Fergus Keane

Pancreatic cancer (PC) is broadly resistant to immune checkpoint blockade, although a subset of homologous recombination-deficient (HRD) tumors exhibits durable immune engagement. The genomic features that distinguish these immune-responsive tumors from immune-inert HRD tumors remain poorly understood. Here we identify a microhomology-mediated end joining (MMEJ) repair scar, the MMEJ Deletion Footprint (MDF), as a genomic readout of POLQ-associated error-prone repair that enriches for frameshift indels. Across the multi-omic discovery cohort integrating tumor genomics, single-nucleus transcriptomics and spatial immune profiling, MDF-high HRD PC exhibited increased frameshift-indel-derived neoantigens and interferon programs. MDF was further associated with remodeling of the myeloid compartment toward MHC II-high dendritic cell-like antigen-presenting macrophage states and the immune synapse architecture marked by increased spatial interaction between APC-like macrophages and cytotoxic CD8 ⁺ T cells. These tissue-level features aligned with a functional trajectory shift of CD8 ⁺ T cells, consistent with effective anti-tumor immunity and was associated with favorable clinical outcomes of patients. Together, our findings position MMEJ-linked repair scarring as actionable biology that connects an HRD genotype to immune organization and suggests rational immunotherapy combinations that may enhance antigen presentation and myeloid activation to extend durable benefit in HRD-lineage cancers.

Purpose:Microsatellite stable (MSS) colorectal cancers, in contrast to microsatellite instability–high colorectal cancers, have few mutations and are insensitive to immune checkpoint blockade (ICB). Colorectal cancers treated with targeted agents often acquire a high number of genomic alterations at progression. We asked whether targeted therapy could be used to generate a high tumor mutational burden (TMB) in MSS colorectal cancer and sensitize these tumors to ICB.Experimental Design:In patients with MSS metastatic colorectal cancer treated with targeted therapy, we evaluated baseline and progression TMB and response to ICB for patients whose tumors developed high TMB. We determined types of alterations, mutational signatures, neoantigenicity, and clonality associated with emergent genomic alterations in cases of acquired high TMB.Results:Among 26 cases, nine acquired high TMB at progression. Three of these patients received ICB but none had a response. In the TMB-high cases, we found no induction of tumor-infiltrating lymphocytes or PD-L1 expression. Acquired genomic alterations consisted predominantly of single-nucleotide variants, were enriched for single base substitution 17a/b mutational signature, and did not enhance predicted MHC class I binding. TMB was higher in plasma, driven by highly subclonal acquired alterations, compared with tissue samples, which harbored few resistance alterations.Conclusions:A substantial number of MSS colorectal cancers acquire high TMB following targeted therapy. However, this change is not associated with sensitization to ICB. The high TMB is due to subclonal alterations unique to individual disease sites that are inadequate to elicit a robust antitumor immune response.See related commentary by Parseghian and Eluri, p. 999

Mutational analyses of cases with and without acquired high TMB

Genomic alterations detected in plasma cfDNA and tumor tissue

Quantitation of tumor-infiltrating lymphocytes

Comparisons of genomic characteristics in patient tumors that acquired versus did not acquire high TMB after targeted therapy

Distribution of single-cell KRAS G12C VAF in clinical samples

Disease characteristics and treatment details

PURPOSE: The incidence of early-onset colorectal cancer (EOCRC; CRC diagnosed before age 50 years) is increasing globally. This study analyses the trend in the Republic of Ireland over a 28-year period. METHODS: Epidemiologic data on CRC incidence were obtained from the National Cancer Registry of Ireland (NCRI) from January 1994 until December 2021. Additional information on age of diagnosis and tumor sidedness for the entire period was obtained, while data relating to stage and sex were available for the study period 1999-2018. Incidence rates were stratified by sex, age group (20-34, 35-49, and ≥ 50 years), and tumor location. RESULTS: Between 1994 and 2021, there were 61,180 cases of CRC among adults older than 20 years in the Republic of Ireland. The age-specific rate (ASPR) annual percentage change (APC) in patients younger than 50 years was 0.97 (95% CI, 0.30 to 1.76) in females and 0.57 (95% CI, 0.08 to 1.30) in males, while in patients age 50 years or older, it was –0.60 (95% CI, –1.03 to –0.15) in females and –0.70 in males (95% CI, –1.18 to –0.16), respectively. CONCLUSION: In line with global trends, the incidence of EOCRC is increasing in Ireland. Further studies investigating the etiology and optimal treatment strategies for this cohort are necessary.

Purpose: Microsatellite stable (MSS) colorectal cancers, in contrast to microsatellite instability–high colorectal cancers, have few mutations and are insensitive to immune checkpoint blockade (ICB). Colorectal cancers treated with targeted agents often acquire a high number of genomic alterations at progression. We asked whether targeted therapy could be used to generate a high tumor mutational burden (TMB) in MSS colorectal cancer and sensitize these tumors to ICB. Experimental Design: In patients with MSS metastatic colorectal cancer treated with targeted therapy, we evaluated baseline and progression TMB and response to ICB for patients whose tumors developed high TMB. We determined types of alterations, mutational signatures, neoantigenicity, and clonality associated with emergent genomic alterations in cases of acquired high TMB. Results: Among 26 cases, nine acquired high TMB at progression. Three of these patients received ICB but none had a response. In the TMB-high cases, we found no induction of tumor-infiltrating lymphocytes or PD-L1 expression. Acquired genomic alterations consisted predominantly of single-nucleotide variants, were enriched for single base substitution 17a/b mutational signature, and did not enhance predicted MHC class I binding. TMB was higher in plasma, driven by highly subclonal acquired alterations, compared with tissue samples, which harbored few resistance alterations. Conclusions: A substantial number of MSS colorectal cancers acquire high TMB following targeted therapy. However, this change is not associated with sensitization to ICB. The high TMB is due to subclonal alterations unique to individual disease sites that are inadequate to elicit a robust antitumor immune response. See related commentary by Parseghian and Eluri, p. 999