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Crippa V, Malighetti F, Villa M, Graudenzi A, Piazza R, Mologni L, Ramazzotti D. Characterization of cancer subtypes associated with clinical outcomes by multi-omics integrative clustering. Comput Biol Med 2023; 162:107064. [PMID: 37267828 DOI: 10.1016/j.compbiomed.2023.107064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/03/2023] [Accepted: 05/27/2023] [Indexed: 06/04/2023]
Abstract
Cancer patients show heterogeneous phenotypes and very different outcomes and responses even to common treatments, such as standard chemotherapy. This state-of-affairs has motivated the need for the comprehensive characterization of cancer phenotypes and fueled the generation of large omics datasets, comprising multiple omics data reported for the same patients, which might now allow us to start deciphering cancer heterogeneity and implement personalized therapeutic strategies. In this work, we performed the analysis of four cancer types obtained from the latest efforts by The Cancer Genome Atlas, for which seven distinct omics data were available for each patient, in addition to curated clinical outcomes. We performed a uniform pipeline for raw data preprocessing and adopted the Cancer Integration via MultIkernel LeaRning (CIMLR) integrative clustering method to extract cancer subtypes. We then systematically review the discovered clusters for the considered cancer types, highlighting novel associations between the different omics and prognosis.
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Affiliation(s)
- Valentina Crippa
- Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy.
| | - Federica Malighetti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy.
| | - Matteo Villa
- Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy.
| | - Alex Graudenzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy.
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy.
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Qiao Y, Jiang X, Li Y, Wang K, Chen R, Liu J, Du Y, Sun L, Li J. Identification of a hypoxia-related gene prognostic signature in colorectal cancer based on bulk and single-cell RNA-seq. Sci Rep 2023; 13:2503. [PMID: 36781976 PMCID: PMC9925779 DOI: 10.1038/s41598-023-29718-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Colorectal cancer (CRC) is the most common and fatal tumor in the gastrointestinal system. Its incidence and mortality rate have increased in recent years. Hypoxia, a persistent physiological tumor feature, plays a vital role in CRC tumorigenesis, metastasis, and tumor microenvironment (TME). Therefore, we constructed a hypoxia-related gene (HRG) nomogram to predict overall survival (OS) and explored the role of HRGs in the CRC TME. The Cancer Genome Atlas (TCGA) dataset was used as the training set, and two Gene Expression Omnibus datasets (GSE39582 and GSE103479) were used as the testing sets. HRGs were identified using the Gene Set Enrichment Analysis (GSEA) database. An HRG prognostic model was constructed in the training set using the least absolute shrinkage and selection operator regression algorithm and validated in the testing sets. Then, we analyzed tumor-infiltrating cells (TICs) using the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm. Furthermore, single-cell next-generation RNA sequencing (RNA-seq) was used to investigate HRG expression in different TICs in the GSE139555 dataset. Finally, reverse transcription polymerase chain reactions (RT-PCR) were used to validate HRG mRNA expression in ten pairs of CRC normal and cancer tissue samples. A six HRG prognostic signature was constructed, with a superior OS prediction ability in CRC patients (area under the receiver operating characteristic curve (AUC) at one year: 0.693, AUC at three years: 0.712, and AUC at five years: 0.780). GSEA enrichment analysis identified six pathways enriched in the high-risk group. The TIC analysis indicated that the high-risk group had lower T-cell expression and higher neutrophil expression than the low-risk group. Furthermore, immune-related genes had an inseparable relationship with the HRG prognostic signature. Based on single-cell RNA-seq data, we found elevated hexokinase 1 (HK1) and glucose-6-phosphate isomerase (GPI) gene expression in natural killer (NK) and CD8+ T cells. RT-PCR in ten CRC normal-tumor tissue pairs showed that expression of the signature's six HRGs varied differently in cancerous and paracancerous tissues. The constructed HRG signature successfully predicted the OS of whole-stage CRC patients. In addition, we showed that the signature's six HRGs were closely associated with the TME in CRC, where hypoxia inhibits the antitumor function of T cells.
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Affiliation(s)
- Yihuan Qiao
- Department of Digestive Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, China
| | - Xunliang Jiang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, 710032, Shaanxi, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Yaoting Li
- Xi'an Gaoxin No. 1 High School, Xi'an, 710119, Shaanxi, China
| | - Ke Wang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, 710032, Shaanxi, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Rujie Chen
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, 710032, Shaanxi, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Jun Liu
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Yongtao Du
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, 710032, Shaanxi, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Li Sun
- Department of Digestive Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, China.
| | - Jipeng Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Air Force Medical University, Xi'an, 710032, Shaanxi, China.
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Pinson A, Xing L, Namba T, Kalebic N, Peters J, Oegema CE, Traikov S, Reppe K, Riesenberg S, Maricic T, Derihaci R, Wimberger P, Pääbo S, Huttner WB. Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals. Science 2022; 377:eabl6422. [PMID: 36074851 DOI: 10.1126/science.abl6422] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neanderthal brains were similar in size to those of modern humans. We sought to investigate potential differences in neurogenesis during neocortex development. Modern human transketolase-like 1 (TKTL1) differs from Neanderthal TKTL1 by a lysine-to-arginine amino acid substitution. Using overexpression in developing mouse and ferret neocortex, knockout in fetal human neocortical tissue, and genome-edited cerebral organoids, we found that the modern human variant, hTKTL1, but not the Neanderthal variant, increases the abundance of basal radial glia (bRG) but not that of intermediate progenitors (bIPs). bRG generate more neocortical neurons than bIPs. The hTKTL1 effect requires the pentose phosphate pathway and fatty acid synthesis. Inhibition of these metabolic pathways reduces bRG abundance in fetal human neocortical tissue. Our data suggest that neocortical neurogenesis in modern humans differs from that in Neanderthals.
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Affiliation(s)
- Anneline Pinson
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Lei Xing
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Takashi Namba
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Nereo Kalebic
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jula Peters
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Sofia Traikov
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Katrin Reppe
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Stephan Riesenberg
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Razvan Derihaci
- Technische Universität Dresden, Universitätsklinikum Carl Gustav Carus, Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, 01307 Dresden, Germany
| | - Pauline Wimberger
- Technische Universität Dresden, Universitätsklinikum Carl Gustav Carus, Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, 01307 Dresden, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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Hao S, Meng Q, Sun H, Li Y, Li Y, Gu L, Liu B, Zhang Y, Zhou H, Xu Z, Wang Y. The role of transketolase in human cancer progression and therapy. Biomed Pharmacother 2022; 154:113607. [PMID: 36030587 DOI: 10.1016/j.biopha.2022.113607] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/02/2022] Open
Abstract
Transketolase (TKT) is an enzyme that is ubiquitously expressed in all living organisms and has been identified as an important regulator of cancer. Recent studies have shown that the TKT family includes the TKT gene and two TKT-like (TKTL) genes; TKTL1 and TKTL2. TKT and TKTL1 have been reported to be involved in the regulation of multiple cancer-related events, such as cancer cell proliferation, metastasis, invasion, epithelial-mesenchymal transition, chemoradiotherapy resistance, and patient survival and prognosis. Therefore, TKT may be an ideal target for cancer treatment. More importantly, the levels of TKTL1 were detected using EDIM technology for the early detection of some malignancies, and TKTL1 was more sensitive and specific than traditional tumor markers. Detecting TKTL1 levels before and after surgery could be used to evaluate the surgery's effect. While targeted TKT suppresses cancer in multiple ways, in some cases, it has detrimental effects on the organism. In this review, we discuss the role of TKT in different tumors and the detailed mechanisms while evaluating its value and limitations in clinical applications. Therefore, this review provides a basis for the clinical application of targeted therapy for TKT in the future, and a strategy for subsequent cancer-related research.
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Affiliation(s)
- Shiming Hao
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Qingfei Meng
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Huihui Sun
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Yunkuo Li
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China
| | - Yao Li
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Liting Gu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Bin Liu
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China
| | - Yanghe Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Honglan Zhou
- Department of Urology, The First Hospital of Jilin University, Changchun 130021, China.
| | - Zhixiang Xu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Yishu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
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TKTL1 Knockdown Impairs Hypoxia-Induced Glucose-6-phosphate Dehydrogenase and Glyceraldehyde-3-phosphate Dehydrogenase Overexpression. Int J Mol Sci 2022; 23:ijms23073574. [PMID: 35408935 PMCID: PMC8999113 DOI: 10.3390/ijms23073574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
Increased expression of transketolase (TKT) and its isoform transketolase-like-1 (TKTL1) has been related to the malignant leukemia phenotype through promoting an increase in the non-oxidative branch of the pentose phosphate pathway (PPP). Recently, it has also been described that TKTL1 can have a role in survival under hypoxic conditions and in the acquisition of radio resistance. However, TKTL1’s role in triggering metabolic reprogramming under hypoxia in leukemia cells has never been characterized. Using THP-1 AML cells, and by combining metabolomics and transcriptomics techniques, we characterized the impact of TKTL1 knockdown on the metabolic reprogramming triggered by hypoxia. Results demonstrated that TKTL1 knockdown results in a decrease in TKT, glucose-6-phosphate dehydrogenase (G6PD) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activities and impairs the hypoxia-induced overexpression of G6PD and GAPDH, all having significant impacts on the redox capacity of NADPH- and NADH-related cells. Moreover, TKTL1 knockdown impedes hypoxia-induced transcription of genes encoding key enzymes and transporters involved in glucose, PPP and amino acid metabolism, rendering cells unable to switch to enhanced glycolysis under hypoxia. Altogether, our results show that TKTL1 plays a key role in the metabolic adaptation to hypoxia in THP-1 AML cells through modulation of G6PD and GAPDH activities, both regulating glucose/glutamine consumption and the transcriptomic overexpression of key players of PPP, glucose and amino acids metabolism.
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Meskers CJW, Franczak M, Smolenski RT, Giovannetti E, Peters GJ. Are we still on the right path(way)?: the altered expression of the pentose phosphate pathway in solid tumors and the potential of its inhibition in combination therapy. Expert Opin Drug Metab Toxicol 2022; 18:61-83. [PMID: 35238253 DOI: 10.1080/17425255.2022.2049234] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The pentose phosphate pathway (PPP) branches from glycolysis and is crucial for cell growth, since it provides necessary compounds for anabolic reactions, nucleotide synthesis, and detoxification of reactive-oxygen-species (ROS). Overexpression of PPP enzymes has been reported in multiple cancer types and linked to therapy resistance, making their inhibition interesting targets for anti-cancer therapies. AREAS COVERED This review summarizes the extent of PPP upregulation across different cancer types, and the non-metabolic functions that PPP-enzymes might contribute to cancer initiation and maintenance. The effects of PPP-inhibition and their combinations with chemotherapeutics are summarized. We searched the databases provided by the University of Amsterdam to characterize the altered expression of the PPP across different cancer types, and to identify the effects of PPP-inhibition. EXPERT OPINION It can be concluded that there are synergistic and additive effects of PPP-inhibition and various classes of chemotherapeutics. These effects may be attributed to the increased susceptibility to ROS. However, the toxicity, low efficacy, and off-target effects of PPP-inhibitors make application in clinical practice challenging. Novel inhibitors are currently being developed, which could make PPP-inhibition a potential therapeutic strategy in the future, especially in combination with conventional chemotherapeutics and the inhibition of other metabolic pathways.
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Affiliation(s)
- Caroline J W Meskers
- Amsterdam University College, Amsterdam, The Netherlands.,Laboratory Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam location VUMC, Cancer Center Amsterdam, The Netherlands
| | - Marika Franczak
- Department of Biochemistry, Medical University of Gdansk, Poland
| | | | - Elisa Giovannetti
- Laboratory Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam location VUMC, Cancer Center Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start Up Unit, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Godefridus J Peters
- Laboratory Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam location VUMC, Cancer Center Amsterdam, The Netherlands.,Department of Biochemistry, Medical University of Gdansk, Poland
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Peng Y, Yang H, Li S. The role of glycometabolic plasticity in cancer. Pathol Res Pract 2021; 226:153595. [PMID: 34481210 DOI: 10.1016/j.prp.2021.153595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 12/28/2022]
Abstract
Dysregulated glycometabolism represented by the Warburg effect is well recognized as a hallmark of cancer that can be driven by oncogenes (e.g., c-Myc, K-ras, and BRAF) and contribute to cellular malignant transformation. The Warburg effect reveals the different glycometabolic patterns of cancer cells, but this unique glycometabolic pattern has the characteristic of plasticity rather than changeless which can vary with different internal or external stimuli during evolution. Glycometabolic plasticity enables cancer cells to modulate glycometabolism to support progression, metastasis, treatment resistance and recurrence. In this review, we report the characteristics of glycometabolic plasticity during different stages of cancer evolution, providing insight into the molecular mechanisms of glycometabolic plasticity in cancer. In addition, we discussed the challenges and future research directions of glycometabolism research in cancer.
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Affiliation(s)
- Yuyang Peng
- Multidisciplinary Center for Pituitary Adenomas of Chongqing, Department of Neurosurgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Hui Yang
- Multidisciplinary Center for Pituitary Adenomas of Chongqing, Department of Neurosurgery, Xinqiao Hospital, Army Medical University, Chongqing, China.
| | - Song Li
- Multidisciplinary Center for Pituitary Adenomas of Chongqing, Department of Neurosurgery, Xinqiao Hospital, Army Medical University, Chongqing, China.
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