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Bonnie Feldman DDS MBA
Y-Dan Bui
Take Charge of All Things
Autoimmune
Take Charge of All Things Autoimmune
+1.310.666.5312
drbonnie360@gmail.com
www.drbonnie360.com
@DrBonnie360
www.facebook.com/YourAutoImmunityConnection
Bonnie Feldman, DDS, MBA
DrBonnie360’s mission is to create a digitally
connected world of personalized care for
autoimmune patients.
We consult with startup companies and
entrepreneurs who are bringing new products
and services that will improve research,
diagnosis, and treatment for autoimmunity.
Y-Dan Bui
Content and Visual Design
UCLA Class of 2016
BS, Biology
Table of Contents
Latest Findings …............................................................................................................
The Invisible Epidemic: Incidence and Prevalence ….......................................................
The Invisible Epidemic: Statistical Invisibility…...............................................................
Polyautoimmunity: No Longer Organ Specific…..............................................................
Data as an Enabling Tool: Getting Closer to Precision Medicine
Big Data: Top-Down Bottom-Up Convergence…..............................................................
Basic Science Foundation For Discovery
Immunology
New Discovery Fuels Collaboration: Immunology & Repertoire Sequencing …................
Omics
Predictive Modeling….....................................................................................................
Systems Biology and Personal Data ….............................................................................
Autoimmunity: Sorting Through the Multiple Causes
Genetics and Autoimmunity
The Genes You Can’t Take Off: What is the Relationship Between Autoimmunity ….......
and Genetics?
Causes of Autoimmunity: Genetics & Genomics …..........................................................
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Table of Contents
Causes of Autoimmunity: Environment …......................................................................
Causes of Autoimmunity: Hormones …..........................................................................
Causes of Autoimmunity: Pathogenesis …......................................................................
Metabolomics
Causes of Autoimmunity: Microbiome Diet …................................................................
Microbiomics
The Microbiome Lifeline ….............................................................................................
The Microbiome Lifeline: Gut as An Organ of Immunity …..............................................
The Microbiome Lifeline: Gut-Brain Axis ….....................................................................
The Microbiome Lifeline: Fixing Your Leaky Gut is Key …................................................
The Microbiome Lifeline: Health Starts in the Mouth …..................................................
Epigenetics
Change Your Fate: What Can Epigenetics do for Autoimmunity? ….................................
A Different Kind of Self Help
Personal Trial and Error: Treatments & Therapies ….......................................................
Treatments & Therapies: Fecal Microbiota Transplants …...............................................
Treatments & Therapies: Prebiotics and Probiotics …......................................................
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Table of Contents
Prevention and Lifestyle Modifications: What We Can Do
Prevention and Lifestyle Modifications ….......................................................................
Prevention and Lifestyle Modifications: Food ….............................................................
Prevention and Lifestyle Modifications: Diet, Food, Nutrition ….....................................
Prevention and Lifestyle Modifications: Nutrigenomics and Autoimmunity …................
Prevention and Lifestyle Modifications: Exercise …........................................................
Prevention and Lifestyle Modifications: Meditation …....................................................
Prevention and Lifestyle Modifications: Community …...................................................
Prevention and Lifestyle Modifications: The Immune System’s Feedback Loops ….........
Prevention and Lifestyle Modifications: Mind-Body Feedback Loops …..........................
Prevention and Lifestyle Modifications: Digital Health …................................................
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© 2017 - All rights reserved.
Latest Findings
© 2017 - All rights reserved.
Latest Findings
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present illness (HPI): results of a blinded comparison." The American journal of
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Latest Findings
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Latest Findings
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The Invisible Epidemic: Incidence & Prevalence
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burden of disease 2010 study." Annals of the rheumatic diseases 73.7 (2014): 1316-1322.
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Across 54 Years of Population-based Data." Journal of Crohn's and Colitis 10.8 (2016): 934-942.
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The Invisible Epidemic: Incidence & Prevalence
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The Invisible Epidemic: Statistical Invisibility
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The Invisible Epidemic: Statistical Invisibility
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© 2017 - All rights reserved.
The Invisible Epidemic: Statistical Invisibility
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MilkenInstitute. 29 Jan 2014. Milken Institute. 6 Jan 2016.
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The Invisible Epidemic: Statistical Invisibility
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Management.” Citph. Jan 2010. Public Health Institute. 12 Jan 2016.
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non-communicable- diseases
© 2017 - All rights reserved.
Polyautoimmunity: No Longer Organ Specific
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syndrome.” Lupus 23.12 (2014): 1273-1275.
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bowel disease patients.” World Journal of Gastroenterology 20.46 (2014): 17463-17467.
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© 2017 - All rights reserved.
Data as an Enabling Tool:
Getting Closer to Precision Medicine
© 2017 - All rights reserved.
Big Data: Top-Down Bottom-Up Convergence
• Dove, Edward, Vural Özdemir, and Yann Joly. “Harnessing Omics Sciences, Population Databases, and
Open Innovation Models for Theranostics‐Guided Drug Discovery and Development.” Drug Development
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es_and_Open_Innovation_Models_for_TheranosticsGuided_Drug_Discovery_and_Development
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518.7539 (2015): 337–43.
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_autoimmune_disease_variants
• Greene, Casey et al. “Understanding multicellular function and disease with human tissue-specific
networks.” Nature Genetics (2015).
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e_with_human_tissue-specific_networks
© 2017 - All rights reserved.
Big Data: Top-Down Bottom-Up Convergence
• Groza, Tudor et al. “The Human Phenotype Ontology: Semantic Unification of Common and
Rare Disease.” The American Journal of Human Genetics (2015).
http://www.researchgate.net/publication/279631558_The_Human_Phenotype_Ontology_Sem
antic_Unification_of_Common_and_Rare_Disease
• Ramos-Casals, Manuel et al. “Google-driven search for big data in autoimmune
geoepidemiology: Analysis of 394,827 patients with systemic autoimmune diseases.”
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driven_search_for_big_data_in_autoimmune_geoepidemiology_Analysis_of_394827_patients
switch_systemic_autoimmune_diseases
© 2017 - All rights reserved.
Big Data: Top-Down Bottom-Up Convergence
• Stanberry, Larissa et al. “Integrative Analysis of Longitudinal Metabolomics Data from a
Personal Multi-Omics Profile.” Metabolites (2013).
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etabolomics_Data_from_a_Personal_Multi-Omics_Profile
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virome.” Science (2015).
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ological_profiling_of_human_populations_using_a_synthetic_human_virome
© 2017 - All rights reserved.
Basic Science Foundation for Discovery
© 2017 - All rights reserved.
Immunology
© 2017 - All rights reserved.
New Discovery Fuels Collaboration: Immunology
& Repertoire Sequencing
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specific immunotherapy.” Nature Communications (2014).
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New Discovery Fuels Collaboration: Immunology
& Repertoire Sequencing
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& Repertoire Sequencing
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Omics
© 2017 - All rights reserved.
Predictive Modeling
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musculoskeletal health.” Scientific Reports (2015).
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Predictive Modeling
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Predictive Modeling
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Specific_Alterations_in_the_Enteric_Virome_in_Inflammatory_Bowel_Disease
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Systems Biology and Personal Data
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© 2017 - All rights reserved.
Autoimmunity:
Sorting through the Multiple Causes
© 2017 - All rights reserved.
Genetics and Autoimmunity
© 2017 - All rights reserved.
The Genes You Can’t Take Off: What is the
Relationship Between Autoimmunity and
Genetics?
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Causes of Autoimmunity: Genetics & Genomics
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© 2017 - All rights reserved.
Causes of Autoimmunity: Genetics & Genomics
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© 2017 - All rights reserved.
Causes of Autoimmunity: Genetics & Genomics
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© 2017 - All rights reserved.
Causes of Autoimmunity: Genetics & Genomics
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(2016). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4938884/
• Topol, Eric. The Patient Will See You Now. New York: Basic Books, 2015. Print.
© 2017 - All rights reserved.
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Taking Charge of All Things Autoimmune

  • 1. © 2017 - All rights reserved. Bonnie Feldman DDS MBA Y-Dan Bui Take Charge of All Things Autoimmune
  • 2. Take Charge of All Things Autoimmune +1.310.666.5312 drbonnie360@gmail.com www.drbonnie360.com @DrBonnie360 www.facebook.com/YourAutoImmunityConnection Bonnie Feldman, DDS, MBA DrBonnie360’s mission is to create a digitally connected world of personalized care for autoimmune patients. We consult with startup companies and entrepreneurs who are bringing new products and services that will improve research, diagnosis, and treatment for autoimmunity. Y-Dan Bui Content and Visual Design UCLA Class of 2016 BS, Biology
  • 3. Table of Contents Latest Findings …............................................................................................................ The Invisible Epidemic: Incidence and Prevalence …....................................................... The Invisible Epidemic: Statistical Invisibility…............................................................... Polyautoimmunity: No Longer Organ Specific….............................................................. Data as an Enabling Tool: Getting Closer to Precision Medicine Big Data: Top-Down Bottom-Up Convergence….............................................................. Basic Science Foundation For Discovery Immunology New Discovery Fuels Collaboration: Immunology & Repertoire Sequencing …................ Omics Predictive Modeling…..................................................................................................... Systems Biology and Personal Data …............................................................................. Autoimmunity: Sorting Through the Multiple Causes Genetics and Autoimmunity The Genes You Can’t Take Off: What is the Relationship Between Autoimmunity …....... and Genetics? Causes of Autoimmunity: Genetics & Genomics ….......................................................... Page 6 Page 10 Page 12 Page 16 Page 18 Page 23 Page 28 Page 31 Page 36 Page 38
  • 4. Table of Contents Causes of Autoimmunity: Environment …...................................................................... Causes of Autoimmunity: Hormones ….......................................................................... Causes of Autoimmunity: Pathogenesis …...................................................................... Metabolomics Causes of Autoimmunity: Microbiome Diet …................................................................ Microbiomics The Microbiome Lifeline …............................................................................................. The Microbiome Lifeline: Gut as An Organ of Immunity ….............................................. The Microbiome Lifeline: Gut-Brain Axis …..................................................................... The Microbiome Lifeline: Fixing Your Leaky Gut is Key …................................................ The Microbiome Lifeline: Health Starts in the Mouth ….................................................. Epigenetics Change Your Fate: What Can Epigenetics do for Autoimmunity? …................................. A Different Kind of Self Help Personal Trial and Error: Treatments & Therapies …....................................................... Treatments & Therapies: Fecal Microbiota Transplants …............................................... Treatments & Therapies: Prebiotics and Probiotics …...................................................... Page 45 Page 49 Page 50 Page 59 Page 62 Page 68 Page 74 Page 77 Page 81 Page 86 Page 89 Page 92 Page 94
  • 5. Table of Contents Prevention and Lifestyle Modifications: What We Can Do Prevention and Lifestyle Modifications …....................................................................... Prevention and Lifestyle Modifications: Food …............................................................. Prevention and Lifestyle Modifications: Diet, Food, Nutrition …..................................... Prevention and Lifestyle Modifications: Nutrigenomics and Autoimmunity …................ Prevention and Lifestyle Modifications: Exercise …........................................................ Prevention and Lifestyle Modifications: Meditation ….................................................... Prevention and Lifestyle Modifications: Community …................................................... Prevention and Lifestyle Modifications: The Immune System’s Feedback Loops …......... Prevention and Lifestyle Modifications: Mind-Body Feedback Loops ….......................... Prevention and Lifestyle Modifications: Digital Health …................................................ Page 97 Page 98 Page 101 Page 103 Page 104 Page 105 Page 106 Page 107 Page 108 Page 110
  • 6. © 2017 - All rights reserved. Latest Findings
  • 7. © 2017 - All rights reserved. Latest Findings • Almario, Christopher V., et al. "Computer-generated vs. physician-documented history of present illness (HPI): results of a blinded comparison." The American journal of gastroenterology 110.1 (2015): 170- 179http://www.nature.com/ajg/journal/v110/n1/full/ajg2014356a.html • Barrett, Jeffrey C., Ian Dunham, and Ewan Birney. "Using human genetics to make new medicines." Nature Reviews Genetics (2015). http://www.nature.com/nrg/journal/v16/n10/full/nrg3998.html • Danese, Silvio, Claudio Fiocchi, and Julián Panés. "Drug development in IBD: from novel target identification to early clinical trials." Gut 65.8 (2016): 1233-1239. http://gut.bmj.com/content/65/8/1233.long
  • 8. © 2017 - All rights reserved. Latest Findings • Harel, Michal, and Yehuda Shoenfeld. "Predicting and preventing autoimmunity, myth or reality?." Annals of the New York Academy of Sciences 1069.1 (2006): 322-345. http://thedr.com/wp-content/uploads/2014/07/AI-Predicting-and-preventing-AI-Myth-or- Reality-Harel-4.pdf • Kaukinen, Katri, Katri Lindfors, and Markku Mäki. "Advances in the treatment of coeliac disease: an immunopathogenic perspective." Nature Reviews Gastroenterology & Hepatology 11.1 (2014): 36-44. http://www.nature.com/nrgastro/journal/v11/n1/abs/nrgastro.2013.141.html • Servick, Kelly. "Can 23andMe have it all?." (2015): 1472-1477. https://www.thekf.org/kf/programs/eminentscientists/es_ach/23andMe-Science-25- September-2015_1:en-us.pdf
  • 9. © 2017 - All rights reserved. Latest Findings • Shoenfeld, Yehuda, et al. "The autoimmunologist: geoepidemiology, a new center of gravity, and prime time for autoimmunity." Journal of autoimmunity 31.4 (2008): 325- 330.http://www.sciencedirect.com/science/article/pii/S0896841108000838
  • 10. © 2017 - All rights reserved. The Invisible Epidemic: Incidence & Prevalence • Cross, Marita, et al. "The global burden of rheumatoid arthritis: estimates from the global burden of disease 2010 study." Annals of the rheumatic diseases 73.7 (2014): 1316-1322. <http://ard.bmj.com/content/73/7/1316.short> • Feldman, Bonnie. “Why is Autoimmune Disease Under-served.” Slideshare (2015). http://bit.ly/1B57pNb • Groza, Tudor et al. “The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.” The American Journal of Human Genetics (2015). http://www.irdirc.org/the- human-phenotype-ontology-semantic-unification-of-common-and-rare-disease/ • Hammer, Turid, et al. "The Faroese IBD Study: Incidence of Inflammatory Bowel Diseases Across 54 Years of Population-based Data." Journal of Crohn's and Colitis 10.8 (2016): 934-942. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962362/>
  • 11. © 2017 - All rights reserved. The Invisible Epidemic: Incidence & Prevalence • Kaplan, Gilaad G. "The global burden of IBD: from 2015 to 2025." Nature Reviews Gastroenterology & Hepatology 12.12 (2015): 720-727. http://www.nature.com/nrgastro/journal/v12/n12/abs/nrgastro.2015.150.html • Malaty, Hoda M., et al. "Rising incidence of inflammatory bowel disease among children: a 12- year study." Journal of Pediatric Gastroenterology and Nutrition 50.1 (2010): 27-31. <http://journals.lww.com/jpgn/Fulltext/2010/01000/Rising_Incidence_of_Inflammatory_Bowel _Disease.11.aspx> • Nakazawa Jackson, Donna. The Autoimmune Epidemic. New York: A Touchstone Book, 2008. Print • “More than 450 Medicines in Development for Rare Diseases.” Medicines in Development (2013). http://phrma.org/Medicines-Development-Rare-Diseases
  • 12. © 2017 - All rights reserved. The Invisible Epidemic: Statistical Invisibility • Anderson, G. “Chronic Care: Making the Case for Ongoing Care.” Robert Wood Johnson Foundation. 7 March 2010. Robert Wood Johnson Foundation. 11 Jan 2016. http://www.rwjf.org/content/dam/farm/reports/reports/2010/rwjf54583 • Brezinski, Elizabeth A. Jaskaran S. Dhillon, and April W. Armstrong. “Economic Burden of Psoriasis in the UnitedStates: A systematic Review.” JAMA Dermatology. 151:6 (2015): 651-658. Web. 2 Feb. 2016. http://bit.ly/1nCOmeg • Conlee, K. D. & Roman, D. H. “The Digital Revolution Comes to US Healthcare.” Scbio. 29 June 2015. Goldman Sachs. 20 Dec 2015. http://www.scbio.org/resources/Documents/Internet%20of%20Things%20- %20Volume%205%20-%20The%20Digital%20Revolution%20comes%20to%20US%20HC%20- %20Jun%2029,%202015%5B1%5D.pdf
  • 13. © 2017 - All rights reserved. The Invisible Epidemic: Statistical Invisibility • “The Cost Burden of Autoimmune Disease: The Latest Front in the War on Healthcare Spending.” Diabetesed. March 2011. American Autoimmune Related Diseases Association (AARDA), National Coalition of Autoimmune Patient Groups (NCAPG). 12 Jan 2016 http://www.diabetesed.net/page/_files/autoimmune-diseases.pdf • Gerteis, J., Izrael, D., Deitz D., LeRoy, L., Ricciardi, R., Miller, T., &amp; Basu, J. “Multiple Chronic Conditions Chart Book.” Agency for Healthcare Research and Quality. Apr 2014. Department of Health & Human Services USA. 12 Jan 2016. http://www.ahrq.gov/sites/default/files/wysiwyg/professionals/prevention- chronic-care/decision/mcc/mccchartbook.pdf
  • 14. © 2017 - All rights reserved. The Invisible Epidemic: Statistical Invisibility • Kubendran, S., King, J. & DeVol, R. “Checkup Time: Chronic Disease and Wellness in America.” MilkenInstitute. 29 Jan 2014. Milken Institute. 6 Jan 2016. http://assets1b.milkeninstitute.org/assets/Publication/ResearchReport/PDF/Checkup-Time- Chronic-Disease-and-Wellness-in-America.pdf • “Primary Care in the New Health Economy: Time for a Makeover.” Pwc. Nov 2015. Health Research Institute. 19 Dec 2015. http://www.pwc.com/us/en/health-industries/our-perspective/primary-care-report- new-health-economy-2015.html • “The Problem: Preventable and Mismanaged Chronic Disease.” FightChronicDisease. Partnership to Fight Chronic Disease. 20 Dec 2015. http://www.fightchronicdisease.org/sites/default/files/docs/PFCDOverview_Upd ated9.29.09.pdf
  • 15. © 2017 - All rights reserved. The Invisible Epidemic: Statistical Invisibility • “The Role of Information and Communications Technology in Chronic Disease Management.” Citph. Jan 2010. Public Health Institute. 12 Jan 2016. http://citph.org/files/2013/11/The-Role- of-ICT- in-Chronic- Disease- Management-Public- Health-Institute.pdf • “The U.S., Government and Global Non-Communicable Diseases.” Kaiser Family Foundation. 7 April 2014. Henry J. Kaiser Family Foundation. 19 Dec 2015. http://kff.org/global-health- policy/fact-sheet/the- u-s- government-and- global- non-communicable- diseases
  • 16. © 2017 - All rights reserved. Polyautoimmunity: No Longer Organ Specific • Franco, -S, and -M Anaya. “The autoimmune tautology with a focus on antiphospholipid syndrome.” Lupus 23.12 (2014): 1273-1275. http://www.researchgate.net/publication/265733380_The_autoimmune_tautology_with_a_fo cus_on_antiphospholipid_syndrome • Zippi, Maddalena. “Extraintestinal manifestations in a large series of Italian inflammatory bowel disease patients.” World Journal of Gastroenterology 20.46 (2014): 17463-17467. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265606/pdf/WJG-20-17463.pdf
  • 17. © 2017 - All rights reserved. Data as an Enabling Tool: Getting Closer to Precision Medicine
  • 18. © 2017 - All rights reserved. Big Data: Top-Down Bottom-Up Convergence • Dove, Edward, Vural Özdemir, and Yann Joly. “Harnessing Omics Sciences, Population Databases, and Open Innovation Models for Theranostics‐Guided Drug Discovery and Development.” Drug Development Research (2012). http://www.researchgate.net/publication/263060822_Harnessing_Omics_Sciences_Population_Databas es_and_Open_Innovation_Models_for_TheranosticsGuided_Drug_Discovery_and_Development • Farh, Kyle et al. “Genetic and epigenetic fine mapping of causal autoimmune disease variants.” Nature 518.7539 (2015): 337–43. http://www.researchgate.net/publication/267753091_Genetic_and_epigenetic_fine_mapping_of_causal _autoimmune_disease_variants • Greene, Casey et al. “Understanding multicellular function and disease with human tissue-specific networks.” Nature Genetics (2015). http://www.researchgate.net/publication/275525447_Understanding_multicellular_function_and_diseas e_with_human_tissue-specific_networks
  • 19. © 2017 - All rights reserved. Big Data: Top-Down Bottom-Up Convergence • Groza, Tudor et al. “The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.” The American Journal of Human Genetics (2015). http://www.researchgate.net/publication/279631558_The_Human_Phenotype_Ontology_Sem antic_Unification_of_Common_and_Rare_Disease • Ramos-Casals, Manuel et al. “Google-driven search for big data in autoimmune geoepidemiology: Analysis of 394,827 patients with systemic autoimmune diseases.” Autoimmunity Reviews (2015). http://www.researchgate.net/publication/274513423_Google- driven_search_for_big_data_in_autoimmune_geoepidemiology_Analysis_of_394827_patients switch_systemic_autoimmune_diseases
  • 20. © 2017 - All rights reserved. Big Data: Top-Down Bottom-Up Convergence • Stanberry, Larissa et al. “Integrative Analysis of Longitudinal Metabolomics Data from a Personal Multi-Omics Profile.” Metabolites (2013). http://www.researchgate.net/publication/256413714_Integrative_Analysis_of_Longitudinal_M etabolomics_Data_from_a_Personal_Multi-Omics_Profile • Xu et al. “Comprehensive serological profiling of human populations using a synthetic human virome.” Science (2015). http://www.researchgate.net/publication/277778734_Viral_immunology._Comprehensive_ser ological_profiling_of_human_populations_using_a_synthetic_human_virome
  • 21. © 2017 - All rights reserved. Basic Science Foundation for Discovery
  • 22. © 2017 - All rights reserved. Immunology
  • 23. © 2017 - All rights reserved. New Discovery Fuels Collaboration: Immunology & Repertoire Sequencing • Burton, Bronwen et al. “Sequential transcriptional changes dictate safe and effective antigen- specific immunotherapy.” Nature Communications (2014). http://scholar.qsensei.com/content/1yq4qh • Caspi, Rachel R. "Immunotherapy of autoimmunity and cancer: the penalty for success." Nature reviews immunology 8.12 (2008): 970-976. <http://www.nature.com/nri/journal/v8/n12/full/nri2438.html> • Koues, Olivia I., et al. "Distinct gene regulatory pathways for human innate versus adaptive lymphoid cells." Cell 165.5 (2016): 1134-1146. http://immunology.ucsf.edu/sites/immunology.ucsf.edu/files/wysiwyg/1-s2.0- S0092867416304056-main.pdf
  • 24. © 2017 - All rights reserved. New Discovery Fuels Collaboration: Immunology & Repertoire Sequencing • Norman, Jason et al. “Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease.” Cell (2015). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312520/ • Poletaev et al. “Immunophysiology versus immunopathology: Natural autoimmunity in human health and disease.” Pathophysiology 19.3 (2012): 221-231. http://www.researchgate.net/publication/230655913_Immunophysiology_versus_immu nopathology_Natural_autoimmunity_in_human_health_and_disease • Ramesh, Manish et al. “Clonal and Constricted T cell repertoire in Common Variable Immune Deficiency.” Clinical immunology (Orlando, Fla.) (2015). http://www.ncbi.nlm.nih.gov/pubmed/25596453
  • 25. © 2017 - All rights reserved. New Discovery Fuels Collaboration: Immunology & Repertoire Sequencing • Robins, Harlan. “Immunosequencing: applications of immune repertoire deep sequencing.” Current Opinion in Immunology 25.5 (2013): 646–52. http://www.researchgate.net/publication/258059445_Immunosequencing_applications_of_i mmune_repertoire_deep_sequencing • Robinson, William. “Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery.” Nature Reviews Rheumatology 11.3 (2015): 171–182. http://www.pubfacts.com/detail/25536486/Sequencing-the-functional-antibody-repertoire- diagnostic-and-therapeutic-discovery
  • 26. © 2017 - All rights reserved. New Discovery Fuels Collaboration: Immunology & Repertoire Sequencing • Spreafico, Roberto et al. “A circulating reservoir of pathogenic-like CD4+ T cells shares a genetic and phenotypic signature with the inflamed synovial micro-environment.” Annals of the Rheumatic Diseases (2014): annrheumdis–2014–206-226. http://www.researchgate.net/publication/269719321_A_circulating_reservoir_of_pathogenic- like_CD4_T_cells_shares_a_genetic_and_phenotypic_signature_with_the_inflamed_synovial_ micro-environment • van der Vlist, Michiel, et al. "Immune checkpoints and rheumatic diseases: what can cancer immunotherapy teach us?." Nature Reviews Rheumatology 12.10 (2016): 593-604. <http://www.nature.com/nrrheum/journal/v12/n10/abs/nrrheum.2016.131.html>
  • 27. © 2017 - All rights reserved. Omics
  • 28. © 2017 - All rights reserved. Predictive Modeling • Ahmed, Usman et al. “Biomarkers of early stage osteoarthritis, rheumatoid arthritis and musculoskeletal health.” Scientific Reports (2015). http://www.researchgate.net/publication/273781983_Biomarkers_of_early_stage_osteoarthrit is_rheumatoid_arthritis_and_musculoskeletal_health • Chopra, Monika, Kulwinder Singh, and Neelam Verma. “AUTOIMMUNE AND INFLAMMATORY DISEASES BIOMARKERS.” International Journal of Biomedical and Advance Research (2012). http://ssjournals.com/index.php/ijbar/article/view/140/140
  • 29. © 2017 - All rights reserved. Predictive Modeling • Dagan, Amir, and Shaye Kivity. "Cutting edge data in autoimmunity: as presented in the 9th international congress of autoimmunity." Cutting Edge in Autoimmunity 61.1 (2015): 1-3. Web https://www.researchgate.net/publication/269177309_Cutting_edge_data_in_autoimmunity_ as_presented_in_the_9th_International_Congress_of_Autoimmunity • Jaberi‐Douraki, Majid et al. “Autoimmune responses in T1DM: quantitative methods to understand onset, progression, and prevention of disease.” Pediatric Diabetes 15.3 (2014): 162–174. http://www.researchgate.net/publication/262339657_Autoimmune_responses_in_T1DM_qua ntitative_methods_to_understand_onset_progression_and_prevention_of_disease
  • 30. © 2017 - All rights reserved. Predictive Modeling • Lee, James, and Kenneth Smith. “Prognosis in autoimmune and infectious disease: new insights from genetics.” Clinical & Translational Immunology 3.5 (2014): 15. http://www.researchgate.net/publication/269715667_Prognosis_in_autoimmune_and_infectio us_disease_new_insights_from_genetics • Norman, Jason et al. “Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease.” Cell (2015). http://www.researchgate.net/publication/271448551_Disease- Specific_Alterations_in_the_Enteric_Virome_in_Inflammatory_Bowel_Disease • Stanberry, Larissa et al. “Integrative Analysis of Longitudinal Metabolomics Data from a Personal Multi-Omics Profile.” Metabolites (2013). http://www.researchgate.net/publication/256413714_Integrative_Analysis_of_Longitudinal_M etabolomics_Data_from_a_Personal_Multi-Omics_Profile
  • 31. © 2017 - All rights reserved. Systems Biology and Personal Data • Alyass, Akram, Michelle Turcotte, and David Meyre. "From big data analysis to personalized medicine for all: challenges and opportunities." BMC medical genomics 8.1 (2015): 33. <https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-015-0108-y> • • Hu, Jessica Xin, Cecilia Engel Thomas, and Søren Brunak. "Network biology concepts in complex disease comorbidities." Nature Reviews Genetics(2016). http://www.nature.com/nrg/journal/v17/n10/full/nrg.2016.87.html • Kim, Ho-Youn, Hae-Rim Kim, and Sang-Heon Lee. “Advances in Systems Biology Approaches for Autoimmune Diseases.” Immune Network 14.2 (2014): 73–80. http://www.pubfacts.com/detail/24851096/Advances-in-systems-biology-approaches-for- autoimmune-diseases
  • 32. © 2017 - All rights reserved. Systems Biology and Personal Data • Greenwood, Veronique. “Disease Networks Show Molecular Connections." Quanta Magazine” (2015). https://www.quantamagazine.org/20150129-networks-reveal-the-connections-of-disease/ • Leung, Elaine et al. “Network-based drug discovery by integrating systems biology and computational technologies.” Briefings in Bioinformatics 14.4 (2013): 491–505. http://www.researchgate.net/publication/230644421_Network- based_drug_discovery_by_integrating_systems_biology_and_computational_technologies • Schork, and Nicholas. “Personalized medicine: Time for one-person trials.” Nature News (2015). http://www.nature.com/polopoly_fs/1.17411!/menu/main/topColumns/topLeftColumn/pdf/5 20609a.pdf
  • 33. © 2017 - All rights reserved. Systems Biology and Personal Data • Smarr, Larry. “Quantifying your body: A how‐to guide from a systems biology perspective.” Biotechnology Journal 7.8 (2012): 980–991. http://lsmarr.calit2.net/repository/Biotech_J._LS_published_article.pdf • Wu, Hao, Valentina Tremaroli, and Fredrik Bäckhed. "Linking microbiota to human diseases: a systems biology perspective." Trends in Endocrinology & Metabolism 26.12 (2015): 758-770. <http://www.sciencedirect.com/science/article/pii/S1043276015001940>
  • 34. © 2017 - All rights reserved. Autoimmunity: Sorting through the Multiple Causes
  • 35. © 2017 - All rights reserved. Genetics and Autoimmunity
  • 36. © 2017 - All rights reserved. The Genes You Can’t Take Off: What is the Relationship Between Autoimmunity and Genetics? • Cho, Judy H., and Marc Feldman. "Heterogeneity of autoimmune diseases: pathophysiologic insights from genetics and implications for new therapies." Nature medicine 21.7 (2015): 730-738. http://www.nature.com/nm/journal/v21/n7/full/nm.3897.html • Ritchie, M., Holzinger, E., Li, R., Pendergrass, S. & Kim, D. Methods of integrating data to uncover genotype-phenotype interactions. Nature Reviews Genetics (2015). http://www.nature.com/nrg/journal/v16/n2/abs/nrg3868.html • Seldin, MF. The genetics of human autoimmune disease: A perspective on progress in the field and future directions. Journal of autoimmunity (2015). https://ucdavis.pure.elsevier.com/en/publications/the- genetics-of-human-autoimmune-disease-a-perspective-on-progres
  • 37. © 2017 - All rights reserved. The Genes You Can’t Take Off: What is the Relationship Between Autoimmunity and Genetics? • Smilek, D. & Clair, W. Solving the puzzle of autoimmunity: critical questions. F1000Prime Reports 7, (2015). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335798/
  • 38. © 2017 - All rights reserved. Causes of Autoimmunity: Genetics & Genomics • Archer, Nassif, and O’Brien. “Genetic variants of SLC11A1 are associated with both autoimmune and infectious diseases: systematic review and meta-analysis.” Genes and Immunity (2015). http://www.researchgate.net/publication/274724921_Genetic_variants_of_SLC11A1_are_asso ciated_with_both_autoimmune_and_infectious_diseases_systematic_review_and_meta- analysis • Castiblanco, John, Mauricio Arcos-Burgos, and Juan-Manuel Anaya. “What is next after the genes for autoimmunity?” BMC Medicine 11 (2013): 197. http://www.biomedcentral.com/1741-7015/11/197 • Cho, Judy H., and Peter K. Gregersen. "Genomics and the multifactorial nature of human autoimmune disease." New England Journal of Medicine365.17 (2011): 1612-1623. http://www.nejm.org/doi/full/10.1056/nejmra1100030
  • 39. © 2017 - All rights reserved. Causes of Autoimmunity: Genetics & Genomics • Cunliffe, Vincent T. "Experience‐sensitive epigenetic mechanisms, developmental plasticity, and the biological embedding of chronic disease risk." Wiley Interdisciplinary Reviews: Systems Biology and Medicine 7.2 (2015): 53-71. https://www.sheffield.ac.uk/polopoly_fs/1.549053!/file/01.Cunliffe2015.pdf • Dieli-Crimi, Romina, Carmen Cénit, and Concepción Núñez. “The genetics of celiac disease: A comprehensive review of clinical implications.” Journal of Autoimmunity (2015). http://thirdworld.nl/the-genetics-of-celiac-disease-a-comprehensive-review-of-clinical-implications • Farh, Kyle et al. “Genetic and epigenetic fine mapping of causal autoimmune disease variants.” Nature 518.7539 (2015): 337–43. http://www.nature.com/nature/journal/v518/n7539/full/nature13835.html
  • 40. © 2017 - All rights reserved. Causes of Autoimmunity: Genetics & Genomics • Groza, Tudor et al. “The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.” The American Journal of Human Genetics (2015). http://www.cell.com/ajhg/abstract/S0002-9297(15)00234-7 • Gupta, Bhawna, and David Hawkins. “Epigenomics of autoimmune diseases.” Immunology and Cell Biology 93.3 (2015): 271–276. https://www.researchgate.net/publication/273703187_Epigenomics_of_autoimmu ne_diseases • Gutierrez-Arcelus, Maria, Stephen S. Rich, and Soumya Raychaudhuri. "Autoimmune diseases — connecting risk alleles with molecular traits of the immune system." Nature Reviews Genetics 17.3 (2016): 160-174. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896831/
  • 41. © 2017 - All rights reserved. Causes of Autoimmunity: Genetics & Genomics • Lee, Hanna J., et al. "Immunogenetics of autoimmune thyroid diseases: a comprehensive review." Journal of autoimmunity 64 (2015): 82-90. http://europepmc.org/articles/pmc4628844 • Lee, James, and Kenneth Smith. “Prognosis in autoimmune and infectious disease: new insights from genetics.” Clinical & Translational Immunology 3.5 (2014). http://www.nature.com/cti/journal/v3/n5/full/cti20148a.html • Marson, Alexander, William Housley, and David Hafler. “Genetic basis of autoimmunity.” Journal of Clinical Investigation (2015). http://www.jci.org/articles/view/78086 • McGarvey, Peter et al. “In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases.” BMC Immunology 15.1 (2014): 61. http://www.researchgate.net/publication/267753091_Genetic_and_epigenetic_fine_mapping_of_c ausal_autoimmune_disease_variants
  • 42. © 2017 - All rights reserved. Causes of Autoimmunity: Genetics & Genomics • Mikacenic, Carmen et al. “Cutting edge: Genetic variation in TLR1 is associated with Pam3CSK4-induced effector T cell resistance to regulatory T cell suppression.” Journal of immunology (Baltimore, Md. : 1950) 193.12 (2014): 5786–90. http://www.researchgate.net/publication/267931277_Cutting_Edge_Genetic_Variation_in_TLR1_Is_Asso ciated_with_Pam(3)CSK(4)-Induced_Effector_T_Cell_Resistance_to_Regulatory_T_Cell_Suppression • “NIH researchers reveal link between powerful gene regulatory elements and autoimmune diseases.” National Institutes Into Health (2015). http://www.nih.gov/news/health/feb2015/niams-17.htm • Oftedal, Bergithe et al. “Dominant Mutations in the Autoimmune Regulator AIRE Are Associated with Common Organ-Specific Autoimmune Diseases.” Immunity (2015). http://www.researchgate.net/publication/278792204_Dominant_Mutations_in_the_Autoimmune_Regul ator_AIRE_Are_Associated_with_Common_Organ-Specific_Autoimmune_Diseases
  • 43. © 2017 - All rights reserved. Causes of Autoimmunity: Genetics & Genomics • Parkes, Miles et al. “Genetic insights into common pathways and complex relationships among immune-mediated diseases.” Nature Reviews Genetics (2013). http://www.researchgate.net/publication/255689274_Genetic_insights_into_common_pathwa ys_and_complex_relationships_among_immune-mediated_diseases._Nat_Rev_Genet • Richardson, Bruce, and Dipak Patel. “Epigenetics in 2013: DNA methylation and miRNA—key roles in systemic autoimmunity.” Nature Reviews Rheumatology 10.2 (2014): 72–74. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332710/ • Ritchie, Marylyn et al. “Methods of integrating data to uncover genotype-phenotype interactions.” Nature Reviews Genetics (2015). http://qpcrupdate.eu/ritchie-et-al-integrative-bioinformatics-nature-2014.pdf
  • 44. © 2017 - All rights reserved. Causes of Autoimmunity: Genetics & Genomics • vel Szic, Katarzyna Szarc, et al. "From inflammaging to healthy aging by dietary lifestyle choices: is epigenetics the key to personalized nutrition?." Clinical epigenetics 7.1 (2015): 33. https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-015-0068-2 • Wang, Xuefeng, Eric Xing, and Daniel Schaid. “Kernel methods for large-scale genomic data analysis.” Briefings in bioinformatics 16.2 (2015): 183–92. http://bib.oxfordjournals.org/content/early/2014/07/22/bib.bbu024.full.pdf+html • Yang, Chin-An, and Bor-Luen Chiang. “Inflammasomes and human autoimmunity: A comprehensive review.” Journal of Autoimmunity (2015). http://www.researchgate.net/publication/49688650_Inflammasomes_and_autoimmunity
  • 45. © 2017 - All rights reserved. Causes of Autoimmunity: Environment • Agmon-Levin, Nancy, Zhexiong Lian, and Yehuda Shoenfeld. "Explosion of autoimmune diseases and the mosaic of old and novel factors." Cellular & molecular immunology 8.3 (2011): 189-192. http://www.nature.com/cmi/journal/v8/n3/full/cmi201070a.html • Anaya, Juan-Manuel, et al. "The autoimmune ecology." Frontiers in immunology 7 (2016). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844615/ • Ballantyne, Sarah. The Paleo Approach. Las Vegas: Victory Belt Publishing Inc, 2013. Print. • Blum, Susan. The Immune System Recovery Plan. New York: Scribner, 2013. Print. • Bogdanos, Dimitrios et al. “Infectome: A platform to trace infectious triggers of autoimmunity.” Autoimmunity Reviews 12.7 (2013): 726740. http://www.researchgate.net/publication/233983999_Infectome_A_platform_to_trace_infecti ous_triggers_of_autoimmunity
  • 46. © 2017 - All rights reserved. Causes of Autoimmunity: Environment • Campbell, Andrew. “Autoimmunity and the Gut.” Autoimmune Diseases 2014 (2014): 152428. http://www.researchgate.net/publication/262886119_Autoimmunity_and_the_Gu t • de St Groth, Barbara Fazekas. "Regulatory T-cell abnormalities and the global epidemic of immuno-inflammatory disease." Immunology and cell biology 90.3 (2012): 256-259. http://www.nature.com/icb/journal/v90/n3/full/icb2011113a.html • Horton, Daniel et al. “Antibiotic Exposure and Juvenile Idiopathic Arthritis: A Case– Control Study” Rutgers University (2015). http://www.sciencedaily.com/releases/2015/07/150720092257.htm
  • 47. © 2017 - All rights reserved. Causes of Autoimmunity: Environment • Javierre, Hernando, and Ballestar. “Environmental triggers and epigenetic deregulation in autoimmune disease.” (2011). http://www.ncbi.nlm.nih.gov/pubmed/22204770 • Nakazawa Jackson, Donna. The Autoimmune Epidemic. New York: A Touchstone Book, 2008. Print. • Obregon-Tito, Alexandra et al. “Subsistence strategies in traditional societies distinguish gut microbiomes.” Nature Communications 6 (2015). http://www.researchgate.net/publication/274071457_Subsistence_strategies_in_traditional_societi es_distinguish_gut_microbiomes • Terato, Kuniaki, Christopher Do, and Hiroshi Shionoya. “Slipping through the Cracks: Linking Low Immune Function and Intestinal Bacterial Imbalance to the Etiology of Rheumatoid Arthritis.” Autoimmune Diseases 2015 (2015). http://www.hindawi.com/journals/ad/2015/636207/
  • 48. © 2017 - All rights reserved. Causes of Autoimmunity: Environment • Vatanen, Tommi, et al. "Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans." Cell 165.4 (2016): 842-853. https://www.uab.edu/medicine/rheumatology/images/Vatanen_et_al_2016.pdf • Velasquez-Manoff, Moises. An Epidemic of Absence. New York: Scribner, 2012. Print. • Vojdani, Aristo. “A Potential Link between Environmental Triggers and Autoimmunity.” Autoimmune Diseases 2014 (2014). http://www.researchgate.net/publication/273894696_Slipping_through_the_Cracks_Linking_Low_I mmune_Function_and_Intestinal_Bacterial_Imbalance_to_the_Etiology_of_Rheumatoid_Arthritis • Vojdani, Aristo, Michael Pollard, and Andrew Campbell. “Environmental Triggers and Autoimmunity.” Autoimmune Diseases 2014 (2014): 798029. http://www.researchgate.net/publication/271221861_Environmental_Triggers_and_Autoimmunity
  • 49. © 2017 - All rights reserved. Causes of Autoimmunity: Hormones • Blum, Susan. The Immune System Recovery Plan. New York: Scribner, 2013. Print. • Perlmutter, David. Grain Brain. New York: Little, Brown and Company, 2013. Print.
  • 50. © 2017 - All rights reserved. Causes of Autoimmunity: Pathogenesis • Altorok, Nezam, et al. "Epigenetics, the holy grail in the pathogenesis of systemic sclerosis." Rheumatology (2014): keu155. https://academic.oup.com/rheumatology/article/54/10/1759/1789830/Epigenetics- the-holy-grail-in-the-pathogenesis-of • Barin, Jobert G., Lawrence D. Tobias, and Daniel A. Peterson. "The microbiome and autoimmune disease: Report from a Noel R. Rose Colloquium." Clinical Immunology 159.2 (2015): 183-188. <http://www.sciencedirect.com/science/article/pii/S1521661615001710> • Blum, Susan. The Immune System Recovery Plan. New York: Scribner, 2013. Print.
  • 51. © 2017 - All rights reserved. Causes of Autoimmunity: Pathogenesis • Brady, David M. "Molecular Mimicry, the Hygiene Hypothesis, Stealth Infections and Other Examples of Disconnect between Medical Research and the Practice of Clinical Medicine in Autoimmune Disease" Open Journal of Rheumatology and Autoimmune Disease (2013): 33-39. Web. http://www.researchgate.net/publication/262068728_Molecular_Mimicry_the_Hygiene_Hypothesi s_Stealth_Infections_and_Other_Examples_of_Disconnect_between_Medical_Research_and_the_P ractice_of_Clinical_Medicine_in_Autoimmune_Disease • Brusca, Abramson, and Scher. “Microbiome and mucosal inflammation as extra-articular triggers for rheumatoid arthritis and autoimmunity.” (2014). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4011633/ • Craft, Joe, and Saeed Fatenejad. “Self antigens and epitope spreading in systemic autoimmunity.” Arthritis & Rheumatism 40.8 (1997): 1374–1382. http://onlinelibrary.wiley.com/doi/10.1002/art.1780400803/pdf
  • 52. © 2017 - All rights reserved. Causes of Autoimmunity: Pathogenesis • Cusick, Libbey, and Fujinami. “Molecular mimicry as a mechanism of autoimmune disease” (2012). http://www.ncbi.nlm.nih.gov/pubmed/22095454 • da Fonseca, Denise Morais, et al. "Microbiota-dependent sequelae of acute infection compromise tissue-specific immunity." Cell 163.2 (2015): 354-366. http://www.sciencedirect.com/science/article/pii/S0092867415010442 • Farh, Kyle et al. “Genetic and epigenetic fine mapping of causal autoimmune disease variants.” Nature 518.7539 (2015): 337–43. http://www.nature.com/nature/journal/v518/n7539/full/nature13835.html#close
  • 53. © 2017 - All rights reserved. Causes of Autoimmunity: Pathogenesis • Gianchecchi, Elena, and Alessandra Fierabracci. "Gene/environment interactions in the pathogenesis of autoimmunity: new insights on the role of toll-like receptors." Autoimmunity reviews 14.11 (2015): 971-983. https://www.researchgate.net/profile/Elena_Gianchecchi/publication/280117764_GeneEnvironme nt_Interactions_in_the_Pathogenesis_of_Autoimmunity_New_Insights_on_the_Role_of_Toll- Like_Receptors/links/56dd7e0a08ae46f1e99f6b8a.pdf • Gomez, Andres, David Luckey, and Veena Taneja. "The gut microbiome in autoimmunity: sex matters." Clinical Immunology 159.2 (2015): 154-162. http://europepmc.org/articles/pmc4560596 • Guo, Haitao, Justin B. Callaway, and Jenny PY Ting. "Inflammasomes: mechanism of action, role in disease, and therapeutics." Nature medicine 21.7 (2015): 677-687. http://www.nature.com/nm/journal/v21/n7/full/nm.3893.html
  • 54. © 2017 - All rights reserved. Causes of Autoimmunity: Pathogenesis • Jeltsch-David, Hélène, and Sylviane Muller. "Autoimmunity, neuroinflammation, pathogen load: A decisive crosstalk in neuropsychiatric SLE." Journal of autoimmunity 74 (2016): 13-26. https://www.researchgate.net/profile/Helene_Jeltsch- David/publication/301772757_Autoimmunity_neuroinflammation_pathogen_load_A_decisive_cros stalk_in_neuropsychiatric_SLE/links/5729ff3708aef7c7e2c4ec78.pdf • Kakodkar, Samir, et al. "The specific carbohydrate diet for inflammatory bowel disease: a case series." Journal of the Academy of Nutrition and Dietetics 115.8 (2015): 1226-1232. http://www.sciencedirect.com/science/article/pii/S2212267215005043 • McLean, Mairi et al. “Does the microbiota play a role in the pathogenesis of autoimmune diseases?” Gut (2014). http://www.researchgate.net/publication/268790142_Does_the_microbiota_play_a_role_in_the_p athogenesis_of_autoimmune_diseases
  • 55. © 2017 - All rights reserved. Causes of Autoimmunity: Pathogenesis • Mu, Q, H Zhang, and XM Luo. “SLE: Another Autoimmune Disorder Influenced by Microbes and Diet?” Frontiers in Immunology (2015) : n. pag. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4663251/ • Proal, Amy D., Paul J. Albert, and Trevor G. Marshall. "The human microbiome and autoimmunity." Current opinion in rheumatology 25.2 (2013): 234-240. http://microbeminded.com/wp- content/uploads/2015/10/Proal_2013_CurrentOpinion-Preprint.pdf • Rao, Meenakshi, and Michael D. Gershon. "The bowel and beyond: the enteric nervous system in neurological disorders." Nature Reviews Gastroenterology & Hepatology 13.9 (2016): 517-528. http://www.nature.com/nrgastro/journal/v13/n9/full/nrgastro.2016.107.html • Roederer, Mario et al. “The genetic architecture of the human immune system: a bioresource for autoimmunity and disease pathogenesis.” Cell 161.2 (2015): 387–403. http://www.cell.com/cell/abstract/S0092-8674(15)00247-0?rss=yes
  • 56. © 2017 - All rights reserved. Causes of Autoimmunity: Pathogenesis • Rosenblum, Michael D., Kelly A. Remedios, and Abul K. Abbas. "Mechanisms of Human Autoimmunity." The Journal of Clinical Investigation 125.6 (2015): 2228-2233. Web. https://www.jci.org/articles/view/78088 • Scher, JU, and SB Abramson. “The Microbiome and Rheumatoid Arthritis.” Nature Reviews Rheumatology 7 (2011) : 569-578. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275101/ Scher, Jose U., et al. "Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis." Elife 2 (2013): e01202. https://elifesciences.org/content/2/e01202 • Smilek, Dawn, and William Clair. “Solving the puzzle of autoimmunity: critical questions.” F1000Prime Reports 7 (2015). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335798/
  • 57. © 2017 - All rights reserved. Causes of Autoimmunity: Pathogenesis • Theofilopoulos, Argyrios, Wolfgang Dummer, and Dwight Kono. “T cell homeostasis and systemic autoimmunity.” Journal of Clinical Investigation 108.3 (2001): 335-340. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC209358/ • Verdu, Elena F., Heather J. Galipeau, and Bana Jabri. "Novel players in coeliac disease pathogenesis: role of the gut microbiota." Nature reviews. Gastroenterology & hepatology 12.9 (2015): 497. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5102016/ • Wen, Haitao, Edward Miao, and Jenny Ting. “Mechanisms of NOD-like Receptor-Associated Inflammasome Activation.” Immunity 39.3 (2013). http://www.cell.com/immunity/abstract/S1074- 7613(13)00389-0
  • 58. © 2017 - All rights reserved. Metabolomics
  • 59. © 2017 - All rights reserved. Causes of Autoimmunity: Microbiome Diet • Gibson, Peter R., et al. "Food components and irritable bowel syndrome." Gastroenterology 148.6 (2015): 1158-1174. http://www.gastrojournal.org/article/S0016-5085(15)00196- 1/abstract • Lerner, Aaron, and Torsten Matthias. “Changes in intestinal tight junction permeability associated with industrial food additives explain the rising incidence of autoimmune disease.” Autoimmunity Reviews (2015). http://www.researchgate.net/publication/272186939_Changes_in_intestinal_tight_junction_p ermeability_associated_with_industrial_food_additives_explain_the_rising_incidence_of_autoi mmune_disease • Manzel, Arndt et al. “Role of ‘Western Diet’ in Inflammatory Autoimmune Diseases.” Current Allergy and Asthma Reports 14.1 (2013): 404. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034518/
  • 60. © 2017 - All rights reserved. Causes of Autoimmunity: Microbiome Diet • Perlmutter, David. Grain Brain. New York: Little, Brown and Company, 2013. Print. • Sonnenburg, Erica, and Justin Sonnenburg. “Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates.” Cell Metabolism (2014). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896489/ • Youm, Yun-Hee et al. “The ketone metabolite β-hydroxybutyrate blocks NLRP3 inflammasome– mediated inflammatory disease.” Nature Medicine 21.3 (2015): 263–9. http://www.researchgate.net/publication/272354552_The_ketone_metabolite_- hydroxybutyrate_blocks_NLRP3_inflammasomemediated_inflammatory_disease
  • 61. © 2017 - All rights reserved. Microbiomics
  • 62. © 2017 - All rights reserved. The Microbiome Lifeline • Ackerman, Jennifer. “The Ultimate Social Network.” Scientific American 306.6 (2012): 36–43. http://www.researchgate.net/publication/225084801_The_ultimate_social_network • Brusca, Samuel, Steven Abramson, and Jose Scher. “Microbiome and mucosal inflammation as extra-articular triggers for rheumatoid arthritis and autoimmunity.” Current Opinion in Rheumatology (2014). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4011633/ • Brüssow, Harald. “Microbiota and the human nature: know thyself.” Environmental Microbiology 17.1 (2015): 10–15. http://www.researchgate.net/publication/269727325_Microbiota_and_the_human_nature_kn ow_thyself
  • 63. © 2017 - All rights reserved. The Microbiome Lifeline • Coit, Patrick, and Amr H. Sawalha. "The human microbiome in rheumatic autoimmune diseases: A comprehensive review." Clinical Immunology 170 (2016): 70-79. http://www.sciencedirect.com/science/article/pii/S1521661616302480 • Garrett, Wendy. “From cell biology to the microbiome: An intentional infinite loop.” The Journal of Cell Biology (2015). http://jcb.rupress.org/content/210/1/7.full.pdf+html • Gordon, Jeffrey I. "Honor thy gut symbionts redux." Science 336.6086 (2012): 1251-1253. http://science.sciencemag.org/content/336/6086/1251 • Hevia, Arancha et al. “Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus.” mBio (2014). http://www.academia.edu/13411926/Intestinal_dysbiosis_associated_with_systemic_lupus_erythe matosus
  • 64. © 2017 - All rights reserved. The Microbiome Lifeline • Kaiko, Gerard E., et al. "The colonic crypt protects stem cells from microbiota-derived metabolites." Cell 165.7 (2016): 1708-1720. http://www.sciencedirect.com/science/article/pii/S0092867416305669 • Kamada, Nobuhiko et al. “Role of the gut microbiota in immunity and inflammatory disease.” Nature Reviews Immunology 13.5 (2013): 321–335. http://www.researchgate.net/publication/236337970_Role_of_gut_microbiota_in_immunity_and_i nflammatory_disease • Kamdar, K et al. “Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease.” Cell Host & Micobe 19.1 (2016) :21-31. http://www.cell.com/cell-host-microbe/pdfExtended/S1931-3128(15)00498-9
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  • 66. © 2017 - All rights reserved. The Microbiome Lifeline • Tamburini, Sabrina, et al. "The microbiome in early life: implications for health outcomes." Nature Medicine 22.7 (2016): 713-722. https://www.researchgate.net/profile/Sabrina_Tamburini2/publication/305037745_The_microbiom e_in_early_life_Implications_for_health_outcomes/links/577fb08908ae9485a439a851.pdf • Waldor, Matthew et al. “Where next for microbiome research?” PLoS biology 13.1 (2015). http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002050 • Wu, Hao, Valentina Tremaroli, and Fredrik Bäckhed. “Linking Microbiota to Human Diseases: A Systems Biology Perspective.” Trends in Endocrinology & Metabolism 26.12 (2015) : 758-770. http://www.cell.com/trends/endocrinology-metabolism/abstract/S1043-2760(15)00194-0
  • 67. © 2017 - All rights reserved. The Microbiome Lifeline • Yurkovetskiy, Leonid, Joseph Pickard, and Alexander Chervonsky. “Microbiota and Autoimmunity: Exploring New Avenues.” Cell Host & Microbe (2015). http://scifeeds.com/journal-article/microbiota-and-autoimmunity-exploring-new-avenues/
  • 68. © 2017 - All rights reserved. The Microbiome Lifeline: Gut As An Organ of Immunity • Bitar, Khalil N., and Elie Zakhem. "Bioengineering the gut: future prospects of regenerative medicine." Nature Reviews Gastroenterology & Hepatology 13.9 (2016): 543-556. https://pdfs.semanticscholar.org/de1d/117e9dcc8b193af65c4288914f9a3e7134ca.pdf • Campbell, Andrew. “Autoimmunity and the Gut.” Autoimmune Diseases 2014 (2014): 152-428. http://www.researchgate.net/publication/262886119_Autoimmunity_and_the_Gut • Cenit, María Carmen, et al. "Intestinal microbiota and celiac disease: cause, consequence or co- evolution?." Nutrients 7.8 (2015): 6900-6923. http://www.mdpi.com/2072-6643/7/8/5314/htm • Glenn Justin, D., and M. Mowry Ellen. "Emerging concepts on the gut microbiome and multiple sclerosis." Journal of Interferon & Cytokine Research (2016). http://online.liebertpub.com/doi/abs/10.1089/jir.2015.0177?journalCode=jir
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  • 71. © 2017 - All rights reserved. The Microbiome Lifeline: Gut As An Organ of Immunity • Mowat, Allan, and William Agace. “Regional specialization within the intestinal immune system.” Nature Reviews Immunology 14.10 (2014): 667–85. http://www.researchgate.net/publication/265862048_Regional_specialization_within_ the_intestinal_immune_system • Sommer, Felix, and Fredrik Bäckhed. "The gut microbiota—masters of host development and physiology." Nature Reviews Microbiology 11.4 (2013): 227-238. http://www.nature.com/nrmicro/journal/v11/n4/full/nrmicro2974.html
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  • 74. © 2017 - All rights reserved. The Microbiome Lifeline: Gut-Brain Axis • Alcock, Joe, Carlo Maley, and Athena Aktipis. “Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms.” BioEssays (2014). https://ucsf.box.com/shared/static/pdz2z4b5fdvwlpr9hfdh.pdf • Brod, Samuel et al. “‘As above, so below’ examining the interplay between emotion and the immune system.” Immunology 143.3 (2014): 311–8. http://www.researchgate.net/publication/263291162_As_above_so_below_Examining_the_int erplay_between_emotion_and_the_Immune_System • Forsythe, Paul et al. “Mood and gut feelings.” Brain, Behavior, and Immunity (2010). https://www.researchgate.net/publication/26252541_Mood_and_gut_feelings
  • 75. © 2017 - All rights reserved. The Microbiome Lifeline: Gut-Brain Axis • Foster, Jane, and Karen-Anne Neufeld. “Gut–brain axis: how the microbiome influences anxiety and depression.” Trends in Neurosciences (2013). http://www.researchgate.net/publication/235404335_Gut- brain_axis_How_the_microbiome_influences_anxiety_and_depression • Hadhazy, Adam. “Think Twice: How the Gut’s ‘Second Brain’ Influences Mood and Well-Being." Scientific American (2010). http://www.scientificamerican.com/article/gut-second-brain/ • Mayer, Emeran et al. “Gut Microbes and the Brain: Paradigm Shift in Neuroscience.” The Journal of Neuroscience (2014). http://www.jneurosci.org/content/34/46/15490.full
  • 76. © 2017 - All rights reserved. The Microbiome Lifeline: Gut-Brain Axis • O’Mahony et al. “Serotonin, tryptophan metabolism and the brain-gut-microbiome axis.” Behavioural Brain Research 277 (2015): 3248. http://www.sciencedirect.com/science/article/pii/S0166432814004768 • Steenbergen, Laura et al. “A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood.” Brain, Behavior, and Immunity (2015). http://www.researchgate.net/publication/274781872_A_randomized_controlled_trial_to_test _the_effect_of_multispecies_probiotics_on_cognitive_reactivity_to_sad_mood
  • 77. © 2017 - All rights reserved. The Microbiome Lifeline: Fixing Your Leaky Gut is Key • De Souza, Heitor, and Claudio Fiocchi. “Immunopathogenesis of IBD: Current State of the Art.” Nature Reviews Gastroenterology & Hepatology (2015) : 13-27 http://www.ncbi.nlm.nih.gov/pubmed/26627550 • Derrien, Muriel, and Johan Vlieg. “Fate, activity, and impact of ingested bacteria within the human gut microbiota.” Trends in Microbiology (2015). http://www.researchgate.net/publication/274405159_Fate_activity_and_impact_of_ingested_ bacteria_within_the_human_gut_microbiota • Fasano, Alessio. “Leaky gut and autoimmune diseases.” Clinical reviews in allergy & immunology 42.1 (2012): 71–8. http://www.researchgate.net/publication/51823457_Leaky_gut_and_autoimmune_diseases
  • 78. © 2017 - All rights reserved. The Microbiome Lifeline: Fixing Your Leaky Gut is Key • Ghosh, Subrata et al. “New tools and approaches for improved management of inflammatory bowel diseases.” Journal of Crohn’s and Colitis 8.10 (2014): 1246–53. http://www.researchgate.net/publication/261756210_New_tools_and_approaches_for_improved_ management_of_inflammatory_bowel_diseases • Kostic, Aleksandar, Ramnik Xavier, and Dirk Gevers. “The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead.” Gastroenterology 146.6 (2014): 1489–99. http://www.researchgate.net/publication/260374207_The_Microbiome_in_Inflammatory_Bowel_D iseases_Current_Status_and_the_Future_Ahead • Sartor, R. Balfour. “The Intestinal Microbiota in Inflammatory Bowel Disease.” Nestle Nutrition Institute Workshop Series 79 (2014) : 29–39. https://uncch.pure.elsevier.com/en/publications/the-intestinal-microbiota-in-inflammat ory-bowel-diseases
  • 79. © 2017 - All rights reserved. The Microbiome Lifeline: Fixing Your Leaky Gut is Key • Sartor, RB, and SK Mazmanian. “Intestinal Microbes in Inflammatory Bowel Diseases.” The American Journal of Gastroenterology … (2012) : 15-21. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985589/ • Strober, Warren. “Impact of the gut microbiome on mucosal inflammation.” Trends in Immunology (2013). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773492/ • Vojdani, Aristo. "For the assessment of intestinal permeability, size matters." Altern Ther Health Med 19.1 (2013): 12-24. http://www.immunoscienceslab.com/Articles/Size%20Matters.pdf • Walsh, Alissa J., Robert V. Bryant, and Simon PL Travis. "Current best practice for disease activity assessment in IBD." Nature Reviews Gastroenterology & Hepatology 13.10 (2016): 567- 579. http://www.nature.com/nrgastro/journal/v13/n10/full/nrgastro.2016.128.html
  • 80. © 2017 - All rights reserved. The Microbiome Lifeline: Fixing Your Leaky Gut is Key • Wlodarska, Marta, Aleksandar Kostic, and Ramnik Xavier. “An Integrative View of Microbiome- Host Interactions in Inflammatory Bowel Diseases.” Cell Host & Microbe (2015). http://www.cell.com/cell-host-microbe/abstract/S1931-3128(15)00166-3 • Zihni, Ceniz, et al. "Tight junctions: from simple barriers to multifunctional molecular gates." Nature reviews Molecular cell biology (2016). http://www.nature.com/nrm/journal/v17/n9/full/nrm.2016.80.html • Zippi, Maddalena. “Extraintestinal manifestations in a large series of Italian inflammatory bowel disease patients.” World Journal of Gastroenterology 20.46 (2014): 17463-17467. http://docrchive.com/document/extraintestinal-manifestations-in-a-large-series-of-italian- inflammatory-bowel-disease-patients-7348008145211277/
  • 81. © 2017 - All rights reserved. The Microbiome Lifeline: Health Starts in the Mouth • Atanasova, Kalina, and Özlem Yilmaz. “Prelude to oral microbes and chronic diseases: past, present and future.” Microbes and Infection (2015). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485946/ • Costalonga, Massimo, and Mark Herzberg. “The oral microbiome and the immunobiology of periodontal disease and caries.” Immunology Letters (2014). http://www.researchgate.net/publication/268079979_The_oral_microbiome_and_the_immunobiology_of_per iodontal_disease_and_caries • Detert, Jacqueline, et al. "The association between rheumatoid arthritis and periodontal disease." Arthritis research & therapy 12.5 (2010): 218. https://arthritis-research.biomedcentral.com/articles/10.1186/ar3106 • He, Jinzhi et al. “The oral microbiome diversity and its relation to human diseases.” Folia Microbiologica (2014). http://www.researchgate.net/publication/264987867_The_oral_microbiome_diversity_and_its_relation_to_h uman_diseases
  • 82. © 2017 - All rights reserved. The Microbiome Lifeline: Health Starts in the Mouth • Marsh, P, and D Bradshaw. “Dental plaque as a biofilm.” Journal of Industrial Microbiology 15.3 (1995): 169–175. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2147593/ • Schwarzberg, Karen et al. “The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease.” PLoS ONE 9.1 (2014). http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086708 • Steinberg, Doron. “Dental Chatter: Bacterial Cross‐Talk in the Biofilm of the Oral Cavity.” Israel Journal of Chemistry (2015). http://onlinelibrary.wiley.com/doi/10.1002/ijch.201400143/abstract
  • 83. © 2017 - All rights reserved. The Microbiome Lifeline: Health Starts in the Mouth • Struzycka, Izabela. “The oral microbiome in dental caries.” Polish journal of microbiology / Polskie Towarzystwo Mikrobiologów = The Polish Society of Microbiologists 63.2 (2014): 127–35. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086708 • Warinner, Christina, Camilla Speller, and Matthew Collins. “A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.” Philosophical Transactions of the Royal Society of London B: Biological Sciences 370.1660 (2015). http://rstb.royalsocietypublishing.org/content/370/1660/20130376
  • 84. © 2017 - All rights reserved. The Microbiome Lifeline: Health Starts in the Mouth • Zarco, Vess, and Ginsburg. “The oral microbiome in health and disease and the potential impact on personalized dental medicine.” Oral Diseases 18.2 (2012): 109–120. http://www.researchgate.net/publication/51628583_The_oral_microbiome_in_health_and_dis ease_and_the_potential_impact_on_personalized_dental_medicine • Zhang, Xuan et al. “The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment.” Nature Medicine (2015). http://www.researchgate.net/publication/280036160_The_oral_and_gut_microbiomes_are_p erturbed_in_rheumatoid_arthritis_and_partly_normalized_after_treatment
  • 85. © 2017 - All rights reserved. Epigenetics
  • 86. © 2017 - All rights reserved. Change your Fate: What can Epigenetics do for Autoimmunity? • Allis, C. David, and Thomas Jenuwein. "The molecular hallmarks of epigenetic control." Nature Reviews Genetics (2016). http://agri.ckcest.cn/ass/NK002-20160822003.pdf • Coppedè, Fabio, and Lucia Migliore. "Epigenetics of autoimmune diseases." Molecular mechanisms and physiology of disease. Springer New York, 2014. 151-173. http://link.springer.com/chapter/10.1007/978-1-4939-0706-9_6#page-1 • Farh, K. et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337–43 (2015). http://www.nature.com/nature/journal/v518/n7539/full/nature13835.html
  • 87. © 2017 - All rights reserved. Change your Fate: What can Epigenetics do for Autoimmunity? • Gupta, B. & Hawkins, D. Epigenomics of autoimmune diseases. Immunol Cell Biol 93, 271–276 (2015). http://www.nature.com/icb/journal/v93/n3/full/icb201518a.html • Jeffries, MA & Sawalha, AH. Autoimmune disease in the epigenetic era: how has epigenetics changed our understanding of disease and how can we expect the field to evolve? Expert review of clinical … (2014). http://www.pubfacts.com/detail/25534978/Autoimmune-disease-in-the-epigene tic-era:-how-has-epigenetics-changed-our-understanding-of-disease-a
  • 88. © 2017 - All rights reserved. A Different Kind of Self Help
  • 89. © 2017 - All rights reserved. Personal Trial and Error: Treatments & Therapies • Bot, Adrian et al. “Target discovery for T cell therapy: next steps to advance Immunotherapies.” Journal for Immunotherapy of Cancer (2015). http://www.immunotherapyofcancer.org/content/pdf/s40425-015-0061-5.pdf • Burton, Bronwen et al. “Sequential transcriptional changes dictate safe and effective antigen- specific immunotherapy.” Nature Communications (2014). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167604/ • Chang, Christopher. “Unmet needs in the treatment of autoimmunity: From aspirin to stem cells.” Autoimmunity Reviews 13 (2014). http://www.researchgate.net/publication/259917083_Unmet_Needs_in_the_Treatment_of_A utoimmunity_From_Aspirin_to_Stem_Cells
  • 90. © 2017 - All rights reserved. Personal Trial and Error: Treatments & Therapies • Curatola, Gerard. “Oral Microbiome Homeostasis: The New Frontier in Oral Care Therapies.” Symbiosis (2013):1-3. http://www.symbiosisonlinepublishing.com/dentistry-oraldisorders-therapy/dentistry- oraldisorders-therapy05.php • Gertner, Jon. “What’s Lurking In Your Microbiome? Possibly, a Cure for Disease.” Fast Company (2015). http://www.fastcompany.com/3039891/gut-check • Nakazawa Jackson, Donna. The Autoimmune Epidemic. New York: A Touchstone Book, 2008. Print. • Olle, Bernat. “Medicines from microbiota.” Nature Biotechnology 31.4 (2013): 309-315. http://www.researchgate.net/publication/236128149_Medicines_from_microbiota
  • 91. © 2017 - All rights reserved. Personal Trial and Error: Treatments & Therapies • Petrof et al. “Microbial ecosystems therapeutics: a new paradigm in medicine?” Beneficial microbes 4.1 (2013): 53-65. http://www.researchgate.net/publication/233963283_Microbial_ecosystems_therapeutics_A_ new_paradigm_in_medicine • Sabatos-Peyton, Catherine A, Johan Verhagen, and David C Wraith. “Antigen-specific immunotherapy of autoimmune and allergic diseases.” Current opinion in immunology 22.5 (2010): 609–15. http://www.researchgate.net/publication/46305185_Antigen- specific_immunotherapy_of_autoimmune_and_allergic_diseases • Velasquez-Manoff, Moises. An Epidemic of Absence. New York: Scribner, 2012. Print.
  • 92. © 2017 - All rights reserved. Treatments & Therapies: Fecal Microbiota Transplants • Borody, Thomas, and Alexander Khoruts. “Fecal microbiota transplantation and emerging applications.” Nature Reviews Gastroenterology and Hepatology 9.2 (2011): 88–96. http://www.researchgate.net/publication/51901488_Borody_TJ_Khoruts_A.._Fecal_microbiota _transplantation_and_emerging_applications._Nat_Rev_Gastroenterol_Hepatol_9_88-96 • Brüssow, Harald. “Microbiota and the human nature: know thyself.” Environmental Microbiology 17.1 (2015): 10–15. http://www.researchgate.net/publication/269727325_Microbiota_and_the_human_nature_kn ow_thyself • Liu, Shirong, et al. "The host shapes the gut microbiota via fecal microRNA." Cell host & microbe 19.1 (2016): 32-43. http://www.sciencedirect.com/science/article/pii/S1931312815004977
  • 93. © 2017 - All rights reserved. Treatments & Therapies: Fecal Microbiota Transplants • Petrof, Elaine, and Alexander Khoruts. “From stool transplants to next-generation microbiota therapeutics.” Gastroenterology 146.6 (2014): 1573-1582. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221437/ • Scher, Jose et al. “Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease.” Arthritis & Rheumatology 67.1 (2015): 128–139. http://www.researchgate.net/publication/266974816_Decreased_Bacterial_Diversity_Characte rizes_the_Altered_Gut_Microbiota_in_Patients_With_Psoriatic_Arthritis_Resembling_Dysbiosi s_in_Inflammatory_Bowel_Disease
  • 94. © 2017 - All rights reserved. Treatments & Therapies: Prebiotics and Probiotics • Bindels, Laure et al. “Towards a more comprehensive concept for prebiotics.” Nature Reviews Gastroenterology & Hepatology (2015). http://www.researchgate.net/publication/274319084_Towards_a_more_comprehensive_concept_f or_prebiotics • Derrien, Muriel, and Johan Vlieg. “Fate, activity, and impact of ingested bacteria within the human gut microbiota.” Trends in Microbiology (2015). http://www.researchgate.net/publication/274405159_Fate_activity_and_impact_of_ingested_bact eria_within_the_human_gut_microbiota • Hemarajata, P, and J Versalovic. “Effects of Probiotics on Gut Microbiota: Mechanisms of Intestinal Immunomodulation and Neuromodulation.” Therapeutic Advances in Gastroenterology. (2012) : 39-51. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539293/
  • 95. © 2017 - All rights reserved. Treatments & Therapies: Prebiotics and Probiotics • Petschow, B et al. “Probiotics, Prebiotics, and the Host Microbiome: The Science of Translation.” Annals of the New York Academy of Sciences (2013) : 1-17. http://onlinelibrary.wiley.com/doi/10.1111/nyas.12303/full • Vieira, Angélica, Mauro Teixeira, and Flaviano Martins. “The Role of Probiotics and Prebiotics in Inducing Gut Immunity.” Frontiers in Immunology 4 (2013): 445. http://www.researchgate.net/publication/259492313_The_Role_of_Probiotics_and_Prebioti cs_in_Inducing_Gut_Immunity
  • 96. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: What We Can Do
  • 97. © 2017 - All rights reserved. Prevention and Lifestyle Modifications • “Translating the Science of Wellness and Healing.” Samueli Institute. 2011. http://www.samueliinstitute.org/File%20Library/About%20Us/SP11_lowres.pdf
  • 98. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Food • Ballantyne, Sarah. The Paleo Approach. Las Vegas: Victory Belt Publishing Inc, 2013. Print. • Blum, Susan. The Immune System Recovery Plan. New York: Scribner, 2013. Print. • Charlebois, Ashley, Greg Rosenfeld, and Brian Bressler. “The Impact of Dietary Interventions on the Symptoms of Inflammatory Bowel Disease: A Systematic Review.” Critical Reviews in Food Science and Nutrition (2015). http://www.researchgate.net/publication/270651195_The_Impact_of_Dietary_Interventions_ on_the_Symptoms_of_Inflammatory_Bowel_Disease_A_Systematic_Review • Clarke, and Mullin. “A Review of Complementary and Alternative Approaches to Immunomodulation.” Nutrition in Clinical Practice 23.1 (2008): 49–62. <http://www.researchgate.net/publication/5647579_A_review_of_complementary_and_altern ative_approaches_to_immunomodulation >
  • 99. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Food • Halmos, Emma, and Peter Gibson. “Dietary management of IBD—insights and advice.” Nature Reviews Gastroenterology & Hepatology 12.3 (2015): 133–146. http://www.researchgate.net/publication/272083767_Dietary_management_of_IBDinsights_a nd_advice • LeBlanc et al. “Bacteria as vitamin suppliers to their host: a gut microbiota perspective” (2013). http://www.researchgate.net/publication/230782474_Bacteria_as_vitamin_suppliers_to_their _host_A_gut_microbiota_perspective • Mullin, Gerard and Kathie Swift. The Inside Tract. New York: Rodale, 2011. Print. • Nakazawa Jackson, Donna. The Autoimmune Epidemic. New York: A Touchstone Book, 2008. Print. • Perlmutter, David. Grain Brain. New York: Little, Brown and Company, 2013. Print.
  • 100. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Food • Sanfilippo, Diane. Practical Paleo: a customized approach to health and a whole-foods lifestyle. Las Vegas: Victory Belt Publishing Inc, 2012. Print. • Subramanian, Sathish et al. “Cultivating Healthy Growth and Nutrition through the Gut Microbiota.” Cell (2015). <http://www.researchgate.net/publication/274259147_Cultivating_Healthy_Growth_and_Nutr ition_through_the_Gut_Microbiota>
  • 101. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Diet, Food, Nutrition • Bonaventura, Paola, et al. "Zinc and its role in immunity and inflammation." Autoimmunity reviews 14.4 (2015): 277-285. https://www.researchgate.net/profile/Paola_Bonaventura/publication/268750493_Zinc_and_its_ Role_in_Immunity_and_Inflammation/links/55fff71b08aeafc8ac8bb226/Zinc-and-its-Role-in- Immunity-and-Inflammation.pdf • Forster, Hannah, et al. "A dietary feedback system for the delivery of consistent personalized dietary advice in the web-based multicenter Food4Me study." Journal of Medical Internet Research 18.6 (2016). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945818/ • Gibson, Peter R., and Susan J. Shepherd. "Evidence‐based dietary management of functional gastrointestinal symptoms: The FODMAP approach." Journal of gastroenterology and hepatology 25.2 (2010): 252-258. http://fodmapliving.com/wp-content/uploads/2012/07/Evidence-Based- FODMAP-approach.pdf
  • 102. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Diet, Food, Nutrition • Tilg, H, and AR Moschen. “Food, Immunity, and the Microbiome.” Gastroenterology 148.6 (2015) : 1107-1119. http://www.sciencedirect.com/science/article/pii/S0016508515000128. • vel Szic, Katarzyna Szarc, et al. "From inflammaging to healthy aging by dietary lifestyle choices: is epigenetics the key to personalized nutrition?." Clinical epigenetics 7.1 (2015): 33. https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-015-0068-2 • Zeevi et al. “Personalized Nutrition by Prediction of Glycemic Responses.” Cell. 163.5 (2015) : 1079-1094. <http://www.cell.com/abstract/S0092-8674(15)01481-6>. • Zmora, N et al. “Taking It Personally: Personalized Utilization of the Human Microbiome in Health and Disease.” Cell Host & Microbe 19.1 (2016) : 12-20. <http://www.cell.com/cell-host-microbe/pdf/S1931-3128(15)00508-9.pdf>.
  • 103. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Nutrigenomics and Autoimmunity • Ferguson, LR. Nutrigenetics, nutrigenomics and inflammatory bowel diseases. Expert review of clinical immunology (2013). http://www.ncbi.nlm.nih.gov/pubmed/23971750 • Gibson, PR, Varney, J, Malakar, S & Muir, JG. Food Components and Irritable Bowel Syndrome. Gastroenterology (2015). at http://www.sciencedirect.com/science/article/pii/S0016508515001961 • Minich, D. M. & Bland, J. S. Personalized lifestyle medicine: relevance for nutrition and lifestyle recommendations. The Scientific World Journal 2013, (2013). http://www.ncbi.nlm.nih.gov/pubmed/23878520 • Xie, G, Li, X, Li, H & Jia, W. Toward personalized nutrition: comprehensive phytoprofiling and metabotyping. Journal of proteome research (2013). http://pubs.acs.org/doi/abs/10.1021/pr301222b
  • 104. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Exercise • Brourman, Sherry, and Randy Rodman. Walk Yourself Well. www.SherryBrourman.com. 2005. Print. • McCaffrey, R., and J. Park. "The benefits of yoga for musculoskeletal disorders: A systematic review of the literature." J Yoga Phys Ther 2.122 (2012): 2.http://www.omicsgroup.info/the- benefits-of-yoga-for-musculoskeletal-disorders-a-systematic-review-of-the-literature-2157- 7595.1000122.pdf • Perlmutter, David. Grain Brain. New York: Little, Brown and Company, 2013. Print.
  • 105. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Meditation • Blum, Susan. The Immune System Recovery Plan. New York: Scribner, 2013. Print. • Nakazawa Jackson, Donna. The Autoimmune Epidemic. New York: A Touchstone Book, 2008. Print.
  • 106. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Community • Kok, BE et al. “How Positive Emotions Build Physical Health Perceived Positive Social Connections Account for the Upward Spiral between Positive Emotions and Vagal Tone.” Psychological Science 24.7 (2013): 1123-1132. <http://pss.sagepub.com/content/24/7/1123.short>.
  • 107. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: The Immune System’s Feedback Loops • Antoni, MH et al. “Cognitive-Behavioral Stress Management Reverses Anxiety-Related Leukocyte Transcriptional Dynamics.” Biological Psychiatry 71.4 (2012): 366-372. <http://www.sciencedirect.com/science/article/pii/S0006322311009656>. • Irwin, MR, and SW Cole. “Reciprocal Regulation of the Neural and Innate Immune Systems.” Nature Reviews Immunology 11.1 (2011) : 625-632. http://www.nature.com/nri/journal/v11/n9/abs/nri3042.html. • Qu, S et al. “Rapid Gene Expression Changes in Peripheral Blood Lymphocytes upon Practice of a Comprehensive Yoga Program.” PloS One 8.4 (2013) : n. pag. . <http://dx.plos.org/10.1371/journal.pone.0061910>.
  • 108. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Mind-Body Feedback Loops • Black, DS, and GM Slavich. “Mindfulness Meditation and the Immune System: A Systematic Review of Randomized Controlled Trials.” Annals of the New York Academy of Sciences 20.1(2016): 1-12. <http://onlinelibrary.wiley.com/doi/10.1111/nyas.12998/full>. • Hill, PL, M Allemand, and BW Roberts. “Examining the Pathways between Gratitude and Self-Rated Physical Health across Adulthood.” Personality and Individual Differences 54.1 (2013): 92-96. <http://www.sciencedirect.com/science/article/pii/S0191886912004011>. • Neff, KD, and CK Germer. “A Pilot Study and Randomized Controlled Trial of the Mindful Self‐compassion Program.” Journal of Clinical Psychology(2013): 1-17. <http://onlinelibrary.wiley.com/doi/10.1002/jclp.21923/full>.
  • 109. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Mind-Body Feedback Loops • Tang, YY, BK Hölzel, and MI Posner. “The Neuroscience of Mindfulness Meditation.” Nature Reviews Neuroscience 16.1 (2015): 213-225. <http://www.nature.com/nrn/journal/v16/n4/abs/nrn3916.html>.
  • 110. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Digital Health • Altshuler, David and et al. "Creating a Global Alliance to Enable Responsible Sharing of Genomic and Clinical Data." 2013 June 3. http://genomicsandhealth.org/about-the-global-alliance/key- documents/white-paper-creating-global-alliance-enable-responsible-shar • Cnossen, Rick, Wendy Nilsen, et al. "White Paper: Data Collection and Mobile Technologies." Precision Medicine Meeting (2014): 1-13 Web http://www.nih.gov/precisionmedicine/whitepapers/Data-Collection-Mobile-Technologies.pdf • Elenko, Eric, Lindsay Underwood, and Daphne Zohar. “Defining digital medicine.” Nature Biotechnology (2015). http://www.researchgate.net/publication/276208474_Defining_digital_medicine
  • 111. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Digital Health • Gehrman, Philip, et al. "Feasibility of Group Cognitive-Behavioral Treatment of Insomnia Delivered by Clinical Video Telehealth." Telemedicine and e-Health 22.12 (2016): 1041-1046. http://online.liebertpub.com/doi/abs/10.1089/tmj.2016.0032 • Housman, Dan. "Marketing Research: Collaboration Proclamation." Medical Marketing & Media (2015): 36- 37. Web. http://www.mmm-online.com/features/marketing-research- collaboration-proclamation/article/400196/ • Maecker, Holden, Tamsin M. Lindstrom, and et al. "New Tools for Classification and Monitoring of Autoimmune Diseases." Nature Reviews Rheumatology. 8.1 (2012): 317-328. Web http://www.researchgate.net/publication/225078353_New_tools_for_classification_and_moni toring_of_autoimmune_diseases
  • 112. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Digital Health • Mandl, Kenneth D., Joshua C. Mandel, and Isaac S. Kohane. "Driving innovation in health systems through an apps-based information economy." Cell systems 1.1 (2015): 8-13. http://www.cell.com/cell-systems/fulltext/S2405-4712(15)00004-6 • Margolis, Peter, Laura Peterson, and Michael Seid. “Collaborative Chronic Care Networks (C3Ns) to transform chronic illness care.” Pediatrics 131.Supplement 4 (2013): S219–S223. http://www.researchgate.net/publication/269912722_Collaborative_Chronic_Care_Networks_ (C3Ns)_to_Transform_Chronic_Illness_Care • Milani, Richard, and Carl Lavie. “Health care 2020: reengineering health care delivery to combat chronic disease.” The American journal of medicine 128.4 (2014): 337–43. http://www.researchgate.net/publication/268692852_Health_Care_2020_Reengineering_Heal th_Care_Delivery_to_Combat_Chronic_Disease
  • 113. © 2017 - All rights reserved. Prevention and Lifestyle Modifications: Digital Health • Spanakis, Emmanouil G., et al. "Technology-Based Innovations to Foster Personalized Healthy Lifestyles and Well-Being: A Targeted Review." Journal of Medical Internet Research 18.6 (2016). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4938884/ • Topol, Eric. The Patient Will See You Now. New York: Basic Books, 2015. Print.
  • 114. © 2017 - All rights reserved. Take Charge of All Things Autoimmune +1.310.666.5312 drbonnie360@gmail.com www.drbonnie360.com @DrBonnie360 www.facebook.com/YourAutoimmunityCon nection Bonnie Feldman, DDS, MBA Business Development for Digital Health