1
|
Colombelli F, Kowalski TW, Recamonde-Mendoza M. A hybrid ensemble feature selection design for candidate biomarkers discovery from transcriptome profiles. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2022.109655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
2
|
Keshavarz-Rahaghi F, Pleasance E, Kolisnik T, Jones SJM. A p53 transcriptional signature in primary and metastatic cancers derived using machine learning. Front Genet 2022; 13:987238. [PMID: 36134028 PMCID: PMC9483853 DOI: 10.3389/fgene.2022.987238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
The tumor suppressor gene, TP53, has the highest rate of mutation among all genes in human cancer. This transcription factor plays an essential role in the regulation of many cellular processes. Mutations in TP53 result in loss of wild-type p53 function in a dominant negative manner. Although TP53 is a well-studied gene, the transcriptome modifications caused by the mutations in this gene have not yet been explored in a pan-cancer study using both primary and metastatic samples. In this work, we used a random forest model to stratify tumor samples based on TP53 mutational status and detected a p53 transcriptional signature. We hypothesize that the existence of this transcriptional signature is due to the loss of wild-type p53 function and is universal across primary and metastatic tumors as well as different tumor types. Additionally, we showed that the algorithm successfully detected this signature in samples with apparent silent mutations that affect correct mRNA splicing. Furthermore, we observed that most of the highly ranked genes contributing to the classification extracted from the random forest have known associations with p53 within the literature. We suggest that other genes found in this list including GPSM2, OR4N2, CTSL2, SPERT, and RPE65 protein coding genes have yet undiscovered linkages to p53 function. Our analysis of time on different therapies also revealed that this signature is more effective than the recorded TP53 status in detecting patients who can benefit from platinum therapies and taxanes. Our findings delineate a p53 transcriptional signature, expand the knowledge of p53 biology and further identify genes important in p53 related pathways.
Collapse
Affiliation(s)
- Faeze Keshavarz-Rahaghi
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Tyler Kolisnik
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
- *Correspondence: Steven J. M. Jones,
| |
Collapse
|
3
|
Baruah VJ, Neog Bora P, Sarmah B, Mahanta P, Sarmah A, Moretti S, Kumar R, Borkotokey S. Game-theoretic link relevance indexing on genome-wide expression dataset identifies putative salient genes with potential etiological and diapeutics role in colorectal cancer. Sci Rep 2022; 12:13409. [PMID: 35927308 DOI: 10.1038/s41598-022-17266-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 07/22/2022] [Indexed: 11/08/2022] Open
Abstract
Diapeutics gene markers in colorectal cancer (CRC) can help manage mortality caused by the disease. We applied a game-theoretic link relevance Index (LRI) scoring on the high-throughput whole-genome transcriptome dataset to identify salient genes in CRC and obtained 126 salient genes with LRI score greater than zero. The biomarkers database lacks preliminary information on the salient genes as biomarkers for all the available cancer cell types. The salient genes revealed eleven, one and six overrepresentations for major Biological Processes, Molecular Function, and Cellular components. However, no enrichment with respect to chromosome location was found for the salient genes. Significantly high enrichments were observed for several KEGG, Reactome and PPI terms. The survival analysis of top protein-coding salient genes exhibited superior prognostic characteristics for CRC. MIR143HG, AMOTL1, ACTG2 and other salient genes lack sufficient information regarding their etiological role in CRC. Further investigation in LRI methodology and salient genes to augment the existing knowledge base may create new milestones in CRC diapeutics.
Collapse
|
4
|
Belotti Y, Tolomeo S, Yu R, Lim WT, Lim CT. Prognostic Neurotransmitter Receptors Genes Are Associated with Immune Response, Inflammation and Cancer Hallmarks in Brain Tumors. Cancers (Basel) 2022; 14:2544. [PMID: 35626148 PMCID: PMC9139273 DOI: 10.3390/cancers14102544] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma multiforme (GBM) is one of the most aggressive forms of cancer. Neurotransmitters (NTs) have recently been linked with the uncontrolled proliferation of cancer cells, but the role of NTs in the progression of human gliomas is still largely unexplored. Here, we investigate the genes encoding for neurotransmitter receptors (NTRs) by analyzing public transcriptomic data from GBM and LGG (low-grade glioma) samples. Our results showed that 50 out of the 98 tested NTR genes were dysregulated in brain cancer tissue. Next, we identified and validated NTR-associated prognostic gene signatures for both LGG and GBM. A subset of 10 NTR genes (DRD1, HTR1E, HTR3B, GABRA1, GABRA4, GABRB2, GABRG2, GRIN1, GRM7, and ADRA1B) predicted a positive prognosis in LGG and a negative prognosis in GBM. These genes were progressively downregulated across glioma grades and exhibited a strong negative correlation with genes associated with immune response, inflammasomes, and established cancer hallmarks genes in lower grade gliomas, suggesting a putative role in inhibiting cancer progression. This study might have implications for the development of novel therapeutics and preventive strategies that target regulatory networks associated with the link between the autonomic nervous system, cancer cells, and the tumor microenvironment.
Collapse
Affiliation(s)
- Yuri Belotti
- Institute for Health Innovation and Technology, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
| | - Serenella Tolomeo
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, Singapore 138632, Singapore;
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore 117600, Singapore
| | - Rongjun Yu
- Department of Management, Hong Kong Baptist University, 34 Renfrew Road, Hong Kong 999077, China;
| | - Wan-Teck Lim
- Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore;
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673, Singapore
| | - Chwee Teck Lim
- Institute for Health Innovation and Technology, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
| |
Collapse
|
5
|
Belotti Y, Lim EH, Lim CT. The Role of the Extracellular Matrix and Tumor-Infiltrating Immune Cells in the Prognostication of High-Grade Serous Ovarian Cancer. Cancers (Basel) 2022; 14:404. [PMID: 35053566 PMCID: PMC8773831 DOI: 10.3390/cancers14020404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer is the eighth global leading cause of cancer-related death among women. The most common form is the high-grade serous ovarian carcinoma (HGSOC). No further improvements in the 5-year overall survival have been seen over the last 40 years since the adoption of platinum- and taxane-based chemotherapy. Hence, a better understanding of the mechanisms governing this aggressive phenotype would help identify better therapeutic strategies. Recent research linked onset, progression, and response to treatment with dysregulated components of the tumor microenvironment (TME) in many types of cancer. In this study, using bioinformatic approaches, we identified a 19-gene TME-related HGSOC prognostic genetic panel (19 prognostic genes (PLXNB2, HMCN2, NDNF, NTN1, TGFBI, CHAD, CLEC5A, PLXNA1, CST9, LOXL4, MMP17, PI3, PRSS1, SERPINA10, TLL1, CBLN2, IL26, NRG4, and WNT9A) by assessing the RNA sequencing data of 342 tumors available in the TCGA database. Using machine learning, we found that specific patterns of infiltrating immune cells characterized each risk group. Furthermore, we demonstrated the predictive potential of our risk score across different platforms and its improved prognostic performance compared with other gene panels.
Collapse
Affiliation(s)
- Yuri Belotti
- Institute for Health Innovation and Technology, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
| | - Elaine Hsuen Lim
- Division of Medical Oncology, National Cancer Center Singapore, 11 Hospital Drive, Singapore 169610, Singapore;
| | - Chwee Teck Lim
- Institute for Health Innovation and Technology, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
| |
Collapse
|
6
|
Belotti Y, Lim SB, Iyer NG, Lim WT, Lim CT. Prognostic Matrisomal Gene Panel and Its Association with Immune Cell Infiltration in Head and Neck Carcinomas. Cancers (Basel) 2021; 13:5761. [PMID: 34830910 DOI: 10.3390/cancers13225761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/13/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary Squamous cell carcinoma of the head and neck (SCCHN) is a heterogeneous group of tumors arising from squamous cells lining different anatomic sites. This type of malignancy has been mainly investigated by focusing primarily on tumor cells, but recent evidence highlighted the importance of the tumor microenvironment (TME) in cancer growth, progression and metastasis. Hence, we hypothesized that dysregulated matrisomal components could have a common association with patient survival, irrespective of the subsite of origin of the SCCHN. Using bioinformatic methods and public datasets, we successfully identified a gene panel with prognostic value in HPV-negative and non-metastatic node-negative tumors and demonstrated its association with immune cell infiltration. Abstract Squamous cell carcinoma of the head and neck (SCCHN) is common worldwide and related to several risk factors including smoking, alcohol consumption, poor dentition and human papillomavirus (HPV) infection. Different etiological factors may influence the tumor microenvironment and play a role in dictating response to therapeutics. Here, we sought to investigate whether an early-stage SCCHN-specific prognostic matrisome-derived gene signature could be identified for HPV-negative SCCHN patients (n = 168), by applying a bioinformatics pipeline to the publicly available SCCHN-TCGA dataset. We identified six matrisome-derived genes with high association with prognostic outcomes in SCCHN. A six-gene risk score, the SCCHN TMI (SCCHN-tumor matrisome index: composed of MASP1, EGFL6, SFRP5, SPP1, MMP8 and P4HA1) was constructed and used to stratify patients into risk groups. Using machine learning-based deconvolution methods, we found that the risk groups were characterized by a differing abundance of infiltrating immune cells. This work highlights the key role of immune infiltration cells in the overall survival of patients affected by HPV-negative SCCHN. The identified SCCHN TMI represents a genomic tool that could potentially aid patient stratification and selection for therapy in these patients.
Collapse
|
7
|
Kim J, Kim SY, Ma SX, Kim SM, Shin SJ, Lee YS, Chang H, Chang HS, Park CS, Lim SB. PPARγ Targets-Derived Diagnostic and Prognostic Index for Papillary Thyroid Cancer. Cancers (Basel) 2021; 13:cancers13205110. [PMID: 34680260 PMCID: PMC8533916 DOI: 10.3390/cancers13205110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Through targeted next-generation sequencing of thyroid cancer-related genes in monozygotic twins with papillary thyroid cancer (PTC), we identified common variants of the gene encoding peroxisome proliferator activated receptor gamma (PPARG). Notably, the expression levels of PPARγ target genes were frequently deregulated in PTC compared to benign tissues and were closely associated with disease-specific survival (DSS) outcomes in a TCGA-PTC cohort. Machine learning-powered personalized scoring index comprising 10 PPARγ targets, termed as PPARGi, achieved a near-perfect accuracy in distinguishing cancers from benign tissues, and further identified a small subpopulation of patients at high-risk across different profiling platforms. Abstract In most cases, papillary thyroid cancer (PTC) is highly curable and associated with an excellent prognosis. Yet, there are several clinicopathological features that lead to a poor prognosis, underscoring the need for a better genomic strategy to refine prognostication and patient management. We hypothesized that PPARγ targets could be potential markers for better diagnosis and prognosis due to the variants found in PPARG in three pairs of monozygotic twins with PTC. Here, we developed a 10-gene personalized prognostic index, designated PPARGi, based on gene expression of 10 PPARγ targets. Through scRNA-seq data analysis of PTC tissues derived from patients, we found that PPARGi genes were predominantly expressed in macrophages and epithelial cells. Machine learning algorithms showed a near-perfect performance of PPARGi in deciding the presence of the disease and in selecting a small subset of patients with poor disease-specific survival in TCGA-THCA and newly developed merged microarray data (MMD) consisting exclusively of thyroid cancers and normal tissues.
Collapse
Affiliation(s)
- Jaehyung Kim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon 16499, Korea;
| | - Soo Young Kim
- Department of Surgery, Ajou University School of Medicine, Suwon 16499, Korea;
| | - Shi-Xun Ma
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Seok-Mo Kim
- Thyroid Cancer Center, Department of Surgery, Institute of Refractory Thyroid Cancer, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.S.L.); (H.C.); (H.-S.C.)
- Correspondence: (S.-M.K.); (S.B.L.); Tel.: +82-2-2019-3370 (S.-M.K.); +82-31-219-5056 (S.B.L.)
| | - Su-Jin Shin
- Department of Pathology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea;
| | - Yong Sang Lee
- Thyroid Cancer Center, Department of Surgery, Institute of Refractory Thyroid Cancer, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.S.L.); (H.C.); (H.-S.C.)
| | - Hojin Chang
- Thyroid Cancer Center, Department of Surgery, Institute of Refractory Thyroid Cancer, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.S.L.); (H.C.); (H.-S.C.)
| | - Hang-Seok Chang
- Thyroid Cancer Center, Department of Surgery, Institute of Refractory Thyroid Cancer, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (Y.S.L.); (H.C.); (H.-S.C.)
| | - Cheong Soo Park
- CHA Ilsan Medical Center, Department of Surgery, Goyang-si 10414, Korea;
| | - Su Bin Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon 16499, Korea;
- Correspondence: (S.-M.K.); (S.B.L.); Tel.: +82-2-2019-3370 (S.-M.K.); +82-31-219-5056 (S.B.L.)
| |
Collapse
|
8
|
Millagaha Gedara NI, Xu X, DeLong R, Aryal S, Jaberi-Douraki M. Global Trends in Cancer Nanotechnology: A Qualitative Scientific Mapping Using Content-Based and Bibliometric Features for Machine Learning Text Classification. Cancers (Basel) 2021; 13. [PMID: 34503227 DOI: 10.3390/cancers13174417] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 01/05/2023] Open
Abstract
This study presents a new way to investigate comprehensive trends in cancer nanotechnology research in different countries, institutions, and journals providing critical insights to prevention, diagnosis, and therapy. This paper applied the qualitative method of bibliometric analysis on cancer nanotechnology using the PubMed database during the years 2000-2021. Inspired by hybrid medical models and content-based and bibliometric features for machine learning models, our results show cancer nanotechnology studies have expanded exponentially since 2010. The highest production of articles in cancer nanotechnology is mainly from US institutions, with several countries, notably the USA, China, the UK, India, and Iran as concentrated focal points as centers of cancer nanotechnology research, especially in the last five years. The analysis shows the greatest overlap between nanotechnology and DNA, RNA, iron oxide or mesoporous silica, breast cancer, and cancer diagnosis and cancer treatment. Moreover, more than 50% of the information related to the keywords, authors, institutions, journals, and countries are considerably investigated in the form of publications from the top 100 journals. This study has the potential to provide past and current lines of research that can unmask comprehensive trends in cancer nanotechnology, key research topics, or the most productive countries and authors in the field.
Collapse
|
9
|
Rohr M, Beardsley J, Nakkina SP, Zhu X, Aljabban J, Hadley D, Altomare D. A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression. Sci Data 2021; 8:214. [PMID: 34381057 PMCID: PMC8358057 DOI: 10.1038/s41597-021-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022] Open
Abstract
Transcriptional profiling of pre- and post-malignant colorectal cancer (CRC) lesions enable temporal monitoring of molecular events underlying neoplastic progression. However, the most widely used transcriptomic dataset for CRC, TCGA-COAD, is devoid of adenoma samples, which increases reliance on an assortment of disparate microarray studies and hinders consensus building. To address this, we developed a microarray meta-dataset comprising 231 healthy, 132 adenoma, and 342 CRC tissue samples from twelve independent studies. Utilizing a stringent analytic framework, select datasets were downloaded from the Gene Expression Omnibus, normalized by frozen robust multiarray averaging and subsequently merged. Batch effects were then identified and removed by empirical Bayes estimation (ComBat). Finally, the meta-dataset was filtered for low variant probes, enabling downstream differential expression as well as quantitative and functional validation through cross-platform correlation and enrichment analyses, respectively. Overall, our meta-dataset provides a robust tool for investigating colorectal adenoma formation and malignant transformation at the transcriptional level with a pipeline that is modular and readily adaptable for similar analyses in other cancer types.
Collapse
Affiliation(s)
- Michael Rohr
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Jordan Beardsley
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Sai Preethi Nakkina
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Xiang Zhu
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Jihad Aljabban
- Department of Medicine, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Dexter Hadley
- Department of Clinical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Deborah Altomare
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
| |
Collapse
|
10
|
van Tilborg D, Saccenti E. Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data. Cancers (Basel) 2021; 13:393. [PMID: 33494351 DOI: 10.3390/cancers13030393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Changes in metabolism are a well-known characteristic of cancer cells. Different cancer types are unique in their genetic aspects, but also in their metabolism, which is in turn, governed by genetics. The aim of our study was to find these differences in metabolic behavior across different cancer types and uncovering intersections between gene expression and metabolic deregulations. We scoured the public domain for metabolomics and transcriptomics data from clinical profiling studies to perform a comprehensive comparison study. By combining evidence from both the genetic and the metabolic aspects, we described the most prominently aberrated pathways across eight different cancer types together with their metabolomic and transcriptomics similarities. Abstract One of the major hallmarks of cancer is the derailment of a cell’s metabolism. The multifaceted nature of cancer and different cancer types is transduced by both its transcriptomic and metabolomic landscapes. In this study, we re-purposed the publicly available transcriptomic and metabolomics data of eight cancer types (breast, lung, gastric, renal, liver, colorectal, prostate, and multiple myeloma) to find and investigate differences and commonalities on a pathway level among different cancer types. Topological analysis of inferred graphical Gaussian association networks showed that cancer was strongly defined in genetic networks, but not in metabolic networks. Using different statistical approaches to find significant differences between cancer and control cases, we highlighted the difficulties of high-level data-merging and in using statistical association networks. Cancer transcriptomics and metabolomics and landscapes were characterized by changed macro-molecule production, however, only major metabolic deregulations with highly impacted pathways were found in liver cancer. Cell cycle was enriched in breast, liver, and colorectal cancer, while breast and lung cancer were distinguished by highly enriched oncogene signaling pathways. A strong inflammatory response was observed in lung cancer and, to some extent, renal cancer. This study highlights the necessity of combining different omics levels to obtain a better description of cancer characteristics.
Collapse
|
11
|
Venkataramana L, Jacob SG, Saraswathi S, Venkata Vara Prasad D. Identification of common and dissimilar biomarkers for different cancer types from gene expressions of RNA-sequencing data. Gene Reports 2020; 19:100654. [DOI: 10.1016/j.genrep.2020.100654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
12
|
Lim SB, Lim CT, Lim WT. Single-Cell Analysis of Circulating Tumor Cells: Why Heterogeneity Matters. Cancers (Basel) 2019; 11:cancers11101595. [PMID: 31635038 PMCID: PMC6826423 DOI: 10.3390/cancers11101595] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 12/31/2022] Open
Abstract
Unlike bulk-cell analysis, single-cell approaches have the advantage of assessing cellular heterogeneity that governs key aspects of tumor biology. Yet, their applications to circulating tumor cells (CTCs) are relatively limited, due mainly to the technical challenges resulting from extreme rarity of CTCs. Nevertheless, recent advances in microfluidics and immunoaffinity enrichment technologies along with sequencing platforms have fueled studies aiming to enrich, isolate, and sequence whole genomes of CTCs with high fidelity across various malignancies. Here, we review recent single-cell CTC (scCTC) sequencing efforts, and the integrated workflows, that have successfully characterized patient-derived CTCs. We examine how these studies uncover DNA alterations occurring at multiple molecular levels ranging from point mutations to chromosomal rearrangements from a single CTC, and discuss their cellular heterogeneity and clinical consequences. Finally, we highlight emerging strategies to address key challenges currently limiting the translation of these findings to clinical practice.
Collapse
Affiliation(s)
- Su Bin Lim
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore 117456, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.
| | - Chwee Teck Lim
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore 117456, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore.
| | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore.
- Office of Academic and Clinical Development, Duke-NUS Medical School, Singapore 169857, Singapore.
- IMCB NCC MPI Singapore Oncogenome Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore.
| |
Collapse
|