Molecular characterization of immunogenic cell death indicates prognosis and tumor microenvironment infiltration in osteosarcoma

Immunogenic cell death: A promising mechanism involving different therapeutic strategies for liver cancer

Hepatocellular carcinoma is a malignant tumor with a high mortality rate that seriously endangers human health. Although there are various treatments for hepatocellular carcinoma, the 5-year survival rate and prognosis of patients are still poor, depending on the stage. The proposal of immunogenic cell death provides a new idea and direction for the treatment of HCC. A variety of drugs act as effective inducers of ICD to induce the immunogenicity of tumor cells, significantly kill tumor cells, activate the body's inherent and adaptive immunity while producing and releasing damage-related molecular patterns, and significantly improve the treatment effect and side effects. This article briefly classifies the existing ICD inducers and describes how DAMPs change in this process. By summarizing the existing ICD-related studies applied to HCC treatment and proposing improvement methods for existing problems, this paper provides a theoretical summary for the future exploration of new therapies for HCC.

Leveraging multiple cell-death patterns based on machine learning to decipher the prognosis, immune, and immune therapeutic response of soft tissue sarcoma

Soft tissue sarcomas (STS) imposes a substantial healthcare burden on society. The progression of these tumors is significantly influenced by diverse modes of programmed cell death (PCD), which can serve as valuable indicators for assessing prognosis and immune therapeutic response in STS. Nonetheless, the precise role of multiple cell death patterns in STS is yet to be clarified. We employed 96 machine-learning algorithm combination frameworks to identify novel cell death-related signatures (CDSigs) with the highest mean c-index, indicating their excellence. The independence test and comparison with previously published models further confirmed the stability and quality of these signatures for survival prediction in STS. The nomogram, comprising the cell death score (CDS) and clinical features, exhibited excellent predictive performance. Additionally, the CDSigs revealed associations with immune checkpoint genes and the immune microenvironment in STS. Furthermore, the results demonstrated that patients with lower CDS had the potential for greater benefit from immune therapeutic responses compared to those with higher CDS. Moreover, STS patients with low-risk scores exhibited heightened sensitivity to doxorubicin, axitinib, cisplatin, and camptothecin. Finally, the RT-qPCR results underscored significant differences in expression levels of several CDSigs genes between STS and normal cells. Overall, we comprehensively analyzed the multiple PCD in STS and established a novel CDSig for STS patients. This novel CDSig holds great promise in deciphering the prognosis, immune, and immune therapeutic response of STS.

PKMYT1 kinase ameliorates cisplatin sensitivity in osteosarcoma

Cisplatin (DDP) remains a cornerstone therapy for osteosarcoma (OS); however, pervasive resistance severely limits its clinical efficacy and worsens patient outcomes. Developing strategies to enhance the chemotherapeutic responsiveness of OS cells is therefore of critical importance. Here, we conducted a kinome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen, coupled with transcriptome sequencing, to identify regulators of DDP sensitivity. This approach revealed protein kinase membrane-associated tyrosine/threonine 1 (PKMYT1) as a key regulator of DDP sensitivity in OS. Subsequent analysis of patient-derived clinical specimens, along with in vitro functional assays, demonstrated that DDP treatment induces the activation of PKMYT1 in OS cells. Importantly, PKMYT1 silencing markedly enhances cellular sensitivity to DDP, indicating its role in promoting chemoresistance. Mechanistically, PKMYT1 induces phosphorylation of nucleophosmin 1 (NPM1) at the S260 site, which competitively impairs NPM1 SUMOylation. This modification interferes with the recruitment of essential DNA damage response factors, including breast cancer suppressor gene 1 (BRCA1), receptor-associated protein 80 (RAP80), and RADiation sensitive protein 51 (RAD51), ultimately affecting double-strand break (DSB) repair. Furthermore, the selective PKMYT1 inhibitor RP6306 was found to synergize with DDP, amplifying its cytotoxic effects in OS cells. Collectively, these findings highlight PKMYT1 as a promising therapeutic target and provide a rationale for combinatorial strategies to overcome DDP resistance in OS.

Integrated analysis of multiple programmed cell death-related prognostic genes and functional validation of apoptosis-related genes in osteosarcoma

Osteosarcoma (OS) is one of the most prevalent bone malignancies with a poor prognosis. Various types of programmed cell death patterns can influence cancer progression and response to treatment. We aimed to integrate different molecular characteristics of cell death for risk stratification and personalized therapy. First, we obtained transcriptomic, single-cell transcriptomic, and clinical information from the TARGET-OS and GEO databases as well as analyzed genes in fourteen cell death patterns to establish the cell death index (CDI) signature. A nomogram constructed from the CDI calculated from seven genes in combination with metastasis could effectively predict the prognosis of OS patients. Subsequently, the prognostic value and immune characteristics in CDI-defined subgroups were analyzed. A construct nomogram model was also constructed with clinical information. Notably, immunohistochemistry confirmed that the expression of GALNT14, a core gene in CDI model, correlated with poor survival. Deficiency of the highly expressed prognostic gene GALNT14 significantly repressed OS progression and OS cell proliferation by promoting apoptosis. We subsequently demonstrated that Bortezomib, a targeted inhibitor of GALNT14, can be used to enhance chemosensitivity. Finally, it was further elucidated that Bortezomib reduces MT2A glycosylation and improves its stability to promote apoptosis in OS cells by inhibiting GALNT14 expression. In summary, integration of multiple cell death genes may improve the ability to stratify risk in patients with OS, and targeting GALNT14 with Bortezomib improves chemotherapy sensitivity and induces apoptosis.

Potential value of immunogenic cell death related-genes in refining European leukemiaNet guidelines classification and predicting the immune infiltration landscape in acute myeloid leukemia

Immunogenic cell death (ICD) is the kind of cell death that triggers the immune system. It affects several tumors, whereas its significance for prognosis in acute myeloid leukemia (AML) remains uncertain. AML categorization by cytogenetic variables is inaccurate. In addition, risk stratification of AML based on cytogenetics is imprecise. The data of AML patients were extracted from 4 databases, a total of 1,537 patients. Univariate and LASSO Cox regression analyses were conducted to construct an ICD risk signature (ICDRS). The ICDRS showed strong prognostic value for AML through Kaplan-Meier, Cox, ROC analyses and nomogram. Combining the ICDRS with the European LeukemiaNet (ELN) classification to redefine the risk stratification can better predict the prognosis of AML. Moreover, the ICDRS was examined to identify gene functional enrichment, immunological characteristics, drug susceptibility, and somatic mutation, which revealed considerable variations among different risk categories. We further validated the expression of ICDRS in the AML bone marrow microenvironment by single-cell RNA (scRNA) analysis. Ultimately, the functional role of CASP1 was proven in AML by a series of in-vitro experiments. Our study highlights the significant impact of ICDRS on AML, which may improve ELN risk classification, predict immune landscapes, and guide personalized therapy.

Predicting bladder cancer survival with high accuracy: insights from MAPK pathway-related genes

The mitogen-activated protein kinase (MAPK) pathway plays a critical role in tumor development and immunotherapy. Nevertheless, additional research is necessary to comprehend the relationship between the MAPK pathway and the prognosis of bladder cancer (BLCA), as well as its influence on the tumor immune microenvironment. To create prognostic models, we screened ten genes associated with the MAPK pathway using COX and least absolute shrinkage and selection operator (LASSO) regression analysis. These models were validated in the Genomic Data Commons (GEO) cohort and further examined for immune infiltration, somatic mutation, and drug sensitivity characteristics. Finally, the findings were validated using The Human Protein Atlas (HPA) database and through Quantitative Real-time PCR (qRT-PCR). Patients were classified into high-risk and low-risk groups based on the prognosis-related genes of the MAPK pathway. The high-risk group had poorer overall survival than the low-risk group and showed increased immune infiltration compared to the low-risk group. Additionally, the nomograms built using the risk scores and clinical factors exhibited high accuracy in predicting the survival of BLCA patients. The prognostic profiling of MAPK pathway-associated genes represents a potent clinical prediction tool, serving as the foundation for precise clinical treatment of BLCA.

GALNT5 functions as a suppressor of ferroptosis and a predictor of poor prognosis in pancreatic adenocarcinoma

Mucin-type O-glycosylation, a posttranslational modification of membrane and secretory proteins, facilitates metastasis and immune escape in tumor cells. N-acetylgalactosaminyl-transferase 5 (GALNT5), the enzyme initiating mucin-type O-glycosylation, is known to advance the progression of various tumors. Yet, the comprehensive role of GALNT5 in pan-cancer scenarios remains to be elucidated. In this research, we conducted a database-centric pan-cancer expression analysis of GALNT5. We examined its aberrant expression, assessed its prognostic implications, and explored the correlations between GALNT5 expression and factors such as ferroptosis, immune cell infiltration levels, and immune checkpoint gene expression across multiple tumor types. To substantiate GALNT5's role, we analyzed cell proliferation, migration, invasion, and ferroptosis in PAAD cells after GALNT5 knockdown. Additionally, RNA-seq was employed to discern potential downstream pathways influenced by GALNT5. Our findings indicate that GALNT5 expression is heightened in the majority of tumors, correlating with the prognosis of multiple cancers. There's a notable association between GALNT5 levels and ferroptosis-related genes, immune cell infiltration, and immune checkpoint genes. In PAAD specifically, the role of GALNT5 was further probed. Knockdown of GALNT5 curtailed the proliferation, migration, and invasion capacities of PAAD cells, concurrently promoting ferroptosis. Moreover, in vivo studies demonstrated that GALNT5 inhibition stunted PAAD tumor growth. The RNA-seq analysis unveiled inflammation and immune-centric pathways, such as the TNF signaling pathway, as potential downstream conduits of GALNT5. In conclusion, our pan-cancer study underscores GALNT5 as a potential therapeutic target for enhancing PAAD prognosis, given its strong ties with ferroptosis and immune cell infiltration. Our experiments further define GALNT5 as a novel suppressor of ferroptosis.

Integrative analysis of TROAP with molecular features, carcinogenesis, and related immune and pharmacogenomic characteristics in soft tissue sarcoma

Soft tissue sarcoma (STS) is an uncommon malignancy that often carries a grim prognosis. Trophinin-associated protein (TROAP) is augmented in a variety of tumors and can affect tumor proliferation. Nevertheless, the prognostic value and specific functions of TROAP in STS are still vague. Herein, we display that TROAP exhibits an augmented trend in STS, and its elevation correlates with a poor prognosis of STS. Furthermore, its reduction is related to increased immune cell infiltration, enhanced stroma, and elevation of immune activation. Meanwhile, the TROAP-derived genomic signature is validated to predict patient prognosis, immunotherapy, and drug response reliably. A nomogram constructed based on age, metastatic status, and a TROAP-derived risk score of an STS individual could be used to quantify the survival probability of STS. In addition, in vitro experiments have demonstrated that TROAP is overexpressed in STS, and the downregulation of TROAP could affect the proliferation, migration, metastasis, and cell cycle of STS cells. In summary, the TROAP expression is elevated in STS tissues and cells, which is related to the poor prognosis and malignant biological behaviors of STS. It could act as a potential prognostic biomarker for diagnosis and treatment of STS.

Prognostic value and immune landscapes of immunogenic cell death-related lncRNAs in hepatocellular carcinoma

BACKGROUND

Both immunogenic cell death (ICD) and long noncoding RNAs (lncRNAs) are strongly associated with tumor development, but the mechanism of action of ICD-associated lncRNAs in hepatocellular carcinoma (HCC) remains unclear.

METHODS

We collected data from 365 HCC patients from The Cancer Genome Atlas (TCGA) database. We formulated a prognostic signature of ICD-associated lncRNAs and a nomogram to predict prognosis. To explore the potential mechanisms and provide clinical guidance, survival analysis, enrichment analysis, tumor microenvironment analysis, tumor mutation burden (TMB), and drug sensitivity prediction were conducted based on the subgroups obtained from the risk score.

RESULTS

A prognostic signature of seven ICD-associated lncRNAs was constructed. Kaplan-Meier (K-M) survival curves showed a more unfavorable outcome in high-risk patients. The nomogram had a higher predictive value than the nomogram constructed without the risk model. Enrichment analysis confirmed that risk lncRNAs were closely associated with cell proliferation and mitosis. Most of the immune checkpoints currently used in therapy (e.g., PDCD1 and CTLA4) appeared to be elevated in high-risk patients. Tumor microenvironment analysis showed differential expression of lymphocytes (including natural killer cells, regulatory T cells, etc.) in the high-risk group. TMB had a higher incidence of mutations in the high-risk group (P=0.004). Chemotherapy drug sensitivity prediction provides effective guidelines for individual therapy. RT-qPCR of human HCC tissues verified the accuracy of the model.

CONCLUSION

We constructed an effective prognostic signature for patients with HCC using seven ICD-lncRNAs, which provides guidance for the prognostic assessment and personalized treatment of patients.