De novo nucleotide biosynthetic pathway and cancer

Metabolic pathway analysis of tumors using stable isotopes

Metabolic reprogramming is pivotal in malignant transformation and cancer progression. Tumor metabolism is shaped by a complex interplay of both intrinsic and extrinsic factors that are not yet fully elucidated. It is of great value to unravel the complex metabolic activity of tumors in patients. Metabolic flux analysis (MFA) is a versatile technique for investigating tumor metabolism in vivo, it has increasingly been applied to the assessment of metabolic activity in cancer in the past decade. Stable-isotope tracing have shown that human tumors use diverse nutrients to fuel central metabolic pathways, such as the tricarboxylic acid cycle and macromolecule synthesis. Precisely how tumors use different fuels, and the contribution of alternative metabolic pathways in tumor progression, remain areas of intensive investigation. In this review, we systematically summarize the evidence from in vivo stable- isotope tracing in tumors and describe the catabolic and anabolic processes involved in altered tumor metabolism. We also discuss current challenges and future perspectives for MFA of human cancers, which may provide new approaches in diagnosis and treatment of cancer.

Deciphering the joint intracellular and extracellular regulatory strategies of toxigenic Microcystis to achieve intraspecific competitive advantage: An integrated multi-omics analysis with novel allelochemicals identified

Global increase in Microcystis-dominated cyanobacterial blooms (MCBs) severely threatens ecological and human health. Intraspecific interaction between microcystin (MC)-producing (MC+) Microcystis and co-existing MC-free (MC-) Microcystis influences the relative abundance of MC+Microcystis, ultimately determining the toxicity and hazard of MCBs. However, specific allelochemicals driving this interaction and underlying molecular mechanisms remain unclear. This study confirmed that intraspecific interaction promoted the competitive advantage of MC+Microcystis over MC-Microcystis and unveiled the joint intracellular and extracellular regulatory strategies of MC+Microcystis based on proteomics-metabolomics analyses and biochemical validation. Intracellularly, MC+Microcystis enhanced pentose phosphate pathway and lipid and fatty acid biosynthesis to maintain cellular functions and membrane stability, but inhibited glycolysis, tricarboxylic acid cycle, and protein biosynthesis to optimize energy utilization for growth and proliferation. Extracellularly, MC+Microcystis released allelochemicals, including cytidine diphosphate-diacylglycerol and N-acyl-homoserine lactones, to inhibit MC-Microcystis growth by 13.53% and 16.39%, respectively, thereby achieving its competitive advantage. In contrast, MC-Microcystis exhibited the suppressed photosynthesis and oxidative phosphorylation, imbalanced anti-inflammatory responses, nucleic acid degradation, and membrane damage, resulting in its competitive disadvantage in co-culture. These findings provide new insights into the competitive dynamics between MC+ and MC-Microcystis, and their involved implications for aquatic ecosystem health.

Exploiting replication stress for synthetic lethality in MYC-driven cancers

The oncoprotein MYC, overexpressed in more than 70% of human cancers, plays a pivotal role in regulating gene transcription and has long been recognized as a promising target for cancer therapy. However, no MYC-targeted drug has been approved for clinical use, largely due to the lack of a well-defined druggable domain and its nuclear localization. MYC-overexpressing cancer cells exhibit increased replication stress, driven by factors such as elevated replication origin firing, nucleotide depletion, replication-transcription conflicts, and heightened reactive oxygen species (ROS) production. Simultaneously, MYC activates compensatory mechanisms, including enhanced DNA repair, checkpoint-mediated cell cycle regulation, and metabolic reprogramming, to mitigate this stress and support cell survival. Interfering with these compensatory pathways exacerbates replication stress, leading to synthetic lethality in MYC-driven cancer cells. In this review, we summarize recent advances in leveraging replication stress to achieve synthetic lethality in MYC-driven cancers. Furthermore, we discuss current strategies targeting replication stress, highlighting new opportunities for the development of therapies against MYC-driven malignancies.

Resilience and vulnerabilities of tumor cells under purine shortage stress

Purine metabolism is a promising therapeutic target in cancer; however how cancer cells respond to purine shortage,particularly their adaptation and vulnerabilities, remains unclear. Using the recently developed purine shortage-inducing prodrug DRP-104 and genetic approaches, we investigated these responses in prostate, lung and glioma cancer models. We demonstrate that when de novo purine biosynthesis is compromised, cancer cells employ microtubules to assemble purinosomes, multi-protein complexes of de novo purine biosynthesis enzymes that enhance purine biosynthesis efficiency. While this process enables tumor cells to adapt to purine shortage stress, it also renders them more susceptible to the microtubule-stabilizing chemotherapeutic drug Docetaxel. Furthermore, we show that although cancer cells primarily rely on de novo purine biosynthesis, they also exploit Methylthioadenosine Phosphorylase (MTAP)-mediated purine salvage as a crucial alternative source of purine supply, especially under purine shortage stress. In support of this finding, combining DRP-104 with an MTAP inhibitor significantly enhances tumor suppression in prostate cancer (PCa) models in vivo. Finally, despite the resilience of the purine supply machinery, purine shortage-stressed tumor cells exhibit increased DNA damage and activation of the cGAS-STING pathway, which may contribute to impaired immunoevasion and provide a molecular basis of the previously observed DRP-104-induced anti-tumor immunity. Together, these findings reveal purinosome assembly and purine salvage as key mechanisms of cancer cell adaptation and resilience to purine shortage while identifying microtubules, MTAP, and immunoevasion deficits as therapeutic vulnerabilities.

IMPDH inhibitors upregulate PD-L1 in cancer cells without impairing immune checkpoint inhibitor efficacy

Tumor cells are characterized by rapid proliferation. In order to provide purines for DNA and RNA synthesis, inosine 5'-monophosphate dehydrogenase (IMPDH), a key enzyme in the de novo guanosine biosynthesis, is highly expressed in tumor cells. In this study we investigated whether IMPDH was involved in cancer immunoregulation. We revealed that the IMPDH inhibitors AVN944, MPA or ribavirin concentration-dependently upregulated PD-L1 expression in non-small cell lung cancer cell line NCI-H292. This effect was reproduced in other non-small cell lung cancer cell lines H460, H1299 and HCC827, colon cancer cell lines HT29, RKO and HCT116, as well as kidney cancer cell line Huh7. In NCI-H292 cells, we clarified that IMPDH inhibitors increased CD274 mRNA levels by enhancing CD274 mRNA stability. IMPDH inhibitors improved the affinity of the ARE-binding protein HuR for CD274 mRNA, thereby stabilizing CD274 mRNA. Guanosine supplementation abolished the IMPDH inhibitor-induced increase in PD-L1 expression. In CT26 and EMT6 tumor models used for ICIs based studies, we showed that despite its immunosuppressive properties, the IMPDH inhibitor mycophenolate mofetil did not reduce the clinical response of checkpoint inhibitors, representing an important clinical observation given that this class of drugs is approved for use in multiple diseases. We conclude that PD-L1 induction contributes to the immunosuppressive effect of IMPDH inhibitors. Furthermore, the IMPDH inhibitor mycophenolate mofetil does not antagonize immune checkpoint blockade.

Lnc-TPT1-AS1/CBP/ATIC Axis Mediated Purine Metabolism Activation Promotes Breast Cancer Progression

The purine biosynthetic pathway was recently identified to play a crucial role in breast cancer progression. However, little was known about the regulatory mechanisms of long non-coding RNA in breast cancer purine metabolism. In this study, we discovered that LncRNA TPT1-AS1 (TPT1-AS1) was downregulated in breast cancer tissues. Its introduction in breast cancer cells markedly suppressed tumor growth and metastasis in xenograft tumor models. Mass spectrometric analysis suggested that the purine biosynthetic pathway was activated in TPT1-AS1-knockdown MCF-7 cells. Inosine monophosphate (IMP), the product of de novo purine biosynthesis, was significantly upregulated. Mechanistically, we found that TPT1-AS1 could physically interact with CBP (CREB-binding protein), which consequently led to the loss of H3K27Ac in the promoter area of ATIC, the key enzyme of IMP synthesis. This process could block breast cancer purine metabolism and inhibit breast cancer progression. In conclusion, our findings illustrate the role of non-coding RNAs in breast cancer purine metabolism reprogramming and present a potential candidate for breast cancer therapy.

Cultivation methods and biology of Lentinula edodes

In this study, the biological applications of cultivation methods related to cultivar selection, vegetative growth, and reproductive development in Lentinula edodes cultivation are briefly reviewed to clarify the current situation and inform future developments. The current cultivars widely used in the main production areas are derived from wild strains distributed in northern Asia. The most effective techniques for cultivar identification are molecular markers identified in two nuclear genome datasets and one mitochondrial genome dataset. The current stage of cultivar breeding is at the junction of Breeding 3.0 (biological breeding) and Breeding 4.0 (intelligent breeding). Plant breeder's rights and patents have different emphases on new breeding variety protection, with the former being the most utilized globally. L. edodes is mostly produced on synthetic logs filled with sawdust substrates. Hardwood sawdust comprises approximately 80% of the substrates. The vegetative growth of L. edodes on synthetic logs involves two distinct stages of mycelial colonization and browning. Mycelia mainly perform glycolysis, tricarboxylic acid cycle, and respiratory metabolism reactions to produce energy and intermediates for synthesizing the structural components of hyphae in the vegetative colonization stage. Upon stimulation by physiological and environmental pressures after colonization, mycelia trigger gluconeogenesis, autophagy, and secondary metabolism, increase metabolic flux of pentose phosphate pathway, activate the glyoxylate cycle, and accumulate melanin on the surface of logs to ensure growth and survival. Sexually competent mycelia can form hyphal knots as a result of reprogrammed hyphal branching patterns after a period of vegetative growth (which varies by cultivar) and stimulation by specific environmental factors. Under a genetically encoded developmental program, hyphal knots undergo aggregation, tissue differentiation, primordium formation, meiosis in the hymenium, stipe elongation, basidiospore production and maturation, and cap expansion to form mature fruiting bodies. Growers can achieve good fruiting body shape and high yield by regulating the number of young fruiting bodies and adjusting specific environmental factors. KEY POINTS: • Cultivar selection becomes less with the increasing technological requirement of L. edodes cultivation. • L. edodes mycelia showed different biological events in the mycelial colonization and browning stages. • Specific cultivar breading may be the next milestone in L. edodes cultivation.

Unraveling the potential contribution of DHHC2 in cancer biology via untargeted metabolomics

DHHC-mediated protein-S-palmitoylation is recognized as a distinct and reversible lipid modification, playing a pivotal role in the progression and prevention of multiple diseases, including cancer and neurodegenerative disorders. Over the past decade, growing evidence indicated the crucial role of DHHC2 in preventing tumorigenesis by palmitoylation of various protein substrates. However, a comprehensive understanding of the specific impact of DHHC2 on cancer cell metabolic regulation remains unclear. To investigate the metabolic changes by DHHC2, we conducted untargeted metabolomic profiling on the HEK-293T cell line with DHHC2-Knockdown (DHHC2-KD), DHHC2-Overexpression (DHHC2-OE) and empty vector control (Ctrl) conditions via LC-MS/MS-based analysis. Our dataset revealed the identification of a total of 73 metabolites encompassing all the conditions, with only 22 showing significant differences in univariate analysis. Furthermore, we performed pathway analysis with metabolites having VIP ≥ 0.7, P value ≤ 0.05, and fold change (FC) > 2 in DHHC2-OE (upregulated) and FC < 0.5 in DHHC2-OE or FC > 2 in DHHC2-KD condition (downregulated). We unveiled significant expression of the pyrimidine metabolism, urea cycle, and aspartate metabolism due to the abundance of onco-metabolites such as glutamine, uridine, and glutamic acid in the DHHC2-KD condition. However, DHHC2 overexpression resulted in a higher expression of metabolites previously reported to be associated with anti-cancer activity, such as betaine and 5'-methylthioadenosine (5'-MTA). Overall, this study sheds light on the changes mediated by DHHC2 in a cancer cell metabolome and suggests avenues for further investigation into other DHHC isoforms and their metabolic aspects.

Biological production of nicotinamide mononucleotide: a review

Nicotinamide mononucleotide (NMN) presents significant therapeutic potential against aging-related conditions, such as Alzheimer's disease, due to its consistent and strong pharmacological effects. Aside from its anti-aging effect, NMN is also an emerging noncanonical cofactor for orthogonal metabolic pathways in the field of biomanufacturing. This has significant advantages in the field of metabolic engineering, allowing cells to produce unnatural chemicals without disrupting the natural cellular processes. NMN is produced through both the chemical and biological methods, with the latter being more environmentally sustainable. The primary biological production pathway centers on the enzyme nicotinamide phosphoribosyltransferase, which transforms nicotinamide and phosphoribosyl pyrophosphate to NMN. Efforts to increase NMN production have been explored in microorganisms, such as: Escherichia coli, Bacillus subtilis, and yeast, serving as biocatalysts, by rewiring their metabolic processes. Although most researchers are focusing on genetically and metabolically manipulating microorganisms to act as biocatalysts, a growing number of studies on cell-free synthesis are emerging as a promising strategy for producing NMN. This review explores the different biological production techniques of NMN employing microorganisms. This article, in particular, is essential to those who are working on NMN production using microbial strain engineering and cell-free systems.

Glutamine availability regulates cDC subsets in tissue

Proliferating tumor cells take up glutamine for anabolic processes engendering glutamine deficiency in the tumor microenvironment. How this might impact immune cells is not well understood. Using multiple mouse models of soft tissue sarcomas, glutamine antagonists, as well as genetic and pharmacological inhibition of glutamine utilization, we found that the number and frequency of conventional dendritic cells (cDC) is dependent on microenvironmental glutamine levels. cDCs comprise two distinct subsets - cDC1 and cDC2, with the former subset playing a critical role in antigen cross-presentation and tumor immunity. While both subsets show dependence on Glutamine, cDC1s are particularly sensitive. Notably, glutamine antagonism did not reduce the frequency of DC precursors but decreased proliferation and survival of cDC1s. Further studies suggest a role of the nutrient sensing mTOR signaling pathway in this process. Taken together, these findings uncover glutamine dependence of cDC1s that is coopted by tumors to escape immune responses.

One Sentence Summary

Type 1 conventional dendritic cells require glutamine to maintain their number in non-lymphoid tissue.

Significance

Immune evasion is a key hallmark of cancer; however, the underlying pathways are diverse, tumor-specific and not fully elucidated. Many tumor cells avidly import glutamine to support their anabolic needs, creating a glutamine-deficient tumor microenvironment (TME). Herein, using mouse models of soft tissue sarcomas, we show that glutamine depletion in TME leads to reduced type 1 conventional dendritic cells - a cell type that is critical for adaptive immune responses. This work is a paradigm for how tumor cell metabolism can regulate anti-tumor immune responses and will be foundational to future efforts targeting glutamine metabolism for cancer immunotherapy.

Emerging roles of FOXK2 in cancers and metabolic disorders

FOXK2, a member of the Forkhead box K (FOXK) transcription factor family, is widely expressed in various tissues and organs throughout the body. FOXK2 plays crucial roles in cell proliferation, differentiation, autophagy, de novo nucleotide biosynthesis, DNA damage response, and aerobic glycolysis. Although FOXK2 is recognized as an oncogene in colorectal cancer and hepatocellular carcinoma, it acts as a tumor suppressor in breast cancer, cervical cancer, and non-small cell lung cancer (NSCLC). This review provides an overview of the recent progress in understanding the regulatory mechanisms of FOXK2 and its downstream targets, highlights the significant impact of FOXK2 dysregulation on cancer etiology, and discusses the potential of targeting FOXK2 for cancer treatment.

A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis

De novo purine nucleotide biosynthesis (DNPNB) consists of sequential reactions that are majorly conserved in living organisms. Several regulation events take place to maintain physiological concentrations of adenylate and guanylate nucleotides in cells and to fine-tune the production of purine nucleotides in response to changing cellular demands. Recent years have seen a renewed interest in the DNPNB enzymes, with some being highlighted as promising targets for therapeutic molecules. Herein, a review of two newly revealed modes of regulation of the DNPNB pathway has been carried out: i) the unprecedent allosteric regulation of one of the limiting enzymes of the pathway named inosine 5'-monophosphate dehydrogenase (IMPDH), and ii) the supramolecular assembly of DNPNB enzymes. Moreover, recent advances that revealed the therapeutic potential of DNPNB enzymes in bacteria could open the road for the pharmacological development of novel antibiotics.

Direct stimulation of de novo nucleotide synthesis by O-GlcNAcylation

O-linked β-N-acetyl glucosamine (O-GlcNAc) is at the crossroads of cellular metabolism, including glucose and glutamine; its dysregulation leads to molecular and pathological alterations that cause diseases. Here we report that O-GlcNAc directly regulates de novo nucleotide synthesis and nicotinamide adenine dinucleotide (NAD) production upon abnormal metabolic states. Phosphoribosyl pyrophosphate synthetase 1 (PRPS1), the key enzyme of the de novo nucleotide synthesis pathway, is O-GlcNAcylated by O-GlcNAc transferase (OGT), which triggers PRPS1 hexamer formation and relieves nucleotide product-mediated feedback inhibition, thereby boosting PRPS1 activity. PRPS1 O-GlcNAcylation blocked AMPK binding and inhibited AMPK-mediated PRPS1 phosphorylation. OGT still regulates PRPS1 activity in AMPK-deficient cells. Elevated PRPS1 O-GlcNAcylation promotes tumorigenesis and confers resistance to chemoradiotherapy in lung cancer. Furthermore, Arts-syndrome-associated PRPS1 R196W mutant exhibits decreased PRPS1 O-GlcNAcylation and activity. Together, our findings establish a direct connection among O-GlcNAc signals, de novo nucleotide synthesis and human diseases, including cancer and Arts syndrome.

Uncovering novel therapeutic targets in glucose, nucleotides and lipids metabolism during cancer and neurological diseases

BACKGROUND

Cell metabolism functions without a stop in normal and pathological cells. Different metabolic changes occur in the disease. Cell metabolism influences biochemical and metabolic processes, signaling pathways, and gene regulation. Knowledge regarding disease metabolism is limited.

OBJECTIVE

The review examines the cell metabolism of glucose, nucleotides, and lipids during homeostatic and pathological conditions of neurotoxicity, neuroimmunological disease, Parkinson's disease, thymoma in myasthenia gravis, and colorectal cancer.

METHODS

Data collection includes electronic databases, the National Center for Biotechnology Information, and Google Scholar, with several inclusion criteria: cell metabolism, glucose metabolism, nucleotide metabolism, and lipid metabolism in health and disease patients suffering from neurotoxicity, neuroinflammation, Parkinson's disease, thymoma in myasthenia gravis. The initial number of collected and analyzed papers is 250. The final analysis included 150 studies out of 94 selected papers. After the selection process, 62.67% remains useful.

RESULTS AND CONCLUSION

A literature search shows that signaling molecules are involved in metabolic changes in cells. Differences between cancer and neuroimmunological diseases are present in the result section. Our finding enables insight into novel therapeutic targets and the development of scientific approaches for cancer and neurological disease onset, outcome, progression, and treatment, highlighting the importance of metabolic dysregulation. Current understanding, emerging research technologies and potential therapeutic interventions in metabolic programming is disucussed and highlighted.

Metabolomics analysis of the metabolic effects of citric acid on Issatchenkia terricola WJL-G4

In current research, yeast species Issatchenkia terricola WJL-G4 was shown to be capable of degrading citric acid, especially in the processing of fruit juice and wine. I. terricola WJL-G4 was able to use citric acid as a carbon source, but the metabolic effects of citric acid on yeast remained unclear. In this study, the metabolic effects of citric acid on I. terricola WJL-G4 were studied using liquid chromatography-mass spectrometry metabolomics technology, with glucose treatment as the control. Results showed that organic acid contents related to the extracellular tricarboxylic acid cycle (TCA) varied greatly. The metabolomics results indicated that I. terricola WJL-G4 might metabolize citric acid through the TCA pathway, and the glycolysis pathway might be inhibited; however, gluconeogenesis proceeded normally during citric acid treatment. Some fatty acids and phospholipids, along with the metabolic pathways of amino acids, vitamins, purines and nicotinamide in I. terricola WJL-G4 were also affected by the citric acid treatment. This work provided a theoretical basis for further study of the mechanism of yeast metabolism of citric acid.

Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being

Phosphoribosyl pyrophosphate synthetase (PRS EC 2.7.6.1) is a rate-limiting enzyme that irreversibly catalyzes the formation of phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate and adenosine triphosphate (ATP). This key metabolite is required for the synthesis of purine and pyrimidine nucleotides, the two aromatic amino acids histidine and tryptophan, the cofactors nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), all of which are essential for various life processes. Despite its ubiquity and essential nature across the plant and animal kingdoms, PRPP synthetase displays species-specific characteristics regarding the number of gene copies and architecture permitting interaction with other areas of cellular metabolism. The impact of mutated PRS genes in the model eukaryote Saccharomyces cerevisiae on cell signalling and metabolism may be relevant to the human neuropathies associated with PRPS mutations. Human PRPS1 and PRPS2 gene products are implicated in drug resistance associated with recurrent acute lymphoblastic leukaemia and progression of colorectal cancer and hepatocellular carcinoma. The investigation of PRPP metabolism in accepted model organisms, e.g., yeast and zebrafish, has the potential to reveal novel drug targets for treating at least some of the diseases, often characterized by overlapping symptoms, such as Arts syndrome and respiratory infections, and uncover the significance and relevance of human PRPS in disease diagnosis, management, and treatment.