Discussion
In this study, we evaluated the prevalence of HLA-I LOH in Chinese
cancer patients using the 1021-gene panel and characterized the genomic
features of patients harboring HLA-I LOH.
Analytical results indicated that HLA-I LOH was widespread in Chinese
cancer patients while varied greatly across cancer types, with an
average incidence of 45.6%. When compared with a western population
cohort containing 83644 samples, Chinese cancer patients shown a higher
incidence of HLA-I LOH (45.6% vs. 17.0%) (Montesion et al., 2020).
Since HLA-I LOH is a common immune evasion mechanism later in tumor
evolution, we speculate that this difference may be due to the different
tumor progression stages of the patients in the study cohort (McGranahan
et al., 2017). The percentage of LOH co-occurrence at all three HLA-I
loci in HLA-I LOH patients is 43.3% (293/676) in Chinese cohort and
85% in the western population cohort, respectively. (Montesion et al.,
2020). Although there is a difference in the frequency of HLA-I LOH, the
proportion of patients with LOH at all three sites concurrently is
roughly equivalent (19.7% in our cohort vs. 14.5% in western cohort)
(Montesion et al., 2020). As confirmed by previous studies, HLA-I LOH is
enriched in squamous cell carcinoma (Montesion et al., 2020). In our
cohort, the highest incidence of HLA-I LOH occurs in cervical squamous
cell carcinoma and lung squamous cell carcinoma. Consistent with prior
researches, the occurrence of HLA-I LOH was accompanied by elevated
tumor mutation burden (TMB), suggesting the genomic instability in
patients harboring HLA-I LOH (Anagnostou et al., 2020; McGranahan et
al., 2017). When focusing on patients harboring HLA-I LOH, the TMB level
of patients with LOH at a single site was lower than with LOH at all
three sites. As one of the important indicators of immunotherapy, high
TMB level indicated better immunotherapy prognosis (Hellmann et al.,
2018; Samstein et al., 2019; Chan et al., 2019; Rizvi et al., 2018).
Considering that the occurrence of multi-loci HLA-I LOH may impair
antigen binding and presentation, the survival benefits of high TMB
levels could be diminished, in which circumstances patients might have a
poor response to immunotherapy. Thus, in clinical practice, the TMB
level should be evaluated along with the occurrence of HLA-I LOH and
number of LOH loci when predicting the response to immunotherapy.
However, when dividing TMB more finely, the relationship between HLA-I
LOH and TMB is more in line with the “Goldilocks” pattern that tumors
with low or high TMB levels show a low incidence of HLA-I LOH, while
higher incidence is presented in between (Supplementary Figure 3A)
(Montesion et al., 2020). Further analysis find that MSI-H patients have
significantly higher TMB levels but lower incidence of HLA-I LOH
compared with MSS patients, which led to the “Goldilocks” phenomenon
in our cohort (Supplementary Figure 3C). Montesion et al. (2020)
hypothesized “HLA-I LOH is selected for in tumors with enough
neoantigens to elicit an immune response but few enough that HLA-I LOH
abrogates immune recognition without eliciting an NK cell response”. We
believe that the reasons behind this phenomenon need to be further
explored by analyzing the genomic differences of those patients. In
addition, the higher incidence of HLA-I LOH in MSS patients suggests
that HLA-I LOH may be one of the reasons for the poor response to
immunotherapy in some MSS patients, prompting the underlying
significance of HLA-I LOH testing in predicting potential benefit
population in MSS patients. Since MSI-H group mainly consist of patients
with gastrointestinal tumors (59.5% [22/37]) in our cohort,
conclusions above might be specifically reflected in these cancer types.
Another important discovery is that patients harboring HLA-I LOH have
unique genomic features, such as increased alteration frequencies of
several signaling pathways and oncogenes. Since the occurrence of HLA-I
LOH is closely related to genomic instability, we first analyzed the
differences in the alterations in DDR pathways (McGranahan et al.,
2017). Results revealed that alteration frequencies of CPF pathway and
FA pathway in the HLA-I LOH group was significantly higher than that of
the HLA-I stable group. In addition, the occurrence of HLA-I LOH was
accompanied by alterations in several important oncogenic signaling
pathways, including p53 pathway, RTK/RAS pathway, Hippo pathway, Notch
pathway and Nrf2 pathway, indicating that HLA-I LOH might involve in
tumor progression by influencing the normal signaling transduction. As a
signaling cascade pathway initiated by activation of RTKs, RTK/RAS
pathway regulates cell proliferation and survival and is frequently
altered in many cancer types (Malumbres & Barbacid, 2003; Sanchez-Vega
et al., 2018). For several oncogenic genes, such as TP53 andLRP1B , the occurrence of HLA-I LOH is related to higher mutation
frequencies. As the central gene of p53 pathway and CPF pathway,TP53 regulates apoptosis, cell cycle arrest, senescence, and DNA
repair (Wade et al., 2013; Sanchez-Vega et al., 2018). The somatic
mutations of this important tumor suppressor may cause genomic
instability and replication stress, which is closely related to
tumorigenesis in various cancer types (Nigro et al., 1989; Baker et al.,
1989; Stracquadanio et al., 2016; Malekzadeh et al., 2019). LRP1Bmay play an essential role in tumorigenesis of NSCLCs, and mutations of
this gene are associated with a higher TMB level (Lan et al., 2019; Wang
et al., 2021). These factors may be involved in positive selection
during tumor evolution and promote the occurrence of HLA-I LOH.
Therefore, the mechanism underlying these observations and the causal
relationship between HLA-I LOH and mutations of certain genes need
further investigation.
One of the major limitations of this study is the insufficient
collection of clinical information, such as smoking history and clinical
outcome, which precluded us to set a cohort to analyze the clinical
significance of our findings. Another shortcoming is that the number of
samples used for analysis is relatively small compared with other large
population studies. In our follow-up study, after enrolling a sufficient
number of patients and collecting adequate clinical data, these
limitations will be overcome. Therefore, deeper mechanism mining and
clinical verification will be achieved.
In general, we confirmed the validity of 1021-gene panel for HLA-I LOH
detection through comparison with whole-exome sequencing (WES). The
1021-gene panel could be applied for HLA-I LOH analysis, provided that
the relevant regions are well captured. We further depicted the
landscape of HLA-I LOH events in Chinese cancer patients and revealed
the genomic features of patients harboring HLA-I LOH. These insights may
provide valuable information for clinical practice and follow-up
immunotherapy research.