Universal DNA methylation age across mammalian tissues

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease

BACKGROUND

DNA methylation is implicated in coronary heart disease (CHD), but current evidence is based on small, cross-sectional studies. We examined blood DNA methylation in relation to incident CHD across multiple prospective cohorts.

METHODS

Nine population-based cohorts from the United States and Europe profiled epigenome-wide blood leukocyte DNA methylation using the Illumina Infinium 450k microarray, and prospectively ascertained CHD events including coronary insufficiency/unstable angina, recognized myocardial infarction, coronary revascularization, and coronary death. Cohorts conducted race-specific analyses adjusted for age, sex, smoking, education, body mass index, blood cell type proportions, and technical variables. We conducted fixed-effect meta-analyses across cohorts.

RESULTS

Among 11 461 individuals (mean age 64 years, 67% women, 35% African American) free of CHD at baseline, 1895 developed CHD during a mean follow-up of 11.2 years. Methylation levels at 52 CpG (cytosine-phosphate-guanine) sites were associated with incident CHD or myocardial infarction (false discovery rate<0.05). These CpGs map to genes with key roles in calcium regulation (ATP2B2, CASR, GUCA1B, HPCAL1), and genes identified in genome- and epigenome-wide studies of serum calcium (CASR), serum calcium-related risk of CHD (CASR), coronary artery calcified plaque (PTPRN2), and kidney function (CDH23, HPCAL1), among others. Mendelian randomization analyses supported a causal effect of DNA methylation on incident CHD; these CpGs map to active regulatory regions proximal to long non-coding RNA transcripts.

CONCLUSION

Methylation of blood-derived DNA is associated with risk of future CHD across diverse populations and may serve as an informative tool for gaining further insight on the development of CHD.

Inflammation-related genes are associated with epigenetic aging in HIV

Chronic inflammation is characteristic of both HIV and aging ("inflammaging") and may contribute to the accelerated aging observed in people living with HIV (PLWH). We examined whether three inflammation-related single-nucleotide polymorphisms (SNPs) were risk factors for accelerated aging and HIV-associated, non-AIDS (HANA) conditions among PLWH. We examined 155 postmortem cases with HIV (mean age = 47.3, 81% male, 68% self-reported White) from the National NeuroAIDS Tissue Consortium who had pre-mortem neurobehavioral/medical/virologic data and epigenomic data from occipital cortex tissue. Accelerated aging was measured according to the Epigenetic Clock; an aging biomarker based on DNA methylation levels. Past or current age-associated HANA conditions including cerebrovascular, liver and kidney disease, chronic obstructive pulmonary disease, cancer, and diabetes were determined via self-report. Epigenetic Aging Z-scores and likelihood of past/current HANA conditions were compared between major allele homozygotes and minor allele carriers for each SNP (IL-6 - 174G>C, IL-10 - 592C>A, TNF-α - 308 G>A) separately. Analyses were adjusted for relevant demographic/clinical factors. Epigenetic aging (e.g., higher Z-scores) was significantly greater in IL-6 C allele carriers (p = .002) and IL-10 CC homozygotes (p = .02) compared to other genotype groups. The likelihood of any past/current HANA condition did not differ by IL-10 genotype but was 3.36 times greater in IL-6 C allele carriers versus others (OR = 3.36, 95%CI = 1.09-10.34, p = .03). TNF-α genotype was not associated with epigenetic aging or HANA conditions. IL-6 and IL-10 SNPs may help to identify PLWH who are at high risk for accelerated aging. These insights into pathophysiological pathways may inform interventional approaches to treat rapid aging among PLWH.

Abstract P1-09-08: Hormonal factors associated with elevation of DNA methylation age in breast tissue of healthy women

Background: Healthy breast tissue appears older than matched peripheral blood, when using a biologic aging measurement based on DNA methylation markers. The underlying cause of this acceleration is not known. We hypothesize that cumulative estrogen exposure is associated with accelerated breast epigenetic aging. In this study, we examined factors associated with breast epigenetic age in a healthy population of women.

Methods: We used breast tissue samples from 232 healthy women donors (119 pre-menopausal, 113 post-menopausal) to the Komen Tissue Bank, with data available on variables related to cumulative estrogen exposure, including age at menarche, gravidity, parity, and menopausal status. DNA methylation experiments were performed using the Illumina EPIC 850K array platform. DNA methylation age (DNAm age) was calculated using the epigenetic clock methods developed by Horvath (2013). Total years of estrogen exposure was calculated as the difference between age at menopause (or current age) - number of live births x 9 months – number of miscarriages x 3 months. Nonparametric group testing was used to compare mean levels of the difference between DNAm age and chronologic age for pre- and post-menopausal groups. We examined the outcome “age acceleration”, calculated using the residuals of the regression of DNAm age versus chronologic age, because it is age-adjusted and independent of cell distribution. Multivariate linear regression models were used to examine for associations between age acceleration and each of our covariates.

Results: Our sample included women aged 19-90 years (mean age 50.7, SD 11.8), with 114 nulliparous women. We confirmed that DNAm age in breast tissue is strongly correlated with chronologic age (ρ=0.89, p&lt;0.0001). The difference between DNAm age and chronologic age is greater at earlier ages, and is significantly greater in premenopausal women (mean 8.9 years, SE 0.04), compared with postmenopausal women (mean 2.7 years, SE 0.05) (p&lt;0.0001). Age acceleration was significantly associated with earlier age at menarche (β=-0.395 for each year, p=0.036). For women with limited total years of exposure to estrogen (&lt;19 years), there was a significant association between age acceleration and total estrogen exposure and β=0.673 for each year, p=0.028).

Conclusion: Acceleration of epigenetic age in breast tissues occurs in healthy women and is most pronounced in the pre-menopausal period. Earlier age at menarche and total years of estrogen exposure are associated with higher degree of acceleration, suggesting that cumulative estrogen exposure drives this process.

Citation Format: Sehl ME, Henry JE, Storniolo AM, Horvath S, Ganz PA. Hormonal factors associated with elevation of DNA methylation age in breast tissue of healthy women [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-09-08.

Abstract P2-04-02: Comparison of DNA methylation patterns in normal breast tissue from women with and without breast cancer

BACKGROUND: Increasing evidence suggests that epigenetic mechanisms play critical roles in the development of breast cancer. However, precise DNA methylation signatures associated with breast cancer susceptibility remain unknown. We sought to compare DNA methylation changes in the normal breast tissue of women with and without breast cancer to identify patterns of aberrant DNA methylation in women with breast cancer.

METHODS:Samples of normal breast tissue were collected from four cohorts of women: age &lt; 50 years with and without breast cancer, and age ≥50 years with and without breast cancer. Normal breast tissue from healthy women was obtained from the Komen Tissue Bank at IU Simon Cancer Center and from women presenting for reduction mammoplasty at Yale New Haven Hospital. Normal breast tissue from women with breast cancer was obtained from patients undergoing adjuvant total mastectomy at Yale Breast Center. DNA was extracted using Qiagen AllPrep Universal kit. Raw data files in idat format were imported to Partek Genomics Suite 6.6 for normalization and differential methylation analysis. Raw intensities were normalized using With Array Normalization (SWAN) method. Principal component analysis (PCA) were performed as quality control. Differentially methylated loci (DML) between control and breast cancer groups were detected when False discovery rate (FDR) &lt; 0.05 and fold change &gt; 1.5. Functional enrichment analysis of genes with DML in the gene body were conducted using METACORE™. Pathways with FDR &lt; 0.05 were selected.

RESULTS: Ninety-three normal breast tissue samples from 89 subjects were analyzed (breast cancer=40, unaffected=53). Comparison of DNA methylation patterns between women with and without breast cancer revealed 200 DMLs. The majority of DMLs (186) were hyper-methylated in breast cancer patients, and 48 DMLs locate in enhancers of genes. 170 DMLs locate in 134 genes, enriched in two pathways: (1) Cell adhesion_Endothelial cell contacts by junctional mechanisms, and (2) Neurophysiological process_Constitutive and regulated NMDA receptor trafficking. Genes associated with cell adhesion and cell contacts included: ACTN2, GJA4, GJA7 and MAGI1. Two hyper-methylated loci were found in enhancers of ACTN2. In addition, one hyper-methylated locus in GJA4, one hyper-methylated and one hypo-methylated loci in GJA7, and two hyper-methylated loci in MAGI1 were detected in breast cancer patients. Genes associated with NMDA receptor trafficking include: TPK1, ADCY4 and LIN7C. One and two loci were found in TPK1 and ADCY4, respectively, that were hyper-methylated in normal breast tissue from cancer patients in the gene body, while a hypo-methylated locus in breast cancer patients was identified in LIN7C.

CONCLUSIONS: Comparison of DNA methylation patterns of normal breast tissue from women with and without breast cancer reveal specific mechanistic pathways and genes that are differentially methylated in women with breast cancer. DNA methylation of normal breast tissue deserves further study as a potential biomarker for breast cancer risk stratification and may lend new insight into mechanisms of breast cancer development.

Citation Format: Hofstatter EW, Zhu Y, Horvath S, Chagpar AB, Wali VB, Bossuyt V, Storniolo AM, Hatzis C, Patwardhan G, Von Wahlde M-K, Butler M, Epstein L, Stavris K, Sturrock T, Au A, Kwei S, Pusztai L. Comparison of DNA methylation patterns in normal breast tissue from women with and without breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-04-02.

Comparison of epigenetic aging in normal breast tissue from women with and without breast cancer

1522

Background: Age is one of the most important risk factors for developing breast cancer. However, why increasing age is associated with increasing incidence of breast cancer remains poorly understood. We hypothesize that accumulated epigenetic alterations in the breast contribute to the development of breast cancer, and that such changes accumulate more rapidly in the breast during the lifetime of women who develop breast cancer as compared to their healthy peers. We therefore sought to identify an epigenetic pattern of accelerated breast tissue “aging” in women with breast cancer. Methods: Samples of normal breast tissue were collected from four cohorts of women: age < 50 years with and without breast cancer, and age ≥50 years with and without breast cancer (BC). Samples were obtained from the Susan G. Komen Tissue Bank at IU Simon Cancer Center, reduction mammoplasties and adjuvant mastectomy specimens at Yale. The Illumina Human 450K BeadChip microarray was used to generate DNA methylation profiles. Data was analyzed using the “Epigenetic Clock”, a published biomarker of aging based on 353 specific CpGs in the human genome. Clinical data collected for each subject included: age, height, weight, ethnicity, medical and reproductive history, tobacco and alcohol use, family history of breast cancer, current medications, and tumor characteristics. Results: Normal breast tissue samples from 90 subjects were analyzed (age < 50 with BC = 22, age < 50 without BC = 30, age ≥50 with BC = 15, age ≥50 without BC = 23). Age range was 24-82 years and 18-82 years for cohorts with and without BC respectively. In the cohort with BC, 95% of tumors were estrogen receptor-positive. Overall, DNA methylation tissue age (DNAmAge) was strongly correlated with chronologic age (r = 0.88, p < 0.001). However, normal breast tissue from women with breast cancer demonstrated significantly accelerated DNAmAge as compared to healthy peers (p < 0.001). Conclusions: Normal breast tissue from women with breast cancer demonstrates evidence of an accelerated epigenetic "aging" process. DNAmAge of normal breast tissue may prove to be a useful tool in identifying those women at highest risk, and lend insight into novel mechanisms of breast cancer prevention.

Generating an image that affords slant perception from stereo, without pictorial cues

This paper describes an algorithm for generating a planar image that when tilted provides stereo cues to slant, without contamination from pictorial gradients. As the stimuli derived from this image are ultimately intended for use in studies of slant perception under magnification, a further requirement is that the generated image be suitable for high-definition printing or display on a monitor. A first stage generates an image consisting of overlapping edges with sufficient density that when zoomed, edges that nearly span the original scale are replaced with newly emergent content that leaves the visible edge statistics unchanged. A second stage reduces intensity clumping while preserving edges by enforcing a broad dynamic range across the image. Spectral analyses demonstrate that the low-frequency content of the resulting image, which would correspond to the pictorial cue of texture gradient changes under slant, (a) has a power fall-off deviating from 1/f noise (to which the visual system is particularly sensitive), and (b) does not offer systematic cues under changes in scale or slant. Two behavioral experiments tested whether the algorithm generates stimuli that offer cues to slant under stereo viewing only, and not when disparities are eliminated. With a particular adjustment of dynamic range (and nearly so with the other version that was tested), participants viewing without stereo cues were essentially unable to discriminate slanted from flat (frontal) stimuli, and when slant was reported, they failed to discriminate its direction. In contrast, non-stereo viewing of a control stimulus with pictorial cues, as well as stereoscopic observation, consistently allowed participants to perceive slant correctly. Experiment 2 further showed that these results generalized across a population of different stimuli from the same generation process and demonstrated that the process did not substitute biased slant cues.

Peripheral blood gene expression profiles linked to monoamine metabolite levels in cerebrospinal fluid

The blood-brain barrier separates circulating blood from the central nervous system (CNS). The scope of this barrier is not fully understood which limits our ability to relate biological measurements from peripheral to central phenotypes. For example, it is unknown to what extent gene expression levels in peripheral blood are reflective of CNS metabolism. In this study, we examine links between central monoamine metabolite levels and whole-blood gene expression to better understand the connection between peripheral systems and the CNS. To that end, we correlated the prime monoamine metabolites in cerebrospinal fluid (CSF) with whole-genome gene expression microarray data from blood (N=240 human subjects). We additionally applied gene-enrichment analysis and weighted gene co-expression network analyses (WGCNA) to identify modules of co-expressed genes in blood that may be involved with monoamine metabolite levels in CSF. Transcript levels of two genes were significantly associated with CSF serotonin metabolite levels after Bonferroni correction for multiple testing: THAP7 (P=2.8 × 10^-8, β=0.08) and DDX6 (P=2.9 × 10^-7, β=0.07). Differentially expressed genes were significantly enriched for genes expressed in the brain tissue (P=6.0 × 10^-52). WGCNA revealed significant correlations between serotonin metabolism and hub genes with known functions in serotonin metabolism, for example, HTR2A and COMT. We conclude that gene expression levels in whole blood are associated with monoamine metabolite levels in the human CSF. Our results, including the strong enrichment of brain-expressed genes, illustrate that gene expression profiles in peripheral blood can be relevant for quantitative metabolic phenotypes in the CNS.

Genomic profiles and predictors of early allograft dysfunction after human liver transplantation

Early hepatic allograft dysfunction (EAD) manifests posttransplantation with high serum transaminases, persistent cholestasis, and coagulopathy. The biological mechanisms are poorly understood. This study investigates the molecular mechanisms involved in EAD and defines a gene expression signature revealing different biological pathways in subjects with EAD from those without EAD, a potential first step in developing a molecular classifier as a potential clinical diagnostic. Global gene expression profiles of 30 liver transplant recipients of deceased donor grafts with EAD and 26 recipients without graft dysfunction were investigated using microarrays of liver biopsies performed at the end of cold storage and after graft reperfusion prior to closure. Results reveal a shift in inflammatory and metabolic responses between the two time points and differences between EAD and non-EAD. We identified relevant pathways (PPARα and NF-κB) and targets (such as CXCL1, IL1, TRAF6, TIPARP, and TNFRSF1B) associated with the phenotype of EAD. Preliminary proof of concept gene expression classifiers that distinguish EAD from non-EAD patients, with Area Under the Curve (AUC) >0.80 were also identified. This data may have mechanistic and diagnostic implications for EAD.

Molecular classifiers for acute kidney transplant rejection in peripheral blood by whole genome gene expression profiling

There are no minimally invasive diagnostic metrics for acute kidney transplant rejection (AR), especially in the setting of the common confounding diagnosis, acute dysfunction with no rejection (ADNR). Thus, though kidney transplant biopsies remain the gold standard, they are invasive, have substantial risks, sampling error issues and significant costs and are not suitable for serial monitoring. Global gene expression profiles of 148 peripheral blood samples from transplant patients with excellent function and normal histology (TX; n = 46), AR (n = 63) and ADNR (n = 39), from two independent cohorts were analyzed with DNA microarrays. We applied a new normalization tool, frozen robust multi-array analysis, particularly suitable for clinical diagnostics, multiple prediction tools to discover, refine and validate robust molecular classifiers and we tested a novel one-by-one analysis strategy to model the real clinical application of this test. Multiple three-way classifier tools identified 200 highest value probesets with sensitivity, specificity, positive predictive value, negative predictive value and area under the curve for the validation cohort ranging from 82% to 100%, 76% to 95%, 76% to 95%, 79% to 100%, 84% to 100% and 0.817 to 0.968, respectively. We conclude that peripheral blood gene expression profiling can be used as a minimally invasive tool to accurately reveal TX, AR and ADNR in the setting of acute kidney transplant dysfunction.

A systematic approach to multifactorial cardiovascular disease: causal analysis

The combination of systems biology and large data sets offers new approaches to the study of cardiovascular diseases. These new approaches are especially important for the common cardiovascular diseases that have long been described as multifactorial. This promise is undermined by biologists' skepticism of the spider web-like network diagrams required to analyze these large data sets. Although these spider webs resemble composites of the familiar biochemical pathway diagrams, the complexity of the webs is overwhelming. As a result, biologists collaborate with data analysts whose mathematical methods seem much like those of experts using Ouija boards. To make matters worse, it is not evident how to design experiments when the network implies that many molecules must be part of the disease process. Our goal is to remove some of this mystery and suggest a simple experimental approach to the design of experiments appropriate for such analysis. We will attempt to explain how combinations of data sets that include all possible variables, graphical diagrams, complementation of different data sets, and Bayesian analyses now make it possible to determine the causes of multifactorial cardiovascular disease. We will describe this approach using the term causal analysis. Finally, we will describe how causal analysis is already being used to decipher the interactions among cytokines as causes of cardiovascular disease.

Biomarkers to predict antidepressant response

During the past several years, we have achieved a deeper understanding of the etiology/pathophysiology of major depressive disorder (MDD). However, this improved understanding has not translated to improved treatment outcome. Treatment often results in symptomatic improvement, but not full recovery. Clinical approaches are largely trial-and-error, and when the first treatment does not result in recovery for the patient, there is little proven scientific basis for choosing the next. One approach to enhancing treatment outcomes in MDD has been the use of standardized sequential treatment algorithms and measurement-based care. Such treatment algorithms stand in contrast to the personalized medicine approach, in which biomarkers would guide decision making. Incorporation of biomarker measurements into treatment algorithms could speed recovery from MDD by shortening or eliminating lengthy and ineffective trials. Recent research results suggest several classes of physiologic biomarkers may be useful for predicting response. These include brain structural or functional findings, as well as genomic, proteomic, and metabolomic measures. Recent data indicate that such measures, at baseline or early in the course of treatment, may constitute useful predictors of treatment outcome. Once such biomarkers are validated, they could form the basis of new paradigms for antidepressant treatment selection.

Computer-aided detection (CAD) as a second reader using perspective filet view at CT colonography: effect on performance of inexperienced readers

AIM

To evaluate whether computer-aided detection (CAD) as a second reader using perspective filet view [three-dimensional (3D) filet] improves the performance of inexperienced readers at computed tomography colonography (CTC) compared with unassisted 3D filet and unassisted two-dimensional (2D) CTC.

MATERIAL AND METHODS

Fifty symptomatic patients underwent CTC and same-day colonoscopy with segmental unblinding. Two inexperienced readers read the CTC studies on 3D filet and 2D several weeks apart. Four months later, readers re-read the cases only evaluating CAD marks using 3D filet. Suspicious CAD marks not previously described on 3D filet were recorded. Jackknife free-response receiver operating characteristic (JAFROC-1) analysis was used to compare the observers' performances in detecting lesions with 3D filet, 2D and 3D filet with CAD.

RESULTS

One hundred and three lesions > or =3mm were detected at colonoscopy with segmental unblinding. CAD alone had a sensitivity of 73% (75/103) at a mean false-positive rate per patient of 12.8 in supine and 11.4 in prone. For inexperienced readers sensitivities with 3D filet with CAD were 58% (60/103) and 48% (50/103) with an improvement of 14-16 percentage points (p<0.05) compared with 2D and of 10-11 percentage points (p<0.05) compared with 3D filet. For inexperienced readers, the false-positive rate was 25-41% and 71-200% higher with 3D filet with CAD compared with 3D filet and 2D, respectively. JAFROC-1 analysis showed no significant differences in per-lesion overall performance among reading modes (p=0.8).

CONCLUSION

CAD applied as a second reader using 3D filet increased both sensitivity and the number of false positives by inexperienced readers compared with 3D filet and 2D, thus not improving overall performance, i.e., the ability to distinguish between lesions and non-lesions.

Primary three-dimensional analysis with perspective-filet view versus primary two-dimensional analysis: evaluation of lesion detection by inexperienced readers at computed tomographic colonography in symptomatic patients

BACKGROUND

"Perspective-filet view" is a novel three-dimensional (3D) viewing technique for computed tomography colonography (CTC). Studies with experienced readers have shown a sensitivity for perspective-filet view similar to that of 2D or 3D endoluminal fly-through in detection of colorectal lesions. It is not known whether perspective-filet view, compared to axial images, improves lesion detection by inexperienced readers.

PURPOSE

To compare primary 3D analysis using perspective-filet view (3D Filet) with primary 2D analysis, as used by inexperienced CTC readers. Secondary aims were to compare lesion detection by 3D Filet when used by experienced and inexperienced readers, and to evaluate the effect of combined 3D Filet + 2D analysis.

MATERIAL AND METHODS

Fifty symptomatic patients were prospectively enrolled. An experienced reader performed 3D Filet analysis followed by complete 2D analysis (3D Filet + 2D), before colonoscopy with segmental unblinding. Two inexperienced readers (readers 2 and 3), blinded to CTC and colonoscopy findings, retrospectively performed 3D Filet analysis and, after 5 weeks, 2D analysis. True positives >or=6 mm detected by the inexperienced readers with 3D Filet and/or 2D were combined to obtain 3D Filet + 2D.

RESULTS

Colonoscopy revealed 116 lesions: 16 lesions >or=10 mm, 19 lesions 6-9 mm, and 81 lesions <or=5 mm. For the experienced reader, sensitivities for lesions >or=6 mm with 3D Filet and 3D Filet + 2D were 77% and 83%, respectively. For the inexperienced readers, sensitivities for lesions >or=6 mm with 3D Filet and 2D were 51% and 57% (reader 2) and 40% and 43% (reader 3), respectively. There was no significant difference between 3D Filet and 2D regarding sensitivity and reading time. For lesions >or=6 mm, 3D Filet + 2D improved the sensitivity of reader 2 to 63% and of reader 3 to 51%.

CONCLUSION

Lesion detection by inexperienced readers using perspective-filet view is comparable to that obtained by 2D. Lesion detection improves by combining 3D Filet + 2D, but not to the level of an experienced reader.

Insulin growth factor-binding protein 2 is a candidate biomarker for PTEN status and PI3K/Akt pathway activation in glioblastoma and prostate cancer

PTEN is an important tumor-suppressor gene associated with many cancers. Through expression profiling of glioblastoma tissue samples and prostate cancer xenografts, we identified a molecular signature for loss of the PTEN tumor suppressor in glioblastoma and prostate tumors. The PTEN signature consists of a minimum of nine genes, several of which are involved in various pathways already implicated in tumor formation. Among these signature genes, the most significant was an increase in insulin growth factor-binding protein 2 (IGFBP-2) mRNA. Up-regulation of IGFBP-2 was confirmed at the protein level by Western blot analysis and validated in samples not included in the microarray analysis. The link between IGFBP-2 and PTEN was of particular interest because elevated serum IGFBP-2 levels have been reported in patients with prostate and brain tumors. To further investigate this link, we determined that IGFBP-2 expression is negatively regulated by PTEN and positively regulated by phosphatidylinositol 3-kinase (PI3K) and Akt activation. In addition, Akt-driven transformation is impaired in IGFBP2(-/-) mouse embryo fibroblasts, implicating a functional role for IGFBP-2 in PTEN signaling. Collectively, these studies establish that PTEN and IGFBP-2 expression are inversely correlated in human brain and prostate cancers and implicate serum IGFBP-2 levels as a potential serum biomarker of PTEN status and PI3K Akt pathway activation in cancer patients.

Stereotactic stimulation of the anterior lobe of the cerebellum in cerebral palsy from a suboccipital approach

The anatomical connections of the anterior lobe of the cerebellum with the reticular formation in the brainstem, upper motor neurons and the limbic system, as well as the results of experimental and clinical observations indicate that this region is a proper area for modulation of certain types of central motor disorders but also of limbic functions. Through a direct stereotacticaly suboccipital approach electrodes were introduced into the anterior lobe of the cerebellum in four patients (3 females and one male, 24, 29, 45 and 19 years old, respectively) suffering from cerebral palsy and being confined to a wheelchair with severe spastic choreoathetoid movements, with minimal hand function, but in good mental state. After a period of test stimulation (up to 10 days), the pulse generators were implanted and chronic high-frequency stimulation was applied (for 37, 58, 9 and 32 months, respectively). In agreement with our previous experience (transtentorial approach in 30 patients), noticeable improvements in spasticity were immediate and a gradual reduction in choreoatetoid movements was observed in the following days to weeks. Improvements in speech, swallowing, respiration, posture, ambulation, and mood states were combined with development of new motor skills. Caution with the proper positioning of the electrode in the target and the selection of optimal program for stimulation are of paramount importance.

Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target

Glioblastoma is the most common primary malignant brain tumor of adults and one of the most lethal of all cancers. Patients with this disease have a median survival of 15 months from the time of diagnosis despite surgery, radiation, and chemotherapy. New treatment approaches are needed. Recent works suggest that glioblastoma patients may benefit from molecularly targeted therapies. Here, we address the compelling need for identification of new molecular targets. Leveraging global gene expression data from two independent sets of clinical tumor samples (n = 55 and n = 65), we identify a gene coexpression module in glioblastoma that is also present in breast cancer and significantly overlaps with the "metasignature" for undifferentiated cancer. Studies in an isogenic model system demonstrate that this module is downstream of the mutant epidermal growth factor receptor, EGFRvIII, and that it can be inhibited by the epidermal growth factor receptor tyrosine kinase inhibitor Erlotinib. We identify ASPM (abnormal spindle-like microcephaly associated) as a key gene within this module and demonstrate its overexpression in glioblastoma relative to normal brain (or body tissues). Finally, we show that ASPM inhibition by siRNA-mediated knockdown inhibits tumor cell proliferation and neural stem cell proliferation, supporting ASPM as a potential molecular target in glioblastoma. Our weighted gene coexpression network analysis provides a blueprint for leveraging genomic data to identify key control networks and molecular targets for glioblastoma, and the principle eluted from our work can be applied to other cancers.

A link between repetitive sequences and gene replication time

Genes display a wide range of replication times in S phase. In general, late replication is associated with transcriptionally repressive states and early replication with transcriptional competence. Rare examples of early-replicating repressive states have also been identified that are consistent with molecular evidence that repressive states are not all uniform in nature. Here we show that the replication times of over 4000 Drosophila genes correlate with the abundance of repetitive sequences in approximately 200-kb regions flanking the genes. In particular, Satellite-Related sequences (SRs) and the simple sequence repeats (SSRs) (CA)n and (ACTG)n were increasingly abundant in the regions flanking progressively later replicating genes, while (CATA)n repeats were more abundant around earlier replicating genes. These four sequences comprise less than 0.5% of the 'euchromatic genome' in Drosophila, yet they account for 5% of the variation of gene replication timing. Although the effect is not strong, it is broad: 99% of the genome is within the region of correlation of at least one of the above repeats. The role of SSRs and non-centromeric SRs in the genome is not known. We propose that SSRs and SRs foster transcriptionally repressive states throughout the genome in order to minimize spurious transcription.

Reg IV: a promising marker of hormone refractory metastatic prostate cancer

The diagnosis and management of prostate cancer is hampered by the absence of markers capable of identifying patients with metastatic disease. In order to identify potential new markers for prostate cancer, we compared gene expression signatures of matched androgen-dependent and hormone refractory prostate cancer xenografts. One candidate gene overexpressed in a hormone refractory xenograft was homologous to the regenerating protein gene family, a group of secreted proteins expressed in the gastrointestinal tract and overexpressed in inflammatory bowel disease and cancer. This gene, Reg IV, was confirmed to be differentially expressed in the LAPC-9 hormone refractory xenograft. Consistent with its up-regulation in a hormone refractory xenograft, it is expressed in several prostate tumors after neoadjuvant hormone ablation therapy. As predicted by its sequence homology, it is secreted from transiently transfected cells. It is also expressed strongly in a majority of hormone refractory metastases represented on two high-density tissue microarrays. In comparison, it is not expressed by any normal prostate specimens and only at low levels in approximately 40% of primary tumors. These data support Reg IV as a candidate marker for hormone refractory metastatic prostate cancer.

Epithelial cell adhesion molecule (KSA) expression: pathobiology and its role as an independent predictor of survival in renal cell carcinoma

PURPOSE

Epithelial cell adhesion molecule (EpCAM) is a widely expressed adhesion molecule in epithelial cancers. The purpose of this study is to determine the protein expression patterns of EpCAM in renal cell carcinoma (RCC) using tissue arrays linked to a clinicopathological database to evaluate both its predictive power in patient stratification and its suitability as a potential target for immunotherapeutic treatment strategies.

EXPERIMENTAL DESIGN

The University of California, Los Angeles kidney cancer tissue microarray contains specimens from 417 patients treated with nephrectomy. EpCAM protein expression in tumors and matched morphologically normal renal tissues was evaluated using anti-EpCAM immunohistochemistry. The resultant expression reactivity was correlated with clinicopathological variables.

RESULTS

EpCAM is consistently expressed in the distal nephron on normal renal epithelium. Clear cell RCCs show minimal and infrequent EpCAM expression, whereas chromophobe and collecting duct RCCs both demonstrate intense and frequent expression. Of 318 clear cell carcinomas used in the analysis, 10% were EpCAM positive in > or = 50% of cells, and 8% of patients would be considered candidates for EpCAM-based therapy, based on high expression [> or = moderate intensity and frequent (> or = 50%) expression] and the need for systemic treatment. EpCAM expression was an independent prognostic factor for improved disease-specific survival, with a multivariate hazard ratio of 0.63 (P = 0.017; 95% confidence interval, 0.43-0.92).

CONCLUSIONS

EpCAM is a novel prognostic molecular marker in RCC patients, and its positive expression is an independent predictor associated with improved survival. However, high expression in morphologically normal renal tissues and minimal or absent expression in clear cell carcinomas will likely limit the utility of this epithelial marker in targeted treatments of this most common RCC type.

Effect of stereotactic high-frequency stimulation in the anterior lobe of the cerebellum in cerebral palsy: a new suboccipital approach

The direct stereotactic suboccipital approach to the anterior lobe of the cerebellum was applied for deep high-frequency stimulation in three patients (for 29, 8 and 3 months) suffering from cerebral palsy. In agreement with our previous experience with a transtentorial approach in 30 patients, spasticity, dyskinesias and behavior were improved during chronic intermittent stimulation (frequency 185 Hz, pulse width 210 micros, voltage individually altered according to motor response at 0.5-4.0 V, 15 min on, 2-6 h off). Patients attained useful motor skill improvements. The results indicate that the method is safe, effective and reasonable.