After the Smoke Clears: Scars on the Immune System 

When a pathogen strikes a community, a variety of immune responses emerge. The COVID-19 pandemic is a prime example of human immunological variance.1  While some individuals walk away asymptomatic, others are hospitalized with life-threatening infections. Individual immune responses to infection are influenced by characteristics such as age and sex, as well as social, economic, and physical environments.

In a paper published in Nature, researchers at the Pasteur Institute reported determinants of human immune variance in a healthy population.2 From a list of over 100 variables, smoking status emerged as a major contributor to innate and adaptive immune responses. Furthermore, they found that the effects on the adaptive immune system persisted long after an individual stopped smoking and associated with epigenetic alterations. Their findings highlight how environmental factors can affect the epigenome and shape an individual’s risk for developing infection and disease.

Photo of Darragh Duffy

Darragh Duffy, an immunologist at the Pasteur Institute, explores the mechanisms that drive individual differences in immune response.  

Pasteur Institute

“We know for multiple reasons why smoking is bad in terms of its cancer risk, but here we’re showing additional information that it’s also probably negatively impacting your immune response. And that it’s a long-lived effect, and it’s also an accumulative effect,” said Darragh Duffy, an immunologist at the Pasteur Institute and coauthor of the study. 

“There is no human immune system; there is everyone’s individual immune system,” said Adrian Liston, an immunologist at the University of Cambridge who was not involved in the study. “We really need to study things at the scale that the group in Paris is studying if we want to understand what’s going to be relevant to human health at a population level.” 

Over a decade ago, the Milieu Intérieur Consortium established a population-based study to explore determinants of human immunological variance.3 Researchers collected blood, stool, and nasal swab samples from 1,000 healthy individuals alongside pages upon pages of health questionnaires. The cohort was equilibrated for men and women in each decade from 20-69 years of age, but only includes individuals from the Western European genetic background. They set out to discover novel factors that affect how an individual’s immune system responds to infection. 

To simulate infection scenarios in the laboratory, the research team systematically exposed the donors’ whole-blood samples to a variety of immune stimulation conditions that capture a breadth of immune cell-inducing agents, including microbes and viruses. “They were representative to have the most diverse responses as possible so that we can see the full dynamic range in which people respond to these simulations,” said Violaine Saint-André, a computational biologist at the Pasteur Institute and coauthor of the study. 

Photo of Violaine Saint-André

Violaine Saint-André, a computational biologist at the Pasteur Institute, studies factors that regulate gene expression.

Thomas Lang, Pasteur Institute

The researchers measured the production of disease-associated cytokines following exposure to stimulation conditions that targeted either the innate immune system, a pre-programmed response network that quickly tackles new infections, or the adaptive immune response, a specialized army of immune cells that provides long-lasting protection from recurrent attacks.

“It is technically very difficult, and it really takes a lot of expertise to be able to run this at scale,” said Liston. “This group in Paris is really a leader in the field.”

To pluck out factors that have strong associations with specific immune phenotypes, Saint-André combed through patient health questionnaires and selected a compilation of socio-demographic, environmental, clinical, and nutritional variables. When she measured their impact on cytokine production in each immune challenge, three variables emerged as major influencers: body mass index, cytomegalovirus latent infection, and smoking. 

“The most striking thing was some of the smoking observations,” said Duffy.

The research team found that smoking compromised both innate and adaptive immune responses across several stimulation conditions, as evidenced by elevated cytokine levels in current smokers relative to individuals who have never smoked. When they looked at the immune phenotypes from past smokers, they observed an innate immune profile that looked similar to non-smokers but an adaptive immune response akin to current smokers. 

“That is very consistent with that conceptual idea that the innate immune system refreshes itself constantly, while the adaptive immune system has this memory that can really last decades,” said Liston.

The authors decided to dig even further into the data in search of the cells that drive smoking’s effects on immune responses. When the researchers incorporated flow cytometry data into their analyses, no specific subsets of cells popped out as mediators of the innate immune response; however, they pinpointed multiple B cells as well as regulatory T cells as major contributors to smoking’s enduring effects on immunity. 

Given smoking’s persistent effects on adaptive immune cells, Saint-André wondered whether epigenetic modifications were to blame. Specifically, she looked into DNA methylation, a biological process that typically inhibits gene transcription. When she analyzed DNA methylation data from more than 850,000 sites in the genome modifications associated with one gene in particular caught her attention. The aryl hydrocarbon receptor (AHR) gene is a metabolizer of xenobiotic toxins, meaning that it gobbles up many of the toxic factors floating in cigarette smoke. The receptor’s activity is curtailed by the AHR repressor (AHRR) gene, which had different methylation patterns across the three smoking groups. Previous studies identified AHRR as a biomarker of smoking cessation, but it was unclear what role the gene played in the health of the individual.4 Now, Duffy and his team have provided evidence that the gene mediates smoking’s enduring effects on the adaptive immune system.

Gray DNA strand and molecules emitting from a burning cigarette, surrounded by smoke. 

Smoking alters short- and long-term immune responses, evidenced by elevations in cytokine levels, and leaves epigenetic marks on genes.   

Bertsy Goic (DrawInScience)

For current smokers, AHRR methylation levels correlated negatively with the number of years spent smoking and the total number of cigarettes smoked across an individual’s lifetime. For past smokers, methylation levels of the gene correlated positively with the number of years since an individual stopped smoking, suggesting that with time, the adaptive immune system shifts towards a methylation profile similar to a never-smoker. Saint-André said that it’s difficult to put an exact number on how long smoking affects immune responses following cessation as it varies across individuals, but it’s on the scale of years. For example, on average, it took around 40 years for past smoker AHRR methylation levels to match the average levels in non-smokers. 

“Anytime you study variation in the immune system, you are studying a population at a snapshot in time, in a single place,” said Liston. The variables that strongly affect immune responses in the cohort studied in France may be different from those of a given population in New Zealand or Senegal or even the French population 30 years ago. He added, “The variation in the population is driven by an environment, which is different, and anytime the environment changes, the relative effect on variation is going to change as well.”

With this limitation in mind, Duffy and his team are collaborating with Pasteur Institutes in Senegal and Hong Kong to ask these same questions in different environments. The team is also excited to begin analyzing longitudinal data that they recently collected from a subset of the original 1,000 donors to explore the effects of aging on immunological variance.

Findings from population-based studies provide insights into the causes and human health consequences of immune variability. These differences could help inform vaccine development or treatment regimens based on an individual’s age or sex. Duffy said that vaccinating smokers and non-smokers differently might be too much of a stretch, but it’s not out of the question to tailor treatments based on an individual’s smoking history, including increasing the dose of anti-inflammatories or steroids to counteract the inflammation.

However, as with many things in health, prevention is key. “The best time to quit smoking is now,” said Duffy. However, he noted that even if someone is unable to quit smoking cold turkey, some benefits come from reducing the number of cigarettes smoked. 


  1. Brodin P, Davis MM. Human immune system variation. Nat Rev Immunol. 2017;17(1):21-29.
  2. Saint-André V, et al. Smoking changes adaptive immunity with persistent effects. Nature. 2024;626(8000):827-835.
  3. Thomas S, et al. The Milieu Intérieur study – an integrative approach for study of human immunological variance. Clin Immunol. 2015;157(2):277-293.
  4. Philibert R, et al. Reversion of AHRR demethylation is a quantitative biomarker of smoking cessation. Front Psychiatry. 2016;7:55.

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