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Development of Allergic Immunity in Early Life 

 

Clare M Lloyd1 & Sejal Saglani1,2 

1Inflammation, Repair & Development Section, National Heart and Lung Institute, Faculty of 

Medicine, Imperial College, London; 2 Dept of Paediatric Respiratory Medicine, Royal 

Brompton Hospital, Royal Brompton Harefield NHS Foundation Trust, London, UK 

 

 

 

 

 

 

 

 

 

 

Contact: 

Inflammation, Repair & Development Section 

National Heart and Lung Institute  

Sir Alexander Fleming Building  

Faculty of Medicine  

Imperial College  

South Kensington  

London SW7 2AZ. UK  

+442075943102 

 

c.lloyd@imperial.ac.uk 

 



	
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 Running Title: Allergic immunity in Early Life 

 

Abstract 

The growth and maturity of the peripheral immune system and subsequent development of 

pulmonary immunity in early life is dictated by host, environmental and microbial factors. 

Dysregulation during the critical window of immune development in the postnatal years 

results in disease which impacts on life-long lung health. Asthma is a common disease in 

childhood and is often preceded by wheezing illnesses during the preschool years. However, 

the mechanisms underlying development of wheeze and how and why only some children 

progress to asthma is unknown. Human studies to date have generally focused on 

peripheral immune development, with little assessment of local tissue pathology in young 

children. Moreover, mechanisms underlying the interactions between inflammation and 

tissue repair at mucosal surfaces in early life remain unknown. Disappointingly, mechanistic 

studies in mice have predominantly used adult models. This review will consider the aspects 

of the neonatal immune system which might contribute to the development of early life 

wheezing disorders and asthma, and discuss the external environmental factors which may 

influence this process.  

 

Key words: Asthma, inflammation, wheezing, immune development 

  



	
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Introduction 

Asthma is a childhood onset disease, with 1.1 million children currently affected in the UK. 

Children diagnosed with asthma by age 7 years already have a deficit in lung function and 

increased bronchial responsiveness as neonates (1). Furthermore, longitudinal birth cohort 

studies have shown wheezing and bronchial hyper-responsiveness in early childhood are 

predictors of newly diagnosed asthma in early adulthood (2), and a prior diagnosis of asthma 

is associated with an increased risk for COPD among never smokers(3). The fundamental 

pathophysiological features of allergic asthma in both adults and children include airway 

hyperresponsiveness, resulting in airway obstruction that is usually reversible, chronic 

inflammation that is predominantly eosinophilic and structural changes of the airway wall, 

termed remodelling. We have shown eosinophilic inflammation and structural airway 

remodelling (4) are already established during the preschool years and become maximal 

and equivalent to the changes seen in adulthood by school age (5). Birth cohort and cross-

sectional studies of preschool children with wheezing have uncovered strong associations 

between lung function and immune responses in early life. Furthermore, children who 

apparently "outgrow" early wheezing illnesses remain at increased risk for relapse or 

recurrence during midlife(6).  

Although approximately one-third of all infants and preschool children have wheezing 

disorders, we do not know why some but not all pre-school children wheeze; and why some 

wheezy children develop asthma, whereas others spontaneously remit. No current 

medication, including inhaled corticosteroids (ICS), can prevent the development of asthma. 

Therefore, a focus on the understanding of the early life pulmonary immune environment is 

essential not only to prevent the development of asthma, but also in the long term to 

contribute to the prevention of COPD (7). This review will consider the impact of various 

intrinsic and extrinsic factors which may impact the development of wheezing and 

progression to asthma (Fig 1). 

 

 



	
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Severe asthma in children 

Although the majority of children with asthma achieve good control with only low-moderate 

doses of maintenance inhaled steroid therapy, approximately 5% remain poorly controlled 

despite maximal prescribed therapy. This small proportion with persistent poor control are a 

significant clinical challenge as they utilise up to 50% of all healthcare resources for asthma 

(8). All children with on-going asthma symptoms despite maximal conventional treatments 

are described as having Problematic Severe Asthma (9). The sub-group in whom persistent 

symptoms result from a failure of basic asthma management have “Difficult Asthma” (DA) 

(10), whilst those who remain symptomatic despite these factors having been addressed 

have “Severe Therapy Resistant Asthma” (STRA) (11). A common definition and guidelines 

for management of severe asthma have recently been proposed for all patients aged 6 years 

and over (10). Although a significant advantage of common guidelines is the ability to trial 

novel treatments using similar criteria, some key differences underlying the evolution and 

pathophysiology of severe asthma between children and adults must be considered, and an 

automatic extrapolation of findings from adult clinical trials to children may not always be 

appropriate. 

Pathophysiology of paediatric asthma 

Asthma is characterised by eosinophilic inflammation, airway hyperresponsiveness (AHR) 

and structural airway remodelling, including increased thickness of the subepithelial reticular 

basement membrane, increased airway smooth muscle mass and angiogenesis (12). All of 

these changes are established in children by school-age, and are present regardless of 

disease severity (13),(14) (5). Asthma has traditionally been thought of as a disease of type 

2 immunity due to increased levels of IL-13, IL-4 and IL-5. As such therapy has been 

directed towards mitigating the effects of these cytokines (15, 16). However, asthma is 

notoriously heterogeneous, with numerous clinical and pathological phenotypes (17) and 



	
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there is evidence that not all patients fit this restrictive, Th2 biased categorisation of disease 

pathology (18). In particular, patients with severe disease may not all have a Th2 phenotype.   

A feature of severe asthma in young children is the early presence of airway remodelling – 

including thickened basement membrane (4). It has been proposed that a normal 

inflammatory response to harmful stimuli is followed by a phase of repair and regulation, 

whereas during chronic disease repeated cycles of inflammation result in exaggerated repair 

culminating in tissue remodelling. However, increasing evidence now confirms that at 

mucosal surfaces, the barrier epithelial cells and underlying stromal cells are active 

immunologically and cooperation with immune effector cells results in development of 

inflammation and repair in parallel, or in disease exaggerated inflammation and abnormal 

remodelling (19). Using both our neonatal model of inhaled allergen exposure and paediatric 

bronchoscopic airway samples we have shown early and parallel onset of inflammatory and 

structural changes is apparent in airway mucosal diseases such as preschool wheezing and 

asthma (20) (4, 21) and cystic fibrosis (22). Specifically, we were among the first to show an 

absence of tissue eosinophilic inflammation or remodeling in infants with recurrent 

respiratory symptoms and wheeze at a year of age (21), but increased inflammation and 

remodeling by 3 years (4) which increased further with age and was established to a similar 

degree to adults by school-age (5, 23). Early life events that result in altered tissue repair are 

likely to be sustained across the life-course and result in down-regulation of cell defence 

mechanisms and impact the ageing trajectory. Although associations between inflammation 

and remodelling are apparent during early life mucosal diseases, nothing is known about the 

interactions between the maturing immune system and remodelling pathways, and whether 

repair pathways are more easily triggered in early life and thus lead to exaggerated repair.	
  

 

Th2 mediators in paediatric severe asthma 

Children with STRA have a persistent airway luminal and tissue eosinophilia and airway 

remodelling despite high dose maintenance steroid therapy. Another key feature of 



	
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childhood severe asthma is the presence of severe atopy with multiple aero-allergen 

sensitisation. This has been found repeatedly in cohorts as a feature of severe disease  (24) 

(23, 25).  However, in our study, in which evidence of type 2 inflammation was sought in 

induced sputum supernatant and bronchoalveolar lavage fluid (two different platforms) and 

immunohistochemistry of bronchial biopsies, evidence for the presence of IL-4, IL-5 and IL-

13 was scarce (23). Furthermore, in a separate unrelated cohort, the paediatric Severe 

Asthma Research Programme (SARP), found neither Type 1 nor Type 2 inflammation 

dominated in children with severe asthma (26). The airway pathology is therefore present 

despite a relative absence of elevated levels of Th2 cytokines. Using an age appropriate 

neonatal mouse model of inhaled allergen challenge, we have shown that the Th2 cytokines, 

IL-5 and IL-13 in particular, are steroid sensitive  (27). An explanation for the paucity of Th2 

mediators in paediatric STRA may be that since significant care is taken to ensure patients 

are compliant with maintenance steroid therapy, levels of Th2 mediators may be dampened.  

 

Innate mediators and severe asthma with fungal sensitisation 

The fact that children with STRA remain symptomatic, even while on inhaled steroids, and in 

50% of cases while on maintenance oral steroids (23) indicates that other molecular 

pathways underlie disease pathology. Although IL-4, IL-5 and IL-13 levels were difficult to 

detect, we did find an increased frequency of patients with elevated IL-33+ cells in the 

submucosa of the airway wall  (27). IL-33 is an innate cytokine derived from the airway 

epithelium that has been associated with the initiation and potentiation of the pathobiology of 

allergic asthma (28, 29).  We have shown using endobronchial biopsies from children with 

STRA that submucosal IL-33 expression was associated with increased thickness of the 

reticular basement membrane, a specific feature of airway remodelling (27). Moreover, in 

vitro culture of primary fibroblasts from the STRA patients’ biopsies showed increased 

secretion of collagen following IL-33 stimulation compared to controls, even in the presence 

of the steroid budesonide. Intranasal administration of rIL-33 to non-allergic mice resulted in 

increased collagen production in the lung, as well as the expected increase in AHR. Using 



	
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our neonatal murine model of inhaled house dust mite exposure, we showed levels of IL-33 

remained elevated in allergen challenged mice, despite steroid therapy, and this was 

associated with persistent AHR and remodelling. Interestingly, levels of IL-13 were 

significantly reduced. Thus it was apparent that IL-33 was relatively steroid resistant and was 

associated with airway remodelling, both of which are features of severe disease in children 

with STRA (27). Conversely, remodelling was absent in HDM-exposed ST2-/- mice that lack 

a functional receptor for IL-33. The fact that IL-33, but not IL-13, was maintained following 

steroid treatment of neonatal HDM-exposed mice, as well as in biopsies from children with 

STRA suggests that IL-33 is resistant to the actions of steroids. This is important because IL-

33 is a cytokine with wide ranging effects on a variety of cells and is thought to bridge innate 

and adaptive immune pathways (30). Numerous experimental models have shown that IL-33 

induces the development of type 2 innate lymphoid cells (ILC2s) (31) (32). These cells 

belong to a recently discovered population that displays none of the usual lineage markers 

for leukocytes but produce effector cytokines. Like effector T cells, ILCs have now been 

classified according to the cytokines that they secrete and the transcription factors that they 

express (33). ILC2 cells are defined by the production of type2 cytokines IL-13, IL-5 and IL-4 

as well as expression of Gata3. We have shown that children with STRA have significantly 

elevated levels of ILC2 cells (defined as Lineage-CD45+CRTH2+) in their blood, broncho-

alveolar lavage and in induced sputum (34). Although present in the blood, numbers were 

very small, and there were significantly higher proportions of ILC2 in the airways, 

demonstrating the propensity of these cells to remain at local tissue sites.  

Although as a group, children with STRA had increased tissue expression of IL-33, the 

heterogeneity of the disease was reflected in the spread of IL-33 levels within the group, 

thus highlighting the need to identify sub-phenotypes of patients in whom any mediator, such 

as IL-33, is the predominant driver of disease. Having shown using our adult murine model 

that exposure to the fungal allergen Alternaria alternata resulted in IL-33 driven exacerbation 

of allergic airways disease (35), we investigated the role of this mediator in the very specific 

clinical sub-phenotype of severe asthma with fungal sensitisation (SAFS) (36). We have 



	
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shown that children with SAFS had evidence of worse allergy than STRA without SAFS, 

despite being prescribed more steroid treatment (37). Using our neonatal mouse model we 

compared disease severity following inhaled HDM exposure to Alternaria exposure, and also 

showed higher serum IgE levels and greater eosinophilia in animals sensitised to Alternaria, 

which was maintained despite administration of steroids. Although levels of Th2 cytokines 

were not different between HDM and Alterrnaria exposure, IL-33 was significantly higher in 

the Alternaria exposed neonatal mice. Moreover, on dividing patients into those with and 

without fungal sensitisation we showed IL-33 was increased in BAL, and 

immunohistochemistry of bronchial biopsies in children with SAFS (37). Interestingly, these 

patients also had higher levels of MMP-9 which is known to be important in regulation of 

extracellular matrix molecules such as collagens within tissues. To date, trials of anti-fungal 

agents have been disappointing in patients with SAFS (38), but these data suggest this sub-

phenotype may be the most amenable to therapeutics that block the action of IL-33. 

 

Neutrophils in childhood severe asthma 

Unlike adults, in whom neutrophilic asthma is a recognised steroid resistant phenotype of 

severe disease (39), we have shown that children with STRA do not have increased 

neutrophils or mast cells in their airways or in bronchial biopsies (23, 40). However, we have 

recently demonstrated that intra-epithelial neutrophils are present in some children with 

STRA (40). Although children with STRA had increased intra-epithelial neutrophils compared 

to controls, what was most interesting was that the epithelial neutrophil expression was high 

in a sub-group of STRA patients and low in others. Challengingly, the neutrophil-high 

children had better asthma outcomes (higher FEV1 percent predicted, better symptom 

control) while being prescribed lower maintenance inhaled steroid doses. However, despite 

the presence of intra-epithelial neutrophils, levels of tissue and luminal IL-17A were not 

increased in STRA, while, epithelial expression of the IL-17R was increased and stimulation 

of primary bronchial epithelial cells with IL-17A led to steroid resistant IL-8 secretion (40) . 



	
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Interestingly, children who grow up in cattle farms and are protected from the development 

of asthma also have increased peripheral neutrophils (41). These data highlight two critical 

issues pertaining to discovery of novel therapies for paediatric STRA. The first is the inability 

to extrapolate findings from adult studies to children and the need for age appropriate 

mechanistic studies, and secondly that targeting inflammatory mediators or cells without 

confirmation of findings from experimental models in human tissue is unlikely to be 

successful as has been demonstrated by initial trial of blocking IL-17 in adult patients (42).  

 

Clinical features and risk factors specific for paediatric disease  

Preschool wheeze and its progression to asthma 

An important clinical phenotype that is very distinct and unique to children is that of 

wheezing in preschool children. Cohort studies have shown that there are several clinical 

phenotypes of wheezing in preschool children with different outcomes by school-age(43). 

Preschool wheezers who develop asthma have a permanent reduction in lung function by 

school-age (44), persisting into adulthood  (45) and increasing susceptibility to chronic 

obstructive pulmonary disease (COPD) (7). The factors that initiate asthma are very different 

from those that perpetuate the disease. No current medication, including inhaled 

corticosteroids (ICS), can prevent progression from preschool wheeze to asthma, but ICS 

are able to control the symptoms of established asthma. Thus investigating the molecular 

mechanisms underlying the inception of preschool wheeze and its progression to asthma is 

essential to identify therapeutic targets that will prevent early and sustained lung function 

abnormalities. Early viral infections (46), bacterial colonization (47) and allergen sensitization 

(48) are important in causing wheeze and the subsequent development of asthma. These 

early life exposures, coupled with genetically determined susceptibility, have a major impact 

on the natural history of the disease. Cumulatively, the data highlight the critical nature of 

this early period in which the maturing immune system meets new environmental exposures, 

and subsequent immune/inflammatory responses in the lung are initiated. This underscores 



	
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the need for animal models of asthma to include young, as well as adult animals, particularly 

when considering the induction of disease. Two clinical phenotypes of preschool wheeze 

have been described (49). In episodic (viral) wheeze, children only wheeze with respiratory 

infections (usually viral), and do not have symptoms at other times. In multiple trigger 

wheeze, children wheeze both with infections, and are symptomatic between infections. 

Importantly, the natural history and clinical management of each phenotype is different (49, 

50). Multiple trigger wheezers are more likely to be atopic, respond to regular inhaled 

steroids, develop an early and permanent reduction in lung function and go on to develop 

asthma in school age. Conversely, episodic wheezers are less atopic, only respond to 

intermittent therapy at the time of symptoms, and are less likely to develop asthma. 

However, the distinctive molecular mechanisms that result in development of each of these 

wheezing subtypes and the factors that dictate progression to allergic asthma remain 

unclear. 

 

Pathology of preschool wheeze 

Preschool multiple trigger wheezers  have a distinct airway inflammatory profile to episodic 

wheezers (51). Multiple trigger wheezers have evidence of eosinophilic airway inflammation 

(52). Children with this phenotype tend to have a good response to treatments for allergic 

asthma, in particular they have reduced symptoms and exacerbations if treated with 

maintenance low dose inhaled steroids (53). Although the inflammatory profile is 

eosinophilic, numbers of mast cells are similar in wheezers and non-wheezers. Little is 

known about the cytokines driving preschool multiple trigger wheeze, although increased 

expression of IL-4 in the submucosa has been reported (51). Since leukotriene-receptor 

antagonists have variable benefit, there are few other therapeutic targets currently available 

for those with severe preschool wheeze that persists despite high-dose inhaled steroids. It is 

known that in addition to eosinophilia, features of airway remodelling, specifically increased 

thickness of the reticular basement membrane, are already present in children with 

persistent, severe wheeze (51, 52). However, neither of these features are predictive of 



	
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asthma development by school-age. The only pathological abnormality that predicts future 

asthma is airway smooth muscle(54), but at present, no biomarkers that represent smooth 

muscle function in preschoolers are known, so this feature cannot be used to identify future 

asthmatics; and in any event, we lack interventions to prevent the evolution of preschool 

wheeze to asthma. 

 

Early sensitisation (55), in particular to inhalant and perennial allergens with high levels of 

specific IgE (56), is an important risk factor determining progression to asthma in school age 

and early, multiple sensitisation predicts a severe disease trajectory (57). In addition, genetic 

susceptibility is an important factor that contributes to childhood severe asthma (58). Several 

genes identified from GWAS have specifically been associated with childhood asthma 

including IL-33, which has also been associated with severe disease in both children (58) 

and adults (59). In addition, when the sub-group of children with severe exacerbations are 

considered, IL-33 was again identified as a susceptibility locus. 

 

 It is clear that there are significant early changes in lung pathology that occur in children 

with these wheezing phenotypes, but what events precipitate these changes and crucially 

what factors mediate progression and propagation of disease through the life course are not 

well understood. Given that it is recognised that asthma and probably preschool wheeze, 

reflect the pathological consequences of a disordered immune system, it seems important to 

consider the immense changes that occur to the immune system during this early life period, 

and how these may impact the lungs, which also continue to develop postnatally.   

 

Development of immunity in early life 

Newborn babies are particularly vulnerable to infection in early life because the immune 

system is not yet developed, but is shaped and educated during this immediate postnatal 

period. Although transfer of maternal antibodies across the placenta provides some 



	
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protection against pathogens, the potential antigenic burden is very high compared to the 

relatively sterile semi-allogeneic environment in utero. It was perceived that babies were 

born in a state of immune tolerance in order to protect them from developing overwhelming 

immune responses upon exposure to the wealth of pathogens encountered on leaving the 

protected in utero environment. This antigenic burden can be intrinsic as well as extrinsic - 

as birth triggers exposure to previously unseen, benign self-antigens to which the neonate 

must develop tolerance in order to prevent later autoimmune reactions. Similarly, immune 

responses must be restrained upon exposure to environmental antigens, such as allergens. 

Robust responses to these antigens would lead to hyper-inflammation that would be 

dangerous and destructive to organs such as the lungs that are still developing postnatally. 

Thus, immune reactions against most antigens are kept under tight control, but mature 

adaptive immune responses can be mobilised when the baby is faced with life threatening, 

dangerous pathogens (60). It is apparent that early life represents a window of both 

vulnerability and opportunity that impacts both immune development and tissue 

homeostasis, therefore it is important to understand how immunity develops in the normal 

lung in order to try and appreciate how allergic immunity develops.  

 

Innate immune mechanisms are compromised during the first months of life. There is 

evidence that expression of TLRs that recognise key molecular signatures on the surfaces of 

pathogens are either absent or expressed at very low levels in the new-born. In fact, it has 

been documented that TLR2 and 4 are largely absent from the murine foetal lung, but 

expression is rapidly upregulated after birth (61). Human studies are much harder to 

perform, but although data in human neonatal lung are rare, nasal mucosal explants taken 

from young children showed enhanced allergen-induced T cell reactivity and proliferation, 

increased production of Th1 cytokines, IL-10 production and TLR4 expression in response to 

TLR stimulation (62).  Investigators have also taken advantage of cord blood as well as 

some studies using peripheral blood from babies. A comprehensive longitudinal profiling 

study of innate immunity over the first 2 years of life revealed qualitative and quantitative 



	
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differences in TLR responses in neonates compared to those in adults. Comparison of 

responses to TLR stimulation in adult and neonatal peripheral blood determined that 

monocytes and dendritic cells from neonates have a reduced capacity to secrete IL-12p70, 

IFN-α and IFN-c, but a greater facility to secrete IL-10 than adult cells(63). These findings 

suggest that rather than neonates being in a state of immune suppression responses to TLR 

stimulation are enhanced at birth, but differences are age specific and progression is not 

linear. Studies with human cord blood have shown that perinatal TLR responses are 

increased – particularly in newborns who subsequently develop allergic disease. Neonates 

from allergic mothers, or those that subsequently developed allergies showed increased 

secretion of TNFα following TLR3, 4, 5 stimulation and enhanced IL-6 after TLR, 4, 5, 

ligands. Crucially, however, T cell derived IFNγ responses to mitogen or allergen were 

suppressed compared to non-allergic subjects (64). Subsequent longitudinal analysis of TLR 

responses in allergic versus non allergic children during the first 5 years of life revealed 

significant differences over time. From birth non-allergic children exhibit increased 

production of  IL-10, TNFα and IL6 in response to TLR stimulation over the first five years of 

life (65). In comparison, allergic children show enhanced cytokine production at birth but this 

decreased over time so that by age 5, this hyperresponsiveness to stimuli had declined and 

cytokine responses were reduced in comparison to similar aged non-allergic children.  A 

comprehensive study of immune development in urban preschool children determined that 

early life environmental exposures are vital in the stimulation of cytokine responses (66). 

Importantly, although cytokine production increased with age, these responses at birth were 

poorly predictive for later responses at aged 1 or 3. Interestingly, exposure to common 

environmental allergens, such as cockroach, mouse or dust mite was associated with 

enhanced cytokines responses at age 3 years, including production of IFN-α and IL-10. 

However, reduced LPS-induced IL-10 responses as birth were related with recurrent 

wheeze, while RSV-induced IL-8, allergen-induced IL4 were both associated with atopy. 

Clearly the cytokine balance during early life is critical in the development of allergic 



	
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responses and is influenced by a variety of external factors. In future, it will be important to 

determine which cells secrete particular cytokines and establish how this fluctuates over time 

as well as determine whether the cellular source of the cytokine during development 

influences pathology.  For example, development of allergic disease in the first year of life in 

high risk children has been associated with reduced responses of T regulatory cells to 

microbial stimuli (67). Collectively, studies show that TLR patterning occurs during the 

perinatal period and that the mother’s allergic status influences this. Although these 

differences in TLR responses may protect the neonate from over-exuberant inflammation to 

microbial infection, they may contribute to the development of inappropriate reactions to 

environmental antigens such as allergens.  

   Neutrophils are a vital component of the innate immune system and are the most prevalent 

leukocyte in human blood. However, both neutrophil numbers and functionality are reduced 

in neonates compared with adults (63). Neonatal neutrophils have reduced expression of 

TLR4, defective MyD88 and p28 signalling (68), and lower levels of CD11b/CD18 which 

reduces their capacity for transmigration and chemotaxis  (69). In addition, neonatal 

neutrophils have reduced phagocytic capacity and impaired intracellular killing (70). 

Collectively, these deficiencies in numbers, mobilization and function increase the 

susceptibility of neonates to sepsis. 

 

Pulmonary macrophages in early life 

   The lungs are colonised with macrophages in the early postnatal period. Macrophages are 

the most predominant leukocyte within the lung and there are at least two distinct 

populations resident at homeostasis: Airway macrophages (AM) that are resident within the 

airspaces and interstitial macrophages (IM) that are situated within the lung parenchyma.  

Each are characterized by their unique location, properties and functions, and populations 

may be identified on the basis of their expression patterns of the integrins CD11b and 

CD11c (71). AMs have high surface expression of CD11c but lack CD11b expression, 

distinguishing them from macrophages present in other tissue compartments. Conversely, 



	
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IMs express high levels of CD11b but only low levels of CD11c. AMs have a critical influence 

in maintaining immunological homeostasis and are able to sense the local environment to 

maintain suppression or initiate the appropriate host defence response.  In contrast, IMs are 

thought to exert a regulatory function within the lung tissue. Whilst AM employ non-specific 

lines of defence (such as high phagocytic ability, the secretion of antimicrobials, nitric oxide 

(NO), tumour necrosis factor (TNF)-α and interferon (IFN)-γ), it has been suggested that 

interstitial macrophages have a greater capacity to release specific cytokines associated 

with the adaptive immune response, such as interleukin (IL)-10 (72). 

   Although once thought to be derived from mononuclear phagocyte precursors recruited 

from the bone marrow it is now accepted that airway macrophages derive from yolk sac 

macrophages and are established prenatally. Experiments with mice show that monocytes 

do not make a significant contribution to tissue macrophage populations under homeostatic 

conditions and furthermore, following depletion of lung macrophages, repopulation of the 

lung occurred by proliferation in situ, rather than replacement from the bone marrow (73-75). 

Given the recognition that tissue residency has a specific impact on macrophage phenotype, 

experiments examining cord blood monocytes are unlikely to be reflective of airway and lung 

macrophage phenotypes. However, these samples are particularly difficult to obtain and 

there is scant information regarding phenotypes of interstitial macrophages in newborns or 

how they impact on development of allergic immunity. Some studies have used bronchial 

lavage samples from babies requiring mechanical ventilation during chronic infections, and 

suggested that phenotypic maturation of monocyte populations was associated with 

gestational age. Preterm infants had increased proportions of non-classical CD14+CD16+ 

monocytes at birth, and immature macrophage phenotypes were associated with 

progression from respiratory distress syndrome to chronic lung disease of prematurity (76).  

Preterm infants with resolving lung injury had greater proportions of mature macrophages, 

than those with progressive lung disease. Since these types of studies rely on lavage of 

ventilated, intubated babies, there is no information regarding the phenoptype of 



	
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macrophages during normal human perinatal development or on the impact of phenotype on 

development of asthma in subsequent childhood.  

 

Perinatal Dendritic cells in the lung 

   Neonatal murine lungs show fewer conventional dendritic cells, coupled with a lower ratio 

of CD103+ to CD11b+ DC (77). However, neonatal lungs matured and were able to prime 

adult naïve CD4T cells as effectively as adult DC. Interestingly, both adult and neonatal 

BCG-primed DC induced Th2 cytokine responses from neonatal lymph node T cells, 

indicating that Th2 skewing is an intrinsic feature of neonatal T cells (77, 78). Similarly, the 

ratio of plasmacytoid (pDC) to myeloid dendritic cells (mDC) is reversed in human cord blood 

dendritic subsets compared to those in adult peripheral blood (79). Both mDC and pDC were 

found to exhibit a more immature phenotype compared to those from adult blood, with lower 

expression of key markers such as MHC class II and ICAM1 as well as the costimulation 

molecules CD80 and CD86. In vitro stimulation assays using TLR ligands such as LPS, poly 

I:C or CpG showed that neonatal (cord blood) mDC failed to mature to the extent of adult 

cDC  (80, 81). The failure of neonatal DC to initiate efficient Th1 responses may rest with a 

specific defect in mDC whereby IL-12(p35) is transcriptionally repressed at the chromatin 

level  (82). Human neonatal APC also show impaired production of type I interferons in 

response to TLR agonists. Allergic children show higher numbers of TLR2+DC at birth, and 

these enhanced levels are maintained throughout the first year of life. This is important 

because these cells are known to produce enhanced levels of inflammatory cytokines such 

as IL-6 (65). Collectively, these defects in innate immune signalling may contribute to the 

propensity of neonatal T cells to generate immune reactions involving type 2 cytokines rather 

than type 1 and with persistent allergen exposure may contribute to the development of 

allergic disease and asthma in children.  

 

T helper cells in early life 



	
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 Early life exposure history shapes development of the immune system - however it is not 

known whether pathology progresses because of an imbalance in regulatory cells vs. 

effector cells, and if so how microbial exposures affect this imbalance. This is important 

since accumulating evidence suggests that these early life microbial exposures are linked to 

subsequent development of wheeze and asthma (83). Although the ontogeny of CD4 

subsets has been examined in peripheral blood during the first year of life there is less 

information regarding the phenotypes of key lymphoid cells within the pulmonary mucosa of 

neonates.  

   The relatively limited exposure to antigen in utero dictates that newborns are more reliant 

on innate immune pathways for protection against infections. However, neonatal mice have 

been shown to be able to mount mature adaptive immune responses in vivo (60, 84). 

Foetally derived CD4+ T cells with an effector memory phenotype have been shown to be 

present in cord blood (85). These cells develop during foetal life within the uterine 

environment which is thought to be relatively sterile, but occur even in the absence of 

pathology or infectious history. Importantly, they exhibit a variety of different effector 

inflammatory functions associated with CD4 T helper cells at birth. Moreover, foetal cells are 

thought to be an important source of type-2 cytokines in early life in both mice and humans 

(60, 86). 

   Nasal associated lymphoid tissue (NALT) is established before birth, while bronchus 

associated lymphoid tissue (BALT) develops postnatally (87). This immature immune system 

is shaped following postnatal exposure to bacteria, viruses and allergens, influencing its 

development and may result in skewing towards health or disease. The majority of studies to 

date have used peripheral blood cells to examine early life immune cell phenotypes. These 

studies have determined that a T helper 2 (Th2) cell preference is required for a healthy 

pregnancy (88), but also that this skew is maintained during the neonatal period, reducing 

gradually during the first 2 years of life (89). In contrast, atopic children retain these foetally 

derived allergen-specific responses (89). This deviation from the physiological in utero Th2 



	
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skewing, with exaggerated Th2 responses in either pregnancy or the first 3 months of life 

has been associated with an increased risk of subsequent childhood asthma or wheeze (90).  

   Interestingly, a skewed Th2 cytokine response was initiated from either adult or neonatal 

BCG-primed DC using neonatal lymph node T cells, indicating that Th2 skewing is an 

intrinsic feature of neonatal T cells (77). In fact, it seems that this skewing of neonatal T cell 

immunity towards type 2 reactions limits inflammatory damage while permitting colonisation 

with neonatal commensal microbes in the intestine.  One of the major effector functions of 

human neonatal T cells has been shown to be production of the chemokine CXCL8, which 

can activate antimicrobial neutrophils and γδT cells. Importantly these T cells were found to 

be rare in adults – highlighting the distinct nature of the neonatal immune system and 

provides a potential protective mechanism against bacterial infection in newborns (91).   

Similarly, γδT cells from newborns show enhanced pleiotropic functional responses when 

compared to αβT cells, and importantly lack the characteristic deficit in IFNγ production.  

Therefore, in the absence of a mature αβT cell compartment, γδT cells are poised at birth to 

contribute to both immuno-protection and immuno-regulation  (92).  

 

Although the mechanisms that facilitate persistence of the neonatal type2 environment are 

unclear, transcriptional profiling of circulating Th2 cells in mice and humans has revealed 

sets of genes that are likely to confer pathological features to Th2 cells that may be either 

unique to specific allergic diseases such as asthma or rhinitis, while others maybe common 

to a range of atopic disorders (93, 94). Interestingly, Th2 cells from asthmatic patients 

specifically displayed increased expression of genes which were predicted to support 

enhanced Th2 survival, proliferation/activation and cytokine production.  Furthermore, the IL-

33/ST2 axis seems to selectively licence memory Th2 cells to promote allergic type 

inflammation via production of IL-5 and thus stimulate eosinophilic inflammation (95, 96). 

These pathogenic effector Th2 cells seem to be a specific subpopulation of Th2 cells with 

enhanced pro-inflammatory function and have been described in patients with eosinophilic 



	
   19	
  

gastrointestinal disease as well as atopic dermatitis (97). The latter patient population were 

children, but the point during immune development when this subpopulation develops has 

yet to be determined.   T cell phenotypes are widely acknowledged to be plastic with 

receptor expression and cytokine production influenced by a wide range of intrinsic and 

extrinsic factors – including allergen exposure as well as age, so it is possible that the 

balance of subsets changes over the lifespan according to particular exposures.  In the 

future, it will be important to examine the temporal shifts in Th subsets of the lifespan in 

order to identify pathways for novel treatment.  

  

  Regulation of inflammation at mucosal sites is controlled by specialized populations of 

tissue resident regulatory T cells that express RORgt or GATA3 - key transcription factors 

normally associated with effector Th populations (98) (99). Described in murine models of 

gut inflammation, these regulatory populations are held in balance by the local microbiota. In 

addition, expression of the IL-33 receptor is thought to define a population of T regulatory 

cells in the gut that is important for accumulation and maintenance of T regulatory cells in an 

inflammatory environment (100). As yet, it is unclear whether they are also present at human 

mucosal sites – including the lung. Normal pregnancy is associated with skewing towards a 

type 2 immune environment which is thought to afford protection to the developing foetus, 

and maybe due to an altered ratio of effector to regulatory T cells (101). Although this 

inequity normally corrects during the first year of life, there is evidence that prolongation of 

the type 2 bias increases the risk of allergy and atopic diseases.  Functional FoxP3+ cells 

with enhanced expression of PD-1 are generated following in vitro activation of naïve cord 

blood derived CD45RO+CD25+CD+ T cells with APC, compared to cells derived from adult 

peripheral blood (102). Longitudinal analysis of infant peripheral blood has determined that 

perinatal Th cells have an enhanced propensity to develop into FoxP3+ T regulatory cells in 

the first 12 months of life but that Th17 cells can already be induced at 3 months (103).  

Additionally, the proportion of both resting naıve T regulatory cells and activated Tregs 

isolated from peripheral blood increase markedly from birth to 6 months of age (104). In 



	
   20	
  

contrast little is known regarding the phenotypes of cells within the airways of infants.   

However, it is important to remember that neonatal thymectomy in mice results in 

development of autoimmune disease, highlighting the importance of a competent regulatory 

population even early in life. CD4+CD25+ T cells are important for the development of 

neonatal tolerance to transplantation antigens.  

 

Innate lymphoid cells in early life 

 Innate lymphoid cells (ILCs) are considered to play an indispensable role in immune 

homeostasis as well as the initiation, regulation and resolution of inflammation (105). ILCs 

are thought to exert particular influence at mucosal surfaces including the airways and 

gastrointestinal (GI) tract, with ILC2s promoting repair following influenza infection in the 

lung, and ILC3s mediating tissue repair following intestinal inflammation (106). They are also 

key players mediating interactions between innate and adaptive type 2 immune pathways 

(107). Despite the proposed importance of these effector cells in immune regulation and 

disease, and the intimate link with T helper cells, nothing is known about their role in immune 

maturation and early life development. Recent evidence indicates that the ILC2 population 

undergoes rapid expansion in the neonatal lung during the first few weeks of life (108) 

(109),(110). 

Factors that may result in accentuated or prolonged Th2 skewing include maternal allergy 

(111) but environmental exposures are also critical as has become apparent from the 

farming exposure studies (112). Growing up in close proximity to cows seems to provide 

protection and incidence of allergic diseases are greatly reduced in children who have grown 

up in farming communities (83). Similarly, diet has a profound influence on the systemic 

microbiome which impacts the developing immune system and thus the trajectory towards 

disease or health (113).  Although it is apparent that the composition of inhaled exposures 

has a direct impact on the airway immune profile, mechanistic studies in experimental 

laboratory models in the context of a developing immune system are scarce, while studies in 

children have predominantly used peripheral blood rather than cells directly isolated from the 



	
   21	
  

lung. Recent data in mice suggests that enhanced neonatal skewing of Th2 immunity after 

exposure to allergens results from hyperactivity of the IL-33-pathway (108). IL-33 production 

during the postnatal phase of lung development is postulated to drive Th2 type immunity, 

thus lowering the threshold for innate immune response to allergen. Similarly, it has been 

shown that the process of birth is enough to trigger IL-33 production from the lungs of 

alveolar epithelial cells of newborn mice which drives the expansion of IL-33R expressing 

innate lymphoid cells (ILC), concomitant with IL-3 driven polarization of airway macrophages 

into an M2 phenotype (109). It is thought that this homeostatic type 2 pathway delays 

antibacterial effector responses, as well as prolonging the in utero derived type 2 

environment. However, it is not known whether human neonates experience a similar wave 

of hyperactivity in IL-33 responses. Thus, it is not known how the balance between effector T 

cells or innate cell subsets differ in the lung following exposure to viruses, bacteria or 

allergens in early life.  

  We have recently shown that ILC2s are present in the airways of children with severe 

therapy resistant asthma (34). Proportions of ILC2 were determined by flow cytometry in 

BAL samples from children with STRA and compared to samples collected from children 

undergoing investigations for recurrent lower respiratory tract infections. Whereas ILC2 were 

extremely rare or absent in this latter group, they were present in BAL from asthmatic 

children. Interestingly, there were relatively higher proportions of ILC2 in the airway samples 

(either BAL or sputum) compared to peripheral blood.  

These are descriptive studies, but mechanistic studies in mouse models have focused solely 

on the use of adult models with environmental exposures in the context of a mature immune 

system. However, since it is known that the neonatal immune system is physiologically 

skewed towards type 2 immunity, and an exaggeration of this skewing results in later 

disease, it is possible that in early life ILCs are less important in disease initiation, or that 

they may be protective. Experiments using adult mouse models have suggested that ILCs 

are vital for the development of an effective adaptive T cell response during classical type 2 

responses initiated by allergens or parasitic worm infections (30) (114). However, given that 



	
   22	
  

the neonatal immune landscape is different from that of the adult it is likely that there will be 

distinct differences in responses to allergens and cytokines in neonatal mice compared to 

adult mice. Indeed, accumulation of pulmonary ILCs at homeostasis occurs postnatally and 

relatively small numbers are present at birth. Conversely, ILC2 are thought to be critical in 

limiting inflammation and promoting tissue repair in order to maintain homeostasis (115). 

Although ILC2 are able to secrete a number of factors that are associated with wound repair, 

such as amphiregulin (116), mechanistic studies have shown that they are involved in 

development of pulmonary fibrosis following bleomycin injury and in patients with liver or 

dermal fibrosis, rather than in the specific repair of tissue following inflammation (117-119). It 

will be important in the future to delineate how ILC2 are able to contribute to the wound 

healing process without causing tissue remodelling. It is possible that those ILC2 associated 

with driving allergic pathology may represent a different subset or that their function may be 

context specific. This is a particularly important point in early life, when the lung is still 

developing, so the phenotypic characteristics of ILC2 during pulmonary immune 

development and their functional role in repair or resolution of inflammation needs to be 

understood.  

 

External influences on the developing immune system 

Although the mechanisms underlying development of early life wheeze are not well 

understood it is clear that a wide variety of external, environmental influences affect the 

developing neonatal immune system and therefore the development of sensitivity to 

allergens as well as to pathogens. It is clear that the postnatal period represents a critical 

window for development of aberrant immune responses, but the maternal environment has a 

significant impact. One of the major influences on the development of neonatal immunity and 

subsequent maintenance of immune homeostasis is our relationship with the microbes that 

live upon and within us. All of our mucosal surfaces, the skin, gut and lungs are colonized by 

dynamic communities of microbes that are integral for our well being. These local microbiota 

are essential for energy harvest from food sources, for metabolism and most importantly 



	
   23	
  

when considering neonatal development, the training and education of local and systemic 

immunity (120). It is clear that robust immune health is associated with a flourishing and 

diverse microbiota, but each of these microbial ecosystems is dynamic and is exquisitely 

sensitive to the environment provoked by changes in diet, intake of drugs and hormonal 

influences.  

   A lack of diversity and resilience in the microbiota has been associated with the rise in 

autoimmune and allergic diseases documented in the developed world. For the neonate the 

first few years of life are associated with the acquisition of a competent microbiota, since the 

uterine environment is relatively sterile. This period represents a critical window for immune 

development, since the composition of the microbiome is affected by the birth process itself, 

whether the baby is breastfed, weaning as well as a whole host of external environmental 

influences such as living in a home with siblings and or pets, spending time in day care and 

living in an urban or rural environment (83). Each of these factors will impact on the diversity 

of the airway microbiota and therefore the education and training of the immune system. We 

have shown that age at first allergen exposure is critical in determining the degree of allergic 

immune responses generated. Neonatal mice exposed to inhaled house dust mite from day 

3 of life had significantly more eosinophilia, AHR and type 2 immune responses compared to 

adult mice (121). Moreoever, if allergen challenge was commenced at day 14, then 

responses were negligible and the mice appeared protected. The formation of the lung 

microbiota is a key parameter in this process. During the first 2 weeks after birth, the 

bacterial load in the lungs increased, and there was a shift in the airway bacterial phyla from 

a predominance of Gammaproteobacteria and Firmicutes towards Bacteroidetes. The 

changes in the microbiota were associated with the decreased aeroallergen responsiveness 

seen at day 14 and the emergence of a Helios(-) Treg cell subset that required interaction 

with programmed death ligand 1 (PD-L1) for development. This demonstrated that the 

airway microbiota induces T regulatory cells early in life, and if its development dysregulated 

during a critical period of development postnatally, can lead to sustained susceptibility to 

allergic airway inflammation in adulthood (121). 



	
   24	
  

 

Maternal influences 

Although once considered a sterile environment the advent of more sensitive methods of 

detection has shown that the womb contains commensal microorganisms which may affect 

development of the foetal immune system, but this concept is not universally accepted (122, 

123). Given that the foetus is nourished by the mothers blood supply it is understandable 

that key aspects of the mother’s wellbeing will affect the foetus. These exposures will affect 

the growth and development of the foetus, but may also influence subsequent development 

of disease.  

   Maternal diet exerts a significant influence on the developing foetus. A recent study 

determined that the nature of maternal diet influenced epigenetic imprinting of immune cells 

and lung stromal cells in utero. Enhanced intake of dietary fibre by the mother was 

associated with increased levels of acetate which primed FoxP3 T regulatory cell mediated 

protection against development of asthma in mice, but critically a similar axis was observed 

in humans (124). Similarly, a recent study showed that supplementation during the last 

trimester of pregnancy with fish oil-derived fatty acids was sufficient to reduce the risk of 

persistent wheeze or asthma and lower respiratory tract infections by one third  (125). 

Deficiency in certain vitamins, particularly vitamins D and A is associated with increased 

asthma risk. Vitamin D has wide ranging effects on immune cells, particularly development 

and functional capacity of T regulatory cells (126). Specifically, lower levels of serum vitamin 

D have been associated with increased airway remodeling and worsened asthma control in 

children with severe asthma (127). We have shown using a neonatal model of inhaled 

allergen exposure, that offspring from mother mice that were fed a vitamin D deficient diet 

had exaggerated airway eosinophilia and Th2 cells with reduced T regulatory cells. In 

addition, if pups were supplemented with a vitamin D sufficient diet at weaning this resulted 

in a significant reduction in serum IgE levels, reduced pulmonary eosinophilia and airway 

remodelling (128). Interestingly, a recent clinical trial determined that supplementation with 

vitamin D during pregnancy elicited a modest reduction in incidence of recurrent wheeze and 



	
   25	
  

asthma in the offspring (129). Although mouse models have determined that maternal 

vitamin A (retinoic acid) affects development of lymphoid tissue inducer cells – thus affecting 

the size of secondary lymphoid organs and setting the threshold for immune responses in 

the offspring, supplementation studies in humans have not shown efficacy in prevention of 

development of asthma (130). Only a weak, inverse association was observed for maternal 

intake of vitamin A and E with childhood allergic rhinitis (131). Conversely, maternal obesity 

has profound effects on immune responses in the baby, giving rise to systemic inflammation 

as well as asthma. Maternal prenatal BMI is associated with increased incidence of 

wheezing and asthma (132).  

    There are multiple longitudinal studies that support the hypothesis that maternal, or 

paternal, smoking has a negative impact on pulmonary health in babies and greatly 

enhances the odds of developing recurrent wheeze or asthma  (133-135). Cigarette smoke 

exposure has been shown to increase expression of specific microRNAs in the blood 

concomitant with lower numbers of T regulatory cells in maternal and cord blood, which was 

associated with an increased risk of atopic disease (136). Infants from smoking mothers also 

display attenuated innate TLR-mediate immune responses compared to infants from 

nonsmoking mothers  (137). Similarly, a number of different studies have shown that traffic 

related air pollution not only affects lung growth, but is associated with an increased 

prevalence of asthma as well as wheezing  (138).    

   Maternal stress is a significant risk factor for wheezing in early life as well as development 

of asthma (132, 139). This may be due to transfer of glucocorticoid hormone across the 

placenta, which has wide ranging effects on the immune system (140). Although it has been 

suggested that maternal stress impacts development of adaptive immune responses in 

neonates, with reduced humoral immunity and reduced capacity for Th1 responses, recent 

studies suggests that the effects may only be transient  (141, 142). 

 

Postnatal Influences  



	
   26	
  

   Immune homeostasis at mucosal surfaces is achieved by maintaining a balance between 

promoting tolerance to environmental particles and mounting rapid immune responses to 

pathogens including viruses and bacteria. Increasing evidence has shown that postnatal 

microbial colonization with commensal bacteria is vital in shaping the developing immune 

system, particularly at mucosal surfaces (120). Neonatal colonization by microbes begins 

soon after birth, is influenced by gestational age, the mother’s microbiota, route of delivery at 

birth and use of antibiotics. Indeed prolonged use of antibiotics also has profound effects on 

the development of the neonatal immune system (143).  

   As the neonate transitions from the relative low microbe environment of the womb into the 

external world, rapid colonisation of mucosal surfaces by microbes takes place. These 

microbes and their metabolic products are arguably the strongest stimulators of early 

immune development and play a vital role in the maturation and education of the developing 

neonatal immune system. The mode of delivery of the infant has a profound effect on the 

microbial load experiences by the baby in the first few days and weeks of life. Caesarean 

and vaginal births result in different species of microbes that colonise the infant from the 

beginning, reflecting the normal flora of the skin and the vagina respectively (144). These 

microbes initially colonise the gastrointestinal tract and this intestinal microbiome undergoes 

dynamic changes during the immediate postnatal period, and this is associated with 

functional development of the immune system. As well as the differences in microbial 

exposure, the very nature of labour including high levels of circulating hormones, the 

pressure on the baby of uterine contractions and the stress of passage through the birth 

canal itself impacts multiple aspects of the neonatal immune system. Collectively, these 

factors elicit the release of a number of pro-inflammatory cytokines, including IL-6, IL-1, IFNγ 

and TNFα which are all measurable in both the maternal circulation and cord blood (145). 

Epidemiologic evidence suggests that children born via caesarian delivery have an 

increased risk for a range of metabolic and immune diseases, including atopic diseases, 

compared to than those born via vaginal delivery. A recent clinical study showed that 



	
   27	
  

exposure of infants delivered by C-section exposed to maternal vaginal fluids soon after birth 

restored the skin, gut and oral microbial communities to a level comparable to that shown in 

babies after a vaginal birth (146). Although the authors did not assess the subsequent long-

term consequences on health or development of immunity it is proof of concept that the 

microbiota can be manipulated postnatally in babies delivered by C-section. This concept is 

not universally accepted however, and an alternative study has suggested that the 

microbiota of each organ reflects that of its mother – regardless of the route of delivery. 

Longitudinal sampling of infants revealed that the microbiota structure and function expands 

and diversifies considerably from birth through the first few months. Thereafter it resembles 

the microbiota from the corresponding maternal body site – irrespective of the mode of 

delivery or other prenatal factors (147).   

    Breast-feeding is an important factor in neonatal immune development, apart from the 

obvious nutritional benefits. Human milk contains a variety of different proteins that aid 

digestion, facilitate maturation of the neonatal gut while also stimulating neonatal immunity 

and providing early antimicrobial protection during this period of immune development 

(133),(140). As well as providing leukocytes and complement proteins from the mother, 

breast milk contains regulatory cytokines such as IL-10 and TGFβ, which promote tolerance 

to antigens, including those in food, in early life (148, 149). Other immune-modulatory 

molecules include immunoglobulins, lysozyme – which can degrade gram-positive bacterial 

cells walls and kappa-casein that blocks pathogen binding to the gut wall, as well as dietary 

nucleotides and lipids. Multiple epidemiologic studies have shown that in developed 

countries a history of breast feeding is associated with reduced risk of severe lower 

respiratory infections, obesity as well as other important childhood diseases, but the effect 

on asthma or wheezing is debated (149). This is possibly because of a lack of clarity 

surrounding the diagnosis of both asthma and wheeze in many studies, but it seems that 

breast feeding for at least 4 months, compared to formula feeding may delay development of 

atopic dermatitis, cows milk allergy and wheezing in early childhood (150).  

 



	
   28	
  

Influence of early life infections 

The developing immune system is shaped by the antigens that are encountered in the 

immediate postnatal period, resulting in colonisation and establishment of the pulmonary 

microbiota and subsequent expression of pattern recognition receptors (PRRs) on resident 

cells such as epithelial cells and airway macrophages.  

Numerous epidemiologic studies have shown that growing up in a farming environment is 

protective against development of asthma and childhood wheeze (83). The strongest 

protective effect has been seen in farming communities which retain traditional farming 

practices with families living in close contact with animals  (41, 112). Amish and  Hutterite 

farming communities share a genetic heritage and many other cultural aspects of life – apart 

from the close contact that the Amish have with their farm animals. However, whereas, 

incidence of allergies, wheeze and asthma are incredibly low in the Amish communities, 

incidence in Hutterite children is similar to that in urban communities. Importantly, the 

strongest protection was afforded to those children that are exposed to farm dust in utero 

(151). Recent analysis showed that although the incidence of asthma is 4 fold lower in the 

Amish population compared to the Hutterites, the level of dust in their homes was much 

higher (41). There were significant differences in the proportions and phenoytpes of innate 

immune cells between the two groups - with lower eosinophils and higher neutrophils in the 

Amish, and the converse in the Hutterites. Cell surface markers such as CXCR4 and CD11b 

were raised on neutrophils from the Hutterite children and their monocytes had raised levels 

of HLA-DR. These data indicate that the farm dust that the Amish were exposed to from very 

early in life has a significant influence on the developing immune system impacting on 

subsequent allergic diseases.  

 

Respiratory infections are common in childhood and the combination of infections 

encountered during this developmental period has an important influence on the immune 

status of the lung. Respiratory infections with viruses or bacteria are the most common 



	
   29	
  

triggers of exacerbations in asthmatic children but there is also evidence that they may be 

precipitating factors in the development of wheeze as well as asthma. Rhinovirus is the most 

commonly attributed driver of viral induced exacerbations. However, infants who develop 

wheeze concomitant with HRV infection are at a significantly enhanced risk for subsequent 

asthma. It has been suggested that host genotype is a significant factor and it is notable that 

variants within the 17q21 locus are associated specifically with asthma in children who 

experiences HRV wheezing illness (152), and expression of ORMDL3 and GSDM – two 

genes found at this locus - were identified in GWAS studies as asthma risk genes (153).  

Cadherin-related family member 3 (CDHR3) was recently identified as an asthma risk gene 

in children with severe asthma and exacerbations (58). This is of particular interest because 

expression of CDHR3 on epithelial cells facilitates both binding and replication of rhinovirus-

C in those cells that would normally be unable to support infection (154).  Moreover, a 

coding SNP associated with enhanced cell-surface expression of CDHR3 protein is related 

to increased risk of wheezing illnesses and hospitalizations for childhood asthma.  

Although the most common infection in childhood is rhinovirus, RSV is also very common in 

babies, and can lead to significant asthma risk. It has been shown that babies that 

experience very early infection with RSV (at less than 3 months of age) have higher Th2 

responses with increased levels of IL-4 (155). However, although viruses have been 

described as causative agents in the development of wheeze and asthma, a prospective 

study in children indicates that the reverse is true. Prospective, repeated characterization of 

a birth cohort demonstrated that allergic sensitization during early life predisposes children to 

more severe viral respiratory illnesses and wheezing but that wheezing respiratory illnesses 

do not increases the risk for subsequent development of allergic sensitization (156).  

   Serial viral infections are a significant risk for wheezing and asthma but in addition certain 

bacterial infections can also enhance risk. A prospective study collected hypopharyngeal 

aspirates in babies at one month and incidence of wheeze monitored for the next 5 years 

(Bisgaard 2007 17928596 (157). Those neonates colonised with S.pneumoniae, H 

influenzae or M.catarrhalis, either alone or in combination, were found to be at increased risk 



	
   30	
  

for recurrent wheeze and asthma by 5 years of age. Thus the nature, pattern and severity of 

infections experienced during childhood influences development of wheezing illness and 

asthma in some children, particularly if they have a susceptible genetic background.  

 

Summary and Future directions. 

Early life immunity is critical in determining lifelong health. Myriad influences on development 

of the pulmonary immune system and the combination of factors encountered by the 

neonate during this window determines heath or disease. All children encounter respiratory 

infections from birth, yet only a proportion develop asthma. The combination of genetic 

together with intrinsic and extrinsic factors dictate whether the immune response is 

appropriately tailored to clear infection versus an exaggerated response which changes the 

course of pulmonary immunity, resulting in disease (Fig 2). The challenge in determining the 

molecular mechanisms underlying this process is to accurately phenotype patients and use 

age-appropriate and tissue specific clinical samples in studies. This represents a significant 

challenge, but with the advent of novel technologies, which allow analysis of gene and 

protein expression at the micro level, this should be achievable. Similarly, it is imperative that 

we use appropriate preclinical models that will enable accurate translation of findings to 

children. Moving forward in our goal of more effective treatment of childhood allergic disease 

will require a shift in mind-set with respect to clinical trial design and more effective 

collaboration between industrial partners, clinicians and academic researchers.  

 

 

 

 

 

 

 

 



	
   31	
  

 

 

 

 

 

 

 

 

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Airways	remodelling

Immune	Development

Microbiome

Infection

Genetics

Lausanne

Wheeze/	
Asthma

Allergen



WHEEZE

Protective Signals Harmful Signals

Diverse Microbiome
Exposure to Farm dust
Pets
Siblings
Diet rich in PUFA, fibre

Serial viral infections
Pollution
Smoke exposure
Poor diet
Allergen exposure

ASTHMA

?

Gene x environment interactions