结直肠癌起始细胞的综合基因组和功能免疫分析，以调节干性特性和对免疫反应的敏感性。

The integrative genomic and functional immunological analyses of colorectal cancer initiating cells to modulate stemness properties and the susceptibility to immune responses.

作者信息

Tout Issam, Bougarn Salim, Toufiq Mohammed, Gopinath Neha, Hussein Ola, Sathappan Abbirami, Chin-Smith Evonne, Rehaman Fazulur, Mathew Rebecca, Mathew Lisa, Wang Kun, Liu Li, Salhab Abdulrahman, Soloviov Oleksandr, Tomei Sara, Hasan Waseem, Da'as Sahar, Bejaoui Yosra, Hajj Nady El, Maalej Karama Makni, Dermime Said, Rasul Kakil, Dellabona Paolo, Casorati Giulia, Turdo Alice, Todaro Matilde, Stassi Giorgio, Ferrone Soldano, Wang Xinhui, Maccalli Cristina

机构信息

Laboratory of Immune Biological Therapy, Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar.

Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.

出版信息

J Transl Med. 2025 Feb 17;23(1):193. doi: 10.1186/s12967-025-06176-0.

DOI:10.1186/s12967-025-06176-0

PMID:39962504

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11834280/

Abstract

BACKGROUND

Colorectal cancer (CRC) initiating cells (CICs) possess self-renewal capabilities and are pivotal in tumor recurrence and resistance to conventional therapies, including immunotherapy. The mechanisms underlying their interaction with immune cells remain unclear.

METHODS

We conducted a multi-omics analysis-encompassing DNA methylation, total RNA sequencing, and microRNAs (miRNAs; N = 800) profiling on primary CICs and differentiated tumor cell lines, including autologous pairs. Functional immunological assays were performed to assess the impact of miRNA modulation.

RESULTS

CICs exhibited distinct methylation patterns, transcriptomic profiles, and miRNA expressions compared to differentiated tumor cells (p < 0.05 or 0.01). Notably, miRNA-15a and -196a were implicated in regulating tumorigenic pathways, such as epithelial-to-mesenchymal transition (EMT), TGF-β signaling, and immune modulation. The transfection of CICs with miRNA mimics led to the downregulation of oncogenic EMT markers (CRKL, lncRNA SOX2-OT, JUNB, SMAD3) and TGF-β pathway, resulting in a significant reduction of the in vitro proliferation and the tumorigenicity and migration in a zebrafish xenograft model. Additionally, miRNA-15a enhanced the expression of antigen processing machinery and decreased the expression of immune checkpoints (PD-L1, PD-L2, CTLA-4) and immunosuppressive cytokines (IL-4). The co-culture of HLA-matched lymphocytes with CICs overexpressing the miRNA-15a, elicited robust tumor-specific immune responses, characterized by a shift toward central and effector memory T cell phenotypes and prevented their terminal differentiation and exhaustion. The combination of miRNA modulation with Indoleamine 2,3-dioxygenase blockade and immunomodulating agents further potentiated these effects.

CONCLUSIONS

Our study demonstrates that the modulation of miRNA-15a in CICs not only suppresses the tumorigenic properties but also enhances their visibility to the immune system by upregulating antigen presentation and reducing immunomodulatory molecules. These findings suggest that combining miRNA modulation with epigenetic or immunomodulatory agents holds significant promise for overcoming treatment resistance in CRC.

摘要

背景

结直肠癌（CRC）起始细胞（CICs）具有自我更新能力，在肿瘤复发和对包括免疫疗法在内的传统疗法的抗性中起关键作用。它们与免疫细胞相互作用的潜在机制仍不清楚。

方法

我们对原发性CICs和分化的肿瘤细胞系（包括自体配对）进行了多组学分析，涵盖DNA甲基化、总RNA测序和微小RNA（miRNA；N = 800）谱分析。进行了功能免疫学测定以评估miRNA调节的影响。

结果

与分化的肿瘤细胞相比，CICs表现出不同的甲基化模式、转录组谱和miRNA表达（p < 0.05或0.01）。值得注意的是，miRNA - 15a和 - 196a参与调节致癌途径，如上皮 - 间质转化（EMT）、TGF - β信号传导和免疫调节。用miRNA模拟物转染CICs导致致癌性EMT标志物（CRKL、lncRNA SOX2 - OT、JUNB、SMAD3）和TGF - β途径的下调，导致体外增殖、肿瘤发生能力和斑马鱼异种移植模型中的迁移能力显著降低。此外，miRNA - 15a增强了抗原加工机制的表达，并降低了免疫检查点（PD - L1、PD - L2、CTLA - 4）和免疫抑制细胞因子（IL - 4）的表达。将HLA匹配的淋巴细胞与过表达miRNA - 15a的CICs共培养，引发了强烈的肿瘤特异性免疫反应，其特征是向中央和效应记忆T细胞表型转变，并防止它们的终末分化和耗竭。miRNA调节与吲哚胺2,3 - 双加氧酶阻断和免疫调节药物的联合进一步增强了这些作用。