Towards an Open-Source Platform to Harmonize and Share Research Results from COVID-19 Interventional and Observational Studies.

As the SARS-CoV-2 virus continues to remain a universal threat on a global scale, a large number of COVID-19 clinical trials and observational studies are being conducted and published. Currently, 9,202 COVID-19 clinical trials have been registered on ClinicalTrials.gov and 293,187 COVID-19 articles were indexed in PubMed. To fully capitalize on the voluminous number of publications reporting COVID-19 interventional and observational studies, their results should be freely accessible via an open-source harmonized shared resource. We introduced ReMeDy (https://remedy.mssm.edu/), an intelligent integrative informatics platform aimed to harmonize and cross-link diverse COVID-19 trial outcomes and observational data. We tested the potential of the platform by uploading 52 COVID-19 clinical trials and 48 COVID-19 observational retrospective studies. ReMeDy was validated based on its capability to store and organize diverse data. The next steps include developing a crowdsourcing functionality coupled with automated outcome extraction using natural language processing.

Gene Expression Markers of Prognostic Importance for Prostate Cancer Risk in Patients with Benign Prostate Hyperplasia.

Comparative analyses utilizing publicly available big data have the potential to generate novel hypotheses and knowledge. However, this approach is underutilized in the realm of cancer research, particularly for prostate cancer. While the general progression of prostate cancer is now well understood, how individual cell types transition from healthy, to pre-cancerous, to cancerous cell types, remains to be further elucidated. To address this, we re-analyzed two publicly available single-cell RNA-seq datasets of prostate cancer and benign prostate hyperplasia cell types. The differential expression analysis of 15,505 epithelial cell profiles across 18,638 genes revealed 791 genes that were up regulated in prostate cancer epithelial cells. Here we report six markers that show significant upregulation in prostate cancer cells relative to BPH epithelial cells: HPN (5.62X), RAC3 (3.51X), CD24 (2.18X), HOXC6 (1.77X), AGR2 (1.71X), and IGFBP2 (1.28X). In particular, the significant differential expression of AGR2 further supports its clinical relevance in supplementing prostate-specific antigen screening for detecting prostate cancer. These findings have the potential to further advance our knowledge of genes governing the development of cancer in prostate epithelial cells. Clinical Relevance- Our results establish the importance of 6 prostate cancer markers (HPN, RAC3, CD24, HOXC6, AGR2, and IGFBP3) in distinguishing between prostate cancer epithelial cells and benign prostate hyperplasia epithelial cells.

X-linked genetic risk factors that promote autoimmunity and dampen remyelination are associated with multiple sclerosis susceptibility.

BACKGROUND: Multiple sclerosis (MS) is a chronic neurodegenerative disease, which has a strong genetic component and is more prevalent in women. MS is caused by an autoimmunity initiated inflammatory response which leads to axon demyelination, followed by axon loss, plaque formation and neurodegeneration. The goal of this article was to explore X-linked genetic factors that are associated with MS susceptibility. METHODS: Using UK Biobank microarray, we analyzed the prevalence of alleles on the X chromosome to identify variants potentially involved in MS. Overall, 488,225 patients across 18,857 markers were analyzed using PLINK. RESULTS: Our results identify 20 SNPs that are significantly more abundant in persons with MS. The genes associated with these SNPs belong to immunity (LAMP2, AVPR2, MTMR8, F8, BCOR, PORCN, and ELF4) and remyelination (NSDHL, HS6ST2, RBM10, TAZ, and AR) pathways that are potentially of great significance for understanding the onset and progression of multiple sclerosis. We further identified a significant 20-fold increase in incidence of MS cases in women with co-occurrences of SNPs associated with myelination and immunity functions. CONCLUSIONS: Our analysis provides novel insights into the roles of X-linked genes in the onset and presentation of multiple sclerosis, identifying 20 SNPs in 14 genes involved primarily in immunity and myelination functions that are significantly more abundant in persons with MS. Our co-occurrence analysis suggests that concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women.

Exploring Determinants of Longevity of Biomedical Databases.

The maintenance of biomedical databases requires ongoing and systematic efforts in keeping them up-to-date which may affect long-term sustainability. Since research has become more reliant on publicly available biomedical data collections, it is important to understand factors affecting their longevity. The aim of this article was to explore potential determinants of biomedical database longevity. To build an analytical dataset, we used Database journal that have been created as an open access platform for presenting biological databases. A stratified analysis of all the original databases published in Database journal between 2009 and 2016 was conducted depending on their accessibility status. Overall, 35% of 518 analyzed databases were not accessible in 2020. We showed that databases with higher citation counts from institutions with higher scientific output were significantly more likely to be currently accessible. Databases from researchers with higher h-index were more likely to be accessible. Further investigation is warranted to identify factors affecting longevity of high impact databases.

Utilizing Shared Big Data to Identify Liver Cancer Dedifferentiation Markers.

Big data reanalysis has the potential to generate novel comparative analyses which aim to generate novel hypotheses and knowledge. However, this approach is underutilized in the realm of cancer research, particularly for cancer stem cells (CSCs). CSCs are a rare subset of tumor cells, which dedifferentiate from healthy adult cells, and have the potential for self-renewal and treatment resistance. This analysis utilizes two publically available single-cell RNA-seq datasets of liver cancer and adult liver cell types to demonstrate how reanalysis of big data can lead to valuable new discoveries. We identify 519 differentially expressed genes between liver CSCs and healthy liver cell types. Here we report the potential novel liver CSC dedifferentiation factor, Msh Homeobox 2, which was significantly upregulated in liver CSCs by 1.36 fold (p-value < 1E-10). These findings have the potential to further advance our knowledge of genes governing the formation of CSCs.

A Web-based Platform to Share Harmonized Results from COVID-19 Clinical Studies.

COVID-19 has caused a worldwide pandemic, accompanied by a high number of deaths and hospitalizations. Multiple preventative vaccines and variety of COVID-19 treatments have been developed and explored. This large volume of scientific work led to an extensive number of COVID-19 publications, which resulted in the necessity to standardize, store, share, and investigate research results in a harmonized manner. Attempts to standardize and share COVID-19 research data have been lacking. The purpose of the ReMeDy platform is to provide an intelligent informatics solution of integrating diverse COVID-19 trial outcomes and omics data across COVID-19 research studies. To test the platform, we utilized 48 COVID-19 observational retrospective studies. The robustness of the platform was validated through the ability to efficiently organize the diverse data elements. Next steps include expanding our database through the inclusion of all published COVID-19 studies. ReMeDy is located at https://remedy.mssm.edu/.

A Platform for Integrating and Sharing Cancer Stem Cell Data.

Advancements in cancer research and treatment have highlighted the need for standardization and sharing of cancer stem cell (CSC) data to facilitate research transparency and to promote collaboration within the scientific community. Although previous applications have attempted to gather and disseminate these data, currently no platform organizes the heterogeneous CSC information into a harmonized project-based framework. The aim of our platform, ReMeDy, is to provide an intelligent informatics solution integrating diverse CSC characteristics, outcomes information, and omics data across clinical, preclinical and in vitro studies. These heterogeneous data streams are organized within a multi-modular framework, subjected to a stringent validation by using standardized ontologies, and stored in a searchable format. To test usefulness of our approach for capturing diverse data related to CSCs, we integrated data from 52 publicly-available CSC projects. We validated the robustness of the platform, by efficiently organizing diverse data elements, and demonstrated its potential for promoting future knowledge discovery driven by aggregation of published data. Next steps include expanding number of uploaded CSC projects and developing additional data visualization tools. The platform is accessible through https://remedy.mssm.edu/.

Intelligent Integrative Platform for Sharing Heterogenuous Stem Cell Research Data.

Recent studies demonstrated that comparative analysis of stem cell research data sets originating from multiple studies can produce new information and help with hypotheses generation. Effective approaches for incorporating multiple diverse heterogeneous data sets collected from stem cell projects into a harmonized project-based framework have been lacking. Here, we provide an intelligent informatics solution for integrating comprehensive characterizations of stem cells with research subject and project outcome information. Our platform is the first to seamlessly integrate information from iPSCs and cancer stem cell research into a single platform, using a multi-modular common data element framework. Heterogeneous data is validated using predefined ontologies and stored in a relational database, to ensure data quality and ease of access. Testing was performed using 103 published, publicly-available iPSC and cancer stem cell projects conducted in clinical, preclinical and in vitro evaluations. We validated the robustness of the platform, by seamlessly harmonizing diverse data elements, and demonstrated its potential for knowledge generation through the aggregation and harmonization of data. Future aims of this project include increasing the database size using crowdsourcing and natural language processing functionalities. The platform is publicly available at https://remedy.mssm.edu/.

ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials.

ABSTRACT: Recent regenerative medicine studies have emphasized the need for increased standardization, harmonization and sharing of information related to stem cell product characterization, to help drive these innovative interventions toward public availability and to increase collaboration in the scientific community. Although numerous attempts and numerous databases have been made to manage these data, a platform that incorporates all the heterogeneous data collected from stem cell projects into a harmonized project-based framework is still lacking. The aim of the database, which is described in this study, is to provide an intelligent informatics solution that integrates comprehensive characterization of diverse stem cell product characteristics with research subject and project outcome information. In the resulting platform, heterogeneous data are validated using predefined ontologies and stored in a relational database, to ensure data quality and ease of access. Testing was performed using 51 published, publically available induced pluripotent stem cell projects conducted in clinical, preclinical and in-vitro evaluations. Future aims of this project include further increasing the database size to include all published stem cell trials and develop additional data visualization tools to improve usability. Our testing demonstrated the robustness of the proposed platform, by seamlessly harmonizing diverse common data elements, and the potential of this platform for driving knowledge generation from the aggregation and harmonization of these diverse data. DATABASE URL: https://remedy.mssm.edu/.

Identification of Liver Cancer Stem Cell Stemness Markers Using a Comparative Analysis of Public Data Sets.

PURPOSE: Comparative reanalysis of single-cell transcriptomics data to gain useful novel insights into cancer stem cells (CSCs), which are a rare subset of cells within tumors, characterized by their capability to self-renew and differentiate, and their role in tumorigenicity. PATIENTS AND METHODS: This project utilized publically available liver single-cell RNA-seq datasets of liver cancer and liver progenitor cell types to demonstrate how shared large amounts of data can generate new and valuable information. The data were analyzed using EdgeR differential expression analysis, with focus on a set of 34 known stemness markers. RESULTS: We showed that the expression of stemness markers SOX9, KRT19, KRT7, and CD24, and Yamanaka factors Oct4 and SOX2 in CSCs was significantly elevated relative to progenitor cell types, potentially explaining their increased differentiation and replication potential. CONCLUSION: These results help to further document the complementary expression changes that give CSCs their distinct phenotypic profile. Our findings have potential significance to advance our knowledge of the important genes relevant to CSCs.

Comparative Analysis of Public Data Sets to Identify Stemness Markers That Differentiate Liver Cancer Stem Cells.

Cancer stem cells (CSCs) represent an important field in translational medicine for generating novel cancer treatments. To identify important stemness markers in liver CSCs that potentially explain their resistance to treatment, we analyzed 10865 single-cell RNA-seq samples across 42684 coding and non-coding genes. Our results show that CSCs have significantly increased expression of two Yamanaka factors (Oct4, 2.14X and SOX2, 1.13X) and three stemness factors (CD44, 3.25X; KRT7, 2.2X; SOX9, 1.71X), relative to liver progenitor cells. Our study demonstrates the potential power of harnessing shared big data for driving translational medicine for novel hypothesis generation.

Introducing a Platform for Integrating and Sharing Stem Cell Research Data.

Advancements in regenerative medicine have highlighted the need for increased standardization and sharing of stem cell products to help drive these innovative interventions toward public availability and to increase collaboration in the scientific community. Although numerous attempts and numerous databases have been made to store this data, there is still a lack of a platform that incorporates heterogeneous stem cell information into a harmonized project-based framework. The aim of the platform described in this study, ReMeDy, is to provide an intelligent informatics solution which integrates diverse stem cell product characteristics with study subject and omics information. In the resulting platform, heterogeneous data is validated using predefined ontologies and stored in a relational database. In this initial feasibility study, testing of the ReMeDy functionality was performed using published, publically-available induced pluripotent stem cell projects conducted in in vitro, preclinical and intervention evaluations. It demonstrated the robustness of ReMeDy for storing diverse iPSC data, by seamlessly harmonizing diverse common data elements, and the potential utility of this platform for driving knowledge generation from the aggregation of this shared data. Next steps include increasing the number of curated projects by developing a crowdsourcing framework for data upload and an automated pipeline for metadata abstraction. The database is publically accessible at https://remedy.mssm.edu/.

Drosophila female reproductive tract gene expression reveals coordinated mating responses and rapidly evolving tissue-specific genes.

Sexual reproduction in internally fertilizing species requires complex coordination between female and male reproductive systems and among the diverse tissues of the female reproductive tract (FRT). Here, we report a comprehensive, tissue-specific investigation of Drosophila melanogaster FRT gene expression before and after mating. We identified expression profiles that distinguished each tissue, including major differences between tissues with glandular or primarily nonglandular epithelium. All tissues were enriched for distinct sets of genes possessing secretion signals that exhibited accelerated evolution, as might be expected for genes participating in molecular interactions between the sexes within the FRT extracellular environment. Despite robust transcriptional differences between tissues, postmating responses were dominated by coordinated transient changes indicative of an integrated systems-level functional response. This comprehensive characterization of gene expression throughout the FRT identifies putative female contributions to postcopulatory events critical to reproduction and potentially reproductive isolation, as well as the putative targets of sexual selection and conflict.

Ovarian fluid proteome variation associates with sperm swimming speed in an externally fertilizing fish.

Sperm velocity is a key trait that predicts the outcome of sperm competition. By promoting or impeding sperm velocity, females can control fertilization via postcopulatory cryptic female choice. In Chinook salmon, ovarian fluid (OF), which surrounds the ova, mediates sperm velocity according to male and female identity, biasing the outcome of sperm competition towards males with faster sperm. Past investigations have revealed proteome variation in OF, but the specific components of OF that differentially mediate sperm velocity have yet to be characterized. Here we use quantitative proteomics to investigate whether OF protein composition explains variation in sperm velocity and fertilization success. We found that OF proteomes from six females robustly clustered into two groups and that these groups are distinguished by the abundance of a restricted set of proteins significantly associated with sperm velocity. Exposure of sperm to OF from females in group I had faster sperm compared to sperm exposed to the OF of group II females. Overall, OF proteins that distinguished between these groups were enriched for vitellogenin and calcium ion interactions. Our findings suggest that these proteins may form the functional basis for cryptic female choice via the biochemical and physiological mediation of sperm velocity.

Towards Intelligent Integration and Sharing of Stem Cell Research Data.

Advancements in regenerative medicine have brought to the fore the need for increased standardization and sharing of stem cell product characterization to help drive these innovative interventions toward public availability. Although numerous attempts have been made to store this data, there is still a lack of a platform that incorporates heterogeneous stem cell information into a harmonized project-based framework. The aim of this project was to introduce and pilot-test an intelligent informatics solution which integrates diverse stem cell product characteristics with study subject and omics information. In the resulting platform, heterogeneous data is validated using predefined ontologies and stored in a NoSQL repository. Pilot-testing was performed on nine sponsored stem cell projects conducting preclinical and intervention evaluations. The pilot-testing demonstrated the robustness of the proposed platform, by seamlessly harmonizing diverse common data elements, and the potential of this platform for driving knowledge generation from the aggregation of this shared data.

Molecular Diversification of the Seminal Fluid Proteome in a Recently Diverged Passerine Species Pair.

Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recently diverged passerine species pair (Passer domesticus and Passer hispaniolensis) using a combination of proteomic and comparative evolutionary genomic approaches. First, we characterized and compared the SF proteome of the two species, revealing consistencies with known aspects of SFP biology and function in other taxa, including the presence and diversification of proteins involved in immunity and sperm maturation. Second, using whole-genome resequencing data, we assessed patterns of genomic differentiation between house and Spanish sparrows. These analyses detected divergent selection on immunity-related SF genes and positive selective sweeps in regions containing a number of SF genes that also exhibited protein abundance diversification between species. Finally, we analyzed the molecular evolution of SFPs across 11 passerine species and found a significantly higher rate of positive selection in SFPs compared with the rest of the genome, as well as significant enrichments for functional pathways related to immunity in the set of positively selected SF genes. Our results suggest that selection on immunity pathways is an important determinant of passerine SF composition and evolution. Assessing the role of immunity genes in speciation in other recently diverged taxa should be prioritized given the potential role for immunity-related proteins in reproductive incompatibilities in Passer sparrows.

Female novelty and male status dynamically modulate ejaculate expenditure and seminal fluid proteome over successive matings in red junglefowl.

Theory predicts that males will strategically invest in ejaculates according to the value of mating opportunities. While strategic sperm allocation has been studied extensively, little is known about concomitant changes in seminal fluid (SF) and its molecular composition, despite increasing evidence that SF proteins (SFPs) are fundamental in fertility and sperm competition. Here, we show that in male red junglefowl, Gallus gallus, along with changes in sperm numbers and SF investment, SF composition changed dynamically over successive matings with a first female, immediately followed by mating with a second, sexually novel female. The SF proteome exhibited a pattern of both protein depletion and enrichment over successive matings, including progressive increases in immunity and plasma proteins. Ejaculates allocated to the second female had distinct proteomic profiles, where depletion of many SFPs was compensated by increased investment in others. This response was partly modulated by male social status: when mating with the second, novel female, subdominants (but not dominants) preferentially invested in SFPs associated with sperm composition, which may reflect status-specific differences in mating rates, sperm maturation and sperm competition. Global proteomic SF analysis thus reveals that successive matings trigger rapid, dynamic SFP changes driven by a combination of depletion and strategic allocation.

Proteins, Transcripts, and Genetic Architecture of Seminal Fluid and Sperm in the Mosquito Aedes aegypti.

The yellow fever mosquito, Aedes aegypti,, transmits several viruses causative of serious diseases, including dengue, Zika, and chikungunya. Some proposed efforts to control this vector involve manipulating reproduction to suppress wild populations or to replace them with disease-resistant mosquitoes. The design of such strategies requires an intimate knowledge of reproductive processes, yet our basic understanding of reproductive genetics in this vector remains largely incomplete. To accelerate future investigations, we have comprehensively catalogued sperm and seminal fluid proteins (SFPs) transferred to females in the ejaculate using tandem mass spectrometry. By excluding female-derived proteins using an isotopic labeling approach, we identified 870 sperm proteins and 280 SFPs. Functional composition analysis revealed parallels with known aspects of sperm biology and SFP function in other insects. To corroborate our proteome characterization, we also generated transcriptomes for testes and the male accessory glands-the primary contributors to Ae. aegypti, sperm and seminal fluid, respectively. Differential gene expression of accessory glands from virgin and mated males suggests that transcripts encoding proteins involved in protein translation are upregulated post-mating. Several SFP transcripts were also modulated after mating, but >90% remained unchanged. Finally, a significant enrichment of SFPs was observed on chromosome 1, which harbors the male sex determining locus in this species. Our study provides a comprehensive proteomic and transcriptomic characterization of ejaculate production and composition and thus provides a foundation for future investigations of Ae. aegypti, reproductive biology, from functional analysis of individual proteins to broader examination of reproductive processes.

Early experiences mediate distinct adult gene expression and reproductive programs in Caenorhabditis elegans.

Environmental stress during early development in animals can have profound effects on adult phenotypes via programmed changes in gene expression. Using the nematode C. elegans, we demonstrated previously that adults retain a cellular memory of their developmental experience that is manifested by differences in gene expression and life history traits; however, the sophistication of this system in response to different environmental stresses, and how it dictates phenotypic plasticity in adults that contribute to increased fitness in response to distinct environmental challenges, was unknown. Using transcriptional profiling, we show here that C. elegans adults indeed retain distinct cellular memories of different environmental conditions. We identified approximately 500 genes in adults that entered dauer due to starvation that exhibit significant opposite ("seesaw") transcriptional phenotypes compared to adults that entered dauer due to crowding, and are distinct from animals that bypassed dauer. Moreover, we show that two-thirds of the genes in the genome experience a 2-fold or greater seesaw trend in gene expression, and based upon the direction of change, are enriched in large, tightly linked regions on different chromosomes. Importantly, these transcriptional programs correspond to significant changes in brood size depending on the experienced stress. In addition, we demonstrate that while the observed seesaw gene expression changes occur in both somatic and germline tissue, only starvation-induced changes require a functional GLP-4 protein necessary for germline development, and both programs require the Argonaute CSR-1. Thus, our results suggest that signaling between the soma and the germ line can generate phenotypic plasticity as a result of early environmental experience, and likely contribute to increased fitness in adverse conditions and the evolution of the C. elegans genome.

Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera.

BACKGROUND: Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aiming to disentangle the molecular ramifications of these processes are progressing, we still know little about the genetic basis of evolutionary transitions in reproductive systems. Here we conduct the first comparative analysis of sperm proteomes in Lepidoptera, a group that exhibits dichotomous spermatogenesis, in which males produce a functional fertilization-competent sperm (eupyrene) and an incompetent sperm morph lacking nuclear DNA (apyrene). Through the integrated application of evolutionary proteomics and genomics, we characterize the genomic patterns potentially associated with the origination and evolution of this unique spermatogenic process and assess the importance of genetic novelty in Lepidopteran sperm biology. RESULTS: Comparison of the newly characterized Monarch butterfly (Danaus plexippus) sperm proteome to those of the Carolina sphinx moth (Manduca sexta) and the fruit fly (Drosophila melanogaster) demonstrated conservation at the level of protein abundance and post-translational modification within Lepidoptera. In contrast, comparative genomic analyses across insects reveals significant divergence at two levels that differentiate the genetic architecture of sperm in Lepidoptera from other insects. First, a significant reduction in orthology among Monarch sperm genes relative to the remainder of the genome in non-Lepidopteran insect species was observed. Second, a substantial number of sperm proteins were found to be specific to Lepidoptera, in that they lack detectable homology to the genomes of more distantly related insects. Lastly, the functional importance of Lepidoptera specific sperm proteins is broadly supported by their increased abundance relative to proteins conserved across insects. CONCLUSIONS: Our results identify a burst of genetic novelty amongst sperm proteins that may be associated with the origin of heteromorphic spermatogenesis in ancestral Lepidoptera and/or the subsequent evolution of this system. This pattern of genomic diversification is distinct from the remainder of the genome and thus suggests that this transition has had a marked impact on lepidopteran genome evolution. The identification of abundant sperm proteins unique to Lepidoptera, including proteins distinct between specific lineages, will accelerate future functional studies aiming to understand the developmental origin of dichotomous spermatogenesis and the functional diversification of the fertilization incompetent apyrene sperm morph.