by Kelly E. Butler
Outside: Biobank photos by Dr. Álvaro Cuesta-Domínguez. Center: PI headshots from Columbia websites
From mid-March to early-June, a team of eighteen CRAC volunteers and fourteen lab technicians diligently pipetted, processed, labeled, and stored COVID-19 patient blood, urine, and nasopharyngeal samples. Led by Dr. Álvaro Cuesta-Domínguez and supervised by Drs. Francesca La Carpia and Sebastian Fernando, these dedicated volunteers were working in the Hod Lab to build a biobank of patient specimens to support COVID-19 research at Columbia. As a result of these efforts, Columbia researchers can now gain insight into many aspects of COVID-19 using over 69,000 samples from over 7,000 unique patients. They can also access de-identified medical records including patient age, symptoms, treatment course, and outcome, as well as survey information for each consented patient. As Dr. Cuesta-Domínguez explained, “the biobank’s strength is having a large number of samples. Researchers can select different groups of patients suffering from uncommon diseases, such as inflammatory or coagulation disorders, and study how these conditions affect COVID-19. With thousands of unique patients, the biobank is truly representative of the local infected population.”
The biobank is an invaluable research tool made all the more impressive by its rapid assembly during a pandemic. But, as Theodore Roosevelt once said, “nothing worth having comes easy.”
The first major challenge was the lack of a biobanking facility. The Hod Lab and Dr. Danielle Pendrick, DrPH, Associate Director of the Columbia University Biobank, have significant experience managing clinical specimens, so they were able to help Drs. Cuesta-Domínguez, La Carpia, and Fernando rapidly prepare the infrastructure needed for a COVID-19 biobank. Reminiscing about overcoming this initial obstacle, Dr. La Carpia explained how the founding team designed the biobank from the ground up in only a few short weeks: “We had to build a biobank facility out of nothing. In an empty lab, we started organizing the space, workflow, and volunteers. We were working long hours, sometimes even on weekends. The lab space was actually under renovation to become Dr. Hod’s Transfusion Biology Lab. Many thanks to Dr. Hod for putting everything aside and making the space available to the biobank team.”
A second major challenge was obtaining patient consent to include residual clinical samples in the COVID-19 biobank. Study coordinators typically meet face-to-face with patients in the hospital or clinic to explain the research and obtain consent, but in-person conversations were not possible due to patient and researcher safety concerns. Fortunately, Dr. Pendrick, Jennifer Williamson-Catania, MS, MPH--the Associate Vice Dean of the Office for Research--and Sheila O’Byrne, PhD--a manager of the Precision Medicine Initiative--were able to work with Dr. Soumitra Sengupta, PhD and his IT team to design and implement a remote consent system. Though it can be difficult to reach patients and families via telephone after a hospital visit, 96% of successfully contacted individuals have agreed to participate in the COVID-19 biobank. This high participation rate was possible because the study was designed with patients in mind: biobank samples were collected from excess materials remaining after clinical tests, so patients did not have to return to the hospital during this already difficult time.
The high study participation rate meant that hundreds and sometimes thousands of samples needed to be processed each day. To support this large-scale initiative, the Center for Advanced Laboratory Medicine (CALM) spent hours collecting the precious samples from the main clinical lab, Dr. Cuesta-Domínguez recruited and led a team of highly experienced CRAC volunteers from across Columbia, and the Departments of Pathology and Precision Medicine offered the help of their technicians. With so many community members lending their hands and expertise, Dr. Cuesta-Domínguez noted that ideas to make the sample processing workflow more efficient arose “naturally and daily.” An assembly line process proved to be most effective; some volunteers labeled thousands of vials, and others pipetted for multiple consecutive hours. The team’s streamlined process paid large dividends: In only ten weeks, the volunteers prepared over 20,000 serum, 11,000 plasma, 11,000 blood mononuclear cells, 3,000 nasopharyngeal, 500 cord blood, and 300 fecal samples.
The COVID-19 biobank is already having a significant positive impact. Just as Ms. Williamson hoped when she first helped launch the project, the biobank has become “a bridge for research questions and a tool for many.” Several different labs have already begun COVID-19 research projects using biobank samples, and they are exploring a wide range of pressing topics such as SARS-CoV-2 genetic variation and the impact of the human microbiome on COVID-19 disease course.
Dr. Krzysztof Kiryluk, MD, a nephrologist, is among the researchers working with the COVID-19 biobank samples. His lab specializes in the genetics of rare kidney diseases such as IgA and membranous nephropathy, conditions in which immune dysregulation damages the kidneys and impairs filtration. Earlier this year, his lab published a genome-wide association study (GWAS) in Nature Communications that identified two new genetic loci--NFKB1 and IRF4--implicated in membranous nephropathy.
Dr. Kiryluk and his team were eager to employ their genetic expertise in the fight against COVID-19. There is significant variation in COVID-19 disease course and prognosis, so the Kiryluk Lab is aiming to identify human genetic markers associated with susceptibility to serious complications of COVID-19. Complications of particular interest include the need for dialysis, dependence on mechanical ventilation, and mortality. As Dr. Kiryluk explained, “the genetic analysis is bread and butter for us. We don’t know if common or rare gene variants are involved, so we will use all of the genetic approaches that are available, including GWAS with SNP arrays and rare variant association analyses based on exome sequencing.”
The Kiryluk Lab has already made large strides towards identifying genetic factors associated with severe COVID-19 infection. The team is currently isolating DNA from nearly 3,000 buffy coat samples, which contain mononuclear blood cells and yield high DNA concentrations suitable for genetic studies. Exome sequencing has already started in collaboration with Dr. David Goldstein, the director of Columbia’s Institute for Genomic Medicine (IGM). Once sequencing is complete, the analysis is expected to be “relatively quick” given the team’s expertise in genetics. It is difficult to predict when the research will be published, but Dr. Kiryluk is “pushing for rapid sharing of data and results” and hopes to share his findings publicly as soon as possible.
Like Dr. Kiryluk, Dr. Wendy Chung, MD, PhD is working to identify genetic factors that make certain people particularly ill upon COVID-19 infection. As a pediatric geneticist, Dr. Chung is focused on why some otherwise healthy young people with COVID-19 develop Severe Multisystem Inflammatory Syndrome in Children (MIS-C), a serious but poorly understood Kawasaki-like illness. MIS-C patients present with persistent fever, hypotension, and dangerous inflammation affecting multiple organs. In New York City alone, COVID-19-associated MIS-C has already sickened over 200 children and caused three pediatric deaths. Dr. Chung noted that both virus and human genetics may contribute to MIS-C, but she suspects that MIS-C “is more due to human genetics and the immunological response than viral factors since the virus does not change much.”
COVID-19 research is already well underway in the Chung Lab. The lab’s COVID-19 team has extracted DNA from around 100 pediatric blood samples and is currently sequencing the genetic material. Using the sequencing data, Chung Lab researchers will conduct rare variant association analyses and identify HLA haplotypes, which in part determine how individual immune systems respond to virus infection. Dr. Chung hypothesizes that different rare gene variants and HLA haplotypes can contribute to MIS-C in COVID-19 infected young people. If this is the case, additional samples from other medical centers may be needed to gather sufficient data on enough patients: “We will have to look at the genetics of kids around the world. As a community, we will come together and share.”
Human genetics likely contribute to the severity of COVID-19 cases, but other factors surely play important roles as well. Dr. Anne-Catrin Uhlemann, MD, PhD, an infectious disease expert, suspects that patients’ particular strain of SARS-CoV-2 in part determines their disease course. To begin characterizing the effects of different strains and identify which are most prevalent in NYC, the Uhlemann Lab is isolating and sequencing viral RNA from nasopharyngeal samples. Combined with information from medical records, strain identification will help elucidate whether certain strains are more likely to cause severe COVID-19 symptoms. Moreover, determining which strains are circulating in NYC may improve the accuracy of future contact tracing and--if combined with similar data from many other studies around the globe--could help track the geographic spread of each SARS-CoV-2 strain. Detailed contact tracing data organized by strain could also reveal that some strains are more infectious than others: “Whether some people are infected with more transmissible strains or are just superspreaders is a hotly debated topic. Genomics alone cannot answer this question. We will need detailed epidemiological assays.”
Dr. Uhlemann further hypothesizes that patient microbiomes can impact COVID-19 disease course: “Depending on its composition, the bacterial microbiome may produce a beneficial immune response, produce metabolites that impact viral infection, or modify disease course through some other chain of events.” To start exploring these hypotheses, the Uhlemann Lab is collaborating with Dr. Harris Wang, PhD and Dr. Daniel Freedberg, MD, MS to characterize COVID-19 patient microbiomes based on nasopharyngeal samples. The team is identifying the bacteria in each sample using 16s ribosomal RNA sequencing, a widely used taxonomy strategy that classifies bacteria based on the ubiquitous and highly conserved 16s ribosomal subunit gene. The researchers will then test for statistical associations between specific types of microbiome bacteria and COVID-19 severity.
Drs. Kiryluk, Chung, and Uhlemann are all eager to share their human, virus, and microbiome sequencing data in a central database available to all Columbia researchers. As Dr. Chung explained, “all of the data will be accessible to the Columbia research community, helping bring expertise to bear on pressing research questions.” Other research teams will thus be able to answer a variety of additional questions without the need for additional samples and time-consuming extraction and sequencing procedures. In this sense, the principal investigators’ willingness to share their data allows more knowledge to be developed from each precious patient sample.
All three Principal Investigators also emphasized that their research is a team effort. For example, Dr. Kiryluk noted that “we have a group interested in high impact questions that need to be addressed as soon as possible. That’s why we got together to do this--the CTSA, Dean’s Office, CRAC volunteers, and genetic and clinical coordinators. The CRAC team did a fantastic job, and we wouldn’t be able to do a lot of these things without them.” Dr. Uhlemann expressed similar gratitude for CRAC: “Eldad, Francesca, Sebastian, and Álvaro coordinated so much and have been fantastic. We are very grateful for the resource.”
Continuing the chain of gratitude, Drs. Cuesta-Domínguez, La Carpia, and Fernando all shared their appreciation for the many CRAC volunteers and lab technicians who helped build the biobank. Expressing sincere thanks, Dr. La Carpia became a bit emotional when sharing final thoughts on the biobank: “The biobank leadership team would like to stress that the volunteers have been amazing. They left the comfort of their apartments during a really stressful time, and many have kids and family. Their generosity and commitment to science and healthcare is amazing. They were all so nice and so humble. We couldn’t see their smiles from behind their masks, but we could feel them. I’m so grateful to all of our volunteers.”
Dr. La Carpia also noted that every volunteer was essential. Labeling thousands of vials and delivering lunch may seem like mundane tasks, but they were instrumental in developing the biobank. “Every person in the chain is important. If one link doesn’t work, then the whole chain is broken.” From the patient bedside, through the biobank, and ultimately to publication, Columbia’s broad spectrum of COVID-19 research is a marvel of scientific collaboration.
Together we can combat both pandemics of our time.
Many thanks to Dr. Barbara Noro, Dr. Natalie Steinemann, Ashlea Morgan, Dr. Paula Croxson, and all of the researchers and biobank team members quoted in this piece for their thoughtful feedback on preliminary drafts.
-Post 5: If not now, when? If not us, who? Perspectives on Stepping Up During Dual Pandemics
-Post 4: Answering the call: CRAC Serology Testing Volunteers Join the Fight Against COVID-19
-Volunteer Profiles: An opportunity to “meet” some of the serology testing volunteers
-Post 3: The human scrub machine
- Post 2: Biobank volunteers process 15,500 samples
- Post 1: The CRAC organizational structure
Covid-19 has changed what matters.
The CRAC team was born as a grassroots response to a pandemic none of us has experienced in their lifetime. CRAC has now grown into a community of like-minded postdocs, students, faculty, and administrators, from across Columbia University - a diverse and inclusive ecosystem of talented individuals with a simple goal: support projects to address what matters now, the fight against covid-19.
These are the stories of how the CRAC ecosystem has evolved and continues to adapt to bring life to efforts that became bigger than the sum of their parts. These are also the stories of single individuals who continue to inspire others with their unheralded efforts.