Maladaptive Genetics: Evolutionary Mismatches, Helminthic Therapy & Complex Disease in the Modern Era

The concept of Evolutionary Mismatches was first expounded on by Ernst Mayr in the 1940’s. That is, certain inherited traits that were once advantageous have become maladaptive in a different or changed environment. The concept of Evolutionary Mismatch is central to understanding the genetic involvement with the rising tide of complex, chronic disease in the modern era, as well as envisioning the means by which a host genotype may become better adapted to his/her environment. Helminthic therapy is the therapeutic colonization of symbiotic microorganisms for the purpose of biome restoration, immunomodulation, and immunotolerance. Helminthic therapy can be seen as a prophylaxis and treatment for individuals who are genetically predisposed to, or who present with inflammatory-based diseases. This article will expand on Evolutionary Mismatch, the Hygiene Hypothesis and the concept of Symbiosis in a medical context, as well as provide a roadmap for research and therapy.

The first wave of genomics research since the mapping of the human genome in the late 1990’s has led to an explosion of data that has identified the associations of various genotypes to modern diseases. While this research has been useful in establishing relationships and associations, lacking is the deeper understanding of how certain genotypes came to exist in various populations, how they evolved from one region to another, and how genotype is related to the presence or absence of microorganisms. The next wave of genomics research should largely be focussed on how and why genotypes came to exist. This future wave of research should investigate degrees of adaption to changing environmental and microbial conditions. By studying the “how” and the “why”, we learn about the pathogenic and symbiotic relationships that have necessarily shaped the development of our immune system, the influence of microorganism interactions with allelic selection, and why genotype critically relates to the environmental and microbial conditions of the host. This has already been studied to some degree, however we must go further and deeper into this subject matter in order to develop better models of how genotypes evolve, adapt and respond to changing microbial and environmental conditions. The majority of chronic diseases in the modern era are inflammatory by nature, and involve complex interactions between host immunity, microorganisms, the body’s terrain and environment. Importantly, microbial conditions have diverged significantly from our evolutionary past. We possess genetics which have historically evolved from diverse pathogenic and microbial interactions, yet now lack the microbial diversity of our ancestors. One result of this situation is an Evolutionary Mismatch, and an increased predisposition to inflammatory-based diseases.

From a chain of research, we’ve learned that the ApoE 4/4 genotype is associated with a roughly 20-fold increased risk of Alzheimer’s disease in the 1st world. However, this risk appears to not be consistent in all geographical regions. For Amazonian forager-horticulturalists who carry the ApoE 4/4 genotype, having increased parasite diversity modifies the risk of Alzheimer’s disease. Increased parasite diversity in this population with this same genotype increases cognitive skills with age, compared to non-ApoE-4 carriers (1). In the 1st world, the ApoE 4/4 genotype lacks the pathogen diversity required to modify the inflammatory predisposition. We learn from other research that ApoE 4/4 is better adapted at controlling the growth of the intracellular parasite plasmodium, which causes malaria (2). Importantly, the immunological effect of helminths and parasites is the induction of a robust TH2 immune response, activation of immunotolerant Regulatory T-cells, while down-regulating TH1 immune activation. ApoE 4/4 genotypes with higher LDL-C values confer protection against hepatitis C infection, and this genotype is associated with spontaneous viral clearance (3). We learn that the ApoE 4/4 genotype generates a more robust innate inflammatory immune response, but is less equipped to regulate redox. The ApoE 4/4 genotype is much better adapted at controlling infections, compared to other ApoE genotypes. If not burdened with a pathogen-rich environment, it can be deduced that ApoE 4/4 genotypes generate more inflammation, which predisposes towards developing an inflammatory condition such as Alzheimer’s or vascular disease.

When a genotype that is better adapted to function in a pathogen diverse environment lacks pathogen diversity, we begin to see the appearance of new diseases. This is Evolutionary Mismatch in real time. It has been argued for decades that the sterility of the 1st world environment, the widespread and multi-generational use of antibiotics and other medical interventions has significantly contributed to the epidemic of inflammatory, allergic, atopic and autoimmune-based diseases, over time. This is a primary concept derived from the ‘Hygiene Hypothesis’. When one considers the combined effect of an absence of certain pathogens and microorganisms with a genotype that is equipped to thrive in a pathogen-rich environment, you end up with an increased incidence of a new disease phenotype. Conversely, when symbiotic helminths are introduced to patients with inflammatory-based diseases, there are measurable benefits and immunological changes that occur.

Autoimmune Disease & Helminth Therapy

Helminthic therapy comprises a large and steadily progressing field of laboratory and clinical research spanning several decades. It involves the ingestion or cutaneous inoculation with certain worms or their ova, which have shown to be commensal and/or symbiotic to the host. “Symbiotic” in this context can be seen as an established, “mutually beneficial” relationship, by the colonization of the worm in the host. Helminthic colonization differs from a “Parasitic Disease”, or a “Parasitic Infection”, because unlike a disease or infection, the helminth is non-pathogenic to the host, and instead yields a benefit. Indeed, the study of how worms and parasites are beneficial (and even essential) under certain conditions forces a reframing and reclassification of the term “pathogenesis”, from a diagnostic perspective.

The large body of evidence suggests that helminthic therapy is advantageous for TH1-driven autoimmune diseases, allergies, asthma and atopy. This is because helminthic treatment induces a strong TH2 immune response, and shifts the patient away from an overreactive TH1 immune profile. Helminth treatment also induces immunotolerance, via the induction of Regulatory T-cells (TREG’s), as well as inducing Tolerogenic factors (24). Moreover, helminths secrete bioactive, immunogenic molecules and peptides into the circulation of the host, modulating dendritic cells, and pattern recognition receptors such as TLR’s (toll like receptors) (25). TLR’s are major therapeutic targets for inflammatory-based diseases. Additionally, research has elucidated that helminths, such as Trichuris Suis are strong inhibitors of chemokines and purinergic receptors, such as CXCL9, and P2X7 (26). Chemokine and purinergic receptors are the subject of ongoing research for a broad number of inflammatory, autoimmune and neuroinflammatory-based diseases (24).

Inoculation with the hookworm Necator Americanus has led to immunologically-induced gluten tolerance in humans with Celiac disease (4, 5). A 2005 study published in the journal ‘Inflammatory Bowel Disease’ found that 21/29 Crohn’s patients (72.4%)  achieved remission with the inoculation of the pig whipworm Trichuris Suis, while achieving a 177-point, mean reduction in the CDAI (Crohn’s disease activity index) (7). In the same year, a randomized controlled trial consisting of 54 Ulcerative Colitis patients found that clinical improvements using Trichuris Suis was achieved in 43% of patients by the 6th week of the study (8). These studies strongly imply that the genes linked to inflammatory bowel disease evolved due to the presence of pathogen richness. Indeed, the evolution of a group of interleukin cytokine genes that are associated with inflammatory bowel diseases, including Celiac and Crohn’s, have been traced to increased pathogen diversity (6).

Animal model research in rheumatoid arthritis has confirmed through systematic meta-analysis, the benefit and potential of helminthic therapy for significantly reducing arthritis scores, while modulating relevant cytokines and immunological markers (10, 11). Similar meta-analysis research has found benefits of Helminthic therapy in SLE (Lupus), including notable improvements in proteinuria, favorable histolgical changes to organ systems, and a wide range of immunomodulatory effects (12).

The effects of helminth treatment in multiple sclerosis (MS) has been studied for several years. With ‘early relapsing-remitting multiple sclerosis’, after 10 months of treatment in patients with the helminth Trichuris Suis, a 34% relative reduction of gandolium-enhancing brain lesions was observed on MRI (20). Other clinical studies have found reduced incidence of MRI-identified brain lesions in MS when using helminthic therapy (21), as well as a stabilization of the gut microbiome (22).

Lack of pathogen diversity among those with autoimmune susceptible genetics creates a void and an evolutionary mismatch to occur, and increases the risk of developing autoimmunity, in the modern world. Helminthic therapy matched to genotype is one major therapeutic lock and key mechanism that provides a real world example of how to effectively control and possibly resolve autoimmune disease.

De-Worming The 3rd World: Lessons To Be Learned

Large scale studies that deworm 3rd populations yield important observational data regarding the effects of helminths, worms and parasites on key biomarkers and disease metrics of metabolic and inflammatory diseases. Large population studies consistently identify that de-worming protocols increase risk factors for the development of metabolic, and inflammatory diseases. Four examples are given below.

A large scale, cluster-randomized controlled trial was conducted over the course of 4 years among 26 fishing villages in Uganda. The study involved a total of 1,898 participants given a quarterly dose of various anti-helminthic drugs, measuring outcomes for a variety of biomarkers: IR HOMA (homeostatic model of insulin resistance), LDL-C, total cholesterol, blood pressure, triglycerides and fasting glucose. Outcomes were assessed after 4 years. While anti-helminthic treatment had no effect on IR HOMA, it did result in a higher mean LDL-C. Infection with the helminth Schistosoma mansoni or Strongyloides, was associated with lower LDL-C values, and lower total cholesterol. Moderate to heavy infection with Schistosoma mansoni was associated with lower triglycerides, lower LDL-C and lower blood pressure (30).

A randomized controlled trial involving 1,566 schoolchildren in Vietnam were given either placebo or anti-helminthic treatment over 12 months. Anti-helminth treatment significantly increased the incidence of allergen skin sensitization (32).

A double-blind, household-cluster-randomized, placebo-controlled clinical trial was conducted on a total of 1,662 subjects living on an island in Indonesia. Enrolled subjects received either the anti-helminthic drug Albendazole or a placebo. As one would expect, Albendazole led to a decrease in IgE and eosinophil levels. At the community level, there was no observable effect on insulin resistance. However, among individuals who were infected with helminths, Albendazole treatment significantly increased insulin resistance (31).

A randomized controlled trial was conducted on 2,507 pregnant women living in Uganda. The design of the study was to determine the effects of the deworming drugs albendazole and praziquantel on perinatal and maternal outcomes. This region of Uganda features high helminthic prevalence but low intensity. The authors found: “Anthelminthic use during pregnancy showed no effect on perinatal mortality or congenital anomalies”. “There was no overall effect of albendazole on maternal anemia, but there was a suggestion of benefit of albendazole among women with moderate to heavy hookworm. There was no effect of either antihelminthic treatment on mean birth weight or on proportion of low birth weight” (33).

The overly ambitious mission to de-worm the 3rd world by the WHO and others, is attacked with much needed criticism (34). It is hardly logical to assume that altruism lies at the heart of de-worming agendas. Knowing that large sized studies consistently have found the appearance of disease metrics following de-worming populations, it is more likely that pharmaceutical interests have financial incentives to establish new markets in 3rd world countries. Furthermore, these de-worming agendas fail to address the biological role, significance, and potential importance of helminthic colonization for human health.

MHC, HLA Pathogen Diversity Genetics & Copy Number Variations (CNV)

MHC & Pathogen Diversity

Autoimmune disease susceptibility is strongly linked to MHC (also known as HLA) genetic inheritance on chromosome 6. This complex region of genes is central to pathogen recognition, consisting of 3 sections, and encodes for the major histocompatibility complex (MHC), which is centrally involved in cell surface antigen recognition. Additionally, the MHC region contains a parade of genes concerned with diverse immunological functions. It has been shown that having a higher variability of HLA genes is directly linked to increased pathogen diversity. Moreover, this pathogen richness association is strongly linked to allelic selection at the MHC-I, HLA-B locus, (18). Importantly, the HLA-B locus includes a large number of ‘B’ serotype antigens, such as HLA-B27, HLA-B51, HLA-B35, HLA-B57, among several others. This region is strongly linked to: ankylosing spondylitis, other spondyloarthropathies, Crohn’s disease, ulcerative colitis, psoriasis, reactive arthritis, Behcet’s disease, as well as adverse drug reactions. Several of the above-listed HLA-B related diseases have research showing benefits from helminthic therapy.

CNV’s (copy number variations) & Parasite Diversity

Copy number variations (CNV’s) are genes or gene sequences which generate duplicate genes on chromosomes. CNV’s make up roughly 4.8-9.5% of the human genome. CNV’s are complex, may lead to genomic instabilities, and are strongly linked to a wide range of diseases including: autoimmunity, Ehlers-Danlos Syndrome (EDS), joint hypermobility, congenital adrenal hyperplasia, Parkinson’s disease, autism spectrum, and psychiatric conditions such as schizophrenia. While CNV’s are known to be associated with various diseases, there is less research available documenting their evolutionary origins. However, when this has been studied, strong evidence links CNV genes, their duplications and complexities to evolutionary pathogen interactions, and pathogenic diversities. This is true of the Fcγ receptor gene (IgG receptor) (13). This is true of the HP (haptoglobulin) and HPR (haptoglobulin-related protein) genes (19). This is also true of the RCCX cluster within MHC-III, including the complement C4 gene (14). This also appears to be the case for the ß-defensin gene (23). This may be true of the SNCA (alpha synuclein) gene, although to date this has not been studied. It is hereby posited that for CNV’s, varying degrees of pathogenic pressures leads to allelic selections, which favor greater or fewer numbers of gene duplications. The presence or absence of pathogen-specific diversities for a given CNV genotype, will influence the function of this gene. Under mismatch conditions, it is posited that CNV genotypes linked to certain diseases, will be more likely to express that disease. By studying the deeper associations of CNV’s to pathogen selective pressures, we will learn about many currently unknown mechanisms of immune interactions between CNV genotype and host pathogen type. CNV research is currently hampered by the technological limitations of CNV sequencing by genomic companies, and therefore this research field is currently under-studied. No doubt, selective pressures from diverse pathogens have shaped the role that certain genes play in immune and neurological responses. It certainly appears that the genomic instabilities hampered by CNV genes may have evolved as a defense or response to high pathogen pressures and parasitic diversities, endemic to certain geographies, and that under mismatch conditions, new disease phenotypes appear.

Evolutionary Mismatch Genes & Helminth Therapeutics: Proposals for Future Research

Understanding Evolutionary Mismatch can greatly expedite our understanding and treatment for a wide range of diseases. It also can pave the way for how research can be better conducted and tailored to individual treatments. We can learn a lot by assembling the disparate areas of research from theoretical, to evolutionary biology, to epidemiology, to clinical trials. For example, clinical trials in autism using helminthic therapy has shown promise for significantly improving repetitive behaviors and irritability (15). Study design and outcomes may be improved upon when including known pathogen-rich genotyping for autistic subjects. A pathogen-rich genotype for autism may be the C4a and C4b genes (part of the RCCX cluster), which have already been strongly linked to autism in two separate studies (16, 17). Because C4a and C4b are known to have evolved due to pathogenic pressures, it could be theorized and studied whether helminthic treatment among autistic subjects who carry the C4a/C4b genotype (termed C4b null alleles with and without C4a gene duplications) is more efficacious or less. This is one example for improving stratification within clinical research studies, based upon pathogen selection-related genes.

The following is a list of proposed research and questions as it pertains to better understanding pathogen richness, genotype, and helminthic therapy. The numerical list of items below serve as a sequential template, that can be modeled and replicated using other genes.

1. Start by using existing genomic research that shows the association between genotype and disease. Example: ApoE 4/4 and Alzheimer’s. Then, establish which genes are associated to pathogen richness. Example: ApoE 4/4
2. Determine the pathogen types that are most associated with evolutionary advantages for each associated gene. Example: conduct pre-clinical studies on ApoE 4/4 to determine which type of microorganisms (viruses, parasites, bacteria) are most adapted with the genotype.
3. Establish biomarkers and/or histological characteristics that are associated with each genotype under pathogen conditions. Example: eosinophilia for ApoE 4/4 with high parasite burden is associated with improved cognition with age, hyperlipidemia for ApoE 4/4 carriers with hepatitis C confers increased viral clearance. Obtain multi-omics data to determine which other biomarkers are related to the genotype under pathogen conditions. Example: Conduct multi-omics testing on populations with ApoE 3/3, 3/4 and 4/4 genotyping, stratified by having high, medium and low parasite burdens. This should yield biomarker data that shows the effect of parasite diversity on ApoE 3/3, 3/4 and 4/4. This data should yield the biomarkers and trends that are present among ApoE 4 carriers, with high parasite burden, who show improved cognition with age, compared against those who don’t have high pathogen burden.
4. Begin longitudinal-type, randomized clinical trials for early onset Alzheimer’s disease among ApoE 4/4 carriers using helminths. Conduct trials comparing helminthic diversity (using multiple helminths) to mono-helminthic treatment (using only 1 helminth), i.e. more than 1 helminth. Use established multi-omics biomarkers obtained from step 3 above.

Ongoing Questions For Studying Genomic Mismatches & Associated Diseases

1. Parkinson’s, Evolutionary Mismatch & Helminthic Therapy – What role does lack of pathogen diversity have on shaping the predisposition to Parkinson’s disease? Epidemiological data suggests that Parkinson’s disease is less prevalent in pathogen-rich geographies, and is more prevalent in the 1st world. Are any of the following Parkinson’s-associated genes linked to evolutionary pathogen-richness? SNCA, LRRK2, MAPT, PARK2. It is worth pointing out that the SNCA gene (alpha synuclein) is a copy number variation (CNV), and triplications of this gene have been identified in severe, early onset Parkinson’s in the United States (35). Because other CNV’s have been identified to have evolved from pathogen diversity, it is worth considering how pathogen diversity relates to the SNCA gene. This is particularly interesting from a research perspective, because the exact function of alpha synuclein is still unclear. It also stands to reason that because alpha synuclein tends to aggregate at the initial onset of Parkinson’s disease within the enteric neurons of the intestines, that synuclein’s function may be directly related to microorganism interaction. However, no such etiological pathogen has been identified to date associated with Parkinson’s, only the presence of alpha synuclein. Researchers could theoretically study alpha synuclein’s behavior in vitro, by using a variety of microorganisms in cell culture, stratified by SNCA genotype.  Parkinson’s & LRRK2. LRRK is a gene that is linked to early onset Parkinson’s disease. It is also known that this gene is essential in innate immune function. Among many other immunological effects, LRRK2 is a target gene of interferon gamma. Research has identified a pleitropic relationship between LRRK2 variants, autoimmune disease and Parkinson’s (27). LRRK2 expression is up-regulated in the intestinal tissues of Crohn’s disease (28). Data suggests that the boosting effect of innate and adaptive immunity is a driver to the progression of Parkinson’s disease. Carriers of a LRRK2 genotype associated with Parkinson’s have higher levels of pro-inflammatory IL1ß (for symptomatic carriers & patients), compared to controls (29). Research involving LRRK2 knockout of Drosophila found improved motor function (28). Do carriers of LRRK2 variants who are predisposed to autoimmunity and Parkinson’s fare better in a parasite-rich environment? Can certain parasites, helminths or their secretory peptides be used to reduce LRRK2 expression, among carriers of the LRRK2 risk genotypes? This seems highly plausible because a) the LRRK2 genotype in question produces more innate inflammation, and b) Crohn’s, a disease that is remissible via helminthic therapy, features elevated LRRK2 in the intestines.
2. Autism & Helminth Trial Study – Do autistic subjects with the C4aC4b genotype (C4BQ0 genotpe) benefit from helminthic therapy, compared to autistic subjects who do not possess the C4aC4b genotype? As discussed earlier, helminthic therapy has been shown to improve some of the features of autism. The C4a and C4b genes are CNV genes that reside within the RCCX gene cluster. The C4 genes have been shown to have evolved due to pathogenic pressures, and their role in the opsonization of parasites has been discussed (14). Of interest, C4 in the brain is strongly linked to synaptic and dendritic pruning mechanisms.
3. Ferritin, HFE, Hemochromatosis & Pathogenic Pressures – The HFE gene provides the instructions for making ferritin. The gene is notorious as being associated with hemochromatosis. Do the HFE genotypes, which predispose to Hemochromatosis and ferritin overload, confer protection to certain types of pathogens? The evolutionary ‘writings on the wall’ provide clues as to the purpose of the HFE gene, given its centralized position within the HLA-1 region on chromosome 6; a location situated with genes of immunological function and defense strategies. It is widely understood that host mechanisms have evolved with intricate iron sequestration and utilization systems, in response to pathogenic pressures. Paradoxically, carriers of the HFE hemochromatosis gene have been shown to have iron-deficient anemia within macrophages (36). It has been proposed that carriers of the HFE hemochromatosis gene may confer increased resistance to certain iron-sequestering bacteria: Chlamydia, Coxiella, Francisella, Legionella, Mycobacterium, Salmonella and Yersinia (36). In 2010 Uzoigwe proposed that parasite fauna served as a selective force in the distribution of the HFE gene (37). Because parasitism is associated with iron-deficient anemia, is it possible that helminthic therapy could be useful in correcting iron-overload conditions among HFE hemochromatosis carriers? Would this be a good or bad strategy? What effect does hookworm therapy have on Ferritin levels among HFE carriers?
4. FUT2 “Non-Secretor” Genotype & Pathogen-Selective Pressures – The FUT2 is a blood group antigen gene that provides instructions for fucosylation, and the deposition of blood group antigens into mucosal fluids, such as the intestinal mucosa. Carriers of the FUT2 “non-secretor” genotype do not secrete blood type antigens into mucosal fluids, and lack terminal fucose molecules on the intestinal microvilli. Thus, pathogenic interactions are distinct. FUT2 non-secretory status is associated with a variety of conditions, such as Crohn’s disease and IBS, pancreatitis and elevated serum lipase, UTI’s in women, and reduced keystone microbial strains such as bifidobacterium and akkermansia (R). It is known that the FUT2 non-secretors carry a reduced risk of susceptibility to certain respiratory viruses, but an increased susceptibility to streptococcus and Neisseria meningitis bacteria. Fumagalli, et al identified FUT2 as one of several blood group antigen genes as having evolved through pathogen-driven selection (38). From a clinical perspective, FUT2 non-secretors often present challenges, and an ongoing need for vigilance with respect to gut and mucosal barrier health. What role does helminth therapy play in balancing the gut ecology and immunology of FUT2 non-secretors?

The Need To Reclassify Terms “Pathogen” & “Parasite” Using a Modern Understanding

With an improved knowledge of the efficacy of helminthic therapy, and with a modern day understanding of symbiosis as it relates to evolution (Margulis), the complex involvement of parasites and helminths on human biology and immunology, there is a critical need to redefine and reclassify the terms “pathogen”, “pathogenesis” and “parasite”. So called “Modern Medicine” as well as “Functional & Integrative Medicine” have historically used its arsenal of killing weapons to destroy, eliminate and sterilize “pathogens” from patients. Before we go any further in describing the potential problems with this approach, its necessary to deconstruct and reclassify the terms “pathogen” and “parasite”. It is also necessary to revisit and redefine the terms “disease-causing” and “pathogenesis” with respect to microorganisms, and their immunological interactions with a host. Because emerging evidence implicates pathogen diversity as inversely related to certain diseases, and helminth treatment as potentially curative to certain individuals who are predisposed to pathogen-rich genotypes, it stands to reason that the terms “pathogenesis”, “pathogen” and “parasite infection” are quite relative and need to be understood within specific contexts. What is bad for one person is essential for someone else. What is “disease-causing” for one individual living within a certain geography, and with various predisposing factors, is a potentially curative treatment for someone else living in a different geography with differing predispositions.

Certain helminths that have been proven to be curative of inflammatory-based diseases are classified as “parasites”, “infective” and “disease-causing” (9). By definition, a parasite feeds off of its host. Whereas with a helminth, there are symbiotic and mutual benefits for both microorganism and host. Clearly, with a more refined understanding, “pathogenesis” is a highly contextual and relative term, which depends upon many different, complex interactive scenarios and conditions (including genotype), for each person. The idea that pathogenesis can be attributed to any one microorganism under any circumstance is not accurate, neither from an evolutionary nor a medical standpoint.