Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

Global research trends on biomarkers for cancer immunotherapy: Visualization and bibliometric analysis

The global burden of cancer continues to grow, posing a significant public health challenge. Although cancer immunotherapy has shown significant efficacy, the response rate is not high. Therefore, the objective of our research was to identify the latest research trends and hotspots on biomarkers from 1993 to 2023. Data were collected from the database Web of Science core collection. Bibliometric analysis and visualization were conducted with CiteSpace(6.3.1), VOSviewer (v1.6.20), R-bibliometrix(v4.3.3), and Microsoft Excel(2019). A total of 2686 literatures were retrieved. The sheer annual volume of publications has shown a rapid upward trend since 2015. The United States has generated the most publications and Harvard University ranked as a leading institution. The global biomarker research on immune checkpoint inhibitors (ICIs) revealed regional differences and in-depth explorations should be promoted in developing countries. Although China has become the second largest country in terms of publication, the average citation per paper and the total link strength were both lower than the other countries. The research on biomarkers mainly concentrated upon the following aspects: PD-1/PD-L1, CTLA-4, gene expression, adverse events, total mutational burden (TMB), body mass index (BMI), gut microbiota, cd8(+)/cd4(+) t-cells, and blood-related biomarkers such as lactate dehydrogenase (LDH), neutrophil-lymphocyte ratio (NLR), cytokines. Furthermore, "artificial intelligence" and "machine learning" have become the most important research hotspot over the last 2 y, which will help us to identify useful biomarkers from complex big data and provide a basis for precise medicine for malignant tumors.

Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts

This study aims to fill the knowledge gap in systematically mapping the evolution of omics-driven tumor immunotherapy research through a bibliometric lens. While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidimensional molecular profiling, their synergistic potential with immunotherapy remains underexplored in large-scale trend analyses. A comprehensive search was conducted using the Web of Science Core Collection for literature related to omics in tumor immunotherapy, up to August 2024. Bibliometric analyses, conducted using R version 4.3.3, VOSviewer 1.6.20, and Citespace 6.2, examined publication trends, country and institutional contributions, journal distributions, keyword co-occurrence, and citation bursts. This analysis of 9,494 publications demonstrates rapid growth in omics-driven tumor immunotherapy research since 2019, with China leading in output (63% of articles) yet exhibiting limited multinational collaboration (7.9% vs. the UK's 61.8%). Keyword co-occurrence and citation burst analyses reveal evolving frontiers: early emphasis on "PD-1/CTLA-4 blockade" has transitioned toward "machine learning," "multi-omics," and "lncRNA," reflecting a shift to predictive modeling and biomarker discovery. Multi-omics integration has facilitated the development of immune infiltration-based prognostic models, such as TIME subtypes, which have been validated across multiple tumor types, which inform clinical trial design (e.g. NCT06833723). Additionally, proteomic analysis of melanoma patients suggests that metabolic biomarkers, particularly oxidative phosphorylation and lipid metabolism, may stratify responders to PD-1 blockade therapy. Moreover, spatial omics has confirmed ENPP1 as a potential novel therapeutic target in Ewing sarcoma. Citation trends underscore clinical translation, particularly mutation-guided therapies. Omics technologies are transforming tumor immunotherapy by enhancing biomarker discovery and improving therapeutic predictions. Future advancements will necessitate longitudinal omics monitoring, AI-driven multi-omics integration, and international collaboration to accelerate clinical translation. This study presents a systematic framework for exploring emerging research frontiers and offers insights for optimizing precision-driven immunotherapy.

A qualitative prognostic biomarker for melanoma based on the relative methylation orderings of CpG loci

Skin cutaneous melanoma (SKCM) is an aggressive tumor with a poor prognosis. We developed SKCM-P8, a novel qualitative prognostic biomarker based on the relative methylation orderings of eight pairs of loci. Analysis of a training cohort and two independent validation datasets revealed a significant difference in overall survival between high- and low-risk groups stratified by SKCM-P8 (p < 0.05, log-rank test), with average area under the curve values of 0.83, 0.80, and 0.61, respectively. The differential methylation loci between high- and low-risk patients were enriched in immune-related biological processes and signaling pathways. Furthermore, low-risk patients exhibited higher CD8+ T cells and B levels, while high-risk patients had higher monocytes. The methylation levels of SKCM-P8 were also correlated with immune cell levels, indicating that they can reflect prognosis-related immune information. The low-risk group had a significantly higher mutation burden (p < 0.05, Wilcoxon test), suggesting potential benefits from immune checkpoint inhibitors. Patients stratified by SKCM-P8 displayed differential responses to therapy and immunotherapy (p < 0.05, Wilcoxon test), with low-risk patients showing better sensitivity and response. Furthermore, SKCM-P8 demonstrated super-predictive accuracy compared to six published models. Overall, SKCM-P8 offers a promising tool for predicting prognosis and guiding therapeutic decisions in SKCM.

Pan-cancer analysis of MET mutation and its association with the efficacy of immune checkpoint blockade

The mesenchymal-epithelial transition factor (MET) proto-oncogene plays important roles during tumor development. Recently, evidence has revealed MET signaling may impact tumor immunogenicity and regulate the immune response. Here we conducted a comprehensive bioinformatic and clinical analysis to explore the characteristics of MET mutation and its association with the outcomes in pan-cancer immunotherapy. In 4149 patients with 12 tumor types treated with immune checkpoint inhibitors, MET mutation indicated favorable overall survival (hazard ratio = 0.61; 95% CI, 0.50-0.74; P < 0.001), progression-free survival (hazard ratio = 0.74; 95% CI, 0.60-0.92; P = 0.01), and objective response rate (40.3% vs. 28.1%; P = 0.003). Moreover, we developed a nomogram to estimate the 12-month and 24-month survival probabilities after the initiation of immunotherapy. Further multi-omics analysis on both intrinsic and extrinsic immune landscapes revealed that MET mutation enhanced tumor immunogenicity, enriched infiltration of immune cells, and improved immune responses. In summary, MET mutation improves cancer immunity and is an independent biomarker for favorable outcomes in pan-cancer immunotherapy. These results may influence clinical practices, guide treatment decision-making, and develop immunotherapy for personalized care.

Shared neoantigens for cancer immunotherapy

Exploration of neoantigens holds the potential to be productive in immuno-oncotherapy. Among tumor-specific antigens, neoantigens result from genetic instability that gives rise to non-synonymous somatic mutations, highly specific to tumor cells. In addition to point mutations, gene rearrangements, indels leading to frameshifts, chromosomal translocations or inversions that may lead to fusion proteins, alternative mRNA splicing, and integration of genetic material of oncogenic viruses into the host genome provide consistent sources of neoantigens that are absent in healthy tissues. Out of these alterations, 2%-3% may generate T cell neoepitopes, possibly detectable by TCRs. Neoantigens are absent in healthy tissues and are thus at low risk of triggering autoimmunity. In addition, the host lymphocytes have not been rendered tolerant toward them and it is possible to induce immune responses against them. Here, we overview the two categories of neoantigens, i.e., private and shared, and their use in immuno-oncotherapy in selected pre-clinical and clinical studies. The vast majority of commonly occurring tumor-specific mutations are cancer causing and are permanently expressed by all malignant tumor cells, preventing the latter from escaping vaccine-induced anti-neoantigen immunity. The use of public neoantigens combined with efficient vaccine platforms can provide non-personalized "off-the-shelf" therapeutic vaccine candidates for broad-spectrum immunotherapy purposes.

Mapping the potential for anti-PD-1 therapy in advanced rare skin carcinomas

This review, focusing on cutaneous adnexal carcinomas, extramammary Paget disease (EMPD), cutaneous angiosarcomas (cAS) and Kaposi sarcoma (KS), summarizes their local recurrence and metastasis rates, tumor mutation burden (TMB), PD-L1 expression, and off-label treatment with systemic anti-PD-1 agents. PD-L1 expression and tumor mutation burden (TMB) were highly variable in adnexal carcinomas (also depending on the histological subtype), cAS and KS tumors, and some responses were noted even in lack of PD-L1 expression or in low-TMB tumors. There were encouraging best overall responses in patients with advanced rare skin carcinomas treated with anti-PD-1 agents in the literature, mostly after failure of other systemic treatments. We identified a total of 3 patients with sebaceous carcinoma (2 with complete response [CR], 1 with partial response [PR]), 5 with porocarcinoma (3 CR, 1 PR, 1 progression of disease [PD]), 2 with spiradenocarcinoma (1 PR, 1 PD), 1 with trichilemmal carcinoma with PR, 9 with EMPD (1 CR, 5 PR, 3 PD), 32 with cAS (5 CR, 18 PR, 9 PD), and 92 with KS (5 CR, 53 PR, 23 SD, 11 PD). However, a large variety of anti-PD-1 agents were used, in monotherapy or in combination with other systemic therapy, in a relatively small number of patients, limiting interpretations on their individual efficacy. The development of clinical guidelines on rare skin carcinomas may provide standardized guidance to physicians towards best care.

Decoding the complex web: cellular and molecular interactions in the lung tumour microenvironment

The lung tumour microenvironment (TME) or stroma is a dynamic space of numerous cells and their released molecules. This complicated web regulates tumour progression and resistance to different modalities. Lung cancer cells in conjunction with their stroma liberate a wide range of factors that dampen antitumor attacks by innate immunity cells like natural killer (NK) cells and also adaptive responses by effector T cells. These factors include numerous growth factors, exosomes and epigenetic regulators, and also anti-inflammatory cytokines. Understanding the intricate interactions between tumour cells and various elements within the lung TME, such as immune and stromal cells can help provide novel strategies for better management and treatment of lung malignancies. The current article discusses the complex network of cells and signalling molecules, which mediate communications in lung TME. By elucidating these multifaceted interactions, we aim to provide insights into potential therapeutic targets and strategies for lung cancer treatment.

NECTIN4 regulates the cell surface expression of CD155 in non-small cell lung cancer cells and induces tumor resistance to PD-1 inhibitors

The development of immune checkpoint inhibitors has changed treatment strategies for some patients with non-small cell lung cancer (NSCLC). However, resistance remains a major problem, requiring the elucidation of resistance mechanisms, which might aid the development of novel therapeutic strategies. The upregulation of CD155, a primary ligand of the immune checkpoint receptor TIGIT, has been implicated in a mechanism of resistance to PD-1/PD-L1 inhibitors, and it is therefore important to characterize the mechanisms underlying the regulation of CD155 expression in tumor cells. The aim of this study was to identify a Nectin that might regulate CD155 expression in NSCLC and affect anti-tumor immune activity. In this study, we demonstrated that NECTIN4 regulated the cell surface expression and stabilization of CD155 by interacting and co-localizing with CD155 on the cell surface. In a syngeneic mouse model, NECTIN4-overexpressing cells exhibited increased cell surface CD155 and resistance to anti-PD-1 antibodies. Of note, combination therapy with anti-PD-1 and anti-TIGIT antibodies significantly suppressed tumor growth. These findings provide new insights into the mechanisms of resistance to anti-PD-1 antibodies and suggest that NECTIN4 could serve as a valuable marker in therapeutic strategies targeting TIGIT.

Whole genome sequencing improves tissue-of-origin diagnosis and treatment options for cancer of unknown primary

Genomics can inform both tissue-of-origin (TOO) and precision treatments for patients with cancer of unknown primary (CUP). Here, we use whole genome and transcriptome sequencing (WGTS) for 72 patients and show diagnostic superiority of WGTS over panel testing (386-523 genes) in 71 paired cases. WGTS detects all reportable DNA features found by panel as well as additional mutations of diagnostic or therapeutic relevance in 76% of cases. Curated WGTS features and a CUP prediction algorithm (CUPPA) trained on WGTS data of known cancer types informs TOO in 71% of cases otherwise undiagnosed by clinicopathology review. WGTS informs treatments for 79% of patients, compared to 59% by panel testing. Finally, WGS of cell-free DNA (cfDNA) from patients with a high cfDNA tumour fraction (>7%), enables high-likelihood CUPPA predictions in 41% of cases. WGTS is therefore superior to panel testing, broadens treatment options, and is feasible using routine pathology samples and cfDNA.

Next-generation immunotherapeutic approaches for blood cancers: Exploring the efficacy of CAR-T and cancer vaccines

Recent advancements in immunotherapy, particularly Chimeric antigen receptor (CAR)-T cell therapy and cancer vaccines, have significantly transformed the treatment landscape for leukemia. CAR-T cell therapy, initially promising in hematologic cancers, faces notable obstacles in solid tumors due to the complex and immunosuppressive tumor microenvironment. Challenges include the heterogeneous immune profiles of tumors, variability in antigen expression, difficulties in therapeutic delivery, T cell exhaustion, and reduced cytotoxic activity at the tumor site. Additionally, the physical barriers within tumors and the immunological camouflage used by cancer cells further complicate treatment efficacy. To overcome these hurdles, ongoing research explores the synergistic potential of combining CAR-T cell therapy with cancer vaccines and other therapeutic strategies such as checkpoint inhibitors and cytokine therapy. This review describes the various immunotherapeutic approaches targeting leukemia, emphasizing the roles and interplay of cancer vaccines and CAR-T cell therapy. In addition, by discussing how these therapies individually and collectively contribute to tumor regression, this article aims to highlight innovative treatment paradigms that could enhance clinical outcomes for leukemia patients. This integrative approach promises to pave the way for more effective and durable treatment strategies in the oncology field. These combined immunotherapeutic strategies hold great promise for achieving more complete and lasting remissions in leukemia patients. Future research should prioritize optimizing treatment sequencing, personalizing therapeutic combinations based on individual patient and tumor characteristics, and developing novel strategies to enhance T cell persistence and function within the tumor microenvironment. Ultimately, these efforts will advance the development of more effective and less toxic immunotherapeutic interventions, offering new hope for patients battling this challenging disease.

Tumour and microenvironment crosstalk in NSCLC progression and response to therapy

The treatment landscape of non-small-cell lung cancer (NSCLC) is evolving rapidly, driven by advances in the development of targeted agents and immunotherapies. Despite this progress, some patients have suboptimal responses to treatment, highlighting the need for new therapeutic strategies. In the past decade, the important role of the tumour microenvironment (TME) in NSCLC progression, metastatic dissemination and response to treatment has become increasingly evident. Understanding the complexity of the TME and its interactions with NSCLC can propel efforts to improve current treatment modalities, overcome resistance and develop new treatments, which will ultimately improve the outcomes of patients. In this Review, we provide a comprehensive view of the NSCLC TME, examining its components and highlighting distinct archetypes characterized by spatial niches within and surrounding tumour nests, which form complex neighbourhoods. Next, we explore the interactions within these components, focusing on how inflammation and immunosuppression shape the dynamics of the NSCLC TME. We also address the emerging influences of patient-related factors, such as ageing, sex and health disparities, on the NSCLC-TME crosstalk. Finally, we discuss how various therapeutic strategies interact with and are influenced by the TME in NSCLC. Overall, we emphasize the interconnectedness of these elements and how they influence therapeutic outcomes and tumour progression.

Impact of radiation therapy on the immunological tumor microenvironment

External beam radiation therapy (RT) is a cornerstone of modern cancer management, being utilized in both curative and palliative settings due to its safety, efficacy, and widespread availability. A primary biological effect of RT is DNA damage, which leads to significant cytostatic and cytotoxic effects. Importantly, malignant cells possess a limited capacity for DNA repair compared to normal cells, and when combined with irradiation techniques that minimize damage to healthy tissues, this creates an advantageous therapeutic window. However, the clinical effectiveness of RT also appears to involve both direct and indirect interactions between RT and non-transformed components of the tumoral ecosystem, particularly immune cells. In this review, we describe the molecular and cellular mechanisms by which irradiated cancer cells modify the immunological tumor microenvironment and how such changes ultimately impact tumor growth.

Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of esophageal adenocarcinoma

Locally advanced esophageal adenocarcinoma remains difficult to treat and the ecological and evolutionary dynamics responsible for resistance and recurrence are incompletely understood. Here, we performed longitudinal multiomic analysis of patients with esophageal adenocarcinoma in the MEMORI trial. Multi-region multi-timepoint whole-exome and paired transcriptome sequencing was performed on 27 patients before, during and after neoadjuvant treatment. We found major transcriptomic changes during treatment with upregulation of immune, stromal and oncogenic pathways. Genetic data revealed that clonal sweeps through treatment were rare. Imaging mass cytometry and T cell receptor sequencing revealed remodeling of the tumor microenvironment during treatment. The presence of genetic immune escape, a less-cytotoxic T cell phenotype and a lack of clonal T cell expansions were linked to poor treatment response. In summary, there were widespread transcriptional and environmental changes through treatment, with limited clonal replacement, suggestive of phenotypic plasticity.

Nivolumab plus low-dose ipilimumab in hypermutated HER2-negative metastatic breast cancer: a phase II trial (NIMBUS)

In the phase II NIMBUS trial, patients with human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC) and high tumor mutational burden (TMB ≥ 9 mut/Mb) received nivolumab (3 mg/kg biweekly) and low-dose ipilimumab (1 mg/kg every 6 weeks) for 2 years or until progression. The primary endpoint was objective response rate (ORR) per RECIST 1.1 criteria. Among 30 patients enrolled, the median TMB was 10.9 mut/Mb (range: 9-110) and the confirmed objective response rate was 20%. Secondary endpoints included progression-free survival, overall survival, clinical benefit rate, and safety and tolerability, including immune-related adverse events (irAEs). A prespecified correlative outcome was to evaluate the ORR in patients with a TMB ≥ 14 mut/Mb. Patients with TMB ≥ 14 mut/Mb (n = 6) experienced higher response rates (60% vs 12%; p = 0.041) and showed a trend towards improved progression-free survival and overall survival compared to patients with TMB < 14 mut/Mb. Exploratory genomic analyses suggested that ESR1 and PTEN mutations may be associated with poor response, while clinical benefit was associated with a decrease or no change in tumor fraction by serial circulating tumor DNA during treatment. Stool microbiome analysis revealed that baseline blood TMB, PD-L1 positivity, and immune-related diarrhea are associated with distinct taxonomic profiles. In summary, some patients with hypermutated HER2-negative MBC experience extended clinical benefit with a dual immunotherapy regimen; a higher TMB, and additional genomic and microbiome biomarkers may optimize patient selection for therapy with nivolumab plus low-dose ipilimumab. (Funded by Bristol Myers Squibb; ClinicalTrials.gov identifier, NCT03789110).

DNA damage repair-related methylated genes RRM2 and GAPDH are prognostic biomarkers associated with immunotherapy for lung adenocarcinoma

Research has highlighted the significant role of methylated genes associated with DNA damage repair in pathogenesis of Lung adenocarcinoma (LUAD). However, the potential of DNA damage repair-related gene (DDRG) methylation as a prognostic biomarker remains underexplored. This study aimed to assess the prognostic value of methylated DDRGs in LUAD. Analysis of the TCGA-LUAD dataset revealed differentially expressed genes (DEGs) and differentially methylated genes (DE-MGs), from which methylated DE-DDRGs were identified. An independent prognostic risk model was constructed based on these methylated DE-DDRGs by integrating risk scores with clinical features. Additionally, the study examined responses to immunotherapy. Results indicated that CLU exhibited hypermethylation and elevated expression in LUAD tissues, while eight other genes (BUB1B, SHCBP1, RRM2, RPL39L, TRIP13, GAPDH, ENO1, and CENPM) showed high expression and hypomethylation. Among these, RRM2 and GAPDH were significantly linked to poorer overall survival. Furthermore, single-sample gene set enrichment analysis (ssGSEA) revealed that patients with LUAD in the high-risk group had lower immune scores and less immune cell infiltration. TIDE analysis suggested that patients in the low-risk group may exhibit greater sensitivity to immune checkpoint inhibitor therapy. In conclusion, RRM2 and GAPDH represent promising prognostic and immunotherapeutic biomarkers, offering new avenues for LUAD treatment strategies.

Atezolizumab plus personalized neoantigen vaccination in urothelial cancer: a phase 1 trial

Features of constrained adaptive immunity and high neoantigen burden have been correlated with response to immune checkpoint inhibitors (ICIs). In an attempt to stimulate antitumor immunity, we evaluated atezolizumab (anti-programmed cell death protein 1 ligand 1) in combination with PGV001, a personalized neoantigen vaccine, in participants with urothelial cancer. The primary endpoints were feasibility (as defined by neoantigen identification, peptide synthesis, vaccine production time and vaccine administration) and safety. Secondary endpoints included objective response rate, duration of response and progression-free survival for participants treated in the metastatic setting, time to progression for participants treated in the adjuvant setting, overall survival and vaccine-induced neoantigen-specific T cell immunity. A vaccine was successfully prepared (median 20.3 weeks) for 10 of 12 enrolled participants. All participants initiating treatment completed the priming cycle. The most common treatment-related adverse events were grade 1 injection site reactions, fatigue and fever. At a median follow-up of 39 months, three of four participants treated in the adjuvant setting were free of recurrence and two of five participants treated in the metastatic setting with measurable disease achieved an objective response. All participants demonstrated on-treatment emergence of neoantigen-specific T cell responses. Neoantigen vaccination plus ICI was feasible and safe, meeting its endpoints, and warrants further investigation. ClinicalTrials.gov registration: NCT03359239 .

Prognostic and predictive value of IDO expression in metastatic melanoma treated with Ipilimumab

BACKGROUND

The tumor microenvironment is crucial for prognosis and response to immunotherapy in several tumor entities.

METHODS

In a multicenter retrospective study, a total of 86 tumor samples from patients with metastatic melanoma were evaluated for baseline expression of indoleamine 2,3-dioxygenase (IDO) and programmed death ligand 1 (PD-L1). Expression patterns of IDO and PD-L1 on tumor cells and antigen-presenting cells (APCs) as determined by immunohistochemical (IHC) staining of paraffin-embedded tissue sections were correlated with response to ipilimumab and overall survival (OS). Statistical analysis was performed using the Spearman correlation, the Mann-Whitney test and Kaplan-Meier estimator.

RESULTS

IDO expression in tumor cells or APCs was not predictive for treatment response. The median OS was 26 months in IDO-positive and IDO-negative patients, regardless of IDO expression in tumor cells or APCs. A correlation of IHC expression scores of IDO and PD-L1 could not be documented.

CONCLUSION

The exact role of IDO in creating an immunosuppressive tumor environment and its reversal needs to be further elucidated.

Novel prognostic biomarkers in small cell lung cancer reveal mutational signatures, genomic mutations, and immune implications

Small cell lung cancer (SCLC) is a highly malignant lung cancer subtype with a dismal prognosis and limited treatment options. This study aimed to identify new prognostic molecular biomarkers for SCLC and explore their immune-related implications for treatment strategies. We analyzed 200 SCLC samples via whole-exome sequencing (WES) and 313 samples by targeted sequencing. A smoking-related SBS4 mutational signature was linked to poorer prognosis and lower tumor mutational burden (TMB), while the APOBEC-mediated SBS13 signature was associated with better prognosis and higher TMB. We identified a molecular subtype with the worst outcomes and lowest TMB in both cohorts. Among 38 high-frequency mutated genes associated with SCLC prognosis, only UNC13A mutations were beneficial. Patients with UNC13A mutations had favorable immune infiltration and tumor immunogenicity. Additionally, TP53 splice site mutations were related to the worst survival outcomes. In conclusion, we discovered new molecular biomarkers for SCLC prognosis. Our findings on their immunological characteristics offer insights for developing novel SCLC treatment strategies.

pTERT mutational status is associated with survival in stage IV melanoma patients receiving first-line immune therapy

BACKGROUND

TERT promoter mutations are the most prevalent mutations in melanoma. In this study, we investigated clinical characteristics and survival after first line therapies in a cohort of melanoma patients with known TERT promoter (pTERT) mutation status.

METHODS

Sequencing data from 2013 to 2021 covering 29 genes and the pTERT status was assessed and 774 melanomas patients with known pTERT status and clinical data were analyzed. Progression free survival (PFS) and overall survival (OS) of 374 melanoma patients in AJCC-stage IV who received first-line immune checkpoint inhibitors (ICI, anti-CTLA4 /anti-PD1 combination therapy or anti-PD1 monotherapy) or targeted therapy (TT) were assessed applying Cox uni-/ multivariable analyses and Kaplan-Meier curves.

RESULTS

The cohort included 573 cutaneous, 69 mucosal, 37 acral and 95 MUP (melanomas of unknown primary) melanoma patients with a median observational time from first diagnosis to patient death or censoring of 38.5 months. TERT promoter mutations were identified in 476 melanomas (61.5 %). Survival analysis of 374 patients with stage IV disease undergoing first-line systemic therapy (ICI or TT) suggested prolonged PFS and OS for patients with pTERT mutation positive tumors (pTERT(+)). Particularly, pTERT(+) patients receiving anti-CTLA4/anti-PD1 therapy showed mPFS of 14.8 months (95 % CI: 7.1-40.3) and mOS of 105.2 months (95 % CI: 27.6-not reached) compared to pTERT(-) patients with mPFS of 5.5 months (95 % CI: 2.7-10.0) and mOS of 14.7 months (95 % CI: 11.7-24.1).

CONCLUSIONS

Our findings suggest that presence of a pTERT mutation in melanomas might favor PFS and OS after first line ICI with the greatest improvement after receiving anti-CTLA4 / anti-PD1. If validated in larger prospective studies, pTERT mutation status may be a valuable prognostic marker for stage IV melanoma patients.

Multi-omics sequencing of gastroesophageal junction adenocarcinoma reveals prognosis-relevant key factors and a novel immunogenomic classification

BACKGROUND

Gastroesophageal junction adenocarcinoma (GEJAC) exhibits distinct molecular characteristics due to its unique anatomical location. We sought to investigate effective and reliable molecular classification of GEJAC to guide personalized treatment.

METHODS

We analyzed the whole genomic, transcriptomic, T-cell receptor repertoires, and immunohistochemical data in 92 GEJAC patients and delineated the landscape of genetic and immune alterations. In addition to COSMIC nomenclature, the de novo nomenclature was also utilized to define signatures and investigate their correlation with survival. A novel molecular subtype was developed and validated in other cohorts.

RESULTS

We found 30 mutated driver genes, 7 novel genomic signatures, 3 copy-number variations, and 2 V-J gene usages related to prognosis that were not identified in previous study. A high frequency of COSMIC-SBS-384-1 and De novo-SV-32-A was associated with more neoantigen generation and a better survival. Using 19 molecular features, we identified three immune-related subtypes (immune inflamed, intermediate, and deserted) with discrete profiles of genomic signatures, immune status, and clinical outcome. The immune deserted subtype (27.2%) was characterized by an earlier KRAS mutation, worse immune reaction, and prognosis than the other two subtypes. The immune inflamed subtypes exhibited the highest levels of neoantigens, TCR/pMHC-binding strength, CD8 + T-cell infiltration, IFN-α/γ response pathways, and survival rate.

CONCLUSIONS

These results emphasize the immune reaction and prognostic value of novel molecular classifications based on multi-omics data and provide a solid basis for better management of GEJAC.

Biomarkers in advanced renal cell carcinoma: current practice and future directions

PURPOSE OF REVIEW

This review focuses on contemporary research into potential prognostic and therapeutic biomarkers for advanced renal cell carcinoma (RCC) published over the past 18 months. Beyond serum lab values, there is no consensus on the use of specific biomarkers for this purpose. Potential biomarkers being investigated consist of genetic, protein, immunologic, and radiologic candidates.

RECENT FINDINGS

New insights in genomic biomarkers include a better understanding of VHL mutational heterogeneity, tumor mutational burden, and the importance of genes like PBRM1 and SETD2 . Protein biomarkers such as C-reactive protein (CRP) and PDZK1 have demonstrated utility in predicting disease progression, therapeutic response, and survival, while immunologic biomarkers like PSMD2, cytokines, and Tregs continue to shed light on the tumor microenvironment and immune evasion. Emerging imaging biomarkers, from CAIX-targeted radiotracers to PSMA-based PET-CT, offer noninvasive diagnostic and prognostic tools that may revolutionize RCC management.

SUMMARY

There are several promising biomarkers currently under investigation for use in advanced RCC.

A redefined InDel taxonomy provides insights into mutational signatures

Despite their deleterious effects, small insertions and deletions (InDels) have received far less attention than substitutions. Here we generated isogenic CRISPR-edited human cellular models of postreplicative repair dysfunction (PRRd), including individual and combined gene edits of DNA mismatch repair (MMR) and replicative polymerases (Pol ε and Pol δ). Unique, diverse InDel mutational footprints were revealed. However, the prevailing InDel classification framework was unable to discriminate these InDel signatures from background mutagenesis and from each other. To address this, we developed an alternative InDel classification system that considers flanking sequences and informative motifs (for example, longer homopolymers), enabling unambiguous InDel classification into 89 subtypes. Through focused characterization of seven tumor types from the 100,000 Genomes Project, we uncovered 37 InDel signatures; 27 were new. In addition to unveiling previously hidden biological insights, we also developed PRRDetect-a highly specific classifier of PRRd status in tumors, with potential implications for immunotherapies.

Mutational signature-based biomarker to predict the response of immune checkpoint inhibitors therapy in cancers

Patients have a limited response rate to immune checkpoint inhibitors (ICIs) therapy. Although several biomarkers have been proposed, their ability to accurately predict the response to ICIs therapy remains unsatisfactory. In addition, mutational signatures were validated to be associated with ICIs therapy. Therefore, we developed a mutational signature-based biomarker (MS-bio) to predict the response to ICIs therapy. Based on differentially mutated genes, we extracted six mutational signatures (single-base substitution (SBS)-A, SBS-B, SBS-C, SBS-D, double-base substitution (DBS)-A, and DBS-B) as MS-bio, and constructed a random forest (RF) model to predict the response. Internal and external validations consistently demonstrated the excellent predictive capability of MS-bio, with an accuracy reaching up to 0.82. Moreover, MS-bio exhibited superior performance compared to existing biomarkers. To further validate the accuracy of MS-bio, we explored its performance in The Cancer Genome Atlas (TCGA) cohort and found that the predicted responders were immunologically "hot". Finally, we found that SBS-C had the highest importance in prediction and was related to T cell differentiation. Overall, here we introduced MS-bio as a novel biomarker for accurately predicting the response to ICIs therapy, thereby contributing to the advancement of precision medicine.

Resistance to PD-1/PD-L1 immune checkpoint blockade in advanced non-small cell lung cancer

Lung cancer is one of the most common malignant tumors, of which non-small cell lung cancer (NSCLC) accounts for about 85 %. Although immune checkpoint inhibitors (ICIs), particularly PD-1/PD-L1 inhibitors, have significantly improved the prognosis of patients with NSCLC. There are still many patients do not benefit from ICIs. Primary resistance remains a major challenge in advanced NSCLC. The cancer-immunity cycle describes the process from antigen release to T cell recognition and killing of the tumor, which provides a framework for understanding anti-tumor immunity. The classical cycle consists of seven steps, and alterations at each stage can result in resistance. This review examines the current status of PD-1/PD-L1 blockade in the treatment of advanced NSCLC and explores potential mechanisms of resistance. We summarize the latest clinical trials of PD-1/PD-L1 inhibitors combined with other therapies and explore potential targets for overcoming primary resistance to PD-1/PD-L1 inhibitors.

Nivolumab plus chemotherapy or ipilimumab in gastroesophageal cancer: exploratory biomarker analyses of a randomized phase 3 trial

First-line nivolumab-plus-chemotherapy demonstrated superior overall survival (OS) and progression-free survival versus chemotherapy for advanced gastroesophageal adenocarcinoma with programmed death ligand 1 combined positive score ≥ 5, meeting both primary end points of the randomized phase 3 CheckMate 649 trial. Nivolumab-plus-ipilimumab provided durable responses and higher survival rates versus chemotherapy; however, the prespecified OS significance boundary was not met. To identify biomarkers predictive of differential efficacy outcomes, post hoc exploratory analyses were performed using whole-exome sequencing and RNA sequencing. Nivolumab-based therapies demonstrated improved efficacy versus chemotherapy in hypermutated and, to a lesser degree, Epstein-Barr virus-positive tumors compared with chromosomally unstable and genomically stable tumors. Within the KRAS-altered subgroup, only patients treated with nivolumab-plus-chemotherapy demonstrated improved OS benefit versus chemotherapy. Low stroma gene expression signature scores were associated with OS benefit with nivolumab-based regimens; high regulatory T cell signatures were associated with OS benefit only with nivolumab-plus-ipilimumab. Our analyses suggest that distinct and overlapping pathways contribute to the efficacy of nivolumab-based regimens in gastroesophageal adenocarcinoma.

Molecular evolution of driver mutations in cancer with microsatellite instability and their impact on tumor progression: Implications for precision medicine in patients with UCEC

Cancer development is driven by genetic alterations, particularly cancer driver mutations (CDMs), which are associated with aggressive phenotypes and shorter survival. In contrast, higher mutation loads caused by microsatellite instability (MSI) or mismatch repair deficiency (MMRd) can induce anti-cancer immunity, leading to tumor shrinkage and improved responses to immune checkpoint inhibitor (ICI) therapies. However, understanding how CDMs and MSI/MMRd influence cancer evolution remains limited. We opted uterine corpus endometrial carcinoma (UCEC) as a model in this study due to its MSI-high/MMRd characteristics. Somatic mutation screening revealed that UCEC has a significantly higher mutation rate in cancer driver genes compared to ovarian cancer (OVCA) and cervical squamous cell carcinoma (CSCC), despite these cancers arising from histologically connected organs in the reproductive tract. Interestingly, these CDMs did not necessarily drive tumor progression. Using a cutoff of 7.0 (mutations/Mb) for tumor mutation burden (TMB), we classified UCEC patients into two groups with distinct clinical features, genetic profiles, and drug sensitivities. Among the known CDMs, TP53 mutations and their functional networks emerged as key drivers in UCEC progression, while mutations in CTNNB1, PTEN, and ARID1A may enhance anti-tumor immunity, correlating with longer overall survivals. Drug screening using GDSC and CTRPv2 databases suggested that GSK-3 inhibitor IX may be effective for treating aggressive UCEC patients with a non-MSI phenotype. Curcumin showed efficacy for UCEC patients with MSI, especially with ICI therapy. Our study highlights the importance of immune regulation and tolerance over CDMs in cancer development, particularly in those with an MSI-high/MMRd phenotype. We propose that TMB could serve as a valuable screening method alongside molecular and histopathological classifications to guide treatment strategies for UCEC patients.

Advances and challenges in cancer immunotherapy: Strategies for personalized treatment

Cancer immunotherapy has transformed oncology by harnessing the immune system to specifically target cancer cells, offering reduced systemic toxicity compared to traditional therapies. This review highlights key strategies, including adoptive cell transfer (ACT), immune checkpoint inhibitors, oncolytic viral (OV) therapy, monoclonal antibodies (mAbs), and mRNA-based vaccines. ACT reinfuses enhanced immune cells like tumor-infiltrating lymphocytes (TILs) to combat refractory cancers, while checkpoint inhibitors (eg, PD-1 and CTLA-4 blockers) restore T-cell activity. OV therapy uses engineered viruses (eg, T-VEC) to selectively lyse cancer cells, and advanced mAbs improve targeting precision. mRNA vaccines introduce tumor-specific antigens to trigger robust immune responses. Despite significant progress, challenges like immune-related side effects, high costs, and immunosuppressive tumor microenvironments persist. This review underscores the need for combination strategies and precision medicine to overcome these barriers and maximize the potential of immunotherapy in personalized cancer treatment.

APOBEC in breast cancer: a dual player in tumor evolution and therapeutic response

The APOBEC (Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like) family of cytidine deaminases has emerged as pivotal a contributor to genomic instability and adaptive immunity through DNA/RNA editing. Accumulating evidence underscores their dual role in breast carcinogenesis-driving tumor heterogeneity via mutagenesis while simultaneously shaping immunogenic landscapes. This review synthesizes current insights into APOBEC-mediated molecular mechanisms, focusing on their clinical implications across breast cancer subtypes. Notably, APOBEC-driven mutagenesis correlates with elevated tumor mutational burden (TMB), replication stress vulnerability, and immune checkpoint inhibitor (ICI) responsiveness. Paradoxically, these mutations also accelerate endocrine therapy resistance and subclonal diversification. We propose APOBEC mutational signatures as predictive biomarkers for ICI efficacy and discuss therapeutic strategies leveraging APOBEC activity, including ATR inhibition and hypermutagenic immunotherapy. Harnessing APOBEC's duality-balancing its pro-immunogenic effects against genomic chaos-may redefine precision oncology in breast cancer.

Potential Mechanisms for Immunotherapy Resistance in Adult Soft-Tissue Sarcoma

Soft-tissue sarcomas represent a diverse group of rare malignancies originating from mesenchymal tissue, accounting for less than 1% of adult cancers in the USA. With over 13,000 new cases and around 5350 deaths annually, patients with metastatic soft-tissue sarcomas face limited therapeutic options and an estimated median overall survival of 18 months. While immunotherapy has demonstrated effectiveness in several cancers, its application in soft-tissue sarcomas remains challenging owing to the tumors' largely "cold" immunological environment, characterized by low levels of tumor-infiltrating lymphocytes and a lack of soft-tissue sarcoma-specific biomarkers. This review examines potential mechanisms underlying immunotherapy resistance in soft-tissue sarcomas, including the complex interplay between innate and adaptive immunity, the tumor microenvironment, and the role of immune-related genes. Despite preliminary findings suggesting correlations between immune profiles and histological subtypes, consistent biomarkers for predicting immunotherapeutic responses across soft-tissue sarcoma types are absent. Emerging strategies focus on converting "cold" tumors to "hot" tumors, enhancing their susceptibility to immunologic activation. While research is ongoing, personalized treatment approaches may offer hope for overcoming the inherent heterogeneity and resistance seen in soft-tissue sarcomas, ultimately aiming to improve outcomes for affected patients.

Interpretable Machine Learning reveals the Role of PANoptosis in the Diagnosis and Subtyping of NAFLD

Non-alcoholic fatty liver disease (NAFLD) is a global health challenge characterized by complex pathogenesis and limited therapeutic options. Emerging evidence highlights PANoptosis-a coordinated interplay of pyroptosis, apoptosis, and necroptosis-as a critical driver of metabolic and immune dysregulation in NAFLD. Here, we integrated multiple datasets and interpretable machine learning to unravel the role of PANoptosis in NAFLD diagnosis, subtyping, and immune microenvironment remodeling. By intersecting differentially expressed genes and PANoptosis-related genes, we identified 9 hub genes (e.g., TRADD, CASP6, TNFRSF1A and TNFAIP3) and constructed a robust diagnostic model (AUC = 0.976) validated via SHAP analysis and nomogram. Unsupervised consensus clustering stratified NAFLD patients into two PANoptosis-driven subtypes (C1/C2 and CA/CB), revealing distinct immune cell infiltration patterns and pathway activation. Single-cell sequencing further localized hub genes to immune cells and revealed their cell communication, implicating their roles in the progression of NAFLD. Molecular docking studies identified fostamatinib and minocycline as potential therapeutic candidates, while pan-cancer analysis revealed that TNFRSF1A overexpression is associated with poor prognosis across multiple cancer types. This study enhances the understanding of PANoptosis as a crucial diagnostic and therapeutic target in NAFLD, providing novel insights into immune-mediated pathogenesis and paving the way for treatment strategies.

Case Report: Two cases of chemotherapy refractory aggressive variant prostate cancer with extreme durable response to PARP inhibitor

Background

Aggressive variant prostate cancer (AVPC) represents a distinct clinical subset characterized by resistance to novel hormone therapies and an unfavorable prognosis, frequently associated with the concurrent loss of tumor suppressor genes (TSG) such as PTEN, RB1, and TP53. While the progression-free survival (PFS) and overall survival (OS) of AVPC are relatively short, the optimal first-line treatment remains unclear.

Presentation

In this case report, we presented two de novo AVPC cases who have ultimately benefited from the usage of PARP inhibitors. The first patient was a 64-year-old male who was diagnosed during prostate biopsy featured by mutations in PTEN, and loss of RB1, BRCA2, ATM, and FANCA. He was treated with docetaxel/albumin-bound paclitaxel and cisplatin in the first line. Second-line therapy was applied with radiotherapy and Olaparib after failure of first-line therapy, resulting in a PSA response sustained for three years. The second case was a 75-year-old male with localized neuroendocrine feature and mutations in TP53, loss of RB1 and HDAC2. He was treated with sustained ADT and chemotherapy in the first-line treatment. Radiotherapy and Fluzoparib + abiraterone was applied as subsequent treatments with a PSA response for 2 years.

Conclusions

These two cases demonstrating a satisfactorily durable response to PARP inhibitors indicating its clinical benefit in AVPC population with detected DNA damage response (DDR) defects. The survival improvement with PARP inhibitors observed in our clinical experiences, along with current advances in tumor sequencing provide more information on future clinical trials and explorations of innovative therapies in AVPC population.

Combinational therapeutic strategies to overcome resistance to immune checkpoint inhibitors

Over the past few years, immune checkpoint inhibitors resulted in magnificent and durable successes in treating cancer; however, only a minority of patients respond favorably to the treatment due to a broad-spectrum of tumor-intrinsic and tumor-extrinsic factors. With the recent insights gained into the mechanisms of resistance, combination treatment strategies to overcome the resistance and enhance the therapeutic potential of immune checkpoint inhibitors are emerging and showing promising results in both pre-clinical and clinical settings. This has been derived through multiple interconnected mechanisms such as enhancing tumor immunogenicity, improving neoantigen processing and presentation in addition to augmenting T cell infiltration and cytotoxic potentials. In the clinical settings, several avenues of combination treatments involving immune checkpoint inhibitors were associated with considerable improvement in the therapeutic outcome in terms of patient's survival and tumor growth control. This, in turn, increased the spectrum of cancer patients benefiting from the unprecedented and durable effects of immune checkpoint inhibitors leading to their adoption as a first-line treatment for certain cancers. Moreover, the significance of precision medicine in cancer immunotherapy and the unmet demand to develop more personalized predictive biomarkers and treatment strategies are also highlighted in this review.

Genetic and transcriptional insights into immune checkpoint blockade response and survival: lessons from melanoma and beyond

BACKGROUND

Integration of immune checkpoint inhibitors (ICIs) with non-immune therapies relies on identifying combinatorial biomarkers, which are essential for patient stratification and personalized treatment.

METHODS

We analyzed genomic and transcriptomic data from pretreatment tumor samples of 342 melanoma patients treated with ICIs to identify mutations and expression signatures associated with ICI response and survival. External validation and mechanistic exploratory analyses were conducted in two additional datasets to assess generalizability.

RESULTS

Responders were more likely to have received anti-PD-1 therapy rather than anti-CTLA-4 and exhibited a higher tumor mutation burden (both P < 0.001). Mutations in the dynein axonemal heavy chain (DNAH) family genes, specifically DNAH2 (P = 0.03), DNAH6 (P < 0.001), and DNAH9 (P < 0.01), were enriched in responders. The combined mutational status of DNAH 2/6/9 effectively stratified patients by progression-free survival (hazard ratio [HR]: 0.69; 95% confidence interval [CI] 0.51-0.92; P = 0.013) and overall survival (HR: 0.58; 95% CI 0.43-0.78; P < 0.001), with consistent association observed in the validation cohort (HR: 0.28; 95% CI 0.12-0.61; P < 0.001). DNAH-altered melanomas exhibited upregulation of chemokine signaling, cytokine-cytokine receptor interaction, and cell cycle-related pathways, along with elevated expression of immune-related signatures in interferon signaling, cytolytic activity, T cell function, and immune checkpoints. Using LASSO logistic regression, we identified a 26-gene composite signature predictive of clinical response, achieving an area under the curve (AUC) of 0.880 (95% CI 0.825-0.936) in the training dataset and 0.725 (95% CI 0.595-0.856) in the testing dataset. High-risk patients, stratified by the expression levels of a 13-gene signature, demonstrated significantly shorter overall survival in both datasets (HR: 3.35; P < 0.001; HR: 2.93; P = 0.002).

CONCLUSIONS

This analysis identified potential molecular determinants of response and survival to ICI treatment. Insights from melanoma biomarker research hold significant promise for translation into other malignancies, guiding individualized anti-tumor immunotherapy.

Targeting B7-H3 enhances the efficacy of neoantigen-based cancer vaccine in combination with radiotherapy

The clinical response to immune checkpoint blockade (ICB) is limited in the majority of patients with colorectal cancer. These immune checkpoint proteins may not only inhibit T-cell-mediated antitumor immunity but also attenuate antigen presentation, including mutation-associated neoantigens. Here, we found that tumor B7-H3 levels may limit the therapeutic response to chemoradiotherapy in patients with locally-advanced rectal cancer. Knockdown of tumor B7-H3 significantly increased antigen presentation to increase T cell infiltration and killing ability, including neoantigen-specific T-cell response. Blockade of B7-H3 significantly augmented neoantigen-specific T cells response and remarkably enhanced the therapeutic efficacy of neoantigen-based cancer vaccines combined with radiotherapy, decreasing the risk of distant tumors in vivo. Taken together, these results demonstrated that targeting B7-H3 significantly enhanced the therapeutic efficacy of neoantigen cancer vaccines as well as radiotherapy by increasing the extent of neoantigen-specific T cells, even for PD-1/PD-L1 blockade-resistant colorectal cancers.

Predicting the Efficacy of Immune Checkpoint Inhibitors in Esophageal Cancer: Changes in Peripheral Blood Lymphocyte Subsets Before and After Immunotherapy

Background

Immunotherapy has demonstrated potential in the treatment of esophageal cancer (EC); however, the overall response rate (ORR) remains below 30% among EC patients. Herein, the use of peripheral blood lymphocyte subsets as biomarkers was explored to evaluate the efficacy of immunotherapy in this patient population.

Methods

Sixty-three patients were enrolled. The patients were diagnosed with EC and treated with immune checkpoint inhibitors (ICIs) at The Fourth Hospital of Hebei Medical University from December 2019 to June 2023. Kaplan-Meier (KM) survival curves were used to reflect differences in survival benefit. The prognostic factors of survival were investigated using the Cox proportional hazards regression model for both univariate and multivariate analyses. Two-tailed P values were reported and statistical significance was defined as P < 0.05.

Results

The results of univariate and multifactorial Cox regression analysis for progression-free survival (PFS) revealed that only CD8+ T lymphocytes demonstrated a significant association with PFS (P = 0.034, P = 0.020). Additionally, the multifactorial Cox regression analysis results for overall survival (OS) revealed a significant association between natural killer (NK) cells and OS (P=0.049). Further, a systematic analysis was conducted on the CD8+ T cell biomarker. The KM survival curves indicated that the group with low CD8+ T cell levels experienced a significantly greater PFS benefit compared to the high CD8+ T cell group (P = 0.030).

Conclusion

The present study reveals that the reduction of both CD8+ T lymphocytes and NK cells in peripheral blood lymphocyte subsets after immunotherapy can serve as superior predictors for the effectiveness of ICIs in patients diagnosed with EC.

Targeting DNA Damage Repair to Enhance Antitumor Immunity in Radiotherapy: Mechanisms and Opportunities

Radiotherapy is a standard cancer treatment that involves the induction of DNA damage. DNA damage repair (DDR) pathways maintain genomic integrity and make tumors resistant to radiotherapy and certain chemotherapies. In turn, DDR dysfunction results in cumulative DNA damage, leading to increased sensitivity for antitumor treatment. Moreover, radiotherapy has been shown to trigger antitumor immunity. Currently, immunotherapy has become a new and widely used standard strategy for treating a broad spectrum of tumor types. Notably, recent studies have demonstrated that DDR pathways play important roles in driving the response to immunotherapy. Herein, we review and discuss how DDR affects antitumor immunity induced by radiotherapy. Furthermore, we summarize the development of strategies for combining DDR inhibitors with radiotherapy and/or immunotherapy to enhance their efficacy against cancers.

Deciphering immune predictors of immunotherapy response: A multiomics approach at the pan-cancer level

Immune checkpoint blockade (ICB) therapy has transformed cancer treatment, yet many patients fail to respond. Employing single-cell multiomics, we unveil T cell dynamics influencing ICB response across 480 pan-cancer and 27 normal tissue samples. We identify four immunotherapy response-associated T cells (IRATs) linked to responsiveness or resistance and analyze their pseudotemporal patterns, regulatory mechanisms, and T cell receptor clonal expansion profiles specific to each response. Notably, transforming growth factor β1 (TGF-β1)+ CD4+ and Temra CD8+ T cells negatively correlate with therapy response, in stark contrast to the positive response associated with CXCL13+ CD4+ and CD8+ T cells. Validation with a cohort of 23 colorectal cancer (CRC) samples confirms the significant impact of TGF-β1+ CD4+ and CXCL13+ CD4+ and CD8+ T cells on ICB efficacy. Our study highlights the effectiveness of single-cell multiomics in pinpointing immune markers predictive of immunotherapy outcomes, providing an important resource for crafting targeted immunotherapies for successful ICB treatment across cancers.

Navigating established and emerging biomarkers for immune checkpoint inhibitor therapy

Immune checkpoint inhibitors (ICIs) have improved outcomes of patients with many different cancers. These antibodies target molecules such as programmed cell death 1 (PD-1) or cytotoxic T lymphocyte associated protein 4 (CTLA-4) which normally function to limit immune activity. Treatment with ICIs reactivates T cells to destroy tumor cells in a highly specific manner, which in some patients, results in dramatic remissions and durable disease control. Over the last decade, much effort has been directed at characterizing factors that drive efficacy and resistance to ICI therapy. Food and Drug Administration (FDA)-approved biomarkers for ICI therapy have facilitated more judicious treatment of cancer patients and transformed the field of precision oncology. Yet, adaptive immunity against cancers is complex, and newer data have revealed the potential utility of other biomarkers. In this review, we discuss the utility of currently approved biomarkers and highlight how emerging biomarkers can further improve the identification of patients who benefit from ICIs.

Comprehensive analysis of prognosis and tumor immune microenvironment of cuproptosis-related gene CDKN2A in lung adenocarcinoma

BACKGROUND

Recent research has increasingly highlighted the significance of various forms of cell death in contributing to tumor heterogeneity and modulating anti-tumor immunity. However, the potential implications of cuproptosis-related genes (CRGs) in lung adenocarcinoma (LUAD) remains poorly explored.

METHODS

We conducted a comprehensive analysis of the expression profiles of 19 CRGs in LUAD based on The Cancer Genome Atlas (TCGA). Utilizing consensus clustering, we stratified the TCGA cohort into two distinct LUAD subtypes (Cluster 1 and Cluster 2). The expression of CDKN2A was further validated across multiple datasets, including TCGA, GEO, Cancer Cell Line Encyclopedia (CCLE), and the Human Protein Atlas (HPA). The prognostic value of the CDKN2A was evaluated through univariate, multivariate, and survival analyses. Gene set enrichment analysis (GSEA) was performed to elucidate the molecular mechanisms associated with the CDKN2A. Additionally, we assessed the levels of immune cell infiltration in LUAD using the CIBERSORT, ESTIMATE, and XCELL algorithms.

RESULTS

By systematically analyzing the genetic alterations of 19 CRGs in LUAD, we found 15 differentially expressed genes between LUAD and adjacent normal tissues. Subsequently, using the consensus clustering method, we classified LUAD patients into two molecular subtypes and cluster 2 had a poor prognosis. CDKN2A emerged as a key gene of interest, exhibiting elevated expression in LUAD and correlating with adverse patient outcomes. Moreover, immunoinfiltration analysis revealed differential levels of immune cell infiltration between the CDKN2A high and CDKN2A low expression groups.

CONCLUSIONS

Our findings indicate that CDKN2A may serve as an effective prognostic biomarker for LUAD and may offer valuable insights into potential immunotherapeutic strategies for these patients.

CLINICAL TRIAL NUMBER

Not applicable.

To Predict the Prognosis and Immunological Characteristics of Pancreatic Cancer Based on Disulfide-Death Gene Death-Related lncRNA

Background: Disulfide-dependent cell death, known as disulfide death, plays a pivotal regulatory role in the onset and progression of various cancers including pancreatic cancer. Despite its significance, little attention has been given to the study of disulfide death-related long non-coding RNAs (lncRNAs) in pancreatic cancer development and progression. Methods: This study utilized data from the Cancer Genome Atlas Project (TCGA) to analyze the transcriptome of pancreatic cancer. Co-expression analysis of genes associated with disulfide death was performed and six lncRNAs closely linked to disulfide death were identified through univariate and multivariate analysis. These lncRNAs were used to develop clinical prognostic models. The prognostic value of this model was then analyzed and further investigations included pathway enrichment analysis, tumor mutation load analysis, immune cell infiltration analysis, analysis of the tumor microenvironment (TME), and drug sensitivity analysis. Results: The developed prognostic model based on disulfide-associated lncRNAs exhibited significant prognostic value, allowing for reliable predictions of patient outcomes in pancreatic adenocarcinoma (PAAD). The analysis revealed that the six identified lncRNAs serve as independent prognostic factors, significantly correlating with patient survival and recurrence rates. Additionally, findings indicated notable differences in immune cell infiltration and drug sensitivity between high-risk and low-risk patient groups, suggesting potential therapeutic targets for enhancing treatment efficacy. Conclusions: Our findings revealed six disulfide death-associated lncRNAs with independent prognostic value, offering a crucial indicator for predicting the prognosis of pancreatic adenocarcinoma (PAAD) patients. Additionally, the analysis of tumor immune invasion and drug sensitivity provides a novel avenue for controlling tumor invasion and metastasis as well as reducing drug tolerance.

HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy

Clear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is considered immunogenic because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor. An earlier case report described a ccRCC patient who was cured by an allogeneic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERV), ERVE-4. We report that ERVE-4 is one of many ERVs that are induced by HIF, translated into HLA-bound peptides in ccRCCs, and capable of generating antigen-specific T cell responses. Moreover, ERV expression can be induced in non-ccRCC tumors with clinical-grade HIF stabilizers. These findings have implications for leveraging ERVs for cancer immunotherapy.

Abscopal Effects and Immunomodulation in Skin Cancer Therapy

Radiation therapy (RT) is a crucial modality in cancer treatment, functioning through direct DNA damage and immune stimulation. However, RT's effects extend beyond targeted cells, influencing neighboring cells through the bystander effect (ByE) and distant sites via the abscopal effect (AbE). The AbE, first described by Mole in 1953, encompasses biological reactions at sites distant from the irradiation field. While RT can enhance antitumor immune responses, it may also contribute to an immunosuppressive microenvironment. To address this limitation, combining RT with immune checkpoint inhibitors (ICIs) has gained renewed interest, aiming to amplify antitumor immune responses. Evidence of AbEs has been observed in various metastatic or advanced cutaneous cancers, including melanoma, basal cell carcinoma, cutaneous lymphoma, Merkel cell carcinoma, and cutaneous squamous cell carcinoma. Clinical studies suggest combining RT with ICIs targeting CTLA-4 and PD-1/PD-L1 may enhance AbE incidence in these cancers. This review primarily explores the current understanding of AbEs in skin cancers, briefly acknowledging the ByE focusing on combining RT with immunomodulation. It focuses on proposed mechanisms, preclinical and clinical evidence, challenges in clinical translation, and future directions for harnessing AbEs in managing advanced skin malignancies. Alternative modalities for inducing abscopal-like responses are also explored. While promising, challenges remain in consistently reproducing AbEs in clinical practice, necessitating further research to optimize treatment combinations, timing, and patient selection.

Identifying patients who benefit more from perioperative immunotherapy combinations for resectable non-small cell lung cancer based on clinical and molecular characteristics: a meta-analysis of randomized clinical trials

PURPOSE

This study aims to identify patient subgroups who benefit more from perioperative immunotherapy combined with chemotherapy (IO-CT) based on clinical and molecular characteristics in resectable non-small cell lung cancer (NSCLC).

METHODS

Randomized controlled trials (RCTs) on perioperative IO-CT were searched. Beneficial differences of IO-CT regimens across different patient subgroups were assessed by pooling trial-specific ratios in event-free survival (EFS), overall survival (OS), pathological complete response (pCR), and major pathological response (MPR).

RESULTS

Six studies (n = 3003) involving five IO-CT regimens were included. Compared to CT alone, all IO-CT regimens significantly improved EFS, OS, MPR, and pCR, but increased toxicity. Toripa-chemo showed the best EFS and nivo-chemo showed the best OS. Patients with PD-L1 ≥ 1% had more EFS benefits compared to those with PD-L1 < 1% (HR [hazard ratio]: 1.55, 95% CI 1.17-2.04). Squamous NSCLC patients had significantly more pCR and MPR benefits than non-squamous NSCLC patients (pCR: OR [odds ratio] 0.68, 95% CI 0.49-0.95; MPR: OR 0.61, 95% CI 0.45-0.82). Former smokers had significantly higher pCR benefits than non-smokers (OR: 2.18; 95% CI 1.21-3.92). Additionally, OS benefit was significantly higher in patients < 65 years compared to those ≥ 65 years (HR ratio: 0.59, 95% CI 0.36-0.95). For MPR, males benefited significantly more from IO-CT compared to females (OR: 1.69, 95% CI 1.18-2.42).

CONCLUSION

Perioperative IO-CT is more effective but more toxic than CT alone in resectable NSCLC. Patients with PD-L1 ≥ 1%, squamous NSCLC, a history of smoking, age < 65 years and male gender may experience greater benefits from perioperative IO-CT.

Durable Response to Pembrolizumab With Chemotherapy in EGFR-Mutated Squamous Cell Lung Cancer: A Case Report

Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) is the standard treatment for EGFR-mutated non-small cell lung cancer (NSCLC), although a small subset of patients does not respond to EGFR-TKI, especially in patients with a smoking history and squamous cell histology. Additionally, even given an initial good response, acquired resistance to EGFR-TKI is inevitable. More individualized treatment could be necessary in certain types of EGFR-mutated NSCLC. We herein report a case of EGFR-mutated metastatic lung squamous cell carcinoma with a high tumor proportion score (TPS) of programmed death ligand 1 (PD-L1), where chemotherapy plus pembrolizumab therapy had a durable efficacy. In this case, chemotherapy plus pembrolizumab therapy was administered, though EGFR-TKI is the standard first-line therapy of EGFR-mutated NSCLC. Three years after treatment initiation, no sign of recurrence was observed. This case suggests that a detailed evaluation of a patient's background is important in making an effective personalized therapeutic strategy.

Unravelling Cancer Immunity: Coagulation.Sig and BIRC2 as Predictive Immunotherapeutic Architects

Immune checkpoint inhibitors (ICIs) represent a groundbreaking advancement in cancer therapy, substantially improving patient survival rates. Our comprehensive research reveals a significant positive correlation between coagulation scores and immune-related gene expression across 30 diverse cancer types. Notably, tumours exhibiting high coagulation scores demonstrated enhanced infiltration of cytotoxic immune cells, including CD8+ T cells, natural killer (NK) cells, and macrophages. Leveraging the TCGA pan-cancer database, we developed the Coagulation.Sig model, a sophisticated predictive framework utilising a coagulation-related genes (CRGs) to forecast immunotherapy outcomes. Through rigorous analysis of ten ICI-treated cohorts, we identified and validated seven critical CRGs: BIRC2, HMGB1, STAT2, IFNAR1, BID, SPATA2, IL33 and IFNG, which form the foundation of our predictive model. Functional analyses revealed that low-risk tumours characterised by higher immune cell populations, particularly CD8+ T cells, demonstrated superior ICI responses. These tumours also exhibited increased mutation rates, elevated neoantigen loads, and greater TCR/BCR diversity. Conversely, high-risk tumours displayed pronounced intratumor heterogeneity (ITH) and elevated NRF2 pathway activity, mechanisms strongly associated with immune evasion. Experimental validation highlighted BIRC2 as a promising therapeutic target. Targeted BIRC2 knockdown, when combined with anti-PD-1 therapy, significantly suppressed tumour growth, enhanced CD8+ T cell infiltration, and amplified IFN-γ and TNF-α secretion in tumour models. Our findings position the Coagulation.Sig model as a novel, comprehensive approach to personalised cancer treatment, with BIRC2 emerging as both a predictive biomarker and a potential therapeutic intervention point.

Mechanisms of primary resistance to immune checkpoint inhibitors in NSCLC

Immune checkpoint inhibitors (ICIs) redefined the therapeutics of non-small cell lung cancer (NSCLC), leading to significant survival benefits and unprecedented durable responses. However, the majority of the patients develop resistance to ICIs, either primary or acquired. Establishing a definition of primary resistance to ICIs in different clinical scenarios is challenging and remains a work in progress due to the changing landscape of ICI-based regimens, mainly in the setting of early-stage NSCLC. The mechanisms of primary resistance to ICIs in patients with NSCLC include a plethora of pathways involving a cross-talk of the tumor cells, the tumor microenvironment and the host, leading to the development of an immunosuppressive phenotype. The optimal management of patients with NSCLC following primary resistance to ICIs represents a significant challenge in current thoracic oncology. Research in this field includes exploring other immunotherapeutic approaches, such as cancer vaccines, and investigating novel antibody-drug conjugates in patients with NSCLC.

Neoantigen-specific tumor-infiltrating lymphocytes in gastrointestinal cancers: a phase 2 trial

Adoptive transfer of unselected autologous tumor-infiltrating lymphocytes (TILs) has mediated meaningful clinical responses in patients with metastatic melanoma but not in cancers of gastrointestinal epithelial origin. In an evolving single-arm phase 2 trial design, TILs were derived from and administered to 91 patients with treatment-refractory mismatch repair proficient metastatic gastrointestinal cancers in a schema with lymphodepleting chemotherapy and high-dose interleukin-2 (three cohorts of an ongoing trial). The primary endpoint of this study was the objective response rate as measured using Response Evaluation Criteria in Solid Tumors 1.0; safety was a descriptive secondary endpoint. In the pilot phase, no clinical responses were observed in 18 patients to bulk, unselected TILs; however, when TILs were screened and selected for neoantigen recognition (SEL-TIL), three responses were seen in 39 patients (7.7% (95% confidence interval (CI): 2.7-20.3)). Based on the high levels of programmed cell death protein 1 in the infused TILs, pembrolizumab was added to the regimen (SEL-TIL + P), and eight objective responses were seen in 34 patients (23.5% (95% CI: 12.4-40.0)). All patients experienced transient severe hematologic toxicities from chemotherapy. Seven (10%) patients required critical care support. Exploratory analyses for laboratory and clinical correlates of response were performed for the SEL-TIL and SEL-TIL + P treatment arms. Response was associated with recognition of an increased number of targeted neoantigens and an increased number of administered CD4+ neoantigen-reactive TILs. The current strategy (SEL-TIL + P) exceeded the parameters of the trial design for patients with colorectal cancer, and an expansion phase is accruing. These results could potentially provide a cell-based treatment in a population not traditionally expected to respond to immunotherapy. ClinicalTrials.gov identifier: NCT01174121 .

Genetic immune escape in cancer: timing and implications for treatment

Genetic immune escape (GIE) alterations pose a significant challenge in cancer by enabling tumors to evade immune detection. These alterations, which can vary significantly across cancer types, may often arise early in clonal evolution and contribute to malignant transformation. As tumors evolve, GIE alterations are positively selected, allowing immune-resistant clones to proliferate. In addition to genetic changes, the tumor microenvironment (TME) and non-genetic factors such as inflammation, smoking, and environmental exposures play crucial roles in promoting immune evasion. Understanding the timing and mechanisms of GIE, alongside microenvironmental influences, is crucial for improving early detection and developing more effective therapeutic interventions. This review highlights the implications of GIE in cancer development and immunotherapy resistance, and emphasizes the need for integrative approaches.

DYNC2H1 mutation as a potential predictive biomarker for immune checkpoint inhibitor efficacy in NSCLC and melanoma

Dynein cytoplasmic 2 heavy chain 1 (DYNC2H1) is reported to play a potential role in cancer immunotherapy. However, the association between DYNC2H1 mutation and the clinical benefit of immunotherapy in non-small cell lung cancer (NSCLC) and melanoma remains to be elucidated. We collected data from three public immune checkpoint inhibitor (ICI)-treated NSCLC cohorts (n = 137 in total) and seven ICI-treated melanoma cohorts (n = 418 in total) to explore the potential of DYNC2H1 mutation as a predictive biomarker. The clinical outcomes, including the objective response rate (ORR) and progression-free survival (PFS), of patients with DYNC2H1 mutations are significantly better than those of patients with wild-type DYNC2H1. Multivariate Cox regression analysis confirmed that DYNC2H1 mutation was an independent predictive factor for ICI efficacy in NSCLC and melanoma. In addition, DYNC2H1 mutation exhibited no prognostic value for NSCLC or melanoma. Tumour mutational burden (TMB) and tumour neoantigen burden (TNB) were significantly higher in patients with DYNC2H1 mutation than in those with wild-type DYNC2H1 in both NSCLC and melanoma cohort. The analysis of immune-related genes and immune cell enrichment revealed an association between DYNC2H1 mutation and increased immune infiltration, revealing a potential mechanism underlying the predictive role of DYNC2H1 mutation in immunotherapy efficacy. In conclusion, DYNC2H1 mutation serves as a predictive biomarker of ICI efficacy in NSCLC and melanoma.

Transcriptional regulation by LKB1 in lung adenocarcinomas: Exploring oxidative stress, neuroglial and amino acid signatures

Lung adenocarcinoma (LUAD) is one of the most prevalent cancer types worldwide and has one of the poorest survival rates. Understanding its developpment is crucial for improving diagnosis, prognosis, and treatment. A key factor in LUAD is the frequent loss-of-function mutations in LKB1/STK11, a kinase that regulates metabolism. These mutations are linked to increased metastasis and worse clinical outcomes. In this study, we analyzed gene expression data from LUAD patients to explore how LKB1 mutations affect cancer behavior. We found that LKB1 mutations in KRAS-driven LUAD lead to widespread gene downregulation. By integrating avalaible protein interaction data, mass spectrometry analysis of LKB1 nuclear partners, and co-immunoprecipitations experiments, we identified BRG1, a chromatin activator and subunit of the BAF complex, as a nuclear partner of LKB1. Further analysis suggested that LKB1 mutations may impair BRG1 activity, disrupting chromatin regulation and gene expression. Notably, LUAD patients with mutated LKB1 showed gene expression patterns indicative of oxidative stress, defective neuronal-glial and neuroinflammation programs, and altered amino acid homeostasis. These changes resemble the roles LKB1 plays in neural crest stem cells, suggesting that LKB1 may reduce tumor aggressiveness in LUAD by maintaining a developmental gene expression program.