COVID Traps Alveoli Cells in a Curious Progenitor State, Squelching Lung Regeneration

Mere weeks into the COVID pandemic, stunning graphics began to appear depicting the path of devastation of SARS-CoV-2 through a human lung. It’s only recently that we’ve come to understand what, exactly, is happening on a cellular level. The new view is thanks to single-cell RNA-sequencing, which analyzes the abundance of messenger RNAs in individual cells. The cells utilize the sets of mRNAs to produce proteins.

normal lung alveoli indicating examples at1 and at2 cells, COVID
Normal lung alveoli indicating examples AT1 and AT2 cells with arrows. Toluidine blue stained section. The new research papers reveal how the AT1, AT2 and other cells in the lung are affected by COVID-19 impairing repair.

Preparing Atlases

Peeks into gene expression provide “atlases” of activities in the tissues and organs that cells build, a little like painting dots and not seeing the big picture until viewed from a distance. The results: a cell-by-cell reconstruction of the lung that researchers can compare to healthy lung topography as well as to lungs in various forms of pneumonia.

Two recent reports in Nature present findings of “RNAseq” applied to lung cells harvested from autopsies of COVID patients within hours of death and flash-frozen. This strategy probes cells in their natural setting, rather than from sputum or hauled out with a bronchoscope. It also circumvents the harsh formalin fix and paraffin embedding of typical cell preps.

The investigations reveal a profound failure of the alveoli to repair themselves underlying the acute respiratory distress syndrome that develops in about 15 percent of people who have COVID. And the root cause is a breakdown of the differentiation of alveoli cells as precursor cells become mired in a progenitor purgatory of sorts.

The Nature paper with first author Johannes C. Melms, from Columbia University’s Department of Pathology & Cell Biology (and dozens of co-authors), analyzes mRNAs from 116,314 lung cells, about 80,000 from 19 COVID patients aged 59 through 89 and from healthy controls. The cells were taken within 10 hours of death and with permission from the patients or their next-of-kin.

The researchers summarize what they found as “a detrimental trifecta of runaway inflammation, direct destruction and impaired regeneration of lung cells involved in gas exchange, and accelerated lung scarring.” That pretty much matches those crazy graphics of the early days.

The second paper, with first author Toni M. Delorey from the Broad Institute, looks at 420 specimens from 11 men and 6 women, aged 30 through 89, taken from kidney, liver, and heart (where the virus goes more rarely) as well as the lungs.

Into the Lungs

A lung consists of a connective tissue scaffold; the epithelia that adhere and bend into the microscopic alveoli where gas exchange occurs; and wandering white blood cells, ready to spew cytokines and engulf pathogens. Overall, RNAseq on cells from the autopsied COVID lungs revealed telltale changes and imbalances.

  • “Pathological” fibroblasts rapidly produce collagen, like covering bubble wrap with thick glue or cement. Lungs stiffen, gas exchange is impaired.
  • B cells churn out antibodies against the virus, while T cells plummet.
  • Monocytes and macrophages proliferate, mopping up viruses while also secreting cytokines, including interleukin (IL)-1beta and IL-6.

Perhaps the most profound change in the COVID lung is to the architecture and functioning of the alveoli, which halts the ability to regenerate.

Melms’ group separated alveoli epithelium from other locations of the lining tissue in the lung, such as the airway epithelium (club, ciliated, basal, and mucous cells) and cycling epithelium (involved in cell division and inflammation), and from fibroblasts. The alveolar epithelium is of two types. In a healthy lung, these cells mostly aggregate in separate clusters. But in COVID, they mix.

AT1 and AT2 cells in COVID

Normally, alveolar type 2 (AT2) epithelial cells serve as caretakers, secreting the surfactant that bathes the air sacs, enabling them to inflate. The type 2 cells also assume a series of stem cell and progenitor forms that divide and give rise to alveolar type 1 (AT1) cells, which comprise the air sacs.

SARS-CoV-2 stops this vital transition of AT2 to AT1 alveoli cells, and the upshot is that the lung, at a microscopic level, can’t heal. So not only does the virus directly destroy alveoli, but it also attacks their ability to regenerate even if they survive. As a result, the lungs basically break down.

The Melms team looked at 20,949 AT1 and AT2 cells. Markers tell the tale, with gene expression going haywire.

In a healthy lung, AT1 cells express CL1C5, which encodes connexin, a protein that is part of gap junctions, connecting cells. Functioning AT1 cells also produce AGER (“advanced glycation end-product”), which oversees development of the alveoli and their repair. Those functions plummet in the AT1 cells of a COVID lung, while production of caveolin-1 also falls, a protein marker of late AT1 maturation.

The AT1 damage unfolds from the compromised AT2 cells. Their production of surfactant proteins drops off, as does a transcription factor, ETV5, which maintains specialization so that the AT2 cells can both support the AT1 cells and divide to give rise to daughter cells that differentiate into AT1 cells.

The researchers conclude, “Overall, these data suggest an incomplete transition of AT2 to AT1 cells in COVID-19.”

In the other Nature paper, Delorey et al describe culturing 4,573 lung organoids from autopsies on 17 people. They note a plunging number of AT2 cells, with an increase in fibroblasts, dendritic cells, macrophages, natural killer cells, and lymphatic and vascular endothelium. Gene expression of the AT2 cells favors programmed cell death, development of adaptive immunity, and inflammation. At the same time, they secrete less surfactant than normal.

Progenitor Cells Run Amok in COVID

From the mayhem ensuing in the COVID lung emerges a cell type apparently caught in the middle, bathed in inflammatory molecules and called “damage-associated transient progenitors,” or DATP cells. A paper in Cell Stem Cell from Jinwook Choi of the Wellcome-MRC Cambridge Stem Cell Institute describes them.

Distinguishing markers of the DATP progenitor cells are a keratin (KRT8), a tight junction protein (CLDN4), and a protein that dampens cell division (CDKN1A). RNAseq data for tumor necrosis factor alpha, p53, and hypoxia response gene HIF-1 alpha, indicate a braking of cell division and a battle to maintain oxygenation. These are the molecular underpinnings of the COVID patient desperately needing oxygen.

DATP cells carry out a program of gene expression called PATS, for “pre-alveolar type-1 transitional cell state,” described in a report in Nature Cell Biology from  Yoshihiko Kobayashi in Purushothama Rao Tata’s group at the Duke University School of Medicine. The PATS-fueled progenitor cells are transient in healthy lungs, but persist in COVID-infected lungs, where their proliferation brings the stifling fibrosis. “Our study thus implicates a transient state associated with senescence in normal epithelial tissue repair and its abnormal persistence in disease conditions,” the researchers write.


The cell atlases of COVID lungs from the single-cell RNA-sequencing may suggest new drug targets or repurposing candidates, and may help to better understand what happens to the lungs of patients who recover from the pneumonia.

“It’s a devastating disease, but the picture we’re getting of the COVID-19 lung is the first step towards identifying potential targets and therapies that disrupt some of the disease’s vicious circuits,” said Benjamin Izar, lead author of the Melms paper.

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