Idiopathic Pulmonary Fibrosis: Rare Variants Link a New Gene and Pathway to Disease
“For quite some time, we have been aware that idiopathic pulmonary fibrosis has a very heritable and presumably genetic component,” says David Zhang, MD, a clinician-researcher in the Division of Pulmonary, Allergy, and Critical Care Medicine at NewYork-Presbyterian/Columbia University Irving Medical Center. “Physicians taking care of patients with pulmonary fibrosis have certainly noticed in their practices that patients often have a family member who has some form of pulmonary fibrosis, whether it is IPF or another fibrotic interstitial lung disease. So, there’s always been this undercurrent of genetics that has led to numerous studies looking at both common and rare mutations. Rare mutations, which may only be found in a handful of individuals, are generally more damaging than common variants. These rare variants often point to specific genes and pathways that cause disease.”
The genetics of idiopathic pulmonary fibrosis are quite complex. Research discoveries by Christine Kim Garcia, MD, PhD, Chief of the Division of Pulmonary, Allergy, and Critical Care Medicine at NewYork-Presbyterian/Columbia and Dr. Zhang’s mentor, had previously implicated the surfactant and telomere pathways in the development of adult-onset pulmonary fibrosis. Dr. Garcia’s laboratory was one of the first to identify rare mutations in the genes encoding telomerase – the enzyme that adds repetitive sequences of DNA to the ends of chromosomes, thus, lengthening the telomere and protecting the chromosome from damage. Subsequently, Dr. Garcia and her colleagues reported that rare mutations in two new genes, PARN and RTEL1, were linked to familial pulmonary fibrosis that also caused telomere shortening and, since then, several additional telomere-related genes have been linked to pulmonary fibrosis and lead to the same final common pathway of excessive telomere shortening.
“The telomere pathway is particularly prominent in IPF,” notes Dr. Zhang. “Many types of mutations in genes, including TERT, TERC, PARN, and RTEL1, relate to telomere biology that manage or maintain the telomere length and have been linked to IPF susceptibility. There are other mutations that we know of in the surfactant pathway, but those tend to be even more rare. However, all of these rare mutations help us understand why the disease occurs in the first place.”
A New Gene, A Non-telomere Pathway
Current research by Dr. Garcia, Dr. Zhang, and their colleagues in the Department of Medicine and the Institute for Genomic Medicine at Columbia, and at other major centers here and abroad, has recently implicated a new gene that not only has both rare and common mutations associated with IPF, but also involves an entirely different pathway. By coalescing analysis of patient DNA sequencing data across large, international, multisite cohorts, the study sought to identify rare pathologic variants in IPF and familial pulmonary fibrosis that are difficult to pinpoint due to their low incidence. Next-generation sequencing and advanced methods for analyzing these data have made it possible to examine the influence of these rare variants on human health. To this end, the investigators:
- Performed gene burden analysis of whole-exome data in 1,725 cases and 23,509 control subjects
- Replicated results in a total of 2,966 cases and 29,817 control subjects
- Tested common variants for disease association
- Conducted functional studies using null and patient-derived cell lines
- Examined human lung single-cell RNA sequencing data
The study by Dr. Zhang and his colleagues, which represents the largest IPF sequencing study to date, led to the identification of KIF15 (kinesin family member 15) as a novel IPF risk gene. This finding, note the authors, “is robust as it is seen in two different genetic models, exceeds genome- and study-wide significance, and is confirmed by the analysis of both discovery and replication cohorts.”
Published in the July 1, 2022, issue of the American Journal of Respiratory and Critical Care Medicine, the study also revealed:
- Both qualifying rare and common genetic variants in KIF15 lead to decreased protein expression and reduced cell proliferation, demonstrating the direct relationship between KIF15 protein expression and cell proliferation
- Male individuals heterozygous for rare deleterious KIF15 alleles develop IPF, whereas female individuals appear to have less severe disease and atypical radiographic features, at least in familial kindreds
“As KIF15 is specifically expressed in replicating cells in the human lung, the gene links a non-telomerase pathway of cell proliferation with IPF susceptibility,” explains Dr. Zhang, who served as lead author on the paper. “The convergence of rare and common KIF15 variants underscores the relevance of this non-telomere pathway of impaired cell proliferation in IPF. These findings open the door to a new avenue of exploration of the genetic underpinnings of IPF.”
The study by Dr. Zhang, Dr. Garcia, and their colleagues, which represents the largest IPF whole-exome sequencing study to date, led to the identification of KIF15 as a novel IPF gene.
“In terms of assessing the impact of this and similar studies, these rare mutations don’t affect the majority of individuals with IPF, but rather they localize within families where multiple individuals in the family have this disease and also have the mutation,” says Dr. Zhang. “The mutations that we find help us to understand an individual’s personalized risk either of developing the disease or having a more severe form of the disease. In the case of some of these more rare damaging mutations, it is more likely that someone else in the family might also inherit that disease risk. That’s very striking because IPF is a very rare condition. It’s rare for one person to have it. It’s incredibly rare for two people in the same family to have it. That strong connection and the disease process behind it is an area of study that we continue to pursue.”
Rare Variants in Patients of Latino Ancestry
In a derivative study, Dr. Zhang and his colleagues conducted the same analysis as they did for the larger KIF15 study, but stratified across different ancestries as a surrogate for ethnicity groups to address the absence of genetic studies in patients with IPF of non-European ancestry. The full cohort included 2,966 multi-ethnic, unrelated cases and 29,817 control subjects. Of these, 241 unrelated patients (8 percent) were grouped into non-European cases. Slightly less than half (n=120) of the non-European cases represented individuals of Latino ancestry; the remainder represented those of African, South Asian, East Asian, and other backgrounds.
“We were able to find for the first time, a significant signal for TERT in individuals of Latino ancestry,” says Dr. Zhang. “While TERT has been described in individuals of Latino ancestry before – short telomere lengths have been indicated for a subset of IPF patients from Spain and Mexico – this is the first time that it has been demonstrated with such a systematic approach.”
Their study showed that enrichment of TERT rare deleterious variants exceeded genome-wide significance for patients of non-European ancestry, and specifically, the Latino subgroup. The researchers also found that for at least two genes (TERT, KIF15), the inclusion of patients of non-European ancestry led to a greater odds ratio in the meta-analysis, demonstrating the increased power of multi-ethnic studies over single-ethnicity studies for improving genetic discoveries.
“Much of the genetic variation between individuals is due to their ancestral makeup,” notes Dr. Zhang. “Because of this complexity and due to the fact that the majority of IPF patients are Caucasian, many genetic studies in IPF have focused on individuals of European ancestry. However, we know that not all studies that are done in one ethnic group are applicable to other groups. With more data being collected along with rigorous statistical methods, we are able to start answering questions specifically in other ethnic groups.”
Important Considerations for Genetic-Based Interventions
Does Environment Play a Role?
“As IPF is a late onset disorder, there may be a component of an environmental-gene interaction between, for example, cigarette smoke or air pollution, that possibly synergizes with the mutation’s effects to spur on the disease,” says Dr. Zhang. “We know that telomere length appears to be a biomarker summarizing a number of different factors, including genetics, environmental exposures, and age, which predicts risk of pulmonary fibrosis.”
“The development of IPF may be similar to the two-hit hypothesis in cancer where a genetic factor causes someone to be vulnerable to the disease and then an environmental factor compounds that risk and pushes the person over the threshold to develop fibrosis,” adds Dr. Zhang. “While environmental aspects will be crucial to understanding the risk of the disease and how to intervene and ideally prevent IPF, our current research focuses on achieving a better mechanistic understanding of the mutations so that we can find more targets to treat.”
Cancer Biology: An Interventional Caveat for IPF
Dr. Zhang notes that KIF15 and TERT have parallel influences on fibrosis and on cancer that is fascinating and also worthy of exploration. “KIF15 and TERT each influence cancer but in the opposite direction. With fibrosis, it is the reduced activity of the proteins (as a result of damaging mutations) that leads to IPF, whereas increased protein activity is seen in malignancies,” says Dr. Zhang. “Studies have shown that high expression levels of TERT or KIF15 in tumors signify poor prognosis. This makes the question of applying genetics to intervention in IPF more challenging. It’s not as simple as finding a way to replenish that gene activity because if we do it wrong then we may have to worry about cancer.”
IPF Genetics: What the Future Holds
“Currently, there are only two FDA approved medications for IPF and neither are specifically targeted to genomics despite the well-known influence of genetics,” adds Dr. Zhang. “While these anti-fibrotic medications decrease the rate of disease progression, they do not reverse the fibrotic process or stop the irreversible decline in lung function. That said, it is remarkable that we have such treatments because 10 years ago this wasn’t the case. With IPF and related mutations, we’re not at the point of being able to intervene upon a mutation because the effects of that mutation are not reversible. Our studies of the biology behind IPF help us understand the impact of the mutation, improve our knowledge of their consequences in terms of turning a normal lung into a scarred lung, and will enable us to consider newer, more potent therapies that are tailored to target the root causes.”
“For KIF15 specifically, I think we’re still at the cusp of understanding how it causes IPF,” adds Dr. Zhang. “We’ve taken the first step to identify this gene and its non-telomere pathway, which definitely looks promising as a new target for future therapies. But, as is the case with the telomere pathway and with the surfactant pathway, we have to put in more legwork to understand the biology behind how these single mutations lead to such a complex disorder. Once we understand that to its fullest, we can take the natural next steps to look for medications or therapies that specifically target this pathway.”
Rare and Common Variants in KIF15 Contribute to Genetic Risk of Idiopathic Pulmonary Fibrosis. Zhang D, Povysil G, Kobeissy PH, Li Q, Wang B, Amelotte M, Jaouadi H, Newton CA, Maher TM, Molyneaux PL, Noth I, Martinez FJ, Raghu G, Todd JL, Palmer SM, Haefliger C, Platt A, Petrovski S, Garcia JA, Goldstein DB, Garcia CK. American Journal of Respiratory and Critical Care Medicine. 2022 Jul 1;206(1):56-69.
Genome-wide Enrichment of TERT Rare Variants in IPF Patients of Latino Ancestry. Zhang D, Povysil G, Newton CA, Maher TM, Molyneaux PL, Noth I, Martinez FJ, Raghu G, Todd JL, Palmer SM, Platt A, Petrovski S, Goldstein DB, Garcia CK. American Journal of Respiratory and Critical Care Medicine. 2022 Jun 6. [Online ahead of print]
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