Yan Xu

scPAS: single-cell phenotype-associated subpopulation identifier

Abstract Despite significant advancements in single-cell sequencing analysis for characterizing tissue sample heterogeneity, identifying the associations between cell subpopulations and disease phenotypes remains a challenging task. Here, we introduce scPAS, a new bioinformatics tool designed to integrate bulk data to identify phenotype-associated cell subpopulations within single-cell data. scPAS employs a network-regularized sparse regression model to quantify the association between each cell in single-cell data and a phenotype. Additionally, it estimates the significance of these associations through a permutation test, thereby identifying phenotype-associated cell subpopulations. Utilizing simulated data and various single-cell datasets from breast carcinoma, ovarian cancer, and atherosclerosis, as well as spatial transcriptomics data from multiple cancers, we demonstrated the accuracy, flexibility, and broad applicability of scPAS. Evaluations on large datasets revealed that scPAS exhibits superior operational efficiency compared to other methods. The open-source scPAS R package is available at GitHub website: https://github.com/aiminXie/scPAS.

LRP8 promotes tumorigenesis in ovarian cancer through inhibiting p53 signaling

AbstractOvarian cancer (OC) is the most lethal gynecological malignancy with a high mortality rate. Low‐density lipoprotein (LDL) receptor‐related protein 8 (LRP8) is a cell membrane receptor belonging LDL receptor family and is involved in several tumor progressions. However, there is limited understanding of how LRP8 mediates OC development. LRP8 expression level was identified in human OC tissues and cells using immunohistochemical staining and quantitative polymerase chain reaction assays, respectively. Functions of LRP8 in OC progression were evaluated by Celigo cell counting, wound healing, transwell and flow cytometry assays, and the xenograft models. The human phospho‐kinase array analysis was used for screening potential signaling involved in OC development. We observed that LRP8 was overexpressed in OC tissues, and high expression of LRP8 was associated with poor prognosis of OC patients. Functionally, LRP8 knockdown remarkably reduced proliferation and migration of OC cells, and induced apoptosis and S phase cycle arrest. LRP8 deficiency attenuated in vivo tumor growth of OC cells. Moreover, the addition of p53 inhibitor partially reversed the effects of LRP8 knockdown on OC cell proliferation and apoptosis, indicating the involvement of p53 signaling in LRP8‐mediated OC progression. This study confirmed that LRP8/p53 axis contributed to OC progression, which might serve as a novel potential therapeutic target for OC patients.

SLAMF7 predicts prognosis and correlates with immune infiltration in serous ovarian carcinoma

Signaling lymphocytic activation molecule family members (SLAMFs) play a critical role in immune regulation of malignancies. This study aims to investigate the prognostic value and function of SLAMFs in ovarian cancer (OC). The expression analysis of SLAMFs was conducted based on The Cancer Genome Atlas Ovarian Cancer Collection (TCGA-OV) and Gene Expression Omnibus (GEO) databases. Immunohistochemistry (IHC) was further performed on tissue arrays (n=98) to determine the expression of SLAMF7. Kaplan-Meier plotter and multivariate Cox regression model were used to evaluate the correlation of SLAMF7 expression with survival outcomes of patients. The molecular function of SLAMF7 in OC was further investigated using Gene Set Enrichment Analysis (GSEA). SLAMF7 mRNA expression were significantly upregulated in OC tumor tissue compared to normal tissue. IHC revealed that SLAMF7 expression was located in the interstitial parts of tumor tissue, and higher SLAMF7 expression was associated with favorable survival outcomes. GSEA demonstrated that SLAMF7 is involved immune-related pathways. Further analysis showed that SLAMF7 had a strong correlation with the T cell-specific biomarker (CD3) but not with the B cell (CD19, CD22, and CD23) and natural killer cell-specific biomarkers (CD85C, CD336, and CD337). Furthermore, IHC analysis confirmed that SLAMF7 was expressed in tumor-infiltrating T cells, and the IHC score of SLAMF7 was positively correlated with CD3 (r=0.85, p<0.001). SLAMF7 is expressed in the interstitial components of clinical OC tissue, and higher SLAMF7 expression indicated a favorable prognosis for patients with OC. Additionally, SLAMF7 is involved in T-cell immune infiltration in OC.

Upregulation of CXCL1 and LY9 contributes to BRCAness in ovarian cancer and mediates response to PARPi and immune checkpoint blockade

Mutations in BRCA1 or BRCA2 (BRCA1/2) cause homologous recombination deficiency (HRD). Ovarian cancer (OvCa) patients harbouring HRD beyond BRCA1/2 mutation result in a state referred to as "BRCAness". OvCa with BRCAness could benefit from PARP inhibitors. This study aims to identify a signature to detect the BRCAness population at the transcriptome level. We used a rank-based algorithm to develop a qualitative BRCAness signature for OvCa. Upregulation of CXCL1 with downregulation of SV2A and upregulation of LY9 with downregulation of CHRNB3 were constructed as the BRCAness signature (2 gene pairs, 2-GPS) for OvCa. OvCa samples that were classified as BRCAness by 2-GPS showed improved overall survival, progression-free survival and exhibited increased multi-omics alterations in homologous recombination genes and enhanced sensitivity to immune checkpoint blockade. BRCAness cells were sensitive to PARP inhibitors. By biological experiments, we validated SKOV3 cells and patients with HRD exhibited higher expression of CXCL1 than SV2A and higher expression of LY9 than CHRNB3 at mRNA level. Both SKOV3 and A2780 with HRD were sensitive to mitomycin C, cisplatin and olaparib. In conclusion, 2-GPS could robustly predict BRCAness OvCa at the individual level and extend the population who may benefit from PARP inhibitors.

Comparison between laparoscopic and abdominal radical hysterectomy for stage IB1 and tumor size &lt;2 cm cervical cancer with visible or invisible tumors: a multicentre retrospective study

To compare 5-year disease-free survival (DFS) and overall survival (OS) rates of laparoscopic radical hysterectomy (LRH) and abdominal radical hysterectomy (ARH) for stage IB1 and tumor size <2 cm with visible or invisible tumors. We retrospectively compared the oncological outcomes of 1,484 cervical cancer patients with IB1 and tumor size <2 cm on final pathology, who received ARH (n=899) or LRH (n=585) between January 2004 and December 2016. Patients were divided into visible tumor subgroup (ARH: n=668, LRH: n=444) and invisible tumor subgroup (ARH: n=231, LRH: n=141) according to tumor type. LRH and ARH showed similar 5-year DFS and OS rates (93.3% vs. 93.1%, p=0.997; 96.2% vs. 97.5%, p=0.351) in total study population. LRH was not associated with worse 5-year DFS rate (hazard ratio [HR]=0.96; 95% confidence interval [CI]=0.58-1.58; p=0.871) or OS rate (HR=1.37; 95% CI=0.65-2.89; p=0.409) by multivariable analysis. In the visible tumor subgroups, LRH and ARH showed similar 5-year DFS and OS rates (91.9% vs. 91.9%, p=0.933; 95.0% vs. 96.9%, p=0.276), and LRH was not associated with worse 5-year DFS or OS rate (p=0.804, p=0.324). In the invisible tumor subgroups, LRH and ARH also showed similar 5-year DFS and OS rates (97.3% vs. 97.1%, p=0.815; 100% vs. 99.5%, p=0.449), and LRH was not associated with worse 5-year DFS rate (p=0.723). Among patients with stage IB1 and tumor size <2 cm, whether the tumor is visible or not, the oncological outcomes of LRH and ARH among cervical cancer patients are comparable. This suggests that LRH may be suitable for stage IB1 and tumor size <2 cm with visible or invisible tumors. International Clinical Trials Registry Platform Identifier: CHiCTR180017778.