Blinded by the UV light: How the focus on transcription-coupled NER has distracted from understanding the mechanisms of Cockayne syndrome neurologic disease
Introduction
Patients with the genetic disease xeroderma pigmentosum (XP) are highly sensitive to sunlight exposure, and have a greater than 10,000× increased risk of cancer on sun exposed areas of the body [1]. Based upon the earlier discovery of nucleotide excision repair [2], the landmark observation by Cleaver [3] that patients with XP are unable to carry out nucleotide excision repair (NER) was the first description of a DNA repair disease. The subsequent discovery that cells from patients with Cockayne syndrome (CS) have a defect in a sub-pathway of NER, referred to as transcription-coupled nucleotide excision repair (TC-NER) [4], [5] led to the identification of CS as a DNA repair disease as well. CS is a rare neurodevelopmental disorder with progeriod features, and sun sensitivity, and the NER defect common to both diseases provided a convincing explanation for the shared sun sensitive phenotype.
The discovery of the TC-NER defect in CS cells brought this extremely rare disease to the attention of world-class scientists working on DNA repair and transcription, resulting in several ground breaking scientific publications, and much progress into understanding the mechanistic basis of TC-NER [6], [7]. In addition, knowledge of the DNA repair defect was essential to the cloning of the genes responsible for CS [8], [9]. However, the association between CS and TC-NER deficiency has had a negative impact as well. Numerous publications on the mechanistic basis of TC-NER, utilizing cells from CS patients, reinforced the association between CS and TC-NER deficiency. Furthermore, the shared NER deficiency in both XP and CS fostered the idea that all of the clinical features of CS, including the neurologic disease, are the result of the TC-NER defect (e.g. [10]). The obvious problem is that while both XP and CS patients have neurologic abnormalities, the nature of the neurologic abnormalities in CS are fundamentally different than those in XP [11], [12].
In my view, much of the confusion in the literature is the result of looking at CS through the lens of the well-known TC-NER deficiency. In fact, cells from CS patients have multiple abnormalities in addition to defective TC-NER. In this work, I will take the opposite approach, starting with a description of the clinical features of CS with a particular emphasis on CS neurologic disease. I then consider which of the various molecular abnormalities that have been described in CS cells, including but not limited to the TC-NER defect, provides the best explanation for the different pathologies of CS neurologic disease. Specifically, I will propose an updated version of the original transcription syndrome hypothesis of CS [13], [14], [15], [16] expanded to include an important role for defective transcription by both RNA polymerase I (RNAPI) and RNA polymerase II (RNAPII) in CS, and argue that this expanded transcription hypothesis provides a better explanation for many aspects of CS neurologic disease than defective DNA repair. I will also consider the implications of the expanded transcription syndrome hypothesis for interpreting recent findings from mouse models of CS. Finally, I will consider the translational implications of different hypotheses for the pathophysiology of CS. As such, this work is not intended to be a comprehensive review of CS, but a different way of looking at the mechanistic basis of CS neurologic disease. Since neurologic disease is of far greater clinical significance to CS patients than sun sensitivity, understanding its mechanistic basis has important implications for the development of treatments and therapies which are urgently needed.
Section snippets
Cockayne syndrome (CS) and CS neurologic disease
CS is a rare autosomal recessive disease, characterized by severe growth failure, neurologic disease, developmental abnormalities, degeneration of multiple organ systems including the eye and ear, cataracts, and, in most (but not all) patients, sun sensitivity [17], [18], [19], [20]. CS can result from mutations in either of two genes: ERCC6 (CSB) or ERCC8 (CSA). In addition, a subset of patients with mutations in the XPB, XPD, and XPG genes have the somatic features of CS, as well as the
Transcription-coupled NER and its relevance to CS
Before assessing the relevance of defective TC-NER for CS neurologic disease, it is necessary to provide some basic information about NER and TC-NER. Since several comprehensive and detailed reviews of various aspects of NER have been recently published in a special issue of DNA Repair [28] here I will give only a basic description of the processes, and refer interested readers to these reviews.
Defective repair of oxidative DNA damage in CS and its relationship to CS neurologic disease
The inability of defective TC-NER to explain the somatic features of CS does not rule out a possible role for defective repair of oxidative DNA damage in the CS phenotype. The concept that CS results from defective repair of oxidative DNA damage is a very popular concept in the literature, and has been reviewed by others [78], [79]. In my view, however, part of the attraction of the oxidative DNA damage hypothesis of CS is based in part on two mutually reinforcing but flawed concepts: CS as a
A New look at an old hypothesis: CS as a RNAPI and RNAPII transcription disease
The identification of the XPD and XPB helicases as components of the transcription factor TFIIH [102], [103] was an important discovery which dramatically impacted our understanding of the relationship between DNA repair, transcription, and human disease. This finding and subsequent work led to the concept that while XP is a DNA repair disorder, CS and trichothiodystrophy (TTD), could be thought of as “transcription syndromes”, i.e. diseases resulting from abnormalities of transcription [13],
An expanded version of the transcription syndrome hypothesis: CS as a RNA polymerase I and II transcription disorder
A combination of defective transcription by RNAPI, coupled with abnormalities in the regulation of transcription by RNAPII, provides plausible explanation for many of the somatic features of CS, including growth defects and aspects of CS neurologic disease. Some examples are given below, and a schematic diagram summarizing this hypothesis is given in Fig. 2. In Fig. 2 and the following text, I have separated the discussion of RNAPI and RNAPII for clarity, and to emphasize the potential role of
Mouse models of CS neurologic disease and their mechanistic interpretation
Several mouse models of CS have been generated, mostly from the Hoeijmakers laboratory, which have had an important impact on the CS field. The first of these was a mouse with a stop codon mutation in Csb [155]. While fibroblasts from these mice were sensitive to killing by UV light, and showed defects in measures of TC-NER, they had an increased incidence of skin cancer in response to UV, in contrast to human CS patients. These mice were slightly smaller than wild-type controls, and displayed
Therapeutic implications
Understanding the mechanistic basis of a human disease is essential for the rational development of treatments and therapies for the patients. At present, the only documented treatment for CS neurologic disease is for tremors and other motor complications that are observed in some CS type I patients [162]. For this reason, I have taken a critical look at multiple mechanisms of CS neurologic disease, because they have quite different implications for additional potential therapies.
As discussed
Summary and concluding remarks
CS is a devastating neurodevelopmental disorder, with growth abnormalities, progeriod features, and sun sensitivity. While it was the sun sensitivity that led to the discovery of the TC-NER defect in CS patients, sun sensitivity is a relatively trivial aspect of the clinical picture compared to the neurologic disease. As such, a better understanding of the mechanistic basis of CS neurologic disease is urgently needed, as it essential to the development of rational therapeutic strategies. In
Acknowledgements
This paper was inspired by meeting patients with CS, and discussions with their families, at events organized by the Share and Care Cockayne syndrome network (http://cockaynesyndrome.net/main/). I also thank Cheryl Marietta, Dr. Rebecca Laposa, and anonymous referees for suggestions and helpful comments on the manuscript, and Nicole Patten for the photomicrograph used in Fig. 1.
The human tissue used in Fig. 1 was obtained from the NICHD Brain and Tissue Bank for Developmental Disorders at the
References (166)
- et al.
Shining a light on xeroderma pigmentosum
J. Invest. Dermatol.
(2012) Nucleotide excision repair of DNA: the very early history
DNA Repair (Amst.)
(2011)- et al.
DNA damage response and transcription
DNA Repair (Amst.)
(2011) - et al.
The Cockayne syndrome group A gene encodes a WD repeat protein that interacts with CSB protein and a subunit of RNA polymerase II TFIIH
Cell
(1995) - et al.
ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne's syndrome and preferential repair of active genes
Cell
(1992) - et al.
Defective DNA repair and neurodegenerative disease
Cell
(2007) - et al.
Neurodegeneration in hereditary nucleotide repair disorders
Brain Dev.
(1999) - et al.
Do all of the neurologic diseases in patients with DNA repair gene mutations result from the accumulation of DNA damage?
DNA Repair (Amst.)
(2008) - et al.
TFIIH: a key component in multiple DNA transactions
Curr. Opin. Genet. Dev.
(1996) - et al.
Xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome: a complex genotype–phenotype relationship
Neuroscience
(2007)
Neuropathology of Cockayne syndrome: evidence for impaired development, premature aging, and neurodegeneration
Mech. Ageing Dev.
Xeroderma pigmentosum/cockayne syndrome complex: first neuropathological study and review of eight other cases
Eur. J. Paediatr. Neurol.
Multistep damage recognition, pathway coordination and connections to transcription, damage signaling, chromatin structure, cancer and aging: current perspectives on the nucleotide excision repair pathway
DNA Repair (Amst.)
Complementation of the xeroderma pigmentosum DNA repair defect in cell-free extracts
Cell
Reconstitution of human DNA repair excision nuclease in a highly defined system
J. Biol. Chem.
DNA repair in an active gene: removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall
Cell
Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene
Cell
Premature aging and cancer in nucleotide excision repair-disorders
DNA Repair (Amst.)
Cockayne syndrome A and B proteins differentially regulate recruitment of chromatin remodeling and repair factors to stalled RNA polymerase II in vivo
Mol. Cell
XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase
DNA Repair (Amst.)
A history of TFIIH: two decades of molecular biology on a pivotal transcription/repair factor
DNA Repair (Amst.)
Regulation of endonuclease activity in human nucleotide excision repair
DNA Repair (Amst.)
DNA polymerases and repair synthesis in NER in human cells
DNA Repair (Amst.)
The xeroderma pigmentosum pathway: decision tree analysis of DNA quality
DNA Repair (Amst.)
Transcription-coupled DNA repair is genomic context-dependent
J. Biol. Chem.
The case for 8,5′-cyclopurine-2′-deoxynucleosides as endogenous DNA lesions that cause neurodegeneration in xeroderma pigmentosum
Neuroscience
A new UV-sensitive syndrome not belonging to any complementation groups of xeroderma pigmentosum or Cockayne syndrome: siblings showing biochemical characteristics of Cockayne syndrome without typical clinical manifestations
Mutat. Res.
Adult-onset neurological degeneration in a patient with Cockayne syndrome and a null mutation in the CSB gene
J. Invest. Dermatol.
The oxidative DNA lesion 8,5′-(S)-cyclo-2′-deoxyadenosine is repaired by the nucleotide excision repair pathway and blocks gene expression in mammalian cells
J. Biol. Chem.
Oxygen free radical damage to DNA. Translesion synthesis by human DNA polymerase eta and resistance to exonuclease action at cyclopurine deoxynucleoside residues
J. Biol. Chem.
Malondialdehyde: a product of lipid peroxidation, is mutagenic in human cells
J. Biol. Chem.
Measurement of (5′R)- and (5′S)-8,5′-cyclo-2′-deoxyadenosines in DNA in vivo by liquid chromatography/isotope-dilution tandem mass spectrometry
Biochem. Biophys. Res. Commun.
Lipid peroxidation-induced DNA damage in cancer-prone inflammatory diseases: a review of published adduct types and levels in humans
Free Radic. Biol. Med.
The current evidence for defective repair of oxidatively damaged DNA in Cockayne syndrome
Free Radic. Biol. Med.
Pathways for repairing and tolerating the spectrum of oxidative DNA lesions
Cancer Lett.
Genetic modulation of senescent phenotypes in Homo sapiens
Cell
Aicardi–Goutieres syndrome (AGS)
Eur. J. Paediatr. Neurol.
Taking a “good” look at free radicals in the aging process
Trends Cell Biol.
Proliferative neural stem cells have high endogenous ROS levels that regulate self-renewal and neurogenesis in a PI3K/Akt-dependant manner
Cell Stem Cell
Host cell reactivation of plasmids containing oxidative DNA lesions is defective in Cockayne syndrome but normal in UV-sensitive syndrome fibroblasts
DNA Repair (Amst.)
Mouse CSB protein is important for gene expression in the presence of a single-strand break in the non-transcribed DNA strand
DNA Repair (Amst.)
Defective repair replication of DNA in xeroderma pigmentosum
Nature
The genetic defect in Cockayne syndrome is associated with a defect in repair of UV-induced DNA damage in transcriptionally active DNA
Proc. Natl. Acad. Sci. U.S.A.
Deficient repair of the transcribed strand of active genes in Cockayne's syndrome cells
Nucleic Acids Res.
Transcription-coupled DNA repair: two decades of progress and surprises
Nat. Rev. Mol. Cell Biol.
Cockayne syndrome: defective repair of transcription?
EMBO J.
Nucleotide excision repair syndromes: molecular basis and clinical symptoms
Philos. Trans. R: Soc. Lond. B: Biol. Sci.
TFIIH: when transcription met DNA repair
Nat. Rev. Mol. Cell Biol.
Cockayne Syndrome
Wide clinical variability among 13 new Cockayne syndrome cases confirmed by biochemical assays
Arch. Dis. Child.
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