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Wang FA, Zhuang Z, Gao F, He R, Zhang S, Wang L, Liu J, Li Y. TMO-Net: an explainable pretrained multi-omics model for multi-task learning in oncology. Genome Biol 2024; 25:149. [PMID: 38845006 PMCID: PMC11157742 DOI: 10.1186/s13059-024-03293-9] [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: 12/14/2023] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Cancer is a complex disease composing systemic alterations in multiple scales. In this study, we develop the Tumor Multi-Omics pre-trained Network (TMO-Net) that integrates multi-omics pan-cancer datasets for model pre-training, facilitating cross-omics interactions and enabling joint representation learning and incomplete omics inference. This model enhances multi-omics sample representation and empowers various downstream oncology tasks with incomplete multi-omics datasets. By employing interpretable learning, we characterize the contributions of distinct omics features to clinical outcomes. The TMO-Net model serves as a versatile framework for cross-modal multi-omics learning in oncology, paving the way for tumor omics-specific foundation models.
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Affiliation(s)
- Feng-Ao Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Zhenfeng Zhuang
- Department of Computer Science at the School of Informatics, Xiamen University, Xiamen, 361005, China
| | - Feng Gao
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200433, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Ruikun He
- BYHEALTH Institute of Nutrition & Health, Guangzhou, 510000, China
| | - Shaoting Zhang
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200433, China
| | - Liansheng Wang
- Department of Computer Science at the School of Informatics, Xiamen University, Xiamen, 361005, China.
| | - Junwei Liu
- Guangzhou National Laboratory, Guangzhou, 510005, China.
| | - Yixue Li
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
- Guangzhou National Laboratory, Guangzhou, 510005, China.
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200030, China.
- GZMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, 511436, China.
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200433, China.
- Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200032, China.
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Ullah I, Khan R, Suhail SM, Ahmad I, Khan FA, Shoaib M, Farid K, Ayari-Akkari A, Morfeine EA. Association of polymorphism in the promotor area of the caprine BMPR1B gene with litter size and body measurement traits in Damani goats. Trop Anim Health Prod 2024; 56:137. [PMID: 38649642 DOI: 10.1007/s11250-024-03991-3] [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: 12/15/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
This study aimed to explore polymorphisms in the promoter region of the caprine BMPR1B (Bone morphogenetic protein receptor 1 beta) gene and its association with body measurement and litter size traits in Damani does. A total of 53 blood samples were collected to analyze the association between the BMPR1B gene polymorphism and 11 phenotypic traits in Damani female goats. The results revealed that three novel SNPs were identified in the promoter region of the caprine BMPR1B gene, including g.67 A > C (SNP1), g.170 G > A(SNP2), and g.501A > T (SNP3), among which the SNP1 and SNP2 were significantly (p < 0.05) associated with litter size and body measurement traits in Damani goats. In SNP1 the AC genotype could be used as a marker for litter size, and the CC genotype for body weight in Damani goats. In SNP2, the genotype GG was significantly (p < 0.05) associated with ear and head length. Therefore, we can conclude from the present study, that genetic variants AC and CC of the caprine BMPR1B gene could be used as genetic markers for economic traits through marker-assisted selection for the breed improvement program of the Damani goat.
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Affiliation(s)
- Inayat Ullah
- Department of Livestock Management, Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan
| | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan.
| | - Syed Muhammad Suhail
- Department of Livestock Management, Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan
| | - Ijaz Ahmad
- Department of Livestock Management, Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan
| | - Farhan Anwar Khan
- College of Veterinary Sciences, Faculty of Animal Husbandry and Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan
| | - Muhammad Shoaib
- College of Veterinary Sciences, Faculty of Animal Husbandry and Veterinary Sciences, The University of Agriculture, Peshawar, Pakistan
| | - Kamran Farid
- Department of Livestock and Dairy Development (Extension) Government of Khyber Pakhtunkhwa, Peshawar, Pakistan
| | - Amel Ayari-Akkari
- Biology Department, College of Science, King Khalid University, P.O. Box 960, Abha, Saudi Arabia
| | - Ekhlas Ali Morfeine
- Biology Department, College of Science, King Khalid University, P.O. Box 960, Abha, Saudi Arabia
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Jiang W, Xu S, Li P. SLC2A3 promotes tumor progression through lactic acid-promoted TGF-β signaling pathway in oral squamous cell carcinoma. PLoS One 2024; 19:e0301724. [PMID: 38625978 PMCID: PMC11020985 DOI: 10.1371/journal.pone.0301724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/21/2024] [Indexed: 04/18/2024] Open
Abstract
BACKGROUNDS Oral squamous cell carcinoma is a malignant tumor of the head and neck, and its molecular mechanism remains to be explored. METHODS By analyzing the OSCC data from the TCGA database, we found that SLC2A3 is highly expressed in OSCC patients. The expression level of SLC2A3 was verified by RT-PCR and western blotting in OSCC cell lines. The function of SLC2A3 in OSCC cell lines and Lactic acid in SLC2A3-knockdown OSCC cells were detected by colony formation, CCK8, transwell, and wound healing assays. The effect of SLC2A3 on tumor growth and metastasis was tested in vivo. GSEA and Western blot were used to analyze and validate tumor phenotypes and signaling pathway molecules. RESULTS We analyzed OSCC datasets in the TCGA database and found that SLC2A3 had abnormally high expression and was associated with poor prognosis. We also found that oral squamous cell carcinoma cells had increased proliferation, migration, invasion, EMT phenotype, and glycolysis due to SLC2A3 overexpression. Conversely, SLC2A3 knockdown had the opposite effect. Our in vivo experiments confirmed that SLC2A3 overexpression promoted tumor growth and metastasis while knockdown inhibited it. We also observed that high SLC2A3 expression led to EMT and the activation of the TGF-β signaling pathway, while knockdown inhibited it. Interestingly, exogenous lactic acid restored the EMT, proliferation, migration, and invasion abilities of oral cancer cells inhibited by knocking down SLC2A3. CONCLUSIONS Our study reveals that SLC2A3 expression was up-regulated in OSCC. SLC2A3 activates the TGF-β signaling pathway through lactic acid generated from glycolysis, thus regulating the biological behavior of OSCC.
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Affiliation(s)
- Wei Jiang
- Guangxi Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
- College of Stomatology, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Sheng Xu
- Department of Dental Laboratory, Guangxi Medical University College of Stomatology, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Ping Li
- Department of Pathology, Guangxi Medical University College of Stomatology, Nanning, Guangxi Zhuang Autonomous Region, China
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Haitzmann T, Schindlmaier K, Frech T, Mondal A, Bubalo V, Konrad B, Bluemel G, Stiegler P, Lackner S, Hrzenjak A, Eichmann T, Köfeler HC, Leithner K. Serine synthesis and catabolism in starved lung cancer and primary bronchial epithelial cells. Cancer Metab 2024; 12:9. [PMID: 38515202 PMCID: PMC10956291 DOI: 10.1186/s40170-024-00337-3] [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: 09/22/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
Serine and glycine give rise to important building blocks in proliferating cells. Both amino acids are either synthesized de novo or taken up from the extracellular space. In lung cancer, serine synthesis gene expression is variable, yet, expression of the initial enzyme, phosphoglycerate dehydrogenase (PHGDH), was found to be associated with poor prognosis. While the contribution of de novo synthesis to serine pools has been shown to be enhanced by serine starvation, the impact of glucose deprivation, a commonly found condition in solid cancers is poorly understood. Here, we utilized a stable isotopic tracing approach to assess serine and glycine de novo synthesis and uptake in different lung cancer cell lines and normal bronchial epithelial cells in variable serine, glycine, and glucose conditions. Under low glucose supplementation (0.2 mM, 3-5% of normal plasma levels), serine de novo synthesis was maintained or even activated. As previously reported, also gluconeogenesis supplied carbons from glutamine to serine and glycine under these conditions. Unexpectedly, low glucose treatment consistently enhanced serine to glycine conversion, along with an up-regulation of the mitochondrial one-carbon metabolism enzymes, serine hydroxymethyltransferase (SHMT2) and methylenetetrahydrofolate dehydrogenase (MTHFD2). The relative contribution of de novo synthesis greatly increased in low serine/glycine conditions. In bronchial epithelial cells, adaptations occurred in a similar fashion as in cancer cells, but serine synthesis and serine to glycine conversion, as assessed by label enrichments and gene expression levels, were generally lower than in (PHGDH positive) cancer cells. In summary, we found a variable contribution of glucose or non-glucose carbon sources to serine and glycine and a high adaptability of the downstream one-carbon metabolism pathway to variable glucose supply.
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Affiliation(s)
- Theresa Haitzmann
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Katharina Schindlmaier
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Tobias Frech
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Ayusi Mondal
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
- Department of Experimental Oncology, European Institute of Oncology, 20139, Milan, Italy
| | - Visnja Bubalo
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Barbara Konrad
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Gabriele Bluemel
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, 5020, Salzburg, Austria
| | - Philipp Stiegler
- Division of General, Visceral and Transplant Surgery, Department of Surgery, Medical University of Graz, 8036, Graz, Austria
| | - Stefanie Lackner
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, 8036, Graz, Austria
| | - Andelko Hrzenjak
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
- Ludwig Boltzmann Institute for Lung Vascular Research, 8010, Graz, Austria
| | - Thomas Eichmann
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, 8036, Graz, Austria
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, 8036, Graz, Austria
| | - Katharina Leithner
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria.
- BioTechMed-Graz, 8010, Graz, Austria.
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Sánchez-Castillo A, Heylen E, Hounjet J, Savelkouls KG, Lieuwes NG, Biemans R, Dubois LJ, Reynders K, Rouschop KM, Vaes RDW, De Keersmaecker K, Lambrecht M, Hendriks LEL, De Ruysscher DKM, Vooijs M, Kampen KR. Targeting serine/glycine metabolism improves radiotherapy response in non-small cell lung cancer. Br J Cancer 2024; 130:568-584. [PMID: 38160212 PMCID: PMC10876524 DOI: 10.1038/s41416-023-02553-y] [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: 10/19/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Lung cancer is the most lethal cancer, and 85% of cases are classified as non-small cell lung cancer (NSCLC). Metabolic rewiring is a cancer hallmark that causes treatment resistance, and lacks insights into serine/glycine pathway adaptations upon radiotherapy. METHODS We analyzed radiotherapy responses using mass-spectrometry-based metabolomics in NSCLC patient's plasma and cell lines. Efficacy of serine/glycine conversion inhibitor sertraline with radiotherapy was investigated by proliferation, clonogenic and spheroid assays, and in vivo using a serine/glycine dependent NSCLC mouse model by assessment of tumor growth, metabolite and cytokine levels, and immune signatures. RESULTS Serine/glycine pathway metabolites were significantly consumed in response to radiotherapy in NSCLC patients and cell models. Combining sertraline with radiotherapy impaired NSCLC proliferation, clonogenicity and stem cell self-renewal capacity. In vivo, NSCLC tumor growth was reduced solely in the sertraline plus radiotherapy combination treatment group. Tumor weights linked to systemic serine/glycine pathway metabolite levels, and were inhibited in the combination therapy group. Interestingly, combination therapy reshaped the tumor microenvironment via cytokines associated with natural killer cells, supported by eradication of immune checkpoint galectin-1 and elevated granzyme B levels. CONCLUSION Our findings highlight that targeting serine/glycine metabolism using sertraline restricts cancer cell recovery from radiotherapy and provides tumor control through immunomodulation in NSCLC.
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Affiliation(s)
- Anaís Sánchez-Castillo
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Elien Heylen
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven, and Leuven Cancer Institute (LKI), Herestraat 49, 3000, Leuven, Belgium
| | - Judith Hounjet
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Kim G Savelkouls
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Natasja G Lieuwes
- Department of Precision Medicine, The M-Lab, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Rianne Biemans
- Department of Precision Medicine, The M-Lab, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Ludwig J Dubois
- Department of Precision Medicine, The M-Lab, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Kobe Reynders
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
- Department of Oncology, Experimental Radiation Oncology, KU Leuven, and Leuven Cancer Institute (LKI), Herestraat 49, 3000, Leuven, Belgium
| | - Kasper M Rouschop
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Rianne D W Vaes
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Kim De Keersmaecker
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven, and Leuven Cancer Institute (LKI), Herestraat 49, 3000, Leuven, Belgium
| | - Maarten Lambrecht
- Department of Radiation Oncology, University Hospital Leuven, Leuven, Belgium
| | - Lizza E L Hendriks
- Department of Pulmonology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Dirk K M De Ruysscher
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Marc Vooijs
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Kim R Kampen
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands.
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven, and Leuven Cancer Institute (LKI), Herestraat 49, 3000, Leuven, Belgium.
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Verstraete P, De Keersmaecker K, Kampen KR. Drivers of de novo Serine/Glycine synthesis in acute leukemia. FEBS Lett 2023; 597:2145-2146. [PMID: 37526379 DOI: 10.1002/1873-3468.14700] [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: 05/02/2023] [Accepted: 06/14/2023] [Indexed: 08/02/2023]
Abstract
Cancer cells hijack metabolic pathways in order to provide themselves with building blocks to support their proliferation and survival. Upregulation and addiction to de novo serine/glycine synthesis is an example of metabolic rewiring in cancer cells whereby serine and glycine are synthesised via a side branch of glycolysis. In this review, we focus on upregulation of endogenous serine/glycine production in acute leukemia, namely T-cell acute leukemia (T-ALL) and acute myeloid leukemia (AML). Several genetic lesions directly driving the serine/glycine addiction in acute leukemia have been established. Additionally, indirect regulation of de novo serine/glycine synthesis is observed in acute leukemia.
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Affiliation(s)
- Paulien Verstraete
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
- Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Kim De Keersmaecker
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
- Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Kim Rosalie Kampen
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
- Leuven Cancer Institute (LKI), Leuven, Belgium
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht, The Netherlands
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