TGFBR2 mutation predicts resistance to immune checkpoint inhibitors in patients with non-small cell lung cancer

Heterogeneity of lymphocyte subsets in predicting immune checkpoint inhibitor treatment response in advanced lung cancer: an analysis across different pathological types, therapeutic drugs, and age groups

Background

Immune checkpoint inhibitor (ICI) has become pivotal in the treatment of advanced lung cancer, yet the absence of reliable biomarkers for assessing treatment response poses a significant challenge. This study aims to explore the predictive value of various lymphocyte subsets in different lung cancer subtypes, thus potentially identifying novel biomarkers to improve ICI treatment stratification and outcomes.

Methods

We conducted a retrospective analysis of 146 stage III or IV lung cancer patients undergoing ICI treatment. The study focused on exploring the relationship between various lymphocyte subsets and the efficacy of ICIs, aiming to determine their predictive value for post-treatment outcomes.

Results

Subgroup analysis revealed a positive correlation (P=0.01) between lower CD3+CD8+ T lymphocyte levels and treatment response in squamous cell carcinoma patients. However, no significance was observed in lung adenocarcinoma patients. Additionally, the predictive ability of lymphocyte subsets for different immunotherapy drugs varies. In individuals receiving anti-programmed cell death ligand 1 (PD-L1) treatment, a lower CD3+CD8+ T lymphocyte levels is significantly associated with a positive treatment outcome (P=0.002), while there is no difference for programmed death 1 (PD-1) drugs. Among patients under 60, higher expression of CD3+CD4+ T lymphocytes (P=0.03) combined with lower CD3+CD8+ T lymphocyte levels (P=0.006) showed a statistically significant association with improved treatment response. However, in patients aged over 60, no discernible correlation was ascertained between lymphocyte subsets and therapeutic response. Through prognostic analysis, two distinct lymphocyte subsets were identified, both exerting considerable impact on progression-free survival subsequent to ICIs treatment: CD3+CD4+ T lymphocytes [hazard ratio (HR) =0.50, P=0.006] and CD3+CD8+ T lymphocytes (HR =1.78, P=0.02).

Conclusions

Our findings underscore the significant heterogeneity in the predictive value of distinct lymphocyte subsets for lung cancer patients undergoing ICI treatment. These findings are particularly salient when considering various pathological types, immunotherapeutic agents, and patient age groups.

Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution

BACKGROUND

Tumors are able to acquire new capabilities, including traits such as drug resistance and metastasis that are associated with unfavorable clinical outcomes. Single-cell technologies have made it possible to study both mutational and transcriptomic profiles, but as most studies have been conducted on model systems, little is known about cancer evolution in human patients. Hence, a better understanding of cancer evolution could have important implications for treatment strategies.

RESULTS

Here, we analyze cancer evolution and clonal selection by jointly considering mutational and transcriptomic profiles of single cells acquired from tumor biopsies from 49 lung cancer samples and 51 samples with chronic myeloid leukemia. Comparing the two profiles, we find that each clone is associated with a preferred transcriptional state. For metastasis and drug resistance, we find that the number of mutations affecting related genes increases as the clone evolves, while changes in gene expression profiles are limited. Surprisingly, we find that mutations affecting ligand-receptor interactions with the tumor microenvironment frequently emerge as clones acquire drug resistance.

CONCLUSIONS

Our results show that lung cancer and chronic myeloid leukemia maintain a high clonal and transcriptional diversity, and we find little evidence in favor of clonal sweeps. This suggests that for these cancers selection based solely on growth rate is unlikely to be the dominating driving force during cancer evolution.

Genomic and Immune Features in an Intrahepatic Cholangiocarcinoma Patient with Microsatellite Instability-High Suffered Rapid Acquired Resistance to PD-1 Inhibitor

Introduction

Intrahepatic cholangiocarcinoma (ICC) is a highly aggressive liver malignancy with poor prognosis. Recently, the development of immune checkpoint inhibitors (ICIs), such as programmed cell death 1 (PD-1) inhibitors, has emerged as a promising strategy in multiple tumor types, including ICC. Microsatellite instability-high (MSI-H) is an important biomarker for ICIs in solid tumors. The response rate in patients with MSI-H is significantly higher than in those with microsatellite stability/microsatellite instability-low. And approximately 80-90% of the patients with MSI-H could maintain sustained clinical benefits once they had an initial response. However, some patients could have primary resistance at the beginning, and some might have acquired resistance after long-term treatment.

Case Presentation

We present the case of an ICC patient with MSI-H who suffered rapid progression after a short-term remission with camrelizumab, a kind of PD-1 inhibitor, as second-line treatment. The patient's genomic and immune features were analyzed by next-generation sequencing and multiplex immunofluorescence staining to explore the possible mechanisms of the rapidly acquired resistance of ICIs in this MSI-H case.

Conclusion

The genomic and immunohistochemical analysis showed that TGFBR2 mutation, loss of HLA B44 supertype, carrying B62 supertype, and increased PD-L1+ cells, macrophages, and Tregs in the tumor microenvironment might be related to the nonsustain benefit of ICIs in this MSI-H patient.

Landscape of Genetic Mutations in Appendiceal Cancers

In appendiceal cancers, the most frequently mutated genes are (i) KRAS, which, when reactivated, restores signal transduction via the RAS-RAF-MEK-ERK signaling pathway and stimulates cell proliferation in the early stages of tumor transformation, and then angiogenesis; (ii) TP53, whose inactivation leads to the inhibition of programmed cell death; (iii) GNAS, which, when reactivated, links the cAMP pathway to the RAS-RAF-MEK-ERK signaling pathway, stimulating cell proliferation and angiogenesis; (iv) SMAD4, exhibiting typical tumor-suppressive activity, blocking the transmission of oncogenic TGFB signals via the SMAD2/SMAD3 heterodimer; and (v) BRAF, which is part of the RAS-RAF-MEK-ERK signaling pathway. Diverse mutations are reported in other genes, which are part of secondary or less critical signaling pathways for tumor progression, but which amplify the phenotypic diversity of appendiceal cancers. In this review, we will present the main genetic mutations involved in appendix tumors and their roles in cell proliferation and survival, and in tumor invasiveness, angiogenesis, and acquired resistance to anti-growth signals.

Genomic characteristics and prognosis of lung cancer patients with MSI-H: A cohort study

BACKGROUND

Microsatellite instability (MSI) is the first pan-cancer biomarker approved to guide immune checkpoint inhibitor therapy for MSI-high (MSI-H) solid tumors. In lung cancer, the MSI-H frequency is very low, and the genetic characteristics and prognosis of lung cancer with MSI-H were rarely reported.

METHODS

Next-generation sequencing and immunohistochemistry were used detect MSI status, tumor mutation burden (TMB) and PD-L1 expression.

RESULTS

Among 12,484 lung cancer patients screened, 66 were found with MSI-H, the proportion was as low as 0.5%. Compared with Microsatellite stability (MSS), TMB was higher in MSI-H lung cancer patients, while PD-L1 expression showed no considerable difference between MSI-H and MSS. After propensity score matching, compared with MSS, the most common companion mutations in MSI-H were TP53, BRCA2, TGFBR2, PTEN and KMT2C. In MSI-H lung adenocarcinoma with EGFR mutation, TGFBR2 and ERBB2 had higher mutation frequency than in MSS.

CONCLUSION

The current study reveals the genetic characteristics of MSI-H lung cancer, which advanced our understanding of MSI-H lung cancer.

Molecules promoting circulating clusters of cancer cells suggest novel therapeutic targets for treatment of metastatic cancers

Treatment of metastatic disease remains among the most challenging tasks in oncology. One of the early events that predicts a poor prognosis and precedes the development of metastasis is the occurrence of clusters of cancer cells in the blood flow. Moreover, the presence of heterogeneous clusters of cancerous and noncancerous cells in the circulation is even more dangerous. Review of pathological mechanisms and biological molecules directly involved in the formation and pathogenesis of the heterotypic circulating tumor cell (CTC) clusters revealed their common properties, which include increased adhesiveness, combined epithelial-mesenchymal phenotype, CTC-white blood cell interaction, and polyploidy. Several molecules involved in the heterotypic CTC interactions and their metastatic properties, including IL6R, CXCR4 and EPCAM, are targets of approved or experimental anticancer drugs. Accordingly, analysis of patient survival data from the published literature and public datasets revealed that the expression of several molecules affecting the formation of CTC clusters predicts patient survival in multiple cancer types. Thus, targeting of molecules involved in CTC heterotypic interactions might be a valuable strategy for the treatment of metastatic cancers.

Aberrant Methylation of the Imprinted C19MC and MIR371-3 Clusters in Patients with Non-Small Cell Lung Cancer

Epigenetic mechanisms have emerged as an important contributor to tumor development through the modulation of gene expression. Our objective was to identify the methylation profile of the imprinted C19MC and MIR371-3 clusters in patients with non-small cell lung cancer (NSCLC) and to find their potential target genes, as well as to study their prognostic role. DNA methylation status was analyzed in a NSCLC patient cohort (n = 47) and compared with a control cohort including COPD patients and non-COPD subjects (n = 23) using the Illumina Infinium Human Methylation 450 BeadChip. Hypomethylation of miRNAs located on chromosome 19q13.42 was found to be specific for tumor tissue. We then identified the target mRNA-miRNA regulatory network for the components of the C19MC and MIR371-3 clusters using the miRTargetLink 2.0 Human tool. The correlations of miRNA-target mRNA expression from primary lung tumors were analyzed using the CancerMIRNome tool. From those negative correlations identified, we found that a lower expression of 5 of the target genes (FOXF2, KLF13, MICA, TCEAL1 and TGFBR2) was significantly associated with poor overall survival. Taken together, this study demonstrates that the imprinted C19MC and MIR371-3 miRNA clusters undergo polycistronic epigenetic regulation leading to deregulation of important and common target genes with potential prognostic value in lung cancer.

Baseline extracellular vesicle TGF-β is a predictive biomarker for response to immune checkpoint inhibitors and survival in non-small cell lung cancer

BACKGROUND

Immune-checkpoint inhibitors (ICIs) are an effective therapeutic strategy, improving the survival of patients with lung cancer compared with conventional treatments. However, novel predictive biomarkers are needed to stratify which patients derive clinical benefit because the currently used and highly heterogenic histological PD-L1 has shown low accuracy. Liquid biopsy is the analysis of biomarkers in body fluids and represents a minimally invasive tool that can be used to monitor tumor evolution and treatment effects, potentially reducing biases associated with tumor heterogeneity associated with tissue biopsies. In this context, cytokines, such as transforming growth factor-β (TGF-β), can be found free in circulation in the blood and packaged into extracellular vesicles (EVs), which have a specific delivery tropism and can affect in tumor/immune system interaction. TGF-β is an immunosuppressive cytokine that plays a crucial role in tumor immune escape, treatment resistance, and metastasis. Thus, we aimed to evaluate the predictive value of circulating and EV TGF-β in patients with non-small-cell lung cancer receiving ICIs.

METHODS

Plasma samples were collected in 33 patients with advanced non-small-cell lung cancer before and during treatment with ICIs. EV were isolated from plasma by serial ultracentrifugation methods and circulating and EV TGF-β expression levels were evaluated by enzyme-linked immunosorbent assay.

RESULTS

Baseline high expression of TGF-β in EVs was associated with nonresponse to ICIs as well as shorter progression-free survival and overall survival, outperforming circulating TGF-β levels and tissue PD-L1 as a predictive biomarker.

CONCLUSION

If validated, EV TGF-β could be used to improve patient stratification, increasing the effectiveness of treatment with ICIs and potentially informing combinatory treatments with TGF-β blockade.

PLAIN LANGUAGE SUMMARY

Treatment with immune-checkpoint inhibitors (ICIs) has improved the survival of some patients with lung cancer. However, the majority of patients do not benefit from this treatment, making it essential to develop more reliable biomarkers to identify patients most likely to benefit. In this pilot study, the expression of transforming growth factor-β (TGF-β) in blood circulation and in extracellular vesicles was analyzed. The levels of extracellular vesicle TGF-β before treatment were able to determine which patients would benefit from treatment with ICIs and have a longer survival with higher accuracy than circulating TGF-β and tissue PD-L1, which is the currently used biomarker in clinical practice.

Cell adhesion molecules and immunotherapy in advanced non-small cell lung cancer: Current process and potential application

Advanced non-small cell lung cancer (NSCLC) is a severe disease and still has high mortality rate after conventional treatment (e.g., surgical resection, chemotherapy, radiotherapy and targeted therapy). In NSCLC patients, cancer cells can induce immunosuppression, growth and metastasis by modulating cell adhesion molecules of both cancer cells and immune cells. Therefore, immunotherapy is increasingly concerned due to its promising anti-tumor effect and broader indication, which targets cell adhesion molecules to reverse the process. Among these therapies, immune checkpoint inhibitors (mainly anti-PD-(L)1 and anti-CTLA-4) are most successful and have been adapted as first or second line therapy in advanced NSCLC. However, drug resistance and immune-related adverse reactions restrict its further application. Further understanding of mechanism, adequate biomarkers and novel therapies are necessary to improve therapeutic effect and alleviate adverse effect.

Novel Necroptosis-Related Gene Signature for Predicting Early Diagnosis and Prognosis and Immunotherapy of Gastric Cancer

Simple Summary

Necroptosis plays an important role in the occurrence and development of many cancers. MLKL is an important component of necroptosis, and has been proved to be closely related to the prognosis of gastric cancer (GC). We determined an early diagnosis (FAP, CCT6A) and prognosis risk score (ZFP36, TP53I3, FAP, CCT6A) model of necroptosis-related genes (NRGs) in GC. Two models, respectively, can effectively predict the occurrence of GC and the prognosis of GC patients. The association between the prognostic risk score and the response to immunotherapy and immune checkpoint inhibitors (ICIs) was also analyzed. FAP was also identified as the core gene in the two models, and the relationship between its expression in GC and ICIs was analyzed. This discovery is the first time that NRGs were combined with immunotherapy for GC and provides a new target for immunotherapy for GC and a more accurate treatment scheme for GC patients.

Abstract

Necroptosis is a kind of programmed necrosis, which is different from apoptosis and pyroptosis. Its molecular mechanism has been described in inflammatory diseases. Gastric cancer (GC) is one of the most common malignancies worldwide with the third highest mortality. However, the role of necroptosis in the occurrence and progression of GC remains largely unexplored. Therefore, we investigated necroptosis-related genes (NRGs) by analyzing public transcriptomic data from GC samples. Our results indicate that 83 of 740 NRGs are dysregulated in GC tissues. Next, we identified necroptosis-associated early diagnosis and prognostic gene signatures for GC using machine learning. 2-NRGs (CCT6A and FAP) and 4-NRGs (ZFP36, TP53I3, FAP, and CCT6A), respectively, can effectively assess the risk of early GC (AUC = 0.943) and the prognosis of GC patients (AUC = 0.866). Through in-depth analysis, we were pleasantly surprised to find that there was a significant correlation between the 4-NRGs and GC immunotherapy effect and immune checkpoint inhibitors (ICIs), which could be used for the evaluation of immunosuppressants. Finally, we identified the core gene FAP, and established the relationship between FAP and ICIs in GC. These findings could provide a new target for immunotherapy for GC and a more effective treatment scheme for GC patients.

Genetic perturbations go spatial

Tissue-tumor interactivity is the culmination of cell intrinsic features and their extrinsic interactions with the environment. Recently in Cell, Dhainaut and Rose et al. established a strategy to track pooled CRISPR-modified cells in vivo using protein barcodes (Pro-Codes) and measure their impact on the tumor microenvironment through multiplexed imaging and spatial transcriptomics of intact tissues.¹.

Spatial CRISPR genomics identifies regulators of the tumor microenvironment

While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying extracellular gene functions, particularly in the tissue context. Here, we developed an approach for spatial functional genomics called Perturb-map. We applied Perturb-map to knock out dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Moreover, we paired Perturb-map and spatial transcriptomics for unbiased analysis of CRISPR-edited tumors. We found that in Tgfbr2 knockout tumors, the tumor microenvironment (TME) was converted to a fibro-mucinous state, and T cells excluded, concomitant with upregulated TGFβ and TGFβ-mediated fibroblast activation, indicating that TGFβ-receptor loss on cancer cells increased TGFβ bioavailability and its immunosuppressive effects on the TME. These studies establish Perturb-map for functional genomics within the tissue at single-cell resolution with spatial architecture preserved and provide insight into how TGFβ responsiveness of cancer cells can affect the TME.

Targeting oncogene and non-oncogene addiction to inflame the tumour microenvironment

Immune checkpoint inhibitors (ICIs) have revolutionized the clinical management of multiple tumours. However, only a few patients respond to ICIs, which has generated considerable interest in the identification of resistance mechanisms. One such mechanism reflects the ability of various oncogenic pathways, as well as stress response pathways required for the survival of transformed cells (a situation commonly referred to as 'non-oncogene addiction'), to support tumour progression not only by providing malignant cells with survival and/or proliferation advantages, but also by establishing immunologically 'cold' tumour microenvironments (TMEs). Thus, both oncogene and non-oncogene addiction stand out as promising targets to robustly inflame the TME and potentially enable superior responses to ICIs.

Immunotherapy for Colorectal Cancer: Mechanisms and Predictive Biomarkers

Simple Summary

Late-stage colorectal cancer treatment often involves chemotherapy and radiation that can cause dose-limiting toxicity, and therefore there is great interest in developing targeted therapies for this disease. Immunotherapy is a targeted therapy that uses peptides, cells, antibodies, viruses, or small molecules to engage or train the immune system to kill cancer. Here, we discuss the preclinical and clinical development of immunotherapy for treatment of colorectal cancer and provide an overview of predictive biomarkers for such treatments. We also consider open questions including optimal combination treatments and sensitization of colorectal cancer patients with proficient mismatch repair enzymes.

Abstract

Though early-stage colorectal cancer has a high 5 year survival rate of 65–92% depending on the specific stage, this probability drops to 13% after the cancer metastasizes. Frontline treatments for colorectal cancer such as chemotherapy and radiation often produce dose-limiting toxicities in patients and acquired resistance in cancer cells. Additional targeted treatments are needed to improve patient outcomes and quality of life. Immunotherapy involves treatment with peptides, cells, antibodies, viruses, or small molecules to engage or train the immune system to kill cancer cells. Preclinical and clinical investigations of immunotherapy for treatment of colorectal cancer including immune checkpoint blockade, adoptive cell therapy, monoclonal antibodies, oncolytic viruses, anti-cancer vaccines, and immune system modulators have been promising, but demonstrate limitations for patients with proficient mismatch repair enzymes. In this review, we discuss preclinical and clinical studies investigating immunotherapy for treatment of colorectal cancer and predictive biomarkers for response to these treatments. We also consider open questions including optimal combination treatments to maximize efficacy, minimize toxicity, and prevent acquired resistance and approaches to sensitize mismatch repair-proficient patients to immunotherapy.

Loss of SMAD4 Is Associated With Poor Tumor Immunogenicity and Reduced PD-L1 Expression in Pancreatic Cancer

Transforming Growth Factor β (TGFβ) is a key mediator of immune evasion in pancreatic ductal adenocarcinoma (PDAC), and the addition of TGFβ inhibitors in select immunotherapy regimens shows early promise. Though the TGFβ target SMAD4 is deleted in approximately 55% of PDAC tumors, the effects of SMAD4 loss on tumor immunity have yet to be fully explored. Using a combination of genomic databases and PDAC specimens, we found that tumors with loss of SMAD4 have a comparatively poor T-cell infiltrate. SMAD4 loss was also associated with a reduction in several chemokines with known roles in T-cell recruitment, which was recapitulated using knockdown of SMAD4 in PDAC cell lines. Accordingly, JURKAT T-cells were poorly attracted to conditioned media from PDAC cells with knockdown of SMAD4 and lost their ability to produce IFNγ. However, while exogenous TGFβ modestly reduced PD-L1 expression in SMAD4-intact cell lines, SMAD4 and PD-L1 positively correlated in human PDAC samples. PD-L1 status was closely related to tumor-infiltrating lymphocytes, particularly IFNγ-producing T-cells, which were more abundant in SMAD4-expressing tumors. Low concentrations of IFNγ upregulated PD-L1 in tumor cells in vitro, even when administered alongside high concentrations of TGFβ. Hence, while SMAD4 may have a modest inhibitory effect on PD-L1 in tumor cells, SMAD4 indirectly promotes PD-L1 expression in the pancreatic tumor microenvironment by enhancing T-cell infiltration and IFNγ biosynthesis. These data suggest that pancreatic cancers with loss of SMAD4 represent a poorly immunogenic disease subtype, and SMAD4 status warrants further exploration as a predictive biomarker for cancer immunotherapy.