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Molecular mechanisms of activating c-MET in KSHV+ primary effusion lymphoma

View Article: PubMed Central - PubMed

ABSTRACT

The oncogenic Kaposi's sarcoma–associated herpesvirus (KSHV) is a principal causative agent of primary effusion lymphoma (PEL), which is mostly seen in immunosuppressed patients. PEL is a rapidly progressing malignancy with a median survival time of approximately 6 months even under the conventional chemotherapy. We recently report that the hepatocyte growth factor (HGF)/c-MET pathway is highly activated in PEL cells and represents a promising therapeutic target (Blood. 2015;126(26):2821-31). However, the underlying mechanisms of c-MET activation within PEL cells remain largely unknown. To solve this puzzle, here we have utilized the next generation sequencing (NGS) based bioinformatics approach to investigate the genomic landscape of the c-MET gene and we found that there's no single nucleotide variations (SNVs) occurred in the c-MET genomic regions in a cohort of PEL samples. Consistently, Sanger sequencing analysis of frequently mutated exons such as exon 10, 14 and 19 shows no mutation of these c-MET exons in PEL cell-lines, which further supports the notion that mutations are not the major mechanism responsible for c-MET activation in PEL. Further, we found that a transmembrane receptor protein, Plexin-B1, is expressed in PEL cell-lines, which is required for c-MET-mediated PEL cell survival via direct protein interaction.

No MeSH data available.


Related in: MedlinePlus

The SNV analysis of c-METThe positions of all single nucleotide variations (SNVs) across the c-MET genomic regions are on the x axis and the sample name on the y axis. Dots indicate a nucleotide difference from the hg19 reference genome, and the color of the dots indicates the number of reads covering that specific SNV on a log10 scale. The TCGA kidney/renal carcinoma and lung adenocarcinoma data sets were used as the positive controls.
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Figure 2: The SNV analysis of c-METThe positions of all single nucleotide variations (SNVs) across the c-MET genomic regions are on the x axis and the sample name on the y axis. Dots indicate a nucleotide difference from the hg19 reference genome, and the color of the dots indicates the number of reads covering that specific SNV on a log10 scale. The TCGA kidney/renal carcinoma and lung adenocarcinoma data sets were used as the positive controls.

Mentions: The human c-MET gene consists of 21 exons and encodes a protein of 1408 amino acids (aa). Structurally, the c-MET protein contains both extracellular and intracellular domains. Its extracellular domain can be further divided into the semaphoring domain, the plexin-semaphorin-integrin domain, and four immunoglobulin-plexin-transcription domains. The intracellular domain of c-MET carries its tyrosine kinase activity (Figure 1) [6, 19]. To date, it is still unclear whether the c-MET gene harbors any oncogenic SNVs and thus leads to its abnormal activation in PEL cells. To investigate the genomic landscape of the c-MET gene, here we have analyzed a cohort of PEL data sets (16 cell-lines isolated and established from HIV+ or HIV- PEL patients, accession no. SRP032975) using a well-established NGS approach as described in the Methods. Our results show that there are no single nucleotide variations (SNVs) in the coding sequence (cds) regions of c-MET, whereas c-MET SNVs were readily detected in the control TCGA kidney/renal carcinoma and lung adenocarcinoma samples (Figure 2). Nevertheless, we indeed noticed that the effective sequencing depth of the c-MET gene of these PEL data sets is significantly lower (around 142-fold lower) than those control TCGA data sets. Thus, it is possible that some potential c-MET mutations may be detectable by using some high-quality deep-sequencing datasets in the future. However, due to the rarity of this disease, these are the only published PEL NGS data sets we can acquire for analysis.


Molecular mechanisms of activating c-MET in KSHV+ primary effusion lymphoma
The SNV analysis of c-METThe positions of all single nucleotide variations (SNVs) across the c-MET genomic regions are on the x axis and the sample name on the y axis. Dots indicate a nucleotide difference from the hg19 reference genome, and the color of the dots indicates the number of reads covering that specific SNV on a log10 scale. The TCGA kidney/renal carcinoma and lung adenocarcinoma data sets were used as the positive controls.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5392335&req=5

Figure 2: The SNV analysis of c-METThe positions of all single nucleotide variations (SNVs) across the c-MET genomic regions are on the x axis and the sample name on the y axis. Dots indicate a nucleotide difference from the hg19 reference genome, and the color of the dots indicates the number of reads covering that specific SNV on a log10 scale. The TCGA kidney/renal carcinoma and lung adenocarcinoma data sets were used as the positive controls.
Mentions: The human c-MET gene consists of 21 exons and encodes a protein of 1408 amino acids (aa). Structurally, the c-MET protein contains both extracellular and intracellular domains. Its extracellular domain can be further divided into the semaphoring domain, the plexin-semaphorin-integrin domain, and four immunoglobulin-plexin-transcription domains. The intracellular domain of c-MET carries its tyrosine kinase activity (Figure 1) [6, 19]. To date, it is still unclear whether the c-MET gene harbors any oncogenic SNVs and thus leads to its abnormal activation in PEL cells. To investigate the genomic landscape of the c-MET gene, here we have analyzed a cohort of PEL data sets (16 cell-lines isolated and established from HIV+ or HIV- PEL patients, accession no. SRP032975) using a well-established NGS approach as described in the Methods. Our results show that there are no single nucleotide variations (SNVs) in the coding sequence (cds) regions of c-MET, whereas c-MET SNVs were readily detected in the control TCGA kidney/renal carcinoma and lung adenocarcinoma samples (Figure 2). Nevertheless, we indeed noticed that the effective sequencing depth of the c-MET gene of these PEL data sets is significantly lower (around 142-fold lower) than those control TCGA data sets. Thus, it is possible that some potential c-MET mutations may be detectable by using some high-quality deep-sequencing datasets in the future. However, due to the rarity of this disease, these are the only published PEL NGS data sets we can acquire for analysis.

View Article: PubMed Central - PubMed

ABSTRACT

The oncogenic Kaposi's sarcoma–associated herpesvirus (KSHV) is a principal causative agent of primary effusion lymphoma (PEL), which is mostly seen in immunosuppressed patients. PEL is a rapidly progressing malignancy with a median survival time of approximately 6 months even under the conventional chemotherapy. We recently report that the hepatocyte growth factor (HGF)/c-MET pathway is highly activated in PEL cells and represents a promising therapeutic target (Blood. 2015;126(26):2821-31). However, the underlying mechanisms of c-MET activation within PEL cells remain largely unknown. To solve this puzzle, here we have utilized the next generation sequencing (NGS) based bioinformatics approach to investigate the genomic landscape of the c-MET gene and we found that there's no single nucleotide variations (SNVs) occurred in the c-MET genomic regions in a cohort of PEL samples. Consistently, Sanger sequencing analysis of frequently mutated exons such as exon 10, 14 and 19 shows no mutation of these c-MET exons in PEL cell-lines, which further supports the notion that mutations are not the major mechanism responsible for c-MET activation in PEL. Further, we found that a transmembrane receptor protein, Plexin-B1, is expressed in PEL cell-lines, which is required for c-MET-mediated PEL cell survival via direct protein interaction.

No MeSH data available.


Related in: MedlinePlus