1
|
Singh N, Sahu DK, Tripathi RK, Mishra A, Shyam H, Shankar P, Jain M, Alam N, Kumar A, Mishra A, Chowdhry R, Singh A, Gupta S, Mehrotra D, Agarwal P, Goel MM, Chaturvedi A, Agarwal SP, Bajpai M, Gupta DK, Bhatt MLB, Kant R. Differentially expressed full-length, fusion and novel isoforms transcripts-based signature of well-differentiated keratinized oral squamous cell carcinoma. Oncotarget 2020; 11:3227-3243. [PMID: 32922662 PMCID: PMC7456611 DOI: 10.18632/oncotarget.27693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022] Open
Abstract
Highly keratinized oral squamous cell carcinoma (OSCC) exhibits an improved response to treatment and prognosis compared with weakly keratinized OSCC. Therefore, we aimed to develop gene transcript signature and to identify novel full-length isoforms, fusion transcript and non-coding RNA to differentiate well-differentiated (WD) with Moderately Differentiated (MD)/Poorly Differentiated (PD)/WD-lymphadenopathy OSCC through, HTA, Isoform sequencing, and NanoString. Additionally, specific copy number gain and loss were also identify in WD keratinized OSCC through Oncoscan array and validated through Real-time PCR in histopathologically characterized FFPE-WD keratinized OSCC. Three-hundred-thirty-eight (338) differentially expressed full-length (FL) transcript isoforms (317 upregulated and 21 down-regulated in OSCC) were identified through Isoform Sequencing using the PacBio platform. Thirty-four (34) highly upregulated differentially expressed transcripts from IsoSeq data were also correlated with HTA2.0 and validated in 42 OSCC samples. We were able to identify 18 differentially expressed transcripts, 12 fusion transcripts, and two long noncoding RNAs. These transcripts were involved in increased cell proliferation, dysregulated metabolic reprogramming, oxidative stress, and immune system markers with enhanced immune rearrangements, suggesting a cancerous nature. However, an increase in proteasomal activity and hemidesmosome proteins suggested an improved prognosis and tumor cell stability in keratinized OSCC and helped to characterize WD with MD/PD/WD with lymphadenopathy OSCC. Additionally, novel isoforms of IL37, NAA10, UCHL3, SPAG7, and RAB24 were identified while in silico functionally validated SPAG7 represented the premalignant phenotype of keratinized (K4) OSCC. Most importantly we found copy number gain and overexpression of EGFR suggest that TKIs may also be used as therapeutics in WD-OSCCs.
Collapse
Affiliation(s)
- Neetu Singh
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Dinesh Kumar Sahu
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Ratnesh Kumar Tripathi
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Archana Mishra
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,Department of Surgery, King George's Medical University, Lucknow, India
| | - Hari Shyam
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Pratap Shankar
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Mayank Jain
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Nawazish Alam
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Anil Kumar
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Abhishek Mishra
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Rebecca Chowdhry
- Department of Periodontology, All India Institute of Medical Sciences, Rishikesh, India
| | - Anjana Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George's Medical University, Lucknow, India
| | - Divya Mehrotra
- Department of Oral and Maxillofacial Surgery, King George's Medical University, Lucknow, India
| | - Preeti Agarwal
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Madhu Mati Goel
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Arun Chaturvedi
- Department of Surgical Oncology, King George's Medical University, Lucknow, India
| | | | - Manish Bajpai
- Department of Physiology, King George's Medical University, Lucknow, India
| | - Devendra Kumar Gupta
- Department of Pediatric Surgery, Super Speciality Pediatric Hospital and Post Graduate Teaching Institute, Noida, India
| | | | - Ravi Kant
- Department of Surgical Oncology, All India Institute of Medical Sciences, Rishikesh, India
| |
Collapse
|
2
|
Singh N, Tripathi AK, Sahu DK, Mishra A, Linan M, Argente B, Varkey J, Parida N, Chowdhry R, Shyam H, Alam N, Dixit S, Shankar P, Mishra A, Agarwal A, Yoo C, Bhatt MLB, Kant R. Differential genomics and transcriptomics between tyrosine kinase inhibitor-sensitive and -resistant BCR-ABL-dependent chronic myeloid leukemia. Oncotarget 2018; 9:30385-30418. [PMID: 30100996 PMCID: PMC6084383 DOI: 10.18632/oncotarget.25752] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/28/2018] [Indexed: 01/11/2023] Open
Abstract
Previously, it has been stated that the BCR-ABL fusion-protein is sufficient to induce Chronic Myeloid Leukemia (CML), but additional genomic-changes are required for disease progression. Hence, we profiled control and tyrosine kinase inhibitors (TKI) alone or in combination with other drug-treated CML-samples in different phases, categorized as drug-sensitive and drug-resistant on the basis of BCR-ABL transcripts, the marker of major molecular-response. Molecular-profiling was done using the molecular-inversion probe-based-array, Human Transcriptomics-Array2.0, and Axiom-Biobank genotyping-arrays. At the transcript-level, clusters of control, TKI-resistant and TKI-sensitive cases were correlated with BCR-ABL transcript-levels. Both at the gene- and exon-levels, up-regulation of MPO, TPX2, and TYMS and down-regulation of STAT6, FOS, TGFBR2, and ITK lead up-regulation of the cell-cycle, DNA-replication, DNA-repair pathways and down-regulation of the immune-system, chemokine- and interleukin-signaling, TCR, TGF beta and MAPK signaling pathways. A comparison between TKI-sensitive and TKI-resistant cases revealed up-regulation of LAPTM4B, HLTF, PIEZO2, CFH, CD109, ANGPT1 in CML-resistant cases, leading to up-regulation of autophagy-, protein-ubiquitination-, stem-cell-, complement-, TGFβ- and homeostasis-pathways with specific involvement of the Tie2 and Basigin signaling-pathway. Dysregulated pathways were accompanied with low CNVs in CP-new and CP-UT-TKI-sensitive-cases with undetectable BCR-ABL-copies. High CNVs (previously reported gain of 9q34) were observed in BCR-ABL-independent and -dependent TKI, non-sensitive-CP-UT/AP-UT/B-UT and B-new samples. Further, genotyping CML-CP-UT cases with BCR-ABL 0-to-77.02%-copies, the identified, rsID239798 and rsID9475077, were associated with FAM83B, a candidate for therapeutic resistance. The presence of BCR-ABL, additional genetic-events, dysregulated-signaling-pathways and rsIDs associated with FAM83B in TKI-resistant-cases can be used to develop a signature-profile that may help in monitoring therapy.
Collapse
Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Anil Kumar Tripathi
- Department of Clinical Hematology, King George's Medical University, Lucknow, India
| | - Dinesh Kumar Sahu
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Archana Mishra
- Department of Cardio Thoracic and Vascular Surgery, King George's Medical University, Lucknow, India
| | | | | | | | - Niranjan Parida
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Rebecca Chowdhry
- Department of Periodontics, King George's Medical University, Lucknow, India
| | - Hari Shyam
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Nawazish Alam
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Shivani Dixit
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Pratap Shankar
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Abhishek Mishra
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Avinash Agarwal
- Department of Medicine, King George's Medical University, Lucknow, India
| | - Chris Yoo
- Systems Imagination, Scottsdale, Arizona, USA
| | | | - Ravi Kant
- All India Institute of Medical Sciences, Rishikesh, India
| |
Collapse
|
3
|
Singh N, Sahu DK, Chowdhry R, Mishra A, Goel MM, Faheem M, Srivastava C, Ojha BK, Gupta DK, Kant R. IsoSeq analysis and functional annotation of the infratentorial ependymoma tumor tissue on PacBio RSII platform. Meta Gene 2015; 7:70-5. [PMID: 26862483 PMCID: PMC4707247 DOI: 10.1016/j.mgene.2015.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/10/2015] [Accepted: 11/16/2015] [Indexed: 12/07/2022] Open
Abstract
Here, we sequenced and functionally annotated the long reads (1–2 kb) cDNAs library of an infratentorial ependymoma tumor tissue on PacBio RSII by Iso-Seq protocol using SMRT technology. 577 MB, data was generated from the brain tissues of ependymoma tumor patient, producing 1,19,313 high-quality reads assembled into 19,878 contigs using Celera assembler followed by Quiver pipelines, which produced 2952 unique protein accessions in the nr protein database and 307 KEGG pathways. Additionally, when we compared GO terms of second and third level with alternative splicing data obtained through HTA Array2.0. We identified four and twelve transcript cluster IDs in Level-2 and Level-3 scores respectively with alternative splicing index predicting mainly the major pathways of hallmarks of cancer. Out of these transcript cluster IDs only transcript cluster IDs of gene PNMT, SNN and LAMB1 showed Reads Per Kilobase of exon model per Million mapped reads (RPKM) values at gene-level expression (GE) and transcript-level (TE) track. Most importantly, brain-specific genes–—PNMT, SNN and LAMB1 show their involvement in Ependymoma. Produced 2952 unique protein accessions in the nr protein database Identified 307 KEGG-pathways with 442 enzyme-codes for 1172 unique-sequences Identified transcript cluster-IDs in Level-2 and -3 GO-terms with alternative splicing index Involvement of PNMT, SNN and LAMB1-brain specific genes in Ependymoma
Collapse
Affiliation(s)
- Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow 226003, India
| | - Dinesh Kumar Sahu
- Imperial Life Sciences, 463 Phase City 2nd, Sector 37, Gurgaon, Haryana 122001, India
| | - Rebecca Chowdhry
- Department of Periodontics, King George's Medical University, Lucknow 226003, India
| | - Archana Mishra
- Department of Biochemistry, King George's Medical University, Lucknow 226003, India
| | - Madhu Mati Goel
- Department of Pathology, King George's Medical University, Lucknow 226003, India
| | - Mohd Faheem
- Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Chhitij Srivastava
- Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Bal Krishna Ojha
- Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Devendra Kumar Gupta
- Department of Pediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ravi Kant
- Department of Surgical Oncology, King George's Medical University, Lucknow, Uttar Pradesh 226003, India
| |
Collapse
|