1,720,974 research outputs found
Cell-free methylated DNA immunoprecipitation and high throughput sequencing technology: diagnostic value in patients with renal cell carcinoma.
No full textBackground
CfmeDNA is a promising biomarker for non-invasive assessment of solid tumors: i) MeDNA is tissue- and tumor-specific ii) cfDNA methylation changes are stable unlike DNA alterations iii) ‘methylation target size’ is larger than identifying specific genomic alterations and, therefore, more sensitive. CfMeDIP-seq is a sensitive assay for genome-wide bisulfite-free cfMeDNA profiling, that requires 1-10 ng input DNA. We tested the feasibility of cfMeDIP-seq to detect ccRCC across TNM stages
Methods
We evaluated plasma cfDNA collected prior to nephrectomy in 46 pts with ccRCC: 25 stage I, 7 stage II, 6 stage III, 8 stage IV. cfMeDIP-seq involves four steps: 1) cfDNA end-repair, A-tailing, and adapter ligation, 2) cfMeDNA immunoprecipitation and enrichment using an Ab targeting 5-methylcytosine (quality control by qPCR to ensure 99% reaction specificity), 3) adapter-mediated PCR to amplify cfMeDNA, and 4) high-throughput NGS for cfMeDNA data. A previously-derived model (Shen et al, Nature, 2018) was used to classify pts as having ccRCC or not based on cfMeDNA. cfMeDIP-seq paired end data was reduced to 300 bp windows of the genome that map to CpG islands, shores, shelves, and FANTOM5 enhancers; a classifier was then built using the top 1,000 most variable fragments between pts with ccRCC and cancer-free controls. Statistical comparisons were performed in the R statistical environment, with the caret package being used for classifier construction and evaluation
Results
The average amount of cfDNA isolated from 1 ml of ccRCC plasma was 19.8±39.8 ng/μL [1.95-260]. Greater than 99% specificity of reaction and <1% of unMeDNA was achieved in 46/46 samples (100%). The previously-derived classifier of ccRCC correctly predicted 46/46 pts (100%) as having ccRCC. Across 3 rounds of 5-fold cross-validation, the classifier performed with a Cohen’s Kappa of 0.93
Conclusion
CfMeDIP-seq is a non-invasive, cost-effective, and sensitive assay to detect cancer-specific cfmeDNA in ccRCC pts prior to nephrectomy. With further validation, cfmeDNA may detect minimal residual disease after nephrectomy for ‘precision’ adjuvant therapy
Very late recurrence of renal cell carcinoma experiencing long-term response to sunitinib: a case report
No full textRenal cell carcinoma (RCC) is responsible for 4% of all neoplasms in adults and for 80% of all primary renal tumors. Metastatic RCC is resistant to all cytotoxic agents and generally prognosis is poor. However, the clinical behavior of RCC is unpredictable, and late recurrences of disease can occur even after several years from the initial surgical approach, so response to the currently available targeted agents is uncertain, due to the lack of reliable prognostic and predictive factors. We report the case of a patient who developed a metastatic recurrence of RCC 16 years after primary treatment, in spite of metastatic disease at diagnosis. At the time of relapse, the disease showed a surprisingly long-term response to Sunitinib, which is maintained after 74 months of treatment. This case report highlights the unpredictable behavior of RCC and underlines the presence of a subset of patients with metastatic RCC achieving long-term response to Sunitinib, despite poor clinical features. In this subset of patients, an important clinical question arises about the appropriate duration of treatment and the need to continue it indefinitely
The prognostic value of stromal and epithelial periostin expression in human breast cancer: correlation with clinical pathological features and mortality outcome
No full textBackground: PN is a secreted cell adhesion protein critical for carcinogenesis. In breast cancer, it is overexpressed compared to normal breast, and a few reports suggest that it has a potential role as a prognostic marker. Methods: Tumour samples obtained at the time of mastectomy from 200 women followed for a median time of 18.7 years (range 0.5-29.5 years) were investigated through IHC with a polyclonal anti-PN antibody using tissue microarrays. Epithelial and stromal PN expression were scored independently according to the percentage of coloured cells; the 60th percentile of PN epithelial expression, corresponding to 1 %, and the median value of PN stromal expression, corresponding to 90 %, were used as arbitrary cut-offs. The relationships between epithelial and stromal PN expression and clinicalpathological features, tumour phenotype and the risk of mortality following surgery were analysed. Appropriate statistics, including the Fine and Gray competing risk proportional hazard regression model, were used. Results: The expression of PN in tumour epithelial cells was significantly lower than that which was observed in stromal cells (p < 0.000). No specific association between epithelial or stromal PN expression and any of the clinicalpathological parameters analysed was found as it was observed in respect to mortality when these variables were analysed individually. However, when both variables were considered as a function of the other one, the expression of PN in the stromal cells maintained a statistically significant predictive value with respect to both all causes and cancerspecific mortality only in the presence of high epithelial expression levels. No significant differences in either all causes or BCa-specific mortality rates were shown according to epithelial expression for tumours displaying higher stromal PN expression rates. However, the trends were opposite for the higher stromal values and the patients with high epithelial expression levels denoted the group with the worst prognosis, while higher epithelial values in patients with lower stromal expression levels denoted the group with the best prognosis, suggesting that PN epithelial/stromal interactions play a crucial role in breast carcinogenesis, most likely due to functional cross-talk between the two compartments. On the basis of PN expression in both compartments, we defined 4 subgroups of patients with different mortality rates with the group of patients characterized by positive epithelial and low stromal PN expression cells showing the lowest mortality risk as opposed to the groups of patients identified by a high PN expression in both cell compartments or those identified by a low or absent PN expression in both cell compartments showing the worst mortality rates. The differences were highly statistically significant and were also retained after multiparametric analysis. Competing risk analysis demonstrated that PN expression patterns characterizing each of previous groups are specifically associated with cancer-specific mortality. Conclusions: Although they require further validation through larger studies, our findings suggest that the patterns of expression of PN in both compartments can allow for the development of IHC "signatures" that maintain a strong independent predictive value of both all causes and, namely, of cancer-specific mortality
Overexpression of Periostin in Tumor Biopsy Samples Is Associated With Prostate Cancer Phenotype and Clinical Outcome
No full textWe retrospectively investigated the prognostic significance of periostin, an extracellular matrix protein, in tumor biopsy samples of 215 patients with prostate cancer. We found that periostin expression can predict the outcome of specific subgroups of patients. In addition to the prostate-specific antigen level and/or Gleason score, the immunohistochemical assessment of periostin expression could be useful in clinical practice to predict the prognosis. Background: Overexpression of periostin (POSTN) is associated with prostate cancer (PCa) aggressiveness. We investigated the prognostic significance of POSTN expression in tumor biopsy samples of patients with PCa. Methods: We scored POSTN expression by immunohistochemistry analysis on 215 PCa biopsy samples using an anti–POSTN-specific antibody. A total immunoreactive score (T-IRS) was calculated by adding the POSTN staining scores of stromal and epithelial tumor cells. Prostate-specific antigen (PSA) progression/recurrence-free survival (PFS), radiographic progression/recurrence-free survival (rPFS), and overall survival (OS) were the study end points. Results: A total of 143 patients received therapy with radical attempt, whereas 72 had locally advanced or metastatic disease and received hormone therapy alone. Median T-IRS was 9 and 12 (range, 0-20), respectively (P = .001). Overall, we found a weak positive correlation of T-IRS with prebiopsy PSA levels (r = 0.166, P = .016) and Gleason score (r = 0.266, P < .000). T-IRS ≥ 8 independently predicted for shorter PSA-PFS and OS (hazard ratio [HR] [95% confidence interval (CI)] ≥ 8 versus < 8: 1.50 [1.06-2.14], P = .024 and 1.92 [1.20-3.07], P = .007, respectively). In the subgroup analysis, the association between T-IRS and patient outcome was retained in patients who received therapy with radical attempt (HR [95% CI] ≥ 8 vs. < 8: rPFS: 2.06 [1.18-3.58], P = .01; OS: 2.36 [1.24-4.50], P = .009) and in those with low to intermediate Gleason scores (HR [95% CI] ≥ 8 vs. < 8: PSA-PFS: 1.65 [1.06-2.59], P = .028; rPFS: 2.09 [1.14-3.87], P = .018; OS: 2.57 [1.31-5.04], P = .006). Conclusion: POSTN T-IRS on PCa biopsy samples independently predicted the risk of recurrence, progression, and death in patients with localized disease and in those with low to intermediate Gleason scores
Comprehensive analysis of plasma methylome reveals distinct patterns of methylation changes between responders and non-responders to neoadjuvant chemotherapy in breast cancer
No full textThe potential of cell-free DNA (cfDNA) methylation profiling in oncology is increasingly recognized for its ability to offer a comprehensive assessment of tumor biology. In this report, we explore the plasma methylome dynamics in patients with early breast cancer (BC) undergoing neoadjuvant chemotherapy (NACT) using an agnostic genome-wide approach with cell-free DNA immunoprecipitation and sequencing (cfMeDIP-seq). Our cohort comprised seven women with triple-positive BC, assessed for cfDNA methylation changes at multiple time points during their treatment course. Genome-wide analysis revealed distinctive patterns of differential methylation in patients achieving pathological complete response (pCR), with no significant epigenomic modifications in patients with residual disease (RD). Gene set enrichment analysis highlighted dynamic variations in functional pathways associated with therapy response, including metabolism, immune response, and response to xenobiotics, with a notable reversibility post-treatment. Principal component analysis of the differentially methylated regions demonstrated a clear distinction between pCR and RD patients, indicating the potential of cfMeDIP-seq for the non-invasive assessment of therapy response. Such findings suggest that cfMeDIP-seq could complement ctDNA offering broader insights into the global modifications induced by chemotherapy. Although future research is needed to validate and expand on our findings, we offer a proof-of-principle of the potential utility of cfMeDIP-seq in the personalized management of BC
a)‐specific mortality following breast surgery
No full textMALDI-TOF MS was used to recognise serum peptidome profiles predictive of mortality in women affected by early BCa. Mortality was analysed based on signal profiling, and appropriate statistics were used. The results indicate that four signals were increased in deceased patients compared with living patients. Three of the four signals were individually associated with all-cause mortality, but only one having mass/charge ratio (m/z) 1,046.49 was associated with BCa-specific mortality and was the only peak to maintain an independent prognostic role after multivariate analysis. Two groups exhibiting different mortality probabilities were identified after clustering patients based on the expression of the four peptides, but m/z 1,046.49 was exclusively expressed in the cluster exhibiting the worst mortality outcome, thus confirming the crucial value of this peptide. The specific role of this peak was confirmed by competing risk analysis. MS findings were validated by ELISA analysis after demonstrating that m/z 1,046.49 structurally corresponded to Angiotensin II (ATII). In fact, mortality results obtained after arbitrarily dividing patients according to an ATII serum value of 255 pg/ml (which corresponds to the 66(th) percentile value) were approximately comparable to those previously demonstrated when the same patients were analysed according to the expression of signal m/z 1,046.49. Similarly, ATII levels were specifically correlated with BCa-related deaths after competing risk analysis. In conclusion, ATII levels were increased in women who exhibited worse mortality outcomes, reinforcing the evidence that this peptide potentially significantly affects the natural history of early BCa. Our findings also confirm that MALDI-TOF MS is an efficient screening tool to identify novel tumour markers and that MS findings can be rapidly validated through less complex techniques, such as ELISA
Prognostic Value of Preoperative Serum Levels of Periostin (PN) in Early Breast Cancer (BCa)
No full textPN is a secreted cell adhesion protein critical for carcinogenesis. Elevated serum levels of PN have been implicated as playing an important role in different types of cancer, and a few reports suggest a potential role as a prognostic marker. We evaluated the prognostic significance of preoperative serum PN concentration in patients with BCa receiving curative surgery. Enzyme-Linked Immunosorbent Assay (ELISA) was performed to determine the preoperative serum PN level in 182 patients. The correlations between serum PN concentration with clinical pathological features and PN expression in primary tumor samples were analyzed. The prognostic impact of serum PN levels with all-cause and BCa-specific mortality was also investigated. Appropriate statistics were used. Elevated serum PN levels were significantly associated with patient age (p = 0.005), adjuvant systemic therapy (p = 0.04) and progesterone receptor (PgR) status (p = 0.02). No correlation between PN preoperative serum levels and other clinical-pathological parameters, including either the epithelial or the stromal PN expression of primary tumor or the combination of the two, was found. Similarly, no association between serum PN levels and either all-cause or BCa-specific mortality was found. However, subgroup analysis revealed a correlation between higher PN serum levels and all-cause mortality in patients with node-negative disease (p = 0.05) and in those with a low PgR expression (p = 0.03). Higher levels of serum PN were also found to correlate with BCa-specific mortality in the subgroup of patients who did not receive any adjuvant systemic therapy (p = 0.04). Our findings suggest that PN was detectable in the serum of early BCa patients before surgery and increased base-line serum levels predicted worse long-term survival outcomes in specific subgroups of patients
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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