Pan-Cancer Analysis of PARP1 Alterations as Biomarkers in the Prediction of Immunotherapeutic Effects and the Association of Its Expression Levels and Immunotherapy Signatures

Abstract

BackgroundPoly (ADP-ribose) polymerases-1 (PARP1) alterations are associated with PARP1 inhibitor resistance, regulating the function of Treg cells and PDL1 expression in tumor cells, and high PARP1 expression is significantly associated with aggressive behavior and chemotherapeutic resistance in several tumors. However, a comprehensive analysis of the predictive values of PARP1 alteration for immune checkpoint inhibitor (ICI) effectiveness in tumors remains unclear, and the associations between its expression and immunotherapy signatures also needs to be explored further.MethodsWe performed some analyses with the cBioPortal online database (https://www.cbioportal.org), TIMER2.0 (Tumor Immune Estimation Resource 2.0, http://timer.comp-genomics.org/) and TCGA database (https://xenabrowser.net or https://portal.gdc.cancer.gov/). Survival analysis was conducted using Kaplan–Meier method, and the associations between PARP1 transcription levels and immune checkpoint gene expression, the number of neoantigens, tumor mutation burden (TMB) levels, and microsatellite instability (MSI) event are analyzed by spearman correlation analysis and visualization of those mentioned above is performed using R, version 3.6.3 (http://www.r-project.org/).ResultsWe found that PARP1 was altered in 1338 (2.9%) out of 45604 patients with diverse tumors, which was associated with markedly higher TMB levels in a variety of tumors (P < 0.01). Impressively, patients with PARP1 alterations in advanced tumors showed better overall survival (OS) in the ICI-treated cohort (P = 0.016). PARP1 altered group was substantially correlated with higher immune infiltrates across most tumors, including CD8+ T cells in colorectal adenocarcinoma (P = 0.0061), endometrial carcinoma (P = 0.0033), stomach cancer (P = 0.033), and cervical cancer (P = 0.026), respectively. The PARP1 altered group showed high expression in transcription (P < 0.001), and higher expression of LAG3, PDCD1, CTLA-4, and TIGIT (P < 0.05). Higher PARP1 expression was present in 27 tumor compared the corresponding normal tissues using the GTEx and TCGA databases and it had a worse OS in several tumors (P < 0.05). Further, high PARP1 expression was significantly associated with six immune cells (B cells, CD4+ T cells, CD8+ T cells, macrophages, neutrophils, and dendritic cells) in most tumors, including colon adenocarcinoma (COAD), head and neck squamous cell carcinoma (HNSC), kidney renal clear cell carcinoma (KIRC), and liver hepatocellular carcinoma (LIHC) (P < 0.05). In particular, CD8+T cell infiltration, was also positively correlated with high PARP1 expression in bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), kidney renal papillary cell carcinoma (KIRP), brain lower grade glioma (LGG), LIHC, pancreatic adenocarcinoma (PAAD), pheochromocytoma and paraganglioma (PCPG), prostate adenocarcinoma (PRAD), rectum adenocarcinoma (READ), testicular germ cell tumors (TGCT), thymoma (THYM), uterine corpus endometrial carcinoma (UCEC), uveal melanoma (UVM) (P < 0.05, no data shown), and PARP1 expression was significantly positively correlated with the transcription levels of some of the 47 immune checkpoint genes, such as CD274, CTLA4, and PDCD1 in several tumors, including PAAD, LIHC, KIRC, HNSC, and BLCA (P < 0.05). A significant positive association between PARP1 expression and the number of immune neoantigen was found within COAD, KIRC, lung adenocarcinoma (LUAD), PAAD and THYM (P < 0.05), and there were also significantly positive correlations between PARP1 expression and TMB in many tumors like adrenocortical carcinoma (ACC), COAD, kidney chromophobe (KICH), LGG, LUAD, READ, skin cutaneous melanoma (SKCM) and stomach adenocarcinoma (STAD) (P < 0.05). In addition, high PARP1 expression was positively associated with microsatellite instability event in COAD, KIRP, BRCA, glioblastoma multiforme (GBM), lung squamous cell carcinoma (LUSC), LGG, READ, UCEC, SKCM and LUAD (P < 0.05).ConclusionsOur results highlight the significance of PARP1 alterations as pan-cancer predictive biomarkers for ICI treatment, and its expression levels seem to be correlated with the status of immunotherapy-associated signatures, thus may be a promising biomarker for predicting ICI response in several tumors.

Identification of Potential Biomarkers for Pan-Cancer Diagnosis and Prognosis Through the Integration of Large-Scale Transcriptomic Data

“…In addition, we found the ICGs expression was higher in tumors with high TMB and having more mutations such as LUSC, LUAD, ESCA, and STAD ( Figure 5C ), reinforcing the point that these tumors may have surprising efficacious against prevailing ICIs ( Liu et al, 2017 ; Tung et al, 2021 ; Xie et al, 2021 ; Zhang et al, 2021 ).…”

DNA damage repair-related gene signature predicts prognosis and indicates immune cell infiltration landscape in skin cutaneous melanoma

“…As a result of such subgroupings, more targeted therapy may be devised. There have been many reports on the prognostic and biological importance of genetic changes linked to cancer such as PARP1 ( 12 , 13 ), NRAS ( 14 ), absent in melanoma-1 (AIM1) ( 15 ), Methylguanine-DNA Methyltransferase (MGMT) ( 16 ) as well as KPNA2 ( 17 ) mutations in SKCM. Nevertheless, the functions of DNA repair genes for the maintenance of genomic stability among SKCM are seldom described.…”

Advance of SOX Transcription Factors in Hepatocellular Carcinoma: From Role, Tumor Immune Relevance to Targeted Therapy

“…Of note, some members have shown remarkable correlation with classic immune checkpoints that have successfully implemented clinical translations, including PD-1 (encoded by PDCD1), PD-L1 (encoded by CD274), and CTLA4 (encoded by CTLA4). In addition, we also revealed that the expression of many SOX members was observably associated with that of human leukocyte antigen (HLA)-I and II molecular [161] (Figure 4B), chemokines (Figure 5A), and chemokines receptors (Figure 5B) in HCC. Taken together, the expression correlation between SOX factors and immune components was close in HCC, suggesting that SOX factors were likely to participate in TIME remodeling of HCC and might act as potential biomarkers for predicting immunotherapy response in HCC.…”

“…Of note, some members have shown remarkable correlation with classic immune checkpoints that have successfully implemented clinical translations, including PD-1 (encoded by PDCD1 ), PD-L1 (encoded by CD274 ), and CTLA4 (encoded by CTLA4 ). In addition, we also revealed that the expression of many SOX members was observably associated with that of human leukocyte antigen (HLA)-I and II molecular [ 161 ] ( Figure 4 B), chemokines ( Figure 5 A), and chemokines receptors ( Figure 5 B) in HCC.…”