Rafael Valentim Fonseca - Academia.edu (original) (raw)

Academic Advisor by Rafael Valentim Fonseca

O objetivo geral deste trabalho consiste em propor uma solução baseada em mecanismos de web semân... more O objetivo geral deste trabalho consiste em propor uma solução baseada em mecanismos de web semântica para integração das informações de prevenção e redução de oferta na área de drogas entre a SENAD e o MJ representado pelo DPF, os quais são integrantes do SISNAD.

Papers by Rafael Valentim Fonseca

Oncotarget, Jan 3, 2015

Epigenetic alterations have emerged as an important cause of microRNA (miRNA) deregulation. In Mu... more Epigenetic alterations have emerged as an important cause of microRNA (miRNA) deregulation. In Multiple Myeloma (MM), a few tumor suppressive miRNAs silenced by DNA hypermethylation have been reported, but so far there are few systemic investigations on epigenetically silenced miRNAs. We conducted genome-wide screening for tumor suppressive miRNAs epigenetically silenced in MM. Four Human MM Cell lines were treated with demethylating agent 5'azacytidine (5'aza). Consistently upregulated miRNAs include miR-155, miR-198, miR-135a*, miR-200c, miR-125a-3p, miR-188-5p, miR-483-5p, miR-663, and miR-630. Methylation array analysis revealed increased methylation at or near miRNA-associated CpG islands in MM patients. Ectopic restoration of miR-155, miR-198, miR-135a*, miR-200c, miR-663 and miR-483-5p significantly repressed MM cell proliferation, migration and colony formation. Furthermore, we derived a 33-gene signature from predicted miRNA target genes that were also upregulated i...

Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 19, 2015

Primary central nervous system lymphoma (PCNSL) is an aggressive non-Hodgkin lymphoma confined to... more Primary central nervous system lymphoma (PCNSL) is an aggressive non-Hodgkin lymphoma confined to the CNS. Whether there is a PCNSL-specific genomic signature and, if so, how it differs from systemic diffuse large B-cell lymphoma (DLBCL) is uncertain. We performed a comprehensive genomic study of tumor samples from 19 immunocompetent PCNSL patients. Testing comprised array-comparative genomic hybridization and whole exome sequencing. Biallelic inactivation of TOX and PRKCD were recurrently found in PCNSL but not in systemic DLBCL, suggesting a specific role in PCNSL pathogenesis. Additionally, we found a high prevalence of MYD88 mutations (79%) and CDKN2A biallelic loss (60%). Several genes recurrently affected in PCNSL were common with systemic DLBCL, including loss of TNFAIP3, PRDM1, GNA13, TMEM30A, TBL1XR1, B2M, CD58, activating mutations of CD79B, CARD11 and translocations IgH-BCL6. Overall, BCR/TLR/NF-κB pathways were altered in >90% of PNCSL, highlighting its value for targ...

Blood, Jan 24, 2014

Cereblon (CRBN) mediates immunomodulatory drug (IMiD) action in multiple myeloma (MM). Using 2 di... more Cereblon (CRBN) mediates immunomodulatory drug (IMiD) action in multiple myeloma (MM). Using 2 different methodologies, we identified 244 CRBN binding proteins and established relevance to MM biology by changes in their abundance after exposure to lenalidomide. Proteins most reproducibly binding CRBN (>fourfold vs controls) included DDB1, CUL4A, IKZF1, KPNA2, LTF, PFKL, PRKAR2A, RANGAP1, and SHMT2. After lenalidomide treatment, the abundance of 46 CRBN binding proteins decreased. We focused attention on 2 of these-IKZF1 and IKZF3. IZKF expression is similar across all MM stages or subtypes; however, IKZF1 is substantially lower in 3 of 5 IMiD-resistant MM cell lines. The cell line (FR4) with the lowest IKZF1 levels also harbors a damaging mutation and a translocation that upregulates IRF4, an IKZF target. Clinical relevance of CRBN-binding proteins was demonstrated in 44 refractory MM patients treated with pomalidomide and dexamethasone therapy in whom low IKZF1 gene expression p...

Clinical Lymphoma Myeloma and Leukemia, 2014

More than 400 preclinical studies report ≥ 1 compound as cytotoxic to multiple myeloma (MM) cells... more More than 400 preclinical studies report ≥ 1 compound as cytotoxic to multiple myeloma (MM) cells; however, few of these agents became relevant in the clinic. Thus, the utility of such assays in predicting future clinical value is debatable. We examined the application of early-phase trial experiences to predict future clinical adoption. We identified 129 drugs explored as single agents in 228 trials involving 7421 patients between 1961 and 2013. All drugs in common use in MM (melphalan, dexamethasone, prednisone, cyclophosphamide, bendamustine, thalidomide, lenalidomide, pomalidomide, bortezomib, carfilzomib, and doxorubicin) demonstrated a best reported response rate of ≥ 22%. Older agents, including teniposide, fotemustine, paclitaxel, and interferon, also appear active by this criterion; however, if mean response rates from all reported trials for an agent are considered, then only drugs with a mean response rate of 15% partial response are in clinical use. Our analysis suggests that thresholds of 20% for best or 15% for mean response are highly predictive of future clinical success. Below these thresholds, no drug has yet reached regulatory approval or widespread use in the clinic. Thus, this benchmark provides 1 element of the framework for guiding choice of drugs for late-stage clinical testing.

Blood, Jan 15, 2015

Dysregulation of cyclin-dependent kinases is a hallmark of myeloma, and specifically, cdk5 inhibi... more Dysregulation of cyclin-dependent kinases is a hallmark of myeloma, and specifically, cdk5 inhibition can enhance the activity of proteasome inhibitors in vitro. Dinaciclib is a novel potent small molecule inhibitor of cyclin-dependent kinases (CDK)1, CDK2, CDK5, and CDK9. Patients with relapsed multiple myeloma and ≤5 prior lines of therapy, with measurable disease, were enrolled. Dinaciclib was administered on day 1 of a 21-day cycle at doses of 30 to 50 mg/m(2). Overall, 27 evaluable patients were accrued; the median number of prior therapies was 4. The dose level of 50 mg/m(2) was determined to be the maximally tolerated dose. The overall confirmed partial response rate (PR) was 3 of 27 (11%), including 1 patient at the 30 mg/m(2) dose (1 very good PR [VGPR]) and 2 patients at the 40 mg/m(2) dose (1 VGPR and 1 PR). In addition, 2 patients at the 50 mg/mg(2) dose achieved a minimal response (clinical benefit rate, 19%). Leukopenia, thrombocytopenia, gastrointestinal symptoms, alo...

Thrombosis Research, 2014

Thrombosis is a marker of poor prognosis in individuals with solid tumors. The expression of tiss... more Thrombosis is a marker of poor prognosis in individuals with solid tumors. The expression of tissue factor (TF) on the cell surface membrane of malignant cells is a pivotal molecular link between activation of coagulation, angiogenesis, metastasis, aggressive tumor behavior and poor survival. Interestingly, thrombosis is associated with shortened survival in solid, but not in lymphoid neoplasias. We sought to study whether the lack of impact of thrombosis on survival in lymphoid neoplasias could be due to a lack of tumor-derived TF expression. We analyzed TF gene (F3) expression in lymphoid (N=114), myeloid (N=49) and solid tumor (N=856) cell lines using the publicly available dataset from the Broad-Novartis Cancer Cell Line Encyclopedia (http://www.broadinstitute.org/ccle/home), and in 90 patient-derived lymphoma samples. TF protein expression was studied by immunohistochemistry (IHC). In sharp contrast to wide F3 expression in solid tumors (74.2%), F3 was absent in all low and high grade T- and B-cell lymphomas, and in most myeloid tumors, except for select acute myeloid leukemias with monocytic component. IHC confirmed the absence of TF protein in all indolent and high-grade B-cell (0/90) and T-cell (0/20) lymphomas, and acute leukemias (0/11). We show that TF in lymphomas does not derive from the malignant cells, since these do not express either F3 or TF protein. Therefore, it is unlikely that thrombosis in patients with lymphoid neoplasms is secondary to tumor-derived tissue factor.

PLoS ONE, 2014

Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis o... more Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR) where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2.

PLoS Genetics, 2014

Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options hav... more Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options have been limited. During the course of a clinical trial of whole genomic sequencing seeking druggable targets, we examined six patients with advanced cholangiocarcinoma. Integrated genome-wide and whole transcriptome sequence analyses were performed on tumors from six patients with advanced, sporadic intrahepatic cholangiocarcinoma (SIC) to identify potential therapeutically actionable events. Among the somatic events captured in our analysis, we uncovered two novel therapeutically relevant genomic contexts that when acted upon, resulted in preliminary evidence of anti-tumor activity. Genome-wide structural analysis of sequence data revealed recurrent translocation events involving the FGFR2 locus in three of six assessed patients. These observations and supporting evidence triggered the use of FGFR inhibitors in these patients. In one example, preliminary anti-tumor activity of pazopanib (in vitro FGFR2 IC 50 <350 nM) was noted in a patient with an FGFR2-TACC3 fusion. After progression on pazopanib, the same patient also had stable disease on ponatinib, a pan-FGFR inhibitor (in vitro, FGFR2 IC 50 <8 nM). In an independent non-FGFR2 translocation patient, exome and transcriptome analysis revealed an allele specific somatic nonsense mutation (E384X) in ERRFI1, a direct negative regulator of EGFR activation. Rapid and robust disease regression was noted in this ERRFI1 inactivated tumor when treated with erlotinib, an EGFR kinase inhibitor. FGFR2 fusions and ERRFI mutations may represent novel targets in sporadic intrahepatic cholangiocarcinoma and trials should be characterized in larger cohorts of patients with these aberrations.

Mayo Clinic Proceedings, 2006

Mayo Clinic Proceedings, 2001

To describe presenting clinical manifestations, long-term disease complications, prognostic indic... more To describe presenting clinical manifestations, long-term disease complications, prognostic indicators, and outcome of pregnancy for women younger than 50 years with essential thrombocythemia. We retrospectively reviewed the records of all patients with essential thrombocythemia evaluated at Mayo Clinic, Rochester, Minn, between 1969 and 1991 and identified 74 young women (median age, 35 years; range, 18-48 years) with essential thrombocythemia. The diagnosis was based on previously established criteria. Median follow-up was 9.2 years (range, 0.2-26.2 years). Overall survival was similar to that of an age- and sex-matched control population. Thrombotic events (except superficial thrombophlebitis) occurred at and after diagnosis in 11 patients (15%) and 13 patients (18%), respectively. A history of thrombosis at diagnosis was significantly associated with recurrent thrombosis (P = .03). A platelet count higher than 1500 x 10(9)/L at diagnosis was significantly associated with gastrointestinal tract bleeding and subsequent development of venous (but not arterial) thrombosis (P = .04). Major hemorrhagic events occurred in only 3 patients (4%) after diagnosis. Only 1 patient developed acute leukemia. Thirty-four pregnancies occurred in 18 patients. Of these, 17 (50%) resulted in live births. Of the 17 patients with unsuccessful pregnancies, 14 had spontaneous abortions, 1 had an ectopic pregnancy, and 2 had elective abortions. Preconception platelet count, thrombotic history, or specific therapy was not useful in predicting pregnancy outcome. Young women with essential thrombocythemia can expect long survival with a low incidence of life-threatening thrombohemorrhagic complications or acute leukemia. There is an increased incidence of first-trimester miscarriages that may not be influenced by specific therapy.

Leukemia Research, 2014

We demonstrate here that no patient with very low CRBN expression responded to IMiD plus dexameth... more We demonstrate here that no patient with very low CRBN expression responded to IMiD plus dexamethasone therapy. In 53 refractory MM patients treated with pomalidomide and dexamethasone, CRBN levels predict for decreased response rates and significant differences in PFS (3.0 vs. 8.9 months, p < 0.001) and OS (9.1 vs. 27.2 months, p = 0.01) (lowest quartile vs. highest three quartiles). While higher CRBN levels can serve as a surrogate for low risk disease, our study demonstrates that low CRBN expression can predict resistance to IMiD monotherapy and is a predictive biomarker for survival outcomes.

Geoscientific Model Development, 2013

Coupled Chemistry Aerosol-Tracer Transport model to the Brazilian developments on the Regional At... more Coupled Chemistry Aerosol-Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CCATT-BRAMS, version 4.5) is an on-line regional chemical transport model designed for local and regional studies of atmospheric chemistry from the surface to the lower stratosphere suitable both for operational and research purposes. It includes gaseous/aqueous chemistry, photochemistry, scavenging and dry deposition. The CCATT-BRAMS model takes advantage of BRAMS-specific development for the tropics/subtropics as well as the recent availability of preprocessing tools for chemical mechanisms and fast codes for photolysis rates. BRAMS includes stateof-the-art physical parameterizations and dynamic formulations to simulate atmospheric circulations down to the meter. This on-line coupling of meteorology and chemistry allows the system to be used for simultaneous weather and chemical composition forecasts as well as potential feedback between the two. The entire system is made of three preprocessing software tools for user-defined chemical mechanisms, aerosol and trace gas emissions fields and the interpolation of initial and boundary conditions for meteorology and chemistry. In this paper, the model description is provided along with the evaluations performed by using observational data obtained from ground-based stations, instruments aboard aircrafts and retrieval from space remote sensing. The evaluation accounts for model applications at different scales from megacities and the Amazon Basin up to the intercontinental region of the Southern Hemisphere.

Atmospheric Environment, 2010

This work describes the development of an urban vehicle emissions inventory for South America, ba... more This work describes the development of an urban vehicle emissions inventory for South America, based on the analysis and aggregation of available inventories for major cities, with emphasis on its application in regional atmospheric chemistry modeling. Due to the limited number of available local inventories, urban emissions were extrapolated based on the correlation between city vehicle density and mobile source emissions of carbon monoxide (CO) and nitrogen oxides (NOx). Emissions were geographically distributed using a methodology that delimits urban areas using high spatial resolution remote sensing products. This numerical algorithm enabled a more precise representation of urban centers. The derived regional inventory was evaluated by analyzing the performance of a chemical weather forecast model in relation to observations of CO, NOx and O 3 in two different urban areas, São Paulo and Belo Horizonte. The gas mixing ratios simulated using the proposed regional inventory show good agreement with observations, consistently representing their hourly and daily variability. These results show that the integration of municipal inventories in a regional emissions map and their precise distribution in fine scale resolutions are important tools in regional atmospheric chemistry modeling.

American Journal of Hematology, 1998

Neoplasms of reticular dendritic origin are extremely rare and include the follicular dendritic c... more Neoplasms of reticular dendritic origin are extremely rare and include the follicular dendritic cell sarcoma (FDCS) and the interdigitating reticulum (or dendritic) cell sarcoma (IDCS). In this article, we review the literature pertaining to the two diseases and describe clinical observations and salient pathologic features, including information provided by authors of FDCS and IDDCS reports. We performed a computerized database search for published articles regarding FDCS and IDDCS. The articles were evaluated critically by the authors. Simple descriptive statistics were used to analyze the data. There are 51 cases of FDCS and 21 cases of IDDCS that are well documented in the literature. The pathologic diagnosis of FDCS and IDDCS is often challenging and requires morphologic, immunophenotypic, cytochemical, and electron-microscopic analysis. Patients with FDCS usually present with cervical or axillary lymphadenopathy, but extranodal disease has been described. In at least some patients, preexisting Castleman's disease has been recognized. Resected localized disease may be prevented from recurrence by consolidative radiotherapy. Chemotherapy regimens have shown nondurable antitumor activity in FDCS. Patients with IDDCS usually present with lymphadenopathy. The clinical course of IDDCS has been variable, but it seems to be more aggressive than that of FDCS. Variable degrees of remission may be achieved with chemotherapy. FDCS and IDDCS are rare neoplasms that may pose difficulty in pathologic diagnosis. IDDCS seems to display a more aggressive behavior than FDCS. Patients with IDDCS and FDCS can eventually die of disease progression. The role of chemotherapy and radiotherapy is not clearly defined.