A Pan-Cancer Landscape of HOX-Related lncRNAs and Their Association With Prognosis and Tumor Microenvironment

Shao, Wei; Ding, Qian; Guo, Yugang; Xing, Juan; Huo, Zheng; Wang, Zhan; Xu, Qian; Guo, Yue

doi:10.3389/fmolb.2021.767856

Cited by 10 publications

(6 citation statements)

References 45 publications

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“…33,34 Cells in this cluster also expressed MEIS1 , which is expressed by differentiating granule cells 35 and HOXB-AS1 , which is a member of a large family of non-coding transcripts that are abnormally expressed in a wide range of cancers. 36 Consistent with the expression of MEIS1 , gene set enrichment analysis suggested this cluster contained mature cells (Supplementary Fig. S3G, H).…”

Section: Resultssupporting

confidence: 56%

Sonic hedgehog medulloblastoma cells in co-culture with cerebellar organoids converge towardsin vivomalignant cell states

van Essen,

Nicheperovich,

Schuster-Böckler

et al. 2024

Preprint

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Background In the malignant brain tumour sonic hedgehog medulloblastoma (SHH-MB) the properties of cancer cells are influenced by their microenvironment, but the nature of those effects and the phenotypic consequences for the tumour are poorly understood. The aim of this study was to identify phenotypic properties of SHH-MB cells that were driven by the non-malignant tumour microenvironment. Methods Human induced pluripotent cells (iPSC) were differentiated to cerebellar organoids to simulate the non-malignant tumour microenvironment. Tumour spheroids were generated from two distinct, long-established SHH-MB cell lines which were co-cultured with cerebellar organoids. We profiled the cellular transcriptomes of malignant and non-malignant cells by performing droplet-based single-cell RNA-sequencing (scRNA-seq). The transcriptional profiles of tumour cells in co-culture were compared with those of malignant cells cultured in isolation and with public SHH-MB datasets of patient tumours and patient- derived xenograft (PDX) models. Results SHH-MB cell lines in organoid co-culture adopted patient tumour-associated phenotypes and showed increased heterogeneity compared to monocultures. Sub-populations of co-cultured SHH-MB cells activated a key marker of differentiating granule cells, NEUROD1 that was not observed in tumour monocultures. Other sub-populations expressed transcriptional determinants consistent with a cancer stem cell (CSC)-like state that resembled cell states identified in vivo. Conclusion For SHH-MB cell lines in co-culture, there was a convergence of malignant cell states towards patterns of heterogeneity in patient tumours and PDX models implying these states were non-cell autonomously induced by the microenvironment. Therefore, we have generated an advanced, novel in vitro model of SHH-MB with potential translational applications.

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Section: Resultssupporting

confidence: 56%

Sonic hedgehog medulloblastoma cells in co-culture with cerebellar organoids converge towardsin vivomalignant cell states

van Essen,

Nicheperovich,

Schuster-Böckler

et al. 2024

Preprint

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“…The prognostic signature we constructed contains four lncRNAs, ANKRD10-IT1, HOXB-AS1, LINC00520 and LINC01165.One of these tumor types is HOXB-AS1, a cancer stimulator that has been linked to prognosis in various types of tumors [ 30 ]. A recent study has shown that HOXB-AS1 plays a part in pathways related to cancer and the immune system, indicating its potential involvement in the development of cancer and immune regulation in various types of cancer [ 31 ]. Furthermore, a notable association is observed between HOXB-AS1 and the immune scores in DLBCL, indicating a positive correlation.…”

Section: Discussionmentioning

confidence: 99%

Development and validation of a combined cuproptosis and immunogenic cell death prognostic model for diffuse large B-cell lymphoma

Wang,

Shi,

et al. 2024

Aging

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Background: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma worldwide with a high degree of heterogeneity. Cuproptosis and immunogenic cell death (ICD) have been considered to be vital for tumor progression. However, current understanding of cuproptosis and immunogenic cell death in DLBCL is still very limited. We aim to explore a prognostic model combining cuproptosis and immunogenic cell death in DLBCL. Methods: Pearson’s correlation analysis was utilized to acquire lncRNAs associated with cuproptosis and immunogenic cell death. Prognostic biomarker identification and model construction involved the use of univariate Cox regression, least absolute shrinkage and selection operator (LASSO) Cox regression, and multivariate Cox regression. We assessed the predictive capability of the risk model by conducting Kaplan-Meier analysis and time-dependent ROC analysis. The analysis and comparison of immune infiltration and drug sensitivity were conducted in this study. Moreover, RT-qPCR was employed to validate the expression of lncRNAs associated with cuproptosis and immunogenic cell death in DLBCL cell lines. Results: We identified 4 prognosis-related lncRNAs (ANKRD10-IT1, HOXB-AS1, LINC00520 and LINC01165) that were correlated with cuproptosis and immunogenic cell death. The model was verified to have a good and independent predictive ability in the prognostic prediction of DLBCL patients. Moreover, significant difference was observed in immune infiltration and drug sensitivity between high- and low-risk groups. Conclusion: Our discoveries could enhance the comprehension of the role of cuproptosis and ICD in DLBCL, potentially offering novel viewpoints and knowledge for personalized and precise treatment of DLBCL individuals.

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“…However, studies on the role of HOX genes on immunity or in the tumor microenvironment are limited. A previous study showed that HOX antisense transcript expression correlates with genes related to immune cell in ltration, speci c immune subtypes, and immune responses to cancer [15]. In colorectal cancer, high HOXC 6 expression is signi cantly associated with activation of cytokine pathways, expression of T cell attraction chemokines, in ltration of immune cells, and expression of immune checkpoint markers [16].…”

Section: Introductionmentioning

confidence: 99%

Effects of HOX family regulator-mediated modification patterns and tumor immunity characteristics on cancer- associated fibroblasts in endometrial cancer

Yang,

Li,

Yang

et al. 2024

Preprint

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Endometrial cancer is one of three major malignant tumors in women. The HOX gene regulates tumor development. However, the potential roles of HOX in the development and progression of endometrial cancer, cancer-associated fibroblasts (CAFs), and tumor microenvironment (TME) cell infiltration remain unknown. Here, a new scoring system was developed to quantify individual HOX patterns in uterine corpus endometrial cancer (UCEC). Meanwhile, our research was verified by immunohistochemistry and real-time quantitative PCR (RT-qPCR) and Single-cell RNA sequencing (scRNA-seq). Our study found that patients in the low HOX score group had abundant anti-tumor immune cell infiltration, good tumor differentiation, and better prognoses. Meanwhile, a high HOX score was associated with blockade of immune checkpoints, which enhances the response to immunotherapy. HOX gene was a pivotal factor in the development and progression of endometrial cancer and in the formation of tumor microenvironment diversity and complexity. HOX genes are involved in the regulation of CAF formation, and thus change microenvironments to promote tumor growth, invasion, and metastasis. In sum, HOX scores can be used as a new biomarker for the diagnosis and prediction of UCEC and to develop more effective therapeutic strategies.

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A Pan-Cancer Landscape of HOX-Related lncRNAs and Their Association With Prognosis and Tumor Microenvironment

Cited by 10 publications

References 45 publications

Sonic hedgehog medulloblastoma cells in co-culture with cerebellar organoids converge towardsin vivomalignant cell states

Sonic hedgehog medulloblastoma cells in co-culture with cerebellar organoids converge towardsin vivomalignant cell states

Development and validation of a combined cuproptosis and immunogenic cell death prognostic model for diffuse large B-cell lymphoma

Effects of HOX family regulator-mediated modification patterns and tumor immunity characteristics on cancer- associated fibroblasts in endometrial cancer

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