2.3. Animals Deficient for DNA-PKcs: Role in Development
Table 3 summarizes the DNA-PKcs-deficient animals and their characteristics. The animals show the SCID phenotype, and the cells show increased sensitivity to IR and defective V(D)J recombinations.
Table 3. DNA-PKcs-deficient animals.
Mice with
scid mutations show the absence of mature T and B lymphocytes [
13]. The
scid mice are highly susceptible to infection by bacteria, viruses and fungi because of an inability to generate an antigen-specific immune response. In addition,
scid mice lack transplant rejection and are used for xenografts. However,
scid mice are termed “leaky”, as they can produce some immunoglobulins and T lymphocytes at increased ages
[100]. Murine
scid mutations lead to a lack of ~2% of the C-terminal region, although the protein expression is greatly diminished, and the protein kinase activity is undetectable. Where the coding joint formation is almost completely abrogated, the signal joint formation remains, at least partially. This has raised the possibility that DNA-PKcs in
scid is not functionally null. As opposed to this, however, DNA-PKcs knockout (DNA-PKcs
−/−) mice, which were generated by three groups independently, were capable of signal joint formation [
82,
83,
84]. In addition, mice with slip mutations, which are generated incidentally by the insertion of a transgene to the DNA-PKcs gene and thought to be functionally null, also show a ~10% ability of signal joint formation without a decrease in fidelity [
85,
86]. These lines of evidence indicate that DNA-PKcs are not absolutely required for signal joint formation.
Knockin mice lacking kinase activity (D3922A substitution in the kinase domain, hereafter referred to as KD for kinase dead) and that lack three autophosphorylation sites (T2605/2634/2643A, hereafter referred to as 3A) were generated [
87,88]. In DNA-PKcs
KD/KD mice, the abundance of DNA-PKcs appeared normal, but its kinase activity was undetectable [
87]. DNA-PKcs
KD/KD mice showed late embryonic lethality, dying before embryonic day 14.5 (E14.5) [
87]. In the brains of DNA-PKcs
KD/KD mice, extensive apoptosis was observed at a level similar to LIG4
−/− or XRCC4
−/− mice (see below) [
87]. In DNA-PKcs
3A/3A mice, the expression of DNA-PKcs and its kinase activity were normal [88]. Although DNA-PKcs
3A/3A mice were born normally in terms of ratio and size, they become smaller within 2 to 3 weeks of age and died shortly after birth [88]. Congenital bone marrow failure and loss of hematopoietic stem cells were observed in DNA-PKcs
3A/3A mice [88]. The lifespans of DNA-PKcs
3A/3A mice were extended in p53
+/− and p53
−/− backgrounds with a concomitant alleviation in lymphocyte development defects [88]. This observation suggests that a shortened lifespan and lymphocyte development defects are at least partially due to p53-mediated DNA damage responses, including apoptosis. Cells from DNA-PKcs
3A/3A mice show an elevated sensitivity to DNA crosslinking agents, as well as IR [88]. These characteristics of DNA-PKcs
3A/3A mice were similar to those of Fanconi’s anemia. More severe phenotypes of DNA-PKcs
KD/KD mice and DNA-PKcs
3A/3A mice than that of DNA-PKcs
−/− mice might be related to the mechanisms of the regulation of DNA-PKcs through phosphorylation by itself and ATM, as we will discuss below.
It might be noted that mice of several strains, including C.B.17, from which
scid mice were derived, have hypomorphic DNA-PKcs, although immunologically normal [
89,
90]. In the Balb/c strain, the expression of DNA-PKcs and DNA-PK kinase activity was 5–10% of the corresponding tissues and cells from the C57BL/6 strain [
89,
90,
91]. There were two nucleotide substitutions in the DNA-PKcs gene and resultant amino acid substitutions in the protein in Balb/c compared to C57BL/6: c.C6418T, p.R2140C and c.A11530G and p.M3844V. The Balb/c mice were susceptible to breast cancer and thymic lymphoma and showed increased apoptosis in the thymuses after irradiation [
90,
91]. The fibroblasts from Balb/c mice showed a reduced DSB repair ability, which is an intermediate of C57BL6 and
scid mice. In crossing experiments, the Balb/c allele was associated with an increased risk of thymic lymphoma and chromosome aberrations [
90,
91].
SCID in horse (Arabian foal) was found earlier than that in mice [
92]. Soon after the finding in mice, SCID horses were shown to be deficient in DNA-PKcs [
93,
94]. Unlike the case of
scid mice, SCID horses are not reported to be leaky and incapable of signal joint formation, as well as coding joint formation [
93,
94]. SCID animals was also found in dogs (Jack Russel Terriers) and shown to harbor mutations in DNA-PKcs [
95,
96]. SCID dogs showed intermediate activity in both the signal joint formation and the coding joint formation [
96]. Thus, the requirement for DNA-PKcs in V(D)J recombination may differ among species. Meek et al. noted that it may be related to an abundance of DNA-PKcs expression and/or DNA-PK kinase activity; the kinase activity, as well as the requirement for DNA-PKcs in V(D)J recombination is the highest in horses and the lowest in mice.
DNA-PKcs
−/− rats, generated through Zinc-finger nuclease (ZFN)-mediated genome editing, showed SCID without leakiness. In addition, DNA-PKcs
−/− rats showed growth retardation, i.e., smaller body sizes than age-matched DNA-PKcs
+/+ or DNA-PK
+/− rats [
97], which was not noticed in mice, horses and dogs. In agreement with this, the fibroblasts from DNA-PKcs
−/− rats showed reduced proliferation and premature senescence [
97]. A reduction in litter size was also noted in DNA-PKcs
−/− rats [
97].
Besides mammals, DNA-PKcs
−/− animals were also generated in zebrafish through transcription activator-like effector nuclease (TALEN)-mediated genome editing [
98,
99]. DNA-PKcs
−/− zebrafish also showed the SCID phenotype and competency for xenograft experiments [
98,
99]. Growth retardation was noted at lower ages, i.e., up to 20 weeks, although it was not obvious thereafter [
98].
Table 4 shows the comparison of the phenotypes of DNA-PKcs
−/− mice and those of other genes, showing similarities and dissimilarities. Ku80
−/− mice mostly show a complete absence of mature B and T lymphocytes and defects in signal joint formation and coding joint formation
[101][102]. Ku70
−/− mice showed SCID with some leakiness; although mature B lymphocytes and serum immunoglobulins were absent, mature T lymphocytes were present, albeit reduced
[103][104]. Mouse embryonic fibroblasts (MEF) from Ku80
−/− mice and Ku70
−/− mice were defective in both coding joint formation and signal joint formation in V(D)J recombination. The reason for the different impact of the loss of Ku80 and Ku70 on the T lymphocytes is not known. It may be noted that Ku70
−/− mice, but not Ku80
−/− mice, showed an increased frequency of thymic lymphoma
[105]. Both Ku80
−/− mice and Ku70
−/− mice showed a reduction in body sizes, i.e., 40–60% of the control and litter sizes [
101,
102,
103], which were not in evident in
scid mice and DNA-PKcs
−/− mice. In conjunction with this, MEF from Ku80
−/− mice and Ku70
−/− mice showed reduced proliferation and premature senescence [
102,
103,
104]. Increased cell death in neuronal development was also observed in Ku70
−/− mice and Ku80
−/− mice
[106], although it was less severe than that observed in LIG4
−/− mice and XRCC4
−/− mice (see next).
Table 4. Gene knockout mice of DNA-PKcs and other NHEJ genes.
LIG4
−/− mice and XRCC4
−/− mice exhibited late embryonic lethality [
107,
108,
109]. MEF from LIG4
−/− mice and XRCC4
−/− mice showed reduced proliferation and premature senescence, as well as an increased sensitivity to IR [
107,
108,
109]. Mature B and T lymphocytes were absent in these mice, and the fibroblasts were defective in both coding joint formation and signal joint formation in V(D)J recombination. In addition, the defective neuronal development associated with greatly increased cell death was manifested in LIG4
−/− mice and XRCC4
−/− mice [
108,
109].
Artemis
−/− mice grew normally but were deficient in lymphocyte development [
110]. Artemis
−/− MEF showed increased IR sensitivity [
110]. While coding joint formation in Artemis
−/− MEF was greatly impaired, signal joint formation was indistinguishable from the wild-type in rate and fidelity [
110]. Since DNA-PKcs
−/− MEF showed mildly reduced fidelity, DNA-PKcs might have an Artemis-independent function in signal joint formation.
XLF
−/− mice did not exhibit overt defects in growth and development [
111]. There was a slight decrease in the number of lymphocytes, but the distribution of mature lymphocytes was normal, although a mild defect in the class switch recombination (CSR) was evident [
111]. However, ES cells or MEFs showed increased IR sensitivity and V(D)J recombination defects in both signal joint formation and coding joint formation [
111]. These results suggested the presence of a lymphocyte-specific mechanism to compensate for a XLF deficiency. XLF is shown to have functional redundancy with ATM
[114], DNA-PKcs
[115] and PAXX (see next). Of note, DNA-PKcs
−/−; XLF
−/− mice showed a reduction in birth ratio and body size at birth [
115]. Additionally, signal joint formation in V(D)J recombination was compromised in DNA-PKcs
−/−; XLF
−/− mice, although it was mostly normal in Artemis
−/−, XLF
−/− mice [
114,
115]. This observation further supports the Artemis-independent function of DNA-PKcs in signal joint formation.
PAXX
−/− mice also showed normal growth and development, although they showed a slightly reduced survival after γ-ray irradiation [
112,
113]. PAXX
−/−; XLF
−/− mice were embryonic lethal, dying between E14.5 and E18.5. A reduced body size became evident at around E10.5 [
112,
113], suggesting possible redundant functions between PAXX and XLF.
These lines of evidence indicate that NHEJ is essential in growth and development. We can also see that the requirement for DNA-PKcs is less pronounced than that of Ku70, Ku80, XRCC4 and LIG4.
2.4. Human Patient and Cells Deficient in DNA-PKcs: Manifested Importance in Human
To date, six human individuals have been reported to harbor homozygous or compound heterozygous mutations in DNA-PKcs, as shown in
Table 5. Five patients (P1 and P3-P5) are of Turkish origin and have a common homozygotic mutation. Of two mutations, i.e., one deletion and one substitution of amino acid in each allele, the latter is considered responsible for the disease
[116]. It is noteworthy that the expression of DNA-PKcs, its autophosphorylation on Ser2056 and kinase activity appeared normal in the fibroblast derived from P1[
116]. Moreover, when exogenously expressed in V3 cells, the mutated gene could accumulate on DNA damage induced by laser micro-irradiation and recruit Artemis there as well[
116]. These lines of evidence indicate that this mutation is hypomorphic, retaining a substantial part of the DNA-PKcs functions. Nevertheless, this mutation increased the length of the P-nucleotide in the coding joint, as in the case of patients with mutations in Artemis, indicating that this mutant might be defective in the activation of Artemis[
116]. Other patients with the same mutations showed granuloma and/or autoimmunity, as well as SCID
[117][118].
Table 5. Human patients deficient in DNA-PKcs.
One patient (P2) of British origin had a distinct compound heterozygotic mutation [
119]. This patient was first given clinical attention due to poor intrauterine growth and, after birth, showed various symptoms, including microcephaly, facial dysmorphism, seizures and other neurological abnormalities, in addition to SCID [
119]. He died at 31 months of age because of intractable seizures [
119]. Unlike the case of P1, the expression of DNA-PKcs in the fibroblast from P2 was very low, and the kinase activity was not detectable [
119]. These observations suggested a more severe defect in DNA-PKcs functions in P2 than in P1, causing growth and neuronal defects in addition to immunodeficiency. Nonetheless, the DNA-PKcs in this patient might have been partially functional, because the treatment of fibroblasts from the patient prolonged the decline of the γ-H2AX foci after IR [
119]. Additionally, the A3574V mutant could partially restore the coding joint proficiency, with normal sequence, to DNA-PKcs-deficient V3 cells, suggesting that this mutant is capable of activating Artemis [
119].
Thus, human individuals with null-functional DNA-PKcs have not been found so far and might not be viable at all. In addition, the attempts to establish Ku70
−/− and Ku80
−/− cells from HCT116 or Nalm-6 failed, and these genes proved indispensable for the viability of human cells
[120][121][122]. The lethality might be due to telomere deletion in the form of telomeric circles, which should be suppressed by Ku86 [
122]. Ku86 was also shown to suppress alternative, DNA polymerase θ-mediated NHEJ (A-NHEJ, A-EJ or TMEJ), which are thought more susceptible to errors than classical NHEJ
[123]. The expression of DNA-PKcs and DNA-PK kinase activity in human cells were reported to be higher than in rodent cells by one or two orders of magnitude [
11,
17,
95]. Human colon cancer HCT116 cells exhibit a haploinsufficiency of DNA-PKcs in terms of various functions; DNA-PKcs
+/- showed a slower proliferation and higher sensitivity to IR and etoposide, as well as a shorter telomere length than DNA-PKcs
+/+ cells [
76] (
Table 1). Ku70 and Ku80 also exhibit haploinsufficiency in terms of cell proliferation, IR sensitivity and telomere length [
120][121][122][123][124]. On the other hand, cells lacking XRCC4 or LIG4 were established from several cell lines and were shown to be viable
[78][79][125]
[126][127][128].This is in contrast to the situation in mice, where the absence of XRCC4 and LIG4 results in more severe consequences than the absence of Ku70 or Ku80. These lines of evidence indicate that the importance of DNA-PKcs and Ku might be manifested in humans as compared to other mammalian species.