Mark Kowarsky

Noninvasive monitoring of infection and rejection after lung transplantation.

Significance Over 3,500 patients receive life-saving lung transplants every year. Nonetheless, complications due to infection and rejection occur frequently and undermine the long-term benefits of lung transplantation. Although clinicians strive to carefully monitor patients, diagnostic options are often limited. Rejection monitoring currently relies on invasive tissue biopsies, and tests of infection are predominately limited to testing one pathogen at a time. This manuscript describes a noninvasive assay based on sequencing of circulating cell-free DNA that simultaneously enables diagnosis of rejection and broad screening of infections. The survival rate following lung transplantation is among the lowest of all solid-organ transplants, and current diagnostic tests often fail to distinguish between infection and rejection, the two primary posttransplant clinical complications. We describe a diagnostic assay that simultaneously monitors for rejection and infection in lung transplant recipients by sequencing of cell-free DNA (cfDNA) in plasma. We determined that the levels of donor-derived cfDNA directly correlate with the results of invasive tests of rejection (area under the curve 0.9). We also analyzed the nonhuman cfDNA as a hypothesis-free approach to test for infections. Cytomegalovirus is most frequently assayed clinically, and the levels of CMV-derived sequences in cfDNA are consistent with clinical results. We furthermore show that hypothesis-free monitoring for pathogens using cfDNA reveals undiagnosed cases of infection, and that certain infectious pathogens such as human herpesvirus (HHV) 6, HHV-7, and adenovirus, which are not often tested clinically, occur with high frequency in this cohort.

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

Glioblastoma (GBM) is the most common primary brain cancer in adults and is notoriously difficult to treat because of its diffuse nature. We performed single-cell RNA sequencing (RNA-seq) on 3,589 cells in a cohort of four patients. We obtained cells from the tumor core as well as surrounding peripheral tissue. Our analysis revealed cellular variation in the tumors genome and transcriptome. We were also able to identify infiltrating neoplastic cells in regions peripheral to the core lesions. Despite the existence of significant heterogeneity among neoplastic cells, we found that infiltrating GBM cells share a consistent gene signature between patients, suggesting a common mechanism of infiltration. Additionally, in investigating the immunological response to the tumors, we found transcriptionally distinct myeloid cell populations residing in the tumor core and the surrounding peritumoral space. Our data provide a detailed dissection of GBM cell types, revealing an abundance of information about tumor formation and migration.

Developmental cell death programs license cytotoxic cells to eliminate histocompatible partners

Significance The colonial tunicate, Botryllus schlosseri, undergoes natural self–nonself recognition that results in formation of a chimera. Following fusion, one chimeric partner is often eliminated in a process of allogeneic resorption, allowing for study of the induction and loss of tolerance. We provide evidence that elimination of one partner in a chimera is an immune cell-based rejection and that the principal cell type to mediate partner elimination is a cytotoxic morula cell (MC). Proinflammatory, blastogenic “takeover” programs render MCs cytolytic and, in collaboration with activated phagocytes, eradicate chimeric partners. These findings identify a conserved strategy for histocompatible elimination through the integrated function of both phagocytic programs and licensing of cytotoxic cells. The coordination of both dimensions of innate immune recognition elicits efficient elimination of chimeric partners. In a primitive chordate model of natural chimerism, one chimeric partner is often eliminated in a process of allogeneic resorption. Here, we identify the cellular framework underlying loss of tolerance to one partner within a natural Botryllus schlosseri chimera. We show that the principal cell type mediating chimeric partner elimination is a cytotoxic morula cell (MC). Proinflammatory, developmental cell death programs render MCs cytotoxic and, in collaboration with activated phagocytes, eliminate chimeric partners during the “takeover” phase of blastogenic development. Among these genes, the proinflammatory cytokine IL-17 enhances cytotoxicity in allorecognition assays. Cellular transfer of FACS-purified MCs from allogeneic donors into recipients shows that the resorption response can be adoptively acquired. Transfer of 1 × 105 allogeneic MCs eliminated 33 of 78 (42%) recipient primary buds and 20 of 76 (20.5%) adult parental adult organisms (zooids) by 14 d whereas transfer of allogeneic cell populations lacking MCs had only minimal effects on recipient colonies. Furthermore, reactivity of transferred cells coincided with the onset of developmental-regulated cell death programs and disproportionately affected developing tissues within a chimera. Among chimeric partner “losers,” severe developmental defects were observed in asexually propagating tissues, reflecting a pathologic switch in gene expression in developmental programs. These studies provide evidence that elimination of one partner in a chimera is an immune cell-based rejection that operates within histocompatible pairs and that maximal allogeneic responses involve the coordination of both phagocytic programs and the “arming” of cytotoxic cells.

Non-Abelian geometric phase in the diamond nitrogen-vacancy center

This paper introduces a theoretical framework for understanding the accumulation of non-Abelian geometric phases in rotating nitrogen-vacancy centers in diamond. Specifically, we consider how degenerate states can be achieved and demonstrate that the resulting geometric phase for multiple paths is non-Abelian. We find that the non-Abelian nature of the phase is robust to fluctuations in the path and magnetic field. In contrast to previous studies of the accumulation of Abelian geometric phases for nitrogen-vacancy centers under rotation we find that the limiting time scale is

Humans are colonized by many uncharacterized and highly divergent microbes

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Simultaneously Monitoring Immune Response and Microbial Infections during Pregnancy through Plasma cfRNA Sequencing

. As such a non-Abelian geometric phase accumulation in nitrogen-vacancy centers has potential advantages for applications as gyroscopes.

Urochordata: Botryllus – Natural Chimerism and Tolerance Induction in a Colonial Chordate

Blood circulates throughout the entire body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analysing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated.

Evolutionary Origin of the Mammalian Hematopoietic System Found in a Colonial Chordate

BACKGROUND Plasma cell-free RNA (cfRNA) encompasses a broad spectrum of RNA species that can be derived from both human cells and microbes. Because cfRNA is fragmented and of low concentration, it has been challenging to profile its transcriptome using standard RNA-seq methods. METHODS We assessed several recently developed RNA-seq methods on cfRNA samples. We then analyzed the dynamic changes of both the human transcriptome and the microbiome of plasma during pregnancy from 60 women. RESULTS cfRNA reflects a well-orchestrated immune modulation during pregnancy: an up-regulation of antiinflammatory genes and an increased abundance of antimicrobial genes. We observed that the plasma microbiome remained relatively stable during pregnancy. The bacteria Ureaplasma shows an increased prevalence and increased abundance at postpartum, which is likely to be associated with postpartum infection. We demonstrated that cfRNA-seq can be used to monitor viral infections. We detected a number of human pathogens in our patients, including an undiagnosed patient with a high load of human parvovirus B19 virus (B19V), which is known to be a potential cause of complications in pregnancy. CONCLUSIONS Plasma cfRNA-seq demonstrates the potential to simultaneously monitor immune response and microbial infections during pregnancy.

CELL-FREE NUCLEIC ACIDS FOR THE ANALYSIS OF THE HUMAN MICROBIOME AND COMPONENTS THEREOF

Chimerism is defined as the coexistence of two or more genomes of separate origin within an individual. In placental mammals such as humans, natural chimerism develops during pregnancy between a mother and fetus and has an important role in the induction of fetal tolerance to maternal tissues. Natural chimerism between kin also occurs in colonial ascidians, the closest extant ancestors of chordates. In the ascidian, Botryllus schlosseri, some colonies fuse to create lifelong chimeric entities of two allogeneic genomes. The decision to fuse in B. schlosseri is governed by a polymorphic histocompatibility gene called the Botryllus histocompatibility factor (BHF). Colonies that share at least one BHF allele fuse upon contact, whereas colonies without any BHF alleles in common ultimately reject. Following vasculature fusion, stem cells from each histocompatible B. schlosseri colony compete to overtake germline or somatic lineages. Stem cell competition may lead to elimination of the other colony’s genome, or it may produce a chimeric colony with mixed genotypes. In this way, chimerism in B. schlosseri represents a nexus between stem cell competition, genome parasitism, and allorecognition. Here we review studies conducted over six decades that led to the discoveries of the nature of the cells that mediate chimerism in colonial ascidians and the gene that controls it.

Non-Invasive Monitoring of Infection and Rejection After Lung Transplantation

Hematopoiesis is an essential process that evolved in multicellular animals. At the heart of this process are hematopoietic stem cells (HSCs), which are multipotent, self-renewing and generate the entire repertoire of blood and immune cells throughout life. Here we studied the hematopoietic system of Botryllus schlosseri, a colonial tunicate that has vasculature, circulating blood cells, and interesting characteristics of stem cell biology and immunity. Self-recognition between genetically compatible B. schlosseri colonies leads to the formation of natural parabionts with shared circulation, whereas incompatible colonies reject each other. Using flow-cytometry, whole-transcriptome sequencing of defined cell populations, and diverse functional assays, we identified HSCs, progenitors, immune-effector cells, the HSC niche, and demonstrated that self-recognition inhibits cytotoxic reaction. Our study implies that the HSC and myeloid lineages emerged in a common ancestor of tunicates and vertebrates and suggests that hematopoietic bone marrow and the B. schlosseri endostyle niche evolved from the same origin.