LARP1 isoform expression in human cancer cell lines

Schwenzer, Hagen; Mouti, Mai Abdel; Neubert, Pia; Morris, Josephine; Stockton, Joanne; Bonham, Sarah; Fellermeyer, Martin; Chettle, James; Fischer, Román; Beggs, Andrew D; Blagden, Sarah P.

doi:10.1080/15476286.2020.1744320

Cited by 15 publications

(10 citation statements)

References 44 publications

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“…500 ng of polyA+ RNA was used in conjunction with the direct RNA sequencing kit (Oxford Nanopore technologies, Oxford, UK [SQK-RNA002]). All protocol steps are as described in [ 37 ]. The reads were aligned to the human (GRCh37) and HPV18 (AY262282.1) genomes using minimap2 [ 38 ] with options “-ax splice -uf -k14” for nanopore direct RNA mapping.…”

Section: Methodsmentioning

confidence: 99%

The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression

et al. 2021

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The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have previously demonstrated that CTCF binds to the E2 open reading frame (ORF) of human papillomavirus (HPV) 18 and functions to repress viral oncogene expression in undifferentiated keratinocytes by co-ordinating an epigenetically repressed chromatin loop within HPV episomes. Keratinocyte differentiation disrupts CTCF-dependent chromatin looping of HPV18 episomes promoting induction of enhanced viral oncogene expression. To further characterise CTCF function in HPV transcription control we utilised direct, long-read Nanopore RNA-sequencing which provides information on the structure and abundance of full-length transcripts. Nanopore analysis of primary human keratinocytes containing HPV18 episomes before and after synchronous differentiation allowed quantification of viral transcript species, including the identification of low abundance novel transcripts. Comparison of transcripts produced in wild type HPV18 genome-containing cells to those identified in CTCF-binding deficient genome-containing cells identifies CTCF as a key regulator of differentiation-dependent late promoter activation, required for efficient E1^E4 and L1 protein expression. Furthermore, our data show that CTCF binding at the E2 ORF promotes usage of the downstream weak splice donor (SD) sites SD3165 and SD3284, to the dominant E4 splice acceptor site at nucleotide 3434. These findings demonstrate that in the HPV life cycle both early and late virus transcription programmes are facilitated by recruitment of CTCF to the E2 ORF.

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Section: Methodsmentioning

confidence: 99%

The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression

et al. 2021

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“…To confirm that LARP1 knockout by CRISPR-Cas9 induced a similar phenotype to siRNA knockdown, we compared the metabolism of LARP1-knockout clones to wild-type OVCAR-8 cells. Through monoclonal selection with puromycin, we thus generated two clones, expressing no full length LARP1 (albeit with low-level expression of the minor isoform of LARP1), 37 along with an additional clone which we confirmed to be genetically identical to wild-type, which we used an additional control for any phenotypic changes induced during the clonal selection process. ( Supplementary Figure 3c ).…”

Section: Resultsmentioning

confidence: 99%

LARP1 regulates metabolism and mTORC1 activity in cancer

Chettle

Dedeić

Fischer

et al. 2022

Preprint

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The protein mammalian target of rapamycin (mTOR) is a master regulator of cell homeostasis. Although mTOR is aberrantly overactivated in 70% ovarian cancers, mTOR cascade inhibitors (such as those blocking the kinase activity of mTOR itself or upstream kinases PI3K/AKT) have demonstrated disappointing activity in ovarian cancer clinical trials. These findings indicate that, despite its pivotal role in normal cells, hyperactivated mTOR does not act as a master regulator of metabolism in this cancer context. Surprisingly, we have identified that the RNA binding protein LARP1, a known phospho-target of mTORC1 and activator of ribosomal biogenesis, is responsible for metabolic reprogramming in mTOR-dysregulated cancers. LARP1 post-transcriptionally regulates the expression of several hundred rate-limiting enzymes involved in multiple aspects of metabolism, including glycolysis and oxidative phosphorylation. Through this mechanism LARP1 sustains ATP production and mTORC1 localisation on the lysosome, thereby activating cell proliferation despite the scarcity of extracellular nutrients. Our findings show that, by sustaining global cellular metabolism in response to growth factor signalling, LARP1 has a central post-transcriptional role in controlling mTORC1 localisation and driving cancer progression, a key cancer hallmark.

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“…These data suggest that the half-life of LARP1 and eIF4G1 proteins may be extended upon ARF or p53 depletion. Upregulation of LARP1 has been seen in many cancers [40][41][42] . Additionally, eIF4G1 is upregulated in many breast cancers 43,44 .…”

Section: Discussionmentioning

confidence: 99%

Upregulation of 5′-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor

Cottrell

Chiou

Weber

2020

Sci Rep

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Tumor cells require nominal increases in protein synthesis in order to maintain high proliferation rates. As such, tumor cells must acquire enhanced ribosome production. How the numerous mutations in tumor cells ultimately achieve this aberrant production is largely unknown. The gene encoding ARF is the most commonly deleted gene in human cancer. ARF plays a significant role in regulating ribosomal RNA synthesis and processing, ribosome export into the cytoplasm, and global protein synthesis. Utilizing ribosome profiling, we show that ARF is a major suppressor of 5′-terminal oligopyrimidine mRNA translation. Genes with increased translational efficiency following loss of ARF include many ribosomal proteins and translation factors. Knockout of p53 largely phenocopies ARF loss, with increased protein synthesis and expression of 5′-TOP encoded proteins. The 5′-TOP regulators eIF4G1 and LARP1 are upregulated in Arf- and p53-null cells.

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LARP1 isoform expression in human cancer cell lines

Cited by 15 publications

References 44 publications

The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression

The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression

LARP1 regulates metabolism and mTORC1 activity in cancer

Upregulation of 5′-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor

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