Application of the AMOCATI R workflow to tumor transcriptomic data delineates the adverse effect of immune cell infiltration in immune-privileged organs

Regnier, P.; Cagnard, N.; Podsypanina, K.; Darrasse-Jeze, G.

doi:10.1101/2024.06.18.596859

Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.06.18.596859

Application of the AMOCATI R workflow to tumor transcriptomic data delineates the adverse effect of immune cell infiltration in immune-privileged organs

Regnier, P.·Cagnard, N.·Podsypanina, K.·Darrasse-Jeze, G.

View original source ↗Export metadata ↓

Abstract

Immune cells are present inside tumor tissue and can alter tumor growth. Expression profiles of human tumors hold transcripts from cancer cells and their microenvironment, including the infiltrating immune cells. Few standardized methods examine tumor immunobiology relying only on tumor transcriptome data. Using a new in-house developed R analysis workflow called AMOCATI, we classified 43 cancer types from 11,176 patients according to the degree of infiltration by 18 distinct immune cell subsets, measured by the abundance of their transcriptomic signature, and calculated its effect on the disease outcome. In about half of cancers affecting organs without immune privilege, immune cell infiltration has beneficial effects. In contrast, immune infiltration in cancers of immune-privileged organs (eye, testis and brain) confers poor prognosis. Moreover, transcriptional evidence of increased immune cell activity in immune-privileged cancer sites is associated with bad prognosis. Thus, our results suggest that the effect of immune infiltration may depend on the origin of the primary tumor. SIGNIFICANCEOur in-house developed computational R approach AMOCATI allows to easily download public transcriptomic and clinical data, classify and analyze them. AMOCATI permitted us to define gene expression signatures associated with short- or long-term survival from 11,176 untreated patient unsorted biopsies in 43 types of cancer. We present the level of infiltration of 18 types of immune cell subsets transcriptomic signatures and 50 immune-related pathways in all these cancers Correlation between immune infiltration of the tumor and survival establishes a link between tumor tissue of origin and the overall effect of immune infiltration on survival. Immune cell infiltration in tumors from immune privileged organs correlate with shorter survival. Contrary to what we observe in hot tumors, biological pathways of immune response are associated with a short-term survival profile in these cancers.

Explore related subjects

cancer biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Regnier, P., Cagnard, N., Podsypanina, K., Darrasse-Jeze, G.. 2024-06-21. Application of the AMOCATI R workflow to tumor transcriptomic data delineates the adverse effect of immune cell infiltration in immune-privileged organs. https://doi.org/10.1101/2024.06.18.596859

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Ex vivo human tumor slices more accurately predict patient responses to an oncolytic virus than in vivo mouse models

Immunotherapies, including oncolytic viruses (OV), are promising therapies that can enhance anti-tumor immune responses. However, preclinical success of immunotherapies in mouse models has not always translated to clinical benefit in cancer patients. This study compared preclinical efficacy and mechanism of action for ASP9801, a vaccinia virus expressing IL-7 and IL-12, using mouse models of colorectal cancer (CRC) in vivo and in human organotypic tumor slice models ex vivo. The murine surrogate for ASP9801 significantly reduced tumor volumes in treated and abscopal tumors in two different CRC models in vivo (MC38 and RO100). Treatment efficacy was accentuated when combined with anti-PD1 treatment, and single-cell RNA sequencing analysis revealed depletion of tumor cells and increased T cell infiltration and activation in both treated and abscopal tumors. However, human tissue analysis ex vivo (E-slices) using PDX models and patient samples showed that ASP9801 is not effective in CRC, consistent with clinical trial results. On the other hand, ASP9801 was highly effective in GBM, indicating indication-specific efficacy of ASP9801, and how E-slice assays can be used to identify treatment-sensitive indications. This study demonstrates the superiority of E-slices over mouse models for predicting clinical response and its utility in planning clinical trials.

cancer biology↗

bioRxiv2026

Immune-cell depleted diffuse large B-cell lymphomas have reduced expression of MHC class I

Immunotherapy has transformed treatment for many cancers. In the aggressive and genetically heterogeneous diffuse large B-cell lymphoma (DLBCL), CD19 CAR T-cell therapy is highly effective, whereas immune checkpoint blockade has shown limited benefit. Loss of MHC expression is a common mechanism to escape T-cell cytotoxicity, and loss of MHC class I (MHC-I) and II are frequent in DLBCL. We applied imaging mass cytometry to diagnostic biopsies from younger, high-risk DLBCL patients to map the tumor microenvironment (TME) spatial architecture in relation to tumor cell MHC expression, mutational status, transcriptomic and proteomic profiles. Neighborhood analyses identified four TME subtypes: immune-cell depleted and three immune-infiltrated types (mixed, CD4 T cell-rich, CD8 T-cell/macrophage-rich). Depleted cases had shorter overall survival (p = 0.033) and increased expression of proteins involved in DNA replication and proliferation markers compared to infiltrated cases. Tumor cell MHC-I expression was heterogeneous. Cases with low frequency of MHC-I-pos tumor cells were enriched for the depleted TME type. MHC-I-pos tumor cells were surrounded by CD4 and CD8 T cells and M1 macrophages, whereas MHC-I-neg tumor cells were closer to other MHC-I-neg tumor cells. These findings suggest that TME-based classification incorporating tumor cell MHC-I status may improve individualized immunotherapy selection.

cancer biology↗

bioRxiv2026

Cross-species analysis links cell-cell communication rewiring to NOTCH2 during serous endometrial carcinogenesis

Cell-cell interactions shape the fate of mutant cells during cancer initiation but how these interactions evolve during progression to pathologically recognizable lesions remain poorly understood. Here, we investigated cell-cell communication during serous endometrial carcinoma (SEC; also known as uterine serous carcinoma) development using a lineage-traceable mouse model and cross-species analyses of the mouse and human neoplastic endometrium. In mice, the early, pre-dysplastic stage was marked by a global decrease in inferred cell-cell interactions, followed by extensive communication network rewiring during neoplastic progression. Pathway-specific analysis revealed a similar pattern for NOTCH signaling, with NOTCH2 emerging as the dominant NOTCH receptor in Trp53/Rb1-mutant immature epithelial cells. Functionally, NOTCH2 promoted the outgrowth of more proliferative mutant organoids. Cross-species transcriptomic analysis identified conserved immature epithelial states in mouse and human neoplastic endometrial epithelium. In human tissues, NOTCH2 was overexpressed in serous endometrial intraepithelial carcinoma, a precursor of SEC, and in overt SEC. Furthermore, elevated NOTCH2 expression was associated with poor patient survival. These findings link cell-cell communication rewiring during experimental SEC development to conserved neoplastic epithelial states and identify NOTCH2 as an early marker and a potential target of disease interception.

cancer biology↗