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Tumor-associated macrophages (TAM) are among the most abundant immune cells in the tumor microenvironment and are important mediators of tumor development and progression. Here, we identified a macrophage-associated long noncoding RNA (lncRNA), MALR, that facilitates progression of esophageal squamous cell carcinoma (ESCC). TAM-mediated secretion of TNFα drove MALR upregulation in ESCC cells. MALR promoted aerobic glycolytic activity and facilitated angiogenesis by activating the HIF1α signaling pathway. Mechanistically, MALR bound the dsRBD1 domain of interleukin enhancer-binding factor 3 (ILF3), promoting ILF3 protein stability and ILF3-mediated liquid–liquid phase separation (LLPS), thereby enhancing HIF1α mRNA stability by preventing PARN-mediated degradation. Loss of MALR suppressed cell line–based and patient-derived xenograft tumor growth. Clinically, high expression of MALR positively correlated with HIF1α target gene expression and indicated poor prognoses for patients with esophageal cancer. Overall, this study uncovers the physiologic roles of MALR/ILF3-mediated LLPS in tumor microenvironment remodeling, highlighting the MALR–ILF3–HIF1α axis as a potential target for cancer therapy.Significance:Secretion of TNFα by tumor-associated macrophages stimulates cancer cells to upregulate lncRNA MALR, which induces ILF3 liquid–liquid phase separation and activation of HIF1α signaling to promote cancer progression.

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Supplementary Methods

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Supplementary Table 1

Supplementary Methods provide experimental details on bioinformatics analysis, standard assays using commercial reagents and kits; Supplementary Figures S1-8 describe additional data to support the function of MNX1-AS1, which promotes the tumorigenesis in both CRC cells and tissues; Supplementary tables S1-6 show clinical information of sequenced patients, detailed screening candidates for validation, regression analysis together with mass spectrometry data used in this study.

Long noncoding RNAs (lncRNA) are involved in tumorigenesis and drug resistance. However, the roles and underlying mechanisms of lncRNAs in colorectal cancer are still unknown. In this work, through transcriptomic profiling analysis of 21 paired tumor and normal samples, we identified a novel colorectal cancer–related lncRNA, MNX1-AS1. MNX1-AS1 expression was significantly upregulated in colorectal cancer and associated with poor prognosis. In vitro and in vivo gain- and loss-of-function experiments showed that MNX1-AS1 promotes the proliferation of colorectal cancer cells. MNX1-AS1 bound to and activated Y-box-binding protein 1 (YB1), a multifunctional RNA/DNA-binding protein, and prevented its ubiquitination and degradation. A marked overlap between genes that are differentially expressed in MNX1-AS1 knockdown cells and transcriptional targets of YB1 was observed. YB1 knockdown mimicked the loss of viability phenotype observed upon depletion of MNX1-AS1. In addition, MYC bound the promoter of the MNX1-AS1 locus and activated its transcription. In vivo experiments showed that ASO inhibited MNX1-AS1, which suppressed the proliferation of colorectal cancer cells in both cell-based and patient-derived xenograft models. Collectively, these findings suggest that the MYC–MNX1-AS1–YB1 axis might serve as a potential biomarker and therapeutic target in colorectal cancer.Significance:This study highlights the discovery of a novel colorectal cancer biomarker and therapeutic target, MNX1-AS1, a long noncoding RNA that drives proliferation via a MYC/MNX1-AS1/YB1 signaling pathway.

Tumor-associated macrophages (TAM) are among the most abundant immune cells in the tumor microenvironment and are important mediators of tumor development and progression. Here, we identified a macrophage-associated long noncoding RNA (lncRNA), MALR, that facilitates progression of esophageal squamous cell carcinoma (ESCC). TAM-mediated secretion of TNFα drove MALR upregulation in ESCC cells. MALR promoted aerobic glycolytic activity and facilitated angiogenesis by activating the HIF1α signaling pathway. Mechanistically, MALR bound the dsRBD1 domain of interleukin enhancer-binding factor 3 (ILF3), promoting ILF3 protein stability and ILF3-mediated liquid–liquid phase separation (LLPS), thereby enhancing HIF1α mRNA stability by preventing PARN-mediated degradation. Loss of MALR suppressed cell line–based and patient-derived xenograft tumor growth. Clinically, high expression of MALR positively correlated with HIF1α target gene expression and indicated poor prognoses for patients with esophageal cancer. Overall, this study uncovers the physiologic roles of MALR/ILF3-mediated LLPS in tumor microenvironment remodeling, highlighting the MALR–ILF3–HIF1α axis as a potential target for cancer therapy. Significance: Secretion of TNFα by tumor-associated macrophages stimulates cancer cells to upregulate lncRNA MALR, which induces ILF3 liquid–liquid phase separation and activation of HIF1α signaling to promote cancer progression.

Background Numerous reports on microRNAs have illustrated their role in tumor growth and metastasis. Recently, a new prognostic factor, miR‐125b‐2‐3p, has been identified for predicting chemotherapeutic sensitivity in advanced colorectal cancer (CRC). However, the specific mechanisms and biological functions of miR‐125b‐2‐3p in advanced CRC under chemotherapy have yet to be elucidated. Methods MiR‐125b‐2‐3p expression was detected by real‐time PCR (RT‐PCR) in CRC tissues. The effects of miR‐125b‐2‐3p on the growth, metastasis, and drug sensitivity of CRC cells were tested in vitro and in vivo. Based on multiple databases, the upstream competitive endogenous RNAs (ceRNAs) and the downstream genes for miR‐125b‐2‐3p were predicted by bioinformatic analysis, followed by the experiments including luciferase reporter assays, western blot assays, and so on. Results MiR‐125b‐2‐3p was significantly lowly expressed in the tissues and cell lines of CRC. Higher expression of miR‐125b‐2‐3p was associated with relatively lower proliferation rates and fewer metastases. Moreover, overexpressed miR‐125b‐2‐3p remarkably improved chemotherapeutic sensitivity of CRC in vivo and in vitro. Mechanistically, miR‐125b‐2‐3p was absorbed by long noncoding RNA (lncRNA) XIST regulating WEE1 G2 checkpoint kinase (WEE1) expression. The upregulation of miR‐125b‐2‐3p inhibited the proliferation and epithelial‐mesenchymal transition (EMT) of CRC induced by lncRNA XIST. Conclusions Lower miR‐125b‐2‐3p expression resulted in lower sensitivity of CRC to chemotherapy and was correlated with poorer survival of CRC patients. LncRNA XIST promoted CRC metastasis acting as a ceRNA for miR‐125b‐2‐3p to mediate WEE1 expression. LncRNA XIST‐miR‐125b‐2‐3p‐WEE1 axis not only regulated CRC growth and metastasis but also contributed to chemotherapeutic resistance to CRC., Low expression of miR‐125b‐2‐3p in CRC was linked to lower chemotherapeutic sensitivity and poor survival. The lncRNA XIST promoted CRC invasion and migration by functioning as a ceRNA for miR‐125b‐2‐3p to mediate WEE1 expression. Our findings suggest that the lncRNA XIST‐miR‐125b‐2‐3p‐WEE1 axis not only regulated CRC growth and metastasis but also contributed to chemotherapeutic resistance to CRC, which may shed light on their targeted applications.

Long noncoding RNAs (lncRNA) are involved in tumorigenesis and drug resistance. However, the roles and underlying mechanisms of lncRNAs in colorectal cancer are still unknown. In this work, through transcriptomic profiling analysis of 21 paired tumor and normal samples, we identified a novel colorectal cancer–related lncRNA, MNX1-AS1. MNX1-AS1 expression was significantly upregulated in colorectal cancer and associated with poor prognosis. In vitro and in vivo gain- and loss-of-function experiments showed that MNX1-AS1 promotes the proliferation of colorectal cancer cells. MNX1-AS1 bound to and activated Y-box-binding protein 1 (YB1), a multifunctional RNA/DNA-binding protein, and prevented its ubiquitination and degradation. A marked overlap between genes that are differentially expressed in MNX1-AS1 knockdown cells and transcriptional targets of YB1 was observed. YB1 knockdown mimicked the loss of viability phenotype observed upon depletion of MNX1-AS1. In addition, MYC bound the promoter of the MNX1-AS1 locus and activated its transcription. In vivo experiments showed that ASO inhibited MNX1-AS1, which suppressed the proliferation of colorectal cancer cells in both cell-based and patient-derived xenograft models. Collectively, these findings suggest that the MYC–MNX1-AS1–YB1 axis might serve as a potential biomarker and therapeutic target in colorectal cancer. Significance: This study highlights the discovery of a novel colorectal cancer biomarker and therapeutic target, MNX1-AS1, a long noncoding RNA that drives proliferation via a MYC/MNX1-AS1/YB1 signaling pathway.

The therapeutic strategies of stage II/III colorectal cancer (CRC) patients after curative surgery remain controversial. In the clinical decision-making process, oncologists need to answer questions such as whether adjuvant chemotherapy is necessary or which therapeutic regimen should be given to each patient. At present, whether adjuvant chemotherapy should be applied is primarily based on histopathological features and clinical risk factors. However, only a fraction of patients can benefit from it. More rigorous stratifying biomarkers are urgently needed to help further distinguishing these populations of patients. Recent progress in next-generation sequencing and high-throughput technologies has greatly promoted biomarker discovery as well as our understanding of the underlying mechanisms in CRC. Novel genetic and epigenetic biomarkers that are associated with prognosis or therapeutic responses have emerged. In this review, we discuss the strategies of biomarker discovery and summarize the status and assess the utility of previously published biomarkers in CRC.

Esophageal squamous cell carcinoma (ESCC) is one of the most life- and health-threatening malignant diseases worldwide, especially in China. Long noncoding RNAs (lncRNAs) have emerged as important regulators of tumorigenesis and tumor progression. However, the roles and mechanisms of lncRNAs in ESCC require further exploration. Here, in combination with a small interfering RNA (siRNA) library targeting specific lncRNAs, we performed MTS and Transwell assays to screen functional lncRNAs that were overexpressed in ESCC. TMPO-AS1 expression was significantly upregulated in ESCC tumor samples, with higher TMPO-AS1 expression positively correlated with shorter overall survival times. In vitro and in vivo functional experiments revealed that TMPO-AS1 promotes the proliferation and metastasis of ESCC cells. Mechanistically, TMPO-AS1 bound to fused in sarcoma (FUS) and recruited p300 to the TMPO promoter, forming biomolecular condensates in situ to activate TMPO transcription in cis by increasing the acetylation of histone H3 lysine 27 (H3K27ac). Targeting TMPO-AS1 led to impaired ESCC tumor growth in a patient-derived xenograft (PDX) model. We found that TMPO-AS1 is required for cell proliferation and metastasis in ESCC by promoting the expression of TMPO, and both TMPO-AS1 and TMPO might be potential biomarkers and therapeutic targets in ESCC.

Background PFKFB3 is a crucial metabolic enzyme which is highly upregulated in cancer cells, prompting much research on potential selective inhibitors of PFKFB3 which all have shown promising tumor inhibitive effects. However, clinical trials such as NCT02044861 on PFKFB3 inhibitors seem resultless. With recent implications of cancer metabolism and tumor immune evasion, we hypothesized that PFKFB3 inhibition and subsequent metabolic reprogramming might affect tumor immune evasion. Methods We examined the function of PFK-15 on tumor cells in vitro and in vivo in immune-deficient nude-mice models and immune-competent mouse models such as C57/BALB/c-CDX models and huPBMC-CDX and PBX models. CO-IP, fluorescent immunohistochemistry, CHIP and dual-luciferase assays were used to investigate the underlying mechanism. Results Inhibition of PFKFB3 using PFK-15 suppressed cell growth in human esophageal cell lines in vitro and in vivo in immune-deficient xenografts. However, inhibition of PFKFB3 caused a marked upregulation in PD-L1 which inactivated cocultured T-cells in vitro and compromised anti-tumor immunity in immune-competent mouse, an effect which could be reversed when PFK-15 was combined with PD-1 mab. Mechanistically, we identified ERK pathway upregulation after treatment with PFK-15, which increased PFKFB3 phosphorylation levels, causing its transformation and increased its binding with HIF-1α, then Phospho-PFKFB3 co-translocated into the nucleus together with HIF-1α by binding with importin α5, whereby nuclear HIF-1α attaches itself to HRE regions on PD-L1 promoter, upregulating PD-L1 expression. Clinically, we observed higher Phospho-PFKFB3 in tumor tissues from non-responders to PD-1 mab treated ESCC patients. Conclusions This study shows that inhibition of PFKFB3 increases immune evasion via the phospho-PFKFB3–HIF-1α–PD-L1 axis. The translational significance of this study lies in the fact that in-vivo experiments in immune-competent mice using the closest to human immune tumor microenvironment model huPBMC-CDX/PDX combining PFKFB3 inhibitors and PD-1 mab resulted in a marked decrease in tumor development. These findings may be of relevance for the design of anti-cancer treatment trials with PFKFB3 inhibitors.

Background Tumor immune evasion is an important hallmark of cancer. The roles of long non-coding RNAs (lncRNAs) in the process of cancer immunosurveillance remain largely unknown. In this study, we aimed to identify oncogenic lncRNAs that are involved in the immunosuppression of esophageal squamous cell carcinoma (ESCC) and investigate underlying mechanisms. Methods High-throughput sequencing and bioinformatics analysis were used to identify lncRNAs that are highly expressed in ESCC tissues and blood. Using the data from a cohort of patients in the clinical trial JSOO1, the relationship between lncRNA expression level and PD-1 mAb response (ORR and DCR) was analyzed. RNA interference and CRISPR-Cas9 were used to explore the functional roles of the lncRNA. In vivo, the human PBMC engrafted humanized xenograft model was established to assess the therapeutic responses of that specific lncRNA inhibitor and its combination with PD-1 mAb. Results Increased expression of LRTIS was observed in ESCC and was correlated with poor prognosis. Conversely, LRTIS high expression group responded better to immunotherapy (ORR 19.56% vs 9.09%, DCR 54.35% vs 18.18%). In vivo, LRTIS knockout significantly inhibited tumor growth in Hu-PBMC mice, and increased sensitivity to PD-1 mAb treatment, as shown by an increased proportion of IFN-γ+CD8+ T cells in xenografts. LRTIS could inhibit the expression of immuno-checkpoints such as PD-L1, PD-L2 and IDO1. Mechanistically, LRTIS was directly associated with MLL1 and significantly affected MLL1 stability by inhibiting its ubiquitination and subsequent proteasomal degradation. LRTIS competitively bonded to MLL1 preventing ASB2 from binding to MLL1, which explained MLL1 ubiquitination inhibition. Knocking out LRTIS, resulted in MLL1 mediated H3K4me decrease in the promoter region of immuno-checkpoints, causing their downregulation. Clinically, dysregulation of LRTIS-MLL1-PD-L1 axis could also be observed in patients. Conclusions The LRTIS plays an essential role in ESCC immunosuppression by binding to and stabilizing MLL1. This study identified a novel immuno-checkpoint regulating lncRNA and revealed a novel mechanism underlying lncRNA-mediated cancer immuno-microenvironment remodeling. Translational studies further implicated that LRTIS is a promising prognostic biomarker for cancer immunotherapy, and a potential target for immunotherapy.