Natural killer-like signature observed post therapy in locally advanced rectal cancer is a determinant of pathological response and improved survival

Radiation-induced changes in gene expression in rectal cancer specimens

PURPOSE

The standard-of-care for locally advanced rectal cancer is radiotherapy-based neoadjuvant therapy followed by surgical resection. This article reviews the evidence of molecular changes at the transcriptome level induced through radiotherapy in rectal cancer.

METHODS

The PubMed search "(radiation OR radiotherapy) cancer (transcriptome OR "gene expression") rectal" was used. The studies taken forward utilised gene-expression data on both pre-treatment and post-treatment rectal adenocarcinoma biospecimens from patients treated with RT-based neoadjuvant strategies.

RESULTS

Twelve publications met the review criteria. There was variation in approaches in terms of design, patient population, cohort size, timing of the post-radiotherapy sampling and method of measuring gene expression. Most of the post-treatment biospecimen retrievals were at resection. The literature indicates a broad upregulation of immune activity through radiotherapy using gene-expression data.

CONCLUSION

Future studies would benefit from standardised prospective approaches to sampling to enable the inclusion of timepoints relevant to the tumour and immune response.

Synergistic treatment strategy: combining CAR-NK cell therapy and radiotherapy to combat solid tumors

Immunotherapy, notably chimeric antigen receptor (CAR) modified natural killer (NK) cell therapy, has shown exciting promise in the treatment of hematologic malignancies due to its unique advantages including fewer side effects, diverse activation mechanisms, and wide availability. However, CAR-NK cell therapies have demonstrated limited efficacy against solid tumors, primarily due to challenges posed by the solid tumor microenvironment. In contrast, radiotherapy, a well-established treatment modality, has been proven to modulate the tumor microenvironment and facilitate immune cell infiltration. With these observations, we hypothesize that a novel therapeutic strategy integrating CAR-NK cell therapy with radiotherapy could enhance the ability to treat solid tumors. This hypothesis aims to address the obstacles CAR-NK cell therapies face within the solid tumor microenvironment and explore the potential efficacy of their combination with radiotherapy. By capitalizing on the synergistic advantages of CAR-NK cell therapy and radiotherapy, we posit that this could lead to improved prognoses for patients with solid tumors.

Implications of Rectal Cancer Radiotherapy on the Immune Microenvironment: Allies and Foes to Therapy Resistance and Patients' Outcome

Aside from surgical resection, locally advanced rectal cancer is regularly treated with neoadjuvant chemoradiotherapy. Since the concept of cancer treatment has shifted from only focusing on tumor cells as drivers of disease progression towards a broader understanding including the dynamic tumor microenvironment (TME), the impact of radiotherapy on the TME and specifically the tumor immune microenvironment (TIME) is increasingly recognized. Both promoting as well as suppressing effects on anti-tumor immunity have been reported in response to rectal cancer (chemo-)radiotherapy and various targets for combination therapies are under investigation. A literature review was conducted searching the PubMed database for evidence regarding the pleiotropic effects of (chemo-)radiotherapy on the rectal cancer TIME, including alterations in cytokine levels, immune cell populations and activity as well as changes in immune checkpoint proteins. Radiotherapy can induce immune-stimulating and -suppressive alterations, potentially mediating radioresistance. The response is influenced by treatment modalities, including the dosage administered and the highly individual intrinsic pre-treatment immune status. Directly addressing the main immune cells of the TME, this review aims to highlight therapeutical implications since efficient rectal cancer treatment relies on personalized strategies combining conventional therapies with immune-modulating approaches, such as immune checkpoint inhibitors.

Alterations in Natural Killer Cells in Colorectal Cancer Patients with Stroma AReactive Invasion Front Areas (SARIFA)

BACKGROUND

Recently, our group introduced Stroma AReactive Invasion Front Areas (SARIFA) as an independent prognostic predictor for a poorer outcome in colon cancer patients, which is probably based on immunologic alterations combined with a direct tumor-adipocyte interaction: the two together reflecting a distinct tumor biology. Considering it is already known that peripheral immune cells are altered in colorectal cancer (CRC) patients, this study aims to investigate the changes in lymphocyte subsets in SARIFA-positive cases and correlate these changes with the local immune response.

METHODS

Flow cytometry was performed to analyze B, T, and natural killer (NK) cells in the peripheral blood (PB) of 45 CRC patients. Consecutively, lymphocytes in PB, tumor-infiltrating lymphocytes (TILs), and CD56+ and CD57+ lymphocytes at the invasion front and the tumor center were compared between patients with SARIFA-positive and SARIFA-negative CRCs.

RESULTS

Whereas no differences could be observed regarding most PB lymphocyte populations as well as TILs, NK cells were dramatically reduced in the PB of SARIFA-positive cases. Moreover, CD56 and CD57 immunohistochemistry suggested SARIFA-status-dependent changes regarding NK cells and NK-like lymphocytes in the tumor microenvironment.

CONCLUSION

This study proves that our newly introduced biomarker, SARIFA, comes along with distinct immunologic alterations, especially regarding NK cells.

Prognostic Model for Clear-cell Renal Cell Carcinoma Based on Natural Killer Cell-related Genes

BACKGROUND

Natural killer (NK) cells are a key factor affecting progression and immune surveillance of clear-cell renal cell carcinoma (ccRCC). This study sought to construct a natural killer cell-related prognostic signature (NKRPS) to predict the outcome of ccRCC patients and to furnish guidance for finding appropriate treatment strategies.

METHODS

From the TCGA and ArrayExpress databases, transcriptomic profiles and relevant clinical information of ccRCC patients were downloaded for the TCGA cohort (n = 515) and the E-MTAB-1980 cohort (n = 101). With the univariate Cox analysis and LASSO-Cox regression algorithm, a NKRPS was built to evaluate patients' prognosis. Receiver operating characteristic (ROC) curves and calibration curves were drawn to estimate the predictive power of the prognostic model. Then, tumor microenvironment (TME), tumor mutational burden (TMB), sensitization to immune checkpoint inhibitors (ICIs) therapy and targeted drug treatment were analyzed in ccRCC patients.

RESULTS

Nine genes (BID, CCL7, CSF2, IL23A, KNSTRN, RHBDD3, PIK3R3, RNF19B and VAV3) were identified to construct a NKRPS. High-risk group displayed undesirable survival compared to low-risk group (P < .05). Moreover, the area under the curve (AUC) of ROC at 1-, 3- and 5-year were 0.766, 0.755, and 0.757, respectively. High-risk group was characterized by superior immune infiltration, higher TMB, and higher expression of 5 ICI-related genes. Additionally, this model enabled to predict the sensitivity of patients to chemotherapy drugs.

CONCLUSION

NKRPS had a strong predictive power on prognosis of ccRCC patients, which may facilitate individualized treatment and medical decision making.

Natural killer cell-related gene signature predicts malignancy of glioma and the survival of patients

Background

Natural killer (NK) cells-based therapies are one of the most promising strategies against cancer. The aim of this study is to investigate the natural killer cell related genes and its prognostic value in glioma.

Methods

The Chinese Glioma Genome Atlas (CGGA) was used to develop the natural killer cell-related signature. Risk score was built by multivariate Cox proportional hazards model. A cohort of 326 glioma samples with whole transcriptome expression data from the CGGA database was included for discovery. The Cancer Genome Atlas (TCGA) datasets was used for validation. GO and KEGG were used to reveal the biological process and function associated with the natural killer cell-related signature. We also collected the clinical pathological features of patients with gliomas to analyze the association with tumor malignancy and patients’ survival.

Results

We screened for NK-related genes to build a prognostic signature, and identified the risk score based on the signature. We found that NK-related risk score was independent of various clinical factors. Nature-killer cell gene expression is correlated with clinicopathological features of gliomas. Innovatively, we demonstrated the tight relation between the risk score and immune checkpoints, and found NK-related risk score combined with PD1/PDL1 patients could predict the patient outcome.

Conclusion

Natural killer cell-related gene signature can predict malignancy of glioma and the survival of patients, these results might provide new view for the research of glioma malignancy and individual immunotherapy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-09230-y.

Dynamic metabolic change of cancer cells induced by natural killer cells at single-cell level studied by label-free mass cytometry

Natural killer cells (NK cells) are important immune cells which have attracted increasing attention in cancer immunotherapy. Due to the heterogeneity of cells, individual cancer cells show different resistance to NK cytotoxicity, which has been revealed by flow cytometry. Here we used label-free mass cytometry (CyESI-MS) as a new tool to analyze the metabolites in Human Hepatocellular Carcinoma (HepG2) cells at the single-cell level after the interaction with different numbers of NK92 MI cells. A large amount of chemical information from individual HepG2 cells was obtained showing the process of cell apoptosis induced by NK cells. Nineteen metabolites which consecutively change during cell apoptosis were revealed by calculating their average relative intensity. Four metabolic pathways were impacted during cell apoptosis which hit 4 metabolites including glutathione (GSH), creatine, glutamic acid and taurine. We found that the HepG2 cells could be divided into two phenotypes after co-culturing with NK cells according to the bimodal distribution of concentration of these 4 metabolites. The correlation between metabolites and different apoptotic pathways in the early apoptosis cell group was established by the 4 metabolites at the single-cell level. This is a new idea of using single-cell specific metabolites to reveal the metabolic heterogeneity in cell apoptosis which would be a powerful means for evaluating the cytotoxicity of NK cells.

Label-free mass cytometry is utilized to study the dynamic metabolic change during apoptosis in HepG2 cells induced by NK92 MI cells at the single-cell level. The metabolic heterogeneity of individual HepG2 cells during apoptosis was revealed.

Prognostic significance of natural killer cell-associated markers in gastric cancer: quantitative analysis using multiplex immunohistochemistry

Background

Natural killer (NK) cells mediate the anti-tumoral immune response as an important component of innate immunity. The aim of this study was to investigate the prognostic significance and functional implication of NK cell-associated surface receptors in gastric cancer (GC) by using multiplex immunohistochemistry (mIHC).

Methods

We performed an mIHC on tissue microarray slides, including 55 GC tissue samples. A total of 11 antibodies including CD57, NKG2A, CD16, HLA-E, CD3, CD20, CD45, CD68, CK, SMA, and ki-67 were used. CD45 + CD3-CD57 + cells were considered as CD57 + NK cells.

Results

Among CD45 + immune cells, the proportion of CD57 + NK cell was the lowest (3.8%), whereas that of CD57 + and CD57- T cells (65.5%) was the highest, followed by macrophages (25.4%), and B cells (5.3%). CD57 + NK cells constituted 20% of CD45 + CD57 + immune cells while the remaining 80% were CD57 + T cells. The expression of HLA-E in tumor cells correlated with that in tumoral T cells, B cells, and macrophages, but not CD57 + NK cells. The higher density of tumoral CD57 + NK cells and tumoral CD57 + NKG2A + NK cells was associated with inferior survival.

Conclusions

Although the number of CD57 + NK cells was lower than that of other immune cells, CD57 + NK cells and CD57 + NKG2A + NK cells were significantly associated with poor outcomes, suggesting that NK cell subsets play a critical role in GC progression. NK cells and their inhibitory receptor, NKG2A, may be potential targets in GC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-03203-8.

Construction and characterization of rectal cancer-related lncRNA-mRNA ceRNA network reveals prognostic biomarkers in rectal cancer

Rectal cancer is an important cause of cancer‐related deaths worldwide. In this study, the differentially expressed (DE) lncRNAs/mRNAs were first identified and the correlation level between DE lncRNAs and mRNAs were calculated. The results showed that genes of highly correlated lncRNA‐mRNA pairs presented strong prognosis effects, such as GPM6A, METTL24, SCN7A, HAND2‐AS1 and PDZRN4. Then, the rectal cancer‐related lncRNA‐mRNA network was constructed based on the ceRNA theory. Topological analysis of the network revealed that the network was maintained by hub nodes and a hub subnetwork was constructed, including the hub lncRNA MIR143HG and MBNL1‐SA1. Further analysis indicated that the hub subnetwork was highly related to cancer pathways, such as ‘Focal adhesion’ and ‘Wnt signalling pathway’. Hub subnetwork also had significant prognosis capability. A closed lncRNA‐mRNA module was identified by bilateral network clustering. Genes in modules also showed high prognosis effects. Finally, a core lncRNA‐TF crosstalk network was identified to uncover the crosstalk and regulatory mechanisms of lncRNAs and TFs by integrating ceRNA crosstalks and TF binding affinities. Some core genes, such as MEIS1, GLI3 and HAND2‐AS1 were considered as the key regulators in tumourigenesis. Based on the authors’ comprehensive analysis, all these lncRNA‐mRNA crosstalks provided promising clues for biological prognosis of rectal cancer.

[Precision medicine and immuno-radiotherapy]

Numerous clinical studies aim to integrate immunotherapy in radiotherapy oncology, either for generating abscopal responses in metastatic patients in combination with radiotherapy, or in the treatment of a locally advanced tumor. The search for biomarkers of response to treatment is a major axis in the development of these therapeutic combinations, to allow the early identification of patients who will benefit from the treatment, in the context of an increasingly personalized approach. We review some of the strategies that can be applied for personalization to combined radiotherapy and immunotherapy treatments.

Targeting NK Cells to Enhance Melanoma Response to Immunotherapies

Natural killer (NK) cells are a key component of an innate immune system. They are important not only in initiating, but also in augmenting adaptive immune responses. NK cell activation is mediated by a carefully orchestrated balance between the signals from inhibitory and activating NK cell receptors. NK cells are potent producers of proinflammatory cytokines and are also able to elicit strong antitumor responses through secretion of perforin and granzyme B. Tumors can develop many mechanisms to evade NK cell antitumor responses, such as upregulating ligands for inhibitory receptors, secreting anti-inflammatory cytokines and recruiting immunosuppressive cells. Enhancing NK cell responses will likely augment the effectiveness of immunotherapies, and strategies to accomplish this are currently being evaluated in clinical trials. A comprehensive understanding of NK cell biology will likely provide additional opportunities to further leverage the antitumor effects of NK cells. In this review, we therefore sought to highlight NK cell biology, tumor evasion of NK cells and clinical trials that target NK cells.

NK cell infiltration is associated with improved overall survival in solid cancers: A systematic review and meta-analysis

The immune landscape of a tumor is highly connected to patient prognosis and response to treatment, but little is known about how natural killer (NK) cells predict overall survival (OS) among patients with solid tumors. We present the first meta-analysis on NK cell infiltration into solid tumors as a prognostic indicator for OS, considering cancer types independently, and together. Samples were collected from 1973 to 2016 with results published between 1989 and 2020. From 53 studies, we found that NK cell infiltration corresponds with decreased risk of death (HR=0.34, 95% CI: 0.26-0.46; p<0.0001). Among studies that investigated the prognostic potential of NK cells in specific regions of the tumor, intraepithelial infiltration was better predictive of OS than NK infiltration in the tumor-adjacent stroma. Generally, NK cell infiltration is lower in advanced-stage and lower-grade tumors; nevertheless, it remains prognostically beneficial. This meta-analysis highlights an important prognostic role of NK cells in solid tumors, but exposes that few studies have considered the contributions of NK cells. Toward NK cell-based immunotherapies, it will be important to understand the conditions under which NK cells can be effective agents of tumor control.

Development of a 15-gene signature for predicting prognosis in advanced colorectal cancer

Advanced colorectal cancer (CRC) is a significant cause of cancer mortality, with a poor prognosis. Here, we identified a novel prognostic signature for predicting survival of advanced CRC. Advanced CRC data were used (training set: n = 267 and validation set: n = 264). The survival analyses were investigated. The functional analysis of the prognostic signature was examined. In this study, our 15-gene signature was established and was an independent prognostic factor of advanced CRC. Stratification analyses also showed that this signature was still powerful for survival prediction in each stratum of age, gender, stage, and metastasis status. In mechanism, our signature involved in DNA replication, DNA damage, and cell cycle. Therefore, our findings suggested that this 15-gene signature has prognostic and predictive value in advanced CRC, which could be further used in personalized therapy for advanced CRC.

Prognostic Significance of Tumor-Infiltrating Natural Killer Cells in Solid Tumors: A Systematic Review and Meta-Analysis

Background: Tumor-infiltrating natural killer (NK) cells (TINKs) are crucial immune cells in tumor defense, and might be related to tumor prognosis. However, the results were discrepant among different studies. The present meta-analysis was performed to comprehensively assess the prognostic value of NK cell markers in solid tumor tissues.

Methods: PubMed, Web of Science, and EMBASE were searched to identify original researches reporting the prognostic significance of TINKs in solid tumors. NK cell markers CD56, CD57, NKp30, and NKp46 were included in the analysis. The hazard ratios (HRs) and 95% confidence intervals (CIs) of pooled overall survival (OS), disease-free survival (DFS), metastasis-free survival (MFS), progression-free survival (PFS), and recurrence-free survival (RFS) were calculated by STATA software 14.0 to assess the prognostic significance.

Results : Of the 56 included studies, there were 18 studies on CD56, 31 studies on CD57, 1 study on NKp30, and 7 studies on NKp46. High levels of CD56, CD57, NKp30, and NKp46 were significantly correlated with better OS of patients with solid malignancies (HR = 0.473, 95%CI: 0.315–0.710, p < 0.001; HR = 0.484, 95%CI: 0.380–0.616, p < 0.001; HR = 0.34, 95%CI: 0.14–0.80, p = 0.014; HR = 0.622, 95%CI: 0.470–0.821, p < 0.001, respectively). Our results also revealed that CD56, CD57, and NKp46 could act as independent prognostic predictors for favorable OS (HR = 0.372, 95%CI: 0.261–0.531, p < 0.001; HR = 0.525, 95%CI: 0.346–0.797, p = 0.003; HR = 0.559, 95%CI: 0.385–0.812, p = 0.002, respectively).

Conclusions : Our results indicated that high levels of NK cell markers in solid tumor tissues could predict favorable prognosis for solid tumor patients.

The Intestinal Tumour Microenvironment

The tumour microenvironment (TME) of intestinal tumours is highly complex and comprises a network of stromal cells, tumour cells, immune cells and fibroblasts, as well as microorganisms. The tumour location, environmental factors and the tumour cells themselves influence the cells within the TME. Immune cells can destroy tumour cells and are associated with better patient prognosis and response to therapy; however, immune cells are highly plastic and easily influenced to instead promote tumour growth. The interaction between local immune cells and the microbiome can lead to progression or regression of intestinal tumours. In this chapter, we will discuss how tumour development and progression can influence, and be influenced by, the microenvironment surrounding it, focusing on immune and fibroblastic cells, and the intestinal microbiota, particularly in the context of colorectal cancer.

The local inflammatory response in colorectal cancer - Type, location or density? A systematic review and meta-analysis

INTRODUCTION

The host anti-tumour inflammatory response is a strong prognostic indicator, and tumour infiltrating lymphocytes (TILs) are believed to have a complimentary role alongside TNM assessment in dictating future management. However, there is wide disagreement regarding the most efficacious and cost-effective method of assessment.

METHODS

A comprehensive literature search was performed of EMBASE, MedLine and PubMed as well as an assessment of references to identify all relevant studies relating to the assessment of the peri-tumoural inflammatory response or TILs and prognosis in colorectal cancer (CRC). A meta-analysis was performed of 67 studies meeting the REMARK criteria using RevMan software.

RESULTS

Intratumoural assessment of both CD3 and CD8 in CRC were significant for disease-free survival (DFS) (combined HRs 0.46; 95%CI: 0.39-0.54 and 0.54; 95%CI: 0.45-0.65), as well as overall survival (OS) and disease-specific survival (DSS). The same was true for assessment of CD3 and CD8 at the invasive margin (DFS: combined HRs 0.45; 95%CI: 0.33-0.61 and 0.51; 95%CI: 0.41-0.62). However, similar fixed effects summaries were also observed for H&E-based methods, like Klintrup-Makinen grade (DFS: HR 0.62; 95%CI: 0.43-0.88). Furthermore, inflammatory assessments were independent of MSI status.

CONCLUSION

The evidence suggests that it is the density of a co-ordinated local inflammatory infiltrate that confers survival benefit, rather than any individual immune cell subtype. Furthermore, the location of individual cells within the tumour microenvironment does not appear to influence survival. The authors advocate a standardised assessment of the local inflammatory response, but caution against emphasizing the importance of any individual immune cell subtype.

Candidate genes and potential mechanisms for chemoradiotherapy sensitivity in locally advanced rectal cancer

The aim of the present study was to investigate candidate genes for chemoradiotherapy (CRT) sensitivity in patients with locally advanced rectal cancer (LARC), and the potential mechanisms of their action. A microarray dataset (GSE98959) was obtained from the Gene Expression Omnibus database that included microRNA (miRNA, miR) expression profiling of 22 samples from patients with LARC who had received preoperative radiotherapy and chemotherapy. Of these patients, 10 responded to the treatment and 12 did not. Differentially expressed miRNAs (DEMs) were identified, followed by the construction of an miRNA-gene network. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) function analyses were performed on the target genes in the miRNA-gene network. Furthermore, a protein-protein interaction (PPI) network was constructed on the basis of the target genes, followed by GO function enrichment and KEGG pathway analysis. A total of 30 DEMs were identified between the responder and non-responder groups. Thiamine metabolism (including miR-371a-3p) was the pathway with the highest enrichment of DEMs. The pathway that was most markedly enriched in the target genes of upregulated miRNAs was the pluripotency of stem cells pathway, as indicated by phosphoinositide-4,5-bisphosphate 3-kinase γ (PIK3CG) and anaphase-promoting complex subunit 2 (APC2). Pathways in cancer exhibited the highest enrichment in the set of target genes of downregulated miRNAs. KEGG pathway and GO function analysis indicated that target genes in the PPI network were enriched in the glioma pathway and assembled in the intracellular signaling cascade function, as indicated by the proto-oncogene NRAS. miR-371a-3p may be a candidate miRNA for CRT sensitivity in LARC via the thiamine metabolism pathway. PIK3CG and APC2 may contribute to CRT sensitivity via signaling pathways regulating the pluripotency of stem cells. Furthermore, NRAS may serve an important role in mediating CRT sensitivity via an intracellular signaling cascade.

Proteomic profiling of rectal cancer reveals acid ceramidase is implicated in radiation response

BACKGROUND

Neoadjuvant chemoradiotherapy (CRT) is used in locally advanced rectal cancer when tumours threaten the circumferential resection margin, with varying response to treatment. This experimental study aimed to identify significantly differentially expressed proteins between patients responding and not responding to CRT, and to validate any proteins of interest.

METHODS

Mass spectrometry (with isobaric tagging for relative quantification) analysis of rectal cancers pre- and post-CRT, and at resection. Validation of proteins of interest was performed by assessing tissue microarray (TMA) immunohistochemistry expression in a further 111 patients with rectal cancer.

RESULTS

Proteomic data are available via ProteomeXchange with identifier PXD008436. Reduced abundance of contributing peptide ions for acid ceramidase (AC) (log fold change -1.526, p = 1.17E-02) was observed in CRT responders. Differential expression of AC was confirmed upon analysis of the TMAs. Cancer site expression of AC in stromal cells from post-CRT resection specimens was observed to be relatively low in pathological complete response (p = 0.003), and relatively high with no response to CRT (p = 0.017).

CONCLUSION

AC may be implicated in the response of rectal cancer to CRT. We propose its further assessment as a novel potential biomarker and therapeutic target.

SIGNIFICANCE

There is a need for biomarkers to guide the use of chemoradiotherapy in rectal cancer, as none are in routine clinical use. We have determined acid ceramidase may have a role in radiation response, based on novel proteomic profiling and validation in a wider dataset using tissue microarrays. The ability to predict or improve response would positively select those patients who will derive benefit, prevent delays in the local and systemic management of disease in non-responders, and reduce morbidity associated with chemoradiotherapy.