Sarath Janga
Permanent URI for this collection
Rapid Detection of Viral Based Infectious Diseases
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan (Hubei, China) in December 2019 has been declared a pandemic by the World Health Organization (WHO) due to its easy human to human transmission, making it a global public health concern. Coronaviruses are enveloped single-stranded ribonucleic acid (RNA) viruses with characteristic “crown” like appearance under two-dimensional transmission electron microscopy. Infections caused by these viruses result in severe pneumonia, fever and breathing difficulty. Currently there is a lack of effective vaccines and antiviral medication that has led to a global outbreak of SARS-CoV-2. Due to rapidly evolving nature of coronaviruses, their identification has become increasingly challenging. Therefore, it is important to develop diagnostic methods that can detect the virus rapidly, to prevent its transmission. Currently, most clinical diagnostic tests for viruses depend on detecting a viral antigen or rely on PCR amplification of viral nucleic acid derived from biological samples. These two approaches offer trade-offs in benefits: antigen tests (including current Point-Of-Care Tests [POCT]) are typically rapid but have low sensitivity, while PCR is more time-consuming but also more sensitive. Irrespective of the test used, most clinical diagnostic facilities report a non-quantitative (binary) diagnostic result, and the data generated have limited capacity to inform insights into epidemiological linkage, vaccine efficacy, or antiviral susceptibility. Hence, there is an urgent need to generate new diagnostic tests that combine POCT, speed, sensitivity, detection of coinfection by other viral strains, and generation of quantitative or semi-quantitative data that can be used to identify drug resistance. Such data may also be used to reconstruct phylogeny to inform surveillance, public health strategy, and vaccine design.
Dr. Sarath Janga's lab has been working to employ “third-generation” portable, real-time bench top sequencers which use nanopores, to develop novel experimental protocols and computational algorithms to not only detect the presence of pathogens but also map their variability across clinical samples, to facilitate public health surveillance. More recently, his lab has been combining an efficient, novel and high-throughput viral RNA isolation methods accompanied with nanopore sequencing to develop automated computational software for real time detection of COVID19.
Dr. Janga's research to detect COVID19 virus strains for developing a rapid, real-time and scalable test that can be used in the clinics to help the healthcare workers, who are at the front lines of care and are getting exposed to infections, is another example of how IUPUI's faculty are TRANSLATING their RESEARCH INTO PRACTICE.
Browse
Recent Submissions
Item Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans(MDPI, 2020-09-25) Srivastava, Rajneesh; Daulatabad, Swapna Vidhur; Srivastava, Mansi; Janga, Sarath Chandra; BioHealth Informatics, School of Informatics and ComputingThe outbreak of a novel coronavirus SARS-CoV-2 responsible for the COVID-19 pandemic has caused a worldwide public health emergency. Due to the constantly evolving nature of the coronaviruses, SARS-CoV-2-mediated alterations on post-transcriptional gene regulations across human tissues remain elusive. In this study, we analyzed publicly available genomic datasets to systematically dissect the crosstalk and dysregulation of the human post-transcriptional regulatory networks governed by RNA-binding proteins (RBPs) and micro-RNAs (miRs) due to SARS-CoV-2 infection. We uncovered that 13 out of 29 SARS-CoV-2-encoded proteins directly interacted with 51 human RBPs, of which the majority of them were abundantly expressed in gonadal tissues and immune cells. We further performed a functional analysis of differentially expressed genes in mock-treated versus SARS-CoV-2-infected lung cells that revealed enrichment for the immune response, cytokine-mediated signaling, and metabolism-associated genes. This study also characterized the alternative splicing events in SARS-CoV-2-infected cells compared to the control, demonstrating that skipped exons and mutually exclusive exons were the most abundant events that potentially contributed to differential outcomes in response to the viral infection. A motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed the enrichment for RBPs such as SRSFs, PCBPs, ELAVs, and HNRNPs, suggesting the sponging of RBPs by the SARS-CoV-2 genome. A similar analysis to study the interactions of miRs with SARS-CoV-2 revealed functionally important miRs that were highly expressed in immune cells, suggesting that these interactions may contribute to the progression of the viral infection and modulate the host immune response across other human tissues. Given the need to understand the interactions of SARS-CoV-2 with key post-transcriptional regulators in the human genome, this study provided a systematic computational analysis to dissect the role of dysregulated post-transcriptional regulatory networks controlled by RBPs and miRs across tissue types during a SARS-CoV-2 infection.Item New Twists in Detecting mRNA Modification Dynamics(Elsevier, 2020-07-01) Anreiter, Ina; Mir, Quoseena; Simpson, Jared T.; Janga, Sarath C.; Soller, Matthias; Medical and Molecular Genetics, School of MedicineModified nucleotides in mRNA are an essential addition to the standard genetic code of four nucleotides in animals, plants, and their viruses. The emerging field of epitranscriptomics examines nucleotide modifications in mRNA and their impact on gene expression. The low abundance of nucleotide modifications and technical limitations, however, have hampered systematic analysis of their occurrence and functions. Selective chemical and immunological identification of modified nucleotides has revealed global candidate topology maps for many modifications in mRNA, but further technical advances to increase confidence will be necessary. Single-molecule sequencing introduced by Oxford Nanopore now promises to overcome such limitations, and we summarize current progress with a particular focus on the bioinformatic challenges of this novel sequencing technology.Item Targeting Bim via a lncRNA Morrbid Regulates the Survival of Preleukemic and Leukemic Cells(Elsevier, 2020-06-23) Cai, Zhigang; Aguilera, Fabiola; Ramdas, Baskar; Daulatabad, Swapna Vidhur; Srivastava, Rajneesh; Kotzin, Jonathan J.; Carroll, Martin; Wertheim, Gerald; Williams, Adam; Janga, Sarath Chandra; Zhang, Chi; Henao-Mejia, Jorge; Kapur, Reuben; Pediatrics, School of MedicineInhibition of anti-apoptotic proteins BCL-2 and MCL-1 to release pro-apoptotic protein BIM and reactivate cell death could potentially be an efficient strategy for the treatment of leukemia. Here, we show that a lncRNA, MORRBID, a selective transcriptional repressor of BIM, is overexpressed in human acute myeloid leukemia (AML), which is associated with poor overall survival. In both human and animal models, MORRBID hyperactivation correlates with two recurrent AML drivers, TET2 and FLT3ITD. Mice with individual mutations of Tet2 or Flt3ITD develop features of chronic myelomonocytic leukemia (CMML) and myeloproliferative neoplasm (MPN), respectively, and combined presence results in AML. We observe increased levels of Morrbid in murine models of CMML, MPN, and AML. Functionally, loss of Morrbid in these models induces increased expression of Bim and cell death in immature and mature myeloid cells, which results in reduced infiltration of leukemic cells in tissues and prolongs the survival of AML mice.Item Integrating Data Science into T32 Training Programs at IUPUI(2019-06-30) Dixon, Brian E.; Stumpff, Julia C.; Kasthurirathne, Suranga N.; Lourens, Spencer; Janga, Sarath; Liu, Yunlong; Huang, KunData science is critically important to the biomedical research enterprise. Many research efforts currently and in the future will employ advanced computational techniques to analyze extremely large datasets in order to discover insights relevant to human health. Therefore the next generation of biomedical scientists requires knowledge of and proficiency in data science. With support from the U.S. National Library of Medicine, a team of faculty from Indiana University-Purdue University Indianapolis (IUPUI) facilitated curricula enhancement for National Institutes of Health (NIH) T32 research training programs with respect to data science. In collaboration with the existing NIH T32 Program Directors at IUPUI and the IU School of Medicine, the interdisciplinary team of faculty drawn from multiple schools and departments examined the existing landscape of data science offerings on campus in parallel with an assessment of the competencies that future biomedical and clinician scientists will require to be comfortable using data science methods to advance their research. The IUPUI campus possesses a rich tapestry of data science education programs across multiple schools and departments. Furthermore, the campus is home to more than a dozen world-class T32 programs funded by the NIH to train biomedical and clinician scientists. However, existing training programs do not currently emphasize data science or provide specific curriculum designed to ensure T32 graduates possess basic competencies in data science. To position the campus for the future, robust T32 programs need to connect with the rapidly growing data science programs. This report summarizes the rationale for the importance of connection and the competencies that future biomedical and clinical scientists will require to be successful. The report further describes the curriculum mapping efforts to link competencies with available degree programs, courses and workshops on campus. The report further recommends next steps for campus leadership, including but not limited to T32 Program Directors, the Office of the Vice Chancellor for Research, the Executive Associate Dean for Research Affairs at the IU School of Medicine, and the President and CEO of the Regenstrief Institute. Together we can strengthen the IUPUI campus and help ensure its T32 graduates are successful in their research careers.Item SARS-CoV-2 contributes to altering the post-transcriptional regulatory networks across human tissues by sponging RNA binding proteins and micro-RNAs(2020-07-06) Srivastava, Rajneesh; Daulatabad, Swapna Vidhur; Srivastava, Mansi; Janga, Sarath Chandra; Department of BioHealth Informatics, IUPUI School of Informatics and ComputingThe outbreak of a novel coronavirus SARS-CoV2 responsible for COVID-19 pandemic has caused worldwide public health emergency. Due to the constantly evolving nature of the coronaviruses, SARS-CoV-2 mediated alteration on post-transcriptional gene regulation across human tissues remains elusive. In this study, we systematically dissected the crosstalk and dysregulation of human post-transcriptional regulatory networks governed by RNA binding proteins (RBPs) and micro-RNAs (miRs), due to SARS-CoV-2 infection. We uncovered that 13 out of 29 SARS-CoV- 2 encoded proteins directly interact with 51 human RBPs of which majority of them were abundantly expressed in gonadal tissues and immune cells. We further performed functional analysis of differentially expressed genes in mock treated versus SARS-CoV-2 infected lung cells that revealed an enrichment for immune response, cytokine mediated signaling, and metabolism associated genes. This study also characterized the alternative splicing events in SARS-CoV-2 infected cells compared to control demonstrating that skipped exons and mutually exclusive exons were the most abundant events that potentially contributed to differential outcomes in response to viral infection. Motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed an enrichment for RBPs such as SRSFs, PCBPs, ELAVs and HNRNPs illustrating the sponging of RBPs by SARS-CoV-2 genome. Similar analysis to study the interactions of miRs with SARS-CoV-2 revealed the potential for several miRs to be sponged, suggesting that these interactions may contribute to altered pos-transcriptional regulation across human tissues. Given the need to understand the interactions of SARS-CoV-2 with key pos-transcriptional regulators in the human genome, this study provides a systematic analysis to dissect the role of dysregulated post-transcriptional regulatory networks controlled by RBPs and miRs, across tissues types during SARS-CoV2 infection.Item Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects(Springer Nature, 2020-03-03) Sarmah, Swapnalee; Srivastava, Rajneesh; McClintick, Jeanette N.; Janga, Sarath C.; Edenberg, Howard J.; Marrs, James A.; Biology, School of ScienceEthanol exposure during prenatal development causes fetal alcohol spectrum disorder (FASD), the most frequent preventable birth defect and neurodevelopmental disability syndrome. The molecular targets of ethanol toxicity during development are poorly understood. Developmental stages surrounding gastrulation are very sensitive to ethanol exposure. To understand the effects of ethanol on early transcripts during embryogenesis, we treated zebrafish embryos with ethanol during pre-gastrulation period and examined the transcripts by Affymetrix GeneChip microarray before gastrulation. We identified 521 significantly dysregulated genes, including 61 transcription factors in ethanol-exposed embryos. Sox2, the key regulator of pluripotency and early development was significantly reduced. Functional annotation analysis showed enrichment in transcription regulation, embryonic axes patterning, and signaling pathways, including Wnt, Notch and retinoic acid. We identified all potential genomic targets of 25 dysregulated transcription factors and compared their interactions with the ethanol-dysregulated genes. This analysis predicted that Sox2 targeted a large number of ethanol-dysregulated genes. A gene regulatory network analysis showed that many of the dysregulated genes are targeted by multiple transcription factors. Injection of sox2 mRNA partially rescued ethanol-induced gene expression, epiboly and gastrulation defects. Additional studies of this ethanol dysregulated network may identify therapeutic targets that coordinately regulate early development.Item Bcl6 and Blimp1 reciprocally regulate ST21 Treg–cell development in the context of allergic airway inflammation(Elsevier, 2020) Koh, Byunghee; Ulrich, Benjamin J.; Nelson, Andrew S.; Panangipalli, Gayathri; Kharwadkar, Rakshin; Wu, Wenting; Xie, Markus M.; Fu, Yongyao; Turner, Matthew J.; Paczesny, Sophie; Janga, Sarath Chandra; Dent, Alexander L.; Kaplan, Mark H.; Pediatrics, School of MedicineBackground Bcl6 is required for the development of T follicular helper cells and T follicular regulatory (Tfr) cells that regulate germinal center responses. Bcl6 also affects the function of regulatory T (Treg) cells. Objective The goal of this study was to define the functions of Bcl6 in Treg cells, including Tfr cells, in the context of allergic airway inflammation. Methods We used a model of house dust mite sensitization to challenge wild-type, Bcl6fl/fl Foxp3-Cre, and Prdm1 (Blimp1)fl/fl Foxp3-Cre mice to study the reciprocal roles of Bcl6 and Blimp1 in allergic airway inflammation. Results In the house dust mite model, Tfr cells repress the production of IgE and Bcl6+ Treg cells suppress the generation of type 2 cytokine–producing cells in the lungs. In mice with Bcl6-deficient Treg cells, twice as many ST2+ (IL-33R+) Treg cells develop as are observed in wild-type mice. ST2+ Treg cells in the context of allergic airway inflammation are Blimp1 dependent, express type 2 cytokines, and share features of visceral adipose tissue Treg cells. Bcl6-deficient Treg cells are more susceptible, and Blimp1-deficient Treg cells are resistant, to acquiring the ST2+ Treg–cell phenotype in vitro and in vivo in response to IL-33. Bcl6-deficient ST2+ Treg cells, but not Bcl6-deficient ST2+ conventional T cells, strongly promote allergic airway inflammation when transferred into recipient mice. Lastly, ST2 is required for the exacerbated allergic airway inflammation in Bcl6fl/fl Foxp3-Cre mice. Conclusions During allergic airway inflammation, Bcl6 and Blimp1 play dual roles in regulating Tfr-cell activity in the germinal center and in the development of ST2+ Treg cells that promote type 2 cytokine responses.Item Splicing factor ESRP1 controls ER-positive breast cancer by altering metabolic pathways(EMBO Press, 2019-02) Gökmen‐Polar, Yesim; Neelamraju, Yaseswini; Goswami, Chirayu P.; Gu, Yuan; Gu, Xiaoping; Nallamothu, Gouthami; Vieth, Edyta; Janga, Sarath C.; Ryan, Michael; Badve, Sunil S.; Pathology and Laboratory Medicine, School of MedicineThe epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) control the epithelial-to-mesenchymal transition (EMT) splicing program in cancer. However, their role in breast cancer recurrence is unclear. In this study, we report that high levels of ESRP1, but not ESRP2, are associated with poor prognosis in estrogen receptor positive (ER+) breast tumors. Knockdown of ESRP1 in endocrine-resistant breast cancer models decreases growth significantly and alters the EMT splicing signature, which we confirm using TCGA SpliceSeq data of ER+ BRCA tumors. However, these changes are not accompanied by the development of a mesenchymal phenotype or a change in key EMT-transcription factors. In tamoxifen-resistant cells, knockdown of ESRP1 affects lipid metabolism and oxidoreductase processes, resulting in the decreased expression of fatty acid synthase (FASN), stearoyl-CoA desaturase 1 (SCD1), and phosphoglycerate dehydrogenase (PHGDH) at both the mRNA and protein levels. Furthermore, ESRP1 knockdown increases the basal respiration and spare respiration capacity. This study reports a novel role for ESRP1 that could form the basis for the prevention of tamoxifen resistance in ER+ breast cancer.Item Human protein-RNA interaction network is highly stable across mammals(BMC, 2019-12-30) Ramakrishnan, Aarthi; Janga, Sarath Chandra; Medical and Molecular Genetics, School of MedicineBackground RNA-binding proteins (RBPs) are crucial in modulating RNA metabolism in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Although previous studies on the conservation of RBP targets have been carried out in lower eukaryotes such as yeast, relatively little is known about the extent of conservation of the binding sites of RBPs across mammalian species. Results In this study, we employ CLIP-seq datasets for 60 human RBPs and demonstrate that most binding sites for a third of these RBPs are conserved in at least 50% of the studied vertebrate species. Across the studied RBPs, binding sites were found to exhibit a median conservation of 58%, ~ 20% higher than random genomic locations, suggesting a significantly higher preservation of RBP-RNA interaction networks across vertebrates. RBP binding sites were highly conserved across primates with weak conservation profiles in birds and fishes. We also note that phylogenetic relationship between members of an RBP family does not explain the extent of conservation of their binding sites across species. Multivariate analysis to uncover features contributing to differences in the extents of conservation of binding sites across RBPs revealed RBP expression level and number of post-transcriptional targets to be the most prominent factors. Examination of the location of binding sites at the gene level confirmed that binding sites occurring on the 3′ region of a gene are highly conserved across species with 90% of the RBPs exhibiting a significantly higher conservation of binding sites in 3′ regions of a gene than those occurring in the 5′. Gene set enrichment analysis on the extent of conservation of binding sites to identify significantly associated human phenotypes revealed an enrichment for multiple developmental abnormalities. Conclusions Our results suggest that binding sites of human RBPs are highly conserved across primates with weak conservation profiles in lower vertebrates and evolutionary relationship between members of an RBP family does not explain the extent of conservation of their binding sites. Expression level and number of targets of an RBP are important factors contributing to the differences in the extent of conservation of binding sites. RBP binding sites on 3′ ends of a gene are the most conserved across species. Phenotypic analysis on the extent of conservation of binding sites revealed the importance of lineage-specific developmental events in post-transcriptional regulatory network evolution.Item Epitranscriptomic code and its alterations in human disease(Elsevier, 2018-10) Kadumuri, Rajashekar Varma; Janga, Sarath Chandra; BioHealth Informatics, School of Informatics and ComputingInnovations in epitranscriptomics have resulted in the identification of more than 160 RNA modifications to date. These developments, together with the recent discovery of writers, readers, and erasers of modifications occurring across a wide range of RNAs and tissue types, have led to a surge in integrative approaches for transcriptome-wide mapping of modifications and protein-RNA interaction profiles of epitranscriptome players. RNA modification maps and crosstalk between them have begun to elucidate the role of modifications as signaling switches, entertaining the notion of an epitranscriptomic code as a driver of the post-transcriptional fate of RNA. Emerging single-molecule sequencing technologies and development of antibodies specific to various RNA modifications could enable charting of transcript-specific epitranscriptomic marks across cell types and their alterations in disease.