Strength of immune selection in tumors varies with sex and age

Abstract

Individual MHC genotype constrains the mutational landscape during tumorigenesis. Immune checkpoint inhibition reactivates immunity against tumors that escaped immune surveillance in approximately 30% of cases. Recent studies demonstrated poorer response rates in female and younger patients. Although immune responses differ with sex and age, the role of MHC-based immune selection in this context is unknown. We find that tumors in younger and female individuals accumulate more poorly presented driver mutations than those in older and male patients, despite no differences in MHC genotype. Younger patients show the strongest effects of MHC-based driver mutation selection, with younger females showing compounded effects and nearly twice as much MHC-II based selection. This study presents evidence that strength of immune selection during tumor development varies with sex and age, and may influence the availability of mutant peptides capable of driving effective response to immune checkpoint inhibitor therapy.

Fig. 1. Sex- and age-specific MHC presentation of observed, RNA-expressed driver mutations.

a, b Box plots denoting the distribution of (a) PHBR-I and (b) PHBR-II scores for expressed driver mutations in female and male pan-cancer patients. c, d Box plots denoting the distribution of (c) PHBR-I and (d) PHBR-II scores for expressed driver mutations in younger and older pan-cancer patients. P values were calculated using the one-tailed Mann–Whitney U test. Median values are shown in each boxplot. All box plots include the median line, the box denotes the interquartile range (IQR), whiskers denote the rest of the data distribution and outliers are denoted by points greater than ±1.5 × IQR. The following effect sizes were calculated using Cliff’s d: (a) r = −0.0654, (b) −0.104, (c) −0.081, (d) −0.0734.

Fig. 2. Integrated sex- and age-specific analysis.

a PHBR-I and b PHBR-II scores for the observed driver mutations in pan-cancer integrated sex- and age-specific patient cohorts. One asterisk indicates p values < 0.05 and two asterisks indicates p values < 0.001. All p values were calculated using a one-tailed Mann–Whitney U test. The Benjamini–Hochberg method was used to adjust for multiple comparisons for (a, b). Median values are shown in each boxplot. Exact p values for (a) include: YF, OM: 0.7e−05; YF, OF: 0.005; YF, YM: 0.008; YM, OM: 0.008; OF, OM: 0.08; OF, YM: 0.22. Exact p values for (f) include: YF, OM: 5.51e−07; YF, YM: 0.0003; YM, OM: 0.035; YF, OF: 0.038; OF, YM: 0.17. Y = younger, O = older, F = female, M = male. All box plots include the median line, the box denotes the interquartile range (IQR), whiskers denote the rest of the data distribution and outliers are denoted by points greater than ±1.5 × IQR.

Fig. 3. Sex-specific exposure analysis with mutational signatures.

a Heatmap of log2 male (blue) to female (pink) ratios of mutational signatures for each tumor type with asterisks denoting a significantly different ratio between male and female sexes. b The percentage of mutations in the set of driver mutations that are part of each mutational signature. c Boxplot comparing MHC-I and MHC-II presentation scores across all possible alleles for C>T or T>C driver mutations (green) versus driver mutations resulting from other base substitutions (yellow); 1,063,975 and 2,051,300 affinity scores were evaluated for C>T or T>C mutations for class I and II, respectively; and 1,851,025 and 3,568,700 affinity scores were evaluated for other mutations for class I and II, respectively. Exact p values were calculated using a one-tailed Mann–Whitney U test: (c) 2.2e−308 and (d) 1.4e−86. Median values are denoted in each boxplot. All box plots include the median line, the box denotes the interquartile range (IQR), whiskers denote the rest of the data distribution and outliers are denoted by points greater than ±1.5 × IQR.

Fig. 4. Sex- and age-specific MHC presentation of observed driver mutations in the validation cohort.

a, b Box plots denoting the distribution of (a) PHBR-I and (b) PHBR-II scores for driver mutations in female and male pan-cancer patients. Exact p values were calculated using a one-tailed Mann–Whitney U test: (a) 0.027 and (b) 0.024, and effect sizes were calculated using Cliff’s d: (a) r = −0.154, (b) r = −0.164. c, d Box plots denoting the distribution of (c) PHBR-I and (d) PHBR-II scores for driver mutations in younger and older pan-cancer patients. Exact p values were calculated using a one-tailed Mann–Whitney U test: (c) 0.022 and (d) 7.9e−04, and effect sizes were calculated using Cliff’s d: (c) r = −0.207, (d) −0.346. e, f Box plots denoting the distribution of (e) PHBR-I and (f) PHBR-II scores for driver mutations among integrated sex- and age-specific pan-cancer patient cohorts. One asterisk indicates p values < 0.05 and two asterisks indicates p values < 0.001. P values were calculated using a one-tailed Mann–Whitney U test. The Benjamini–Hochberg method was used to adjust for multiple comparisons for (e, f). Median values are shown in each boxplot. Exact p values for (e) include: YM, OM: 0.024; YF, OM: 0.028; OF, OM: 0.070; YF, OF: 0.56; YF, YM: 0.49; OF, YM: 0.50. Exact p values for (f) include: YF, OF: 0.0083; YF, OM: 0.013; OF, YM: 0.023; YM, OM: 0.045; YF, YM: 0.24; OF, OM: 0.34. Y = younger, O = older, F = female, M = male. All box plots include the median line, the box denotes the interquartile range (IQR), whiskers denote the rest of the data distribution and outliers are denoted by points greater than ±1.5 × IQR.

Fig. 5. Proposed model of the relationship between immune selection and immunotherapy in cancer patients.

Young females experience the strongest immune response, rendering their diagnosed tumors more invisible to the immune system and difficult to treat with ICB. On the other extreme, old males experience the weakest immune response, leaving their diagnosed tumors more visible to the immune system and open to attack when stimulated with ICB. Blue dots indicate immunologically visible driver mutations while red dots indicate immunologically invisible driver mutations at various time points.