designed the study. gene expression of single cells from human HCC tumor and para-tumor tissues using the Smart-seq 2 sequencing method. Based on differentially expressed genes, we identified heterogeneous subclones in HCC tissues, including five HCC and two hepatocyte subclones. We then carried out hub-gene co-network and functional annotations analysis followed pseudo-time analysis with regulated transcriptional factor co-networks to determine HCC cellular trajectory. We found that MLX interacting protein like (MLXIPL) was commonly upregulated in the single cells and tissues and associated with a poor survival rate in HCC. KDU691 Mechanistically, MLXIPL activation is crucial for promoting cell proliferation and inhibits cell apoptosis by KDU691 accelerating cell glycolysis. Taken KDU691 together, our work identifies the heterogeneity of HCC subclones, and suggests MLXIPL might be a promising therapeutic target for HCC. values between different groups using value cut-off 0.01. Single-cell trajectory analysis We used diffusion mapping and Monocle to perform a pseudo-time analysis. Cells were chosen based on Seurat cluster identification results. Then, the key genes were obtained through Function in Monocle R package and filtered by the significance of R package and ranked by value to build a co-expression KDU691 regulatory network as above described. Cell culture and transfection L02, SMMC-7721, HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (Hyclone). All of the cell lines were from ATCC. Cells used in the experiments were authenticated by using short tandem repeat profiling. HCC cells were plated at a density of 2??105/well in a six-well plate 24?h before transfection. Transfection was performed using Lipofectamine 2000 transfection reagent (Thermo Fisher), according to the manufacturers protocol. Transfection efficiency was verified using quantitative reverse transcription-quantitative PCR (qRT-PCR) and western blotting. Quantitative reverse transcription-quantitative PCR (qRT-PCR) Total RNA was extracted from transfected cells using the TRIzol reagent (Invitrogen), and the concentration was measured by NanoDrop1000 Spectrophotometer (Agilent). cDNA was reversed transcribed by the Superscript RT kit (TOYOBO) according to the manufacturers instructions. qRT-PCR amplification was performed using the SYBR Prime Script qRT-PCR kit (Takara). All quantization was normalized to the level of internal control GAPDH. Primer sequences are shown in Supplementary Table 7. Western blot analysis Tissues and cells were lysed with a modified buffer, and western blotting was performed as described previously41. The primary antibodies were as follows: MLXIPL (Abcam, ab92809), GLUT1 (Abcam, ab115730), PKM1 (Abcam, ab116271), PKM2 (Abcam, ab137852), LDHA (Abcam, ab84716), and -actin (Abbkine, A01011). And images were captured using an Amersham Imager 600 System (GE Healthcare). Immunohistochemistry All the specimens embedded in paraffin blocks were cut at 3C4?m and air-dried overnight. The tissue sections were deparaffinized, rehydrated, and subjected to heat-induced antigen retrieval with sodium citrate buffer (10?mM sodium citrate, 0.05% Tween-20 (pH 6.0)), which was followed by incubation with 3% hydrogen peroxide for 5?min to block endogenous peroxidase activity. Sections were then incubated with the appropriate primary antibody and were sequentially incubated with biotinylated goat anti-mouse IgG. For signal detection, the VECTASTAIN ABC kit (Vector Laboratories) was used according to the manufacturers instructions. CCK8 assay In all, 1000 cells were plated in 96-well plates in 100?l media. 10?l Cell Counting Kit (CCK8) (Yeasen) solution was added into medium for 30?min before measuring absorbance at a wavelength of 450?nm by a microplate reader (Thermo KDU691 Scientific) daily for continuous 5 days. Apoptosis analysis Transfected cells were washed twice with ice-cold water, and stained with 5?l of annexin V-FITC and 1?l propidium iodide (PI, 1?mg/ml) for EIF4EBP1 15?min, and subjected to analysis on a flow cytometer (BD Biosciences). Glucose uptake and lactate production SMMC-7721 and HepG2 cells transfected with MLXIPL OE plasmid or siRNAs were seeded in.