Distinct Immune Features Research Articles

A causal relationship between distinct immune features and acute or chronic pancreatitis: results from a mendelian randomization analysis

ObjectivesThis study aimed to thoroughly examining the causal link between immune traits and four types of pancreatitis, using mendelian randomization. MethodsData on 731 immune traits were collected from the genome-wide association study (GWAS) database as exposure. Information regarding acute pancreatitis (AP), alcohol-induced acute pancreatitis (AAP), chronic pancreatitis (CP), and alcohol-induced chronic pancreatitis (ACP) were acquired from the FinnGen Consortium as outcomes. Mendelian randomization (MR) using inverse variance weighting (IVW) evaluated the links between immune traits and pancreatitis. We evaluated the robustness of the IVW results through sensitivity analyses and validated them using meta-analysis with AP and CP data from the UK Biobank in the GWAS catalog. ResultsA total of 36 immune traits showed significant associations with susceptibility of four types of pancreatitis, including AP (7 traits), AAP (8 traits), CP (14 traits), and ACP (7 traits). Twenty characteristics were found to be potential risk factors for pancreatitis, identified in B Cells (5 traits), conventional dendritic cells (cDCs, 2 traits), maturation stage of T cells (2 traits), monocytes (2 traits), myeloid cells (2 traits), T cells, B cells, natural killer cells (TBNK, 2 traits), and regulatory T cells (Treg cells, 5 traits). Multiple sensitivity analyses confirmed the validity of the findings. Meta-analysis confirmed a solid causal relationship between CX3CR1 on CD14− CD16−of monocyte panel and the susceptibility of CP. ConclusionsOur MR study identified immune traits causally linked to acute and chronic pancreatitis, offering new insights for early clinical intervention and immune cell-targeted therapies.

Angiogenesis related genes based prognostic model of glioma patients developed by multi-omics approach

IntroductionGlioma, particularly glioblastoma (GBM), is a highly malignant brain tumor with poor prognosis despite current therapeutic approaches. The tumor microenvironment (TME), plays a crucial role in glioma progression by promoting invasion and drug resistance. Angiogenesis, the formation of new blood vessels, is a tightly regulated process involving endothelial cell activation, proliferation, and migration. In cancer, angiogenesis becomes dysregulated, leading to excessive blood vessel formation.MethodsWe enrolled bulk data of TCGA-LGG/GBM, CGGA-693, and CGGA-325 cohorts, scRNA data of GSE162631, GSE84465, and GSE138794 cohorts. Identification of malignant cells was conducted by “copycat” R package. The “AUCell” R package scored the activity of target gene set of each single cell. Consensus clustering was applied using the “ConsensusClusterPlus” R package, while tumor-infiltrating immune cells were determined using “IOBR” R package. To construct a prognostic model, we used LASSO and multiCOX algorithms based on the expression levels of the 15 hub genes, the efficacy of which was verified by KM and ROC analysis.ResultsWe identified 4 different malignant cell subclusters in glioma and disclosed their distinct gene expression patterns and interactions within TME. We identified differentially expressed immune-related genes (DE-ARGs) in glioma and found 15 genes that were specifically expressed in the malignant glioma cell populations. Glioma cells with higher expression of these DE-ARGs were associated with gliogenesis, glial cell development, and vasculature development. We found that tumor-infiltrating monocytes were the main interacting cell type within glioma TME. Using the expression patterns of the 15 screened DE-ARGs, we categorized glioma samples into 2 molecular clusters with distinct immune features, suggesting a possible relationship between angiogenesis and immune activation and recruitment. We constructed a prognostic model based on the expression levels of the 15 DE-ARGs and evaluated its predictive ability for glioma patient outcomes, which displayed exceedingly high efficacy.ConclusionWe characterized different malignant cell subclusters in glioma and investigate their gene expression patterns and interactions within TME. We constructed a prognostic model based on the expression levels of the 15 DE-ARGs and evaluated its predictive ability for glioma patient outcomes, which displayed exceedingly high efficacy.

Integrative genomic and transcriptomic profiling of pulmonary sarcomatoid carcinoma identifies molecular subtypes associated with distinct immune features and clinical outcomes.

Pulmonary sarcomatoid carcinoma (PSC)is a rare and aggressive subtype of non-small cell lung cancer (NSCLC),characterized by the presence of epithelial and sarcoma-like components. The molecular and immune landscape of PSC has not been well defined. Multiomics profiling of 21 pairs of PSCs with matched normal lung tissues was performed through targeted high-depth DNA panel, whole-exome, and RNA sequencing. We describe molecular and immune features that define subgroups of PSC with disparate genomic and immunogenic features as well as distinct clinical outcomes. In total, 27 canonical cancer gene mutations were identified, with TP53 the most frequently mutated gene, followed by KRAS. Interestingly, most TP53 and KRAS mutations were earlier genomic events mapped to the trunks of the tumors, suggesting branching evolution in most PSC tumors. We identified two distinct molecular subtypes of PSC, driven primarily by immune infiltration and signaling. The Immune High (IM-H)subtype was associated with superior survival, highlighting the impact of immune infiltration on the biological and clinical features of localized PSCs. We provided detailed insight into the mutational landscape of PSCand identified two molecular subtypes associated with prognosis. IM-H tumors were associated with favorable recurrence-free survival and overall survival, highlighting the importance of tumor immune infiltration in the biological and clinical features of PSCs.

Abstract 1162: Tumor-immune microenvironment associated with obesity in triple-negative breast cancer in the Mayo Clinic cohort

Abstract Background: Previous studies demonstrated that obesity is associated with poor outcomes and significantly worse pathological complete response (pCR) in triple-negative breast cancer (TNBC) treated with conventional chemotherapy. Emerging studies described a phenomenon termed the obesity paradox, which referred to improved outcomes observed in obese patients treated with immune checkpoint inhibitors (ICIs). Our study aimed to determine distinct immune features in TNBC across body mass index (BMI). Methods: Characteristics and outcomes of TNBC patients treated with neoadjuvant pembrolizumab-based chemotherapy at Mayo Clinic were collected. Normal BMI was defined as 18-25 kg/m2, overweight 25-30, and obese BMI ≥ 30. NanoString CosMx, a spatial multi-omics single-cell imaging (SMI), was performed in 75 samples from the Mayo Clinic TNBC cohort (Leon-Ferre BCRT 2018). Differential expression as log 2-fold change (FC) was estimated from the linear mixed model with significance defined as two-sided p< 0.05. Results: Between 2021-2023, there were 108 TNBC patients treated with neoadjuvant pembrolizumab. 25.9% were obese, 32.4% were overweight, and 41.7% had normal BMI. In contrast to previous studies with conventional chemotherapy, obese patients numerically had a higher pCR rate of 71.4% with pembrolizumab-based chemotherapy compared to 55.6% in normal and 62.9% in overweight patients. However, this difference did not reach statistical significance (obese vs. normal weight, OR 2.26, 95%CI 0.89-6.06, p 0.094). We further evaluated spatially-resolved immune features associated with obesity using CosMx SMI in 75 samples from the MC TNBC cohort. Obese patients had significantly higher intratumoral B cells (log2FC 1.88, p 0.017), stromal B cells (log2FC 2.79, p 0.001), stromal plasmablasts (log2FC 1.94, p 0.047), and stromal macrophages (log2FC 1.80, p 0.017) compared to patients with normal BMI. Obese patients also had significantly lower intratumoral myeloid dendritic cells (mDC) (log2FC -1.27, p 0.037). Similar trends were observed after standardizing cell counts per 100 tumor or stromal cells, including higher intratumoral B cells (log2FC 3.00, p 0.001), intratumoral plasmablasts (log2FC 2.00, p 0.006), intratumoral natural killer (NK) cells (log2FC 1.66, p 0.044), and stromal B cells (log2FC 1.50, p 0.008). Differential gene analyses for intratumoral B cells revealed that genes (CD74, HLA-C, HLA-DRB1, HLA-DRA, HLA-DRB) associated with the positive regulation of type 2 immune or chemokine response were upregulated. Conclusions: Using in-depth analysis with spatially defined context, our study showed that obese TNBC patients had significantly higher B cell infiltration, which is associated with improved outcomes with ICIs. Future research on how obesity alters the immune microenvironment is needed to identify potential pathways to improve outcomes with ICIs in TNBC. Citation Format: Songhan Pang, Yi Liu, Yaohua Ma, Zhuo Li, Roberto A. Leon-Ferre, David Zahrieh, David W. Hillman, Judy C. Boughey, James N. Ingle, Krishna R. Kalari, Fergus J. Couch, Matthew P. Goetz, Keith L. Knutson, Saranya Chumsri, E. Aubrey Thompson. Tumor-immune microenvironment associated with obesity in triple-negative breast cancer in the Mayo Clinic cohort [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 1162.

1483-P: Distinct Immune Features in the Partial Remission Phase of Type 1 Diabetes Identified by Single-Cell RNA Sequencing and Functional Analysis

Type 1 diabetes (T1D) patients might experience a transient partial remission (PR) stage. However, the immunological mechanisms responsible for the PR stage still need to be elucidated. Here, we have applied single-cell RNA sequencing to delineate the immune underpinnings of peripheral immune cells among healthy individuals, new-onset T1D patients, and T1D patients in the PR phase. Combined with cohort validation and functional assays, the expansion of TIGIT+ CCR7− Tregs as well as the decrease of CD226+ CCR7− CD8+ T cells helps to maintain a window in which to transit the immune balance in the remission stage via the TGF-β signal. These findings, especially the identified cell subsets may provide novel mechanism for future therapeutic interventions. Disclosure X.Li: None. T.Zhong: None. X.Li: None. L.Kang: None. R.Tang: None.

Multi-modal molecular programs regulate melanoma cell state

Melanoma cells display distinct intrinsic phenotypic states. Here, we seek to characterize the molecular regulation of these states using multi-omic analyses of whole exome, transcriptome, microRNA, long non-coding RNA and DNA methylation data together with reverse-phase protein array data on a panel of 68 highly annotated early passage melanoma cell lines. We demonstrate that clearly defined cancer cell intrinsic transcriptomic programs are maintained in melanoma cells ex vivo and remain highly conserved within melanoma tumors, are associated with distinct immune features within tumors, and differentially correlate with checkpoint inhibitor and adoptive T cell therapy efficacy. Through integrative analyses we demonstrate highly complex multi-omic regulation of melanoma cell intrinsic programs that provide key insights into the molecular maintenance of phenotypic states. These findings have implications for cancer biology and the identification of new therapeutic strategies. Further, these deeply characterized cell lines will serve as an invaluable resource for future research in the field.

Immulectin-2 from the ghost moth, Thitarodes xiaojinensis (Lepidoptera: Hepialidae), modulates cellular and humoral responses against fungal infection

C type-lectins constitute a large family of pattern recognition receptors, playing important roles in insect immune defenses. Thitarodes xiaojinensis larvae showed distinct immune features after Ophiocordyceps sinensis, Cordyceps militaris, or Beauveria bassiana infection. Based on transcriptome and immunoblot analysis, we found that immulectin-2 (IML2) was induced after T. xiaojinensis larvae were infected by C. militaris or B. bassiana but maintained at a low level after larvae injected with O. sinensis or Ringer's buffer. Recombinant IML2 (rIML2) could promote melanization, encapsulation, phagocytosis, and hemocyte aggregation in vitro. RNA interference with IML2 induced a significant reduction in the transcript levels of various antimicrobial peptides. Importantly, we found that the abundance of O. sinensis blastospores coated with rIML2 dramatically decreased in the host hemolymph. Overall, this study demonstrated that T. xiaojinensis IML2 modulates cellular and humoral responses to entomopathogenic fungi, broadening our view of the immune interaction between O. sinensis and its host.

Data-Driven Kidney Transplant Phenotyping as a Histology-Independent Framework for Biomarker Discovery.

In transplant medicine, clinical decision making largely relies on histology of biopsy specimens. However, histology suffers from low specificity, sensitivity, and reproducibility, leading to suboptimal stratification of patients. We developed a histology-independent immune framework of kidney graft homeostasis and rejection. We applied tailored RNA deconvolution for leukocyte enumeration and coregulated gene network analysis to published bulk human kidney transplant RNA transcriptomes as input for unsupervised, high-dimensional phenotype clustering. We used framework-based graft survival analysis to identify a biomarker that was subsequently characterized in independent transplant biopsy specimens. We found seven immune phenotypes that confirm known rejection types and uncovered novel signatures. The molecular phenotypes allow for improved graft survival analysis compared with histology, and identify a high-risk group in nonrejecting transplants. Two fibrosis-related phenotypes with distinct immune features emerged with reduced graft survival. We identified lysyl oxidase-like 2 (LOXL2)-expressing peritubular CD68+ macrophages as a framework-derived biomarker of impaired allograft function. These cells precede graft fibrosis, as demonstrated in longitudinal biopsy specimens, and may be clinically useful as a biomarker for early fibrogenesis. This study provides a comprehensive, data-driven atlas of human kidney transplant phenotypes and demonstrates its utility to identify novel clinical biomarkers.

Immune subtyping for pancreatic cancer with implication in clinical outcomes and improving immunotherapy

BackgroundEmerging evidence has shown that intra-tumor immune features are associated with response to immune checkpoint blockade (ICB) therapy. Accordingly, patient stratification is needed for identifying target patients and designing strategies to improve the efficacy of ICB therapy. We aimed to depict the specific immune features of patients with pancreatic cancer and explore the implication of immune diversity in prognostic prediction and individualized immunotherapy.MethodsFrom transcriptional profiles of 383 tumor samples in TCGA, ICGC, and GEO database, robust immune subtypes which had different response immunotherapy, including ICB therapy, were identified by consensus clustering with five gene modules. DEGs analysis and tumor microarray were used to screen and demonstrate potential targets for improving ICB therapy.ResultsThree subtypes of pancreatic cancer, namely cluster 1–3 (C1–C3), characterized with distinct immune features and prognosis, were generated. Of that, subtype C1 was an immune-cold type in lack of immune regulators, subtype C2, with an immunosuppression-dominated phenotype characterized by robust TGFβ signaling and stromal reaction, showed the worst prognosis, subtype C3 was an immune-hot type, with massive immune cell infiltration and in abundance of immune regulators. The disparity of immune features uncovered the discrepant applicability of anti-PD-1/PD-L1 therapy and potential sensitivity to other alternative immunotherapy for each subtype. Patients in C3 were more suitable for anti-PD-1/PD-L1 therapy, while patients in the other two clusters may need combined strategies targeted on other immune checkpoints or oncogenic pathways. A promising target for improving anti-PD-1/PD-L1 treatment, TGM2, was screened out and its role in the regulation of PD-L1 was investigated for the first time.ConclusionCollectively, immune features of pancreatic cancer contribute to distinct immunosuppressive mechanisms that are responsible for individualized immunotherapy. Despite pancreatic cancer being considered as a poor immunogenic cancer type, the derived immune subtypes may have implications in tailored designing of immunotherapy for the patients. TGM2 has potential synergistic roles with ICB therapy.

Immune microenvironment features and efficacy of PD-1/PD-L1 blockade in non-small cell lung cancer patients with EGFR or HER2 exon 20 insertions.

BackgroundInsertions in exon 20 (Ex20ins) of epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) are relatively insensitive to first‐ and second‐generation EGFR‐tyrosine kinase inhibitors (TKIs) in non‐small cell lung cancer (NSCLC). This study aimed to investigate the immune microenvironment features and efficacy of PD‐1/PD‐L1 blockade of NSCLC with EGFR and HER2 Ex20ins.MethodsClinical characteristics, coexisting mutations, and outcomes to EGFR‐TKIs and immune checkpoint blockade were reviewed for NSCLC patients with exon 20 mutations of EGFR or HER2. Data obtained included the molecular spectrum (extended genotyping for mutations in 324 cancer‐related genes), as well as tumor mutational burden (TMB), PD‐L1 protein expression, and the abundance of CD4+ and CD8+ tumor‐infiltrating lymphocytes (TILs).ResultsA total of 1270 NSCLC patients were identified. Of these, 504 (39.7%) cases had EGFR mutations and 6.9% (35/504) of them had EGFR Ex20ins. Meanwhile, 21 (1.7%) cases with HER2 Ex20ins were detected. Comprehensive genomic profiling identified A767_V769dup variant (25.0%) was the most common type in tumors with EGFR Ex20ins. Co‐occurring mutations were not uncommon including TP53 (45%), PIK3CA (20%), CDKN2A (10%), and EGFR amplification (20%). The average TMB was 3.3 mutations/megabase. PD‐L1 expression in patients with EGFR Ex20ins was significantly higher than for those with HER2 mutations (48.6% vs. 19.0%, P = 0.027). High TMB and PD‐L1 expression was independently associated with significantly poor prognosis (P = 0.025, P = 0.045, respectively) while there was no association between CD4+/CD8+ TILs and prognosis in EGFR or HER2 mutant NSCLC. Finally, patients harboring EGFR Ex20ins seemed to be sensitive to PD‐1/PD‐L1 blockage whereas it showed limited efficacy in patients with HER2 Ex20ins.ConclusionsNSCLC patients with EGFR/HER2 Ex20ins had similar genomic characteristics and distinct immune features. Patients with EGFR Ex20ins had significantly higher PD‐L1 expression than those with HER2 mutations, which may be the potential reason for the different responses to PD‐1/PD‐L1 blockage.

Abstract 2675: Single-CellRNA-Seq reveals the transcriptional landscape of the immune microenvironment in chemical induced liver cancer

Abstract The immune cell types as well as their numbers and activities in the tumor microenvironment (TME) may contribute to tumor progression, metastasis, prognosis and clinical response to cancer immunotherapies. Hepatocellular Carcinoma (HCC) is a type of highly heterogeneous solid tumor, causing high morbidity and mortality in the world, especially in China, however, the immune microenvironment of HCC has not been well-defined so far. In the present work, we first employed single-cell RNA sequencing on diethylnitrosamine (DEN)-induced mouse HCC model to depict the changing landscape of the immune cell composition, lineages and functional activities in TME during tumorigenesis, showing the distinct immune features in precancerous and cancerous lesions. The data indicated that the tumor-associated immune changes appeared early in pathological progression and the specific subsets of T and B cells were preferentially enriched in TME of HCC. We identified the signature genes for these specific cell subsets, and then mapped them onto the HCC RNA-seq dataset of human The Cancer Genome Atlas (TCGA) database. We found a cluster of naïve B cells characterized by high expression of CD38 was associated with better prognosis of human HCC. In addition, the inter-cellular interaction map was established based on the receptor-ligand bonding at single cell resolution. Taken together, this study will be helpful to the comprehensive understanding of dynamic immune microenvironment and cellular networks, especial naïve B cells, during HCC pathogenesis, which could provide a novel insight into the therapeutics for the HCC. Citation Format: Jian He. Single-CellRNA-Seq reveals the transcriptional landscape of the immune microenvironment in chemical induced liver cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2675.

Immune microenvironment features and efficacy of PD-1/PD-L1 blockade in non-small cell lung cancer (NSCLC) patients with EGFR or HER2 exon 20 insertions.

e21540 Background: This study aimed to investigate the immune microenvironment features and efficacy of PD-1/PD-L1 blockade of NSCLC with insertions in exon 20 (Ex20ins) of EGFR or HER2. Methods: Molecular spectrum, tumor mutational burden (TMB), PD-L1 protein expression, and the abundance of CD4+ and CD8+ tumor-infiltrating lymphocytes (TILs) were reviewed for NSCLC patients with Ex20ins of EGFR or HER2. Results: Thirty-five patients carrying EGFR Ex20ins and 21 patients harboring HER2 Ex20ins were retrospectively enrolled between April 2016 and September 2018. The average TMB was 3.3 mutations/megabase. PD-L1 expression in patients with EGFR Ex20ins was significantly higher than those with HER2 mutations (48.6% vs. 19.0%, P=0.027). High TMB and PD-L1 expression was independently associated with considerably poor prognosis (P=0.025, P=0.045; respectively). Finally, patients harboring EGFR Ex20ins seemed to be sensitive to PD-1/PD-L1 blockage whereas it showed limited efficacy in patients with HER2 Ex20ins. Conclusions: NSCLC patients with EGFR/ HER2 Ex20ins had distinct immune features. Patients with EGFR Ex20ins had significantly higher PD-L1 expression than those with HER2 mutations, which may be the underlying reason for the different responses to PD-1/PD-L1 blockage.

Immune Function and Micronutrient Requirements Change over the Life Course.

As humans age, the risk and severity of infections vary in line with immune competence according to how the immune system develops, matures, and declines. Several factors influence the immune system and its competence, including nutrition. A bidirectional relationship among nutrition, infection and immunity exists: changes in one component affect the others. For example, distinct immune features present during each life stage may affect the type, prevalence, and severity of infections, while poor nutrition can compromise immune function and increase infection risk. Various micronutrients are essential for immunocompetence, particularly vitamins A, C, D, E, B2, B6, and B12, folic acid, iron, selenium, and zinc. Micronutrient deficiencies are a recognized global public health issue, and poor nutritional status predisposes to certain infections. Immune function may be improved by restoring deficient micronutrients to recommended levels, thereby increasing resistance to infection and supporting faster recovery when infected. Diet alone may be insufficient and tailored micronutrient supplementation based on specific age-related needs necessary. This review looks at immune considerations specific to each life stage, the consequent risk of infection, micronutrient requirements and deficiencies exhibited over the life course, and the available evidence regarding the effects of micronutrient supplementation on immune function and infection.