Genomics Personalized Medicine and Oral Disease 1st edition by Stephen Sonis ISBN 3319179411 978-3319179414

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ISBN 10:   3319179411
ISBN 13:   978-3319179414
Author:   Stephen Sonis 

The objective of this book is to catalyze the application of genomics to the diagnosis and treatment of oral diseases by comprehensively presenting focused discussions on the current state of knowledge. The first section book provides basic information about genetics, genomics and personalized medicine and the informatical methods available to apply and organize genetic data so that it has clinical relevance. Recognizing the genetic robustness of the oral cavity, the introductory section includes chapters on the oral micro biome and host genomics and response to infectious agents. The next two sections contain chapters which describe the genomics of specific oral diseases and conditions, including the genetic basis for mechanism and risk of treatment toxicities associated with cancer therapy and bisphosphonates. Four chapters focus on gene-based therapies and the pharmacogenomics applied to oral disease. The final chapter presents a provocative summary which describes a comprehensive vision of the melding of genomics to personalized medicine and the potential actionable outcomes that will likely affect clinical practice in the upcoming years.

 Genomics, Personalized Medicine and Oral Disease 1st Table of contents:

1. The Fundamentals: Chromosomes, DNA and Genes (Figure 1)
2. Mutations and Variations in Genes
3. Epigenetics
4. Personalized Medicine
5. References
6. Current and Evolving Technologies
7. Background on Genomic-Based Technologies
8. Genomic Isolation Methods
9. Genomics-Based Analytical Methods
10. Microarrays
11. QRT-PCR
12. Digital PCR
13. Next Generation Sequencing
14. NGS Platforms
15. Pyrosequencing
16. Sequencing by Synthesis
17. Sequencing by Ligation
18. Ion Semiconductor
19. “Third-Generation” Sequencing
20. Single-Molecule Real-Time
21. Nanopore DNA Sequencing
22. Sequencing NGS Methods in Development
23. NGS in the Clinic
24. Conclusion
25. References
26. The Oral Microbiome and Its Relationship to Genomics and Oral Disease
27. What Metagenomics Has Revealed about the Oral Microbiome
28. Concepts and Advances in Microbiome and Metagenomics
29. Quantitative Approaches to Microbiome Analysis
30. Overview of Technologies Applied to Metagenomic Microbiome Research
31. Transcriptomic Approaches
32. Proteomics
33. Metabolomics
34. In vitro Models Supporting ‘Omic’ Analysis
35. Progress in Defining a ‘Healthy’ or ‘Core’ Oral Microbiome
36. Progress in Microbiome Characterization in Disease States
37. Periodontal Disease and Endodontic Periodontal Disease
38. Cariogenesis
39. Carcinogenesis
40. ‘Infectogenomics’: Relationship between Host Genetic Factors and Oral Microbiota
41. Characterization of Genetics Supporting Disease Emergence
42. Genetics and Periodontal Disease (PD)
43. Is there Genetic Predisposition Supporting Cariogenesis?
44. Advances in Proteomics in Assessing the Microbiome in Health and Disease States
45. Implications for Diagnostic and Therapeutic Approaches
46. Metagenomic and other ‘Omic’ Resources
47. Human Microbiome Project (HMP)
48. Human Oral Microbiome Database (HOMD: https://www.homd.org/)
49. Core Human Oral Microbiome Database (CORE: https://microbiome.osu.edu) and other 16s rRNA gene refere
50. OralCard
51. References
52. Host Genomics and Response to Infectious Agents
53. The Virus
54. Pathogenesis and Clinical Course
55. Host Immune Response to HSV-1 and Virus Evasion from Host Immunosurveillance
56. Innate Cytokine Response to Virus Molecular Patterns
57. Cellular Immunity
58. Humoral Immunity
59. Genetics, Genomics and Susceptibility to HSV-1 Infection
60. Lessons from Mouse Experimental HSV-1 Infection
61. TLR-IFN Pathways and Herpes Simplex Encephalitis
62. HLA Polymorphism
63. Diversity of NK-cell Receptors for HLA Class I
64. Diversity of Cellular Receptors for Immunoglobulin G
65. Genome-Wide Association Studies, Cold Sore Susceptibility Gene 1 and Apolipoprotein E—A Connection
66. Perspectives
67. References
68. Developmental Anomalies – Clefts
69. Introduction
70. Orofacial Development
71. Orofacial Cleft Epidemiology and Co-Morbidities
72. Epidemiology
73. Genetic Epidemiology
74. Co-Morbidities
75. Orofacial Cleft Phenotypes
76. Orofacial Cleft Genetics
77. Lessons Learned from Genetic Studies of Syndromic Orofacial Clefts
78. Lessons Learned from Genetic Studies of Nonsyndromic Orofacial Clefts
79. Orofacial Clefts and Other Developmental Anomalies: Future Directions and Challenges for Personalize
80. Reference
81. Caries
82. Dental Caries: Public Health and Pathogenesis
83. Family-Based Studies
84. Genetic Association and Bioinformatics Studies
85. Dental Caries Phenotypes
86. Revisiting GWAS Using Innovative Phenotypes
87. Prospects and Challenges for Personalized Medicine
88. References
89. Periodontal Disease
90. Epidemiology
91. Etiopathogenesis
92. Role of the Oral Microflora in the Disease Etiology of Periodontitis
93. Adipositas as a Likely Susceptibility Factor of PD
94. Current Strategies to Identify the Genetic Basis of PD
95. Candidate Gene Association Studies (CGAS)
96. Genome-Wide Association Studies (GWAS)
97. Validated Genetic Risk Factors of PD
98. NPY (Neuropeptide Y)
99. ANRIL (CDKN2BAS)
100. PLG (Plasminogen)
101. GLT6D1 (Glycosyltransferase 6 Domain Containing 1)
102. Other Genetic Risk Loci of PD
103. Application of Genomics to Guide Diagnosis of PD
104. Application of Genomics to Guide Prevention and Treatment of PD
105. Outlook
106. References
107. Aphthous Stomatitis
108. Introduction and Concepts
109. Clinical Classification
110. TH1 Polarization of Immune Response in RAS
111. TNF-α as the Key Cytokine for RAS
112. Importance of the Professional Antigen-Presenting Cells to the Maintenance of Bucal Tolerance
113. Importance of the Epithelial Cell in Maintaining Buccal Tolerance
114. Importance of the Epithelial Celular Permeability to the Maintenance of Buccal Tolerance
115. Importance of the TLR in the Control of Immune Response and the Permeability of the Buccal Mucosa
116. Future Perspectives
117. Conclusion
118. References
119. Lichen Planus
120. Introduction
121. Methods
122. Results
123. Discussion
124. Experimental Evidence of Leader Genes Involvement in OLP
125. Topological Analysis
126. OLP-Related miRNAs
127. Limitations
128. Conclusions
129. References
130. Blistering Diseases – Pemphigoid
131. Introduction
132. Bullous Pemphigoid (BP)
133. Incidence
134. Pathogenesis
135. Clinical Presentation
136. Diagnosis
137. Treatment
138. Differential Diagnosis
139. Prognosis
140. Mucous Membrane Pemphigoid
141. Introduction
142. Incidence
143. Pathogenesis
144. Clinical Presentation
145. Diagnosis
146. Treatment
147. Differential Diagnosis
148. Prognosis
149. Pemphigoid Gestationis
150. Introduction
151. Incidence
152. Pathogenesis
153. Clinical Presentations
154. Diagnosis
155. Treatment
156. Differential Diagnosis
157. Prognosis
158. Linear IgA Bullous Disease
159. Introduction
160. Incidence
161. Pathogenesis
162. Clinical Presentation
163. Diagnosis
164. Differential Diagnosis
165. Treatment
166. Prognosis
167. Epidermolysis Bullosa Acquisita
168. Introduction
169. Incidence
170. Pathogenesis
171. Clinical Presentation
172. Diagnosis
173. Treatment
174. Differential Diagnosis
175. Prognosis
176. Pemphigus
177. Introduction
178. Pemphigus Vulgaris
179. Introduction
180. Incidence
181. Pathogenesis
182. Clinical Presentation
183. Diagnosis
184. Differential Diagnosis
185. Pemphigus Vegetans
186. Pemphigus Foliaceus
187. Introduction
188. Pathogenesis
189. Incidence
190. Clinical Presentation
191. Differential Diagnosis
192. Pemphigus Erythematosus
193. Introduction
194. Pathogenesis
195. Clinical Presentation
196. Diagnosis
197. IgA Pemphigus
198. Introduction
199. Incidence
200. Pathogenesis
201. Clinical Features
202. Diagnosis
203. Paraneoplastic Pemphigus
204. Introduction
205. Incidence
206. Clinical Features
207. Diagnosis
208. Differential Diagnosis
209. Pemphigus Herpetiformis
210. Introduction
211. Incidence
212. Pathogenesis
213. Clinical Features
214. Diagnosis
215. Differential Diagnosis
216. Investigations for Pemphigus Diseases
217. Treatment and Prognosis of Pemphigus Diseases
218. References
219. Salivary Gland Diseases
220. Introduction
221. Autoimmune Diseases
222. Granulomatous Diseases
223. Congenital Malformations
224. References
225. Premalignant Lesions
226. Introduction to Oral Epithelial Premalignancy
227. Pathobiological Mechanisms of OED
228. Chromosomal Instability Predisposes an Individual to Malignant Transformation
229. Loss of Heterozygosity
230. DNA Aneuploidy
231. Telomerase Dysfunction
232. Altered Signaling Pathways Enhance Oncogenesis or Deteriorate Tumor Suppression
233. TP53 Signaling Pathway
234. Cyclin D1 Signaling Pathway
235. Retinoblastoma Signaling Pathway
236. Receptor Tyrosine Kinase Signaling Pathway
237. “Super Competition” as the Potential Mechanism to Pioneer and Dominate the Precancerized Fields
238. Current Understanding of HPV-associated OED
239. Future Perspectives and Conclusion
240. References
241. Oral Cancer
242. Clinical and Epidemiological Features
243. Germline Predisposition
244. Somatic Genetic Events and Clonal Tumor Evolution
245. Major Genetic Abnormalities and Pathways
246. p53/Rb/CDKN2A
247. Notch/p63
248. EGFR/RAS/PIK3CA/PTEN/CASPASE8
249. TGFβ/SMAD/FAT1
250. Alterations in the Epigenome and Epigenetic Regulators
251. Additional Genes/Pathways
252. Adenoid Cystic Carcinoma
253. Conclusions
254. References
255. Bisphosphonate Related Osteonecrosis of the Jaw
256. Epidemiology and Time-to-Event Statistics
257. Genome-Wide Pharmacogenetics of Osteonecrosis of the Jaw
258. Discussion on Genomics and Etiology of ONJ
259. Lessons Learned
260. References
261. Gene Therapy for Xerostomia
262. Introduction
263. First Steps Towards Gene Therapy
264. Preclinical Proof of Concept
265. Clinical Study
266. References
267. Gene Therapy for Mucositis
268. Introduction
269. Oral Cavity/Oropharyngeal Radiation Mucositis
270. The Logic of Mitochondrial Targeted Radiation Protection
271. Molecular Mechanism of MnSOD Transgene Mediated Irradiation Protection
272. Animal Models of Irradiation-Induced Mucositis
273. MnSOD-Plasmid Liposome Gene Therapy for Radiation Protection
274. Transition to Small Molecule Radioprotectors, the Role of Formulations for Drug Delivery
275. GS-Nitroxide Small Molecule Radioprotective Therapy
276. Application of JP4-039 (GS-Nitroxide) in Organ Specific Radioprotection
277. GS-Nitroxides as Radioprotectors for the Oral Cavity/Oropharynx: Comparative Effectiveness to Other
278. Preclinical Evaluation of JP4-039/F15 as an Oral Cavity/Oropharyngeal Radioprotector: The Importance
279. Conclusions and Plans for Future Developments
280. Pharmacogenomics for Oral Disease
281. Pharmacogenomics
282. Pharmacogenomic Approaches to Correct X-linked Hypohidrotic Ectodemal Dysplasia
283. Personalized Oral and Head and Neck Oncology
284. Periodontitis
285. Dental Caries
286. Conclusion
287. References
288. Personalized Medicine, Genomics and Oral Diseases: The Future
289. Introduction
290. Pharmacogenomics
291. A Pharmacogenomics’ Story—Pharmacokinetics
292. Genomics and Pharmacodynamics
293. A Pharmacogenomics’ Story—Pharmacodynamics
294. Challenges of Applying Genomics to Individualized Medicine
295. Conclusions
296. References

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