Journal: Nature

Article Title: ACLY inhibition promotes tumour immunity and suppresses liver cancer

doi: 10.1038/s41586-025-09297-0

Figure Lengend Snippet: a , Volcano plot of bulk RNA-seq of tumours showing upregulated and downregulated genes at early or late timepoints from Acly- KO ( n = 12) versus WT ( n = 9) mice. Significance was determined by Wald test with a false discovery-adjusted threshold of 5% as implemented in DESeq2. Horizontal dashed lines demarcate the P value threshold at a 5% false discovery rate (FDR). b , Gene Ontology analysis of selected biological processes involving significantly upregulated genes in tumours from Acly -KO ( n = 12) versus WT ( n = 9) mice. FC, fold change. c , Top 10 Gene Ontology biological processes (GOBP) from clusters identified among significantly upregulated gene sets in tumours from Acly -KO ( n = 12) versus WT ( n = 9) mice. NES, normalized enrichment score. d , Correlation between B cell populations and Acly expression in tumours from WT ( n = 9) and Acly -KO ( n = 12) mice. Confidence bands denote the upper and lower bounds of the 95% confidence interval. Significance of association was determined by a two-sided Student’s t -test of regression coefficients and at a false discovery-adjusted threshold of 5%. e – p , Spatial transcriptomic analysis of livers from WT and Acly -KO mice and vehicle or EVT0185-treated mice. Cluster analysis representing the number of cell types in the liver and tumour ( e , k ). Umapharmony integration analysis showing increased B cells in Acly- KO ( f ) and in EVT0185-treated ( l ) mice. The top upregulated pathways in HCC cells from Acly -KO ( g ) and EVT0185-treated ( m ) mice. Statistical analysis was performed using Fisher’s exact test. Expression level of metabolic genes ( h , n ). Expression of markers of subtypes of B cells ( i , o ). The box-and-whisker plots are defined by the median with the first quartile (Q1), third quartile (Q3), minimum (Q1 − 1.5 × interquartile range (IQR)) and maximum (Q3 + 1.5 × IQR). Cxcl13 expression levels in HCC cells ( j , p ). GC, germinal centre; HSC, hepatic stellate cell; MZ, marginal zone; Tr, regulatory; VSMC, vascular smooth muscle cell.

Article Snippet: Liver tumour CXCL13 protein levels were determined using the mouse CXCL13/BLC/BCA-1 Quantikine ELISA Kit (MCX130, R&D Systems) following the manufacturer’s instructions.

Techniques: RNA Sequencing, Expressing, Whisker Assay

Journal: Nature

Article Title: ACLY inhibition promotes tumour immunity and suppresses liver cancer

doi: 10.1038/s41586-025-09297-0

Figure Lengend Snippet: a-b , Immune cell markers expressed in different cell types in a , WT and Acly KO and b , Vehicle and EVT0185-treated mice. c , Top upregulated pathways in B cells in Acly KO or EVT0185-treated mice (spatial transcriptomics analysis). Statistical analysis was performed using Fisher’s Exact test. d and e , Single seq analysis of d , WD-DEN and e , WD-CCl 4 mouse livers showing top upregulated pathways in B cells. Statistical analysis was performed using a one-sided hypergeometric test (enrichGO); p-values adjusted by Benjamini-Hochberg. f , Cxcl13 mRNA expression analyzed from publicly available RNA-seq dataset in WT and Acly KO DEN tumors cultured in vitro ( GSE223966 ) . Boxplot lines represent the first quartile, median, and third quartile. Whiskers connect the minimum and maximum values. Significance was ascertained by an unpaired two-tailed t-test between Acly KO vs WT (n = 4 hepatocellular carcinoma cell lines derived from DEN-induced tumors in Acly f/f mice).

Article Snippet: Liver tumour CXCL13 protein levels were determined using the mouse CXCL13/BLC/BCA-1 Quantikine ELISA Kit (MCX130, R&D Systems) following the manufacturer’s instructions.

Techniques: Expressing, RNA Sequencing, Cell Culture, In Vitro, Two Tailed Test, Derivative Assay

Journal: Nature

Article Title: ACLY inhibition promotes tumour immunity and suppresses liver cancer

doi: 10.1038/s41586-025-09297-0

Figure Lengend Snippet: a and b , Quantification of lipid droplet area was extrapolated by converting the PLIN-2 signal into a mask and quantifying the area covered by this mask per 400 × 400 micron field of view (FOV). These calculations were performed in ImageJ using custom scripts. Each dot represents a single FOV, Wilcoxon non-parametric unpaired two-sided test. Acly KO (n = 188) vs WT (n = 170) FOVs from n = 4 mice/group. c , CXCL13 protein level in tumors from WT and Acly KO mice; mean ± SEM, n = 5 mice/group; unpaired two-tailed t-test. d , Representative images showing B cells at tumor centre and periphery (Orange star: Tumor front (border-periphery), Black star: Surrounding non-tumoral hepatic tissue). e , B cell aggregations in Acly KO tumor (Orange star: Tumor, Black star: Non-tumoral liver tissue, Blue star: B Cell aggregations). f , Heatmap of cell neighborhoods hierarchically sorted by cell phenotype and showing relative cell abundances. ( g-j, l-n ) WD-DEN mice treated with Vehicle or EVT0185. g , Representative MIBI images of liver tumors. h , B cell, and i , T cell counts from regions representing the tumor lesion interface with the liver; mean ± SEM, n = 4 mice/group; unpaired Wilcoxon non-parametric unpaired two-sided test. j , CD19+ positive cells count/mm 2 tumor area; mean ± SEM, Vehicle (n = 29) and EVT0185 (n = 21) lesions; unpaired two-tailed t-test. k , CD3+ positive cells count/mm 2 tumor area; mean ± SEM, WT (n = 12) and Acly KO (n = 10) lesions; unpaired two-tailed t-test. l , CD3+ positive cells count/mm 2 tumor area; mean ± SEM, Vehicle (n = 29) and EVT0185 (n = 21) lesions; unpaired two-tailed t-test. m , Percentage of mice with/without B cells in TLS. n , TLS in EVT-treated mouse compared with vehicle control. o , GO enrichment analysis showing upregulated pathways related to complement activation in B cells in the EVT0185-treated group relative to Vehicle. Statistical analysis was performed using one-sided hypergeometric test (enrichGO); p-values adjusted by Benjamini-Hochberg.

Article Snippet: Liver tumour CXCL13 protein levels were determined using the mouse CXCL13/BLC/BCA-1 Quantikine ELISA Kit (MCX130, R&D Systems) following the manufacturer’s instructions.

Techniques: Two Tailed Test, Control, Activation Assay

Journal: Nature

Article Title: ACLY inhibition promotes tumour immunity and suppresses liver cancer

doi: 10.1038/s41586-025-09297-0

Figure Lengend Snippet: a , Differential expression analysis comparing MASH-HCC (n = 53) and non-tumor adjacent liver (n = 29), MASH liver (n = 74), cirrhotic liver (n = 8), and healthy liver tissue (n = 6); two-tailed t-test; 5% FDR as implemented in limma. b , Overlap between significantly upregulated and downregulated genes in each pairwise comparison. c , Gene expression of lipogenic enzymes acetyl-CoA carboxylase ( ACACA or ACACB ), ACSS2 , and FASN across disease states (MASH-HCC, n = 53; non-tumor adjacent, n = 29; MASH liver, n = 74; cirrhotic liver, n = 8; healthy liver, n = 6). Boxplot lines represent the first quartile, median, and third quartile. Whiskers connect the minimum and maximum values. d , ACLY upregulation in human MASH-HCC compared to all other tissue types using scRNAseq samples. Significance assessed using Wilcoxon rank-sum tests comparing each condition to MASH-HCC, with p-values adjusted using the Benjamini-Hochberg method. Exact p-adj values: vs healthy P adj = 6.9 × 10 −247 , vs MALSD P adj = 1.0 × 10 −16 , vs non-tumor adjacent P adj = 1.6 × 10 −18 . e , Differential expression analysis of genes associated with ACLY expression in MASH-HCC; two-tailed t-test; 5% FDR as implemented in limma. f , Principal component embeddings of genes differentially expressed with respect to ACLY expression validate stratification of MASH-HCC tissues by high, medium, and low ACLY expression levels. g , Upregulation of CXCL13 among human MASH-HCC samples with reduced (bottom tertile, n = 18) relative to elevated (top tertile, n = 18) ACLY expression. Significance determined by two-tailed t-test with a false discovery adjusted threshold of 5% as implemented in limma. Boxplot lines represent the first quartile, median, and third quartile. Whiskers connect the minimum and maximum values. h , Identification of co-expression modules associated with ACLY expression and immune features. i , Significant biological processes associated with the immune and ACLY associated gene co-expression module.

Article Snippet: Liver tumour CXCL13 protein levels were determined using the mouse CXCL13/BLC/BCA-1 Quantikine ELISA Kit (MCX130, R&D Systems) following the manufacturer’s instructions.

Techniques: Quantitative Proteomics, Two Tailed Test, Comparison, Gene Expression, Expressing