Utility of Circulating Cell-Free RNA Analysis for the Characterization of Global Transcriptome Profiles of Multiple Myeloma Patients

Chen, Maoshan; Mithraprabhu, Sridurga; Ramachandran, Malarmathy; Choi, Kawa; Khong, Tiffany; Spencer, Andrew

doi:10.3390/cancers11060887

Cited by 25 publications

(29 citation statements)

References 72 publications

(75 reference statements)

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“…TPM (transcripts per million reads mapped) method was used to normalize the gene expression for each sample. The numbers of reads aligned to Eucalyptus genes were calculated by htseq-count, as described [55].…”

Section: Genome Mapping and Gene Expression Pro Lingmentioning

confidence: 99%

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Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

Xiao

Zhang

et al. 2020

Preprint

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Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2,687 up-regulated and 2,581 down-regulated genes shared. Next, we identified 2,003 up-regulated and 1,958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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Section: Genome Mapping and Gene Expression Pro Lingmentioning

confidence: 99%

“…We next ltered the variants by the read depth (> 100) and obtained the nal variants for E. camaldulensis and E. grandis x urophylla samples. The variants were annotated by ANNOVAR, as previously described [55], and variants from noncoding regions and synonymous variants were discarded.…”

Section: Variant Callingmentioning

confidence: 99%

Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

Xiao

Zhang

et al. 2020

Preprint

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“…More recently, a study characterized the peripheral blood plasma transcriptomic profile of newly diagnosed and relapsed and refractory MM patients, and this was compared to that of healthy individuals [100]. The authors not only identified differences in the expression of protein-coding genes but also reported variations in the levels of some non-coding genes; these include antisense genes such as FAM83C-AS1, ZNF32-AS1, TMC3-AS1, and TAT-AS1, long intergenic noncoding RNA (LincRNA) such as LINC00863, LINC01123, LINC00349, LINC00677, and LINC00462, and microRNAs including miR-301A, miR-378H, miR-425, and miR-647 [100].…”

Section: Ev-ncrnas As Diagnostic and Prognostic Biomarkers In MMmentioning

confidence: 99%

Emerging Insights on the Biological Impact of Extracellular Vesicle-Associated ncRNAs in Multiple Myeloma

Raimondo

Urzì

Conigliaro

et al. 2020

ncRNA

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Increasing evidence indicates that extracellular vesicles (EVs) released from both tumor cells and the cells of the bone marrow microenvironment contribute to the pathobiology of multiple myeloma (MM). Recent studies on the mechanisms by which EVs exert their biological activity have indicated that the non-coding RNA (ncRNA) cargo is key in mediating their effect on MM development and progression. In this review, we will first discuss the role of EV-associated ncRNAs in different aspects of MM pathobiology, including proliferation, angiogenesis, bone disease development, and drug resistance. Finally, since ncRNAs carried by MM vesicles have also emerged as a promising tool for early diagnosis and therapy response prediction, we will report evidence of their potential use as clinical biomarkers.

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“…TPM (transcripts per million reads mapped) method was used to normalize the gene expression in each sample. Numbers of reads aligned to the Eucalyptus genes were calculated by htseq-count, as described [54].…”

Section: Genome Mapping and Gene Expression Pro Lingmentioning

confidence: 99%

“…We next ltered the variants by the read depth (> 100) and obtained the nal variants for E. camaldulensis and E. grandis x urophylla samples. The variants were annotated by ANNOVAR, as previously described [54], and variants from noncoding regions and synonymous variants were discarded based on the annotation.…”

Section: Variant Callingmentioning

confidence: 99%

Transcriptome Analysis Identifies Genes Involved in the Somatic Embryogenesis of Eucalyptus

Xiao

Zhang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood due to its increasing importance for fiber and energy in the word. Somatic embryogenesis is one method to provide large-scale commercial use for the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the SE of Eucalyptus on transcriptional level.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus cultivars – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). In total, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively. Comparison of DEGs showed that they shared 2,687 up-regulated and 2,581 down-regulated genes. Next, we found 2,003 up-regulated and 1,958 down-regulated genes specifically identified in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. Our results will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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Utility of Circulating Cell-Free RNA Analysis for the Characterization of Global Transcriptome Profiles of Multiple Myeloma Patients

Cited by 25 publications

References 72 publications

Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

Emerging Insights on the Biological Impact of Extracellular Vesicle-Associated ncRNAs in Multiple Myeloma

Transcriptome Analysis Identifies Genes Involved in the Somatic Embryogenesis of Eucalyptus

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