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New Technique Provides Detailed Map of Lung Pathology in COVID-19

A team led by investigators at Weill Cornell Medicine and NewYork-Presbyterian has used advanced technology and analytics to map, at single-cell resolution, the cellular landscape of diseased lung tissue in severe COVID-19 and other infectious lung diseases.

In the study, published online March 29 in Nature, the researchers imaged autopsied lung tissue in a way that simultaneously highlighted dozens of molecular markers on cells. Analyzing these data using novel analytical tools revealed new insights into the causes of damage in these lung illnesses and a rich data resource for further research.


lung sections from early and late-stage COVID-19 patients showing fibrosis

Immune cells (red) migrate near the cells that cause fibrosis (green) in late COVID-19. Images courtesy of André Rendeiro.


“COVID-19 is a complex disease, and we still don’t understand exactly what it does to a lot of organs, but with this study we were able to develop a much clearer understanding of its effects on the lungs,” said co-senior author Dr. Olivier Elemento, professor of physiology and biophysics, director of the Caryl and Israel Englander Institute for Precision Medicine, associate director of the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine at Weill Cornell Medicine and co-Director of the WorldQuant Initiative for Quantitative Prediction, which funded the technology for single cell analysis of tissue. “I think the technological approach we used here is going to become standard for studying such diseases.”

Researchers create rapid tests, analytics for COVID-19

Two distinct diagnostic tests, a host/pathogen RNA sequencing platform, and spatially resolved tissue mapping tools, were created by a multidisciplinary team of Weill Cornell Medicine and NewYork-Presbyterian Hospital-led researchers and used to map SARS-CoV-2 infections at the height of the initial COVID-19 outbreak in New York City.

These alternatives to the gold standard RT-PCR test expand the repertoire of tools available to the public health community and together offer the benefits of speed, simplicity and in-depth knowledge about the virus.

The multidisciplinary study, published March 12 in Nature Communications, demonstrates that a test called reverse transcription loop-mediated isothermal amplification (RT-LAMP) can quickly and accurately detect the presence of SARS-CoV-2 in patient samples using simple equipment, while a second approach that captures and sequences the viral RNA allows investigators to identify and track the evolution of variants. The investigators further demonstrated that total RNA sequencing yields insights into both viral sequence evolution as well as human responses to the viral infection.

“We are entering a new era of fast and accurate tools that can tell us when and how viral variants arise and move in specific populations,” said senior author Dr. Christopher Mason, co-director of the WorldQuant Initiative for Quantitative Prediction and a professor of physiology and biophysics at Weill Cornell Medicine. “We hope our innovations will be used like a weather report to identify viral outbreaks, improve tracking and tracing efforts to protect people from infection, and improve treatment interventions for patients.”

Dr. Luigi Marchionni Promoted to Vice Chair, Computational and Systems Pathology

We are delighted to announce the promotion of Luigi Marchionni, MD, PhD, to Vice Chair, Computational and Systems Pathology effective March 1, 2021.

Luigi Marchionni, MD, PhD
Vice Chair, Computational and Systems Pathology

Dr. Marchionni is truly an outstanding computational biologist. He works to develop novel tools for integration and analysis of “omics” data from distinct patients, model organisms, and technological platforms. Dr. Marchionni’s research, through the integration of multi-modal data, aims at the development of novel prediction algorithms for disease prognostication and therapy selection, and the integration of such multimodal predictors into current patients clinical management.

Dr. Marchionni has authored over 100 peer-reviewed publications, with many as primary or senior author, in journals that include Genome Research, PNAS, Cancer Research, Modern Pathology, Bioinformatics, Molecular Cancer Research, Nature Communications, and Science Translational Medicine. A subset of his work embodies multidisciplinary research publications in which Dr. Marchionni has served as the biocomputational expert that designed the analysis and key analytics data assessments for many collaborative studies. 

Dr. Marchionni is currently leading the Department initiative to establish the Pathology Cloud Research Data Warehouse (CRDP), a powerful, HIPAA-compliant, CPU/GPU-scalable, cloud computing infrastructure, fitted with state-of-the analytical pipelines, that aims at streamlining clinical research and innovation on integrated imaging, molecular, and health care data, by leveraging secure and scalable data analysis pipelines.

Please join us in congratulating Luigi!

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