Background
During cancer development, tumor cells may elicit cytotoxic T-lymphocyte (CTL)-mediated immune responses–partly a consequence of accumulated gene mutations that are translated into altered peptides [
1]. Tumor cell expression of HLA class I-antigen complexes is essential for CTL recognition of aberrant peptides and subsequent activation [
2]. Consequently, alteration of HLA class I cell surface expression provides an effective mechanism by which tumors can escape immune detection [
3,
4]. Multiple mechanisms have been shown to underlie defects in HLA class I expression by tumor cells. They include mutations in the individual HLA class I genes
HLA-A,
-B and
-C, located on chromosome 6p21.3) [
5]; mutations in
β2-microglobulin (
β2m) [
6‐
9], molecule required for cell surface expression of HLA class I antigens; and defects in components of the HLA class I-associated antigen-processing machinery (APM) [
9‐
11]. The APM consists of proteasome components delta, MB1 and Z; the immunoproteasome components LMP2, LMP7 and LMP10; peptide transporters TAP1 and TAP2; and chaperones Calnexin, Calreticulin, ERp57, and Tapasin. The immunoproteasome generates peptides mostly, although not exclusively from endogenous proteins, TAP1 and TAP2 facilitate peptide translocation from the cytosol into the lumen of the endoplasmic reticulum, where the peptides are loaded onto the HLA class I molecules with the aid from the several chaperones [
12].
Chromosomal instability (CIN) and microsatellite instability (MIN) are the two major forms of genetic instability in colorectal cancer. Combined with distinct somatic mutation patterns and epigenetic modifications, CIN and MIN lead to the development of sporadic colorectal cancer [
13]. MIN sporadic tumors, which constitute approximately 15% of all colorectal cancer cases and up to 40% of the tumors localized on the right side (preceding the splenic flexure) of the colon [
14], have a phenotype resulting from the epigenetic inactivation of the mismatch repair gene
hMLH1. Its inactivation destroys a cell's ability to repair base-base mismatches and small insertions or deletions in repetitive stretches, leading to an accumulation of frameshift mutations that get translated into abnormal peptide sequences. When these mutations are accumulated to large extent in the cell genome the tumors are said to possess high-microsatellite instability (MSI-H) [
15]. Hence, it is expected that genes containing microsatellite sequences within their coding regions are more susceptible to somatic mutations, as seen in the
TGFβ-RII gene.
TGFβ-RII's third exon contains a microsatellite repeat of 10 adenines that is frequently targeted by frameshift mutations in MSI-H tumors [
16]. MSI-H is also the hallmark of hereditary non-polyposis colorectal cancer (HNPCC), in which germline mutations of
hMLH1,
hMSH2,
hMSH6 and
PMS2 can be found. HNPCC constitutes approximately 2–4% of all CRC cases [
17]. Tumors with MSI-H are thought to be more able to stimulate a CTL-mediated immune response due to their frequent generation of the aberrant frameshift peptides [
18]. Therefore, these tumors are subjected to a greater selective pressure which favors the outgrowth of tumor cells with the ability to escape from recognition and destruction by host immune system.
Various studies have identified HLA alterations in colorectal cancer [
19‐
21], including the prevalence of HLA class I alterations in MSI-H tumors [
8,
22]. However, the latter studies did not compare the frequency of alterations between hereditary and sporadic MSI-H tumors neither the mechanisms that led to HLA class I alterations in each subgroup. It was suggested that MSI-H sporadic and hereditary tumors follow parallel evolutionary pathways during tumorigenesis in terms of both genotype and phenotype [
23]. As far as HLA class I defects are concerned it was never investigated whether these different tumors present distinct escape mechanisms from the immune system. In the present study, we compared the frequency of defects in HLA class I expression in right-sided sporadic (MSI-H and microsatellite-stable (MSS) sub-groups) colon tumors and in HNPCC tumors and studied the mechanisms underlying any abnormalities in these subgroups.
Methods
Patient material and tissue microarrays
Two tissue microarrays were constructed from formalin-fixed, paraffin-embedded tissues as described previously [
24]. One array, previously described [
25], included colorectal tumor specimens from 129 suspected HNPCC patients with MSI-H colon tumors of which 75 cases were analyzed in the present study after confirmation of their HNPCC status: 73.3% (n = 55) of the latter possessed a germline pathogenic mutation in
hMLH1 (n = 24),
hMSH2 (n = 18),
hMSH6 (n = 12) or
PMS2 (n = 1), the remaining were MSI-H, without methylation of the
hMLH1 promoter and/or with immunohistochemical loss of the MSH2/MSH6 heterodimer and/or possessed a very young age at diagnosis of colon cancer (<50 yrs old). All cases possessed a positive family history for MSI-H tumors. The second tissue array included 3 tumor tissue cores from 81 sporadic right-sided colon cancer cases resected between 1990 and 2005 at the Leiden University Medical Center (Leiden, The Netherlands) and at the Rijnland Hospital (Leiderdorp, The Netherlands). The 81 patients in the latter array consisted of 47 females and 34 males with a mean age of 71.15 years (SD= 9.958). Approximately 60% (n = 48) of these cases were classified as MSS while the remaining (n = 33) possessed a MSI-H phenotype. The microsatellite instability status of the tumors was determined according to recommendations of the National Cancer Institute/ICG-HNPCC [
15]. Moreover all MSI-H sporadic cases have lost the expression of the MLH1/PMS2 heterodimer as assessed by immunohistochemistry. The sporadic status of the MSI-H right-sided tumors (RST) was confirmed by methylation analysis of the
hMLH1 promoter using a methylation-specific MLPA assay as previously described [
26]. All MSI-H sporadic cases presented with hypermethylation at the
hMLH1 promoter.
The present study falls under approval by the Medical Ethical Committee of the LUMC (protocol P01–019). Cases were analyzed following the medical ethnical guidelines described in the Code Proper Secondary Use of Human Tissue established by the Dutch Federation of Medical Sciences [
27].
Immunohistochemistry
Standard three-step, indirect immunohistochemistry was performed on 4-μm tissue sections transferred to glass slides using a tape-transfer system (Instrumedics, Hackensack, NJ), including citrate antigen retrieval, blockage of endogenous peroxidase and endogenous avidin-binding activity, and di-aminobenzidine development.
The following primary antibodies were used: the mAb HCA2 which recognizes β2m-free HLA-A (except -A24), -B7301 and -G heavy chains [
28,
29] ; the mAb HC10, which recognizes a determinant expressed on all β2m-free HLA-B and C heavy chains and on β2m-free HLA-A10, -A28, -A29, -A30, -A31, -A32 and -A33 heavy chains (supernatant kindly provided by Dr. J. Neefjes, NKI, Amsterdam, The Netherlands and Dr. H. L. Ploegh, MIT, Boston, MA) [
28,
30]; TAP1 specific mAb NOB1; LMP2-specific mAb SY-1; LMP7-specific mAb HB2; LPM10-specific mAb TO-7; Calnexin-specific mAb TO-5; Calreticulin-specific mAb TO-11; Tapasin-specific mAb TO-3; ERp57-specific mAb TO-2 [
31‐
33]; TAP2-specific mAb (BD Biosciences Pharmingen, San Diego, CA); rabbit anti-β2m polyclonal Ab (A 072; DAKO Cytomation, Glostrup, Denmark); anti-MLH1 (clone G168–728; BD Biosciences) and anti-PMS2 (clone A16-4; BD Biosciences). Secondary reagents used were biotinylated rabbit anti-mouse IgG antibodies (DAKO Cytomation), goat anti-rabbit IgG antibodies (DAKO Cytomation), and biotinylated-peroxidase streptavidin complex (SABC; DAKO Cytomation).
Loss of expression was defined by complete lack of staining in membrane and cytoplasm (HCA2, HC10, and anti-β2m), in the nucleus (anti-MLH1 and anti-PMS2), in the peri-nucleus/endoplasmic reticulum (NOB1, anti-TAP2, TO-2, TO-3, TO-5, TO-7, and TO-11), or in the cytoplasm (SY-1, HB2, and TO-7), but with concurrent staining in normal epithelium, stroma or infiltrating leukocytes. HLA class I expression was considered to be lost when one of the HLA class I antigen-specific antibodies gave a negative result alongside a positive internal control (lymphocytic infiltrate).
Flow cytometric sorting
The flow cytometric sorting procedure, including tissue preparation, staining and flow cytometry analysis was performed as described previously [
34]. Briefly, 2 mm diameter punches from selected areas of formalin-fixed paraffin embedded colorectal carcinomas were digested enzymatically in a mixture of 0.1% collagenase I-A (Sigma-Aldrich, St Louis, MO, USA) and 0.1% dispase (Gibco BRL, Paisley, UK). After determination of cell concentration, one million cells were incubated with 100 μl of mAb mixture directed against keratin and vimentin containing clones MNF116 (anti-keratin; IgG1; DAKOCytomation, Golstrup, Denmark), AE1/AE3 (anti-keratin; IgG1; Chemicon International Inc, Temecula, CA, USA), and V9-2b (anti-vimentin; IgG2b; Department of Pathology, LUMC [
35]). Next day, cells were incubated with 100 μl of premixed FITC and RPE-labelled goat F(ab')2 anti-mouse subclass-specific secondary reagents (Southern Biotechnology Associates, Birmingham, AL, USA). After washing, cells were incubated with 10 μM propidium iodide (PI) and 0.1% DNase-free RNase (Sigma). The next day cells were analyzed by flow cytometry. A standard FACSCalibur (BD Biosciences) was used for the simultaneous measurement of FITC, RPE, and PI. Tumor and normal cell populations were flow-sorted using a FACSVantage flow-sorter (BD Biosciences) using the FACSCalibur filter settings. Sorting was only performed on samples included in the RST array due to shortage of material from the HNPCC cases. DNA from flow-sorted tumor material was isolated as described by Jordanova
et al. [
36]. DNA from non-sorted material was isolated using Chelex extraction as described previously [
37].
LOH and fragment analysis
Markers for loss of heterozygosity (LOH) analysis were chosen from the dbMHC database [
38] to map the chromosome 6p21.3 region between HLA-A and TAP2. They were MOGc, D6S510, C125, C141, D6S2444, TAP1 and M2426. A "linker" sequence of 5'-GTTTCTT was added to the 5' terminus of all reverse primers [
39]. LOH was defined as allelic imbalance >2 in the HNPCC cases (non-sorted) and allelic imbalance >5 in the sorted RST [
40].
To detect frame-shift mutations in the
HLA-A,
HLA-B,
β2m, LMP2,
LMP7,
LMP10,
TAP1,
TAP2,
Calnexin,
Calreticulin,
ERp57 and
Tapasin genes, 28 pairs of primers (Table
1) were constructed surrounding non-polymorphic microsatellite regions within the coding regions.
Table 1
Primers used in fragment analysis
HLA A 4th ex | CCTGAATTTTCTGACTCTTCCCGT | GTTTCTTTCCCGCTGCCAGGTCAGTGT | 7(C) |
HLA A 5th ex | CCATCGTGGGCATCATTG | GTTTCTTTCAGTGAGACAAGAAATCTC | 3(GGA) |
HLA B 2nd ex | GCTTCATCTCAGTGGGCTAC | GTTTCTTCTCGCTCTGGTTGTA | 3(GA) + 3(CA) |
β2m 1st ex | GGCTGGGCACGCGTTTAAT | GTTTCTTAGGGAGAGAAGGACCAGAG | 4(CT) |
β2m 2nd ex (1) | TACCCTGGCAATATTAATGTG | GTTTCTTGATAGAAAGACCAGTCCTTGC | 4(GA) + 5(A) |
β2m 2nd ex (2) | CTTACTGAAGAATGGAGAGAG | GTTTCTTGACTACTCATACACAACTTTCA | 5(A) |
TAP1 1st ex | TAAATGGCTGAGCTTCTCGC | GTTTCTTAGAGCTAGCCATTGGCA | 5(C) |
TAP1 3rd ex | ACAGCCACTTGCAGGGAG | GTTTCTTTATGAACAGTACATGGCGTAT | 5(T) |
TAP1 8th ex | CTGCCCTGCTGCAGAATCTG | GTTTCTTCAAGCCACCTGCTTCCAT | 5(G) |
TAP1 10th ex | CTCTGCAGAGGTAGACGAGG | GTTTCTTATTAAGAAGATGACTGCCTCAC | 5(G) |
TAP1 11th ex | AGCACCTCAGCCTGGTGGA | GTTTCTTGCAGGTCTGAGAAGGCTTTC | 6(G) + 5(A) |
TAP2 2nd ex | TTCCTCAAGGGCTGCCAGGAC | GTTTCTTGCTCCAAGGGGCTGAAG | 6(C) |
TAP2 9th ex | CCTACGTCCTGGTGAGGTGA | GTTTCTTCTGGCTGTGCAGGTAGC | 5(G) |
Tapasin 2nd ex | TTGGTTCGTGGAGGATGC | GTTTCTTCCTAGAGACTCACCGTGTAC | 5(G) |
Tapasin 3rd ex | CTTCCTTCTCTACACTCAGACC | GTTTCTTAGGACTGGGCTGGATATGC | 5(C) |
Tapasin 4th ex | CCTGTCTTCCTCAGTGGTAC | GTTTCTTGAGCAGATGTCCCTTACCC | 6(C) |
Tapasin 5th ex | TGCTCATTTCGTCCTCTTTCC | GTTTCTTGTTCCCACTCCACCTCCAG | 5(G) |
Calnexin 7th ex | GAAGGATCAGTTCCATGACAAG | GTTTCTTCTGCATCTGGCCTCTTAGC | 5(A) |
Calnexin 8th ex | TCTGCTCAATGACATGACTCC | GTTTCTTTGAAGACAGTTCCCCAAGAC | 5(A) |
Calnexin 11th ex | AACCTTTCAGAATGACTCCTTTTAG | GTTTCTTCAAGCAGCAAACACGAACC | 8(T) |
Calreticulin 3rd ex | CTACCGTCCCGTCTCAGG | GTTTCTTTCTGTCTGGTCCAAACTATTAGG | 5(G) |
Calreticulin 6th ex | GACAAGCCCGAGCATATCC | GTTTCTTCACCTTGTACTCAGGGTTCTG | 5(C) |
ERp57 5th ex | CACTTATTGCTTCTTCCTTGTG | GTTTCTTAATACTTGGTCAGGAGATTCAAC | 6(T) |
ERp57 6th ex | CTTCTGCTATCTGCCTACTGAG | GTTTCTTTCAAGCAAATAAATCCCAGACAAG | 6(A) |
ERp57 13th ex | ACTTTTAAGCTGATCTTTCTGTTTT | GTTTCTTTTAGAGATCCTCCTGTGCCTT | 6(C) |
LMP2 2nd ex | GAGGGCATCAAGGCTGTTC | GTTTCTTGCAGACACTCGGGAATCAG | 5(G) |
LMP2 6th ex | CCCTCTCTCCAACTTGAAACC | GTTTCTTTGTAATAGTGACCAGGTAGATGAC | 5(G) |
LMP7 1st ex | GGCTTTCGCTTTCACTTCC | GTTTCTTGAGATCGCATAGAGAAACTGTAG | 6(C) |
Statistics
Significance values were calculated using the software package SPSS 10.0.7 (SPSS Inc., Chicago, IL, USA).
Discussion
Abnormalities in HLA class I cell surface expression are commonly observed in tumors and are interpreted as a mechanism by which tumor cells evade the host immune system [
1]. In colorectal cancer, especially in MSI-H tumors, the high degree of lymphocytic infiltrate in some cases may suggest an active immune response during tumor development [
41,
42]. Moreover, MSI-H tumors might cause increased immune reactivity as a consequence of the high amounts of aberrant frameshift peptides they generate [
8,
18]. A selective pressure by CTLs upon these tumors would favor the outgrowth of tumor cells that lost HLA class I expression at the cell surface allowing them to surpass the action of the immune system.
Applying immunohistochemistry on tissue arrays, we compared HLA class I expression in both sporadic RST (MSI-H and MSS sub-groups) and HNPCC tumors. RST were chosen because of the high percentage of MSI-H cases in this specific tumor type [
43]. Indeed, immunohistochemical staining with mAb showed that HLA class I loss was frequent in the MSI-H cases analyzed when compared to their MSS counterpart. This finding supports the hypothesis that MSI-H tumors face greater selective pressure to lose HLA class I expression, as described by Kloor
et al[
8]. However, we have shown for the first time that distinct molecular mechanisms underlie HLA class I loss in sporadic MSI-H and HNPCC colon cancers. In the latter, HLA class I loss was preferentially associated with that of β2m, while in the former HLA class I loss was associated with that of one or more APM components (p < 0.0001).
We investigated the genetic abnormalities underlying the HLA class I loss of expression. They included LOH on chromosome region 6p21.3 (encompassing HLA class I and TAP genes), mutations in APM components and mutations in β2m.
Loss of heterozygosity at 6p21.3 was most prevalent in MSS tumors. This is consistent with the observation that these tumors frequently possess gross chromosomal aberrations and are often aneuploid [
13]. Moreover, since LOH events in MSS tumors normally comprise large areas of a chromosome, LOH on 6p21 might not be a direct consequence of selective pressure directed to the loss of HLA expression but instead to other genes within the same chromosomal region. The general absence of LOH in MSI-H tumors suggests that this is not the major mechanism by which the cells abrogate HLA class I expression.
The genome's coding regions contain multiple microsatellite repeats, which are considered hotspots for mutations in mismatch repair-deficient tumors [
43]. Such repeats are also present within the exons of the APM components,
β2m,
HLA-A and
HLA-B genes. In about half of the MSI-H cases, loss of expression of HLA class I was concordant with the detection of one or more mutations in these genes. We have discovered novel mutations in the antigen presenting machinery genes;
Tapasin,
Erp57,
Calreticulin and
Calnexin in colorectal cancer. Previous reports associated the loss of HLA class I expression in MSI-H tumors with defects on β2m molecule [
7,
9]. However, the authors did not distinguish the sporadic/hereditary nature of the tumors that were studied. We cannot exclude that the MSI-H cases included in these studies were mainly HNPCC tumors.
The reason sporadic MSI-H tumors would target APM members for inactivation and HNPCC would target the β2m chaperon is unclear. One possibility worth further exploration is that the various mutations suggest different immune-escape mechanisms for thwarting distinct anti-tumor responses. HNPCC tumors can have an age of onset before the 5
th decade of life while sporadic MSI-H tumors appear generally around the 7
th decade of life [
43]; one would therefore predict that the alertness and robustness of the immune system would be higher in HNPCC patients leading to a stronger, or at least different selective pressure on the latter. Furthermore it has been recently suggested that the JC polyoma virus plays a role in the oncogenicity of colon tumors with an identical phenotype to sporadic MSI-H tumors [
44]. Although speculative, the presence of the JC virus might be implicated in a different immune response between sporadic MSI-H and HNPCC tumors.
The advantages of different escape mechanisms (loss of APM members vs. abrogation of β2m) are not understood. The only known function of APM members is facilitating the expression of HLA classical molecules in complex with endogenous peptides. Thus, one would expect that only these HLA molecules would be affected by failure of the antigen processing machinery. On the other hand, it is accepted that cell surface expression of non-classical HLA molecules (e.g. HLA -G, -E) also depends on β2m, so the function of these highly specialized molecules would be compromised if β2m were mutated or lost. These molecules might play an important role in regulation of immune cell activity by inhibiting or activating its function. Therefore, MSI-H sporadic tumors that have lost expression of both HLA and an APM component and HNPCC tumors with lost β2m expression might behave differently or present a different kind of interaction with cells from the immune system. For instance, Yamamoto
et al. have described a correlation between β2m mutations and unfavorable prognosis in colorectal cancer [
45].
We separately analyzed the presence of the characteristic
BRAF V600E somatic mutations in the RST cohort (data not shown). Forty-percent of MSI-H sporadic tumors presented with this mutation which was absent in the MSS tumors. It was previously described that this mutation is also absent in HNPCC tumors [
46]. V600E was distributed equally between tumors that lost vs. retained expression of HLA class I in the sporadic MSI-H cases.
Competing interests
The author(s) declare that they have no competing interests.
Authors' contributions
JWD – Contributed to the conception and design of the study, performed flow sorting procedure and was involved in the interpretation of data.
NM – Generated the RST array, performed the immunohistochemistry, flow sorting procedure, LOH and fragment analysis, was involved in the interpretation of data and drafting of the manuscript
SF – Contributed to the conception and design of the study, and critically reviewed the manuscript
MvP – Performed the MSI analysis on HNPCC cases and methylation-specific MLPA assay.
CC – Contributed to the conception and design of the study, and critically reviewed the manuscript
GJF – Contributed to the conception and design of the study, and to critical revision of the manuscript
TvW – Critically reviewed the manuscript.
HM – Contributed to the conception and design of the study, and is responsible for the study.
All authors read and approved the final manuscript.