Single-cell lineage tracing approaches in hematology research: technical considerations

The coordinated differentiation of hematopoietic stem and progenitor cells (HSPCs) into the various mature blood cell types is responsible for sustaining blood and immune system homeostasis. The cell fate decisions underlying this important biological process are made at the level of single cells. Methods to trace the fate of single cells are therefore essential for understanding hematopoietic system activity in health and disease and have had a major impact on how we understand and represent hematopoiesis. Here, we discuss the basic methodologies and technical considerations for three important clonal assays: single-cell transplantation, lentiviral barcoding, and Sleeping Beauty barcoding. This perspective is a synthesis of presentations and discussions from the 2019 International Society for Experimental Hematology (ISEH) Annual Meeting New Investigator Technology Session and the 2019 ISEH Winter Webinar.

Tomato TFT1 is required for PAMP-triggered immunity and mutations that prevent T3S effector XopN from binding to TFT1 attenuate Xanthomonas virulence

XopN is a type III effector protein from Xanthomonas campestris pathovar vesicatoria that suppresses PAMP-triggered immunity (PTI) in tomato. Previous work reported that XopN interacts with the tomato 14-3-3 isoform TFT1; however, TFT1's role in PTI and/or XopN virulence was not determined. Here we show that TFT1 functions in PTI and is a XopN virulence target. Virus-induced gene silencing of TFT1 mRNA in tomato leaves resulted in increased growth of Xcv ΔxopN and Xcv ΔhrpF demonstrating that TFT1 is required to inhibit Xcv multiplication. TFT1 expression was required for Xcv-induced accumulation of PTI5, GRAS4, WRKY28, and LRR22 mRNAs, four PTI marker genes in tomato. Deletion analysis revealed that the XopN C-terminal domain (amino acids 344–733) is sufficient to bind TFT1. Removal of amino acids 605–733 disrupts XopN binding to TFT1 in plant extracts and inhibits XopN-dependent virulence in tomato, demonstrating that these residues are necessary for the XopN/TFT1 interaction. Phos-tag gel analysis and mass spectrometry showed that XopN is phosphorylated in plant extracts at serine 688 in a putative 14-3-3 recognition motif. Mutation of S688 reduced XopN's phosphorylation state but was not sufficient to inhibit binding to TFT1 or reduce XopN virulence. Mutation of S688 and two leucines (L64,L65) in XopN, however, eliminated XopN binding to TFT1 in plant extracts and XopN virulence. L64 and L65 are required for XopN to bind TARK1, a tomato atypical receptor kinase required for PTI. This suggested that TFT1 binding to XopN's C-terminal domain might be stabilized via TARK1/XopN interaction. Pull-down and BiFC analyses show that XopN promotes TARK1/TFT1 complex formation in vitro and in planta by functioning as a molecular scaffold. This is the first report showing that a type III effector targets a host 14-3-3 involved in PTI to promote bacterial pathogenesis.

Bacterial pathogens of plants and animals employ the type III secretion system to secrete and translocate effector proteins into host cells to suppress defense responses. Biochemical analyses have revealed that several effector proteins mimic host enzyme activities to directly interfere with pathogen perception, defense signal transduction, and/or secretion of antimicrobial compounds. The XopN effector from Xanthomonas campestris pathovar vesicatoria, the causal agent of bacterial spot on tomato and pepper plants, suppresses PAMP-triggered immunity (PTI) but structural modeling predicts it encodes a unique scaffolding-like protein with no obvious enzymatic fold. We postulate that XopN mediates its virulence function by associating with host proteins regulating defense. XopN was previously shown to physically interact with the tomato 14-3-3 protein TFT1 in planta. The significance of TFT1 in plant immune signaling and the relevance of the XopN/TFT1 interaction were not determined. Here we show that TFT1 is a positive regulator of PTI in tomato required to inhibit Xcv growth. Moreover, we provide evidence that TFT1 is a bona fide target of XopN because mutations that disrupt XopN/TFT1 binding also eliminate XopN-dependent virulence in tomato. This is the first example of a bacterial effector targeting a 14-3-3 associated with host immunity.

Novel approach for the development of new antibodies directed against transposase-derived proteins encoded by human neogenes

Molecular domestication of several DNA transposons has occurred during the evolution of the primate lineage, and has led to the emergence of at least 42 new genes known as neogenes. Because these genes are derived from transposons, they encode proteins that are related to certain recombinases, known as transposases. Consequently, they may make an important contribution to the genetic instability of some human cells. In order to investigate the role of these neogenes, we need to be able to study their expression as proteins, for example in tumours, which often provide good models of genetic instability. In order to perform such studies, polyclonal antibodies directed against the proteins expressed by neogenes are obtained using a recently developed new method of Nanospheres/DNA immunisation in laboratory mammals. In this chapter, we describe a fully integrated process of producing antibodies that consists of a series of steps starting with the preparation and synthetic formulation of plasmids encoding neogenes, and culminating in the final production and confirmation of the quality of these polyclonal antibodies.

Redirecting specificity of T-cell populations for CD19 using the Sleeping Beauty system

Genetic modification of clinical-grade T cells is undertaken to augment function, including redirecting specificity for desired antigen. We and others have introduced a chimeric antigen receptor (CAR) to enable T cells to recognize lineage-specific tumor antigen, such as CD19, and early-phase human trials are currently assessing safety and feasibility. However, a significant barrier to next-generation clinical studies is developing a suitable CAR expression vector capable of genetically modifying a broad population of T cells. Transduction of T cells is relatively efficient but it requires specialized manufacture of expensive clinical grade recombinant virus. Electrotransfer of naked DNA plasmid offers a cost-effective alternative approach, but the inefficiency of transgene integration mandates ex vivo selection under cytocidal concentrations of drug to enforce expression of selection genes to achieve clinically meaningful numbers of CAR(+) T cells. We report a new approach to efficiently generating T cells with redirected specificity, introducing DNA plasmids from the Sleeping Beauty transposon/transposase system to directly express a CD19-specific CAR in memory and effector T cells without drug selection. When coupled with numerical expansion on CD19(+) artificial antigen-presenting cells, this gene transfer method results in rapid outgrowth of CD4(+) and CD8(+) T cells expressing CAR to redirect specificity for CD19(+) tumor cells.

New concepts in the regulation of an ancient reaction: transposition by RAG1/RAG2

The lymphoid-specific factors, recombination-activating gene 1 (RAG1) and RAG2, initiate V(D)J recombination by introducing DNA double-stand breaks at specific sites in the genome. In addition to this critical endonuclease activity, the RAG proteins catalyze other chemical reactions that can affect the outcome of V(D)J recombination, one of which is transposition. While the transposition activity of the RAG proteins is thought to have been critical for the evolution of modern antigen-receptor loci, it has also been proposed to contribute to chromosomal translocations and lymphoid malignancy. A major challenge has been to determine how the transposition activity of the RAG proteins is regulated in vivo. Although a variety of mechanisms have been suggested by recent studies, a clear resolution of this issue remains elusive.

Oral administration of hapten inhibits in vivo induction of specific cytotoxic CD8+ T cells mediating tissue inflammation: a role for regulatory CD4+ T cells

We investigated whether oral tolerance could block the development of an inflammatory response mediated by CD8+ T cells, using a mouse model of oral tolerance of contact sensitivity (CS) to the hapten 2, 4-dinitrofluorobenzene (DNFB). In this system, the skin inflammatory response is initiated by hapten-specific class I-restricted cytotoxic CD8+ T (CTL) cells, independently of CD4 help. Oral delivery of DNFB before skin sensitization blocked the CS response by impairing the development of DNFB-specific CD8+ effector T cells in secondary lymphoid organs. This was shown by complete inhibition of DNFB-specific CTL and proliferative responses of CD8+ T cells, lack of specific IFN-gamma-producing CD8+ T cells, and inability of CD8+ T cells to transfer CS in RAG20/0 mice. RT-PCR and immunohistochemical analysis confirmed that recruitment of CD8+ effectors of CS in the skin at the site of hapten challenge was impaired in orally tolerized mice. Sequential anti-CD4 Ab treatment showed that only depletion of CD4+ T cells during the afferent phase of CS abrogated oral tolerance induction by restoring high numbers of specific CD8+ effectors in lymphoid organs, whereas CD4 depletion during the efferent phase of CS did not affect oral tolerance. These data demonstrate that a single intragastric administration of hapten can block in vivo induction of DNFB-specific CD8+ CTL responsible for tissue inflammation and that a subset of regulatory CD4+ T cells mediate oral tolerance by inhibiting expansion of specific CD8+ effectors in lymph nodes.

Effect of deregulated IL-7 transgene expression on B lymphocyte development in mice expressing mutated pre-B cell receptors

Deregulated overexpression of IL-7 under the control of the promoter of the Ealpha gene of MHC class II in IL-7-transgenic mice changes B cell development in wild-type mice and in mutants which limit B cell development at various cellular stages. While the introduction of deregulated IL-7 production does not change the size of the pro-B and pre-B I compartments in the bone marrow of wild-type and lambda5-/- mice, it increases these compartments 2.5- to fivefold in mice which cannot make immature and mature B cells, i. e. in RAG-2-/-, tmmuH-/-, and RAG-2-/- mice expressing a transgenic muH chain. Excessive IL-7 production also increases four- to fivefold the pre-B II compartment in all those mouse strains where it can be formed (i. e. in wild-type, lambda5-/- and muH chain-transgenic RAG-2-/- mice), while no pre-B- II-like cells appear in excessively IL-7-stimulated bone marrow of mice devoid of pre-B II cells (i. e. in tmmuH-/- and RAG-2-/- mice). In the spleen of all IL-7-transgenic mice significant numbers of both pro-B and pre-B I cells are detectable and increased numbers of pre-B II and immature B cells appear in the spleen of mouse strains which are capable of making them. The capacity of the spleen to accommodate expanded numbers of these B-lineage cells as well as mature B cells is much larger than that of the bone marrow of the IL-7-transgenic mice probably because the bone limits cellular expansion and provokes spillover into the peripheral lymphoid organs.