methylation, genomics, and sibo - nhri genomics and sibo ... • in the following slides the header...

Lincoln College of Postprofessional, Graduate and Continuing Education

Methylation, Genomics, and SIBO

Instructor:

Paul Anderson, NMD

200 East Roosevelt Road Lombard, Illinois 60148-4583 630/889-6622 Phone / 630/889-6482 Fax

www.nuhs.edu (Continuing Education)

Copyright © 2017 by National University of Health Sciences. All Rights reserved.

Material attached may not be reproduced in any form without written permission.

Faculty and Instructors representing NUHS/Lincoln College of Postprofessional, Graduate and Continuing

Education are responsible for disclosing any financial interest, research grants, program support, or other

matters that create any suggestion of a conflict of interest.

Methylation, Genomics and SIBO

Paul S. Anderson, NMD2017 Integrative SIBO Conference

Saturday 4:00 – 5:30 PMAll material © PS Anderson unless noted

Abstract

The world of clinical genomics and nutrigenomics specifically has become an incredibly fast growth and high learning curve area of integrative medicine. Genomics as they affect GI health and SIBO specifically are still in their infancy but are impactful in the pathologies involved and healing from them. Dr. Anderson will use his knowledge of clinical genomics to propose ways in which ones genes and the epigenetic factors stressing them factor in to SIBO as a pathology and more importantly in healing. A mixture of data, clinical experiences and outcomes and case examples will be used.

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OutlineI. Introduction and Presentation of Thesis 20 min / 5 min

• How genomics relate to GI function and healing• Overview of mechanisms

o Epigenetic effects and SNP triggeringo Methyl Cycle SNPso Immunologic SNPs

• Statement of thesis – Nutrigenomics can augment the therapy and healing of a SIBO patient

II. Methyl Cycle Genomics and GI Function 20 min / 15 min

• How specifically the methyl cycle affects GI health• Salient SNP patterns to assess

III. Other Genomics and GI Function 20 min / 15 min

• Secretor status SNPs• IgA related SNPs• Other Immunologic SNPs

• MALT‐GALT Related SNPs• Type‐1 and other Immune related SNPs• Biofilm related SNPs

IV. Therapeutic Inclusion of Nutrigenomics in SIBO Patients 30 min / 15 min

• Nutrigenomic therapies for Methyl Cycle SNPs in SIBO• Nutrigenomic therapies for Immunologic and Other SNPs in SIBO


Financial Disclosures:

• No relevant financial conflicts to disclose.

• I have no affiliations with any testing company. The use of images depicting particular test reports does not indicate endorsement of said reports.


Introduction:

How Genomics Relate to

GI Function and Health


Important Note:

•Many SIBO cases are cleared without the inclusion (knowingly) of any of this information.

• In my experience mindfulness of this information improves outcomes and speed of treatment / strength of recovery.

• I believe genomic factors should be included in all assessments of GI disorders, and especially those cases that do not clear or do not stay cleared.


Overview

• The GI tract has two groups of genomic effectors that

crossover its function:

• Direct: Such as IgA, FUT, Celiac, etc…

• Indirect: Such as Methylation, Biofilms,

Neurotransmission etc…


What tissue specific activities does the methyl cycle have and how do they affect health?


Methylation effects on physiology and health:

• Neurotransmitter (central and peripheral) function:

• Most neurotransmitters have a methylation step in

synthesis or degradation:

• Formation: DA‐NE‐Epi‐Serotonin

• Reduction (partial) Histamine

9(c) PS Anderson ‐ www.ConsultDrA.com 2017


• Detoxification• Many Phase‐2 pathways up‐regulate with faster methylation• Detoxification of CO2/NH4 [Urea]• Biotransformation of some toxins

• Importance in rapidly dividing tissues:• Bone marrow function• GI repair and maintenance • Muscle (skeletal, cardiac and smooth)



•DNA Turnover – Cell replication and repair

•All Purine syntheses and half Pyrimidine syntheses

is predicated on a methylfolate step

•No methylation = Very slow or NO DNA repair /

replication11(c) PS Anderson ‐ www.ConsultDrA.com 2017

NUCLEOTIDE METABOLISM• PURINE BIOSYSTHESIS

• PYRIMIDINE BIOSYNTHESIS


5‐MTHF

5‐MTHF

Curr Gastroenterol Rep. 2010 October ; 12(5): 340–348. doi:10.1007/s11894‐010‐0130‐3.

The possible relationship between the quiescent and the actively cycling nature of the ISCs (Intestinal Stem Cells) needs to be further explored.

Moreover, it is critical to understand the genetic elements that determine stem cell fate and the basis by which regeneration occurs in order to better understand stem cell plasticity and the contribution made by the stem cell compartment to malignant disease. It is hoped that future studies in this area will provide a better platform to develop therapies to regenerate damaged intestinal epithelia as seen after radiation injuries or inflammatory bowel disease (eg, Crohn's disease).


Adam S. Darwich, Umair Aslam, Darren M. Ashcroft, and Amin Rostami‐Hodjegan. Meta‐Analysis of the Turnover of Intestinal Epithelia in Preclinical Animal Species and Humans. DMD December 2014 vol. 42 no. 12 2016‐2022

Cell turnover across the entire GI tract has a mean of 3‐9 days per cell turnover – If there is normal methyl

cycle support.(c) PS Anderson ‐ www.ConsultDrA.com 2017 14

Aside from physiologic and biochemical

extrapolations – is anyone researching the

genomic – GI connection?

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Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.230318.113.


… These tight junction components have been shown to affect several signaling and transcriptional pathways, and changes in the expression of tight junction proteins are associated with several disease conditions, such as cancer. Here, we will review how tight junction proteins participate in the regulation of gene expression and cell proliferation, as well as how they are regulated themselves by different mechanisms involved in gene expression and cell differentiation.



…These results suggest that DNA methylation patterns are important to consider in multi‐omic analyses of microbiome samples seeking to discover the diversity of bacterial functions and may differ between disease states.

So:

• There is no portion of the GI system which is not affected by genomic influences.

• In some dysfunctional / disease patterns this influence can be life long and create significant dysfunction leading to disease and poor outcome of therapy.

•Assessing and treating nutrigenomic areas in patients such as this can improve outcomes.


Note:

•The rest of the presentation will assume some

basic genomic / nutrigenomic understanding.

•Resources will be provided for deeper CME on

this topic at the end of the presentation.


A brief review:


SNP

Single Nucleotide Polymorphism ‐ (genetics) genetic variation in a DNA sequence that occurs when a single nucleotide in a genome is altered; SNPs are usually considered to be point mutations that have been evolutionarily successful enough to recur in a significant proportion of the population of a speciesVariations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, and other agents.As of 23 July 2013, dbSNP listed 62,676,337 SNPs in humans.National Center for Biotechnology Information, United States National Library of Medicine. 2013. NCBI dbSNP build 138 for human.

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GENETIC ‐ GENOMIC

• Genomics: discipline in genetics that applies recombinant DNA, DNA

sequencing methods, and bioinformatics to sequence, assemble, and

analyze the function and structure of genomes (the complete set of

DNA within a single cell of an organism).National Human Genome Research Institute (2010‐11‐08). "A Brief Guide to Genomics". Genome.gov.

Concepts of genetics (10th ed.). San Francisco: Pearson Education. 2012. ISBN 9780321724120.

National Human Genome Research Institute (2010‐11‐08). "FAQ About Genetic and Genomic Science". Genome.gov.

Culver, Kenneth W.; Mark A. Labow (2002‐11‐08). "Genomics". In Richard Robinson (ed.). Genetics. Macmillan Science Library. Macmillan Reference USA. ISBN 0028656067.

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GENETIC ‐ GENOMIC

• Contrast; the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.

National Human Genome Research Institute (2010‐11‐08). "A Brief Guide to Genomics". Genome.gov.

Concepts of genetics (10th ed.). San Francisco: Pearson Education. 2012. ISBN 9780321724120.

National Human Genome Research Institute (2010‐11‐08). "FAQ About Genetic and Genomic Science". Genome.gov.

Culver, Kenneth W.; Mark A. Labow (2002‐11‐08). "Genomics". In Richard Robinson (ed.). Genetics. Macmillan Science Library. Macmillan Reference USA. ISBN 0028656067.


Note:

• In the following slides the header “Epigenetics” is being used in a very

broad sense, including some factors not technically “epigenetic” but

fitting the role of factors that affect gene expression, phenotypic

outcome and other interactions that can minimize or exaggerate

expression of potentially pathogenic SNPs or other phenotypic

determinants.


Epigenetics: Patient and family history

• There are “upstream” epigenetic factors that are terribly interesting

but we won’t really look at deeply – i.e. experiences of parent or

grandparent affect your epigenome…

• Also newer epi or “paragenetic” information (dads stressed sperm

affects your DNA etc…)

• But:


EPIGENETIC

“Denoting processes by which heritable modifications in gene function occur

without a change in the sequence of the DNA”

Epigenetics is the study of changes in gene expression caused by certain base

pairs in DNA, or RNA, being "turned off" or "turned on" again, through

chemical reactions. In biology, and specifically genetics, epigenetics is mostly

the study of heritable changes that are not caused by changes in the DNA

sequenceSpector, Tim (2012). Identically Different: Why You Can Change Your Genes. London: Weidenfeld & Nicolson. p. 8.


EPIGENETIC

To a lesser extent, epigenetics also describes the study of stable, long‐

term alterations in the transcriptional potential of a cell that are not

necessarily heritable. Unlike simple genetics based on changes to the

DNA sequence (the genotype), the changes in gene expression or

cellular phenotype of epigenetics have other causes, thus use of the

term epi‐ (Greek: επί‐ over, outside of, around) ‐genetics. Spector, Tim (2012).

Identically Different: Why You Can Change Your Genes. London: Weidenfeld & Nicolson. p. 8.


EPIGENETIC

The term also refers to the changes themselves: functionally relevant

changes to the genome that do not involve a change in the nucleotide

sequence. Examples of mechanisms that produce such changes are

DNA methylation and histone modification, each of which alters how

genes are expressed without altering the underlying DNA sequenceSpector, Tim (2012). Identically Different: Why You Can Change Your Genes. London: Weidenfeld & Nicolson. p. 8.


Further reading for the interested:


• Gordana Supic , Maja Jagodic & Zvonko Magic (2013) Epigenetics:A New Link Between Nutrition and Cancer, Nutrition and Cancer, 65:6, 781‐792, DOI:10.1080/01635581.2013.805794

• Mark H. Vickers. Early Life Nutrition, Epigenetics and Programming of Later Life Disease. Nutrients 2014, 6, 2165‐2178; doi:10.3390/nu6062165. www.mdpi.com/journal/nutrients

• Michael Daniel and Trygve O. Tollefsbol. Epigenetic linkage of aging, cancer and nutrition. The Journal of Experimental Biology (2015) 218, 59‐70 doi:10.1242/jeb.107110

• Anna Maria Mileo and Stefania Miccadei. Polyphenols as Modulator of Oxidative Stress in Cancer Disease: New Therapeutic Strategies. Oxidative Medicine and Cellular Longevity. Volume 2016, Article ID 6475624, 17 pages. http://dx.doi.org/10.1155/2016/6475624

• Karen S. Bishop and Lynnette R. Ferguson. The Interaction between Epigenetics, Nutrition and the Development of Cancer. Nutrients 2015, 7, 922‐947; doi:10.3390/nu7020922


So:

• Presence of a SNP does not mean it is activated / expressing

• Epigenetic factors are not “tested” but rather assessed in total

• The more epigenetic stressors the more likely a SNP will be active and

expressing

• Many epigenetically activated SNPs can be inactivated / silenced by

proper treatment


The Methyl Cycle and

GI Function


As mentioned:Methylation effects on GI physiology and

health:

• Affects GI Stem cells, Microbiome, Tight junction function etc…

• DNA Turnover – Cell replication and repair

• All Purine syntheses and half Pyrimidine syntheses is predicated on a methylfolate step

• No methylation = Very slow or NO DNA repair / replication


What are the components of the methyl cycle and what makes them work?


Methyl Cycle – Sulfur AA Interactions (simplified)

5‐10‐Methyl‐THF

Folate [B‐3] DHF [B‐3—DHF reductase] TetraHydroFolate

[B‐3 ‐‐‐MTHFR / B2]

[MTR‐MTRR]

Methionine / SAM‐e [Betaine / B12‐‐‐‐MethSynth] 5‐MTHF

[AHCY] [BHMT Back up to MTRR…]

CH3 Homocysteine

[B6 ------- CBS]Cystathionine

(Toxic-S) [B6]Sulfite Cysteine [Mg---GSH Synthase (GSTP/GSTM)] Glutathione

[B3][Mo ------Sulfite Oxidase]

[B6]Sulfate(Helpful-S) Taurine

© PS Anderson 2017


Quick Methylation Points:

• The whole cycle must be considered and assessed (not just MTHFR).• In order to normalize (to the degree possible) any methylation imbalances with a nutrigenomic strategy all parts of the methyl cycle must be treated.

• Additionally care should be given in “jump starting” the methyl cycle without assuring collateral ‐ downstream pathways are working first. This avoids the common “detox” and other reactions seen with methylation support applied too quickly.


Where in biochemistry does the methyl cycle exist and what pathways does it intersect with?



Main graphic: http://blog.healthpost.co.nz/wp‐content/uploads/BComplex140729‐diagram.jpg Yellow and Brown additions by PS Anderson

Sulfite Reduction

Phase‐2 Priming

Catecholamine Reduction

Ornithine‐Arginine cycling /

Removal of CO2 and NH4

Histamine partial

reduction

A few of the places affected by increased methyl cycle activity

Most Common Negative Reactions:

• Negative reaction:• Agitation• Anxiety• Sulfur ‐ Sulfite intolerance• Sleeplessness• Allergic reactions• GI Upset• Fatigue• Memory problems

• Likely causes:• COMT – MAO SNP’s

• CBS SNP’s

• Sulfation pathway defects

• Histamine metabolism

• Phase‐2 overload


Other Genomic / SNP areas

to Consider in

GI Health


Immune System – Genomics

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Cell LinesBone Marrow:

Hemocytoblast

Myeloid Stem

Lymphoid Megakaryocyte

Stem Proerythroblast

MonoblastMyeloblast

B-Cells NK Cells Platelets Retic’s

Peripheral Tissues: PLT RBC’s WBC’sCell Mediated Immunity Ab (Humoral) Immunity Immunological Surveillance

Thymus:

Lymphoid Stem Cells

T-Cell Lines

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Immune Response1 – ANTIGEN PRESENTATION

2 – T‐CELL ACTIVATION / CMI

3 – B‐CELL ACTIVATION / Ab IMMUNITY

3A – ANTIGEN – ANTIBODY REACTION4 – CLASSIC COMPLIMENT

1A – ALTERNATE COMPLIMENT

2A – KILLER T‐CELL ACTION

ATTACK ON INVADER

= cytokine


Antibody – Humoral Response

• Ig‐A: “Secretory”• Primarily the secretory form is the useful kind. (found in tears, saliva, mucus…) Prevents bacteria, viruses, and toxin from attaching to mucosal linings.

• Ig‐E: “Allergy”• Type‐1 immediate hypersensitivity (allergy) reactions. Parasite infection.

• Ig‐M: “First Responder”. • Elevated in acute infection. Basis for ABO‐blood type antigen / transfusion reaction.

• Ig‐G: “Long Term”• Most common type. Focuses NK cells to their targets. Used in passive immunization (gamma‐globulin injection).


Compliment

• Activation of endogenous proteins (mainly enzyme precursors) in case of immunologic need.

• Two pathways:• Classical: activated by antigen – antibody (AG/AB) reaction• Alternate: goes ‘around’ the AG/AB reaction, activates the compliment cascade in the middle (at the C‐3 locus) without the Ag / Ab reaction.

• Large polysaccharide in the cell membranes of some pathogens stimulate this reaction.

• Less effective than Classical pathway


Ig issues: Frequency in the chronically ill:

• Selective Ig‐excess:• Ig A excess common in acute and chronic smoldering infections

• Ig M excess common in acute and chronic smoldering infections

• IgE Elevation

• Common in IBD – Parasites / Helminths – significant dysbiosis

• Generally resolve with acute / chronic immune treatment


Ig issues: Frequency in the chronically ill:

• Selective Ig‐deficiency:

• All potentially can happen and are more common in these cases

• IgG specific selective deficiency:

• Low levels (functional) common

• Must follow – May respond to IgG Tx.

• Screening:• IgG Subclasses: IgG1,2,3,4: Test Number: 209601


Ig: Considerations

Consider these SNP’s in the overall constitution of the patient and their

susceptibilities:

• More IgE SNP’s = more Type‐1 and Histamine reactions

• More IgA SNP’s = more mucosal issues

• More IgG SNP’s = more immune memory issues

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HLA and Celiac

Ruiz‐Ortiz E1, Montraveta M, Cabré E, Herrero‐Mata MJ, Pujol‐Borrell R, Palou E, Faner R. HLA‐DQ2/DQ8 and HLA‐DQB1*02 homozygosity typing by real‐time polymerase chain reaction for the assessment of celiac disease genetic risk: evaluation of a Spanish celiac population. Tissue Antigens. 2014 Dec;84(6):545‐53. doi: 10.1111/tan.12472. PMID: 25413104

Abstract• Celiac disease (CD) is a complex autoimmune disorder caused by ingestion of gluten in genetically susceptible individuals….Finally, we assessed the clinical relevance of this real‐time PCR‐based assay by studying a cohort of fully characterized patients. As expected, all CD patients had at least one of the CD‐associated alleles, and the highest CD risk was indicated by the presence of the HLA‐DQ2.5 heterodimer (HLA‐DQA1*05‐DQB1*02) with HLA‐DQB1*02 in homozygosity.

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RAD Complex and Ig

• Mre11, Rad50, and Nbs1 form an evolutionarily conserved protein complex (Mre11‐Rad50‐Nbs1, MRN) that has been proposed to function as a DNA damage sensor. Hypomorphic mutations in Mre11 and Nbs1 result in the human …

• Here, we use Cre‐loxP‐mediated recombination to restrict Nbs1 deletion to B lymphocytes. We find that disruption of Nbs1 results in the accumulation of high levels of spontaneous DNA damage…

• Moreover, we show that Ig class‐switch recombination (CSR) is diminished in Nbs1‐deficient B cells. The CSR defect is B cell‐intrinsic, independent of switch‐region transcription, and a consequence of inefficient recombination at the DNA level. Our findings reveal that Nbs1 is critical for efficient Ig CSR and maintenance of the integrity of chromosomal structure and number.

PMID: 15668392


DARC

• INTRODUCTION: Chemokines are regulated by a family of 'atypical' chemokine receptors, D6, DARC and CCX‐CKR, each of which efficiently internalizes its cognate chemokine ligands. Development of monoclonal antibodies (MAbs) that would recognize CCX‐CKR on the cell surface will be helpful to identify primary CCX‐CKR‐expressing cell types and analyze the fate of CCX‐CKR after ligand binding to the receptor.

• RESULTS: A panel of MAbs reacting with CCX‐CKR expressed on the cell surface was prepared. The panel was a small one, consisting of only ten MAbs, but was rich in terms of diversity of the Ig isotypes and of the epitopes. Epitope analyses revealed that all the 10 MAbs recognized at least three different, although very close, peptide structures of the N‐terminal domain. Three MAbs, namely, 2F11, 13E11 and 14F10, were selected to represent the panel. All of the MAbs were applicable for flow cytometry and immunoflurescent assays and immunoprecipitation. The reactivity of the 2F11 MAb was also confirmed by western blotting. Endogenous expression of CCX‐CKR on human hepatocytes and hepatic tumor cell lines was demonstrated using the 13E11 MAb. Interestingly, binding of the 13E11 MAb with B300‐19 cells expressing CCX‐CKR resulted in induction of CCX‐CKR internalization.

PMID: 21184834


FCER1

• IgE has long been known as a therapeutic target for allergic disease, but the difficulty has been in selecting agents that don't trigger cross linkage of IgE when bound to its high affinity receptor (FceR1) on mast cells and basophils.

• By “designing” a monoclonal antibody (mAb) which targets that part of IgE that binds to that binds to the a‐chain of FceR1, the allergic cascade can be effectively interrupted and diseases such as asthma greatly improved, providing a substantial part of their phenotype engages IgE.

Holgate World Allergy Organization Journal 2014, 7:17


IL‐13

• IL‐13 are able to induce an immunoglobulin isotype switch to IgE in B cells. A major question is to what extent these cytokines contribute to the production of IgE in allergic patients. To address this question we used an in vitro culture system in which the production of IgE is dependent on endogenously produced IL‐4 and IL‐13.

• Our results indicate that, at least in vitro, IgE production in allergic asthma patients is more dependent on IL‐13 than in non‐atopics, due to enhanced IL‐13 production and to enhanced IgE production in response to IL‐13.

Van Der Pouw Kraan TCTM, Van Der Zee JS, Boeije LCM, DE Groot ER, Stapel SO, Aarden LA. The role of IL‐13 in IgE synthesis by allergic asthma patients. Clinical and Experimental Immunology. 1998;111(1):129‐135. doi:10.1046/j.1365‐2249.1998.00471.x.



FCGR2

• Also known as: CD32; FCG2; FcGR; CD32A; CDw32; FCGR2; IGFR2; FCGR2A1

• Summary: This gene encodes one member of a family of immunoglobulin Fc receptor genes found on the surface of many immune response cells. The protein encoded by this gene is a cell surface receptor found on phagocytic cells such as macrophages and neutrophils, and is involved in the process of phagocytosis and clearing of immune complexes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2008 ‐ NLM]


TNFRSF

• Tumor necrosis factor (TNF) receptor superfamily (TNFRSF), agonistic antibodies have been used to stimulate TNFRSF receptors in vitro and in vivo. TNFRSF receptor‐specific antibodies of the IgM subclass and secondary cross‐linked or aggregation prone dimeric antibodies typically display superior agonistic activity compared with dimeric antibodies….

Cell Death and Differentiation (2015) 22, 1727–1741; doi:10.1038/cdd.2015.109; published online 21 August 2015

• TNFRSF13B/TACI defects have been associated with CVID pathogenesis and/or phenotype, especially the development of benign lymphoproliferation and autoimmunity. Our purpose was to investigate the role … Both mutations identified in TH patients have been assessed as deleterious for protein function, while the patient with the R202H mutation and sarcoidosis exhibited also sIgG4D. Our study further supports the notion that… but may be also found frequently in distinct clinical phenotypes, including benign lymphoproliferation and IgG subclass deficiencies.

Speletas M, Salzer U, Florou Z, et al. Heterozygous Alterations of TNFRSF13B/TACI in Tonsillar Hypertrophy and Sarcoidosis. Clinical and Developmental Immunology. 2013;2013:532437. doi:10.1155/2013/532437.

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CFH

• We carried out a genome‐wide association study of IgA nephropathy, a major cause of kidney failure worldwide. We studied 1,194 cases … as well as a common deletion of CFHR1 and CFHR3 at chromosome 1q32 and a locus at chromosome 22q12 that each surpassed genome‐wide significance.

• These five loci explain 4–7% of the disease variance and up to a tenfold variation in inter individual risk. Many of the alleles that protect against IgA nephropathy impart increased risk for other autoimmune or infectious diseases, and IgA nephropathy

• Nature Genetics 43, 321–327 (2011) doi:10.1038/ng.787


IFIH1

• To understand the genetic predisposition to selective immunoglobulin A deficiency (IgAD), we performed a genome‐wide association study in 430 affected individuals (cases) from Sweden and Iceland and 1,090 ethnically matched controls, and we performed replication studies in two independent European cohorts. In addition to the known association of HLA with IgAD, we identified association with a nonsynonymous variant in IFIH1 (rs1990760G>A, P = 7.3 x 10(‐10)) which was previously associated with type 1 diabetes and systemic lupus erythematosus. Variants in CLEC16A, another known autoimmunity locus, showed suggestive evidence for association (rs6498142C>G, P = 1.8 x 10(‐7)), and 29 additional loci were identified with P < 5 x 10(‐5). A survey in IgAD of 118 validated non‐HLA autoimmunity loci indicated a significant enrichment for association with autoimmunity loci as compared to non‐autoimmunity loci (P = 9.0 x 10(‐4)) or random SNPs across the genome (P < 0.0001). These findings support the hypothesis that autoimmune mechanisms may contribute to the pathogenesis of IgAD.

PMID: 20694011


TRAF1

• This protein and TRAF2 form a heterodimeric complex, which is required for TNF‐alpha‐mediated activation of MAPK8/JNK and NF‐kappaB. The protein complex formed by this protein and TRAF2 also interacts with inhibitor‐of‐apoptosis proteins (IAPs), and thus mediates the anti‐apoptotic signals from TNF receptors. The expression of this protein can be induced by Epstein‐Barr virus (EBV). EBV infection membrane protein 1 (LMP1) is found to interact with this and other TRAF proteins; this interaction is thought to link LMP1‐mediated B lymphocyte transformation to the signal transduction from TNFR family receptors. [NLM]

• Also related to IgA Nephropathy etc…


HLA‐DQA2

• Related to IgA:

• Nephropathy

• Deficiency

• Crosstalk


Ig: Therapy Considerations

Consider these SNP’s in the overall constitution of the patient and their susceptibilities:

• More IgE SNP’s = more Type‐1 and Histamine reactions• See any of the “Histamine CME” from Dr. Anderson

• More IgA SNP’s = more mucosal issues• See below

• More IgG SNP’s = more immune memory issues


Immunoglobulin Stimulation (IgA)

• Colostrum:• Crooks CV, Wall CR, Cross ML, Rutherfurd‐Markwick KJ. The effect of bovine colostrum supplementation on salivary IgA in distance runners. Int J Sport Nutr Exerc Metab. 2006 Feb;16(1):47‐64. PMID:16676703

• Sacro b.:• Amir Qamar, et.al. Saccharomyces boulardii Stimulates Intestinal Immunoglobulin A Immune Response to Clostridium difficile Toxin A in Mice. Infect Immun. 2001 Apr; 69(4): 2762–2765. doi: 10.1128/IAI.69.4.2762‐2765.2001. PMCID: PMC98222

• Zanello G, et.al. Saccharomyces boulardii effects on gastrointestinal diseases Curr. Issues Mol. Biol. 11: 47‐58.


Immunoglobulin Stimulation (IgA)

• Mushrooms:• van Nevel CJ1, Decuypere JA, Dierick N, Molly K. The influence of Lentinusedodes (Shiitake mushroom) preparations on bacteriological and morphological aspects of the small intestine in piglets. Arch Tierernahr. 2003 Dec;57(6):399‐412. PMID: 14982320

• Thymus:• Lin CY, Hsu HC, Chen CL, Shen EY. Treatment of combined immunodeficiency with thymic extract (Thymostimulin). Ann Allergy. 1987 May;58(5):379‐84. PMID: 3578932


Immunoglobulin Stimulation (IgG)

• Methylation and Marrow Support

• Mitochondrial Support

• Immune Balancing


Immunogenomics

A BIG topic. I did a webinar for Key2Health you can order and it goes through this topic in a 90 minute webinar format.

“Immunology and genetics: Where to look on the SNP profile for immune affecting genetics and what you can do about them.”http://www.keycompounding.com/providers/webinar‐immunology‐and‐genetics‐where‐to‐look‐on‐the‐snp‐profile‐for‐immune‐affecting‐genetics‐and‐what‐you‐can‐do‐about‐them/

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FUT2


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Wacklin P, Tuimala J, Nikkila¨ J, Tims S, Ma¨kivuokko H, et al. (2014) Faecal Microbiota Composition in Adults Is Associated with the FUT2 Gene Determining the Secretor Status. PLoS ONE 9(4): e94863. doi:10.1371/journal.pone.0094863

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FUT2

Our findings based on the microbiota profiling with three methods (PCR‐DGGE, pyrosequencing and the HITChip) showed that the composition of the intestinal microbiota was associated with the secretor status and with the determinant of the secretor status, the FUT2 gene polymorphism. The secretor status/FUT2 appeared to be one of the host genetic features contributing to the human microbiota and inter‐individual microbiota variation. This demonstrates that a single host gene can have a significant effect on the intestinal microbiotacomposition in healthy adults.The human intestinal microbiota has recently been tentatively clustered into three main types, called enterotypes, suggested to be characterised by a few key genera [16]. The drivers of these clusters, which are still under debate [17], [18], are not fully known, but diet, environment and host genetics have been proposed. Indeed, long‐term diet has been reported to explain part of the enterotypes [19] and immunity‐related host gene GTPase family M gene (IRGM) (SNP rs1747270) has been associated to

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FUT2Several autoimmune diseases such as the inflammatory bowel disease (IBD) [9], [21], and type I diabetes [10] have been associated with the FUT2 polymorphism. By studying microbiota of IBD patients with known FUT2 genotypes Rausch et al. showed that the FUT2 genotype could contribute to the susceptibility for IBD through altered microbiota composition [14]. The present study comparing the fecal microbiota in 14 non‐secretors and 57 secretors showed that even healthy non‐secretors and secretors have differences in their intestinal microbiota. Similarly, differences in composition of mucosal microbiota between healthy nonsecretors and secretors were suggested in study by Rausch et al. on the basis of only three healthy non‐secretors [14]. Actually, we observed that the bacteria belonging to Blautia et rel., Dorea formicigenerans et rel., Ruminococcus gnavus et rel., and Clostridium sphenoides et rel., were significantly more abundant in the nonsecretors than in the secretors. Interestingly, all these taxa have been associated with IBS and/or IBD in several studies [22–24] and may thus indicate that non‐secretors have propensity for intestinal aberrations. In addition to IBD, higher susceptibility to e.g. coeliac disease [25] and diabetes type 1 [26] has been associated with the dysbiosis of microbiota and in separate studies also with non‐secretor status [10], [27]. Based on these examples it is tempting to speculate that the FUT2 genotype may be a relevant factor that induces alterations in the microbiota composition and plays a role in aetiology of the several diseases involving hostmicrobiota interactions.


FUT2

This study shows that non‐secretors have an altered intestinalmicrobiota community and strengthens the evidence indicatingthat the FUT2 polymorphism influence on the intestinal microbiota.The secretor status is one of the drivers of host‐associatedvariation in the microbiota composition and, together with otherfactors it may contribute to the clustering of microbiota intoenterotypes.


Yeast, Alcohol and Aldehyde

Metabolism and SNPs



Acetaldehyde ExposureAlcoholOne of the main significant acetaldehyde exposure routes is through alcohol (ethanol) consumption. Ethanol metabolism starts with the conversion of alcohol to acetaldehyde, which is at least 30 times more toxic than alcohol. Ideally, acetaldehyde is then oxidized to acetic acid and ultimately into Acetyl‐CoA, which will be used for cellular energy. Unfortunately, in many if not most people, this conversion is slow and not always efficient due to genetic variations of the enzymes that perform this step, insufficient nutrient cofactors or exposure to related chemicals utilizing the same metabolic enzymes and nutrients. The result may be high acetaldehyde levels, which can cause significant damage to the liver where the bulk of alcohol metabolism occurs.1 Other alcohol metabolism sites that expose tissue to acetaldehyde’s damaging effects are the pancreas, gastrointestinal tract and in particular, the brain.2‐3 Alcohol may result in “drunkenness”—the central nervous system effects of relaxation, loss of coordination and inhibition of judgment—but acetaldehyde is responsible for the “hangover,” the toxic side effects that can eventually damage the brain.


Acetaldehyde ExposureCandidaAnother important exposure route to toxic acetaldehyde levels is through its production by the opportunistic yeast, Candida albicans. In small numbers, this yeast may be kept in check in the gut by the immune system and friendly bacteria such as Lactobacillus sp. and Bifidobacterium sp. But in many people, increasing carbohydrates, especially sweets, will cause chronic Candidiasis. Candida produces acetaldehyde in the GI tract by sugar fermentation. The typical American diet along with drug and antibiotic therapies, hypochlorhydria (low stomach acid), chronic stress, environmental toxins, etc. have altered gut integrity and immunity and predisposed millions of people to yeast overgrowth or the “Candida Syndrome.”4 A person with this condition who also drinks beer, wine or liqueurs not only produces acetaldehyde from the alcohol but also delivers more sugar for yeast production of acetaldehyde, creating a double‐barreled dose. Acetaldehyde produced in the gut can eventually reach more parts of the body, flooding the system and increasing the risk for damage.5


Acetaldehyde ExposurePollutionThrough the burning of tobacco, petroleum fuels, natural gas, wood and trash, aldehydes, including acetaldehyde, are present in the air we breathe. Vehicle and factory exhaust can create a chronic but significant exposure source to those who live near heavily trafficked areas or who spend hours commuting on freeways. Acetaldehyde contributes to photochemical “smog” formation when it reacts with other volatile substances in the air. Open car windows increase exposure, as does breathing in acetaldehyde‐containing fumes near gas pumps. Cigarette smokers and others around them are exposed through inhaling smoke. According to the Environmental Protection Agency (EPA), wood smoke from campfires, wood‐burning stoves and residential fireplaces is more toxic than cigarette smoke. But the acetaldehyde level released from burning items such as plastics, styrofoamand batteries is even higher.6 While acetaldehyde exposure from auto exhaust and cigarettes may be less than that from alcohol, research shows that low dose chronic exposure may still be sufficient to gradually damage proteins, enzymes and other cellular structures in the brain and other organs.7Furthermore, most fragrances today are made from synthetic chemicals, many of which are toxic. Air fresheners, scented candles, cleaning products, cologne or perfume and more can create a source of chronic exposure to many toxic chemicals including acetaldehyde. Children and babies are particularly susceptible. Additionally, the Environmental Working Group (EWG) lists acetaldehyde as one of the contaminants released from polyethylene plastic bottles.8


Prior Slide References1. Zakhari S. Overview: How is alcohol metabolized by the body? Alcohol Research & Health. 2006;29(4):245‐254.2. Edenberg H J. The genetics of alcohol metabolism: Role of alcohol dehydrogenase and aldehyde dehydrogenase variants. Alcohol Research & Health. 2007;30(1):5‐13.3. Vonlaufen A, Wilson JS, Pirola RC, Apte MV. Role of alcohol metabolism in chronic pancreatitis. Alcohol Research & Health. 2007;30(1):38‐54.4. Galland LD. Nutrition and Candida albicans, 1986 A year in Nutritional Medicine, ed. J. Bland. New Canaan. Keats Pub. 1986 pg. 203‐238.5. Truss CO. Metabolic Abnormalities in Patients with Chronic Candidiasis: The Acetaldehyde Hypothesis. J Orthomolecular Psychiatry. 1984;13(2):66‐93.6. www.fs.fed.us/t‐d/pubs/htmlpubs/htm04232327/page01.htm (US Forest Service‐Dept of Agriculture). What’s Burning in your Campfire? Garbage In, Toxics Out.7 Sorrell MF, Tuma DJ. The Functional Implications of Acetaldehyde Binding to Cell Constituents. Ann NY Acad Sci. 1987;492:50‐62.8. www.EWG.org, accessed on 5/10/10.


ADH

Alcohol dehydrogenases (ADH) (EC 1.1.1.1) are a group of dehydrogenase enzymes that occur in many organisms and facilitate the interconversion between alcohols and aldehydes or ketones with the reduction of nicotinamide adenine dinucleotide (NAD+ to NADH). In humans and many other animals, they serve to break down alcohols that otherwise are toxic, and they also participate in generation of useful aldehyde, ketone, or alcohol groups during biosynthesis of various metabolites. In yeast, plants, and many bacteria, some alcohol dehydrogenases catalyze the opposite reaction as part of fermentation to ensure a constant supply of NAD+.



http://www.inchem.org/documents/jecfa/jecmono/v48je17.htm


http://www.gbhealthwatch.com/Trait‐Asian‐Flush.php

Acetaldehyde and Nutrient DeficienciesIn addition to its toxic effects, acetaldehyde induces deficiencies of nutrients used for its detoxification. As an example, vitamin B1 (thiamine) is depleted through alcohol and acetaldehyde detoxification.16 B1 is essential in carbohydrate metabolism for energy production, of which the brain uses 20 percent. Acetaldehyde‐induced B1 depletions exacerbate the already low B1 levels common in the population due to diuretics and other drugs, over‐consumption of simple carbohydrates (dysglycemia) and adrenal stress. In addition to its many functions, thiamine, the “nerve vitamin,” is critical to nerves and neurotransmitters. Even mild, chronic B1 deficiency can produce brain‐related symptoms such as emotional instability, confusion, depression, fatigue, irritability, headaches, sensitivity to noise, insomnia, decreased short‐term memory, brain‐fog and a feeling of impending doom.17‐18Relevant to this time of year, B1deficiency‐related lactic acidosis can make people more vulnerable to bug bites, since many insects, particularly mosquitoes, are attracted to mild acids.19Furthermore, people with chemical sensitivities to aldehydes may also be sensitive to seemingly unrelated substances like sulfites (preservatives) from wines and foods, and the smell of chlorine from pools and bleach.19. Fradin MS. Mosquitoes and Mosquito Repellents: A Clinician’s Guide. Ann Intern Med. June 1998;128(11):931‐940.20. Molybdenum. Monograph. Altern Med Rev. 2006;11(2):156‐161.21. Schmitt WH, et al. Molybdenum for Candida albicans Patients and other Problems. The Digest of Chiropractic Economics. Jan‐Feb. 1991;31(4):56‐63.


Acetaldehyde and Nutrient DeficienciesThe under appreciated essential trace mineral molybdenum is also involved with acetaldehyde metabolism. A molybdenum deficiency not only affects this process but also other enzymes in the body that require molybdenum as a cofactor—for example, sulfite oxidase, responsible for converting irritating sulfites into harmless sulfates for use in liver detoxification and cartilage. Sulfur‐containing amino acids, as important free radical scavengers, also use this molybdenum‐dependent pathway. Molybdenum has been shown to reduce sulfite sensitivity by increasing sulfite oxidase activity.20 Sulfites also destroy vitamin B1’s biological activity, contributing to a deficiency. Nutrient depletion leads to sensitivity to other chemicals that use these same pathways. This has been demonstrated in patients with Candidiasis as the excess stress put on the enzyme systems to detoxify acetaldehyde often leave them with sensitivities to multiple chemicals especially fragrances. Supplementing with the appropriate cofactors may improve an individual’s ability to handle Candida‐generated acetaldehyde.2119. Fradin MS. Mosquitoes and Mosquito Repellents: A Clinician’s Guide. Ann Intern Med. June 1998;128(11):931‐940.20. Molybdenum. Monograph. Altern Med Rev. 2006;11(2):156‐161.21. Schmitt WH, et al. Molybdenum for Candida albicans Patients and other Problems. The Digest of Chiropractic Economics. Jan‐Feb. 1991;31(4):56‐63.



B‐1

ALD2

• ALDH2 plays a crucial role in maintaining low blood levels of acetaldehyde during alcohol oxidation. In this pathway, the intermediate structures can be toxic, and health problems arise when those intermediates cannot be cleared.[3] When high levels of acetaldehyde occur in the blood, facial flushing, light headedness, palpitations, nausea, and general “hangover” symptoms occur. These symptoms are indicative of a disease known as the Alcohol flush reaction, also known as “Asian Flush” or “Oriental Flushing Syndrome”.[6]

3 Crabb DW, Matsumoto M, Chang D, You M (February 2004). "Overview of the role of alcohol dehydrogenase and aldehyde dehydrogenase and their variants in the genesis of alcohol‐related pathology". The Proceedings of the Nutrition Society 63 (1): 49–63. doi:10.1079/PNS2003327. PMID 15099407.6 Thomasson HR, Edenberg HJ, Crabb DW; et al. (April 1991). "Alcohol and aldehyde dehydrogenase genotypes and alcoholism in Chinese men". American Journal of Human Genetics 48 (4): 677–81. PMC 1682953. PMID 2014795.


ALD2

Aldehyde dehydrogenase is a polymorphic enzyme[3] responsible for the oxidation of aldehydes to carboxylic acids, which leave the liver and are metabolized by the body’s muscle and heart.[3] There are three different classes of these enzymes in mammals: class 1 (low Km, cytosolic), class 2 (low Km, mitochondrial), and class 3 (high Km, such as those expressed in tumors, stomach, and cornea). In all three classes, constitutive and inducible forms exist. ALDH1 and ALDH2 are the most important enzymes for aldehyde oxidation, and both are tetrameric enzymes composed of 54kDA subunits. These enzymes are found in many tissues of the body but are at the highest concentration in the liver.[3]3 Crabb DW, Matsumoto M, Chang D, You M (February 2004). "Overview of the role of alcohol dehydrogenase and aldehyde dehydrogenase and their variants in the genesis of alcohol‐related pathology". The Proceedings of the Nutrition Society 63 (1): 49–63. doi:10.1079/PNS2003327. PMID 15099407.

(c) PS Anderson ‐ www.ConsultDrA.com ‐ 2016 93 (c) PS Anderson ‐ www.ConsultDrA.com ‐ 2016 94

http://jn.nutrition.org/content/128/2/459S/F1.expansion

CYP’s (Phase‐1) in the GI TractThelen K, Dressman JB. Cytochrome P450‐mediated metabolism in the human gut wall. J Pharm Pharmacol. 2009 May;61(5):541‐58. doi: 10.1211/jpp/61.05.0002. PMID: 19405992OBJECTIVE:Although the human small intestine serves primarily as an absorptive organ for nutrients and water, it also has the ability to metabolise drugs. Interest in the small intestine as a drug‐metabolising organ has been increasing since the realisation that it is probably the most important extrahepatic site of drug biotransformation.KEY FINDINGS:Among the metabolising enzymes present in the small intestinal mucosa, the cytochromes P450 (CYPs) are of particular importance, being responsible for the majority of phase I drug metabolism reactions. Many drug interactions involving induction or inhibition of CYP enzymes, in particular CYP3A, have been proposed to occur substantially at the level of the intestine rather than exclusively within the liver, as originally thought. CYP3A and CYP2C represent the major intestinal CYPs, accounting for approximately 80% and 18%, respectively, of total immunoquantified CYPs. CYP2J2 is also consistently expressed in the human gut wall. In the case of CYP1A1, large interindividual variation in the expression levels has been reported. Data for the intestinal expression of the polymorphic CYP2D6 are conflicting. Several other CYPs, including the common hepatic isoform CYP2E1, are expressed in the human small intestine to only a very low extent, if at all. The distribution of most CYP enzymes is not uniform along the human gastrointestinal tract, being generally higher in the proximal regions of the small intestine.SUMMARY:This article reviews the current state of knowledge of CYP enzyme expression in human small intestine, the role of the gut wall in CYP‐mediated metabolism, and how this metabolism limits the bioavailability of orally administered drugs. Possible interactions between drugs and CYP activity in the small intestine are also discussed.


Mitochondria


Mitochondria

• While we have spoken about mitochondria in the original (Key2Health and CCNM) series on genomics, and in many other settings such as the immune and fatigue oriented CME on the ConsultDrA website, it is critical to remember that mitochondria need support in chronic GI disease.

• The longer the dysregulation the more the mitochondria get “run down”.

• In an immunologically challenged person if they have a number of mito‐SNP’s their resistance, bone marrow function and recovery will be significantly affected.


Mitochondrial Damage

• Big topic – Involved in the pathology of most chronic – slow resolution cases

• Slow to repair, but as it does the major symptoms lessen or are eliminated

• Concepts are:• Clean up (curcumin)• Restore energy (Poly‐MVA, B‐Vitamins, Iron [ferritin over 30‐40 minimum], Thyroid etc.)

• Repair (Phospholipids, ALA, Carnitine, Taurine)• Attend to cell ReDox: Omegas / Tocopherols / Ascorbate / Glutathione

98(c) PS Anderson‐www.ConsultDrA.com ‐ 2016

Mitochondrial Damage

• Big topic – Involved in the pathology of most chronic ID folks

• Slow to repair, but as it does the major symptoms lessen or are

eliminated

• Again a whole 90 min course is available:

https://www.consultdranderson.com/product/mitochondrial‐function/

99(c) PS Anderson‐www.ConsultDrA.com ‐ 2016

Cofactors to consider:

• Nicotinamide / NADH• Co‐Q‐10• Riboflavin‐5‐phosphate• Iron• Proline• Ca, Mg, K, Zn,Cu,Cr [positive]• Cd [negative]

(c) PS Anderson 2014 100

•Structure 19, 833–843, June 8, 2011•African Journal of Food Science Vol. 4(5) pp. 200‐222, May 2010•J. Anim. Sci. Vol. 91, E‐Suppl. 2/J. Dairy Sci. Vol. 96, E‐Suppl. 1

Biofilms:

They make tests falsely negative, slow healing

and cause the “recurrent” cases we see all

the time.


Some (of the many) resources:

• Brown HL, Reuter M, Hanman K, Betts RP, van Vliet AHM (2015) Prevention of Biofilm Formation and Removal of Existing Biofilms by Extracellular DNases of Campylobacter jejuni. PLoS ONE 10(3):e0121680. doi:10.1371/journal.pone.0121680

• npj Biofilms and Microbiomes (2015) 1, 15005; doi:10.1038/npjbiofilms.2015.5; published online 25 March 2015

• Di Pasquale P. et.al. (2016) Exposure of E.coli to DNA‐MethylatingAgents Impairs Biofilm Formation and Invasion of Eukaryotic Cells via Down Regulation of the N‐Acetylneuraminate Lyase NanA. Front.Microbiol.7:147.doi: 10.3389/fmicb.2016.00147


Biofilm Agents – A Spectrum:

1. Prevention:A. Inhibit: Quorum Sensing

I. Organism cell signaling with auto‐inducers which determines gene expression, virulence, resistance, and the development of biofilms.

B. Inhibit: Initial Attachment of Biofilm ColoniesC. Inhibit: Organism Efflux Pump / Multi Drug Resistance Pump

Inhibitors2. Active therapies:

A. Bacteriostatic & ‘cidal agentsB. Direct biofilm disruption agents


Oral Biofilm Rx: Results

Phase‐1 (attachment / early biofilm) Phase‐2 Later Biofilm

• As compared to preventive phase‐1 agents?• As compared to other phase‐2 agents?BOTTOM LINE: YOU CANNOT TREAT PHASE‐2 BIOFILMS (which all your chronically ill folks have) WITH PHASE‐1 THERAPIES.


Biofilm Agents – A Spectrum: 1‐Prevention

• Enzymes

• Aromatics

• Tannins

• Phenolics

• Xylitol, Stevia

• Black cumin

• Etc…


Biofilm Agents – A Spectrum: 2‐ Active Therapy

• Antimicrobial Therapies

• Natural (including Black Cumin)

• Synthetic

• Direct Biofilm Disruption

• Agents that actually disrupt and “open” the biofilm


Oral Biofilm – Bismuth‐Thiol Complex

• STRONGEST PHASE‐2 AGENT AVAILABLE:

• More than the sum of its parts

• Pharmacology very different from individual parts


Oral Biofilm Rx: FAQ

• Isn’t bismuth toxic?

• Not in this form. This is neither bismuth nor thiol. The reason a reactive form

of bismuth and thiol(s) are mixed is to create a NEW molecule. The new

molecule is what disrupts the biofilm.



• Won’t it chelate my patient?

• Same answer – no. The Dithiol is bound to the bismuth so the toxicity of

bismuth and chelating ability of the thiols are negated.



• Does the initiation of immune symptoms after starting the agent

mean it is not working?

• No. In fact it means it is working. You may need more anti‐infective,

endocrine, inflammatory or other support as the symptoms mean the

immune system may be “seeing” the ID agents for the first time (due to

opening of the biofilm).


Biofilm Rx: FAQ

• In all your research and human trial is IV administered biofilm therapy

more likely to “stir up” or aggravate a patient or is oral biofilm Rx

more likely?

• In almost every case we have seen MUCH more aggravation in oral biofilm

therapy. Far less with IV therapies.

• This is likely due to the fact that biofilms are thought to start in the GI tract.


Oral Biofilm Rx:

• Any compounding pharmacy can make these capsules based on the strongest ingredients available in the studies mentioned.

• Initial testing on humans shows very good tolerance.

• Formula:• DMPS 25mg/ Alpha Lipoic Acid 100mg/ Bismuth Subnitrate 200mg per Capsule

• Ideally no substitutions• DMSA 100 mg can sub for DMPS• Bismuth Subcitrate can sub for Subnitrate (will make product weaker)


Oral Biofilm Rx:

• Bis‐thiol dosing:

• Approximates the most potent – most researched biofilm drugs• Uses the most (available) forms and combinations of medication chemistry

• DOSE:• 1 cap QD away from food, 3X a week for one week as a test dose• 1‐4 caps QD to BID away from food 3‐5X a week• Extra doses (on the “off days”) are helpful in dermatologic flares during therapy for dermatologic and ‘Herx’ type reactions

• Once an immunologic reaction is reached the dose may need to be decreased as needed


Oral Biofilm Rx:

• Normal trial is for 60 – 120 days during other anti‐infective therapy• May be used much longer if clinically indicated

• Usual trajectory of therapy:• First 30‐60 days may have no change

• Eventually (when the biofilm Rx breaks the biofilm open) the patient will typically exhibit signs of an immune reaction. This can be any cytokine based reaction.

• This is the time when a balance must be struck:


Biofilm Rx Support:

• This “balance is gained typically by allowing the biofilm Rx to continue and modulating anti‐infective Rx along with enough Adrenal (and occasionally Thyroid) support.

• If the patient is on non‐Rx adrenal support they may need 5‐10X the dose for a time.

• If they are on low dose hydrocortisone and adrenal support they often will need more hydrocortisone (sometimes 2‐4X for a time).


What is next?

Phase‐1 (attachment / early biofilm) Phase‐2 Later Biofilm

• After you have broken through the biofilm and therapy is progressing (which may take 3‐12 months) then you can phase in the “phase‐1” agents to clean up the biofilms that are most clinically significant –AND – keep them from re‐forming.


Biofilms

• While we do not have the time to delve as deeply as necessary into this topic I have a full 90 minute webinar which can be obtained at the URL below.

• It develops the concepts of phases of biofilms and how those phases affect treatment (and why most ‘biofilm therapies’ do not work.)

• Additionally specific recommendations are given for each phase of biofilm activity and natural as well as Compounded Rx agents available.

https://www.consultdranderson.com/product/biofilms‐update/


Nutrigenomics in SIBO


Important Note:

•Many SIBO cases are cleared without the inclusion (knowingly) of any of this information.

• In my experience mindfulness of this information improves outcomes and speed of treatment / strength of recovery.

• I believe genomic factors should be included in all assessments of GI disorders, and especially those cases that do not clear or do not stay cleared.


“A.L.T.O.S.”

• ASSESS Sn/Sx and SNP’s

• Start LOW and work up

• TREAT the patient not just the SNP’s

• Treat from the OUTSIDE in

• Monitor SIGNS AND SYMPTOMS to adjust therapy


Concept:

• A genetic slow‐down or absence of an enzyme system will cause:

• Slower production of the enzyme, nucleotide, neurotransmitter etc

• Slower elimination of the used product

• Imbalance in products

• Excess consumption of collateral (or possibly primary) pathway cofactors

• All of the above


Treatment Order: Outside ‐ In

• Diet – GI [within other therapeutic limitations]

• Colorful veggies / flavinoids

• Avoid sensitivities and sugar

• Long term of course but you can’t out supplement a shitty diet

• Inflammation and Phase‐2 Support

• Most “SNP” support eventually hits some oxidative pathway or another

• Many post SNP Tx reactions are Phase 1 2 back ups etc


Treatment Order: Outside ‐ In

• Trace Minerals + Magnesium + MVM If tolerated• Almost all patients are trace mineral deficient• NO B‐vitamin Tx can work without its collateral trace element• Always consider Taurine in Magnesium sensitive people• Also K+ in Magnesium sensitive people

• Non Methyl Donor additions ‐ as indicated(B1,2,3,5,6)• See dosing below

• Methyl Support – as indicated• See dosing below• Watch for aggravations:

• Insomnia / Anxiety / Agitation• Pain / Detox‐like Sx…

(c) PS Anderson ‐ www.ConsultDrA.com 2016 123 (c) PS Anderson www.ConsultDrA.com 2016 124

Main graphic: http://blog.healthpost.co.nz/wp‐content/uploads/BComplex140729‐diagram.jpg Yellow, Red and Brown additions by PS Anderson

Sulfite Reduction

Phase‐2 Priming

Catecholamine Reduction

Ornithine‐Arginine cycling /

Removal of CO2 and NH4

Histamine partial

reduction

A few of the places affected by increased methyl cycle activity

Consider in first phase of

Tx


Tx


Tx


Tx


Tx

Nutrient dosing over time:

Time

Dose:

High [Pharmacologic]

Repletion

Test Dose

????


Nutrient dosing over time:

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing


Nutrient dosing over time: B‐1 Example

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing50 ‐ 100mg 500 – 1000 mg 100 ‐ 300 mg

“Test dose” “Replete and compensate” “Maintain”



Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing10 ‐ 50 mg 70 ‐ 300 mg 15 ‐ 50 dep. on SNP’s



Nutrient dosing over time: B‐3 ExampleExpressed as Niacinamide dose form:

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing100 ‐ 500 mg 1000 – 3000 mg 50 – 500 mg dep. on SNP’s




Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing250 mg 1500 ‐ 3000mg 100 ‐ 250



Nutrient dosing over time: P‐5‐P Example

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing10 ‐ 50 mg 70 ‐ 300 mg 15 ‐ 50 dep. on SNP’s



Nutrient dosing over time: 5‐MTHF / Folinic Acid Example

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing200 ‐ 400 mcg 1 to 15 mg 400 mcg – 5 mg dep. on SNP’s



Forms of Folate:• Folic Acid

requires DHFreductase

• Folinic Acid / Leukovorin (formyl-THF)No DHFreductase required

• 5-Methyltetrahydrofolate

FOLNADH/B3THFB3+DHF-reductase

(Graphics) http://web2.iadfw.net/uthman/nutritional_anemia/nutritional_anemia.html 133(c) PS Anderson ‐ www.ConsultDrA.com 2016

Nutrient dosing over time: B‐12 ExampleMethyl – Hydroxy or Adeno forms

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing200 ‐ 400 mcg 1 to 10 mg 1 – 5 mg dep. on SNP’s



Nutrient dosing over time: Vitamin‐C ExampleGiven in divided doses

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing500 – 1000 mg Bowel Tolerance 1 ‐ 2 grams



Nutrient dosing over time: Magnesium ExampleCitrate or Glycinate form – Divided Doses

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing100 ‐ 200 mg Bowel Tolerance 150 – 400 mg



Nutrient dosing over time: Copper Example

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing1‐3 mg 2‐6 mg 1‐3 mg



Nutrient dosing over time: Taurine Example

Time

Dose:


Repletion

Test Dose

Acute Replete / Pharmacologic Maintenance / BalanceDosing Dosing Dosing250‐500 mg 1000‐4000 mg 500‐1000 mg



VITAMIN GENERAL ENZYME SUPPORT FUNCTION

B-1

B-2

B-3

B-5

B-6

BH4 a.k.a.

(tetrahydro-

biopterin)

SAMe

ALDEHYDE transfer / DECARBOXYLATION

H+ Transfer / FMN – FAD (Flavins)

H+ Transfer / NAD – NADP

ACYL Group Transfer / Co-A

AMINO Group transfer / De-& Trans “aminations” [DAO, GAD, GABA]

NOS Cofactor / Superoxide anion producer; SAMe Cofactor in Hydroxylase

reactions

COMT, 5HT AND TYR Hydroxylase Support

ASCGSHBIOTIN

H+ Transfer / Hydroxylation of Proline& LysineGlutathione TransferaseCARBOXYLATION


Cofactors: Inorganic / Metal Ions

Ion Examples of enzymes containing this ionCupric Cytochrome oxidase

Ferrous or FerricCatalase / Cytochrome (via Heme)

Nitrogenase / Hydrogenase

MagnesiumGlucose 6‐phosphatase

HexokinaseDNA polymerase

Manganese Arginase

MolybdenumNitrate reductase / Nitrogenase

Sulfite OxidaseNickel Urease

ZincAlcohol dehydrogenase

Carbonic anhydrase / DNA polymerase


Remember:

• If your patient is healthy and you are providing preventive assessment and

treatment your therapeutic role is neither this complicated nor aggressive.

• Assure proper diet with precursors

• Support globally based on MTHFR status, family history, age etc…

• Since you do not know how toxic or how many SNP’s they have – Be as

balanced in supplementation as possible and work up.


In non‐resolving cases what time frame does

it take to have all these therapies effect

outcomes?


Online Genomics CME

Key2Health CE Series:• http://www.keycompounding.com/providers/webinars/introduction‐to‐clinical‐genomics/ [PART‐1: SIX CLASSES]

• http://www.keycompounding.com/providers/webinars/level‐ii‐advanced‐genomic‐medicine‐series/ [PART‐2: SEVEN CLASSES]

CCNM 6‐Part Genomics CME• http://www.ccnm.edu/nd‐careers/continuing‐education/on‐demand/genomic‐medicine‐new‐applications‐clinical‐practice


Thanks!

Questions?


methylation, genomics, and sibo - nhri genomics and sibo ... • in the following slides the header...

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