in SEC pathogenesis, highlight aberrant cell-cell interactions in pre-dysplastic stages, and provide a new platform for comparative identification and characterization of novel, clinically relevant prognostic and diagnostic markers and potential therapeutic modalities.
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Alsofyani AA, Nedjadi T. Gelsolin, an Actin-Binding Protein: Bioinformatic Analysis and Functional Significance in Urothelial Bladder Carcinoma. Int J Mol Sci 2023; 24:15763. [PMID: 37958747 PMCID: PMC10647509 DOI: 10.3390/ijms242115763] [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: 05/28/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 11/15/2023] Open
Abstract
The involvement of the actin-regulatory protein, gelsolin (GSN), in neoplastic transformation has been reported in different cancers including bladder cancer. However, the exact mechanism by which GSN influences bladder cancer development is not well understood. Here, we sought to reveal the functional significance of GSN in bladder cancer by undertaking a comprehensive bioinformatic analysis of TCGA datasets and through the assessment of multiple biological functions. GSN expression was knocked down in bladder cancer cell lines with two siRNA isoforms targeting GSN. Proliferation, migration, cell cycle and apoptosis assays were carried out. GSN expression, enrichment analysis, protein-protein interaction and immune infiltration analysis were verified through online TCGA tools. The data indicated that GSN expression is associated with bladder cancer proliferation, migration and enhanced cell apoptosis through regulation of NF-κB expression. GSN expression correlated with various inflammatory cells and may influence the immunity of the tumor microenvironment. Computational analysis identified several interacting partners which are associated with cancer progression and patient outcome. The present results demonstrate that GSN plays an important role in bladder cancer pathogenesis and may serve as a potential biomarker and therapeutic target for cancer therapy.
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Affiliation(s)
| | - Taoufik Nedjadi
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Jeddah 21423, Saudi Arabia;
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The Transcription Factor Twist1 Has a Significant Role in Mycosis Fungoides (MF) Cell Biology: An RNA Sequencing Study of 40 MF Cases. Cancers (Basel) 2023; 15:cancers15051527. [PMID: 36900319 PMCID: PMC10000433 DOI: 10.3390/cancers15051527] [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: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
The purpose of this RNA sequencing study was to investigate the biological mechanism underlying how the transcription factors (TFs) Twist1 and Zeb1 influence the prognosis of mycosis fungoides (MF). We used laser-captured microdissection to dissect malignant T-cells obtained from 40 skin biopsies from 40 MF patients with stage I-IV disease. Immunohistochemistry (IHC) was used to determinate the protein expression levels of Twist1 and Zeb1. Based on RNA sequencing, principal component analysis (PCA), differential expression (DE) analysis, ingenuity pathway analysis (IPA), and hub gene analysis were performed between the high and low Twist1 IHC expression cases. The DNA from 28 samples was used to analyze the TWIST1 promoter methylation level. In the PCA, Twist1 IHC expression seemed to classify cases into different groups. The DE analysis yielded 321 significant genes. In the IPA, 228 significant upstream regulators and 177 significant master regulators/causal networks were identified. In the hub gene analysis, 28 hub genes were found. The methylation level of TWIST1 promoter regions did not correlate with Twist1 protein expression. Zeb1 protein expression did not show any major correlation with global RNA expression in the PCA. Many of the observed genes and pathways associated with high Twist1 expression are known to be involved in immunoregulation, lymphocyte differentiation, and aggressive tumor biology. In conclusion, Twist1 might be an important regulator in the disease progression of MF.
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Ren S, Zhu Y, Wang S, Zhang Q, Zhang N, Zou X, Wei C, Wang Z. The pseudogene DUXAP10 contributes to gefitinib resistance in NSCLC by repressing OAS2 expression. Acta Biochim Biophys Sin (Shanghai) 2023; 55:81-90. [PMID: 36471952 PMCID: PMC10157544 DOI: 10.3724/abbs.2022176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
Gefitinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI),is the currently recommended first-line therapy for advanced EGFR-mutant lung cancer, and understanding the mechanism of resistance is the key to formulating therapeutic strategies for EGFR-TKIs. In this study, we evaluate the expression patterns and potential biological functions of the pseudogene DUXAP10 in gefitinib resistance. We find that pseudogene DUXAP10 expression is significantly upregulated in NSCLC gefitinib-resistant cells and tissues. Gain and loss of function assays reveal that knockdown of DUXAP10 by siRNA reverses gefitinib resistance both in vitro and in vivo. Furthermore, DUXAP10 interacts with the histone methyltransferase enhancer of zeste homolog 2 (EZH2) to repress the expression of 2',5'-oligoadenylate synthetase (OAS2). Overall, our study highlights the pivotal role of DUXAP10 in gefitinib resistance, and the DUXAP10/EZH2/OAS2 axis might be a promising therapeutic target to overcome acquired gefitinib resistance in NSCLC.
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Affiliation(s)
- Shengnan Ren
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Department of OncologySir Run Run HospitalNanjing Medical UniversityNanjing210011China
| | - Ya Zhu
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Siying Wang
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Qinqiu Zhang
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Niu Zhang
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Xiaoteng Zou
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Chenchen Wei
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Zhaoxia Wang
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
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Zhang L, Deng Y, Liu S, Zhang W, Hong Z, Lu Z, Pan Z, Wu X, Peng J. Lymphovascular invasion represents a superior prognostic and predictive pathological factor of the duration of adjuvant chemotherapy for stage III colon cancer patients. BMC Cancer 2023; 23:3. [PMID: 36593480 PMCID: PMC9808960 DOI: 10.1186/s12885-022-10416-7] [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: 08/09/2022] [Accepted: 12/06/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Lymphovascular invasion (LVI) and perineural invasion (PNI) can indicate poor survival outcomes in colorectal cancer, but few studies have focused on stage III colon cancer. The current study aimed to confirm the prognostic value of LVI and PNI and identify patients who could benefit from a complete duration of adjuvant chemotherapy based on the two pathological factors. METHODS We enrolled 402 consecutive patients with stage III colon cancer who received colon tumor resection from November 2007 to June 2016 at Sun Yat-sen University Cancer Center. Survival analyses were performed by using Kaplan-Meier method with log-rank tests. Risk factors related to disease-free survival (DFS) and overall survival (OS) were identified through Cox proportional hazards analysis. RESULTS 141 (35.1%) patients presented with LVI, and 108 (26.9%) patients with PNI. The LVI-positive group was associated with poorer 3-year DFS (86.5% vs. 76.3%, P = 0.001) and OS (96.0% vs. 89.1%, P = 0.003) rates compared with the LVI-negative group. The PNI-positive group showed a worse outcome compared with the PNI-negative group in 3-year DFS rate (72.5% vs. 86.7%, P < 0.001). Moreover, LVI-positive group present better 3-year DFS and OS rate in patients completing 6-8 cycles of adjuvant chemotherapy than those less than 6 cycles (3-year DFS: 80.0% vs. 64.9%, P = 0.019; 3-year OS: 93.2% vs. 76.3%, P = 0.002). CONCLUSIONS LVI is a superior prognostic factor to PNI in stage III colon cancer patients undergoing curative treatment. PNI status can noly predict the 3-year DFS wihout affecting the 3-year OS. Furthermore, LVI also represents an effective indicator for adjuvant chemotherapy duration.
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Affiliation(s)
- Linjie Zhang
- grid.488530.20000 0004 1803 6191Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Road East, Guangdong 510060 Guangzhou, P. R. China
| | - Yuxiang Deng
- grid.440601.70000 0004 1798 0578Department of Thyroid and Breast Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, 518000 Shenzhen, P. R. China
| | - Songran Liu
- grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Road East, Guangdong 510060 Guangzhou, P. R. China
| | - Weili Zhang
- grid.488530.20000 0004 1803 6191Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Road East, Guangdong 510060 Guangzhou, P. R. China
| | - Zhigang Hong
- grid.488530.20000 0004 1803 6191Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Road East, Guangdong 510060 Guangzhou, P. R. China
| | - Zhenhai Lu
- grid.488530.20000 0004 1803 6191Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Road East, Guangdong 510060 Guangzhou, P. R. China
| | - Zhizhong Pan
- grid.488530.20000 0004 1803 6191Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Road East, Guangdong 510060 Guangzhou, P. R. China
| | - Xiaojun Wu
- grid.488530.20000 0004 1803 6191Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Road East, Guangdong 510060 Guangzhou, P. R. China
| | - Jianhong Peng
- grid.488530.20000 0004 1803 6191Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng Road East, Guangdong 510060 Guangzhou, P. R. China
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Wang Y, Bi X, Luo Z, Wang H, Ismtula D, Guo C. Gelsolin: A comprehensive pan-cancer analysis of potential prognosis, diagnostic, and immune biomarkers. Front Genet 2023; 14:1093163. [PMID: 37035750 PMCID: PMC10076574 DOI: 10.3389/fgene.2023.1093163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction: Gelsolin (GSN), a calcium-regulated actin-binding protein, is out of balance in various cancers. It can mediate cytoskeletal remodeling and regulate epithelial-mesenchymal conversion (EMT), but the studies on GSN function in pan-cancer are limited. Methods: We studied the transcription level, prognostic impact, diagnostic value, genetic, epigenetic modification, methylation level and immune significance of GSN in pan-cancer to fully comprehend the function of GSN in various malignancies based on multiple databases like The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Results: Pan-cancer research showed that GSN was downregulated in most tumors and expressed differently in immunological and molecular subtypes of many cancers. GSN had varying impacts on the prognosis of various tumor types. However, all had moderate to high diagnostic efficiency, and serum GSN had good diagnostic value in breast cancer patients (AUC = 0.947). Moreover, GSN was a distinguishing prognosis factor for some specific cancer types. The GSN protein was hypophosphorylated, and its promoter was hypermethylated in most cancers. GSN was linked to the infiltration level of several immunity cells and was essential in anti-tumor immune cell infiltration. KEGG and GSEA analyses showed that GSN was vital in the functions and proteoglycans processes in cancer, chemokine signaling pathway and other immune-related pathways, DNA methylation and cell cycle. Discussion: In conclusion, GSN possesses the ability to be a predictive, diagnostic, and immune indicator in pan-cancer.
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Affiliation(s)
- Yiyang Wang
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiaojuan Bi
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine Institute, Urumqi, China
| | - Zhiwen Luo
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Haiyan Wang
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Dilimulati Ismtula
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Dilimulati Ismtula, ; Chenming Guo,
| | - Chenming Guo
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Dilimulati Ismtula, ; Chenming Guo,
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DNA methylome in pancreatic cancer identified novel promoter hyper-methylation in NPY and FAIM2 genes associated with poor prognosis in Indian patient cohort. Cancer Cell Int 2022; 22:334. [PMID: 36329447 PMCID: PMC9635159 DOI: 10.1186/s12935-022-02737-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is one of the leading cancers worldwide and has a poor survival, with a 5-year survival rate of only 8.5%. In this study we investigated altered DNA methylation associated with PDAC severity and prognosis. Methods Methylome data, generated using 450 K bead array, was compared between paired PDAC and normal samples in the TCGA cohort (n = 9) and our Indian cohort (n = 7). The total Indian Cohort (n = 75) was split into cohort 1 (n = 7), cohort 2 (n = 22), cohort 3 (n = 26) and cohort 4 (n = 20).Validation of differential methylation (6 selected CpG loci) and associated gene expression for differentially methylated genes (10 selected gDMs) were carried out in separate validation cohorts, using MSP, RT-PCR and IHC correlations between methylation and gene expression were observed in TCGA, GTEx cohorts and in validation cohorts. Kaplan–Meier survival analysis was done to study differential prognosis, during 2–5 years of follow-up. Results We identified 156 DMPs, mapped to 91 genes (gDMs), in PDAC; 68 (43.5%) DMPs were found to be differentially methylated both in TCGA cohort and our cohort, with significant concordance at hypo- and hyper-methylated loci. Enrichments of “regulation of ion transport”, “Interferon alpha/beta signalling”, “morphogenesis and development” and “transcriptional dysregulation” pathways were observed among 91 gDMs. Hyper-methylation of NPY and FAIM2 genes with down-regulated expression in PDAC, were significantly associated with poor prognosis in the Indian patient cohort. Conclusions Ethnic variations among populations may determine the altered epigenetic landscape in the PDAC patients of the Indian cohort. Our study identified novel differentially methylated genes (mainly NPY and FAIM2) and also validated the previously identified differentially methylated CpG sites associated with PDAC cancer patient’s survival. Comparative analysis of our data with TCGA and CPTAC cohorts showed that both NPY and FAIM2 hyper-methylation and down-regulations can be novel epigenetically regulated genes in the Indian patient population, statistically significantly associated with poor survival and advanced tumour stages. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02737-1.
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Clinical Implication of Perineural and Lymphovascular Invasion in Rectal Cancer Patients Who Underwent Surgery After Preoperative Chemoradiotherapy. Dis Colon Rectum 2022; 65:1325-1334. [PMID: 34856592 DOI: 10.1097/dcr.0000000000002219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Lymphovascular and perineural invasion are well-known negative prognostic indicators in rectal cancer, but previous studies on their significance are not consistent. OBJECTIVE This study assessed the prognostic value of lymphovascular and perineural invasion in rectal cancer patients who received preoperative chemoradiotherapy followed by curative resection. DESIGN This is a retrospective analysis. SETTING This study was performed at a tertiary cancer center. PATIENTS Rectal cancer patients who underwent curative resection after preoperative chemoradiotherapy between January 2000 and December 2010. MAIN OUTCOME MEASURES The primary outcomes were disease-free survival and overall survival. The survival rates were estimated using Kaplan-Meier analysis, and group comparisons were conducted using a log-rank test. RESULTS Of the 1156 included patients, 109 (9.4%) presented with lymphovascular invasion and 137 (11.9%) presented with perineural invasion. Lymphovascular and perineural invasion were associated with T and N downstaging after preoperative chemoradiotherapy ( p < 0.001). In the ypN0 patients, the 5-year disease-free survival rates were 70.8% and 78.5% ( p = 0.150) for the lymphovascular invasion and absent groups, respectively. In the perineural invasion group, the 5-year disease-free survival rate was 59.0% compared to 80.2% in the absent group ( p = 0.001). Among the ypN+ patients, the 5-year disease-free survival rates were 36.9% and 44.4% for the lymphovascular invasion and absent groups, respectively ( p = 0.211). The perineural invasion group had a poorer 5-year disease-free survival rate compared to the absent group (29.7% vs 46.7%; p = 0.011). By multivariable analyses, perineural invasion correlated with a poor disease-free survival (HR 1.412, 95% CI 1.082-1.843; p = 0.011) and also in ypN0 subgroup analysis (HR 1.717, 95% CI 1.093-2.697; p = 0.019). LIMITATIONS This study was a retrospective study conducted at a single center. CONCLUSIONS Perineural invasion is a reliable independent predictor of recurrence in rectal cancer patients treated with preoperative chemoradiotherapy. Patients with perineural invasion should be considered for closer surveillance even with ypN0 status. See Video Abstract at http://links.lww.com/DCR/B833 .IMPLICACIÓN CLÍNICA DE LA INVASIÓN PERINEURAL Y LINFOVASCULAR EN PACIENTES CON CÁNCER DE RECTO SOMETIDOS A CIRUGÍA DESPUÉS DE QUIMIORRADIOTERAPIA PREOPERATORIA. ANTECEDENTES La invasión linfovascular y perineural en cancer de recto, son indicadores pronósticos negativos bien conocidos, pero estudios previos sobre su significancia, no son consistentes. OBJETIVO El estudio evaluó el valor pronóstico de la invasión linfovascular y perineural en pacientes con cáncer de recto sometidos a quimiorradioterapia preoperatoria seguida de resección curativa. DISEO Es un análisis retrospectivo. ENTORNO CLINICO El estudio se realizó en un centro oncológico terciario. PACIENTES Pacientes con cáncer de recto sometidos a resección curativa después de quimiorradioterapia preoperatoria entre enero de 2000 y diciembre de 2010. PRINCIPALES MEDIDAS DE VALORACION Los resultados primarios fueron la supervivencia libre de enfermedad y la supervivencia general. Las tasas de supervivencia se estimaron mediante el análisis de Kaplan-Meier y las comparaciones de grupos se realizaron mediante una prueba de rango logarítmico. RESULTADOS De los 1156 pacientes incluidos, 109 (9,4%) presentaron invasión linfovascular y 137 (11,9%) invasión perineural. La invasión linfovascular y perineural se asoció con reducción del estadio de T y N después de la quimiorradioterapia preoperatoria ( p < 0,001). En los pacientes ypN0, las tasas de supervivencia libre de enfermedad a 5 años fueron del 70,8% y el 78,5% ( p = 0,150) para los grupos con y sin invasión linfovascular, respectivamente. En el grupo de invasión perineural, la tasa de supervivencia libre de enfermedad a 5 años fue del 59,0%, en comparación con el 80,2% en el grupo ausente ( p = 0,001). Entre los pacientes ypN +, las tasas de supervivencia sin enfermedad a 5 años fueron del 36,9% y 44,4% para los grupos con y sin invasión linfovascular, respectivamente ( p = 0,211). El grupo de invasión perineural mostró una tasa de supervivencia libre de enfermedad a 5 años menor, en comparación con el grupo ausente (29,7% versus 46,7%, p = 0,011). Mediante análisis multivariable, la invasión perineural se correlacionó con una pobre tasa de supervivencia de enfermedad (índice de riesgo 1,412; intervalo de confianza del 95%: 1,082-1,843; p = 0,011) y también en el análisis de subgrupos ypN0 (índice de riesgo 1,717; intervalo de confianza del 95%: 1,093-2,697; p = 0,019). LIMITACIONES Estudio retrospectivo realizado en un solo centro. CONCLUSIONES La invasión perineural es un predictor independiente y confiable de recurrencia en pacientes con cáncer de recto tratados con quimiorradioterapia preoperatoria. Los pacientes con invasión perineural deben considerarse para una vigilancia más estrecha incluso con estadio ypN0. Consulte Video Resumen en http://links.lww.com/DCR/B833 . (Traducción-Dr. Fidel Ruiz Healy ).
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Gao L, Ren R, Shen J, Hou J, Ning J, Feng Y, Wang M, Wu L, Sun Y, Wang H, Wang D, Cao J. Values of OAS gene family in the expression signature, immune cell infiltration and prognosis of human bladder cancer. BMC Cancer 2022; 22:1016. [PMID: 36162993 PMCID: PMC9510761 DOI: 10.1186/s12885-022-10102-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/15/2022] [Indexed: 12/24/2022] Open
Abstract
Background Bladder cancer (BLCA) is one of the most common genitourinary malignancies in the world, but its pathogenic genes have not been fully identified and the treatment outcomes are still unsatisfactory. Although the members of 2', 5'-oligoadenylate synthetase (OAS) gene family are known involved in some tumorous biological processes, the roles of the OAS gene family in BLCA are still undetermined. Methods By combining vast bioinformatic datasets analyses of BLCA and the experimental verification on clinical BLCA specimen, we identified the expressions and biological functions of OAS gene family members in BLCA with comparison to normal bladder tissues. Results The expression levels of OAS gene family members were higher in BLCA than in normal bladder tissues. The expression levels of most OAS genes had correlations with genomic mutation and methylation, and with the infiltration levels of CD4 + T cells, CD8 + T cells, neutrophils, and dendritic cells in the microenvironment of BLCA. In addition, high expressions of OAS1, OAS2, OAS3, and OASL predicted better overall survival in BLCA patients. Conclusions The highly expressed OAS genes in BLCA can reflect immune cells infiltration in the tumor microenvironment and predict the better overall survival of BLCA, and thus may be considered as a signature of BLCA. The study provides new insights into the diagnosis, treatment, and prognosis of BLCA. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10102-8.
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Affiliation(s)
- Lijuan Gao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China.,Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Ruimin Ren
- Department of Urology, Shanxi Bethune Hospital (Third Hospital of Shanxi Medical University), Taiyuan, 030032, China
| | - Jing Shen
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China.,Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Jiayi Hou
- Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, 030012, China
| | - Junya Ning
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China.,Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Yanlin Feng
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China.,Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Meiyue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China.,Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Lifei Wu
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China
| | - Yaojun Sun
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China.,Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Huang Wang
- Department of Urology, Shanxi Bethune Hospital (Third Hospital of Shanxi Medical University), Taiyuan, 030032, China
| | - Deping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China. .,Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China.
| | - Jimin Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, 030001, China. .,Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China.
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11
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2D-DIGE-MS Proteomics Approaches for Identification of Gelsolin and Peroxiredoxin 4 with Lymph Node Metastasis in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14133189. [PMID: 35804959 PMCID: PMC9265116 DOI: 10.3390/cancers14133189] [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: 05/24/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 02/07/2023] Open
Abstract
Background/Aims: A combination of fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry approach was used to search for potential markers for prognosis and intervention of colorectal cancer (CRC) at different stages of lymph node metastasis (LMN). This quantitative proteomic survey aimed to investigate the LNM-associated proteins and evaluate the clinicopathological characteristics of these target proteins in CRC from stage I to stage IV. Methods: Sixteen CRC cases were categorized into paired non-LNM and LNM groups, and two-dimensional difference gel electrophoresis and MS proteome analysis were performed. Differential protein expression between non-LNM and LNM CRC was further validated in a tissue microarray, including 40 paraffin-embedded samples by immunohistochemistry staining. Moreover, a Boyden chamber assay, flow cytometry, and shRNA were used to examine the epithelial–mesenchymal transition and mechanism invasiveness of the differentially expressed proteins in DLD-1 cells and in vivo xenograft mouse model. Results: Eighteen differentially expressed proteins were found between non-LNM and LNM CRC tissues. Among them, protein levels of Gelsolin (GSN) and peroxiredoxin 4 (PRDX4) were abundant in node-positive CRC. Downregulation of GSN and PRDX4 markedly suppressed migration and invasiveness and also induced cell cycle G1/S arrest in DLD-1. Mechanistically, the EGFR/RhoA/PKCα/ERK pathways are critical for transcriptional activation of histone modification of H3 lysine 4 trimethylation (H3K4me3) of GSN and PRDX4 promoters, resulting in upregulation of GSN, PRDX4, Twist-1/2, cyclinD1, proliferating cell-nuclear antigen, β-catenin, N-cadherin, and matrix metalloprotein-9. Conclusions: GSN and PRDX4 are novel regulators in CRC lymph node metastasis to potentially provide new insights into the mechanism of CRC progression and serve as a biomarker for CRC diagnosis at the metastatic stage.
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12
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Zhang ZJ, Wang KP, Huang YP, Jin C, Jiang H, Xiong L, Chen ZY, Wen Y, Liu ZT, Mo JG. Comprehensive Analysis of the Potential Immune-Related Biomarker ATG101 that Regulates Apoptosis of Cholangiocarcinoma Cells After Photodynamic Therapy. Front Pharmacol 2022; 13:857774. [PMID: 35592424 PMCID: PMC9110647 DOI: 10.3389/fphar.2022.857774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/24/2022] [Indexed: 12/04/2022] Open
Abstract
Autophagy related gene 101 (ATG101) plays a significant role in the occurrence and development of tumours by responding to stress. Our research aims to illustrate the correlation between the expression of ATG101 and tumor prognosis and its potential role and mechanism in tumor immunity and photodynamic therapy (PDT). First, integrated analysis of The Cancer Genome Atlas and Genotype-Tissue Expression portals were used to analyse the expression of ATG101. Then, Kaplan–Meier curves was applied in cholangiocarcinoma (CHOL) and liver hepatocellular carcinoma (LIHC) datasets for survival analysis. Next, the relationship between ATG101 expression and six immune cells, the immune microenvironment and immune checkpoints was analysed. Besides, the relationship between the expression of ATG101 and methyltransferase. GSEA was used to study the function and the related transcript factors of ATG101 in CHOL and LIHC. The effect of PDT on ATG101 was verified by microarray, qPCR and western blot. Then the effect of ATG101 and its regulatory factors on apoptosis were verified by siRNA, lentivirus transfection and Chip-qPCR. Comprehensive analysis showed that ATG101 was overexpressed in different tumours. Kaplan–Meier curves found that ATG101 was associated with poor prognosis in tumours (including CHOL and LIHC). We found that ATG101 can be used as a target and prognostic marker of tumour immunotherapy for different tumours. We also found that ATG101 regulates DNA methylation. GSEA analysis showed that ATG101 may play a critical role in CHOL and LIHC. Subsequent validation tests confirmed that the up-regulated ATG101 after PDT treatment is not conducive to the occurrence of apoptosis of cholangiocarcinoma cells. The high expression of ATG101 may be induced by the early stress gene EGR2. Our study highlights the significance of ATG101 in the study of tumour immunity and photodynamic therapy from a pan-cancer perspective.
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Affiliation(s)
- Zi-Jian Zhang
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Kun-Peng Wang
- Department of General Surgery, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
| | - Yun-Peng Huang
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chong Jin
- Department of General Surgery, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
| | - Hao Jiang
- Department of General Surgery, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
| | - Li Xiong
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhao-Yi Chen
- Department of General Surgery, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
| | - Yu Wen
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhong-Tao Liu
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jing-Gang Mo
- Department of General Surgery, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, China
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13
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Motoo I, Nanjo S, Ando T, Yamashita S, Ushijima T, Yasuda I. Methylation silencing of ULK2 via epithelial-mesenchymal transition causes transformation to poorly differentiated gastric cancers. Gastric Cancer 2022; 25:325-335. [PMID: 34554345 DOI: 10.1007/s10120-021-01250-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/09/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Diffuse-type gastric cancers (DGC) typically have a poor prognosis related to their invasion and metastasis, in which the epithelial-mesenchymal transition (EMT) is the initiation step. ULK2 plays a role in the autophagy initiation, which might provide a survival advantage in cancer cells. Although knock-down of ULK2 reportedly induces autophagy and EMT in a lung cancer cell line, the mechanism of EMT via the down-regulation of ULK2, as well as its clinical significance, remains yet unclear. The present study, therefore, aims at clarifying this mechanism and its clinical significance in gastric cancers. METHODS We examined ULK2 mRNA expression in gastric cancer tissues and normal gastric tissues of healthy people. The effects of knock-downed ULK2 were examined in two gastric cancer cells, which were investigated in terms of their gene expression changes by the mRNA microarray. RESULTS ULK2 was strongly expressed in intestinal-type cancers but was scarcely expressed in DGC by immunohistochemical staining. Furthermore, we found that ULK2 was methylated in DGC and was unmethylated in corresponding adjacent normal tissues. Then, we validated whether knock-down of ULK2 could induce autophagy, cell migration, and EMT in NUGC3 and MKN45 cells. Using mRNA microarray analysis, we confirmed that knock-down of ULK2 changed expressions of oncogenic genes associated with cell migration and EMT. Autophagy inhibitor suppressed cell migration and EMT induced by knock-down of ULK2 in NUGC3 and MKN45. CONCLUSION Methylation silencing of ULK2 could induce cell migration and EMT by means of autophagy induction, causing transformation to poorly differentiated cancers.
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Affiliation(s)
- Iori Motoo
- Department of Gastroenterology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Sohachi Nanjo
- Department of Gastroenterology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.
| | - Takayuki Ando
- Department of Gastroenterology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Ichiro Yasuda
- Department of Gastroenterology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
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14
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Wu Y, Zheng J, Yan Y, Liu J, Zhou Y. Gelsolin Can Be a Prognostic Biomarker and Correlated with Immune Infiltrates in Gastric Cancer. Int J Gen Med 2022; 15:927-936. [PMID: 35115818 PMCID: PMC8803610 DOI: 10.2147/ijgm.s339940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/24/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Gelsolin (GSN) is the most widely expressed actin-severing protein in humans, which could regulate cell morphology, differentiation, movement and apoptosis. This study aims to explore the GSN as a prognostic biomarker of stomach adenocarcinoma (STAD). METHODS In this study, we used several online databases to comprehensively analyze the role of GSN in STAD. Oncomine and HPA databases were used to explore the GSN expression in various cancer, especially in gastric cancer. Then, UALCAN database was used to evaluate the relationship between GSN expression and promoter methylation in clinical characteristics. Finally, we used TIMER to analyze the correlation between GSN expression and immune infiltrates in gastric cancer. RESULTS GSN was down-regulated in gastric cancer, and decreased expression of GSN was related to worse survival. The GSN expression was significantly related to tumor purity in STAD and significantly correlated with infiltrating level of various immune cells, especially the dendritic cells. CONCLUSION Our study proposes that GSN can be served as the biomarker of disease and neoantigen for STAD treatment, which can improve the deficiency of disease-specific targeted therapies currently exist.
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Affiliation(s)
- Yingmei Wu
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, People’s Republic of China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510000, People’s Republic of China
| | - Junhui Zheng
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, People’s Republic of China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510000, People’s Republic of China
| | - Yanhua Yan
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, People’s Republic of China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510000, People’s Republic of China
| | - Jiduo Liu
- Department of Clinical Laboratory, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510000, People’s Republic of China
| | - Yingchun Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510000, People’s Republic of China
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15
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Susceptibility to disease (tropical theileriosis) is associated with differential expression of host genes that possess motifs recognised by a pathogen DNA binding protein. PLoS One 2022; 17:e0262051. [PMID: 35061738 PMCID: PMC8782480 DOI: 10.1371/journal.pone.0262051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/15/2021] [Indexed: 12/04/2022] Open
Abstract
Background Knowledge of factors that influence the outcome of infection are crucial for determining the risk of severe disease and requires the characterisation of pathogen-host interactions that have evolved to confer variable susceptibility to infection. Cattle infected by Theileria annulata show a wide range in disease severity. Native (Bos indicus) Sahiwal cattle are tolerant to infection, whereas exotic (Bos taurus) Holstein cattle are susceptible to acute disease. Methodology/Principal findings We used RNA-seq to assess whether Theileria infected cell lines from Sahiwal cattle display a different transcriptome profile compared to Holstein and screened for altered expression of parasite factors that could generate differences in host cell gene expression. Significant differences (<0.1 FDR) in the expression level of a large number (2211) of bovine genes were identified, with enrichment of genes associated with Type I IFN, cholesterol biosynthesis, oncogenesis and parasite infection. A screen for parasite factors found limited evidence for differential expression. However, the number and location of DNA motifs bound by the TashAT2 factor (TA20095) were found to differ between the genomes of B. indicus vs. B. taurus, and divergent motif patterns were identified in infection-associated genes differentially expressed between Sahiwal and Holstein infected cells. Conclusions/Significance We conclude that divergent pathogen-host molecular interactions that influence chromatin architecture of the infected cell are a major determinant in the generation of gene expression differences linked to disease susceptibility.
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16
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Ahmed M, Lai TH, Kim W, Kim DR. A Functional Network Model of the Metastasis Suppressor PEBP1/RKIP and Its Regulators in Breast Cancer Cells. Cancers (Basel) 2021; 13:6098. [PMID: 34885208 PMCID: PMC8657175 DOI: 10.3390/cancers13236098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
Drug screening strategies focus on quantifying the phenotypic effects of different compounds on biological systems. High-throughput technologies have the potential to understand further the mechanisms by which these drugs produce the desired outcome. Reverse causal reasoning integrates existing biological knowledge and measurements of gene and protein abundances to infer their function. This approach can be employed to appraise the existing biological knowledge and data to prioritize targets for cancer therapies. We applied text mining and a manual literature search to extract known interactions between several metastasis suppressors and their regulators. We then identified the relevant interactions in the breast cancer cell line MCF7 using a knockdown dataset. We finally adopted a reverse causal reasoning approach to evaluate and prioritize pathways that are most consistent and responsive to drugs that inhibit cell growth. We evaluated this model in terms of agreement with the observations under treatment of several drugs that produced growth inhibition of cancer cell lines. In particular, we suggested that the metastasis suppressor PEBP1/RKIP is on the receiving end of two significant regulatory mechanisms. One involves RELA (transcription factor p65) and SNAI1, which were previously reported to inhibit PEBP1. The other involves the estrogen receptor (ESR1), which induces PEBP1 through the kinase NME1. Our model was derived in the specific context of breast cancer, but the observed responses to drug treatments were consistent in other cell lines. We further validated some of the predicted regulatory links in the breast cancer cell line MCF7 experimentally and highlighted the points of uncertainty in our model. To summarize, our model was consistent with the observed changes in activity with drug perturbations. In particular, two pathways, including PEBP1, were highly responsive and would be likely targets for intervention.
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Affiliation(s)
| | | | | | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 527-27, Korea; (M.A.); (T.H.L.); (W.K.)
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17
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Dong C, Rao N, Du W, Gao F, Lv X, Wang G, Zhang J. mRBioM: An Algorithm for the Identification of Potential mRNA Biomarkers From Complete Transcriptomic Profiles of Gastric Adenocarcinoma. Front Genet 2021; 12:679612. [PMID: 34386038 PMCID: PMC8354214 DOI: 10.3389/fgene.2021.679612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/06/2021] [Indexed: 12/09/2022] Open
Abstract
Purpose In this work, an algorithm named mRBioM was developed for the identification of potential mRNA biomarkers (PmBs) from complete transcriptomic RNA profiles of gastric adenocarcinoma (GA). Methods mRBioM initially extracts differentially expressed (DE) RNAs (mRNAs, miRNAs, and lncRNAs). Next, mRBioM calculates the total information amount of each DE mRNA based on the coexpression network, including three types of RNAs and the protein-protein interaction network encoded by DE mRNAs. Finally, PmBs were identified according to the variation trend of total information amount of all DE mRNAs. Four PmB-based classifiers without learning and with learning were designed to discriminate the sample types to confirm the reliability of PmBs identified by mRBioM. PmB-based survival analysis was performed. Finally, three other cancer datasets were used to confirm the generalization ability of mRBioM. Results mRBioM identified 55 PmBs (41 upregulated and 14 downregulated) related to GA. The list included thirteen PmBs that have been verified as biomarkers or potential therapeutic targets of gastric cancer, and some PmBs were newly identified. Most PmBs were primarily enriched in the pathways closely related to the occurrence and development of gastric cancer. Cancer-related factors without learning achieved sensitivity, specificity, and accuracy of 0.90, 1, and 0.90, respectively, in the classification of the GA and control samples. Average accuracy, sensitivity, and specificity of the three classifiers with machine learning ranged within 0.94–0.98, 0.94–0.97, and 0.97–1, respectively. The prognostic risk score model constructed by 4 PmBs was able to correctly and significantly (∗∗∗p < 0.001) classify 269 GA patients into the high-risk (n = 134) and low-risk (n = 135) groups. GA equivalent classification performance was achieved using the complete transcriptomic RNA profiles of colon adenocarcinoma, lung adenocarcinoma, and hepatocellular carcinoma using PmBs identified by mRBioM. Conclusions GA-related PmBs have high specificity and sensitivity and strong prognostic risk prediction. MRBioM has also good generalization. These PmBs may have good application prospects for early diagnosis of GA and may help to elucidate the mechanism governing the occurrence and development of GA. Additionally, mRBioM is expected to be applied for the identification of other cancer-related biomarkers.
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Affiliation(s)
- Changlong Dong
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Nini Rao
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenju Du
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Fenglin Gao
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoqin Lv
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Guangbin Wang
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Junpeng Zhang
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
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18
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Mining the plasma-proteome associated genes in patients with gastro-esophageal cancers for biomarker discovery. Sci Rep 2021; 11:7590. [PMID: 33828156 PMCID: PMC8027878 DOI: 10.1038/s41598-021-87037-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/15/2021] [Indexed: 12/22/2022] Open
Abstract
Gastro-esophageal (GE) cancers are one of the major causes of cancer-related death in the world. There is a need for novel biomarkers in the management of GE cancers, to yield predictive response to the available therapies. Our study aims to identify leading genes that are differentially regulated in patients with these cancers. We explored the expression data for those genes whose protein products can be detected in the plasma using the Cancer Genome Atlas to identify leading genes that are differentially regulated in patients with GE cancers. Our work predicted several candidates as potential biomarkers for distinct stages of GE cancers, including previously identified CST1, INHBA, STMN1, whose expression correlated with cancer recurrence, or resistance to adjuvant therapies or surgery. To define the predictive accuracy of these genes as possible biomarkers, we constructed a co-expression network and performed complex network analysis to measure the importance of the genes in terms of a ratio of closeness centrality (RCC). Furthermore, to measure the significance of these differentially regulated genes, we constructed an SVM classifier using machine learning approach and verified these genes by using receiver operator characteristic (ROC) curve as an evaluation metric. The area under the curve measure was > 0.9 for both the overexpressed and downregulated genes suggesting the potential use and reliability of these candidates as biomarkers. In summary, we identified leading differentially expressed genes in GE cancers that can be detected in the plasma proteome. These genes have potential to become diagnostic and therapeutic biomarkers for early detection of cancer, recurrence following surgery and for development of targeted treatment.
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19
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Deveaux AE, Allen TA, Al Abo M, Qin X, Zhang D, Patierno BM, Gu L, Gray JE, Pecot CV, Dressman HK, McCall SJ, Kittles RA, Hyslop T, Owzar K, Crawford J, Patierno SR, Clarke JM, Freedman JA. RNA splicing and aggregate gene expression differences in lung squamous cell carcinoma between patients of West African and European ancestry. Lung Cancer 2021; 153:90-98. [PMID: 33465699 DOI: 10.1016/j.lungcan.2021.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Despite disparities in lung cancer incidence and mortality, the molecular landscape of lung cancer in patients of African ancestry remains underexplored, and race-related differences in RNA splicing remain unexplored. MATERIALS AND METHODS We identified differentially spliced genes (DSGs) and differentially expressed genes (DEGs) in biobanked lung squamous cell carcinoma (LUSC) between patients of West African and European ancestry, using ancestral genotyping and Affymetrix Clariom D array. DSGs and DEGs were validated independently using the National Cancer Institute Genomic Data Commons. Associated biological processes, overlapping canonical pathways, enriched gene sets, and cancer relevance were identified using Gene Ontology Consortium, Ingenuity Pathway Analysis, Gene Set Enrichment Analysis, and CancerMine, respectively. Association with LUSC survival was conducted using The Cancer Genome Atlas. RESULTS 4,829 DSGs and 267 DEGs were identified, including novel targets in NSCLC as well as genes identified previously to have relevance to NSCLC. RNA splicing events within 3 DSGs as well as 1 DEG were validated in the independent cohort. 853 DSGs and 29 DEGs have been implicated as potential drivers, oncogenes and/or tumor suppressor genes. Biological processes enriched among DSGs and DEGs included metabolic process, biological regulation, and multicellular organismal process and, among DSGs, ion transport. Overlapping canonical pathways among DSGs included neuronal signaling pathways and, among DEGs, cell metabolism involving biosynthesis. Gene sets enriched among DSGs included KRAS Signaling, UV Response, E2 F Targets, Glycolysis, and Coagulation. 355 RNA splicing events within DSGs and 18 DEGs show potential association with LUSC patient survival. CONCLUSION These DSGs and DEGs, which show potential biological and clinical relevance, could have the ability to drive novel biomarker and therapeutic development to mitigate LUSC disparities.
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Affiliation(s)
- April E Deveaux
- Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Tyler A Allen
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Muthana Al Abo
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xiaodi Qin
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Dadong Zhang
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Brendon M Patierno
- Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Lin Gu
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jhanelle E Gray
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Chad V Pecot
- Department of Medicine, Division of Hematology/Oncology, University of North Carolina, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, 27599, USA
| | - Holly K Dressman
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Shannon J McCall
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Rick A Kittles
- Department of Population Sciences, Division of Health Equities, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Terry Hyslop
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kouros Owzar
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jeffrey Crawford
- Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Steven R Patierno
- Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jeffrey M Clarke
- Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jennifer A Freedman
- Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
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20
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Wang X, Cao Y, Ding M, Liu J, Zuo X, Li H, Fan R. Oncological and prognostic impact of lymphovascular invasion in Colorectal Cancer patients. Int J Med Sci 2021; 18:1721-1729. [PMID: 33746588 PMCID: PMC7976558 DOI: 10.7150/ijms.53555] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
Objectives: Lymphovascular invasion (LVI) is correlated with unfavorable prognoses in several types of cancers. We aimed to identify the informative features associated with LVI and to determine its prognostic value in colorectal cancer (CRC) patients. Methods: We retrospectively analyzed 1,474 CRC patients admitted in Wuhan Union Hospital between 2013 and 2017 as the development cohort and 549 CRC patients from The Cancer Genome Atlas (TCGA) database as the validation cohort. Logistical and Cox regression analyses were conducted to determine the oncological and prognostic significance of LVI in CRC patients. A survival nomogram based on LVI status was established using the Wuhan Union cohort and validated using TCGA cohort. Results: The LVI detection rates were 21.64% in the Wuhan Union cohort and 35.15% in TCGA cohort. LVI was closely correlated with advanced T stage, N stage, and TNM stage. LVI positivity was an independent biomarker for unfavorable overall survival (hazard ratio [HR]=2.25, 95% confidence interval [CI]=1.70-2.96, P<0.0001) and worse disease-free survival (HR=2.34, 95% CI=1.76-3.12, P<0.0001) in CRC patients. The survival nomogram incorporating LVI exhibited good predictive performance and reliability in the Wuhan Union cohort and TCGA cohort. Conclusion: LVI is a significant indicator of advanced stage and is remarkably correlated with worse prognosis in CRC patients. The survival nomogram incorporating LVI may assist clinicians to better strategize the therapeutic options for patients with CRC.
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Affiliation(s)
- Xiaofei Wang
- Department of radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yinghao Cao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Miaomiao Ding
- Department of Ultrasonography, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Junqi Liu
- Department of radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaoxiao Zuo
- Department of radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongfei Li
- Department of radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruitai Fan
- Department of radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Su H, Chang C, Hao J, Xu X, Bao M, Luo S, Zhao C, Liu Q, Wang X, Zhou Z, Zhou H. Identification of Genomic Alterations of Perineural Invasion in Patients with Stage II Colorectal Cancer. Onco Targets Ther 2020; 13:11571-11582. [PMID: 33204110 PMCID: PMC7667198 DOI: 10.2147/ott.s264616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose The molecular mechanism of perineural invasion (PNI) in stage II colorectal cancer (CRC) remains not to be defined clearly. This study aims to identify the genomic aberrations related to PNI in stage II CRC. Patients and Methods Using array-based comparative genomic hybridization (array-CGH), primary tumor tissues and paracancerous normal tissues of stage II CRC with PNI and without PNI were analyzed. We identified genomic aberrations by using Genomic Workbench and MD-SeeGH and validated the aberrations of selected genes by real-time polymerase chain reaction (PCR). Gene ontology (GO) and pathway analysis were performed to determine the most likely biological effects of these genes. Results The most frequent gains in stage II CRC were at 7q11.21-q11.22, 8p11.21, 8p12-p11.23, 8q11.1-q11.22, 13q12.13-q12.2, and 20q11.21-q11.23 and the most frequent losses were at 17p13.1-p12, 8p23.2, and 118q11.2-q23. Four high-level amplifications at 8p11.23-p11.22, 18q21.1, 19q11-q12, and 20q11.21-q13.32 and homozygous deletions at 20p12.1 were discovered in Stage II CRC. Gains at 7q11.21-q22.1, 16p11.2, 17q23.3-q25.3, 19p13.3-p12, and 20p13-p11.1, and losses at 11q11-q12.1, 11p15.5-p15.1, 18p11.21, and 18q21.1-q23 were more commonly found in patients with PNI by frequency plot comparison together with detailed genomic analysis. It is also observed that gains at 8q11.1-q24.3, 9q13-q34.3, and 13q12.3-q13.1, and losses at 8p23.3-p12, 17p13.3-p11.2, and 21q22.12 occurred more frequently in patients without PNI. Further validation showed that the expression of FLT1, FBXW7, FGFR1, SLC20A2 and SERPINI1 was significantly up-regulated in the NPNI group compared to the PNI group. GO and pathway analysis revealed some genes enriched in specific pathways. Conclusion These involved genomic changes in the PNI of stage II CRC may be useful to reveal the mechanisms underlying PNI and provide candidate biomarkers.
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Affiliation(s)
- Hao Su
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Chen Chang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Jiajie Hao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Xin Xu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Mandula Bao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Shou Luo
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Chuanduo Zhao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Xishan Wang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Zhixiang Zhou
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Haitao Zhou
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
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Zhao J, Zhang X, Cheng M, Guan J, Gai J, Fu L, Zhang R, Du T, Li Q. Expression of IFN-induced 2'-5'-oligoadenylate synthetases correlates with immune infiltration, revealing potential targets and new biomarkers for basal-like breast cancer prognosis. Int Immunopharmacol 2020; 88:106916. [PMID: 32882665 DOI: 10.1016/j.intimp.2020.106916] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/15/2020] [Accepted: 08/16/2020] [Indexed: 10/23/2022]
Abstract
Triple-negative breast cancer has been classified as basal-like immune activated (BLIA), basal-like immune-suppressed (BLIS), and two other subtypes, suggesting potential immune therapeutic targets for basal-like breast cancer (BLBC). 2'-5'-Oligoadenylate synthetases (OASs), identified from differentially expressed genes (DEGs) between BLIA and BLIS breast cancers (GSE76124), are involved in antiviral activity induced by interferons. However, the association between the four OASs and prognosis or tumor-infiltrating immune cells (TIICs) remains unclear. Expression, survival data, and immune correlations for OASs in BLBC were assessed using bioinformatics tools. We found that OASs were highly expressed in BLIA breast cancer. Survival analysis suggested that high transcriptional levels of OASs were associated with better overall survival, relapse-free survival, and distant metastasis-free survival in patients with BLBC. Moreover, the prognostic value of OASs with respect to different clinicopathological factors, and especially according to lymph node metastasis, in patients with BLBC was further assessed. Our findings elucidated the expression, prognostic role, and effect of OASs in TIICs on BLBC, which might promote the development of OAS-targeted immunotherapy for BLBC.
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Affiliation(s)
- Jinming Zhao
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Xiupeng Zhang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Ming Cheng
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Jingqian Guan
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Junda Gai
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Lin Fu
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China; Department of Pathology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Ruochen Zhang
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT, United States
| | - Tengjiao Du
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Qingchang Li
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China; Department of Pathology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China.
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Mass Spectrometric Comparison of HPV-Positive and HPV-Negative Oropharyngeal Cancer. Cancers (Basel) 2020; 12:cancers12061531. [PMID: 32545200 PMCID: PMC7352546 DOI: 10.3390/cancers12061531] [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: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Squamous cell carcinoma of the head and neck (HNSCC) consist of two distinct biological entities. While the numbers of classical, tobacco-induced HNSCC are declining, tumors caused by human papillomavirus (HPV) infection are increasing in many countries. HPV-positive HNSCC mostly arise in the oropharynx and are characterized by an enhanced sensitivity towards radiotherapy and a favorable prognosis. To identify molecular differences between both entities on the protein level, we conducted a mass spectrometric comparison of eight HPV-positive and nine HPV-negative oropharyngeal tumors (OPSCC). Overall, we identified 2051 proteins, of which 31 were found to be differentially expressed. Seventeen of these can be assorted to three functional groups, namely DNA replication, nuclear architecture and cytoskeleton regulation, with the differences in the last group potentially reflecting an enhanced migratory and invasive capacity. Furthermore, a number of identified proteins have been described to directly impact on DNA double-strand break repair or radiation sensitivity (e.g., SLC3A2, cortactin, RBBP4, Numa1), offering explanations for the differential prognosis. The unequal expression of three proteins (SLC3A2, MCM2 and lamin B1) was confirmed by immunohistochemical staining using a tissue microarray containing 205 OPSCC samples. The expression levels of SLC3A2 and lamin B1 were found be of prognostic relevance in patients with HPV-positive and HPV-negative OPSCC, respectively.
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A prognostic index based on an eleven gene signature to predict systemic recurrences in colorectal cancer. Exp Mol Med 2019; 51:1-12. [PMID: 31578316 PMCID: PMC6802642 DOI: 10.1038/s12276-019-0319-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/12/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
Approximately half of colorectal cancer (CRC) patients experience disease recurrence and metastasis, and these individuals frequently fail to respond to treatment due to their clinical and biological diversity. Here, we aimed to identify a prognostic signature consisting of a small gene group for precisely predicting CRC heterogeneity. We performed transcriptomic profiling using RNA-seq data generated from the primary tissue samples of 130 CRC patients. A prognostic index (PI) based on recurrence-associated genes was developed and validated in two larger independent CRC patient cohorts (n = 795). The association between the PI and prognosis of CRC patients was evaluated using Kaplan–Meier plots, log-rank tests, a Cox regression analysis and a RT-PCR analysis. Transcriptomic profiling in 130 CRC patients identified two distinct subtypes associated with systemic recurrence. Pathway enrichment and RT-PCR analyses revealed an eleven gene signature incorporated into the PI system, which was a significant prognostic indicator of CRC. Multivariate and subset analyses showed that PI was an independent risk factor (HR = 1.812, 95% CI = 1.342–2.448, P < 0.001) with predictive value to identify low-risk stage II patients who responded the worst to adjuvant chemotherapy. Finally, a comparative analysis with previously reported Consensus Molecular Subgroup (CMS), high-risk patients classified by the PI revealed a distinct molecular property similar to CMS4, associated with a poor prognosis. This novel PI predictor based on an eleven gene signature likely represents a surrogate diagnostic tool for identifying high-risk CRC patients and for predicting the worst responding patients for adjuvant chemotherapy. A prognostic tool that searches for eleven genes associated with colorectal cancer recurrence shows promise in initial trials. The complexity of colorectal cancer (CRC) makes it challenging to treat. A significant number of patients relapse or experience metastasis even after surgical intervention, and fail to respond to post-surgical chemotherapy. Yong Sung Kim at the Korea Research Institute of Bioscience and Biotechnology, Daejeon, and Jin Cheon Kim from the University of Ulsan, Seoul, South Korea, and co-workers, conducted RNA-sequencing analysis on samples from 130 patients with CRC, 58 of whom had suffered relapse. They pinpointed eleven genes strongly associated with recurrence-free survival. They used these to develop a prognostic tool to identify high-risk patients and those more likely to respond poorly to chemotherapy. The tool was validated on a further 795 patients with CRC.
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25
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Wang J, Wang Y, Kong F, Han R, Song W, Chen D, Bu L, Wang S, Yue J, Ma L. Identification of a six‐gene prognostic signature for oral squamous cell carcinoma. J Cell Physiol 2019; 235:3056-3068. [PMID: 31538341 DOI: 10.1002/jcp.29210] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/03/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Jiaying Wang
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Yuanyong Wang
- Department of Thoracic Surgery Affiliated Hospital of Qingdao University Qingdao China
| | - Fanzhi Kong
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Rui Han
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Wenbin Song
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Di Chen
- Department of Gastroenterology Affiliated Hospital of Qingdao University Qingdao China
| | - Lingxue Bu
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Shuangyi Wang
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Jin Yue
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
| | - Lei Ma
- Department of Stomatology Affiliated Hospital of Qingdao University Qingdao Shandong China
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