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Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, Liao W, Oh DH, Cleaver JE, LeBoit PE, Costello JF, Lehmann AR, Gray JW, Spellman PT, Arron ST, Huh N, Purdom E, Cho RJ. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Rep 2014; 9:1228-34. [PMID: 25456125 DOI: 10.1016/j.celrep.2014.10.031] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/26/2014] [Accepted: 10/11/2014] [Indexed: 12/25/2022] Open
Abstract
Somatic mutations in cancer are more frequent in heterochromatic and late-replicating regions of the genome. We report that regional disparities in mutation density are virtually abolished within transcriptionally silent genomic regions of cutaneous squamous cell carcinomas (cSCCs) arising in an XPC(-/-) background. XPC(-/-) cells lack global genome nucleotide excision repair (GG-NER), thus establishing differential access of DNA repair machinery within chromatin-rich regions of the genome as the primary cause for the regional disparity. Strikingly, we find that increasing levels of transcription reduce mutation prevalence on both strands of gene bodies embedded within H3K9me3-dense regions, and only to those levels observed in H3K9me3-sparse regions, also in an XPC-dependent manner. Therefore, transcription appears to reduce mutation prevalence specifically by relieving the constraints imposed by chromatin structure on DNA repair. We model this relationship among transcription, chromatin state, and DNA repair, revealing a new, personalized determinant of cancer risk.
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Affiliation(s)
- Christina L Zheng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Sciences University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Nicholas J Wang
- Department of Biomedical Engineering, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Jongsuk Chung
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Kyunggi-do 446-712, Korea
| | - Homayoun Moslehi
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Joseph S Hur
- Headquarters, Samsung Electronics, Seocho-gu, Seoul 137-857, Korea
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Swapna S Vemula
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Agne Naujokas
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kami E Chiotti
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service, St John's Institute of Dermatology, Guy's and St Thomas' NHS Trust, London SE1 9RT, UK
| | - Andrew J Blumberg
- Department of Mathematics, University of Texas, Austin, Austin, TX 78712, USA
| | - Celeste V Bailey
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Gary M Fudem
- Department of Surgery, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Frederick G Mihm
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Bari B Cunningham
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Isaac M Neuhaus
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dennis H Oh
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA; Dermatology Research Unit, Veterans Affairs Medical Center, San Francisco, San Francisco, CA 94121, USA
| | - James E Cleaver
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Philip E LeBoit
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RH, UK
| | - Joe W Gray
- Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR 97239, USA; Department of Biomedical Engineering, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Paul T Spellman
- Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Sarah T Arron
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nam Huh
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Kyunggi-do 446-712, Korea
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA.
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Abstract
The use of free scapular fasciocutaneous flaps for reconstruction of recalcitrant grade 6 venous stasis ulcers has shown excellent early success rates. Venous refilling times measured postoperatively over the flaps by photoplethysmography have noted improvements to normal levels. Preliminary anatomic studies have demonstrated valves in the circumflex scapular veins of flaps used in reconstruction. The purpose of this study was to investigate and document the number, morphology, size, and location of valves in the human dorsal thoracic fascia. Ten scapular flaps were obtained from unembalmed cadavers and injected with methyl methacrylate. Each flap cast was divided into four parts: proximal, right and left, and distal, right and left. We reduced the size of specimens (the largest being 24 x 11 mm) and studied them in a scanning electron microscope. We identified all valves, estimated the diameter of the corresponding vein, calculated the depth of the valvular sinus, and related it to the corresponding venous size. Light microscopy and transmission electron microscopy were used as assisting tools applied to glutaraldehyde-fixed specimens. Analysis of injected specimens showed that valves were most abundant in veins with a luminal diameter of 30 to 120 microns (59.3 percent of 905 valves). The depth of valves became larger with increasing venous diameter. The sizes of valve sinuses were not different for individual valves. Except for veins larger than 1000 microns in diameter, there was no significant difference between the number of valves in different parts of an individual flap, nor were there significant differences between the valve numbers in different flaps. Most valves were bicuspid; only in the vein category of 30 to 120 microns were unicuspid valves encountered. Valves sometimes were located in series in a short segment of a vein; occasionally, they were found at the merging site of two veins. Transmission electron microscopy showed that valve leaflets had collagen fibers that ascended toward the tip of the leaflet and occasionally were accompanied by elastic fibers. Myofibroblasts were regularly present in the valve leaflets. These data show that fasciocutaneous flaps from the scapular region have numerous valves (90 valves on average in each flap) in the venous microcirculation. The microvenous valves in the dorsal thoracic fascia appear to be structurally similar to valves in larger veins. These valves may play a role in the improved hemodynamics and promising clinical outcome of patients with chronic venous insufficiency who have undergone free scapular flap reconstruction.
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Affiliation(s)
- S Aharinejad
- Department of Anatomy and Cell Biology, University of Massachusetts Medical Center, Worcester, USA
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