Comprehensive characterization of MCL-1 in patients with colorectal cancer: Expression, molecular profiles, and outcomes

Abstract

Myeloid cell leukemia 1 (MCL-1) is a member of the B-cell lymphoma 2 protein family and has anti-apoptotic functions. Deregulation of MCL-1 has been reported in several cancers, including lung and breast cancer. In the present study, the association of MCL-1 expression with molecular features in colorectal cancer (CRC) has been highlighted. CRC samples from Caris Life Sciences (Phoenix, AZ) were analyzed using NextGen DNA sequencing, whole transcriptome sequencing, whole exome sequencing, and immunohistochemistry (IHC); and stratified based on MCL-1 expression as top quartile MCL-1^high (Q4) and bottom quartile MCL-1^low (Q1). Immune cell infiltration (CI) in the tumor microenvironment (TME) was measured using RNA deconvolution analysis (QuanTIseq). MCL-1^high tumors were associated with an increased rate of programmed death ligand 1 IHC, higher T cell-inflamed signature, interferon score, microsatellite instability-high and tumor mutational burden-high status. MCL-1^high was associated with higher mutation rates of BCOR, TP53, KMT2D, ASXL1, KDM6A, ATM, MSH6, SPEN, KRAS, STK11, GNAS, RNF43, and lower mutation rates of CDKN1B, NRAS, and APC, and copy number amplifications in several genes. MCL-1^high TME had higher CI of M1 and M2 macrophages, B cells, natural killer cells, neutrophils, and T-regulatory cells infiltration, and lower CI of myeloid dendritic cells. Higher MCL-1 expression is significantly associated with favorable clinical outcomes in CRC cohorts. Our data showed a strong correlation between MCL-1 and distinct immune biomarkers and TME CI in CRC. Our findings suggest MCL-1 is a potential modulator of antitumor immunity, TME, and biomarker in CRC.

Keywords: MCL‐1; colorectal cancer; infiltration; mutations; rectal tumors; tumor microenvironment.

FIGURE 1

Correlation of MCL‐1 ^high (Q4) and MCL‐1 ^low (Q1) expression with immune‐oncology‐related markers, programmed death ligand 1 (PD‐L1) expression, TMB status (high), and dMMR/MSI‐H status in (A) all CRC and (B) pMMR/MSS cohorts. **q < 0.05 by chi‐squared or Fisher exact test was considered statistically significant. dMMR, deficient mismatch repair; IHC, immunohistochemistry; MCL‐1, myeloid cell leukemia 1; MSI‐H, microsatellite instability‐high; TMB, tumor mutation burden. (C) Gene co‐alterations associated with MCL‐1 ^high (Q4) and MCL‐1 ^low (Q1) colorectal cancer (CRC) patients. Mutations in genes involved in signaling pathways important in cancer (including apoptosis, cell cycle, DNA damage response, etc.) were correlated with MCL‐1 expression, and q < 0.05 by chi‐squared or Fisher exact test was considered statistically significant. DDR, DNA damage repair; NGS, next‐generation sequencing. (D) Gene co‐amplifications or copy number amplifications (CNA) associated with MCL‐1 ^high (Q4) and MCL‐1 ^low (Q1) CRC patients. Copy number amplifications in genes involved in signaling pathways important in cancer (including apoptosis, cell cycle, DNA damage response, etc.) were correlated with MCL‐1 expression, and q < 0.05 by chi‐squared or Fisher exact test was considered statistically significant.

FIGURE 2

Association of MCL‐1 expression with (A) T cell inflamed, MCL‐1 ^high (Q4) significantly correlated (q < 0.00001) with higher T‐cell inflamed signature in proficient mismatch repair (pMMR)/microsatellite stable (MSS) colorectal cancer (CRC) cohort; and (B) interferon‐gamma (IFN‐γ) score Tumor Inflammatio Signature (TIS) in pMMR/MSS CRC cohort, MCL‐1 ^high (Q4) significantly correlated (q < 0.00001) with higher IFN‐γ expression in pMMR/MSS CRC cohort. (C) Box plot representing MCL‐1 expression according to primary tumor side. No significant difference was observed in right‐ versus left‐sided tumors; however, rectal tumors showed the highest MCL‐1 expression (p < .05). (D) T‐cell inflamed distribution in the MCL‐1 ^high versus MCL‐1 ^low CRC cohort in the pMMR/MSS subgroup. Significantly more inflamed tumors were seen in Q4 compared to Q1. (E) Box plot representing MCL‐1 expression according to consensus molecular subtypes (CMS). Among the CMS subtypes, CMS4 tumors showed the highest MCL‐1 expression (p < .05). MCL‐1, myeloid cell leukemia 1.

FIGURE 3

Tumor microenvironment cell infiltration according to MCL‐1 expression in proficient mismatch repair/microsatellite stable tumors for (A) B cells, (B) macrophages M1, (C) macrophages M2, (D) monocytes, (E) neutrophils, (F) natural killer (NK) cells, (G) CD4+ T‐cells (non‐reg), (H) CD8+ T‐cells, (I) T‐regulatory (T‐reg) cells, (J) myeloid dendritic cells, and (K) uncharacterized cells (q < 0.001). MCL‐1, myeloid cell leukemia 1.

FIGURE 4

Immune checkpoint‐related marker expression and its association with MCL‐1 expression (Q1 and Q4) in proficient mismatch repair/microsatellite stable tumors, (A) cytotoxic T‐lymphocyte‐associated protein 4 (CTLA4), (B) interferon gamma (IFNG), (C) indoleamine 2, 3‐dioxygenase 1 (IDO1), (D) CD274, (E) CD80, (F) lymphocyte activation Gene 3 (LAG3), (G) programmed cell death protein 1 (PDCD1), (H) hepatitis A virus cellular receptor 2 (HAVCR2), (I) CD86, and (J) programmed cell death 1 ligand 2 (PDCD1LG2) (q < 0.001). MCL‐1, myeloid cell leukemia 1.

FIGURE 5

Association of MCL‐1 expression with (A) overall survival (OS), (B) efficacy of regorafenib, (C) efficacy of bevacizumab, (D) efficacy of immune checkpoint inhibitors (ICIs) in all colorectal cancer (CRC) patients, (E) overall survival, (F) efficacy of regorafenib, (G) efficacy of bevacizumab, (H) efficacy of ICIs in proficient mismatch repair/microsatellite stable tumors (pMMR/MSS) CRC patients. Kaplan–Meier OS curve of all CRC/pMMR/MSS CRC patients receiving different treatments classified by MCL‐1 expression, MCL‐1 ^high (Q4) and MCL‐1 ^low (Q1). MCL‐1, myeloid cell leukemia 1; TOT, time on treatment.