Neoadjuvant chemotherapy with trastuzumab in HER2-positive breast cancer: pathologic complete response rate, predictive and prognostic factors

Buzatto, I.P.C.; Ribeiro-Silva, A.; Andrade, J.M.; Carrara, H.H.A.; Silveira, W.A.; Tiezzi, D.G.

doi:10.1590/1414-431x20165674

NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models (2020)
Journal Article
McDonald, J. T., Stainforth, R., Miller, J., Cahill, T., Abraham da Silveira, W., Rathi, K. S., …Beheshti, A. (2020). NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models. Cancers, 12(2), Article 381. https://doi.org/10.3390/cancers12020381

Background: Ionizing radiation from galactic cosmic rays (GCR) is one of the major risk factors that will impact the health of astronauts on extended missions outside the protective effects of the Earth's magnetic field. The NASA GeneLab project has... Read More about NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models.

Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver (2019)
Journal Article
Beheshti, A., chakravarty, K., Fogle, H., Fazelinia, H., Abraham da Silveira, W., Boyko, V., …V. Costes, S. (2019). Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver. Scientific reports, 9, Article 19195. https://doi.org/10.1038/s41598-019-55869-2

Spaceflight has several detrimental effects on the physiology of astronauts, many of which are recapitulated in rodent models. Mouse studies performed on the Space Shuttle showed disruption of lipid metabolism in liver. However, given that these anim... Read More about Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver.

The effects of rosiglitazone on the neonatal rat cardiomyocyte transcriptome: a temporal analysis (2019)
Journal Article
Abraham da Silveira, W., Vazquez-Hidalgo, E., Bartolotta, E., Renaud, L., Paolini, P., & Hardiman, G. (2019). The effects of rosiglitazone on the neonatal rat cardiomyocyte transcriptome: a temporal analysis. Pharmacogenomics, 20(16), 1125-1141. https://doi.org/10.2217/pgs-2019-0077

Aim: The objective was to determine via high-throughput RNA sequencing the temporal effects of rosiglitazone (Avandia®) on the neonatal rat ventricular myocyte transcriptome.

Materials & methods: Neonatal rat ventricular myocytes (NRVMs) were exp... Read More about The effects of rosiglitazone on the neonatal rat cardiomyocyte transcriptome: a temporal analysis.

Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina (2019)
Journal Article
Overbey, E. G., Abraham da Silveira, W., Stanbouly, S., Nishiyama, N. C., Roque-Torres, G. D., Pecaut, M. J., …Wen Mao, X. (2019). Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina. Scientific reports, 9, Article 13304. https://doi.org/10.1038/s41598-019-49453-x

Extended spaceflight has been shown to adversely affect astronaut visual acuity. The purpose of this study was to determine whether spaceflight alters gene expression profiles and induces oxidative damage in the retina. Ten week old adult C57BL/6 mal... Read More about Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina.

Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae (2019)
Journal Article
Overbey, E. G., Paul, A. M., da Silveira, W. A., Tahimic, C. G., Reinsch, S. S., Szewczyk, N., …Mao, X. W. (2019). Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae. International Journal of Molecular Sciences, 20(17), Article 4094. https://doi.org/10.3390/ijms20174094

Spaceflight poses many challenges for humans. Ground-based analogs typically focus on single parameters of spaceflight and their associated acute effects. This study assesses the long-term transcriptional effects following single and combination spac... Read More about Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae.

Gene expression and immunohistochemical analyses identify SOX2 as major risk factor for overall survival and relapse in Ewing sarcoma patients (2019)
Journal Article
Sannino, G., Marchetto, A., Ranft, A., Jabar, S., Zacherl, C., Alba-Rubio, R., …Grünewald, T. G. (2019). Gene expression and immunohistochemical analyses identify SOX2 as major risk factor for overall survival and relapse in Ewing sarcoma patients. EBioMedicine, 47, 156-162. https://doi.org/10.1016/j.ebiom.2019.08.002

Background: Up to 30-40% of Ewing sarcoma (EwS) patients with non-metastatic disease develop local or metastatic relapse within a time span of 2-10 years. This is in part caused by the absence of prognostic biomarkers that can identify high-risk pati... Read More about Gene expression and immunohistochemical analyses identify SOX2 as major risk factor for overall survival and relapse in Ewing sarcoma patients.

GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature (2019)
Journal Article
Couch, D., Yu, Z., Nam, J. H., Allen, C., Ramos, P. S., da Silveira, W. A., …Chung, D. (2019). GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature. PLoS ONE, 14(7), Article e0219195. https://doi.org/10.1371/journal.pone.0219195

In systems biology, inference of functional associations among genes is compelling because the construction of functional association networks facilitates biomarker discovery. Specifically, such gene associations in human can help identify putative b... Read More about GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature.

Primary cilia defects causing mitral valve prolapse (2019)
Journal Article
Toomer, K. A., Yu, M., Fulmer, D., Guo, L., Moore, K. S., Moore, R., …Norris, R. A. (2019). Primary cilia defects causing mitral valve prolapse. Science Translational Medicine, 11(493), Article eaax0290. https://doi.org/10.1126/scitranslmed.aax0290

Mitral valve prolapse (MVP) affects 1 in 40 people and is the most common indication for mitral valve surgery. MVP can cause arrhythmias, heart failure, and sudden cardiac death, and to date, the causes of this disease are poorly understood. We now d... Read More about Primary cilia defects causing mitral valve prolapse.

A Human Skin Model Recapitulates Systemic Sclerosis Dermal Fibrosis and Identifies COL22A1 as a TGFβ Early Response Gene that Mediates Fibroblast to Myofibroblast Transition (2019)
Journal Article
Watanabe, T., Baker Frost, D., Mlakar, L., Heywood, J., da Silveira, W. A., Hardiman, G., & Feghali-Bostwick, C. (2019). A Human Skin Model Recapitulates Systemic Sclerosis Dermal Fibrosis and Identifies COL22A1 as a TGFβ Early Response Gene that Mediates Fibroblast to Myofibroblast Transition. Genes, 10(2), Article 75. https://doi.org/10.3390/genes10020075

Systemic sclerosis (SSc) is a complex multi-system autoimmune disease characterized by immune dysregulation, vasculopathy, and organ fibrosis. Skin fibrosis causes high morbidity and impaired quality of life in affected individuals. Animal models do... Read More about A Human Skin Model Recapitulates Systemic Sclerosis Dermal Fibrosis and Identifies COL22A1 as a TGFβ Early Response Gene that Mediates Fibroblast to Myofibroblast Transition.

Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods (2019)
Book Chapter
Courtney, S. M., da Silveira, W. A., Hazard, E. S., & Hardiman, G. (2019). Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods. In Tumor Profiling (169-184). New York: Humana Press. https://doi.org/10.1007/978-1-4939-9004-7_12

RNA sequencing (RNA-seq) is revolutionizing the study of cancer by providing a highly sensitive and robust tool to interrogate the transcriptome. It leverages the power of deep sequencing technology and provides global and multidimensional views of t... Read More about Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods.

Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses (2019)
Journal Article
Abraham da Silveira, W., Hazard, E. S., Chung, D., & Hardiman, G. (2019). Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses. Methods in Molecular Biology, 185-204. https://doi.org/10.1007/978-1-4939-9004-7_13

RNAseq is a powerful technique enabling global profiles of transcriptomes in healthy and diseased states. In this chapter we review pipelines to analyze the data generated by sequencing RNA, from raw data to a system level analysis. We first give an... Read More about Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses.

Identification of a Subtype of Poorly Differentiated Invasive Ductal Carcinoma of the Breast Based on Vimentin and E-cadherin Expression (2018)
Journal Article
Orlandini, L. F., Reis, F. J. C. D., da Silveira, W. A., Tiezzi, M. G., de Andrade, J. M., Ribeiro-Silva, A., …Tiezzi, D. G. (2018). Identification of a Subtype of Poorly Differentiated Invasive Ductal Carcinoma of the Breast Based on Vimentin and E-cadherin Expression. Revista Brasileira de Ginecologia e Obstetrícia, 40(12), 779-786. https://doi.org/10.1055/s-0038-1673700

Objective: The use of molecular markers can identify a subgroup of tumors with distinct recurrence patterns. The present study aimed to characterize the immunohistochemical expression of vimentin (VIM), of E-cadherin (CDH1), and of cytokeratin 5 (CK5... Read More about Identification of a Subtype of Poorly Differentiated Invasive Ductal Carcinoma of the Breast Based on Vimentin and E-cadherin Expression.

Systems analysis of the liver transcriptome in adult male zebrafish exposed to the non-ionic surfactant nonylphenol (2018)
Journal Article
Huff, M., Abraham da Silveira, W., Starr Hazard, E., Courtney, S. M., Renaud, L., & Hardiman, G. (2019). Systems analysis of the liver transcriptome in adult male zebrafish exposed to the non-ionic surfactant nonylphenol. General and Comparative Endocrinology, 271, 1-14. https://doi.org/10.1016/j.ygcen.2018.10.016

Nonylphenol (NP) arises from the environmental degradation of nonylphenol ethoxylates. It is a ubiquitous environmental contaminant and has been detected at levels up to 167 nM in rivers in the United States. NP is an endocrine disruptor (ED) that ca... Read More about Systems analysis of the liver transcriptome in adult male zebrafish exposed to the non-ionic surfactant nonylphenol.

miRmapper: A Tool for Interpretation of miRNA–mRNA Interaction Networks (2018)
Journal Article
Da Silveira, W. A., Renaud, L., Simpson, J., Glen, W. B., Hazard, E. S., Chung, D., & Hardiman, G. (2018). miRmapper: A Tool for Interpretation of miRNA–mRNA Interaction Networks. Genes, 9(9), Article 458. https://doi.org/10.3390/genes9090458

It is estimated that 30% of all genes in the mammalian cells are regulated by microRNA (miRNAs). The most relevant miRNAs in a cellular context are not necessarily those with the greatest change in expression levels between healthy and diseased tissu... Read More about miRmapper: A Tool for Interpretation of miRNA–mRNA Interaction Networks.

Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio) (2018)
Journal Article
Renaud, L., da Silveira, W. A., Glen, W. B., Hazard, E. S., & Hardiman, G. (2018). Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio). Current Genomics, 19(7), 615-629. https://doi.org/10.2174/1389202919666180503124522

Background: Cellular homeostasis is regulated by the intricate interplay between a plethora of signaling pathways and "energetic sensors" in organs. In order to maintain energy balance, induction or repression of metabolic pathways must be regulated... Read More about Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio).

Systems Analysis of the Liver Transcriptome in Adult Male Zebrafish Exposed to the Plasticizer (2-Ethylhexyl) Phthalate (DEHP) (2018)
Journal Article
Huff, M., Carnevali, O., da Silveira, W. A., Renaud, L., & Hardiman, G. (2018). Systems Analysis of the Liver Transcriptome in Adult Male Zebrafish Exposed to the Plasticizer (2-Ethylhexyl) Phthalate (DEHP). Scientific reports, 8, Article 2118. https://doi.org/10.1038/s41598-018-20266-8

The organic compound diethylhexyl phthalate (DEHP) represents a high production volume chemical found in cosmetics, personal care products, laundry detergents, and household items. DEHP, along with other phthalates causes endocrine disruption in male... Read More about Systems Analysis of the Liver Transcriptome in Adult Male Zebrafish Exposed to the Plasticizer (2-Ethylhexyl) Phthalate (DEHP).

Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information (2018)
Journal Article
Wei, W., Sun, Z., da Silveira, W. A., Yu, Z., Lawson, A., Hardiman, G., …Chung, D. (2019). Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information. Statistical Methods in Medical Research, 28(7), 2137-2149. https://doi.org/10.1177/0962280217752980

Identification of cancer patient subgroups using high throughput genomic data is of critical importance to clinicians and scientists because it can offer opportunities for more personalized treatment and overlapping treatments of cancers. In spite of... Read More about Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information.

The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome (2017)
Journal Article
Renaud, L., Silveira, W. A. D., Hazard, E. S., Simpson, J., Falcinelli, S., Chung, D., …Hardiman, G. (2017). The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome. Genes, 8(10), Article 269. https://doi.org/10.3390/genes8100269

Ubiquitous exposure to bisphenol A (BPA), an endocrine disruptor (ED), has raised concerns for both human and ecosystem health. Epigenetic factors, including microRNAs (miRNAs), are key regulators of gene expression during cancer. The effect of BPA e... Read More about The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome.

Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype (2017)
Journal Article
da Silveira, W. A., Palma, P. V. B., Sicchieri, R. D., Villacis, R. A. R., Mandarano, L. R. M., Oliveira, T. M. G., …Tiezzi, D. G. (2017). Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype. Scientific reports, 7, Article 2851. https://doi.org/10.1038/s41598-017-02761-6

Breast cancer is the most common cancer in women worldwide and metastatic dissemination is the principal factor related to death by this disease. Breast cancer stem cells (bCSC) are thought to be responsible for metastasis and chemoresistance. In thi... Read More about Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype.

Neoadjuvant chemotherapy with trastuzumab in HER2-positive breast cancer: pathologic complete response rate, predictive and prognostic factors (2017)
Journal Article
Buzatto, I., Ribeiro-Silva, A., Andrade, J., Carrara, H., Silveira, W., & Tiezzi, D. (2017). Neoadjuvant chemotherapy with trastuzumab in HER2-positive breast cancer: pathologic complete response rate, predictive and prognostic factors. #Journal not on list, 50(2), Article e5674. https://doi.org/10.1590/1414-431x20165674

The purpose of this study was to retrospectively review the pathologic complete response (pCR) rate from patients (n=86) with stage II and III HER2-positive breast cancer treated with neoadjuvant chemotherapy at our institution from 2008 to 2013 and... Read More about Neoadjuvant chemotherapy with trastuzumab in HER2-positive breast cancer: pathologic complete response rate, predictive and prognostic factors.

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