Tertiary lymphoid structures in cancer and beyond

The fibroinflammatory response in cancer

Fibroinflammation refers to the highly integrated fibrogenic and inflammatory responses mediated by the concerted function of fibroblasts and innate immune cells in response to tissue perturbation. This process underlies the desmoplastic remodelling of the tumour microenvironment and thus plays an important role in tumour initiation, growth and metastasis. More specifically, fibroinflammation alters the biochemical and biomechanical signalling in malignant cells to promote their proliferation and survival and further supports an immunosuppressive microenvironment by polarizing the immune status of tumours. Additionally, the presence of fibroinflammation is often associated with therapeutic resistance. As such, there is increasing interest in targeting this process to normalize the tumour microenvironment and thus enhance the treatment of solid tumours. Herein, we review advances made in unravelling the complexity of cancer-associated fibroinflammation that can inform the rational design of therapies targeting this.

Multimodal spatial proteomic profiling in acute myeloid leukemia

Acute myeloid leukemia (AML) resides in an immune-rich microenvironment, yet, immune-based therapies have faltered in eliciting durable responses. Bridging this paradox requires a comprehensive understanding of leukemic interactions within the bone marrow microenvironment. We optimized a high-throughput tissue-microarray-based pipeline for high-plex spatial immunofluorescence and mass cytometry imaging on a single slide, capturing immune, tumor, and structural components. Using unbiased clustering on the spatial K function, we unveiled the presence of tertiary lymphoid-like aggregates in bone marrow, which we validated using spatial transcriptomics and an independent proteomics approach. We then found validated TLS signatures predictive of outcomes in AML using an integrated public 480-patient transcriptomic dataset. By harnessing high-plex spatial proteomics, we open the possibility of discovering novel structures and interactions that underpin leukemic immune response. Further, our study's methodologies and resources can be adapted for other bone marrow diseases where decalcification and autofluorescence present challenges.

Clinical and Fundamental Research Progressions on Tumor-Infiltrating Lymphocytes Therapy in Cancer

Malignant tumors represent a significant threat to human health. Among the various therapeutic strategies available, cancer immunotherapy-encompassing adoptive cell transfer (ACT) and immune checkpoint blockade therapy-has emerged as a particularly promising approach following surgical resection, radiotherapy, chemotherapy, and molecular targeted therapies. This form of treatment elicits substantial antigen-specific immune responses, enhances or restores anti-tumor immunity, thereby facilitating the control and destruction of tumor cells, and yielding durable responses across a range of cancers, which can lead to the eradication of tumor lesions and the prevention of recurrence. Tumor-infiltrating lymphocytes (TILs), a subset of ACT, are characterized by their heterogeneity and are found within tumor tissues, where they play a crucial role in mediating host antigen-specific immune responses against tumors. This review aims to explore recent advancements in the understanding of TILs biology, their prognostic implications, and their predictive value in therapeutic contexts.

Fibroblasts in immune responses, inflammatory diseases and therapeutic implications

Once regarded as passive bystander cells of the tissue stroma, fibroblasts have emerged as active orchestrators of tissue homeostasis and disease. From regulating immunity and controlling tissue remodelling to governing cell growth and differentiation, fibroblasts assume myriad roles in guiding normal tissue development, maintenance and repair. By comparison, in chronic inflammatory diseases such as rheumatoid arthritis, fibroblasts recruit and sustain inflammatory leukocytes, become dominant producers of pro-inflammatory factors and catalyse tissue destruction. In other disease contexts, fibroblasts promote fibrosis and impair host control of cancer. Single-cell studies have uncovered striking transcriptional and functional heterogeneity exhibited by fibroblasts in both normal tissues and diseased tissues. In particular, advances in the understanding of fibroblast pathology in rheumatoid arthritis have shed light on pathogenic fibroblast states in other chronic diseases. The differentiation and activation of these fibroblast states is driven by diverse physical and chemical cues within the tissue microenvironment and by cell-intrinsic signalling and epigenetic mechanisms. These insights into fibroblast behaviour and regulation have illuminated therapeutic opportunities for the targeted deletion or modulation of pathogenic fibroblasts across many diseases.

Recent advances in biomarkers for predicting the efficacy of immunotherapy in non-small cell lung cancer

Lung cancer continues to be the primary cause of cancer-related deaths globally, with non-small cell lung cancer (NSCLC) accounting for approximately 85% of all instances. Recently, immune checkpoint inhibitors (ICIs) have transformed the treatment approach for NSCLC, however, only a subset of patients experiences significant benefits. Therefore, identifying reliable biomarkers to forecast the efficacy of ICIs is crucial for ensuring the safety and effectiveness of treatments, becoming a major focus of current research efforts. This review highlights the recent advances in predictive biomarkers for the efficacy of ICIs in the treatment of NSCLC, including PD-L1 expression, tertiary lymphoid structures (TLS), tumor-infiltrating lymphocytes (TILs), tumor genomic alterations, transcriptional signatures, circulating biomarkers, and the microbiome. Furthermore, it underscores the pivotal roles of liquid biopsy, sequencing technologies, and digital pathology in biomarker discovery. Special attention is given to the predictive value of TLS, circulating biomarkers, and transcriptional signatures. The review concludes that the integration of multiple biomarkers holds promise for achieving more accurate efficacy predictions and optimizing personalized immunotherapy strategies. By providing a comprehensive overview of the current progress, this review offers valuable insights into biomarker-based precision medicine for NSCLC and outlines future research directions.

Immunocytes in the tumor microenvironment: recent updates and interconnections

The tumor microenvironment (TME) is a complex, dynamic ecosystem where tumor cells interact with diverse immune and stromal cell types. This review provides an overview of the TME's evolving composition, emphasizing its transition from an early pro-inflammatory, immune-promoting state to a later immunosuppressive milieu characterized by metabolic reprogramming and hypoxia. It highlights the dual roles of key immunocytes-including T lymphocytes, natural killer cells, macrophages, dendritic cells, and myeloid-derived suppressor cells-which can either inhibit or support tumor progression based on their phenotypic polarization and local metabolic conditions. The article further elucidates mechanisms of immune cell plasticity, such as the M1/M2 macrophage switch and the balance between effector T cells and regulatory T cells, underscoring their impact on tumor growth and metastasis. Additionally, emerging therapeutic strategies, including checkpoint inhibitors and chimeric antigen receptor (CAR) T and NK cell therapies, as well as approaches targeting metabolic pathways, are discussed as promising avenues to reinvigorate antitumor immunity. By integrating recent molecular insights and clinical advancements, the review underscores the importance of deciphering the interplay between immunocytes and the TME to develop more effective cancer immunotherapies.

Correlation analysis of tertiary lymphoid structure parameters with the prognosis of patients with locally advanced rectal cancer after neoadjuvant chemotherapy: a retrospective study

BACKGROUND

The tertiary lymphoid structures (TLSs) are positively correlated with the prognosis of many solid tumors, including colorectal cancer. However, their prognostic significance in patients with locally advanced rectal cancer (LARC) after neoadjuvant chemotherapy remains unclear. This study aimed to explore the correlation between TLS parameters and the prognosis of LARC patients receiving neoadjuvant chemotherapy.

METHODS

This retrospective study included patients with LARC treated at the Harbin Medical University Cancer Hospital from 2012 to 2021. The quantity, area, and density of TLSs in the tumor, normal, and total tissues from surgical specimens were determined. Overall survival (OS) was calculated from surgery to death from any cause. The correlation between TLS parameters and prognosis was assessed using Kaplan-Meier survival analysis and Cox regression analysis. Multiplex immunofluorescence (mIF) staining was used to analyze TLS maturity and immune composition.

RESULTS

This study included 114 patients, of whom 46.5% were over 60 years old, and 70.2% were male. TLS parameters in tumor region were smaller than those in normal and total regions (P < 0.001). A larger TLS area and higher density in the total region (HR = 0.371, P = 0.023 for area; HR = 0.250, P = 0.005 for density) were significantly associated with better OS. Moreover, a higher total-region TLS density was correlated with low carcinoembryonic antigen (CEA) levels (P = 0.028), positive responses to neoadjuvant therapy (P < 0.001), and tumor regression (P < 0.001). Subgroup analysis revealed that combining total-region TLS density with clinicopathologic features such as sex, age, cTNM stage, CEA levels, and extramural vascular invasion further stratified prognosis. Additionally, mIF analysis showed that a high TLS density was associated with a higher TLS maturity (P = 0.014); mature TLSs exhibited greater infiltration of CD20⁺ B cells and CD21⁺ follicular dendritic cells compared to non-mature TLSs.

CONCLUSIONS

TLS parameters, particularly TLS density, are promising prognostic biomarkers for LARC patients undergoing neoadjuvant chemotherapy.

TRIAL REGISTRATION

not applicable.

Activation-induced cytidine deaminase in tertiary lymphoid structures: dual roles and implications in cancer prognosis

Activation-induced cytidine deaminase (AID) serves as a critical molecular orchestrator in the germinal center (GC) reaction within secondary lymphoid organs (SLOs), driving the production of high-affinity antibodies through somatic hypermutation. While its pathological implications are well-documented - including ectopic expression in non-B cell populations and transcriptional dysregulation linked to hematological malignancies and solid tumorigenesis - the cellular provenance of AID in solid tumors remains an unresolved paradox. This review advances two principal hypotheses: (1) AID may derive from tertiary lymphoid structures (TLSs), ectopic immune niches mirroring SLO organization, and (2) exhibits context-dependent transcriptional duality, capable of both potentiating and suppressing gene expression based on microenvironmental cues. Through systematic analysis of AID/GC involvement across cancer subtypes, we delineate mechanistic connections between lymphoid neogenesis and tumor progression. Our examination extends to TLS architecture, revealing three critical dimensions: (i) structural organization and cellular heterogeneity, (ii) developmental trajectories, and (iii) bidirectional interactions with tumor microenvironments. Crucially, we establish functional parallels between tumor-infiltrating B cells (TIL-Bs) in SLOs versus TLSs, while elucidating the differential roles of AID in canonical GC versus TLS-associated GC formation. This synthesis ultimately proposes that AID's functional dichotomy - acting as both oncogenic collaborator and tumor suppressor - underlies the paradoxical prognostic associations observed with TLS presence across malignancies. The review thereby provides a conceptual framework reconciling AID's dual functionality with the context-dependent immunobiology of tumor-associated lymphoid structures.

Helicobacter pylori CagA and Cag type IV secretion system activity have key roles in triggering gastric transcriptional and proteomic alterations

Colonization of the human stomach with cag pathogenicity island (PAI)-positive Helicobacter pylori strains is associated with increased gastric cancer risk compared to colonization with cag PAI-negative strains. To evaluate the contributions of the Cag type IV secretion system (T4SS) and CagA (a secreted bacterial oncoprotein) to gastric molecular alterations relevant for carcinogenesis, we infected Mongolian gerbils with a Cag T4SS-positive wild-type (WT) H. pylori strain, one of two Cag T4SS mutant strains (∆cagT or ∆cagY), or a ∆cagA mutant for 12 weeks. Histologic staining revealed a biphasic distribution of gastric inflammation severity in WT-infected animals and minimal inflammation in animals infected with mutant strains. Atrophic gastritis (a premalignant condition), dysplasia, and gastric adenocarcinoma were only detected in WT-infected animals with high inflammation scores. Transcriptional profiling, liquid chromatography-tandem mass spectrometry analysis of micro-extracted tryptic peptides, and imaging mass spectrometry revealed more than a thousand molecular alterations in gastric tissues from WT-infected animals with high inflammation scores compared to uninfected tissues and few alterations in tissues from other groups of infected animals. Proteins with altered abundance in animals with severe Cag T4SS-induced inflammation mapped to multiple pathways, including the complement/coagulation cascade and proteasome pathway. Proteins exhibiting markedly increased abundance in tissues from H. pylori-infected animals with severe inflammation included calprotectin components, proteins involved in proteasome activation, polymeric immunoglobulin receptor (PIGR), interferon-inducible guanylate-binding protein (GBP2), lactoferrin, lysozyme, superoxide dismutase, and eosinophil peroxidase. These results demonstrate key roles for CagA and Cag T4SS activity in promoting gastric mucosal inflammation, transcriptional alterations, and proteomic alterations relevant to gastric carcinogenesis.IMPORTANCEHelicobacter pylori colonizes the stomachs of about half of humans worldwide, and its presence is the primary risk factor for the development of stomach cancer. H. pylori strains isolated from humans can be broadly classified into two groups based on whether they contain a chromosomal cag pathogenicity island, which encodes a secreted effector protein (CagA) and components of a type IV secretion system (T4SS). In experiments using a Mongolian gerbil model, we found that severe gastric inflammation and gastric transcriptional and proteomic alterations related to gastric cancer development were detected only in animals infected with a wild-type H. pylori strain containing CagA and an intact Cag T4SS. Mutant strains lacking CagA or Cag T4SS activity successfully colonized the stomach without inducing detectable pathologic host responses. These findings illustrate two different patterns of H. pylori-host interaction.

Characterisation and Clinical Relevance of Tertiary Lymphoid Structures in Primary Biliary Cholangitis

BACKGROUND AND AIMS

The pathological characteristics of lymphocyte infiltration in the hepatic portal tracts of patients with primary biliary cholangitis (PBC) remain unclear. Tertiary lymphoid structures (TLSs) are ectopic lymphoid tissues associated with the exacerbation of autoimmune reactions. Here, we evaluate the role of TLSs in PBC and investigate their potential therapeutic value.

METHODS

We recruited 75 patients with PBC and 53 control patients with liver biopsies who were followed more than 2 years. TLSs and their maturity were identified by the amount and spatial distribution of immune cells. Bulk RNA sequencing of liver was performed in PBC patients with different TLS maturity. The sphingosine-1-phosphate receptor (S1PRs) modulator FTY720 was administered to dnTGFβRII mice to assess the role of TLSs on cholangitis.

RESULTS

TLSs presented in 61.3% (46/75) of liver tissues from patients with PBC, including 26 patients with mature TLS (mTLS) and 20 patients with immature TLS (imTLS). The proportion of mTLS was higher in PBC compared with chronic hepatitis B and autoimmune hepatitis. PBC patients with mTLS exhibited the highest serum levels of biochemical indicators, immune globulin and proportions of liver cirrhosis. Gene sets for lymphocyte migration and chemokine signalling pathways were enriched in patients with PBC presenting with TLS. FTY720 inhibited TLS formation and relieved cholangitis and fibrosis in dnTGFβRII mice.

CONCLUSION

TLSs are characteristics of lymphocyte accumulation in the portal tracts of PBC, of which the maturity of TLSs correlates with the inflammation and fibrosis of PBC. Targeting TLSs formation is a potential treatment of PBC.

Inorganic Nanomaterials Meet the Immune System: An Intricate Balance

The immune system provides defense against foreign agents that are considered harmful for the organism. Inorganic nanomaterials can be recognized by the immune system as antigens, inducing an immune reaction dependent on the patient's immunological anamnesis and from several factors including size, shape, and the chemical nature of the nanoparticles. Furthermore, nanomaterials-driven immunomodulation might be exploited for therapeutic purposes, opening new horizons in oncology and beyond. In this scenario, we present a critical review of the state of the art regarding the preclinical evaluation of the effects of the most promising metals for biomedical applications (gold, silver, and copper) on the immune system. Because exploiting the interactions between the immune system and inorganic nanomaterials may result in a game changer for the management of (non)communicable diseases, within this review we encounter the need to summarize and organize the plethora of sometimes inconsistent information, analyzing the challenges and providing the expected perspectives. The field is still in its infancy, and our work emphasizes that a deep understanding on the influence of the features of metal nanomaterials on the immune system in both cultured cells and animal models is pivotal for the safe translation of nanotherapeutics to the clinical practice.

FOXP3/TLS; a prognostic marker in patients with bladder carcinoma without muscle invasion

OBJECTIVE

Bladder carcinoma (BC) is a common type of cancer. Approximately 20% of BC patients have non-muscle invasive bladder cancer (NMIBC). Despite adequate BCG treatment, recurrence occurs in approximately 40% of the patients. There is no adequate prognostic marker for recurrence in a group of patients. Forkhead box P3 (FOXP3) is a regulatory T cell marker that sometimes exhibits anti-tumoral effects and can be used as a tumor marker. T-cell immunoglobulin and mucin domain 3 (TIM-3) is an immune checkpoint inhibitor of T cells. Tertiary lymphoid structures (TLS) increase malignancy and inflammation in non-lymphoid organs. Therefore, we aimed to evaluate the prognostic value of FOXP3, TIM-3, and TLS in patients with NMIBC.

METHODS

Patients with pathologically confirmed NMIBC were included in this study. Stromal and intraepithelial cells were evaluated separately using immunohistochemistry, and FOXP3, TIM-3, TLS, FOXP3/TLS, and TIM-3/TLS were calculated and noted. The cutoff value was determined using ROC analysis. Recurrence-free survival (RFS) and overall survival (OS) were evaluated using univariate and multivariate Cox proportional hazard analyses.

RESULTS

The study included ninety-six patients. FOXP3/TLS high group had a better RFS than FOXP3/TLS low group (P = 0.001; HR, 0.079; 95% CI, 0.019-0.337). This was also significant in the multivariate analysis (P = 0.018; HR, 0.125; 95% CI, 0.022-0.705). In the group receiving BCG, FOXP3/TLS, FOXP3-TLS, TIM-3-TLS and TIM-3/TLS elevation were lower in patients with relapse than in patients without relapse and were statistically significant. Combined TIM-3 and FOXP3 elevation was found to be good prognostic regardless of whether it was found in intraepithelial, stromal or TLS.

CONCLUSION

FOXP3/TLS elevation is a good prognostic and predictive marker in all non-muscle invasive bladder cancer cases and in the subgroup receiving BCG. Elevation of FOXP3-TLS, TIM-3-TLS, and TIM-3/TLS is associated with longer RFS in patients receiving BCG. Combined TIM-3 and FOXP3 elevation is indicative of a low recurrence rate in NMIBC.

Pipelines for lymphocyte homeostasis maintenance during cancer immunotherapy

In general, increasing lymphocyte entry into tumor microenvironment (TME) and limiting their efflux will have a positive effect on the efficacy of immunotherapy. Current studies suggest maintenance lymphocyte homeostasis during cancer immunotherapy through the two pipelines tumor-associated high endothelial venules and lymphatic vessels. Tumor-associated high endothelial venules (TA-HEVs) play a key role in cancer immunotherapy through facilitating lymphocyte trafficking to the tumor. While tumor-associated lymphatic vessels, in contrast, may promote the egress of lymphocytes and restrict their function. Therefore, the two traffic control points might be potential to maintain lymphocyte homeostasis in cancer during immunotherapy. Herein, we highlight the unexpected roles of lymphocyte circulation regulated by the two gateways for through reviewing the biological characters and functions of TA-HEVs and tumor-associated lymphatic vessels in the entry, positioning and exit of lymphocyte cells in TME during anti-tumor immunity.

Multiple mechanisms and applications of tertiary lymphoid structures and immune checkpoint blockade

BACKGROUND

Immune checkpoint blockade (ICB) inhibits tumor immune escape and has significantly advanced tumor therapy. However, ICB benefits only a minority of patients treated and may lead to many immune-related adverse events. Therefore, identifying factors that can predict treatment outcomes, enhance synergy with ICB, and mitigate immune-related adverse events is urgently needed.

MAIN TEXT

Tertiary lymphoid structures (TLS) are ectopic lymphoid tissues that arise from the tumor periphery. They have been found to be associated with better prognosis and improved clinical outcomes after ICB therapy. TLS may help address the problems associated with ICB. The multiple mechanisms of action between TLS and ICB remain unknown. This paper described potential mechanisms of interaction between the two and explored their potential applications.

Deciphering key roles of B cells in prognostication and tailored therapeutic strategies for lung adenocarcinoma: a multi-omics and machine learning approach towards predictive, preventive, and personalized treatment strategies

Background

Lung adenocarcinoma (LUAD) remains a significant global health challenge, with an urgent need for innovative predictive, preventive, and personalized medicine (PPPM) strategies to improve patient outcomes. This study leveraged multi-omics and machine learning approaches to uncover the prognostic roles of B cells in LUAD, thereby reinforcing the PPPM approach.

Methods

We integrated multi-omics data, including bulk RNA, ATAC-seq, single-cell RNA, and spatial transcriptomics sequencing, to characterize the B cell landscape in LUAD within the PPPM framework. Subsequently, we developed an integrative machine learning program that generated the Scissor+ related B cell score (SRBS). This score was validated in the training and validation sets, and its prognostic value was assessed along with clinical features to develop predictive nomograms. This study further assessed the role of SRBS and SRBS genes in response to immunotherapy and identified personalized drug targets for distinct risk subgroups, with gene expression verified experimentally to ensure tailored medical interventions.

Results

Our analysis identified 79 Scissor+ B cell genes linked to LUAD prognosis, supporting the predictive aspect of PPPM. The SRBS model, which utilizes multiple machine learning algorithms, performed excellently in predicting prognosis and clinical transformation, embodying the preventive and personalized aspects of PPPM. Multifactorial analysis confirmed that SRBS was an independent prognostic factor. We observed varying biological functions and immune cell infiltration in the tumor immune microenvironment (TIME) between the high- and low-SRBS groups, underscoring personalized treatment approaches. Notably, patients with elevated SRBS may exhibit resistance to immunotherapy but show increased sensitivity to chemotherapy and targeted therapies. Additionally, we found that LDHA, as an SRBS gene with significant clinical implications, may regulate the sensitivity of LUAD cells to cisplatin.

Conclusion

This study presents a B cell-associated gene signature that serves as a prognostic marker to facilitate personalized treatment for patients with LUAD, adhering to the principles of PPPM.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-024-00390-4.

Analyze the Diversity and Function of Immune Cells in the Tumor Microenvironment From the Perspective of Single-Cell RNA Sequencing

BACKGROUND

Cancer development is closely associated with complex alterations in the tumor microenvironment (TME). Among these, immune cells within the TME play a huge role in personalized tumor diagnosis and treatment.

OBJECTIVES

This review aims to summarize the diversity of immune cells in the TME, their impact on patient prognosis and treatment response, and the contributions of single-cell RNA sequencing (scRNA-seq) in understanding their functional heterogeneity.

METHODS

We analyzed recent studies utilizing scRNA-seq to investigate immune cell populations in the TME, focusing on their interactions and regulatory mechanisms.

RESULTS

ScRNA-seq reveals the functional heterogeneity of immune cells, enhances our understanding of their role in tumor antibody responses, and facilitates the construction of immune cell interaction networks. These insights provide guidance for the development of cancer immunotherapies and personalized treatment approaches.

CONCLUSION

Applying scRNA-seq to immune cell analysis in the TME offers a novel pathway for personalized cancer treatment. Despite its promise, several challenges remain, highlighting the need for further advancements to fully integrate scRNA-seq into clinical applications.

Clinicopathological and prognostic value of tertiary lymphoid structures in lung cancer: a meta-analysis

OBJECTIVE

The purpose of this meta-analysis was to examine the clinicopathological and prognostic significance of tertiary lymphocytic infiltrates in lung cancer.

METHOD

A systematic search was performed in many databases, including PubMed, Web of Science, Cochrane Library, Embase, CNKI, Wangfangdate, and CBM, up until January 2024. We calculated the hazard ratio (HR), odds ratios (OR), and confidence interval (CI), and accomplished this meta-analysis with Stata 15 software.

RESULT

14 studies, including 3101 patients, were subjected to analysis. High TLS detection was associated with a longer OS (HR = 0.545, 95% CI: 0.359-0.827, p = 0.004), DFS (HR = 0.431, 95% CI: 0.350-0.531, p < 0.001), and RFS (HR = 0.430, 95% CI: 0.325-0.569, p < 0.001). Meanwhile, it was observed that a higher detection of TLS was significantly correlated with the administration of adjuvant chemotherapy (OR = 1.505, 95% CI: 1.017-2.225, p = 0.041). Not only that, but there was a higher occurrence of significantly elevated TLS detection in the early N stages (N = 0) compared to the advanced N stages (N = 1, 2, and 3) (OR = 1.604, 95% CI: 1.021-2.521, p = 0.04).

CONCLUSION

Elevated detection of TLS has been observed to be correlated with extended OS, DFS, and RFS in cases of lung cancer. This finding suggests that TLS could potentially serve as a valuable prognostic biomarker for lung cancer.

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE

Recent advances in spatial transcriptomics (ST) technologies have transformed our ability to profile gene expression while retaining the crucial spatial context within tissues. However, existing ST platforms suffer from high costs, long turnaround times, low resolution, limited gene coverage, and small tissue capture areas, which hinder their broad applications. Here we present iSCALE, a method that predicts super-resolution gene expression and automatically annotates cellular-level tissue architecture for large-sized tissues that exceed the capture areas of standard ST platforms. The accuracy of iSCALE were validated by comprehensive evaluations, involving benchmarking experiments, immunohistochemistry staining, and manual annotation by pathologists. When applied to multiple sclerosis human brain samples, iSCALE uncovered lesion associated cellular characteristics that were undetectable by conventional ST experiments. Our results demonstrate iSCALE's utility in analyzing large-sized tissues with automatic and unbiased tissue annotation, inferring cell type composition, and pinpointing regions of interest for features not discernible through human visual assessment.

Development of a tertiary lymphoid structure-based prognostic model for breast cancer: integrating single-cell sequencing and machine learning to enhance patient outcomes

Background

Breast cancer, a highly prevalent global cancer, poses significant challenges, especially in advanced stages. Prognostic models are crucial to enhance patient outcomes. Tertiary lymphoid structures (TLS) within the tumor microenvironment have been associated with better prognostic outcomes.

Methods

We analyzed data from 13 independent breast cancer cohorts, totaling over 9,551 patients. Using single-cell RNA sequencing and machine learning algorithms, we identified critical TLS-associated genes and developed a TLS-based predictive model. This model stratified patients into high and low-risk groups. Genomic alterations, immune infiltration, and cellular interactions within the tumor microenvironment were assessed.

Results

The TLS-based model demonstrated superior accuracy compared to traditional models, predicting overall survival. High TLS patients had higher tumor mutation burden and more chromosomal alterations, correlating with poorer prognosis. High-risk patients exhibited a significant depletion of CD4+ T cells, CD8+ T cells, and B cells, as evidenced by single-cell and bulk transcriptomic analyses. In contrast, immune checkpoint inhibitors demonstrated greater efficacy in low-risk patients, whereas chemotherapy proved more effective for high-risk individuals.

Conclusions

The TLS-based prognostic model is a robust tool for predicting breast cancer outcomes, highlighting the tumor microenvironment's role in cancer progression. It enhances our understanding of breast cancer biology and supports personalized therapeutic strategies.

POU2F2+ B cells enhance antitumor immunity and predict better survival in non small cell lung cancer

Immune checkpoint inhibitors are an effective adjuvant therapy for non-small cell lung cancer (NSCLC). Recent studies have highlighted the critical role of tumor-infiltrating B cells in tumor immunity. However, research specifically focusing on B cells in NSCLC is limited. This study aims to elucidate the role of POU2F2+ B cells in patient survival and immune cell infiltration in NSCLC. Pseudotime analysis was performed to identify B cell pseudotime-related gene sets from two single-cell RNA sequencing (scRNA-seq) datasets of NSCLC. Differentially expressed genes (DEGs) were identified from two NSCLC immunotherapy-related bulk RNA sequencing datasets. A Venn diagram was used to determine core genes shared between these datasets. Kaplan-Meier survival curves were utilized to analyze overall survival (OS). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed based on the differential genes between POU2F2+ and POU2F2- B cells. CIBERSORT analysis was conducted to compare the proportions of immune cell subpopulations between groups. Multiplex immunohistochemistry (mIHC) was used to localize POU2F2+ cells and measure distances between different immune cells. Three hallmark genes, POU2F2, CD2, and CST7, were identified as being associated with B cell maturation and immunotherapy efficacy in NSCLC. High expression of POU2F2 was associated with poorer OS in both LUAD and LUSC. However, the POU2F2+ B cell score specifically correlated with the OS of LUAD but not with LUSC. Further analysis using scRNA-seq and mIHC methods revealed that POU2F2 is predominantly expressed in B cells. In LUAD tumor tissues, POU2F2+ CD20+ B cells were spatially further from PD-1+ CD8+ T cells and CD206+ CD68+ macrophages compared to POU2F2- CD20+ B cells. In LUSC tumor tissues, POU2F2+ CD20+ B cells were spatially further from CD206+ CD68+ macrophages but showed no significant spatial difference from PD-1+ CD8+ T cells compared to POU2F2- CD20+ B cells. In patients with high POU2F2+ B cell scores, LUAD tissues showed an increased proportion of CD8+ T cells and M1 macrophages, and a decreased proportion of M2 macrophages. In contrast, in LUSC tissues, a high POU2F2+ B cell score was associated only with an increased proportion of M1 macrophages, with no significant differences in the proportions of CD8+ T cells or M2 macrophages between groups. This study elucidates the significant role of POU2F2+ B cells in influencing survival and immune cell infiltration in NSCLC. Our findings highlight POU2F2 as a novel target for NSCLC immunotherapy. Targeting POU2F2 may modulate the tumor immune microenvironment, enhance the infiltration and activity of critical immune cells, and ultimately improve patient survival.

The Impact of Tertiary Lymphoid Structures on Tumor Prognosis and the Immune Microenvironment in Colorectal Cancer

Background: Colorectal cancer (CRC) ranks as the third most common cancer worldwide. Tertiary lymphoid structures (TLSs), organized immune cell aggregates in non-lymphoid tissues, are linked to chronic inflammation and tumorigenesis. However, the precise relationship between TLSs and CRC prognosis remains unclear. This study aimed to develop a TLS-associated genetic signature to predict CRC prognosis and support clinical applications. Methods: Utilizing the TCGA database, we analyzed TLS-related gene expression in CRC versus normal tissues. Prognostic models were constructed using Cox and Kaplan-Meier analyses. CRC samples were stratified into high and low TLS groups via ssGSEA, with validation in the GSE75500 dataset. We identified clinical characteristics associated with TLS scores, created prognostic nomograms, analyzed the top 50 differential genes, assessed tumor mutations, estimated immune infiltration using CIBERSORT, and examined correlations between TLS scores and immune checkpoints. Results: A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes. Survival analysis indicated significantly better outcomes for the TLS-high group. Cox regression identified stage IV and M1 as independent factors influencing TLS scores. Nomogram analysis demonstrated that combining TLS scores with clinical features enhances prognostic accuracy. TLS scores were closely associated with immune checkpoint genes, suggesting potential immunotherapy benefits for TLS-high patients. Conclusions: This study developed and validated a TLS-based prognostic model for CRC, exploring relevant immune cells. The model holds promise for predicting clinical prognosis and treatment responsiveness in CRC patients.

Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity

Biliary tract cancer (BTC), encompassing diseases such as intrahepatic (ICC), extrahepatic cholangiocarcinoma (ECC), and gallbladder cancer, is not only increasing but also poses a significant and urgent health threat due to its high malignancy. Genomic differences point to the possibility that these subtypes represent distinct diseases. Elucidation of the specific distribution of T-cell subsets, critical to cancer immunity, across these diseases could provide better insights into the unique biology of BTC subtypes and help identify potential precision medicine strategies. To address this, we conducted single-cell RNA sequencing and T-cell receptor sequencing on CD3+ T cells from 36 samples from 16 patients with BTC across all subtypes and analyzed 355 pathologic slides to examine the spatial distribution of T cells and tertiary lymphoid structures. Compared with ICC and gallbladder cancer, ECC possessed a unique immune profile characterized by T-cell exhaustion, elevated CXCL13 expression in CD4+ T helper-like and CD8+CXCL13+ exhausted T cells, more mature tertiary lymphoid structures, and fewer desert immunophenotypes. Conversely, ICC displayed an inflamed immunophenotype with an enrichment of IFN-related pathways and high expression of LGALS1 in activated regulatory T cells, associated with immunosuppression. Inhibition of LGALS1 reduced tumor growth and regulatory T-cell prevalence in ICC mouse models. Overall, this study unveils T-cell diversity across BTC subtypes at the single-cell and spatial level that could open paths for tailored immunotherapies. Significance: Single-cell and spatial analyses detailed the T-cell characteristics specific to anatomic subtypes of biliary tract cancer, identifying unique immunologic features that could potentially be harnessed to improve patient outcomes.

The Society for Immunotherapy of Cancer Perspective on Tissue-Based Technologies for Immuno-Oncology Biomarker Discovery and Application

With immuno-oncology becoming the standard of care for a variety of cancers, identifying biomarkers that reliably classify patient response, resistance, or toxicity becomes the next critical barrier toward improving care. Multiparametric, multi-omics, and computational platforms generating an unprecedented depth of data are poised to usher in the discovery of increasingly robust biomarkers for enhanced patient selection and personalized treatment approaches. Deciding which developing technologies to implement in clinical settings ultimately, applied either alone or in combination, relies on weighing pros and cons, from minimizing patient sampling to maximizing data outputs, and assessing the reproducibility and representativeness of findings, while lessening data fragmentation toward harmonization. These factors are all assessed while taking into consideration the shortest turnaround time. The Society for Immunotherapy of Cancer Biomarkers Committee convened to identify important advances in biomarker technologies and to address advances in biomarker discovery using multiplexed IHC and immunofluorescence, their coupling to single-cell transcriptomics, along with mass spectrometry-based quantitative and spatially resolved proteomics imaging technologies. We summarize key metrics obtained, ease of interpretation, limitations and dependencies, technical improvements, and outward comparisons of these technologies. By highlighting the most interesting recent data contributed by these technologies and by providing ways to improve their outputs, we hope to guide correlative research directions and assist in their evolution toward becoming clinically useful in immuno-oncology.

Amelioration of breast cancer therapies through normalization of tumor vessels and microenvironment: paradigm shift to improve drug perfusion and nanocarrier permeation

Breast cancer (BC) is the most commonly diagnosed cancer among women. Chemo-, immune- and photothermal therapies are employed to manage BC. However, the tumor microenvironment (TME) prevents free drugs and nanocarriers (NCs) from entering the tumor premises. Formulation scientists rely on enhanced permeation and retention (EPR) to extravasate NCs in the TME. However, recent research has demonstrated the inconsistent nature of EPR among different patients and tumor types. In addition, angiogenesis, high intra-tumor fluid pressure, desmoplasia, and high cell and extracellular matrix density resist the accumulation of NCs in the TME. In this review, we discuss TME normalization as an approach to improve the penetration of drugs and NCSs in the tumor premises. Strategies such as normalization of tumor vessels, reversal of hypoxia, alleviation of high intra-tumor pressure, and infiltration of lymphocytes for the reversal of therapy failure have been discussed in this manuscript. Strategies to promote the infiltration of anticancer immune cells in the TME after vascular normalization have been discussed. Studies strategizing time points to administer TME-normalizing agents are highlighted. Mechanistic pathways controlling the angiogenesis and normalization processes are discussed along with the studies. This review will provide greater tumor-targeting insights to the formulation scientists.

Determining the status of tertiary lymphoid structures in invasive pulmonary adenocarcinoma based on chest CT radiomic features

OBJECTIVES

The aim of this study was to determine the status of tertiary lymphoid structures (TLSs) using radiomic features in patients with invasive pulmonary adenocarcinoma (IA).

METHODS

In this retrospective study, patients with IA from November 2015 to March 2024 were recruited from two independent centers (center 1, training and internal test data set; center 2, external test data set). TLS was divided into two groups according to hematoxylin-eosin staining. Radiomic features were extracted, and support vector machine (SVM) were implemented to predict the status of TLSs. Receiver operating characteristic (ROC) curves were used to analyze diagnostic performance. Furthermore, visual assessments of the test set were also conducted by two thoracic radiologists and compared with the radiomics results.

RESULTS

A total of 456 patients were included (training data set, n = 278; internal test data set, n = 115; external test data set, n = 63). The area under the curve (AUC) of the radiomics model on the validation set, the internal test set, and the external test set were 0.781 (95% confidence interval (CI): 0.659-0.905;), 0.804 (95% CI: 0.723-0.884;) and 0.747 (95% CI: 0.621-0.874;), respectively. In the visual assessments, the mean CT value and air bronchogram were important indicators of TLS, the AUC was 0.683. In the external test set, the AUC of the clinical model was 0.632.

CONCLUSIONS

The radiomics model has a higher AUC than the clinical model and effectively discriminates TLSs in patients with IA.

CRITICAL RELEVANCE STATEMENT

This study demonstrates that the radiomics-based model can differentiate TLSs in patients with IA. As a non-invasive biomarker, it enhances our understanding of tumor prognosis and management.

KEY POINTS

TLSs are closely related to favorable clinical outcomes in non-small cell lung cancer. Radiomics from Chest CT predicted TLSs in patients with IA. This study supports individualized clinical decision-making for patients with IA.

Mature tertiary lymphoid structure associated CD103+ CD8+ Trm cells determined improved anti-tumor immune in breast cancer

Background

Although tertiary lymphoid structures (TLS) play crucial roles in the anti-tumor immune response and are associated with favorable prognoses in many solid tumors, the precise mechanisms by which TLSs enhance anti-tumor immunity remain poorly understood. The current study aimed to explore the relationship between the maturity of tertiary lymphoid structures and their key immune cells in combating breast cancer.

Patients and methods

In this study, we utilized immunofluorescence and H&E staining to detect tumor-resident memory T cells (Trm) and assess the maturity of TLS, analyzing their distribution and proportion in an annotated cohort of 95 breast cancer patients.

Results

The presence of tumor-associated TLSs was correlated with an improved prognosis in patients with breast cancer. The proportion of CD8+CD103+ resident memory T cells and natural killer (NK) cells within the TLSs was significantly higher than that in areas outside of these structures. Additionally, the proportions of CD103+ CD8+ Trm cells and NK cells were significantly increased with the gradual maturation of TLS. Furthermore, the secretion function of effector molecules by CD8+ CD103+ Trm cells and NK cells within TLSs was significantly enhanced, indicating a strong correlation between the effector function of CD103+ CD8+ Trm and NK cells and the maturity of TLSs.

Conclusion

Our study identifies potential additional prognostic information for the clinical prognosis of breast cancer patients, underscoring the prognostic significance of immune cells within TLS, with a particular focus on CD103+ CD8+ Trm cells and NK cells.

Tumor aggression-defense index-a novel indicator to predicts recurrence and survival in stage II-III colorectal cancer

BACKGROUND

Although the TNM staging system plays a critical role in guiding adjuvant chemotherapy for colorectal cancer (CRC), its precision for risk stratification in stage II and III CRC patients with proficient DNA mismatch repair (pMMR) remains limited. Therefore, precise predictive models and research on postoperative treatments are crucial for enhancing patient survival and improving quality of life.

METHODS

This retrospective study analyzed 1051 pMMR CRC patients who underwent radical resection and were randomly assigned to training (n = 736) and validation (n = 315) groups. Immunohistochemistry and hematoxylin and eosin staining were utilized to evaluate regulatory-Immunoscore (RIS), tertiary lymphoid structures (TLS), and tumor budding (TB). The Tumor Aggression-Defense Index (TADI) was derived through a multi-factor COX regression model. Subgroup analysis demonstrated potential of TADI in guiding personalized adjuvant therapy for stage II and III CRC.

RESULTS

Univariate and multivariate Cox analysis indicated that TADI was an independent prognostic indicator. Among stage II CRC, chemotherapy was significantly correlated with improved recurrence times in individuals with intermediate (95% CI 0.19-0.59, P < 0.001) and high (95% CI 0.36-0.95, P = 0.031) TADI. In stage III CRC receiving adjuvant chemotherapy, a duration of 3 months or longer was notably associated with a prolonged time to recurrence in those with high TADI (95% CI 0.40-0.98, P = 0.041) compared to durations of less than 3 months.

CONCLUSION

The TADI serves as an effective parameter for predicting the survival outcomes of stage I-III pMMR CRC patients and guiding precision treatment strategies.

Tertiary lymphoid structures and cancer immunotherapy: From bench to bedside

Tertiary lymphoid structures (TLSs) are organized ectopic lymphoid aggregates within the tumor microenvironment that serve as crucial sites for the development of adaptive antitumor cellular and humoral immunity. TLSs have been consistently documented in numerous cancer types, correlating with improved prognosis and enhanced responses to immunotherapy, especially immune-checkpoint blockade (ICB). Given the potential role of TLSs as predictive biomarkers for the efficacy of ICB in cancer patients, the therapeutic manipulation of TLSs is gaining significant attention as a promising avenue for cancer treatment. Herein, we comprehensively review the composition, definition, and detection methods of TLSs in humans. We also discuss the contributions of TLSs to antitumor immunity, their prognostic value in cancer patients, and their association with therapeutic response to ICB-based immunotherapy. Finally, we present preclinical data supporting the potential of therapeutically manipulating TLSs as a promising approach for innovative cancer immunotherapy.

Role of tertiary lymphoid structures and B cells in clinical immunotherapy of gastric cancer

Gastric cancer is a common malignant tumor of the digestive tract, and its treatment remains a significant challenge. In recent years, the role of various immune cells in the tumor microenvironment in cancer progression and treatment has gained increasing attention. Immunotherapy, primarily based on immune checkpoint inhibitors, has notably improved the prognosis of patients with gastric cancer; however, challenges regarding therapeutic efficacy persist. Histological features within the tumor microenvironment, such as tertiary lymphoid structures (TLSs), tumor-infiltrating lymphocytes, and the proportion of intratumoral stroma, are emerging as potentially effective prognostic factors. In gastric cancer, TLSs may serve as local immune hubs, enhancing the ability of immune cells to interact with and recognize tumor antigens, which is closely linked to the effectiveness of immunotherapy and improved survival rates in patients. However, the specific cell type driving TLS formation in tumors has not yet been elucidated. Mature TLSs are B-cell regions containing germinal centers. During germinal center formation, B cells undergo transformations to become mature cells with immune function, exerting anti-tumor effects. Therefore, targeting B cells within TLSs could provide new avenues for gastric cancer immunotherapy. This review, combined with current research on TLSs and B cells in gastric cancer, elaborates on the relationship between TLSs and B cells in the prognosis and immunotherapy of patients with gastric cancer, aiming to provide effective guidance for precise immunotherapy.

Multimodal profiling uncovers tertiary lymphoid structures as a critical determinant of immunotherapy response and prognosis in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC), historically termed 'lymphoepithelioma-like carcinoma' due to its rich lymphocyte infiltration, benefit from PD-1 blockade treatment. However, a comprehensive understanding of its tumor microenvironment (TME) remains elusive, hindering the identification of effective biomarkers for immunotherapy. We leveraged multimodal profiling data, including gene expression, immunohistochemistry, and multiplex immunohistochemistry, from three independent cohorts of NPC patients with a total of 327 patients to dissect the TME in NPC. Unsupervised hierarchical clustering of TME cell populations in the discovery cohort revealed two novel subtypes with distinct prognosis: 'Immune Inflamed' and 'Immune Deficient'. Intriguingly, the most significant differences between the two subtypes were the abundance of B cells and tertiary lymphoid structures (TLS), with a nearly two-fold increase in TLS presence in the Immune Inflamed subtype. The prognostic significance of TLS was confirmed in three independent NPC cohorts, surpassing the prognostic value of individual immune cell subsets. Mechanistically, TLS enhanced anti-tumor immunity by increasing T and B cell receptor repertoire diversity, promoting infiltration of plasma cells, macrophages, and natural killer cells, and consequently increasing antibody-dependent cell-mediated cytotoxicity and antibody-dependent phagocytosis. Finally, TLS status robustly predicted prognosis in a cohort of NPC patients treated with PD-1 blockade, and its prognostic value was consistent across a pan-cancer immunotherapy cohort of 10 tumors and 1158 patients, although with context-specific effects depending on cancer type and immunotherapy modality. In conclusion, this study provides compelling evidence that TLS is a robust indicator of overall immune response within TME and have great potential to guide individualized immunotherapy.

Imaging Mass Cytometry to Decipher the Maturation of Tertiary Lymphoid Structures

In the realm of inflammation, including conditions like cancers, infections, and autoimmune diseases, the emergence of tertiary lymphoid structures (TLS) holds significant implications for prognosis and treatment response. Yet, traditional methodologies such as immunohistochemistry and immunofluorescence falter in capturing the nuanced complexities of TLS, necessitating innovative approaches, like imaging mass cytometry (IMC), to unravel their significance. With the capacity to concurrently assess nearly 40 markers within the same tissue section, IMC transcends the constraints of traditional approaches.This chapter delineates the IMC methodology tailored for TLS visualization and subsequent quantification. By leveraging IMC on formalin-fixed, paraffin-embedded (FFPE) sections of human colorectal cancer (CRC) tissues, we aim to establish a standardized protocol that elucidates the intricacies of TLS dynamics and composition.

Mouse Models Enable the Functional Investigation of Tertiary Lymphoid Structures in Cancer

Tertiary lymphoid structures (TLSs) are organized lymphoid aggregates that form within nonlymphoid tissue, including tumors, in response to persistent inflammatory stimulation. In cancer patients, TLSs are generally associated with positive clinical outcomes. However, the cellular composition and spatial distribution of TLSs can vary depending on the underlying disease state, complicating interpretations of their prognostic significance. Murine models are indispensable for providing a deeper insight into the mechanisms involved in TLS formation and function. Studies using these models can complement current clinical efforts to characterize TLSs via genetic sequencing and histopathology of human samples. Several features of TLSs resemble that of secondary lymphoid organs (SLOs). Consequently, vascular system components and structural support elements are important for TLS formation and maintenance. Furthermore, TLSs in different tissue environments can exhibit distinct characteristics, necessitating careful consideration when selecting mouse models for study. Herein, we discuss critical aspects to consider when modeling TLSs and describe recent findings of TLS studies in the mouse lung and intestinal gut environments as examples to highlight the importance of considering tissue-specific regulatory mechanisms for TLSs. In this chapter, we also summarize the mechanistic insights derived from murine models on the formation and function of TLSs, which may translate to the future therapeutic modulation of TLS in disease.

Automated Quantification of Tertiary Lymphoid Structures in Human Tumor Samples Using Immunofluorescence and AI-Powered Analysis Pipeline

The tumor microenvironment (TME) is a complex entity comprising not only tumor cells but also immune, stromal, and endothelial cells. Preclinical and clinical studies indicate that the density, localization, function, and organization of immune infiltration can influence survival probability and treatment response in many cancers. Among these cell organizations, the clustering of T and B cells into tertiary lymphoid structures (TLS) has been associated with favorable clinical outcomes. In this protocol, we propose a protocol for 7-plex immunofluorescence staining for identifying six cell types enriched in TLS in formalin-fixed paraffin-embedded (FFPE) human tumor sections. Additionally, we provide a detailed methodology for quantifying these cell subtypes using the Halo-AI analysis software. This approach will enable a more precise and detailed characterization of TLS in the TME, opening new avenues for understanding their role in anticancer treatment response.

Prognostic significance of tertiary lymphoid structures in gastric neuroendocrine carcinoma with association to delta-like ligand 3 and neuroendocrine expressions

BACKGROUND

Gastric neuroendocrine carcinomas (NECs) are rare cancers with highly aggressive behavior. Although tertiary lymphoid structures (TLSs) are well-known prognostic factors in various cancers, their role in gastric NECs remain unexplored. Unique immunohistochemical subtypes of pulmonary NECs have been discovered, however, their feasibility in gastric NECs is unknown.

METHODS

The presence and maturation of TLSs (lymphoid aggregates, primary and secondary follicles) were assessed in 48 surgically resected gastric NECs and were compared with immunohistochemical subtypes, using a panel of ASCL1, NeuroD1, POU2F3, YAP1, and DLL3 with three neuroendocrine (NE) markers.

RESULTS

Patients with secondary follicles had significantly better overall survival (OS) and recurrence-free survival (RFS; both, p = 0.004) than those without them. Based on the hierarchical clustering, gastric NECs were classified into all low/negative (31%), high-YAP1 (19%), high-DLL3/low-NE (29%), and high-NE (21%) expression groups. The high-DLL3/low-NE group was associated with absent TLSs (p = 0.026) and showed the worst OS (p = 0.026). Distant metastasis and a lack of secondary follicles were poor independent prognostic factors of OS and RFS.

CONCLUSION

The assessment of TLSs is a feasible and potent biomarker for gastric NECs, thus enabling better prognosis and more effective immunotherapy. Furthermore, gastric NECs can be categorized as four immunohistochemically distinct groups, of which the high-DLL3/low-NE group has the worst OS with lack of TLSs.

Tertiary Lymphoid Structure in Dental Pulp: The Role in Combating Bacterial Infections

Tertiary lymphoid structure (TLS) is associated with various pathologies, including those of cancers and chronic infections. Depending on the organ, multiple factors regulate the formation of TLS. However, the role of TLS in immune response and the molecules that drive its formation remain uncertain. The dental pulp, includes a few immune cells surrounded by rigid mineralized tissue, and opens to the outside through the apical foramen. Owing to this special organization, the dental pulp generates a directional immune response to bacterial infection. Considering this aspect, the dental pulp is an ideal model for comprehensively studying the TLS. In the present study, single-cell RNA sequencing of healthy and inflamed human dental pulp reveals known markers of TLS, including C-C motif chemokine ligand 19 (CCL19), lysosome-associated membrane glycoprotein 3 (LAMP3), CC chemokine receptor 7 (CCR7), and CD86, present in inflamed dental pulp. Compared with the healthy pulp, types and proportions of immune cells increase, along with enhanced cellular communication. Multiple immunofluorescence staining reveals that typical TLS emerges in dental pulp with pulpitis, consistent with the high expression of CC chemokine ligand 3 (CCL3), which may be a key driver of TLS formation. Moreover, TLS is also observed in a mouse model of pulpitis. These findings collectively offer insights into the formation and function of TLS in response to infection.

Methods for Selective Gene Expression Profiling in Single Tertiary Lymphoid Structure Using Laser Capture Microdissection

Tertiary lymphoid structures (TLS) are de novo lymphoid formations that are induced within tissues during inflammatory episodes. TLS have been reported at various anatomic sites and in many different contexts like cancer, infections, autoimmunity, graft rejection, and idiopathic diseases. These inducible, ectopic, and transient lymphoid structures exhibit the prototypical architecture found within secondary lymphoid organs (SLO) and have been increasingly recognized as a major driver of local adaptive immune reaction. As TLS emerge within tissues, the isolation in situ and the molecular characterization of these structures are challenging to perform. Laser capture microdissection (LCM) is a powerful tool to isolate selective structural components and cells from frozen or paraffin-embedded tissues. We and other groups previously applied LCM to decipher the molecular network within TLS and uncover their intrinsic connection with the local microenvironment. In this chapter, we describe a detailed LCM method for selecting and isolating TLS in situ to perform comprehensive downstream molecular analyses.

Tertiary lymphoid structures in colorectal cancer - organization and immune cell interactions

Tertiary lymphoid structures (TLS), formerly recognized as Crohn's-like structures, serve as crucial biomarkers for evaluating the progression of colorectal cancer (CRC). Understanding their spatial distribution, cellular composition, and interactions within CRC is paramount for comprehending the immune response in the tumor microenvironment (TME). TLS are comprised of a T-cellular compartment and a B-cellular compartment, the latter encompassing follicular dendritic cells (FDCs), high endothelial venules (HEVs), and lymphatic vessels. While T helper cells predominate in cancer TLS, the specific functions of their subpopulations remain inadequately understood. Notably, T follicular helper (Tfh) cells play a central role in the activation of CD8+ T cells, and both Tfh cells and Tfh-associated genes have been linked to enhanced CRC survival. In stage II CRC TLS, an escalation in the number of FoxP3+ T regulatory cells (Tregs) is regarded as a negative prognostic factor. Moreover, within TLS, T lymphocytes shield B lymphocytes from the immunosuppressive effects of the TME. B lymphocyte activation is succeeded by class recombination (CSR) and somatic hypermutation (SHM). Dendritic cells (DCs) constitute a vital cellular component of the TLS T compartment. During steady state and early stages of CRC, specialized antigen-presenting cells such as DCs migrate to regional lymph nodes through afferent lymphatics. They deliver MHC antigen-derived peptide complexes (tumor antigens) to naïve CD4+ and CD8+ T cells, which subsequently infiltrate the tumor site as antigen-specific T cells. Key DC markers studied in TLS include CD83 and DC-LAMP. Research has indicated that the DC-LAMP gene signature in tumor TLS reflects Th1 cell targeting, cytotoxicity, and T cell activation. This review comprehensively outlines the functions performed by distinct cell subsets within tertiary lymphoid structures (TLS) in tumors.

The systemic inflammation response index (SIRI) predicts survival in advanced non-small cell lung cancer patients undergoing immunotherapy and the construction of a nomogram model

BACKGROUND

Inflammation and immune evasion are associated with tumorigenesis and progression. The Systemic Inflammation Response Index (SIRI) has been proposed as a pre-treatment peripheral blood biomarker. This study aims to compare the relationship between SIRI, various serum biomarkers, and the prognosis of NSCLC patients before and after treatment.

METHODS

A retrospective study was conducted on advanced NSCLC patients treated with anti-PD-1 drugs from December 2018 to September 2021. Peripheral blood markers were measured pre- and post-treatment, and hazard ratios were calculated to assess the association between serum biomarkers and progression-free survival (PFS) and overall survival (OS). Kaplan-Meier curves and Cox proportional hazards models were employed for survival analysis. A nomogram model was built based on multivariate Cox proportional hazards regression analysis using the R survival package, with internal validation via the bootstrap method (1,000 resamples). Predictive performance was expressed using the concordance index (C-index), and calibration plots illustrated predictive accuracy.The application value of the model was evaluated by decision curve analysis (DCA).

RESULTS

Among 148 advanced NSCLC patients treated with PD-1 inhibitors, the median PFS was 12.9 months (range: 5.4-29.2 months), and the median OS was 19.9 months (range: 9.6-35.2 months). Univariate analysis identified pre- and post-treatment SIRI, mGRIm-Score, and PNI as independent prognostic factors for both PFS and OS (p < 0.05). Multivariate analysis demonstrated that high post-SIRI and post-mGRIm-Score independently predicted poor PFS (P < 0.001, P = 0.004) and OS (P = 0.048, P = 0.001). The C-index of the nomogram model for OS was 0.720 (95% CI: 0.693-0.747) and for PFS was 0.715 (95% CI: 0.690-0.740). Internal validation via bootstrap resampling (B = 1,000) showed good agreement between predicted and observed OS and PFS at 1, 2, and 3 years, as depicted by calibration plots.

CONCLUSION

SIRI is an important independent predictor of early progression in advanced NSCLC patients treated with PD-1 inhibitors and may assist in identifying patients who will benefit from PD-1 inhibitors therapy in routine clinical practice.

Comprehensive Analysis of Tertiary Lymphoid Structures in Pancreatic Cancer: Molecular Characteristics and Prognostic Implications

Purpose:

The molecular properties of TLSs in pancreatic cancer are still not well comprehended. This research delved into the molecular properties of intratumoral TLSs in pancreatic cancer through the exploration of multi-omics data.

Methods:

Seven key genes were identified through Cox regression analysis and random survival forest analysis from a total of 5908 genes related to TLSs. These genes were utilized to construct a prognosis model, which was subsequently validated in two independent cohorts. Additionally, the study investigated the molecular features of different populations of TLSs from multiple perspectives. The model’ s forecasting accuracy was verified by analyzing nomogram and decision curves, taking into account the patients’ clinical traits.

Results:

The analysis of immune cell infiltration showed a notably greater presence of Macrophage M0 cells in the group at high risk than in the low-risk group. The pathway enrichment analysis demonstrated the activation among common cancer-related pathways, including ECM receptor interaction, pathways in cancer, and focal adhesion, in the high-risk group. Additionally, the methylation study revealed notable disparities in DNA methylation between two TLS groups across four regions: TSS200, 5’ UTR, 1stExon, and Body. A variety of notably distinct sites were linked with PVT1. Furthermore, by constructing a competing endogenous RNA network, several mRNAs and lncRNAs were identified that compete for the binding of hsa-mir-221.

Conclusion:

Overall, this research sheds light on the molecular properties of TLSs across various pancreatic cancer stages and suggests possible focal points for the treatment of pancreatic cancer.

Tertiary lymphoid structures in colorectal cancer

BACKGROUND

Tertiary lymphoid structures (TLS) are ectopic clusters of immune cells found in non-lymphoid tissues, particularly within the tumor microenvironment (TME). These structures resemble secondary lymphoid organs and have been identified in various solid tumors, including colorectal cancer (CRC), where they are associated with favorable prognosis. The role of TLS in modulating the immune response within the TME and their impact on cancer prognosis has garnered increasing attention in recent years.

OBJECTIVE

This review aims to summarize the current understanding of TLS in CRC, focusing on their formation, function, and potential as prognostic markers and therapeutic targets. We explore the mechanisms by which TLS influence the immune response within the TME and their correlation with clinical outcomes in CRC patients.

METHODS

We conducted a comprehensive review of recent studies that investigated the presence and role of TLS in CRC. The review includes data from histopathological analyses, immunohistochemical studies, and clinical trials, examining the association between TLS density, composition, and CRC prognosis. Additionally, we explored emerging therapeutic strategies targeting TLS formation and function within the TME.

RESULTS

The presence of TLS in CRC is generally associated with an improved prognosis, particularly in early-stage disease. TLS formation is driven by chronic inflammation and is characterized by the organization of B and T cell zones, high endothelial venules (HEVs), and follicular dendritic cells (FDCs). The density and maturity of TLS are linked to better patient outcomes, including reduced recurrence rates and increased survival. Furthermore, the interplay between TLS and immune checkpoint inhibitors (ICIs) suggests potential therapeutic implications for enhancing anti-tumor immunity in CRC.

CONCLUSIONS

TLS represent a significant prognostic marker in CRC, with their presence correlating with favorable clinical outcomes. Ongoing research is required to fully understand the mechanisms by which TLS modulate the immune response within the TME and to develop effective therapies that harness their potential. The integration of TLS-focused strategies in CRC treatment could lead to improved patient management and outcomes.

Multi-Algorithm-Integrated Tertiary Lymphoid Structure Gene Signature for Immune Landscape Characterization and Prognosis in Colorectal Cancer Patients

PURPOSE

Colorectal cancer (CRC) is a common malignancy with a low survival rate as well as a low response rate to immunotherapy. This study aims to develop a risk model based on tertiary lymphoid structure (TLS)-associated gene signatures to enhance predictions of prognosis and immunotherapy response.

METHODS

TLS-associated gene data were obtained from TCGA-CRC and GEO cohorts. A comprehensive analysis using univariate Cox regression identified TLS-associated genes with significant prognostic implications. Subsequently, multiple algorithms were employed to select the most influential genes, and a stepwise Cox regression model was constructed. The model's predictive performance was validated using independent datasets (GSE39582, GSE17536, and GSE38832). To further investigate the immune microenvironment, immune cell infiltration in high-risk (HRG) and low-risk (LRG) groups was assessed using the CIBERSORT and ssGSEA algorithms. Additionally, we evaluated the model's potential to predict immune checkpoint blockade therapy response using data from The Cancer Imaging Archive, the TIDE algorithm, and external immunotherapy cohorts (GSE35640, GSE78200, and PRJEB23709). Immunohistochemistry (IHC) was employed to characterize TLS presence and CCL2 gene expression.

RESULTS

A three-gene (CCL2, PDCD1, and ICOS) TLS-associated model was identified as strongly associated with prognosis and demonstrated predictive power for CRC patient outcomes and immunotherapy efficacy. Notably, patients in the low-risk group (LRG) had a higher overall survival rate as well as a higher re-response rate to immunotherapy compared to the high-risk group (HRG). Finally, IHC results confirmed significantly elevated CCL2 expression in the TLS regions.

CONCLUSIONS

The multi-algorithm-integrated model demonstrated robust performance in predicting patient prognosis and immunotherapy response, offering a novel perspective for assessing immunotherapy efficacy. CCL2 may function as a TLS modulator and holds potential as a therapeutic target in CRC.

Research trends, hotspots and future directions of tertiary lymphoid structures in cancer: a comprehensive informatics analysis and visualization study

Many studies have reported the presence of tertiary lymphoid structures (TLSs) in cancer, but the research progress of TLSs in cancer has not been systematically analyzed. Therefore, we analyzed the global scientific knowledge in the field using informatics methods. The results showed that TLSs in cancer have received increasing attention since the 21st century, with an annual publication growth rate of 27.86%. Unsupervised hierarchical clustering based on machine learning further categorized the research features into four clusters, with the cluster related to immunotherapy being considered an emerging cluster. TLSs and immunotherapy were identified as the top two hotspots with the highest occurrence frequency and total link strength. The Walktrap algorithm indicated that "TLSs, carcinoma, prognostic value" and "high endothelial venules, germinal-centers, node-like structures" are important to TLSs but remain underexplored, representing promising research directions. These findings suggest that cancer-related TLSs have brought new insights into antitumor immunity, and targeting TLSs has the potential to transform the landscape of antitumor immunotherapy.

Global trends in tertiary lymphoid structures: a bibliometric analysis from 2014 to 2023

AIM AND BACKGROUND

Tertiary lymphoid structures (TLS) are increasingly recognized for their role in immunity. Despite growing interest, a systematic bibliometric analysis of TLS-related research has been lacking. To provide a comprehensive overview of current research trends and hotspots, we conducted a bibliometric analysis using data from the Web of Science Core Collection.

METHODS

We retrieved TLS-related publications from the Science Citation Index Expanded within the Web of Science Core Collection from January 2014 to December 2023. Co-occurrence analysis with "VOSviewer" identified current status and research hotspots, while "CiteSpace" was used for co-citation analysis to assess knowledge evolution and bursts. Thematic evolution was explored using bibliometrics to identify emerging keyword trends. Additionally, we examined country/region, institutional, and author contributions and collaborations. Tables were created using Microsoft Word.

RESULTS

A total of 785 publications were analyzed, showing a continuous growth trend from 2017 to 2023, indicating escalating interest in TLS among researchers. Leading countries in TLS research were China (231 publications), the United States (212 publications), and France (89 publications). The most productive institution and author were the "Institut national de la santé et de la recherche médicale" (70 publications) and Catherine Sautes-Fridman (21 publications), respectively. Key topics included TLS, B cells, and immunotherapy. Recent research has focused on mechanisms linking TLS with cancers, such as immunotherapy, tumor microenvironment, tumor-infiltrating lymphocytes, prognosis, and immune checkpoint inhibitors, highlighting an expanding area of study. Additionally, TLS' potential as a biomarker for predicting immunotherapy efficacy across different cancer types remains a burgeoning research direction.

CONCLUSIONS

This study provides a comprehensive analysis of global TLS-related publications, revealing key literature metrics and identifying influential articles and emerging research concerns. These findings contribute valuable insights into the role of TLS in immunotherapy and suggest future directions for this dynamic field.

Proteomic profile of the antibody diversity in circulating extracellular vesicles of lung adenocarcinoma

Immunoglobulin diversity encompasses B-cell receptor, T-cell receptor, and antibody diversity. Existing studies have focused more on the role of B-cell and T-cell receptor diversity in tumor immunity, while the role of antibody diversity is less understood. This study examined and compared the blood extracellular vesicles (EVs) of lung cancer patients and healthy individuals using proteomics and bioinformatics analyses. The results revealed that among the 270 identified proteins, those involved in defense mechanisms were the most abundant. Most of these were antibody subtypes, accounting for 50.00%. Similarly, of the 40 identified EVs differentially expressed proteins (DEPs), 29 were involved in defense mechanisms (72.50%), with a higher proportion being antibody subtypes (82.76%). Furthermore, 24 DEP antibody subtypes were implicated in 18 immune reaction-related signaling pathways. These findings suggest that human serum EVs contain a significant number of antibody subtypes, and the antibody subtypes from lung cancer serum EVs differ from those of healthy controls (HCs). The variations in antibody diversity may be closely associated with lung cancer tumor immunity.

Preferential activation of type I interferon-mediated antitumor inflammatory signaling by CuS/MnO2/diAMP nanoparticles enhances anti-PD-1 therapy for sporadic colorectal cancer

Converting the "cold" tumor microenvironment (TME) to a "hot" milieu has become the prevailing approach for enhancing the response of immune-excluded/immunosuppressed colorectal cancer (CRC) patients to immune checkpoint blockade (ICB) therapy. During this process, inflammation accompanied by different kinds of chemokines/cytokines inevitably occurs. However, some activated inflammatory signals exhibit protumor potency. Therefore, strategies that preferentially activate antitumor inflammatory signaling rather than tumor-promoting signaling need to be developed. Herein, we constructed a STING agonist-loaded CuS/MnO2 bimetallic nanosystem, termed diAMP-BCM. BCM with an optimized Cu/Mn ratio efficiently promoted the activation of proinflammatory signaling, and in combination with the STING agonist diAMP, diAMP-BCM controllably activated tumoricidal inflammatory signaling in APCs. DiAMP-BCM can efficiently generate ROS and promote the activation of STING, which induces the apoptosis of cancer cells and promotes the recruitment of monocytes while facilitating the polarization of macrophages and maturation of DCs. MC38 and CT26 CRC models were established to evaluate the in vivo antitumor effects of diAMP-BCM. Combined with ICB therapy, diAMP-BCM enables the rebuilding of tumor milieus with efficient tumor growth inhibition and alleviation of T-cell exhaustion, particularly in distal tumors, in sporadic colorectal cancer therapy. This study established a nanoplatform to promote the preferential activation of antitumor inflammatory signaling, rebuild the T-cell repertoire and alleviate T-cell exhaustion to enhance cancer ICB immunotherapy.

Single-cell landscape identified SERPINB9 as a key player contributing to stemness and metastasis in non-seminomas

Embryonal carcinoma (EC), characterized by a high degree of stemness similar to that of embryonic stem cells, is the most malignant subtype within non-seminomatous testicular germ cell tumors (TGCTs). However, the mechanisms underlying its malignancy remain unknown. In this study, we employed single-cell RNA sequencing to analyze four non-seminoma samples. Our differential expression analysis revealed high expression of SERPINB9 in metastatic EC cells. We conducted in vitro experiments to further investigate SERPINB9's role in the progression of EC. Functionally, the knockdown of SERPINB9 in NCCIT and NTERA-2 leads to a diminished migratory capability and decreased cis-platin resistance, as demonstrated by Transwell migration assay and drug sensitivity assay. Moreover, embryoid bodies showed reduced size and lower OCT4 expression, alongside heightened expression of differentiation markers AFP, ACTA2, and CD57 in shSERPINB9 cells. In vivo, the role of SERPINB9 in maintaining cancer stemness was validated by the limiting dilution assay. Mechanistically, Bulk RNA-seq further showed downregulation of ERK1/2 signaling and WNT signaling pathways with concomitant upregulation of differentiation pathways subsequent to SERPINB9 knockdown. Additionally, the analysis indicated increased levels of cytokines linked to tertiary lymphoid structures (TLS), such as IL6, IL11, IL15, CCL2, CCL5, and CXCL13 in shSERPINB9 cells, which were further validated by ELISA. Our research indicates that SERPINB9 plays a key role in driving tumor progression by enhancing tumor stemness and suppressing TLS. This study stands as the first to elucidate the molecular signature of non-seminomas at a single-cell level, presenting a wealth of promising targets with substantial potential for informing the development of future therapeutic interventions.

Tertiary lymphoid structures in ovarian cancer

Ovarian cancer (OC) is a significant cause of cancer-related mortality in women worldwide. Despite advances in treatment modalities, including surgery and chemotherapy, the overall prognosis for OC patients remains poor, particularly for patients with advanced or recurrent disease. Immunotherapy, particularly immune checkpoint blockade (ICB), has revolutionized cancer treatment in various malignancies but has shown limited efficacy in treating OC, which is primarily attributed to the immunologically. Tertiary lymphoid structures (TLSs), which are ectopic aggregates of immune cells, have emerged as potential mediators of antitumor immunity. This review explores the composition, formation, and induction of tumor associated TLS (TA-TLS) in OC, along with their role and therapeutic implications in disease development and treatment. By elucidating the roles TA-TLSs and their cellular compositions played in OC microenvironment, novel therapeutic targets may be identified to overcome immune suppression and enhance immunotherapy efficacy in ovarian cancer.

Characteristics and Significance of Tertiary Lymphoid Structures Based on Molecular Subtypes in Endometrial Cancer

The purpose of this study is to investigate the characteristics and significance of tertiary lymphoid structures (TLSs) in endometrial cancer (EC) based on molecular subtypes. A total of 220 patients with EC were retrospectively enrolled, including 20 with polymerase epsilon ultramutated (POLE-mut), 63 with mismatch repair deficient, 32 with p53 abnormal, and 105 with no specific molecular profile. The presence and maturity of TLSs were determined by immunohistochemical markers (CD3, CD20, CD21, and Bcl6). Disease-free survival served as the endpoint event. TLSs were found in 91 out of 220 patients (41.1%), with 68 located in peritumoral tissues and 37 exhibiting well-formed germinal center structures. The presence and different maturity of TLSs were closely associated with tumor-infiltrating lymphocytes and the programmed cell death ligand-1 expression. Moreover, TLSs displayed heterogeneity across different molecular subtypes. Notably, the TLSs, tumor-infiltrating lymphocytes, and expression of the programmed cell death ligand-1 were significantly enriched in POLE-mut EC. Multivariate logistic regression analysis showed the presence of TLSs (odds ratio: 3.483, 95% CI: 1.044-11.623, P = 0.042) as a potential predictor of POLE-mut EC. Kaplan-Meier survival curves revealed that molecular subtypes significantly stratified prognosis in patients with EC (P = 0.002), whereas TLSs did not. Multivariate Cox regression analysis indicated that The International Federation of Gynecology and Obstetrics stage and Ki-67 expression were independent prognostic factors affecting disease-free survival in patients with EC, and TLSs were not included. In conclusion, TLSs in EC exhibit heterogeneity based on molecular subtypes, necessitating further exploration to determine their clinical application value.

Lymphocyte Function in Tertiary Lymphoid Structures Predicts Hepatocellular Carcinoma Outcome

An increasing number of studies have revealed a correlation between tertiary lymphoid structures (TLSs) and the outcome of hepatocellular carcinoma (HCC). Nevertheless, the associations between the heterogeneity of cellular composition and the overall survival (OS) in HCC remain unexplored. Here, we evaluated the cancer tissues from 150 HCC individuals using multiplex immunofluorescence to determine the presence and characteristics of TLS and to investigate the relationship between intra-TLS immunologic activity, TLS maturation, and intratumoral immune cell infiltration. Prognostic factors influencing the outcome were identified through both univariate and multivariate analyses. Additionally, the levels of cytotoxic T-lymphocyte antigen-4 (CTLA-4), programmed death 1, programmed death-ligand 1, and lymphocyte activation gene-3 were determined, as well as their relationship with TLS features were determined. TLS was detected in 71 (47.3%) of the 150 HCC cases and was related to higher intratumoral infiltration levels of lymphocytes. Additionally, intra-TLS lymphocyte proliferation correlated with that of intratumoral lymphocytes, and the presence of TLS and a high proportion of mature TLS demonstrated a significant correlation with better prognosis (P = .013 and P = .03, respectively). Among TLS-positive tumors, a high proportion of B cells expressing activation-induced cytidine deaminase and a high proportion of CD8+ T cells expressing CD45RO were significantly related to improved OS (P = .01 and P < .001, respectively). Comparatively, a high proportion of CD21+CD20+ B cells demonstrated a significant correlation with poorer OS (P < .001). A markedly reduced number of CTLA-4+ cells in the stromal regions in TLS-negative tumors was observed compared with TLS-positive tumors (P = .01). These findings reveal a correlation between TLS presence and improved OS in HCC patients. However, TLS exhibited significant variation in maturation state, T- and B-cell proliferation, and expression of markers related to B- and T-cell function. Notably, these characteristics were also found to possess prognostic significance, indicating that certain TLS might hinder tumor immunity by inhibiting immune cells, whereas others may foster antigen-driven immune responses, likely influenced by the composition and functional status of intra-TLS lymphocytes.

Tertiary lymphoid structures as potential biomarkers for cancer prediction and prognosis

Tertiary lymphoid structures (TLSs) are ectopic lymphocyte aggregates formed in non-lymphoid tissues, including cancers, and are loci for the generation of in situ anti-tumor immune responses, which play a crucial role in cancer control. The state of TLS presence in cancer and its composition can significantly impact the treatment response and prognosis of patients. TLSs have the potential to serve as predictive and prognostic biomarkers for cancer. However, the mechanisms underlying TLS formation in cancer and how the essential components of TLSs affect cancer are not fully understood. In this review, we summarized TLS formation in cancer, the value of the TLS in different states of existence, and its key constituents for cancer prediction and prognosis. Finally, we discussed the impact of cancer treatment on TLSs.