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Stefano Calza

Publications and source records attributed to Stefano Calza.

13 recordsLinked to original sources
PubMed2026

A contextual activity score (CAS) for inferring ADAR-associated transcriptional activity across RNA-seq, single-cell, and spatial transcriptomics.

BACKGROUND AND OBJECTIVE: Adenosine-to-inosine RNA editing, catalyzed by Adenosine Deaminases Acting on RNA (ADARs), is a widespread modification involved in neural function, immune regulation, and cancer. The Alu Editing Index (AEI) is the standard metric to estimate ADAR activity but requires raw sequencing reads and is poorly suited for single-cell and spatial transcriptomic data. This study aimed to develop an alternative framework for inferring ADAR-associated transcriptional activity from gene expression data across diverse transcriptomic technologies. METHODS: We developed the Contextual Activity Score (CAS), a framework based on transcriptional signatures from ADAR perturbation experiments. Context-specific signatures were generated for human neurons, mouse neurons, and cancer models to infer ADAR1 and ADAR2 activity. CAS was computed from normalized gene expression matrices using regulon-based enrichment analysis. Performance was evaluated by comparing with the Alu Editing Index across bulk RNA sequencing datasets, simulated sequencing depths, and library preparation protocols. RESULTS: CAS showed strong concordance with the Alu Editing Index across multiple datasets, while remaining robust to reduced sequencing depth and different library protocols. Unlike the Alu Editing Index, CAS can be applied to single-cell and spatial transcriptomic data and enables the independent assessment of ADAR2 activity. In cancer and neuronal contexts, CAS captured biologically meaningful variations in ADAR-associated transcriptional activity at sample, cell-type, and spatial levels. CONCLUSION: CAS provides a scalable approach applicable across multiple RNA-seq protocols for estimating ADAR-associated transcriptional activity using gene expression data. This method, implemented in an open-source R package for broad adoption, expands the ability to study ADAR-associated transcriptional activity across transcriptomic modalities where direct editing quantification is challenging, such as single-cell and spatial transcriptomics.

Adenosine Deaminase↗
PubMed2007

Gene expression in 16q is associated with survival and differs between Sørlie breast cancer subtypes.

We have investigated the relationship between gene expression and chromosomal positions in 402 breast cancer patients. Using an overrepresentation approach based on Fisher's exact test, we identified disproportionate contributions of specific chromosomal positions to genes associated with survival. Our major finding is that the gene expression in the long arm of chromosome 16 stands out in its relationship to survival. This arm contributes 36 (18%) and 55 (11%) genes to lists negatively associated with recurrence-free survival (set to sizes 200 and 500). This is a highly disproportionate contribution from the 313 (2%) genes in this arm represented on the used Affymetrix U133A and B microarray platforms (Bonferroni corrected Fisher test: P < 2.2 x 10(-16)). We also demonstrate differential expression in 16q across tumor subtypes, which suggests that the ERBB2, basal, and luminal B tumors progress along a high grade-poor prognosis path, while luminal A and normal-like tumors progress along a low grade-good prognosis path, in accordance with a previously proposed model of tumor progression. We conclude that important biological information can be extracted from gene expression data in breast cancer by studying non-random connections between chromosomal positions and gene expression. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.

Breast Neoplasms↗
PubMed2006

Gail model for prediction of absolute risk of invasive breast cancer: independent evaluation in the Florence-European Prospective Investigation Into Cancer and Nutrition cohort.

BACKGROUND: The Gail model 2 (GM) for predicting the absolute risk of invasive breast cancer has been used for counseling and to design intervention studies. Although the GM has been validated in US populations, its performance in other populations is unclear because of the wide variation in international breast cancer rates. METHODS: We used data from a multicenter case-control study in Italy and from Italian cancer registries to develop a model (IT-GM) that uses the same risk factors as the GM. We evaluated the accuracy of the IT-GM and the GM using independent data from the Florence-European Prospective Investigation Into Cancer and Nutrition (EPIC) cohort. To assess model calibration (i.e., how well the model predicts the observed numbers of events in subsets of the population), we compared the number of expected incident breast cancers (E) predicted by these models with the number of observed incident breast cancers (O), and we computed the concordance statistic to measure discriminatory accuracy. RESULTS: The overall E/O ratios were 0.96 (95% confidence interval [CI] = 0.84 to 1.11) and 0.93 (95% CI = 0.81 to 1.08) for the IT-GM and the GM, respectively. The IT-GM was somewhat better calibrated than GM in women younger than 50 years, but the GM was better calibrated when age at first live birth categories were considered (e.g., 20- to 24-year age-at-first-birth category E/O = 0.68, 95% CI = 0.53 to 0.94 for the IT-GM and E/O = 0.75, 95% CI = 0.58 to 1.03 for the GM). The concordance statistic was approximately 59% for both models, with 95% confidence intervals indicating that the models perform statistically significantly better than pure chance (concordance statistic of 50%). CONCLUSIONS: There was no statistically significant evidence of miscalibration overall for either the IT-GM or the GM, and the models had equivalent discriminatory accuracy. The good performance of the IT-GM when applied on the independent data from the Florence-EPIC cohort indicates that GM can be improved for use in populations other than US populations. Our findings suggest that the Italian data may be useful for revising the GM to include additional risk factors for breast cancer.

Breast Neoplasms↗
PubMed2006

Estimation of false discovery proportion under general dependence.

MOTIVATION: Wide-scale correlations between genes are commonly observed in gene expression data, due to both biological and technical reasons. These correlations increase the variability of the standard estimate of the false discovery rate (FDR). We highlight the false discovery proportion (FDP, instead of the FDR) as the suitable quantity for assessing differential expression in microarray data, demonstrate the deleterious effects of correlation on FDP estimation and propose an improved estimation method that accounts for the correlations. METHODS: We analyse the variation pattern of the distribution of test statistics under permutation using the singular value decomposition. The results suggest a latent FDR model that accounts for the effects of correlation, and is statistically closer to the FDP. We develop a procedure for estimating the latent FDR (ELF) based on a Poisson regression model. RESULTS: For simulated data based on the correlation structure of real datasets, we find that ELF performs substantially better than the standard FDR approach in estimating the FDP. We illustrate the use of ELF in the analysis of breast cancer and lymphoma data. AVAILABILITY: R code to perform ELF is available in http://www.meb.ki.se/~yudpaw.

Algorithms↗
PubMed2006

Differential gene expression profiles between tumor biopsies and short-term primary cultures of ovarian serous carcinomas: identification of novel molecular biomarkers for early diagnosis and therapy.

OBJECTIVE: To identify novel molecular biomarkers useful for the early diagnosis and therapy of ovarian cancer by gene expression profiling. To compare the genetic fingerprints of flash-frozen ovarian serous carcinomas to those of matched highly purified primary tumor cell cultures. METHODS: Gene expression profiles of 19 flash-frozen ovarian serous papillary carcinoma (OSPC) were analyzed and compared to 15 controls (highly purified human ovarian surface epithelium short-term cultures, HOSE) using oligonucleotide microarrays complementary to >14,500 human genes. In addition, gene expression profiling of 5 highly purified primary OSPC cultured in vitro for less than 2 weeks was compared to flash-frozen ovarian carcinoma biopsies obtained from matched samples. Quantitative RT-PCR and IHC staining techniques were used to validate microarray data at RNA and protein levels for some of the differentially expressed genes. RESULTS: Unsupervised analysis of gene expression data readily distinguished normal tissue from flash-frozen OSPC and identified 901 and 557 genes that exhibited >3-fold up-regulation or down-regulation, respectively, in OSPC when compared to HOSE. Mammaglobin 2, an ovarian secreted protein, was identified as the top differentially expressed gene in OSPC (19 out 19 OSPC versus 0 out of 15 HOSE) with over 827-fold up-regulation relative to HOSE. The claudin and kallikrein family of proteins including the clostridium perfringens enterotoxin receptors claudin 3 and 4, kallikreins 6, 7, 8, 10, 11 and the immunomodulatory molecule B7-H4 were found among the most highly overexpressed genes in OSPC when compared to HOSE. Genetic fingerprints of flash-frozen OSPC were found to have high correlation with those of purified primary OSPC short-term in vitro cultures with only 31 out of 8,637 genes (0.35%) differentially expressed between the two groups. CONCLUSIONS: Short-term in vitro culture of primary ovarian carcinomas may greatly increase the purity of ovarian tumor RNA available for gene expression profiling without causing major alteration in OSPC fingerprints. Mammaglobin 2, kallikreins 6, 7, 8, 10, 11, claudin 3 and 4 and B7-H4 gene expression products represent candidate biomarkers endowed with great potential for early screening and therapy of OSPC patients.

Adult↗
PubMed2006

Correlation of fetal DNA levels in maternal plasma with Doppler status in pathological pregnancies.

OBJECTIVES: To evaluate whether intrauterine growth restriction (IUGR) as seen in preeclampsia is associated with high levels of fetal DNA in maternal circulation, and whether fetal DNA is related to altered uterine and/or umbilical artery Doppler velocimetry. METHODS: Fetal DNA quantification was performed by real-time PCR on SRY sequences in 64 male-bearing pregnant women with IUGR and/or preeclampsia and 89 controls. RESULTS: Fetal DNA content was significantly elevated in IUGR pregnancies similar to preeclampsia and correlated with altered umbilical Doppler velocimetry, while no correlation was found with uterine Doppler status. CONCLUSION: Increased fetal DNA levels in maternal plasma may be a sign of placental or fetal pathology even in the presence of normal uterine Doppler velocimetry, allowing a more precise diagnostic evaluation. The finding that elevated fetal DNA in IUGR pregnancies correlates with abnormal umbilical Doppler velocimetry suggests that fetal DNA release is associated more with fetal chronic hypoxia than with fetal size.

Arteries↗
PubMed2006

Dental amalgam and mercury levels in autopsy tissues: food for thought.

Eighteen cadavers from routine autopsy casework were subject to a study of tissue levels of total mercury in brain, thyroid, and kidney samples by atomic absorption. On these same cadavers, all dental amalgam fillings (the most important source of inorganic mercury exposure in the general population, according to the World Health Organization (WHO) were charted. Total mercury levels were significantly higher in subjects with a greater number of occlusal amalgam surfaces (>12) compared with those with fewer occlusal amalgams (0-3) in all types of tissue (all P < or = 0.04). Mercury levels were significantly higher in brain tissues compared with thyroid and kidney tissues in subjects with more than 12 occlusal amalgam fillings (all P < or = 0.01) but not in subjects with 3 or less occlusal amalgams (all P > or = 0.07).

Brain Chemistry↗
PubMed2006

Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients.

BACKGROUND: Molecular markers and the rich biological information they contain have great potential for cancer diagnosis, prognostication and therapy prediction. So far, however, they have not superseded routine histopathology and staging criteria, partly because the few studies performed on molecular subtyping have had little validation and limited clinical characterization. METHODS: We obtained gene expression and clinical data for 412 breast cancers obtained from population-based cohorts of patients from Stockholm and Uppsala, Sweden. Using the intrinsic set of approximately 500 genes derived in the Norway/Stanford breast cancer data, we validated the existence of five molecular subtypes--basal-like, ERBB2, luminal A/B and normal-like--and characterized these subtypes extensively with the use of conventional clinical variables. RESULTS: We found an overall 77.5% concordance between the centroid prediction of the Swedish cohort by using the Norway/Stanford signature and the k-means clustering performed internally within the Swedish cohort. The highest rate of discordant assignments occurred between the luminal A and luminal B subtypes and between the luminal B and ERBB2 subtypes. The subtypes varied significantly in terms of grade (p < 0.001), p53 mutation (p < 0.001) and genomic instability (p = 0.01), but surprisingly there was little difference in lymph-node metastasis (p = 0.31). Furthermore, current users of hormone-replacement therapy were strikingly over-represented in the normal-like subgroup (p < 0.001). Separate analyses of the patients who received endocrine therapy and those who did not receive any adjuvant therapy supported the previous hypothesis that the basal-like subtype responded to adjuvant treatment, whereas the ERBB2 and luminal B subtypes were poor responders. CONCLUSION: We found that the intrinsic molecular subtypes of breast cancer are broadly present in a diverse collection of patients from a population-based cohort in Sweden. The intrinsic gene set, originally selected to reveal stable tumor characteristics, was shown to have a strong correlation with progression-related properties such as grade, p53 mutation and genomic instability.

Breast Neoplasms↗
PubMed2005

Multidimensional local false discovery rate for microarray studies.

MOTIVATION: The false discovery rate (fdr) is a key tool for statistical assessment of differential expression (DE) in microarray studies. Overall control of the fdr alone, however, is not sufficient to address the problem of genes with small variance, which generally suffer from a disproportionally high rate of false positives. It is desirable to have an fdr-controlling procedure that automatically accounts for gene variability. METHODS: We generalize the local fdr as a function of multiple statistics, combining a common test statistic for assessing DE with its standard error information. We use a non-parametric mixture model for DE and non-DE genes to describe the observed multi-dimensional statistics, and estimate the distribution for non-DE genes via the permutation method. We demonstrate this fdr2d approach for simulated and real microarray data. RESULTS: The fdr2d allows objective assessment of DE as a function of gene variability. We also show that the fdr2d performs better than commonly used modified test statistics. AVAILABILITY: An R-package OCplus containing functions for computing fdr2d() and other operating characteristics of microarray data is available at http://www.meb.ki.se/~yudpaw.

Algorithms↗
PubMed2005

Fetal DNA detection in maternal plasma throughout gestation.

The presence of fetal DNA in maternal plasma may represent a source of genetic material which can be obtained noninvasively. We wanted to assess whether fetal DNA is detectable in all pregnant women, to define the range and distribution of fetal DNA concentration at different gestational ages, to identify the optimal period to obtain a maternal blood sample yielding an adequate amount of fetal DNA for prenatal diagnosis, and to evaluate accuracy and predictive values of this approach. This information is crucial to develop safe and reliable non-invasive genetic testing in early pregnancy and monitoring of pregnancy complications in late gestation. Fetal DNA quantification in maternal plasma was carried out by real-time PCR on the SRY gene in male-bearing pregnancies to distinguish between maternal and fetal DNA. A cohort of 1,837 pregnant women was investigated. Fetal DNA could be detected from the sixth week and could be retrieved at any gestational week. No false-positive results were obtained in 163 women with previous embryo loss or previous male babies. Fetal DNA analysis performed blindly on a subset of 464 women displayed 99.4, 97.8 and 100% accuracy in fetal gender determination during the first, second, and third trimester of pregnancy, respectively. No SRY amplification was obtained in seven out of the 246 (2.8%) male-bearing pregnancies. Fetal DNA from maternal plasma seems to be an adequate and reliable source of genetic material for a noninvasive prenatal diagnostic approach.

Cohort Studies↗
PubMed2003

Application of a latent variable model for a multicenter study on early effects due to mercury exposure.

A latent variable model was applied to the results of an Italian multicenter nation-wide cross-sectional study to assess the earliest health effects due to mercury (Hg) exposure caused by occupation, dental amalgams (DENTAM) and fish eating (FISH). The studied population included subjects recruited from four different geographical areas. A total number of 122 workers from chloroalkali plants and production of thermometers and neon lamps formed the occupationally exposed group, whereas 196 subjects, recruited from the same areas and not occupationally exposed to mercury, formed the control group. Neuropsychological functions were assessed with neurobehavioral testing including vigilance, motor and cognitive function, tremor measurements, and with symptoms concerning neuropsychological and mood assessment. Neuroendocrine function was examined with the measurement of prolactin (PRL) level. Parameters of immunological and renal function were also measured. The target population was characterized by the number and surface of dental amalgams and consumption of fish. In the exposed workers the average urinary mercury (U-Hg) was 10.4+/-6.9 (geometric mean 8.3, range 0.2-35.2) microg/g creatinine, whereas in the control group it was 1.9+/-2.8 (geometric mean 1.2, range 0.1-33.2) microg/g creatinine. The preliminary results indicated that finger tapping (FT) and the Branches alternate movement task (BAMT) coordination test were associated with the occupational exposure (OCCEXP). PRL was significantly decreased among the exposed workers, and inversely related to U-Hg. Among the immunological and renal parameters, cytokine serum interleuchin-8 (sIL8) and beta(2) micro globulin (beta(2)MG) were lower in the exposed group and negatively correlated to U-Hg. Small-size fish consumption was associated to a beneficial effect on symptoms reporting. No effects were observed concerning dental amalgams. After first evaluating the relationship between mercury exposure and each indicator of effect, further assessment was performed to identify the earliest effects related to mercury exposure among those who resulted in being associated in the preliminary elaboration. Two latent variables "exposure" and "effect" were identified, integrating respectively the different forms of exposure (occupational, due to dental amalgams and fish consumption) and the indicators of effects (FT, BAMT, PRL, sIL8, beta(2)MG). Confounding factors (age, alcohol, body mass index (BMI)) were considered in the same model. This further analysis showed that an inverse association of occupational exposure to mercury with PRL and BAMT, with Hg-U mediating the effect on PRL, was predominant with respect to the other form of mercury exposure, the other indicators of effect and the confounders. In conclusion, this study supports the finding of alterations of neuroendocrine secretion and motor coordination at very low occupational exposure levels of inorganic mercury, below the current ACGIH Biological Exposure Index. These changes occur at lower levels than other subtle effects on the renal function and the immunitary system. On the contrary, dental amalgams and small-size fish consumption do not seem to be associated to any adverse health effect at these exposure levels.

Adult↗
PubMedDate not supplied

EPIC-Italy cohorts and multipurpose national surveys. A comparison of some socio-demographic and life-style characteristics.

BACKGROUND: EPIC-Italy cohort study recruited subjects who voluntarily accepted to participate in the project. From the self-selected bases of the population sample, some bias could derive in the data interpretation when risk estimation for cancer disease related to life-style factors is the principal concern. Knowledge of the bias related to self-selected sampling is important for better directing the interpretation of the EPIC-Italy study results. METHODS: We investigated the characteristics of volunteer subjects recruited in the EPIC-Italy cohorts and compared them with those of the randomly selected subjects recruited in the Multipurpose ISTAT Surveys realized in the same period (1993-1998) in which the EPIC-cohorts were recruited. RESULTS: We found some differences, and in particular a different attitude towards cigarettes smoking and wine consumption, between the EPIC cohort and the Multipurpose ISTAT Surveys, as well as among geographical areas within the EPIC cohort. CONCLUSIONS: The uneven distribution of some characteristics suggests that the self-selected subjects were characterized by an overall lower consumption of wine and cigarette smoking even when the educational level was considered. This could suggest a generally more healthy life-style among subjects recruited on a volountary bases.

Adult↗