Genetic altitude regions for various reasons such as

signature/signals/evidence of High altitude acclimatization




High altitude (HA) is considered to be an elevation
between 1,500–3,500 metres (4,900–11,500 ft) above sea level.  Very high altitude is an elevation between
3,500–5,500 metres (11,500–18,000 ft) while extreme altitude is considered
to be an elevation above 5,500 metres (18,000 ft) (International Society
for Mountain Medicine.  Retrieved 22 December 2005).  High altitude regions include Tibetan plateau
in the Himalayas (with long term resident populations of Tibetans, Ladakhis and
Sherpas), the Andean altiplano (with resident populations of Quechua and
Aymara), the Semien Plateau of North Africa (with resident population of
Ethiopians), Tien-Shan and Pamir mountains in Asia (populated by the
Kyrgyz).  More than 140 million people
live at elevation more than 2500 m above sea level, of these 80 million live in
Asia (Hornbein and Schoene 2001), where the major population density is at
elevations exceeding 3500m.  Apart from
residential people, millions of sojourners visit to the high altitude regions
for various reasons such as recreational activity, travelling, mountaineering,
climbing, trekking, personnel duty and many others purposes.

high altitude, the atmospheric or barometric pressure, and thus the partial
pressure of oxygen, is considerably less than at sea level.  Due to decrease in pressure, the air expands
rises up and become less dense. 
Therefore, although the percentage of oxygen (20.93% ) in air  remains constant up to an altitude of 100,000
meters  (328,083 feet) (Clausen, 1977),
but the number of oxygen molecules per breath is reduced, causing diminished
oxygen diffusion from the alveoli to blood. 
This condition is called hypobaric
hypoxia.  This reduced inspired
partial pressure of oxygen results in marked declines in maximal oxygen
consumption (VO2 max), element that need to be compensated for
body’s energy requirements.  Hypoxia at
high altitude triggers a cascade of 
favorable  physiological changes
that try to minimize the decrements to an lowland individual’s physical and
cognitive work performance level and health under these extreme conditions (Fulco
et al 2000; Banderet et al 2002).  This
process is known as altitude
acclimatization.  Several
physiological changes that permit this acclimatization, including  hyperventilation, hypoxic pulmonary
increased in red blood cell production , decreased plasma volume,
increased hematocrit (polycythemia),
increased myoglobin content  and  a
higher concentration of capillaries in skeletal muscle, increased mitochondria,
increased aerobic enzyme concentration and right ventricular
hypertrophy (Young
et al 2002, West 2006). These changes tend to decrease the gradient of
oxygen partial pressure from ambient air to tissues. Nevertheless, even after
initial acclimatization, there is reduction in physical work capacity with fall
in arterial oxygen saturation, decrease in maximal heart rate and reduction in
maximum oxygen uptake capacity (VO2max) (Fulco et al 1998, Muza et al 2004,
McSherry PE 2007).  It is well known that
the potential to withstand and acclimatize at high altitude are highly
individualized, and differ based upon the rate of ascent and degree of
altitude, as well as fitness level and genetics (Armstrong 2000, Reeves et al
1993).  Some individuals fail to
acclimatize properly regardless of their time at altitude, while others are
never troubled, provided they ascend slowly. 
Insufficient altitude adjustment may result in several
pathophysiological conditions that have become known as high altitude sicknesses. 
The variables that may affect the chances of developing such illnesses
are age, health, experience at high altitude, and genetic inheritance.  About 50% sea level sojourners who climb speedily
to high altitude develop acute mountain
sickness (AMS).  Common symptoms of
AMS include nausea, loss of appetite, severe headache, lack of energy, and
disturbed sleep.  Symptoms can develop
within 12 hours of arrival, and worsen on the following 2 days, resolving only
after about 3 days at high altitude as acclimatization begins to take place (West
2012).  For the avoidance of acute
mountain sickness (AMS), altitude acclimatization is the best approach (AMS)
(Forgey 2006).  While the pathogenesis of
AMS has been disputed, there is data that supports its relation to increased
intracranial pressure subsequent to hypobaric hypoxia (West 2012).  There are also drugs such as acetazolamide
that one can take at the beginning of ascent which help to prevent sickness by
acting as a respiratory stimulant (Armstrong 2000).  In rare cases, altitude sickness can become
severe and cause edema in the brain or lungs known as High-altitude cerebral edema (HACE) or High altitude pulmonary
edema (HAPE).  AMS can progress to HACE
in as little as 12 hours, but normally requires at least 3 days.  Fortunately, the incidence of HACE is
relatively rare, and occurs in less than 1% of all individuals exposed to
hypoxic environments (Armstrong 2000). 
Fluid accumulation in the brain may be caused by cytotoxic edema (cell
swelling due to increased intracellular osmolarity), vasogenic oedema (leak of
the blood-brain barrier with extravasation of proteins and fluid into the
interstitial space), or both.  It is
crucial that HACE is treated at the first signs of a change in consciousness
and ataxia.  Rapid descent is critical
for treatment, as well as supplemental oxygen and the drug Dexamethasone (West
2012).  High-altitude pulmonary edema (HAPE) is another potentially fatal
form of high altitude illness that occurs in otherwise healthy unacclimatized
sea level soujorners who rapidly ascend to high altitude (above 3000 m).  A prior history of HAPE (Bartsch et al 1991),
rapid ascent to high altitude (Bartsch 1999), strenuous exercise at high
altitude (Grissom  2006), preexisting
respiratory infection (Durmowicz et al 1997) and genetic factors (Grocott and
Montgomery 2008)  are some of the
proposed reasons for HAPE. Symptoms of HAPE, characterised by tightness in
chest, cough, gurgling sound, difficulty in breathing, typically develops 2-4
days after arrival at high altitude and as the disease progresses,  frothy pink sputum develop which is the
hallmark of HAPE.  Clinical
investigations suggest that the increased pulmonary vascular permeability and
pulmonary hypertension possibly due to exaggerated  and inhomogeneous hypoxic pulmonary
vasoconstriction (HPV) (Maggiorini et al 2001), (Hopkins et al 2005), (Dehnert
et al 2006), transarteriolar leakage (Whayne et al 1968), which leads to
vascular leakage through over perfusion, capillary stress failure, resulting in
high concentration of vascular proteins and red blood cells in the alveolar
fluid are known to be causally linked to HAPE. 
Augmented hypoxic pulmonary vasoconstrictor (HPV) response to hypoxia
(Bartsch 1997), (Stream and Grissom 2008) and increased pulmonary artery
systolic pressure (PASP) during exercise in normoxia (Grunig et al 2000) have
also been reported in susceptible individuals. 
Beside hypoxia induced damage to endothelial cells-derived vasodilator
nitric oxide (NO) (Duplain et al 2000), (Busch et al 2001), cell adhesion
molecules, activation of cytokines and chemokines may involve in lung
inflammatory response (West 2000).  Notably,
individuals who develop HAPE run a significant risk of recurrence suggesting
involvement of genetic component in its etiology although little is known about
the genetic basis of HAPE.  If left
untreated, HAPE can be fatal within 12 hours (Armstrong 2000).  Genetic predisposition and individual
susceptibility in cases of HAPE has been postulated (Schoene RB 2004).  It is considered a multifactorial condition whose
origin and progression are governed both by genetic and environmental factors
(Patel and Peacock 2001).  Ascending
slowly, climbing and sleeping at low altitudes and restricting physical
activity can prevent HAPE.  Although the
exact mechanism underlying the development of HAPE remains unclear. 


contrary, highland populations residing in regions like the Himalayas and
Tibetan plateau are able to survive at high altitude without having gone
through the same slow acclimatization process as sea level sojourners.  Highland population (resident  at altitude >2500 meters for hundreds of
generations) who have adapted to HA environment ,  evolved a set of physiological
characteristics (Rupert et al 2001 , Beall 2007) distinctive from sea level
population due to genetic selection that off set high altitude hypoxic stress
(Beall 2006 , Beall et al 2010).  Hence,
adaptation is an instance of evolutionary process by which an organisms react
to long-term environmental stress by irreversible genetic changes.  The word -‘adaptation’ generally denotes to
the natives. High altitude adaptive physiological feature is improved aerobic
performance in native compared with lowlanders, as revealed in high resting
ventilation, better oxygen saturation , low hypoxic pulmonary vasoconstrictor
response, and low hemoglobin (Hb) concentration compared with acclimatized
lowlanders (Wu and Kayser 2006; Beall 2007, Garruto et al 2003, Zhuang  et al 1996, Droma et al 1991).  All these adaptive features very likely have
a genetic basis (Moore 2001; Wu and Kayser 2006; Beall 2007; Grocott and
Montgomery 2008).  Several genome-wide

studies of Tibetan highlanders have been reported the
natural selection of two important candidate genes EGLN1 (prolyl-hydroxylase-2
PHD2) and EPAS1 (endothelial PAS
domain protein 1; also known as hypoxia-inducible factor-2a HIF-2a) which
were significantly associated with the decreased Hb concentration as compared
with acclimatized lowlanders (Beall et al 2010, Simonson et al 2010, Yi et al
2010, Jeong et al 2014). Apart from these two known genes that have biological
relevance to hypoxia adaptation (Yi  et
al 2010, Simonson   et al 2010, Wuren
et al 2014, Jha et al 2016), several other candidate gene loci PPARA (Peroxisome Proliferator Activated
Receptor Alpha)  and HBB (hemoglobin
subunit beta) have been highlighted in recent studies.


            It is also well-known fact that the
variation in genetic makeup makes individuals to be susceptible /tolerant or
adapted to an environmental factors.  The
human genome is a sequence of 3.3 billion letters over the nucleotide-alphabet
A, G, C, T (adenine, guanine, cytosine, thymine), this huge amount of data
requires massive computational analysis for deciphering the genetic architecture
of an individual. Each individual inherits one allele copy from each parent, so
that the individual genotype at an SNP site is AA, BB, or AB.  In 99.5 percent of the positions on the
genome, the same nucleotide is shared among the individuals.  However, about 0.1percent of genetic variation
is unique (Jorde and
Wooding 2004), which occurs both within and
among populations
.  These genetic variations include
different nucleotide occurrences, called single nucleotide polymorphisms (SNPs
– pronounced ‘snips’), deletion/insertion of one or more nucleotides, or
variations in the number of multiple nucleotide repetitions. Causes of differences between individuals
include independent assortment, the exchange of genes (crossing over and recombination) during meiosis and
various mutational events
while population differences arise due to numerous causes, including random
genetic drift, the influence of small migrant populations (the “founder
effect”), and differences in selective pressures acting in different
environments. As of 2017, the Single Nucleotide Polymorphism Database (dbSNP), listed 324 million variants found in
sequenced human genomes (NCBI (2017-05-08). SNPs are the most
frequent type of variation in the human genome, occurring once every several
hundred base pairs throughout the genome. 
Due to their high abundance in the genome, SNPs already serve as the
predominant marker type.  About 3% to 5% of human SNPs are functional
which affects some factor such as gene splicing or messenger RNA
or protein, and so causes a phenotypic
difference between population.  Neutral,
or synonymous SNPs are still useful as genetic markers in genome-wide
association studies, because
of their sheer number and the stable inheritance over generations (Collins et al 1998).         

            Individuals with different genotypes
are affected differently by exposure to the same environmental factors, and
thus gene-environment interactions can result in different disease phenotypes. 
Simple Mendelian diseases (such as Huntington disease or Sickle Cell Anemia)
are caused by an abnormal alteration of a single gene.  Because of the polygenic nature of the human
response to high altitude hypobaric hypoxia and the potential for strong environmental
influence or selection pressure, it is more likely that several genetic loci,
each with a small but significant contribution, will be responsible for the
phenotypic outcome. It could also be the case that long-term exposure to high
altitude provides a natural positive adaptive pressure to alleles at certain
loci, whereas variation at the same loci may underlie high altitude illnesses,
such as high altitude pulmonary edema.


 Understanding of human genetic variations for
research and clinical purposes have been greatly facilitated by advancements
from low-resolution candidate gene approach to the recent technological
platforms of high-throughput whole genome sequencing (WGS).  The genetic approaches, such as                                                       candidate gene, sequencing, and
genome wide association, have been successful in depicting the convergent
evolution of the HA populations living in altitude environment (Aggarwal S et
al 2010, Beall CM et al 2010, Bigham A et al 2010, Mishra A et al 2013, Peng Y,
et al 2011, Simonson TS et al 2010, Wang et al 2011,  Xu S et al 2011, Yi X,  et al 2010).  Several recent studies have examined the
genetic basis of HAPE, focusing mainly on genetic polymorphisms in the
beta2-adrenergic receptor (Stobdan T et al 2010), vascular endothelial growth
factor (Hanaoka et al 2009), the renin angiotensin system (Hotta et al 2004),
and pulmonary surfactant proteins A1 and A2 (Saxena  et al 2005) in subjects susceptible to HAPE.
Polymorphisms within these genes may explain individual variation in hypoxic
responses and perhaps indicate susceptibility to high-altitude disease.
Understanding the impact of these variations will not only elucidate the
pathophysiological mechanisms of HAPE but will also help in understanding of
the adaptations of the human body to high 
altitude environment. However, the precise role of these genes in HAPE
pathogenesis remains unclear. Our understanding of the genetic etiology of high
altitude acclimatization and/or maladaptation is still limited due to the
enormous number of genetic variations on the human genome, as well as the
complex interplay of multiple genes and environmental factors underlying


genetic basis of high altitude acclimatization/adaptation, limited studies are
available and the majority of studies conducted thus far have taken a candidate
gene approach.  However, in this area
there is much more research need to be done in Indian populations.  India is unique in context of population
structure having both sea level dwellers and high altitude natives.  It will be important to study the genetic
architecture of those who acclimatized/adapted or get maladapted under high
altitude hypoxic stress in order to identify the markers of high altitude
environment.  In this thesis, to identify
more candidate genes and biochemical pathways that may underlie physiology of high
altitude acclimatization/adaptation or maladaptation in Indian population, we
have used genome-wide high throughput techniques (beadchip array for gene
expression, SNP array, exome sequencing), which are considered to be unbiased
by prior assumptions regarding sequence alteration responsible for phenotypic
variation. Findings presented in this thesis are the outcome of investigations
carried to evaluate the significant single nucleotide variations (SNVs) in  acclimatized sea level population and HAPE
patient as well as in genome of  high
altitude natives of Ladakh and differential gene expression profile between
HAPE patients and acclimatized controls (individuals from sea level).  Such study will be relevant for assessment of
health and disease status at altitude.