IU Indianapolis ScholarWorks :: Browsing by Author "Neelamraju, Yaseswini"

Browsing by Author "Neelamraju, Yaseswini"

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Database of RNA binding protein expression and disease dynamics (READ DB)
(Oxford University Press, 2015-07-25) Hashemikhabi, Seyedsasan; Neelamraju, Yaseswini; Janga, Sarath Chandra; BioHealth Informatics, School of Informatics and Computing
RNA Binding Protein (RBP) Expression and Disease Dynamics database (READ DB) is a non-redundant, curated database of human RBPs. RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop portal for understanding the expression, evolutionary trajectories and disease dynamics of RBPs in the context of post-transcriptional regulatory networks.
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks
(Nature Publishing Group, 2016-05-10) Nishtala, Sneha; Neelamraju, Yaseswini; Janga, Sarath Chandra; Department of BioHealth Informatics, School of Informatics and Computing
RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks
Evolutionary dynamics of RNA-binding proteins expression levels in mammals
Badve, Abhijit; Sarsani, Vishal; Neelamraju, Yaseswini; Janga, Sarath Chandra
RNA binding proteins (RBPs) play important roles in controlling the posttranscriptional fate of RNA molecules, yet their evolutionary dynamics remains largely unknown. As expression profiles of genes encoding for RBPs can yield insights about their evolutionary trajectories on the posttranscriptional regulatory networks across species, we performed a comparative analyses of RBP expression profiles across 8 tissues (brain, cerebellum, heart, lung, liver, lung, skeletal muscle, testis) in 11 mammals (human, chimpanzee, gorilla, orangutan, macaque, rat, mouse, platypus, opossum, cow) and chicken & frog (evolutionary outgroups). Noticeably, orthologous gene expression profiles suggest a significantly higher expression level for RBPs than their non-RBP gene counterparts - which include other protein-coding and non-coding genes, across all the mammalian tissues studied here. This trend is significant irrespective of the tissue and species being compared, though RBP gene expression distribution patterns were found to be generally diverse in nature. Our analysis also shows that RBPs are expressed at a significantly lower level in human and mouse tissues compared to their expression levels in equivalent tissues in other mammals chimpanzee, orangutan, rat, etc. which are all likely exposed to diverse natural habitats and ecological settings compared to more stable ecological environment humans and mice might have been exposed, thus reducing the need for complex and extensive post-transcriptional control. Further analysis of the similarity of orthologous RBP expression profiles between all pairs of tissue-mammal combinations clearly showed the grouping of RBP expression profiles across tissues in a given mammal, in contrast to the clustering of expression profiles for non-RBPs, which frequently grouped equivalent tissues across diverse mammalian species together, suggesting a significant evolution of RBPs expression after speciation events. Calculation of species specificity indices (SSis) for RBPs across various tissues, to identify those that exhibited restricted expression to few mammals, revealed that about 30% of the RBPs are species-specific in at least one tissue studied here, with lung, liver, kidney & testis exhibiting a significantly higher proportion of species specifically expressed RBPs. We conducted a differential expression analysis of RBPs in human, mouse and chicken tissues to study the evolution of expression levels in recently evolved species i.e. humans and mice than evolutionarily distant species i.e. chicken. We identified more than 50% of the orthologous RBPs to be differentially expressed in at-least one tissue compared between human and mouse but not so between human and the outgroup i.e. chicken in which RBP expression levels are relatively conserved. Among the studied tissues brain, liver and kidney showed a higher fraction of differentially expressed RBPs, which may suggest hyper regulatory activities by RBPs in these tissues with species evolution. Overall, this study forms a foundation for understanding the evolution of expression levels of RBPs in mammals, facilitating a snapshot of the wiring patterns of post-transcriptional regulatory networks in mammalian genomes.
Expression levels of SF3B3 correlate with prognosis and endocrine resistance in estrogen receptor-positive breast cancer
(Nature Publishing Group, 2015-05) Gökmen-Polar, Yesim; Neelamraju, Yaseswini; Goswami, Chirayu P.; Gu, Xiaoping; Nallamothu, Gouthami; Janga, Sarath Chandra; Badve, Sunil; Department of Pathology and Laboratory Medicine, IU School of Medicine
De novo or acquired resistance to endocrine therapy limits its utility in a significant number of estrogen receptor-positive (ER-positive) breast cancers. It is crucial to identify novel targets for therapeutic intervention and improve the success of endocrine therapies. Splicing factor 3b, subunit 1 (SF3B1) mutations are described in luminal breast cancer albeit in low frequency. In this study, we evaluated the role of SF3B1 and SF3B3, critical parts of the SF3b splicing complex, in ER-positive endocrine resistance. To ascertain the role of SF3B1/SF3B3 in endocrine resistance, their expression levels were evaluated in ER-positive/endocrine-resistant cell lines (MCF-7/LCC2 and MCF-7/LCC9) using a real-time quantitative reverse transcription PCR (qRT-PCR). To further determine their clinical relevance, expression analysis was performed in a cohort of 60 paraffin-embedded ER-positive, node-negative breast carcinomas with low, intermediate, and high Oncotype DX recurrence scores. Expression levels of SF3B1 and SF3B3 and their prognostic value were validated in large cohorts using publicly available gene expression data sets including The Cancer Genome Atlas. SF3B1 and SF3B3 levels were significantly increased in ERα-positive cells with acquired tamoxifen (MCF-7/LCC2; both P<0.0002) and fulvestrant/tamoxifen resistance (MCF-7/LCC9; P=0.008 for SF3B1 and P=0.0006 for SF3B3). Expression levels of both MCF-7/LCC2 and MCF-7/LCC9 were not affected by additional treatments with E2 and/or tamoxifen. Furthermore, qRT-PCR analysis confirmed that SF3B3 expression is significantly upregulated in Oncotype DX high-risk groups when compared with low risk (P=0.019). Similarly, in publicly available breast cancer gene expression data sets, overexpression of SF3B3, but not SF3B1, was significantly correlated with overall survival. Furthermore, the correlation was significant in ER-positive, but not in ER-negative tumors.
The Human RBPome: From Genes and Proteins to Human Disease
(2015) Neelamraju, Yaseswini; Hashemikhabir, Seyedsasan; Janga, Sarath Chandra
RNA Binding Proteins (RBPs) play a central role in mediating post transcriptional regulation of genes. However, less is understood about them and their regulatory mechanisms. In this study, we construct a repertoire of 1344 genes encoding RBPs identified from several experimental studies and present a comprehensive analysis to understand their characteristics at a global scale. The domain architecture of RBPs enabled us to classify them into three groups - Classical (29%), Non-classical (19%) and Unclassified (52%). A higher percentage of proteins with unclassified domains reveals the presence of various uncharacterized motifs that can potentially bind RNA. In addition, enrichment of various unconventional superfamilies' suggest that RBPs could form an integral part of the cellular architecture. RBPs were found to be highly disordered compared to non-RBPs (p<2.2e-16, Fisher's exact test), indicating a dynamic regulatory role of RBPs in cellular functioning. Evolutionary analysis in 62 different species showed that RBPs are highly conserved compared to non-RBPs (p<2.2e-16, Wilcox-test), reflecting a conservation of various biological processes like mRNA splicing, ribosome biogenesis. Expression patterns of RBPs from human proteome map revealed that majority (~60%) of the RBPs are tissue-specific. Additionally, non-classical proteins were found to be highly expressed than the classical proteins (p<0.05, Wilcox test) in ~50% of the tissues. RBPs were also seen to be highly associated with several neurological disorders, cancer and inflammatory diseases. Further, anatomical context like B cells, T-cells, Fetal Liver and Fetal Brain were found to be enriched, implying a prominent role of RBPs in mediating immune responses and different developmental stages. These analyses are made accessible to researchers in the form of a database called RNA Binding protein expression and disease dynamics database (READ DB).
The human RBPome: From genes and proteins to human disease
(Elsevier, 2015-09) Neelamraju, Yaseswini; Hashemikhabir, Seyedsasan; Janga, Sarath Chandra; Department of BioHealth Informatics, School of Informatics and Computing
RNA binding proteins (RBPs) play a central role in mediating post transcriptional regulation of genes. However less is understood about them and their regulatory mechanisms. In this study, we construct a catalogue of 1344 experimentally confirmed RBPs. The domain architecture of RBPs enabled us to classify them into three groups — Classical (29%), Non-classical (19%) and unclassified (52%). A higher percentage of proteins with unclassified domains reveals the presence of various uncharacterised motifs that can potentially bind RNA. RBPs were found to be highly disordered compared to Non-RBPs (p < 2.2e-16, Fisher's exact test), suggestive of a dynamic regulatory role of RBPs in cellular signalling and homeostasis. Evolutionary analysis in 62 different species showed that RBPs are highly conserved compared to Non-RBPs (p < 2.2e-16, Wilcox-test), reflecting the conservation of various biological processes like mRNA splicing and ribosome biogenesis. The expression patterns of RBPs from human proteome map revealed that ~ 40% of them are ubiquitously expressed and ~ 60% are tissue-specific. RBPs were also seen to be highly associated with several neurological disorders, cancer and inflammatory diseases. Anatomical contexts like B cells, T-cells, foetal liver and foetal brain were found to be strongly enriched for RBPs, implying a prominent role of RBPs in immune responses and different developmental stages. The catalogue and meta-analysis presented here should form a foundation for furthering our understanding of RBPs and the cellular networks they control, in years to come. This article is part of a Special Issue entitled: Proteomics in India.
Integrative analysis identifies an older female-linked AML patient group with better risk in ECOG-ACRIN Cancer Research Group's clinical trial E3999
(Springer Nature, 2022-09-23) Rapaport, Franck; Seier, Kenneth; Neelamraju, Yaseswini; Hassane, Duane; Baslan, Timour; Gildea, Daniel T.; Haddox, Samuel; Lee, Tak; Murdock, H. Moses; Sheridan, Caroline; Thurmond, Alexis; Wang, Ling; Carroll, Martin; Cripe, Larry D.; Fernandez, Hugo; Mason, Christopher E.; Paietta, Elisabeth; Roboz, Gail J.; Sun, Zhuoxin; Tallman, Martin S.; Zhang, Yanming; Gönen, Mithat; Levine, Ross; Melnick, Ari M.; Kleppe, Maria; Garrett-Bakelman, Francine E.; Medicine, School of Medicine
Mutational Landscape of RNA Binding Proteins in Human Cancers
(2017) Neelamraju, Yaseswini; Gomez-Perez, Abel; Lopez-Bigas, Nuria; Janga, Sarath Chandra
RNA Binding proteins (RBPs) are a class of regulatory molecules pivotal in orchestrating several post-transcriptional mechanisms. Recent studies have shown a significant number of them to be up-regulated in various cancer genomes and few of them were also shown to be contributing directly to cancer progression (1). Although variations in the gene expression levels of these proteins across cancers have been known, the cause for such alteration remains to be understood. A plausible hypothesis for this aberrant expression of RNA Binding proteins could be attributed to the occurrence of atypical mutations in the genes encoding for these proteins. In the present study, we aim to delineate the mutational landscape of ~1300 RNA Binding proteins (2) in ~6000 cancer genomes from The Cancer Genome Atlas (TCGA). Our analysis revealed that RBPs have an average of ~3 mutations per Mb across 26 tumor types. We identified ~600 RBPs to be significantly mutated in at least one tumor type (Corrected p<0.01, Fisher's exact test) suggesting that RBPs are as likely to be mutated as NonRBPs (p=0.9, Fisher's exact test). Among these, genes encoding for KMT2C, AHNAK and PLEC were found to be significantly mutated in at least 9 cancers suggesting common players of regulation across different tumor types. Furthermore, a comparison of different mutation types among significantly and non-significantly mutated RBPs revealed that the former genes are highly enriched for mutation types like inframe deletion (p < 8E-06, Wilcox test) and missense mutation (p < 3E-05, Wilcox test). Further, we identified RBPs (driver genes) whose function could be impaired due to the nonsynonymous SNPs, using OncodriveFM framework. We identify ~200 RBPs which can be defined as drivers in at least one tumor type (Corrected p<0.01). Of these, AHNAK was found to be mutated in at least 11 tumor types suggesting a common regulatory pathway affected in majority of the tumor types. Further analysis of the RNA levels of the driver genes between the patient groups with and without these deleterious mutations revealed ~30 RBPs (15% of the drivers) to be significantly altered in their expression levels between these groups (p < 0.05, Wilcox test). Protein-protein interaction network analysis of the driver genes identified in at least two tumor types revealed the presence of a cluster of mutated proteins involved in the spliceosomal machinery suggesting a plausible mechanism for tumorigenesis.
Mutational landscape of RNA-binding proteins in human cancers
(Taylor & Francis, 2018-01-02) Neelamraju, Yaseswini; Gonzalez-Perez, Abel; Bhat-Nakshatri, Poornima; Nakshatri, Harikrishna; Janga, Sarath Chandra; BioHealth Informatics, School of Informatics and Computing
RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is limited. Here, we delineate the mutational landscape of ∼1300 RBPs in ∼6000 cancer genomes. Our analysis revealed that RBPs have an average of ∼3 mutations per Mb across 26 cancer types. We identified 281 RBPs to be enriched for mutations (GEMs) in at least one cancer type. GEM RBPs were found to undergo frequent frameshift and inframe deletions as well as missense, nonsense and silent mutations when compared to those that are not enriched for mutations. Functional analysis of these RBPs revealed the enrichment of pathways associated with apoptosis, splicing and translation. Using the OncodriveFM framework, we also identified more than 200 candidate driver RBPs that were found to accumulate functionally impactful mutations in at least one cancer. Expression levels of 15% of these driver RBPs exhibited significant difference, when transcriptome groups with and without deleterious mutations were compared. Functional interaction network of the driver RBPs revealed the enrichment of spliceosomal machinery, suggesting a plausible mechanism for tumorogenesis while network analysis of the protein interactions between RBPs unambiguously revealed the higher degree, betweenness and closeness centrality for driver RBPs compared to non-drivers. Analysis to reveal cancer-specific Ribonucleoprotein (RNP) mutational hotspots showed extensive rewiring even among common drivers between cancer types. Knockdown experiments on pan-cancer drivers such as SF3B1 and PRPF8 in breast cancer cell lines, revealed cancer subtype specific functions like selective stem cell features, indicating a plausible means for RBPs to mediate cancer-specific phenotypes. Hence, this study would form a foundation to uncover the contribution of the mutational spectrum of RBPs in dysregulating the post-transcriptional regulatory networks in different cancer types.
Prognostic Impact of HOTAIR Expression is Restricted to ER-Negative Breast Cancers
(Nature, 2015-03) Gökmen-Polar, Yesim; Vladislav, I. Tudor; Neelamraju, Yaseswini; Janga, Sarath Chandra; Badve, Sunil
Expression of HOX transcript antisense intergenic RNA (HOTAIR), a large intergenic noncoding RNA (lincRNA), has been described as a metastases-associated lincRNA in various cancers including breast, liver and colon cancer cancers. We sought to determine if expression of HOTAIR could be used as a surrogate for assessing nodal metastases and evaluated RNA in situ hybridization (RNA-ISH) assay in a tissue microarray constructed from 133 breast cancer patients. The prognostic value of HOTAIR was further validated in large cohorts using The Cancer Genome Atlas (TCGA) breast cancer subjects. RNA-ISH analysis was successful in 94 cases (17% cases scored 0, 32.9% scored 1, 30.8% scored 2, and 19.1% scored 3). The expression of HOTAIR did not correlate with nodal metastasis regardless of the scoring intensity or with other study parameters (age, tumor size and grade, expression status). Further analysis of TCGA dataset showed that HOTAIR expression was lower in ductal carcinomas but higher in ER-negative tumors. Overexpression of HOTAIR was not associated with nodal metastases or prognosis in ER-positive patients. Its function as a poor prognostic indicator in ER-negative patients was restricted to node-positive patients. HOTAIR appears to be a marker for lymphatic metastases rather than hematogenous metastases in ER-negative patients.

Browsing by Author "Neelamraju, Yaseswini"

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