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PubMed1989

Characterization of bacteria that suppress rhizoctonia damping-off in bark compost media by analysis of Fatty Acid biomarkers.

Examination of cucumber roots (Cucumis sativus L.) grown in bark compost media and of the surrounding edaphic substrate showed profiles of polar lipid fatty acids commonly found in bacteria. The composition of fatty acids in these profiles differed significantly between roots grown in a medium naturally suppressive to Rhizoctonia damping-off and roots from a conducive medium. Cucumber roots from the suppressive medium had higher proportions of cis-vaccenic acid (18:1 omega 7c) and the iso-branched monoenoic fatty acid i17:1 omega 8 but lower proportions of several iso- and anteiso-branched fatty acids compared with roots from the conducive medium. The concentrations of the bacterial fatty acids were significantly lower in the surrounding media. However, the suppressive and conducive growth substrates had differences in the composition of the bacterial fatty acids similar to those found between the cucumber roots proper. These results suggest major differences in bacterial community composition between suppressive and conducive systems. Fatty acid analyses were also utilized to examine the effects on bacterial community composition of root colonization by Flavobacterium balustinum 299, a biocontrol agent. The concentration of the most prominent fatty acid in this bacterium, i17:1 omega 8, was increased on roots produced from inoculated seeds in a medium rendered suppressive by the treatment. This change was concomitant with a significant increase in the concentration of 18:1 omega 7c, not present in the lipids of the antagonist, indicating a shift in the microflora from a conducive to a suppressive bacterial community.

Journal Article↗
PubMed2004

Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets.

Accurate normalization is an absolute prerequisite for correct measurement of gene expression. For quantitative real-time reverse transcription-PCR (RT-PCR), the most commonly used normalization strategy involves standardization to a single constitutively expressed control gene. However, in recent years, it has become clear that no single gene is constitutively expressed in all cell types and under all experimental conditions, implying that the expression stability of the intended control gene has to be verified before each experiment. We outline a novel, innovative, and robust strategy to identify stably expressed genes among a set of candidate normalization genes. The strategy is rooted in a mathematical model of gene expression that enables estimation not only of the overall variation of the candidate normalization genes but also of the variation between sample subgroups of the sample set. Notably, the strategy provides a direct measure for the estimated expression variation, enabling the user to evaluate the systematic error introduced when using the gene. In a side-by-side comparison with a previously published strategy, our model-based approach performed in a more robust manner and showed less sensitivity toward coregulation of the candidate normalization genes. We used the model-based strategy to identify genes suited to normalize quantitative RT-PCR data from colon cancer and bladder cancer. These genes are UBC, GAPD, and TPT1 for the colon and HSPCB, TEGT, and ATP5B for the bladder. The presented strategy can be applied to evaluate the suitability of any normalization gene candidate in any kind of experimental design and should allow more reliable normalization of RT-PCR data.

Biomarkers, Tumor↗
PubMed2005

High expression of a new marker PCA-1 in human prostate carcinoma.

PURPOSE: Identifying the genetic factors involved in prostate carcinogenesis is critical. Novel cancer-specific markers aid in early detection, in differentiating between cancer and nonmalignant disorders, and in monitoring clinical of prostate disease. We therefore examined differential gene displays in an attempt to identify genes that may be involved in prostate carcinogenesis. EXPERIMENTAL DESIGN: Applying fluorescent differential display analysis to human prostate carcinomas, we have identified and cloned several cDNA transcripts. Antisera were raised against synthetic peptides and used in Western blot and immunohistochemical analyses. The mRNAs were also analyzed by real-time reverse transcription-PCR. For functional analysis, we assessed methylmethane sulfonate (MMS)-induced toxicity in COS-7 cells after cDNA transfection. RESULTS: We identified a gene, designated prostate cancer antigen-1 (pca-1), which shows high mRNA expression in prostate carcinoma. Database analysis of the deduced amino acid sequence of PCA-1 indicated high similarity to Escherichia coli AlkB, a DNA alkylation damage repair enzyme. By immunohistochemical analysis, PCA-1 was expressed in a high number of both prostate carcinoma samples and in the atypical cells within high-grade prostatic intraepithelial neoplasias but not in benign prostatic hyperplasia or normal adjacent tissues. PCA-1-transfected COS-7 cells further showed resistance against MMS-induced cell death. CONCLUSIONS: These findings suggest that PCA-1 could be a useful diagnostic marker. Furthermore, because this human counterpart of AlkB exhibits a protective function against alkylation damage in mammalian cells, PCA-1 may also serve as a therapeutic target molecule for prostate cancer.

Amino Acid Sequence↗
PubMed2005

Novel genes associated with malignant melanoma but not benign melanocytic lesions.

PURPOSE: Cutaneous melanoma is a common, aggressive cancer with increasing incidence. The identification of melanoma-specific deregulated genes could provide molecular markers for lymph node staging assays and further insight into melanoma tumorigenesis. EXPERIMENTAL DESIGN: Total RNA isolated from 45 primary melanoma, 18 benign skin nevi, and 7 normal skin tissue specimens were analyzed on an Affymetrix Hu133A microarray containing 22,000 probe sets. RESULTS: Hierarchical clustering revealed a distinct separation of the melanoma samples from the benign and normal specimens. Novel genes associated with malignant melanoma were identified. Differential gene expression of two melanoma-specific genes, PLAB and L1CAM, were tested by a one-step quantitative reverse transcription-PCR assay on primary malignant melanoma, benign nevi, and normal skin samples, as well as on malignant melanoma lymph node metastasis and melanoma-free lymph nodes. The performance of the markers was compared with conventional melanoma markers such as tyrosinase, gp100, and MART1. CONCLUSION: Our study systematically identified novel melanoma-specific genes and showed the feasibility of using a combination of PLAB and L1CAM in a reverse transcription-PCR assay to differentiate clinically relevant samples containing benign or malignant melanocytes.

Adolescent↗
PubMed2006

Radiation-guided gene therapy of cancer.

Gene therapy has been proposed as a means to combat cancer. However, systemic toxicity observed in preclinical trials suggested the importance of selectively targeted delivery and inducible gene expression in tumor tissues. Discovery of radiation-inducible promoter sequences provides one way to minimize inadvertent toxicity from gene therapy in normal tissues. Radiation is administered to selectively induce cytotoxic gene expression in the targeted tumor tissues. With promising results from phase II clinical trials using TNF-expressing adenovirus, it is possible to have radiation-guided gene therapy regimes once the tumor-targeted delivery has been achieved. Tumor endothelium is an attractive biological target for gene therapy, because it has the advantage of stability, accessibility, and bioavailability for therapeutic agents. Technological development of DNA microarray, proteomic profiling, and phage-displayed libraries accelerates the identification of tumor-specific endothelial biomarkers and discovery of its relevant affinity reagents for targeted delivery. The application of radiation-guided gene delivery, its amplification, as well as expression of gene therapy presents great opportunities to be employed as an alternative cancer treatment.

Animals↗
PubMed2006

An improved procedure for gene selection from microarray experiments using false discovery rate criterion.

BACKGROUND: A large number of genes usually show differential expressions in a microarray experiment with two types of tissues, and the p-values of a proper statistical test are often used to quantify the significance of these differences. The genes with small p-values are then picked as the genes responsible for the differences in the tissue RNA expressions. One key question is what should be the threshold to consider the p-values small. There is always a trade off between this threshold and the rate of false claims. Recent statistical literature shows that the false discovery rate (FDR) criterion is a powerful and reasonable criterion to pick those genes with differential expression. Moreover, the power of detection can be increased by knowing the number of non-differential expression genes. While this number is unknown in practice, there are methods to estimate it from data. The purpose of this paper is to present a new method of estimating this number and use it for the FDR procedure construction. RESULTS: A combination of test functions is used to estimate the number of differentially expressed genes. Simulation study shows that the proposed method has a higher power to detect these genes than other existing methods, while still keeping the FDR under control. The improvement can be substantial if the proportion of true differentially expressed genes is large. This procedure has also been tested with good results using a real dataset. CONCLUSION: For a given expected FDR, the method proposed in this paper has better power to pick genes that show differentiation in their expression than two other well known methods.

Algorithms↗
PubMed2006

Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

BACKGROUND: Genetic markers hold great promise for refining our ability to establish precise prognostic prediction for diseases. The development of comprehensive gene expression microarray technology has allowed the selection of relevant marker genes from a large pool of candidate genes in early-phased, developmental prognostic marker studies. The primary analytical task in such studies is to select a small fraction of relevant genes, typically from a list of significant genes, for further investigation in subsequent studies. RESULTS: We develop a methodology for predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays. Key components in this methodology include building prediction models, assessing predictive performance of prediction models, and assessing significance of prediction results. As particular specifications, we assume Cox proportional hazard models with a compound covariate. For assessing predictive accuracy, we propose to use the cross-validated log partial likelihood. To assess significance of prediction results, we apply permutation procedures in cross-validated prediction. As an additional key component peculiar to prognostic prediction, we also consider incorporation of standard prognostic factors. The methodology is evaluated using both simulated and real data. CONCLUSION: The developed methodology for prognostic prediction using a subset of significant genes can provide new insights based on predictive capability, possibly incorporating standard prognostic factors, in selecting a fraction of relevant genes for subsequent studies.

Biomarkers↗
PubMed2006

The influence of MMP-14, TIMP-2 and MMP-2 expression on breast cancer prognosis.

INTRODUCTION: Matrix metalloproteinase (MMP)-2 is very active at degrading extracellular matrix. It is under the influence of an activator, membrane type 1 MMP (MMP-14), and the tissue inhibitor of metalloproteases (TIMP)-2. We hypothesized that the individual expression of these three markers or their balance may help to predict breast cancer prognosis. METHODS: MMP-2, MMP-14 and TIMP-2 expression has been evaluated by 35S mRNA in situ hybridization on paraffin material of 539 breast cancers without distant metastasis at diagnosis and with a median follow-up of 9.2 years. RESULTS: MMP-2 and MMP-14 mRNA was detected primarily in reactive stromal cells whereas TIMP-2 mRNA was expressed by both stromal and cancer cells. Of the three molecules, an adjusted Cox model revealed that high MMP-14 mRNA (> or = 10% cells) alone predicted a significantly shorter overall survival (p = 0.031) when adjusted for clinical factors (tumor size and number of involved lymph nodes). Prognostic significance was lost when further adjusted for Her-2/neu and urokinase-type plasminogen activator (p = 0.284). Furthermore, when all three components were analyzed together, the survival was worst for patients with high MMP-2/high MMP-14/low TIMP-2 (5 year survival = 60%) and best with low MMP-2/low MMP-14/high TIMP-2 (5 year survival = 74%), but the difference did not reach statistical significance (p = 0.3285). CONCLUSION: Of the MMP-14/TIMP-2/MMP-2 complex, MMP-14 was the factor most significantly associated with the outcome of breast cancer and was an independent factor of poor overall survival when adjusted for clinical prognostic factors, but not for certain ancillary markers.

Adult↗
PubMed2007

Comparative analysis of predictive biomarkers for therapeutical strategies in colorectal cancer.

BACKGROUND: Prognostic information regarding the risk of postoperative tumor recurrence defined by a profile of serological, morphological and/or molecular markers can have potential value, particularly for patients with colorectal carcinoma (CRC) of the International Union Against Cancer (UICC) stage II/III who may benefit from adjuvant chemotherapy after surgery. METHODS: A retrospective study of 783 patients with CRC (UICC I-III) including a subgroup analysis of 116 subjects was conducted to determine preoperative serum carcinoembryonic antigen (CEA), carbohydrate antigen (CA) 19-9, and p53 serum levels. In addition, protein and gene expression of p53, CEA, and adenomatous polyposis coli (APC) was assessed in the tumors of those patients. The values of all serological, morphological, and molecular parameters were correlated with clinicopathological characteristics for their predictive value of tumor recurrence over a mean follow-up period of 32 +/- 6.2 months. RESULTS: Serum CEA but not CA 19-9 or p53 was a significant prognostic factor for disease-free survival, along with UICC and T/N stage. When comparing elevated CEA, CA 19-9, and p53 serum levels with expression of the markers in the tumors, their overall expression was found to be 61.3% in the serum versus 93.5% in the tumor in analyzed patients (n = 116). In particular, all patients in UICC stages I-III who demonstrated at least three elevated markers (CEA/CA 19-9/p53) in serum and/or in the tumor presented with tumor recurrence/metastases. CONCLUSION: Overall increased p53, CEA, and CA 19-9 serum levels and their marker expression in the tumor may be used at the time of primary tumor removal for defining patients at risk for tumor recurrence.

Adenocarcinoma↗
PubMed2005

Effects of nonylphenol and triclosan on production of plasma vitellogenin and testosterone in male South African clawed frogs (Xenopus laevis).

We investigated the effects of nonylphenol (NP) and triclosan (TCS) on production of vitellogenin (Vg), testosterone (T), and hepatic cytochrome P450 1A and 2B activities in male South African clawed frogs (Xenopus laevis). In a 14-d waterborne exposure test, no significant differences in the level of plasma Vg synthesis in male frogs were observed among the control, 10, 50, and 100 microg/l NP and 20, 100, and 200 microg/l TCS treatment groups. Intraperitoneal injection of male frogs with 2, 20, and 200 microg/g body weight NP resulted in no significant differences in plasma Vg levels among the control and all treatment groups. However, the levels of plasma Vg in all TCS treatment groups (intraperitoneal injection of 4, 40, and 400 microg/g body weight) were lower than that in the solvent control group, and male frogs injected with high doses of NP or TCS had lower T levels than the control group. No significant differences in hepatic cytochrome P450 1A and 2B activities were observed among the all treatment groups. Male frogs injected with 20 microg/g body weight of estradiol-17beta had significantly higher plasma Vg levels than the control group. These results suggest that profiles of plasma Vg and T production in male Xenopus laevis could be useful biomarkers for detecting hormonally active agents.

Animals↗
PubMed2006

Effects of storage time and exogenous protease inhibitors on plasma protein levels.

Plasma biomarker analysis requires intact unbiased starting material. We analyzed the effects on plasma protein profiles of protease inhibitor cocktails and preprocessing storage. Plasma from 12 healthy subjects collected with and without protease inhibitors was prepared immediately and after 2 hours of room temperature storage. The samples were analyzed by a multiplexed enzyme-linked immunosorbent assay that captured 99 chemokines and cytokines. Unsupervised hierarchical analysis clustered the samples into 4 groups; one composed predominantly of samples processed immediately, another of samples processed after 2 hours, and the remaining two were a mix of immediate and 2-hour samples. The mixed and immediate group protein profiles were similar. However, among the immediate and 2-hour samples, the levels of 37 factors differed significantly: all were greater after 2 hours. The dramatic changes in protein levels during storage were independent of protease inhibitors and are likely due to cytokine production and/or release by leukocytes and platelets.

Blood Preservation↗
PubMed2005

Overexpression of glutathione s-transferase alpha in clear cell renal cell carcinoma.

To determine its diagnostic value, we evaluated glutathione S-transferase alpha (GST-alpha) expression in a large number of renal cell carcinomas (RCCs). GST-alpha messenger RNA (mRNA) levels from 70 renal neoplasms were analyzed with complementary DNA (cDNA) microarray chips containing 21,632 cDNA clones. Furthermore, 348 primary renal tumors and 24 metastatic RCCs were subjected to immunohistochemical analysis with a GST-alpha-specific antibody. GST-alpha mRNA was elevated significantly (11.4-fold) in a majority of clear cell RCCs (28/43 [65.1%]; 28/39 [71.8%] with adjustments for informative spots) compared with other kidney tumors (1/27 [3.7%]). Strong and diffuse GST-alpha immunoreactivity was demonstrated in a majority of clear cell (166/202 [82.2%]; mean intensity, 2.41) and metastatic clear cell RCCs (17/24 [70.8%]; mean intensity, 2.62). Other renal tumor types did not exhibit significant GST-alpha immunoreactivity, confirming mRNA results. Through cDNA microarrays and immunohistochemical analysis, we demonstrated GST-alpha as a biomarker for clear cell RCCs.

Adenocarcinoma, Clear Cell↗
PubMed2003

From microarrays to new therapeutic approaches in bladder cancer.

Bladder cancer is a model tumor progressing from superficial to locally invasive and finally metastatic disease. The likelihood of progression is determined to a large extent by the molecular profile of the tumor. From the pre-genomic era only p53 emerged as the molecular prognostic factor able to add value to existing clinical and pathological features of bladder cancer, however it was not introduced to the clinic. Microarray technologies enable us to study expression of thousands of genes in the tumor tissue. This method has already proven to add information to clinical classifiers, to find new tumor suppressor genes and to define p53 related pathways of cell-cycle regulation. In the last decade, progress in the treatment of locally invasive and metastatic bladder cancer was minimal; large Phase III trials with neo/adjuvant chemotherapy were inconclusive. The new paradigm of treatment tailored to an individual patient could be realized in bladder cancer for his chronic clinical course with opportunities to obtain tumor samples for microarray studies. Molecular profiling of two samples taken at the superficial stage and at cystectomy should enable us to study the microevolution of the tumor, to tailor existing treatment options, and to introduce new biologicals to the clinic.Introduction

Apoptosis↗
PubMed2003

Medulloblastomas: do molecular and biologic markers indicate different prognoses and treatments?

The origin and histological classification of embryonal tumors, which make up the largest group of malignant pediatric brain malignancies, are two controversial issues. However, in recent years, progress has been made in our understanding of the molecular genetic abnormalities that govern their onset and/or progression. Several of these abnormalities appear to involve alterations in the signaling system controlling normal cerebellar development. An improved understanding of both the biology and clinical relevance of these molecular defects is probably the only means by which neuro-oncologists will improve the management of these tumors, thus reducing disease- and treatment-related morbidity and mortality.

Animals↗
PubMed2006

Preoperatively molecular staging with CM10 ProteinChip and SELDI-TOF-MS for colorectal cancer patients.

OBJECTIVES: To detect the serum proteomic patterns by using SELDI-TOF-MS (surface enhanced laser desorption/ ionization-time of flight-mass spectrometry) technology and CM10 ProteinChip in colorectal cancer (CRC) patients, and to evaluate the significance of the proteomic patterns in the tumour staging of colorectal cancer. METHODS: SELDI-TOF-MS and CM10 ProteinChip were used to detect the serum proteomic patterns of 76 patients with colorectal cancer, among them, 10 Stage I, 19 Stage II, 16 Stage III and 31 Stage IV samples. Different stage models were developed and validated by support vector machines, discriminant analysis and time-sequence analysis. RESULTS: The Model I formed by 6 protein peaks (m/z: 2759.58, 2964.66, 2048.01, 4795.90, 4139.77 and 37761.60) could be used to distinguish local CRC patients (Stage I and Stage II) from regional CRC patients (Stage III) with an accuracy of 86.67% (39/45). The Model II formed by 3 protein peaks (m/z: 6885.30, 2058.32 and 8567.75) could be used to distinguish locoregional CRC patients (Stage I, Stage II and Stage III) from systematic CRC patients (Stage IV) with an accuracy of 75.00% (57/76). The Model III could distinguish Stage I from Stage II with an accuracy of 86.21% (25/29). The Model IV could distinguish Stage I from Stage III with accuracy of 84.62% (22/26). The Model V could distinguish Stage II from Stage III with accuracy of 85.71% (30/35). The Model VI could distinguish Stage II from Stage IV with accuracy of 80.00% (40/50). The Model VII could distinguish Stage III from Stage IV with accuracy of 78.72% (37/47). Different stage groups could be distinguished by the two-dimensional scattered spots figure obviously. CONCLUSION: This method showed great success in preoperatively determining the colorectal cancer stage of patients.

Adolescent↗
PubMed2006

Cyclooxygenase-2 and inducible nitric oxide synthase expression in thyroid neoplasms and their clinicopathological correlation.

To evaluate the expressions of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) in thyroid neoplasms in a Korean population, we studied a total of 154 cases: papillary carcinoma of classical type (PTC), 86; follicular adenoma (FA), 21; follicular carcinoma (FC), 35; medullary carcinoma (MC), 3; undifferentiated carcinoma (UC), 5; and Hurthle cell neoplasm (HN), 4. Using immunohistochemical staining, COX-2 expression was detected in 62 (72.1%) PTC specimens, 5 (23.8%) FA specimens, 10 (28.6%) FC specimens, 0 (0.0%) MC specimens, 1 (20.0%) UC specimen, and 3 (75%) HN specimens. iNOS expression was detected in 66 (76.7%) PTC specimens, 4 (19.0%) FA specimens, 13 (37.1%) FC specimens, 0 (0.0%) MC specimens, 3 (60.0%) UC specimens, and 4 (100%) HN specimens. The results showed that COX-2 and iNOS were frequently expressed in the PTC and HN specimens, and iNOS was more frequently overexpressed in the FC specimens than in the FA specimens. In PTC, COX-2 and iNOS were significantly overexpressed in patients over 45 yr of age (p=0.029, p=0.041), and iNOS expression was increased in patients with a large primary tumor (p=0.028). These results suggest that the upregulation of COX-2 and iNOS may contribute to the tumor progression of thyroid gland, particularly in PTC and HN, and iNOS may play an adjuvant role during the tumor progression of FC.

Adult↗
PubMed2024

Developing a machine learning-based prognosis and immunotherapeutic response signature in colorectal cancer: insights from ferroptosis, fatty acid dynamics, and the tumor microenvironment.

INSTRUCTION: Colorectal cancer (CRC) poses a challenge to public health and is characterized by a high incidence rate. This study explored the relationship between ferroptosis and fatty acid metabolism in the tumor microenvironment (TME) of patients with CRC to identify how these interactions impact the prognosis and effectiveness of immunotherapy, focusing on patient outcomes and the potential for predicting treatment response. METHODS: Using datasets from multiple cohorts, including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we conducted an in-depth multi-omics study to uncover the relationship between ferroptosis regulators and fatty acid metabolism in CRC. Through unsupervised clustering, we discovered unique patterns that link ferroptosis and fatty acid metabolism, and further investigated them in the context of immune cell infiltration and pathway analysis. We developed the FeFAMscore, a prognostic model created using a combination of machine learning algorithms, and assessed its predictive power for patient outcomes and responsiveness to treatment. The FeFAMscore signature expression level was confirmed using RT-PCR, and ACAA2 progression in cancer was further verified. RESULTS: This study revealed significant correlations between ferroptosis regulators and fatty acid metabolism-related genes with respect to tumor progression. Three distinct patient clusters with varied prognoses and immune cell infiltration were identified. The FeFAMscore demonstrated superior prognostic accuracy over existing models, with a C-index of 0.689 in the training cohort and values ranging from 0.648 to 0.720 in four independent validation cohorts. It also responses to immunotherapy and chemotherapy, indicating a sensitive response of special therapies (e.g., anti-PD-1, anti-CTLA4, osimertinib) in high FeFAMscore patients. CONCLUSION: Ferroptosis regulators and fatty acid metabolism-related genes not only enhance immune activation, but also contribute to immune escape. Thus, the FeFAMscore, a novel prognostic tool, is promising for predicting both the prognosis and efficacy of immunotherapeutic strategies in patients with CRC.

Ferroptosis↗