We're not too far into 2014 and we already have a contender for "favorite paper of the year". This treat is the story behind that paper - one that remarkably interconnects phylosymbiosis with human health.
Kodaman et al, PNAS 2014
Contributed by Carrie L. Shaffer, PhD
Twitter @CLShafferPhD
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| Electron micrograph of H. pylori (Source) |
Global dissemination
of Helicobacter by modern humans
One of the most successful
human pathogens in recorded history is Helicobacter
pylori, a Gram-negative bacterium that has colonized the gastric niche of
modern humans since our migration out of Africa approximately 60,000 years
ago. Since leaving Africa, H. pylori has diversified in parallel
with its human host. Because of the
predominantly vertical transmission of H.
pylori within family units and the chronic carriage of H. pylori for nearly the entire lifetime of an individual, we have
the remarkable ability to trace human migrations by analyzing H. pylori genetic signatures. Recent evidence suggests that H. pylori has colonized humans for at
least 100,000 years, and points to a second exodus out of Africa 52,000 years
ago that resulted in generation of a hybrid European lineage of H. pylori strains (Moodley et al.).
Today, H. pylori colonizes the gastric mucosa of at least 3 billion people
worldwide. Gastric colonization by H.
pylori results in the development of asymptomatic chronic non-atrophic
gastritis in all cases. However, in a
small percentage of cases, severe gastric disease can manifest, including emergence
of peptic ulcers and gastric adenocarcinoma, which is currently the second
leading cause of all cancer-related deaths worldwide. In contrast to the United
States, where the prevalence of gastric cancer is low, the incidence of gastric
adenocarcinoma varies globally with the highest rates occurring in Japan,
China, South America, and Eastern European nations.
Because of its diverse and
segregated geographic and ethnic landscape, the South American country of
Colombia serves as an ideal natural laboratory for the study of H. pylori-related disease and its
association with gastric adenocarcinoma. Separated by only 200 kilometers, the
Colombian towns of Tuquerres and Tumaco have sharply contrasting rates of
gastric cancer. Tuquerres, located in
the altitude of the Andes Mountains, has one of the highest rates of gastric
cancer in the world (approximately 150 cases/100,000 people), whereas the
coastal town of Tumaco has a gastric cancer rate of just 6 cases per 100,000
people, despite a nearly universal rate of H.
pylori colonization throughout Colombia.
Health outcomes echoing
a continued legacy of European colonization
A rich history of settlement
by native Amerindians coupled with both colonization and conquest by Spanish
invaders and the introduction of African slave trades led to racial and ethnic
segregation within Colombia. People
residing in modern day Tuquerres are mainly of mestizo (Spanish and Amerindian)
descent, while the residents of Tumaco are primarily of mulatto (African and
Spanish) descent. These observations led
us to the central question of our recently published paper in PNAS (Kodaman et
al.): Are the rates of gastric cancer in Colombia governed by human or Helicobacter ancestry? We reasoned that
a 25-fold difference in the rate of stomach cancer between the two populations could
be attributed to differences in the host genetic composition; differences in
host immune responses to chronic infection; phylogeographic origin and/or virulence
factors harbored by H. pylori; environmental
factors such as diet and smoking status; or a combination thereof.
Our previous work (de Sablet et
al.) demonstrated that European H.
pylori ancestry is strongly predictive of increased premalignant lesions
and epithelial DNA damage in both Colombian populations, while African H. pylori phylogeographic origin is
associated with reduced severity in histologic disease parameters. These findings are significant because we were able to show that in this region, the
genetic ancestry of H. pylori is both
a risk factor for development of gastric disease and a determinant of gastric
disease severity, irrespective of the presence of the major virulence factors
CagA (an oncoprotein present in some strains of H. pylori) and VacA (a secreted toxin present in all strains of H. pylori). However, this study was constrained to a
small subset of our larger cohort, and thus, we wanted to further investigate
how Helicobacter phylogeographic
origin contributes to development of gastric cancer.
In our follow-up study, we
expanded the number of patients analyzed to 242 (122 from Tumaco and 120 from
Tuquerres), and focused our efforts on analyzing human ancestry in parallel
with the phylogeographic origin of the H.
pylori cultured from patient-matched gastric biopsies. Using Immunochip analysis to genotype nearly
200,000 SNPs in each patient’s blood sample, we determined that human ancestry
closely followed expected patterns based on historical events: the people of
coastal Tumaco trace the majority of their ancestry to Africa (58%), while the
mountain population of Tuquerres are largely of Amerindian (67%) and European
(31%) descent. We used multilocus sequence typing (MLST) to determine the
matched H. pylori phylogeographic
origin from each patient, and classified each isolate into an ancestral
haplotype based on analysis of housekeeping gene sequences using STRUCTURE. Helicobacter
phylogeography recapitulated our previous report indicating that the bacteria
derived from ancestral European, African, and East Asian (Amerindian)
lineages. The matched human and Helicobacter ancestries were then
correlated to histopathology scores from gastric biopsies taken from each
patient in order to determine if either human or H. pylori genetic ancestry was associated with disease severity.
The answer surprised us: we found that perturbation of human-Helicobacter phylosymbiosis can shift a
benign infection to a potentially catastrophic relationship that results in disease
progression to gastric cancer. Rather
than either the human or the bacterial ancestry acting alone, the contribution
of bacterial-host genetic interplay was found to be the most significant factor
for predicting disease outcome. This
result was even more captivating when we analyzed the influence of the major
carcinogenic virulence factor CagA on the progression of advanced gastric
disease within this cohort – human-microbe
incompatibility had a greater effect on the risk for developing severe disease than
the bona fide Helicobacter oncoprotein. We went on to show that disruption of human-Helicobacter phylosymbiosis accounts
almost entirely for the differences we observe in stomach cancer risk between
Tumaco and Tuquerres. To our
knowledge, this study was the first report of matched genetic analysis of the
host and pathogen with subsequent correlation of human-microbe phylosymbiosis to clinical outcome.
Reflections of a
distant past
So what do our results mean?
One theory is that invasion of Colombia by the Spanish conquistadors introduced
ancestral European H. pylori to the
Amerindian populations, and these bacteria replaced the East Asian H. pylori strains naturally harbored by
the Tuquerres population. It is thought that
H. pylori of European ancestral
origin may be more virulent than some other lineages, including H. pylori of ancestral African and
Amerindian haplogroups. Since many people are often co-infected by multiple H. pylori strains, it is reasonable to
hypothesize that H. pylori of
European lineage could have outcompeted strains of Amerindian lineage in native
Colombians. Alternatively, co-infection with multiple H. pylori strains and the natural competence of the bacterium leads
to a propensity of H. pylori to
uptake DNA for recombination, resulting in generation of new strains that are
entirely unique at the DNA level. Another possibility is that differences in
virulence factors between H. pylori
phylogenetic lineages could provide a competitive advantage during
co-infection. In fact, analysis of the cag
pathogenicity island (which encodes components of a molecular machine used by H. pylori to inject CagA into gastric
epithelial cells) in several Amerindian H.
pylori isolates revealed numerous changes, including gene rearrangements,
indels of approximately 11.2 kb (one quarter the size of the entire
pathogenicity island), and gene inversions (Olbermann et al.). Despite these dramatic variations in
macrodiversity, the Amerindian isolates retained functional secretion system
machinery, suggesting that the changes are non-deleterious to pathogenicity
island function, and are likely under neutral or positive selection. Strikingly,
our study reveled that patients with a high proportion of Amerindian ancestry
who are infected with H. pylori
strains that have a substantial percentage of African lineage (>20%) develop
the most severe gastric lesions. Perhaps the frequent differences in
macrodiversity found in Amerindian H.
pylori isolates are essential for maintenance of host-microbe phylosymbiosis
in the native Colombian population.
The results of our study
provide insight into an ongoing debate in the field regarding classification of
H. pylori as a pathogen rather than a
commensal. While it is true that H. pylori colonization is associated
with a significantly increased risk for development of gastric disease, H. pylori may provide some benefits to
its host. For example, it has been
suggested that H. pylori colonization
is protective against development of esophageal reflux, cancer of the upper
stomach, and cancer of the esophagus. H. pylori may help to prevent Mycobacterium tuberculosis infection
from progressing to active tuberculosis, and may play a role in providing
protection from development of asthma and other allergic diseases. The protective advantages of this fascinating
microbe are intriguing, but nonetheless, additional investigation will be
required to determine the mechanisms by which H. pylori provides such advantages to its host. Our study points towards co-analysis of host
and microbe genomic variation to identify those at highest gastric cancer risk
so that we can selectively target H.
pylori eradication.
Finally, our study brings new
perspective to the so-called ‘African Enigma,’ a theory that describes the
discordant prevalence of H. pylori
infection and H. pylori-related
disease in continental Africa. Our findings suggest that maintenance of a
harmonious host-microbe phylosymbiotic relationship can account for the low
incidence of gastric disease throughout Africa in spite of H. pylori colonization rates estimated at greater than 90%. In future investigations, it will be
important to recapitulate our findings in cohorts from diverse sites including
Africa, East Asia, and additional locations within Central and South America in
order to determine the extent to which human-Helicobacter phylosymbiosis dictates disease outcome in global
populations.
