Abstract Background Since the pathophysiology of clear cell renal cell carcinoma (ccRCC) was still unknown, finding novel therapeutic targets to support current treatment approaches was crucial. Methods We conducted an RNA-Sequencing analysis using data from the TCGA-KIRC dataset, with our own clinical data serving as validation. Kaplan–Meier survival curves, univariate and multivariate studies of overall survival, and differential expression analysis were all used. Furthermore, we explored the correlation between LGALS1 (Galectin-1) and clinical characteristics in ccRCC patients by leveraging proteomics data from the CPTAC analysis. Additionally, the Single-cell RNA-Sequencing (scRNA-Seq) analysis elucidated the cellular landscape of LGALS1 using the [32]GSE159115 database, complemented by pathway enrichment analysis via GO and KEGG datasets. Lastly, we performed an immunohistochemistry (IHC) analysis on ccRCC tissue microarrays and scored the staining intensity. While p < 0.05 was used for other analyses, p < 0.1 was deemed significant in multivariate analysis. Results As shown in TCGA and confirmed in our clinical data, higher LGALS1 expression in ccRCC was associated with a bad prognosis. Proteomics analysis in the CPTAC dataset revealed that LGALS1 levels were statistically significant across different grade and stage groups of patients. The high expression was confirmed on the IHC chip, with tumor tissue displaying a higher staining intensity score. Additionally, scRNA-Seq analysis identified that the differential expression of LGALS1 primarily occurred in endothelial and epithelial cells, along with associated signaling pathways. Conclusions We performed a multi-omics analysis using transcriptomics, proteomics, single-cell omics, and our clinical data, confirming LGALS1 as a possible target for ccRCC. Keywords: LGALS1, ccRCC, Multi-omics analysis, Single-cell RNA-Seq Introduction According to the American Cancer Society, in 2025, renal carcinoma is expected to cause 80,980 new cases and 14,510 fatalities in the United States [[33]1]. Clear cell renal cell carcinoma (ccRCC) was the most common histological subtype of renal carcinoma, accounting for approximately 85% of cases [[34]2]. Often exhibiting no symptoms, patients with ccRCC were discovered by chance during regular imaging tests [[35]3]. The deletion of the Von Hippel-Lindau (VHL) gene, a key molecular hallmark of ccRCC, played a pivotal role in its pathogenesis [[36]4]. The primary treatment modality for localized ccRCC was surgical resection. Surgical excision was the main therapy option for localized ccRCC. A number of variables, such as tumor size, renal pelvic involvement, and other pertinent considerations, influenced the decision between partial and radical nephrectomy [[37]5]. Furthermore, chemotherapy and radiation therapy did not usually work in ccRCC. Tyrosine kinase inhibitors (TKIs), such axitinib, and immune checkpoint inhibitors that target the PD-1/PD-L1 pathway, like pembrolizumab, were the most widely used adjuvant treatments [[38]6]. Patients with metastatic ccRCC often experienced poor outcomes. For instance, those treated with nivolumab typically had a median progression-free survival of approximately 11.3 months [[39]7]. A member of the beta-galactoside-binding protein family, Galectin-1 (LGALS1) played a role in regulating interactions between cells and between cells and matrices [[40]8]. It was identified as being closely associated with inflammation, fibrosis, immunity, and other biological processes, particularly in carcinomas [[41]9]. Researchers found that atherosclerosis and abdominal aortic aneurysms are caused by pathological vascular remodeling when the LGALS1 gene is silenced [[42]10]. In a hypertonic glucose environment, LGALS1 was found to interact with and potentiate the effects of the receptor for activated protein C kinase 1, thereby promoting inflammation in diabetic nephropathy. At the same time, Li and colleagues identified a compound called Bruceine A that targets this gene, which had the potential to inhibit the aforementioned pathological biological processes [[43]11]. By improving STING protein stability, LGALS1 was discovered to mediate the migration and accumulation of myeloid-derived suppressor cells, preserving the NF-κB signaling pathway in tumor cells [[44]12]. Additionally, earlier research found that LGALS1 was significantly expressed and linked to a poor prognosis acute myeloid leukemia [[45]13] and glioblastoma [[46]14]. We performed a comprehensive clinical data analysis, integrating information from multiple databases, with the objective of identifying potential risk factors for ccRCC. The ultimate objective of this effort was to identify potential treatment targets for this illness. The expression levels of the target gene were investigated, and prognostic and survival analyses were performed simultaneously. Furthermore, the expression of the gene was validated in ccRCC tissue samples. Utilizing single-cell sequencing technology, we elucidated the cytological landscape of the selected gene and its associated signaling pathways. Method and materials RNA-Seq analysis of LGALS1 in ccRCC TCGA-KIRC RNA-Seq data and clinical information were obtained from The Cancer Genome Atlas (TCGA) database, containing 72 controls and 539 cancer samples. All tumor specimens were histopathologically confirmed as ccRCC. The follow-up spanned 3,668 days, during which 367 deaths occurred. The transcripts per million (TPM) approach was used to standardize the expression levels of LGALS1. The “limma” package in R was used to do differential expression analysis, with a p-value cutoff of less than 0.05. Log-rank testing was used to assess the association between LGALS1 expression and patients’ overall survival (OS) as determined by Kaplan-Meier survival curves. The predictive value of LGALS1 expression was assessed using univariate and multivariate Cox regression analyses of OS, controlling for clinical variables such age, gender, tumor stage, grade, and race. These investigations shed light on the possible significance of LGALS1’s RNA expression in ccRCC. Proteomics analysis of LGALS1 in ccRCC We accessed the UALCAN website ([47]http://ualcan.path.uab.edu/index.html) and navigated to the “Proteomics” section to explore the protein expression of LGALS1 in ccRCC [[48]15]. We selected the ccRCC dataset and used boxplots and t-tests or Wilcoxon rank-sum tests to analyze the protein expression levels of LGALS1 across tumor and normal tissues. Furthermore, we investigated associations between clinical characteristics such tumor stage and grade and LGALS1 expression. These analyses provided insights into the potential protein expression significance of LGALS1 in ccRCC. Single-cell RNA-Seq (scRNA-Seq) analysis of LGALS1 in ccRCC ScRNA-Seq analyses of the expression of LGALS1 in ccRCC were conducted by analyzing the [49]GSE159115 dataset from the Gene Expression Omnibus (GEO) database ([50]https://www.ncbi.nlm.nih.gov/geo/). The data were preprocessed and normalized using the “Seurat” R package. Cells were clustered and annotated based on known markers, as the previous article described [[51]16]. The TSNE and violin plots were used to visualize the results of a differential expression study that compared the expression of LGALS1 in different cells between tumor and normal samples. The LGALS1-associated pathways were obtained using the “irGSEA” R package, and the physiological process connected to LGALS1 in specific cells of ccRCC was obtained using the GO enrichment approach. Immunohistochemistry (IHC) chip After excluding samples with missing or erroneous data, 93 tumor specimens and 87 matched peritumoral tissues were included; all were obtained surgically. Histopathologic review confirmed ccRCC in every tumor sample. The IHC analysis of LGALS1 in ccRCC was conducted using tissue microarrays by SHANGHAI OUTDO BIOTECH CO. LTD. The LGALS1 antibody was purchased from Proteintech (Cat. No. 11858-1-AP; Wuhan, China). The expression of LGALS1 in the cytoplasm of cancer and peritumoral tissues was evaluated using the IHC analysis of LGALS1 in ccRCC tissue microarrays. The percentage of positive cells was assessed on a range of 0–100%, while the staining intensity was rated as 0 (negative), 1 (1+), 2 (2+), or 3 (3+). The staining intensity score and the percentage of positive cells score were multiplied to determine the final score. Nonparametric tests were used to analyze the expression levels of LGALS1 in ccRCC and peritumoral tissues. The median postoperative follow-up of these patients was 106 days, during which 31 deaths occurred. Kaplan-Meier survival analysis and log-rank tests were employed to evaluate the correlation between LGALS1 expression levels and OS in ccRCC patients. Besides, the clinical data for the cohort were analyzed using the Cox proportional-hazards model to assess the influence of various factors on survival. In addition, the variables that exhibited statistical significance in the univariate analysis were incorporated into the subsequent multivariate analysis. Specifically, the variates included LGALS1 expression, sex (male vs. female), age (≤ 60 vs. > 60 years), tumor size (≤ 5 cm vs. > 5 cm), and TNM stage: stage I–II (T1–2 N0 M0) vs. stage III–IV (all other TNM stages). Statistical analysis All statistical analyses were performed using R software (version 4.3.2), and a significance level of P < 0.05 was applied. Differential expression analysis was performed via t-tests or Wilcoxon rank-sum tests. Kaplan-Meier survival analysis and log-rank tests were used to analyze the OS prognostic value in ccRCC. Results The mRNA expression and prognosis correlation of LGALS1 in ccRCC Our analysis of TCGA-KIRC data revealed that LGALS1 expression in tumor tissues was significantly higher than that in normal tissues (p < 2.22 × 10⁻¹⁶), as shown in Fig. [52]1A. Moreover, as illustrated in Fig. [53]1B, we conducted paired analyses that further confirmed the statistically significant difference (p < 7.7 × 10⁻¹²). The survival analysis depicted in Fig. [54]1C revealed that patients with high LGALS1 expression had poorer survival outcomes. Furthermore, we carried out univariate analysis (Fig. [55]1D) and multivariate analysis (Fig. [56]1E) using these data from TCGA. And we came to the conclusion that, although the T and M stages were only significant in univariate analysis, age, grade, and stage clearly affected the survival and prognosis of patients with ccRCC. Surprisingly, LGALS1 was found to be a risk factor for ccRCC; both analyses supported this finding. This implied that LGALS1 might be a valuable therapeutic target and predictive biomarker. We set a more permissive p-value threshold to enhance the sensitivity of our analysis. A p-value of less than 0.1 was considered statistically significant in multiple factor analysis. Fig. 1. [57]Fig. 1 [58]Open in a new tab Analysis results from transcriptomics using RNA-Seq data from the TCGA database: A and B: Expression levels of LGALS1 in normal and tumor groups (A: unpaired analysis; B: paired analysis); C: Kaplan-Meier survival curves; D: Univariate Cox regression analysis of OS; E: Multivariate Cox regression analysis of OS The protein expression and prognosis correlation of LGALS1 in ccRCC With an emphasis on the gene and its phosphorylated version, we investigated the protein-level expression of LGALS1 and its correlation with clinical outcomes in the CPTAC study. The expression level of LGALS1 was significantly higher in tumor tissues (LGALS1: Fig. [59]2A; phosphorylated form: Fig. [60]2D). Additionally, we assessed the expression levels of the gene in subgroups of ccRCC patients at different stages and grades. The expression level of LGALS1 was elevated across all tumor grades compared to normal tissues, as shown in Fig. [61]2B, and the same trend was observed for its phosphorylated form in Fig. [62]2E. The similar conclusion for the stage group was shown by Fig. [63]2C and F for LGALS1 and its phosphorylated version, respectively: tumor tissues expressed more LGALS1 than normal tissues. All p-value was less than 0.05. Fig. 2. [64]Fig. 2 [65]Open in a new tab Analysis results from proteomics utilizing the CPTAC database: A, B, and C: Expression levels of LGALS1 in different patient groups categorized by clinical features (A: normal and ccRCC groups; B: different grade groups; C: various stage groups); D, E, and F: Expression levels of phosphorylated LGALS1 in the same groups as above Validation the expression and clinical correlation of LGALS1 in ccRCC samples IHC tissue chips were conducted using tumor and surrounding normal tissues from patients with ccRCC, which allowed for an intuitive display of the variations in LGALS1 levels within the same patient. The expression of LGALS1 was greater in the tumor tissue, as seen in Fig. [66]3A. The IHC score, as integrated in Fig. [67]3B, revealed that tumors exhibited a higher score than in adjacent non-tumor tissue (p < 0.001). Specifically, the median IHC score was 1.013 for tumor tissue and 0.264 for matched normal tissue. The clinical data of the same patients was then examined, and the results were in agreement with the two databases mentioned above. The group with high LGALS1 levels exhibited worse OS, as shown in Fig. [68]3C (p < 0.0001). Additionally, Fig. [69]3D revealed that the area under the ROC curve was 0.9388, with the p-value being less than 0.0001. Age, TNM stages, and LGALS1 were found to be statistically significant factors affecting the outcomes of ccRCC patients in both univariate and multivariate analyses (Fig. [70]3E). Fig. 3. [71]Fig. 3 [72]Open in a new tab IHC analysis and survival analysis of LGALS1: A IHC staining of tissue microarrays targeting LGALS1; B IHC scores comparing cancerous and peritumoral tissues; C Kaplan-Meier survival analysis of OS; D ROC curve analysis distinguishing tumor from normal tissue; E Univariate and multivariate analyses of OS. LGALS1 was also known as GAL-1 The scRNA-Seq analysis in ccRCC As presented in Fig. [73]4A, we intuitively depicted the expression of LGALS1 across various cellular subtypes in ccRCC. A deeper shade of red in the UMAP graphic denoted higher expression levels. Moreover, Fig. [74]4B showed the levels of LGALS1 in various cell types. Besides, we found that endothelial and epithelial cells showed especially high expression levels. The expression levels of LGALS1 in endothelial and epithelial cells differed significantly from those in other cell types, as shown by the violin plot in Fig. [75]4C. When matched with the normal group, the endothelial and epithelial cells in the tumor group were found to have higher expression levels of LGALS1 (Fig. [76]4D). Fig. 4. [77]Fig. 4 [78]Open in a new tab Single-cell omics analysis results using the [79]GSE159115 dataset: A Expression of LGALS1 in ccRCC tissue at a cytological field of view; B Expression levels of LGALS1 in various cell subtypes within ccRCC; C Violin plot showing differential expression of LGALS1 among different cell types; D Differential expression analysis between tumor and normal groups across cell subtypes LGALS1 in ccRCC endothelial cells: expression and pathways Figure [80]5A displayed the violin plot of LGALS1 expression in endothelial cells, which showed that tumor endothelial cells had a substantially greater level of LGALS1 than did normal endothelium cells. Furthermore, we separated the cells into two groups based on the LGALS1 median level. As shown in Fig. [81]5B, tumor endothelial cells were more likely to be part of the group with high LGALS1 expression. Furthermore, the UMAP plot in Fig. [82]5C intuitively illustrated the expression of LGALS1 in endothelial cells. The KEGG and GO databases were used for the ensuing pathway enrichment study. The results of the former investigation indicated that endothelial cells with increased expression of LGALS1 may be associated with the epithelial-mesenchymal transition (EMT), fatty acid metabolism, oxidative phosphorylation, and other pathways (Fig. [83]5D). While in Fig. [84]5E, data from the GO dataset revealed that these cells might be related to functions such as growth factor binding, cytokine binding, and others. Fig. 5. [85]Fig. 5 [86]Open in a new tab Specific scRNA-Seq analysis results of LGALS1 in endothelial cells: A Violin plot of LGALS1 expression levels in normal and tumor endothelial cells; B Boxplots of LGALS1 expression grouped by median level; C LGALS1 expression levels in tumor endothelial cells; D Pathway enrichment analysis using the KEGG database; E Pathway enrichment analysis using the GO database LGALS1 in ccRCC epithelial cells: expression and pathways Normal and malignant cells differed statistically significantly in their expression of LGALS1 within their epithelial cells (Fig. [87]6A). Furthermore, tumor epithelial cells showed a noticeably greater percentage of strong LGALS1 expression, as seen in Fig. [88]6B. The overall expression of LGALS1 in epithelial cells was intuitively depicted among all epithelial cells in Fig. [89]6C. The pathway enrichment analysis using the KEGG database in Fig. [90]6D revealed that epithelial cells with high LGALS1 levels tended to activate pathways such as MTORC1 signaling, interferon-gamma response, and TNF-alpha signaling via NFκB, among others. As Fig. [91]6E showed, electron transfer activity, NADH dehydrogenase activity, and other associated processes may be important in epithelial cells with high LGALS1 expression, according to the GO dataset’s later analysis. Fig. 6. [92]Fig. 6 [93]Open in a new tab The distinctive results of the scRNA-Seq analysis of LGALS1 in epithelial cells: A LGALS1 level in a violin plot of normal and malignant epithelial cells; B LGALS1 expression boxplots arranged by median level; C LGALS1 level in malignant epithelial cells; D and E pathway enrichment analysis (D: KEGG database; E GO database) Discussion Several studies highlighted the relationship between LGALS1 and ccRCC [[94]17]. Previous study concluded that LGALS1, which was overexpressed in ccRCC, was associated with the TNF-alpha signaling pathway, as evidenced by RNA-Seq data from the GEO database [[95]18]. Fang et al. identified LGALS1 as a prognostic biomarker of ccRCC by building a gene co-expression network using data from the TCGA and GEO databases [[96]19]. Transcriptomics, proteomics, single-cell omics, and other multi-omics data were combined for ccRCC in our work. As a result, LGALS1 was identified as a possible candidate biomarker deserving of additional research. Specifically, we identified that LGALS1 was highly expressed at both the transcriptional and translational levels, and that its high expression was associated with worse OS, which served as an independent prognostic factor for ccRCC. Subsequently, publicly available scRNA-Seq data revealed that the high expression of LGALS1 predominantly occurred in endothelial and epithelial cells within ccRCC tissue. The primary cytological features observed in ccRCC were the absence of renal-specific endothelial cells and epithelial cells, coupled with extensive immune cell infiltration [[97]20]. The upregulation of endothelial cells in ccRCC tumor thrombus likely promoted cancer progression through cancer-related vasculature formation and cell proliferation [[98]21]. Our knowledge of the highly vascularized features of ccRCC was improved when it was demonstrated that CD105 was elevated in both tumor and vascular endothelium cells [[99]22]. Targeting the function of cancer-associated endothelial cells was currently a first-line treatment strategy in ccRCC [[100]23]. Anti-angiogenic drugs, such as axitinib and bevacizumab, functioned by inhibiting the proliferation and function of endothelial cells, thereby impeding tumor-associated angiogenesis [[101]24]. Targeting the HIF2α axis might represent a promising therapeutic strategy to inhibit the malignant behavior of endothelial cells, thereby suppressing tumor progression [[102]25]. We identified LGALS1 as a potential gene that was particularly enriched in the ccRCC endothelial cells. Mechanistically, it could affect how these cells behaved in the signaling pathways for EMT, oxidative phosphorylation, and apoptosis signaling pathways, which warranted further investigation. Notably, ccRCC is fundamentally a metabolic disorder, driven by VHL inactivation and characterized by marked lipid accumulation and mitochondrial dysfunction [[103]26]. Specifically, lipid metabolism in ccRCC was typified by augmented uptake from both endogenous synthesis and exogenous acquisition, coupled with diminished β-oxidation [[104]27]. Consequently, signaling cascades such as mTOR–SREBP and PI3K–Akt were hyper-activated, collectively fueling tumor progression [[105]28]. Glucose metabolism is reprogrammed, with carbon flux shifting from glycolysis to the pentose phosphate pathway [[106]29]. Previous studies delineated a spectrum of key signaling cascades and master regulators governing glucose and lipid metabolism in ccRCC progression. Bombelli et al. demonstrated that HIF-1 alpha repressed the 36-kDa Annexin A3, thereby diminishing lipid endocytosis and driving intracellular lipid accumulation in ccRCC [[107]30]. Moreover, MUC1 was discovered to be cooperate with HIF-1 alpha to transcriptionally up-regulate LDH-A while repressing LDH-B, which stalled glycolytic flux, leading to the intracellular accumulation of glycolytic intermediates and a consequent surge in carbon flow through the pentose phosphate pathway [[108]31]. Our scRNA-seq profiling further implicates LGALS1 in ccRCC metabolic reprogramming, revealing that endothelial cells with high LGALS1 exhibit marked up-regulation of cholesterol homeostasis, fatty-acid metabolism, and oxidative phosphorylation pathways. The role of LGALS1 in ccRCC appeared to hinge partly on glucose and lipid metabolism, yet the precise upstream triggers and downstream effectors remain to be elucidated. Previous research demonstrated that epithelial cells were of critical importance in the tumorigenesis and progression of ccRCC. Researchers discovered that epithelial cells facilitate the infiltration of immune cells and the enrichment of associated inflammatory factors [[109]16]. According to Xu et al., a high-fat diet and exposure to polystyrene microplastics may cause renal epithelial cells’ extracellular matrix architecture to be disrupted, which could lead to ROS-mediated ccRCC carcinogenesis [[110]32]. A total of 219 malignant epithelial cell-related genes (MECRGs) were identified, which enabled the establishment of a prognostic model associated with their signatures [[111]33]. Following that, the prognostic model was assessed for its high accuracy in predicting tumor growth and metastasis as well as various biological traits, such as necrotic apoptosis, cuproptosis, immune cell infiltration, and immunotherapy response [[112]33]. Furthermore, the propensity for tumor initiation and metastasis was intimately linked to the EMT pathways [[113]34]. Wu and colleagues identified that tumor epithelial cells in ccRCC often exhibited a mesenchymal transition tendency, which might be mediated by eight associated genes [[114]35]. Our study investigated the expression of LGALS1 and its related pathways in epithelial cells of ccRCC, identifying potential target gene and pathways that modulated the malignant behavior of these cells, thereby enhancing our understanding of the progression mechanisms of ccRCC. The interplay between the immune microenvironment and tumor heterogeneity could further influence the efficacy of immunotherapy, thereby affecting patient prognosis [[115]36]. A number of cell subtypes in ccRCC affected immune cell behavior through a variety of biological mechanisms. Endothelial cells, for instance, might be linked to immune cell homing, whereas epithelial cells were probably linked to immune cell infiltration [[116]16]. Moreover, by up-regulating the expression of immune checkpoint molecules like PD-L1 and CTLA-4, the EMT signaling pathway might cause immunological suppression and immune escape in a variety of malignancies [[117]37]. Furthermore, interferon-gamma signaling within cancer cells might concurrently enhance PD-L1 expression and decrease TRAILR2 levels. This dual effect was identified as possibly leading to T cell exhaustion and antagonizing the cytotoxicity of PD-1(+) TRAIL(+) NK/ILC1 cells, ultimately impeding the functions of both adaptive and innate immunity [[118]38]. Furthermore, the recruitment of CD8(+) cells was reduced in the hepatocellular carcinoma model by LGALS1-mediated overexpression of PD-L1 in vascular endothelial cells [[119]39]. Previous studies on ccRCC also found that the level of LGALS1 was associated with predicting the efficacy of immunotherapy targeting PD-L1 [[120]18]. Future research on the immunoregulatory function of LGALS1 in ccRCC was necessary, especially to understand the processes underlying immunotherapy based on PD1/PD-L1. There were several disadvantages to our work. Firstly, it should be noted that the TCGA and UALCAN datasets, which were widely utilized in research, predominantly consisted of data from individuals of Caucasian descent. On the other hand, the number of patients included in our own clinical data, which was centered on the Asian community, was relatively limited. In order to more easily identify the correlations between LGALS1 levels and tumor grades, stages, and other clinical characteristics in the tissues of Chinese ccRCC patients, a large-scale observational investigation would be necessary in the future. Moreover, the specific mechanisms underlying the elevated LGALS1 levels and the potential roles that this gene played in epithelial and endothelial cells within ccRCC merited careful selection and in-depth investigation. Additionally, particular attention should be paid to its relationship with tumor immune behavior and glucose and lipid metabolism. This approach could enhance our comprehension of the pathogenesis of ccRCC, thereby identifying potential new therapeutic targets. Furthermore, the development of potential drugs targeting LGALS1 and other key molecules in associated pathways was eagerly anticipated, which would provide additional therapeutic strategy options to complement current treatments. Lastly, it should be emphasized that LGALS1 expression in ccRCC was validated solely by IHC chip. therefore, validation in vitro studies were imperative when exploring its mechanistic role in future investigations. Conclusions LGALS1 was identified as a risk factor for ccRCC due to its high expression in tumors and association with worse survival and poor prognosis, supported by TCGA database, CPTAC analysis, and our clinical studies. Furthermore, the increased LGALS1 expression in tumors was validated by our IHC chip analysis of tumor and paracancerous tissues from ccRCC patients. Additionally, scRNA-Seq analysis revealed that LGALS1 was predominantly highly expressed in endothelial and epithelial cells within tumors, along with the identification of related pathways associated with the gene. In summary, LGALS1 was identified as a prospective biomarker and therapeutic target for ccRCC. Acknowledgements