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Shen HT, Hung CS, Davis C, Su CM, Liao LM, Shih HM, Lee KD, Ansar M, Lin RK. Hypermethylation of the Gene Body in SRCIN1 Is Involved in Breast Cancer Cell Proliferation and Is a Potential Blood-Based Biomarker for Early Detection and a Poor Prognosis. Biomolecules 2024; 14:571. [PMID: 38785978 PMCID: PMC11118508 DOI: 10.3390/biom14050571] [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: 04/10/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Breast cancer is a leading cause of cancer mortality in women worldwide. Using the Infinium MethylationEPIC BeadChip, we analyzed plasma sample methylation to identify the SRCIN1 gene in breast cancer patients. We assessed SRCIN1-related roles and pathways for their biomarker potential. To verify the methylation status, quantitative methylation-specific PCR (qMSP) was performed on genomic DNA and circulating cell-free DNA samples, and mRNA expression analysis was performed using RT‒qPCR. The results were validated in a Western population; for this analysis, the samples included plasma samples from breast cancer patients from the USA and from The Cancer Genome Atlas (TCGA) cohort. To study the SRCIN1 pathway, we conducted cell viability assays, gene manipulation and RNA sequencing. SRCIN1 hypermethylation was identified in 61.8% of breast cancer tissues from Taiwanese patients, exhibiting specificity to this malignancy. Furthermore, its presence correlated significantly with unfavorable 5-year overall survival outcomes. The levels of methylated SRCIN1 in the blood of patients from Taiwan and the USA correlated with the stage of breast cancer. The proportion of patients with high methylation levels increased from 0% in healthy individuals to 63.6% in Stage 0, 80% in Stage I and 82.6% in Stage II, with a sensitivity of 78.5%, an accuracy of 90.3% and a specificity of 100%. SRCIN1 hypermethylation was significantly correlated with increased SRCIN1 mRNA expression (p < 0.001). Knockdown of SRCIN1 decreased the viability of breast cancer cells. SRCIN1 silencing resulted in the downregulation of ESR1, BCL2 and various cyclin protein expressions. SRCIN1 hypermethylation in the blood may serve as a noninvasive biomarker, facilitating early detection and prognosis evaluation, and SRCIN1-targeted therapies could be used in combination regimens for breast cancer patients.
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Affiliation(s)
- Hsieh-Tsung Shen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- EG BioMed US Inc., Covina, CA 91722, USA;
| | - Chin-Sheng Hung
- EG BioMed US Inc., Covina, CA 91722, USA;
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
- Division of Breast Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei 110301, Taiwan
| | - Clilia Davis
- International Master Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
| | - Chih-Ming Su
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan;
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
| | - Li-Min Liao
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235041, Taiwan;
| | - Hsiu-Ming Shih
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
| | - Kuan-Der Lee
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- Comprehensive Cancer Center, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Muhamad Ansar
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Ruo-Kai Lin
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110301, Taiwan; (H.-T.S.); (H.-M.S.); (K.-D.L.)
- EG BioMed US Inc., Covina, CA 91722, USA;
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 110301, Taiwan
- Graduate Institute of Pharmacognosy, Ph.D. Program in Drug Discovery and Development Industry, Masters Program for Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei 110301, Taiwan
- Clinical Trial Center, Taipei Medical University Hospital, Taipei 110301, Taiwan
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Dubey AK, Kaur I, Madaan R, Raheja S, Bala R, Garg M, Kumar S, Lather V, Mittal V, Pandita D, Gundamaraju R, Singla RK, Sharma R. Unlocking the potential of oncology biomarkers: advancements in clinical theranostics. Drug Metab Pers Ther 2024; 39:5-20. [PMID: 38469723 DOI: 10.1515/dmpt-2023-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/11/2024] [Indexed: 03/13/2024]
Abstract
INTRODUCTION Cancer biomarkers have revolutionized the field of oncology by providing valuable insights into tumor changes and aiding in screening, diagnosis, prognosis, treatment prediction, and risk assessment. The emergence of "omic" technologies has enabled biomarkers to become reliable and accurate predictors of outcomes during cancer treatment. CONTENT In this review, we highlight the clinical utility of biomarkers in cancer identification and motivate researchers to establish a personalized/precision approach in oncology. By extending a multidisciplinary technology-based approach, biomarkers offer an alternative to traditional techniques, fulfilling the goal of cancer therapeutics to find a needle in a haystack. SUMMARY AND OUTLOOK We target different forms of cancer to establish a dynamic role of biomarkers in understanding the spectrum of malignancies and their biochemical and molecular characterization, emphasizing their prospective contribution to cancer screening. Biomarkers offer a promising avenue for the early detection of human cancers and the exploration of novel technologies to predict disease severity, facilitating maximum survival and minimum mortality rates. This review provides a comprehensive overview of the potential of biomarkers in oncology and highlights their prospects in advancing cancer diagnosis and treatment.
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Affiliation(s)
- Ankit Kumar Dubey
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Ishnoor Kaur
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Reecha Madaan
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Shikha Raheja
- Jan Nayak Ch. Devi Lal Memorial College of Pharmacy, Sirsa, Haryana, India
| | - Rajni Bala
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine & Stem Cell Research, 77282 Amity University, Sector-125 , Noida, India
| | - Suresh Kumar
- Department of Pharmaceutical Sciences and Drug Research, 429174 Punjabi University Patiala , Patiala, India
| | - Viney Lather
- Amity Institute of Pharmacy, 77282 Amity University , Noida, India
| | - Vineet Mittal
- Department of Pharmaceutical Sciences, 29062 Maharshi Dayanand University , Rohtak, Haryana, India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, PushpVihar, 633274 Govt. of NCT of Delhi , New Delhi, India
- Centre for Advanced Formulation and Technology (CAFT), Delhi Pharmaceutical Sciences and Research University, PushpVihar, Govt. of NCT of Delhi, New Delhi, India
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Lab, School of Health Sciences, 8785 University of Tasmania , Launceston, Tasmania, Australia
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rajeev K Singla
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- School of Pharmaceutical Sciences, 34753 Lovely Professional University , Phagwara, Punjab, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, 80095 Banaras Hindu University , Varanasi, Uttar Pradesh, India
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Cohen SE, Betancourt J, Soo Hoo GW. Pleural Uptake Patterns in F18Fluorodeoxyglucose-Positron Emission Tomography (FDG-PET) Scans Improve the Identification of Malignant Pleural Effusions. J Clin Med 2023; 12:6977. [PMID: 38002592 PMCID: PMC10672363 DOI: 10.3390/jcm12226977] [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: 09/09/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND The confirmation of malignant pleural effusions (MPE) requires an invasive procedure. Diagnosis can be difficult and may require repeated thoracentesis or biopsies. F18Fluorodeoxyglucose-Positron Emission Tomography (FDG-PET) can characterize the extent of malignant involvement in areas of increased uptake. Patterns of uptake in the pleura may be sufficient to obviate the need for further invasive procedures. METHODS This is a retrospective review of patients with confirmed malignancy and suspected MPE. Patients who underwent diagnostic thoracentesis with cytology and contemporaneous FDG-PET were identified for analysis. Some underwent confirmatory pleural biopsy. The uptake pattern on FDG-PET underwent blinded review and was categorized based on the pattern of uptake. RESULTS One hundred consecutive patients with confirmed malignancy, suspected MPE and corresponding FDG-PET scans were reviewed. MPE was confirmed in 70 patients with positive pleural fluid cytology or tissue pathology. Of the remaining patients, 15 had negative cytopathology, 14 had atypical cells and 1 had reactive cells. Positive uptake on FDG-PET was noted in 76 patients. The concordance of malignant histology and positive FDG-PET occurred in 58 of 76 patients (76%). Combining histologically confirmed MPE with atypical cytology, positive pleural FDG-PET uptake had a positive predictive value of 91% for MPE. An encasement pattern had a 100% PPV for malignancy. CONCLUSION Positive FDG-PET pleural uptake represents an excellent method to identify MPE, especially in patients with an encasement pattern. This may eliminate the need for additional invasive procedures in some patients, even when initial pleural cytology is negative.
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Affiliation(s)
| | - Jaime Betancourt
- West Los Angeles Veterans Affairs Healthcare Center, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA; (J.B.); (G.W.S.H.)
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Guy W. Soo Hoo
- West Los Angeles Veterans Affairs Healthcare Center, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA; (J.B.); (G.W.S.H.)
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
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Gupta SRR, Mittal P, Kundu B, Singh A, Singh IK. Silibinin: an inhibitor for a high-expressed BCL-2A1/BFL1 protein, linked with poor prognosis in breast cancer. J Biomol Struct Dyn 2023:1-11. [PMID: 37837418 DOI: 10.1080/07391102.2023.2268176] [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: 03/14/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Breast cancer (BC) accounts for 30% of all diagnosed cases of cancer in women and remains a leading cause of cancer-related deaths among women worldwide. The current study looks for a protein from the anti-apoptotic/pro-survival BCL-2 family whose overexpression reduces survivability in BC patients and a potential inhibitor for the protein. We found BCL-2A1/BFL1 protein with high expression linked to low survivability in BC. The protein shows prognosis in 8 out of 29 categories, whereas no other family member manifests this property. Out of 7379 compounds, three small molecules (CHEMBL9509, CHEMBL2104550 and CHEMBL3545011) form an H-bond with BCL-2A1/BFL1 protein's unique residue Cys55. Of the three small molecules, we found CHEMBL9509 (Silibinin) to be a potent inhibitor. The compound forms a stable H-bond with the residue Cys55 with the lowest binding energy compared to the other two compounds. It remains stable in the BH3 binding region for more than 100 ns, whereas the other two detach from the region. Additionally, the compound is found to be better than Venetoclax and Nematoclax. We firmly believe in the compound CHEMBL9509 potency to halt BC's progression by inhibiting the BCL-2A1/BFL1 protein, increasing patients' survivability.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shradheya R R Gupta
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Pooja Mittal
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- Norris Comprehensive Cancer Center, Division of Medical Oncology, University of Southern California, Los Angeles, USA
| | - Bishwajit Kundu
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi (South Campus), New Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- Norris Comprehensive Cancer Center, Division of Medical Oncology, University of Southern California, Los Angeles, USA
- Institute of Eminence, Delhi School of Public Health, University of Delhi, Delhi, India
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Chen J, Zou X. Prognostic significance of lactate dehydrogenase and its impact on the outcomes of gastric cancer: a systematic review and meta-analysis. Front Oncol 2023; 13:1247444. [PMID: 37727205 PMCID: PMC10505930 DOI: 10.3389/fonc.2023.1247444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/07/2023] [Indexed: 09/21/2023] Open
Abstract
Background The prognostic significance of lactate dehydrogenase (LDH) and its impact on the outcomes of gastric cancer (GC) is still unclear. We assessed the link between the levels of LDH and the overall survival (OS) and disease-free survival (DFS) in GC patients. Methods A comprehensive search (both electronic and manual) was carried out in PubMed via MEDLINE, Web of Science (WoS), Experta Medical Database (Embase), and CENTRAL (Cochrane Library) databases for citations that evaluated the strength of association between LDH cut-off levels and OS and/or DFS in GC. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated using a random-effects model, and heterogeneity was assessed. Results Eighteen studies with 5328 patients were included in our review. The overall pooled HR for OS was 1.48 (95% CI: 1.22-1.80) with high heterogeneity (I2 = 86%). Subgroup analyses showed that the link between LDH and OS was more prominent in Caucasian (HR 1.50 95% CI [0.80, 2.81], p=0.21) than in Asian cohorts (HR, 1.51 95% CI [1.21, 1.87], p=0.002). No significant overall association between LDH and OS (HR = 1.12, 95% CI: 0.76-1.65, p = 0.58) was found. Similar subgroup analyses results were reported for the association between LDH and DFS. Conclusion In patients with GC, elevated LDH levels may correlate with worse OS and DFS, but the association is not significant. LDH is a significant predictor of OS but not of DFS. Further studies with larger sample sizes and more standardized criteria for defining elevated LDH levels are needed to confirm our findings. Systematic review registration https://www.crd.york.ac.uk/prospero, identifier CRD42023412449.
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Affiliation(s)
| | - Xiaoyue Zou
- Department of Clinical Laboratory, First affiliated Hospital of Huzhou University, Huzhou, China
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6
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Jin N, Qiao B, Zhao M, Li L, Zhu L, Zang X, Gu B, Zhang H. Predicting cervical lymph node metastasis in OSCC based on computed tomography imaging genomics. Cancer Med 2023; 12:19260-19271. [PMID: 37635388 PMCID: PMC10557859 DOI: 10.1002/cam4.6474] [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: 05/12/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND To investigate the correlation between computed tomography (CT) radiomic characteristics and key genes for cervical lymph node metastasis (LNM) in oral squamous cell carcinoma (OSCC). METHODS The region of interest was annotated at the edge of the primary tumor on enhanced CT images from 140 patients with OSCC and obtained radiomic features. Ribonucleic acid (RNA) sequencing was performed on pathological sections from 20 patients. the DESeq software package was used to compare differential gene expression between groups. Weighted gene co-expression network analysis was used to construct co-expressed gene modules, and the KEGG and GO databases were used for pathway enrichment analysis of key gene modules. Finally, Pearson correlation coefficients were calculated between key genes of enriched pathways and radiomic features. RESULTS Four hundred and eighty radiomic features were extracted from enhanced CT images of 140 patients; seven of these correlated significantly with cervical LNM in OSCC (p < 0.01). A total of 3527 differentially expressed RNAs were screened from RNA sequencing data of 20 cases. original_glrlm_RunVariance showed significant positive correlation with most long noncoding RNAs. CONCLUSIONS OSCC cervical LNM is related to the salivary hair bump signaling pathway and biological process. Original_glrlm_RunVariance correlated with LNM and most differentially expressed long noncoding RNAs.
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Affiliation(s)
- Nenghao Jin
- Medical School of Chinese PLABeijingChina
- Department of Stomatology, The First Medical CentreChinese PLA General HospitalBeijingChina
| | - Bo Qiao
- Medical School of Chinese PLABeijingChina
- Department of Stomatology, The First Medical CentreChinese PLA General HospitalBeijingChina
| | - Min Zhao
- Pharmaceutical Diagnostics, GE HealthcareBeijingChina
- Research Center of Medical Big Data, Chinese PLA General HospitalBeijingChina
| | - Liangbo Li
- Medical School of Chinese PLABeijingChina
- Department of Stomatology, The First Medical CentreChinese PLA General HospitalBeijingChina
| | - Liang Zhu
- Medical School of Chinese PLABeijingChina
- Department of Stomatology, The First Medical CentreChinese PLA General HospitalBeijingChina
| | - Xiaoyi Zang
- Medical School of Chinese PLABeijingChina
- Department of Stomatology, The First Medical CentreChinese PLA General HospitalBeijingChina
| | - Bin Gu
- Department of Stomatology, The First Medical CentreChinese PLA General HospitalBeijingChina
| | - Haizhong Zhang
- Department of Stomatology, The First Medical CentreChinese PLA General HospitalBeijingChina
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Alfahed A. Molecular pathology of colorectal cancer: The Saudi situation in perspective. Saudi Med J 2023; 44:836-847. [PMID: 37717975 PMCID: PMC10505285 DOI: 10.15537/smj.2023.44.9.20230257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide, and one of the most common causes of cancer deaths. In recent times, significant advancements have been made in elucidating the molecular alterations of the disease, and the results have been an improved understanding of CRC biology, as well as the discovery of biomarkers of diagnostic, prognostic, and therapeutic significance. In this review, an evaluation is carried out of the molecular pathology research of CRC emanating from Saudi Arabia. The verdict is that the data on the molecular alterations in CRC from Saudi patients is at best modest. This dearth of molecular pathology data is aptly reflected in the paucity of molecular markers recommended for testing by the Saudi National Cancer Centre guidelines for CRC management. Large scale multi-institutional and multiregional translational studies are required to generate molecular data that would inform diagnostic, prognostic, and risk-stratification guidelines for Saudi CRC patients.
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Affiliation(s)
- Abdulaziz Alfahed
- From the Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj, Kingdom of Saudi Arabia
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8
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Chaithanya P, Meshram RJ. Chemo Markers as Biomarkers in Septic Shock: A Comprehensive Review of Their Utility and Clinical Applications. Cureus 2023; 15:e42558. [PMID: 37637638 PMCID: PMC10460194 DOI: 10.7759/cureus.42558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Sepsis is a life-threatening condition characterized by a dysregulated host response to infection, often leading to septic shock. Early diagnosis and prompt intervention are crucial for improving patient outcomes. Chemo markers, which are measurable biological substances associated with the pathophysiology of septic shock, have emerged as potential biomarkers for the identification, risk stratification, and management of this condition. This comprehensive review aims to thoroughly evaluate the utility and clinical applications of chemo markers in septic shock. The review begins by discussing the criteria for ideal chemo markers, including specificity, sensitivity, dynamic range, stability, non-invasiveness, and prognostic value. These characteristics ensure accurate diagnosis, early detection, effective monitoring, and prediction of clinical outcomes. Furthermore, the review explores the role of chemo markers in monitoring treatment response and disease progression, highlighting their ability to serve as objective indicators for assessing the effectiveness of interventions and making timely adjustments in management strategies. Moreover, the prognostic value of chemo markers in predicting outcomes is discussed, emphasizing their association with mortality, hospital stays, and the development of complications. Integration of chemo markers into prognostic models or scoring systems enhances risk stratification and informs therapeutic decisions. The review also delves into recent advances in chemo marker research and technology, emphasizing the potential for discovering novel chemo markers with enhanced diagnostic and prognostic capabilities. It highlights the use of high-throughput proteomics, genomics, and transcriptomics in identifying specific molecular signatures associated with septic shock. This contributes to a deeper understanding of the complex immune and inflammatory responses involved. In conclusion, chemo markers have emerged as valuable biomarkers in septic shock, offering potential utility in diagnosis, risk stratification, treatment monitoring, and prediction of outcomes. Continued research, validation, and integration into clinical practice are necessary to fully realize their potential in improving patient care and outcomes in septic shock.
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Affiliation(s)
- Pulivarthi Chaithanya
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Revat J Meshram
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Medical Sciences, Wardha, IND
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Neves Rebello Alves L, Dummer Meira D, Poppe Merigueti L, Correia Casotti M, do Prado Ventorim D, Ferreira Figueiredo Almeida J, Pereira de Sousa V, Cindra Sant'Ana M, Gonçalves Coutinho da Cruz R, Santos Louro L, Mendonça Santana G, Erik Santos Louro T, Evangelista Salazar R, Ribeiro Campos da Silva D, Stefani Siqueira Zetum A, Silva Dos Reis Trabach R, Imbroisi Valle Errera F, de Paula F, de Vargas Wolfgramm Dos Santos E, Fagundes de Carvalho E, Drumond Louro I. Biomarkers in Breast Cancer: An Old Story with a New End. Genes (Basel) 2023; 14:1364. [PMID: 37510269 PMCID: PMC10378988 DOI: 10.3390/genes14071364] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer is the second most frequent cancer in the world. It is a heterogeneous disease and the leading cause of cancer mortality in women. Advances in molecular technologies allowed for the identification of new and more specifics biomarkers for breast cancer diagnosis, prognosis, and risk prediction, enabling personalized treatments, improving therapy, and preventing overtreatment, undertreatment, and incorrect treatment. Several breast cancer biomarkers have been identified and, along with traditional biomarkers, they can assist physicians throughout treatment plan and increase therapy success. Despite the need of more data to improve specificity and determine the real clinical utility of some biomarkers, others are already established and can be used as a guide to make treatment decisions. In this review, we summarize the available traditional, novel, and potential biomarkers while also including gene expression profiles, breast cancer single-cell and polyploid giant cancer cells. We hope to help physicians understand tumor specific characteristics and support decision-making in patient-personalized clinical management, consequently improving treatment outcome.
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Affiliation(s)
- Lyvia Neves Rebello Alves
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Débora Dummer Meira
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Luiza Poppe Merigueti
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Matheus Correia Casotti
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Diego do Prado Ventorim
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo (Ifes), Cariacica 29150-410, ES, Brazil
| | - Jucimara Ferreira Figueiredo Almeida
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Valdemir Pereira de Sousa
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Marllon Cindra Sant'Ana
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Rahna Gonçalves Coutinho da Cruz
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Luana Santos Louro
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, ES, Brazil
| | - Gabriel Mendonça Santana
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, ES, Brazil
| | - Thomas Erik Santos Louro
- Escola Superior de Ciências da Santa Casa de Misericórdia de Vitória (EMESCAM), Vitória 29027-502, ES, Brazil
| | - Rhana Evangelista Salazar
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Danielle Ribeiro Campos da Silva
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Aléxia Stefani Siqueira Zetum
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Raquel Silva Dos Reis Trabach
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
| | - Flávia Imbroisi Valle Errera
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Flávia de Paula
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Eldamária de Vargas Wolfgramm Dos Santos
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
| | - Elizeu Fagundes de Carvalho
- Instituto de Biologia Roberto Alcântara Gomes (IBRAG), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20551-030, RJ, Brazil
| | - Iúri Drumond Louro
- Núcleo de Genética Humana e Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, ES, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória 29047-105, ES, Brazil
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10
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Dixit S, Kumar A, Srinivasan K. A Current Review of Machine Learning and Deep Learning Models in Oral Cancer Diagnosis: Recent Technologies, Open Challenges, and Future Research Directions. Diagnostics (Basel) 2023; 13:diagnostics13071353. [PMID: 37046571 PMCID: PMC10093759 DOI: 10.3390/diagnostics13071353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cancer is a problematic global health issue with an extremely high fatality rate throughout the world. The application of various machine learning techniques that have appeared in the field of cancer diagnosis in recent years has provided meaningful insights into efficient and precise treatment decision-making. Due to rapid advancements in sequencing technologies, the detection of cancer based on gene expression data has improved over the years. Different types of cancer affect different parts of the body in different ways. Cancer that affects the mouth, lip, and upper throat is known as oral cancer, which is the sixth most prevalent form of cancer worldwide. India, Bangladesh, China, the United States, and Pakistan are the top five countries with the highest rates of oral cavity disease and lip cancer. The major causes of oral cancer are excessive use of tobacco and cigarette smoking. Many people’s lives can be saved if oral cancer (OC) can be detected early. Early identification and diagnosis could assist doctors in providing better patient care and effective treatment. OC screening may advance with the implementation of artificial intelligence (AI) techniques. AI can provide assistance to the oncology sector by accurately analyzing a large dataset from several imaging modalities. This review deals with the implementation of AI during the early stages of cancer for the proper detection and treatment of OC. Furthermore, performance evaluations of several DL and ML models have been carried out to show that the DL model can overcome the difficult challenges associated with early cancerous lesions in the mouth. For this review, we have followed the rules recommended for the extension of scoping reviews and meta-analyses (PRISMA-ScR). Examining the reference lists for the chosen articles helped us gather more details on the subject. Additionally, we discussed AI’s drawbacks and its potential use in research on oral cancer. There are methods for reducing risk factors, such as reducing the use of tobacco and alcohol, as well as immunization against HPV infection to avoid oral cancer, or to lessen the burden of the disease. Additionally, officious methods for preventing oral diseases include training programs for doctors and patients as well as facilitating early diagnosis via screening high-risk populations for the disease.
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Affiliation(s)
- Shriniket Dixit
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore 632014, India
| | - Anant Kumar
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Kathiravan Srinivasan
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore 632014, India
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11
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Al-Showbaki L, Wilson B, Tamimi F, Molto C, Mittal A, Cescon DW, Amir E. Changes in circulating tumor DNA and outcomes in solid tumors treated with immune checkpoint inhibitors: a systematic review. J Immunother Cancer 2023; 11:jitc-2022-005854. [PMID: 36792122 PMCID: PMC9933752 DOI: 10.1136/jitc-2022-005854] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Quantification of circulating tumor DNA (ctDNA) levels is a reliable prognostic tool in several malignancies. Dynamic changes in ctDNA levels in response to treatment may also provide prognostic information. Here, we explore the value of changes in ctDNA levels in response to immune checkpoint inhibitors (ICIs). METHODS We searched MEDLINE (host: PubMed) for trials of ICIs in advanced solid tumors in which outcomes were reported based on change in ctDNA levels. ctDNA reduction was defined as reported in individual trials. Typically, this was either >50% reduction or a reduction to undetectable levels. We extracted HRs and related 95% CIs and/or p values comparing ctDNA reduction versus no reduction for progression-free survival (PFS) and/or overall survival (OS). Data were then pooled in a meta-analysis. Variation in effect size was examined using subgroup analyses. RESULTS Eighteen trials were included in the meta-analysis. ctDNA levels were detectable in all participants in all studies prior to initiation of ICIs. A reduction in ctDNA measured 6-16 weeks after starting treatment was associated with significantly better PFS (HR 0.20; 95% CI, 0.14 to 0.28; p<0.001). Similarly, OS was superior in patients with reduced ctDNA levels (HR 0.18; 95% CI, 0.12 to 0.26; p<0.001). The results were consistent across all disease sites, lines of treatment, magnitude of change (to undetectable vs >50% reduction) and whether treatment exposure comprised single or combination ICIs. CONCLUSIONS In advanced solid tumors, a reduction in ctDNA levels in response to ICIs is associated with substantial improvements in outcome. ctDNA change is an early response biomarker which may allow for de-escalation of cross-sectional imaging in patients receiving ICIs or support treatment de-escalation strategies.
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Affiliation(s)
- Laith Al-Showbaki
- Division of Hematology and Medical Oncology, Department of Medicine, The University of Jordan, Amman, Jordan
| | - Brooke Wilson
- Division of Medical Oncology and Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Faris Tamimi
- Division of Medical Oncology and Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Consolacion Molto
- Division of Medical Oncology and Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Abhenil Mittal
- Division of Medical Oncology and Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - David W Cescon
- Division of Medical Oncology and Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Eitan Amir
- Division of Medical Oncology and Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
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12
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Xin J, Gu D, Chen S, Ben S, Li H, Zhang Z, Du M, Wang M. SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival. Nucleic Acids Res 2023; 51:D1160-D1167. [PMID: 35947748 PMCID: PMC9825440 DOI: 10.1093/nar/gkac677] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 01/30/2023] Open
Abstract
Genome-wide association studies (GWASs) underlying case-control design have uncovered hundreds of genetic loci involved in tumorigenesis and provided rich resources for identifying risk factors and biomarkers associated with cancer susceptibility. However, the application of GWAS in determining the genetic architecture of cancer survival remains unestablished. Here, we systematically evaluated genetic effects at the genome-wide level on cancer survival that included overall survival (OS) and cancer-specific survival (CSS), leveraging data deposited in the UK Biobank cohort of a total of 19 628 incident patients across 17 cancer types. Furthermore, we assessed the causal effects of risk factors and circulating biomarkers on cancer prognosis via a Mendelian randomization (MR) analytic framework, which integrated cancer survival GWAS dataset, along with phenome-wide association study (PheWAS) and blood genome-wide gene expression/DNA methylation quantitative trait loci (eQTL/meQTL) datasets. On average, more than 10 traits, 700 genes, and 4,500 CpG sites were prone to cancer prognosis. Finally, we developed a user-friendly online database, SUrvival related cancer Multi-omics database via MEndelian Randomization (SUMMER; http://njmu-edu.cn:3838/SUMMER/), to help users query, browse, and download cancer survival results. In conclusion, SUMMER provides an important resource to assist the research community in understanding the genetic mechanisms of cancer survival.
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Affiliation(s)
- Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Silu Chen
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Huiqin Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
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13
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Zheng D, He X, Jing J. Overview of Artificial Intelligence in Breast Cancer Medical Imaging. J Clin Med 2023; 12:jcm12020419. [PMID: 36675348 PMCID: PMC9864608 DOI: 10.3390/jcm12020419] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/26/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023] Open
Abstract
The heavy global burden and mortality of breast cancer emphasize the importance of early diagnosis and treatment. Imaging detection is one of the main tools used in clinical practice for screening, diagnosis, and treatment efficacy evaluation, and can visualize changes in tumor size and texture before and after treatment. The overwhelming number of images, which lead to a heavy workload for radiologists and a sluggish reporting period, suggests the need for computer-aid detection techniques and platform. In addition, complex and changeable image features, heterogeneous quality of images, and inconsistent interpretation by different radiologists and medical institutions constitute the primary difficulties in breast cancer screening and imaging diagnosis. The advancement of imaging-based artificial intelligence (AI)-assisted tumor diagnosis is an ideal strategy for improving imaging diagnosis efficient and accuracy. By learning from image data input and constructing algorithm models, AI is able to recognize, segment, and diagnose tumor lesion automatically, showing promising application prospects. Furthermore, the rapid advancement of "omics" promotes a deeper and more comprehensive recognition of the nature of cancer. The fascinating relationship between tumor image and molecular characteristics has attracted attention to the radiomic and radiogenomics, which allow us to perform analysis and detection on the molecular level with no need for invasive operations. In this review, we integrate the current developments in AI-assisted imaging diagnosis and discuss the advances of AI-based breast cancer precise diagnosis from a clinical point of view. Although AI-assisted imaging breast cancer screening and detection is an emerging field and draws much attention, the clinical application of AI in tumor lesion recognition, segmentation, and diagnosis is still limited to research or in limited patients' cohort. Randomized clinical trials based on large and high-quality cohort are lacking. This review aims to describe the progress of the imaging-based AI application in breast cancer screening and diagnosis for clinicians.
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14
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Dong F, Yan W, Dong W, Shang X, Xu Y, Liu W, Wu Y, Wei W, Zhao T. DNA-enabled fluorescent-based nanosensors monitoring tumor-related RNA toward advanced cancer diagnosis: A review. Front Bioeng Biotechnol 2022; 10:1059845. [DOI: 10.3389/fbioe.2022.1059845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
As a burgeoning non-invasive indicator for reproducible cancer diagnosis, tumor-related biomarkers have a wide range of applications in early cancer screening, efficacy monitoring, and prognosis predicting. Accurate and efficient biomarker determination, therefore, is of great importance to prevent cancer progression at an early stage, thus reducing the disease burden on the entire population, and facilitating advanced therapies for cancer. During the last few years, various DNA structure-based fluorescent probes have established a versatile platform for biological measurements, due to their inherent biocompatibility, excellent capacity to recognize nucleic and non-nucleic acid targets, obvious accessibility to synthesis as well as chemical modification, and the ease of interfacing with signal amplification protocols. After decades of research, DNA fluorescent probe technology for detecting tumor-related mRNAs has gradually grown to maturity, especially the advent of fluorescent nanoprobes has taken the process to a new level. Here, a systematic introduction to recent trends and advances focusing on various nanomaterials-related DNA fluorescent probes and the physicochemical properties of various involved nanomaterials (such as AuNP, GO, MnO2, SiO2, AuNR, etc.) are also presented in detail. Further, the strengths and weaknesses of existing probes were described and their progress in the detection of tumor-related mRNAs was illustrated. Also, the salient challenges were discussed later, with a few potential solutions.
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15
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Elderdery AY, Alhamidi AH, Elkhalifa AME, Althobiti MM, Eltayeb Omer N, Alsugoor MH, Alsuhaymi N, Atebien EM, Hamza SMA, Alzahrani B, Alanazi F, Subbiah SK, Mok PL. Synthesis, Characterization, and Antimicrobial and Antiproliferative Effects of CuO-TiO 2-Chitosan-Escin Nanocomposites on Human Leukemic MOLT4 Cells. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12213753. [PMID: 36364538 PMCID: PMC9655830 DOI: 10.3390/nano12213753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/15/2022] [Accepted: 10/19/2022] [Indexed: 05/13/2023]
Abstract
Nanocomposites comprised of CuO-TiO2-chitosan-escin, which has adjustable physicochemical properties, provide a solution for therapeutic selectivity in cancer treatment. By controlling the intrinsic signaling primarily through the mitochondrial signaling pathway, we desired nanocomposites with enhanced anticancer activity by containing CuO-TiO2-chitosan-escin. The metal oxides CuO and TiO2, the natural polymer chitosan, and a phytochemical compound escin were combined to form CuO-TiO2-chitosan-escin nanocomposites. The synthesized nanocomposites were confirmed and characterized using FTIR spectroscopy, TEM, and UV-Vis absorption spectroscopy. A human leukemia cell line (MOLT-4) was used to assess the efficacy and selectivity of nanocomposites. Based on a cytotoxicity study, CuO-TiO2-chitosan-escin nanocomposites had inhibition concentrations (IC50) of 13.68, 8.9, and 7.14 µg/mL against human T lymphoblast cells after 24, 48, and 72 h of incubation, respectively. Compared with untreated MOLT-4 cells, CuO-TiO2-chitosan-escin nanocomposite-treated cells significantly increased (p < 0.05) caspase-3, -8, and -9 and decreased the levels of antioxidant enzymes GR, SOD, and GSH. Furthermore, MDA for lipid peroxidase and ROS levels significantly increased (p < 0.05) in the treated cells than in the untreated cells. Remarkably, CuO-TiO2-chitosan-escin nanocomposite-mediated control of cell cycles were mainly achieved through the activation of caspase-3, -8, and -9.
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Affiliation(s)
- Abozer Y. Elderdery
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 42421, Saudi Arabia
- Health Sciences Research Unit, Jouf University, Sakaka 42421, Saudi Arabia
- Correspondence: (A.Y.E.); (P.L.M.)
| | - Abdulaziz H. Alhamidi
- Clinical Laboratory Sciences Department, College of Applied Medical Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed M. E. Elkhalifa
- Department of Public Health, College of Health Sciences, Saudi Electronic University, Riyadh 13316, Saudi Arabia
| | - Maryam M. Althobiti
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, Shaqra 15572, Saudi Arabia
| | | | - Mahdi H. Alsugoor
- Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Makkah 21912, Saudi Arabia
| | - Naif Alsuhaymi
- Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Makkah 21912, Saudi Arabia
| | - Entesar M. Atebien
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, Shaqra 15572, Saudi Arabia
| | - Siddiqa M. A. Hamza
- College of Medicine, Department of Pathology, Umm Alqura University Algunfuda, Mecca 24382, Saudi Arabia
| | - Badr Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 42421, Saudi Arabia
| | - Fehaid Alanazi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences-AlQurayyat, Jouf University, Sakaka 42421, Saudi Arabia
| | - Suresh Kumar Subbiah
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Chennai 600073, India
| | - Pooi Ling Mok
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: (A.Y.E.); (P.L.M.)
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16
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Bektas S, Kaptan E. RNA-Seq transcriptome analysis reveals Maackia amurensis leukoagglutinin has antitumor activity in human anaplastic thyroid cancer cells. Mol Biol Rep 2022; 49:9257-9266. [PMID: 36057880 PMCID: PMC9441018 DOI: 10.1007/s11033-022-07759-6] [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: 02/08/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022]
Abstract
Background Lectins are carbohydrate-binding molecules that can bind specifically to the sugar residues of glycoconjugates and are found in almost all organisms. Plant lectins subjected to many studies reported exhibiting anti-cancer activity. This study aimed to investigate the possible molecular mechanisms of Maackia amurensis leukoagglutinin II (MAL-II) treated ATCCs. Methods and results We tested the effects of MAL-II, which is isolated from Amur seeds, on cancerous features of 8505C human anaplastic thyroid cancer cells (ATCCs) on a large scale using RNA-Seq. Transcriptome analysis was performed using Illumina next-generation sequencing technology by using cDNA libraries obtained from total RNA isolates of ATCCs treated with 0.25 µM MAL-II for 24 h. Gene ontology and pathway enrichment analysis were performed for the systematic analysis of gene functions. Moreover, we validated RNA-Seq findings using qPCR. Our results showed that many cancer-related genes such as TENM4, STIM2, SYT12, PIEZO2, ABCG1, SPNS2, ARRB1, and IRX5 were downregulated and many anticancer genes such as HSPA6, G0S2, TNFAIP3, GEM, GADD45G, RND1, SERPINB2, and IL24 were upregulated. Also, pathway enrichment analysis showed that differentially expressed genes were found to be associated with Ras, p53, and apoptosis signaling pathways, which are some important signal transduction pathways in development, proliferation, stem cell control, and carcinogenesis. Conclusion Collectively, our results show that MAL-II treatment reveals significant antitumor activity by changing the expression of many cancer-related genes and implies that MAL-II treatment might be a potential candidate molecule to inhibit the malignancy of human anaplastic thyroid cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07759-6.
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Affiliation(s)
- Suna Bektas
- Department of Biology, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey
| | - Engin Kaptan
- Department of Biology, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.
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17
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Barrientos K, Arango JP, Moncada MS, Placido J, Patiño J, Macías SL, Maldonado C, Torijano S, Bustamante S, Londoño ME, Jaramillo M. Carbon dot-based biosensors for the detection of communicable and non -communicable diseases. Talanta 2022; 251:123791. [DOI: 10.1016/j.talanta.2022.123791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 10/16/2022]
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18
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Meisami AH, Abbasi M, Mosleh-Shirazi S, Azari A, Amani AM, Vaez A, Golchin A. Self-propelled micro/nanobots: A new insight into precisely targeting cancerous cells through intelligent and deep cancer penetration. Eur J Pharmacol 2022; 926:175011. [PMID: 35568064 DOI: 10.1016/j.ejphar.2022.175011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/13/2022]
Abstract
Cancer overlooks are globally one of the most dangerous and life-threatening tribulations. While significant advances have been made in the targeted delivery of anti-cancer medications over the last few years, several challenges, such as low efficacy and strong toxic effects, remain to be addressed. Micro/nanomotors have been thoroughly studied for both effective cancer detection and treatment, as demonstrated by significant advancements in the architecture of smart and functional micro/nanomotor biomedical systems. Able to self-propelled within fluid media, micro/nanomotors have attractive vehicles to maximize the efficacy of tumor delivery. Here, we present the current developments in the delivery, detection, and imaging-guided treatment of micro/nanomotors in the clinical field, including cancer-related specific targeted drug delivery, and then discuss the barriers and difficulties encountered by micro/nanomotors throughout the medical process. Furthermore, this paper addresses the potential growth of micro/nanomotors for medical applications, and sets out the current drawbacks and future research directions for more advancement.
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Affiliation(s)
- Amir Hossein Meisami
- Department of Emergency Medicine, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Milad Abbasi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sareh Mosleh-Shirazi
- Department of Materials Science and Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Arezo Azari
- Department of Applied Cell Sciences and Tissue Engineering, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ahmad Vaez
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ali Golchin
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran; Department of Clinical Biochemistry and Applied Cell Sciences, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
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Sharma M, Bakshi AK, Mittapelly N, Gautam S, Marwaha D, Rai N, Singh N, Tiwari P, Aggarwal N, Kumar A, Mishra PR. Recent updates on innovative approaches to overcome drug resistance for better outcomes in cancer. J Control Release 2022; 346:43-70. [DOI: 10.1016/j.jconrel.2022.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/07/2023]
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Petroušková P, Hudáková N, Maloveská M, Humeník F, Cizkova D. Non-Exosomal and Exosome-Derived miRNAs as Promising Biomarkers in Canine Mammary Cancer. Life (Basel) 2022; 12:life12040524. [PMID: 35455015 PMCID: PMC9032658 DOI: 10.3390/life12040524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023] Open
Abstract
Canine mammary cancer (CMC), similar to human breast cancer (HBC) in many aspects, is the most common neoplasm associated with significant mortality in female dogs. Due to the limited therapy options, biomarkers are highly desirable for early clinical diagnosis or cancer progression monitoring. Since the discovery of microRNAs (miRNAs or miRs) as post-transcriptional gene regulators, they have become attractive biomarkers in oncological research. Except for intracellular miRNAs and cell-free miRNAs, exosome-derived miRNAs (exomiRs) have drawn much attention in recent years as biomarkers for cancer detection. Analysis of exosomes represents a non-invasive, pain-free, time- and money-saving alternative to conventional tissue biopsy. The purpose of this review is to provide a summary of miRNAs that come from non-exosomal sources (canine mammary tumor, mammary tumor cell lines or canine blood serum) and from exosomes as promising biomarkers of CMC based on the current literature. As is discussed, some of the miRNAs postulated as diagnostic or prognostic biomarkers in CMC were also altered in HBC (such as miR-21, miR-29b, miR-141, miR-429, miR-200c, miR-497, miR-210, miR-96, miR-18a, miR19b, miR-20b, miR-93, miR-101, miR-105a, miR-130a, miR-200c, miR-340, miR-486), which may be considered as potential disease-specific biomarkers in both CMC and HBC.
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Affiliation(s)
- Patrícia Petroušková
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Nikola Hudáková
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Marcela Maloveská
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Filip Humeník
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Dasa Cizkova
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 10 Bratislava, Slovakia
- Correspondence: ; Tel.: +421-918-752-157
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Peng X, Wang HJ. A Generalized Quantile Tree Method for Subgroup Identification. J Comput Graph Stat 2022. [DOI: 10.1080/10618600.2022.2032723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Xiang Peng
- Department of Statistics, George Washington University
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Chen JQ, Zhang N, Su ZL, Qiu HG, Zhuang XG, Tao ZH. Integrated Analysis to Obtain Potential Prognostic Signature in Glioblastoma. Front Integr Neurosci 2022; 15:717629. [PMID: 35069135 PMCID: PMC8766324 DOI: 10.3389/fnint.2021.717629] [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: 05/31/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most malignant and multiple tumors of the central nervous system. The survival rate for GBM patients is less than 15 months. We aimed to uncover the potential mechanism of GBM in tumor microenvironment and provide several candidate biomarkers for GBM prognosis. In this study, ESTIMATE analysis was used to divide the GBM patients into high and low immune or stromal score groups. Microenvironment associated genes were filtered through differential analysis. Weighted gene co-expression network analysis (WGCNA) was performed to correlate the genes and clinical traits. The candidate genes’ functions were annotated by enrichment analyses. The potential prognostic biomarkers were assessed by survival analysis. We obtained 81 immune associated differentially expressed genes (DEGs) for subsequent WGCNA analysis. Ten out of these DEGs were significantly associated with targeted molecular therapy of GBM patients. Three genes (S100A4, FCGR2B, and BIRC3) out of these genes were associated with overall survival and the independent test set testified the result. Here, we obtained three crucial genes that had good prognostic efficacy of GBM and may help to improve the prognostic prediction of GBM.
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Affiliation(s)
- Jia-Qi Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China
- Department of Clinical Laboratory, The People’s Hospital of Lishui, Lishui, China
| | - Nuo Zhang
- Beijing Rehabilitation Hospital of Capital Medical University, Beijing, China
| | - Zhi-Lin Su
- Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Hui-Guo Qiu
- Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Xin-Guo Zhuang
- Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Zhi-hua Tao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China
- *Correspondence: Zhi-hua Tao,
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Fawzy A, Alqelaiti YA, Almatrafi MM, Almatrafi OM, Alqelaiti EA. Common Sensitive Prognostic Marker in Breast Cancer and their Clinical Significance: A Review Article. ARCHIVES OF PHARMACY PRACTICE 2022. [DOI: 10.51847/t8d3bp2l19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Askari N, Hadizadeh M. Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2022; 15:232-240. [PMID: 36311956 PMCID: PMC9589132 DOI: 10.22037/ghfbb.v15i3.2465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/10/2022] [Indexed: 11/16/2022]
Abstract
Aim The current study analyzed the miRNA microarray dataset (GSE66274) and gene expression microarray dataset (GSE38129) with similar samples to achieve a better understanding of miRNA-mRNA interactions. Background The most common form of esophageal cancer is esophageal squamous cell carcinoma (ESCC). While, miRNAs are well recognized as having a critical regulatory role in human cancer, their responsibilities and mechanisms of miRNA-mRNA in ESCC are unknown. Methods Differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) were identified using the LIMMA package in R. In total, 478 DEmRNA (224 upregulated and 254 downregulated) and 39 DEmiRNA (15 upregulated and 24 downregulated) were screened. The RNAInter database analyzed miRNA-mRNA interactions; then, the miRNA-mRNA network was visualized by Cytoscape software. ClusterProfiler packages were used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEmRNA as targets of DEmiRNAs. Results KEGG pathway analysis indicated that the p53 signaling pathway, ECM-receptor interaction, and AGE-RAGE signaling pathway were significant. Cellular response to amino acid stimulus, negative regulation of apoptotic signaling pathway, and endoderm formation were most prevalent in the biological process category. Additionally, the collagen-containing extracellular matrix, actomyosin complex collagen trimers, basement membrane, and extracellular matrix structural constituent were more enriched. Conclusion Overall, the present survey provides evidence that could support the prognosis of esophageal tumors in the future.
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Affiliation(s)
- Nahid Askari
- Department of Biotechnology, Institute of Sciences and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Morteza Hadizadeh
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
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25
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Current advances in prognostic and diagnostic biomarkers for solid cancers: Detection techniques and future challenges. Biomed Pharmacother 2021; 146:112488. [PMID: 34894516 DOI: 10.1016/j.biopha.2021.112488] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/19/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
Solid cancers are one of the leading causes of cancer related deaths, characterized by rapid growth of tumour, and local and distant metastases. Current advances on multimodality care have substantially improved local control and metastasis-free survival of patients by resection of primary tumour. The major concern in disease prognosis is the timely detection of resectable or metastatic tumour, thus reinforcing the need for identification of biomarkers for premalignant lesions of solid cancer. This ultimately improves the outcome for the patients. Therefore, the purpose of this review is to update the recent advancements on prognostic and diagnostic biomarkers to enhance early detection of common solid cancers including, breast, lung, colorectal, prostate and stomach cancer. We also provide an insight into Food and Drug Administration (FDA)-approved solid cancers biomarkers; various conventional techniques used for detection of prognostic and diagnostic biomarkers and discuss approaches to turn challenges in this field into opportunities.
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Acar V, Couto Fernandez FL, Buscariolo FF, Novais AA, Matheus Pereira RA, de Campos Zuccari DAP. Immunohistochemical Evaluation of PARP and Caspase-3 as Prognostic Markers in Prostate Carcinomas. Clin Med Res 2021; 19:183-191. [PMID: 34933951 PMCID: PMC8691432 DOI: 10.3121/cmr.2021.1607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/27/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022]
Abstract
Prostate cancer is the second most common neoplasm among men, with a high mortality rate in advanced stages. Poly (ADP-ribose) polymerase (PARP) plays an important role in repair to DNA damage, being associated with resistance to tumor cell death. Conversely, Caspase-3 is a crucial mediator of programmed cell death, being highly expressed in apoptotic cells. The aim of the present study was to characterize the expression of PARP and Caspase-3 by immunohistochemistry in patients with advanced prostate cancer. PARP and Caspase-3 were independently correlated to patients' evolution, in accordance with the classification of prognostic groups. The increase in PARP expression was positively correlated with tumor patients with poor prognosis (P < 0.0001). In contrast, a decrease in Caspase-3 expression was identified in patients with poor prognosis, when compared with prostate cancer patients with good prognosis (P = 0.0007). Numerically, 92.3% of patients previously classified with poor prognosis showed higher PARP expression, while 93.75% of patients previously classified with good prognosis showed higher levels of Caspase-3. We conclude that PARP and Caspase-3 are potential prognostic markers for prostate cancer patients with different prognosis.
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Affiliation(s)
- Vitoria Acar
- Academic Student, São José do Rio Preto Medical School - FAMERP
| | | | | | - Adriana Alonso Novais
- Post-doctoral student, Cancer Molecular Research Laboratory, São José do Rio Preto Medical School - FAMERP
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da Cunha IW, de Almeida Coudry R, de Macedo MP, de Assis EACP, Stefani S, Soares FA. A call to action: molecular pathology in Brazil. SURGICAL AND EXPERIMENTAL PATHOLOGY 2021. [DOI: 10.1186/s42047-021-00096-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Background
Adoption of molecular pathology in Brazil is currently very limited. Of note, there are no programs for training new molecular pathologists in the country; thus, documents compiling nationally applicable information on molecular pathology are few.
Methods
A selected panel of Brazilian experts in fields related to molecular pathology were provided with a series of relevant questions to address prior to the multi-day conference. Within this conference, each narrative was discussed and edited by the entire group, through numerous drafts and rounds of discussion until a consensus was achieved.
Results
The panel proposes specific and realistic recommendations for implementing molecular pathology in cancer care in Brazil. In creating these recommendations, the authors strived to address all barriers to the widespread use and impediments to access mentioned previously within this manuscript.
Conclusion
This manuscript provides a review of molecular pathology principles as well as the current state of molecular pathology in Brazil. Additionally, the panel proposes practical and actionable recommendations for the implementation of molecular pathology throughout the country in order to increase awareness of the importance molecular pathology in Brazil.
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Adeoye J, Tan JY, Choi SW, Thomson P. Prediction models applying machine learning to oral cavity cancer outcomes: A systematic review. Int J Med Inform 2021; 154:104557. [PMID: 34455119 DOI: 10.1016/j.ijmedinf.2021.104557] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Machine learning platforms are now being introduced into modern oncological practice for classification and prediction of patient outcomes. To determine the current status of the application of these learning models as adjunctive decision-making tools in oral cavity cancer management, this systematic review aims to summarize the accuracy of machine-learning based models for disease outcomes. METHODS Electronic databases including PubMed, Scopus, EMBASE, Cochrane Library, LILACS, SciELO, PsychINFO, and Web of Science were searched up until December 21, 2020. Pertinent articles detailing the development and accuracy of machine learning prediction models for oral cavity cancer outcomes were selected in a two-stage process. Quality assessment was conducted using the Quality in Prognosis Studies (QUIPS) tool and results of base studies were qualitatively synthesized by all authors. Outcomes of interest were malignant transformation of precancer lesions, cervical lymph node metastasis, as well as treatment response, and prognosis of oral cavity cancer. RESULTS Twenty-seven articles out of 950 citations identified from electronic and manual searching were included in this study. Five studies had low bias concerns on the QUIPS tool. Prediction of malignant transformation, cervical lymph node metastasis, treatment response, and prognosis were reported in three, six, eight, and eleven articles respectively. Accuracy of these learning models on the internal or external validation sets ranged from 0.85 to 0.97 for malignant transformation prediction, 0.78-0.91 for cervical lymph node metastasis prediction, 0.64-1.00 for treatment response prediction, and 0.71-0.99 for prognosis prediction. In general, most trained algorithms predicting these outcomes performed better than alternate methods of prediction. We also found that models including molecular markers in training data had better accuracy estimates for malignant transformation, treatment response, and prognosis prediction. CONCLUSION Machine learning algorithms have a satisfactory to excellent accuracy for predicting three of four oral cavity cancer outcomes i.e., malignant transformation, nodal metastasis, and prognosis. However, considering the training approach of many available classifiers, these models may not be streamlined enough for clinical application currently.
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Affiliation(s)
- John Adeoye
- Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Jia Yan Tan
- Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region.
| | - Siu-Wai Choi
- Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region.
| | - Peter Thomson
- Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region
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Reddy S, Hung LH, Sala-Torra O, Radich JP, Yeung CC, Yeung KY. A graphical, interactive and GPU-enabled workflow to process long-read sequencing data. BMC Genomics 2021; 22:626. [PMID: 34425749 PMCID: PMC8381503 DOI: 10.1186/s12864-021-07927-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/10/2021] [Indexed: 12/18/2022] Open
Abstract
Background Long-read sequencing has great promise in enabling portable, rapid molecular-assisted cancer diagnoses. A key challenge in democratizing long-read sequencing technology in the biomedical and clinical community is the lack of graphical bioinformatics software tools which can efficiently process the raw nanopore reads, support graphical output and interactive visualizations for interpretations of results. Another obstacle is that high performance software tools for long-read sequencing data analyses often leverage graphics processing units (GPU), which is challenging and time-consuming to configure, especially on the cloud. Results We present a graphical cloud-enabled workflow for fast, interactive analysis of nanopore sequencing data using GPUs. Users customize parameters, monitor execution and visualize results through an accessible graphical interface. The workflow and its components are completely containerized to ensure reproducibility and facilitate installation of the GPU-enabled software. We also provide an Amazon Machine Image (AMI) with all software and drivers pre-installed for GPU computing on the cloud. Most importantly, we demonstrate the potential of applying our software tools to reduce the turnaround time of cancer diagnostics by generating blood cancer (NB4, K562, ME1, 238 MV4;11) cell line Nanopore data using the Flongle adapter. We observe a 29x speedup and a 93x reduction in costs for the rate-limiting basecalling step in the analysis of blood cancer cell line data. Conclusions Our interactive and efficient software tools will make analyses of Nanopore data using GPU and cloud computing accessible to biomedical and clinical scientists, thus facilitating the adoption of cost effective, fast, portable and real-time long-read sequencing. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07927-1.
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Affiliation(s)
| | - Ling-Hong Hung
- School of Engineering and Technology, University of Washington, 98402, Tacoma, WA, USA
| | - Olga Sala-Torra
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA
| | - Jerald P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA.,Clinical Research Division, Kurt Enslein Endowed Chair, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA.,Department of Medicine, University of Washington, 98109, Seattle, WA, USA
| | - Cecilia Cs Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, 98109, Seattle, WA, USA
| | - Ka Yee Yeung
- School of Engineering and Technology, University of Washington, 98402, Tacoma, WA, USA.
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Papenberg BW, Ingles J, Gao S, Feng J, Allen JL, Markwell SM, Interval ET, Montague PA, Wen S, Weed SA. Copy number alterations identify a smoking-associated expression signature predictive of poor outcome in head and neck squamous cell carcinoma. Cancer Genet 2021; 256-257:136-148. [PMID: 34130230 PMCID: PMC8273756 DOI: 10.1016/j.cancergen.2021.05.011] [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: 10/13/2020] [Revised: 04/23/2021] [Accepted: 05/23/2021] [Indexed: 11/17/2022]
Abstract
Cigarette smoking is a risk factor for the development of head and neck squamous cell carcinoma (HNSCC), partially due to tobacco-induced large-scale chromosomal copy-number alterations (CNAs). Identifying CNAs caused by smoking is essential in determining how gene expression from such regions impact tumor progression and patient outcome. We utilized The Cancer Genome Atlas (TCGA) whole genome sequencing data for HNSCC to directly identify amplified or deleted genes correlating with smoking pack-year based on linear modeling. Internal cross-validation identified 35 CNAs that significantly correlated with patient smoking, independent of human papillomavirus (HPV) status. The most abundant CNAs were chromosome 11q13.3-q14.4 amplification and 9p23.1/9p24.1 deletion. Evaluation of patient amplicons reveals four different patterns of 11q13 gene amplification in HNSCC resulting from breakage-fusion-bridge (BFB) events. . Predictive modeling identified 16 genes from these regions that denote poorer overall and disease-free survival with increased pack-year use, constituting a smoking-associated expression signature (SAES). Patients with altered expression of signature genes have increased risk of death and enhanced cervical lymph node involvement. The identified SAES can be utilized as a novel predictor of increased disease aggressiveness and poor outcome in smoking-associated HNSCC.
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Affiliation(s)
| | | | - Si Gao
- Department of Biostatistics USA
| | | | - Jessica L Allen
- Department of Biochemistry, Program in Cancer Cell Biology USA
| | | | - Erik T Interval
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University, Morgantown, West Virginia, 26506 USA
| | - Phillip A Montague
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University, Morgantown, West Virginia, 26506 USA
| | | | - Scott A Weed
- Department of Biochemistry, Program in Cancer Cell Biology USA.
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Shih CY, Chattopadhyay A, Wu CH, Tien YW, Lu TP. Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants. BMC Bioinformatics 2021; 22:350. [PMID: 34182919 PMCID: PMC8240296 DOI: 10.1186/s12859-021-04243-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An individual's genetics play a role in how RNA transcripts are generated from DNA and consequently in their translation into protein. Transcriptional and translational profiling of patients furnishes the information that a specific marker is present; however, it fails to provide evidence whether the marker correlates with response to a therapeutic agent. A comparative analysis of the frequency of genetic variants, such as single nucleotide polymorphisms (SNPs), in diseased and general populations can identify pathogenic variants in individual patients. This is in part because SNPs have considerable effects on protein function and gene expression when they occur in coding regions and regulatory sequences, respectively. Therefore, a tool that can help users to obtain the allele frequency for a corresponding transcript is the need of the day. Several annotation tools such as SNPnexus and VariED are publicly available; however, none of them can use transcript IDs as input and provide the corresponding genomic positions of variants. RESULTS In this study, we developed an R package, called transcript annotation tool (TransAT), that provides (i) SNP ID and genomic position for a user-provided transcript ID from patients, and (ii) allele frequencies for the SNPs from publicly available global populations. All data elements are extracted, collected, and displayed in an easily downloadable format in two simple command lines. TransAT is available on Windows/Linux/MacOS and is operative for R version 4.0.4 or later. It is available at https://github.com/ShihChingYu/TransAT and can be downloaded and installed using devtools::install_github("ShihChingYu/TransAT", force=T) on the R execution page. Thereafter, all functions can be executed by loading the package into R with library(TransAT). CONCLUSIONS TransAT is a novel tool that seamlessly provides genetic annotations for queried transcripts. Such easily obtainable information would be greatly advantageous for physicians, assisting them to make individualized decisions about specific drug treatments. Moreover, allele frequencies from user-chosen global ethnic populations will highlight the importance of ethnicity and its effect on patient pathogenicity.
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Affiliation(s)
- Ching-Yu Shih
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan
| | - Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan
| | - Chien-Hui Wu
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Wen Tien
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan.
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan.
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Alimardani M, Moghbeli M, Rastgar-Moghadam A, Shandiz FH, Abbaszadegan MR. Single nucleotide polymorphisms as the efficient prognostic markers in breast cancer. Curr Cancer Drug Targets 2021; 21:768-793. [PMID: 34036920 DOI: 10.2174/1568009621666210525151846] [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: 10/24/2020] [Revised: 03/15/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Breast cancer (BC) is known as the most common malignancy in women. Environmental and genetic factors are associated with BC progression. Genetic polymorphisms have been reported as important risk factors of BC prognosis and drug response. Main body: Therefore, in the present review, we have summarized all single nucleotide polymorphisms (SNPs) which have been significantly associated with drug response in BC patients around the world. We have also categorized the reported SNPs based on their related genes functions to clarify the molecular biology of drug responses in BC. CONCLUSION The majority of SNPs were reported in detoxifying enzymes, which introduced such genes as the main genetic risk factors during BC drug responses. This review paves the way for introducing a prognostic panel of SNPs for the BC patients in the world.
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Affiliation(s)
- Maliheh Alimardani
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Azam Rastgar-Moghadam
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Homaei Shandiz
- Department of Radiotherapy/Oncology, Omid Hospital, Mashhad University of Medical Science, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Kashyap D, Garg VK, Sandberg EN, Goel N, Bishayee A. Oncogenic and Tumor Suppressive Components of the Cell Cycle in Breast Cancer Progression and Prognosis. Pharmaceutics 2021; 13:pharmaceutics13040569. [PMID: 33920506 PMCID: PMC8072616 DOI: 10.3390/pharmaceutics13040569] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023] Open
Abstract
Cancer, a disease of inappropriate cell proliferation, is strongly interconnected with the cell cycle. All cancers consist of an abnormal accumulation of neoplastic cells, which are propagated toward uncontrolled cell division and proliferation in response to mitogenic signals. Mitogenic stimuli include genetic and epigenetic changes in cell cycle regulatory genes and other genes which regulate the cell cycle. This suggests that multiple, distinct pathways of genetic alterations lead to cancer development. Products of both oncogenes (including cyclin-dependent kinase (CDKs) and cyclins) and tumor suppressor genes (including cyclin-dependent kinase inhibitors) regulate cell cycle machinery and promote or suppress cell cycle progression, respectively. The identification of cyclins and CDKs help to explain and understand the molecular mechanisms of cell cycle machinery. During breast cancer tumorigenesis, cyclins A, B, C, D1, and E; cyclin-dependent kinase (CDKs); and CDK-inhibitor proteins p16, p21, p27, and p53 are known to play significant roles in cell cycle control and are tightly regulated in normal breast epithelial cells. Following mitogenic stimuli, these components are deregulated, which promotes neoplastic transformation of breast epithelial cells. Multiple studies implicate the roles of both types of components-oncogenic CDKs and cyclins, along with tumor-suppressing cyclin-dependent inhibitors-in breast cancer initiation and progression. Numerous clinical studies have confirmed that there is a prognostic significance for screening for these described components, regarding patient outcomes and their responses to therapy. The aim of this review article is to summarize the roles of oncogenic and tumor-suppressive components of the cell cycle in breast cancer progression and prognosis.
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Affiliation(s)
- Dharambir Kashyap
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh 160 012, Punjab, India;
| | | | - Elise N. Sandberg
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
| | - Neelam Goel
- University Institute of Engineering and Technology, Panjab University, Chandigarh 160 014, Punjab, India
- Correspondence: (N.G.); or (A.B.)
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
- Correspondence: (N.G.); or (A.B.)
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Kashyap D, Garg VK, Goel N. Intrinsic and extrinsic pathways of apoptosis: Role in cancer development and prognosis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 125:73-120. [PMID: 33931145 DOI: 10.1016/bs.apcsb.2021.01.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Apoptosis, also named programmed cell death, is a fundament process required for morphogenetic homeostasis during early development and in pathophysiological conditions. It is come into existence in 1972 by work of Kerr, Wyllie and Currie and later on investigated during the research on development of the C. elegans. Trigger by several stimuli, apoptosis is necessary during the embryonic development and aging as homeostatic mechanism to control the cell population and also play a key role as defense mechanism against the immune responses and elimination of damaged cells. Cancer, a genetic disease, is a growing burden on the health and economy of both developing and developed countries. Every year there is tremendously increasing in the number of new cancer cases and mortality rate. Although, there is a significant improvement have been made in biotechnological and bioinformatic fields however, the therapeutic advantages and cancer etiology is still under explored. Several studies determined the deregulation of different apoptotic components during the cancer development and progression. Apoptosis relies on activation of distinct signaling pathways that are often deregulated in cancer. Thus, exploring the single or more than one apoptotic component underlying their expression in carcinogenesis could help to track the disease progression. Current book chapter will provide the several evidences supporting the use of different apoptotic components as prognosis and prediction markers in various human cancer types.
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Affiliation(s)
- Dharambir Kashyap
- Department of Histopathology, Postgraduation Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | | | - Neelam Goel
- Department of Information Technology, UIET, Panjab University, Chandigarh, India.
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Advani D, Sharma S, Kumari S, Ambasta RK, Kumar P. Precision Oncology, Signaling and Anticancer Agents in Cancer Therapeutics. Anticancer Agents Med Chem 2021; 22:433-468. [PMID: 33687887 DOI: 10.2174/1871520621666210308101029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The global alliance for genomics and healthcare facilities provides innovational solutions to expedite research and clinical practices for complex and incurable health conditions. Precision oncology is an emerging field explicitly tailored to facilitate cancer diagnosis, prevention and treatment based on patients' genetic profile. Advancements in "omics" techniques, next-generation sequencing, artificial intelligence and clinical trial designs provide a platform for assessing the efficacy and safety of combination therapies and diagnostic procedures. METHOD Data were collected from Pubmed and Google scholar using keywords: "Precision medicine", "precision medicine and cancer", "anticancer agents in precision medicine" and reviewed comprehensively. RESULTS Personalized therapeutics including immunotherapy, cancer vaccines, serve as a groundbreaking solution for cancer treatment. Herein, we take a measurable view of precision therapies and novel diagnostic approaches targeting cancer treatment. The contemporary applications of precision medicine have also been described along with various hurdles identified in the successful establishment of precision therapeutics. CONCLUSION This review highlights the key breakthroughs related to immunotherapies, targeted anticancer agents, and target interventions related to cancer signaling mechanisms. The success story of this field in context to drug resistance, safety, patient survival and in improving quality of life is yet to be elucidated. We conclude that, in the near future, the field of individualized treatments may truly revolutionize the nature of cancer patient care.
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Affiliation(s)
- Dia Advani
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Sudhanshu Sharma
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
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Rishabh K, Khadilkar S, Kumar A, Kalra I, Kumar AP, Kunnumakkara AB. MicroRNAs as Modulators of Oral Tumorigenesis-A Focused Review. Int J Mol Sci 2021; 22:ijms22052561. [PMID: 33806361 PMCID: PMC7961687 DOI: 10.3390/ijms22052561] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/23/2022] Open
Abstract
Oral cancers constitute the majority of head and neck tumors, with a relatively high incidence and poor survival rate in developing countries. While the five-year survival rates of the oral cancer patients have increased to 65%, the overall survival for advanced stages has been at 27% for the past ten years, emphasizing the necessity for further understanding the etiology of the disease, diagnosis, and formulating possible novel treatment regimens. MicroRNAs (miRNAs), a family of small non-coding RNA, have emerged as master modulators of gene expression in various cellular and biological process. Aberrant expression of these dynamic molecules has been associated with many human diseases, including oral cancers. The deregulated miRNAs have been shown to control various oncogenic processes, including sustaining proliferative signaling, evading growth suppressors, resisting cell death activating invasion and metastasis, and inducing angiogenesis. Hence, the aberrant expression of miRNAs associated with oral cancers, makes them potential candidates for the investigation of functional markers, which will aid in the differential diagnosis, prognosis, and development of novel therapeutic regimens. This review presents a holistic insight into our understanding of the role of miRNAs in regulating various hallmarks of oral tumorigenesis.
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Affiliation(s)
- Kumar Rishabh
- Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam 781039, India; (K.R.); (S.K.); (A.K.); (I.K.)
| | - Soham Khadilkar
- Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam 781039, India; (K.R.); (S.K.); (A.K.); (I.K.)
| | - Aviral Kumar
- Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam 781039, India; (K.R.); (S.K.); (A.K.); (I.K.)
| | - Ishu Kalra
- Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam 781039, India; (K.R.); (S.K.); (A.K.); (I.K.)
| | - Alan Prem Kumar
- Cancer Science Institute of Singapore, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- National University Cancer Institute, National University Health System, Singapore 119074, Singapore
- Correspondence: authors: (A.P.K.); (A.B.K.)
| | - Ajaikumar B. Kunnumakkara
- Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati, Assam 781039, India; (K.R.); (S.K.); (A.K.); (I.K.)
- Correspondence: authors: (A.P.K.); (A.B.K.)
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Joseph AO, Li YH, Salako O, Doi S, Balogun OD, Awofeso OM, Abdulkareem F, Onitilo AA. A review of breast cancer pathology reports in Nigeria. Ecancermedicalscience 2021; 15:1190. [PMID: 33889199 PMCID: PMC8043685 DOI: 10.3332/ecancer.2021.1190] [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: 10/27/2020] [Indexed: 11/21/2022] Open
Abstract
Background Diagnosis and treatment of cancer rely heavily on imaging, histopathology and molecular information. Incomplete or missing tumour information can hinder the delivery of high-quality care in oncology practice, especially in resource-limited countries. To evaluate the completeness of histopathology reporting in a real-world setting and identify areas for future cancer care delivery research efforts, we retrospectively analysed reports from patients diagnosed with breast cancer who received care at a high-volume oncology department at a hospital in Lagos, Nigeria. Methods Demographic, institutional and histopathology characteristics were retrospectively obtained from 1,001 patient records from 2007 to 2016. Completeness was defined as reporting five tumour features (tumour histology, tumour grade, laterality, oestrogen receptor (ER) or progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2)) for biopsy specimens and seven tumour features (tumour size, tumour histology, tumour grade, laterality, ER/PR, HER2 and lymph node involvement) for surgical specimens. Results The mean age of patients was 48.6 ± 11.7 years with a predominantly female population (99.3%). A majority of pathologic reports were produced after 2011, and two-thirds of the reports originated from centres or labs within Lagos, Nigeria (67.7%). Most reports documented primary site (98.0%) and specimen type (85.0%) while other characteristics were less often recorded. This led to substantial variation in reporting between biopsy (13.4%) and surgical (6.1%) specimens for an overall low pathology report completeness <10%. Conclusion The majority of patient records analysed lacked complete documentation of breast cancer histopathological characteristics commonly used in oncology practice. Our study highlights a need to identify and address the contributing factors for incomplete histopathological reporting in Nigeria and will guide future clinical programmatic developments.
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Affiliation(s)
- Adedayo O Joseph
- NSIA-LUTH Cancer Treatment Center, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Ya-Huei Li
- Cancer Care and Research Center, Marshfield Clinic Research Institute, Marshfield, Wisconsin 54449, USA
| | - Omolola Salako
- Department of Radiotherapy, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Suhail Doi
- Department of Population Medicine, College of Medicine, Doha, Qatar
| | - Onyinye D Balogun
- Department of Radiation Oncology, Weill Cornell Medicine, New York 10065, USA
| | | | | | - Adedayo A Onitilo
- Cancer Care and Research Center, Marshfield Clinic Research Institute, Marshfield, Wisconsin 54449, USA.,Department of Oncology, Marshfield Clinic Health System-Weston Center, 3501 Cranberry Blvd, Weston, WI 54476, USA.,https://orcid.org/0000-0001-9185-0606
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Saegusa T, Zhao Z, Ke H, Ye Z, Xu Z, Chen S, Ma T. Detecting survival-associated biomarkers from heterogeneous populations. Sci Rep 2021; 11:3203. [PMID: 33547332 PMCID: PMC7865037 DOI: 10.1038/s41598-021-82332-y] [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: 07/27/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Detection of prognostic factors associated with patients' survival outcome helps gain insights into a disease and guide treatment decisions. The rapid advancement of high-throughput technologies has yielded plentiful genomic biomarkers as candidate prognostic factors, but most are of limited use in clinical application. As the price of the technology drops over time, many genomic studies are conducted to explore a common scientific question in different cohorts to identify more reproducible and credible biomarkers. However, new challenges arise from heterogeneity in study populations and designs when jointly analyzing the multiple studies. For example, patients from different cohorts show different demographic characteristics and risk profiles. Existing high-dimensional variable selection methods for survival analysis, however, are restricted to single study analysis. We propose a novel Cox model based two-stage variable selection method called "Cox-TOTEM" to detect survival-associated biomarkers common in multiple genomic studies. Simulations showed our method greatly improved the sensitivity of variable selection as compared to the separate applications of existing methods to each study, especially when the signals are weak or when the studies are heterogeneous. An application of our method to TCGA transcriptomic data identified essential survival associated genes related to the common disease mechanism of five Pan-Gynecologic cancers.
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Affiliation(s)
- Takumi Saegusa
- grid.164295.d0000 0001 0941 7177Department of Mathematics, University of Maryland, College Park, MD 20742 USA
| | - Zhiwei Zhao
- grid.164295.d0000 0001 0941 7177Department of Mathematics, University of Maryland, College Park, MD 20742 USA
| | - Hongjie Ke
- grid.164295.d0000 0001 0941 7177Department of Mathematics, University of Maryland, College Park, MD 20742 USA
| | - Zhenyao Ye
- grid.164295.d0000 0001 0941 7177Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD 20740 USA
| | - Zhongying Xu
- grid.21925.3d0000 0004 1936 9000Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213 USA
| | - Shuo Chen
- grid.411024.20000 0001 2175 4264Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Tianzhou Ma
- grid.164295.d0000 0001 0941 7177Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD 20740 USA
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Abstract
The discovery that all cells secrete extracellular vesicles (EVs) to shuttle proteins and nucleic acids to recipient cells suggested they play an important role in intercellular communication. EVs are widely distributed in many body fluids, including blood, cerebrospinal fluid, urine and saliva. Exosomes are nano-sized EVs of endosomal origin that regulate many pathophysiological processes including immune responses, inflammation, tumour growth, and infection. Healthy individuals release exosomes with a cargo of different RNA, DNA, and protein contents into the circulation, which can be measured non-invasively as biomarkers of healthy and diseased states. Cancer-derived exosomes carry a unique set of DNA, RNA, protein and lipid reflecting the stage of tumour progression, and may serve as diagnostic and prognostic biomarkers for various cancers. However, many gaps in knowledge and technical challenges in EVs and extracellular RNA (exRNA) biology, such as mechanisms of EV biogenesis and uptake, exRNA cargo selection, and exRNA detection remain. The NIH Common Fund-supported exRNA Communication Consortium was launched in 2013 to address major scientific challenges in this field. This review focuses on scientific highlights in biomarker discovery of exosome-based exRNA in cancer and its possible clinical application as cancer biomarkers.
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Affiliation(s)
- Christine Happel
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aniruddha Ganguly
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute at the National Institutes of Health, Bethesda, MD 20892, USA
| | - Danilo A Tagle
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
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Systems Biology and Biomarkers in Necrotizing Soft Tissue Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1294:167-186. [PMID: 33079369 DOI: 10.1007/978-3-030-57616-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
In necrotizing soft tissue infection (NSTI) there is a need to identify biomarker sets that can be used for diagnosis and disease management. The INFECT study was designed to obtain such insights through the integration of patient data and results from different clinically relevant experimental models by use of systems biology approaches. This chapter describes the current state of biomarkers in NSTI and how biomarkers are categorized. We introduce the fundamentals of top-down systems biology approaches including analysis tools and we review the use of current methods and systems biology approaches to biomarker discover. Further, we discuss how different "omics" signatures (gene expression, protein, and metabolites) from NSTI patient samples can be used to identify key host and pathogen factors involved in the onset and development of infection, as well as exploring associations to disease outcomes.
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[Multimodal, multiparametric and genetic breast imaging]. Radiologe 2021; 61:183-191. [PMID: 33464404 DOI: 10.1007/s00117-020-00801-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
CLINICAL/METHODOLOGICAL ISSUE Multiparametric magnetic resonance imaging (MRI) aims to visualize and quantify biological, physiological and pathological processes at the cellular and molecular level and provides valuable information about key processes in cancer development and progression. "Omics" strategies (genomics, transcriptomics, proteomics, metabolomics) have many uses in oncology. STANDARD RADIOLOGICAL METHODS Multiparametric MRI of the breast currently includes T2-weighted, diffusion-weighted and dynamic contrast-enhanced MRI (DCE-MRI) METHODOLOGICAL INNOVATIONS: Additional parameters such as proton magetic resonance spectroscopy (MRS), chemical exchange saturation transfer (CEST), blood oxygen level-dependent (BOLD), hyperpolarized (HP) MRI or lipid MRS are currently being developed and are being evaluated in breast cancer diagnostics. ACHIEVEMENTS Radiogenomics is a new direction in medical science that has been made possible by significant advances in imaging and image analysis methods, as well as the development of techniques to extract and correlate various imaging parameters with "omics" data. The aim of radiogenomics is to correlate imaging characteristics (phenotypes) with gene expression patterns, gene mutations and other genome-associated properties and is the evolution of the correlation between radiology and pathology from the anatomical-histological to the molecular level. Quantitative and qualitative imaging biomarkers provide insights into the complex tumor biology. Initial results suggest that radiogemics will play an important role in the diagnosis, prognosis, and treatment of breast cancer. PRACTICAL RECOMMENDATIONS This article provides an overview of the current state of radiogenomics of the breast and future applications and challenges.
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Niedziałkowski P, Bojko M, Ryl J, Wcisło A, Spodzieja M, Magiera-Mularz K, Guzik K, Dubin G, Holak TA, Ossowski T, Rodziewicz-Motowidło S. Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode. Bioelectrochemistry 2021; 139:107742. [PMID: 33517203 DOI: 10.1016/j.bioelechem.2021.107742] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/22/2023]
Abstract
This work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10-18 to 10-8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10-14 M for PD-L1 (S/N = 3.3) and at a concentration of 10-14 M via cyclic voltammetry (CV). Additionally, high-resolution X-ray photoelectron spectroscopy (XPS), contact angle, and surface free energy measurements were applied to confirm the functionalization of the electrode. We investigated the selectivity of the electrode for other proteins: Programmed Death-1 (PD-1), cluster of differentiation 160 (CD160), and B- and T-lymphocyte attenuator (BTLA) at concentrations of 10-8 M. Differentiation between PD-L1 and PD-1 was achieved based on the analysis of the capacitance effect frequency dispersion at the surface of the modified Au electrode with BMS-8 after incubation at various concentrations of PD-L1 and PD-1 proteins in the range of 10-18 to 10-8 M. Significant differences were observed in the heterogeneity of PD-L1 and PD-1. The results of the quasi-capacitance studies demonstrate that BMS-8 strongly and specifically interacts with the PD-L1 protein.
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Affiliation(s)
- Paweł Niedziałkowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Magdalena Bojko
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Jacek Ryl
- Department of Electrochemistry, Corrosion and Materials Engineering, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, Gdansk 80-233, Poland
| | - Anna Wcisło
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marta Spodzieja
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | | | - Katarzyna Guzik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tadeusz Ossowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sylwia Rodziewicz-Motowidło
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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Pandey I, Misra V, Pandey AT, Ramteke PW, Agrawal R. Artificial intelligence technologies empowering identification of novel diagnostic molecular markers in gastric cancer. INDIAN J PATHOL MICR 2021; 64:S63-S68. [PMID: 34135140 DOI: 10.4103/ijpm.ijpm_950_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In recent clinical practice the molecular diagnostics have been significantly empowered and upgraded by the use of Artificial Intelligence and its assisted technologies. The use of Machine leaning and Deep Learning Neural network architectures have brought in a new dimension in clinical oncological research and development. These algorithm based software system with enhanced digital image analysis have emerged into a new branch of digital pathology and contributed immensely towards precision medicine and personal diagnostics. In India, gastric cancer is one of the most common cancers in males as well as in females. Various molecular biomarkers are associated with gastric cancer development and progression of which HER2 protein, a transmembrane tyrosine kinase (TK) receptor of epidermal growth factor receptors (EGFRs) family is of prime importance. The EGF receptor expression in gastric cancer is linked with its prognostics and theragnostics. These expressions are assessed by immunohistochemistry (IHC) and molecular techniques such as Fluorescence in-situ hybridization (FISH), as per recommendations for HER2 targeted immunotherapy. These have motivated the software giants like Google Inc. to produce innovative state of art technologies mimicking human traits such as learning and problem solving skill sets. This field is still under development and is slowly evolving and capturing global importance in recent times. A literature search on PubMed was performed to access updated information for this manuscript.
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Affiliation(s)
- Ishan Pandey
- Department of Pathology, MotiLal Nehru Medical College, Prayagraj, India
| | - Vatsala Misra
- Department of Pathology, MotiLal Nehru Medical College, Prayagraj, India
| | | | | | - Ranjan Agrawal
- Department of Pathology, Rohilkhand Medical College and Hospital, Bareilly, Uttar Pradesh, India
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Mohanty SS, Sahoo CR, Padhy RN. Role of hormone receptors and HER2 as prospective molecular markers for breast cancer: An update. Genes Dis 2020; 9:648-658. [PMID: 35782984 PMCID: PMC9243349 DOI: 10.1016/j.gendis.2020.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/24/2020] [Accepted: 12/12/2020] [Indexed: 11/18/2022] Open
Abstract
This review provides an updated account on the current methods, principles and mechanism of action of therapies for the detection of molecular markers of therapeutic importance in the prognosis of breast cancer progression and recurrence, which includes estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor2 (HER2). Indeed, hormone-receptors namely, ER, PR, proto-oncogene HER2 are the basic molecular markers that are recognized and established prognostic factors and predictors of response, for therapeutic practice. These markers can be detected by using immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), which are established, faster and cost effective detection methods. These molecular markers along with clinicopathological prognostic parameters give the best prediction of the prognosis of cancer recurrence and progress. Finally, hormone receptors and HER2 as molecular markers are of prime therapeutic importance and have the capability to take part in future drug development techniques.
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Affiliation(s)
- Swati Sucharita Mohanty
- Cytogenetics Laboratory, P.G. Department of Zoology, Utkal University, Bhubaneswar, Odisha 751004, India
- Central Research Laboratory, Institute of Medical Sciences & SUM Hospital, Siksha ‘O’ Anusandhan Deemed to be University, Bhubaneswar, Odisha 751003, India
- Corresponding author. Cytogenetics Laboratory, P.G. Department of Zoology, Utkal University, Bhubaneswar 751004, Odisha, India.
| | - Chita Ranjan Sahoo
- Central Research Laboratory, Institute of Medical Sciences & SUM Hospital, Siksha ‘O’ Anusandhan Deemed to be University, Bhubaneswar, Odisha 751003, India
| | - Rabindra Nath Padhy
- Central Research Laboratory, Institute of Medical Sciences & SUM Hospital, Siksha ‘O’ Anusandhan Deemed to be University, Bhubaneswar, Odisha 751003, India
- Corresponding author.
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Bioinformatics-Based Identification of a circRNA-miRNA-mRNA Axis in Esophageal Squamous Cell Carcinomas. JOURNAL OF ONCOLOGY 2020; 2020:8813800. [PMID: 33061972 PMCID: PMC7542503 DOI: 10.1155/2020/8813800] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
Background Esophageal squamous cell carcinoma (ESCC) has a poor prognosis due to the lack of early disease symptoms. Using bioinformatics tools, this study aimed to discover differentially expressed nonprotein-coding RNAs and genes with potential prognostic relevance in ESCC. Methods Two microRNAs (miRNAs) and one circular RNA (circRNA) microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differential expression of miRNAs (DEMs) and circRNAs (DECs) was, respectively, identified in ESCC tissue and compared to adjacent healthy tissue. Further analysis was performed using the miRNA microarray datasets, where miRTarBase was used to predict which messenger RNAs (mRNAs) was present. This was followed by protein-protein interaction (PPI) network, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) analyses. Moreover, cytoHubba and UALCAN were used to predict the important nodes and perform patient survival analysis, respectively. The miRNA-associated circRNAs were predicted using the ENCORI website. The interaction between DECs and the predicted circRNAs was also determined. A circRNA-miRNA-mRNA axis was constructed. Results Associated with RAP1B and circ_0052867, two miRNAs (miR-133b and miR-139-5p) were identified as being differentially expressed and downregulated across the two datasets. Finally, the circ_0052867/miR-139-5p/RAP1B regulatory axis was established. Conclusion This study provides support for the possible mechanisms of disease progression in ESCC.
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Zhou X, Xiao C, Han T, Qiu S, Wang M, Chu J, Sun W, Li L, Lin L. Prognostic biomarkers related to breast cancer recurrence identified based on Logit model analysis. World J Surg Oncol 2020; 18:254. [PMID: 32977823 PMCID: PMC7519567 DOI: 10.1186/s12957-020-02026-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND This study intended to determine important genes related to the prognosis and recurrence of breast cancer. METHODS Gene expression data of breast cancer patients were downloaded from TCGA database. Breast cancer samples with recurrence and death were defined as poor disease-free survival (DFS) group, while samples without recurrence and survival beyond 5 years were defined as better DFS group. Another gene expression profile dataset (GSE45725) of breast cancer was downloaded as the validation data. Differentially expressed genes (DEGs) were screened between better and poor DFS groups, which were then performed function enrichment analysis. The DEGs that were enriched in the GO function and KEGG signaling pathway were selected for cox regression analysis and Logit regression (LR) model analysis. Finally, correlation analysis between LR model classification and survival prognosis was analyzed. RESULTS Based on the breast cancer gene expression profile data in TCGA, 540 DEGs were screened between better DFS and poor DFS groups, including 177 downregulated and 363 upregulated DEGs. A total of 283 DEGs were involved in all GO functions and KEGG signaling pathways. Through LR model screening, 10 important feature DEGs were identified and validated, among which, ABCA3, CCL22, FOXJ1, IL1RN, KCNIP3, MAP2K6, and MRPL13, were significantly expressed in both groups in the two data sets. ABCA3, CCL22, FOXJ1, IL1RN, and MAP2K6 were good prognostic factors, while KCNIP3 and MRPL13 were poor prognostic factors. CONCLUSION ABCA3, CCL22, FOXJ1, IL1RN, and MAP2K6 may serve as good prognostic factors, while KCNIP3 and MRPL13 may be poor prognostic factors for the prognosis of breast cancer.
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Affiliation(s)
- Xiaoying Zhou
- Department of Nursing, Wuxi Higher Health Vocational Technology School, Wuxi, 2140128, Jiangsu, China
| | - Chuanguang Xiao
- Department of Breast Thyroid Surgery, Central Hospital of Zibo, Zibo, 255036, Shandong, China
| | - Tong Han
- Department of Rehabilitation Medicine, Xinxiang Medical University, Xinxiang, 453000, Henan, China
| | - Shusheng Qiu
- Department of Breast Thyroid Surgery, Central Hospital of Zibo, Zibo, 255036, Shandong, China
| | - Meng Wang
- Department of Nursing, Wuxi Higher Health Vocational Technology School, Wuxi, 2140128, Jiangsu, China
| | - Jun Chu
- Department of Nursing, Wuxi Higher Health Vocational Technology School, Wuxi, 2140128, Jiangsu, China
| | - Weike Sun
- Department of Breast Thyroid Surgery, Central Hospital of Zibo, Zibo, 255036, Shandong, China
| | - Liang Li
- Department of Breast Thyroid Surgery, Central Hospital of Zibo, Zibo, 255036, Shandong, China
| | - Lili Lin
- Department of Pharmacy, Wuxi Higher Health Vocational Technology School, No. 305, Xinguang Road, Wuxi, 214028, Jiangsu, China.
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Hasan S. An Overview of Promising Biomarkers in Cancer Screening and Detection. Curr Cancer Drug Targets 2020; 20:831-852. [PMID: 32838718 DOI: 10.2174/1568009620666200824102418] [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: 05/13/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 11/22/2022]
Abstract
Applications of biomarkers have been proved in oncology screening, diagnosis, predicting response to treatment as well as monitoring the progress of the disease. Considering the crucial role played by them during different disease stages, it is extremely important to evaluate, validate, and assess them to incorporate them into routine clinical care. In this review, the role of few most promising and successfully used biomarkers in cancer detection, i.e. PD-L1, E-Cadherin, TP53, Exosomes, cfDNA, EGFR, mTOR with regard to their structure, mode of action, and reports signifying their pathological significance, are addressed. Also, an overview of some successfully used biomarkers for cancer medicine has been presented. The study also summarizes biomarker-driven personalized cancer therapy i.e., approved targets and indications, as per the US FDA. The review also highlights the increasingly prominent role of biomarkers in drug development at all stages, with particular reference to clinical trials. The increasing utility of biomarkers in clinical trials is clearly evident from the trend shown, wherein ~55 percent of all oncology clinical trials in 2019 were seen to involve biomarkers, as opposed to ~ 15 percent in 2001, which clearly proves the essence and applicability of biomarkers for synergizing clinical information with tumor progression. Still, there are significant challenges in the implementation of these possibilities with strong evidence in cost-- effective manner.
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Affiliation(s)
- Saba Hasan
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Lucknow, India
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Arora C, Kaur D, Lathwal A, Raghava GP. Risk prediction in cutaneous melanoma patients from their clinico-pathological features: superiority of clinical data over gene expression data. Heliyon 2020; 6:e04811. [PMID: 32913910 PMCID: PMC7472860 DOI: 10.1016/j.heliyon.2020.e04811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Risk assessment in cutaneous melanoma (CM) patients is one of the major challenges in the effective treatment of CM patients. Traditionally, clinico-pathological features such as Breslow thickness, American Joint Committee on Cancer (AJCC) tumor staging, etc. are utilized for this purpose. However, due to advancements in technology, most of the upcoming risk prediction methods are gene-expression profile (GEP) based. In this study, we have tried to develop new GEP and clinico-pathological features-based biomarkers and assessed their prognostic strength in contrast to existing prognostic methods. We developed risk prediction models using the expression of the genes associated with different cancer-related pathways and got a maximum hazard ratio (HR) of 2.52 with p-value ~10-8 for the apoptotic pathway. Another model, based on combination of apoptotic and notch pathway genes boosted the HR to 2.57. Next, we developed models based on individual clinical features and got a maximum HR of 2.45 with p-value ~10-6 for Breslow thickness. We also developed models using the best features of clinical as well as gene-expression data and obtained a maximum HR of 3.19 with p-value ~10-9. Finally, we developed a new ensemble method using clinical variables only and got a maximum HR of 6.40 with p-value ~10-15. Based on this method, a web-based service and an android application named 'CMcrpred' is available at (https://webs.iiitd.edu.in/raghava/cmcrpred/) and Google Play Store respectively to facilitate scientific community. This study reveals that our new ensemble method based on only clinico-pathological features overperforms methods based on GEP based profiles as well as currently used AJCC staging. It also highlights the need to explore the full potential of clinical variables for prognostication of cancer patients.
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Affiliation(s)
- Chakit Arora
- Department of Computational Biology, IIIT- Delhi, New-Delhi, India
| | - Dilraj Kaur
- Department of Computational Biology, IIIT- Delhi, New-Delhi, India
| | - Anjali Lathwal
- Department of Computational Biology, IIIT- Delhi, New-Delhi, India
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Lee YJ, Seo HW, Baek JH, Lim SH, Hwang SG, Kim EH. Gene expression profiling of glioblastoma cell lines depending on TP53 status after tumor-treating fields (TTFields) treatment. Sci Rep 2020; 10:12272. [PMID: 32704022 PMCID: PMC7378235 DOI: 10.1038/s41598-020-68473-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/24/2020] [Indexed: 01/20/2023] Open
Abstract
Glioblastoma is frequently associated with TP53 mutation, which is linked to a worse prognosis and response to conventional treatments (chemoradiotherapy). Therefore, targeting TP53 is a promising strategy to overcome this poor therapeutic response. Tumor-treating fields (TTFields) are a recently approved treatment for newly diagnosed glioblastoma, which involves direct application of low-intensity, intermediate-frequency alternating electric fields to the tumor, thereby offering a local tumor-killing effect. However, the influence of TP53 mutation status on the effectiveness of TTFields is controversial. Here, we identified the key gene signatures and pathways associated with TTFields in four glioblastoma cell lines varying in TP53 mutation status using gene profiling and functional annotation. Overall, genes associated with the cell cycle, cell death, and immune response were significantly altered by TTFields regardless of TP53 status. TTFields appeared to exert enhanced anti-cancer effects by altering the immune system in the inflammatory environment and regulating cell cycle- and cell death-related genes, but the precise genes influenced vary according to TP53 status. These results should facilitate detailed mechanistic studies on the molecular basis of TTFields to further develop this modality as combination therapy, which can improve the therapeutic effect and minimize side effects of chemoradiotherapy.
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Affiliation(s)
- Yeon-Joo Lee
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences (KIRAMS), Seoul, South Korea
| | - Hyun Wook Seo
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences (KIRAMS), Seoul, South Korea
| | - Jeong-Hwa Baek
- Radiation Biology Research Team, Research Center, Dongnam Institute of Radiological and Medical Sciences, Busan, 46033, Republic of Korea
| | - Sun Ha Lim
- Department of Biochemistry, School of Medicine, Daegu Catholic University, 33, 17-gil, Duryugongwon-ro, Nam-gu, Daegu, Korea
| | - Sang-Gu Hwang
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences (KIRAMS), Seoul, South Korea.
| | - Eun Ho Kim
- Department of Biochemistry, School of Medicine, Daegu Catholic University, 33, 17-gil, Duryugongwon-ro, Nam-gu, Daegu, Korea.
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Atutornu J, Hayre CM. A Survey Exploring Personalised Medicine amongst Radiography Academics within the United Kingdom. J Med Imaging Radiat Sci 2020; 51:443-450. [PMID: 32620522 PMCID: PMC7327469 DOI: 10.1016/j.jmir.2020.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 11/18/2022]
Abstract
Introduction This article explores the application of personalized medicine (PM) within the academic environment in the United Kingdom. There is a growing acceptance of the utility of PM in health care and the role medical imaging can play. In response, this article explored the views and opinions of diagnostic and therapeutic academics and the utilization of PM in education. Methods This study primarily adopted a quantitative approach using an online survey. However, participants were also encouraged to provide qualitative comments in response to open-ended questions. The survey was distributed to radiography and radiotherapy academic departments, which received a response rate of 29%. Results The findings identify some important considerations. On the one hand some participants reported teaching PM on their programmes (24%, n = 16), whereas 30% (n = 20) did not. Importantly, the remaining academics (46%) were either unsure or did not know what PM was. This finding, coincided with qualitative commentary, highlights some discrepancies linked to knowledge and understanding of PM within higher education and highlights areas where academics may need additional support. Conclusion This article concludes by recognizing the challenges of delivering PM by some academics. It is noted that although the findings cannot be fully generalized, it does highlight fragmented understanding of PM among academic staff. This is important to reflect upon following the increasing requirements for radiography to become “more personalized.”
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Affiliation(s)
- Jerome Atutornu
- Diagnostic Radiography, School of Health and Sports Science, University of Suffolk, Ipswich, United Kingdom.
| | - Christopher M Hayre
- Diagnostic Radiography, School of Dentistry and Health Sciences, Charles Sturt University, New South Wales, Australia
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