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Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes.

Liang F, Qu H, Lin Q, Yang Y, Ruan X, Zhang B, Liu Y, Yu C, Zhang H, Fang X, Hao X - World J Surg Oncol (2015)

Bottom Line: Among them, FABP1 (negative group) and CYP2A13 (positive group) were the only 2 protein-encoding genes with expression levels in the 8th to 10th deciles.Using a false discovery rate threshold of <0.05, 62 up-regulated genes and 98 down-regulated genes were discovered in the NSLN positive group.Furthermore, 10 gene fusions were identified in this group with the most frequently fused gene being IGLL5.

View Article: PubMed Central - PubMed

Affiliation: Affiliated Hospital of Academy of Military Medical Sciences, 8 Dongdajie, Fengtai District, Beijing, 100071, China. lfpeakcool@126.com.

ABSTRACT

Background: Non-sentinel lymph node (NSLN) status prediction with molecular biomarkers may make some sentinel lymph node (SLN) positive breast cancer patients avoid the axillary lymph node dissection, but the available markers remain limited.

Methods: SLN positive patients with and without NSLN invasion were selected, and genes differentially expressed or fused in SLN metastasis were screened by next-generation RNA sequencing.

Results: Six candidates (all ER/PR+, HER2-, Ki-67 <20%) with metastatic SLNs selected from 305 patients were equally categorized as NSLN negative and positive. We identified 103 specifically expressed genes in the NSLN negative group and 47 in the NSLN positive group. Among them, FABP1 (negative group) and CYP2A13 (positive group) were the only 2 protein-encoding genes with expression levels in the 8th to 10th deciles. Using a false discovery rate threshold of <0.05, 62 up-regulated genes and 98 down-regulated genes were discovered in the NSLN positive group. Furthermore, 10 gene fusions were identified in this group with the most frequently fused gene being IGLL5.

Conclusions: The biomarkers screened in present study may broaden our understanding of the mechanisms of breast cancer metastasis to the lymph nodes and contribute to the axillary surgery selection for SLN positive patients.

No MeSH data available.


Related in: MedlinePlus

Distribution of sequencing base quality. a Base quality of paired-end reads for NSLN negative group. b Base quality of paired-end reads for NSLN positive group. The base quality of sequencing reads was greater than 25 in five samples except for 67167 whose base quality was slightly lower (≥20)
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Fig1: Distribution of sequencing base quality. a Base quality of paired-end reads for NSLN negative group. b Base quality of paired-end reads for NSLN positive group. The base quality of sequencing reads was greater than 25 in five samples except for 67167 whose base quality was slightly lower (≥20)

Mentions: As showed in Additional file 1, the extracted RNA concentrations for each sample were all >100 ng/μl and their OD260/OD280 ratio ranged from 1.78 to 2.03, which ensured that the samples could be used for downstream experiments. We successfully generated cDNA libraries of 350–500 bp and obtained 18–27 million (range 18,549,392–27,137,861; mean 22,775,012) high-quality sequencing reads with a sequencing quality of >25 for each base in five samples and >20 in sample 67161 (Fig. 1). The raw sequence data has been deposited in a public repository (Gene Expression Omnibus (GEO)) with the access number GSE64850. After filtering the repetitive or very low complexity reads (0.16 % of the sequenced reads on average), we mapped an average of 52.27 % (range 19.57–67.22 %) of the reads to the human genome (UCSC version hg19) (Additional file 2).Fig. 1


Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes.

Liang F, Qu H, Lin Q, Yang Y, Ruan X, Zhang B, Liu Y, Yu C, Zhang H, Fang X, Hao X - World J Surg Oncol (2015)

Distribution of sequencing base quality. a Base quality of paired-end reads for NSLN negative group. b Base quality of paired-end reads for NSLN positive group. The base quality of sequencing reads was greater than 25 in five samples except for 67167 whose base quality was slightly lower (≥20)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4551378&req=5

Fig1: Distribution of sequencing base quality. a Base quality of paired-end reads for NSLN negative group. b Base quality of paired-end reads for NSLN positive group. The base quality of sequencing reads was greater than 25 in five samples except for 67167 whose base quality was slightly lower (≥20)
Mentions: As showed in Additional file 1, the extracted RNA concentrations for each sample were all >100 ng/μl and their OD260/OD280 ratio ranged from 1.78 to 2.03, which ensured that the samples could be used for downstream experiments. We successfully generated cDNA libraries of 350–500 bp and obtained 18–27 million (range 18,549,392–27,137,861; mean 22,775,012) high-quality sequencing reads with a sequencing quality of >25 for each base in five samples and >20 in sample 67161 (Fig. 1). The raw sequence data has been deposited in a public repository (Gene Expression Omnibus (GEO)) with the access number GSE64850. After filtering the repetitive or very low complexity reads (0.16 % of the sequenced reads on average), we mapped an average of 52.27 % (range 19.57–67.22 %) of the reads to the human genome (UCSC version hg19) (Additional file 2).Fig. 1

Bottom Line: Among them, FABP1 (negative group) and CYP2A13 (positive group) were the only 2 protein-encoding genes with expression levels in the 8th to 10th deciles.Using a false discovery rate threshold of <0.05, 62 up-regulated genes and 98 down-regulated genes were discovered in the NSLN positive group.Furthermore, 10 gene fusions were identified in this group with the most frequently fused gene being IGLL5.

View Article: PubMed Central - PubMed

Affiliation: Affiliated Hospital of Academy of Military Medical Sciences, 8 Dongdajie, Fengtai District, Beijing, 100071, China. lfpeakcool@126.com.

ABSTRACT

Background: Non-sentinel lymph node (NSLN) status prediction with molecular biomarkers may make some sentinel lymph node (SLN) positive breast cancer patients avoid the axillary lymph node dissection, but the available markers remain limited.

Methods: SLN positive patients with and without NSLN invasion were selected, and genes differentially expressed or fused in SLN metastasis were screened by next-generation RNA sequencing.

Results: Six candidates (all ER/PR+, HER2-, Ki-67 <20%) with metastatic SLNs selected from 305 patients were equally categorized as NSLN negative and positive. We identified 103 specifically expressed genes in the NSLN negative group and 47 in the NSLN positive group. Among them, FABP1 (negative group) and CYP2A13 (positive group) were the only 2 protein-encoding genes with expression levels in the 8th to 10th deciles. Using a false discovery rate threshold of <0.05, 62 up-regulated genes and 98 down-regulated genes were discovered in the NSLN positive group. Furthermore, 10 gene fusions were identified in this group with the most frequently fused gene being IGLL5.

Conclusions: The biomarkers screened in present study may broaden our understanding of the mechanisms of breast cancer metastasis to the lymph nodes and contribute to the axillary surgery selection for SLN positive patients.

No MeSH data available.


Related in: MedlinePlus