Publications

Peer-reviewed publications resulting from work I have been involved in.

  • Gene expression profiling during intensive cardiovascular lifestyle modification: Relationships with vascular function and weight loss. December 12, 2017
    Related Articles Gene expression profiling during intensive cardiovascular lifestyle modification: Relationships with vascular function and weight loss. Genom Data. 2015 Jun;4:50-3 Authors: Blackburn HL, McErlean S, Jellema GL, van Laar R, Vernalis MN, Ellsworth DL Abstract Heart disease and related sequelae are a leading cause of death and healthcare expenditure throughout the world. Although many patients opt for surgical interventions, lifestyle modification programs focusing on nutrition and exercise have shown substantial health benefits and are becoming increasing popular. We conducted a year-long lifestyle modification program to mediate cardiovascular risk through traditional risk factors and to investigate how molecular changes, if present, may contribute to long-term risk reduction. Here we describe the lifestyle intervention, including clinical and molecular data collected, and provide details of the experimental methods and quality control parameters for the gene expression data generated from participants and non-intervention controls. Our findings suggest successful and sustained modulation of gene expression through healthy lifestyle changes may have beneficial effects on vascular health that cannot be discerned from traditional risk factor profiles. The data are deposited in the Gene Expression Omnibus, series GSE46097 and GSE66175. PMID: 26484175 [PubMed]
  • Importance of substantial weight loss for altering gene expression during cardiovascular lifestyle modification. December 12, 2017
    Related Articles Importance of substantial weight loss for altering gene expression during cardiovascular lifestyle modification. Obesity (Silver Spring). 2015 Jun;23(6):1312-9 Authors: Ellsworth DL, Mamula KA, Blackburn HL, McDyer FA, Jellema GL, van Laar R, Costantino NS, Engler RJ, Vernalis MN Abstract OBJECTIVE: To examine relationships between weight loss through changes in lifestyle and peripheral blood gene expression profiles. METHODS: A prospective nonrandomized trial was conducted over 1 year in participants undergoing intensive lifestyle modification to reverse or stabilize progression of coronary artery disease. Cardiovascular risk factors, inflammatory biomarkers, and gene expression as a function of weight loss were assessed in 89 lifestyle participants and 71 retrospectively matched controls undergoing usual care. RESULTS: Substantial weight loss (-15.2 ± 3.8%) in lifestyle participants (n = 33) was associated with improvement in selected cardiovascular risk factors and significant changes in peripheral blood gene expression from pre- to post-intervention: 132 unique genes showed significant expression changes (false discovery rate corrected P-value
  • Translating a gene expression signature for multiple myeloma prognosis into a robust high-throughput assay for clinical use. December 12, 2017
    Related Articles Translating a gene expression signature for multiple myeloma prognosis into a robust high-throughput assay for clinical use. BMC Med Genomics. 2014 May 17;7:25 Authors: van Laar R, Flinchum R, Brown N, Ramsey J, Riccitelli S, Heuck C, Barlogie B, Shaughnessy JD Abstract BACKGROUND: Widespread adoption of genomic technologies in the management of heterogeneous indications, including Multiple Myeloma, has been hindered by concern over variation between published gene expression signatures, difficulty in physician interpretation and the challenge of obtaining sufficient genetic material from limited patient specimens. METHODS: Since 2006, the 70-gene prognostic signature, developed by the University of Arkansas for Medical Sciences (UAMS) has been applied to over 4,700 patients in studies performed in 4 countries and described in 17 peer-reviewed publications. Analysis of control sample and quality control data compiled over a 12-month period was performed. RESULTS: Over a 12 month period, the 70-gene prognosis score (range 0-100) of our multiple myeloma cell-line control sample had a standard deviation of 2.72 and a coefficient of variance of 0.03. The whole-genome microarray profile used to calculate a patient's GEP70 score can be generated with as little as 15 ng of total RNA; approximately 30,000 CD-138+ plasma cells. Results from each GEP70 analysis are presented as either low (70-gene score
  • Gene expression differences in adipose tissue associated with breast tumorigenesis. December 12, 2017
    Related Articles Gene expression differences in adipose tissue associated with breast tumorigenesis. Adipocyte. 2014 Apr 1;3(2):107-14 Authors: Sturtz LA, Deyarmin B, van Laar R, Yarina W, Shriver CD, Ellsworth RE Abstract Long thought to function only as an inert energy storage depot, the role of adipose tissue in breast tumorigenesis has been largely ignored. In light of increasing rates of obesity and use of breast conserving therapy and autologous fat grafting, improved understanding of the role of adipose tissue in tumor etiology is crucial. Thus, adipose tissue adjacent to and distant from invasive breast tumors (n = 20), or adjacent to non-malignant diagnoses (n = 20) was laser microdissected from post-menopausal women. Gene expression data were generated using microarrays and data analyzed to identify significant patterns of differential expression between adipose tissue groups at the individual gene and molecular pathway level. Pathway analysis revealed significant differences in immune response between non-malignant, distant, and tumor-adjacent adipose tissue, with the highest response in tumor-adjacent and lowest in non-malignant adipose tissue. Adipose tissue from invasive breasts exhibits increased expression of anti-inflammatory genes such as MARCO and VSIG4 while genes differentially expressed between tumor-adjacent and distant adipose tissue such as SPP1, RRM2, and MMP9, are associated with increased cellular proliferation, invasion, and angiogenesis. These data suggest that molecular profiles of adipose tissue differ depending on presence of or proximity to tumor cells. Heightened immunotolerance in adipose tissue from invasive breasts provides a microenvironment favorable to tumorigenesis. In addition, tumor-adjacent adipose tissue demonstrates expression of genes associated with tumor growth and progression. Thus, adipose tissue is not an inert component of the breast microenvironment but plays an active role in tumorigenesis. PMID: 24719783 [PubMed]
  • Intensive cardiovascular risk reduction induces sustainable changes in expression of genes and pathways important to vascular function. December 12, 2017
    Related Articles Intensive cardiovascular risk reduction induces sustainable changes in expression of genes and pathways important to vascular function. Circ Cardiovasc Genet. 2014 Apr;7(2):151-60 Authors: Ellsworth DL, Croft DT, Weyandt J, Sturtz LA, Blackburn HL, Burke A, Haberkorn MJ, McDyer FA, Jellema GL, van Laar R, Mamula KA, Chen Y, Vernalis MN Abstract BACKGROUND: Healthy lifestyle changes are thought to mediate cardiovascular disease risk through pathways affecting endothelial function and progression of atherosclerosis; however, the extent, persistence, and clinical significance of molecular change during lifestyle modification are not well known. We examined the effect of a rigorous cardiovascular disease risk reduction program on peripheral blood gene expression profiles in 63 participants and 63 matched controls to characterize molecular responses and identify regulatory pathways important to cardiovascular health. METHODS AND RESULTS: Dramatic changes in dietary fat intake (-61%; P
  • BreastPRS is a gene expression assay that stratifies intermediate-risk Oncotype DX patients into high- or low-risk for disease recurrence. December 12, 2017
    Related Articles BreastPRS is a gene expression assay that stratifies intermediate-risk Oncotype DX patients into high- or low-risk for disease recurrence. Breast Cancer Res Treat. 2013 Jun;139(3):705-15 Authors: D'Alfonso TM, van Laar RK, Vahdat LT, Hussain W, Flinchum R, Brown N, John LS, Shin SJ Abstract Molecular prognostic assays, such as Oncotype DX, are increasingly incorporated into the management of patients with invasive breast carcinoma. BreastPRS is a new molecular assay developed and validated from a meta-analysis of publically available genomic datasets. We applied the assay to matched fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tumor samples to translate the assay to FFPE. A linear relationship of the BreastPRS prognostic score was observed between tissue preservation formats. BreastPRS recurrence scores were compared with Oncotype DX recurrence scores from 246 patients with invasive breast carcinoma and known Oncotype DX results. Using this series, a 120-gene Oncotype DX approximation algorithm was trained to predict Oncotype DX risk groups and then applied to series of untreated, node-negative, estrogen receptor (ER)-positive patients from previously published studies with known clinical outcomes. Correlation of recurrence score and risk group between Oncotype DX and BreastPRS was statistically significant (P 
  • Recreational Music-Making alters gene expression pathways in patients with coronary heart disease. December 12, 2017
    Related Articles Recreational Music-Making alters gene expression pathways in patients with coronary heart disease. Med Sci Monit. 2013 Feb 25;19:139-47 Authors: Bittman B, Croft DT, Brinker J, van Laar R, Vernalis MN, Ellsworth DL Abstract BACKGROUND: Psychosocial stress profoundly impacts long-term cardiovascular health through adverse effects on sympathetic nervous system activity, endothelial dysfunction, and atherosclerotic development. Recreational Music Making (RMM) is a unique stress amelioration strategy encompassing group music-based activities that has great therapeutic potential for treating patients with stress-related cardiovascular disease. MATERIAL/METHODS: Participants (n=34) with a history of ischemic heart disease were subjected to an acute time-limited stressor, then randomized to RMM or quiet reading for one hour. Peripheral blood gene expression using GeneChip® Human Genome U133A 2.0 arrays was assessed at baseline, following stress, and after the relaxation session. RESULTS: Full gene set enrichment analysis identified 16 molecular pathways differentially regulated (P
  • Effect of ASCO/CAP guidelines for determining ER status on molecular subtype. December 12, 2017
    Related Articles Effect of ASCO/CAP guidelines for determining ER status on molecular subtype. Ann Surg Oncol. 2013 Jan;20(1):87-93 Authors: Deyarmin B, Kane JL, Valente AL, van Laar R, Gallagher C, Shriver CD, Ellsworth RE Abstract BACKGROUND: Determination of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status is standard for predicting prognosis and determining treatment options for patients with breast cancer. In 2010, the American Society of Clinical Oncology (ASCO) and College of American Pathologists (CAP) issued guidelines that tumors with ≥1% positively staining cells should be considered ER positive. Here, we determined how this cutoff relates to molecular subtype. METHODS: Clinicopathological characteristics were compared between ER-negative, ER-positive, and low-ER-staining (1-10%) tumors using chi-square analysis with P
  • Genomic signatures for predicting survival and adjuvant chemotherapy benefit in patients with non-small-cell lung cancer. December 12, 2017
    Related Articles Genomic signatures for predicting survival and adjuvant chemotherapy benefit in patients with non-small-cell lung cancer. BMC Med Genomics. 2012 Jul 02;5:30 Authors: Van Laar RK Abstract BACKGROUND: Improved methods are needed for predicting prognosis and the benefit of delivering adjuvant chemotherapy (ACT) in patients with non-small-cell lung cancer (NSCLC). METHODS: A novel prognostic algorithm was identified using genomic profiles from 332 stage I-III adenocarcinomas and independently validated on a separate series of 264 patients with stage I-II tumors, compiled from five previous studies. The prognostic algorithm was used to interrogate genomic data from a series of patients treated with adjuvant chemotherapy. Those genes associated with outcome in the adjuvant treatment setting, independent to prognosis were used to train an algorithm able to classify a patient as either a responder or non-responder to ACT. The performance of this signature was independently validated on a separate series of genomic profiles from patients enrolled in a randomized controlled trial of cisplatin/vinorelbine vs. observation alone (JBR.10). RESULTS: NSCLC patients exhibiting the high-risk, poor-prognosis form of the 160-gene prognosis signature experienced a 2.80-times higher rate of 5-year disease specific death (log rank P 
  • Design and multiseries validation of a web-based gene expression assay for predicting breast cancer recurrence and patient survival. December 12, 2017
    Related Articles Design and multiseries validation of a web-based gene expression assay for predicting breast cancer recurrence and patient survival. J Mol Diagn. 2011 May;13(3):297-304 Authors: Van Laar RK Abstract Gene expression analysis is a valuable tool for determining the risk of disease recurrence and overall survival of an individual patient with breast cancer. The purpose of this study was to create and validate a robust prognostic algorithm and implement it within an online analysis environment. Genomic and clinical data from 477 clinically diverse patients with breast cancer were analyzed with Cox regression models to identify genes associated with outcome, independent of standard prognostic factors. Percentile-ranked expression data were used to train a "metagene" algorithm to stratify patients as having a high or low risk of recurrence. The classifier was applied to 1016 patients from five independent series. The 200-gene algorithm stratifies patients into risk groups with statistically and clinically significant differences in recurrence-free and overall survival. Multivariate analysis revealed the classifier to be the strongest predictor of outcome in each validation series. In untreated node-negative patients, 88% sensitivity and 44% specificity for 10-year recurrence-free survival was observed, with positive and negative predictive values of 32% and 92%, respectively. High-risk patients appear to significantly benefit from systemic adjuvant therapy. A 200-gene prognosis signature has been developed and validated using genomic and clinical data representing a range of breast cancer clinicopathological subtypes. It is a strong independent predictor of patient outcome and is available for research use. PMID: 21458382 [PubMed – indexed for MEDLINE]
  • Implementation of a novel microarray-based diagnostic test for cancer of unknown primary. December 12, 2017
    Related Articles Implementation of a novel microarray-based diagnostic test for cancer of unknown primary. Int J Cancer. 2009 Sep 15;125(6):1390-7 Authors: van Laar RK, Ma XJ, de Jong D, Wehkamp D, Floore AN, Warmoes MO, Simon I, Wang W, Erlander M, van't Veer LJ, Glas AM Abstract Patients with carcinoma of unknown primary (CUP) present with metastatic disease for which the primary site cannot be found, despite extensive standard investigation. Here, we describe the development and implementation of the first clinically available microarray-based test for this cancer type (CUPPrint), based on 633 individual tumors representing 30 carcinoma and 17 noncarcinoma classes. Tissue of origin prediction for either fresh frozen or paraffin-embedded tumor samples is achieved with the use of a custom 8-pack 1.9k microarray and robust classification algorithm. An expression profile of 495 genes was used to predict tumor origin by applying a k-nearest neighbor algorithm. Internal cross-validation and analysis of an independent, previously published, 229-sample dataset revealed that clinically informative predictions were made for up to 94% of samples analyzed. Analysis of 13 previously published CUP specimens yielded predicted tumor origins that supported the clinical suspicion in 12 cases (92%). Microarray profiling presents a promising tool to assist in the identification of the primary tumor and might direct a more tailored treatment for CUP patients. PMID: 19536816 [PubMed – indexed for MEDLINE]
  • Gene expression profiling to identify the histogenetic origin of metastatic adenocarcinomas of unknown primary. December 12, 2017
    Related Articles Gene expression profiling to identify the histogenetic origin of metastatic adenocarcinomas of unknown primary. J Clin Oncol. 2008 Sep 20;26(27):4435-41 Authors: Horlings HM, van Laar RK, Kerst JM, Helgason HH, Wesseling J, van der Hoeven JJ, Warmoes MO, Floore A, Witteveen A, Lahti-Domenici J, Glas AM, Van't Veer LJ, de Jong D Abstract PURPOSE: Patients with adenocarcinoma of unknown primary origin (ACUP) constitute approximately 4% of all malignancies. For effective treatment of these patients, it is considered optimal to identify the primary tumor origins. Currently, the success rate of the diagnostic work-up is only 20% to 30%. Our goal was to evaluate the contribution of gene expression profiling for routine clinical practice in patients with ACUP. PATIENTS AND METHODS: Formalin-fixed, paraffin-embedded (FFPE) samples were obtained from 84 patients with a known primary adenocarcinoma and from 38 patients with ACUP. An extensive immunohistochemical panel classified 16 of the patients with ACUP, whereas 22 patients remained unclassified for their histogenetic origin. Information about staging procedures and clinical follow-up were available in all patient cases. The expression data were analyzed in relation to clinicopathologic variables and immunohistochemical results. RESULTS: The gene expression-based assay classified the primary site correctly in 70 (83%) of 84 patient cases of primary and metastatic tumors of known origin, with good sensitivity for the majority of the tumor classes and relatively poor sensitivity for primary lung adenocarcinoma. Gene expression profiling identified 15 (94%) of 16 patients with initial ACUP who were classified by immunohistochemistry, and it made a valuable contribution to a potential site of origin in 14 of the 22 patients with ACUP. CONCLUSION: The gene expression platform can classify correctly from FFPE samples the majority of tumors classes both in patients with known primary and in patients with ACUP. Therefore, gene expression profiling represents an additional analytic approach to assist with the histogenetic diagnosis of patients with ACUP. PMID: 18802156 [PubMed – indexed for MEDLINE]
  • Comparison of gene expression profiles predicting progression in breast cancer patients treated with tamoxifen. December 12, 2017
    Related Articles Comparison of gene expression profiles predicting progression in breast cancer patients treated with tamoxifen. Breast Cancer Res Treat. 2009 Jan;113(2):275-83 Authors: Kok M, Linn SC, Van Laar RK, Jansen MP, van den Berg TM, Delahaye LJ, Glas AM, Peterse JL, Hauptmann M, Foekens JA, Klijn JG, Wessels LF, Van't Veer LJ, Berns EM Abstract BACKGROUND: Molecular signatures that predict outcome in tamoxifen treated breast cancer patients have been identified. For the first time, we compared these response profiles in an independent cohort of (neo)adjuvant systemic treatment naïve breast cancer patients treated with first-line tamoxifen for metastatic disease. METHODS: From a consecutive series of 246 estrogen receptor (ER) positive primary tumors, gene expression profiling was performed on available frozen tumors using 44K oligoarrays (n = 69). A 78-gene tamoxifen response profile (formerly consisting of 81 cDNA-clones), a 21-gene set (microarray-based Recurrence Score), as well as the HOXB13-IL17BR ratio (Two-Gene-Index, RT-PCR) were analyzed. Performance of signatures in relation to time to progression (TTP) was compared with standard immunohistochemical (IHC) markers: ER, progesterone receptor (PgR) and HER2. RESULTS: In univariate analyses, the 78-gene tamoxifen response profile, 21-gene set and HOXB13-IL17BR ratio were all significantly associated with TTP with hazard ratios of 2.2 (95% CI 1.3-3.7, P = 0.005), 2.3 (95% CI 1.3-4.0, P = 0.003) and 4.2 (95% CI 1.4-12.3, P = 0.009), respectively. The concordance among the three classifiers was relatively low, they classified only 45-61% of patients in the same category. In multivariate analyses, the association remained significant for the 78-gene profile and the 21-gene set after adjusting for ER and PgR. CONCLUSION: The 78-gene tamoxifen response profile, the 21-gene set and the HOXB13-IL17BR ratio were all significantly associated with TTP in an independent patient series treated with tamoxifen. The addition of multigene assays to ER (IHC) improves the prediction of outcome in tamoxifen treated patients and deserves incorporation in future clinical studies. PMID: 18311582 [PubMed – indexed for MEDLINE]
  • Gene-expression and immunohistochemical study of specific T-cell subsets and accessory cell types in the transformation and prognosis of follicular lymphoma. December 12, 2017
    Related Articles Gene-expression and immunohistochemical study of specific T-cell subsets and accessory cell types in the transformation and prognosis of follicular lymphoma. J Clin Oncol. 2007 Feb 1;25(4):390-8 Authors: Glas AM, Knoops L, Delahaye L, Kersten MJ, Kibbelaar RE, Wessels LA, van Laar R, van Krieken JH, Baars JW, Raemaekers J, Kluin PM, van't Veer LJ, de Jong D Abstract PURPOSE: Despite the generally favorable clinical course in follicular lymphoma (FL), a minority of patients have a poor prognosis-with death within 3 years of diagnosis-most often due to transformation to aggressive disease. PATIENTS AND METHODS: In this study, we analyzed the potential of predicting early transformation on the basis of gene expression and immunologic parameters in FL biopsy samples taken at diagnosis. RESULTS: At the gene-expression level, FL is a highly uniform disease at the time of diagnosis, precluding the detection of sufficiently validated prognostic gene-expression profiles suitable for a clinical setting. Combinations of differentially expressed genes indicate that immunologic mechanisms play a differential role in the risk of early transformation. Using immunohistochemistry for specific cell populations, the spatial distribution to neoplastic follicles and the activation of CD4-positive T-helper cells (P = .002) and specifically T-helper 1 (P = .004) were shown to be highly discriminatory to predict early transformation. A role for functional modulation of follicular dendritic cells could also be supported (P = .04). Other cell populations, including CD68-positive macrophages and regulatory T cells, were not differentially present. CONCLUSION: These results support the identification of FL as an immunologically functional disease in which an interaction of the tumor cells and the functional composition of the microenvironment determines the clinical behavior. PMID: 17200149 [PubMed – indexed for MEDLINE]
  • Empirical array quality weights in the analysis of microarray data. December 12, 2017
    Related Articles Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics. 2006 May 19;7:261 Authors: Ritchie ME, Diyagama D, Neilson J, van Laar R, Dobrovic A, Holloway A, Smyth GK Abstract BACKGROUND: Assessment of array quality is an essential step in the analysis of data from microarray experiments. Once detected, less reliable arrays are typically excluded or "filtered" from further analysis to avoid misleading results. RESULTS: In this article, a graduated approach to array quality is considered based on empirical reproducibility of the gene expression measures from replicate arrays. Weights are assigned to each microarray by fitting a heteroscedastic linear model with shared array variance terms. A novel gene-by-gene update algorithm is used to efficiently estimate the array variances. The inverse variances are used as weights in the linear model analysis to identify differentially expressed genes. The method successfully assigns lower weights to less reproducible arrays from different experiments. Down-weighting the observations from suspect arrays increases the power to detect differential expression. In smaller experiments, this approach outperforms the usual method of filtering the data. The method is available in the limma software package which is implemented in the R software environment. CONCLUSION: This method complements existing normalisation and spot quality procedures, and allows poorer quality arrays, which would otherwise be discarded, to be included in an analysis. It is applicable to microarray data from experiments with some level of replication. PMID: 16712727 [PubMed – indexed for MEDLINE]
  • Location of, immunogenicity of and relationships between neutralization epitopes on the attachment protein (G) of Hendra virus. December 12, 2017
    Related Articles Location of, immunogenicity of and relationships between neutralization epitopes on the attachment protein (G) of Hendra virus. J Gen Virol. 2005 Oct;86(Pt 10):2839-48 Authors: White JR, Boyd V, Crameri GS, Duch CJ, van Laar RK, Wang LF, Eaton BT Abstract Epitopes involved in a protective immune response to Hendra virus (HeV) (Henipavirus, Paramxyoviridae) were investigated by generating five neutralizing monoclonal antibodies (mAbs) to the virus attachment protein (G) of HeV (HeV G) and sequencing of the G gene of groups of neutralization-escape variants selected with each mAb. Amino acid substitutions occurred at eight distinct sites on HeV G. Relationships between these sites were investigated in binding and neutralization assays using heterologous combinations of variants and mAbs. The sites were also mapped to a proposed structural model for the attachment proteins of Paramyxoviridae. Their specific locations and the nature of their interactions with the mAb panel provided the first functional evidence that HeV G in fact resembled the proposed structure. Four sites (aa 183-185, 417, 447 and 570) contributed to a major discontinuous epitope, on the base of the globular head, that was similar to immunodominant virus neutralization sites found in other paramyxoviruses. Amino acid similarity between HeV and Nipah virus was relatively highly conserved at these sites but decreased significantly at the other sites identified in this study. These included another discontinuous epitope on the base of the head region defined by sites aa 289 and 324 and well separated epitopes on the top of the head at sites aa 191-195 and 385-356. The latter epitope corresponded to immunodominant neutralization sites found in Rinderpest virus and Measles virus. PMID: 16186240 [PubMed – indexed for MEDLINE]
  • An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. December 12, 2017
    Related Articles An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. Cancer Res. 2005 May 15;65(10):4031-40 Authors: Tothill RW, Kowalczyk A, Rischin D, Bousioutas A, Haviv I, van Laar RK, Waring PM, Zalcberg J, Ward R, Biankin AV, Sutherland RL, Henshall SM, Fong K, Pollack JR, Bowtell DD, Holloway AJ Abstract Gene expression profiling offers a promising new technique for the diagnosis and prognosis of cancer. We have applied this technology to build a clinically robust site of origin classifier with the ultimate aim of applying it to determine the origin of cancer of unknown primary (CUP). A single cDNA microarray platform was used to profile 229 primary and metastatic tumors representing 14 tumor types and multiple histologic subtypes. This data set was subsequently used for training and validation of a support vector machine (SVM) classifier, demonstrating 89% accuracy using a 13-class model. Further, we show the translation of a five-class classifier to a quantitative PCR-based platform. Selecting 79 optimal gene markers, we generated a quantitative-PCR low-density array, allowing the assay of both fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue. Data generated using both quantitative PCR and microarray were subsequently used to train and validate a cross-platform SVM model with high prediction accuracy. Finally, we applied our SVM classifiers to 13 cases of CUP. We show that the microarray SVM classifier was capable of making high confidence predictions in 11 of 13 cases. These predictions were supported by comprehensive review of the patients' clinical histories. PMID: 15899792 [PubMed – indexed for MEDLINE]
  • Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. December 12, 2017
    Related Articles Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3697-702 Authors: Peart MJ, Smyth GK, van Laar RK, Bowtell DD, Richon VM, Marks PA, Holloway AJ, Johnstone RW Abstract Histone deacetylase inhibitors (HDACis) inhibit tumor cell growth and survival, possibly through their ability to regulate the expression of specific proliferative and/or apoptotic genes. However, the HDACi-regulated genes necessary and/or sufficient for their biological effects remain undefined. We demonstrate that the HDACis suberoylanilide hydroxamic acid (SAHA) and depsipeptide regulate a highly overlapping gene set with at least 22% of genes showing altered expression over a 16-h culture period. SAHA and depsipeptide coordinately regulated the expression of several genes within distinct apoptosis and cell cycle pathways. Multiple genes within the Myc, type beta TGF, cyclin/cyclin-dependent kinase, TNF, Bcl-2, and caspase pathways were regulated in a manner that favored induction of apoptosis and decreased cellular proliferation. APAF-1, a gene central to the intrinsic apoptotic pathway, was induced by SAHA and depsipeptide and shown to be important, but not essential, for HDACi-induced cell death. Overexpression of p16(INK4A) and arrest of cells in G(1) can suppress HDACi-mediated apoptosis. Although p16(INK4A) did not affect the genome-wide transcription changes mediated by SAHA, a small number of apoptotic genes, including BCLXL and B-MYB, were differentially regulated in a manner consistent with attenuated HDACi-mediated apoptosis in arrested cells. We demonstrate that different HDACi alter transcription of a large and common set of genes that control diverse molecular pathways important for cell survival and proliferation. The ability of HDACi to target multiple apoptotic and cell proliferation pathways may provide a competitive advantage over other chemotherapeutic agents because suppression/loss of a single pathway may not confer resistance to these agents. PMID: 15738394 [PubMed – indexed for MEDLINE]
  • Genomic analysis of a spontaneous model of breast cancer metastasis to bone reveals a role for the extracellular matrix. December 12, 2017
    Related Articles Genomic analysis of a spontaneous model of breast cancer metastasis to bone reveals a role for the extracellular matrix. Mol Cancer Res. 2005 Jan;3(1):1-13 Authors: Eckhardt BL, Parker BS, van Laar RK, Restall CM, Natoli AL, Tavaria MD, Stanley KL, Sloan EK, Moseley JM, Anderson RL Abstract A clinically relevant model of spontaneous breast cancer metastasis to multiple sites, including bone, was characterized and used to identify genes involved in metastatic progression. The metastatic potential of several genetically related tumor lines was assayed using a novel real-time quantitative RT-PCR assay of tumor burden. Based on this assay, the tumor lines were categorized as nonmetastatic (67NR), weakly metastatic to lymph node (168FARN) or lung (66cl4), or highly metastatic to lymph node, lung, and bone (4T1.2 and 4T1.13). In vitro assays that mimic stages of metastasis showed that highly metastatic tumors lines were more adhesive, invasive, and migratory than the less metastatic lines. To identify metastasis-related genes in this model, each metastatic tumor was array profiled against the nonmetastatic 67NR using 15,000 mouse cDNA arrays. A significant proportion of genes relating to the extracellular matrix had elevated expression in highly metastatic tumors. The role of one of these genes, POEM, was further investigated in the model. In situ hybridization showed that POEM expression was specific to the tumor epithelium of highly metastatic tumors. Decreased POEM expression in 4T1.2 tumors significantly inhibited spontaneous metastasis to the lung, bone, and kidney. Taken together, our data support a role for the extracellular matrix in metastatic progression and describe, for the first time, a role for POEM in this process. PMID: 15671244 [PubMed – indexed for MEDLINE]
  • Options available–from start to finish–for obtaining data from DNA microarrays II. December 12, 2017
    Related Articles Options available–from start to finish–for obtaining data from DNA microarrays II. Nat Genet. 2002 Dec;32 Suppl:481-9 Authors: Holloway AJ, van Laar RK, Tothill RW, Bowtell DD Abstract Microarray technology has undergone a rapid evolution. With widespread interest in large-scale genomic research, an abundance of equipment and reagents have now become available and affordable to a large cross section of the scientific community. As protocols become more refined, careful investigators are able to obtain good quality microarray data quickly. In most recent times, however, perhaps one of the biggest obstacles researchers face is not the manufacture and use of microarrays at the bench, but storage and analysis of the array data. This review discusses the most recent equipment, reagents and protocols available to the researcher, as well as describing data analysis and storage options available from the evolving field of microarray informatics. PMID: 12454642 [PubMed – indexed for MEDLINE]