Telomerase Mutations in Families with Idiopathic Pulmonary Fibrosis
Mary Y. Armanios, M.D., Julian J.-L. Chen, Ph.D., Joy D. Cogan, Ph.D., Jonathan K. Alder, B.A., Roxann G. Ingersoll, B.S., Cheryl Markin, B.S., William E. Lawson, M.D., Mingyi Xie, B.S., Irma Vulto, B.S., John A. Phillips, III, M.D., Peter M. Lansdorp, M.D., Ph.D., Carol W. Greider, Ph.D., and James E. Loyd, M.D.
Background Idiopathic pulmonary fibrosis is progressive andoften fatal; causes of familial clustering of the disease areunknown. Germ-line mutations in the genes hTERT and hTR, encodingtelomerase reverse transcriptase and telomerase RNA, respectively,cause autosomal dominant dyskeratosis congenita, a rare hereditarydisorder associated with premature death from aplastic anemiaand pulmonary fibrosis.
Methods To test the hypothesis that familial idiopathic pulmonaryfibrosis may be caused by short telomeres, we screened 73 probandsfrom the Vanderbilt Familial Pulmonary Fibrosis Registry formutations in hTERT and hTR.
Results Six probands (8%) had heterozygous mutations in hTERTor hTR; mutant telomerase resulted in short telomeres. Asymptomaticsubjects with mutant telomerase also had short telomeres, suggestingthat they may be at risk for the disease. We did not identifyany of the classic features of dyskeratosis congenita in fiveof the six families.
Conclusions Mutations in the genes encoding telomerase componentscan appear as familial idiopathic pulmonary fibrosis. Our findingssupport the idea that pathways leading to telomere shorteningare involved in the pathogenesis of this disease.
Idiopathic pulmonary fibrosis has a predictable, progressiveclinical course that ultimately leads to respiratory failure.Irreversible fibrosis is the hallmark of the disease, whichhas a characteristic radiographic appearance most often associatedwith the pathological lesion of usual interstitial pneumonia.Although both genetic and environmental factors have been implicated,the cause of idiopathic pulmonary fibrosis is unknown —as, indeed, its name implies. Treatment approaches that targetthe immune system have not proved to be successful.1 From 2to 20% of patients with idiopathic pulmonary fibrosis have afamily history of the disease; inheritance appears to be autosomaldominant with variable penetrance.1,2,3 Aside from one largekindred with a mutation in the gene encoding surfactant proteinC in affected family members, the genetic basis of familialforms of idiopathic pulmonary fibrosis is not understood.4
Telomerase is a specialized polymerase that adds telomere repeatsto the ends of chromosomes.5 It has two essential components:a catalytic component, telomerase reverse transcriptase (hTERT),and an RNA component (hTR); the latter provides the templatefor nucleotide addition by hTERT.6,7,8 The addition of telomericrepeats (a repeat comprising the six nucleotides — TTAGGG— complementary to the template in hTR) onto the endsof the chromosome partly offsets the shortening that occursduring DNA replication. Telomeres shorten with each cell divisionand ultimately activate a DNA damage response that leads toapoptosis or cell-cycle arrest.9,10,11,12,13 Telomere lengththus limits the replicative capacity of tissues and has beenimplicated in age-related disease.9,10,11,14,15
Dyskeratosis congenita is a rare hereditary disorder initiallydescribed on the basis of a triad of mucocutaneous manifestations:skin hyperpigmentation, oral leukoplakia, and nail dystrophy.16The most common cause of death in patients with dyskeratosiscongenita is bone marrow failure due to aplastic anemia. Pulmonarydisease is present in 20% of patients and is the second mostcommon cause of death.16,17,18 The X-linked form of dyskeratosiscongenita is severe and associated with mutations in the DKC1gene.19 Autosomal dominant cases of dyskeratosis congenita arerare, can present later in adulthood, and often lack the classicskin manifestations. In some families, the hematopoietic defectsdevelop first, implying that despite the originally given name,the dyskeratosis is not canonical.20 Heterozygous mutationsin hTR and hTERT, the essential components of telomerase, underliethe genetic defect in families with dominant inheritance, indicatingthat half the usual dose of telomerase is inadequate for telomeremaintenance, and tissues of high turnover, such as the bonemarrow, are susceptible.21,22,23,24 In autosomal dominant dyskeratosiscongenita, anticipation can be seen in which phenotypes presentearlier and more severely in successive generations.21,24,25This pattern implies that in these patients, it is not the telomerasemutation itself but the short telomeres that determine the severityof the disease.14,24,26
We recently identified a pedigree with autosomal dominant dyskeratosiscongenita that carried a null hTERT allele but lacked the typicalmucocutaneous features.24 In this kindred, pulmonary fibrosiswas dominantly transmitted and was the only manifestation ofdisease in one mutation carrier. The clinical presentation andpattern of fibrosis in this subject were typical of the idiopathicform of the disease. Since familial idiopathic pulmonary fibrosisis also dominantly inherited, we hypothesized that telomereshortening causes this disease and that mutations in telomerasemay contribute to it.
Methods
Subjects
Subjects and their families were recruited into the VanderbiltFamilial Pulmonary Fibrosis Registry on the basis of the presenceof two or more cases of idiopathic pulmonary fibrosis. (We didnot limit families to those in which only first-degree relativeswere affected.) Subjects were excluded from the study if theyhad a secondary cause of pulmonary fibrosis or if they had skinmanifestations suggestive of dyskeratosis congenita. Subjectswere recruited from the Vanderbilt Idiopathic Pulmonary FibrosisClinic or were referred from other sites in North America between1996 and 2004. The study was approved by the local institutionalreview boards, and written informed consent was obtained fromall subjects. Diagnostic confirmation was based on a detailedclinical assessment (Table 1, and Table 1 of the Supplementary Appendix,available with the full text of this article at www.nejm.org).We used the consensus classification of idiopathic interstitialpneumonia in individual cases.27 At the time the registry wasaccessed, all 73 probands were reported by their cliniciansto be North Americans of European descent.
Table 1. Mutations in Telomerase and Associated Clinical Features of the Six Probands.
Sequence Analysis
Genomic DNA was isolated from peripheral blood with the useof standard methods. We amplified and sequenced hTR in bothdirections, as described previously.21 We amplified and sequencedthe 16 exons of hTERT and its 3' untranslated region with theuse of primers listed in Table 2 of the Supplementary Appendix.Amplicons of hTERT were sequenced in one direction, and suspectedchanges were confirmed in the opposite strand. Mutations inthe probands and their relatives were confirmed by bidirectionalsequencing. Sequences were inspected manually with the use ofSequencher software, and variants were compared with publicdatabases. Coding and noncoding variants are listed in Table3 of the Supplementary Appendix.
Telomeres and Telomerase
A reverse-transcriptase–polymerase-chain-reaction (RT-PCR)assay was performed with the use of RNA isolated from peripheralblood to make complementary DNA (cDNA). Primers were designedto span exons where a mutation was predicted to alter splicing;primer sequences are available on request. PCR products werecloned, and the sequence was verified.
The average length of telomeres was measured in peripheral-bloodlymphocytes by flow fluorescence in situ hybridization (FISH),as described previously.28
Point mutations were generated, and the telomerase complex wasreconstituted in vitro.24 Telomerase activity was assayed withoutamplification, with the use of a modified direct assay.29,30
Results
Mutations Affecting Telomerase Components
Of 73 probands who were screened, 6 (8%) had heterozygous mutationsin hTERT or hTR. Five probands had mutations in hTERT (two missense,two splice junction, and one frameshift), and one proband hada mutation in hTR (Table 1, and Figure 1 of the Supplementary Appendix).None of the hTERT mutations were present in 623 unaffected subjects,as determined in other studies.23,31 Of these subjects, 140described themselves as white, with the rest describing themselvesas black, Hispanic, or Asian. The hTR mutation was also absentin 194 healthy controls. Of these subjects, 123 described themselvesas white, with the remaining subjects describing themselvesas black, Hispanic, or Asian.22
Mutations Associated with Disease and Short Telomeres
To determine whether telomerase mutations segregated with idiopathicpulmonary fibrosis in families, we examined the pedigrees. Thepattern of inheritance was consistent with autosomal dominantinheritance of the disease (Figure 1). The mutant allele waspresent in affected subjects and was generally absent in asymptomaticsubjects of the same generation. We identified mutation carrierswho did not have symptoms of the disease. These subjects wereon average 11 years younger than the probands at the time ofdiagnosis (Figure 1). This observation is consistent with thevariable penetrance associated with familial idiopathic pulmonaryfibrosis and also suggests that the onset of disease may beage dependent.
Figure 1. Pedigrees of Six Probands with Telomerase Mutations.
Arrows point to the proband in each family, and bold italic numbers indicate subjects for whom DNA was available for sequencing. Subjects in whom telomere length was measured are indicated by asterisks. Mutation status is indicated by the symbols shown in the key, with squares indicating male sex and circles indicating female sex. Deceased family members are indicated by slashes through the symbols. In Family D, Subject DII.1 is an obligate carrier, given that two of his children carry the mutation and the mother does not. A total of 19 subjects with confirmed idiopathic pulmonary fibrosis are included among the six families shown. The seven asymptomatic carriers in younger generations were on average 11 years younger than the probands at the time of diagnosis: 40, 44, 46, 50, 52, 55, and 68 years of age. In Family F, three subjects had aplastic anemia, and Subject FIII.16 died from acute myeloid leukemia, probably in the setting of aplastic anemia. IPF denotes idiopathic pulmonary fibrosis.
To assess whether mutant telomerase is associated with shorttelomeres, we measured the telomere length in lymphocytes. Theaverage telomere length was significantly less in the probandsand asymptomatic mutation carriers than in their relatives whodid not carry the mutation (P=0.006) (Figure 2A). A comparisonof the telomere length in mutation carriers with that in 400healthy controls, according to age,23 showed that mutation carriersfell below the 10th percentile of the controls (P=0.018), whereastheir relatives who were noncarriers clustered near the median(P=0.575) (Figure 2B). Mutant telomerase was therefore associatedwith short telomeres.
Figure 2. Telomere Length in Mutation Carriers and Their Relatives.
Panel A shows the average length of telomeres in lymphocytes in eight carriers and seven noncarriers of the genetic mutation, and Panel B shows telomere length as a function of age. The three oldest mutation carriers are the probands in Family A, Family E, and Family F. The 12 other subjects who were examined are indicated in Figure 1 by an asterisk. Identifiers refer to subjects from the pedigrees in Figure 1. I bars represent standard errors. Telomere lengths in mutation carriers were significantly less than the median value for their age (P=0.018 by the Wilcoxon signed-rank test), whereas telomere lengths in noncarriers did not differ significantly from the median for their age (P=0.575).
Impaired Activity of Mutant Telomerase
We next examined the consequences of hTERT and hTR mutationson telomerase function. We first examined the two missense mutationsin hTERT, glutamine replacing leucine at residue 55 (Leu55Gln)and methionine replacing threonine at residue 1110 (Thr1110Met).The Leu55Gln substitution identified in the proband of FamilyA is in a highly conserved region of the N-terminal; an aminoacid substitution of Leu55 may alter telomerase RNA bindingand thus the catalytic efficiency of telomerase.32 The Thr1110residue is also highly conserved and lies in the C-terminalof hTERT, a domain that is thought to mediate recruitment oftelomerase to the telomere.33 Both mutant versions of hTERT(Leu55Gln and Thr1110Met) had impaired activity, as comparedwith the wild-type enzyme (Figure 3C and 3D). Since heterozygousmutations sometimes interfere with the function of the wild-typeallele, we assayed the telomerase activity of a mixture of wild-typeand mutant versions of the enzyme and observed no dominant negativeeffect (data not shown).
Figure 3. Biochemical Consequences of Telomerase Mutations in Probands.
Panel A shows conserved domains of hTERT with missense mutations, as indicated. Colors indicate conserved domains in hTERT shared with other reverse transcriptases. The Leu55Gln mutation lies in the telomerase essential N-terminal (TEN) domain, and Thr1110Met is in one of four conserved C-terminal domains. Panel B shows the secondary structure of hTR, with the site of the mutation indicated by an asterisk. The 98 GA substitution lies in a critical helix of the pseudoknot domain, which contains the telomere template and is responsible for binding to TERT. Panel C shows the telomerase activity of mutant hTERT and hTR alleles, as measured by the direct assay and the intensity and pattern of the repetitive ladder. Panel D shows the quantitation of telomerase activity at the second major band, as indicated by the arrowhead in Panel C. Mean activity was calculated on the basis of three to five experiments; the I bars represent standard errors. Panel E shows the results of an RT-PCR assay across exons 9 through 11 from a subject with an hTERT 9-2 AC mutation, indicating that the heterozygous mutation at this consensus splice junction leads to the skipping of exon 10. As a result, the mutant TERT lacks the essential motif C of the reverse-transcriptase domain.
We also examined the effect of the hTR 98 GA substitution (observedin the proband of Family F) on telomerase activity. This mutationis predicted to impair base pairing in a helix in the essentialpseudoknot domain of hTR.34 Moreover, since 98G is conservedin telomerase RNA in all vertebrates, a mutation at this siteis expected to alter activity.34 When telomerase was reconstitutedwith the mutant hTR 98A allele, activity was severely impaired(Figure 3C and 3D).
We next examined the potential consequences of the three mutationsin hTERT. The deletion of nucleotide C at codon 112 in the probandof Family C leads to a frameshift mutation and is predictedto result in a nonfunctional, truncated protein. Both splice-junctionmutations in Family B and Family D occur at consensus sequencesthat are conserved in 99.9% of all eukaryotic genes and aretherefore predicted to alter splicing. We examined the cDNAof primary cells from a subject in Family D who carried theIVS9-2 AC mutation and observed skipping of exon 10 but retentionof the reading frame (Figure 3E). According to these findings,obtained by RT-PCR, synthesis of a protein of nearly full lengthis predicted. However, this mutant TERT is predicted to lackan essential motif (the C motif) in the reverse-transcriptasedomain and thus to result in a functionally null protein (Figure 3A).8
Clinical Review
We reexamined the probands for the most common features of dyskeratosiscongenita. None of the probands had cytopenias (Table 1), andnone had any of the classic features of dyskeratosis congenitaat the time of diagnosis. To discern whether these six familieshad hidden cases of dyskeratosis congenita, we requeried familymembers and medical records for evidence of aplastic anemia.We identified no cases of aplastic anemia in five of the sixfamilies. In Family F, we identified three subjects with aplasticanemia and a fourth subject with probable aplastic anemia (Figure 1).In this family, subjects with a hematopoietic defect died ata younger age (25, 26, 31, and 81 years, with a mean of 41 years)than did those with idiopathic pulmonary fibrosis (76, 70, 63,57, 60, and 66 years, with a mean of 65 years). We also exploredthe possibility that asymptomatic mutation carriers with shorttelomeres had cytopenias that reflected early changes of aplasticanemia. We examined complete blood counts in members of fiveof the families — Family A, Family B, Family C, FamilyD, and Family E — and found no abnormalities.
To assess whether the pulmonary fibrosis in the probands couldbe differentiated from other cases of idiopathic pulmonary fibrosis,we reviewed the clinical data. The presentation, age at onset,and findings on computed tomography were indistinguishable fromthose of other cases of the disease (Table 1 and Figure 4).None of these subjects had a response to trials of immunosuppressivetherapy. In all cases, the proband had undergone lung biopsy,and five of the six probands had the common lesion of usualinterstitial pneumonia. A biopsy specimen obtained from thesixth proband showed idiopathic interstitial pneumonia, notclassifiable. Different idiopathic interstitial pneumonia pathologicallesions have been described in the same patient, as well asin members of the same family with the disease, underscoringthe need for precise molecular characterization.4,35
Figure 4. High-Resolution Computed Tomographic Images of the Midlung (Panel A through Panel D) and Bases (Panel E through Panel H) in Probands in Four Families.
Subject numbers are shown in the upper right-hand corners of the panels. In all four probands, subpleural honeycombing and increased reticular densities are visible in the views at the bases. These changes extend up to the midlung and apexes in some subjects with more advanced stages of disease (e.g., Subject DIII.2).
Discussion
We have shown that mutant telomerase is associated with familialidiopathic pulmonary fibrosis, which suggests that the spectrumof disease caused by telomere shortening is more extensive thanpreviously appreciated and that a subgroup of families withpulmonary fibrosis falls on that spectrum.
Short dysfunctional telomeres activate a DNA damage responsethat leads to cell death or cell-cycle arrest. This responseis manifested clinically as organ failure in tissues of highturnover (bone marrow, skin, and gastrointestinal tract) inpatients with, and in an animal model of, dyskeratosis congenita.14,24The presence of pulmonary fibrosis in dyskeratosis congenita,along with the presence of telomerase mutations in some familieswith idiopathic pulmonary fibrosis, suggests that bronchoalveolarepithelium is also constantly replaced and relies on local progenitorreserves that are limited by short telomeres.
On the basis of these findings, we propose that the fibroticlesion in patients with short telomeres is provoked by a lossof alveolar cells rather than by a primary fibrogenic process,such as one that would seem to occur in autoimmune disease associatedwith lung fibrosis. This view is supported by the fact thatmisfolded surfactant protein C (present in affected subjectscarrying a mutation in the corresponding gene) appears to betoxic to alveolar cells.4 Therefore, it is possible that insome types of fibrosis, damage of epithelial cells leads toa remodeling response that appears clinically as usual interstitialpneumonia. Taken together, these considerations may explainthe lack of success in reversing idiopathic fibrosis with agentsthat modulate immune or inflammatory signals and support theidea that at least in some cases, strategies aimed at preventingthe loss of alveolar cells, or local responses to such cellloss, may have a greater clinical impact.
Although mutations in the essential components of telomerasedo not seem to account for a majority of cases of familial pulmonaryfibrosis, telomere shortening as a process may still contributeto the pathogenesis. There is evidence that short telomeres,rather than telomerase mutations, correlate with disease indyskeratosis congenita. In an animal model of dyskeratosis congenita,wild-type mice who inherit short telomeres appear to have anoccult genetic disease and display phenotypes similar to thosein mice that are heterozygous for mutant telomerase RNA.14 Acquiredstates that increase tissue turnover are also associated withshort telomeres. One study showed that both current and formersmokers had shorter telomeres than did age-matched nonsmokers.36In addition, there is some evidence that telomeres of the alveolarepithelium in smokers are shorter than those of the alveolarepithelium in nonsmokers.37 It is therefore possible that somatictelomere shortening, caused by conditions that increase cellturnover (e.g., smoking), could contribute to fibrosis. In astudy evaluating disease onset in relatives of familial probandswith idiopathic pulmonary fibrosis, cigarette smoking and olderage were the strongest predictors.35 Because telomere shorteningoccurs with aging and can be acquired, it may contribute tothe disease pathogenesis even in persons with wild-type telomerase.
Our study will have clinical implications, assuming that ourfindings are replicated by other investigators. As suggestedby the experience in aplastic anemia,23 patients who carry eitherhTERT or hTR mutations are unlikely to have a response to immunosuppressionand may be good candidates for investigational clinical trials.The presence of a diagnostic genetic test gives patients atrisk and their clinicians a chance to consider early screeningand evaluation tailored to identification of complications ofdyskeratosis congenita. Patients with dyskeratosis congenita,especially those with severe forms, have a predisposition tocancers of the skin, hematopoietic system, and oral mucosa.
Finally, telomere length may serve as a surrogate marker forthe identification of patients at greatest risk for carryingmutant telomerase genes. In our series of 15 subjects, longertelomeres appeared to predict the absence of a telomerase mutation,although this finding requires verification in larger studies.Since the consequences of carrying mutant telomerase genes canappear in adulthood as either idiopathic pulmonary fibrosisor aplastic anemia without dyskeratosis, the consideration ofsuch cases as part of a syndrome of telomere shortening mayheighten the index of suspicion and facilitate diagnosis.
Supported by a grant (NCI K08 118416) from the National Institutesof Health (NIH) (to Dr. Armanios), the Richard C. Ross JohnsHopkins School of Medicine Clinician Scientist Award (to Dr.Armanios), the Maryland Cigarette Restitution Fund (to JohnsHopkins University), a grant from the Johns Hopkins Institutefor Cellular Engineering Pilot Program (to Dr. Greider), a grant(HL K08 85406) from the NIH and the Francis Family Foundation(to Dr. Lawson), a grant (AI29524) from the NIH and grants (MOP38075and GMH79042) from the Canadian Institute of Health Research(to Dr. Lansdorp), a Vanderbilt Discovery Grant and the RudyW. Jacobson endowment (to Dr. Loyd), and a grant (M01 RR-00095)from the National Center for Research Resources of the NIH tosupport the Vanderbilt Clinical Research Center.
Dr. Lansdorp reports being a founding shareholder in RepeatDiagnostics, a company that specializes in length measurementof leukocyte telomeres with the use of flow FISH. No other potentialconflict of interest relevant to this article was reported.
We thank the subjects and their families who participated inthis study and their clinicians, especially Drs. Adaani Frostand Keith E. Kelly and nurses Wendi Mason and Rhonda Greer;the Johns Hopkins Fragment Analysis Laboratory and Laura Kasch-Semenzafor their help with DNA sequencing; Melissa Prince for technicalassistance; and Dr. David Valle for his valuable advice.
Source Information
From the Department of Oncology (M.Y.A., C.W.G.), the Graduate Program in Cellular and Molecular Medicine (J.K.A.), the Institute of Genetic Medicine (R.G.I.), and the Department of Molecular Biology and Genetics (C.W.G.), Johns Hopkins University School of Medicine, Baltimore; the Department of Chemistry and Biochemistry (J.J.-L.C., M.X.) and the School of Life Sciences (J.J.-L.C.), Arizona State University, Tempe; the Departments of Pediatrics (J.D.C., J.A.P.) and Medicine (C.M., W.E.L., J.E.L.), Vanderbilt University School of Medicine, Nashville; the Veterans Affairs Medical Center, Nashville (W.E.L.); and the Terry Fox Laboratory (I.V., P.M.L.) and the British Columbia Cancer Agency and the Department of Medicine (P.M.L.), University of British Columbia, Vancouver, BC, Canada.
Address reprint requests to Dr. Armanios at the Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans St., CRB 186, Baltimore, MD 21231, or at marmani1{at}jhmi.edu.
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