Biological Informatics Research Articles

A Method Utilizing an Image Visibility Graph to Portray the Arrangement of Genomic Data Sequencing, Gene Frequencies for The Peptidoglycan-Associated Lipoprotein (Pal) Gene in Brucella Spp., and Prevalence of Brucellosis in Nineveh

Brucellosis is a disease triggered by various Gram-negative bacteria (Brucella spp.), impacting animals through miscarriages and causing fever in humans. The verified reality that peptidoglycan-associated lipoprotein (Pal) proteins eist in multiple bacteria and display remarkable vaccine potential shifts the spotlight to this protein and its importance within bacterial systems. Furthermore, gaining insight into the implications of mutations in this protein becomes of utmost importance. Biological informatics software was utilized to carry out a comparative study of the Pal gene across different species of Brucella bacteria. Computational methods were employed to represent sequences using both CGR and FCGR techniques. The Pal protein’s secondary and tertiary structures were built, and comparisons were drawn regarding mutations present among various Brucella species. An assessment of instances of infection was conducted, and statistical analyses were eecuted concerning brucellosis in the Nineveh region. While no significant differences were observed in the Pal gene among Brucella species, noticeable variations became evident when employing CGR and FCGR methodologies. FCGR proves to be more precise for visualization compared to CGR. Particularly, B. endophytica ehibited the most notable changes in the Pal protein when compared to the standard type within the species. The frequency of brucellosis infections increases in correlation with rising population numbers. The initial CGR images might not ehibit noticeable differences, but utilizing the FCGR method makes it easier to distinguish these variations. This affirms that FCGR is more effective for assessing the degree of dissimilarities. The presence of brucellosis poses a concern, especially in regions characterized by dense populations. It is important to emphasize public education regarding the adoption of suitable health precautions to thwart the disease, coupled with the importance of vaccination.

Abstract 859: Development of non-smoking lung cancers by indoor carcinogenic aerosols through epigenetic reprogramming of lung stem cells: Bioinformatics and artificial intelligence analysis

Abstract Several scientific studies discovered the toxic effects of indoor aerosols on different organs’ adult stem cells of the human body. The most importantly, the indoor toxic aerosols comprised of numerous carcinogens namely, sodium dodecyl sulfate, phthalic acids from floor cleaners, formaldehyde, acetaldehyde, benzene, toluene, ethyl benzene, xylenes, from air fresheners, Hydramethylnon, Pyrethrins, imiprothrin, cypermethrin, tetramethrin, prallethrin and permethrin from ant and roach Killer. However, there was a lack of analysis revealing the mechanism of toxic effects and epigenetic reprogramming of human lung stem cells and development of non-smoking lung cancers. In this study, we analyzed the toxic effects of these chemicals and the mechanism of epigenetic reprograming on lung epithelial cells using Comparative Toxico-genomics Database (CTD), database of Environmental Health Perspectives (EHP), National Institute of Environmental Health Sciences (NIEHS), Google search browser with generative artificial intelligence (AI) and other biological informatics methods (Reactome, Cytoscape PSICQUIC services, and ChEMBL database). We observed from CTD analysis that the chemical gene interactions as risk factors from indoor aerosols showed transcriptionally highly expressed of 31 common genes, by phthalic acids, sodium dodecyl sulfate, from the total of 1347 genes, 107 common genes by formaldehyde, acetaldehyde from the total of 4193 genes and all other toxic ingredients of indoor aerosols. The epigenetic mechanism of histone modifications (H3K4me3, H3K9me3, H3K27me3, H3K27ac, H3K36me3, H3K4me1, Hsa-mir-1301 of lung epithelial, and miRNAs have been revealed by NIH Roadmap Epigenomics Mapping Consortium and the lung tissue arrays were analyzed with AI and matplotlib program. The heterogenic adult stem cell reprogramming is regulated by epigenetic bivalent histone modifications at transcript starts sequences (TSS) of target genes and our current study revealed that CD44, CD80, ALDH2, ALDH3A1, ALDH3B2 are epigenetically reprogrammed with close interaction of other genes by these toxic ingredients of indoor aerosols. Therefore, our results are significant for the carcinogenic effects of indoor aerosols causing for development of lung cancer epigenetically, which may give a clue for the prevention and treatment of nonsmoking lung cancer. Citation Format: Juan Anderson, Mariah Delgado, Malcolm Lovett, Maya Saunders, Geovannie Lake, Samuel Darko, Rose M. Stiffin, Ayivi Huisso, Marilyn Sherman, Latoya Appleton, Amalya Mihnea, Swarnava Das, Mohammad M. Algahtani, Ravi Vadapalli, Biswarup Basu, Arunima Biswas, Noor Neha, Madhumita Das, Marco A. Ruiz, Mayur Doke, Jayanta K. Das. Development of non-smoking lung cancers by indoor carcinogenic aerosols through epigenetic reprogramming of lung stem cells: Bioinformatics and artificial intelligence analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 859.

Exploration of hub genes involved in PCOS using biological informatics methods.

Background:The aim of this study was to find underlying genes and their interaction mechanism crucial to the polycystic ovarian syndrome (PCOS) by analyzing differentially expressed genes (DEGs) between PCOS and non-PCOS subjects.Methods:Gene expression data of PCOS and non-PCOS subjects were collected from gene expression omnibus (GEO) database. GEO2R were used to calculating P value and logFC. The screening threshold of DEGs was P < .05 and | FC | ≥ 1.2. GO annotation and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathway enrichment analysis was performed by using DAVID (2021 Update). The protein-protein interaction (PPI) network of DEGs was constructed by using the STRING database, and the hub genes were recognized through Hubba plugin of Cytoscape software.Results:PCOS and non-PCOS subjects shared a total of 174 DGEs, including 14 upregulated and 160 downregulated genes. The GO biological processes enriched by DEGs mainly involved actin cytoskeleton organization, positive regulation of NF-κB signaling pathway, and positive regulation of canonical Wnt signaling pathway. The DEGs were significantly enriched in cytoplasm, nucleus and cytosol. Their molecular functions mainly focused on protein binding, calmodulin binding and glycerol-3-phosphate dehydrogenase activity. The PI3K/Akt signaling pathway and glycosaminoglycan biosynthesis were highlighted as critical pathways enriched by DEGs. 10 hub genes were screened from the constructed PPI network, of which EGF, FN1 and TLR4 were mainly enriched in the PI3K/Akt signaling pathway.Conclusion:In this study, a total of 174 DEGs and 10 hub genes were identified as new candidate targets for insulin resistance (IR) in PCOS individuals, which may provide a new direction for developing novel treatment strategies for PCOS.

Screening differential circular RNAs expression profiles in Vulvar Lichen Sclerosus

BackgroundVulvar lichen sclerosus (VLS) is one of the most common clinical manifestations of vulva. Thirteen percent of women have symptomatic vulvar diseases. The aim of this study is to investigate the expression profile of circular RNA (circRNAs) in vulvar lichen sclerosus, and to identify the underlying core genes of VLS.MethodsWe removed rRNA for sequencing, and screened the differentially expressed messenger RNA (mRNAs), long non-coding RNA (lncRNAs) and single-stranded circRNA in 20 groups of VLS tissues and 20 groups of healthy female vulvar skin tissues. Bioinformatics analysis was used to analyze its potential functions.ResultsA total of 2545 differentially expressed mRNAs were assessed in VLS patients, of which 1541 samples were up-regulated and 1004 samples were down-regulated. A total of 1453 differentially expressed lncRNAs were assessed, of which 812 samples were up-regulated and 641 samples were down-regulated. A total of 79 differentially expressed circRNAs were assessed, of which 54 were up-regulated and 25 were down-regulated. The differential expression of circRNAs was closely related to biological processes and molecular functions. The differences in circRNAs were mainly related to the “human T-cell leukemia virus 1 infection” signaling pathway and the “axon guidance” signaling pathway.ConclusionThe profile of abnormal regulation of circRNA exists in VLS. According to biological informatics analysis, the dysregulation of circRNAs may be related to the pathogenesis and pathological process of VLS.

Detecting Alterations in Fractal Fibrin Patterns using Light Microscopy

Fibrin is produced from the polymerization of fibrinogen at the completion of the coagulation cascade. Alterations in the structure and pattern of fibrin in plasma clots have been associated with various disease states such as pulmonary embolism, myocardial infarction, and hemophilia. Assessing these structural changes often requires confocal microscopy with fluorescently labeled fibrinogen or electron microscopy. Here, we demonstrate a novel method whereby pathophysiological alterations in fibrin patterns can be detected using light microscopy. Images of plasma clots from the partial thromboplastin time test were analyzed for alterations in fractal patterns using The Workflow of Matrix Biology Informatics. Factor VIII and Factor IX deficiencies showed significant changes in lacunarity, branchpoints, and total pattern area. We also detected significant changes in fibrin patterns altered by hyperglycemia, a known risk factor for thrombosis and embolisms. This work has direct clinical relevance as it utilizes readily available technology that can be applied in the clinical laboratory to screen patient samples for fibrin alterations when clotting time tests are prolonged. This diagnostic information could be utilized in the identification of various diseases that affect blood clot formation.

Investigation of hub genes involved in Turner syndrome using biological informatics methods.

This study aimed to explore candidate genes and their potential interaction mechanism critical to the pathophysiology of Turner syndrome by using the Gene Expression Omnibus database. GSE58435 data set was obtained by querying the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened using R and subsequently annotated by Gene Ontology. Functional enrichment analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes database for annotation, visualization, and integrated discovery. A protein-protein interaction network of different genes was constructed based on the STRING database, in which hub genes were explored through Cytoscape software. The expression of the hub genes was verified by analyzing the gene expression in the GSE46687 data set. A total of 733 differential genes were identified. These differentially expressed genes were significantly enriched in nucleoplasm and nucleus. Their molecular function was concentrated on DNA binding and transcription, coronary artery, and adipose tissue development. According to the annotation of Kyoto Encyclopedia of Genes and Genomes, the identified DEGs were mainly enriched in inflammatory mediator regulation of TRP channels, osteoclast differentiation. A total of 10 hub genes (HIST1H2BA, TRIM71, HIST1H2BB, HIST1H4D, TNF, TP53BP1, CDCA8, EGF, HMG20B, and BCL9) were identified from the constructed protein-protein interaction network. These genes were discovered to be highly expressed in osteoclasts, ovaries, digestive tract, blood, and lymphatic tissues through the online application of human protein atlas. In this study, 733 DEGs and 10 hub genes were identified. They would be new candidate targets in Turner syndrome.

The methodology of food design. Part 2. Digital nutritiology in personal food

Atherosclerosis (the main cause of a wide range of cardiovascular diseases) and other multifactorial diseases depend on several nutrition factors, defined in general by lifestyle that directly and constantly affects the human body. The modern level of science and technology development is able to form a diet, taking into account all personal characteristics in such a way that makes nutrition an effective preventive measure against diseases in order to keep a person healthy. The purpose of this article is to define and study all the limitations (the scope of its coverage in the scientific literature) that arose in the process of research aimed to formation of an integrated personal approach to designing of nutrition to prevent atherosclerosis. The object of the study was scientific literature, which is available in open source and free access databases: PubMed, ScienceDirect, eLIBRARY.RU, www.fips.ru, Patentscope. The language of search is Russian and English, search depth is 12 years. In the course of the research two food design concepts were found that affect process of digitalization in the food sector: the concept “FoodTech” (food technology) and digital nutritiology. It was established that in Russia only one company — LLC “City Supermarket” (Moscow), that works with the brand “Azbuka Vkusa” — acts in the sphere of “FoodTech” on the Russian market. This company selects personalized food, taking into account the results of personal nutrigenetic tests, in cooperation with LLC “Genotech” (Moscow). There is a need to use biological information, statistical information processing (nutrigenetic studies, nutrigenomic research) and machine-aided data processing (machine learning) for further generation of automatic algorithm that compiles personal recommendations. The relevance of generation of a national domestic database on chemical composition of food products (presented in the market) to simplify the preparation of individual personal diets is observed. We underline the necessity to use the test-organisms, i. e. dorio fish / zebrafish (Danio rerio) and nematodes (Caenorhabditis elegans)), which were used to determine the activity of candidate substances — the biologically active substances that feature antiatherosclerotic properties. In the future the authors plan to conduct a nutrigenomic and nutrigenetic study, using digital achievements. To collect information about consumers, it is necessary to apply digital devices, and use biological informatics to process the results; after that it is necessary to generate the algorithm for automatic selection of personalized dietary recommendations.

Abstract 2104: 3D spheroid: A rapid drug screening model for epigenetic clinical targets against heterogenic cancer stem cells

Abstract Recent scientific studies showed that transcript start sequences (TSS) are regulated by epigenetic bivalent histone modifications (H3K4me3 and H3K27me3) of target genes for heterogenic cancer stem cells (CSCs) reprogramming. Most of these studies are based on monolayer or 2D culture grew cancer cells. Studies of 3D spheroid models showed a rapid screening of anticancer drugs against CSCs. The 3D-spheroid models closely mimic in vivo tumor microenvironment (TME). Hence, 3D spheroid in vitro model development is a standout amongst other portrayed cancer models regarding 3D cell culture based on its similitude to physiological tumor tissues. Our previous studies of 3D spheroid models showed the effectiveness of small molecules targeted to the bivalent histone modifications against the CSCs in pancreatic cancer. The current study is aimed to explore the epigenetic clinical targets of bivalent histone modifications with the expression of heterogenic CSCs (CD133, CD15 CD44, CD49f, CD24, ALDH1A3, CXCR4) of 3D spheroids in glioblastomas, oral, and colorectal cancers (CRC). The Cancer Stem Cells Therapeutic Target Database Version 2.0 (CSCTTv2.0) reported the highest expression of CSCs in glioblastomas, oral and CRCs that showed resistance to anticancer drugs (such as Bevacizumab, 5-FU, cisplatin, cetuximab, oxaliplatin). The biological informatics methods (String; Cytoscape, BioGrid, Reactome, MatrixDB, Pubchem database) were used in our current study. The NCBI Gene Expression Omnibus (GEO) database showed only 4 studies of 3D spheroids of CSCs which revealed drug-resistant heterogenic CSCs, in 7 samples of glioblastoma spheroids and 4 samples of CSCs in MCF-7 breast cancer spheroids from 6 samples; drug-resistant CSCs of MDA-MB 231 spheroids from 6 samples; CSCs of colorectal cancer (CRC) spheroids from 6 samples, but the clinical the target of bivalent histone modifications with heterogenic CSCs in the glioblastomas, oral and CRCs have not been explored earlier using 3D spheroids for rapid drug screening. The protein-protein interaction (PPI) network of the current study showed a relationship of closely related 17 significant genes. Among these 17 genes, a total of 6 CSCs was closely associated with epigenetic bivalent histone modifications through KDM7A, PHF1and EZH2. We also found from Cytoscape analysis of Reactome network that UniProtKB - P61073 (CXCR4_HUMAN) has significant interaction with other target network genes from 106 network data and it has been mentioned that Plerixafor, an antagonist inhibits CXCR4 activity. Therefore, it is important in designing any small molecules or drugs against heterogenic CSCs of glioblastomas, oral, and CRC with epigenetic target of histone bivalent modifications using a 3D spheroid model which could be rapid screening model for anticancer drug discovery and our current study highlighted this important relationship. Citation Format: Madhumita Das, Maylet Cortes Santana, Stephanie Barraque, Jhoselyn Cardenas, Johnny Amaya Galindo, Misael Cortes, Jose Ramos, Alberto Sanchez Prado, Melissa Tejeda Castillo, Victor Villar, Claudy Vincent, Elizabeth Justo, Mariano Mendez, Indira Mera, Juan Pachon, Kamila Perez, Adara Marin, Nabendu Murmu, Maharaj Biswas, Marco Ruiz, Jayanta Kumar Das. 3D spheroid: A rapid drug screening model for epigenetic clinical targets against heterogenic cancer stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2104.

Induction of ferroptosis by ATF3 elevation alleviates cisplatin resistance in gastric cancer by restraining Nrf2/Keap1/xCT signaling

BackgroundCurrently, resistance against cisplatin (DDP) is a frequent problem for the success of advanced gastric carcinoma (GC) chemotherapy. Here, we sought to investigate the function of activating transcription factor 3 (ATF3) n GC chemoresistance.MethodsExpression of ATF3 was determined in GC cell lines (MNK45, SGC7901, and BGC823) and cisplatin (DDP)-resistant cells (SGC7901/DDP and BGC823/DDP). Biological informatics was performed to analyze ATF3 expression and prognosis in GC patients. Cisplatin resistance was evaluated. Ferroptosis was detected after ATF3 transfection of cells. The underlying molecular mechanism was also investigated.ResultsTranscripts of ATF3 were decreased in GC cells and GC tissues. Kaplan–Meier plotter analysis revealed that ATF3 expression was positively related to the overall survival of GC patients. In particular, lower levels of ATF3 were observed in cisplatin-resistant SGC7901/DDP and BGC823/DDP relative to their parental cells. Notably, ATF3 elevation sensitized cisplatin-resistant cells to cisplatin. Mechanically, compared with parental cells, SGC7901/DDP and BGC823/DDP cells exhibited lower ferroptosis evident by lower ROS, MDA and lipid peroxidation and higher intracellular GSH levels. However, ATF3 elevated ferroptosis in SGC7901/DDP and BGC823/DDP cells. Intriguingly, ATF3 overexpression together with ferroptosis activator erastin or RSL3 treatment further enhanced ferroptosis and cisplatin resistance; however, the ferroptosis suppressor liproxstatin-1 reversed the function of ATF3 in ferroptosis and cisplatin resistance. Additionally, cisplatin-resistant cells exhibited stronger activation of Nrf2/Keap1/xCT signaling relative to parental cells, which was restrained by ATF3 up-regulation. Importantly, restoring Nrf2 signaling overturned ATF3-mediated ferroptosis and cisplatin resistance.ConclusionATF3 may sensitize GC cells to cisplatin by induction of ferroptosis via blocking Nrf2/Keap1/xCT signaling, supporting a promising therapeutic approach for overcoming chemoresistance in GC.

USE OF MEDICAL INFORMATION SYSTEMS IN PROFESSIONAL TRAINING OF FUTURE DOCTORS

In the process of work, the doctor has to process a significant amount of information, establish contacts with different departments of the medical institution or between different institutions, work with a significant flow of patients, making decisions concerning human life and health. Modern medical information systems, which are widely implemented in various areas of health care, allow to optimize the doctor's activity, provide him with quick access to databases and resources of the clinic, improve the efficiency of diagnosis, reduce the error rate. Graduates of higher educational medical institutions must be able to apply them in their professional activities, know their advantages and disadvantages. This is facilitated by the inclusion of topic on Medical Information Systems (MIS) in the curriculum of the discipline «Medical Informatics». The aim of the article is to consider the main approaches to the organization of students'’work with modern medical software in medical informatics classes on the example of experience in studying the topic «Medical Information Systems» at National Pirogov Memorial Medical University. Research methods: theoretical analysis of methodical approaches to the study of information systems in universities and generalization of experimental experience of teachers of the Department of Biological Physics, Medical Equipment and Informatics. Effective formation of practical skills of work with MIS at future doctors is promoted by observance of the following sequence of actions: comparison of the capabilities of Medods, MedElement, Doctor Eleks, Meduchet SQL, EMCiMED platforms; work in a virtual university clinic with the Doctor Eleks software package; diagnosis of diseases using training expert systems «RG-lungs», «Diarrhea», Wero. The method of organization of practical work of students with medical information systems described in the article is used in the educational process by teachers of VNMU for the fifth year. This allowed to form in our graduates an understanding of the peculiarities of the work of various departments of medical institutions.

Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis

Inflammatory bowel disease (IBD) is a chronic, recurrent inflammatory disease of the gastrointestinal (GI) tract. Ulcerative colitis (UC) is a type of IBD. Pregnane X Receptor (PXR) is a member of the nuclear receptor superfamily. In order to deepen understanding and exploration of the molecular mechanism of regulation roles of PXR on UC, biological informatics analysis was performed. First, 878 overlapping differentially expressed genes (DEGs) between UC and normal samples were obtained from the Gene Expression Omnibus (GEO) database (GSE59071 and GSE38713) by using the "limma" R language package. Then WGCNA analysis was performed by 878 DEGs to obtain co-expression modules that were positively and negatively correlated with clinical traits. GSEA analysis of PXR results obtained the signal pathways enriched in the PXR high and low expression group and the active genes of each signal pathway. Then the association of PXR with genes that are both active in high expression group and negatively related to diseases (gene set 1), or both active in low expression group and negatively related to diseases (gene set 2) was analyzed by String database. Finally, carboxylesterase 2 (CES2), ATP binding cassette subfamily G member 2 (ABCG2), phosphoenolpyruvate carboxykinase (PCK1), PPARG coactivator 1 alpha (PPARGC1A), cytochrome P450 family 2 subfamily B member 6 (CYP2B6) from gene set 1 and C-X-C motif chemokine ligand 8 (CXCL8) from gene set 2 were screened out. After the above analysis and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) verification, we speculated that PXR may exert a protective role on UC by promoting CES2, ABCG2, PCK1, PPARGC1A, CYP2B6 expression and inhibiting CXCL8 expression in their corresponding signal pathway in intestinal tissue.

A FIJI macro for quantifying pattern in extracellular matrix.

Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end, we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. This pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation and tutorial video. Although developed with the extracellular matrix in mind, TWOMBLI is versatile and can be applied to vascular and cytoskeletal networks. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.

TEACHING OF MEDICAL AND BIOLOGICAL PHYSICS AND MEDICAL INFORMATICS IN EUROPEAN UNIVERSITIES

This review article discusses some of the problems associated with teaching fundamental medical disciplines «Medical and Biological Physics» and «Medical Informatics» in 10 universities from 7 European countries. A comparison is made of the organization of teaching these natural disciplines (in particular, the volume of classroom hours) at the Bogomolets National Medical University and other European medical universities for the specialty «Medicine». It was found that in the absolute majority of 8 out of 9 European universities (medical faculties) more classroom hours are allocated for the study of obligatory physical disciplines (for some universities 2–3 times more) than at the Bogomolets National Medical University. The discipline «Medical Informatics and Foundations of Scientific Research» is approved in the working curriculum of the Bogomolets National Medical University for the 2021-2022 academic year not as obligatory, but as a variable discipline which students of the 1st year of study can choose with a prior probability that is equal to 0.5. The importance of teaching the disciplines «Medical and biological physics» and «Medical informatics» as an integral part of the medical industry and medical education is emphasized. It is these directions of science and technology as well as academic disciplines (together with biomedical engineering) that provided a reliable basis to create precision and high-tech medical equipment for diagnostics and treatment, ranging from X-ray and cardiography devices and ending at the moment with the Da Vinci surgical robotic system for minimally invasive interventions, as well as medical imaging system using combined positron emission tomography and magnetic resonance imaging.

Abstract PO-003: Bivalent histone modifications: Clinical targets against pancreatic cancer stem cell heterogeneity

Abstract Bivalent histone modifications, the pre-transcriptional regulators were known as the chief orchestra underlining the mechanism of development for pancreatic cancer stem cells (PANCSCs) recently. The histone bivalency methylations are related to the transcriptional activation as well as repression of the prominent histone methylations (H3K4me3 and H3K27me3) at the transcript start sequence (TSS). These epigenetic changes are recognized to initiate heterogenic cancer stem cells (CSCs) reprogramming. Recent studies showed that the heterogenic CSCs are more resistant to anti-tumor drug therapy. Our previous study showed the relationship between bivalent histone modifications with the expression of pancreatic CSCs(CD44, CD24, CD133, Ep-CAM, ALDH1A3). Our current study is focused on the importance of designing anti-cancer drugs or epigenetic small molecules against bivalent histone modifications (to inhibit the upregulation of H3K4me3 or down-regulation of H3K27me3) related the expression of heterogenic pancreatic CSCs (CD44, CD24, CD133, Ep-CAM, ALDH1A3). The Cancer Stem Cells Therapeutic Target Database Version 2.0 (CSCTTv2.0) reported the high CD133 as PAN CSCs and high CD133, CD44 showed resistance to anticancer drugs (such as docetaxel, 5-FU, irinotecan, oxaliplatin) in many cancers. The Gemcitabine, a nucleoside analog, and Metformin are only drugs used for pancreatic cancer treatment and showed resistance against heterogenic PANCSCs. The biological informatics analyses (Cytoscape database, HPIDb, Spike, BioGrid, Reactome, MBInfo) were deployed in our study to find the effect of bivalent histone modifications on the TSS of the target genes in heterogenic PANCSCs and we found the effect at TSS of target genes CD44, and EZH2/ENX1. We also found a novel small molecule KY-02111 has an effect to reduce the expression of heterogenic PANCSCs at tumorigenic in vitro 3D spheroids model of PANC-1ORGR (Gemcitabine resistant) cells. Therefore, our preliminary study may give an important clue to find further the role of KY-02111 against the heterogenic pancreatic CSCs by inhibiting the upregulation of H3K4me3 or down-regulation of H3K27me3 as a clinical target for pancreatic cancer therapy. Citation Format: Madhumita Das, Mayur Doke, Edwin Gonzalez, Daima Diaz, Bryan Pineda, Jonathan Celli, Marco Ruiz, Jayanta K. Das. Bivalent histone modifications: Clinical targets against pancreatic cancer stem cell heterogeneity [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-003.

Functional benefit and molecular mechanism of vitamin C against perfluorooctanesulfonate-associated leukemia

Perfluorooctanesulfonate (PFOS) is a persistent pollutant that can induce toxic effects, including leukemia, on blood cells. Vitamin C (VC), a functional nutrient, has been found to possess potent cytoprotective effects. However, there are currently no reports on its ability to treat PFOS-associated leukemia. This study used a molecular networking analysis to reveal the functional action and pharmacological mechanism of VC against PFOS-associated leukemia. The biological informatics findings revealed a total of 17 intersection targets against PFOS-associated leukemia. In addition, seven core-functional targets, including tumor protein p53 (TP53), mitogen-activated protein kinase 1 (MAPK1), estrogen receptor 1 (ESR1), sirtuin 1 (SIRT1), nitric oxide synthase 3 (NOS3), myeloid cell leukemia-1 (MCL1), and telomerase reverse transcriptase (TERT), were screened and identified. Notably, the molecular docking findings indicated that TP53, MAPK1, and ESR1 were potent pharmacological targets of VC against PFOS-associated leukemia. Moreover, the pharmacological functions including biological processes, cell components, and molecular pathways of VC against PFOS-associated leukemia were determined. According to the computational findings, we conclude that VC protects against PFOS-associated leukemia action by suppressing leukemia-associated cell proliferation and tumor growth. The validated genes of TP53, MAPK1, ESR1 may become potential biomarkers for monitoring and treating PFOS-associated leukemia.

Investigation of hub genes involved in diabetic nephropathy using biological informatics methods.

BackgroundThe aim of this study was to find genes with significantly aberrant expression in diabetic nephropathy (DN) and determine their underlying mechanisms.MethodsGSE30528 and GSE1009 were obtained by querying the Gene Expression Omnibus (GEO) database. The difference in target gene expression between normal renal tissues and kidney tissues in patients with DN was screened by using the GEO2R tool. Using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database, differentially expressed genes (DEGs) were analysed by Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Then, the protein-protein interactions (PPIs) of DEGs were analyzed by Cytoscape with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the hub genes in this PPI network were recognized by centrality analysis.ResultsThere were 110 genes with significant expression differences between normal and DN tissues. The differences in gene expression involved many functions and expression pathways, such as the formation of the extracellular matrix and the construction of the extracellular domain. The correlation analysis and subgroup analysis of 14 hub genes and the clinical characteristics of DN showed that CTGF, ALB, PDPN, FLT1, IGF1, WT1, GJA1, IGFBP2, FGF9, BMP2, FGF1, BMP7, VEGFA, and TGFBR3 may be involved in the progression of DN.ConclusionsWe confirmed the differentially expressed hub genes and other genes which may be the novel biomarker and target candidates in DN.

Abstract 2431: Identification of the underlining relationship of bivalent histone modifications with pancreatic cancer stem cells by bioinformatic analysis

Abstract Epigenetic alterations are known to involve in cancer stem cells (CSCs) reprogramming. CSCs have been reported to be more resistant to anti-tumor treatments than the non-stem cancer cells, suggesting that surviving CSCs could be responsible for tumor relapse after therapy. The most relevant epigenetic alteration, histone modification has been shown in recent scientific studies to contribute to the regulation of cancer stem cell features in tumor metastasis, progression and response to chemotherapy. The pre-transcriptional regulator, bivalent histone modifications were reported to be involved in the development of CSCs recently. The synchronous presence of functionally opposite histone marks at transcript start sequence (TSS) is known as “Bivalency”. The H3K4me3 as well as H3K27me3, the prominent histone methylations of bivalency, are concerned in transcriptional activation and transcriptional repression respectively. The balance between H3K4me3 and H3K27me3 results in diverse chromatin architectures, ensuing in different transcription states of downstream genes: “poised”, “activated” or “repressed”. The current study is aimed to explore the relationship of bivalent histone modifications, (upregulation or expression of H3K4me3, and down-regulation or repression H3K27me3) the epigenetic regulations with the expression of pancreatic cancer stem cells (CD44, CD24, CD133, Ep-CAM, ALDH1A3) in pancreatic cancer. Protein expression profiles were analyzed using biological informatics methods (string database; Cytoscape database, BioGrid, Reactome, MatrixDB, NCBI Gene and NCBI epigenomics metadata analyses) to identify the relationship of bivalent histone modifications with expressed genes of pancreatic cancer stem cells (CD44, CD24, CD133, Ep-CAM, ALDH1A3). NCBI Biosystems database showed that 197 genes are involved in the Integrated Pancreatic Cancer Pathway model using KEGG database, but the relationship of bivalent histone modifications with the expression of pancreatic cancer stem cells (CD44, CD24, CD133, Ep-CAM, ALDH1A3) in pancreatic cancer has not been showed earlier. Our analysis showed the protein-protein interaction (PPI) network was constructed for such a relationship of closely related 45 significant genes. Among these 45 genes, a total of 7 pancreatic cancer stem cell markers (CSCs) was closely associated with upregulation or expression of H3K4me3, and down-regulation or repression H3K27me3 through EZH2 and PHF19 with a high degree of interaction in the PPI network. We are also able to analyze the role of H3K27ac in regulating target genes in 18 samples of pancreatic cancer cell lines using the ChIP-sequences data set of study SRA 109996 from NCBI NLM Sequence Read Archive from Run Browser Accession number ERR2708462. Therefore, this study identified the significant relationship of bivalent histone modifications associated with pancreatic CSCs which may be the novel biomarkers and target candidates in designing drugs against pancreatic cancer. This work was part of the honors option project (HOP) of Natalia Ortega mentored by Dr. Jayanta K. Das, at MDC north campus. Citation Format: Natalia Ortega, Madhumita Das, Marco A. Ruiz, Jairo Ramos, Jayanta Kumar Das. Identification of the underlining relationship of bivalent histone modifications with pancreatic cancer stem cells by bioinformatic analysis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2431.

Comparison of aflatoxin production of Aspergillus flavus at different temperatures and media: Proteome analysis based on TMT

Aflatoxin production of Aspergillus flavus is affected by abiotic factors such as temperature, water activity, oxidative stress, etc. These factors likely affect different metabolic pathways and result in altered aflatoxin production. Aflatoxin was determined in liquid media at 28 °C, solid media at 28 °C and solid media at 37 °C. The proteomic method was used to elucidate the mechanism of aflatoxin production in A. flavus in liquid media at 28 °C, solid media at 28 °C and solid media at 37 °C. Potential factors affecting aflatoxin production were found by GO and KEGG analysis. A. flavus produces more aflatoxin at 28 °C compared to 37 °C. Our study also found that A. flavus cultured on solid media produced more aflatoxin than in liquid media. In this study, we identified 5029 proteins from A. flavus NRRL3357, in which 1547 differential proteins were identified between liquid media and solid-state media, while 546 differential proteins were identified between 28 °C and 37 °C. Biological informatics analysis showed that these differential proteins were widely involved in a variety of biological processes, molecular functions, and cellular components, and were associated with multiple metabolic pathways. Compared to the liquid media, extracellular hydrolase for nutrient uptake and proteins related to sclerotia development were differentially expressed on solid media (p < 0.05). Enzymes involved in oxidative stress showed significantly down-regulated in liquid media and up-regulated at 28 °C (p < 0.05). Furthermore, our research also revealed aflatoxin synthesis is a complex process that is affected by a variety of factors such as nutrient uptake, oxidative stress, sclerotia development, G protein signaling pathways and valine, leucine and isoleucine degradation, and a speculative model summarizing the regulation of aflatoxin biosynthesis in A. flavus is presented.

Identification of primary genes in glomeruli compartment of immunoglobulin A nephropathy by bioinformatic analysis.

The current study is aimed to explore the specific genes which are responsible for the manifestation of Immunoglobulin A nephropathy (IgAN). Gene expression profiles GSE37460, GSE93798 and GSE104948 were analyzed using biological informatics methods to identify differentially expressed genes (DEGs) in IgAN glomeruli samples which were then compared to normal control samples. Subsequently, the DEGs were overlapped to explore genes with significant expression in at least two profiles. Finally, the enrichment analysis was conducted and the protein-protein interaction (PPI) network was constructed for the overlapping DEGs. A total of 28 genes were up-regulated and 10 genes were down-regulated. The up-regulated genes including CD44 and FN1 were chiefly involved in extracellular matrix receptors interaction pathway. In addition, CX3CR1 and CCL4 were associated with chemokine signaling pathway. ITGB2, PTPRC, FN1, and FCER1G were hub genes with a high degree of interaction in the PPI network. Therefore, this study identified many significant genes associated with extracellular matrix expansion and inflammatory mechanism which may be the novel biomarker and target candidates in IgAN.

Linking Biodiversity Data Using Evolutionary History

All life on earth is linked by a shared evolutionary history. Even before Darwin developed the theory of evolution, Linnaeus categorized types of organisms based on their shared traits. We now know these traits derived from these species’ shared ancestry. This evolutionary history provides a natural framework to harness the enormous quantities of biological data being generated today. The Open Tree of Life project is a collaboration developing tools to curate and share evolutionary estimates (phylogenies) covering the entire tree of life (Hinchliff et al. 2015, McTavish et al. 2017). The tree is viewable at https://tree.opentreeoflife.org, and the data is all freely available online. The taxon identifiers used in the Open Tree unified taxonomy (Rees and Cranston 2017) are mapped to identifiers across biological informatics databases, including the Global Biodiversity Information Facility (GBIF), NCBI, and others. Linking these identifiers allows researchers to easily unify data from across these different resources (Fig. 1). Leveraging a unified evolutionary framework across the diversity of life provides new avenues for integrative wide scale research. Downstream tools, such as R packages developed by the R OpenSci foundation (rotl, rgbif) (Michonneau et al. 2016, Chamberlain 2017) and others tools (Revell 2012), make accessing and combining this information straightforward for students as well as researchers (e.g. https://mctavishlab.github.io/BIO144/labs/rotl-rgbif.html). For example, a recent publication by Santorelli et al. 2018 linked evolutionary information from Open Tree with species locality data gathered from a local field study as well as GBIF species location records to test a river-barrier hypothesis in the Amazon. By combining these data, the authors were able test a widely held biogeographic hypothesis across 1952 species in 14 taxonomic groups, and found that a river that had been postulated to drive endemism, was in fact not a barrier to gene flow. However, data provenance and taxonomic name reconciliation remain key hurdles to applying data from these large digital biodiversity and evolution community resources to answering biological questions. In the Amazonian river analysis, while they leveraged use of GBIF records as a secondary check on their species records, they relied on their an intensive local field study for their major conclusions, and preferred taxon specific phylogenetic resources over Open Tree where they were available (Santorelli et al. 2018). When Li et al. 2018 assessed large scale phylogenetic approaches, including Open Tree, for measuring community diversity, they found that synthesis phylogenies were less resolved than purpose-built phylogenies, but also found that these synthetic phylogenies were sufficient for community level phylogenetic diversity analyses. Nonetheless, data quality concerns have limited adoption of analyses data from centralized resources (McTavish et al. 2017). Taxonomic name recognition and reconciliation across databases also remains a hurdle for large scale analyses, despite several ongoing efforts to improve taxonomic interoperability and unify taxonomies, such at Catalogue of Life + (Bánki et al. 2018). In order to support innovative science, large scale digital data resources need to facilitate data linkage between resources, and address researchers' data quality and provenance concerns. I will present the model that the Open Tree of Life is using to provide evolutionary data at the scale of the entire tree of life, while maintaining traceable provenance to the publications and taxonomies these evolutionary relationships are inferred from. I will discuss the hurdles to adoption of these large scale resources by researchers, as well as the opportunities for new research avenues provided by the connections between evolutionary inferences and biodiversity digital databases.