Introduction

Rare diseases are a large and highly heterogeneous group of disorders that collectively represent a signi cant healthcare burden. Indeed, according to current estimates, there are approximately 7000 such conditions, which share the common qualities of being infrequent and unusual. In the United States, where as many as 30 million individuals are living with a rare disease, the Rare Disease Act of 2002 and the US Orphan Drug Act de ne a rare disease or condition as one that “(a) affects less than 200,000 persons in the United States, or (b) affects more than 200,000 in the United States but for which there is no reasonable expectation that the cost of developing and making available in the United States a drug for such disease or condition will be recovered from sales in the United States of such drug” [1]. However, the concept of rare disease is not uniform around the world. For instance, the European Union (EU) considers as rare a disease that affects fewer than 1 in 2000 people, whereas in Japan, a rare disease is one that affects less than 1 in 2500 people [2].

Rare diseases are generally poorly studied and incompletely understood; consequently, often no effective therapy is available for these conditions. Individuals who have the misfortune to be diagnosed with a rare disease feel isolated and orphaned; hence, the commonly applied term “orphan” disease. An estimated 27–36 million people are affected by a rare or ultra-rare condition in Europe and about 350 million are affected worldwide. Overall, about 10% of all diseases are classi ed as rare, and their cumulative prevalence ranges between 6% and 8% [3]. Despite an urgent need, boosting research in rare diseases is dif cult for several reasons:

P. Spagnolo (*) · N. Bernardinello

Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy

e-mail: paolo.spagnolo@unipd.it

\1.\ Many diseases lack a real “research community.”

\2.\ Experts are often scattered within a country or even internationally, which makes gathering different expertise in a multidisciplinary approach unfeasible.

\3.\ Resources needed to conduct research may be similarly scattered or altogether lacking, e.g., databases, biobanks, and registries.

\4.\ Research into rare diseases is more costly and time-­ consuming than in other areas, and funding is generally scarce and uncertain.

\5.\ Scientists are often more interested in mechanisms than in how mechanistic interventions might improve disease management, so they may fail to collaborate with clinicians-­scientists to identify novel treatments.

\6.\ Clinicians and scientists may be reluctant to pursue a career in the eld of rare diseases due to the limited commercial interest in these conditions.

These factors need to be overcome in order to make substantial advances in the implementation of research and clinical care for rare diseases to take place and for gaps in knowledge to be lled.

Challenges to Overcome in Order to Undertake Quality Clinical Research

In order to undertake clinical research, there needs to be adequate numbers of patients gathered, either in a single center or through clinical networks, to enable obtaining meaningful data. However, in rare diseases, this task is problematic for a number of reasons, including a general paucity of prevalence and incidence data, often despite the existence of registries; small numbers of patients with any individual disease; variable genetic effects with incomplete penetrance that affect disease expression and phenotype; occurrence of some genetic diseases in only certain populations worldwide; and limited knowledge of gene–environment interactions. Due to considerable challenges to an accurate diagnosis, patients

often present late in their disease when it may be inappropriate to enroll them in clinical research studies.

Lack of Reliable Data on Prevalence

In order to plan clinical studies, a number of feasibility issues need to be addressed, especially how many individuals are likely to be enrolled. The prevalence of rare lung diseases varies widely and may be dif cult to estimate for a number of reasons. For instance, the prevalence of a “common” rare disease, such as sarcoidosis, is as high as 160 per 100,000 people in Sweden but is much lower in other countries [4–6]; conversely, disorders such as pulmonary alveolar microlithiasis, surfactant protein (SP)-A-related lung disease, or idiopathic pulmonary hemosiderosis are exceedingly rare, having only been described in case reports or small case series. The lungs may also be involved as a rare manifestation of more common disorders, including, among others, Marfan syndrome, Ehlers–Danlos syndrome, Gaucher disease, or Niemann–Pick type C disease.

Small Number of Patients

When planning clinical studies of rare diseases or trials of orphan drugs, investigators are faced with a number of challenges that are usually not encountered in clinical trials of common diseases [7]. Obvious drawbacks include the small size of the trial population and the fact that patients are often geographically dispersed [8]. This is particularly true for disorders with a geographic predilection (e.g., Hermansky– Pudlak syndrome in individuals of Puerto Rican ancestry) or gender predominance (lymphangioleiomyomatosis (LAM) in women of childbearing age). In these circumstances, it is particularly dif cult to undertake randomized, double-blind, placebo-controlled studies, which represent the most robust and highest quality data for developing evidence-based recommendations. In addition, in order to prove ef cacy in a study with small patient numbers, the compound under investigation needs to show a stronger treatment effect compared to studies with large numbers of patients; furthermore, small studies need more robust methods of data analysis. Indeed, drawing conclusions from trials performed in a limited number of patients may be misleading, if not dangerous. Good examples include initial studies investigating antiestrogen therapy—consisting of surgical castration by oophorectomy, administration of tamoxifen, progesterone, and a gonadotropin-releasing hormone (GnRH) agonist or a luteinizing hormone-releasing hormone—that claimed bene cial effects in LAM [9, 10]. Subsequent careful scrutiny of some of these studies revealed that while the treatment under investigation might have improved some aspects of the dis-

ease, such as chylothorax or chylous ascites, other affected organs, including the lungs, were not affected and, in some instances, showed disease progression. Accordingly, the most recentAmerican Thoracic Society/Japanese Respiratory Society Clinical Practice Guidelines have suggested not using hormonal therapy (i.e., progestins, gonadotropin-­ releasing hormone (GnRH) agonists, selective estrogen receptor modulators like tamoxifen, and oophorectomy) as treatment for LAM [11, 12].

Genetic Component, Variable Degree

of Penetrance, and Environmental Interactions

It is estimated that approximately 70% of rare diseases have a genetic origin [2]. However, the importance (and the complexity) of the interactions between host/genetic factors and environmental triggers has become clear only recently. Idiopathic pulmonary brosis (IPF), the most common and severe of the idiopathic interstitial pneumonias, is a complex and heterogeneous disease associated with sequence variants in many genes, including genes involved in telomere biology (i.e., TERT, TERC, RTEL1, TINF2, PARN, and DKC1), alveolar stability (i.e., SFTPC, SFTPA, SFTPA2, and ABCA3), cell–cell adhesion (DSP and DPP9), and host defense (MUC5B) [13]. However, a common gain-of-function variant in the promoter region of MUC5B (rs35705950) is the strongest risk factor for both sporadic and familiar IPF, accounting for approximately 30% of the total risk of developing the disease [14]. Familial pulmonary brosis (FPF), which is de ned by the presence of at least two cases of pulmonary brosis (not only IPF) in the same family, represents approximately 10% of all cases and is inherited in an autosomal dominant manner with incomplete penetrance [15]. FPF is characterized by substantial phenotypic heterogeneity, which may be due to a complex interaction between genetic factors and brogenic triggers, including cigarette smoke, outdoor pollution, microaspiration of gastric content, and viral infection (a “two-hit” concept) [16]. Different combinations of genetic abnormalities and individual triggers may also account for the variable disease course and prognosis. Another good example of gene–trigger interactions includes chronic beryllium disease in which a strong genetic component requires less antigenic stimulus (i.e., beryllium) to cause the disease, whereas stronger environmental exposures are needed in individuals with “weaker” susceptibility genotypes [17, 18].

Rare genetic lung diseases generally affect individuals from birth through about age 60 and are uncommon in the elderly. Some conditions display racial and ethnic prevalence. For instance, sarcoidosis varies in prevalence and severity across ethnic boundaries [5]. Available measures of prevalence suggest that it is not a common disease. Mass sur-

veys in the United Kingdom in the 1950s and 1960s disclosed radiographic abnormalities consistent with sarcoidosis in 9 [17, 18] to 36 [19] per 100,000 persons screened. Similar studies in Scandinavia, carried out over the same decades, revealed a combined prevalence of 28 per 100,000 examined persons [20]. In 1964, Bauer and Lofgren summarized thendings from 29 surveys carried out in 24 countries; the results varied widely from a prevalence of 0.2 per 100,000 in Portugal, Brazil, and Uruguay to the highest gure of 64 per 100,000 in Sweden [21]. In general, the prevalence is higher, the greater the degrees of latitude from the equator for reasons­ that are not understood. In the United States, sarcoidosis is more common in African Americans than in Whites. Applying cumulative incidence estimates, the lifetime risk of sarcoidosis is 2.4% for African Americans and 0.85% for American Whites [22]. The wide variation in these estimates presumably refects the differences in diagnostic labeling and in the age, gender, and morbid distributions of the screened populations. In addition, speci c sarcoidosis phenotypes are more prevalent in certain populations, such as uveitis and cardiac involvement in Japanese, Löfgren syndrome (an acute and generally self-limiting form of sarcoidosis characterized by bilateral hilar lymph adenopathy, erythema nodosum/arthralgia, and uveitis) in Scandinavians, and lupus pernio (a chronic purplish indurated lesion mainly seen on the ears, cheeks, lips, and nose) in Puerto Ricans. Rare lung diseases may also display regional variations. This is the case of Hermansky–Pudlak syndrome (HPS), a rare autosomal recessive disorder characterized by oculocutaneous albinism, bleeding diathesis, and lung brosis [23]. HPS has a prevalence of 1 in 1800 in Puerto Rico but is exceedingly rare in the rest of the world [24, 25]. Pulmonary alveolar microlithiasis, a rare autosomal recessive disease characterized by calcium phosphate deposits in the distal airspaces, is another example of a condition with a geographic predilection, occurring predominantly in Japan and Turkey [26, 27].

Identifying Causation/Disease Pathogenesis

The cause and pathophysiology of the majority of rare diseases are unknown. However, over the past two decades, research has led to the identi cation of genes responsible for approximately 50% of the estimated 7000 rare monogenic diseases. This markedly increased discovery rate of causative genes is the result of dramatic improvements in DNA sequencing technologies (i.e., next-generation sequencing, whole-exome sequencing, and whole-genome sequencing) and the associated data analysis [28]. However, interactions between causative and disease-modi er genes remain largely unknown. The environment, including microorganisms, may also play a role in disease pathogenesis, particularly in the

presence of a patient’s compromised immune system, making these disorders phenotypically heterogeneous and complex. Incomplete knowledge of the disease pathogenesis, in turn, complicates disease management, which is often based on expert opinions.

Unclear/Imprecise Defnitions

Rare lung diseases are often dif cult to diagnose because of inconsistent case de nitions. For instance, hepatopulmonary syndrome, a rare disorder de ned by the triad of liver disease, intrapulmonary vascular dilatation, and abnormal gas exchange [29], may also be a rare complication of more common chronic liver diseases, such as liver cirrhosis [30]. Because the de nition of an “abnormal gas exchange” varies widely in the published literature [31], the use of diverse diagnostic thresholds has led to variable disease prevalence, thus rendering it dif cult to compare studies and complicating patient recruitment due to inconsistent selection criteria. Expert consensus statements and guidelines—not available for most rare diseases—would undoubtedly facilitate consistent disease de nitions.

Disease Complexity

Pulmonary involvement in rare diseases may represent only one end of a spectrum of clinical manifestations. This is the case, for instance, of Birt–Hogg–Dubé (BHD) syndrome, an autosomal dominant disorder caused by germline mutations in the FLCN (folliculin) gene located on chromosome 17p11.2 and characterized by skin brofolliculomas, multiple lung cysts, spontaneous pneumothorax, and renal cancer [32]. BHD-associated skin lesions may also include angio - bromas, which are more typically associated with tuberous sclerosis. In turn, tuberous sclerosis may manifest with pneumothorax (caused by rupture of lung cysts), renal cysts, or tumors and should therefore be considered in the differential diagnosis of BHD syndrome [33]. The diagnosis of BHD syndrome is based on both clinical features and histology. However, the wide variability of clinical expression and the sporadic (in the majority of cases) occurrence of renal cancer or pneumothorax make the diagnosis challenging.

Several Forms of Disease: The Paradigm

of Pulmonary Alveolar Proteinosis (PAP)

Pulmonary alveolar proteinosis (PAP) is a rare condition characterized by the accumulation of surfactants within alveolar macrophages and alveoli. PAP is now recognized as a highly heterogeneous syndrome belonging to a large group