The development of the human lymph node

KanCell: dissecting cellular heterogeneity in biological tissues through integrated single-cell and spatial transcriptomics

KanCell is a deep learning model based on Kolmogorov-Arnold networks (KAN) designed to enhance cellular heterogeneity analysis by integrating single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data. ST technologies provide insights into gene expression within tissue context, revealing cellular interactions and microenvironments. To fully leverage this potential, effective computational models are crucial. We evaluate KanCell on both simulated and real datasets from technologies such as STARmap, Slide-seq, Visium, and Spatial Transcriptomics. Our results demonstrate that KanCell outperforms existing methods across metrics like PCC, SSIM, COSSIM, RMSE, JSD, ARS, and ROC, with robust performance under varying cell numbers and background noise. Real-world applications on human lymph nodes, hearts, melanoma, breast cancer, dorsolateral prefrontal cortex, and mouse embryo brains confirmed its reliability. Compared with traditional approaches, KanCell effectively captures non-linear relationships and optimizes computational efficiency through KAN, providing an accurate and efficient tool for ST. By improving data accuracy and resolving cell type composition, KanCell reveals cellular heterogeneity, clarifies disease microenvironments, and identifies therapeutic targets, addressing complex biological challenges.

Early life imprinting of intestinal immune tolerance and tissue homeostasis

Besides its canonical role in protecting the host from pathogens, the immune system plays an arguably equally important role in maintaining tissue homeostasis. Within barrier tissues that interface with the external microenvironment, induction of immune tolerance to innocuous antigens, such as commensal, dietary, and environmental antigens, is key to establishing immune homeostasis. The early postnatal period represents a critical window of opportunity in which parallel development of the tissue, immune cells, and microbiota allows for reciprocal regulation that shapes the long-term immunological tone of the tissue and subsequent risk of immune-mediated diseases. During early infancy, the immune system appears to sacrifice pro-inflammatory functions, prioritizing the establishment of tissue tolerance. In this review, we discuss mechanisms underlying early life windows for intestinal tolerance with a focus on newly identified RORγt+ antigen-presenting cells-Thetis cells-and highlight the role of the intestinal microenvironment in shaping intestinal immune system development and tolerance.

Development of the immune system in the human embryo

The fetal immune system is highly specialized which is to generate both tolerogenic and protective immune responses to tolerate both self- and maternal-antigens. Fetal T cells with pro-inflammatory potential are born in a tolerogenic environment and are tightly controlled by both cell-intrinsic and -extrinsic mechanisms. Fetal B-1 and B-2 B cells involved in innate and adaptive immune responses, respectively, arise in staggered waves of development from distinct progenitors. Innate immune responses are the key to the protection against infection and adaptive immunity creates memory after an initial response to a specific pathogen. This review aims to discuss the recent advances in understanding the development of immune system in fetus. IMPACT: During gestation, essential developmental changes occur to survive the neonates. At early stage, developmental signals and changes may be influenced due to immune deficiencies.

Development of immune organs and functioning in humans and test animals: Implications for immune intervention studies

A healthy immune status is mostly determined during early life stages and many immune-related diseases may find their origin in utero and the first years of life. Therefore, immune health optimization may be most effective during early life. This review is an inventory of immune organ maturation events in relation to developmental timeframes in minipig, rat, mouse and human. It is concluded that time windows of immune organ development in rodents can be translated to human, but minipig reflects the human timeframes better; however the lack of prenatal maternal-fetal immune interaction in minipig may cause less responsiveness to prenatal intervention. It is too early to conclude which immune parameters are most appropriate, because there are not enough comparative immune parameters. Filling these gaps will increase the predictability of results observed in experimental animals, and guide future intervention studies by assessing relevant parameters in the right corresponding developmental time frames.

Human fetal lymphoid tissue-inducer cells are interleukin 17-producing precursors to RORC+ CD127+ natural killer-like cells

The human body contains over 500 individual lymph nodes, yet the biology of their formation is poorly understood. Here we identify human lymphoid tissue-inducer cells (LTi cells) as lineage-negative RORC+ CD127+ cells with the functional ability to interact with mesenchymal cells through lymphotoxin and tumor necrosis factor. Human LTi cells were committed natural killer (NK) cell precursors that produced interleukin 17 (IL-17) and IL-22. In vitro, LTi cells gave rise to RORC+ CD127+ NK cells that retained the ability to produce IL-17 and IL-22. Postnatally, similar populations of LTi cell-like cells and RORC+ CD127+ NK cells were present in tonsils, and both secreted IL-17 and IL-22 but no interferon-gamma. Our data indicate that lymph node organogenesis is controlled by an NK cell precursor population with adaptive immune features and demonstrate a previously unappreciated link between the innate and adaptive immune systems.

Development of human lymph nodes and Peyer's patches

In contrast to our understanding of murine lymphoid organogenesis, detailed knowledge on the mechanisms of human lymph node development is virtually lacking. This is mainly due to the obvious difficulties that accompany research using human fetal organs. In this review we will highlight current knowledge on human lymph node and Peyer's patch development and will temporally align observations made in humans with data available from murine studies. In the final paragraphs we will put this knowledge in the context of human malignancies in which interactions between lymphocytes and stroma, resembling those seen in lymphoid organs, are recapitulated.

Development, maturation and subsequent activation of follicular dendritic cells (FDC): immunohistochemical observation of human fetal and adult lymph nodes

To elucidate the processes involved in development and activation of human follicular dendritic cells (FDC), immunohistochemistry was performed on paraffin sections of fetal lymph nodes (FLN) obtained from archived autopsy material, and of adult reactive lymph nodes (ARLNs) excised for diagnostic purpose, using a panel of antibodies. Our study showed that tiny clusters of CNA.42(+ )KiM4p(+) cells, surrounded by some B-lymphocytes, initially arose in the cortical area of underdeveloped FLN around the 20th gestational week. No co-expression of CD21 and CD35 was found. In the relatively developed FLN of the same gestational age, small eddies of immature FDC, which expressed CD21, CD35, and nerve growth factor receptor (NGFR), as well as CNA.42 and KiM4p, were observed within ill-defined aggregations of B-lymphocytes. As gestation progressed, more B-lymphocytes assembled in a compact manner and formed primary lymphoid follicles containing an extending web of mature FDC, which expressed CNA.42, KiM4p, CD21, CD35, NGFR, and sometimes CD23 and X-11. In well-developed secondary follicles of ARLNs, activated FDC expressed additional molecules such as CD55, CD106, and S100alpha. Our observations identified the processes of phenotypic alteration of human FDC and established practical indicators determining their developmental stage and functional phase.

Transplantation and growth characteristics of human fetal lymph node in immunodeficient mice

OBJECTIVE

The lymph node is an integral component of the immune system and the major site of antigen-dependent lymphocyte proliferation and differentiation. Development of animal models possessing functional primary human lymph nodes will have a significant impact on research in lymphopoiesis and immune response. To date, successful transplantation of primary human lymph nodes in rodents has not yet been reported. This work was undertaken to develop a reliable methodology to engraft primary human fetal lymph nodes in immunodeficient mice.

MATERIALS AND METHODS

Three different sets of parameters, including three different transplantation sites in the mice, two different strains of immunodeficient mice, and two different preconditioning regimens, were evaluated. The growth characteristics of the implanted primary human fetal lymph nodes were examined 3 months after transplantation by histologic, immunocytochemical, and flow cytometric methods.

RESULTS

Transplantation of primary human fetal lymph nodes into subcutaneous pouches in the ears in severe combined immunodeficiency (SCID) mice preconditioned with etoposide reproducibly give rise to >80% engraftment. The engrafted primary human fetal lymph nodes undergo massive growth (>200-fold) and retain the same histology and cellular composition as fresh human fetal lymph nodes from the same donors.

CONCLUSIONS

We report, for the first time, the development of a reliable methodology to successfully engraft human fetal lymph node in SCID mice. The engrafted human lymph nodes are visible and accessible to experimental manipulations. This SCID-hu mouse model with human lymph node should provide a physiologically relevant system to investigate lymphopoiesis, immunologic response, and virus-mediated immunosuppression.

Follicular dendritic cells share a membrane-bound protein with fibroblasts

The expression of a fibroblast antigen (AS02) on a proportion of CD21+ follicular dendritic cells (FDCs) provides evidence in support of their fibroblastic reticular origin. This antigen is expressed on the membrane of tissue fibroblasts but is absent from lymphocytes, macrophages or granulocytes. The distribution of AS02 in conjunction with other FDC markers (DRC-1, RFD3, CD23, IgM, and vitronectin) showed six types of FDCs. AS02 is present in the outer layers of primary and secondary follicles, but gradually decreases and disappears in the centre of germinal centres. In contrast, there is a progressive up-regulation of the other FDC markers. AS02 is re-expressed in involuting FDCs. Intermediate forms from fibroblastic to dendritic appearance are also apparent and occasionally FDC processes contain collagen type I and IV fibres, a characteristic feature of fibroblasts. In pathological follicles the normal differentiation pattern is disrupted, with persistence of the fibroblast marker, possibly due to altered interactions between FDCs and disrupted lymphocytic patterns. These findings provide new evidence for a local differentiation pathway of fibroblasts to mature FDCs.

Stromal cell organisation in the mouse lymph node. A light and electron microscopic investigation using the zinc iodide-osmium technique

The organisation of the stromal cell compartment in the mouse lymph node was studied by light and electron microscopy after tissue impregnation by the zinc iodide-osmium (ZIO) method. Fibroblastic reticular cells (FRCs) represented the main stromal cell population. These cells were located both in the cortical region and in the medulla and exhibited various configurations. In the cortex, FRCs were fusiform in shape and came into close proximity with the floor of the subcapsular sinus. In the medulla, the FRCs were shaped like irregular dendritic cells which formed a complex 3-dimensional network. The FRCs surrounded vascular structures such as capillaries and/or high endothelial venules; in these instances they were organised in a discontinuous sheath-like fashion around the vessel wall. By light and electron microscopy, FRCs have been observed to come in close spatial relationship with a number of cells in the lymph node, including sinus endothelial cells, the endothelium of high endothelial venules and capillaries, various types of lymphocytes, follicular dendritic cells and interdigitating cells. These microanatomical features are consistent with the proposal that FRCs may be involved in the communicative networks between the different lymph node compartments. In particular, the FRCs may be involved in the transport of molecules from the sinus compartment to the high endothelial venules or to the distinct cell populations in the lymphoid parenchyma.

Development and cell phenotypes in primary follicles of foetal sheep lymph nodes

Lymph nodes from sheep foetuses and postnatal lambs were examined to determine the participation of different leucocyte populations in primary follicle formation, with special emphasis on the emergence and subsequent development of follicular dendritic cells during late gestation and early postnatal life. A series of immune and enzyme histochemical markers was used. The first 5'-nucleotidase-positive primary follicles were found at 80 days gestational age (gestation in sheep is 150 days) in superficial cervical lymph nodes. In the last month of gestation the primary follicles possessed follicular dendritic cells, macrophages, dendritic cells, and CD5-positive lymphocytes, in addition to IgM-positive cells. Follicular dendritic cells in primary follicles were found to be ultrastructurally immature. These follicular dendritic cells were characterised by a few, course surface projections and many ribosomes attached to the endoplasmic reticulum. A final differentiation to mature follicular dendritic cells was coincident with the postnatal germinal centre reaction. Computer-assisted morphometric analysis demonstrated that the size of 5'-nucleotidase-positive primary follicles in the distal jejunal lymph node, but not in the superficial cervical lymph node, increased significantly during late gestation. It was concluded that stromal cells in primary follicles of foetal sheep lymph nodes were a continuously developing population but that ultrastructural maturity was only achieved in the germinal centres of postnatal lambs.

Ontogeny of reticular cells in the ileal Peyer's patch of sheep and goats

The ontogeny of reticular cells in the ileal Peyer's patch of sheep from 70 days gestational age was studied by light and electron microscopy and by enzyme histochemistry. Small to medium-sized lymphocytes were seen in the lamina propria at 97 days, when the stroma was essentially still mesenchymal. By 110 days, the stromal cells in the dome/follicle primordia had differentiated into reticular fibroblasts, whose processes and fibers were seen to surround groups of lymphocytes. With advancing age the number and size of primordia increased, and proliferation was obvious among the lymphocytes. Processes of reticular cells increased in number and penetrated between individual lymphocytes of the groups. Coarser desmosome-like contacts were seen between the reticular cells from 115 days onwards. A central light area in the follicle was apparent from 130 days onwards. The fine structure of the stromal cells in this light follicle center developed towards but never became similar to that of follicular dendritic cells in a typical germinal center. The fine interdigitating end branches of the stromal cells were less numerous, and the dense homogeneous material present in between the end branches was not observed in the ileal Peyer's patch follicle. Instead, small particles and vesicles were seen between the various cell types of the light center and were not restricted to the intercellular spaces between the stromal cells. In the dark peripheral zone of the follicle, the stromal cells retained more immature features. The follicle became bordered by a capsule at an early stage. This capsule was formed by multiple layers of flattened fibroblasts separated by small amounts of intercellular material only. The alkaline phosphatase, Mg(2+)-dependent adenosine triphosphatase and 5' nucleotidase reactivities of the follicular dendritic cells in the ileal Peyer's patch were similar to those of early prenatal primary follicles of sheep lymph nodes. This study indicates that the stromal cells of the ileal Peyer's patch are mesenchymal in nature and different from those of germinal centers and the epithelial stromal cells of bursa Fabricii of birds.

The ontogeny of human lymphocyte recirculation: high endothelial cell antigen (HECA-452) and CD44 homing receptor expression in the development of the immune system

In the present report we have studied the expression of a lymphocyte homing receptor, the CD44 antigen, and of HECA-452, a high endothelial-specific antigen, during the development of the human immune system. We found that prothymocyte immigrants of the thymus already expressed the CD44 antigen. Similarly, the first peripheral T lymphocytes in fetal lymph nodes, tonsils and gut-associated lymphoid tissue were also CD44+. Cortical thymocytes and germinal center cells were CD44-. CD44 antigen expression was, thus, not limited to mature recirculating lymphocytes. This suggests that CD44 may not only be involved in recirculation of mature lymphocytes but also in the migration of prothymocytes to their site of maturation, i.e. the thymus. High endothelial venules (HEV) were not demonstrable at the early onset of lymphocyte immigration into the developing lymphoid organs. However, when large-scale influx of lymphocytes occurred, it paralleled HEV development. HECA-452 antigen expression preceded the morphological transformation of endothelium into a HEV phenotype. Expression of this antigen therefore, independently reflected the specialized nature of high endothelium. In a patient with complete DiGeorge's syndrome normal HEV developed, indicating that the presence of T lymphocytes is not a requirement for HEV development. Interestingly, a subpopulation of venules located in the thymic medulla near the cortico-medullary junction expressed the HECA-452 antigen. These vessels, which had flat or intermediately high endothelium, are probably involved in lymphocyte migration to the thymus.

Lissencephaly, abnormal lymph nodes, and T-cell deficiency in one patient

We report on a child with lissencephaly type I, abnormal lymph nodes, and immunodeficiency, associated with recurrent infections, autoimmune disease, spastic tetraplegia, and psychomotor retardation. Diagnostic measures included cranial computer tomography (CT) and magnetic resonance imaging (MRI) scanning, several in vivo and in vitro immunological tests, and histology of skin, lymph nodes, and liver including electron microscopy and immunohistology. Despite medical supervision, the child died at age 4 years. A common pathogenetic mechanism of defective migration of neurons and the dysmaturation of lymph nodes is most probable. The T-cell deficiency may represent a common defect of the development of both neuronal and lymphatic tissue, as the six-layered cerebral cortex and the B-cell areas in lymph nodes develop at about the same gestational age. A common defect could also be assumed involving genetically determined cell surface proteins.

Terminal deoxynucleotidyl transferase-positive B cell precursors in fetal lymph nodes and extrahemopoietic tissues

Terminal deoxynucleotidyl transferase (TdT)-positive B cell precursors populate fetal lymph nodes (LN) of mid-term (16th-22th week) fetuses. These cells have a B cell phenotype (HLA-DR, CD45R, CD22, mu) and lack mature differentiation antigens (CD1c, CD20, L26). TdT+ cells are also present in the extranodal mesenteric mesenchyme, pancreas and LN primordia. Extranodal TdT+ cells are found among proliferating (i.e. Ki-67+) B cells and lack leukocyte function-associated antigen (LFA-1) and HLA-DQ; these latter molecules are acquired by nodal TdT+ elements. Adult LN, adult and fetal spleen contain less TdT+ cells than fetal LN. The fetal LN contains the full range of the B cell differentiation compartment, from the TdT+ precursor cell to the mature B lymphocyte.

Immunohistological analysis of human fetal lymph nodes

A panel of monoclonal antibodies directed against various lymphoid and non-lymphoid cell subsets was used to study the lymph nodes of human fetuses of 16-40 weeks. B cells were of intermediate size and were present at all ages in primitive follicles and in the outer cortex. The fetal B-cell immunophenotype is indicative of an intermediate stage of development, just preceding the differentiation to mature B cell. Forty to sixty per cent Leu1+ B cells were observed in the follicles until the end of the second trimester. At all stages, T cells showed an immunophenotype similar to type III thymocytes, different from adult peripheral T cells, with a marked predominance of CD4+ T cells. Leu7+ NK cells were generally absent. OKIa+ interdigitating reticulum cells were present in T-cell areas. Some axillary lymph nodes showed strongly CD1+ dendritic cells, probably Langerhans' cells. Macrophages and granulocytes were present in varying numbers. Altogether, our results indicate that fetal lymph nodes are quite well differentiated at an early fetal age, although T and B cells do not (yet) show adult immunophenotypes. The expression of the CD38 antigen may be a main marker related to the immaturity of fetal T and B cells.

Immuno-architecture of human fetal lymphoid tissues

Spleen, thymus and lymph node of human fetuses from the 12th to the 38rd week (spleen from 9 weeks) were investigated in an immunohistological study on B5-fixed paraffin embedded tissues, employing a panel of recently developed monoclonal antibodies, reactive with antigens resistant against fixation and paraffin embedment. The monoclonal antibodies included were MT1, MT2, MB1, MB2, MB3, LN1, LN2, LN3, LeuM1, Leu7, VIE-G4, together with polyclonal antibodies reactive with immunoglobulin heavy and light chains, and with lysozyme and S100-protein. The preservation of morphological detail together with immunoperoxidase staining of cellular subsets, allowed an accurate determination of the ontogenic development of the different cell types in situ, in relation to their micro-environment. The use of paraffin tissue reactive (monoclonal) antibodies gives an extra dimension to the study of fetal lymphoid tissues. This is of particular advantage in studies on very fragile tissues as in early embryonal and fetal ontogeny.

Sarcoma arising from interdigitating reticulum cells: report of a case, studied with light and electron microscopy, and enzyme- and immunohistochemistry

The morphological, enzyme- and immunohistochemical features of a sarcoma arising from interdigitating reticulum cells (IDRC) are presented. These cells are normal constituents of the T-dependent region of lymphoid organs, and their function is largely unresolved. The immunohistochemical findings in the present case indicate that neoplastic IDRC are morphologically and phenotypically similar to normal IDRC in lymphoid organs. Functionally however, neoplastic IDRC more closely resemble IDRC in the fetal lymph node and in the thymus, where they are thought to play a role in the final differentiation of immature thymocytes into mature peripheral T-lymphocytes.

The development of the human spleen. Ultrastructural studies in fetuses from the 14th to 24th week of gestation

Splenic tissue of human fetuses from the 14th to the 24th week of gestation (menstrual age) were investigated by light- and electron microscopy to describe the development of the red and white pulp in close relationship to the differentiation of the vascular tree. Special interest is focussed on the differentiation of the T-cell- and the B-cell regions and their specific stationary cells. The preliminary stage, here called the "primary vascular reticulum," lasts up to the 14th gestational week (gw). Numerous erythrocytes, normoblasts and macrophages are seen among a network of mesenchymal cells and argyrophilic fibers. Hematopoiesis, especially erythropoiesis, can be recognized. The characteristic organ structure becomes established during the subsequent transformation stage of the fetal spleen, beginning with the 15th gw. Splenic lobules begin to form during the 15th to 17th gw. They consist of a central artery, surrounded by a sheath of lightly stained stationary cells which resemble myofibroblasts. At the periphery of these lobules the red pulp forms. Initially mobile cells are distributed throughout the reticulum. Soon they begin to accumulate in the venous sinuses, which develop from lacunae among the reticular network and come into contact with the venous system. The endothelial wall of these sinuses remains discontinuous, confirming the theory of the "open" vascularization of the spleen. The development of the larger veins is correlated with the differentiation of the splenic trabeculae. The development of the white pulp is correlated with the stage of lymphoid colonization within the spleen, beginning around the 18th gw. An accumulation of lymphocytes around the central arteries can be recognized during the 19th and 20th gw. These lymphoid cells show morphological and immunohistochemical characteristics of T-precursor cells. Within the now assembling periarterial lymphoid sheath (PALS) a few precursors of interdigitating cells (IDC) are recognizable, giving evidence for the differentiation of the T-cell region. Around the 23rd gw the assemblage of primary follicles is discernible at the periphery of the PALS. Precursors of the follicular dendritic reticulum cell (FDRC), the specific stationary cell of the B-cell region, have been recognized. This observation leads to the conclusion that the small primary follicles represent the beginning formation of the B-cell region. The significance of the vascular system for the differentiation of the specific splenic organization is discussed.

Histiocytic and dendritic reticulum cells in follicular structures of follicular lymphoma and reactive hyperplasia. A quantitative electron microscopical analysis

Histiocytic reticulum cells (HRC) and dendritic reticulum cells (DRC) are integral parts of germinal centres. These cell types are also present in follicles of follicular lymphomas, the neoplastic analogues of physiological germinal centres. In this study the distribution and ultrastructural appearances of HRC and DRC present in normal germinal centres and in neoplastic follicles were established by means of morphometric methods. The number of HRC was significantly lower in malignant follicles than in their reactive counterparts. Quantitative analysis of the cytoplasm and phagolysosomes suggest that HRC are smaller and that their activity is lower in malignant follicles. DRC were present in smaller numbers in these structures, as measured by nuclear counts and their relative volume within the follicles. The ultrastructural features indicate that DRC in follicular lymphoma are functionally less active than in reactive lymph nodes. The possibility that differences between the reticulum cells from reactive and neoplastic follicles may be related to the absence of an immune reaction in malignant follicular lymphoma is discussed. The frequency and appearance of HRC and DRC are suitable as additional parameters to differentiate reactive secondary germinal centres from their malignant analogues.