Biomedical subjects

Jeanne Kowalski

Publications and source records attributed to Jeanne Kowalski.

11 recordsLinked to original sources

PubMed2007

Nested, non-parametric, correlative analysis of microarrays for heterogenous phenotype characterization.

We present a non-parametric approach for qualitatively selecting candidate genes to characterize several criteria that are nested among genes selected on the basis of their individual, similar effects upon an array-wide closeness measure. In this setting, a goal is to obtain a reliable characterization of phenotypes, based on very high-dimensional data from a few samples. As opposed to a distance-based approach, the proposed measure defines closeness based on gene signal profiles (functionals) rather than on isolated (numerical) differences in each gene between samples. By using such a measure to characterize intensity differences, we effectively separate biological from artifactual variation in expression, due to tissue effects or signal calibration. Based on this measure, we successively examine the significance of the following: a set of similarly behaved genes relative to all arrayed genes, a set of candidate genes relative to similarly behaved genes, individual candidate genes relative to non-candidates, and the direction, as over- or under-expressed, of candidate genes. In each setting, sample pairs are the units of analysis, with U-statistics the theoretical framework. We illustrate the method on a microarray experiment, where the goal is to select sets of genes that characterize a type of skin cancer and its histological subtypes.

Genetic Heterogeneity↗

PubMed2005

Egr-2 and Egr-3 are negative regulators of T cell activation.

T cell receptor engagement in the absence of proper accessory signals leads to T cell anergy. E3 ligases are involved in maintaining the anergic state. However, the specific molecules responsible for the induction of anergy have yet to be elucidated. Using microarray analysis we have identified here early growth response gene 2 (Egr-2) and Egr-3 as key negative regulators of T cell activation. Overexpression of Egr2 and Egr3 was associated with an increase in the E3 ubiquitin ligase Cbl-b and inhibition of T cell activation. Conversely, T cells from Egr3(-/-) mice had lower expression of Cbl-b and were resistant to in vivo peptide-induced tolerance. These data support the idea that Egr-2 and Egr-3 are involved in promoting a T cell receptor-induced negative regulatory genetic program.

Adaptor Proteins, Signal Transducing↗

PubMed2005

Group-based HIV risk reduction intervention for adolescent girls: evidence of feasibility and efficacy.

The purposes of this pilot study were (a) to assess the feasibility of a community-based, small group HIV risk reduction intervention with adolescent girls, and (b) to obtain preliminary evidence of the efficacy of this theoretically-guided intervention using a controlled design. The feasibility of the intervention was demonstrated by successfully implementing it with 33 sexually-active, single girls. Preliminary evidence of the efficacy of the intervention was obtained using a randomized trial with 62 sexually-active, single girls. Data obtained at a 3-month follow-up assessment showed that girls who received the HIV-related intervention improved their HIV-related knowledge and enhanced their motivation for risk reduction compared to girls who received a control (health promotion) intervention. Effect sizes suggest that the HIV intervention also reduced several risk behaviors (e.g., vaginal sex without a condom, giving oral sex, and alcohol and drug use before sex). Challenges to implementation and suggestions for intervention enhancement are discussed.

Adolescent↗

PubMed2005

Downregulation of NDUFA1 and other oxidative phosphorylation-related genes is a consistent feature of basal cell carcinoma.

Basal cell carcinoma (BCC) is the most common cutaneous malignancy that, like other tumours, possesses a heterogeneous genetic composition. In order to select genes with consistent changes in expression among these tumours, we analysed BCC microarray expression data by using a novel approach, termed correlative analysis of microarrays (CAM). CAM is a nested, non-parametric method designed to qualitatively select candidates based on their individual, similar effects upon an array-wide closeness measure. We applied the CAM method to expression data generated by two-channel cDNA microarray experiments, where 21 BCC and patient-matched normal skin specimens were examined. Fifteen candidate genes were selected, with six overexpressed and nine underexpressed in BCC vs. normal skin. Five of the nine consistently downregulated genes in the tumour samples are involved in mitochondrial function and the oxidative phosphorylation (OXPHOS) pathway. One of these genes was the 7.5-kDa subunit, NADH dehydrogenase (ubiquinone) alpha subcomplex-1 (NDUFA1), an accessory component of OXPHOS complex-I that is essential for respiratory activity. These findings support the hypothesis that irregularities in mitochondrial function are involved in neoplasia. Suppression of NDUFA1 expression could represent a key pathogenic mechanism in the development of BCC.

Basal Cell Carcinoma↗

PubMed2005

CCAAT/enhancer binding protein alpha (C/EBPalpha) and C/EBPalpha myeloid oncoproteins induce bcl-2 via interaction of their basic regions with nuclear factor-kappaB p50.

The CEBPA gene is mutated in 10% of acute myeloid leukemia (AML) cases. We find that CEBPA and Bcl-2 RNA levels correlate highly in low-risk human AMLs, suggesting that inhibition of apoptosis via induction of bcl-2 by CCAAT/enhancer binding protein alpha (C/EBPalpha) or its mutant variants contributes to transformation. C/EBPalphap30, lacking a NH2-terminal transactivation domain, or C/EBPalphaLZ, carrying in-frame mutations in the leucine zipper that prevent DNA binding, induced bcl-2 in hematopoietic cell lines, and C/EBPalpha induced bcl-2 in normal murine myeloid progenitors and in the splenocytes of H2K-C/EBPalpha-Emu transgenic mice. C/EBPalpha protected Ba/F3 cells from apoptosis on interleukin-3 withdrawal but not if bcl-2 was knocked down. Remarkably, C/EBPalphaLZ oncoproteins activated the bcl-2 P2 promoter despite lack of DNA binding, and C/EBPalphap30 also activated the promoter. C/EBPalpha and the C/EBPalpha oncoproteins cooperated with nuclear factor-kappaB (NF-kappaB) p50, but not p65, to induce bcl-2 transcription. Endogenous C/EBPalpha preferentially coimmunoprecipitated with p50 versus p65 in myeloid cell extracts. Mutation of residues 297 to 302 in the C/EBPalpha basic region prevented induction of endogenous bcl-2 or the bcl-2 promoter and interaction with p50 but not p65. These findings suggest that C/EBPalpha or its mutant variants tether to a subset of NF-kappaB target genes, including Bcl-2, via p50 to facilitate gene activation and offer an explanation for preferential in-frame rather than out-of-frame mutation of the leucine zipper with sparing of the basic region in C/EBPalphaLZ oncoproteins. Targeting interaction between C/EBPalpha basic region and NF-kappaB p50 may contribute to the therapy of AML and other malignancies expressing C/EBPs.

Adult↗

PubMed2004

Microarray and serial analysis of gene expression analyses identify known and novel transcripts overexpressed in hematopoietic stem cells.

The human CD34(+)/CD38(-)/Lin(-) cell subset, comprising approximately 1-10% of the CD34(+) cell population, contains few of the less primitive hematopoietic (lineage-committed) progenitor cells (HPCs) but most of the primitive in vivo engrafting (lympho-)hematopoietic stem cells (HSCs). We analyzed gene expression in CD34(+)/CD38(-)/Lin(-) cell populations isolated from normal human adult donor bone marrow, neonatal placental/umbilical cord blood, and mobilized adult donor peripheral blood stem-progenitor cells. As measured by Affymetrix microarrays, 4746 genes were expressed in CD34(+)/CD38(-)/Lin(-) cells from all three tissues. We also determined the transcriptomes of the stem cell-depleted, HPC-enriched CD34(+)/[CD38/Lin](++) cell population from each tissue. Comparison of CD34(+)/CD38(-)/Lin(-) (HSC-enriched) versus CD34(+)/[CD38/Lin](++) (HPC-enriched, HSC-depleted) cells from each tissue yielded 81 genes overrepresented and 90 genes underrepresented, common to all three of the CD34(+)/CD38(-)/Lin(-) cell populations. These transcripts, which are selectively expressed in HSCs from all three tissues, include a number of known genes (e.g., transcription factors, receptors, and signaling molecules) that might play roles in key functions (e.g., survival, self-renewal, differentiation, and/or migration/adhesion) of human HSCs. Many genes/transcripts of unknown function were also detected by microarray analysis. Serial analysis of gene expression of the bone marrow HSC and HPC populations confirmed expression of most of the overrepresented transcripts for which reliable serial analysis of gene expression tags were detected and additionally suggested that current microarrays do not detect as many as 30% of the transcripts expressed in HSCs, including a number of previously unknown transcripts. This work is a step toward full definition of the transcriptome of normal human HSCs and may identify new genes involved in leukemogenesis and cancer stem cells.

ADP-ribosyl Cyclase↗

PubMed2004

Hypermethylation of CpG islands in primary and metastatic human prostate cancer.

Aberrant DNA methylation patterns may be the earliest somatic genome changes in prostate cancer. Using real-time methylation-specific PCR, we assessed the extent of hypermethylation at 16 CpG islands in DNA from seven prostate cancer cell lines (LNCaP, PC-3, DU-145, LAPC-4, CWR22Rv1, VCaP, and C42B), normal prostate epithelial cells, normal prostate stromal cells, 73 primary prostate cancers, 91 metastatic prostate cancers, and 25 noncancerous prostate tissues. We found that CpG islands at GSTP1, APC, RASSF1a, PTGS2, and MDR1 were hypermethylated in >85% of prostate cancers and cancer cell lines but not in normal prostate cells and tissues; CpG islands at EDNRB, ESR1, CDKN2a, and hMLH1 exhibited low to moderate rates of hypermethylation in prostate cancer tissues and cancer cell lines but were entirely unmethylated in normal tissues; and CpG islands at DAPK1, TIMP3, MGMT, CDKN2b, p14/ARF, and CDH1 were not abnormally hypermethylated in prostate cancers. Receiver operator characteristic curve analyses suggested that CpG island hypermethylation changes at GSTP1, APC, RASSF1a, PTGS2, and MDR1 in various combinations can distinguish primary prostate cancer from benign prostate tissues with sensitivities of 97.3-100% and specificities of 92-100%. Hypermethylation of the CpG island at EDNRB was correlated with the grade and stage of the primary prostate cancers. PTGS2 CpG island hypermethylation portended an increased risk of recurrence. Furthermore, CpG island hypermethylation patterns in prostate cancer metastases were very similar to the primary prostate cancers and tended to show greater differences between cases than between anatomical sites of metastasis.

Adult↗

PubMed2004

Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes.

MOTIVATION: We present a statistical framework for the analysis of high-dimensional microarray data, where the goal is to compare intensities among several groups based on as few as a single sample from each group. In this setting, it is of interest to compare gene expression among several phenotypes to define candidate genes that simultaneously characterize several criteria, simultaneously, among the comparison groups. We motivate the approach by a comparative microarray experiment in which clones of a cell were singly exposed to several distinct but related conditions. The experiment was conducted to elucidate genes involved in pathways leading to T cell clonal anergy. RESULTS: By integrating inference principles within a bioinformatics setting, we introduce a two-stage approach to select candidate genes that characterize several criteria. The method is unified in its non-parametric approach to inference and description. For inference, we construct a testable hypothesis based on the criteria of interest in a high-dimensional space, while preserving the dependence among genes. Upon rejecting the null, we estimate the cardinality of a set of individual candidate genes (or gene pairs) that depict the events of interest. With this estimate, we then select individual genes (or gene pairs) based upon a two-dimensional ranking that examines relations within and between genes, among comparison groups, using singular value decomposition in combination with inner product concepts.

Algorithms↗

PubMed2004

Role of LAG-3 in regulatory T cells.

Regulatory T cells (Tregs) limit autoimmunity but also attenuate the magnitude of antipathogen and antitumor immunity. Understanding the mechanism of Treg function and therapeutic manipulation of Tregs in vivo requires identification of Treg-selective receptors. A comparative analysis of gene expression arrays from antigen-specific CD4(+) T cells differentiating to either an effector/memory or a regulatory phenotype revealed Treg-selective expression of LAG-3, a CD4-related molecule that binds MHC class II. Antibodies to LAG-3 inhibit suppression by induced Tregs both in vitro and in vivo. Natural CD4(+)CD25(+) Tregs express LAG-3 upon activation, which is significantly enhanced in the presence of effector cells, whereas CD4(+)CD25(+) Tregs from LAG-3(-/-) mice exhibit reduced regulatory activity. Lastly, ectopic expression of LAG-3 on CD4(+) T cells significantly reduces their proliferative capacity and confers on them suppressor activity toward effector T cells. We propose that LAG-3 marks regulatory T cell populations and contributes to their suppressor activity.

Adoptive Transfer↗

PubMed2004

Clinical and epidemiologic characterization of photosensitivity in HIV-positive individuals.

BACKGROUND: An increased prevalence and severity of cutaneous photosensitivity has been recognized in association with human immunodeficiency virus (HIV) infection. However, this disorder remains poorly characterized in terms of its epidemiology, predisposing factors, clinical, and environmental associations. METHODS: To define the risk factors associated with the presence of photosensitivity among HIV-positive individuals, a cross-sectional study of 631 primary patient visits to an urban HIV Dermatology clinic between January 1997 and August 2001, inclusive, was conducted. A multivariate model was fit to estimate adjusted odds ratios for risk factors associated with photosensitivity diagnosis. Subsequently, a case-series of the patients with photosensitivity was reported. RESULTS: The overall prevalence of photosensitivity was 5.4%, while African-Americans (AA) exhibited a prevalence of 7.3%. In the multivariate model, using highly active anti-retroviral therapy (HAART) (OR=2.82, 95% CI: 1.13, 7.03) and being AA (OR=6.68, 95% CI: 1.56, 28.65) significantly increased the odds of photosensitivity. Patients with photosensitivity were more likely to present during periods of higher ultraviolet (UV) index (P=0.08). Two distinct clinical morphologies were noted: lichenoid and non-lichenoid, eczematous. Sub-morphologies in the non-lichenoid group were suggestive of differences in immunologic profile and estimated UV exposure. CONCLUSION: Photosensitivity associated with HIV infection is an increasingly recognized dermatologic condition with a heterogeneous clinical presentation. AA ethnicity and HAART were independent indicators for the diagnosis of photosensitivity, whereas CD4+ and UV exposure had non-significant associations. The subtleties in these and other clinical variables may directly aid in the recognition and diagnosis of this poorly characterized disorder.

Adult↗

PubMed2003

Do patients drop out prematurely from exposure therapy for PTSD?

Many studies have demonstrated the efficacy of exposure therapy in the treatment of chronic post-traumatic stress disorder (PTSD). Despite the convincing outcome literature, a concern that this treatment may exacerbate symptoms and lead to premature dropout has been voiced on the basis of a few reports. In this paper, we examined the hypothesis that treatments that include exposure will be associated with a higher dropout rate than treatments that do not include exposure. A literature search identified 25 controlled studies of cognitive-behavioral treatment for PTSD that included data on dropout. The results indicated no difference in dropout rates among exposure therapy, cognitive therapy, stress inoculation training, and EMDR. These findings are consistent with previous research about the tolerability of exposure therapy.

Humans↗