(Micro)Chimerism & Treatment: Immune Tolerance, Transplantation, and Precision Therapeutics
Pregnancy-derived microchimerism exerts durable immunological and clinical consequences that extend from early development to transplantation and autoimmunity. Bidirectional trafficking of maternal and fetal cells establishes antigen-specific tolerance or sensitization shaped by HLA disparity, with implications for transplant compatibility, graft-versus-leukemia effects, and longterm immune regulation. Mechanistic frameworks linking non-inherited maternal antigens and inherited paternal antigens to immune education underscore how gestational exposure can promote either tolerance or pathogenic alloimmunity. In parallel, emerging antigen-specific therapeutic tools like CAR T cells provide experimental avenues to directly test the contribution of rare chimeric populations to autoimmune disease. Technological innovation is central to these advances: high-resolution single-cell transcriptomics and novel bioinformatic tools now enable detection of exceedingly rare foreign-genotype cells across blood, tissues, and transplant samples, revealing diverse cellular fates and lifelong persistence. Expansion and characterization of microchimeric populations further suggests developmental routes for durable engraftment and biological functionality. This interdisciplinary session highlights microchimerism as a biologically embedded determinant of immunity, disease risk, and therapeutic opportunity and provides insight into fascinating technological developments.
Wednesday, 27.05.2026, Day 1
Time: 14:00 – 15:30
Consequences of pregnancy-derived microchimerism for outcome after transplantation
Michael Eikmans
Leiden University Medical Center, The Netherlands
Microchimerism can cause immune recognition between mother and fetus. Differences in human leukocyte antigen (HLA) genes between two hosts is a main driver of immune reactions. The child inherits one set of HLA genes from the mother and one from the father. The mother may develop immunity by forming antibodies and effector- and regulatory T cells, which are specific against the inherited paternal antigens (IPA) of the fetus. Vice versa, T cells from the fetus may show reactivity to non-inherited maternal antigens (NIMA).
Likewise, exposure of a recipient to a transplanted organ or cells from a genetically different individual leads to immune reactions. Previous studies have emphasized the possible consequence of microchimerism for outcome of transplantation performed later in life. For instance, immune recognition by the pregnant woman may lead to HLA antibody development, forming a hurdle when a transplant is given containing HLA antigens to which those antibodies are directed to. Alternatively, maternal exposure during pregnancy in the womb leads to immune tolerance. If a patient, having developed tolerance toward the NIMA, is offered a donor kidney containing a mismatched antigen that is the same as the NIMA, there is no significant negative impact on transplant outcome.
In this lecture I focus on maternal microchimerism (mMC) in the fetus. Umbilical cord blood (UCB) from the newborn can be used as a source for cell transplantation in patients suffering from leukemia. Clinical studies provided indirect evidence that mMC cells in fetal blood mediate graft-versus-leukemia effects in the recipient after UCB transplantation. Attempts for enriching these cells are discussed along with questions including: which cell types are these chimeric cells? How are these chimeric cells maintained and not cleared by the host’s immune system? Why would these cells not directly attack host cells, but would exert alloreactivity in a recipient?
Strategies to test the role of microchimerism in autoimmune disease through antigen-specific therapeutic development
Anne M. Stevens
Executive Medical Director, Century Therapeutics
Adjunct Clinical Professor, Pediatric Rheumatology, Stanford University
Retired Professor, Pediatric Rheumatology, University of Washington
Attending Physician, Pediatric Rheumatology, Renown Regional Medical Center, Reno, NV
Maternal and fetal microchimerism (MMc, FMc) derived during pregnancy have been associated with various aspects of health and disease. In the context of interactive genetic backgrounds, both FMc and MMc have been implicated in the triggering and perpetuation of chronic autoimmune diseases. Functional studies in vitro and in mouse models support a role for loss of allogeneic T cell regulation of fetal-maternal tolerance contributing to chronic inflammation. Novel strategies to target cells with an antigen-specific CAR T cell or bispecific large molecule therapeutics opens up a pathway toward treatment of autoimmunity via depletion of small numbers of pathogenic chimeric cells expressing non-inherited maternal or fetal antigens. Innovative therapeutic development approaches targeting antigen-specific T and B lymphocytes will be discussed with relevance to applying technologies to definitively test roles of MMc and FMc in the pathogenesis of autoimmune disease.
Cellector: A tool to detect foreign genotype cells in scRNAseq data with applications in leukemia and microchimerism.
Haynes Heaton
Haynes Heaton1,†,*, Reza Behboudi1,†, Colin Ward1, Minindu Weerakoon1, Sami Kanaan2, Skylar Reichle1, Nathan Hunter1, Scott Furlan2,3
1 Auburn University, Auburn, AL 36849
2 Fred Hutchison Cancer Center
3 Seattle Childrens Hospital, Department of Pediatrics
†These authors contributed equally to this work
* Correspondence: haynesheaton@auburn.edu
The existence of rare, genetically distinct cells can occur in various samples such as transplant patient samples, naturally occurring microchimerism between maternal and fetal tissues, and cancer samples with sufficient mutational burden. Computational methods for detecting these foreign cells are vital to studying these biological conditions. An application that is of particular interest is that of leukemia patients post hematopoietic cell transplant (HCT). In many leukemias, a primary therapy is HCT, after which, the primary genotype of the bone marrow and blood cells should be of donor origin. If cells exist that are of the patient’s genotype and the cell type lineage of the particular leukemia, this is known as measurable residual disease (MRD). If the MRD is high enough, this may represent a relapse of the patient’s leukemia. Furthermore, accurately estimating the MRD is important for driving clinical decision making for these patients. Using high throughput single cell RNAseq (scRNA-seq) such as drop-seq1, 10x Genomics2, Seq-Well3, InDrops4 among others, one can use the expressed genetic variants in the RNAseq reads to detect microchimeric cells. Unlike multiplexed single cell experiments, one cannot biochemically tag these cells for demultiplexing5,6. Tools made for demultiplexing cells by genotype such as souporcell7,8, vireo9, and scSplit10 rely on clustering based systems that don’t perform well with highly skewed cluster sizes, which microchimerism has by definition. Other tools such as Demuxlet11 require knowledge of the genotypes up front which may be costly, not possible, or unavailable. Here we present Cellector, a computational method for identifying rare foreign genotype cells in single cell RNAseq (scRNAseq) datasets. Cellector uses a sparse beta-binomial anomaly detection method to identify cells with different genotypes than the majority of the sample. We show cellector accurately detects microchimeric cells down to an exceedingly low percentage of these cells present (0.05% or lower) even when the cells come from related individuals which represent the most common donors for HCT.
Cellector is freely available under an MIT open-source license at https://github.com/wheaton5/cellector.
A novel approach to investigate breastmilk T cell antigen-specific responses
Blair Armistead
Yonghou Jiang1, Jennifer E. Stolarczuk2, Sharon Kung2, John Houck1, Victoria L. Campbell3, David M. Koelle3,4,5, Alisa Kachikis2, Whitney E. Harrington1,7,8, Blair Armistead1,8
1 Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
2 University of Washington School of Medicine, Department of Obstetrics and Gynecology, Seattle, WA, USA
3 University of Washington School of Medicine, Department of Medicine, Seattle, Washington, USA
4 Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
5 University of Washington School of Medicine, Department of Laboratory Medicine & Pathology, Seattle, Washington, USA
6 Benaroya Research Institute, Seattle, Washington, USA
7 University of Washington, Department of Global Health, Seattle, Washington, USA
8 University of Washington School of Medicine, Department of Pediatrics, Seattle, WA USA
Abstract
Breastmilk plays a pivotal role in infant health and development, providing both nutritional and immunological benefits. In addition to protective antibodies, breastmilk contains immune cells, including T cells, which have an unknown role in human infant immunity. However, multiple studies in animals have shown that milk-derived T cells can traffic to peripheral organs of nursing offspring as a form of maternal microchimerism (MMc) and provide protection from infection. Further study is needed to understand the potential of breastmilk T cells to exert pathogen-specific effector functions at the maternal-infant interface. To-date, direct ex vivo functional analyses and T cell receptor sequencing of breastmilk T cells have been limited by low T cell frequency. To overcome this barrier, we optimized a method to expand breastmilk T cells in culture using cell sorting and mitotic stimulation. With this approach, we generated expanded breastmilk T cell (EBM T cell) cultures from n=4 lactating women, resulting in a ~1,000-fold increase in T cells from the original sample. Because each donor reported receipt of SARS-CoV-2 (SARS2) mRNA vaccination and/or history of SARS2 infection, we used SARS2 Spike as a model for detecting antigen-specific responses in EBM T cell cultures. In EBM T cell cultures from 2 of 2 donors tested, we identified SARS2 Spike-specific CD8+ T cells using an HLA-matched, Spike-loaded tetramer. To assess antigen-specific functional responses, we stimulated EBM T cells from one donor with a SARS2 Spike peptide pool, using autologous irradiated PBMC for antigen presenting function. Spike-stimulated EBM T cells contained CD4+ and CD8+ T cells expressing activation-induced markers, suggesting that their antigen-specific functionality was preserved. Together, our findings show that our novel approach is a valuable platform for investigating pathogen-specific responses in breastmilk T cells, with relevance to the study of breastmilk-derived MMc in infants.
Is the skin the preferred target of twin microchimerism in mice in all cross combinations: allogeneic, congenic and semi-allogeneic?
Yoan Ghaffar
Yoan GHAFFAR1, Chahinez ARIF1, Mathilde GIASSI 1, Marielle MARTIN1, Isabelle AUGER1, Catherine DUEZ1 and Nathalie LAMBERT1.
INSERM U1097 ARTHEMIS Aix Marseille University, France
During pregnancy, bidirectional cell exchange—especially between twins—represents a significant but often overlooked source of microchimerism. This mouse study investigates two key questions: What are the preferred niches for littermate microchimeric cells (LMc), and what factors influence the quantity of cells transferred between twins?
Previous work by the team showed that an embryo’s location in the uterine horn affects the amount of LMc it receives. Here, we examine how genetic relationships (allogeneic, semi-allogeneic, congenic) influence the passage and persistence of LMc from embryonic to adult stages. We use crosses where the father is heterozygous for the TdTomato fluorescence gene, allowing tracking of TdTomato+ LMc cells in offspring that did not inherit the gene. Crosses are as follows : C57BL6 X C57BL6-Tom+ (congeneic), DBA/2 X C57BL6-Tom+ (allogeneic), and D2BL6 X C57BL6-Tom+ mice, with respectively 6, 17, and 22 offspring dissected at embryonic, young adult, or older adult stages. About 20 tissues per offspring are tested for TdTomato presence via quantitative PCR, and organ sections are preserved for microscopy.
Preliminary results show that, as previously observed in semi-allogeneic crosses, the skin is the preferred niche for LMc in allogeneic crosses with respectively 4/4 embryos, and 5/5 of young adults. Congenic crosses have not yet been tested. Further analysis is needed to characterize these skin-resident cells. These findings echo earlier lab work identifying cells from a vanished twin in a 40-year-old man with scleroderma-like syndrome, suggesting that twin microchimerism may play a role in skin-targeted autoimmune diseases such as scleroderma.
Characterization of human amniotic fluid stem cells and their potential role in maternal microchimerism
Bernadette L. Bramreiter
Bernadette L. Bramreiter1, Katja Sallinger1, Emiel Slaats1, Julia Schönberger1, Katharina Schuch1, Philipp Klaritsch², Herbert Fluhr², Thomas Kroneis1
1: Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
2: Department of Obstetrics and Gynaecology, Medical University of Graz, Graz, Austria
Objective
Microchimerism (MC) is defined as the presence of a small population of genetically distinct cells within a host. During pregnancy, bidirectional cell trafficking across the feto-maternal interface results in maternal and fetal microchimerism. Since microchimeric cells represent cell types derived from all three germ layers, we assume cells with stem cell-like properties to be responsible for the establishment of lifelong MC. However, the cellular routes and mechanisms remain unclear. We hypothesize that maternal cells reach the fetus via ingestion of fetally-derived amniotic fluid (AF) and subsequent transmigration into fetal tissues, potentially through the gastrointestinal tract, and that these cells represent a subpopulation of amniotic fluid stem cells (AFSCs).
Methods
Stem cells were isolated from AF using CD117-targeting microbeads and characterized using a 16-marker multicolor flow cytometry panel designed to identify AFSCs and distinguish them from other progenitor and contaminating populations. Markers included CD27, CD34, CD44, CD45, CD73, CD90, CD105, CD117, HLA-ABC, HLA-DR, SSEA-3, SSEA-4, Tra-1-60, Tra-1-81, and OCT3/4. Pluripotency was assessed by trilineage differentiation into early germ layer intermediates. Potential maternal microchimeric cells were identified in male pregnancies using XIST and RPS4Y1-specific padlock probes and/or X Y-FISH.
Results
AFSCs expressed pluripotency-associated markers, including OCT3/4 and CD117, and lacked lineage-specific markers such as CD34 and CD45. Upon differentiation, AFSCs generated early germ layer intermediates expressing lineage specific morphology and markers such as FOXA2 (endoderm), CD144 (mesoderm), and Nestin (ectoderm). Maternal cells were detected in three of four AFSC samples.
Conclusion
The presence of maternal cells within the AFSC compartment supports a potential role for feto-maternal cell trafficking in the AF and suggests AFSCs as a potential source of maternal microchimeric cells.