Diagnostic strategies for endometrial cancer have been evolving, with cytologic analysis being considered a key method in integrated oncologic diagnostics because of its less invasive nature and adaptability to various assessments. Liquid-based cytology (LBC) has emerged as a promising method for intact DNA preservation; it exhibits improved efficiency in advanced sequencing applications such as next-generation sequencing. However, despite the use of LBC in panel assays, its application in whole-exome sequencing (WES) for comprehensive genomic profiling remains underexplored.

To investigate whether molecular classification is possible based on WES using DNA derived from LBC specimens.

We combined WES with targeted gene panel analysis to compare genomic findings of LBC and traditional tissue samples obtained from 7 cases of endometrial cancer. We investigated pathogenic mutations, tumor mutational burden, and microsatellite instability, and achieved molecular classification with high accuracy.

We found a substantial concordance between LBC and traditional tissue samples in terms of pathogenic mutation detection, with a 95% match in the LBC samples and 94% in the tissue samples. Notably, our results highlight the importance of combining WES with panel-based analysis in identifying the ultramutated status of a case that had been missed during panel analysis.

Our findings emphasize the potential of LBC samples in the precise and noninvasive genomic analysis of cases of endometrial cancer and offer a new avenue for developing diagnostic and therapeutic strategies in precision oncology.

T cells are crucial effector cells in the endogenous defense against cancer, yet the clinical impact of their quantity, diversity, and dynamics remains underexplored. Here, we investigate the clinical relevance of the T cell receptor (TCR) repertoire in patients with bladder cancer. In advanced-stage disease, low pre-treatment peripheral TCR diversity is associated with worse overall survival (p = 0.024), particularly when coupled with low circulating T cell fractions (p = 0.00049). These low-diversity repertoires are dominated by hyper-expanded clones that persist throughout treatment. Further longitudinal analysis reveals reductions in TCR diversity after treatment, indicating adverse effects on the immune system. In early-stage disease, immunotherapy increases TCR diversity in patients with good outcomes. Furthermore, single-cell sequencing identifies most hyper-expanded clones as cytotoxic T cells, while non-expanded clones are predominantly naive T cells. Overall, this highlights TCR diversity as a promising biomarker, offering opportunities for tailored oncological treatments to enhance clinical outcomes.

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.

Uveal melanoma (UM) is the most common intraocular malignancy in adults, representing a rare but aggressive melanoma subtype with a distinct molecular landscape, unique metastatic behavior and limited therapeutic options in the metastatic setting. This review provides an in-depth analysis of the latest evidence on the evolving treatment landscape of metastatic UM.

For liver-only metastatic disease, locoregional therapies provide significant benefit compared to systemic therapies. The recent approval of tebentafusp-tebn, a bispecific gp100 peptide-HLA-directed CD3 T-cell engager, marks a pivotal advancement for HLA-A*02:01-positive patients with unresectable/metastatic UM, demonstrating a clinically significant survival benefit. Several clinical studies are currently active, examining emerging locoregional and systemic treatments for metastatic UM, with promising early data. Despite effective local disease control through radiotherapy and enucleation, approximately 50% of patients develop metastatic disease, predominantly in the liver, with a median survival of less than one year. The approval of tebentafusp represents a landmark achievement in UM treatment, while promising experimental combinations have demonstrated clinical utility in late phase clinical trials, offering hope for further improvement in patient survival.

Immune checkpoint inhibitors (ICIs) have revolutionized colon cancer treatment, but their efficacy is largely restricted by the limited presence of CD8+ cytotoxic T lymphocytes (CTLs). However, the specific genetic alterations that impact the CD8+ CTL infiltration in colon cancer remain poorly understood. Here, we analyzed clinical and multi-omics data from the Memorial Sloan-Kettering Cancer Center (MSKCC) ICIs-treated and The Cancer Genome Atlas (TCGA) colon adenocarcinoma (COAD) cohorts to screen the key mutations that may influence the efficacy of immunotherapy. We found that patients with NCOA3 mutations exhibit better response to immunotherapy and higher CD8+ CTL infiltration. In vitro and in vivo experiments revealed that mutant NCOA3 increases the efficacy of anti-PD-L1 and CD8+ CTL recruitment by upregulating C-X-C motif chemokine ligand 9 (CXCL9), which is dependent on its impaired intrinsic histone acetyltransferase activity. Mechanistically, wild-type NCOA3 as histone acetyltransferase upregulates Heat shock protein 90 alpha (HSP90α) by enhancing histone H3 lysine 27 acetylation (H3K27ac) at its promoter region. Increased HSP90α stabilizes Enhancer of zeste homolog 2 (EZH2), which then increase the histone H3 lysine 27 trimethylation (H3K27me3) at the CXCL9 promoter region, thereby suppressing the expression of CXCL9. Targeted inhibition of NCOA3 by small molecular inhibitor SI-2 improves the efficacy of PD-L1 blockade therapy. NCOA3 could serve as a novel biomarker and potential target to improve the efficacy of immunotherapy.

Immune checkpoint inhibitors (ICIs) are becoming more prominent in the treatment of gastric cancer (GC). However, predictive biomarkers of response to ICIs in HER2-negative patients remain incompletely understood.

A total of 47 patients diagnosed with HER2-negative advanced GC who underwent ICI regimens were eligible for this study. Plasma samples with paired white blood cells prior to treatments were collected from these 47 patients. Variations of circulating tumor DNA (ctDNA) was evaluated by next-generation sequencing followed by its significance analysis.

A total of 658 somatic mutations involving 203 genes were identified in all ctDNA. Mutations in MEN1, MLH1, CEBPA, ATR, GNAQ, and FOXL2 genes were more frequent in responders (P < 0.05). Compared with wild-type patients, patients with CEBPA or IRS2 mutations had prolonged median progression-free survival (mPFS, P = 0.0056). Patients with co-occurring mutations in IRS2/CEBPA, IRS2/POLD1, TP53/PIK3CA, or POLD1/CEBPA had longer mPFS compared with others (P = 0.003; 0.006; 0.0166; 0.0315; respectively). Both alteration of CDKN2A alone and co-mutations with MSH6 were significantly associated with superior overall survival (OS, P = 0.0289; 0.0355; respectively). In addition, higher on-treatment ctDNA concentration or variant allele frequency (VAF) were associated with poorer response (P < 0.05). Additionally, the increased molecular alterations of POLE, FGFR2 and MDC1 seemed to indicate the acquired resistance to ICIs.

Variation signatures captured by ctDNA as well as the kinetics of ctDNA could predict the clinical benefits of ICB in HER2-negative GC patients, which was worth further validated in large cohort.

This study explored the relationship between mRNA expression profiles obtained through next-generation sequencing (NGS) and 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) texture analysis in patients with treatment-resistant oral squamous cell carcinoma (OSCC) who were treated with molecular-targeted drugs. We analyzed the correlation between 18F-FDG PET texture features and NGS data in a small cohort of five patients with recurrent or metastatic OSCC who received molecular-targeted drugs after surgery. Patients were categorized into two groups based on treatment response: responders (n = 3) and non-responders (n = 2). To validate our findings, we examined transcriptomic data from 292 OSCC patients in The Cancer Genome Atlas (TCGA) database.

The gene ankyrin repeat and SOCS box containing two (ASB2) was significantly overexpressed in non-responders and strongly correlated with specific PET radiomic features, including GLRLM_GLNU, GLRLM_RLNU, and GLZLM_GLNU (p < 0.05). High ASB2 expression was also associated with poor prognosis in OSCC patients (p < 0.05) and decreased overall survival, as shown by Kaplan-Meier analysis of the TCGA database (p = 0.017).

Integrating ASB2 expression data with 18F-FDG PET texture features could potentially improve the prediction of treatment outcomes in treatment-resistant OSCC patients undergoing molecular-targeted therapy.

Ciliated adenocarcinomas are rare non-terminal respiratory unit-type lung adenocarcinomas characterised by ciliated cells with nuclear atypia and glandular or papillary architecture. A few cases of ciliated adenocarcinoma of the lung have been reported. These adenocarcinomas are negative for TTF1 and have either KRAS (25%) or EGFR (9%) mutations. A case of a well-differentiated adenocarcinoma with papillary architecture, focal residual cilia, apical snouts, and CHEK2 and p53 mutations diagnosed at stage IV(T4NxM0) is reported. The article describes the cytomorphological features of this tumour, the potential pitfalls, diagnostic limitations, challenges identified in cytology specimens, and the necessary work-up for a definitive diagnosis. The differential diagnosis of papillary lesions of the lung and the clinical significance of CHEK2 mutations are also discussed in this article.

The molecular landscape of lung neuroendocrine neoplasms is still poorly characterized, making it difficult to develop a molecular classification and personalized therapeutic approaches. Significant clinical heterogeneity of these malignancies has been highlighted among poorly differentiated histotypes and within the subgroup of well-differentiated neuroendocrine tumors (NET). Currently, the main prognostic factors of lung NET include stage, histotype, grade, peripheral location, and demographic parameters. To gain deeper insights into the genomic underpinnings of lung NETs, we conducted a pilot investigation to uncover potential genetic mutations and copy number variations (CNVs) implicated in their pathogenesis.

Formalin-fixed, paraffin-embedded intraoperative tumor biopsies and matched peripheral blood mononuclear cell samples were collected from six consecutive patients with lung NETs. The whole exome sequencing (WES) was performed to profile germline and somatic mutations, identify novel genetic alterations, and detect CNVs. Clinical and pathological data were systematically documented at diagnosis and during follow-up.

The WES analysis identified a subset of mutations shared between germline and somatic; some were of particular clinical interest as they were associated with tumor proliferation and potential therapeutic targets such as the genes KDM5C, ATR, COL7A1, NOTCH4, PTPRS, SMO, SPEN, SPTA1, TAF1. These mutations were predominantly linked to chromatin remodeling and were involved in critical oncogenic pathways such as Notch and Wnt signaling.

This pilot study highlights the potential role of NGS analysis on solid biopsy in the assessment of the mutational profile of lung NET. A comparison of germline and somatic mutations is critical to identifying putative tumor driver mutations. In perspective, the enrichment of a subpopulation of cancer cells in the blood, with one or more specific mutations, is information of enormous clinical relevance, either for prognosis or therapeutic decisions. Translational studies on large prospective series are required to establish the role of liquid biopsy in lung NET.

Prostate cancer (PCa) remains a leading cause of cancer-related mortality, necessitating robust prognostic models and personalized therapeutic strategies. This study integrated bulk RNA sequencing, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomics to construct a prognostic model based on genes shared between ferroptosis and fatty acid metabolism (FAM). Using the TCGA-PRAD dataset, we identified 73 differentially expressed genes (DEGs) at the intersection of ferroptosis and FAM, of which 19 were significantly associated with progression-free survival (PFS). A machine learning-based prognostic model, optimized using the Lasso + Random Survival Forest (RSF) algorithm, achieved a high C-index of 0.876 and demonstrated strong predictive accuracy (1-, 2-, and 3-year AUCs: 0.77, 0.75, and 0.78, respectively). The model, validated in the DFKZ cohort, stratified patients into high- and low-risk groups, with the high-risk group exhibiting worse PFS and higher tumor mutation burden (TMB). Functional enrichment analysis revealed distinct pathway activities, with high-risk patients showing enrichment in immune-related and proliferative pathways, while low-risk patients were enriched in metabolic pathways. Immune microenvironment analysis revealed heightened immune activity in high-risk patients, characterized by increased infiltration of CD8 + T cells, regulatory T cells, and M2 macrophages, alongside elevated TIDE scores, suggesting immune evasion and resistance to immunotherapy. In contrast, low-risk patients exhibited higher infiltration of plasma cells and neutrophils and demonstrated better responses to immune checkpoint inhibitors (ICIs). Spatial transcriptomics and scRNA-seq further elucidated the spatial distribution of model genes, highlighting the central role of macrophages in mediating risk stratification. Additionally, chemotherapy sensitivity analysis identified potential therapeutic agents, such as Erlotinib and Picolinic acid, for low-risk patients. In vitro experiments showed that overexpression of CD38 in the PC-3 cell line led to elevated lipid peroxidation (C11-BODIPY) and reactive oxygen species (ROS), suggesting increased cell ferroptosis. These findings provide a comprehensive framework for risk stratification and personalized treatment in PCa, bridging molecular mechanisms with clinical outcomes.

Locally advanced cervical cancer remains a significant therapeutic challenge, with high rates of recurrence and metastasis despite advances in chemoradiation. Immunotherapy, particularly immune checkpoint inhibitors targeting the PD-1/PD-L1 axis, has emerged as a promising strategy to enhance treatment efficacy. This review explores the integration of immunotherapy with standard chemoradiation, highlighting the potential of PD-1 inhibitors, such as pembrolizumab, in improving progression-free survival (PFS) among high-risk patients. Furthermore, the role of predictive biomarkers, including microsatellite instability (MSI) and tumor mutational burden (TMB), is examined to refine patient selection and personalize therapeutic approaches. Emerging strategies, including the use of nivolumab, ipilimumab, and maintenance immunotherapy, are also discussed. While preliminary clinical data are encouraging, further research is required to optimize treatment combinations, establish robust patient selection criteria, and enhance long-term outcomes in cervical cancer management.

Homologous recombination (HR) and mismatch repair (MMR) act as guardians of the human genome, and defects in HR or MMR are causative in at least a quarter of all malignant tumors. Although these DNA repair-deficient tumors are eligible for effective targeted therapies, fully reliable diagnostic strategies based on functional assay have yet to be established, potentially limiting safe and proper application of the molecular targeted drugs. Here we show that transient transfection of artificial DNA substrates enables ultrarapid detection of HR and MMR. This finding led us to develop a diagnostic strategy that can determine the cellular HR/MMR status within one day without the need for control cells or tissues. Notably, the accuracy of this method allowed the discovery of a pathogenic RAD51D mutation, which was missed by existing companion diagnostic tests. Our methods, termed HR eye and MMR eye, are applicable to frozen tumor tissues and roughly predict the response to therapy. Overall, the findings presented here could pave the way for accurately assessing malignant tumors with functional defects in HR or MMR, a step forward in accelerating precision medicine.

Background: Defective DNA repair systems result in the accumulation of mutations, loss of genomic integrity, and eventually cancer. Following initial malignant transformation due to specific DNA damage and defective DNA repair, cancer cells become reliant upon other DNA repair pathways for their survival. The co-occurrence of specific repair deficiencies brings catastrophic outcomes such as cell death for cancer cells and thus holds promise as a potential therapeutic strategy. Exploring the co-occurrence and mutual exclusivity of mutational signatures provides valuable knowledge regarding combinations of defective repair pathways that are cooperative and confer selective advantage to cancer cells and those that are detrimental and cannot be tolerated by them. Methods: Taking advantage of mutational signature profiling, we analyzed whole-genome sequences of 1014 breast cancers to reveal the underlying mutational processes and their interrelationships. Results: We found an inverse relationship between deficiencies of homologous recombination (HRd) and non-homologous end joining (NHEJd) with reactive oxygen species (ROS). Moreover, HRd and NHEJd co-occurred with APOBEC but were mutually exclusive with mismatch repair deficiency (MMRd) and ROS. Our analysis revealed that SBS8 and SBS39 signatures of currently unknown etiology correlate with NHEJd. ID1 and ID2 signatures co-occur with ROS and have mutual exclusivity with HRd, SBS8, SBS39 and NHEJd. The ID4 signature, with currently unknown etiology, has mutual exclusivity with HRd and NHEJd and co-occurred with ROS. On the other hand, the ID15 signature, with currently unknown etiology, co-occurred with SBS8, SBS39, HRd, NHEJd and DBS2, while having an inverse relationship with MMRd and ROS. Comparing the mutational signatures of HRd and non-HRd TNBC genomes reveals the unique presence of ROS signatures in non-HRd tumors and the lack of ROS signature in HRd tumors. Conclusion: Taken together, these analyses indicate the possible application of mutation signatures and their interactions in advancing patient stratification and suggest appropriate therapies targeting the make-up of individual tumors' mutational processes. Ultimately, this information provides the opportunity to discover promising synthetic lethal candidates targeting DNA repair systems.

We compared genomic alterations and a homologous recombination deficiency (HRD) signature (HRDsig) in primary tumors from stage I-III to those in de novo stage IV breast cancers and from stage I-III cancers with early (<2 years after diagnosis) versus late (>2 years) recurrence.

De-identified genomic and clinical data of primary breast cancers (stage I-III N = 910, stage IV N = 783) from the United States, the nationwide clinico-genomic database of Flatiron Health and Foundation Medicine were analyzed. Genomic results included the mutation status of 324 cancer-related genes and HRDsig, a DNA scar-based measure of HRD.

No significant differences were observed in the frequencies of genomic alterations across disease stages, or between stage I-III cancers with early versus late relapse. Overall, the most prevalent biomarkers were PIK3CA mutation and HRDsig positivity. HRDsig positivity was observed in 82% of germline or somatic g/sBRCA1/2 or germline PALB2 (gPALB2) mutated cancers, 13.1% in cancers with other HR-repair (HRR) gene alterations (ATM, BARD1, BRIP1, CDK12, CHEK1, CHEK2, FANCL, somatic PALB2 (sPALB2), RAD51B, RAD51C, RAD51D and RAD54L), and also in 16.5% of HRR wild-type cancers. HRDsig positivity was observed across receptor subtypes and was the highest in TNBC (30%), followed by ER+/HER2- cancers (17%), then HER2 + cancers (8.7%).

Early-stage (I-III) and de novo stage IV breast cancers shared a similar prevalence of targetable genomic alterations and overall genomic landscape. HRDsig identified approximately 16% of breast cancers without g/sBRCA/gPALB2 alteration that might potentially benefit from PARP inhibitors or platinum-based treatments and should be tested in future clinical studies.

Identifying host genetic factors modulating immune checkpoint inhibitor (ICI) efficacy is experimentally challenging. Our approach, utilizing the Collaborative Cross mouse genetic resource, fixes the tumor genomic configuration while varying host genetics. We find that response to anti-PD-1 (aPD1) immunotherapy is significantly heritable in four distinct murine tumor models (H2: 0.18-0.40). For the MC38 colorectal carcinoma system, we map four significant ICI response quantitative trait loci (QTLs) with significant epistatic interactions. The differentially expressed genes within these QTLs that define responder genetics are highly enriched for processes involving antigen processing and presentation, allograft rejection, and graft vs. host disease (all p < 1 × 10-10). Functional blockade of two top candidate immune targets, GM-CSF and IL-2RB, completely abrogates the MC38 transcriptional response to aPD1 therapy. Thus, our in vivo experimental platform is a powerful approach for discovery of host genetic factors that establish the tumor immune microenvironment propitious for ICI response.

Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by limited targeted therapies and high recurrence rates. While immune checkpoint inhibitors (ICIs) have shown promise, their efficacy as monotherapy is limited. Clinically, ICIs demonstrate significant benefit primarily when combined with chemotherapy, particularly in the neoadjuvant setting for early-stage TNBC, which yields superior outcomes compared to adjuvant therapy. This review elucidates the tumor immunological principles underlying these observations. We discussed how the suppressive tumor microenvironment (TME), progressive T cell exhaustion, and associated epigenetic scarring constrain ICI monotherapy effectiveness. Crucially, we highlight the immunological advantages of the neoadjuvant approach: the presence of the primary tumor provides abundant antigens, and intact tumor-draining lymph nodes (TDLNs) act as critical sites for ICI-mediated priming and expansion of naïve and precursor exhausted T cells. This robust activation within TDLNs enhances systemic anti-tumor immunity and expands the T cell repertoire, a process less effectively achieved in the adjuvant setting after tumor resection. These mechanisms provide a strong rationale for the improved pathological complete response (pCR) rates and event-free survival observed with neoadjuvant chemoimmunotherapy, as demonstrated in trials like KEYNOTE-522. We further explore the implications for adjuvant therapy decisions based on treatment response, the challenges of ICI resistance, the need for predictive biomarkers, management of immune-related adverse events (irAEs), and future therapeutic directions. Understanding the dynamic interplay between chemotherapy, ICIs, T cells, and the TME, particularly the role of TDLNs in the neoadjuvant context, is essential for optimizing immunotherapy strategies and improving outcomes for patients with TNBC.

High tumor mutational burden (TMB-H) is an established biomarker for a favorable response to immune checkpoint inhibitors. However, tumor mutational burden (TMB) in invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) has not been sufficiently investigated.

We collected data of patients with ILC or IDC from the Center for Cancer Genomics and Advanced Therapeutics database between June 2019 and August 2023. Furthermore, we examined the clinicopathological factors and TMB status.

Patients with ILC (n = 170) had a median TMB score of 4.00 mut/Mb (interquartile range, 2.00-7.14 mut/Mb), whereas those with IDC (n = 2598) had a score of 3.90 mut/Mb (2.00-6.00 mut/Mb). TMB-H was more common in patients with ILC than in those with IDC (18.2% vs. 10.1%, P < 0.001), particularly in the ER+ /HER2- subtype. Multivariate analysis revealed that the pathological diagnosis of ILC (P = 0.006), tissue samples collected from metastatic sites (P < 0.001), and older age (50 years, P < 0.001) were independent factors for TMB-H.

Patients with ILC were more likely to have TMB-H than those with IDC. The findings of this study would be invaluable in selecting treatment strategies for patients with ILC.

Precision oncology is making remarkable advancements in optimizing patient care by personalizing treatments. To date, the US Food and Drug Administration (FDA) has approved poly(ADP-ribose) polymerase inhibitors (PARPi) olaparib (Lynparza, AstraZeneca and Merck) and talazoparib (Talzenna, Pfizer Oncology Together™) for germline or somatic BRCA1/2-mutated metastatic breast cancer (BC) patients, and PI3K inhibitor alpelisib (Piqray, Novartis) plus fulvestrant for patients with hormone receptor-positive human epidermal growth factor receptor 2-negative (HR+HER2-) PIK3CA-mutated advanced BC. In addition, the FDA approved capivasertib (Trucap, AstraZeneca) for HR+HER2- locally advanced or metastatic BC patients with one or more AKT1, PIK3CA, or PTEN alterations. Finally, the FDA recently approved elacestrant (Orserdu, Stemline Therapeutics, Inc.) for postmenopausal patients with ER+ HER2- ESR1-mutated advanced or metastatic BC with disease progression following at least one line of endocrine therapy.

This study presents a single institutional retrospective review of genomic reports of patients with BC. Analysis of genomic reports of 1361 BC sequencing reports was performed for 1010 patients with BC from 2013 to 2023 (23% of patients had multiple reports). Eligible patients had at least one primary or metastatic tumor. Multiple sequencing platforms were used for FFPE specimens including Tempus xT targeted next-generation sequencing (NGS), Foundation One Medicine, HopeSeq, Ashion Analytics GEM ExTra, and Exact Sciences Oncomap. Liquid biopsies were performed by Guardant, Tempus, and Foundation One Medicine. Chart reviews were performed to collect patient characteristics. BRCA1/2-mutated, metastatic BC patients who initiated treatment with olaparib or talazoparib, and PIK3CA-mutated, HR+ metastatic BC patients who initiated treatment with alpelisib were reported. In addition, patients with ESR1 or AKT1/PIK3CA/PTEN mutations were identified. Clinical outcomes, including progression-free survival (PFS) and overall survival (OS) were analyzed for BRCA1/2 and PIK3CA-mutated patients who received PARPi or alpelisib. Survival curves were generated using the Kaplan Meier method.

A cohort of 1010 BC patients with 1361 genomic reports was identified. A total of 935/1361 (69%) specimens were formalin-fixed paraffin-embedded (FFPE) tumor biopsies and 426/1361 (31%) were liquid biopsies. Receptor status included 65% HR+HER2-, 8% HR+HER2+, 4% HR-HER2+, and 23% TNBC. Racial and ethnic distribution of these patients included 50% non-Hispanic White, 26% Hispanic, 17% Asian, 6% African American, 1% other (Native Hawaiian or Other Pacific Islander, American Indian or Alaska Native, or unknown). Sequencing platforms included 30% Tempus xT, 31% Foundation One, 10% HopeSeq, 20% GEM ExTra, and 9% Exact Sciences. Liquid biopsies included 79% Guardant, 20% Tempus, and 1% Foundation One. Of 1010 patients, the most common mutations were TP53 (44%), PIK3CA (38%), ESR1 (14%), PTEN (12%), CCND1 (11%), FGFR1 (10%), CDH1 (10%), ERBB2 (9%), MYC (9%), FGF3 (8%), GATA3 (8%), FGF19 (8%), FGF4 (7%), ARID1A (6%), RB1 (5%), BRCA2 (5%), MAP3K1 (4%), AKT1 (4%), NF1 (4%), MLL3 (4%), ZNF703 (4%), CDKN2A (4%), BRCA1 (4%), MCL1 (3%), ATM (3%), PALB2 (1%), and CHEK2 (1%). The majority of reports with tumor mutation burden (TMB) results (97%) had low or intermediate TMB. A total of 784 actionable mutations in 1010 patients were reported, including 381/1010 (38%) PIK3CA; 144/1010 (14%) ESR1; 122/1010 (12%) PTEN; 48/1010 (5%) BRCA2; 36/1010 (4%) BRCA1; 41/1010 (4%) AKT1; and 12/1010 (1%) PALB2. Of the 96/1010 (10%) patients with BRCA1, BRCA2, or PALB2 mutations not including variants of uncertain significance (VUS), 33/96 (34.4%) received olaparib and 3/96 (3%) received talazoparib in the metastatic setting, and 28 were eligible for response (one had toxicity, two were lost to follow-up, and two went to hospice). Median PFS was 9.0 months and median OS was 21.8 months for patients receiving PARPi. Of the 381/1010 (38%) patients with PIK3CA mutations, 84/381 (22%) received alpelisib and 41 were eligible for response (22 had toxicity, 13 were discontinued, six were lost to follow-up, and two went to hospice). Median PFS was 7.9 months and median OS was 31.2 months for patients receiving alpelisib. A total of 544/1010 (54%) patients had AKT1, PIK3CA, or PTEN mutations which are now FDA approved for capivasertib in HR+HER2- metastatic BC patients. In addition, 144/1010 (14%) patients had ESR1 mutations which are FDA approved for elacestrant in HR+HER2- metastatic BC patients.

In this study, a total of 784 clinically actionable mutations were reported for 1010 patients with genomic sequencing. Of these, 96/1010 (10%) patients had at least one actionable mutation in homologous recombination repair genes (BRCA1, BRCA2, PALB2) and 36/96 (37.5%) patients received PARP inhibitors (33 olaparib and three talazoparib). In addition, 381/1010 (38%) patients had at least one clinically actionable PIK3CA mutation, and 84/381 (22%) received alpelisib. Additionally, 544/1010 (54%) of patients had either AKT1 (41/1010), PIK3CA (381/1010), or PTEN (122/1010) alterations that were FDA approved in November 2023 for capivasertib in the treatment of HR+HER2- metastatic BC (MBC) patients. Furthermore, 144/1010 (14%) patients in this study had at least one ESR1 mutation, a clinically actionable mutation that was FDA approved in January 2023 for elacestrant in the treatment of ER+HER2- MBC patients (44% detected by liquid biopsy). Future studies are needed to determine the efficacy of elacestrant and capivasertib for patients with these mutations, and to tailor strategies for optimal patient quality of life and cancer outcome.

Immune checkpoint inhibitors and molecular-targeted therapies have dominated recent cancer treatment. However, these treatments face challenges, such as primary and acquired resistance, indicating that not all patients benefit from them. Therefore, the search for new molecular targets is crucial. In addition, immune checkpoint inhibitors have exhibited racial differences in their effectiveness for certain neoplasms. Hence, understanding the genomic landscape of cancers in various racial groups is important. In Japan, health insurance has covered comprehensive genomic profiling since 2019, and the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) has accumulated genetic abnormalities along with clinical data of patients with various cancers. These data are crucial for advancing cancer research and drug development. This review discusses the genetic abnormalities of the major skin malignancies including melanoma, cutaneous squamous cell carcinoma (cSCC), and extramammary Paget's disease (EMPD), and proposes potential treatment strategies by comparing C-CAT data analysis with other genetic studies. The C-CAT data have emphasized unique genetic alterations in tumors of the Japanese population, particularly racial differences in tumor mutational burden in cutaneous melanoma and cSCC, indicating the importance of personalized treatment strategies that consider racial differences.

Novel treatment options for metastatic renal cell carcinomas (RCC) include specific MET inhibitors, GAS6/AXL inhibitors, and SRC inhibitors. The interplay between c-MET, SRC, AXL expression, and their gene mutation patterns in different renal carcinoma subtypes is unclear. To improve the understanding of these signaling pathways, we analyzed c-MET, AXL, and SRC expression in 590 clear cell RCC (ccRCC) and 127 papillary RCC (pRCC) by immunohistochemistry and integrated sequencing data to investigate the frequency of MET, AXL, and SRC gene mutations, their expression levels, and the presence of splice variants. In TCGA and in Foundation Medicine, Inc. (FMI) datasets, AXL and SRC gene alterations were extremely rare (<2%) or absent in ccRCC (n = 531 and 2,781, respectively) and pRCC (n = 290 and 566, respectively). On the other hand, MET mutations or amplifications were found in 9.7% (TCGA) and 10.2% (FMI) of pRCC. We show that strong SRC staining intensity by immunohistochemistry is associated with high tumor stage, high grade, and shorter survival in ccRCC (p < 0.001 each). AXL expression correlates with high stage and grade in ccRCC (p < 0.001 each). Both SRC and AXL expression were independent prognostic parameters in multivariate analysis (p < 0.05). MET expression is associated with longer survival in pRCC (p < 0.05). Our TCGA data analysis aligns with SRC immunohistochemistry findings on tumor stage and shorter survival in ccRCC. TCGA expression data showed a moderate positive correlation between AXL and c-MET in pRCC. In addition, we identified alternative splicing events reported for AXL in pRCC, and MET and SRC in ccRCC, across various alternative splicing databases. In conclusion, we identified high SRC expression as a biomarker for poor prognosis of ccRCC. Our data demonstrate c-MET, AXL, and SRC signaling pathway interactions independent of c-MET, AXL, and SRC mutations in ccRCC.

The molecular landscape of cutaneous melanoma is complex and heterogeneous, and a deeper understanding of the genesis and progression of the tumor driven by genetic alterations is essential for the development of effective diagnostic and therapeutic strategies. Molecular diagnostics and the use of biomarkers are increasingly playing a role in treatment decisions. However, further research is urgently needed to elucidate the relationships between complex genetic alterations and the effectiveness of target therapies (although BRAF mutation is still the only targeted genetic alteration). Further research is required to exploit other targetable genetic alterations such as NRAS, KIT or rare mutations. Treatment guidelines for cutaneous melanoma are continually evolving based on data from recent and ongoing clinical trials. These advancements reflect changes mainly in the optimal timing of systemic therapy and the choice of combination therapies increasingly tailored to molecular profiles of individual tumors. Mono- or combination immunotherapies demonstrated unprecedented success of melanoma treatment; still, there is room for improvement: though several factors of primary or acquired resistance are known, they are not part of patient management as biomarkers. The novel developments of cancer vaccines to treat melanoma (melanoma-marker-based or personalized neoantigen-based) are encouraging; introduction of them into clinical practice without proper biomarkers would be the same mistake made in the case of first-generation immunotherapies.

Colorectal cancer (CRC) patients benefit more from immune checkpoint inhibitor therapy, but they only account for around 15% of all patients. The remaining patients still lack effective therapeutic biomarkers to predict their prognosis.

We performed whole-exome sequencing (WES) to analyze 84 CRC specimens, classifying them into different groups based on their microsatellite status (MS), tumor mutation burden (TMB), homologous recombination deficiency (HRD) score, and clinicopathological features, which might be associated with clinical outcomes. Survival analysis and multivariable Cox regression modeling were employed to identify prognostic indicators. Comparative genomic profiling evaluated somatic mutations, copy number variations (CNVs), and pathway activation patterns across clinical subgroups.

The characteristics of the cohort (N = 84) revealed a median age of 52 years, with a male predominance (61.9%) and a majority of patients presenting with stage IV disease (77%). The HRD-high (HRD-H) subgroup accounted for 16.7%, while 19.0% of cases were microsatellite instability-high (MSI-H) and 22.6% were TMB-high (TMB-H). Multivariable analysis identified HRD-H as an independent predictor of overall survival (OS: HR = 0.19, 95% CI 0.12-0.94, p = 0.002). Comparative genomics demonstrated distinct mutation landscapes between HRD-H and HRD-low subgroups. In microsatellite-stable (MSS) patients, HRD-H status correlated with enriched SMAD4 mutations (p < 0.01) and differential activation of TGF-β/MYC signaling pathways compared to HRD-H-MSI counterparts.

HRD status serves as a novel independent prognostic biomarker in CRC. Our multi-parametric genomic framework delineates stratification-specific molecular signatures, advocating for HRD-integrated molecular diagnostics to optimize CRC management.

Dedifferentiated liposarcoma (DDLPS) is a rare and aggressive subtype of soft tissue sarcoma, characterized by limited treatment options and poor prognosis. Despite surgical resection being the only potentially curative treatment for localized DDLPS, the recurrence rate remains high, and systemic chemotherapy, typically anthracycline-based, shows limited efficacy in advanced stages. While immune checkpoint inhibitors (ICIs) have shown promise in various sarcoma subtypes, including DDLPS, their role as a first-line treatment remains unclear.

We conducted a systematic meta-analysis to evaluate the efficacy of ICIs in treating patients with DDLPS. A total of 25 studies encompassing 245 patients were included. Data on overall response rate (ORR), progression-free survival, and grade III-V treatment-related adverse events were analyzed. We assessed treatment efficacy based on the line of therapy and treatment regimens, including ICI monotherapy, dual ICI therapy, and ICI combinations with other modalities.

The pooled ORR for all ICI-based treatments was 7%. First-line ICI therapy yielded a significantly higher ORR of 22%, compared to 4% in later-line treatment. The combination of ICI with anthracyclines demonstrated the highest ORR of 52%. In contrast, ICI regimens combined with trabectedin or other agents showed limited efficacy. Sensitivity analysis confirmed the stability of results, and publication bias was not detected.

This meta-analysis supports the potential role of ICIs, particularly in combination with anthracyclines, as a first-line therapeutic strategy for DDLPS. These results provide a foundation for future prospective studies aimed at optimizing immunotherapy approaches for this rare and challenging malignancy.

One of the most prevalent malignant tumors worldwide, stomach cancer still has a high incidence and fatality rate in China, and the number of young people developing early-onset gastric cancer is steadily increasing. The 5-year survival rate of stomach cancer is typically 30%-35%, the prognosis is bad, the patients' quality of life is low, and the progression of advanced gastric cancer cannot be effectively managed despite the use of surgical surgery, chemotherapy, and other medicines. We urgently need molecular biomarkers with high specificity and sensitivity to increase the early gastric cancer detection rate, extend patient survival, and improve patient quality of life. The initial diagnosis of gastric cancer primarily depends on gastroscopy and biopsy, and invasive procedures cause significant discomfort to patients. Similar to this, treating advanced and metastatic stomach cancer is a pressing issue that requires attention. More and more immune checkpoint molecules have been discovered, and corresponding inhibitors are gradually being applied to clinical diagnosis and treatment. Recently, some non-coding RNAs have begun to be used as new targets for the treatment of gastric cancer. Some non-coding RNAs are highly present in the serum or urine of gastric cancer patients and can be used as diagnostic markers or prognostic indicators. Many clinical trials targeting non-coding RNAs have also shown good therapeutic effects. In general, targeting non-coding RNAs has shown good therapeutic effects. The biomarkers for gastric cancer detection and treatment are reviewed in this article, focusing on the new non-coding RNAs used in diagnosis, prognosis, and treatment. Patients with stomach cancer should have access to more precise and efficient diagnosis and treatment choices as a result of ongoing technological advancements and thorough research.

Immunotherapy is used extensively in treating non-small cell lung cancer (NSCLC) patients. Nevertheless, in contrast to lung adenocarcinoma (LUAD), the endeavors to develop effective targeted treatments for lung squamous cell carcinoma (LUSC) have not yielded positive outcomes. Hence, it is crucial to discover biomarkers for immunotherapy and investigate more potent treatments, which is an immediate requirement for individuals with LUSC. The LUSC somatic mutation data were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. Multivariate analysis was performed to create a signature related to tumor mutation burden (TMB). Next, we utilized the CIBERSORT algorithm to assess the correlation between TMB and immune infiltrates. Additionally, we identified prognostic immune cells of LUSC through Kaplan-Meier analysis. The TCGA and ICGC cohorts covered a combined total of 11 genes that were frequently mutated. SYNE1 and TTN mutation correlated with an increased TMB and suggested a positive clinical outlook. A TMB-related signature (SYNE1 and TTN) was constructed based on this. The outlook for the high-risk group in LUSC was considerably poorer than the low-risk group (p = 0.004). In LUSC, there was a correlation between the TMB-related signature and immune infiltrates, and a positive response to anti-PD-L1 therapy was observed in individuals with low-risk scores. Furthermore, based on Kaplan-Meier analysis, plasma cells were identified as predictive immune cells in LUSC samples. In conclusion, the GSEA examination demonstrated that the TMB-associated signature stimulated immune system-related signaling pathways. To sum up, the TMB-associated signature could be marker to anticipate the immune reaction in individuals with LUSC.

PPP1R3G, a regulatory subunit of protein phosphatase 1, plays a critical role in glycogen metabolism and has been implicated in various cancers. This study provides a comprehensive pan-cancer analysis of PPP1R3G, evaluating its expression, diagnostic and prognostic significance, and potential as a therapeutic target.

We performed an extensive pan-cancer analysis of PPP1R3G using several databases to assess its expression and investigate its correlations with clinical outcomes. Our investigation included assessing PPP1R3G's impact on survival, its correlation with immune checkpoints and tumor stemness scores, and its prognostic significance. We also explored its relationship with immunomodulators, genomic profiles, and immunological characteristics, as well as its response to immunotherapy and involvement in various biological pathways.

PPP1R3G expression varied significantly across different cancers and correlated with both diagnostic and prognostic outcomes. Moreover, PPP1R3G was significantly linked to immune checkpoints, immunomodulators, prognosis, immunoregulatory genes, tumor stemness, cellular function, and immune infiltration across numerous cancer types. Further analysis of PPP1R3G-related gene enrichment, mutation profiles, RNA modifications, and genomic heterogeneity revealed that missense mutations were the predominant alteration affecting PPP1R3G.

Overall, the expression of PPP1R3G is closely associated with various cancers and may serve as a potential biomarker for cancer detection.

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.

Despite harboring the highest tumor mutational burden of all cancers, basal cell carcinoma (BCC) has low immunogenicity. Here, we demonstrate that BCC's low immunogenicity is associated with epigenomic suppression of antigen presentation machinery reminiscent of its cell of origin. Primary BCC had low T cell infiltrates and low human leukocyte antigen class I (HLA-I) expression compared with cutaneous squamous cell carcinoma (SCC) and normal keratinocytes. Forkhead box C1 (Foxc1), a regulator of quiescence in hair follicle stem cells, was expressed in BCC. Foxc1 bound to promoter of interferon regulatory factor 1 and HLA-I genes, leading to their deacetylation and reduced expression. A histone deacetylase inhibitor, entinostat, overcame Foxc1's effect and upregulated HLA-I in BCC. Topical entinostat plus imiquimod immunotherapy blocked BCC development in mice. Collectively, our findings demonstrate that low BCC immunogenicity is associated with a stem-like quiescent program preserved in the tumor cells, which can be blocked to enable BCC immunotherapy.

Cervical cancer (CC) is a major global health issue, ranking sixth in cancer-related mortality. The tumor microenvironment (TME) plays a crucial role in tumor growth. This study explored the cellular composition and immunological landscape of CC using various genomic data sources.

Data from the Cancer Genome Atlas and Gene Expression Omnibus were analyzed, including single-cell RNA sequencing, spatial transcriptome analysis, and survival data. Gene set variation analysis (GSVA) identified pathways in CD8+ cells, macrophages, and epithelial cells. Immunohistochemistry assessed marker expression in CC and normal tissues. Tumor immune dysfunction and exclusion (TIDE) scores differentiated high- and low-macrophage groups. Cell-cell communication analyses highlighted interactions between macrophages and epithelial cells.

Macrophage markers correlated with overall survival (OS) and disease-free survival (DFS). Epithelial cell subgroups 1 and 4, along with CD8+ T cells, were associated with OS. TIDE scores varied between groups. Specific ligand-receptor interactions were found between macrophages and epithelial cell subgroup 1. Triptolide was effective in epithelial cell subgroup 1, while memantine was more effective in macrophages.

Epithelial-macrophage interactions in the TME are crucial for CC progression and treatment, offering a potential immunotherapeutic strategy.

DLX4 is involved in the regulation of embryonic development, but its function in cancer remains unclear. Here, we conducted a pan-cancer analysis to investigate the molecular mechanisms of DLX4, with a particular emphasis on its role in renal cancer.

A comprehensive analysis of DLX4 was performed, focusing on differences in expression, prognostic value, somatic mutations, methylation modifications, and immune landscapes across various cancer types using multiple databases. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were utilized to explore the potential biological functions. Additionally, we evaluated the expression profile, prognostic significance, and immune infiltration of DLX4 in Kidney Renal Clear Cell Carcinoma (KIRC). The effect of DLX4 on KIRC was further validated by Spatial Transcriptomics, Real-time PCR (RT-PCR), and Immunohistochemistry experiments.

DLX4 was found to be upregulated in 26 cancer types and associated with poor prognosis. It was also correlated with tumor mutational burden (TMB), microsatellite instability, mismatch repair, and methylation, and was significantly enriched in pathways related to cell proliferation. In KIRC, DLX4 expression increased along with TMB and immune scores, likely due to the infiltration of regulatory T cells (Tregs) and T-helper 2 (Th2) cells. Spatial transcriptomics revealed a strong correlation between DLX4 localization and tumor cells. Experimental validation confirmed that DLX4 expression is significantly upregulated in renal cancer tissues.

Our study explored the mechanisms of DLX4 in pan-cancer, especially in renal clear cell carcinoma, identifying it as a promising biomarker and therapeutic target.

Immune checkpoint inhibitors (ICIs) have significantly advanced cancer therapy, yet their efficacy in tumors with low tumor mutational burden (TMB) remains suboptimal. In this study, we aimed to elucidate the impact of somatic mutations on overall survival (OS) in TMB-low patients treated with ICIs and to explore the potential for personalized treatment selection through machine learning.

We conducted a comprehensive analysis of 1172 TMB-low (TMB < 10 mutations per megabase) patients with cancer receiving ICIs, examining the association between specific gene mutations and OS. Additionally, we developed a decision tree model (DTM) to predict OS based on clinical features and tumor mutational profiles.

Our findings reveal that mutations in DAXX, HLA-A, H3C2, IGF1R, CTNNB1, SMARCA4, KMT2D, and TP53 are significantly associated with poorer survival outcomes in the multivariate analysis. Remarkably, for renal cell carcinoma (RCC) patients, VHL mutations predicted improved OS following ICI even when adjusted for age, sex, and microsatellite instability (MSI) status in both multivariate analysis and the DTM model.

These results reinforce the prevailing notion that TMB alone does not predict ICI response, highlighting the critical role of individual gene mutations in TMB-low tumors under ICI therapy. Furthermore, our study demonstrates the promise of machine learning models in optimizing ICI treatment decisions, paving the way for more precise and effective therapeutic strategies in this patient population.

Antibody-dependent cellular phagocytosis (ADCP) is an immune biological process and plays a biological role in the clearance of tumor cells and the response to immune checkpoint inhibitors. However, the effects of ADCP on stomach adenocarcinoma (STAD) remain unclear. Clinical and genomic data were extracted from multiple datasets. The ADCP-related signature was established using Cox least absolute shrinkage and selection operator regression. Expression of the C5a receptor also known as complement component 5a receptor 1 in the tumor and adjacent-normal tissues was calculated using immunohistochemistry staining. Validation of the signature was conducted in the training and validation cohorts by Cox regression and log-rank tests. Furthermore, the immune infiltrates, the tumor immune dysfunction and exclusion score, and tumor mutation burden score were calculated using the corresponding algorithms, and Mann-Whitney U tests were used to evaluate the differences between groups. Seventy-three hub genes with predictive performance were identified to establish an ADCP-related signature. Accordingly, a 27-gene signature was established, C5a receptor also known as complement component 5a receptor 1, one of the signature genes, had higher expression in tumors than adjacent-normal samples, and its predictive performance was validated in the GSE84437 and The Cancer Genome Atlas cohorts. We found that the ADCP-related signature is an excellent prognostic predictor of STAD. Moreover, the molecular characteristics and some indices of response to immunotherapy differed between the high- and low-risk groups. We constructed a 27-gene signature that is associated with the prognosis and response to STAD-based immunotherapy and provide insights into the biological mechanisms underlying this predictive function.

Sarcomas are traditionally considered "cold" tumors with poor response to immunotherapy. However, evidence accumulating over the last years shows that immune checkpoint inhibitors (ICIs) may have a role in selected sarcoma patients according to predictive markers. Here, we report the case of a woman diagnosed with a primary cardiac undifferentiated sarcoma. Following failure of standard first line chemotherapy, high-throughput sequencing (HTS) revealed a high tumor mutational burden (TMB), pathogenic mutations in FAT1 and NOTCH2 and a microsatellite instability (MSI)-associated signature. Immunohistochemistry confirmed mismatch repair-deficiency (MMRd) and abundant CD8+ tumor-infiltrating lymphocytes (TILs), in the absence of tertiary lymphoid structures. The patient was, therefore, treated with the ICI pembrolizumab, reaching a complete response that continues to persist at last follow-up, more than seven years from initial diagnosis and nearly six years from initiation of ICI treatment. This case illustrates the importance of performing HTS in rare sarcomas given the availability of efficient therapies, such as those for tumors displaying high TMB or MMRd/MSI. In agreement with other reports, it supports the contention that MMRd/MSI status and high numbers of TILs are valuable predictive markers of response to immunotherapy in sarcomas.

Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer associated with poor prognosis. While chemotherapy remains the conventional treatment approach, its efficacy is limited and often accompanied by significant toxicity. Advances in precision-targeted therapies have expanded treatment options for TNBC, including immunotherapy, poly (ADP-ribose) polymerase inhibitors, androgen receptor inhibitors, cell cycle-dependent kinase inhibitors, and signaling pathway inhibitors. However, the heterogeneous nature of TNBC contributes to variations in treatment outcomes, underscoring the importance of identifying intrinsic molecular subtypes for personalized therapy. Additionally, due to patient-specific variability, the therapeutic response to targeted treatments is inconsistent. This highlights the need to strategize patients based on potential therapeutic targets for targeted drugs to optimize treatment strategies. This review summarizes the classification strategies and immunohistochemical (IHC) biomarkers for TNBC subtypes, along with potential targets for identifying indications for targeted drug therapy. These insights aim to support the development of personalized treatment approaches for TNBC patients.

Cancer-associated fibroblasts (CAF) represent significant constituents within the extracellular matrix (ECM) across a range of cancers. Nevertheless, there exists a scarcity of direct proof concerning the function of CAF in glioblastoma (GBM).

This study endeavors to probe the participation of CAF in GBM by developing and validating a CAF-risk signature and exploring its correlation with immune infiltration and immunotherapy responsiveness.

To fulfill these objectives, mRNA expression profiles of GBM samples and their corresponding clinical data were retrieved from two databases. First, stromal CAF-associated genes were identified by weighted gene co-expression network analysis (WGCNA). This method constructs co-expression networks and pinpoints gene modules with similar expression patterns to detect relevant genes. Subsequently, a CAF-risk signature was established via univariate and LASSO Cox regression analyses. Thereafter, gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA) were carried out to investigate the underlying molecular mechanisms. The immune status was evaluated with several R packages, and the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm was utilized to assess the response to immunotherapy. Validation was performed using single-cell RNA sequencing (scRNA) datasets, the Cancer Cell Line Encyclopedia (CCLE), and the Human Protein Atlas (HPA). Eventually, a 5-gene (ITGA5, MMP14, FN1, COL5A1, and COL6A1) prognostic CAF model was constructed. Notably, immune infiltration analysis demonstrated a significant correlation between Treg, Macrophage, and CAF risk scores. Moreover, TIDE analysis suggested a decreased responsiveness to immunotherapy in high CAF-risk patients. In addition, GSEA showed significant enrichment of the transforming growth factor alpha (TGF-α), inflammatory response, and epithelial-mesenchymal transition (EMT) pathways in this subgroup. Finally, the validation through scRNA, CCLE, and HPA datasets confirmed these findings.

The 5-gene CAF-risk signature exhibited accurate prognostic predictions and efficiently evaluated clinical immunotherapy responses among GBM patients. These results offer robust evidence regarding the implication of CAF in GBM and underscore the potential clinical value of personalized anti-CAF therapies in conjunction with immunotherapy.