Naomi Rapier-Sharman

Background/Objectives: Breast cancer is diagnosed in 2.3 million women each year and kills 685,000 (~30% of patients) worldwide. The prognosis for many breast cancer subtypes has improved due to treatments targeting the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). In contrast, patients with triple-negative breast cancer (TNBC) tumors, which lack all three commonly targeted membrane markers, more frequently relapse and have lower survival rates due to a lack of tumor-selective TNBC treatments. We aim to investigate TNBC mechanistic markers that could be targeted for treatment. Methods: We performed a secondary TNBC analysis of 196 samples across 10 publicly available bulk RNA-sequencing studies to better understand the molecular mechanism(s) of disease and predict robust mechanistic markers that could be used to improve the mechanistic understanding of and diagnostic capabilities for TNBC. Results: Our analysis identified ~12,500 significant differentially expressed genes (FDR-adjusted p-value < 0.05), including KIF14 and ELMOD3, and two significantly modulated pathways. Additionally, our novel findings include highly accurate mechanistic markers identified using machine learning methods, including CIDEC (97.1% accuracy alone), CD300LG, ASPM, and RGS1 (98.9% combined accuracy), as well as TNBC subtype-differentiating mechanistic markers, including the targets PDE3B, CFD, IFNG, and ADM, which have associated therapeutics that can potentially be repurposed to improve treatment options. We then experimentally and computationally validated a subset of these findings. Conclusions: The results of our analyses can be used to better understand the mechanism(s) of disease and contribute to the development of improved diagnostics and/or treatments for TNBC.

Background/Objectives: Systemic lupus erythematosus (lupus) and B-cell lymphoma (lymphoma) co-occur at higher-than-expected rates and primarily depend on B cells for their pathology. These observations implicate shared inflammation-related B cell molecular mechanisms as a potential cause of co-occurrence. Methods: We consequently implemented a novel Immune Imbalance Transcriptomics (IIT) algorithm and applied IIT to lupus, lymphoma, and healthy B cell RNA-sequencing (RNA-seq) data to find shared and contrasting mechanisms that are potential therapeutic targets. Results: We observed 7143 significantly dysregulated genes in both lupus and lymphoma. Of those genes, we found 5137 to have a significant immune imbalance, defined as a significant dysregulation by both diseases, as analyzed by IIT. Gene Ontology (GO) term and pathway enrichment of the IIT genes yielded immune-related “Neutrophil Degranulation” and “Adaptive Immune System”, which validates that the IIT algorithm isolates biologically relevant genes in immunity and inflammation. We found that 344 IIT gene products are known targets for established and/or repurposed drugs. Among our results, we found 48 known and 296 novel lupus targets, along with 151 known and 193 novel lymphoma targets. Known disease drug targets in our IIT results further validate that IIT isolates genes with disease-relevant mechanisms. Conclusions: We anticipate the IIT algorithm, together with the shared and contrasting gene mechanisms uncovered here, will contribute to the development of immune-related therapeutic options for lupus and lymphoma patients.

Breast cancer is diagnosed in 2.3 million women each year, and kills 685,000 (~30% of patients) worldwide. Breast cancer prognosis for many subtypes has improved due to treatments targeting Estrogen Receptor (ER), Progesterone Receptor (PR), and Human Epidermal growth factor Receptor 2 (HER2). In contrast, patients with triple-negative breast cancer (TNBC) tumors, which lack all three commonly-targeted membrane biomarkers, more frequently relapse and have lower survival due to lack of tumor-selective TNBC treatments. We performed a secondary TNBC analysis of 196 samples across 10 publicly available bulk RNA-sequencing studies to better understand the molecular mechanism(s) of disease and predict robust biomarkers that could be used to improve diagnostic capabilities for TNBC. Our analysis identified ~12,500 significant differentially expressed genes (FDR-adjusted p-value < 0.05) including KIF14 and ELMOD3, and two significantly modulated pathways. Additionally, our novel findings include highly-accurate biomarkers from machine learning methods including CIDEC (97.1% accurate alone), CD300LG, ASPM, and RGS1 (98.9% combined accuracy); as well as TNBC subtype-differentiating biomarkers. We then experimentally and computationally validated a subset of these findings. The results from our analyses can be used to better understand the mechanism(s) of disease and contribute to the development of improved diagnostics and/or treatments for TNBC.

Mosquito-borne pathogens plague much of the world, yet rapid and simple diagnosis is not available for many affected patients. Using a custom stereolithography 3D printer, we created microfluidic devices with affinity monoliths that could retain, noncovalently attach a fluorescent tag, and detect oligonucleotide and viral RNA. We optimized the fluorescent binding and sample load times using an oligonucleotide sequence from chikungunya virus (CHIKV). We also tested the specificity of CHIKV capture relative to genetically similar Sindbis virus. Moreover, viral RNA from both viruses was flowed through capture columns to study the efficiency and specificity of the column for viral CHIKV. We detected ~10⁷ loaded viral genome copies, which was similar to levels in clinical samples during acute infection. These results show considerable promise for development of this platform into a rapid mosquito-borne viral pathogen detection system.

We report here the results of a transcriptomic meta-analysis of public data for B-cell Non-Hodgkin’s Lymphomas (BCNHL). In 2016, there were 461,000 cases of Non-Hodgkin’s lymphoma worldwide, resulting in 240,000 deaths that year. BCNHLs pose a significant disease burden worldwide, making up 85-90% of BCNHL cases. BCNHL subtypes include Burkitt’s lymphoma, marginal-zone B-cell lymphomas, follicular lymphoma, diffuse large B-cell lymphoma, and mantle cell lymphoma. There is a growing need to understand the mechanisms of BCNHL pathology. The scientific community has spent a great deal of time and effort to identify the hallmarks of cancer. Since cancers of different subtypes can be considered parallel systems, we have performed a meta-analysis including as many BCNHL subtypes as possible to determine common underlying mechanisms. We performed a transcriptomic meta-analysis of publicly available RNA-sequencing data for BCNHL, consisting of 322 relevant samples across seven distinct studies in the NCBI Gene Expression Omnibus (GEO). To our knowledge, no BCNHL meta-analysis of this magnitude has previously been performed. We found ~10,400 significant differentially expressed genes (FDR p-value <= 0.05) and 33 significantly modulated pathways (FDR p-value <= 0.05). We observed potential common mechanisms for BCNHL’s differentially expressed genes and signaling pathways. Our findings include a significant class of proteoglycans not previously associated with lymphomas as well as significant upregulation of extracellular matrix-associated proteins. This meta-analysis offers fresh insights into the inner workings and mechanisms of B-cell lymphomas that could give rise to improved diagnostics and/or therapeutics. Citation Format: Naomi Rapier-Sharman, Brett E. Pickett. Transcriptomic meta-analysis of non-Hodgkin’s B-cell lymphomas reveals reliance on pathways associated with extracellular matrix [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2709.

H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we characterize antigenic drift events observed in the hemagglutinin (HA) sequence of the pandemic H1N1 lineage from 2015–2019. We observed the substitutions S200P, K147N, and P154S, together with other mutations in structural, functional, and/or epitope regions in 2015–2019 HA protein sequences from the Mountain West region of the United States, the larger United States, Europe, and other Northern Hemisphere countries. We reconstructed multiple phylogenetic trees to track the relationships and spread of these mutations and tested for evidence of selection pressure on HA. We found that the prevalence of amino acid substitutions at positions 147, 154, 159, 200, and 233 significantly changed throughout the studied geographical regions between 2015 and 2019. We also found evidence of coevolution among a subset of these amino acid substitutions. The results from this study could be relevant for future epidemiological tracking and vaccine prediction efforts. Similar analyses in the future could identify additional sequence changes that could affect the pathogenicity and/or infectivity of this virus in its human host.

Publicly available RNA-sequencing (RNA-seq) data are a rich resource for elucidating the mechanisms of human disease; however, preprocessing these data requires considerable bioinformatic expertise and computational infrastructure. Analyzing multiple datasets with a consistent computational workflow increases the accuracy of downstream meta-analyses. This collection of datasets represents the human intracellular transcriptional response to disorders and diseases such as acute lymphoblastic leukemia (ALL), B-cell lymphomas, chronic obstructive pulmonary disease (COPD), colorectal cancer, lupus erythematosus; as well as infection with pathogens including Borrelia burgdorferi, hantavirus, influenza A virus, Middle East respiratory syndrome coronavirus (MERS-CoV), Streptococcus pneumoniae, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We calculated the statistically significant differentially expressed genes and Gene Ontology terms for all datasets. In addition, a subset of the datasets also includes results from splice variant analyses, intracellular signaling pathway enrichments as well as read mapping and quantification. All analyses were performed using well-established algorithms and are provided to facilitate future data mining activities, wet lab studies, and to accelerate collaboration and discovery.