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Uqaili AA, Usman G, Bhatti U, Nasir H, Zia R, Akram MA, Jawad FA, Farid A, AbdelGawwad MR, Almutairi SM, Elshikh MS, Hussain S, Rasheed RA. Bioinformatics, RNA sequencing, and targeted bisulfite sequencing analyses identify the role of PROM2 as a diagnostic and prognostic biomarker. Am J Transl Res 2023; 15:5389-5407. [PMID: 37692961 PMCID: PMC10492044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
OBJECTIVES Prominin 2 (PROM2) gene has been reported as a molecular biomarker of human cancers; however, its role is still controversial. This study was therefore arranged to seek the role of PROM2 in different cancers with Bioinformatics and in vitro analyses. METHODS A combination of bioinformatics and molecular experiments. RESULTS Through the utilization of Bioinformatics analysis, it was observed that in 19 out of the 24 human cancers studied, there was a significant increase in the expression of PROM2 compared to the respective control samples. Additionally, the overexpression of PROM2 was linked specifically to a decrease in overall survival (OS) among breast cancer (BRCA), lung adenocarcinoma (LUAD), and uterine corpus endometrial carcinoma (UCEC) patients. Furthermore, advanced molecular investigations were conducted, encompassing RNA sequencing (RNA-seq) as well as targeted bisulfite sequencing (bisulfite-seq) assessments of PROM2. These analyses were performed across an array of lung cancer cell lines (A549, ABC-1, EBC-1, and LK-2) and a normal control lung cell line (MRC-9). Results of these analysis revealed overexpression and reduced methylation of PROM2 within lung cancer cell lines, relative to the corresponding control cell line. This suggests that PROM2 assumes a substantial function in the advancement and course of BRCA, LUAD, and UCEC cancers. Subsequent pathway analysis revealed that genes enriched by PROM2 are actively engaged in four pivotal pathways. Additionally, intriguing associations were observed between PROM2 expression, tumor purity, infiltration of CD8+ T immune cells, and genetic modifications. Moreover, we also predicted a few MicroRNAs (miRNAs), transcription factors (TFs), and potential drugs that could help to understand and better manage these cancers via designing appropriate therapies targeting PROM2. CONCLUSION Via this study, we effectively revealed PROM2 overexpression as a potential diagnostic and prognostic biomarker of survival in BRCA, LUAD, and UCEC.
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Affiliation(s)
- Arsalan Ahmed Uqaili
- Department of Physiology, Liaquat University of Medical and Health SciencesJamshoro 76090, Pakistan
| | - Gulzar Usman
- Department of Community Medicine, LUMHSJamshoro 76090, Pakistan
| | - Urooj Bhatti
- Department of Physiology, LUMHSJamshoro 76090, Pakistan
| | - Hilal Nasir
- Clinical and Translational Oncology, Scuola Superiore Meridionale, Naples Federico II UniversityNaples 80131, Italy
| | - Rabeea Zia
- Pakistan Kidney and Liver Institute and Research CenterLahore 54000, Pakistan
| | - Muhammad Aitzaz Akram
- Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Fahim Ali Jawad
- Centre of Agricultural Biochemistry and Biotechnology-University of Agriculture FaisalabadFaisalabad 38040, Pakistan
| | - Afshan Farid
- Department of Botany, PMAS Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Mohamed Ragab AbdelGawwad
- Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of SarajevoSarajevo 71210, Bosnia and Herzegovina
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. 2455, Riyadh 11451, Saudi Arabia
| | - Sajid Hussain
- Department of Botany, PMAS Arid Agriculture UniversityRawalpindi 46000, Pakistan
| | - Rabab Ahmed Rasheed
- Histology & Cell Biology Department, Faculty of Medicine, King Salman International UniversitySouth Sinai, Egypt
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Harabajsa S, Šefčić H, Klasić M, Milavić M, Židovec Lepej S, Grgić I, Zajc Petranović M, Jakopović M, Smojver-Ježek S, Korać P. Infection with human cytomegalovirus, Epstein-Barr virus, and high-risk types 16 and 18 of human papillomavirus in EGFR-mutated lung adenocarcinoma. Croat Med J 2023; 64:84-92. [PMID: 37131310 PMCID: PMC10183960 DOI: 10.3325/cmj.2023.64.84] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/30/2023] [Indexed: 04/11/2024] Open
Abstract
AIM To assess the frequency of human cytomegalovirus (HCMV), Epstein-Barr virus (EBV), and high-risk types of human papillomavirus (HPV16 and HPV18) infections in lung adenocarcinoma samples. METHODS Lung adenocarcinoma cytological smears and their DNA isolates were obtained from patients hospitalized at the Department for Lung Diseases Jordanovac, Zagreb, in 2016 and 2017. Overall, 67 lung adenocarcinoma samples were examined: 34 with epidermal growth factor receptor gene (EGFR) mutations and 33 without EGFR mutations. The EGFR mutation status and virus presence were assessed with a polymerase chain reaction, and random samples were additionally tested for EBV with Sanger sequencing. HCMV, EBV, HPV16, and HPV18 infections were evaluated in relation to EGFR mutation, smoking status, and sex. A meta-analysis of available data about HPV infection in non-small cell lung cancer was performed. RESULTS More frequent HCMV, EBV, HPV16, and HPV18 infections were observed in lung adenocarcinoma samples with EGFR mutations than in samples without these mutations. Coinfection of the investigated viruses was observed only in lung adenocarcinoma samples with mutated EGFR. In the group with EGFR mutations, smoking was significantly associated with HPV16 infection. The meta-analysis showed that non-small cell lung cancer patients with EGFR mutations had a higher odds of HPV infection. CONCLUSION HCMV, EBV, and high-risk HPV infections are more frequent in EGFR-mutated lung adenocarcinomas, which indicates a possible viral impact on the etiology of this lung cancer subtype.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Petra Korać
- Petra Korać, Department of Biology, Division of Molecular Biology, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia,
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Lin FW, Yeh MH, Lin CL, Wei JCC. Association between Breast Cancer and Second Primary Lung Cancer among the Female Population in Taiwan: A Nationwide Population-Based Cohort Study. Cancers (Basel) 2022; 14:cancers14122977. [PMID: 35740640 PMCID: PMC9221143 DOI: 10.3390/cancers14122977] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
PURPOSE A special association between breast cancer and second primary lung cancer in Taiwanese women has been discovered not only in clinical practice, but also in a large population-based study. We hereby investigate the association between breast cancer and second primary lung cancer in Taiwanese women. METHODS This study was conducted from the National Health Insurance Research Database (NHIRD) from Taiwan National Health Insurance (NHI). Patients older than 18 years old and hospitalized with a first diagnosis of breast cancer during 2000 to 2012 were enrolled in the breast cancer group. Patients who were cancer free were frequency-matched with the breast cancer group by age (every five-year span) and index year. The ratio of breast cancer group to non-breast cancer group was 1:4. The event as the outcome in this study was lung cancer. The comorbidities viewed as important confounding factors included coronary artery disease, stroke, hypertension, diabetes, chronic obstructive pulmonary disease, hyperlipidemia, tuberculosis, chronic kidney disease, and chronic liver disease and cirrhosis. We estimated the hazard ratios (HRs), adjusted hazard ratios (aHRs), and 95% confidence intervals (CIs) for risk of lung cancer in the breast cancer group and non-breast cancer group using Cox proportional hazard models. Sensitivity analysis was also done using propensity score matching. All of the statistical analyses were performed using SAS statistical software, version 9.4 (SAS Institute Inc., Cary, NC). RESULTS There were 94,451 breast cancer patients in the breast cancer group and 377,804 patients in the non-breast cancer group in this study. After being stratified by age, urbanization level, and comorbidities, the patients with breast cancer had a significantly higher risk of lung cancer compared with the patients without breast cancer, particularly for those who aged between 20 and 49 years (aHR = 2.10, 95% CI = 1.71-2.58), 50 and 64 years (aHR = 1.35, 95% CI = 1.15-1.58), and those without any comorbidities (aHR = 1.92, 95% CI = 1.64-2.23). CONCLUSION Patients with breast cancer had a significantly higher risk of developing second primary lung cancer compared with patients without breast cancer, particularly in younger groups and in those without any comorbidities. The special association may be attributed to some potential risk factors such as genetic susceptibility and long-term exposure to PM2.5, and is supposed to increase public awareness. Further studies are necessary given the fact that inherited genotypes, different subtypes of breast cancer and lung cancer, and other unrecognized etiologies may play vital roles in both cancers' development.
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Affiliation(s)
- Fan-Wen Lin
- Department of Surgery, Chung Shan Medical University Hospital, Taichung 40201, Taiwan;
| | - Ming-Hsin Yeh
- Division of Breast Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
- Correspondence:
| | - Cheng-Li Lin
- Management Office for Health Data, China Medical University Hospital, Taichung 40202, Taiwan;
- College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - James Cheng-Chung Wei
- Department of Allergy, Immunology & Rheumatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan;
- Institute of Medicine, College of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 40201, Taiwan
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Olaya-Galán NN, Blume S, Tong K, Shen H, Gutierrez MF, Buehring GC. In vitro Susceptibility of Human Cell Lines Infection by Bovine Leukemia Virus. Front Microbiol 2022; 13:793348. [PMID: 35359744 PMCID: PMC8964291 DOI: 10.3389/fmicb.2022.793348] [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: 10/12/2021] [Accepted: 01/28/2022] [Indexed: 12/17/2022] Open
Abstract
Evidence of the presence of bovine leukemia virus (BLV) in human beings and its association with breast cancer has been published in the literature, proposing it as a zoonotic infection. However, not enough evidence exists about transmission pathways nor biological mechanisms in human beings. This study was aimed at gathering experimental evidence about susceptibility of human cell lines to BLV infection. Malignant and non-malignant human cell lines were co-cultured with BLV-infected FLK cells using a cell-to-cell model of infection. Infected human cell lines were harvested and cultured for 3 to 6 months to determine stability of infection. BLV detection was performed through liquid-phase PCR and visualized through in situ PCR. Seven out of nine cell lines were susceptible to BLV infection as determined by at least one positive liquid-phase PCR result in the 3-month culture period. iSLK and MCF7 cell lines were able to produce a stable infection throughout the 3-month period, with both cytoplasmic and/or nuclear BLV-DNA visualized by IS-PCR. Our results support experimental evidence of BLV infection in humans by demonstrating the susceptibility of human cells to BLV infection, supporting the hypothesis of a natural transmission from cattle to humans.
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Affiliation(s)
- Nury N Olaya-Galán
- Ph.D. Program in Biomedical and Biological Sciences, School of Medicine and Human Health, Universidad del Rosario, Bogotá, Colombia.,Grupo de Enfermedades Infecciosas, Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Skyler Blume
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Kan Tong
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - HuaMin Shen
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Maria F Gutierrez
- Grupo de Enfermedades Infecciosas, Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Gertrude C Buehring
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
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Abstract
This overview of the molecular pathology of lung cancer includes a review of the most salient molecular alterations of the genome, transcriptome, and the epigenome. The insights provided by the growing use of next-generation sequencing (NGS) in lung cancer will be discussed, and interrelated concepts such as intertumor heterogeneity, intratumor heterogeneity, tumor mutational burden, and the advent of liquid biopsy will be explored. Moreover, this work describes how the evolving field of molecular pathology refines the understanding of different histologic phenotypes of non-small-cell lung cancer (NSCLC) and the underlying biology of small-cell lung cancer. This review will provide an appreciation for how ongoing scientific findings and technologic advances in molecular pathology are crucial for development of biomarkers, therapeutic agents, clinical trials, and ultimately improved patient care.
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Affiliation(s)
- James J Saller
- Departments of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Theresa A Boyle
- Departments of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
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6
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Wu M, Shi QM, Duan SL, Ou-yang DJ, Chen P, Tu B, Huang P. Insights into the Association Between QSER1 and M2 Macrophages and Remarkable Malignancy Characteristics in Hepatocellular Carcinoma. Int J Gen Med 2022; 15:1765-1775. [PMID: 35210841 PMCID: PMC8863346 DOI: 10.2147/ijgm.s352574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/08/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Glutamine and serine rich 1 (QSER1), as a DNA methylation modulator, play a crucial role in transforming tumor cells. Previous studies have shown that QSER1 plays a role in regulating the progression of various malignancies and that QSER1 dysfunction is connected with precancerous lesions of hepatocellular carcinoma (HCC) as well as HCC prognosis. However, little is known about the detailed contribution of QSER1 in HCC. Patients and Methods Various statistical methods such as Kaplan–Meier method, AUC analysis, GSEA, and immune-infiltration analysis were used to evaluate the relationship between QSER1 expression and clinical features, prognostic factors, and potential functional mechanisms of QSER1. Results QSER1 expression was negatively correlated with clinicopathological features (clinical stage, pathological grade, TP53 mutation, lymph node metastasis) and clinical outcome (overall survival versus recurrence). Functional enrichment analysis further suggested that QSER1 is involved in multiple pathways related to DNA replication and tumor immunity. TIMER analysis indicated that high QSER1 expression was significantly associated with higher macrophage infiltration and poorer macrophage-related outcomes. In particular, QSER1 was significantly more associated with M2 macrophages than M1 macrophages. Conclusion Overall, elevated QSER1 is a potential prognostic marker for HCC and is associated with immune infiltration in HCC.
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Affiliation(s)
- Min Wu
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Qi-man Shi
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Sai-Li Duan
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Deng-jie Ou-yang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Pei Chen
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Biao Tu
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, Hunan, 410008, People’s Republic of China
| | - Peng Huang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, Hunan, 410008, People’s Republic of China
- Correspondence: Peng Huang, Email
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Wang Q, Wang Y, Wang YJ, Ma N, Zhou YJ, Zhuang H, Zhang XH, Li C, Pei YH, Liu SL. Dissection of the Functional Mechanism of Human Gut Bacterial Strain AD16 by Secondary Metabolites' Identification, Network Pharmacology, and Experimental Validation. Front Pharmacol 2021; 12:706220. [PMID: 34803669 PMCID: PMC8602878 DOI: 10.3389/fphar.2021.706220] [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: 05/27/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota plays important roles in several metabolic processes, such as appetite and food intake and absorption of nutrients from the gut. It is also of great importance in the maintenance of the health of the host. However, much remains unknown about the functional mechanisms of human gut microbiota itself. Here, we report the identification of one anticancer gut bacterial strain AD16, which exhibited potent suppressive effects on a broad range of solid and blood malignancies. The secondary metabolites of the strain were isolated and characterized by a bioactivity-guided isolation strategy. Five new compounds, streptonaphthalenes A and B (1-2), pestaloficins F and G (3-4), and eudesmanetetraiol A (5), together with nine previously known compounds, were isolated from the effective fractions of AD16. Structures of the new compounds were established by 1D and 2D NMR and MS analysis, and the absolute configurations were determined by the CD method. The analysis of network pharmacology suggested that 3, 2, and 13 could be the key components for the anti-NSCLC activity of AD16. In addition to the PI3K–Akt signaling pathway, the proteoglycans in cancer pathway could be involved in the anti-NSCLC action of AD16.
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Affiliation(s)
- Qin Wang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yao Wang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Ya-Jing Wang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Nan Ma
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yu-Jie Zhou
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
| | - He Zhuang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Xing-Hua Zhang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chang Li
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yue-Hu Pei
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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8
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Evidence of bovine leukemia virus circulating in sheep and buffaloes in Colombia: insights into multispecies infection. Arch Virol 2021; 167:807-817. [PMID: 34762149 PMCID: PMC8581130 DOI: 10.1007/s00705-021-05285-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/15/2021] [Indexed: 12/18/2022]
Abstract
Bovine leukemia virus (BLV) is the causative agent of leukemia/lymphoma in cattle. However, previous evidence has shown its presence in other species of livestock as well as in humans, suggesting that other species can be accidental hosts of the virus. In viral infections, receptors that are common to different animal species are proposed to be involved in cross-species infections. For BLV, AP3D1 has been proposed to be its receptor, and this protein is conserved in most mammalian species. In Colombia, BLV has been reported in cattle with high prevalence rates, but there has been no evidence of BLV infections in other animal species. In this study, we tested for the virus in sheep (n = 44) and buffaloes (n = 61) from different regions of Colombia by nested PCR, using peripheral blood samples collected from the animals. BLV was found in 25.7% of the animals tested (12 buffaloes and 15 sheep), and the results were confirmed by Sanger sequencing. In addition, to gain more information about the capacity of the virus to infect these species, the predicted interactions of AP3D1 of sheep and buffaloes with the BLV-gp51 protein were analyzed in silico. Conserved amino acids in the binding domains of the proteins were identified. The detection of BLV in sheep and buffaloes suggests circulation of the virus in multiple species, which could be involved in dissemination of the virus in mixed livestock production settings. Due to the presence of the virus in multiple species and the high prevalence rates observed, integrated prevention and control strategies in the livestock industry should be considered to decrease the spread of BLV.
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Corredor-Figueroa AP, Olaya-Galán NN, Velandia-Álvarez S, Muñoz M, Salas-Cárdenas SP, Ibáñez-Pinilla M, Patarroyo MA, Gutiérrez MF. Co-Circulation of Bovine Leukemia Virus Haplotypes among Humans, Animals, and Food Products: New Insights of Its Zoonotic Potential. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18094883. [PMID: 34064361 PMCID: PMC8124648 DOI: 10.3390/ijerph18094883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 01/09/2023]
Abstract
Bovine leukemia virus (BLV) is the causative agent of leukemia/lymphoma in cattle. It has been found in humans and cattle-derived food products. In humans, it is described as a potential risk factor for breast cancer development. However, the transmission path remains unclear. Here, a molecular epidemiology analysis was performed to identify signatures of genetic flux of BLV among humans, animals, and food products. Sequences obtained from these sources in Colombia were used (n = 183) and compared with reference sequences available in GenBank. Phylogenetic reconstruction was performed in IQ-TREE software with the maximum likelihood algorithm. Haplotype (hap) distribution among the population was carried out with a median-joining model in Network5.0. Recombination events were inferred using SplitsTree4 software. In the phylogenetic analysis, no specific branches were identified for the Colombian sequences or for the different sources. A total of 31 haps were found, with Hap 1, 4, 5 and 7 being shared among the three sources of the study. Reticulation events among the different sources were also detected during the recombination analysis. These results show new insights about the zoonotic potential of BLV, showing evidence of genetic flux between cattle and humans. Prevention and control strategies should be considered to avoid viral dissemination as part of the One Health program policies.
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Affiliation(s)
- Adriana P. Corredor-Figueroa
- Grupo de Enfermedades Infecciosas, Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogota 110231, Colombia; (A.P.C.-F.); (S.V.-Á.); (S.P.S.-C.); (M.F.G.)
- Vicerrectoría de Investigación, Universidad ECCI, Bogota 111311, Colombia
| | - Nury N. Olaya-Galán
- Grupo de Enfermedades Infecciosas, Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogota 110231, Colombia; (A.P.C.-F.); (S.V.-Á.); (S.P.S.-C.); (M.F.G.)
- PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogota 111221, Colombia
- Correspondence: ; Tel.: +57-3002081160
| | - Sebastian Velandia-Álvarez
- Grupo de Enfermedades Infecciosas, Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogota 110231, Colombia; (A.P.C.-F.); (S.V.-Á.); (S.P.S.-C.); (M.F.G.)
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogota 111221, Colombia;
| | - Sandra P. Salas-Cárdenas
- Grupo de Enfermedades Infecciosas, Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogota 110231, Colombia; (A.P.C.-F.); (S.V.-Á.); (S.P.S.-C.); (M.F.G.)
| | - Milcíades Ibáñez-Pinilla
- Research Department, Hospital Universitario Mayor Méderi—Universidad del Rosario, Bogota 111411, Colombia;
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogota 111321, Colombia;
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogota 111321, Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogota 110231, Colombia
| | - Maria F. Gutiérrez
- Grupo de Enfermedades Infecciosas, Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogota 110231, Colombia; (A.P.C.-F.); (S.V.-Á.); (S.P.S.-C.); (M.F.G.)
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Nain Z, Rana HK, Liò P, Islam SMS, Summers MA, Moni MA. Pathogenetic profiling of COVID-19 and SARS-like viruses. Brief Bioinform 2021; 22:1175-1196. [PMID: 32778874 PMCID: PMC7454314 DOI: 10.1093/bib/bbaa173] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/23/2020] [Accepted: 07/08/2020] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus (2019-nCoV) has recently emerged, causing COVID-19 outbreaks and significant societal/global disruption. Importantly, COVID-19 infection resembles SARS-like complications. However, the lack of knowledge about the underlying genetic mechanisms of COVID-19 warrants the development of prospective control measures. In this study, we employed whole-genome alignment and digital DNA-DNA hybridization analyses to assess genomic linkage between 2019-nCoV and other coronaviruses. To understand the pathogenetic behavior of 2019-nCoV, we compared gene expression datasets of viral infections closest to 2019-nCoV with four COVID-19 clinical presentations followed by functional enrichment of shared dysregulated genes. Potential chemical antagonists were also identified using protein-chemical interaction analysis. Based on phylogram analysis, the 2019-nCoV was found genetically closest to SARS-CoVs. In addition, we identified 562 upregulated and 738 downregulated genes (adj. P ≤ 0.05) with SARS-CoV infection. Among the dysregulated genes, SARS-CoV shared ≤19 upregulated and ≤22 downregulated genes with each of different COVID-19 complications. Notably, upregulation of BCL6 and PFKFB3 genes was common to SARS-CoV, pneumonia and severe acute respiratory syndrome, while they shared CRIP2, NSG1 and TNFRSF21 genes in downregulation. Besides, 14 genes were common to different SARS-CoV comorbidities that might influence COVID-19 disease. We also observed similarities in pathways that can lead to COVID-19 and SARS-CoV diseases. Finally, protein-chemical interactions suggest cyclosporine, resveratrol and quercetin as promising drug candidates against COVID-19 as well as other SARS-like viral infections. The pathogenetic analyses, along with identified biomarkers, signaling pathways and chemical antagonists, could prove useful for novel drug development in the fight against the current global 2019-nCoV pandemic.
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Affiliation(s)
- Zulkar Nain
- Department of Genetic Engineering and Biotechnology, East West University, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh
| | - Pietro Liò
- Artificial Intelligence Group at the University of Cambridge
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Lathwal A, Kumar R, Raghava GPS. In-silico identification of subunit vaccine candidates against lung cancer-associated oncogenic viruses. Comput Biol Med 2021; 130:104215. [PMID: 33465550 DOI: 10.1016/j.compbiomed.2021.104215] [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: 07/22/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
Globally, ~20% of cancer malignancies are associated with virus infections. Lung cancer is the most prevalent cancer and has a 10% 5-year survival rate when diagnosed at stage IV. Cancer vaccines and oncolytic immunotherapy are promising treatment strategies for better clinical outcomes in advanced-stage cancer patients. Here, we used a reverse vaccinology approach to devise subunit vaccine candidates against lung cancer-causing oncogenic viruses. Protein components (945) from nine oncogenic virus species were systematically analyzed to identify epitope-based subunit vaccine candidates. Best vaccine candidates were identified based on their predicted ability to stimulate humoral and cell-mediated immunity and avoid self-tolerance. Using a rigorous integrative approach, we identified 125 best antigenic epitopes with predicted B-cell, T-cell, and/or MHC-binding capability and vaccine adjuvant potential. Thirty-two of these antigenic epitopes were predicted to have IL-4/IFN-gamma inducing potential and IL-10 non-inducing potential and were predicted to bind 15 MHC-type I and 49 MHC-type II alleles. All 32 epitopes were non-allergenic and 31 were non-toxic. The identified epitopes showed good conservancy and likely bind a broad class of human HLA alleles, indicating promiscuous potential. The majority of best antigenic epitopes were derived from Human papillomavirus and Epstein-Barr virus proteins. Of the 32 epitopes, 25 promiscuous epitopes were related to E1 and E6 envelope genes and were present in multiple viral strains/species, potentially providing heterologous immunity. Further validating our results, 38 antigenic epitopes were also present in the largest experimentally-validated epitope resource, Immune Epitope Database and Analysis Resource. We further narrowed the selection to 29 antigenic epitopes with the highest immunogenic/immune-boosting potential. These epitopes possess tremendous therapeutic potential as vaccines against lung cancer-causing viruses and should be validated in future experiments. All findings are available at https://webs.iiitd.edu.in/raghava/vlcvirus/.
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Affiliation(s)
- Anjali Lathwal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
| | - Rajesh Kumar
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India.
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
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Jyotsana N, King MR. The Impact of COVID-19 on Cancer Risk and Treatment. Cell Mol Bioeng 2020; 13:285-291. [PMID: 32837583 PMCID: PMC7323371 DOI: 10.1007/s12195-020-00630-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023] Open
Abstract
Millions of people are being infected with COVID-19 around the globe. Though the majority of them will recover, cancer patients remain at a higher risk to SARS-CoV-2 infection and its related severe outcomes. Understanding how viruses contribute to human cancers provides us with new opportunities for preventing or treating virus-associated cancers. However, a limited amount of research has been done to date in the context of how viral infections impact cancer at the cellular level and vice versa. Therefore, in light of the COVID-19 global infection, this review highlights the need for better understanding of the biology of viral infections in cancer patients, to enable novel therapies to co-target viral infections and cancer.
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Affiliation(s)
- Nidhi Jyotsana
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN USA
| | - Michael R King
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN USA
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Lee TY, Huang KY, Chuang CH, Lee CY, Chang TH. Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication. Comput Biol Chem 2020; 87:107277. [PMID: 32512487 DOI: 10.1016/j.compbiolchem.2020.107277] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/30/2020] [Indexed: 12/25/2022]
Abstract
Lung cancer is the most occurring cancer type, and its mortality rate is also the highest, among them lung adenocarcinoma (LUAD) accounts for about 40 % of lung cancer. There is an urgent need to develop a prognosis prediction model for lung adenocarcinoma. Previous LUAD prognosis studies only took single-omics data, such as mRNA or miRNA, into consideration. To this end, we proposed a deep learning-based autoencoding approach for combination of four-omics data, mRNA, miRNA, DNA methylation and copy number variations, to construct an autoencoder model, which learned representative features to differentiate the two optimal patient subgroups with a significant difference in survival (P = 4.08e-09) and good consistency index (C-index = 0.65). The multi-omics model was validated though four independent datasets, i.e. GSE81089 for mRNA (n = 198, P = 0.0083), GSE63805 for miRNA (n = 32, P = 0.018), GSE63384 for DNA methylation (n = 35, P = 0.009), and TCGA independent samples for copy number variations (n = 94, P = 0.0052). Finally, a functional analysis was performed on two survival subgroups to discover genes involved in biological processes and pathways. This is the first study incorporating deep autoencoding and four-omics data to construct a robust survival prediction model, and results show the approach is useful at predicting LUAD prognostication.
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Affiliation(s)
- Tzong-Yi Lee
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China; School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen, China; School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China.
| | - Kai-Yao Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China; School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen, China; School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China.
| | - Cheng-Hsiang Chuang
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan.
| | - Cheng-Yang Lee
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei City, Taiwan.
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei City, Taiwan; Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei City, Taiwan.
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Martins SF, Mariano V, Rodrigues M, Longatto-Filho A. Human papillomavirus (HPV) 16 infection is not detected in rectal carcinoma. Infect Agent Cancer 2020; 15:17. [PMID: 32165915 PMCID: PMC7059378 DOI: 10.1186/s13027-020-00281-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction Persistence of human papillomavirus (HPV) infections is associated with squamous cell carcinomas of different human anatomic sites. Several studies have suggested a potential role for HPV infection, particularly HPV16 genotype, in rectal cancer carcinogenesis.. The aim of this study was to assess the frequency of oncogenic HPV 16 viral DNA sequences in rectal carcinomas cases retrieved from the pathology archive of Braga Hospital, North Portuga. Methods TaqMan-based type-specific real-time PCR for HPV 16 was performed using primers and probe targeting HPV16 E7 region. Results Most of the rectal cancer patients (88.5%, n = 206 patients), were symptomatic at diagnosis. The majority of the lesions (55.3%, n = 129) presented malignancies of polypoid/vegetant phenotype. 26.8% (n = 63) had synchronic metastasis at diagnosis. 26.2% (n = 61) patients had clinical indication for neoadjuvant therapy. Most patients with rectal cancer were stage IV (19.7% patients), followed by stage IIA (19.3%) and stage I (18.5%). All cases of the present series tested negative for HPV16. Conclusion The total of negative tests for HPV 16 infection is a robust argument to support the assumption that HPV 16 infection, despite of previous evidences, is not involved in rectal cancer carcinogenesis and progression.
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Affiliation(s)
- Sandra F Martins
- 1Life and Health Science Research Institute (ICVS), School of Health Sciences, School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal.,Coloproctology Unit, Braga Hospital, Braga, Portugal
| | - Vânia Mariano
- Molecular Oncology Research Center, Barretos, São Paulo, Brazil
| | | | - Adhemar Longatto-Filho
- 1Life and Health Science Research Institute (ICVS), School of Health Sciences, School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal.,Molecular Oncology Research Center, Barretos, São Paulo, Brazil.,5Laboratory of Medical Investigation (LIM) 14, Faculty of Medicine, University of Sao Paulo, Sao Paulo, Brazil
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Human papillomavirus is not associated to non-small cell lung cancer: data from a prospective cross-sectional study. Infect Agent Cancer 2019; 14:18. [PMID: 31388352 PMCID: PMC6679449 DOI: 10.1186/s13027-019-0235-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
Background The pathogenesis of lung cancer is triggered by a combination of genetic and environmental factors, being the tobacco smoke the most important risk factor. Nevertheless, the incidence of lung cancer in non-smokers is gradually increasing, which demands the search for different other etiological factors such as occupational exposure, previous lung disease, diet among others. In the early 80’s a theory linked specific types of human papillomavirus (HPV) to lung cancer due to morphological similarities of a subset of bronchial squamous cell carcinomas with other HPV-induced cancers. Since then, several studies revealed variable rates of HPV DNA detection. The current study aimed to provide accurate information on the prevalence of HPV DNA in lung cancer. Methods Biopsies were collected from 77 newly diagnosed non-small cell lung cancer (NSCLC) patients treated at the Thoracic Oncology Department at Barretos Cancer Hospital. The samples were formalin fixed and paraffin embedded (FFPE), histologic analysis was performed by an experienced pathologist. DNA was extracted from FFPE material using a commercial extraction kit and HPV DNA detection was evaluated by multiplex PCR and HPV16 specific real-time PCR. Results HPV was not identified in any of the samples analysed (69). Conclusions Our data demonstrated a lack of HPV DNA in a series of NSCL cancers.
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