title: Sample preparation method considerations for integrated transcriptomic and proteomic analysis of tumors.
abstract: Sample processing protocols that enable compatible recovery of differentially expressed transcripts and proteins are necessary for integration of the multiomics data applied in the analysis of tumors. In this pilot study, we compared two different isolation methods for extracting RNA and protein from laryngopharyngeal tumor tissues and the corresponding adjacent normal sections. In Method 1, RNA and protein were isolated from a single tissue section sequentially and in Method 2, the extraction was carried out using two different sections and two independent and parallel protocols for RNA and protein. RNA and protein from both methods were subjected to RNA-seq and iTRAQ-based LC-MS/MS analysis, respectively. Analysis of data revealed that a higher number of differentially expressed transcripts and proteins were concordant in their regulation trends in Method 1 as compared to Method 2. Cross-method comparison of concordant entities revealed that RNA and protein extraction from the same tissue section (Method 1) recovered more concordant entities that are missed in the other extraction method (Method 2) indicating heterogeneity in distribution of these entities in different tissue sections. Method 1 could thus be the method of choice for integrated analysis of transcriptome and proteome data.
authors: Strand Life Sciences, Bangalore, India.
authors: Anupama Rajan
authors: AR
authors: Bhat
authors: Institute of Bioinformatics, International Tech Park, Bangalore, India.|Manipal University, Madhav Nagar, Manipal, India.
authors: Manoj Kumar
authors: MK
authors: Gupta
authors: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.
authors: Priya
authors: P
authors: Krithivasan
authors: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.
authors: Kunal
authors: K
authors: Dhas
authors: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.
authors: Jayalakshmi
authors: J
authors: Nair
authors: Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, India.|Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore, India.
authors: Ram Bhupal
authors: RB
authors: Reddy
authors: Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore, India.
authors: Holalugunda Vittalamurthy
authors: HV
authors: Sudheendra
authors: Institute of Bioinformatics, International Tech Park, Bangalore, India.
authors: Sandip
authors: S
authors: Chavan
authors: Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, India.|Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore, India.
authors: Harsha
authors: H
authors: Vardhan
authors: Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, India.
authors: Sujatha
authors: S
authors: Darsi
authors: Institute of Bioinformatics, International Tech Park, Bangalore, India.
authors: Lavanya
authors: L
authors: Balakrishnan
authors: Strand Life Sciences, Bangalore, India.
authors: Shanmukh
authors: S
authors: Katragadda
authors: Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, India.
authors: Vikram
authors: V
authors: Kekatpure
authors: Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, India.|Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore, India.
authors: Amritha
authors: A
authors: Suresh
authors: Strand Life Sciences, Bangalore, India.
authors: Pramila
authors: P
authors: Tata
authors: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.
authors: Binay
authors: B
authors: Panda
authors: Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, India.|Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore, India.
authors: Moni A
authors: MA
authors: Kuriakose
authors: Institute of Bioinformatics, International Tech Park, Bangalore, India.|Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health, Bangalore, India.
authors: Ravi
authors: R
authors: Sirdeshmukh
mesh_terms: D053000:Analytic Sample Preparation Methods / Q000379:methods*; D020869:Gene Expression Profiling; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics; D018511:Systems Integration
keywords: Head and neck cancer; Multiomics data integration; Proteomics; Transcriptomics; Tumor heterogeneity