Tumor-inﬁltrating immature innate lymphoid cells in colorectal cancer are biased toward ILC1/tissue-resident NK cell differentiation

Sep 23, 2026

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Peritoneal metastases in colorectal cancer affect a substantial subset of patients and are associated with poor outcomes, yet the role of dysregulated innate lymphoid cells in CRC with peritoneal spread remains unclear. This study analyzes colorectal primary tumors and CRC-PM using single-cell RNA sequencing, flow cytometry, and differentiation assays. Tumors display depletion of ILC3 and enrichment for ILC1, tissue-resident NK cells, and conventional NK cells, with two immature ILC populations that differentiate toward an ILC1/trNK-like program.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages19

Reading Time48 min

AccessFree to download

Article overview

Patient cohort and sample analyses

Immune infiltration patterns across tissues

Immature ILC differentiation toward ILC1/trNK-like cells

Article [https://doi.org/10.1038/s41467-026-71085-9](https://doi.org/10.1038/s41467-026-71085-9) Tumor-inﬁltrating immature innate lymphoid cells in colorectal cancer are biased toward ILC1/tissue-resident NK cell differentiation Received: 18 June 2025 | Accepted: 3 March 2026 | | --- | | | | Check for updates | Anne Marchalot 1, Malin Ljunggren2, Christopher Stamper1, Whitney Weigel1, Christopher Andrew Tibbitt1, Isabel Meininger1, Ram Vinay Pandey1, Miriam Franklin 1, John Washington Bassett1, Lorenz Wirth1, Colorectal Study Group*, Ulrik Lindforss2, Gabriella Jansson-Palmer2, Caroline Nordenvall2,4 & Jenny Mjösberg 1,3,4 Peritoneal metastases (PM) occur in 10% of patients with colorectal cancer (CRC) and are linked to poor outcomes. Although dysregulated innate lymphoid cells (ILC) have been described in CRC, their function in CRC-PM remains unclear. Here, we analyze tumor samples from CRC and CRC-PM patients using single-cell RNA sequencing (11 patients), ﬂow cytometry (8 patients) and differentiation assays (24 patients). Healthy colon, primary CRC and CRC-PM tumors are inﬁltrated by heterogeneous populations of ILC3, ILC2, ILC1, tissue resident (tr)NK cells and conventional (c)NK cells. Compared to healthy colons, primary CRC and CRC-PM tumors are depleted of ILC3 but enriched for ILC1, trNK cells and cNK cells. CRC and CRC-PM tumors harbor two immature ILC populations, early NK and naïve (n)ILC, with nILCs being transcriptionally skewed toward ILC1 and trNK cells. Indeed, co-culture of isolated nILCs with OP9-DL1 cells induces intratumoral nILC differentiation into ILC1/trNK-like cells. These ﬁndings help understand the immune pathogenesis of CRC and CRC-PM and provide insights for future ILC1 and NK cellbased therapies. Colorectal cancer (CRC) is the second leading cause of cancer-related death globally1. Around 5% of CRC patients present with peritoneal metastasis (PM) at diagnosis2,3, and around 5% ofCRC patients develop PM later3,4. Patients with right-sided colon cancer, locally advanced CRC, especially those with obstructive or perforated tumors, or those undergoing emergency or non-radical resections, are at an even greater risk3. Historically, CRC-PM patients were treated palliatively, but now hyperthermic intraperitoneal chemotherapy (HIPEC) combined with cytoreductive surgery (CRS) offers a potential cure fora subgroup of patients5. However, HIPEC efﬁcacy is debated6 and up to 25% of patients experience serious postoperative complications, and the risk of recurrence is high7. Immune checkpoint blockade has shown encouraging results for patients with microsatellite instability high (MSI-high) metastatic CRC8, but only around 8% of patients with metastatic CRC have MSI-high tumors9. Hence, more research is needed on immunotherapies for patients with microsatellite stable (MSS) 1Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden. 2Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden. 3 Department of Medicine Huddinge, Clinical Lung-and Allergy Research Unit, Karolinska Institutet, Stockholm, Sweden. 4These authors contributed equally: Caroline Nordenvall, Jenny Mjösberg. *A list of authors and their afﬁliations appears at the end of the paper. [e-mail:](e-mail: jenny.mjosberg@ki.se)[ jenny.mjosberg@ki.se](e-mail: jenny.mjosberg@ki.se) Table1| Patient characteristics of samples used for single-cell RNA-sequencing | Characteristic | Subgroup | Primary colon tumors
N =6 (%) | Peritoneal
metastasis N =7 (%) | | --- | --- | --- | --- | | Biological sex | Female (%) | 2 (33) | 2 (29) | | | Male (%) | 4 (6%) | 5 (71) | | Age at surgery | Mean years (range) | 66 (34–90) | 59 (34–72) | | Tissues donateda | Normal colon (%) | 6 (100) | 2 (29) | | | Colorectal primary tumor (%) | 6 (100) | 2 (29) | | | Peritoneal metastasis (%) | 2 (33) | 7 (100) | | American so

FAQs

What clinical problem does the study address in colorectal cancer?

The study focuses on peritoneal metastases in colorectal cancer, which occur in a measurable fraction of patients and are linked to poor outcomes.

How were tumor and metastasis immune cells analyzed in the study?

Tumor samples from colorectal cancer and CRC-PM patients were analyzed using single-cell RNA sequencing, flow cytometry, and differentiation assays.

What immune cell changes distinguish primary CRC and CRC-PM from healthy colon?

Compared with healthy colon, primary CRC and CRC-PM show depletion of ILC3 and enrichment for ILC1, tissue-resident NK cells, and conventional NK cells.

Sep 23, 2026

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