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Open Access Publications from the University of California

Scholarly Works (9 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2015)

Non-coding RNAs play pivotal roles in a wide variety of molecular processes. The functions of long non-coding RNAs (lncRNAs), in particular, have deep implications for both development and oncogenesis. Dysregulated expression of lncRNAs has been found in various cancers, but had not been comprehensively described in B lymphoblastic leukemia (B acute lymphoblastic leukemia; B-ALL). We completed a gene expression profiling study in human B-ALL samples and found differential lncRNA expression in samples with particular cytogenetic abnormalities. We determined that lncRNA expression could discriminate between B-ALL with specific karyotype abnormalities as well as, predict patient survival. Two promising lncRNAs from our study, designated B-ALL associated long RNAs (BALRs), have the highest expression in B-ALL samples carrying the MLL rearrangement when compared non-MLL rearranged and normal CD19+ cells. MLL rearranged B-ALL cases have a very poor prognosis and occur frequently in infants, making them particularly difficult to treat. This thesis investigates the role of lncRNAs BALR-2 and BALR-6 in MLL translocated B-ALL.

In the first part of this thesis work, we found that high expression of BALR-2 was correlated with diminished response to prednisone treatment. Knockdown led to a reduction in proliferation, increased apoptosis, and increased sensitivity to prednisolone treatment. Conversely, overexpression of the lncRNA caused increased cell growth and resistance to prednisone treatment. Remarkably, BALR-2 expression was repressed by prednisolone treatment and its dysregulation led to changes in the glucocorticoid response pathway in human and mouse B-cells. These findings indicate an important role for BALR-2 in the pathogenesis of B-ALL.

Much like BALR-2, siRNA mediated knockdown of BALR-6 in human B-ALL cell lines caused decreased proliferation and increased apoptosis. Additionally, overexpression of BALR-6 isoforms caused a significant increase in progenitor populations in mice and increased proliferation in mammalian cell lines. To understand the functional role of BALR-6, differential expression analysis from cell lines with knockdown was carried out. The analysis indicated an enrichment of genes involved in leukemia. Among these genes were SP1 and its known target genes. Luciferase reporter assays uncovered a positive regulatory role for BALR-6 in SP1 mediated transcription. Together, these data elucidate a role for BALR-6 in transcriptional regulation.

Thus, this thesis identifies novel non-coding RNA transcripts that regulate gene expression, and thereby pathogenesis in B-ALL with MLL rearrangement. This work suggests novel diagnostic, prognostic, and therapeutic utility for lncRNAs in B-ALL.

    Cover page: The Role of Long Non-coding RNAs in B-acute Lymphoblastic Leukemia
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2012)
    Abstract MicroRNAs are small RNA molecules that regulate gene expression and play critical roles in B cell development and malignancy. miRNA expression is important globally, as B cell specific knockouts of Dicer show profound defects in B cell development; and is also critical at the level of specific miRNAs. In this review, we discuss miRNAs that are involved in normal B cell development in the bone marrow and during B cell activation and terminal differentiation in the periphery. Next, we turn to miRNAs that are dysregulated during diseases of B cells, including malignant diseases and autoimmunity. Further study of miRNAs and their targets will lead to a better understanding of B cell development, and should also lead to the development of novel therapeutic strategies against B cell diseases.
      Cover page: MicroRNAs in B cell development and malignancy
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2019)
      Probiotics are considered to have multiple beneficial effects on the human gastrointestinal tract, including immunomodulation, pathogen inhibition, and improved host nutrient metabolism. However, extensive characterization of these properties is needed to define suitable clinical applications for probiotic candidates. Lactobacillus johnsonii 456 (LBJ 456) was previously demonstrated to have anti-inflammatory and anti-genotoxic effects in a mouse model. Here, we characterize its resistance to gastric and bile acids as well as its ability to inhibit gut pathogens and adhere to host mucosa. While bile resistance and in vitro host attachment properties of LBJ 456 were comparable to other tested probiotics, LBJ 456 maintained higher viability at lower pH conditions compared to other tested strains. LBJ 456 also altered pathogen adhesion to LS 174T monolayers and demonstrated contact-dependent and independent inhibition of pathogen growth. Genome analyses further revealed possible genetic elements involved in host attachment and pathogen inhibition. Importantly, we show that ingestion of Lactobacillus johnsonii 456 over a one week yogurt course leads to persistent viable bacteria detectable even beyond the period of initial ingestion, unlike many other previously described probiotic species of lactic acid bacteria.
        Cover page: A novel probiotic, Lactobacillus johnsonii 456, resists acid and can persist in the human gut beyond the initial ingestion period
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2015)
        miR-146a is a NF-κB induced microRNA that serves as a feedback regulator of this critical pathway. In mice, deficiency of miR-146a results in hematolymphoid cancer at advanced ages as a consequence of constitutive NF-κB activity. In this study, we queried whether the deficiency of miR-146a contributes to B-cell oncogenesis. Combining miR-146a deficiency with transgenic expression of c-Myc led to the development of highly aggressive B-cell malignancies. Mice transgenic for c-Myc and deficient for miR-146a were characterized by significantly shortened survival, increased lymph node involvement, differential involvement of the spleen and a mature B-cell phenotype. High-throughput sequencing of the tumors revealed significant dysregulation of approximately 250 genes. Amongst these, the transcription factor Egr1 was consistently upregulated in mice deficient for miR-146a. Interestingly, transcriptional targets of Egr1 were enriched in both the high-throughput dataset and in a larger set of miR-146a-deficient tumors. miR-146a overexpression led to downregulation of Egr1 and downstream targets with concomitant decrease in cell growth. Direct targeting of the human EGR1 by miR-146a was seen by luciferase assay. Together our findings illuminate a bona fide role for miR-146a in the modulation of B-cell oncogenesis and reveal the importance of understanding microRNA function in a cell- and disease-specific context.
          Cover page: MicroRNA-146a modulates B-cell oncogenesis by regulating Egr1
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2015)

          Unlabelled

          Long noncoding RNAs (lncRNA) have been found to play a role in gene regulation with dysregulated expression in various cancers. The precise role that lncRNA expression plays in the pathogenesis of B-acute lymphoblastic leukemia (B-ALL) is unknown. Therefore, unbiased microarray profiling was performed on human B-ALL specimens, and it was determined that lncRNA expression correlates with cytogenetic abnormalities, which was confirmed by qRT-PCR in a large set of B-ALL cases. Importantly, high expression of BALR-2 correlated with poor overall survival and diminished response to prednisone treatment. In line with a function for this lncRNA in regulating cell survival, BALR-2 knockdown led to reduced proliferation, increased apoptosis, and increased sensitivity to prednisolone treatment. Conversely, overexpression of BALR-2 led to increased cell growth and resistance to prednisone treatment. Interestingly, BALR-2 expression was repressed by prednisolone treatment and its knockdown led to upregulation of the glucocorticoid response pathway in both human and mouse B cells. Together, these findings indicate that BALR-2 plays a functional role in the pathogenesis and/or clinical responsiveness of B-ALL, and that altering the levels of particular lncRNAs may provide a future direction for therapeutic development.

          Implications

          lncRNA expression has the potential to segregate the common subtypes of B-ALL, predict the cytogenetic subtype, and indicate prognosis.
            Cover page: LncRNA Expression Discriminates Karyotype and Predicts Survival in B-Lymphoblastic Leukemia
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2015)

            Background

            A new class of non-coding RNAs, known as long non-coding RNAs (lncRNAs), has been recently described. These lncRNAs are implicated to play pivotal roles in various molecular processes, including development and oncogenesis. Gene expression profiling of human B-ALL samples showed differential lncRNA expression in samples with particular cytogenetic abnormalities. One of the most promising lncRNAs identified, designated B-ALL associated long RNA-6 (BALR-6), had the highest expression in patient samples carrying the MLL rearrangement, and is the focus of this study.

            Results

            Here, we performed a series of experiments to define the function of BALR-6, including several novel splice forms that we identified. Functionally, siRNA-mediated knockdown of BALR-6 in human B-ALL cell lines caused reduced cell proliferation and increased cell death. Conversely, overexpression of BALR-6 isoforms in both human and mouse cell lines caused increased proliferation and decreased apoptosis. Overexpression of BALR-6 in murine bone marrow transplantation experiments caused a significant increase in early hematopoietic progenitor populations, suggesting that its dysregulation may cause developmental changes. Notably, the knockdown of BALR-6 resulted in global dysregulation of gene expression. The gene set was enriched for leukemia-associated genes, as well as for the transcriptome regulated by Specificity Protein 1 (SP1). We confirmed changes in the expression of SP1, as well as its known interactor and downstream target CREB1. Luciferase reporter assays demonstrated an enhancement of SP1-mediated transcription in the presence of BALR-6. These data provide a putative mechanism for regulation by BALR-6 in B-ALL.

            Conclusions

            Our findings support a role for the novel lncRNA BALR-6 in promoting cell survival in B-ALL. Furthermore, this lncRNA influences gene expression in B-ALL in a manner consistent with a function in transcriptional regulation. Specifically, our findings suggest that BALR-6 expression regulates the transcriptome downstream of SP1, and that this may underlie the function of BALR-6 in B-ALL.
              Cover page: BALR-6 regulates cell growth and cell survival in B-lymphoblastic leukemia
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2017)

              Background

              Long non-coding RNAs (lncRNAs) play a variety of cellular roles, including regulation of transcription and translation, leading to alterations in gene expression. Some lncRNAs modulate the expression of chromosomally adjacent genes. Here, we assess the roles of the lncRNA CASC15 in regulation of a chromosomally nearby gene, SOX4, and its function in RUNX1/AML translocated leukemia.

              Results

              CASC15 is a conserved lncRNA that was upregulated in pediatric B-acute lymphoblastic leukemia (B-ALL) with t (12; 21) as well as pediatric acute myeloid leukemia (AML) with t (8; 21), both of which are associated with relatively better prognosis. Enforced expression of CASC15 led to a myeloid bias in development, and overall, decreased engraftment and colony formation. At the cellular level, CASC15 regulated cellular survival, proliferation, and the expression of its chromosomally adjacent gene, SOX4. Differentially regulated genes following CASC15 knockdown were enriched for predicted transcriptional targets of the Yin and Yang-1 (YY1) transcription factor. Interestingly, we found that CASC15 enhances YY1-mediated regulation of the SOX4 promoter.

              Conclusions

              Our findings represent the first characterization of this CASC15 in RUNX1-translocated leukemia, and point towards a mechanistic basis for its action.
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2021)
                Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control oncogenic transcriptional programs. Current approaches to identifying MTFs rely on ChIP-seq data, which is unavailable for many cancers. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes including predictions for cancer types/subtypes for which MTFs are unknown, including e.g. PAX8, SOX17, and MECOM as candidates in ovarian cancer (OvCa). In OvCa cells, consistent with known MTF properties, these factors are required for viability, lie proximal to superenhancers, co-occupy regulatory elements globally, co-bind loci encoding OvCa biomarkers, and are sensitive to pharmacologic inhibition of transcription. Our predictions of MTFs, especially for tumor types with limited understanding of transcriptional drivers, pave the way to therapeutic targeting of MTFs in a broad spectrum of cancers.
                  Cover page: Predicting master transcription factors from pan-cancer expression data
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2019)

                  Objective

                  Genome-wide association studies (GWASs) for epithelial ovarian cancer (EOC) have focused largely on populations of European ancestry. We aimed to identify common germline variants associated with EOC risk in Asian women.

                  Methods

                  Genotyping was performed as part of the OncoArray project. Samples with >60% Asian ancestry were included in the analysis. Genotyping was performed on 533,631 SNPs in 3238 Asian subjects diagnosed with invasive or borderline EOC and 4083 unaffected controls. After imputation, genotypes were available for 11,595,112 SNPs to identify associations.

                  Results

                  At chromosome 6p25.2, SNP rs7748275 was associated with risk of serous EOC (odds ratio [OR] = 1.34, P = 8.7 × 10-9) and high-grade serous EOC (HGSOC) (OR = 1.34, P = 4.3 × 10-9). SNP rs6902488 at 6p25.2 (r2 = 0.97 with rs7748275) lies in an active enhancer and is predicted to impact binding of STAT3, P300 and ELF1. We identified additional risk loci with low Bayesian false discovery probability (BFDP) scores, indicating they are likely to be true risk associations (BFDP <10%). At chromosome 20q11.22, rs74272064 was associated with HGSOC risk (OR = 1.27, P = 9.0 × 10-8). Overall EOC risk was associated with rs10260419 at chromosome 7p21.3 (OR = 1.33, P = 1.2 × 10-7) and rs74917072 at chromosome 2q37.3 (OR = 1.25, P = 4.7 × 10-7). At 2q37.3, expression quantitative trait locus analysis in 404 HGSOC tissues identified ESPNL as a putative candidate susceptibility gene (P = 1.2 × 10-7).

                  Conclusion

                  While some risk loci were shared between East Asian and European populations, others were population-specific, indicating that the landscape of EOC risk in Asian women has both shared and unique features compared to women of European ancestry.
                    Cover page: Genome-wide association studies identify susceptibility loci for epithelial ovarian cancer in east Asian women
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