Abundance Of Tumor-infiltrating Lymphocytes Research Articles

Tumor-infiltrating lymphocytes and immune-related adverse events in advanced melanoma

The predictive value of tumor-infiltrating lymphocytes (TILs) in immune-related adverse event (irAE) development remains unknown, although an association between tumor immunogenicity and irAEs has been suggested. We investigated the association between TIL abundance in pretreatment primary and metastasis specimens and the subsequent development of severe irAEs. We retrospectively identified patients with advanced cutaneous melanoma who received first-line anti-programmed cell death protein 1 (PD-1) with or without anti-cytotoxic T-lymphocyte associated protein 4 (anti-CTLA-4) from 10 hospitals in the Netherlands. TILs were scored on representative hematoxylin and eosin (H&E) stains of the primary melanoma and pretreatment melanoma metastasis as 'absent', 'nonbrisk', or 'brisk'. A univariable logistic regression analysis was carried out to assess the association between the TIL scores and the development of severe irAEs. Fine and Gray subdistribution hazard models were used to estimate the cumulative incidence of severe irAEs. Of the 1346 eligible patients, 536 patients had primary melanoma specimens available, and 613 patients had metastasis specimens available. Severe irAEs occurred in 15% of anti-PD-1-treated patients and 49% of anti-PD-1+ anti-CTLA-4-treated patients. The presence of TILs was not associated with the occurrence of grade ≥3 irAEs in primary melanoma specimens (P= 0.70) nor pretreatment metastasis specimens (P= 0.91). In the univariable analysis, patients with brisk TILs did not have a higher chance of developing severe irAEs compared with patients with absent TILs, for both primary specimen (odds ratio 1.15, 95% confidence interval 0.60-2.18) and metastasis specimen (odds ratio 0.77, 95% confidence interval 0.37-1.59). There was also no significant difference in the lifetime risk or timing of the development of severe irAEs in patients with TILs present compared with patients with TILs absent. There was no association between the TIL scores on H&E-stained slides from the primary melanoma or pretreatment metastasis and the development of grade 3 or higher irAEs. Additionally, no correlation was found between the presence of TILs and the timing of irAEs.

Abstract PO1-28-04: PILHLE-001: neoadjuvant pyrotinib combined with chemotherapy in HR-positive, HER2-low (IHC 2+/FISH-negative) early breast cancer

Abstract Background: Hormone receptor (HR)-positive/HER2-low (IHC 2+/FISH negative or IHC 1+) breast cancers (BCs) represent the largest proportion of breast carcinomas. However, its response to neoadjuvant chemotherapy or endocrine therapy is the lowest, with a residual cancer burden (RCB) 0/I rate around 15%. Previous studies have demonstrated that pyrotinib (P), a pan-HER tyrosine kinase inhibitor, exhibits excellent response in HER2-positive early or advanced BC (E/ABC). In-vitro experiments have shown that pyrotinib can effectively inhibit colony formation in HER2-low (IHC 2+/FISH negative) BC cells. This PILHLE-001 study (NCT05165225) aimed to evaluate the efficacy and safety of neoadjuvant pyrotinib plus chemotherapy in HR-positive/HER2-low (IHC 2+/FISH negative) EBC patients with potential biomarkers. Methods: PILHLE-001, as a single-arm, single-center phase Ⅱ trial, enrolled patients with previously untreated HR-positive (ER or PR > 1%) and HER2-low (IHC 2+/FISH negative) invasive EBC (TNM stage II-III) to receive pyrotinib 320mg QD and four Q3W of epirubicin-cyclophosphamide followed by four Q3W of docetaxel. MammaPrint/BluePrint at baseline (t0) was assessed. Breast magnetic resonance imaging (MRI) was conducted at t0, the end of cycle 2 neoadjuvant therapy (t1), and the end of all neoadjuvant therapy. Immune cell subpopulations assay and gene sequencing of tumor tissues with whole blood control samples were performed at t0 and surgery (t2). Additional core biopsy was administered to reassess Ki67 and tumor infiltrating lymphocytes (TILs) at t1. The primary outcome was RCB 0/I rate. The short-term secondary outcomes included pathological complete response (pCR, ypT0/is ypN0) rate, objective response rate (ORR), breast conservation surgery (BCS) rate, safety, and exploratory biomarkers analysis. Results: From July 2021 to March 2023, 48 patients were enrolled and treated. The median age of the patients was 48 years (range 28-66), 43 (90%) had cT1-2 tumors, 30 (63%) showed no node involvement, 37 (77%) had tumours with TNM stage II, and 47 (98%) had ER expression ≥ 50%. Twenty-eight (61%) of 46 patients had MammaPrint high risk. Out of the 48 patients, 26 (54.2%) achieved RCB 0/I, with a 95% confidence interval of 39.2% to 68.6%. The RCB 0/I rate was particularly higher in tumors with no lymph node involvement (73.3%), TNM stage II (64.9%), or abundant tumor-infiltrating lymphocytes (66.7%). Three (6.3%) patients obtained a pCR. The rate of BCS was 60.4% (29/48). The ORR was 45.8% (22/48) at t1 and 81.3% (39/48) at the end of all neoadjuvant therapy, respectively. No patients had progressive disease. All treatment-related adverse events (AEs) were mostly of grade 1 or 2 severity. Grade ≥ 3 AEs occurred in 21 (44%) patients, with the most prevalent being diarrhea [10 (21%)]. All AEs were reversible with symptomatic treatment and no treatment-related deaths occurred. Patients with MammaPrint risk-low BC had a lower RCB 0/I rate than those with risk-high BC (60.7% vs. 44.4%), although the difference was not statistically significant. Baseline specific immune cell subpopulations (lower PD-1, higher CD3, etc.) or the presence of non-altered PIK3CA were significantly associated with a higher likelihood of achieving RCB 0/I. Similarly, objective response, greater declines in specific MRI quantitative parameters (Ktrans and Kep), greater declines in Ki67, or more increased TILs at t1 were also significantly associated with a higher rate of RCB 0/I. Conclusions: The PILHLE-001 trial first revealed that neoadjuvant pyrotinib plus chemotherapy has encouraging efficacy and acceptable toxicity in patients with HR-positive/HER2-low (IHC 2+/FISH negative) EBC, and this regimen warrants further investigation in phase III randomized controlled trials. Citation Format: Chang Gong, Yuan Xia, Yingying Zhu, Yaping Yang, Wenqian Yang, Louis W.C. Chow, Li Ling, Yunjie Zeng, Jiajie Zhong, Ziliang Cheng, Jun Shen, Qun Lin, Yinduo Zeng, Qiang Liu, Erwei Song. PILHLE-001: neoadjuvant pyrotinib combined with chemotherapy in HR-positive, HER2-low (IHC 2+/FISH-negative) early breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-28-04.

Diffuse Pleural Mesotheliomas with Genomic Near-Haploidization: A Newly Recognized Subset with Distinct Clinical, Histologic, and Molecular Features.

Diffuse pleural mesotheliomas (DPM) with genomic near-haploidization (GNH) represent a novel subtype first recognized by The Cancer Genome Atlas project; however, its clinicopathologic and molecular features remain poorly defined. We analyzed clinical genomic profiling data from 290 patients with DPM using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay. Allele-specific copy number analysis was performed using the Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing (FACETS) algorithm. A total of 210 patients were evaluable for loss of heterozygosity (LOH) analysis using FACETS from MSK-IMPACT tumor:normal sequencing data. In this cohort, GNH, defined as LOH across >80% of the genome, was detected in 10 cases (4.8%). Compared with non-GNH tumors, GNH DPMs were associated with younger age and less frequent self-reported history of occupational asbestos exposure. Histologically, GNH DPMs were enriched in biphasic subtype (80% vs. 14.5%) and showed abundant tumor-infiltrating lymphocytes (TILs). Genomic analysis revealed a higher frequency of TP53 alterations, whereas SETDB1 mutations were present in nearly all and only in this subset. The clinicopathologic and molecular findings were further validated in a separate cohort. Despite the younger age, patients with GNH DPMs had a shorter overall survival (10.9 vs. 25.4 months, P = 0.004); the poor prognostic impact of GNH remained significant after controlling for biphasic histology. Of three patients with GNH DPMs who received immune checkpoint blockade, two achieved a clinician-assessed partial response. GNH defines an aggressive subtype of mainly biphasic DPMs in younger patients with recurrent alterations in SETDB1 and TP53. The enrichment in biphasic histology and TILs, together with our preliminary immune checkpoint blockade response data and anecdotal clinical trial data, suggests that further evaluation of immunotherapy may be warranted in this subset.

Tumor-Infiltrating Lymphocytes in Triple-Negative Breast Cancer.

The association of tumor-infiltrating lymphocyte (TIL) abundance in breast cancer tissue with cancer recurrence and death in patients with early-stage triple-negative breast cancer (TNBC) who are not treated with adjuvant or neoadjuvant chemotherapy is unclear. To study the association of TIL abundance in breast cancer tissue with survival among patients with early-stage TNBC who were treated with locoregional therapy but no chemotherapy. Retrospective pooled analysis of individual patient-level data from 13 participating centers in North America (Rochester, Minnesota; Vancouver, British Columbia, Canada), Europe (Paris, Lyon, and Villejuif, France; Amsterdam and Rotterdam, the Netherlands; Milan, Padova, and Genova, Italy; Gothenburg, Sweden), and Asia (Tokyo, Japan; Seoul, Korea), including 1966 participants diagnosed with TNBC between 1979 and 2017 (with follow-up until September 27, 2021) who received treatment with surgery with or without radiotherapy but no adjuvant or neoadjuvant chemotherapy. TIL abundance in breast tissue from resected primary tumors. The primary outcome was invasive disease-free survival [iDFS]. Secondary outcomes were recurrence-free survival [RFS], survival free of distant recurrence [distant RFS, DRFS], and overall survival. Associations were assessed using a multivariable Cox model stratified by participating center. This study included 1966 patients with TNBC (median age, 56 years [IQR, 39-71]; 55% had stage I TNBC). The median TIL level was 15% (IQR, 5%-40%). Four-hundred seventeen (21%) had a TIL level of 50% or more (median age, 41 years [IQR, 36-63]), and 1300 (66%) had a TIL level of less than 30% (median age, 59 years [IQR, 41-72]). Five-year DRFS for stage I TNBC was 94% (95% CI, 91%-96%) for patients with a TIL level of 50% or more, compared with 78% (95% CI, 75%-80%) for those with a TIL level of less than 30%; 5-year overall survival was 95% (95% CI, 92%-97%) for patients with a TIL level of 50% or more, compared with 82% (95% CI, 79%-84%) for those with a TIL level of less than 30%. At a median follow-up of 18 years, and after adjusting for age, tumor size, nodal status, histological grade, and receipt of radiotherapy, each 10% higher TIL increment was associated independently with improved iDFS (hazard ratio [HR], 0.92 [0.89-0.94]), RFS (HR, 0.90 [0.87-0.92]), DRFS (HR, 0.87 [0.84-0.90]), and overall survival (0.88 [0.85-0.91]) (likelihood ratio test, P < 10e-6). In patients with early-stage TNBC who did not undergo adjuvant or neoadjuvant chemotherapy, breast cancer tissue with a higher abundance of TIL levels was associated with significantly better survival. These results suggest that breast tissue TIL abundance is a prognostic factor for patients with early-stage TNBC.

Abstract 99: Versican regulates T cell abundance within the colorectal cancer microenvironment

Abstract Background: Clinical benefit from immunotherapy is seen in a minority of patients with metastatic colorectal cancer (CRC). Identifying how the tumor microenvironment (TME) influences immune infiltration and treatment response is an unmet need. Versican (VCAN), a chondroitin sulfate proteoglycan, common in the CRC TME has immunoregulatory properties and can be cleaved releasing an immunostimulatory product, versikine (Vkine). Here we evaluate the impact of the abundance of VCAN and Vkine on CD8+ T cell infiltration in CRC. Methods: Samples include 306 primary colon tumors, an additional 176 primary CRCs with matched liver metastases (175 samples), and 328 normal samples (238 colon and 90 liver). Samples were stained via immunohistochemistry (IHC) for VCAN, Vkine, and CD8. CD8+ tumor infiltrating lymphocytes (TILs) were counted per high powered field (HPF, 400X magnification) and presented as averages. Intensity of VCAN and Vkine expression were scored from 0-3+. Samples designated a 0/1 were considered low accumulation and samples scored as a 2/3+ were designated high. Samples scored low for VCAN but high for Vkine were designated VCAN proteolytic predominant (VPP) and all other combinations considered VCAN proteolytic weak (VPW). To create an in vitro model, the mouse MC38 cell line was CRISPR engineered to over-express VCAN. Conditioned media was then concentrated and added to a collagen matrix in a transwell with activated T cells. The number of cells and their subtype that migrated through the matrix were evaluated with flow cytometry. Results: VCAN accumulation was highest in cancerous stroma with 58% of cancers being VCAN high and only 14% of adjacent normal tissues (p&amp;lt;0.001). Vkine accumulation was similar between groups, with 67% of tumors and 54% of adjacent normal samples scored as Vkine high. The VPP phenotype was least common in tumor tissues with only 27% of tumor samples designated VPP versus 43% of adjacent normal samples (p&amp;lt;0.001). VCAN high tumors had significantly fewer TILs with 4 TILs/HPF vs 13 in the VCAN low tumors (p&amp;lt;0.001). High levels of Vkine correlated with greater TIL abundance (Vkine high: 10 TILs/HPF, Vkine low: 5 TILs/HPF; p=0.02). Versican proteolysis had the strongest correlation with TIL abundance in cancers (VPP: 18 TILs/HPF, VPW: 5 TILS/HPF; p&amp;lt;0.001). In vitro, the addition of VCAN containing media into transwell matrices reduced both CD4+ and CD8+ T cell migration through the matrix (Control: 4277 CD8+ T cells, VCAN: 2603 CD8+ T cells; p&amp;lt;0.001 and Control: 7770 CD4+ T cells, VCAN: 5340 CD4+ T cells; p=0.007). Conclusions: VCAN accumulation in human CRCs is common and correlates with reduced TIL abundance, whereas VCAN proteolysis correlates with increased TILs. In vitro, VCAN demonstrated the ability to reduce T cell migration. Future studies will explore the mechanism by which VCAN abundance leads to decreased T cell infiltration and the importance of this as an immunotherapy biomarker. Citation Format: Sean Kraus, Philip Emmerich, Mitch Hayes, Kristina Matkowskyj, Wei Zhang, Cheri Pasch, Fotis Asimakopoulos, Dustin A. Deming. Versican regulates T cell abundance within the colorectal cancer microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 99.

Abstract 6179: Machine learning (ML)-spatial quantification of the tumor microenvironment (TME) identifies differences associated with response to bintrafusp alfa (BA) vs pembrolizumab (PEM) treatment in the Phase 3 INTR@PID Lung 037 study

Abstract Background: ML digital pathology models can accurately quantify predictive biomarkers like PD-L1.1 We combined tissue conserving ML assessment of the TME in hematoxylin and eosin (H&amp;E)-stained whole slide images (WSI) with RNAseq for high-dimensional TME quantification for biomarker discovery. The orthogonal methods were applied to a retrospective analysis of a Phase 3 trial directly comparing BA, a first-in-class bifunctional fusion protein composed of the extracellular domain of TGF-βRII (a TGF-β “trap”) fused to a human IgG1 monoclonal antibody blocking PD-L1, and the anti-PD-1 PEM. Methods: Non-small cell lung cancer ML models previously trained to exhaustively quantify cell types and tissue regions in H&amp;E-stained tissue were refined and deployed on 273 WSI from the INTR@PID Lung 037 study/NCT03631706. Human interpretable features (HIFs) describing the complex spatial organization of the TME were extracted from model predictions. HIFs were selected for analysis using K-means consensus clustering and describe the frequency of lymphocytes in cancer epithelium (cTILs); macrophages, fibroblasts, and granulocytes in stroma; and the abundance of cancer cells relative to all other cells in tumor. Bulk RNAseq was performed for 186 samples yielding 177 WSI-RNAseq pairs. Spearman correlation between HIFs and gene expression or signature was computed. Top gene associations were analyzed via gene-set enrichment analysis. HIFs were used for immunophenotyping (immune excluded, inflamed, and desert) via prespecified cutoffs on tumor-infiltrating lymphocyte abundance, and for biomarker discovery via Cox modeling of PFS and OS. Results: Gene expression and signatures were associated with HIFs quantifying immune spatial abundance in TME (e.g., cTILs vs. immune checkpoint signature2). Improved PFS and OS were associated with an immune-inflamed phenotype for PEM (PFS, HR=0.36, p=0.007, 95% CI 0.17-0.75; OS, HR=0.37, p=0.065, 95% CI 0.13-1.06). In interaction with BA, stromal macrophages were associated with improved survival (PFS, HR=0.72, p=0.062, 95% CI 0.53-1.02; OS, HR=0.62, p=0.058, 95% CI 0.38-1.02) and an increased likelihood of treatment response (odds ratio=1.61, p=0.015). PFS and OS were nearly identical between arms in immune-excluded cases (PEM vs. BA PFS, HR=0.93, p=0.73, 95% CI 0.63-1.39; OS, HR=1.09, p=0.77, 95% CI 0.62-1.92. Conclusion: Together HIFs and immunophenotyping enabled response prediction to BA and PEM. PEM response was greater for immune-inflamed tumors, while BA response was associated with macrophage infiltration of stroma. ML-based spatial analysis of the TME shows promise for immunotherapy biomarker discovery and validation. 1V Baxi, et al. Modern Pathology. 2022; 35(1):23-32. 2S Mariathasan, et al. Nature. 2018; 554(7693):544-548. Citation Format: John Abel, Andreas Machl, Aslihan Gerhold-Ay, Limin Yu, Darpan Sanghavi, Ben Trotter, Neel Patel, Ylaine Gerardin, Ramprakash Srinivasan, Sergine Brutus, Thomas Mrowiec. Machine learning (ML)-spatial quantification of the tumor microenvironment (TME) identifies differences associated with response to bintrafusp alfa (BA) vs pembrolizumab (PEM) treatment in the Phase 3 INTR@PID Lung 037 study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6179.

Prognostic significance of alveolar collapse in lung invasive adenocarcinoma and its relationship with tumor infiltrating lymphocytes

This study aims to investigate the correlations between alveolar collapse, tumor size, and tumor infiltrating lymphocytes (TILs), while also evaluating the prognostic significance of alveolar collapse in invasive lung adenocarcinoma. 355 patients with solitary invasive lung adenocarcinoma were divided into two groups based on the maximum diameter of alveolar collapse: alveolar collapse ≤ 5 mm group and alveolar collapse > 5 mm group. Differences in clinicopathological characteristics, tumor size, TILs, and prognosis were compared between the two groups. The alveolar collapse > 5 mm group had a higher mean age, larger tumor diameter, and increased TILs levels compared to the alveolar collapse ≤ 5 mm group (P < 0.05). A moderate positive correlation was observed between alveolar collapse and tumor size (r = 0.646, P < 0.001). Lung adenocarcinoma with alveolar collapse > 5 mm demonstrated superior 5-year survival and acted as an independent prognostic indicator (HR=0.152, P = 0.004) in multivariate Cox regression analysis, alongside tumor size (HR=10.172, P = 0.034) and lymph node metastasis (HR=2.88, P = 0.017). The size of alveolar collapse is associated with TILs abundance, suggesting that the immune microenvironment may play a crucial role in alveolar collapse formation. Pathologists should take note of alveolar collapse in lung adenocarcinoma.

A pan-cancer analysis revealing the role of LFNG, MFNG and RFNG in tumor prognosis and microenvironment

BackgroundFringe is a glycosyltransferase involved in tumor occurrence and metastasis. However, a comprehensive analysis of the Fringe family members lunatic fringe (LFNG), manic fringe (MFNG), radical fringe (RFNG) in human cancers is lacking.MethodsIn this study, we performed a pan-cancer analysis of Fringe family members in 33 cancer types with transcriptomic, genomic, methylation data from The Cancer Genome Atlas (TCGA) project. The correlation between Fringe family member expression and patient overall survival, copy number variation, methylation, Gene Ontology enrichment, and tumor-infiltrating lymphocytes (TILs) was investigated by using multiple databases, such as cBioPortal, Human Protein Atlas, GeneCards, STRING, MSigDB, TISIDB, and TIMER2. In vitro experiments and immunohistochemical assays were performed to validate our findings.ResultsHigh expression levels of LFNG, MFNG, RFNG were closely associated with poor overall survival in multiple cancers, particularly in pancreatic adenocarcinoma (PAAD), uveal melanoma (UVM), and brain lower-grade glioma (LGG). Copy number variation analysis revealed that diploid and gain mutations of LFNG was significantly increased in PAAD and stomach adenocarcinoma (STAD), and significantly associated with the methylation levels in promoter regions. Significant differential genes between high and low expression groups of these Fringe family members were found to be consistently enriched in immune response and T cell activation pathway, extracellular matrix adhesion pathway, RNA splicing and ion transport pathways. Correlation between the abundance of tumor-infiltrating lymphocytes (TILs) and LFNG, MFNG, and RFNG expression showed that high LFNG expression was associated with lower TIL levels, particularly in PAAD. In vitro experiment by using pancreatic cancer PANC1 cells showed that LFNG overexpression promoted cell proliferation and invasion. Immunohistochemical assay in 90 PAAD patients verified the expression level of LFNG and its relationship with the prognosis.ConclusionsOur study provides a relatively comprehensive understanding of the expression, mutation, copy number, promoter methylation level changes along with prognosis values of LFNG, MFNG, and RFNG in different tumors. High LFNG expression may serve as a poor prognosis molecular marker for PAAD.

Machine learning-based identification of glycosyltransferase-related mRNAs for improving outcomes and the anti-tumor therapeutic response of gliomas.

Background: Glycosyltransferase participates in glycosylation modification, and glycosyltransferase alterations are involved in carcinogenesis, progression, and immune evasion, leading to poor outcomes. However, in-depth studies on the influence of glycosyltransferase on clinical outcomes and treatments are lacking. Methods: The analysis of differentially expressed genes was performed using the Gene Expression Profiling Interactive Analysis 2 database. A total of 10 machine learning algorithms were introduced, namely, random survival forest, elastic network, least absolute shrinkage and selection operator, Ridge, stepwise Cox, CoxBoost, partial least squares regression for Cox, supervised principal components, generalized boosted regression modeling, and survival support vector machine. Gene Set Enrichment Analysis was performed to explore signaling pathways regulated by the signature. Cell-type identification by estimating relative subsets of RNA transcripts was used for estimating the fractions of immune cell types. Results: Here, we analyzed the genomic and expressive alterations in glycosyltransferase-related genes in gliomas. A combination of 80 machine learning algorithms was introduced to establish the glycosyltransferase-related mRNA signature (GRMS) based on 2,030 glioma samples from The Cancer Genome Atlas Program, Chinese Glioma Genome Atlas, Rembrandt, Gravendeel, and Kamoun cohorts. The GRMS was identified as an independent hazardous factor for overall survival and exhibited stable and robust performance. Notably, gliomas in the high-GRMS subgroup exhibited abundant tumor-infiltrating lymphocytes and tumor mutation burden values, increased expressive levels of hepatitis A virus cellular receptor 2 and CD274, and improved progression-free survival when subjected to anti-tumor immunotherapy. Conclusion: The GRMS may act as a powerful and promising biomarker for improving the clinical prognosis of glioma patients.

Significance of high expression of C5orf46 in gastric cancer and potential intervention of tarditional Chinese medicine based on bioinformatics, molecular docking, and cell experiments

This study aims to investigate the expression, prognosis, and clinical significance of C5orf46 in gastric cancer and to study the interaction between the active components of C5orf46 and tarditional Chinese medicine. The ggplot2 package was utilized for differential expression analysis of C5orf46 in gastric cancer tissues and normal tissues. The survival package was used for survival analysis, univariate regression analysis, and multivariate regression analysis. Nomogram analysis was used to assess the connection between C5orf46 expression in gastric cancer and overall survival. The abundance of tumor-infiltrating lymphocytes was calculated by GSVA package. Coremine database, Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) database, and PubChem database were used to search the potential components corresponding to C5orf46 gene and tarditional Chinese medicine. Molecular docking was performed to explore the binding affinity of potential components to C5orf46. Cell experiments were performed to explore the expression of C5orf46 gene in cells of the blank group, model group, and drug administration groups. As compared with normal tissues, C5orf46 expression was higher in gastric cancer tissues, which had more significant predictive effects in the early stages(T2, N0, and M0). The more advanced the tumor node metastasis(TNM) stage, the higher the C5orf46 expression and the lower the probability of survival of patients with gastric cancer. The expression of C5orf46 positively correlated with the helper T cells1 in gastric cancer and the macrophage infiltration level in gastric cancer, and negatively correlated with B cells, central memory T cells, helper T cells 17, and follicular helper T cells. Seven potential components of C5orf46 were obtained, and three active components were obtained after the screening, which matched five tarditional Chinese medicines, namely, Sojae Semen Nigrum, Jujubae Fructus, Trichosanthis Fructus, Silybi Fructus, and Bambusae Concretio Silicea. Molecular docking revealed that sialic acid and adeno-sine monophosphate(AMP) had a good binding ability to C5orf46. The results of real-time quantitative polymerase chain reaction(RT-qPCR) and Western blot showed that, as compared with the model group, the mRNA and protein expression levels of C5orf46 were significantly lower in the drug administration groups. The lowest expression level was found at the concentration of 40 μmol·L~(-1). The results of this study provide ideas for the clinical development of traditional Chinese medicine compounds for the treatment of gastric cancer as well as other cancers.

Characteristic differences in the abundance of tumor-infiltrating lymphocytes and intratumoral developing T cells in thymoma, with special reference to PD-1 expression.

Though programmed cell death-1 (PD-1) inhibitors mainly target tumor-infiltrating lymphocytes (TILs) expressing PD-1, developing T cells in thymus also express PD-1 in their process of maturation. To predict the therapeutic effect of PD-1 inhibitors for thymoma, it is necessary to clarify the proportions of TILs and intratumoral developing T cells. The expressions of CD4, CD8, and PD-1 on T cells were analyzed by flow cytometry in 31 thymomas. The amount of T cell receptor excision circles (TRECs), which can be detected in newly formed naïve T cells in the thymus, was evaluated using sorted lymphocytes from thymomas by quantitative PCR. The expressions of granzyme B (GZMB) and lymphocyte activation gene-3 (LAG-3) in PD-1 + CD8 T cells were analyzed by image cytometry using multiplex immunohistochemistry. The PD-1 + rate in both CD4 and CD8 T cells was significantly higher in type AB/B1/B2 than in type A/B3 thymomas. The amounts of TRECs in CD4 and CD8 T cells were significantly higher in type AB/B1/B2 than in type A/B3 thymomas and comparable to normal thymus. PD-1 expression at each stage of T cell development of type AB/B1/B2 thymomas was comparable to that of normal thymus. Both the percentages and cell densities of PD-1 + CD8 T cells expressing GZMB or LAG-3, which are known to contain tumor-reactive T cells, were significantly lower in type AB/B1/B2 thymomas. Most PD-1 + T cells in type AB/B1/B2 thymomas are intratumoral developing T cells and are not TILs.

Abstract 4647: Potential of TIMP3 regulating the versican status in the colorectal cancer tumor microenvironment

Abstract Background: In colorectal cancer (CRC), versican (VCAN) accumulation has been found to negatively correlate with CD8+ tumor infiltrating lymphocyte (TIL) abundance and its proteolysis into versikine (Vkine) positively correlates with TIL abundance. TIMP3 has demonstrated the ability to inhibit several ADAMTS proteases able to cleave VCAN to Vkine. Here we investigate the correlation of TIMP3 accumulation in CRCs with the VCAN status and CD8+ T cell infiltration. Methods: Matched primary and metastatic CRC samples from 156 patients who had resected oligometastatic CRC were stained for VCAN, Vkine, TIMP3, and CD8+ TILs. VCAN, Vkine, and TIMP3 were scored using an intensity binning system ranging from 0-3+ and T cells in the epithelium were reported per high power field (HPF). Tumors were designated as high (2 or 3+) or low (0 or 1) for both VCAN and Vkine and positive (+; 1-3) or negative (0) for TIMP3. Tumors designated VCAN low and Vkine high are considered VCAN proteolytic predominant (VPP) and all other combinations are considered VCAN proteolytic weak (VPW). Results: Across the whole dataset, 52% of cancers were VCAN high and 24% were VPP. TIMP3 was detected in 33% of cancers. The frequency of TIMP3 was similar between primary and metastatic tumors (39% and 29%, respectively). Of the VCAN high cancers, 42% were TIMP3+ whereas 61% of the TIMP3+ samples are VCAN high. Of the Vkine high cancers, 44% were TIMP3+ and 36% of VPP cancers were TIMP3+. The prevalence of the VPP phenotype was similar between the TIMP3+ and negative cancers. Additionally, among the TIMP3+ samples 68% were Vkine high versus 46% in TIMP3 negative cancers (p=0.001). VCAN proteolysis correlates with higher CD8+ TIL abundance, thus we assessed the number of CD8+ TILs in TIMP3+ and negative tumors. The TIMP3+ cancers had a median of 2 CD8+ TILs/HPF and the TIMP3 negative cancers has a median of 3 CD8+ TILs/HPF. For VPP cancers, those that were also TIMP3+ had a median of 3 CD8+ TILs/HPF compared to TIMP3 negative cancers which had a median of 6 CD8+ TILs/HPF (p=0.2). Conclusions: TIMP3 correlates with higher levels of VCAN accumulation but does not correlate with lower levels of proteolysis. Future studies are needed to better clarify the impact of TIMP3 and other mediators in regulating VCAN accumulation and proteolysis in the tumor microenvironment. Citation Format: Anna Field, Sean Kraus, Kristina Matkowskyj, Dustin Deming, Cheri A. Pasch, Wei Zhang. Potential of TIMP3 regulating the versican status in the colorectal cancer tumor microenvironment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4647.

Abstract 1991: Remodeling the microenvironment of osteosarcoma lung metastases with inhaled CSF-1Ri immunotherapy

Abstract Osteosarcoma (OS) metastasizes primarily and almost exclusively to the lungs. The survival rate decreases significantly for patients who develop OS lung metastasis (OSLM). Purpose: To assess the safety and efficacy of colony-stimulating factor-1 receptor inhibitor (CSF-1Ri) (Pexidartinib; PLX) in shifting the OSLM tumor microenvironment (TME) to an anti-tumorigenic state upon local delivery to lungs of a syngeneic mouse model of OSLM. Methods: The safety of PLX upon repeated pulmonary administration (9 doses, every other day at 2 mg/kg) in healthy BALB/c mice was assessed using health scoring, pulmonary mechanics, molecular and cellular composition of bronchoalveolar lavage fluid (BALF), blood count and plasma biochemistry, and H&amp;E of lungs and liver. To establish the OSLM model, murine OS cells, expressing bioluminescent and fluorescent genes (K7M2-Luc-tdT), were used. Mice bearing OSLM were randomized into two groups (vehicle and PLX) and treated over 3 weeks. Tumor burden was evaluated using bioluminescent imaging (BLI) and lung weight. The treatment impact on the abundance and phenotype of tumor-associated macrophages (TAMs) and their CSF-1R expression as well as on the abundance of tumor-infiltrating lymphocytes and their expression to PD-1 were investigated using immunofluorescence, flow cytometry, and western blot. Results: PLX is well tolerated upon local lung administration with all safety markers indicating no alteration compared to naïve and vehicle controls. Treatment did not affect health scores. We did not detect any functional or mechanical alteration on the lungs or systemically (including liver); no marked differences in pulmonary function parameters, proinflammatory cytokines, nor infiltrating differential cell count obtained from BALF were observed. Both total blood count and liver enzymes were within normal range. As a measure of efficacy, treatment with PLX via local lung administration reduced tumor burden, indicated by the in vivo BLI and lung weight. Notably, PLX significantly decreased the abundance of total TAMs, with a more pronounced effect on pro-tumorigenic alternatively-activated (M2-like) TAMs phenotype, thus leading to a 22-fold increase in M1/M2 ratio. PLX further led to a marked decrease in tumor-promoting T regulatory cells (Treg), increase in the CD8/Treg ratio, and decrease in PD-1+ percentage in CD8 T cells in the TME, indicating a shift to a more immunogenic tumor phenotype. Conclusions: We demonstrated that repeated doses of PLX is safe upon local delivery to the lungs of murine model of OSLM, with no alternations in lungs or liver tissue. We further showed that PLX reduces tumor burden, which correlates with a change in the immune phenotype of the OSLM toward a more anti-tumorigenic profile. These results are clinically relevant as PLX has been approved by the FDA, thus opening opportunities for its repurposing to support standard of care therapy in OSLM. Citation Format: Fatemah S. Sunbul, Sulaiman S. Alhudaithi, Rashed M. Almuqbil, Hanming Zhang, Raneem R. Aldaqqa, Shane Albin, Rebecca L. Heise, Valentina Robila, Matthew S. Halquist, Sarah W. Gordon, Paula D. Bos, Sandro R. da Rocha. Remodeling the microenvironment of osteosarcoma lung metastases with inhaled CSF-1Ri immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1991.

Abstract P2-20-12: Abundance of tumor-infiltrating lymphocytes is associated with pathologic complete response to neoadjuvant chemotherapy but not with survival in ER-positive/HER2-negative breast cancer

Abstract INTRODUCTION: Abundance of tumor infiltrating lymphocytes (TILs) is well known to be associated with achievement of pathologic complete response (pCR) after neoadjuvant chemotherapy and is a surrogate of better survival in triple negative breast cancer (TNBC). However, the association remains unclear in ER-positive/HER2-negative, which is the most common subtype in breast cancer. Further, pathological quantification of TILs is known for its ambiguity. We hypothesized that abundance of TILs, quantified by transcriptomic signatures, in ER-positive/HER2-negative is associated with different biology and is not a surrogate of survival unlike in TNBC. METHODS: A total of 6035 primary breast cancer patients from three cohorts (TCGA, METABRIC, and SCAN-B) with full transcriptome and clinical data were analyzed. Lymphocyte fractionation in the tumor microenvironment of a bulk tumor was estimated from the transcriptome using two different deconvolution tools, CIBERSORTx and xCell. RESULTS: First, the correlation between TIL score measured histologically on TCGA patients and gene expression of CD3D, CD3E, CD3G, CD8A, CD4, and total lymphocytes, and total T-cells measured by xCell or CIBERSORTx were analyzed. Total sum of lymphocytes by xCell correlated the strongest, thus it was adopted as the TIL score. The TIL score strongly correlated with CD3G, CD3E, CD3D, CD8A, and CD4 gene expressions in both TCGA and GSE96058 cohorts (all r &amp;gt; 0.48). Among the infiltrated cells; M1 and M2 macrophages, dendritic cells, mast cells and monocytes were all higher, and microvascular endothelial cells and pericytes were lower in TIL score high tumors in ER-positive/HER2-negative (all p &amp;lt; 0.01) where M2 and mast cells were not in HER2+ and TNBC in both 2 cohorts. Enrichment of immune related gene sets IL2/Stat5 signaling, IL6/Jak/Stat3 signaling, inflammatory response, and Complement were less in high TIL group of ER-positive/HER2-negativethan HER2 and TNBC. In agreement, cytolytic activity was lower in TIL high of ER-positive/HER2-negative compared from TNBC. On the other hand, high TIL group in ER-positive/HER2-negative had significantly higher intratumor heterogeneity, homologous recombination deficiency, mutation burden, and neoantigens, which were not the case in the other subtypes. In agreement, all the cell proliferation-related gene sets; E2F targets, G2M checkpoint, mitotic spindle, Myc targets v1 and v2, were more strongly enriched in high TIL group of ER-positive/HER2-negative compared from HER2+ and TNBC. MKI67 gene expression and Nottingham histological Grade were uniformly elevated with high TIL regardless of subtypes. In three independent neoadjuvant cohorts, we found that pathologic complete response rates of high TIL group. On the other hand, high TIL group did not show any survival benefit compared with low TIL group in ER-positive/HER2-negative, unlike in HER2+ or TNBC. CONCLUSION: High tumor-infiltrating lymphocytes in ER-positive/HER2-negative breast cancer was associated with less immune response and higher genetic alteration and cell proliferation compared to the other subtypes, leading to better response of neoadjuvant chemotherapy, but no benefit in survival outcome. Citation Format: Rongrong Wu, Masayuki Nagahashi, Masanori Oshi, Yasuo Miyoshi, Takashi Ishikawa, Kazuaki Takabe. Abundance of tumor-infiltrating lymphocytes is associated with pathologic complete response to neoadjuvant chemotherapy but not with survival in ER-positive/HER2-negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-20-12.

Triple-Negative Breast Cancer and Predictive Markers of Response to Neoadjuvant Chemotherapy: A Systematic Review.

Around 40-50% of all triple-negative breast cancer (TNBC) patients achieve a pathological complete response (pCR) after treatment with neoadjuvant chemotherapy (NAC). The identification of biomarkers predicting the response to NAC could be helpful for personalized treatment. This systematic review provides an overview of putative biomarkers at baseline that are predictive for a pCR following NAC. Embase, Medline and Web of Science were searched for articles published between January 2010 and August 2022. The articles had to meet the following criteria: patients with primary invasive TNBC without distant metastases and patients must have received NAC. In total, 2045 articles were screened by two reviewers resulting in the inclusion of 92 articles. Overall, the most frequently reported biomarkers associated with a pCR were a high expression of Ki-67, an expression of PD-L1 and the abundance of tumor-infiltrating lymphocytes, particularly CD8+ T cells, and corresponding immune gene signatures. In addition, our review reveals proteomic, genomic and transcriptomic markers that relate to cancer cells, the tumor microenvironment and the peripheral blood, which also affect chemo-sensitivity. We conclude that a prediction model based on a combination of tumor and immune markers is likely to better stratify TNBC patients with respect to NAC response.

Prognostic Significance of Tumor-Infiltrating Lymphocytes Determined Using LinkNet on Colorectal Cancer Pathology Images.

Tumor-infiltrating lymphocytes (TILs) have a significant prognostic value in cancers. However, very few automated, deep learning-based TIL scoring algorithms have been developed for colorectal cancer (CRC). We developed an automated, multiscale LinkNet workflow for quantifying TILs at the cellular level in CRC tumors using H&E-stained images from the Lizard data set with annotations of lymphocytes. The predictive performance of the automatic TIL scores () for disease progression and overall survival (OS) was evaluated using two international data sets, including 554 patients with CRC from The Cancer Genome Atlas (TCGA) and 1,130 patients with CRC from Molecular and Cellular Oncology (MCO). The LinkNet model provided outstanding precision (0.9508), recall (0.9185), and overall F1 score (0.9347). Clear continuous TIL-hazard relationships were observed between and the risk of disease progression or death in both TCGA and MCO cohorts. Both univariate and multivariate Cox regression analyses for the TCGA data demonstrated that patients with high TIL abundance had a significant (approximately 75%) reduction in risk for disease progression. In both the MCO and TCGA cohorts, the TIL-high group was significantly associated with improved OS in univariate analysis (30% and 54% reduction in risk, respectively). The favorable effects of high TIL levels were consistently observed in different subgroups (classified according to known risk factors). The proposed deep-learning workflow for automatic TIL quantification on the basis of LinkNet can be a useful tool for CRC. is likely an independent risk factor for disease progression and carries predictive information of disease progression beyond the current clinical risk factors and biomarkers. The prognostic significance of for OS is also evident.

Identification and experimental validation of a tumor-infiltrating lymphocytes-related long noncoding RNA signature for prognosis of clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is a common aggressive malignant tumor of the urinary system. Given the heterogeneity of the tumor microenvironment, immunotherapy may not fully exert its role in the treatment of advanced patients. Long noncoding RNA (lncRNA) has been reported to be critically associated with the differentiation and maturation of tumor-infiltrating lymphocytes (TILs), which work against tumor cells. In this study, we identified 10 TIL-related lncRNAs (AL590094.1, LINC02027, LINC00460, AC147651.1, AC026401.3, LINC00944, LINC01615, AP000439.2, AL162586.1, and AC084876.1) by Pearson correlation, univariate Cox regression, Lasso regression, and multivariate Cox regression based on The Cancer Genome Atlas (TCGA) database. A risk score model was established based on these lncRNAs. Next, a nomogram was constructed to predict the overall survival. By employing differentially expressed genes (DEGs) between groups with high and low risk scores, gene ontology (GO) enrichment analysis was performed to identify the major biological processes (BP) related to immune DEGs. We analyzed the mutation data of the groups and demonstrated that SETD2 and BAP1 had the highest mutation frequency in the high-risk group. The "CIBERSORT" R package was used to detect the abundance of TILs in the groups. The expression of lymphocyte markers was compared. We also determined the expression of two lncRNAs (AC084876.1 and AC026401.3) and their relationship with lymphocyte markers in the kidney tissue of ccRCC patients and showed that there was a positive correlation between AC084876.1 and FoxP3. Proliferation, migration, and invasion of AC084876.1-downregulated ccRCC cell lines were inhibited, and the expression of PD-L1 and TGF-β secretion decreased. To our knowledge, this is the first bioinformatics study to establish a prognostic model for ccRCC using TIL-related lncRNAs. These lncRNAs were associated with T-cell activities and may serve as biomarkers of disease prognosis.

TMPRSS4 is a novel biomarker and correlated with immune infiltration in thyroid carcinoma

Transmembrane protease serine 4 (TMPRSS4) is a cancer-associated protease associated with prognosis in various types of cancer. Mechanistically, TMPRSS4 mainly regulates malignant phenotypes, such as tumor invasion and metastasis, by either the epithelial to mesenchymal transition (EMT) program or promoting the proliferation of cancer cells. To date, TMPRSS4 and immune infiltration in thyroid carcinoma (TC) are largely unknown. Thus, this paper evaluated the expression of TMPRSS4 in tumor tissue through the Tumor Immune Estimation Resource (TIMER) database, and Oncomine, and its correlation with clinical parameters by UALCAN databases. Furthermore, we analyzed its prognostic value from Kaplan-Meier Plotter database, and the relationship between TMPRSS4 and the abundance of tumor-infiltrating lymphocytes (TILs) in TC in TISIDB, screening potential immune targets to explore novel mechanisms for the clinical management of TC. Finally, we assessed the correlation between TMPRSS4 and some immune markers to uncover a potential immune-related biomarker in TC patients by TIMER2.0. The results revealed that TMPRSS4 was highly expressed in TC and was also associated with lymphatic metastasis, advanced stage, histological subtype, and favorable clinical outcome. The stratified analysis based on immune cell content showed that decreased TMPRSS4 had worse prognosis in CD8+ T cell-enriched TC patients. TMPRSS4 was positively correlated with tumor immune infiltration and the expression of gene markers of immune cells. Notably, its expression was lower in the lymphocyte-depleted subtype than in other immunosubtypes in TC. Moreover, TMPRSS4 was closely related to chemokines as well as their receptors and the immunosuppressive checkpoints CTLA-4, PD-1, and HLA-G. In conclusion, TMPRSS4 may act as a novel biomarker predicting prognosis and immune infiltration in TC.

Establishment of a gastric cancer cell line with high microsatellite instability, OCUM-13, derived from Borrmann type-2 primary tumor.

Gastric cancer (GC) with microsatellite instability (MSI) has been reported to be sensitive to immunotherapy, however some of GC cases with MSI remain resistant to immunotherapy. Cancer cell lines showing MSI might be useful for the analysis of mechanisms of immunotherapy, while only a few GC cell lines with MSI are available so far. In this study, we established a unique GC cell line with MSI, OCUM-13, from a primary GC with abundant tumor-infiltrating lymphocytes. MSI assay indicated that OCUM-13 cells as well as the primary tumor showed a band shift in more than 3 of 5 microsatellite loci, suggesting that OCUM-13 did have high MSI. The subcutaneous inoculation of OCUM-13 cells into mice performed tumor formation. Insulin-like growth factor 1 receptor inhibitor decreased the growth of OCUM-13 cells. The newly established cell line with MSI, OCUM-13, might be useful for the analysis of cancer therapy for GC with MSI.

The Abundance of Tumor-Infiltrating CD8+ Tissue Resident Memory T Lymphocytes Correlates with Patient Survival in Glioblastoma.

Glial tumors alone account for 40% of all CNS tumors and present a low survival rate. The tumor microenvironment is a critical regulator of tumor progression and therapeutic effectiveness in glioma. Growing evidence from numerous studies of human solid tumor-infiltrating CD8+ T cells indicates that tissue-resident memory T cells (TRM) represent a substantial subpopulation of tumor-infiltrating lymphocytes (TILs). Although it is reported that some types of cancer patients with high immune infiltration tend to have better outcomes than patients with low immune infiltration, it seems this does not happen in gliomas. This study aimed to characterize TRMs cells in the glioma tumor microenvironment to identify their potential predictive and prognostic role and the possible therapeutic applications. Fluorescence activated cell sorting (FACS) analysis and immunofluorescence staining highlighted a statistically significant increase in CD8+ TRM cells (CD103+ and CD69+ CD8+ T cells) in gliomas compared to control samples (meningioma). In-silico analysis of a dataset of n = 153 stage IV glioma patients confirmed our data. Moreover, the gene expression analysis showed an increase in the expression of TRM-related genes in tumor tissues compared to normal tissues. This analysis also highlighted the positive correlation between genes associated with CD8+ TRM and TILs, indicating that CD8+ TRMs cells are present among the infiltrating T cells. Finally, high expression of Integrin subunit alpha E (ITGAE), the gene coding for the integrin CD103, and high CD8+ TILs abundance were associated with more prolonged survival, whereas high ITGAE expression but low CD8+ TILs abundance were associated with lower survival.