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PURPOSE Pembrolizumab or nivolumab plus chemotherapy was approved as a first-line treatment for high programmed cell death ligand 1 (PD-L1)–expressing esophageal squamous cell carcinoma (ESCC) by the European Medicines Agency, whereas the US Food and Drug Administration approved this regimen regardless of PD-L1 expression. The superiority of programmed death-1 (PD-1) antibody plus chemotherapy over chemotherapy alone in patients with low PD-L1–expressing ESCC remains debatable. METHODS Post hoc analysis of the Chinese JUPITER-06 study focusing on efficacy stratified by PD-L1 tumor proportion score (TPS; using JS311 antibody) was conducted. Electronic databases were searched to identify eligible randomized controlled trials for meta-analysis. Study-level pooled analyses of hazard ratios (HRs) for overall survival and progression-free survival and odds ratios for objective response rate according to PD-L1 expression were performed. RESULTS The post hoc analysis of JUPITER-06 showed more prominent clinical benefit with PD-1 antibody plus chemotherapy than with chemotherapy alone in both the high and low PD-L1–expressing subgroups. Five randomized controlled trials were included in the meta-analysis, and two PD-L1 expression scoring criteria, TPS (≥ 1%/< 1%) and combined positive score (CPS, ≥ 10/< 10), were analyzed. Significant overall survival benefit by adding PD-1 antibody to chemotherapy was observed in both the TPS < 1% (HR, 0.74; 95% CI, 0.56 to 0.97) and CPS < 10 (HR, 0.77; 95% CI, 0.66 to 0.89) subgroups. Similarly, significantly prolonged progression-free survival was observed in both the TPS < 1% (HR, 0.66; 95% CI, 0.50 to 0.86) and CPS < 10 (HR, 0.63; 95% CI, 0.47 to 0.84) subgroups. In addition, the objective response rate of the TPS < 1% subgroup was significantly improved (odds ratio, 1.71; 95% CI, 1.27 to 2.29). In all high PD-L1–expressing subgroups, the pooled benefit of PD-1 antibody plus chemotherapy was significantly better than that of chemotherapy. CONCLUSION This study provided novel evidence supporting the superiority of PD-1 antibody plus chemotherapy to chemotherapy alone in patients with advanced ESCC with low PD-L1 expression. Further studies of predictive biomarkers are warranted.

ObjectiveMethionine metabolism is involved in a myriad of cellular functions, including methylation reactions and redox maintenance. Nevertheless, it remains unclear whether methionine metabolism, RNA methylation and antitumour immunity are molecularly intertwined.DesignThe antitumour immunity effect of methionine-restricted diet (MRD) feeding was assessed in murine models. The mechanisms of methionine and YTH domain-containing family protein 1 (YTHDF1) in tumour immune escape were determined in vitro and in vivo. The synergistic effects of MRD or YTHDF1 depletion with PD-1 blockade were also investigated.ResultsWe found that dietary methionine restriction reduced tumour growth and enhanced antitumour immunity by increasing the number and cytotoxicity of tumour-infiltrating CD8+T cells in different mouse models. Mechanistically, the S-adenosylmethionine derived from methionine metabolism promoted the N6-methyladenosine (m6A) methylation and translation of immune checkpoints, including PD-L1 and V-domain Ig suppressor of T cell activation (VISTA), in tumour cells. Furthermore, MRD or m6A-specific binding protein YTHDF1 depletion inhibited tumour growth by restoring the infiltration of CD8+T cells, and synergised with PD-1 blockade for better tumour control. Clinically, YTHDF1 expression correlated with poor prognosis and immunotherapy outcomes for cancer patients.ConclusionsMethionine and YTHDF1 play a critical role in anticancer immunity through regulating the functions of T cells. Targeting methionine metabolism or YTHDF1 could be a potential new strategy for cancer immunotherapy.

BackgroundWhile recent studies have separately explored mutational signatures and the tumor microenvironment (TME), there is limited research on the associations of both factors in a pan-cancer context.Materials and methodsWe performed a pan-cancer analysis of over 8,000 tumor samples from The Cancer Genome Atlas (TCGA) project. Machine learning methods were employed to systematically explore the relationship between mutational signatures and TME and develop a risk score based on TME-associated mutational signatures to predict patient survival outcomes. We also constructed an interaction model to explore how mutational signatures and TME interact and influence cancer prognosis.ResultsOur analysis revealed a varied association between mutational signatures and TME, with the Clock-like signature showing the most widespread influence. Risk scores based on mutational signatures mainly induced by Clock-like and AID/APOBEC activity exhibited strong pan-cancer survival stratification ability. We also propose a novel approach to predict transcriptome decomposed infiltration levels using genome-derived mutational signatures as an alternative approach for exploring TME cell types when transcriptome data are unavailable. Our comprehensive analysis revealed that certain mutational signatures and their interaction with immune cells significantly impact clinical outcomes in particular cancer types. For instance, T cell infiltration levels only served as a prognostic biomarker in melanoma patients with high ultraviolet radiation exposure, breast cancer patients with high homologous recombination deficiency signature, and lung adenocarcinoma patients with high tobacco-associated mutational signature.ConclusionOur study comprehensively explains the complex interplay between mutational signatures and immune infiltration in cancer. The results highlight the importance of considering both mutational signatures and immune phenotypes in cancer research and their significant implications for developing personalized cancer treatments and more effective immunotherapy.

ObjectiveCirculating tumour DNA (ctDNA) sequencing is increasingly used in the clinical management of patients with colorectal cancer. However, the genomic heterogeneity in ctDNA during treatments and its impact on clinical outcomes remain largely unknown.DesignWe conducted a prospective cohort study (NCT04228614) of 171 patients with unresectable metastatic colorectal cancer (mCRC) who underwent first-line treatment and prospectively collected blood samples with or without tumour samples from patients at baseline and sequentially until disease progression or last follow-up.ResultsThe RAS/BRAF alterations in paired baseline tissue and plasma samples from 63 patients displayed a favourable concordance (81.0%, 51/63). After a period of first-line treatment (median time between baseline and last liquid biopsy, 4.67 months), 42.6% (26/61) of RAS-mutant patients showed RAS clearance and 50.0% (5/10) of BRAF-mutant patients showed BRAF clearance, while 3.6% (3/84) and 0.7% (1/135) of patients showed new RAS or BRAF mutations in ctDNA. Patients with plasma RAS/BRAF clearance showed similar progression-free survival (PFS) and overall survival (OS) with patients who remained RAS/BRAF wild-type, while much better outcomes than those who remained RAS/BRAF mutant. Patients who gained new RAS/BRAF mutations showed similar prognosis as those who maintained RAS/BRAF mutations, and shorter PFS and OS than those who remained RAS/BRAF wild-type.ConclusionThis prospective, serial and large-scale ctDNA profiling study reveals the temporal heterogeneity of mCRC-related somatic variants, which should be given special attention in clinical practice, as evidenced by the finding that the shift in plasma RAS/BRAF mutational status can yield a drastic change in survival outcomes.

Metabolic inhibition via PFKFB3 inhibition has demonstrated considerable tumor inhibitory effects in various studies; however, PFKFB3 inhibition did not show satisfactory tumor inhibition when used in clinical trials. PFKFB3 is a crucial metabolic enzyme that is highly upregulated in cancer cells and directly affects tumor glycolysis. Here, we showed that PFKFB3 inhibition suppresses tumors in vitro and in vivo in immune-deficient xenografts. However, this inhibition induces the upregulation of PD-L1 levels, which inactivated cocultured T-cells in vitro, compromises anti-tumor immunity in vivo, and reduced anti-tumor efficacy in an immune-competent mouse model. Functionally, PD-1 mAb treatment enhances the efficacy of PFKFB3 inhibition in immunocompetent and hu-PBMC NOG mouse models. Mechanistically, PFKFB3 inhibition increases phosphorylation of PFKFB3 at residue Ser461, which increases interaction with HIF-1α, and their colocalization into the nucleus, where HIF-1α transcriptionally upregulate PD-L1 expression and causes subsequent tumor immune evasion. Higher phos-PFKFB3 correlated with higher PD-L1 expression, lower CD8 and GRZMB levels, and shorter survival time in ESCC patients.

Methionine metabolism is involved in a myriad of cellular functions, including methylation reactions and redox maintenance. Nevertheless, it remains unclear whether methionine metabolism, RNA methylation and antitumour immunity are molecularly intertwined.The antitumour immunity effect of methionine-restricted diet (MRD) feeding was assessed in murine models. The mechanisms of methionine and YTH domain-containing family protein 1 (YTHDF1) in tumour immune escape were determined in vitro and in vivo. The synergistic effects of MRD or YTHDF1 depletion with PD-1 blockade were also investigated.We found that dietary methionine restriction reduced tumour growth and enhanced antitumour immunity by increasing the number and cytotoxicity of tumour-infiltrating CD8Methionine and YTHDF1 play a critical role in anticancer immunity through regulating the functions of T cells. Targeting methionine metabolism or YTHDF1 could be a potential new strategy for cancer immunotherapy.

Gastrointestinal cancer causes countless deaths every year due to therapeutic resistance. However, whether metabolic alterations contribute to chemoresistance is not well understood. In this study, we report that fatty acid (FA) catabolism was activated in gastrointestinal cancer cells treated with oxaliplatin, which exhibited higher expression of the rate-limiting enzymes carnitine palmitoyltransferase 1B (CPT1B) and CPT2. The clinical analysis also showed that high expression of these enzymes was associated with poor oxaliplatin-based chemotherapy outcomes in patients. Furthermore, genetic or pharmacological inhibition of CPT2 with perhexiline disturbed NADPH and redox homeostasis and increased reactive oxygen species (ROS) generation and cell apoptosis in gastrointestinal cancer cells following oxaliplatin treatment. Specifically, the combination of oxaliplatin and perhexiline significantly suppressed the progression of gastrointestinal cancer in cell-based xenograft and patient-derived xenograft (PDX) models. Mechanistically, CPT2 was transcriptionally upregulated by nuclear factor of activated T cells 3 (NFATc3), which translocated to the nucleus in response to oxaliplatin treatment. In summary, our study suggests that the inhibition of CPT-mediated FA catabolism combined with conventional chemotherapy is a promising therapeutic strategy for patients with gastrointestinal cancers.

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.

Nowadays, the direct matrix converter (DMC) is a well-accepted topology for AC/AC conversion. In DMC topology, the commutation method should be considered to avoid the short circuit at the input and open circuit at the output during commutations. The DMC with the conventional three-step commutation of input voltage type can produce sinusoidal output with low voltage error and low harmonic distortion. However, the inrush current during the commutation process results in stability problem and/or protective issue. In this paper, a novel three-step commutation is proposed to simultaneously maintain output voltage error cancellation advantage and avoid instantaneous short circuits during commutations. Accordingly, the proposed method removes the inrush current and reduces the THD. Moreover, it causes the switching losses to reduce by providing soft switching. The simulation study has been accomplished, and its results demonstrate the effectiveness of the proposed method.

Background Although immune checkpoint inhibitor (ICI) is regarded as a breakthrough in cancer therapy, only a limited fraction of patients benefit from it. Cancer stemness can be the potential culprit in ICI resistance, but direct clinical evidence is lacking. Methods Publicly available scRNA-Seq datasets derived from ICI-treated patients were collected and analyzed to elucidate the association between cancer stemness and ICI response. A novel stemness signature (Stem.Sig) was developed and validated using large-scale pan-cancer data, including 34 scRNA-Seq datasets, The Cancer Genome Atlas (TCGA) pan-cancer cohort, and 10 ICI transcriptomic cohorts. The therapeutic value of Stem.Sig genes was further explored using 17 CRISPR datasets that screened potential immunotherapy targets. Results Cancer stemness, as evaluated by CytoTRACE, was found to be significantly associated with ICI resistance in melanoma and basal cell carcinoma (both P < 0.001). Significantly negative association was found between Stem.Sig and anti-tumor immunity, while positive correlations were detected between Stem.Sig and intra-tumoral heterogenicity (ITH) / total mutational burden (TMB). Based on this signature, machine learning model predicted ICI response with an AUC of 0.71 in both validation and testing set. Remarkably, compared with previous well-established signatures, Stem.Sig achieved better predictive performance across multiple cancers. Moreover, we generated a gene list ranked by the average effect of each gene to enhance tumor immune response after genetic knockout across different CRISPR datasets. Then we matched Stem.Sig to this gene list and found Stem.Sig significantly enriched 3% top-ranked genes from the list (P = 0.03), including EMC3, BECN1, VPS35, PCBP2, VPS29, PSMF1, GCLC, KXD1, SPRR1B, PTMA, YBX1, CYP27B1, NACA, PPP1CA, TCEB2, PIGC, NR0B2, PEX13, SERF2, and ZBTB43, which were potential therapeutic targets. Conclusions We revealed a robust link between cancer stemness and immunotherapy resistance and developed a promising signature, Stem.Sig, which showed increased performance in comparison to other signatures regarding ICI response prediction. This signature could serve as a competitive tool for patient selection of immunotherapy. Meanwhile, our study potentially paves the way for overcoming immune resistance by targeting stemness-associated genes.

The genetic basis of colorectal cancer (CRC) and its clinical associations remain poorly understood due to limited samples or targeted genes in current studies. Here, we perform ultradeep whole-exome sequencing on 1015 patients with CRC as part of the ChangKang Project. We identify 46 high-confident significantly mutated genes, 8 of which mutate in 14.9% of patients: LYST, DAPK1, CR2, KIF16B, NPIPB15, SYTL2, ZNF91, and KIAA0586. With an unsupervised clustering algorithm, we propose a subtyping strategy that classisfies CRC patients into four genomic subtypes with distinct clinical characteristics, including hypermutated, chromosome instability with high risk, chromosome instability with low risk, and genome stability. Analysis of immunogenicity uncover the association of immunogenicity reduction with genomic subtypes and poor prognosis in CRC. Moreover, we find that mitochondrial DNA copy number is an independent factor for predicting the survival outcome of CRCs. Overall, our results provide CRC-related molecular features for clinical practice and a valuable resource for translational research.

4054 Background: Circulating tumor DNA (ctDNA) is a promising biomarker for detecting molecular residual disease (MRD) and relapse after definitive treatment in multiple solid cancers. However, the significance of ctDNA is rarely clarified in locoregional gastric cancer (GC). Here, we conducted a prospective and observational study to evaluate the utility of ctDNA in predicting the recurrence risk of GC. Methods: From October 2016 to June 2019, 100 patients with stage II/III resectable GC were recruited in this study (NCT02887612). Primary tumors and plasma samples were collected perioperatively and after adjuvant chemotherapy (ACT). Somatic variants were captured via a targeted sequencing panel of 425 cancer-related genes. The plasma of patients was defined as ctDNA positive only if one or more variants detected in the plasma presented in at least 2% of the primary tumors. All the patients received curative-intent standard-of-care therapy. Results: Preoperative ctDNA was detectable in 38 (38.0%) patients but showed limited value for predicting recurrence. After surgery (median days, 4), the plasma of 25 (25.0%) patients were still ctDNA positive and they had higher recurrence risk than the non-positive patients (hazard ratio [HR], 2.74 (95% CI: 1.37–5.48); P = 0.003). Forty-one patients had evaluable plasma after ACT and 10 (24.4%) of them who were ctDNA positive had remarkably higher recurrence and death risk compared with ctDNA-negative patients (recurrence-free survival [RFS] HR = 14.99 (95% CI: 3.08–72.96); P < 0.001; overall survival HR, 11.88 (95% CI: 2.38–59.24); P < 0.001). In particular, post-ACT ctDNA achieved better predictive performance (sensitivity, 77.8%; specificity, 90.6%) than both postoperative ctDNA and post-treatment tumor biomarkers (i.e., CEA, CA199, and CA72-4). In all multivariate analyses, ctDNA positivity was an independent factor of RFS. Patients with ERBB4 mutation in their primary tumors had poorer RFS compared to those were ERBB4 wildtype (HR = 3.46 (95% CI: 1.32–9.03); P = 0.007). A comprehensive model incorporating ctDNA status for recurrence risk prediction showed a higher concordance index (0.78; 95%CI, 0.71–0.84) than the model without ctDNA status (0.71; 95%CI, 0.64–0.79; P = 0.009). Conclusions: Postoperative and post-ACT ctDNA was associated with MRD and high risk of relapse in patients with stage II/III GC and can be utilized to guide GC management in post-surgical settings.

The acidic tumor microenvironment provides an energy source driving malignant tumor progression. Adaptation of cells to an acidic environment leads to the emergence of cancer stem cells. The expression of the vitamin D receptor (VDR) is closely related to the initiation and development of colorectal carcinoma (CRC), but its regulatory mechanism in CRC stem cells is still unclear. Our study revealed that acidosis reduced VDR expression by downregulating peroxisome proliferator-activated receptor delta (PPARD) expression. Overexpression of VDR effectively suppressed the stemness and oxaliplatin resistance of cells in acidosis. The nuclear export signal in VDR was sensitive to acidosis, and VDR was exported from the nucleus. Chromatin immunoprecipitation (ChIP) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analyses showed that VDR transcriptionally repressed SRY-box 2 (SOX2) by binding to the vitamin D response elements in the promoter of SOX2, impairing tumor growth and drug resistance. We demonstrated that a change in the acidic microenvironment combined with overexpression of VDR substantially restricted the occurrence and development of CRC in vivo. These findings reveal a new mechanism by which acidosis could affect the stemness of CRC cells by regulating the expression of SOX2 and show that abnormal VDR expression leads to ineffective activation of vitamin D signaling, resulting in a lack of efficacy of vitamin D in antineoplastic process.

Objectives Although the genomic landscape of small‐cell carcinoma of the oesophagus (SCCE) has been dissected, its transcriptome‐level aberration and immune microenvironment status are unknown. Methods Using ultra‐deep whole transcriptome sequencing, we analysed the expression profile of nine paired SCCE samples and compared the transcriptome with public transcriptomic data set of normal oesophageal mucosa and other cancer types. Based on the transcriptome data, the immune signatures were investigated. The genomic data of 55 SCCE samples were also applied for immune checkpoint blockade therapy (ICBT) biomarker evaluation including microsatellite instability (MSI) status, tumor mutation burden (TMB) and neoantigen burden (TNB). Also, we evaluated the CD8, CD68 and programmed death‐ligand 1 (PD‐L1) in 62 retrospective SCCE samples with IHC assay. Results Differential expression analysis revealed that the cell cycle, p53, and Wnt pathways are significantly deregulated in SCCE. Immune microenvironment analysis showed that high leucocyte infiltration and adaptive immune resistance did occur in certain individuals, while the majority showed a relatively suppressive immune status. Immune checkpoints such as CD276 and LAG‐3 were upregulated, and higher M2 macrophage infiltration in tumor tissues. Furthermore, normal tissues adjacent to the tumors of SCCE presented a more activated inflammatory status than tumor‐free healthy controls. These observations showed that ICBT might benefit SCCE patients. As the critical biomarker of ICBT, TMB of SCCE was 3.64 with the predictive objective response rate 13.2%, while the PD‐L1‐positive rate was 43%. Conclusions Our study systematically characterized the immune microenvironment in small‐cell carcinoma of the esophagus and provided evidence that several patients with SCCE may benefit from immune checkpoint blockade therapy., In this study, transcriptomic aberrance and immune microenvironment of small‐cell carcinoma of the esophagus (SCCE) was comprehensively characterized with transcriptome and immunohistochemistry analysis. Assessment of immune checkpoint blockade (ICB) treatment biomarkers provides a rationale for use of ICB treatment in patients with SCCE.

Background Immune checkpoint inhibitors (ICIs) have achieved impressive success in different cancer types, yet responses vary and predictive biomarkers are urgently needed. Growing evidence points to a link between DNA methylation and anti-tumor immunity, while clinical data on the association of genomic alterations in DNA methylation-related genes and ICI response are lacking. Methods Clinical cohorts with annotated response and survival data and matched mutational data from published studies were collected and consolidated. The predictive function of specific mutated genes was first tested in the discovery cohort and later validated in the validation cohort. The association between specific mutated genes and tumor immunogenicity and anti-tumor immunity was further investigated in the Cancer Genome Altas (TCGA) dataset. Results Among twenty-one key genes involving in the regulation of DNA methylation, TET1-mutant (TET1-MUT) was enriched in patients responding to ICI treatment in the discovery cohort (P 0.05 in both two non-ICI-treated cohorts). In TCGA dataset, TET1-MUT was strongly associated with higher tumor mutational burden and neoantigen load, and inflamed pattern of tumor-infiltrating T lymphocytes, immune signatures and immune-related gene expressions. Conclusions TET1-MUT was strongly associated with higher ORR, better DCB, longer PFS, and improved OS in patients receiving ICI treatment, suggesting that TET1-MUT is a novel predictive biomarker for immune checkpoint blockade across multiple cancer types.

Background Long non-coding RNAs (lncRNAs) are emerging as key molecules in gastric cancer(GC), yet their potential molecular mechanisms are not well understood. The aim of our study is to identify lncRNAs that are up-regulated in gastric cancer tissues and explore their function in gastric cancer metastasis. Methods RNA sequencing of 48 paired gastric tumor and non-tumor tissues in SYSUCC was conducted. The upregulated lncRNAs were selected and overlapped with those in TCGA database. A siRNA library was established using the top 50 lncRNAs highly expressed in GC and used to identify lncRNAs that significantly affected cell migration based on transwell assays. The expression of our focused lncRNA CRCAL-2(ColoRectal Cancer Associated LncRNA-2) was measured using quantitative reverse transcription PCR assays and lncRNA in situ hybridization. In vivo,cell-based and patient-derived xenograft (PDX) models were used to further explore roles of CRCAL-2 in GC metastasis. Then, RNA pull-down, mass spectrometry analyses, western blot and RNA-binding protein immunoprecipitation (RIP) were performed to identify interaction proteins and related mechanisms of CRCAL-2. Results LncRNA CRCAL-2, significantly overexpressed in the tumor tissues, was identified as the key regulator of GC metastasis. Upregulated CRCAL-2 in GC correlated with poor overall survival. Knockdown of CRCAL-2 significantly reduced GC cells migration, invasion, and metastasis of xenograft tumors in nude mice. Mechanistically, CRCAL-2 promoted GC metastasis by directly interacting with and stabilizing the nuclear transport protein RAN, resulting in increasement of nuclear import of beta-catenin and ultimately, activation of downstream targeted EMT(Epithelial-Mesenchymal Transition) genes. Additionally, the transcription factor YY1 could bind to the promoter of CRCAL-2 to upregulate its expression. Conclusions Our results suggest that YY1/CRCAL2/beta-catenin axis play a crucial role in GC metastasis, and the newly identified lncRNA CRCAL-2 might be developed as a biomarker and potential therapeutic target of GC in patients.

Additional file 3: Table S1. Related to Fig. 2A_Key genes involving in the regulation of DNA methylation. (DOCX 16 kb)

Additional file 2: Figure S2. Related to Fig. 6_Flowchart of data processing of the TCGA dataset. (PDF 107 kb)

Additional file 6: Figure S4. Related to Fig. 6C_The differences of tumor-infiltrating leukocytes between TET1-MUT and TET1-WT tumors. (Mann-Whitney U test with Bonferroni correction. *, P

Additional file 3. Supplementary methods.

Additional file 4: Table S2. Related to Fig. 3_ Patient characteristics between TET1-MUT and TET1-WT subgroups of the discovery cohort. (DOCX 16 kb)

Additional file 13: Table S6. Correlation between LINRIS/IGF2BP2 expression and clinicopathological features in 220 CRC patients.

Additional file 5: Figure S3. Related to Fig. 4_Kaplan-Meier curves investigating the prognostic impact of TET1-MUT in the TCGA cohort. (PDF 471 kb)

Additional file 10: Figure S5, related to Fig. 5. In vivo experiments elucidated the effect of the inhibition of LINRIS in CRC. (A) qPCR detection shows the relative RNA levels of LINRIS in tumors in two PDX experiments. Error bars, SD of four independent experiments. *P

Additional file 1: Figure S1. Related to Fig. 2B_Flowchart of data processing for the pan-cancer alteration frequency analysis of TET1. (PDF 107 kb)

Additional file 4: Figure S1, related to Fig. 1. Identification of LINRIS as an oncogenic lncRNA in CRC. (A) Volcano plots of downregulated and upregulated lncRNA, including LINRIS, based on RNA-seq. (B) LINRIS was highly expressed in CRC tissues (T, n = 21) compared with the expression in normal colon tissues (N). *P

Additional file 7: Figure S2, related to Fig. 2. LINRIS was associated with IGF2BP2 in CRC. (A) The protein score graph of the 18 proteins identified by the RNA pull-down and LC-MS. (B) The emPAI graph of the 18 proteins identified by RNA pull-down assays and LC-MS. (C) Protein cover graph of the 18 proteins identified by RNA pull-down assays and LC-MS. (D) Immunofluorescence assays identifying the subcellular location of IGF2BP2 in the indicated cells. Bar scale: 50 μm. (E) Computational secondary structure of LINRIS predicted with RNAfold. (F) In vitro-synthesized full-length (FL) and 450–640 nt fragments of LINRIS were incubated with protein lysates from HCT116 cells. RNA pull-down and Western blotting assays were then performed. The data shown represent three independent experiments. (G) qPCR detection of LINRIS levels in 11 CRC cell lines. The data are shown as the mean ± SD; n = 3 independent experiments, two-tailed Student’s t-test, *P

Background: Accumulating evidence has demonstrated that microRNAs regulate diverse tumorigenic processes and play important roles in tumor metastasis and growth. Recently, miR-125b-2-3p was identified as a meaningful prognostic factor for predicting chemotherapeutic sensitivity in advanced colorectal cancer (CRC). However, the biological functions and molecular mechanisms of miR-125b-2-3p in the chemotherapy of advanced CRC have yet to be elucidated. Methods: MiR-125b-2-3p expression was detected by real-time PCR in CRC tissues. Gain-of-function experiments were performed to assess the effect of miR-125b-2-3p on CRC growth, metastasis, invasion and drug sensitivity in vitro and in vivo. Based on multiple databases, the competitive endogenous RNAs (ceRNAs) and target genes for miR-125b-2-3p were predicted and have been confirmed by bioinformatic analysis, luciferase reporter assays, rescue experiments and western blot assays. Findings: MiR-125b-2-3p expression was significantly downregulated in CRC tissues and cell lines. MiR-125b-2-3p overexpression was correlated with lower proliferation rates, fewer metastases and better chemotherapeutic sensitivity in vitro and in vivo. Mechanistically, miR-125b-2-3p was regulated by lncRNA XIST and influenced the expression of the WEE1 G2 checkpoint kinase (WEE1). Interpretation: These findings suggested that the lncRNA XIST-miR-125b-2-3p-WEE1 axis not only regulated CRC growth and metastasis but also contributed to chemotherapeutic resistance, thus identifying a potential therapeutic target for CRC. Funding: National Natural Science Foundation of China (81572392), Guangdong special support program (2016TQ03R614), National Key RD Natural Science Foundation of Guangdong Province (2014A030312015); Science and Technology Program of Guangdong (2019B020227002); Science and Technology Program of Guangzhou (201904020046, 201803040019, 201704020228). Declaration of Interest: The authors declare no conflicts of interest. Ethical Approval: This study was approved by the institutional ethics review board of SYSUCC (Guangzhou, China). Our animal study was approved by the Institutional Animal Care and Use Committee of Sun Yat-sen University.

Additional file 6: Table S4. Effect of factors on OS in the CRC patients in the univariate and multivariate Cox regression model.

Additional file 5: Table S3. Correlation between LINRIS expression and clinicopathological features in 118 CRC patients.

Additional file 7: Figure S5. Related to Fig. 6E_ The expression levels of immune-related genes, such as chemokines (A), cytolytic activity associated genes (B) and immune checkpoints (C) in TET1-MUT tumors versus TET1-WT tumors. (Mann-Whitney U test with Bonferroni correction. *, P

Additional file 2: Table S2. The sequences of siRNAs or shRNAs used in this article.

Additional file 8: Figure S3, related to Fig. 3. LINRIS is involved in the autophagic degradation of IGF2BP2. (A) Western blotting shows the levels of IGF2BP2 in the indicated cells with the knockdown of LINRIS after treatment with or without 3-MA (10 mg/ml) for 24 h. GAPDH was used as the loading control. (B) Confocal microscopy of HCT116 cells treated with or without EBSS for 3 h. Scale bar, 50 μm. (C) Western blotting shows the knockout of ATG5 in DLD-1 cells with sgRNA (sg-ATG5) compared with that in control cells. GAPDH was used as the loading control. (D) DLD-1 cells with the knockout of ATG5 and control cells were transfected with shRNAs specific for LINRIS. Cell lysates were analyzed by immunoblotting with GAPDH as the loading control.

Additional file 12: Table S5. Correlation between IGF2BP2 expression and clinicopathological features in 220 CRC patients.

Background/Aims: Small cell carcinoma of the esophagus (SCCE) is a rare and highly deadly malignancy with rapid disease progress and extensive metastasis, whereas present therapy for the cancer is limited, making the identification of a new treatment strategy an area of intense research. We previous reported the genomic characteristics and alterations of the SCCE, but the transcriptome abnormality of the cancer has not been investigated yet. Method: we performed an RNA Sequencing on nine paired samples from patients with SCCE and conducted a series of comprehensive analysis on the data. DESeq2 and GSEA were applied on transcriptome of SCCE tumor tissue and their para-normal to identify differential expressive genes and associated pathways. Besides, with MCP-counter and a list of immunity related genes, we also compared immune signal of the expression data in pair. By applying a rigorous batch removing strategy, including preprocessing raw data in identical method and RUVSeq, transcriptome data of healthy esophageal mucosa from GTEx was involved as control samples in comparison. In addition, we applied CIBERSORT to calculate the fraction of different tumor infiltrated leukocytes (TILs) of SCCE and compare the number with those of other cancers that have been proven to be potentially responsive to immunotherapy. Results: We identified 1486 and 1782 genes were significantly up-regulated and down-regulated in SCCE tumor tissue against their para-normal, respectively. Pathway analysis revealed the E2F Target and G2M checkpoint are significantly enriched in tumor tissue. Immune signal analysis across the samples in pair showed that in 3 out of 9 paired sample, immunity reaction upregulates in tumor tissue. T-SNE cluster across transcriptome data of SCCE tumor tissue, their para-normal and healthy esophageal mucosa showed the para-normal tissue, namely the normal tissue adjacent to tumor, is more similar to tumor tissue than the healthy. CIBERSORT analysis showed the difference in TILs fraction between SCCE and the compared cancers. For example, the relative fraction of plasma cell of SCCE is higher than those of ESCC(P=0.040), CIN type of STAD(P=0.040), while lower than those of SCLC(P=0.020). M2 macrophages is higher in SCCE than ESCC(P=0.002), EAC(P Conclusion: In summary, our analysis provides transcriptome evidence that immunotherapy might be an efficient treatment strategy for small cell esophagus cancer. Citation Format: Qi Zhao, Yan-xing Chen, Ying-nan Wang, Qi-nian Wu, Hui Sheng, JIa-jia Hu, Yun-xin Lu, Ze-xian Liu, Zhi-xiang Zuo, Feng Wang, Rui-hua Xu. Systematic transcriptome analysis of small cell carcinoma of esophagus suggests a possibility for immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4242.