1
|
Zou S, Yang C, Zhang J, Zhong D, Meng M, Zhang L, Chen H, Fang L. Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer. J Transl Med 2024; 22:175. [PMID: 38369542 PMCID: PMC10874565 DOI: 10.1186/s12967-024-04984-4] [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: 11/17/2023] [Accepted: 02/12/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the leading cancer worldwide. Microbial agents have been considered to contribute to the pathogenesis of different disease. But the underlying relevance between CRC and microbiota remain unclear. METHODS We dissected the fecal microbiome structure and genomic and transcriptomic profiles of matched tumor and normal mucosa tissues from 41 CRC patients. Of which, the relationship between CRC-associated bacterial taxa and their significantly correlated somatic mutated gene was investigated by exome sequencing technology. Differentially expressed functional genes in CRC were clustered according to their correlation with differentially abundant species, following by annotation with DAVID. The composition of immune and stromal cell types was identified by XCELL. RESULTS We identified a set of 22 microbial gut species associated with CRC and estimate the relative abundance of KEGG ontology categories. Next, the interactions between CRC-related gut microbes and clinical phenotypes were evaluated. 4 significantly mutated gene: TP53, APC, KRAS, SMAD4 were pointed out and the associations with cancer related microbes were identified. Among them, Fusobacterium nucleatum positively corelated with different host metabolic pathways. Finally, we revealed that Fusobacterium nucleatum modified the tumor immune environment by TNFSF9 gene expression. CONCLUSION Collectively, our multi-omics data could help identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC.
Collapse
Affiliation(s)
- Shaomin Zou
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Chao Yang
- Department of Computer Science, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Jieping Zhang
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Dan Zhong
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Manqi Meng
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Lu Zhang
- Department of Computer Science, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Honglei Chen
- Gastrointestinal Endoscopy Center, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China.
| | - Lekun Fang
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China.
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, 510655, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
| |
Collapse
|
2
|
Shuvalov O, Kirdeeva Y, Daks A, Fedorova O, Parfenyev S, Simon HU, Barlev NA. Phytochemicals Target Multiple Metabolic Pathways in Cancer. Antioxidants (Basel) 2023; 12:2012. [PMID: 38001865 PMCID: PMC10669507 DOI: 10.3390/antiox12112012] [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: 09/12/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer metabolic reprogramming is a complex process that provides malignant cells with selective advantages to grow and propagate in the hostile environment created by the immune surveillance of the human organism. This process underpins cancer proliferation, invasion, antioxidant defense, and resistance to anticancer immunity and therapeutics. Perhaps not surprisingly, metabolic rewiring is considered to be one of the "Hallmarks of cancer". Notably, this process often comprises various complementary and overlapping pathways. Today, it is well known that highly selective inhibition of only one of the pathways in a tumor cell often leads to a limited response and, subsequently, to the emergence of resistance. Therefore, to increase the overall effectiveness of antitumor drugs, it is advisable to use multitarget agents that can simultaneously suppress several key processes in the tumor cell. This review is focused on a group of plant-derived natural compounds that simultaneously target different pathways of cancer-associated metabolism, including aerobic glycolysis, respiration, glutaminolysis, one-carbon metabolism, de novo lipogenesis, and β-oxidation of fatty acids. We discuss only those compounds that display inhibitory activity against several metabolic pathways as well as a number of important signaling pathways in cancer. Information about their pharmacokinetics in animals and humans is also presented. Taken together, a number of known plant-derived compounds may target multiple metabolic and signaling pathways in various malignancies, something that bears great potential for the further improvement of antineoplastic therapy.
Collapse
Affiliation(s)
- Oleg Shuvalov
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia; (Y.K.); (A.D.); (O.F.)
| | - Yulia Kirdeeva
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia; (Y.K.); (A.D.); (O.F.)
| | - Alexandra Daks
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia; (Y.K.); (A.D.); (O.F.)
| | - Olga Fedorova
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia; (Y.K.); (A.D.); (O.F.)
| | - Sergey Parfenyev
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia; (Y.K.); (A.D.); (O.F.)
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland;
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Nickolai A. Barlev
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia; (Y.K.); (A.D.); (O.F.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana 20000, Kazakhstan
| |
Collapse
|
3
|
Tsuji Y, Hara T, Meng S, Sato H, Arao Y, Ofusa K, Ishii H. Role of RNA methylation in the regulation of pancreatic cancer stem cells (Review). Oncol Lett 2023; 26:336. [PMID: 37427348 PMCID: PMC10326658 DOI: 10.3892/ol.2023.13922] [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: 02/02/2023] [Accepted: 04/21/2023] [Indexed: 07/11/2023] Open
Abstract
Pancreatic cancer stem cells (CSCs) play a key role in the initiation and progression of pancreatic adenocarcinoma (PDAC). CSCs are responsible for resistance to chemotherapy and radiation, and for cancer metastasis. Recent studies have indicated that RNA methylation, a type of RNA modification, predominantly occurring as m6A methylation, plays an important role in controlling the stemness of cancer cells, therapeutic resistance against chemotherapy and radiation therapy, and their overall relevance to a patient's prognosis. CSCs regulate various behaviors of cancer through cell-cell communication by secreting factors, through their receptors, and through signal transduction. Recent studies have shown that RNA methylation is involved in the biology of the heterogeneity of PDAC. The present review provides an update on the current understanding of RNA modification-based therapeutic targets against deleterious PDAC. Several key pathways and agents that can specifically target CSCs have been identified, thus providing novel insights into the early diagnosis and efficient treatment of PDAC.
Collapse
Affiliation(s)
- Yoshiko Tsuji
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Tomoaki Hara
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Sikun Meng
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Hiromichi Sato
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yasuko Arao
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Ken Ofusa
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Prophoenix Division, Food and Life-Science Laboratory, IDEA Consultants, Inc., Osaka, Osaka 559-8519, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| |
Collapse
|
4
|
Takeda Y, Chijimatsu R, Ofusa K, Kobayashi S, Doki Y, Eguchi H, Ishii H. Cancer metabolism challenges genomic instability and clonal evolution as therapeutic targets. Cancer Sci 2022; 113:1097-1104. [PMID: 35112433 PMCID: PMC8990295 DOI: 10.1111/cas.15279] [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: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 11/29/2022] Open
Abstract
Although cancer precision medicine has improved diagnosis and therapy, refractory cancers such as pancreatic cancer remain to be challenging targets. Clinical sequencing has identified the significant alterations in driver genes and traced their clonal evolutions. Recent studies indicated that the tumor microenvironment elicits alterations in cancer metabolism, although its involvement in the cause and development of genomic alterations has not been established. Genomic abnormalities can contribute to the survival of selected subpopulations, recently recognized as clonal evolution, and dysfunction can lead to DNA mutations. Here, we present the most recent studies on the mechanisms of cancer metabolism involved in the maintenance of genomic stability to update current understanding of such processes. Sirtuins, which are NAD+-dependent protein deacetylases, appear to be involved in the control of genomic stability. Alterations of deleterious subpopulations would be exposed to selective pressure for cell survival. Recent studies indicated that a new type of cell death, ferroptosis, determines the survival of clones and exert cancer-restricting or -promoting effects to surrounding cells in the tumor microenvironment. Suppressing genomic instability and eliminating deleterious clones by cell death will contribute to the improvement of cancer medicine. Furthermore, the elucidation of the mechanisms involved is seen as a bridgehead to the pharmacologic suppression of such refractory cancers as pancreatic cancer.
Collapse
Affiliation(s)
- Yu Takeda
- Department of Gastroenterological SurgeryGraduate School of MedicineOsaka UniversitySuitaJapan
| | - Ryota Chijimatsu
- Department of Medical Data ScienceGraduate School of MedicineCenter of Medical Innovation and Translational ResearchOsaka UniversitySuitaJapan
| | - Ken Ofusa
- Department of Medical Data ScienceGraduate School of MedicineCenter of Medical Innovation and Translational ResearchOsaka UniversitySuitaJapan
- Prophoenix DivisionFood and Life‐Science LaboratoryIdea Consultants, IncOsaka‐cityJapan
| | - Shogo Kobayashi
- Department of Gastroenterological SurgeryGraduate School of MedicineOsaka UniversitySuitaJapan
| | - Yuichiro Doki
- Department of Gastroenterological SurgeryGraduate School of MedicineOsaka UniversitySuitaJapan
| | - Hidetoshi Eguchi
- Department of Gastroenterological SurgeryGraduate School of MedicineOsaka UniversitySuitaJapan
| | - Hideshi Ishii
- Department of Medical Data ScienceGraduate School of MedicineCenter of Medical Innovation and Translational ResearchOsaka UniversitySuitaJapan
| |
Collapse
|
5
|
Tatekawa S, Ofusa K, Chijimatsu R, Vecchione A, Tamari K, Ogawa K, Ishii H. Methylosystem for Cancer Sieging Strategy. Cancers (Basel) 2021; 13:5088. [PMID: 34680237 PMCID: PMC8534198 DOI: 10.3390/cancers13205088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 12/14/2022] Open
Abstract
As cancer is a genetic disease, methylation defines a biologically malignant phenotype of cancer in the association of one-carbon metabolism-dependent S-adenosylmethionine (SAM) as a methyl donor in each cell. Methylated substances are involved in intracellular metabolism, but via intercellular communication, some of these can also be secreted to affect other substances. Although metabolic analysis at the single-cell level remains challenging, studying the "methylosystem" (i.e., the intercellular and intracellular communications of upstream regulatory factors and/or downstream effectors that affect the epigenetic mechanism involving the transfer of a methyl group from SAM onto the specific positions of nucleotides or other metabolites in the tumor microenvironment) and tracking these metabolic products are important research tasks for understanding spatial heterogeneity. Here, we discuss and highlight the involvement of RNA and nicotinamide, recently emerged targets, in SAM-producing one-carbon metabolism in cancer cells, cancer-associated fibroblasts, and immune cells. Their significance and implications will contribute to the discovery of efficient methods for the diagnosis of and therapeutic approaches to human cancer.
Collapse
Affiliation(s)
- Shotaro Tatekawa
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (S.T.); (K.T.)
| | - Ken Ofusa
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (K.O.); (R.C.)
- Food and Life-Science Laboratory, Prophoenix Division, Idea Consultants, Inc., Osaka 559-8519, Japan
| | - Ryota Chijimatsu
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (K.O.); (R.C.)
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Rome “Sapienza”, Santo Andrea Hospital, Via di Grottarossa, 1035-00189 Rome, Italy;
| | - Keisuke Tamari
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (S.T.); (K.T.)
| | - Kazuhiko Ogawa
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (S.T.); (K.T.)
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (K.O.); (R.C.)
| |
Collapse
|