Routine Immunohistochemical Analysis of Mismatch Repair Proteins in Colorectal Cancer—A Prospective Analysis

Epigenetic MLH1 silencing concurs with mismatch repair deficiency in sporadic, naturally occurring colorectal cancer in rhesus macaques

BACKGROUND

Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers.

METHODS

We conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP). We furthermore employed Monte-Carlo simulations to in-silico model alterations in DNA topology in transcription-factor binding site-rich promoter regions upon experimentally demonstrated DNA methylation.

RESULTS

Similar cancer histology, progression patterns, and co-morbidities could be observed in rhesus as reported for human CRC patients. IHC identified loss of MLH1 and PMS2 in all cases, with functional microsatellite instability. DNA sequencing revealed the close genetic relatedness to human CRCs, including a similar mutational signature, chromosomal instability, and functionally-relevant mutations affecting KRAS (G12D), TP53 (R175H, R273*), APC, AMER1, ALK, and ARID1A. Interestingly, MLH1 mutations were rarely identified on a somatic or germline level. Transcriptomics not only corroborated the similarities of rhesus and human CRCs, but also demonstrated the significant downregulation of MLH1 but not MSH2, MSH6, or PMS2 in rhesus CRCs. Methylation-specific qPCR suggested CIMP-positivity in 9/16 rhesus CRCs, but all 16/16 exhibited significant MLH1 promoter hypermethylation. DNA hypermethylation was modelled to affect DNA topology, particularly propeller twist and roll profiles. Modelling the DNA topology of a transcription factor binding motif (TFAP2A) in the MLH1 promoter that overlapped with a methylation-specific probe, we observed significant differences in DNA topology upon experimentally shown DNA methylation. This suggests a role of transcription factor binding interference in epigenetic silencing of MLH1 in rhesus CRCs.

CONCLUSIONS

These data indicate that epigenetic silencing suppresses MLH1 transcription, induces the loss of MLH1 protein, abrogates mismatch repair, and drives genomic instability in naturally occurring CRC in rhesus macaques. We consider this spontaneous, uninduced CRC in immunocompetent, treatment-naïve rhesus macaques to be a uniquely informative model for human CRC.

Diagnosis of patients with Lynch syndrome lacking the Amsterdam II or Bethesda criteria

BACKGROUND

Lynch Syndrome (LS) is an autosomal dominant inheritance disorder characterized by genetic predisposition to develop cancer, caused by pathogenic variants in the genes of the mismatch repair system. Cases are detected by implementing the Amsterdam II and the revised Bethesda criteria, which are based on family history.

MAIN BODY

Patients who meet the criteria undergo posterior tests, such as germline DNA sequencing, to confirm the diagnosis. However, these criteria have poor sensitivity, as more than one-quarter of patients with LS do not meet the criteria. It is very likely that the lack of sensitivity of the criteria is due to the incomplete penetrance of this syndrome. The penetrance and risk of developing a particular type of cancer are highly dependent on the affected gene and probably of the variant. Patients with variants in low-penetrance genes have a lower risk of developing a cancer associated with LS, leading to families with unaffected generations and showing fewer clear patterns. This study focuses on describing genetic aspects of LS cases that underlie the lack of sensitivity of the clinical criteria used for its diagnosis.

CONCLUSION

Universal screening could be an option to address the problem of underdiagnosis.

Microsatellite Status Detection of Colorectal Cancer: Evaluation of Inconsistency between PCR and IHC

Objective: An essential component of precision medical treatment for colorectal cancer (CRC) is the use of microsatellite state in combination with polymerase chain reaction (PCR) and immunohistochemistry (IHC) as the primary clinical detection methods. Microsatellite instability-high (MSI-H) or mismatch-repair deficiency (dMMR) accounts for about 15% of all CRC patients. Characterized by a high mutation burden, MSI-H is a predictive biomarker of immune checkpoint inhibitors (ICIs). Misdiagnosis of microsatellite status has been shown to be an important cause of resistance to immune checkpoint inhibitors. Therefore, a rapid and accurate assessment of microsatellite status can be beneficial for precision medicine in CRC. Methods: We evaluated the rate of discordance between PCR and IHC detection of microsatellite status from a cohort of patients that had 855 colorectal cancers. PCR-based microsatellite assay was performed using a set of five monomorphic mononucleotide makers (NR-24, BAT-25, CAT-25, BAT-26, MONO-27) and two polymorphic pentanucleotide (Penta D and Penta E). IHC was used to detect the absence of mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). The inconsistency rates of the two assays were evaluated. Results: Among 855 patients,15.6% (134 to 855) cases were identified as MSI-H by PCR, whereas 16.9% (145 to 855) cases were identified as dMMR by IHC. There were 45 patients with discordant results between IHC and PCR. Of these, 17 patients were classified as MSI-H/pMMR and 28 patients as MSS/dMMR. When the clinicopathological characteristics of these 45 patients were compared to those of the 855 patients, it was found that more patients were younger than 65 years old (80% to 63%), more were male (73% to 62%), more were located in the right colon (49% to 32%), and more were poorly differentiated (20% to 15%). Conclusion: Our study demonstrated a high concordance between the PCR and IHC results. In order to reduce the ineffective treatment of ICIs due to MSI misdiagnosis, the patient's age, gender, tumor location and degree of differentiation should be included in the clinician's selection of MSI testing in colorectal cancer.

Clinical, Pathological, and Molecular Characteristics in Colorectal Cancer

Colorectal cancer (CRC) is the third most diagnosed cancer worldwide, and the second leading cause of death in patients with cancer [...].