Fenton reactions drive nucleotide and ATP syntheses in cancer

Diffuse tumors: Molecular determinants shared by different cancer types

Most cancer types have both diffuse and non-diffuse subtypes, which have rather distinct morphologies, namely scattered tiny tumors vs. one solid tumor, and different levels of aggressiveness. However, the causes for forming such distinct subtypes remain largely unknown. Using the diffuse and non-diffuse gastric cancers (GCs) as the illustrative example, we present a computational study based on the transcriptomic data from the TCGA and GEO databases, to address the following questions: (i) What are the key molecular determinants that give rise to the distinct morphologies between diffuse and non-diffuse cancers? (ii) What are the main reasons for diffuse cancers to be generally more aggressive than non-diffuse ones of the same cancer type? (iii) What are the reasons for their distinct immunoactivities? And (iv) why do diffuse cancers on average tend to take place in younger patients? The study is conducted using the framework we have previously developed for elucidation of general drivers cancer formation and development. Our main discoveries are: (a) the level of (poly-) sialic acids deployed on the surface of cancer cells is a significant factor contributing to questions (i) and (ii); (b) poly-sialic acids synthesized by ST8SIA4 are the key to question (iii); and (c) the circulating growth factors specifically needed by the diffuse subtype dictate the answer to question (iv). All these predictions are substantiated by published experimental studies. Our further analyses on breast, prostate, lung, liver, and thyroid cancers reveal that these discoveries generally apply to the diffuse subtypes of these cancer types, hence indicating the generality of our discoveries.

Intravenous Injection of PEI-Decorated Iron Oxide Nanoparticles Impacts NF-kappaB Protein Expression in Immunologically Stressed Mice

Nanoparticle-based formulations are considered valuable tools for diagnostic and treatment purposes. The surface decoration of nanoparticles with polyethyleneimine (PEI) is often used to enhance their targeting and functional properties. Here, we aimed at addressing the long-term fate in vivo and the potential "off-target" effects of PEI decorated iron oxide nanoparticles (PEI-MNPs) in individuals with low-grade and persistent systemic inflammation. For this purpose, we synthesized PEI-MNPs (core-shell method, PEI coating under high pressure homogenization). Further on, we induced a low-grade and persistent inflammation in mice through regular subcutaneous injection of pathogen-associated molecular patterns (PAMPs, from zymosan). PEI-MNPs were injected intravenously. Up to 7 weeks thereafter, the blood parameters were determined via automated fluorescence flow cytometry, animals were euthanized, and the organs analyzed for iron contents (atomic absorption spectrometry) and for expression of NF-κB associated proteins (p65, IκBα, p105/50, p100/52, COX-2, Bcl-2, SDS-PAGE and Western blotting). We observed that the PEI-MNPs had a diameter of 136 nm and a zeta-potential 56.9 mV. After injection in mice, the blood parameters were modified and the iron levels were increased in different organs. Moreover, the liver of animals showed an increased protein expression of canonical NF-κB signaling pathway members early after PEI-MNP application, whereas at the later post-observation time, members of the non-canonical signaling pathway were prominent. We conclude that the synergistic effect between PEI-MNPs and the low-grade and persistent inflammatory state is mainly due to the hepatocytes sensing infection (PAMPs), to immune responses resulting from the intracellular metabolism of the uptaken PEI-MNPs, or to hepatocyte and immune cell communications. Therefore, we suggest a careful assessment of the safety and toxicity of PEI-MNP-based carriers for gene therapy, chemotherapy, and other medical applications not only in healthy individuals but also in those suffering from chronic inflammation.

Acid-base Homeostasis and Implications to the Phenotypic Behaviors of Cancer

Acid-base homeostasis is a fundamental property of living cells, and its persistent disruption in human cells can lead to a wide range of diseases. In this study, we conducted a computational modeling analysis of transcriptomic data of 4750 human tissue samples of 9 cancer types in The Cancer Genome Atlas (TCGA) database. Built on our previous study, we quantitatively estimated the average production rate of OH- by cytosolic Fenton reactions, which continuously disrupt the intracellular pH (pHi) homeostasis. Our predictions indicate that all or at least a subset of 43 reprogrammed metabolisms (RMs) are induced to produce net protons (H+) at comparable rates of Fenton reactions to keep the pHi stable. We then discovered that a number of well-known phenotypes of cancers, including increased growth rate, metastasis rate, and local immune cell composition, can be naturally explained in terms of the Fenton reaction level and the induced RMs. This study strongly suggests the possibility to have a unified framework for studies of cancer-inducing stressors, adaptive metabolic reprogramming, and cancerous behaviors. In addition, strong evidence is provided to demonstrate that a popular view that Na+/H+ exchangers along with lactic acid exporters and carbonic anhydrases are responsible for the intracellular alkalization and extracellular acidification in cancer may not be justified.

Cytochrome b561 regulates iron metabolism by activating the Akt/mTOR pathway to promote Breast Cancer Cells proliferation

Breast cancer (BC) is the leading cause of cancer-related mortality in women, necessitating the development of novel therapeutic targets. While cytochrome b561 (CYB561) expression is associated with poor prognosis in BC, the precise role of CYB561 in BC and its potential mechanisms remain unclear. In the present study, we found that CYB561 plays an essential role in BC growth. CYB561 expression was up-regulated in surgically resected cancerous tissues and in six BC cell lines. Lentivirus-mediated CYB561 knockdown in BC cells significantly reduced their proliferation, migration, and invasiveness. CYB561 participates in the regulation of iron metabolism in BC. CYB561 knockdown reduced total iron content, increased ferrous iron content, and down-regulated the expression of proteins associated with iron metabolism (transferrin receptor 1, divalent metal transporter 1, and ferritin heavy chain 1). Conversely, up-regulation of CYB561 through co-incubation with exogenous iron (ferric ammonium citrate) produced contrary outcomes. Additionally, CYB561 activated the protein kinase B/mammalian target of rapamycin (Akt/mTOR) signaling pathway in BC cells. Down-regulation of CYB561 expression inhibited the Akt/mTOR signaling pathway activity. The application of an mTOR agonist (MHY1485) rescued this negative effect, as well as the inhibitory effect of CYB561 knockdown on cell proliferation. Importantly, the dual mTOR inhibitor MLN0128 (50 nM, 48 h) down-regulated CYB561 expression and the iron metabolism-related proteins transferrin receptor, divalent metal transporter 1, and ferritin heavy chain 1, whereas the mTOR agonist MHY1485 rescued the down-regulation of CYB561 knockdown on iron metabolism-related proteins. We conclude that CYB561 promotes the proliferation of BC cells by regulating iron metabolism through the activation of the Akt/mTOR signaling pathway.

Engineered inhaled nanocatalytic therapy for ischemic cerebrovascular disease by inducing autophagy of abnormal mitochondria

Mitochondrial dysfunction and subsequent accumulation of reactive oxygen species (ROS) are key contributors to the pathology of ischemic cerebrovascular disease. Therefore, elimination of ROS and damaged mitochondria is crucial for the effective treatment of this disease. For this purpose, we designed an inhalation nanotherapeutic agent, P/D@Mn/Co3O4, to treat ischemic cerebrovascular disease. Mn/Co3O4 effectively removed excess ROS from cells, reduced acute cellular oxidative stress, and protected neural cells from apoptosis. Furthermore, it depleted the H+ surrounding mitochondria and depolarized the mitochondrial membrane potential, inducing mitophagy and eliminating abnormal mitochondria, thereby avoiding the continuous overproduction of ROS by eliminating the source of ROS regeneration. On intranasal administration, Mn/Co3O4 encapsulated by platelet membranes and 2,3-(dioxy propyl)-trimethylammonium chloride can bypass the blood-brain barrier, enter the brain through the trigeminal and olfactory pathways, and target inflammatory regions to remove ROS and damaged mitochondria from the lesion area. In rat models of stroke and vascular dementia, P/D@Mn/Co3O4 effectively inhibited the symptoms of acute and chronic cerebral ischemia by scavenging ROS and damaged mitochondria in the affected area. Our findings indicate that the nanotherapeutic agent developed in this study can be used for the effective treatment of ischemic cerebrovascular disease.

Brain metastases: It takes two factors for a primary cancer to metastasize to brain

Brain metastasis of a cancer is a malignant disease with high mortality, but the cause and the molecular mechanism remain largely unknown. Using the samples of primary tumors of 22 cancer types in the TCGA database, we have performed a computational study of their transcriptomic data to investigate the drivers of brain metastases at the basic physics and chemistry level. Our main discoveries are: (i) the physical characteristics, namely electric charge, molecular weight, and the hydrophobicity of the extracellular structures of the expressed transmembrane proteins largely affect a primary cancer cell’s ability to cross the blood-brain barrier; and (ii) brain metastasis may require specific functions provided by the activated enzymes in the metastasizing primary cancer cells for survival in the brain micro-environment. Both predictions are supported by published experimental studies. Based on these findings, we have built a classifier to predict if a given primary cancer may have brain metastasis, achieving the accuracy level at AUC = 0.92 on large test sets.

Emerging Mechanisms and Targeted Therapy of Ferroptosis in Neurological Diseases and Neuro-oncology

Ferroptosis is a novel type of cell death characterized by iron-dependent lipid peroxidation that involves a variety of biological processes, such as iron metabolism, lipid metabolism, and oxidative stress. A growing body of research suggests that ferroptosis is associated with cancer and neurodegenerative diseases, such as glioblastoma, Alzheimer's disease, Parkinson's disease, and stroke. Building on these findings, we can selectively induce ferroptosis for the treatment of certain cancers, or we can treat neurodegenerative diseases by inhibiting ferroptosis. This review summarizes the relevant advances in ferroptosis, the regulatory mechanisms of ferroptosis, the participation of ferroptosis in brain tumors and neurodegenerative diseases, and the corresponding drug therapies to provide new potential targets for its treatment.

Understanding the Potential and Risk of Bacterial Siderophores in Cancer

Siderophores are iron chelating molecules produced by nearly all organisms, most notably by bacteria, to efficiently sequester the limited iron that is available in the environment. Siderophores are an essential component of mammalian iron homeostasis and the ongoing interspecies competition for iron. Bacteria produce a broad repertoire of siderophores with a canonical role in iron chelation and the capacity to perform versatile functions such as interacting with other microbes and the host immune system. Siderophores are a vast area of untapped potential in the field of cancer research because cancer cells demand increased iron concentrations to sustain rapid proliferation. Studies investigating siderophores as therapeutics in cancer generally focused on the role of a few siderophores as iron chelators; however, these studies are limited and some show conflicting results. Moreover, siderophores are biologically conserved, structurally diverse molecules that perform additional functions related to iron chelation. Siderophores also have a role in inflammation due to their iron acquisition and chelation properties. These diverse functions may contribute to both risks and benefits as therapeutic agents in cancer. The potential of siderophore-mediated iron and bacterial modulation to be used in the treatment of cancer warrants further investigation. This review discusses the wide range of bacterial siderophore functions and their utilization in cancer treatment to further expand their functional relevance in cancer detection and treatment.

Quantitative estimation of intracellular oxidative stress in human tissues

Oxidative stress is known to be involved in and possibly a key driver of the development of numerous chronic diseases, including cancer. It is highly desired to have a capability to reliably estimate the level of intracellular oxidative stress as it can help to identify functional changes and disease phenotypes associated with such a stress, but the problem proves to be very challenging. We present a novel computational model for quantitatively estimating the level of oxidative stress in tissues and cells based on their transcriptomic data. The model consists of (i) three sets of marker genes found to be associated with the production of oxidizing molecules, the activated antioxidation programs and the intracellular stress attributed to oxidation, respectively; (ii) three polynomial functions defined over the expression levels of the three gene sets are developed aimed to capture the total oxidizing power, the activated antioxidation capacity and the oxidative stress level, respectively, with their detailed parameters estimated by solving an optimization problem and (iii) the optimization problem is so formulated to capture the relevant known insights such as the oxidative stress level generally goes up from normal to chronic diseases and then to cancer tissues. Systematic assessments on independent datasets indicate that the trained predictor is highly reliable and numerous insights are made based on its application results to samples in the TCGA, GTEx and GEO databases.

Molecular Subtyping of Cancer Based on Robust Graph Neural Network and Multi-Omics Data Integration

Accurate molecular subtypes prediction of cancer patients is significant for personalized cancer diagnosis and treatments. Large amount of multi-omics data and the advancement of data-driven methods are expected to facilitate molecular subtyping of cancer. Most existing machine learning–based methods usually classify samples according to single omics data, fail to integrate multi-omics data to learn comprehensive representations of the samples, and ignore that information transfer and aggregation among samples can better represent them and ultimately help in classification. We propose a novel framework named multi-omics graph convolutional network (M-GCN) for molecular subtyping based on robust graph convolutional networks integrating multi-omics data. We first apply the Hilbert–Schmidt independence criterion least absolute shrinkage and selection operator (HSIC Lasso) to select the molecular subtype-related transcriptomic features and then construct a sample–sample similarity graph with low noise by using these features. Next, we take the selected gene expression, single nucleotide variants (SNV), and copy number variation (CNV) data as input and learn the multi-view representations of samples. On this basis, a robust variant of graph convolutional network (GCN) model is finally developed to obtain samples’ new representations by aggregating their subgraphs. Experimental results of breast and stomach cancer demonstrate that the classification performance of M-GCN is superior to other existing methods. Moreover, the identified subtype-specific biomarkers are highly consistent with current clinical understanding and promising to assist accurate diagnosis and targeted drug development.

Targeting Cellular Iron Homeostasis with Ironomycin in Diffuse Large B-cell Lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common hematological malignancy. Although more than half of patients with DLBCL achieve long-term remission, the majority of remaining patients succumb to the disease. As abnormal iron homeostasis is implicated in carcinogenesis and the progression of many tumors, we searched for alterations in iron metabolism in DLBCL that could be exploited to develop novel therapeutic strategies. Analysis of the iron metabolism gene expression profile of large cohorts of patients with DLBCL established the iron score (IS), a gene expression-based risk score enabling identification of patients with DLBCL with a poor outcome who might benefit from a suitable targeted therapy. In a panel of 16 DLBCL cell lines, ironomycin, a promising lysosomal iron-targeting small molecule, inhibited DLBCL cell proliferation at nanomolar concentrations compared with typical iron chelators. Ironomycin also induced significant cell growth inhibition, ferroptosis, and autophagy. Ironomycin treatment resulted in accumulation of DNA double-strand breaks, delayed progression of replication forks, and increased RPA2 phosphorylation, a marker of replication stress. Ironomycin significantly reduced the median number of viable primary DLBCL cells of patients without major toxicity for nontumor cells from the microenvironment and presented low toxicity in hematopoietic progenitors compared with conventional treatments. Significant synergistic effects were also observed by combining ironomycin with doxorubicin, BH3 mimetics, BTK inhibitors, or Syk inhibitors. Altogether, these data demonstrate that a subgroup of high-risk patients with DLBCL can be identified with the IS that can potentially benefit from targeting iron homeostasis.

SIGNIFICANCE

Iron homeostasis represents a potential therapeutic target for high-risk patients with DLBCL that can be targeted with ironomycin to induce cell death and to sensitize tumor cells to conventional treatments.

Contributing factors common to COVID‑19 and gastrointestinal cancer

The devastating complications of coronavirus disease 2019 (COVID-19) result from the dysfunctional immune response of an individual following the initial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple toxic stressors and behaviors contribute to underlying immune system dysfunction. SARS-CoV-2 exploits the dysfunctional immune system to trigger a chain of events, ultimately leading to COVID-19. The authors have previously identified a number of contributing factors (CFs) common to myriad chronic diseases. Based on these observations, it was hypothesized that there may be a significant overlap between CFs associated with COVID-19 and gastrointestinal cancer (GIC). Thus, in the present study, a streamlined dot-product approach was used initially to identify potential CFs that affect COVID-19 and GIC directly (i.e., the simultaneous occurrence of CFs and disease in the same article). The nascent character of the COVID-19 core literature (~1-year-old) did not allow sufficient time for the direct effects of numerous CFs on COVID-19 to emerge from laboratory experiments and epidemiological studies. Therefore, a literature-related discovery approach was used to augment the COVID-19 core literature-based ‘direct impact’ CFs with discovery-based ‘indirect impact’ CFs [CFs were identified in the non-COVID-19 biomedical literature that had the same biomarker impact pattern (e.g., hyperinflammation, hypercoagulation, hypoxia, etc.) as was shown in the COVID-19 literature]. Approximately 2,250 candidate direct impact CFs in common between GIC and COVID-19 were identified, albeit some being variants of the same concept. As commonality proof of concept, 75 potential CFs that appeared promising were selected, and 63 overlapping COVID-19/GIC potential/candidate CFs were validated with biological plausibility. In total, 42 of the 63 were overlapping direct impact COVID-19/GIC CFs, and the remaining 21 were candidate GIC CFs that overlapped with indirect impact COVID-19 CFs. On the whole, the present study demonstrates that COVID-19 and GIC share a number of common risk/CFs, including behaviors and toxic exposures, that impair immune function. A key component of immune system health is the removal of those factors that contribute to immune system dysfunction in the first place. This requires a paradigm shift from traditional Western medicine, which often focuses on treatment, rather than prevention.

A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data

The metabolic heterogeneity and metabolic interplay between cells are known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single-cell metabolomics technology, we are yet to establish systematic understanding of the intra-tissue metabolic heterogeneity and cooperative mechanisms. To mitigate this knowledge gap, we developed a novel computational method, namely, single-cell flux estimation analysis (scFEA), to infer the cell-wise fluxome from single-cell RNA-sequencing (scRNA-seq) data. scFEA is empowered by a systematically reconstructed human metabolic map as a factor graph, a novel probabilistic model to leverage the flux balance constraints on scRNA-seq data, and a novel graph neural network-based optimization solver. The intricate information cascade from transcriptome to metabolome was captured using multilayer neural networks to capitulate the nonlinear dependency between enzymatic gene expressions and reaction rates. We experimentally validated scFEA by generating an scRNA-seq data set with matched metabolomics data on cells of perturbed oxygen and genetic conditions. Application of scFEA on this data set showed the consistency between predicted flux and the observed variation of metabolite abundance in the matched metabolomics data. We also applied scFEA on five publicly available scRNA-seq and spatial transcriptomics data sets and identified context- and cell group-specific metabolic variations. The cell-wise fluxome predicted by scFEA empowers a series of downstream analyses including identification of metabolic modules or cell groups that share common metabolic variations, sensitivity evaluation of enzymes with regards to their impact on the whole metabolic flux, and inference of cell-tissue and cell-cell metabolic communications.

Ferroportin and FBXL5 as Prognostic Markers in Advanced Stage Clear Cell Renal Cell Carcinoma

PURPOSE

Advanced stage clear cell renal cell carcinoma (ccRCC) involves a poor prognosis. Several studies have reported that dysfunctions in iron metabolism‒related proteins may cause tumor progression and metastasis of this carcinoma. In this study, we investigated the impact of the expression of iron metabolism‒related proteins on patient prognoses in advanced stage ccRCCs.

MATERIALS AND METHODS

All of 143 advanced stage ccRCC specimens were selected following validation with double blind reviews. Several clinicopathological parameters including nuclear grade, perirenal fat invasion, renal sinus fat invasion, vascular invasion, necrosis, and sarcomatoid/rhabdoid differentiation were compared with the expression of ferroportin (FPN), and F-Box and leucine rich repeat protein 5 (FBXL5), by immunohistochemistry. FPN and FBXL5 mRNA level of ccRCC from The Cancer Genome Atlas database were also analyzed for validation.

RESULTS

FPN and FBXL5 immunohistochemistry showed membrane and cytoplasmic expression, respectively. Based on the H-score, cases were classified as low or high expression with a cutoff value of 20 for FPN and 15 for FBXL5, respectively. Low expression of FPN and FBXL5 were significantly associated with patient death (p=0.022 and p=0.005, respectively). In survival analyses, low expression of FPN and FBXL5 were significantly associated with shorter overall survival (p=0.003 and p=0.004, respectively). On multivariate analysis, low expression of FBXL5 (hazard ratio, 2.001; p=0.034) was significantly associated with shorter overall survival.

CONCLUSION

FPN and FBXL5 can be used as potential prognostic markers and therapeutic targets for advanced stage ccRCC.

DFT mechanistic study on the formation of 8-oxoguanine and spiroiminodihydantoin mediated by iron Fenton reactions

Fenton reactions unavoidably take place in the human body and have been demonstrated to cause oxidative DNA damage. However, the molecular-level understanding of DNA damage mediated by Fenton reactions is limited. Herein, density functional theory (DFT) calculations were made to investigate the counterion effects on aqueous Fenton reactions and the detailed mechanisms of chemical modifications to guanine induced by Fenton reactions. Our calculations show that the activation energy of the Fenton reaction catalyzed by a pure aquo complex [FeII(H2O)6]2+ is too high to agree with experiments, whereas complexation with counteranions reduces the activation energy to a reasonable range. This result suggests that FeII-counteranion complexes are the real catalyst for fast aqueous Fenton reactions. In addition, we found that the Fenton oxidation mediated by FeII bonded to the N7 atom of guanine can result in the formation of 8-oxoguanine and spiroiminodihydantoin through multiple reaction pathways, including the electrophilic addition of ˙OH, H-abstraction by ˙OH, and oxygen atom transfer of oxoiron(iv) species. The activation of hydrogen peroxide by ferrous iron is the rate-determining step. The guanine N7-bound iron ion and the coordinated counteranion were found to play an important role in the Fenton oxidation of guanine.

Comprehensive analysis of ferritin subunits expression and positive correlations with tumor-associated macrophages and T regulatory cells infiltration in most solid tumors

Ferritin is the most important iron storage form and is known to influence tumor immunity. We previously showed that expression of ferritin light chain (FTL) and ferritin heavy chain (FTH1) subunits is increased in head and neck squamous cell carcinoma (HNSC). Here, we analyzed solid tumor datasets from The Cancer Genome Atlas and Genotype-Tissue Expression databases to investigate correlations between FTL and FTH1 expressions and (i) patient survival, using univariate, multivariate, Kaplan-Meier and Receiver Operator Characteristic analysis; and (ii) tumor-infiltrating immune cell subsets, using the bioinformatics tools Estimation of Stomal and Immune cells in Malignant Tumor tissues, Microenvironment Cell Population-counter, Tumor Immune Estimation Resource, and Tumor Immunology Miner. We found that FTL and FTH1 are upregulated and downregulated, respectively, in most of the human cancers analyzed. Tumor FTL levels were associated with prognosis in patients with lower grade glioma (LGG), whereas FTH1 levels were associated with prognosis in patients with liver hepatocellular carcinoma, HNSC, LGG, and kidney renal papillary cell carcinoma. In many cancers, FTL and FTH1 levels was significantly positively correlated with tumor infiltration by tumor-associated macrophages and T regulatory cells. These results suggest an important role for FTL and FTH1 in regulating tumor immunity to solid cancers.

Iron Metabolism in the Tumor Microenvironment-Implications for Anti-Cancer Immune Response

New insights into the field of iron metabolism within the tumor microenvironment have been uncovered in recent years. Iron promotes the production of reactive oxygen species, which may either trigger ferroptosis cell death or contribute to malignant transformation. Once transformed, cancer cells divert tumor-infiltrating immune cells to satisfy their iron demand, thus affecting the tumor immunosurveillance. In this review, we highlight how the bioavailability of this metal shapes complex metabolic pathways within the tumor microenvironment and how this affects both tumor-associated macrophages and tumor-infiltrating lymphocytes functions. Furthermore, we discuss the potentials as well as the current clinical controversies surrounding the use of iron metabolism as a target for new anticancer treatments in two opposed conditions: (i) the “hot” tumors, which are usually enriched in immune cells infiltration and are extremely rich in iron availability within the microenvironment, and (ii) the “cold” tumors, which are often very poor in immune cells, mainly due to immune exclusion.

MRPL27 contributes to unfavorable overall survival and disease-free survival from cholangiocarcinoma patients

Objective: This study aimed to investigate the roles of MRPL27 in survival from cholangiocarcinoma patients in The Cancer Genome Atlas (TCGA) database. Methods: In TCGA-CHOL profile, MRPL27 gene expression and clinical data were obtained. Cox regression models were used to evaluate the potential links between MRPL27 and cholangiocarcinoma survival. Enrichment analysis of MRPL27 was conducted in Metascape and Gene Set Enrichment Analysis (GSEA) databases. Results: 36 cholangiocarcinoma patients were included in this analysis. MRPL27 mRNA was significantly upregulated in tumor tissues in cholangiocarcinoma patients including intrahepatic, distal and hilar/perihilar cholangiocarcinoma cases (all p < 0.01). Cholangiocarcinoma patients with high MRPL27 had worse overall survival (OS) and disease-free survival (DFS) compared to those with low MRPL27 (all p < 0.05). Univariate and multivariate Cox models indicated that MRPL27 should be a risk factor for the OS and DFS in cholangiocarcinoma patients (both p < 0.01). Bioinformatic analysis revealed that MRPL27 mainly involved in the processes of mitochondrial translation elongation, respiratory electron transport, ATP synthesis, and inner mitochondrial membrane organization. No mutations of MRPL27 were screened in cholangiocarcinoma patients. Conclusion: Upregulated in tumors, MRPL27 contributes to unfavorable survival in cholangiocarcinoma patients.

Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur

Data from the SEER reports reveal that the occurrence rate of a cancer type generally follows a unimodal distribution over age, peaking at an age that is cancer-type specific and ranges from 30+ through 70+. Previous studies attribute such bell-shaped distributions to the reduced proliferative potential in senior years but fail to explain why some cancers have their occurrence peak at 30+ or 40+. We present a computational model to offer a new explanation to such distributions. The model uses two factors to explain the observed age-dependent cancer occurrence rates: cancer risk of an organ and the availability level of the growth signals in circulation needed by a cancer type, with the former increasing and the latter decreasing with age. Regression analyses were conducted of known occurrence rates against such factors for triple negative breast cancer, testicular cancer and cervical cancer; and all achieved highly tight fitting results, which were also consistent with clinical, gene-expression and cancer-drug data. These reveal a fundamentally important relationship: while cancer is driven by endogenous stressors, it requires sufficient levels of exogenous growth signals to happen, hence suggesting the realistic possibility for treating cancer via cleaning out the growth signals in circulation needed by a cancer.

Metabolic reprogramming in cancer: the bridge that connects intracellular stresses and cancer behaviors

Extensive changes in cellular metabolisms have been observed in cancer. They are probably induced by the same intracellular stressor, persistent off-balance in intracellular pH across possibly all adult cancers. It is these altered metabolisms that gives rise to a variety of cancerous behaviors such as continuous cell division, metastasis and drug resistance.

Co-expression based cancer staging and application

A novel method is developed for predicting the stage of a cancer tissue based on the consistency level between the co-expression patterns in the given sample and samples in a specific stage. The basis for the prediction method is that cancer samples of the same stage share common functionalities as reflected by the co-expression patterns, which are distinct from samples in the other stages. Test results reveal that our prediction results are as good or potentially better than manually annotated stages by cancer pathologists. This new co-expression-based capability enables us to study how functionalities of cancer samples change as they evolve from early to the advanced stage. New and exciting results are discovered through such functional analyses, which offer new insights about what functions tend to be lost at what stage compared to the control tissues and similarly what new functions emerge as a cancer advances. To the best of our knowledge, this new capability represents the first computational method for accurately staging a cancer sample. The R source code used in this study is available at GitHub (https://github.com/yxchspring/CECS).

Altered Iron Metabolism and Impact in Cancer Biology, Metastasis, and Immunology

Iron is an essential nutrient that plays a complex role in cancer biology. Iron metabolism must be tightly controlled within cells. Whilst fundamental to many cellular processes and required for cell survival, excess labile iron is toxic to cells. Increased iron metabolism is associated with malignant transformation, cancer progression, drug resistance and immune evasion. Depleting intracellular iron stores, either with the use of iron chelating agents or mimicking endogenous regulation mechanisms, such as microRNAs, present attractive therapeutic opportunities, some of which are currently under clinical investigation. Alternatively, iron overload can result in a form of regulated cell death, ferroptosis, which can be activated in cancer cells presenting an alternative anti-cancer strategy. This review focuses on alterations in iron metabolism that enable cancer cells to meet metabolic demands required during different stages of tumorigenesis in relation to metastasis and immune response. The strength of current evidence is considered, gaps in knowledge are highlighted and controversies relating to the role of iron and therapeutic targeting potential are discussed. The key question we address within this review is whether iron modulation represents a useful approach for treating metastatic disease and whether it could be employed in combination with existing targeted drugs and immune-based therapies to enhance their efficacy.

Elucidation of Functional Roles of Sialic Acids in Cancer Migration

Sialic acids (SA), negatively charged nine-carbon sugars, have long been implicated in cancer metastasis since 1960's but its detailed functional roles remain elusive. We present a computational analysis of transcriptomic data of cancer vs. control tissues of eight types in TCGA, aiming to elucidate the possible reason for the increased production and utilization of SAs in cancer and their possible driving roles in cancer migration. Our analyses have revealed for all cancer types: (1) the synthesis and deployment enzymes of SAs are persistently up-regulated throughout the progression for all but one cancer type; and (2) gangliosides, of which SAs are part, tend to converge to specific types that allow SAs to pack at high densities on cancer cell surface as a cancer advances. Statistical and modeling analyses suggest that (i) a highly plausible reason for the increased syntheses of SAs is to produce net protons, used for neutralizing the OH⁻ persistently generated by elevated intracellular iron metabolism coupled with chronic inflammation in cancer tissues; (ii) the level of SA accumulation on cancer cell surface strongly correlates with the stage of cancer migration, as well as multiple migration-related characteristics such as altered cell-cell adhesion, mechanical stress, cell protrusion, and contraction; and (iii) the pattern of SA deployment correlates with the 5-year survival rate of a cancer type. Overall, our study provides strong evidence for that the continuous accumulation of SAs on cancer cell surface gives rise to increasingly stronger cell-cell repulsion due to their negative charges, leading to cell deformation by electrostatic force-induced mechanical compression, which is known to be able to drive cancer cell migration established by recent studies.

CaMeRe: A Novel Tool for Inference of Cancer Metabolic Reprogramming

Metabolic reprogramming is prevalent in cancer, largely due to its altered chemical environments such as the distinct intracellular concentrations of O₂, H₂O₂ and H⁺, compared to those in normal tissue cells. The reprogrammed metabolisms are believed to play essential roles in cancer formation and progression. However, it is highly challenging to elucidate how individual normal metabolisms are altered in a cancer-promoting environment; hence for many metabolisms, our knowledge about how they are changed is limited. We present a novel method, CaMeRe (CAncer MEtabolic REprogramming), for identifying metabolic pathways in cancer tissues. Based on the specified starting and ending compounds, along with gene expression data of given cancer tissue samples, CaMeRe identifies metabolic pathways connecting the two compounds via collection of compatible enzymes, which are most consistent with the provided gene-expression data. In addition, cancer-specific knowledge, such as the expression level of bottleneck enzymes in the pathways, is incorporated into the search process, to enable accurate inference of cancer-specific metabolic pathways. We have applied this tool to predict the altered sugar-energy metabolism in cancer, referred to as the Warburg effect, and found the prediction result is highly accurate by checking the appearance and ranking of those key pathways in the results of CaMeRe. Computational evaluation indicates that the tool is fast and capable of handling large metabolic network inference in cancer tissues. Hence, we believe that CaMeRe offers a powerful tool to cancer researchers for their discovery of reprogrammed metabolisms in cancer. The URL of CaMeRe is http://csbl.bmb.uga.edu/CaMeRe/.

Metabolic Reprogramming in Cancer Is Induced to Increase Proton Production

Considerable metabolic reprogramming has been observed in a conserved manner across multiple cancer types, but their true causes remain elusive. We present an analysis of around 50 such reprogrammed metabolisms (RM) including the Warburg effect, nucleotide de novo synthesis, and sialic acid biosynthesis in cancer. Analyses of the biochemical reactions conducted by these RMs, coupled with gene expression data of their catalyzing enzymes, in 7,011 tissues of 14 cancer types, revealed that all RMs produce more H⁺ than their original metabolisms. These data strongly support a model that these RMs are induced or selected to neutralize a persistent intracellular alkaline stress due to chronic inflammation and local iron overload. To sustain these RMs for survival, cells must find metabolic exits for the nonproton products of these RMs in a continuous manner, some of which pose major challenges, such as nucleotides and sialic acids, because they are electrically charged. This analysis strongly suggests that continuous cell division and other cancerous behaviors are ways for the affected cells to remove such products in a timely and sustained manner. As supporting evidence, this model can offer simple and natural explanations to a range of long-standing open questions in cancer research including the cause of the Warburg effect. SIGNIFICANCE: Inhibiting acidifying metabolic reprogramming could be a novel strategy for treating cancer.

Structure of the flavonoid catechin in solution: NMR and quantum chemical investigations

DFT-PCM statistical index scan curves and ¹H-NMR profiles reveal conformational changes when a solid catechin sample is dissolved in acetone solvent.

Why the Reactive Oxygen Species of the Fenton Reaction Switches from Oxoiron(IV) Species to Hydroxyl Radical in Phosphate Buffer Solutions? A Computational Rationale

It has been shown that the major reactive oxygen species (ROS) generated by the aqueous reaction of Fe(II) and H2O2 (i.e., the Fenton reaction) are high-valent oxoiron(IV) species, whereas the hydroxyl radical plays a role only in very acidic conditions. Nevertheless, when the Fenton reaction is conducted in phosphate buffer solutions, the resulting ROS turns into hydroxyl radical even in neutral pH conditions. The present density functional theory (DFT) study discloses the underlying principle for this phenomenon. Static and dynamic DFT calculations indicate that in phosphate buffer solutions, the iron ion is highly coordinated by phosphoric acid anions. Such a coordination environment substantially raises the pK a of coordinated water on Fe(III). As a consequence, the Fe(III)-OH intermediate, resulting from the reductive decomposition of H2O2 by ferrous ion is relatively unstable and will be readily protonated by phosphoric acid ligand or by free proton in solution. These proton-transfer reactions, which become energetically favorable when the number of phosphate coordination goes up to three, prevent the Fe(III)-OH from hydrogen abstraction by nascent •OH to form Fe(IV)=O species. On the basis of this finding, a ligand design strategy toward controlling the nature of ROS produced in the Fenton reaction is put forth. In addition, it is found that while phosphate buffers facilitate •OH radical generation in the Fenton reaction, phosphoric acid anions can act as •OH radical scavengers through hydrogen atom transfer reactions.

Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name

It has been observed that both cancer tissue cells and normal proliferating cells (NPCs) have the Warburg effect. Our goal here is to demonstrate that they do this for different reasons. To accomplish this, we have analyzed the transcriptomic data of over 7000 cancer and control tissues of 14 cancer types in TCGA and data of five NPC types in GEO. Our analyses reveal that NPCs accumulate large quantities of ATPs produced by the respiration process before starting the Warburg effect, to raise the intracellular pH from ∼6.8 to ∼7.2 and to prepare for cell division energetically. Once cell cycle starts, the cells start to rely on glycolysis for ATP generation followed by ATP hydrolysis and lactic acid release, to maintain the elevated intracellular pH as needed by cell division since together the three processes are pH neutral. The cells go back to the normal respiration-based ATP production once the cell division phase ends. In comparison, cancer cells have reached their intracellular pH at ∼7.4 from top down as multiple acid-loading transporters are up-regulated and most acid-extruding ones except for lactic acid exporters are repressed. Cancer cells use continuous glycolysis for ATP production as way to acidify the intracellular space since the lactic acid secretion is decoupled from glycolysis-based ATP generation and is pH balanced by increased expressions of acid-loading transporters. Co-expression analyses suggest that lactic acid secretion is regulated by external, non-pH related signals. Overall, our data strongly suggest that the two cell types have the Warburg effect for very different reasons.

Systematic analyses of glutamine and glutamate metabolisms across different cancer types

BACKGROUND

Glutamine and glutamate are known to play important roles in cancer biology. However, no detailed information is available in terms of their levels of involvement in various biological processes across different cancer types, whereas such knowledge could be critical for understanding the distinct characteristics of different cancer types. Our computational study aimed to examine the functional roles of glutamine and glutamate across different cancer types.

METHODS

We conducted a comparative analysis of gene expression data of cancer tissues versus normal control tissues of 11 cancer types to understand glutamine and glutamate metabolisms in cancer. Specifically, we developed a linear regression model to assess differential contributions by glutamine and/or glutamate to each of seven biological processes in cancer versus control tissues.

RESULTS

While our computational predictions were consistent with some of the previous observations, multiple novel predictions were made: (1) glutamine is generally not involved in purine synthesis in cancer except for breast cancer, and is similarly not involved in pyridine synthesis except for kidney cancer; (2) glutamine is generally not involved in ATP production in cancer; (3) glutamine's contribution to nucleotide synthesis is minimal if any in cancer; (4) glutamine is not involved in asparagine synthesis in cancer except for bladder and lung cancers; and (5) glutamate does not contribute to serine synthesis except for bladder cancer.

CONCLUSIONS

We comprehensively predicted the roles of glutamine and glutamate metabolisms in selected metabolic pathways in cancer tissues versus control tissues, which may lead to novel approaches to therapeutic development targeted at glutamine and/or glutamate metabolism. However, our predictions need further functional validation.