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1.
Biochem Pharmacol ; : 116393, 2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38942088

ABSTRACT

The incidence of colorectal cancer (CRC) in patients under 50 has been increasing over the past several decades. The factors underlying the increase in early onset colorectal cancer (EOCRC) are not entirely clear, although several genetic and clinical differences with late onset colorectal cancer (LOCRC) have been noted. EOCRC cases are often diagnosed at a more advanced stage, raising the possibility that these cancers progress more rapidly than LOCRC cases. The impact of age on cancer progression is an intriguing topic and numerous lines of research have found that a young tissue environment is often more promotional. In fact, a less hospitable promotional tissue environment in older individuals may offset the increased cancer risk associated with the increased mutational load associated with age. Here we address how youthful aspects of angiogenesis, the tumor immune response, and the oxidative stress response may contribute to the rapid progression of EOCRC. Understanding the factors promoting EOCRC may provide insight into why EOCRC cases are increasing.

2.
J Diabetes Sci Technol ; : 19322968231153419, 2023 Feb 11.
Article in English | MEDLINE | ID: mdl-36772835

ABSTRACT

BACKGROUND: The objective of this work is to develop a highly miniaturized, low-power, biosensing platform for continuous glucose monitoring (CGM). This platform is based on an application-specific integrated circuit (ASIC) chip that interfaces with an amperometric glucose-sensing element. To reduce both size and power requirements, this custom ASIC chip was implemented using 65-nm complementary metal oxide semiconductor (CMOS) technology node. Interfacing this chip to a frequency-counting microprocessor with storage capabilities, a miniaturized transcutaneous CGM system can be constructed for small laboratory animals, with long battery life. METHOD: A 0.45 mm × 1.12 mm custom ASIC chip was first designed and implemented using the Taiwan Semiconductor Manufacturing Company (TSMC) 65-nm CMOS technology node. This ASIC chip was then interfaced with a multi-layer amperometric glucose-sensing element and a frequency-counting microprocessor with storage capabilities. Variation in glucose levels generates a linear increase in frequency response of this ASIC chip. In vivo experiments were conducted in healthy Sprague Dawley rats. RESULTS: This highly miniaturized, 65-nm custom ASIC chip has an overall power consumption of circa 36 µW. In vitro testing shows that this ASIC chip produces a linear (R2 = 99.5) frequency response to varying glucose levels (from 2 to 25 mM), with a sensitivity of 1278 Hz/mM. In vivo testing in unrestrained healthy rats demonstrated long-term CGM (six days/per charge) with rapid glucose response to glycemic variations induced by isoflurane anesthesia and tail vein injection. CONCLUSIONS: The miniature footprint of the biosensor platform, together with its low-power consumption, renders this CMOS ASIC chip a versatile platform for a variety of highly miniaturized devices, intended to improve the quality of life of patients with type 1 and type 2 diabetes.

3.
J Cell Sci ; 136(1)2023 01 01.
Article in English | MEDLINE | ID: mdl-36606487

ABSTRACT

53BP1 (also known as TP53BP1) is a key mediator of the non-homologous end joining (NHEJ) DNA repair pathway, which is the primary repair pathway in interphase cells. However, the mitotic functions of 53BP1 are less well understood. Here, we describe 53BP1 mitotic stress bodies (MSBs) formed in cancer cell lines in response to delayed mitosis. These bodies displayed liquid-liquid phase separation characteristics, were close to centromeres, and included lamin A/C and the DNA repair protein RIF1. After release from mitotic arrest, 53BP1 MSBs decreased in number and moved away from the chromatin. Using GFP fusion constructs, we found that the 53BP1 oligomerization domain region was required for MSB formation, and that inclusion of the 53BP1 N terminus increased MSB size. Exogenous expression of 53BP1 did not increase MSB size or number but did increase levels of MSB-free 53BP1. This was associated with slower mitotic progression, elevated levels of DNA damage and increased apoptosis, which is consistent with MSBs suppressing a mitotic surveillance by 53BP1 through sequestration. The 53BP1 MSBs, which were also found spontaneously in a subset of normally dividing cancer cells but not in non-transformed cells (ARPE-19), might facilitate the survival of cancer cells following aberrant mitoses. This article has an associated First Person interview with the first author of the paper.


Subject(s)
DNA Repair , Neoplasms , Tumor Suppressor p53-Binding Protein 1 , Humans , Chromatin , DNA Damage , DNA End-Joining Repair , Mitosis , Neoplasms/genetics , Tumor Suppressor p53-Binding Protein 1/genetics , Tumor Suppressor p53-Binding Protein 1/metabolism , Cell Line, Tumor
4.
Mol Cancer Res ; 20(1): 56-61, 2022 01.
Article in English | MEDLINE | ID: mdl-34670862

ABSTRACT

Stromal cells play a central role in promoting the progression of colorectal cancer. Here, we analyze molecular changes within the epithelial and stromal compartments of dysplastic aberrant crypt foci (ACF) formed in the ascending colon, where rapidly developing interval cancers occur. We found strong activation of numerous neutrophil/monocyte chemokines, consistent with localized inflammation. The data also indicated a decrease in interferon signaling and cell-based immunity. The immune checkpoint and T-cell exhaustion gene PDCD1 was one of the most significantly upregulated genes, which was accompanied by a decrease in cytotoxic T-cell effector gene expression. In addition, CDKN2A expression was strongly upregulated in the stroma and downregulated in the epithelium, consistent with diverse changes in senescence-associated signaling on the two tissue compartments. IMPLICATIONS: Decreased CD8 T-cell infiltration within proximal colon ACF occurs within the context of a robust inflammatory response and potential stromal cell senescence, thus providing new insight into potential promotional drivers for tumors in the proximal colon.


Subject(s)
Colonic Neoplasms/genetics , Epithelial Cells/metabolism , Stromal Cells/metabolism , Colonic Neoplasms/pathology , Female , Humans , Male , Middle Aged , Tumor Microenvironment
5.
Methods ; 198: 76-87, 2022 02.
Article in English | MEDLINE | ID: mdl-34628030

ABSTRACT

Pathway analysis is a popular method aiming to derive biological interpretation from high-throughput gene expression studies. However, existing methods focus mostly on identifying which pathway or pathways could have been perturbed, given differential gene expression patterns. In this paper, we present a novel pathway analysis framework, namely rPAC, which decomposes each signaling pathway route into two parts, the upstream portion of a transcription factor (TF) block and the downstream portion from the TF block and generates a pathway route perturbation analysis scheme examining disturbance scores assigned to both parts together. This rPAC scoring is further applied to a cohort of gene expression data sets which produces two summary metrics, "Proportion of Significance" (PS) and "Average Route Score" (ARS), as quantitative measures discerning perturbed pathway routes within and/or between cohorts. To demonstrate rPAC's scoring competency, we first used a large amount of simulated data and compared the method's performance against those by conventional methods in terms of power curve. Next, we performed a case study involving three epithelial cancer data sets from The Cancer Genome Atlas (TCGA). The rPAC method revealed specific pathway routes as potential cancer type signatures. A deeper pathway analysis of sub-groups (i.e., age groups in COAD or cancer sub-types in BRCA) resulted in pathway routes that are known to be associated with the sub-groups. In addition, multiple previously uncharacterized pathways routes were identified, potentially suggesting that rPAC is better in deciphering etiology of a disease than conventional methods particularly in isolating routes and sections of perturbed pathways in a finer granularity.


Subject(s)
Gene Expression Regulation , Transcription Factors , Gene Expression , Humans , Signal Transduction/genetics , Transcription Factors/genetics , Transcription Factors/metabolism
6.
Metabolomics ; 17(9): 80, 2021 09 03.
Article in English | MEDLINE | ID: mdl-34480220

ABSTRACT

INTRODUCTION: A methyl donor depleted (MDD) diet dramatically suppresses intestinal tumor development in Apc-mutant mice, but the mechanism of this prevention is not entirely clear. OBJECTIVES: We sought to gain insight into the mechanisms of cancer suppression by the MDD diet and to identify biomarkers of cancer risk reduction. METHODS: A plasma metabolomic analysis was performed on ApcΔ14/+ mice maintained on either a methyl donor sufficient (MDS) diet or the protective MDD diet. A group of MDS animals was also pair-fed with the MDD mice to normalize caloric intake, and another group was shifted from an MDD to MDS diet to determine the durability of the metabolic changes. RESULTS: In addition to the anticipated changes in folate one-carbon metabolites, plasma metabolites related to fatty acid metabolism were generally decreased by the MDD diet, including carnitine, acylcarnitines, and fatty acids. Some fatty acid selectivity was observed; the levels of cancer-promoting arachidonic acid and 2-hydroxyglutarate were decreased by the MDD diet, whereas eicosapentaenoic acid (EPA) levels were increased. Machine-learning elastic net analysis revealed a positive association between the fatty acid-related compounds azelate and 7-hydroxycholesterol and tumor development, and a negative correlation with succinate and ß-sitosterol. CONCLUSION: Methyl donor restriction causes dramatic changes in systemic fatty acid metabolism. Regulating fatty acid metabolism through methyl donor restriction favorably effects fatty acid profiles to achieve cancer protection.


Subject(s)
Colonic Neoplasms , Lipid Metabolism , Animals , Arachidonic Acid , Colonic Neoplasms/prevention & control , Diet , Fatty Acids , Mice
7.
J Cell Mol Med ; 25(18): 9011-9027, 2021 09.
Article in English | MEDLINE | ID: mdl-34414662

ABSTRACT

Excitotoxic events underlying ischaemic and traumatic brain injuries activate degenerative and protective pathways, particularly in the hippocampus. To understand opposing pathways that determine the brain's response to excitotoxicity, we used hippocampal explants, thereby eliminating systemic variables during a precise protocol of excitatory stimulation. N-methyl-d-aspartate (NMDA) was applied for 20 min and total RNA isolated one and 24 h later for neurobiology-specific microarrays. Distinct groups of genes exhibited early vs. delayed induction, with 63 genes exclusively reduced 24-h post-insult. Egr-1 and NOR-1 displayed biphasic transcriptional modulation: early induction followed by delayed suppression. Opposing events of NMDA-induced genes linked to pathogenesis and cell survival constituted the early expression signature. Delayed degenerative indicators (up-regulated pathogenic genes, down-regulated pro-survival genes) and opposing compensatory responses (down-regulated pathogenic genes, up-regulated pro-survival genes) generated networks with temporal gene profiles mirroring coexpression network clustering. We then used the expression profiles to test whether NF-κB, a potent transcription factor implicated in both degenerative and protective pathways, is involved in the opposing responses. The NF-κB inhibitor MG-132 indeed altered NMDA-mediated transcriptional changes, revealing components of opposing expression signatures that converge on the single response element. Overall, this study identified counteracting avenues among the distinct responses to excitotoxicity, thereby suggesting multi-target treatment strategies and implications for predictive medicine.


Subject(s)
Brain Injuries, Traumatic/therapy , Gene Expression Regulation/drug effects , Hippocampus/drug effects , N-Methylaspartate , NF-kappa B/metabolism , Protective Agents , Animals , N-Methylaspartate/administration & dosage , N-Methylaspartate/pharmacology , Protective Agents/administration & dosage , Protective Agents/pharmacology , Rats , Rats, Sprague-Dawley
8.
Biochem Pharmacol ; 186: 114486, 2021 04.
Article in English | MEDLINE | ID: mdl-33631189

ABSTRACT

Ferroptosis is a recently defined form of programmed cell death that is different from apoptosis. It is an iron-dependent programmed cell death and the accumulation of lipid hydroperoxides to lethal levels make ferroptosis distinct. Ferroptosis can be effectively regulated by a number of cellular variables including iron content, amino acid uptake, polyunsaturated fatty acid incorporation, glutathione biosynthesis, and NADPH levels. A number of severe and common degenerative diseases in humans such as Parkinson's disease and Huntington's disease, as well as several acute injury scenarios, such as stroke, intracerebral hemorrhage, traumatic brain injury, and ischemia-reperfusion injury are likely to be linked to ferroptosis. Ferroptosis may play a critical role in tumor-suppression and has been proposed as a potential target for cancer therapy. However, regulating ferroptosis in vivo remains difficult due to a lack of compounds that can effectively activate or repress ferroptosis. Here we review the cellular mechanisms underlying ferroptosis and the pathophysiological circumstances where its regulation could be beneficial.


Subject(s)
Drug Delivery Systems/methods , Ferroptosis/drug effects , Ferroptosis/physiology , Lipid Peroxidation/drug effects , Lipid Peroxidation/physiology , Animals , Antineoplastic Agents/administration & dosage , Apoptosis/drug effects , Apoptosis/physiology , Cerebrovascular Disorders/drug therapy , Cerebrovascular Disorders/metabolism , Humans , Nervous System Diseases/drug therapy , Nervous System Diseases/metabolism , Neuroprotective Agents/administration & dosage , Reactive Oxygen Species/antagonists & inhibitors , Reactive Oxygen Species/metabolism
9.
Cell Stress Chaperones ; 25(4): 667-677, 2020 07.
Article in English | MEDLINE | ID: mdl-32253741

ABSTRACT

We present new data on the effects of HBOT on human kidney (HK-2) cell metabolism using a SeaHorse XF Analyzer to evaluate separately the state of mitochondrial and glycolytic energy metabolism. The data are discussed in the context of the concept of cellular caloristasis networks. The information on the changes in cellular energy metabolism stimulated by HBOT presented here provides new insights into the cellular energy state and mitochondrial environment in which sHSPs function. These data will be useful in forming testable hypotheses about the functions of translocated sHSPs in human mitochondria responding to stressors.


Subject(s)
Energy Metabolism , Glycolysis , Hyperbaric Oxygenation , Mitochondria/metabolism , Oxygen/metabolism , Cell Line , Humans , Oxidative Stress
10.
Sci Rep ; 9(1): 9029, 2019 06 21.
Article in English | MEDLINE | ID: mdl-31227749

ABSTRACT

Transcriptome data can provide information on signaling pathways active in cancers, but new computational tools are needed to more accurately quantify pathway activity and identify tissue-specific pathway features. We developed a computational method called "BioTarget" that incorporates ChIP-seq data into cellular pathway analysis. This tool relates the expression of transcription factor TF target genes (based on ChIP-seq data) with the status of upstream signaling components for an accurate quantification of pathway activity. This analysis also reveals TF targets expressed in specific contexts/tissues. We applied BioTarget to assess the activity of TBX21 and GATA3 pathways in cancers. TBX21 and GATA3 are TF regulators that control the differentiation of T cells into Th1 and Th2 helper cells that mediate cell-based and humoral immune responses, respectively. Since tumor immune responses can impact cancer progression, the significance of our pathway scores should be revealed by effective patient stratification. We found that low Th1/Th2 activity ratios were associated with a significantly poorer survival of stomach and breast cancer patients, whereas an unbalanced Th1/Th2 response was correlated with poorer survival of colon cancer patients. Lung adenocarcinoma and lung squamous cell carcinoma patients had the lowest survival rates when both Th1 and Th2 responses were high. Our method also identified context-specific target genes for TBX21 and GATA3. Applying the BioTarget tool to BCL6, a TF associated with germinal center lymphocytes, we observed that patients with an active BCL6 pathway had significantly improved survival for breast, colon, and stomach cancer. Our findings support the effectiveness of the BioTarget tool for transcriptome analysis and point to interesting associations between some immune-response pathways and cancer progression.


Subject(s)
Computational Biology/methods , Gene Expression Profiling/methods , Immune System/metabolism , Neoplasms/genetics , Signal Transduction/genetics , T-Lymphocytes/metabolism , Cell Differentiation/genetics , Cell Differentiation/immunology , GATA3 Transcription Factor/genetics , Humans , Immune System/cytology , Immune System/immunology , Kaplan-Meier Estimate , Neoplasms/classification , Neoplasms/pathology , Proto-Oncogene Proteins c-bcl-6/genetics , Signal Transduction/immunology , T-Box Domain Proteins/genetics , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , T-Lymphocytes/cytology , T-Lymphocytes/immunology , Th1 Cells/immunology , Th1 Cells/metabolism , Th2 Cells/immunology , Th2 Cells/metabolism
11.
Sci Rep ; 9(1): 4954, 2019 03 20.
Article in English | MEDLINE | ID: mdl-30894570

ABSTRACT

The platinum-based chemotherapeutic agent, oxaliplatin, is used to treat advanced colorectal cancer (CRC). Unfortunately, nearly all patients acquire resistance to oxaliplatin after long-term use, limiting its therapeutic efficacy. Since COX-2 and PGE2 signaling can impact colon cancer cell proliferation and survival, we examined how this pathway was affected in an oxaliplatin resistant colon cancer cell line. PGE2 levels were significantly elevated in oxaliplatin-resistant HT29 cells (OXR) compared to naïve parental HT29 cells (PAR). This increase was associated with elevated COX-2 (17.9-fold; P = 0.008) and reduced 15-hydroxyprostaglandin dehydrogenase (2.9-fold; P < 0.0001) expression. RNAi knockdown of microsomal prostaglandin E synthase-1, the rate-limiting enzyme in PGE2 synthesis, sensitized OXR cells to oxaliplatin. Downstream effects of PGE2 in OXR cells were also examined. Selective inhibition of the EP4 PGE2 receptor by the small molecule inhibitor, L-161,982 enhanced oxaliplatin-induced apoptosis in OXR cells. L-161,982 also reduced expression of the colonic stem cell markers, CD133 and CD44, and inhibited tumor sphere formation. The accumulation of intracellular reactive oxygen species (ROS), a key component of oxaliplatin cytotoxicity, was significantly increased by EP4 inhibition (2.4 -fold; P < 0.0001). Overall, our findings uncover an important role for the COX-2/PGE2/EP4 signaling axis in oxaliplatin resistance via regulation of oxidative stress.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/pharmacology , Colonic Neoplasms/drug therapy , Oxaliplatin/pharmacology , Receptors, Prostaglandin E, EP4 Subtype/antagonists & inhibitors , Thiophenes/pharmacology , Triazoles/pharmacology , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Colonic Neoplasms/pathology , Cyclooxygenase 2/genetics , Cyclooxygenase 2/metabolism , Dinoprostone/metabolism , Drug Resistance, Neoplasm/drug effects , Drug Synergism , Gene Knockdown Techniques , HT29 Cells , Humans , Oxaliplatin/therapeutic use , Oxidative Stress/drug effects , RNA, Small Interfering/metabolism , Reactive Oxygen Species/metabolism , Receptors, Prostaglandin E, EP4 Subtype/metabolism , Signal Transduction/drug effects , Signal Transduction/genetics , Thiophenes/therapeutic use , Triazoles/therapeutic use
12.
Cell Stress Chaperones ; 23(6): 1143-1152, 2018 11.
Article in English | MEDLINE | ID: mdl-30374882

ABSTRACT

Diabetic kidney disease (DKD) is the leading cause of end-stage renal failure in the western world. Current treatment of diabetic kidney disease relies on nutritional management and drug therapies to achieve metabolic control. Here, we discuss the potential application of hyperbaric oxygen therapy (HBOT) for the treatment of diabetic kidney disease (DKD), a treatment which requires patients to breathe in 100% oxygen at elevated ambient pressures. HBOT has traditionally been used to diabetic foot ulcers (DFU) refractory to conventional medical treatments. Successful clinic responses seen in the DFU provide the underlying therapeutic rationale for testing HBOT in the setting of DKD. Both the DFU and DKD have microvascular endothelial disease as a common underlying pathologic feature. Supporting evidence for HBOT of DKD comes from previous animal studies and from our preliminary prospective clinical trial reported here. We report urinary metabolomic data obtained from patients undergoing HBOT for DFU, before and after exposure to 6 weeks of HBOT. The preliminary data support the concept that HBOT can reduce biomarkers of renal injury, oxidant stress, and mitochondrial dysfunction in patients receiving HBOT for DFU. Further studies are needed to confirm these initial findings and correlate them with simultaneous measures of renal function. HBOT is a safe and effective treatment for DFU and could also be for individuals with DKD.


Subject(s)
Diabetic Foot/metabolism , Diabetic Foot/therapy , Diabetic Nephropathies/metabolism , Diabetic Nephropathies/therapy , Hyperbaric Oxygenation/methods , Mitochondria/metabolism , Animals , Biomarkers/metabolism , Humans , Metabolomics , Models, Animal , Oxidative Stress , Prospective Studies , Treatment Outcome
13.
Mol Cancer Res ; 16(9): 1361-1372, 2018 09.
Article in English | MEDLINE | ID: mdl-29769406

ABSTRACT

AK3 compounds are mitotic arrest agents that induce high levels of γH2AX during mitosis and apoptosis following release from arrest. We synthesized a potent AK3 derivative, AK306, that induced arrest and apoptosis of the HCT116 colon cancer cell line with an EC50 of approximately 50 nmol/L. AK306 was active on a broad spectrum of cancer cell lines with total growth inhibition values ranging from approximately 25 nmol/L to 25 µmol/L. Using biotin and BODIPY-linked derivatives of AK306, binding to clathrin heavy chain (CLTC/CHC) was observed, a protein with roles in endocytosis and mitosis. AK306 inhibited mitosis and endocytosis, while disrupting CHC cellular localization. Cells arrested in mitosis by AK306 showed the formation of multiple microtubule-organizing centers consisting of pericentrin, γ-tubulin, and Aurora A foci, without apparent centrosome amplification. Cells released from AK306 arrest were unable to form bipolar spindles, unlike nocodazole-released cells that reformed spindles and completed division. Like AK306, CHC siRNA knockdown disrupted spindle formation and activated p53. A short-term (3-day) treatment of tumor-bearing APC-mutant mice with AK306 increased apoptosis in tumors, but not normal mucosa. These findings indicate that targeting the mitotic CHC complex can selectively induce apoptosis and may have therapeutic value.Implication: Disruption of clathrin with a small-molecule inhibitor, AK306, selectively induces apoptosis in cancer cells by disrupting bipolar spindle formation. Mol Cancer Res; 16(9); 1361-72. ©2018 AACR.


Subject(s)
Clathrin Heavy Chains/metabolism , Piperazines/pharmacology , Spindle Apparatus/drug effects , Animals , Apoptosis/drug effects , Apoptosis/physiology , Clathrin Heavy Chains/genetics , Colonic Neoplasms/drug therapy , Colonic Neoplasms/genetics , Colonic Neoplasms/metabolism , Gene Knockdown Techniques , HCT116 Cells , Humans , Male , Mice , Mitosis/drug effects , Molecular Targeted Therapy , Piperazines/chemistry , Spindle Apparatus/genetics , Spindle Apparatus/metabolism , Structure-Activity Relationship , Transfection
14.
Biochem Pharmacol ; 147: 1-8, 2018 01.
Article in English | MEDLINE | ID: mdl-29128368

ABSTRACT

Cancer cells have long been noted for alterations in centrosome structure, number, and function. Colorectal cancers are interesting in this regard since two frequently mutated genes, APC and CTNNB1 (ß-catenin), encode proteins that directly interact with the centrosome and affect its ability to direct microtubule growth and establish cell polarity. Colorectal cancers also frequently display centrosome over-duplication and clustering. Efforts have been directed toward understanding how supernumerary centrosomes cluster and whether disrupting this clustering may be a way to induce aberrant/lethal mitoses of cancer cells. Given the important role of the centrosome in establishing spindle polarity and regulating some apoptotic signaling pathways, other approaches to centrosome targeting may be fruitful as well. Basic information on the nature and extent of centrosome defects in colorectal cancer, including why they over-duplicate and whether this over-duplication compensates for their functional defects, could provide a framework for the development of novel approaches for the therapeutic targeting of colorectal cancer.


Subject(s)
Centrosome/physiology , Colonic Neoplasms/genetics , Colonic Neoplasms/metabolism , Gene Targeting , Animals , Cell Polarity/physiology , Centrioles/genetics , Centrioles/metabolism , Colonic Neoplasms/therapy , Gene Targeting/trends , Humans , RNA Interference/physiology , beta Catenin/genetics , beta Catenin/metabolism
15.
Methods ; 124: 3-12, 2017 07 15.
Article in English | MEDLINE | ID: mdl-28647608

ABSTRACT

We propose a new way of analyzing biological pathways in which the analysis combines both transcriptome data and mutation information and uses the outcome to identify "routes" of aberrant pathways potentially responsible for the etiology of disease. Each pathway route is encoded as a Bayesian Network which is initialized with a sequence of conditional probabilities which are designed to encode directionality of regulatory relationships encoded in the pathways, i.e. activation and inhibition relationships. First, we demonstrate the effectiveness of our model through simulation in which the model was able to easily separate Test samples from Control samples using fictitiously perturbed pathway routes. Second, we apply our model to analyze the Breast Cancer data set, available from TCGA, against many cancer pathways available from KEGG and rank the significance of identified pathways. The outcome is consistent with what have already been reported in the literature. Third, survival analysis has been carried out on the same data set by using pathway routes as features. Overall, we envision that our model of using pathway routes for analysis can further refine the conventional ways of subtyping cancer patients as it can discover additional characteristics specific to individual's tumor.


Subject(s)
Algorithms , Breast Neoplasms/genetics , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Mutation , Neoplasm Proteins/genetics , Bayes Theorem , Breast Neoplasms/metabolism , Breast Neoplasms/mortality , Breast Neoplasms/pathology , DNA Mutational Analysis , Female , Gene Expression Profiling , Humans , Neoplasm Proteins/metabolism , Signal Transduction , Survival Analysis , Transcriptome
16.
Cancer Prev Res (Phila) ; 9(10): 812-820, 2016 Oct.
Article in English | MEDLINE | ID: mdl-27530130

ABSTRACT

The role of folate one-carbon metabolism in colorectal cancer development is controversial, with nutritional intervention studies producing conflicting results. It has been reported that ApcMin/+ mice maintained on a diet deficient in the methyl donors folic acid, methionine, choline, and vitamin B12, and supplemented with homocysteine, show a greater than 95% reduction in intestinal tumor development. The present study extends these findings and shows that tumor protection afforded by dietary methyl donor deficiency (MDD) is long-lasting. After 11 weeks of MDD, tumor protection persisted for at least an additional 7 weeks of methyl donor repletion (22.2 ± 3.5 vs. 70.2 ± 4.6 tumors per mouse; P < 0.01). Sustained tumor protection was associated with a reduction in intestinal crypt length (26%, P < 0.01), crypt cell division and crypt fission, and an increase in apoptosis of both normal crypts and tumors (4.9- and 3.2-fold, respectively, P < 0.01). MDD also caused a significant reduction in the number of Dclk1-positive cells in the intestine (62%, P < 0.01), a long-lived crypt cell with cancer stem cell potential. Several undesirable effects associated with methyl donor restriction (e.g., reduced body weight gain) were shown to be transient and readily reversible following methyl donor repletion. Taken together, these results indicate that even temporary dietary methyl donor restriction in adenoma-prone mice can induce persistent changes to the intestinal epithelium and provide long-lasting tumor protection. These data also suggest that transient reductions in dietary methyl donor consumption should be considered when studying the impact of folate on colon cancer risk in humans. Cancer Prev Res; 9(10); 812-20. ©2016 AACR.


Subject(s)
Adenoma/metabolism , Diet , Intestinal Neoplasms/metabolism , Animals , Choline/metabolism , Folic Acid/metabolism , Methionine/deficiency , Mice , Mice, Inbred C57BL , Mice, Transgenic , Random Allocation , Vitamin B 12/metabolism
17.
Mol Cancer Res ; 14(9): 795-804, 2016 09.
Article in English | MEDLINE | ID: mdl-27353028

ABSTRACT

UNLABELLED: Although the progression of mutated colonic cells is dependent upon interactions between the initiated epithelium and surrounding stroma, the nature of these interactions is poorly understood. Here, the development of an ultrasensitive laser capture microdissection (LCM)/RNA-seq approach for studying the epithelial and stromal compartments of aberrant crypt foci (ACF) is described. ACF are the earliest identifiable preneoplastic lesion found within the human colon and are detected using high-definition endoscopy with contrast dye spray. The current analysis focused on the epithelium of ACF with somatic mutations to either KRAS, BRAF, or APC, and expression patterns compared with normal mucosa from each patient. By comparing gene expression patterns among groups, an increase in a number of proinflammatory NF-κB target genes was identified that was specific to ACF epithelium, including TIMP1, RELA, and RELB Distinct transcriptional changes associated with each somatic mutation were observed and a subset of ACF display BRAF(V600E)-mediated senescence-associated transcriptome characterized by increased expression of CDKN2A Finally, LCM-captured ACF-associated stroma was found to be transcriptionally distinct from normal-appearing stroma, with an upregulation of genes related to immune cell infiltration and fibroblast activation. Immunofluorescence confirmed increased CD3(+) T cells within the stromal microenvironment of ACF and an abundance of activated fibroblasts. Collectively, these results provide new insight into the cellular interplay that occurs at the earliest stages of colonic neoplasia, highlighting the important role of NF-κB, activated stromal fibroblasts, and lymphocyte infiltration. IMPLICATIONS: Fibroblasts and immune cells in the stromal microenvironment play an important role during the earliest stages of colon carcinogenesis. Mol Cancer Res; 14(9); 795-804. ©2016 AACR.


Subject(s)
Cell Communication/genetics , Colonic Neoplasms/genetics , Colonic Neoplasms/pathology , Cellular Senescence/genetics , Epithelial Cells/pathology , Humans , Intestinal Mucosa/pathology , Neoplasm Staging , Stromal Cells/pathology , Transcription, Genetic , Transcriptome , Up-Regulation
18.
PLoS One ; 11(4): e0153818, 2016.
Article in English | MEDLINE | ID: mdl-27097159

ABSTRACT

Mitotic inhibitors are widely utilized chemotherapeutic agents that take advantage of mitotic defects in cancer cells. We have identified a novel class of piperazine-based mitotic inhibitors, of which AK301 is the most potent derivative identified to date (EC50 < 200 nM). Colon cancer cells arrested in mitosis with AK301 readily underwent a p53-dependent apoptosis following compound withdrawal and arrest release. This apoptotic response was significantly higher for AK301 than for other mitotic inhibitors tested (colchicine, vincristine, and BI 2536). AK301-treated cells exhibited a robust mitosis-associated DNA damage response, including ATM activation, γH2AX phosphorylation and p53 stabilization. The association between mitotic signaling and the DNA damage response was supported by the finding that Aurora B inhibition reduced the level of γH2AX staining. Confocal imaging of AK301-treated cells revealed multiple γ-tubulin microtubule organizing centers attached to microtubules, but with limited centrosome migration, raising the possibility that aberrant microtubule pulling may underlie DNA breakage. AK301 selectively targeted APC-mutant colonocytes and promoted TNF-induced apoptosis in p53-mutant colon cancer cells. Our findings indicate that AK301 induces a mitotic arrest state with a highly active DNA damage response. Together with a reversible arrest state, AK301 is a potent promoter of a mitosis-to-apoptosis transition that can target cancer cells with mitotic defects.


Subject(s)
Apoptosis/drug effects , Cell Cycle Checkpoints/drug effects , Mitosis/drug effects , Piperazines/pharmacology , Adenomatous Polyposis Coli Protein/genetics , Animals , Ataxia Telangiectasia Mutated Proteins/metabolism , Caspase 3/metabolism , Colon/cytology , DNA Breaks/drug effects , HCT116 Cells , HT29 Cells , Humans , Mice , Mutation , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism
19.
Cancer Prev Res (Phila) ; 8(5): 387-99, 2015 May.
Article in English | MEDLINE | ID: mdl-25873367

ABSTRACT

One variable that may affect the ability of vitamin D to reduce colon cancer risk is the expression of its high-affinity receptor, VDR. Here, we show that vitamin D does not reduce tumor formation in Apc(Δ14/+) mice and that VDR expression is lost in the majority of the colon tumor cells. The extent of VDR loss corresponded inversely to the level of ß-catenin nuclear localization and could be observed in early lesions composed of just a few crypts. Analysis of reported VDR regulators showed that the repressing class I histone deacetylases (HDAC) were significantly elevated in the tumors (up to 4-fold), whereas the VDR-activating retinoid X receptors (RXR) were downregulated (∼50%). Expression of the Slug repressor was also increased, but was found primarily in stromal cells. Analysis of epigenetically active compounds on colon cell lines and intestinal organoids showed that HDAC inhibitors were particularly adept at stimulating VDR expression. Treatment of tumor-bearing Apc(Δ14/+) mice with the HDAC inhibitor panobinostat increased VDR expression in the tumors and normal mucosa. The RXR agonist bexarotene failed to activate VDR expression, indicating that RXR ligands were not limiting. Analysis of human microarray data indicated that VDR mRNA is frequently downregulated in colon adenomas, which correlated positively with RXRA expression and inversely with HDAC 2 and 8 expression. Human adenomas showed variable VDR protein expression levels, both between and within individual lesions. Determining the mechanisms of VDR regulation in colon neoplasms may significantly enhance our ability to use vitamin D as a cancer prevention agent.


Subject(s)
Adenocarcinoma/genetics , Adenoma/genetics , Colonic Neoplasms/genetics , Receptors, Calcitriol/genetics , Adenocarcinoma/pathology , Adenoma/pathology , Animals , Colonic Neoplasms/pathology , Colonic Polyps/genetics , Colonic Polyps/pathology , Female , Gene Expression Regulation, Neoplastic/drug effects , Genes, APC , HCT116 Cells , HT29 Cells , Humans , Male , Mice , Mice, Transgenic , Receptors, Calcitriol/metabolism , Tumor Cells, Cultured , Vitamin D/pharmacology
20.
Cell Stress Chaperones ; 20(3): 495-505, 2015 May.
Article in English | MEDLINE | ID: mdl-25648080

ABSTRACT

The disease burden from diabetic kidney disease is large and growing. Effective therapies are lacking, despite an urgent need. Hyperbaric oxygen therapy (HBOT) activates Nrf2 and cellular antioxidant defenses; therefore, it may be generally useful for treating conditions that feature chronic oxidative tissue damage. Herein, we determined how periodic exposure to oxygen at elevated pressure affected type 2 diabetes mellitus-related changes in the kidneys of db/db mice. Two groups of db/db mice, designated 2.4 ATA and 1.5 ATA, were treated four times per week with 100 % oxygen at either 1.5 or 2.4 ATA (atmospheres absolute) followed by tests to assess kidney damage and function. The sham group of db/db mice and the Hets group of db/+ mice were handled but did not receive HBOT. Several markers of kidney damage were reduced significantly in the HBOT groups including urinary biomarkers neutrophil gelatinase-associated lipocalin (NGAL) and cystatin C (CyC) along with significantly lower levels of caspase-3 activity in kidney tissue extracts. Other stress biomarkers also showed trends to improvement in the HBOT groups, including urinary albumin levels. Expressions of the stress response genes NRF2, HMOX1, MT1, and HSPA1A were reduced in the HBOT groups at the end of the experiment, consistent with reduced kidney damage in treated mice. Urinary albumin/creatinine ratio (ACR), a measure of albuminuria, was significantly reduced in the db/db mice receiving HBOT. All of the db/db mouse groups had qualitatively similar changes in renal histopathology. Glycogenated nuclei, not previously reported in db/db mice, were observed in these three experimental groups but not in the control group of nondiabetic mice. Overall, our findings are consistent with therapeutic HBOT alleviating stress and damage in the diabetic kidney through cytoprotective responses. These findings support an emerging paradigm in which tissue oxygenation and cellular defenses effectively limit damage from chronic oxidative stress more effectively than chemical antioxidants.


Subject(s)
Diabetes Mellitus, Type 2/urine , Diabetic Nephropathies/urine , Hyperbaric Oxygenation , Renal Insufficiency/urine , Albuminuria/prevention & control , Albuminuria/urine , Animals , Biomarkers/urine , Creatinine/urine , Diabetes Mellitus, Type 2/therapy , Diabetic Nephropathies/prevention & control , Male , Mice, Obese , Oxidative Stress , Renal Insufficiency/prevention & control
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