Identification of novel transcripts deregulated in buccal cancer by RNA-seq

Sajnani, Manisha R.; Patel, Amrutlal K.; Bhatt, Vaibhav D.; Tripathi, Ajai K.; Ahir, Viral B.; Shankar, Vangipuram; Shah, Siddharth; Shah, Tejas; Koringa, Prakash G.; Jakhesara, Subhash J.; Joshi, Chaitanya G.

doi:10.1016/j.gene.2012.07.036

Cited by 19 publications

(17 citation statements)

References 48 publications

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“…They include squamous cell carcinomas of the tongue, floor of the mouth, buccal mucosa, lips, hard and soft palate, and gingiva . In the Indian subcontinent, OSCC of the BM and GB are more common due to the habit of chewing betel quid with or without smokeless tobacco …”

Section: Discussionmentioning

confidence: 99%

“…The most commonly affected site in the Indian subcontinent is the buccal mucosa (BM) and gingivo-buccal sulcus (GB) due to the habit of pouching of betel quid comprising betel leaf, areca nut, and slaked lime with or without smokeless tobacco within the cheek. 2,3 OSCC has a poor prognosis due to its invasive growth pattern, lymph-node metastasis, and high recurrence rate. Despite recent advances in cancer treatment, the overall survival rate is approximately 50% and has not changed significantly over the last few decades.…”

Section: Introductionmentioning

confidence: 99%

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Pathway based prognostic gene expression profile of buccal and gingivo‐buccal oral squamous cell carcinoma in smokeless tobacco chewers

et al. 2018

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Background The objective was to study comprehensive mRNA expression profiles of buccal mucosa oral squamous cell carcinoma (OSCC‐BM) and gingivo‐buccal OSCC (OSCC‐GB) in smokeless tobacco chewers to understand the biological behavior of OSCC at these specific sites and identify diagnostic and prognostic markers. Methods High throughput RNA sequencing transcriptome of fresh buccal mucosa (4 samples) and gingivo‐buccal (4 samples) OSCC with normal oral mucosa (3 samples) was performed on Illumina NextSeq500 paired end sequencing with 75x2bp. Results In the comparison between OSCC and normal, there were 402 differentially expressed genes (DEGs); between OSCC‐BM and normal, there were 467 DEGs; and between OSCC‐GB and normal oral tissue, there were 608 DEGs. Pathway‐based analysis of gene expression was done. The inflammation mediated by chemokine and cytokine signaling pathway had the maximum gene hits. Conclusions FZD2 and its interactions with the cadherins have a role in invasion and metastasis. immunosurveillance is evident in OSCC‐GB with the downregulation of CADM1.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Pathway based prognostic gene expression profile of buccal and gingivo‐buccal oral squamous cell carcinoma in smokeless tobacco chewers

et al. 2018

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“…Despite the extensive longitudinal changes in DNA methylation described above, we found that, in general, probes located within genes associated with RNA metabolism (for example, spliceosome components) and control of gene expression (for example, transcription factors) were consistently more discordant within twin pairs at both birth and 18 months of age. Of interest, this class of genes has previously been shown to have altered levels of transcription in buccal cancer [59]. …”

Section: Discussionmentioning

confidence: 99%

Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance

et al. 2013

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BackgroundThe extent to which development- and age-associated epigenetic changes are influenced by genetic, environmental and stochastic factors remains to be discovered. Twins provide an ideal model with which to investigate these influences but previous cross-sectional twin studies provide contradictory evidence of within-pair epigenetic drift over time. Longitudinal twin studies can potentially address this discrepancy.ResultsIn a pilot, genome-scale study of DNA from buccal epithelium, a relatively homogeneous tissue, we show that one-third of the CpGs assayed show dynamic methylation between birth and 18 months. Although all classes of annotated genomic regions assessed show an increase in DNA methylation over time, probes located in intragenic regions, enhancers and low-density CpG promoters are significantly over-represented, while CpG islands and high-CpG density promoters are depleted among the most dynamic probes. Comparison of co-twins demonstrated that within-pair drift in DNA methylation in our cohort is specific to a subset of pairs, who show more differences at 18 months. The rest of the pairs show either minimal change in methylation discordance, or more similar, converging methylation profiles at 18 months. As with age-associated regions, sites that change in their level of within-pair discordance between birth and 18 months are enriched in genes involved in development, but the average magnitude of change is smaller than for longitudinal change.ConclusionsOur findings suggest that DNA methylation in buccal epithelium is influenced by non-shared stochastic and environmental factors that could reflect a degree of epigenetic plasticity within an otherwise constrained developmental program.

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“…Among the three GO terms with the most significant fold enrichment, five proteins (FGF2, TGFB1, PTK2, JAK2, and GH1) with the highest fold changes were selected as the further subjects. In addition, 10 of the 43 downregulated proteins were involved in tumor suppression and were thus selected for the subsequent analysis (Figure B, right panel and Table S5, Supporting Information).…”

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confidence: 99%

Circ‐MALAT1 Functions as Both an mRNA Translation Brake and a microRNA Sponge to Promote Self‐Renewal of Hepatocellular Cancer Stem Cells

Chen

Kong

et al. 2019

Advanced Science

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Both circular RNAs (circRNAs) and cancer stem cells (CSCs) are separately known to be involved in cancer, but their interaction remains unclear. Here, the regulation of hepatocellular CSC self‐renewal is discovered by a circRNA, circ‐MALAT1, which is produced by back‐splicing of a long noncoding RNA, MALAT1. Circ‐MALAT1 is highly expressed in CSCs from clinical hepatocellular carcinoma samples under the mediation of an RNA‐binding protein, AUF1. Surprisingly, circMALAT1 functions as a brake in ribosomes to retard PAX5 mRNA translation and promote CSCs' self‐renewal by forming an unprecedented ternary complex with both ribosomes and mRNA. The discovered braking mechanism of a circRNA, termed mRNA braking, along with its more traditional role of miRNA sponging, uncovers a dual‐faceted pattern of circRNA‐mediated post‐transcriptional regulation for maintaining a specific cell state.

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Identification of novel transcripts deregulated in buccal cancer by RNA-seq

Cited by 19 publications

References 48 publications

Pathway based prognostic gene expression profile of buccal and gingivo‐buccal oral squamous cell carcinoma in smokeless tobacco chewers

Pathway based prognostic gene expression profile of buccal and gingivo‐buccal oral squamous cell carcinoma in smokeless tobacco chewers

Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance

Circ‐MALAT1 Functions as Both an mRNA Translation Brake and a microRNA Sponge to Promote Self‐Renewal of Hepatocellular Cancer Stem Cells

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