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Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients.

Lim EL, Trinh DL, Scott DW, Chu A, Krzywinski M, Zhao Y, Robertson AG, Mungall AJ, Schein J, Boyle M, Mottok A, Ennishi D, Johnson NA, Steidl C, Connors JM, Morin RD, Gascoyne RD, Marra MA - Genome Biol. (2015)

Bottom Line: Of these 25 miRNAs, six miRNAs are significantly associated with survival in our validation cohort.Abundant expression of miR-28-5p, miR-214-5p, miR-339-3p, and miR-5586-5p is associated with superior outcome, while abundant expression of miR-324-5p and NOVELM00203M is associated with inferior outcome.Our comprehensive sequence analysis of the DLBCL miRNome identifies candidate novel miRNAs and miRNAs associated with survival, reinforces results from previous mutational analyses, and reveals regulatory networks of significance for lymphomagenesis.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue samples for validation.

Results: We identify known and candidate novel miRNAs, 25 of which are associated with survival independently of cell-of-origin and International Prognostic Index scores, which are established indicators of outcome. Of these 25 miRNAs, six miRNAs are significantly associated with survival in our validation cohort. Abundant expression of miR-28-5p, miR-214-5p, miR-339-3p, and miR-5586-5p is associated with superior outcome, while abundant expression of miR-324-5p and NOVELM00203M is associated with inferior outcome. Comparison of DLBCL miRNA-seq expression profiles with those from other cancer types identifies miRNAs that were more abundant in B-cell contexts. Unsupervised clustering of miRNAs identifies two clusters of patients that have distinct differences in their outcomes. Our integrative miRNA and mRNA expression analyses reveal that miRNAs increased in abundance in DLBCL appear to regulate the expression of genes involved in metabolism, cell cycle, and protein modification. Additionally, these miRNAs, including one candidate novel miRNA, miR-10393-3p, appear to target chromatin modification genes that are frequent targets of somatic mutation in non-Hodgkin lymphomas.

Conclusions: Our comprehensive sequence analysis of the DLBCL miRNome identifies candidate novel miRNAs and miRNAs associated with survival, reinforces results from previous mutational analyses, and reveals regulatory networks of significance for lymphomagenesis.

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Profiling miRNA in DLBCL. (a) miRNA sequence analysis identifies several small RNA species, with the majority of reads aligning to miRNA loci. The pie chart depicts the proportion and origin of miRNA-seq aligned reads. Reported proportions are averaged across the 92 DLBCL and 15 centroblast libraries. (b) Expression of candidate novel miRNA across DLBCL and centroblast libraries. Column labels represent the type of sample: Dark Blue: ABC-DLBCL; Light Blue: GCB-DLBCL; Gray: Unclassified-DLBCL; Orange: Centroblasts. Row labels are annotated to indicate whether the miRNA was more abundantly expressed in a sample category. (c) Expression of B-cell enriched candidate novel miRNAs (NOVELM00010M, miR-10398-3p and NOVELM00260M) in DLBCL, centroblasts, and other cancers. BLCA: bladder urothelial carcinoma; BRCA: breast invasive carcinoma; CESC: cervical squamous cell carcinoma and endocervical adenocarcinoma; COAD: colon adenocarcinoma; HNSC: head and neck squamous cell carcinoma; KICH: kidney chromophobe; KIRC: kidney renal clear cell carcinoma; KIRP: kidney renal papillary cell carcinoma; LGG: brain lower grade glioma; LIHC: liver hepatocellular carcinoma; LUAD: lung adenocarcinoma; LUSC: lung squamous cell carcinoma; OV: ovarian serous cystadenocarcinoma; PAAD: pancreatic adenocarcinoma; PRAD: prostate adenocarcinoma; READ: rectum adenocarcinoma; SARC: sarcoma; SKCM: skin cutaneous melanoma; STAD: stomach adenocarcinoma; THCA: thyroid carcinoma; UCEC: uterine corpus endometrial carcinoma. Blue: DLBCL; Orange: Centroblast.
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Fig1: Profiling miRNA in DLBCL. (a) miRNA sequence analysis identifies several small RNA species, with the majority of reads aligning to miRNA loci. The pie chart depicts the proportion and origin of miRNA-seq aligned reads. Reported proportions are averaged across the 92 DLBCL and 15 centroblast libraries. (b) Expression of candidate novel miRNA across DLBCL and centroblast libraries. Column labels represent the type of sample: Dark Blue: ABC-DLBCL; Light Blue: GCB-DLBCL; Gray: Unclassified-DLBCL; Orange: Centroblasts. Row labels are annotated to indicate whether the miRNA was more abundantly expressed in a sample category. (c) Expression of B-cell enriched candidate novel miRNAs (NOVELM00010M, miR-10398-3p and NOVELM00260M) in DLBCL, centroblasts, and other cancers. BLCA: bladder urothelial carcinoma; BRCA: breast invasive carcinoma; CESC: cervical squamous cell carcinoma and endocervical adenocarcinoma; COAD: colon adenocarcinoma; HNSC: head and neck squamous cell carcinoma; KICH: kidney chromophobe; KIRC: kidney renal clear cell carcinoma; KIRP: kidney renal papillary cell carcinoma; LGG: brain lower grade glioma; LIHC: liver hepatocellular carcinoma; LUAD: lung adenocarcinoma; LUSC: lung squamous cell carcinoma; OV: ovarian serous cystadenocarcinoma; PAAD: pancreatic adenocarcinoma; PRAD: prostate adenocarcinoma; READ: rectum adenocarcinoma; SARC: sarcoma; SKCM: skin cutaneous melanoma; STAD: stomach adenocarcinoma; THCA: thyroid carcinoma; UCEC: uterine corpus endometrial carcinoma. Blue: DLBCL; Orange: Centroblast.

Mentions: We observed that 310 known miRNAs (3p or 5p strands of 221 miRNA species in miRBase version 19) were expressed at levels of at least 10 reads per million (RPM) in at least 10% of the samples. Our threshold for calling expressed miRNAs (>10 RPM in >10% samples) was based on miRBase criteria [16] for high confidence miRNAs. In addition to miRNAs, which accounted for 60% of the aligned miRNA-seq reads, our pipeline also identified the expression of other classes of small RNAs. For example, an average of 9% of the aligned reads mapped to rRNAs and 6% to snoRNAs. Other non-coding RNAs (tRNAs, snRNAs, scRNAs) and DNA repeat elements were represented by fewer reads (FigureĀ 1a; Additional file 3: Table S3).Figure 1


Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients.

Lim EL, Trinh DL, Scott DW, Chu A, Krzywinski M, Zhao Y, Robertson AG, Mungall AJ, Schein J, Boyle M, Mottok A, Ennishi D, Johnson NA, Steidl C, Connors JM, Morin RD, Gascoyne RD, Marra MA - Genome Biol. (2015)

Profiling miRNA in DLBCL. (a) miRNA sequence analysis identifies several small RNA species, with the majority of reads aligning to miRNA loci. The pie chart depicts the proportion and origin of miRNA-seq aligned reads. Reported proportions are averaged across the 92 DLBCL and 15 centroblast libraries. (b) Expression of candidate novel miRNA across DLBCL and centroblast libraries. Column labels represent the type of sample: Dark Blue: ABC-DLBCL; Light Blue: GCB-DLBCL; Gray: Unclassified-DLBCL; Orange: Centroblasts. Row labels are annotated to indicate whether the miRNA was more abundantly expressed in a sample category. (c) Expression of B-cell enriched candidate novel miRNAs (NOVELM00010M, miR-10398-3p and NOVELM00260M) in DLBCL, centroblasts, and other cancers. BLCA: bladder urothelial carcinoma; BRCA: breast invasive carcinoma; CESC: cervical squamous cell carcinoma and endocervical adenocarcinoma; COAD: colon adenocarcinoma; HNSC: head and neck squamous cell carcinoma; KICH: kidney chromophobe; KIRC: kidney renal clear cell carcinoma; KIRP: kidney renal papillary cell carcinoma; LGG: brain lower grade glioma; LIHC: liver hepatocellular carcinoma; LUAD: lung adenocarcinoma; LUSC: lung squamous cell carcinoma; OV: ovarian serous cystadenocarcinoma; PAAD: pancreatic adenocarcinoma; PRAD: prostate adenocarcinoma; READ: rectum adenocarcinoma; SARC: sarcoma; SKCM: skin cutaneous melanoma; STAD: stomach adenocarcinoma; THCA: thyroid carcinoma; UCEC: uterine corpus endometrial carcinoma. Blue: DLBCL; Orange: Centroblast.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4308918&req=5

Fig1: Profiling miRNA in DLBCL. (a) miRNA sequence analysis identifies several small RNA species, with the majority of reads aligning to miRNA loci. The pie chart depicts the proportion and origin of miRNA-seq aligned reads. Reported proportions are averaged across the 92 DLBCL and 15 centroblast libraries. (b) Expression of candidate novel miRNA across DLBCL and centroblast libraries. Column labels represent the type of sample: Dark Blue: ABC-DLBCL; Light Blue: GCB-DLBCL; Gray: Unclassified-DLBCL; Orange: Centroblasts. Row labels are annotated to indicate whether the miRNA was more abundantly expressed in a sample category. (c) Expression of B-cell enriched candidate novel miRNAs (NOVELM00010M, miR-10398-3p and NOVELM00260M) in DLBCL, centroblasts, and other cancers. BLCA: bladder urothelial carcinoma; BRCA: breast invasive carcinoma; CESC: cervical squamous cell carcinoma and endocervical adenocarcinoma; COAD: colon adenocarcinoma; HNSC: head and neck squamous cell carcinoma; KICH: kidney chromophobe; KIRC: kidney renal clear cell carcinoma; KIRP: kidney renal papillary cell carcinoma; LGG: brain lower grade glioma; LIHC: liver hepatocellular carcinoma; LUAD: lung adenocarcinoma; LUSC: lung squamous cell carcinoma; OV: ovarian serous cystadenocarcinoma; PAAD: pancreatic adenocarcinoma; PRAD: prostate adenocarcinoma; READ: rectum adenocarcinoma; SARC: sarcoma; SKCM: skin cutaneous melanoma; STAD: stomach adenocarcinoma; THCA: thyroid carcinoma; UCEC: uterine corpus endometrial carcinoma. Blue: DLBCL; Orange: Centroblast.
Mentions: We observed that 310 known miRNAs (3p or 5p strands of 221 miRNA species in miRBase version 19) were expressed at levels of at least 10 reads per million (RPM) in at least 10% of the samples. Our threshold for calling expressed miRNAs (>10 RPM in >10% samples) was based on miRBase criteria [16] for high confidence miRNAs. In addition to miRNAs, which accounted for 60% of the aligned miRNA-seq reads, our pipeline also identified the expression of other classes of small RNAs. For example, an average of 9% of the aligned reads mapped to rRNAs and 6% to snoRNAs. Other non-coding RNAs (tRNAs, snRNAs, scRNAs) and DNA repeat elements were represented by fewer reads (FigureĀ 1a; Additional file 3: Table S3).Figure 1

Bottom Line: Of these 25 miRNAs, six miRNAs are significantly associated with survival in our validation cohort.Abundant expression of miR-28-5p, miR-214-5p, miR-339-3p, and miR-5586-5p is associated with superior outcome, while abundant expression of miR-324-5p and NOVELM00203M is associated with inferior outcome.Our comprehensive sequence analysis of the DLBCL miRNome identifies candidate novel miRNAs and miRNAs associated with survival, reinforces results from previous mutational analyses, and reveals regulatory networks of significance for lymphomagenesis.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue samples for validation.

Results: We identify known and candidate novel miRNAs, 25 of which are associated with survival independently of cell-of-origin and International Prognostic Index scores, which are established indicators of outcome. Of these 25 miRNAs, six miRNAs are significantly associated with survival in our validation cohort. Abundant expression of miR-28-5p, miR-214-5p, miR-339-3p, and miR-5586-5p is associated with superior outcome, while abundant expression of miR-324-5p and NOVELM00203M is associated with inferior outcome. Comparison of DLBCL miRNA-seq expression profiles with those from other cancer types identifies miRNAs that were more abundant in B-cell contexts. Unsupervised clustering of miRNAs identifies two clusters of patients that have distinct differences in their outcomes. Our integrative miRNA and mRNA expression analyses reveal that miRNAs increased in abundance in DLBCL appear to regulate the expression of genes involved in metabolism, cell cycle, and protein modification. Additionally, these miRNAs, including one candidate novel miRNA, miR-10393-3p, appear to target chromatin modification genes that are frequent targets of somatic mutation in non-Hodgkin lymphomas.

Conclusions: Our comprehensive sequence analysis of the DLBCL miRNome identifies candidate novel miRNAs and miRNAs associated with survival, reinforces results from previous mutational analyses, and reveals regulatory networks of significance for lymphomagenesis.

Show MeSH
Related in: MedlinePlus