Loss‐of‐Function Genetic Screening Identifies Aldolase A as an Essential Driver for Liver Cancer Cell Growth Under Hypoxia

Abstract

Accepted ArticleThis article is protected by copyright. All rights reserved Hypoxia is a common feature of tumor microenvironment (TME), which promotes tumor progression, metastasis and therapeutic drug resistance via a myriad of cell activities in tumor and stroma cells. While targeting hypoxic TME is emerging as a promising strategy for treating solid tumors, preclinical development of this approach is lacking in the study of hepatocellular carcinoma (HCC). From a genome-wide CRISPR/Cas9 gene knockout screening, we identified aldolase A (ALDOA), a key enzyme in glycolysis and gluconeogenesis, as an essential driver for HCC cell growth under hypoxia. Knockdown of ALDOA in HCC cells leads to lactate depletion, and consequently inhibits tumor growth. Supplementation of lactate partly rescues the inhibitory effects mediated by ALDOA knockdown. Upon hypoxia, ALDOA is induced by HIF-1α and FTO-mediated m6A modification through transcriptional and post-transcriptional regulation, respectively. Analysis of TCGA shows that elevated levels of ALDOA are significantly correlated with poor prognosis of HCC patients. In a screen of FDA-approved drugs based on structured hierarchical virtual platforms, we identify sulfamonomethoxine derivative cpd-5 as a potential inhibitor to target ALDOA, evidenced by the anti-tumor activity of cpd-5 in preclinical patient-derived xenograft models of HCC. Conclusion:Our work identifies ALDOA as an essential driver for HCC cell growth under hypoxia, and we demonstrate that inhibition of ALDOA in hypoxic TME is a promising therapeutic strategy for treating HCC.

Measurement of Circulating Tumor Cells to Track Hepatocellular Carcinoma Progression After Liver Transplantation-Case Report

“…Subsequently, cell were incubated with Goat polyclonal Secondary Antibody to Mouse IgG H&L (Alexa Fluor ® 488) (ab150113, Abcam, USA) preadsorbed at 1/1000 dilution, Goat polyclonal Secondary Antibody to Rabbit IgG - H&L (Alexa Fluor ® 594) (ab150080, Abcam, USA) at 1/1000 dilution and Nuclear DNA was labelled with DAPI for 1 hour. Image was acquired with Fluorescence inverted microscope (Nikon Ti2, Japan) ( 8 ).…”

N6-Methyladenosine RNA Modification: An Emerging Immunotherapeutic Approach to Turning Up Cold Tumors

“…Mechanistically, FTO increases metabolic reprogramming and survival of VHL-deficient ccRCC cells by targeting SLC1A5 in a hypoxia-inducible factor (HIF)independent way (Xiao et al, 2020). Furthermore, Niu et al (2021) recently showed that the posttranscriptional regulation of the abnormal expression of aldolase A (ALDOA) under hypoxia was positively modulated by FTO-mediated m 6 A RNA modification in a YTHDF2-dependent manner in liver cancer cells, and hypoxia-mediated high level of ALDOA contributed to liver cancer development by promoting glycolysis metabolism and its terminal product lactate expression. Additionally, FTO promotes tumor cell glycolysis by activating PI3K/AKT signaling or in a YTHDF2-dependent manner (Liu et al, 2017;Liu et al, 2021d).…”

The Contextual Essentiality of Mitochondrial Genes in Cancer

“…Many of these essential NEMGs have also been identified in other studies where single cell line genome-wide CRISPR-Cas9 deletion screens have been undertaken, using different cancer cell lines (Arroyo et al, 2016;Jain et al, 2016;Bao et al, 2021;Niu et al, 2021;Thomas et al, 2021). Interestingly, while there is broad pathway-level agreement between these independent studies, there is little gene-to-gene agreement, and in some cases, gene hits identified from the CRISPR-Cas9 deletion screen could not be verified in validation experiments using the primary screening cell line or additional cell lines (Jain et al, 2020).…”

“…The DepMap project (Tsherniak et al, 2017), and other independent genome-wide CRISPR-Cas9 deletion screens (e.g., To et al, 2019), constitute powerful resources for understanding gene essentiality in cancer cells. However, only a few screens use culture conditions that reflect features of the (solid) tumor microenvironment (TME) (Arroyo et al, 2016;Jain et al, 2020;Bao et al, 2021;Niu et al, 2021;Thomas et al, 2021). The TME is central to promoting tumorigenesis and disease progression, and comprises features that are distinct from surrounding normal tissue (Egeblad et al, 2010;Elia and Haigis, 2021).…”

“…To mimic conditions of the TME, several recent genomewide CRISPR-Cas9 deletion screens have been carried out under conditions of hypoxia (Jain et al, 2020;Bao et al, 2021;Niu et al, 2021;Thomas et al, 2021), or glucose deprivation (Arroyo et al, 2016;Thomas et al, 2021), using different cancer cell types. Importantly, while there are differences in the essentiality of specific genes identified between studies, there is broad agreement in the findings across these studies showing that the essentiality of both non-mitochondrial and mitochondrial genes is dependent on the environmental context in which cells are cultured (Figure 2).…”