Manjari Kiran

University of Hyderabad

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Anindya Dutta

University of Alabama at Birmingham

Ajay Chatrath

University of Virginia

Canan Kuscu

University of Tennessee Health Science Center

Shekhar Saha

University of Virginia

Brian J. Reon

University of Virginia

Bruno Takao Real Karia

Universidade Federal de São Paulo

David Wotton

University of Virginia

Marty W. Mayo

University of Virginia

Aakrosh Ratan

University of Virginia

Pankaj Kumar

University of Virginia

Cooperative Institutions

Institute of Navigation

University of Virginia

University of Hyderabad

University of Tennessee Health Science Center

Centre for DNA Fingerprinting and Diagnostics

University of North Carolina at Chapel Hill

Institute of Medical Sciences

Johns Hopkins University

Banaras Hindu University

Harvard University

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Sirtuin 7 in cell proliferation, stress and disease: Rise of the Seventh Sirtuin!

Cellular Signalling (2014)

Shashi Kiran Tarique Anwar Manjari Kiran Gayatri Ramakrishna

Epigenome

Sirtuin 1

10.1016/j.cellsig.2014.11.026

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Citations (103)

Figure S3 from Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation

Shekhar Saha Manjari Kiran Canan Kuscu Ajay Chatrath David Wotton

Specificity of DRAIC's association with IKK by depletion of IKK complex using siRNA and immunoprecipitation of the residual subunit of IKK complex in LNCaP cells

IκB kinase

10.1158/0008-5472.22424476.v1

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Supplementary Table 2 from LINC00152 Promotes Invasion through a 3′-Hairpin Structure and Associates with Prognosis in Glioblastoma

Brian J. Reon Bruno Takao Real Karia Manjari Kiran Anindya Dutta

List of oligonucleotides used in this study.

10.1158/1541-7786.22512955.v1

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Additional file 2 of The pan-cancer landscape of prognostic germline variants in 10,582 patients

Figshare (2020)

Ajay Chatrath Roza Przanowska Shashi Kiran Zhangli Su Shekhar Saha

Table S2. A. 70 Prognostic Germline Variants Identified in Analyis 1. B. Five Prognostic Germline Variants Identified in Analysis 2. C. 103 Prognostic Germline Variants Identified in Analysis 3. D. 9 Prognostic Germline Variants Identified in Analysis 4. E. 1 Prognostic Germline Variants Identified in Analysis 5. F. 3 Prognostic Germline Variants Identified in Analyis 6. (XLSX 48 kb)

10.6084/m9.figshare.11864022

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Additional file 4 of The pan-cancer landscape of prognostic germline variants in 10,582 patients

Figshare (2020)

Ajay Chatrath Roza Przanowska Shashi Kiran Zhangli Su Shekhar Saha

Table S5. Literature review results for the genes that the prognostic germline variants were found in or near (Fig. 6a–c). (XLSX 26 kb)

10.6084/m9.figshare.11864037

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Figure S3 from Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation

Shekhar Saha Manjari Kiran Canan Kuscu Ajay Chatrath David Wotton

Specificity of DRAIC's association with IKK by depletion of IKK complex using siRNA and immunoprecipitation of the residual subunit of IKK complex in LNCaP cells

IκB kinase

10.1158/0008-5472.22424476

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A prognostic signature for lower-grade gliomas based on expression of long noncoding RNAs

bioRxiv (Cold Spring Harbor Laboratory) (2018)

Manjari Kiran Ajay Chatrath Xiwei Tang Daniel M. Keenan Anindya Dutta

Abstract Diffuse low-grade and intermediate-grade gliomas (together known as lower-grade gliomas, WHO grade II and III) develop in the supporting glial cells of brain and are the most common types of primary brain tumor. Despite a better prognosis for lower-grade gliomas, 70% of patients undergo high-grade transformation within 10 years, stressing the importance of better prognosis. Long non-coding RNAs (lncRNAs) are gaining attention as potential biomarkers for cancer diagnosis and prognosis. We have developed a computational model, UVA8, for prognosis of lower-grade gliomas by combining lncRNA expression, Cox regression and L1-LASSO penalization. The model was trained on a subset of patients in TCGA. Patients in TCGA, as well as a completely independent validation set (CGGA) could be dichotomized based on their risk score, a linear combination of the level of each prognostic lncRNA weighted by its multivariable cox regression coefficient. UVA8 is an independent predictor of survival and outperforms standard epidemiological approaches and previous published lncRNA-based predictors as a survival model. Guilt-by-association studies of the lncRNAs in UVA8, all of which predict good outcome, suggest they have a role in suppressing interferon stimulated response and epithelial to mesenchymal transition. The expression levels of 8 lncRNAs can be combined to produce a prognostic tool applicable to diverse populations of glioma patients. The 8 lncRNA (UVA8) based score can identify grade II and grade III glioma patients with poor outcome and thus identify patients who should receive more aggressive therapy at the outset.

Lasso

10.1101/442616

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Citations (8)

Figure S2 from Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation

Shekhar Saha Manjari Kiran Canan Kuscu Ajay Chatrath David Wotton

DRAIC KO validation

IκB kinase

10.1158/0008-5472.22424479.v1

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Supplementary Figure 5 from LINC00152 Promotes Invasion through a 3′-Hairpin Structure and Associates with Prognosis in Glioblastoma

Brian J. Reon Bruno Takao Real Karia Manjari Kiran Anindya Dutta

LINC00152 full length and deletion mutants. A) Predicted secondary structures of LINC00152 deletion mutants. M2 and M3 lack the protein bound stem-loop. M8 is highlighted by the boxed area (nucleotides 280-401). On the other hand, M4 through M8 contain the protein bound stem-loop (highlighted by the boxed area). B) Schematics of LINC00152 siRNA and primers relative to LINC00152 sequence.

Schematic

10.1158/1541-7786.22512964

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Supplementary Table 2 from LINC00152 Promotes Invasion through a 3′-Hairpin Structure and Associates with Prognosis in Glioblastoma

Brian J. Reon Bruno Takao Real Karia Manjari Kiran Anindya Dutta

List of oligonucleotides used in this study.

Table (database)

10.1158/1541-7786.22512955

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