Biology subjects

Thangarajan, R.

Publications and source records attributed to Thangarajan, R..

4 recordsLinked to original sources

bioRxiv2022

Locus-specific enrichment analysis of 5-hydroxymethylcytosine revealed novel genes associated with breast carcinogenesis

BackgroundAn imbalance in DNA methylation is a hallmark epigenetic alteration in cancer. The conversion of 5-methylcytosine (5-mC) to 5-hydroxymethyl cytosine (5-hmC), which causes the imbalance, results in aberrant gene expression. The precise functional role of 5-hydroxymethylcytosine in breast cancer remains elusive. In this study, we describe the landscape of 5-mC and 5-hmC and their association with breast cancer development. ResultsWe found a distinguishable global loss of 5-hmC in the localized and invasive types of breast cancer, which correlate strongly with TET expression. Genome-wide analysis revealed a unique 5-mC and 5-hmC signature in breast cancer. The differentially methylated regions (DMRs) were primarily concentrated in the proximal regulatory regions such as the promoters and UTRs, while the differentially hydroxymethylated regions (DhMRs) were densely packed in the distal regulatory regions such as the intergenic regions (>-5 kb from TSSs). Our results indicate 4809 DMRs and 4841 DhMRs associated with breast cancer. Validation of nine 5-hmC enriched loci in a distinct set of breast cancer and normal samples, positively correlated with their corresponding gene expression. The novel 5-hmC candidates such as TXNL1, CNIH3, and BNIPL implicate a pro-oncogenic role in breast cancer. Therefore, 5-hmC modified regions could be used as promising diagnostic and therapeutic markers for breast cancer. ConclusionGlobal loss of 5-hmC is associated with down-regulation of the TET 1 and TET3 genes. Genome-wide profiling has revealed a profound imbalance in the region-specific distribution of 5-mC and 5-hmC in breast cancer. Predominant 5-hmC modifications are localized at distal gene regulatory sites. Novel 5-hmC candidates associated with breast cancer have been identified. Hence, these results provide new insights in the loci-specific accumulation of 5-mC and 5-hmC which are aberrantly methylated and demethylated in breast cancer.

cancer biology↗

bioRxiv2020

Detection of M-Protein in Acetonitrile Precipitates of Serum using MALDI-TOF Mass Spectrometry

Purpose of the researchMultiple myeloma and plasmacytomas belong to a group of disorders, namely plasma cell dyscrasias and are identified by the presence of a monoclonal protein (M-protein). MALDI-TOF-mass spectrometry (MS) has demonstrated superior analytical sensitivity for the detection of M-protein and is now used for screening of M-protein at some centres. We present the results of an alternative methodology for M-protein analysis by MALDI-TOF MS. MethodsSerum samples from patients with newly diagnosed multiple myeloma or plasmacytoma with positive M-protein detected by serum protein electrophoresis, immunofixation electrophoresis and serum free light chain analysis, underwent direct reagent-based extraction process using Acetonitrile (ACN) precipitation. Serum{kappa} and{lambda} light chains were validated using immunoenrichment by anti-{kappa} and anti-{lambda} biotin-labelled antibodies immobilised on streptavidin magnetic beads. MALDI-TOF MS measurements were obtained for intact proteins using alpha-cyano-4-hydroxycinnamic acid as matrix. The images obtained were overlaid on apparently healthy donor serum samples to confirm the presence of M-protein. Principle resultsCharacteristic M-protein peaks were observed in the ACN precipitates of serum in the predicted mass ranges for{kappa} and{lambda} . The{kappa} and{lambda} peaks were confirmed by immunoenrichment analysis. Twenty-seven patient samples with either newly diagnosed multiple myeloma or plasmacytoma with monoclonal gammopathy detected by the standard methods were chosen for Acetonitrile precipitation and analysed by MALDI-TOF MS. All 27 patient samples demonstrated a peak suggestive of M-protein with mass/charge (m/z) falling within the{kappa} and{lambda} range. The concordance rate with serum immunofixation electrophoresis and free light chain analysis was above 90%. Major conclusionsWe report the results of a low-cost reagent-based extraction process using Acetonitrile precipitation to enrich for{kappa} and{lambda} light chains, which can be used for the screening and qualitative analysis of M-protein.

biochemistry↗

bioRxiv2019

Identification of lncRNAs associated with early stage breast cancer and their prognostic implications

Breast cancer is a common malignancy among women with the highest incidence rate worldwide. Dysregulation of long non-coding RNAs occurring in the preliminary stages of breast carcinogenesis is poorly understood. In this study, RNA sequencing was done to identify long non-coding RNA expression profiles associated with early-stage breast cancer. RNA sequencing was done in 6 invasive ductal carcinoma (IDC) tissues along with paired normal tissue samples, 7 ductal carcinoma in situ (DCIS) tissues and 5 apparently normal breast tissues. We identified 375 differentially expressed lncRNAs (DElncRNAs) in IDC tissues compared to paired normal tissues. Antisense transcripts ([~]58%) were the largest subtype among DElncRNAs. About 20% of the 375 DElncRNAs were supported by typical split readings leveraging their detection confidence. Validation was done in n=52 IDC and paired normal tissue by qRT-PCR for the identified targets (ADAMTS9-AS2, EPB41L4A-AS1, WDFY3-AS2, RP11-295M3.4, RP11-161M6.2, RP11-490M8.1, CTB-92J24.3 and FAM83H-AS)1. We evaluated the prognostic significance of DElncRNAs based on TCGA datasets and overexpression of FAM83H-AS1 was associated with patient poor survival. We confirmed that the down-regulation of ADAMTS9-AS2 in breast cancer was due to promoter hypermethylation through in-vitro silencing experiments and pyrosequencing.

cancer biology↗

bioRxiv2018

RNA sequencing identifies dysregulated circular RNAs in early-stage breast cancer

BackgroundBreast cancer is a major cause of cancer related death in women worldwide. Molecular diagnostic markers that are detectable in early-stage breast cancer can aid in effective clinical intervention. Circular RNAs are a recently identified group of non-coding RNA with potential role in cancer development and progression. In this study, we aimed to identify circular RNAs specific for early stage breast cancer.\n\nMethodCircular RNA expression profile was analyzed in early-stage breast cancer tissues (N=5), matched normal counterparts (N=5) and absolute normal samples (N=5) by RNA-sequencing that enables a comprehensive analysis of RNA expression across the transcriptome. Two different algorithms, find_circ and DCC were used to identify the differentially expressed circular RNAs.\n\nResultsA total of 58 and 87 circular RNAs were found to be differentially expressed by find_circ and DCC algorithms, respectively, among which 26 circular RNAs were common. Hsa_circ_0001946 (CDR1-as) was found to be upregulated in early stage breast cancer along with other novel circular RNAs (hsa_circ_0008225, hsa_circ_0007766, hsa_circ_0016601). We also found that a few of the identified circular RNAs harbor microRNA binding sites which can lead to microRNA sponging activity and pre-microRNA sequences which can generate mature microRNAs. The identified circular RNAs that are differentially regulated in early stage breast cancer can be of potential diagnostic/prognostic importance.\n\nConclusionCircular RNA are differentially expressed in the early-stage breast cancer with potential application in early diagnosis and prognosis. The differentially expressed circular RNA can sequester microRNA and can act as microRNA precursor as well.

cancer biology↗