A second wind

Rajarshi Pal first created lung cells — unintentionally — in a laboratory dish nearly two decades ago, while pursuing his doctoral studies at the Manipal Institute of Regenerative Medicine in Bengaluru. The developmental biologist had set out to coax human embryonic pluripotent stem cells — undifferentiated cells that can turn into any type of tissue in the human body — into forming liver cells. Some resisted and turned into lung cells instead. Pal wasn't entirely surprised. Controlling cell differentiation is a challenge. The lung and liver both emerge from the endoderm, one of three primary germ layers that form the body's tissues and organs.

However, he regarded these interlopers with interest. He knew that the human lungs are the site of complex, intractable diseases with no known cure. One day, he thought, he might be able to make lung cells because he wanted to do so — and not by accident. Pal is now the Co-founder of and Chief Scientist at the biotech start-up Eyestem Research, which develops regenerative therapies to replace cells damaged or lost due to incurable diseases. Pal's team has grown lung alveolar epithelial cells from induced pluripotent stem cells (iPSCs) — cells coaxed back into an embryonic-like state from somatic (non-reproductive) cells. For its cell therapies, Eyestem scientists primarily use iPSCs derived from reprogrammed cells of the skin, umbilical cord blood, and a category of white blood cells known as peripheral blood mononuclear cells. Alveolar epithelial cells are fundamental to lung health and are impaired in several diseases. 

The lung is a large organ with an aggressive immune system. So, an effective stem cell therapy for the organ must, on average, comprise a billion lung cells. The challenge is to make a large number of such cells while retaining the alveolar characteristics. Having achieved this in the lab from an iPSC cell line, the next hurdle for Pal is to repeat and reproduce these studies in multiple cell lines to demonstrate robustness and consistency to regulators. "It is a work in progress, but we are reasonably confident we can," he says. 

Eyestem's goal is a cell therapy to treat Idiopathic Pulmonary Fibrosis (IPF), a progressive and eventually lethal disease affecting millions of people worldwide and hundreds of thousands in India. IPF causes thickening and irreversible scarring of the tissue around the lung's alveoli, or air sacs, reducing oxygen entry into the bloodstream. Fibrosis can have known causes such as damage from tuberculosis (TB) or occupational exposure to specific pollutants. Most fibrosis, though, is termed idiopathic, a term for diseases with unknown causes. "After nearly three decades of research to identify novel drugs to inhibit and reverse lung fibrosis, the search for definitive solutions is still on," says Pal.

Several iPSC-derived cell therapies are in human trials for serious diseases, a result of advances in stem cell engineering. In Japan, two therapies have received conditional approval but not for lung disease. These treatments are an example of a swathe of breakthrough technologies that have advanced over the last two decades and are now being brought to the human lung. These technologies enable a close look at lungs in health and disease, opening avenues to test drugs and therapeutics, and raising hopes for novel diagnostics and treatments.

The lung is often one of the first points of contact in the body for chemicals, dust, microbes, and other airborne substances. This makes it an important organ for scientists to study, especially when pollutants increase in quantity, variety, and toxicity. Studying the lung helps scientists understand inflammation, immunity, how the body repairs itself, and other aspects of biology. In the developed world, human lung tissue is not difficult to obtain after surgery or transplant. It is also possible to image the lung or view it through bronchoscopy, a procedure that can collect cells, tissue, and fluids from the airways and lungs. Several technologies are maturing simultaneously and making it easier to study the organ. Such research has implications for diseases that have so far stubbornly resisted treatment. 

For example, single-cell sequencing (See 'Taming tumours',) was discovered by the end of the first decade of this century. Microfluidics, single-cell RNA sequencing, and other methods made its commercial exploitation possible a decade ago. By 2020, single-cell sequencing had become mainstream in biology labs around the world. The technique was important for biologists, especially lung researchers, because they had by then stopped seeing tissues as a monolithic mass. Cells of many tissues, such as the lung, become specialised depending on their location. Single-cell sequencing became a powerful technique when combined with spatial transcriptomics, which could pinpoint a cell's location. Spatial transcriptomics became widespread only a few years ago, and is still developing. Also maturing alongside these two technologies are organ-on-a-chip, CRISPR-based gene manipulation, new forms of high-resolution imaging, and artificial intelligence (AI). Since 2020, these have converged into a powerful network of technologies.

Consider Eyestem. Safety and efficacy studies of its alveolar epithelial cells in mice, a de rigueur precursor to human trials, are underway at its collaborator, the Singapore-based A*STAR Institute of Molecular and Cell Biology (IMCB), which has access to mouse models genetically engineered to accept foreign grafts. IMCB will use sophisticated live-cell imaging techniques to follow the cells from injection to harvest to understand where they go, what they do, and how long they survive.

At the BRIC-Institute for Stem Cell Science and Regenerative Medicine (inStem), Bengaluru, Arjun Guha, a cell and developmental biologist and Associate Professor, founded the Lung Repair and Plasticity Lab a decade ago. Starting with fundamental questions, the lab can now address more clinically relevant ones, he says. Its researchers seek to understand how the lung responds at a cellular level to disease, injury, or stress. They closely study cell plasticity, or the ability of cells to morph from one state or type to another. Cell plasticity is integral to lung repair, and is also so tightly regulated that it enables the system to cope with stressors. "In response to injury, cells that have day jobs can proliferate and make other types of cells," says Guha. Such plasticity is integral to maintaining and repairing many organs. "The lung is a particularly phenomenal example of that," Guha says. 

Scientists at the lab study how cell plasticity contributes to the lung's ability to remain resilient under stress and repair itself after injury. They also examine whether these processes can ultimately be targeted to enhance repair or prevent disease. The key question is not just whether cells can change state, but when, why, and how that plasticity is engaged, and whether it can be harnessed or regulated therapeutically. In their experiments, cells in some parts of the lung appeared more plastic than others, and behaved unusually in microenvironments in response to injury. "The question was what makes these environments different and why cells behave funnily here and not elsewhere," says Guha. This inquiry has revealed a mechanism, observed in mouse models, that the lung seems to use specifically to repair fibrotic alveoli. The next step is to determine, through collaborations with clinicians, whether this mechanism is also present in the human lung by culturing cells from human lung tissue and testing them. 

Guha's lab is combining single-cell sequencing and spatial multi-omics to identify cells in the injured part of the lung, pinpoint their location, determine their molecular states, and see how those states change in response to injury or stress. It is working with an Indian start-up with expertise in spatial multi-omics, a technique to map diverse molecular data on DNA, RNA, proteins, etc., while tracking cells' physical location. This multi-omics data can then be integrated with the already burgeoning set of single-cell sequencing data, derived from patient samples, in the public domain. This approach will particularly help in understanding interactions between immune and epithelial cells, and how such interactions influence the response to injury and repair. 

Understanding lung diseases is a major step towards treating them. At Kolkata's CSIR-Indian Institute of Chemical Biology (CSIR-IICB), U. Mabalirajan orients his research to gain new insights into three chronic lung diseases: steroid-resistant asthma (SRA), Chronic Obstructive Pulmonary Disease (COPD) and IPF. These remain major therapeutic challenges, says Mabalirajan, Principal Scientist and Deputy Head, Cell Biology & Physiology. These diseases are associated with substantial suffering and, in the case of COPD and IPF, early death. His research involves studying the complex cellular and molecular mechanisms by which these diseases begin and progress in the lung, a process researchers call pathogenesis. 

Lung cancer has seen considerable progress in precision medicine, with the discovery of specific biomarkers such as gene mutations that can act as drug targets. Infectious diseases such as TB and pneumonia are treated with antibiotics. But current therapies for non-infectious, non-cancerous diseases, those in Mabalirajan's crosshairs, largely focus on controlling symptoms, reducing flare-ups, and slowing disease progression rather than a definitive cure. By shedding light on the pathogenesis, Mabalirajan hopes to identify new targets for precision medicine. This global quest involves different approaches. For instance, earlier this year, the U.S.-based Insilico Medicine moved a novel targeted therapy candidate for IPF into advanced human trials. Its target and chemical structure were both arrived at using AI.

At CSIR-IICB, Mabalirajan uses a combination of single-cell transcriptomic sequencing, wet lab experiments with mouse models, and validation in human lung tissue to identify proteins involved in pathogenesis. In a recent instance, his lab found that pulmonary neuroendocrine cells — rare sensory epithelial cells found along the airways and enriched at airway branch points — play a role in COPD pathogenesis. The researchers sampled the blood of 150 patients with end-stage COPD and found abnormally high levels of a neurotransmitter secreted by this cell type. It is not yet known whether these levels are the cause or the effect of disease progression. 

However, blocking its activity in mouse models reduced lung injury, according to Mabalirajan. The scientist believes this could be a result of the cell's protective response to harmful stimuli such as cigarette smoke, which becomes damaging when exposure is chronic. The next step for his group is to find drug targets involved in the regulation of this cell type, followed by discovering drugs that act on these targets. Mabalirajan is also pursuing another approach to treating lung fibrosis — chimeric antigen receptor T-cell (CAR-T) therapy — in collaboration with a CAR expert. CAR-T has been used successfully to treat certain blood cancers (See 'Cheaper, better cancer cure'), but it is early days for CAR-Ts in respiratory disease. 

In the human gut, microorganisms such as bacteria thrive on undigested fibre and complex carbohydrates that the body cannot digest on its own. "The gut is like an Asian food store," says Sudipto Saha, Professor of Biological Sciences at Kolkata's Bose Institute. "But the lung is more like Antarctica where no food is available." 

Yet, it has been established for several years now that, far from being sterile, the healthy lung has a microbiome or community of microorganisms, albeit in far fewer numbers than the gut. For nutrients, they feed on mucus (a carbohydrate source) and blood, among other things. A 2010 study by researchers (bit.ly/asthma-microbiome) first showed that the bronchial tree contains a characteristic microbiota and suggested that this was disturbed in asthmatic airways. The work, followed by other studies in 2011, spurred lung-related microbiome research. The studies were enabled by sequencing technology, which opened up an avenue to identify even bacteria that could not be cultured for any reason.

Saha researches the interaction between the lung microbiome and host immune cells in obstructive pulmonary diseases such as asthma and COPD. The lung microbiome is a complex network in which even bacteria that are few in number play a role in disease by releasing molecules that feed other bacteria, allowing them to grow dominant and cause inflammation. Saha calls the former keystone bacteria, and they can be targets for drugs. The metabolic pathways of these bacteria could also reveal targets.

In the gut, a change in the number of a few bacteria may not be significant as there are others that act as buffers. In the lung, which has a smaller microbial mass, even minor imbalances matter. For instance, metabolites released by certain bacteria can pass through the plasma membrane and contact host immune cells, which in turn release pro-inflammatory cytokines that damage the airways. "It is a dynamic system, and we are still understanding it."

As the host is also a source of metabolites, the lab uses an 'omics' approach to identify bacterial metabolites. This involves bioinformatics — bringing computer science, maths, and statistics to sequencing data of the genome and the complete set of metabolites (metabolome). In March 2026, Saha's lab published an open-access database of microbiome data related to 19 pulmonary diseases and healthy groups. This was manually curated from raw data from global studies conducted between 2012 and 2024 (bit.ly/lung-microbiome). Saha says this resource helps researchers identify bacterial groups and their microbial signatures to find the "true" biomarkers for these diseases. In parallel, his lab also studies the role of mitochondrial dysfunction in lung diseases, focusing on the proteome — proteins within and outside the mitochondria involved in their optimal functioning.

Building a good model is important in lung research. Although human lung architecture remains the same, different parts of the lung behave differently across space and time. Mouse models remain relevant because they provide a vital perspective on how the lung behaves at different stages, from the embryo to old age. Nevertheless, scientists are also developing novel methods to model the lung for purposes that include experimental research and testing of pharmaceuticals (See 'Bellows to Mend'). 

At the Division of Tissue Culture, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST) in Thiruvananthapuram, PhD scholar Joseph Xavier has procured primary human airway smooth muscle cells and cultured them on a hydrogel matrix on a chip to create a micro-environment similar to the one seen in the actual human lung (bit.ly/lungonchip-smoothmuscle). With the right cues, the cells aligned, connected, and assembled into a smooth muscle fibre. "This is exactly what happens in vivo," he says. 

Using the chip, Joseph and fellow researchers model alveolar smooth muscle remodelling in disease or injury. When they exposed the cells to an inflammatory cytokine (protein) at higher-than-normal levels, they observed an alteration or thickening of the cell fibres. Such thickening, driven by the uncontrolled growth of airway smooth muscle cells, is a hallmark of airway remodelling in lung diseases such as asthma, he explains. "That's what we want to mimic in the system."

Joseph says that the chip developed at SCTIMST is easier to fabricate than comparable chips available elsewhere. The lung chip is one component of a multi-organ chip that includes lung, liver, and kidney cells, designed to study drug absorption and excretion. Other approaches include organoids, three-dimensional, self-organising clusters of cells that mimic the structure and function of organs. Organoids are typically created to model tissues and organs with multiple interconnected cell types. Eyestem has whole-lung organoids, developed from healthy and patient-specific iPSC cell lines, to model complex lung diseases, with the hope that experiments on them will be more physiologically relevant. An ideal organoid replicates the exact lamination or architecture of human tissue. If a specific marker is expressed on the periphery of a layer of cells or tissue in a human, it is expressed in the same location in the organoid as well. 

At the Bose Institute, Saha's lab is in talks with the Indian Institute of Technology Kharagpur, the All India Institute of Medical Sciences Kalyani, and the software company TCS to create digital lung models of patients with lung diseases such as asthma and COPD for pre-clinical drug testing. The model will incorporate data from sources such as computed tomography (CT) imaging to generate the lung tree, spirometry and oscillometry tests for lung function and air movement within the lungs, and omics data.

Despite their substantial global disease burden, many chronic non-infectious lung diseases remain poorly studied, with important gaps in the understanding of disease mechanisms. Lung diseases such as COPD are especially complex, involving an interplay between genes and the environment. Lung function is best from adolescence to middle age, then declines from around the 50s. 

Disease progression also unfolds over time. An obvious example is damage from smoking. A person starting to smoke as a teenager may feel no adverse effects until much later in life. So, fully understanding what happens in the lung calls for longitudinal studies, where subjects are followed over 10–15 years.

A decade ago, the lung as a model was not as well researched as other tissues and organs such as the brain and the heart. That gap has substantially narrowed with major advances in lung biology, single-cell and spatial approaches, organoid and organ-on-chip models, and human lung studies. But much remains to be understood about how the lung responds to the complex environmental challenges it encounters in the real world, including injury, infection, pollutants, and other stresses. "There is a lot to do but also the opportunity to do a lot," Guha says.

India has a disproportionately high burden of chronic respiratory diseases, which are increasingly contributing to the overall disease burden, according to the 2018 Global Burden of Disease Study (1990-2016). Chronic respiratory diseases such as COPD and asthma accounted for 10.9% of all deaths. Pollution, not a major cause for concern in developed countries, is a significant factor. For instance, while COPD is a smoker's disease in the West, a substantial number of Indian COPD patients are non-smokers. The reasons behind the disease could include inhaling smoke from biomass-fuelled stoves, lung damage from TB, repeated lower respiratory tract infections or poor lung development in childhood, and long-term exposure to industrial pollution. Indians also have an intrinsic susceptibility to lung dysfunction. Longevity is expected to lead to a rise in COPD and other lung diseases. 

Novel diagnostics and drugs emerge in the developed world and find their way to India. Even data — whether from longitudinal studies or sequencing databases — are generated from western populations. Researchers also currently import human lung tissue samples from the West as lung transplants in the country are rare. 

According to pulmonologist Anurag Agrawal, Dean of BioSciences and Health Research at the Trivedi School of Biosciences, and Head of the Koita Centre for Digital Health, Ashoka University, Sonipat, emerging lung transplant programmes in the country could improve access to healthy and diseased lung tissue for study. This could help translate experimental biology to the human lung and address critical issues such as the drivers of fibrosis in Indian patients.

Indian hospitals and research institutions are part of the Air Pollution Exposure on Adolescents Lungs (APEAL) study, which assesses the burden of impaired lung function in Indian children and identifies key factors contributing to pollution-induced lung injury. The study cohort includes over 4,000 adolescents from four cities, categorised by PM2.5 levels. One research paper based on secondary analysis of the study data found that a substantial proportion of the cohort had bronchial hyperresponsiveness (BHR), described as increased sensitivity to — and airway contraction from inhaling — a variety of stimuli despite being asymptomatic. BHR is an early marker for future chronic lung disease such as COPD. 

The findings showed a dose-dependent association with PM2.5, age, and undernutrition (bit.ly/apealstudy-BHR). Mabalirajan at CSIR-IICB, which is a part of the second phase of APEAL, will measure 40 immune parameters in serum samples from the cohort. Some hospitals are measuring microRNA in breath and respiratory stress parameters. Such studies yield a wealth of data that can be mined to unveil disease sensitivity and resistance patterns. 

Guha of inStem has been taking steps to build a seed network of researchers, clinicians, and technology companies to enable lung research in the country. Such a network would be closely connected with the international research community and enable the transfer of novel technologies, their global benchmarking, and wide dissemination to solve problems relevant to India. "We need to develop the capacity to address our own lung health challenges, while leveraging and contributing to the global ecosystem," he says.

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