Mar 7, 2022 / Neuroscience / Oncology / Immunology

Xperience 2022: Making the impossible possible with single cell and spatial technologies

Jeanene Swanson

On February 22, 2022, 10x Genomics held its annual Xperience event, which showcased our current and upcoming products for single cell and spatial analysis. We also heard from several scientists who used our single cell and spatial assays to perform visionary research and drive discoveries that simply would not be possible using bulk RNA sequencing analyses. In this post, we feature several publications that were highlighted during the event, and discuss how our Chromium single cell and Visium spatial products are being used to gain insights into neurodegenerative conditions like Alzheimer’s disease and Lewy body dementia, complex tissues like the human endometrium, and vaccine response as it pertains to immune tolerance.

Unveiling novel culprits of neurodegenerative disease

Last fall, we granted the inaugural Early Career Investigator Award (ECIA), which recognizes one exceptional early-stage researcher who is advancing our understanding of the pathophysiology of Alzheimer’s disease (AD) and related dementias, to David Michael Gate, PhD, an assistant professor at Northwestern University. Dr. Gate spoke during Xperience 2022 about his research at the intersection of the brain and immune system, how spatial transcriptomics will advance a newfound ability to probe autopsy tissue samples, and his own groundbreaking studies utilizing single cell techniques.

In a study published in Nature in 2020 (1), Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer's disease, Dr. Gate, then at Stanford University, led a team that applied single cell RNA sequencing (scRNA-seq) of immune cells from the cerebrospinal fluid (CSF) of multiple cohorts of patients with AD and mild cognitive impairment (MCI) to reveal changes that may be useful as potential biomarkers in the early identification of dementia.

Specifically, they first used mass spectrometry on peripheral blood mononuclear cells (PBMCs) of patients with AD and MCI to uncover an immune signature of AD that consisted of an increased number of a subset of proinflammatory peripheral T cells, a CD8+ T effector memory CD45RA+ (TEMRA) cell. They then turned to the Chromium Single Cell Immune Profiling assay to perform scRNA-seq on PBMCs of a second cohort, finding an increase in T-cell receptor (TCR) and cytokine signaling in CD8+ TEMRA cells in MCI and AD. By applying single cell TCR sequencing (scTCR-seq) in a third cohort, they were able to show that clonally expanded CD8+ TEMRA cells exist in the CSF of patients with AD.

While inflammation—a result of the innate immune response—is a hallmark of AD, their findings emphasize a role for the adaptive immune response and highlight the complex interactions of immune cells within the brain over the course of this neurodegenerative disease.

In more recent work published in Science in 2021 (2), CD4+ T cells contribute to neurodegeneration in Lewy body dementia, Dr. Gate again led a team that reported that T cells invade the brains of people with Lewy body dementia (LBD), hone to synuclein aggregates, and are found in association with IL17A+ dopaminergic neurons. They first performed immunohistochemistry to initially identify T cells located in the substantia nigra of LBD and Parkinson’s disease (PD) patients.

Next, to determine which type of T cell might have infiltrated the central nervous system, the researchers analyzed CSF of healthy controls and people with PD or LBD. Using Single Cell Immune Profiling, they performed both scRNA-seq and scTCR-seq to reveal that CD4+ T cells were most altered in LBD, expressing large amounts of the chemokine receptor CXCR4. The data suggests that these cells are somehow being recruited into the CSF and, hence, the brain.

The findings are significant as the identification of these CXCR4+ T cells may have clinical implications. Antagonists for this receptor have been developed to treat various types of cancer and HIV infection. Several are in clinical trials, and the FDA has approved one, plerixafor (3). While such drugs hold potential for treating LBD, Dr. Gate said they are not ready for clinical trials.

Spatially mapping a moving target, the human endometrium

In another example of how single cell technologies are game-changing for some neglected fields of study, a paper published in 2021 in Nature Genetics (4), Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro, showcased how Roser Vento-Tormo, PhD, of the Wellcome Sanger Institute led a team that used both Chromium Single Cell Gene Expression and Visium Spatial Gene Expression to create a single cell transcriptomic map of the full-thickness human uterus. Performing scRNA-seq and single nucleus RNA sequencing alongside spatial transcriptomics on samples of postmortem uterine and endometrial biopsy tissues, they identified five main types of cells. They then were able to systematically map the location of these cell types within the endometrium and myometrium, notably during its proliferative phase.

In complex tissues such as the uterus, which is constantly undergoing cellular changes across the menstrual cycle, the location of a cell can determine its activity and function. Dr. Vento-Tormo found that epithelial cells in the glands secrete molecules that provide nutrition to the embryo while epithelial cells in the lumen are key for fetal implantation. Using spatial transcriptomics, their results revealed two new progenitors with unique spatial coordinates that have the ability to differentiate into lumenal and glandular cells.

Single cell analysis lends view on outsmarting vaccine immune tolerance

In a Nature study published in 2021 (5), Systems vaccinology of the BNT162b2 mRNA vaccine in humans, researchers led by Prabhu Arunachalam, PhD, in the Stanford University lab of Bali Pulendran, PhD, used Single Cell Gene Expression + Feature Barcode to demonstrate that two shots of the Pfizer-BioNTech mRNA vaccine led to a subset of myeloid cells with a profile that showed reduced AP-1 accessibility and increased expression of interferon genes. This profile is similar to the one found by another study (6) out of Dr. Pulendran’s lab, where they showed that adding an adjuvant (in this case, AS03, a squalene-based adjuvant containing alpha-tocopherol) to the avian influenza (H5N1) vaccine can and does lead to epigenomic changes in myeloid cells, which in turn lead to an antiviral state and protection against other viruses, such as Dengue virus or Zika virus.

The results obtained by Dr. Arunachalam suggest that this type of vaccine can prime the innate immune system for an even stronger response following a booster shot. Ultimately, it may be possible to design new vaccines—whether those with adjuvants or mRNA-based ones—that provide broader protection from variants or other, unrelated viruses.

To discover more about 10x Genomics single cell and spatial products—and how they’re leading to impactful research in areas as diverse as neuroscience, immunology, and oncology—watch the on-demand recording of Xperience 2022.


  1. Gate D, et al. Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer's disease. Nature 577: 399–404 (2020). doi: 10.1038/s41586-019-1895-7
  2. Gate D, et al. CD4+ T cells contribute to neurodegeneration in Lewy body dementia. Science 374: 868–874 (2021). doi: 10.1126/science.abf7266
  3. De Clercq E. Mozobil® (Plerixafor, AMD3100), 10 years after its approval by the US Food and Drug Administration. Antivir Chem Chemother 27: 2040206619829382 (2019). doi: 10.1177/2040206619829382
  4. Garcia-Alonso L, et al. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nat Genet 53: 1698–1711 (2021). doi: 10.1038/s41588-021-00972-2.
  5. Arunachalam PS, et al. Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature 596: 410–416 (2021). doi: 10.1038/s41586-021-03791-x
  6. Wimmers F, et al. The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. Cell 184: 3915–3935.e21 (2021). doi: 10.1016/j.cell.2021.05.039