830 Artificial intelligence-powered spatial analysis of tumor-infiltrating lymphocytes reveals immune-excluded phenotype related to APOBEC signature and clonal evolution of cancer

BackgroundLittle is known about bridging clonal heterogeneity into the resistance of immune checkpoint inhibitors (ICI). Recent reports showed that excluded tumor-infiltrating lymphocytes (TIL) into stroma assessed by an artificial intelligence (AI)-powered spatial TIL analyzer, Lunit SCOPE IO, was related to loss-of-heterozygosity of HLA genes which would be one of crucial resistance pathways of ICI.1 In the current study, we hypothesized that Immune-excluded phenotype called by Lunit SCOPE IO would be related to clonal heterogeneity resulted from genome-wide accidents during early carcinogenesis which may cause an improper targeting of TIL for diverse clones with multiple genomic aberrations.MethodsFor spatial TIL analysis, we applied Lunit SCOPE IO1 which automatically detects TIL and segmentizes cancer area and stroma, then it classified Immune phenotype of 1 mm2-sized grid in H&E image. Inflamed score or Immune-excluded score were defined as the proportion of Inflamed phenotype, which is high intra-tumoral TIL density, or Immune-excluded phenotype, which is exclusively high TIL density only in stroma, within a whole-slide image, respectively. We evaluated the correlation of Immune phenotype with APOBEC mutational signature by single-base substitution (SBS) signature 2 and/or SBS13,2 whole-genome doubling, and subclonal genome fraction which reflects intra-tumoral heterogeneity,3 and clusters of T cell receptor (TCR) repertoire 4 derived from previous reports of The Cancer Genome Atlas (TCGA), consists of 7,467 tumor samples from 22 cancer types.Abstract 830 Table 1Correlation between immune phenotype and clonal evolution of cancer [* Median (95% confidence interval)]ResultsIn the TCGA pan-carcinoma database, APOBEC mutational signature was significantly correlated with increased ratio of cancer stroma to cancer epithelium (median 0.866 vs 1.19, fold change +37.4%), and increased TIL density in cancer stroma (median 558 vs 764 / mm2, fold change +36.9%), but it was not correlated with intra-tumoral TIL density (median 63 vs 59 / mm2, fold change -6.3%). Interestingly, Immune-excluded score (IES) called by Lunit SCOPE IO was positively correlated with APOBEC mutational signature as well as expression levels of APOBEC1, APOBEC3A, and APOBEC3B, whole-genome doubling, and subclonal genome fraction, respectively, while Inflamed score (IS) or immune cytolytic activity (GZMA and PRF1 expressions) was negatively or not significantly correlated to those variables (table 1). TCR repertoire was expanded in the tumor samples with high IS (spearman rho = 0.279), but it was not increased in those with high IES (spearman rho = -0.0595).ConclusionsThere is a significant correlation between distinct TIL deposition in stroma, or Immune-excluded phenotype, with APOBEC-attributed clonal expansion of cancer, without proper expansion of TCR repertoire.ReferencesOck CY, Park C, Paeng K, Yoo D, Kim S, Park S, Lee SH, Mok T, Bang YJ. Artificial intelligence-powered spatial analysis of tumor-infiltrating lymphocytes reveals distinct genomic profile of immune excluded phenotype in pan-carcinoma. Cancer Res 2021;81(Supp 13):1908.Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V, PCAWG Mutational Signatures Working Group, Getz G, Rozen SG, Stratton MR, PCAWG Consortium. The repertoire of mutational signatures in human cancer. Nature 2020;578(7793):94–101.Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cancer Genome Atlas Research Network, Cherniack AD, Beroukhim R, Meyerson M. Genomic and functional approaches to understanding cancer aneuploidy. Cancer Cell 2018;33(4):676–689.e3.Zhang H, Liu L, Zhang J, Chen J, Ye J, Shukla S, Qiao J, Zhan X, Chen H, Wu CJ, Fu YX, Li B. Investigation of antigen-specific T-Cell receptor clusters in human cancers. Clin Cancer Res 2020;26(6):1359–1371.

823 Spatial analysis of tumor-infiltrating lymphocytes correlates with the response of metastatic colorectal cancer patients treated with vactosertib in combination with pembrolizumab

BackgroundPreviously, we presented a promising anti-tumor efficacy (ORR: 16%, mOS: 15.8 months, RECIST) of the combination of vactosertib, a potent and selective TGF-β receptor I, and pembrolizumab (vac+pem) in patients with microsatellite stable metastatic colorectal cancer (MSS mCRC, MP-VAC-204 study). Recent reports showed immune-excluded TIL located in stroma would be closely related to TGF-β signature, which may harbor the primary resistance of pembrolizumab. In this study, we performed an exploratory biomarker analysis of TIL resided in either intra-tumoral or stromal area in pathology slides, and we hypothesized that spatial features of TIL would correlate with the response of vac+pem.MethodsPathology slides stained with H&E were obtained from 31 patients at baseline and 14 patients at cycle 2 in MSS mCRC patients in MP-VAC-204 study. For spatial TIL analysis, we applied an artificial intelligence -powered H&E analyzer, named Lunit SCOPE IO, which automatically detects TIL, tumor and stroma. It calculates the proportion of immune phenotype consists of inflamed, as high TIL density inside tumor area, or immune-excluded, as high TIL density in stroma in whole-slide images. Additionally, PD-L1 and CD8 were stained using multiplex immunohistochemistry to validate immune phenotype assessed by Lunit SCOPE IO.ResultsAt baseline, the proportion of immune-excluded area (immune-excluded score, IES) was positively correlated with the density of CD8-positive cells in stroma area measured by mIHC (coefficient = 0.349), but it was not related to the density of PD-L1-positive cells (coefficient = -0.226). Area under receiver operating characteristics to predict the responder as partial response by RECIST v1.1 by IES and PD-L1 were 0.741 and 0.528. The overall response rate of vac+pem in the patients with high IES > 42.3% was 25% (4 out of 16), while no response was observed in those with low IES (0 out of 15). Overall survival (OS) of vac+pem was significantly prolonged in those with high IES > 42.3% compared to low IES (median OS: not reached versus 6.8 months, P = 0.0097), but it was not different according to PD-L1 level. After treatment of vac+pem, while IES was decreased regardless of treatment response, the proportion of inflamed area was increased in the responders (N=3) but decreased in the non-responders (N=11).ConclusionsImmune-excluded score which reflects TGF-β-driven TIL exclusion into stroma is correlated with anti-tumor response of vac+pem in MSS mCRC. Further investigation on spatial TIL analysis as a potential biomarker should be warranted. (Clinical trial information: NCT03724851)

Profound systemic alteration of the immune phenotype and an immunoglobulin switch in Erdheim–Chester disease in a single-center of 78 patients

Erdheim–Chester disease (ECD) is a rare, systemic, non-Langerhans cell histiocytosis neoplasm, which is characterized by the infiltration of CD63+ CD1a- histiocytes in multiple tissues. The BRAFV600E mutation is frequently present in individuals with ECD and has been detected in hematopoietic stem cells and immune cells from the myeloid and systemic compartments. Immune cells and proinflammatory cytokines are present in lesions, suggesting ECD involves immune cell recruitment. Although a systemic cytokine Th-1-oriented signature has been reported in ECD, the immune cell network orchestrating the immune response in ECD has yet to be described. To address this question, the phenotypes of circulating leukocytes were investigated in a large, single-center cohort of 78 patients with ECD and compared with a group of 21 control individuals. Major perturbations in the abundance of systemic immune cells were detected in patients with ECD, with a decrease in circulating plasmacytoid, myeloid 1, and myeloid 2 dendritic cells, mostly in BRAFV600E carriers, in comparison with individuals in the control group. Similarly, a marked decrease in blood T-helper, cytotoxic, and B lymphocyte numbers was observed in patients with ECD, relative to the control group. Measurement of circulating immunoglobulin concentrations revealed an immunoglobulin G switch, from IgG1 to IgG4 subclasses, which are more frequently associated with the BRAF mutation. First-line therapies, including pegylated IFNlland vemurafenib, were able to correct most of these alterations. This study reports a profound disturbance in the systemic immune phenotype in patients with ECD, providing important new information and helping to understand the physiopathological mechanisms involved in this rare disease and in the therapeutic management of patients.

Asymptomatic COVID-19 Individuals Tend to Establish Relatively Balanced Innate and Adaptive Immune Responses

The sharp increase in the proportion of asymptomatic cases and the potential risk of virus transmission have greatly increased the difficulty of controlling the COVID-19 pandemic. The individual immune response is closely associated with clinical outcomes and pathogenic mechanisms of COVID-19. However, the clinical characteristics and immunophenotyping features of immune cells of asymptomatic individuals remain somewhat mysterious. To better understand and predict the disease state and progress, we performed a comprehensive analysis of clinical data, laboratory indexes and immunophenotyping features in 41 patients with SARS-CoV-2 (including 24 asymptomatic cases and 17 symptomatic individuals). Firstly, from the perspective of demographic characteristics, the rate of asymptomatic infection was significantly higher in those with younger age. Secondly, the laboratory test results showed that some indexes, such as CRP (acute phase reaction protein), D-Dimer and fibrinogen (the marker for coagulation) were lower in the asymptomatic group. Finally, symptomatic individuals were prone to establishing a non-protective immune phenotype by abnormally decreasing the lymphocyte count and percentage, abnormally increasing the Th17 percentage and decreasing Treg percentage, which therefore cause an increase in the neutrophil/lymphocyte ratio (NLR), monocytes/lymphocytes ratio (MLR) and Th17/Treg ratio. On the other hand, asymptomatic individuals tended to establish a more effective and protective immune phenotype by maintaining a normal level of lymphocyte count and percentage and a high level of NK cells. At the same time, asymptomatic individuals can establish a relatively balanced immune response through maintaining a low level of monocytes, a relatively low level of Th17 and high level of Treg, which therefore lead to a decrease in MNKR and Th17/Treg ratio and finally the avoidance of excessive inflammatory responses. This may be one of the reasons for their asymptomatic states. This study is helpful to reveal the immunological characteristics of asymptomatic individuals, understand immune pathogenesis of COVID-19 and predict clinical outcomes more precisely. However, owing to small sample sizes, a future study with larger sample size is still warranted.

Optimization of Blood Handling and Peripheral Blood Mononuclear Cell Cryopreservation of Low Cell Number Samples

Background: Rural/remote blood collection can cause delays in processing, reducing PBMC number, viability, cell composition and function. To mitigate these impacts, blood was stored at 4 °C prior to processing. Viable cell number, viability, immune phenotype, and Interferon-γ (IFN-γ) release were measured. Furthermore, the lowest protective volume of cryopreservation media and cell concentration was investigated. Methods: Blood from 10 individuals was stored for up to 10 days. Flow cytometry and IFN-γ ELISPOT were used to measure immune phenotype and function on thawed PBMC. Additionally, PBMC were cryopreserved in volumes ranging from 500 µL to 25 µL and concentration from 10 × 106 cells/mL to 1.67 × 106 cells/mL. Results: PBMC viability and viable cell number significantly reduced over time compared with samples processed immediately, except when stored for 24 h at RT. Monocytes and NK cells significantly reduced over time regardless of storage temperature. Samples with >24 h of RT storage had an increased proportion in Low-Density Neutrophils and T cells compared with samples stored at 4 °C. IFN-γ release was reduced after 24 h of storage, however not in samples stored at 4 °C for >24 h. The lowest protective volume identified was 150 µL with the lowest density of 6.67 × 106 cells/mL. Conclusion: A sample delay of 24 h at RT does not impact the viability and total viable cell numbers. When long-term delays exist (>4 d) total viable cell number and cell viability losses are reduced in samples stored at 4 °C. Immune phenotype and function are slightly altered after 24 h of storage, further impacts of storage are reduced in samples stored at 4 °C.