DOI: 10.5061/dryad.18931zdb1
title: LARP1 drives steatosis to hepatocellular carcinoma progression in MASH mouse models

description: Background: This study focuses on the role of an RNA binding protein,
 La-related protein 1 or LARP1 in progression of metabolic
 dysfunction–associated steatotic liver disease (MASLD). A knockout mouse
 model of the S-adenosylmethionine (SAMe) synthetic enzyme, methionine
 adenosyltransferase 1A (Mat1a-KO) spontaneously develops MASH and
 progresses to HCC. We discovered that LARP1 is strongly induced in Mat1a
 KO during the MASH stage (Ramani 2022, PMC8766892). RNA‑sequencing from
 LARP1‑overexpressing liver cancer cells and from Larp1‑silenced Mat1a KOs
 revealed that LARP1 regulates mRNAs controlling key metabolic pathways,
 including peroxisomal β‑oxidation (Sirtuin 5, SIRT5), aerobic glycolysis
 (c‑MYC), and oxidative phosphorylation/mitochondrial ribosomal proteins
 (MRPL13, MRPL50, MRPL59). This dataset is bulk RNA sequencing data from
 the above studies.  Our findings from RNA sequencing reveal a
 novel role for LARP1 in regulating metabolic pathways associated with
 MASLD progression through its dysregulation of key mRNAs involved in these
 pathways.
description: Experiment 1: Total RNA from human Huh7 liver cancer cells
 overexpressing an empty vector (EV) or a LARP1 vector was subject to
 polyribosome profiling to separate the actively translating ribosomal
 fraction and the non-translating fraction (NTR). The NTR and polysome
 fractions from EV or LARP1 OV groups was submitted for RNA sequencing (BGI
 Americas Inc.) and Poisson distribution and DEGseq2 analysis was performed
 on the same using human reference (GCF_000001405.38_GRCh38.p12).
 Experiment 2: Total RNA was isolated from the livers of WT (CAS),
 Mat1a KO, and Mat1a KO mice injected with a Larp1 CRISPR silencing vector
 (Larp1 si). Bulk RNA sequencing was performed as in experiment 1 and
 Poisson distribution and DEGseq2 analysis was performed by using mouse
 reference (Mus_musculus_NCBI_GCF_000001635.27_GRCm39).
description: # LARP1 drives steatosis to hepatocellular carcinoma progression in MASH
 mouse models **Dataset DOI:**
 **[10.5061/dryad.18931zdb1](https://doi.org/10.5061/dryad.18931zdb1)**
 **Description of the data and file structure** The purpose of this RNA
 sequencing data is to identify mRNA targets of LARP1 that are dysregulated
 in MASLD mouse models and are reversed when LARP1 is silenced. Two kinds
 of data are presented. The first experiment shows that forced expression
 of LARP1 in liver cancer cell lines changes the translationally active
 polyribosomal fraction of mRNAs. The second experiment silences LARP1 in
 the Mat1a KO, a MASLD mouse model and demonstrates that this modulates
 LARP1's mRNA targets in the liver. **Files and variables** **File:
 expt_1_raw_FPKM.csv** **Description:** This file contains raw Fragments
 Per Kilobase of transcript per Million mapped reads or FPKM values of each
 mRNA from polyribosome and non-translating fractions of Huh7 liver cancer
 cells overexpressing LARP1 or an empty vector **Variables** * Gene Symbol:
 Gene symbols are the symbol of the gene corresponding to each mRNA. *
 Transcripts ID: Transcript ID is the ID of the transcripts or mRNAs
 encoded by each gene symbol. * Type: Is the type of molecule, in this case
 it is messenger RNA or mRNA * 1_CTRL FPKM: FPKM values of non-translating
 fraction mRNA obtained from polyribosome profiling of RNA from Huh7 cells
 transfected with empty vector (EV). * 2_CTRL FPKM: FPKM values of
 non-translating fraction mRNA obtained from polyribosome profiling of RNA
 from Huh7 cells transfected with empty vector (EV). * 5_CTRL FPKM: FPKM
 values of polyribosomal fraction mRNA obtained from polyribosome profiling
 of RNA from Huh7 cells transfected with empty vector (EV) * 6_CTRL
 FPKM: FPKM values of polyribosomal fraction mRNA obtained from
 polyribosome profiling of RNA from Huh7 cells transfected with empty
 vector (EV) * C_3 FPKM: FPKM values of non-translating fraction obtained
 from polyribosome profiling of RNA from Huh7 cells transfected with LARP1
 vector (LARP1 OV) * C_4 FPKM: FPKM values of non-translating fraction
 obtained from polyribosome profiling of RNA from Huh7 cells transfected
 with LARP1 vector (LARP1 OV) * C_7 FPKM: FPKM values of polyribosomal
 fraction obtained from polyribosome profiling of RNA from Huh7 cells
 transfected with LARP1 vector (LARP1 OV) * C_8 FPKM: FPKM values of
 polyribosomal fraction obtained from polyribosome profiling of RNA from
 Huh7 cells transfected with LARP1 vector (LARP1 OV) * 3_4_case Average
 FPKM: Average FPKM value of two replicates (**C_3 FPKM and C_4 FPKM**) of
 non-translating fraction obtained from polyribosome profiling of RNA from
 Huh7 cells transfected with LARP1 vector (LARP1 OV) * 5_6_CTRL Average
 FPKM: Average FPKM value of two replicates (**5_CTRL FPKM and 6_CTRL
 FPKM**) of polyribosomal fraction mRNA obtained from polyribosome
 profiling of RNA from Huh7 cells transfected with empty vector (EV) *
 7_8_case Average FPKM: Average FPKM value of two replicates (**C_7 FPKM
 and C_8 FPKM**) of polyribosomal fraction obtained from polyribosome
 profiling of RNA from Huh7 cells transfected with LARP1 vector (LARP1 OV)
 * 1_2_CTRL Average FPKM: Average FPKM value of two replicates (**1_CTRL
 FPKM and 2_CTRL FPKM**) of non-translating fraction mRNA obtained from
 polyribosome profiling of RNA from Huh7 cells transfected with empty
 vector (EV). **File: expt_2_raw_FPKM.csv** **Description:** This file
 contains raw Fragments Per Kilobase of transcript per Million mapped reads
 or FPKM of mRNAs from livers of wild type (WT), MAT1A KO, and MAT1A KO
 with Larp1 silencing (Larp1 si). CR1, 2, 3,7,8,9 are WT liver mRNA.
 CR4,5,6 are MAT1A KO liver mRNA. CR10,11,12,13,14 are MAT1A KO+Larp1 Si
 liver mRNAs. **Variables** * RNA ID: The accession number of the RNA *
 Symbol:Gene symbols are the symbol of the gene corresponding to each mRNA.
 * Type: Is the type of molecule, in this case it is messenger RNA or mRNA
 * CR1 FPKM: FPKM value of mRNA from WT liver injected with a CAS empty
 vector * CR2 FPKM: FPKM value of mRNA from WT liver injected with a CAS
 empty vector * CR3 FPKM: FPKM value of mRNA from WT liver injected with a
 CAS empty vector * CR4 FPKM: FPKM value of mRNA from Mat1a KO liver * CR5
 FPKM: FPKM value of mRNA from Mat1a KO liver * CR6 FPKM: FPKM value of
 mRNA from Mat1a KO liver * CR7 FPKM: FPKM value of mRNA from WT liver
 injected with a CAS empty vector * CR8 FPKM: FPKM value of mRNA from WT
 liver injected with a CAS empty vector * CR9 FPKM: FPKM value of mRNA from
 WT liver injected with a CAS empty vector * CR10 FPKM: FPKM value of mRNA
 from Mat1a KO liver injected with Larp1 si vector * CR11 FPKM: FPKM value
 of mRNA from Mat1a KO liver injected with Larp1 si vector * CR12
 FPKM: FPKM value of mRNA from Mat1a KO liver injected with Larp1 si vector
 * CR13 FPKM: FPKM value of mRNA from Mat1a KO liver injected with Larp1 si
 vector * CR14 FPKM: FPKM value of mRNA from Mat1a KO liver injected with
 Larp1 si vector **File: Log2FC_dyrad_submission.xlsx**
 **Description:** This excel file contains the key definitions and the
 calculatable log2 (fold change) or Log2 (FC) comparing FPKM values of
 different groups in experiments 1 and 2 using DEGSEQ2 analysis method.
 Cells in which the values were not calculatable are marked as N/A.
 **Variables** * Log2FC expt 1: * EV (polysome/NTR) log2FC: The log of fold
 change (FC) of polysomal mRNA versus non-translating mRNA fraction from
 empty vector transfected Huh7 cells.   * LARP1 OV (polysome/NTR) log2FC:
 The log of fold change (FC) of polysomal mRNA versus non-translating mRNA
 fraction   from LARP1 OV transfected Huh7 cells      * EV (polysome/NTR) P
 value: P value of comparison of polysome to NTR in EV samples   * LARP1 OV
 (polysome/NTR) P value P value of comparison of polysome to NTR in LARP1
 OV samples   * Log2FC expt 2: * Mat1a-KO vs. WT (log2 (CASE_1 / CTRL):
 Log2Fold change of Mat1a KO total liver RNA compared to WT livers. *
 Mat1a-KO+Larp1 si vs. WT (log2 (CASE_2 / CTRL): Log2Fold change of Mat1a
 KO+Larp1 si total liver RNA compared to WT livers. * Pvalue(CASE_1 /
 CTRL)   - Statistical P value for Mat1a-KO vs WT log2FC * Pvalue(CASE_2/
 CTRL)-Statistical P value for Mat1a-KO+Larp1 si vs. WT log2FC  
 **Code/software** To access CSV or excel files, microsoft excel is needed.
 **Access information** Other publicly accessible locations of the data: *
 None Data was derived from the following sources: * Data was derived from
 RNA sequencing run by BGI Americas Inc. (Cambridge MA) from 2022-2023.