The Konnikova Lab

Mucosal Immune Development

The research laboratory of Liza Konnikova, MD, is focused on understanding how neonatal mucosal immunity develops and its role in the pathogenesis of diverse diseases such as sepsis, preterm labor, necrotizing enterocolitis and very early onset IBD.

To improve our understanding of mucosal immunity, her team uses a number of single-cell based techniques, including mass cytometry or CyTOF to understand diverse interactions between the immune and epithelial components of the gastrointestinal (GI) tract both during development, from fetal to adult tissue, as well as in disease. Broadly, the team is interested at how GI and mucosal immunity develops and how its dysregulation leads to disease.

To better elucidate causes of preterm labor, Dr. Konnikova’s lab is applying these techniques to gain a better understanding of placental immune development from first to third trimester.

Areas of Focus

Maintenance of mucosal homeostasis is key to proper development of both healthy microbiome and proper immune development. Dysregulation of this process can lead to both uncontrolled inflammation and autoimmune diseases. Using human samples, the Konnikova Lab focuses on understanding how proper mucosal immunity develops and how its dysregulation leads to disease.

Members of the Konnikova Lab team are currently focused on these subject areas:

CyTOF analysis of peripheral blood and small and large intestinal immune cells of a patient.

CyTOF analysis of peripheral blood and small and large intestinal immune cells of a patient.

Placental Immune Development

Using various techniques, members of the Konnikova Lab team are studying the placental immune development throughout human gestation period. Focusing on the various layers of placenta, we are analyzing the immunophenotype and functionality of immune cells present.

CyTOF analysis of different regions of the placenta.

CyTOF analysis of different regions of the placenta.

Immunofluorescence and in situ hybridization image of first trimester placenta.

Immunofluorescence and in situ hybridization image of first trimester placenta.

Gastrointestinal Immune Development and Disease

The gastrointestinal (GI) tract is one of the largest immune organs in the body. It is also host to 500 to 1000 different bacterial species and as much as 1014 bacteria. The majority of these bacteria represent commensals that play an important role in the development and maintenance of the host immune system. The careful interplay between the immune cells and the commensal bacteria allow for the host’s immune system’s ability to respond to pathogenic bacteria but to be tolerant to the commensal ones. However, how homeostasis is established and maintained in humans is very poorly understood.

Through translational studies of human tissue throughout gestation as well as from neonates and young children, the Konnikova Lab is interested in deciphering how homeostasis is established and maintained.

Dysregulation of the GI immune homeostasis leads to a number of diseases such as necrotizing enterocolitis (NEC), very early onset inflammatory bowel disease (VEO-IBD) and IBD. To facilitate with studying mucosal immunity in health and diseases, we have adapted mass cytometry (CyTOF) to perform deep immunophenotyping and functional analysis of immune cells at mucosal surfaces. Additionally, we have developed a cryopreservation method to store tissue directly with preservation of viability and functionality. These advances have allowed us to study immune dysregulation in various diseases such as NEC, VEOIBD and IBD.

CyTOF analysis of immune cells in the small intestine of a VEOIBD patient (P1) and patients with and without IBD. Kotlarz et al, Nature Genetics, 2018.

CyTOF analysis of immune cells in the small intestine of a VEOIBD patient (P1) and patients with and without IBD. Kotlarz et al, Nature Genetics, 2018.

FACS analysis of Th17 and IL17 production in an IL10 receptor deficient patient. Shouval and Konnikova et al, IBD, 2017.

FACS analysis of Th17 and IL17 production in an IL10 receptor deficient patient. Shouval and Konnikova et al, IBD, 2017.

Developing a Pipeline of Simultaneously Analyzing CyTOF and Clinical Data

CyTOF is an innovative approach that combines both mass spectrometry and cytometry providing the ability to detect up to 40 antigens in a single sample at a single cell resolution. This technique is ideal for identifying rare functionally distinct subpopulations of cells and to compare them between different conditions. It has been successfully used in a number of settings including detection of extremely rare metastasis in peripheral blood.

To visualize the complex multidimensional data produced by CyTOF, a number of algorithms have been developed. However, there are no commercially available pipelines to automatically define computer-generated clustering or to associate clinical data such as disease phenotype, patient age, and sex, with the clustering.

In collaboration with George Tseng, ScD, from the University of Pittsburgh Graduate School of Public Health, we are working on building such a pipeline.

CyTOF: Single Cell Analysis of >40 Parameters

Lab Team & Contact Information

Liza Konnikova, MD, PhD, FAAP

Principal Investigator
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Erica Prochaska, MD

Anne-Marie Rick, MD
Research Fellow

Jessica Toothaker
Graduate Student Researcher - Immunology

Alex Denny

Austin Oldham
Undergraduate Researcher

Courteney Avon
Undergraduate Researcher

Cindy Vogt

Contact Us

The Konnikova Lab
UPMC Children’s Hospital of Pittsburgh
John G. Rangos Sr. Research Center, Suite 7127
4401 Penn Avenue
Pittsburgh, PA 15224

News & Activities

That's PediatricsResearching Early Immune Development, a podcast featuring Liza Konnikova, MD, was added to the “That’s Pediatrics” series.

Clinical Studies

Currently Liza Konnikova, MD, PhD, FAAP and her team are conducting patient-oriented research investigations that are focused on: 1) Understanding causes of necrotizing enterocolitis (NEC) and 2) Understanding causes of premature delivery.

Identifying Infants At High Risk For NEC

NEC is the leading cause of death in preterm infants. Despite advances in neonatal care, the survival of infants with NEC remains low – less than 50 percent in many cases. In part, this is due to our inability to predict which infants are at risk for the development of NEC and the subsequent failure to utilize preventative strategies.

The Konnikova Lab has identified that signaling via the innate immune receptor, Toll-like receptor 4 (TLR4) plays a key role in the development of NEC. We now seek to identify novel biomarkers for NEC in a longitudinal cohort study of infants with NEC, who are born at a major neonatal center, by assessing the TLR4 signaling capacity of these neonates using combined in vitro and in silico approaches. In so doing, we hope to advance the field by identifying newborns that are at risk for NEC development, thus creating a window for early prophylactic and interventional therapies.

Immunophenotyping of Placenta Specimens and Cord Blood

Every year more than 500,000 infants are born prematurely (prior to 37-weeks' gestation) in the United States, which is equivalent to one in every eight babies being born prematurely. Preterm birth (PTB) has been correlated with greater risk for many conditions that require an infant to spend time in Neonatal Intensive Care Units (NICU). However, the underlying causes of PTB have not been completely elucidated.

A link between preterm birth and placental inflammation has been reported in both infection-driven and non-infection-driven cases of PTB, but the specific cell types and signaling pathways involved remain unclear. Infants born preterm are at greater risk for multiple complications including sepsis, particularly in the first few days of life which can lead to severe neurodevelopmental complications or death in afflicted infants. Evidence suggests immune dysregulation may contribute to both the onset of PTB and increased risk of sepsis.

The role of the placenta in immune regulation and its impact on the outcomes of the neonate has not been fully explored. This has in part been difficult due to the large repertoire of cells and signaling molecules related to immune homeostasis that need to be investigated. To address this issue, our study utilizes the placenta and cord blood samples collected through the Magee Obstetric Maternal & Infant (MOMI) Biobank and processes them using mass cytometry (CyTOF) to simultaneously analyze 40 antibody cell surface and signaling markers at single cell resolutions to comprehensively evaluate cell populations. CyTOF also has the potential to aid in uncovering inflammatory signaling cascades by segregating cell types based on intracellular phosphorylated proteins and stimulated cytokine concentrations. In the current study we aim to systematically characterize the immune profile of the placenta and cord blood. We will then take the immune profile and correlate it to the clinical presentation of the mother and the clinical outcomes of the neonate.


High Dimensional Immune Phenotyping and Transcriptional Analyses Reveal Robust Recovery of Viable Human Immune and Epithelial Cells from Frozen Gastrointestinal Tissue
Konnikova L, Boschett G, Rahman A, Mitsialis V, Lord J, Richmond C, Tomov VT, Gordon W, Jelinsky S, Canavan J, Liss A, Wall S, Field M, Zhou F, Goldsmith JD, Bewtra M, Breault DT, Merad M, Snapper SB
2018 May

Human TGF-β1 Deficiency Causes Severe Inflammatory Bowel Disease and Encephalopathy
Kotlarz D, Marquardt B, Barøy T, Lee WS, Konnikova L, Hollizeck S, Magg T, Lehle AS, Walz C, Borggraefe I, Hauck F, Bufler P, Conca R, Wall SM, Schumacher EM, Misceo D, Frengen E, Bentsen BS, Uhlig HH, Hopfner KP, Muise AM, Snapper SB, Strømme P, Klein C
Nature Genetics
2018 Feb 26

Enhanced TH17 Responses in Patients with IL10 Receptor Deficiency and Infantile-onset IBD
Shouval DS, Konnikova L, Griffith AE, Wall SM, Biswas A, Werner L, Nunberg M, Kammermeier J, Goettel JA, Anand R, Chen H, Weiss B, Li J, Loizides A, Yerushalmi B, Yanagi T, Beier R, Conklin LS, Ebens CL, Santos FGMS, Sherlock M, Goldsmith JD, Kotlarz D, Glover SC, Shah N, Bousvaros A, Uhlig HH, Muise AM, Klein C, Snapper SB
Inflammatory Bowel Diseases
2017 Nov

Impact of Antibiotics on Necrotizing Enterocolitis and Antibiotics-associated Diarrhea
Silverman MA, Konnikova L, Gerber JS
Gastorenterology Clinics of North America
2017 Mar

Late Enteral Feedings Are Associated with Intestinal Inflammation and Adverse Neonatal Outcomes
Konnikova Y, Zaman MM, Makda M, D'Onofrio D, Freedman SD, Martin CR
PLos One
2015 Jul 14

See the complete List of Dr. Konnikova’s published work.

Opportunities to Join

We’d Like to Hear From You!

Researchers interested in positions within the Konnikova Lab should contact Dr. Konnikova via email to explore opportunities.