Epigenome-Driven Strategies for Personalized Cancer Immunotherapy

Fighting cancer remains one of the greatest challenges for science in the 21st century. Advances in immunotherapy against different types of cancer have greatly contributed to the treatment, remission, and cure of patients. In this context, knowledge of epigenetic phenomena, their relationship with tumor cells and how the immune system can be epigenetically modulated represent some of the greatest advances in the development of anticancer therapies. Epigenetics is a rapidly growing field that studies how environmental factors can affect gene expression without altering DNA sequence. Epigenomic changes include DNA methylation, histone modifications, and non-coding RNA regulation, which impact cellular function. Epigenetics has shown promise in developing cancer therapies, such as immunotherapy, which aims to stimulate the immune system to attack cancer cells. For example, PD-1 and PD-L1 are biomarkers that regulate the immune response to cancer cells and recent studies have shown that epigenetic modifications can affect their expression, potentially influencing the efficacy of immunotherapy. New therapies targeting epigenetic modifications, such as histone deacetylases and DNA methyltransferases, are being developed for cancer treatment, and some have shown promise in preclinical studies and clinical trials. With growing understanding of epigenetic regulation, we can expect more personalized and effective cancer immunotherapies in the future. This review highlights key advances in the use of epigenetic and epigenomic tools and modern immuno-oncology strategies to treat several types of tumors.

ALTERED PLASMA CYTOKINE CONCENTRATIONS ARE ASSOCIATED WITH THE CLINICAL SEVERITY OF PATIENTS WITH COVID-19

Introduction

The novel Coronavirus (SARS-CoV-2), responsible for severe acute respiratory syndrome, has emerged as a threat to humans since December 2019, and the search for a better understanding of the pathophysiology of coronavirus disease 2019 (COVID-19) and its definitive treatment is still in progress.

Objective

To evaluate the plasma pro- and anti-inflammatory cytokines in COVID-19 patients and their associations with the disease severity and outcome.

Methods

Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR)-confirmed COVID-19 unvaccinated patients at the Hospital de Clínicas (HC), UNICAMP, Campinas, SP, were enrolled. Clinical and laboratory data were extracted from the medical records, and the plasma cytokines levels were quantified using LUMINEX and ELISA.

Results

There were 154 COVID-19 patients (99 survivors and 55 non-survivors) with male:female of 1.4:1, and a median age of 60 years. The non-survivors were older than survivors (65 vs. 55 years, p < 0.0001); and coronary artery disease and autoimmunity, disease severity, and oxygen therapy, intensive care, and intubation were associated with mortality. Non-survivors had higher leukocyte and neutrophil counts, and RDW and lower lymphocyte count at diagnosis. Non-survivors had higher levels of pro-inflammatory (TNF-α, IL-6, IFN-γ, CCL3, IL-17/IL-17A, IL-8, G-CSF, CCL2/MCP-1) and anti-inflammatory (IL-1ra and IL-27) cytokines, but lower TGF-β levels than the survivors. TNF-α levels were positively correlated with all studied cytokines except TGF-β, while TGF-β levels were negatively correlated with TNF-α, IL-6, CCL3, G-CSF, and IL-27. IL-27 levels were significantly correlated with all the cytokines except IL-37 and IL-17E. More than half (55.2%) of our patients had severe COVID-19, 18.8% had moderate, 16.2% had critical, 5.2% had mild, and 4.5% were asymptomatic. Majority of the patients (68.2%) required ICU care and had higher TNF-α, IL-6, IL-8, IL-17, CCL3, CCL2, IL-1ra, and IL-27 than others. 59.7% of the patients required endotracheal intubation and had higher TNF-α, IL-6, IL-8, CCL3, CCL2, and IL-1ra than those who did not have intubation. TNF-α, IL-6, and IL-8 had the highest Area Under the Receiver Operating Characteristics (AUROC) curve, sensitivity, and specificity for predicting mortality in these COVID-19 patients.

Discussion and conclusion

The altered levels of pro- and anti-inflammatory cytokines support the role of SARS-CoV-2 in inducing cytokine storm, and higher concentrations seen in the deceased patients meant a more severe storm. Also, the increased leukocytes and neutrophils in our patients could have led to the release of reactive oxygen species, and end-organ damage, thus leading to poor outcomes. This study showed that the levels of these cytokines could be used as markers of mortality in COVID-19. It is possible to suggest that TNF, IL-6, and IL-8 levels at diagnosis could be efficient predictors of fatal outcomes in COVID-19 patients. If properly measured at diagnosis, these markers could be useful for triaging and predicting the outcome of COVID-19, thus guiding the treatment of the COVID-19.

Funding

CNPq (#190374/2017-9), CAPES, FAPESP and FAEPEX (#338619).

Antitumoral activity of liraglutide, a new DNMT inhibitor in breast cancer cells in vitro and in vivo

Breast cancer (BC) is the most frequently diagnosed female cancer and second leading cause of death. Despite the discovery of many antineoplastic drugs for BC, the current therapy is not totally efficient. In this study, we investigated the potential of repurposing the well-known diabetes type II drug liraglutide to modulate epigenetic modifications in BC cells lines in vitro and in vivo via Ehrlich mice tumors models. The in vitro results revealed a significant reduction on cell viability, migration, DNMT activity and displayed lower levels of global DNA methylation in BC cell lines after liraglutide treatment. The interaction between liraglutide and the DNMT enzymes resulted in a decrease profile of DNA methylation for the CDH1, ESR1 and ADAM33 gene promoter regions and, consequently, increased their gene and protein expression levels. To elucidate the possible interaction between liraglutide and the DNMT1 protein, we performed an in silico study that indicates liraglutide binding in the catalytic cleft via hydrogen bonds and salt bridges with the interdomain contacts and disturbs the overall enzyme conformation. The in vivo study was also able to reveal that liraglutide and the combined treatment of liraglutide and paclitaxel or methotrexate were effective in reducing tumor growth. Moreover, the modulation of CDH1 and ADAM33 mouse gene expression by DNA demethylation suggests a role for liraglutide in DNMT activity in vivo. Altogether, these results indicate that liraglutide may be further analysed as a new adjuvant treatment for BC.

Artificial intelligence and the future of life sciences

Over the past few decades, the number of health and 'omics-related data' generated and stored has grown exponentially. Patient information can be collected in real time and explored using various artificial intelligence (AI) tools in clinical trials; mobile devices can also be used to improve aspects of both the diagnosis and treatment of diseases. In addition, AI can be used in the development of new drugs or for drug repurposing, in faster diagnosis and more efficient treatment for various diseases, as well as to identify data-driven hypotheses for scientists. In this review, we discuss how AI is starting to revolutionize the life sciences sector.

Beneficial Effects of Soluble Guanylyl Cyclase Stimulation and Activation in Sickle Cell Disease Are Amplified by Hydroxyurea: In Vitro and In Vivo Studies

The complex pathophysiology of sickle cell anemia (SCA) involves intravascular hemolytic processes and recurrent vaso-occlusion, driven by chronic vascular inflammation, which result in the disease’s severe clinical complications, including recurrent painful vaso-occlusive episodes. Hydroxyurea, the only drug frequently used for SCA therapy, is a cytostatic agent, although it appears to exert nitric oxide/soluble guanylyl cyclase (sGC) modulating activity. As new drugs that can complement or replace the use of hydroxyurea are sought to further reduce vaso-occlusive episode frequency in SCA, we investigated the effects of the sGC agonists BAY 60-2770 (sGC activator) and BAY 41-2272 (sGC stimulator) in the presence or absence of hydroxyurea on SCA vaso-occlusive mechanisms and cell recruitment both ex vivo and in vivo. These agents significantly reduced stimulated human SCA neutrophil adhesive properties ex vivo in association with the inhibition of surface β2-integrin activation. A single administration of BAY 60-2770 or BAY 41-2272 decreased tumor necrosis factor cytokine–induced leukocyte recruitment in a mouse model of SCA vaso-occlusion. Importantly, the in vivo actions of both agonists were significantly potentiated by the coadministration of hydroxyurea. Erythroid cell fetal hemoglobin (HbF) elevation is also a major goal for SCA therapy. BAY 41-2272 but not BAY 60-2770 at the concentrations employed significantly induced γ-globin gene transcription in association with HbF production in cultured erythroleukemic cells. In conclusion, sGC agonist drugs could represent a promising approach as therapy for SCA, for use either as stand-alone treatments or in combination with hydroxyurea.

Targeted next-generation sequencing identified novel mutations associated with hereditary anemias in Brazil

Hereditary anemias are a group of heterogeneous disorders including hemolytic anemias and hyporegenerative anemias, as congenital dyserythropoietic anemia (CDA). Causative mutations occur in a wide range of genes leading to deficiencies in red cell production, structure, or function. The genetic screening of the main genes is important for timely diagnosis, since routine laboratory tests fail in a percentage of the cases, appropriate treatment decisions, and genetic counseling purposes. A conventional gene-by-gene sequencing approach is expensive and highly time-consuming, due to the genetic complexity of these diseases. To overcome this problem, we customized a targeted sequencing panel covering 35 genes previously associated to red cell disorders. We analyzed 36 patients, and potentially pathogenic variants were identified in 26 cases (72%). Twenty variants were novel. Remarkably, mutations in the SPTB gene (β-spectrin) were found in 34.6% of the patients with hereditary spherocytosis (HS), suggesting that SPTB is a major HS gene in the Southeast of Brazil. We also identified two cases with dominant HS presenting null mutations in trans with α-LELY in SPTA1 gene. This is the first comprehensive genetic analysis for hereditary anemias in the Brazilian population, contributing to a better understanding of the genetic basis and phenotypic consequences of these rare conditions in our population.

Endothelial Nitric Oxide Synthase (eNOS) Gene Polymorphisms and Markers of Hemolysis, Inflammation and Endothelial Dysfunction in Brazilian Sickle Cell Anemia Patients

The impaired bioavailability of endogenous nitric oxide (NO) in sickle cell anemia (SCA) may be influenced by polymorphisms in the endothelial nitric oxide synthase gene (eNOS). We compared allelic/genotypic frequencies of the eNOS polymorphisms T-786C, VNTR4a/b and G894T between 89 adult SCA patients and 100 healthy controls, and investigated the relationship between these SNPs and markers of hemolysis [lactate dehydrogenase (LDH), indirect bilirubin (IB) and reticulocyte counts], inflammation [interleukins IL-1β, IL-6, IL-8, Tumor Necrosis Factor (TNF-α) and C-reactive protein (CRP)] and endothelial dysfunction (ED) [soluble vascular cell adhesion molecule-1 (sVCAM-1), soluble intercellular adhesion molecule-1 (sICAM-1), soluble L-selectin (sL-selectin), von Willebrand Factor (vWF) antigen and D-dimers] in the patients. The frequencies of the mutant -786C allele and -786C/C genotype were significantly higher in patients (p = 0.02 and p = 0.04, respectively) but not significantly correlated with the markers. For VNTR4a/b and G894T, the allelic/genotypic frequencies did not statistically differ between patient and control groups. Patients carrying the 4a allele and those with the 894G/G genotype showed a significant decrease in IB (p = 0.02 and p = 0.04, respectively), and only patients with the 4a allele exhibited reduced IL-1β (p = 0.01). The correlation profiles between markers of inflammation and ED significantly differed between patients carrying the mutant alleles and those with wild-type genotypes. This appears to be the first report on the relationship between eNOS gene polymorphisms and markers of hemolysis, inflammation and ED in Brazilian SCA patients. Our results indicate that the SNPs analyzed may influence the phenotypic variability of these patients.

Effect of allogeneic mesenchymal stem cells (MSCs) on corneal wound healing in dogs

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Allogeneic MSCs are safety to be transplanted by subconjunctival route.

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Allogeneic MSCs therapy seems to be efficient in improving corneal healing in dogs.

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Allogeneic MSCs therapy applied to depth corneal ulcers promoted healing in 14 days.

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The paracrine effect of MSCs must provide a rapid corneal wound healing.

Antifungal drugs: New insights in research & development

The need for better antifungal therapy is commonly accepted in view of the high mortality rates associated with systemic infections, the low number of available antifungal classes, their associated toxicity and the increasing number of infections caused by strains with natural or acquired resistance. The urgency to expand the range of therapeutic options for the treatment of fungal infections has led researchers in recent decades to seek alternative antifungal targets when compared to the conventional ones currently used. Although new potential targets are reported, translating the discoveries from bench to bedside is a long process and most of these drugs fail to reach the patients. In this review, we discuss the development of antifungal drugs focusing on the approach of drug repurposing and the search for novel drugs for classical targets, the most recently described gene targets for drug development, the possibilities of immunotherapy using antibodies, cytokines, therapeutic vaccines and antimicrobial peptides.

Evaluation of sociodemographic, clinical, and laboratory markers of sickle leg ulcers among young nigerians at a tertiary health institution

Background

Sickle leg ulcer (SLU) is a chronic and debilitating complication of sickle cell disease (SCD) associated with huge physical and psychosocial discomfort. The occurrence of SLU has remained steady despite successful preventive strategies and advances in SCD care. Although multifactorial factors have been implicated in SLU, these are not fully understood, and data on how these relate to young Nigerian SCD patients are scanty.

Aims

This study aims to evaluate the sociodemographic, clinical, and laboratory markers of SLU in a young Nigerian SCD cohort.

Patients and Methods

This study involved 109 young SCD patients and 67 healthy peers. The sociodemographic and laboratory parameters of the participants were examined in addition to the evaluation of the SCD cohort for SLU.

Results

Only the HbSS patients had SLU. This was found in six of them giving a prevalence of 5.9% (6/101). Their median age was 17, range 14-21 years. There was a preceding history of trauma in 4 (66.7%), and this included a case of traditional scarifications for local therapeutic purposes. Two of the three (66.7%) males with SLU also had priapism (P = 0.0132). Patients with SLU were older, had less frequent bone pain crises, and significantly belonged to the low socioeconomic class (P < 0.05). Although patients with SLU had relatively higher lactate dehydrogenase, platelet count, aspartate transaminase, bilirubin, white blood cell, and lower Hb concentration and HbF, these did not attain statistical significance (P > 0.05).

Conclusion

This study confirms that SLU is common among young SCD patients with HbSS genotype, low socioeconomic background, and older age. It also suggests that SLU could be more related to hemolysis-associated SCD phenotypes among the patients.

Down regulation of ADAM33 as a Predictive Biomarker of Aggressive Breast Cancer

Breast cancer is a heterogeneous disease with differences in its clinical, molecular and biological features. Traditionally, immunohistochemical markers together with clinicopathologic parameters are used to classify breast cancer and to predict disease outcome. Triple-negative breast cancer (TNBC) is a particular type of breast cancer that is defined by a lack of expression of hormonal receptors and the HER2 gene. Most cases of TNBC also have a basal-like phenotype (BLBC) with expression of cytokeratin 5/6 and/or EGFR. A basal marker alone is insufficient for a better understanding of the tumor biology of TNBC. In that regard, the ADAM33 gene is silenced by DNA hypermethylation in breast cancer, which suggests that ADAM33 might be useful as a molecular marker. In the present study, we have produced monoclonal antibodies against the ADAM33 protein and have investigated the role of ADAM33 protein in breast cancer. We used 212 breast tumor samples and lower levels of ADAM33 were correlated with TNBC and basal-like markers. A lower level of ADAM33 was also correlated with shorter overall survival and metastasis-free survival and was considered an independent prognostic factor suggesting that ADAM33 is a novel molecular biomarker of TNBC and BLBC that might be useful as a prognostic factor.

Expression of miR-18a and miR-210 in Normal Breast Tissue as Candidate Biomarkers of Breast Cancer Risk

miRNAs are noncoding RNAs with abnormal expression in breast cancer; their expression in high-risk benign breast tissue may relate to breast cancer risk. We examined miRNA profiles in contralateral unaffected breasts (CUB) of patients with breast cancer and validated resulting candidates in two additional sample sets. Expression profiles of 754 mature miRNAs were examined using TaqMan Low Density Arrays in 30 breast cancer samples [15 estrogen receptor (ER)-positive and 15 ER-negative] and paired CUBs and 15 reduction mammoplasty controls. Pairwise comparisons identified miRNAs with significantly differential expression. Seven candidate miRNAs were examined using qRT-PCR in a second CUB sample set (40 cases, 20 ER+, 20 ER-) and 20 reduction mammoplasty controls. Further validation was performed in 80 benign breast biopsy (BBB) samples; 40 from cases who subsequently developed breast cancer and 40 from controls who did not. Logistic regression, using tertiles of miRNA expression, was used to discriminate cases from controls. Seven miRNAs were differentially expressed in tumors and CUBs versus reduction mammoplasty samples. Among them, miR-18a and miR-210 were validated in the second CUB set, showing significantly higher expression in tumor and CUBs than in reduction mammoplasty controls. The expression of miR-18a and miR-210 was also significantly higher in BBB cases than in BBB controls. When both miR-18a and miR-210 were expressed in the upper tertiles in BBB, OR for subsequent cancer was 3.20, P = 0.023. miR-18a and miR-210 are expressed at higher levels in CUBs of patients with breast cancer, and in BBB prior to cancer development, and are therefore candidate breast cancer risk biomarkers. Cancer Prev Res; 10(1); 89-97. ©2016 AACR.

Epigenomes as therapeutic targets

Epigenetics is a molecular phenomenon that pertains to heritable changes in gene expression that do not involve changes in the DNA sequence. Epigenetic modifications in a whole genome, known as the epigenome, play an essential role in the regulation of gene expression in both normal development and disease. Traditional epigenetic changes include DNA methylation and histone modifications. Recent evidence reveals that other players, such as non-coding RNAs, may have an epigenetic regulatory role. Aberrant epigenetic signaling is becoming to be known as a central component of human disease, and the reversible nature of the epigenetic modifications provides an exciting opportunity for the development of clinically relevant therapeutics. Current epigenetic therapies provide a clinical benefit through disrupting DNA methyltransferases or histone deacetylases. However, the emergence of next-generation epigenetic therapies provides an opportunity to more effectively disrupt epigenetic disease states. Novel epigenetic therapies may improve drug targeting and drug delivery, optimize dosing schedules, and improve the efficacy of preexisting treatment modalities (chemotherapy, radiation, and immunotherapy). This review discusses the epigenetic mechanisms that contribute to the disease, available epigenetic therapies, epigenetic therapies currently in development, and the potential future use of epigenetic therapeutics in a clinical setting.

Fibronectin affects transient MMP2 gene expression through DNA demethylation changes in non-invasive breast cancer cell lines

Metastasis accounts for more than 90% of cancer deaths. Cells from primary solid tumors may invade adjacent tissues and migrate to distant sites where they establish new colonies. The tumor microenvironment is now recognized as an important participant in the signaling that induces cancer cell migration. An essential process for metastasis is extracellular matrix (ECM) degradation by metalloproteases (MMPs), which allows tumor cells to invade local tissues and to reach blood vessels. The members of this protein family include gelatinase A, or MMP-2, which is responsible for the degradation of type IV collagen, the most abundant component of the basal membrane, that separates epithelial cells in the stroma. It is known that fibronectin is capable of promoting the expression of MMP-2 in MCF7 breast cancer cells in culture. In addition, it was already shown that the MMP2 gene expression is regulated by epigenetic mechanisms. In this work, we showed that fibronectin was able to induce MMP2 expression by 30% decrease in its promoter methylation. In addition, a histone marker for an open chromatin conformation was significantly increased. These results indicate a new role for fibronectin in the communication between cancer cells and the ECM, promoting epigenetic modifications.

Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects

Background

Mechanisms underlying the development of virus-induced asthma exacerbations remain unclear. To investigate if epigenetic mechanisms could be involved in virus-induced asthma exacerbations, we undertook DNA methylation profiling in asthmatic and healthy nasal epithelial cells (NECs) during Human Rhinovirus (HRV) infection in vitro.

Methods

Global and loci-specific methylation profiles were determined via Alu element and Infinium Human Methylation 450 K microarray, respectively. Principal components analysis identified the genomic loci influenced the most by disease-status and infection. Real-time PCR and pyrosequencing were used to confirm gene expression and DNA methylation, respectively.

Results

HRV infection significantly increased global DNA methylation in cells from asthmatic subjects only (43.6% to 44.1%, p = 0.04). Microarray analysis revealed 389 differentially methylated loci either based on disease status, or caused by virus infection. There were disease-associated DNA methylation patterns that were not affected by HRV infection as well as HRV-induced DNA methylation changes that were unique to each group. A common methylation locus stood out in response to HRV infection in both groups, where the small nucleolar RNA, H/ACA box 12 (SNORA12) is located. Further analysis indicated that a relationship existed between SNORA12 DNA methylation and gene expression in response to HRV infection.

Conclusions

We describe for the first time that Human rhinovirus infection causes DNA methylation changes in airway epithelial cells that differ between asthmatic and healthy subjects. These epigenetic differences may possibly explain the mechanism by which respiratory viruses cause asthma exacerbations.

Comparison of precision and accuracy of linear measurements performed by two different imaging software programs and obtained from 3D-CBCT images for Le Fort I osteotomy

OBJECTIVE

The purpose of this study was to compare the precision and accuracy of linear measurements for Le Fort I osteotomy performed by two different imaging software programs and obtained from three-dimensional cone beam CT (3D-CBCT) images.

METHODS

The study population consisted of 11 dried skulls submitted to CBCT, which generated 3D images. Linear measurements were based on craniometric anatomical landmarks pre-defined by the authors as specifically used for Le Fort I osteotomy and were identified by two radiologists twice each, independently, using Vitrea 3.8.1 (Vital Images Inc., Plymouth, MN) and open-source digital imaging communication in medicine viewer OsiriX 1.2 64-bit (Pixmeo, Geneva, Switzerland). Subsequently, a third examiner made physical measurements using a digital caliper (167 series; Mitutoyo Sul Americana Ltd, Suzano, SP, Brazil).

RESULTS

The results demonstrated a statistically significant difference between OsiriX and the gold standard, especially in the pterygoid process (TPtg L = 0.019, LLpPtg R = 0.016 and LLpPtg L = 0.012). Vitrea showed no statistical difference in comparison with the gold standard, and showed a high level of accuracy in all the measurements performed. The major difference found was 0.42 mm (LLpPtg R). Interexaminer analysis ranged from 0.90 to 0.97 using Vitrea and from 0.8 to 0.97 using OsiriX. Intraexaminer correlation coefficient ranged from 0.90 to 0.98 and from 0.84 to 0.98 for Examiners 1 and 2, respectively, using Vitrea and from 0.93 to 0.99 for Examiner 1 and from 0.64 to 0.96 for Examiner 2 using OsiriX.

CONCLUSION

Vitrea may be considered as precise and accurate, insofar as it was able to perform all the 3D linear measurements. On the other hand, linear measurements performed using OsiriX were not successful in producing accurate linear measurements for Le Fort I osteotomy.

Clinical characteristics of alopecia areata in Down syndrome

This study was undertaken to better understand clinical characteristics, environmental and physical events in Down syndrome (DS) and alopecia areata (AA). This cross-sectional study included 18 DS patients who were currently presenting or had presented AA. We evaluated gender, age, location and type of AA, presence of autoimmune disease or atopy, AA in first-degree relatives, and environmental, physical, and clinical intercurrences. The mean age of study subjects was 11.6 (SD ± 5.5) years and mean age at AA onset 7.2 (2.5 to 15.2) years. The duration of alopecia episodes varied, with a mean of 2.7 (0.1 to 18.7) years. Recurrence of AA was reported in 27.7% (5/18) of subjects, with a mean number of recurrences of 3.6. Localized type AA was seen in 83.4% of individuals, with the most frequent location on the scalp (100%). Seven of the individuals presented atopy. Fourteen individuals had undergone environmental and/or clinical intercurrences. In conclusion, the most frequent presentation of AA in DS is the non-recurrent, localized form on the scalp, with a varied period of duration. Changes in the individuals' routine occurred in more than half of the study group. We suggest further studies of the psychology and immunogenetics in the etiopathology of AA in DS.

Differentially expressed miRNAs in retinoblastoma

MicroRNAs (miRNAs) are short non-coding RNA transcripts that have the ability to regulate the expression of target genes, and have been shown to influence the development of various tumors. The purpose of our study is to identify aberrantly expressed miRNAs in retinoblastoma for the discovery of potential therapeutic targets for this disease, and to gain a greater understanding of the mechanisms driving retinoblastoma progression. We report 41 differentially expressed miRNAs (p<0.05) in 12 retinoblastomas as compared to three normal human retinae. Of these miRNAs, many are newly identified as being differentially expressed in retinoblastoma. Further, we report the validations of five of the most downregulated miRNAs in primary human retinoblastomas (p<0.05), human retinoblastoma cell lines, and mouse retinoblastoma cell lines. This serves as the largest and most comprehensive retinoblastoma miRNA analysis to date with corresponding clinical and pathological characteristics. This is an essential step in the discovery of miRNAs associated with retinoblastoma progression, and in the identification of potential therapeutic targets for this disease.

Lack of association between MDM2 SNP309 and TP53 Arg72Pro polymorphisms with clinical outcomes in myelodysplastic syndrome

MDM2/p53 pathway plays an important role in the control of apoptotic and proliferation mechanisms, and alterations in this pathway have been described in myelodysplastic syndromes (MDS). We investigated the frequency of MDM2 SNP309, TP53 Arg72Pro polymorphisms in de novo MDS and the association of these polymorphisms with clinical characteristics. Our results showed that the frequencies of genotypes for MDM2 SNP309 and TP53 Arg72Pro did not differ between MDS and healthy controls and that these polymorphisms were not associated with clinical and laboratory parameters, disease progression and overall survival, suggesting that MDM2 and TP53 polymorphisms are not involved in risk for MDS, or in the clinical and laboratory characteristics of the disease.

A new β⁰-thalassemia frameshift mutation [β 48 (-T)] in a Uruguayan family

We describe here a new frameshift mutation of β-thalassemia in a Uruguayan family with Italian ancestry [β48 (-T); HBB:c.146delT]. This frameshift results in formation of premature stop codon (TGA) 40 bp downstream and in a short unstable product that is degraded in the cell.

Epigenetically reprogramming metastatic tumor cells with an embryonic microenvironment

We have previously shown that the microenvironment of human embryonic stem cells (hESCs) is able to change and reprogram aggressive cancer cells to a less aggressive state. Some mechanisms implicated in the phenotypic changes observed after this exposure are mainly associated with the Nodal signaling pathway, which plays a key role in tumor cell plasticity. However, several other molecular mechanisms might be related directly and/or indirectly to these changes, including microRNA (miRNA) regulation and DNA methylation.

AIM

To further explore the epigenetic mechanisms potentially underlying the phenotypic changes that occur after exposing metastatic melanoma cells to a hESC microenvironment.

MATERIALS & METHODS

A total of 365 miRNAs were screened using the TaqMan® Low Density Arrays. We also evaluated whether DNA methylation could be one of the factors regulating the expression of the inhibitor of Nodal, Lefty, in hESCs (where it is highly expressed) vs melanoma cells (where it is not expressed).

RESULTS

Using these experimental approaches, we identified miRNAs that are up- and down-regulated in melanoma cells exposed to a hESC microenvironment, such as miR-302a and miR-27b, respectively. We also demonstrate that Notch4 is one of the targets of miR-302a, which is upstream of Nodal. Additionally, one of the mechanisms that might explain the absence of the inhibitor of Nodal, Lefty, in cancer cells is silencing by DNA methylation, which provides new insights into the unregulated expression of Nodal in melanoma.

CONCLUSION

These findings suggest that epigenetic changes such as DNA methylation and regulation by microRNAs might play a significant role in tumor cell plasticity and the metastatic phenotype.

Identification of microRNAs as potential prognostic markers in ependymoma

Introduction

We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers.

Materials and Methods

We have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features.

Results

We have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival.

Conclusion

We have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas.

Analysis of the workers head transcriptome of the Asian subterranean termite, Coptotermes gestroi

The lower termite, Coptotermes gestroi (Isoptera: Rhinotermitidae), is originally from Southeast Asia and has become a pest in Brazil. The main goal of this study was to survey C. gestroi transcriptome composition. To accomplish this, we sequenced and analyzed 3003 expressed sequence tags (ESTs) isolated from libraries of worker heads. After assembly, 695 uniESTs were obtained from which 349 have similarity with known sequences. Comparison with insect genomes demonstrated similarity, primarily with genes from Apis mellifera (28%), Tribolium castaneum (28%) and Aedes aegypti (10%). Notably, we identified two endogenous cellulases in the sequences, which may be of interest for biotechnological applications. The results presented in this work represent the first genomic study of the Asian subterranean termite, Coptotermes gestroi.

Neutrophils of rheumatoid arthritis patients on anti-TNF-α therapy and in disease remission present reduced adhesive functions in association with decreased circulating neutrophil-attractant chemokine levels

Neutrophils participate in the initiation and progression of rheumatoid arthritis (RA) although the exact mechanisms responsible for neutrophil accumulation in rheumatoid joints are not understood. This study compared the adhesive and chemotactic functions of neutrophils from RA patients in activity (DAS28 > 3.2) and not in activity (DAS28 < 2.6) and observed the effects of different treatment approaches on these functions. Neutrophils were isolated from healthy controls (CON), and patients with active or inactive RA in use of therapy not specific for RA (NSAIDs), in use of DMARDs and in use of anti-TNF-α therapy. Adhesive and chemotactic properties were evaluated using in vitro assays; adhesion molecule expression was assessed by flow cytometry and real-time PCR and circulating chemokines were determined by ELISA. No significant alterations in the adhesive and chemotactic properties of neutrophils from active RA were observed when compared to CON neutrophils, independently of treatment regimen. In contrast, neutrophils from RA patients in disease remission presented reduced adhesive properties and a lower spontaneous chemotactic capacity, in association with decreased adhesion molecule expression, although profiles of alterations differed for those patients on DMARDs and those on anti-TNF-α therapy. Circulating levels of the major neutrophilic chemokines, IL-8 and epithelial neutrophil activating peptide-78, were also significantly decreased in those patients demonstrating a clinical response. Remission of RA appears to be associated with ameliorations in aspects important for neutrophil adhesion and chemotaxis; whether these alterations contribute to decrease neutrophil migration to the synovial fluid, with consequent improvements in the clinical manifestations of RA, remains to be determined.

The impact of epigenomics on future drug design and new therapies

The future of drug design and the development of new therapeutics will rely on our ability to unravel the complexities of the epigenome in normal and disease states. Proper epigenetic regulation is essential for normal differentiation in embryogenesis and development. Conversely, abnormal epigenetic regulation is a feature of complex diseases, including cancer, diabetes, heart disease and other pathologies. Epigenetic therapies hold promise for a wide range of biological applications, from cancer treatment to the establishment of induced pluripotent stem cells. The creation of more specific and effective epigenetic therapies, however, requires a more complete understanding of epigenomic landscapes. Here, we give a historical overview of the epigenomics field and how epigenetic modifications can affect embryo development and disease etiology. We also discuss the impact of current and future epigenetic drugs.

Abstract 168: Differential microRNA expression profiles of breast cancer and matched benign breast samples stratified by ER status

Background: The identification of women at high risk for breast cancer remains a challenge. Robust risk markers that better stratify women for their probability of developing breast cancer would represent a significant advance for breast cancer prevention research. microRNAs (miRNAs) are a large group of non-coding RNAs, generally 18-25 nt long, which block messenger RNA (mRNA) translation and affect mRNA stability. Since the molecular signature of ER-positive breast cancer differs from that of ER-negative breast cancer, we hypothesized that miRNA profile differences may be reflected in the contralateral normal breast tissue of women with breast cancer.Methods:we used a well-annotated set of samples comprised of matched contra-lateral benign breast tissue (MCBB) from 30 women (15 ER positive and 15 ER negative tumor with their corresponding MCBBs matched for age and race) to generate expression profiles of 754 mature miRNAs by TaqMan Low Density Arrays (TLDAs). Following background subtraction, miRNA levels were normalized against controls and compared across groups using tests of contrast on estimated parameters from a full ANOVA model with Empirical Bayes variance correction and False Discovery Rate (FDR) control at p≪0.05 using the Benjamini-Hochberg method. Following this strategy, we have performed different pair-wise comparisons as follows: 1) ER+ to ER- tumors, 2) ER+ tumor to MCBB tissue, 3) ER- tumor to MCBB, and 4) MCBB tissue from women with ER+ versus ER- tumors.Results: We observe clear patterns of differential expression between ER+ and ER- tumors. Four miRNAs were significantly down-regulated in ER+ tumors compared to ER-negative, whereas miR190b was significantly up-regulated in ER- lesions. More striking were the patterns of differential expression of 23 miRNAs in ER- breast cancer tissue compared to MCCB. A similar analysis in ER+ breast cancer and MCBB yeilded at least 29 miRNAs with significantly differential expression. Among these differentially expressed miRNAs, nine miRNAs were common in the ER- and ER+ cancers, and the remainder were distinct. Notably, we found that miR-18a and miR-18b expression were more than 50-fold higher in ER- cancer samples compared to MCBB, but when we compared ER+ tumor to MCBB, we found no significant difference in miR-18b expression. On the other hand, miR-96 and miR-183 are over-expressed in both ER+ and ER- tumors when compared to the MCBB set. Comparing MCBB from women with ER-and ER+ breast cancer yielded no significant differences. Conclusion: we see striking differences in the patterns of miRNA expression differences between breast cancer samples and matched contralateral benign tissue when stratified by ER status.The majority of the miRNAs identified in our analyses are novel. These findings have significant potential for the identification of new ER- status specific and biologically significant molecular biomarkers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 168. doi:10.1158/1538-7445.AM2011-168

DataGenno: building a new tool to bridge molecular and clinical genetics

Clinical genetics is one of the most challenging fields in medicine, with thousands of children born every year with congenital defects that have no satisfactory diagnosis. There are more than 6,000 known single-gene disorders that can cause birth defects or diseases in approximately 1 in every 200 births. Clinical and molecular information on genetic diseases and syndromes are widespread in the literature, and there are few databases combining this information. Therefore, it is very challenging for health care professionals and researchers to translate the latest advances in science and medicine into effective clinical interventions and new treatments. In order to overcome this obstacle and promote networking, we are building DataGenno, an online medical and scientific portal. DataGenno has been developed to be a source of information on genetic diseases and syndromes for the needs of all heath care professionals and researchers. Our database will be able to integrate both clinical and molecular aspects of genetic diseases in a fully interactive environment. DataGenno’s system already contains clinical and molecular information for 300 diseases, with approximately 6,000 signs and symptoms of these diseases in a database combined with a search engine. Our main goal is to cover all genetic diseases described to date, providing not only clinical information such as morphological and anatomical features but also the most comprehensive molecular genetics/genomics features and available testing information. We are also developing ways to connect DataGenno’s portal with Electronic Health Records in order to improve the efficiency of patient care. Additionally, DataGenno’s system and search engine will be able to provide tools that will facilitate the discovery and description of new genetic syndromes. In conclusion, we believe that DataGenno‘s portal will be a helpful and innovative tool for health care professionals, scientists, genetic counselors, and other professionals in the clinical genetics field.