Aspects of lymphocyte developmental biology

Computational epitope-based vaccine design with bioinformatics approach; a review

The significance of vaccine development has gained heightened importance in light of the COVID-19 pandemic. In such critical circumstances, global citizens anticipate researchers in this field to swiftly identify a vaccine candidate to combat the pandemic's root cause. It is widely recognized that the vaccine design process is traditionally both time-consuming and costly. However, a specialized subfield within bioinformatics, known as "multi-epitope vaccine design" or "reverse vaccinology," has significantly decreased the time and costs of the vaccine design process. The methodology reverses itself in this subfield and finds a potential vaccine candidate by analyzing the pathogen's genome. Leveraging the tools available in this domain, we strive to pinpoint the most suitable antigen for crafting a vaccine against our target. Once the optimal antigen is identified, the next step involves uncovering epitopes within this antigen. The immune system recognizes particular areas of an antigen as epitopes. By characterizing these crucial segments, we gain the opportunity to design a vaccine centered around these epitopes. Subsequently, after identifying and assembling the vital epitopes with the assistance of linkers and adjuvants, our vaccine candidate can be formulated. Finally, employing computational techniques, we can thoroughly evaluate the designed vaccine. This review article comprehensively covers the entire multi-epitope vaccine development process, starting from obtaining the pathogen's genome to identifying the relevant vaccine candidate and concluding with an evaluation. Furthermore, we will delve into the essential tools needed at each stage, comparing and introducing them.

Insight into the long-term impact of birth weight on intestinal development, microbial settlement, and the metabolism of weaned piglets

Infant mortality of low birth body weight (LBBW) piglets can reach 10% and is mainly due to gut and immune system immaturity which can lead to a higher risk in the long term. This study aimed to assess the impact of birth body weight (BBW) on piglet metabolism, gut status, and microbial profile from weaning to 21 d postweaning. At birth, 32 piglets were selected for their BBW and inserted into the normal BBW (NBBW:1.38 ± 0.09 g) or the LBBW (0.92 ± 0.07 g) group. The piglets were weighed weekly from weaning (d0) to d21. At d9 and d21, 8 piglets/group were slaughtered to obtain the distal jejunum for morphology, immunohistochemistry, and gene expression analysis, colon content for microbiota and short-chain fatty acid (SCFA) analysis, and intestinal content for pH measurement. Blood was collected for metabolomic, haptoglobin (Hp), and reactive oxygen metabolite (ROM) analysis. The LBBW group had a lower body weight (BW) throughout the study (P < 0.01), a lower average daily gain from d9-d21 (P = 0.002), and lower feed intake (P = 0.02). The LBBW piglets had lower Hp at d9 (P = 0.03), higher ROMs at d21 (P = 0.06), and a net alteration of the amino acid (AA) metabolism at d9 and d21. A higher expression of NFKB2 was observed in the LBBW piglets at d9 (P = 0.003) and d21 (P < 0.001). MYD88 expression was enhanced in NBBW piglets at d9 (P < 0.001). The LBBW piglets had a lower villus height, absorptive mucosal surface (P = 0.01), and villus height:crypt depth ratio (P = 0.02), and a greater number of T-lymphocytes in both the epithelium and the crypts (P < 0.001) at d21. At d21, the LBBW piglets had higher lactic acid, acetate, butyrate, and valerate, and also higher SCFA in the colon (P < 0.05). The LBBW piglets had a higher Shannon index (P = 0.01) at d9 and a higher abundance of SCFA-fermenting bacteria. In conclusion, the present study confirmed that LBBW could impact the gut mucosal structure, immunity, and inflammatory and oxidative status, leading to an altered AA metabolism, and delaying the recovery from weaning.

The development of T cells from stem cells in mice and humans

T cells develop from hematopoietic stem cells in the specialized microenvironment of the thymus. The main transcriptional players of T-cell differentiation such as Notch, Tcf-1, Gata3 and Bcl11b have been identified, but their role and regulation are not yet completely understood. In humans, functional experiments on T-cell development have traditionally been rather difficult to perform, but novel in vitro culture systems and in vivo xenograft models have allowed detailed studies on human T-cell development. Recent work has allowed the use of human severe combined immunodeficiency stem cells to unravel developmental checkpoints for human thymocyte development.

Thy28 protects against anti-CD3-mediated thymic cell death in vivo

Apoptotic cell death plays a pivotal role in the development and/or maintenance of several tissues including thymus. Deregulated thymic cell death is associated with autoimmune diseases including experimental autoimmune encephalomyelitis (EAE), a prototype murine model for analysis of human multiple sclerosis. Because Thy28 expression is modulated during thymocyte development, we tested whether Thy28 affects induction of EAE as effectively as antigen-induced thymocyte deletion using Thy28 transgenic (TG) mice. Thy28 TG mice showed partial resistance to anti-CD3 monoclonal antibody (mAb)-induced thymic cell death in vivo, as assessed by annexin V-expression and loss of mitochondrial membrane potential. The resistance to anti-CD3 mAb-induced cell death in Thy28 TG mice appeared to correlate with a decreased c-Jun N-terminal kinase phosphorylation and reduced down-regulation of Bcl-xL. Moreover, thymic hyperplasia was detected in Thy28 TG mice, although thymocyte development was unaltered. Development of peripheral lymphoid tissues including spleen and lymph nodes was also unaltered. Thy28 TG spleen T cells showed an increased production of IFN-γ, but not IL-17, in response to both anti-CD3 and anti-CD28 mAbs. Finally, Thy28 TG mice displayed accelerated induction of EAE as assessed by disease incidence, clinical score, and pathology following immunization with myelin oligodendrocyte glycoprotein compared with control WT mice. These findings suggest that modulation of Thy28 expression plays a crucial role in the determination of thymic cell fate, which may contribute to the development of EAE through proinflammatory cytokine production.

Loss of adenomatous polyposis coli gene function disrupts thymic development

Loss of the adenomatous polyposis coli (APC) protein is a common initiating event in colon cancer. Here we show that thymocyte-specific loss of APC deregulated beta-catenin signaling and suppressed Notch-dependent transcription. These events promoted the proliferation of cells of the double-negative 3 and 4 stages and reduced rearrangements between the variable, diversity and joining regions of the gene encoding T cell receptor (TCR) beta, encouraging developmental progression of aberrant thymocytes lacking pre-TCR and alphabeta TCR. Simultaneously, the loss of APC prolonged the mitotic metaphase-to-anaphase checkpoint and impaired chromosome segregation, blocking development beyond the double-negative 4 stage. The result was extensive thymic atrophy and increased frequencies of thymocytes with chromosomal abnormalities. Thus, loss of APC in immature thymocytes has consequences distinct from those of deregulation of beta-catenin signaling and is essential for T cell differentiation.

Modulation of mThy28 nuclear protein expression during thymocyte development

We have recently shown that down-regulation of mouse Thy28 (mThy28) protein expression appears to be accompanied by apoptotic processes. Thymocytes from mice contain moderate amounts of mThy28 protein and undergo proliferation, differentiation, or apoptosis during murine thymic maturation. As a first step to examine the potential role of the mThy28 protein in the thymocyte development, such as positive-negative selection, the expression of mThy28 protein in the thymocyte subsets was examined. Thymocytes are separated into four subpopulations by the expression levels of CD4 and CD8: CD4-CD8- (DN), CD4+CD8+ (DP), and CD4+CD8- or CD4-CD8+ (SP). Flow cytometry analysis using three-color staining demonstrated that the mThy28 expression in immature DP cells is lower than that in DN and SP cells. The down-regulation of the mThy28 expression in the DP stage was also detected by Western blotting and reverse transcription-polymerase chain reaction (RT-PCR). The immunostaining method also showed that mThy28 protein was expressed in the medulla containing mature thymocytes, but not the cortex having immature thymocytes. The mThy28 protein in the thymocytes was mainly localized in the nucleus, as recently demonstrated in lymphoma cells, indicating that the mThy28 protein resides in the nucleus, irrespective of the cyclic or resting stage of the cell cycle. Together, the observation that mThy28 expression is down-modulated during the DP stage suggests that mThy28 protein might play some role in the positive-negative selection step in thymic maturation.

Evolution of the thymus size in response to physiological and random events throughout life

During embryogenesis and in the early stages of life, the thymus is a crucial organ for the generation of the T cell repertoire. T cells are generated from hematopoietic stem cells already differentiated to precursor T cells in the bone marrow. These cells enter the thymus guided by chemotactic factors secreted by this organ. The complex maturation process takes place that ensures self-tolerance and homeostasis. Thymocytes that show autoreactivity do not leave the thymus, but rather die by apoptosis. The final percentage of mature T cells that survive to migrate from the thymus to the periphery is very low: at most 5%, under optimal conditions. The highest migration occurs in childhood and adulthood, at least in mice and humans; however, it declines throughout life and is minimal in the elderly. Under normal circumstances, the thymus commences involution soon after birth, and this involution correlates with the capacity to export mature T cells to the periphery. Hormones, cytokines, and neurotransmitters all play a role in this age-associated process, but the reasons for and mechanisms of this involution remain unknown. Apart from physiological conditions that change throughout life and govern age-related thymus evolution, random states and events provoked by intrinsic or extrinsic factors can induce either thymus involution, as in reversible transient thymic hypoplasias, or thymic hyperplasias. The age-associated involution, unlike transient involutions, follows a regular pattern for all individuals, though there are clear differences between the sexes. Nevertheless, even the age-associated involution seems to be reversible, raising the possibility of therapeutic strategies aimed at enhancing thymus function in the elderly.

Spontaneous chronic colitis in TCR alpha-mutant mice; an experimental model of human ulcerative colitis

Mice with targeted disruption of the T cell receptor alpha gene (TCR alpha-/-) spontaneously develop chronic colitis. Colonic inflammation begins at 6-8 weeks of age and chronic colitis is established in about 60% of mice by 16-20 weeks of age. The disease is also associated with autoantibodies (anti-tropomyosin antibodies, anti-neutrophil cytoplasmic antibodies) and an oligoclonal immune response to luminal bacterial antigens. Although T cells, but not B cells or autoantibodies, are essential for the development of colitis, B cells and/or autoantibodies may have a regulatory role in the pathogenesis of this colitis because the colitis is more severe in B cell deficient TCR alpha-/- mice. Cytokines, specifically IL-4 and IL-1, also play an important role in the development of colitis in TCR alpha-/- mice. Enteric bacteria located in the large intestine are an important factor in the pathogenesis of this colitis because germ-free TCR alpha-/- mice do not develop colitis and appendectomy at an early age delays the onset of this colitis. The colitis in TCR alpha-/- mice resembles human ulcerative colitis and provides a useful model to study the pathogenesis of human inflammatory bowel disease.

Human Immunodeficiency Virus nef Gene Expression Affects Generation and Function of Human T Cells, But Not Dendritic Cells

Human immunodeficiency virus (HIV)-infected individuals develop an acquired immune deficiency syndrome (AIDS) due to loss in their lymphocyte numbers and cellular defects in T cells and antigen-presenting cells (APC). HIV infection of the thymus results in deficient replenishment of the peripheral naive T-cell pool. The HIVnef gene was shown to be important for progression towards AIDS and cellular depletion of the infected thymus. Here, we demonstrate by retroviral gene transfer that nef expression, in the absence of other HIV genes, impaired human thymic T-cell development. Thymocytes were generated in reduced numbers and downmodulated CD4 and CD8β cell surface expression. T cells grown from nef-expressing thymocytes were hyperproliferative in vitro upon T-cell receptor triggering. Mature dendritic cells (DC) were functional and had normal surface CD4 levels despite nef expression. Thus, nefexpression alone may contribute to AIDS development by reduced T-cell generation and T-cell hyperresponsiveness.

Molecular and cellular aspects of induced thymus development in recombinase-deficient mice

Thymus development and microenvironment organization require stage- and site-specific cross-talk between thymocyte and stroma. In this study we have used recombinase-activating gene-deficient (RAG-2(-/-)) mice to analyze regulated gene expression both in thymocytes and stromal cells following injection of anti-CD3 monoclonal antibodies as inducer of thymus development. We show that IFN-gamma, TNF-alpha and lymphotactin are transcriptionally regulated in thymocytes, whereas cytoskeletal keratin 14, IL-1alpha and TNF-alpha are regulated in the stroma, quantitatively reproducing the variations associated with beta selection of thymocytes. In addition, RAG-2(-/-) thymus development is associated with entry of epithelial cells into the cell cycle. The histochemical evidence that expanded RAG-2(-/-) thymus becomes undistinguishable from wild-type cortex further suggests that cross-talk phenomena occurring during beta selection of thymocyte are reproduced in this system.

GKLF in thymus epithelium as a developmentally regulated element of thymocyte-stroma cross-talk

Gut-enriched Krüppel-like factor (GKLF) is a transcriptional regulator expressed in differentiated epithelia. We identified GKLF transcript as a regulated element in thymic epithelium of recombinase-deficient mice during thymus development induced by anti-CD3 antibody injection. This treatment recapitulates the organogenetic process depending on productive rearrangement of T cell receptor (TCR) beta gene with thymocytes expansion and acquisition of the CD4+8+ double positive phenotype. In wildtype mice, GKLF is expressed very early in embryogenesis and becomes intensely up-regulated in thymus epithelium at day 18 of gestation when TCR beta expressing cells have selectively expanded and express both CD4 and CD8. The results presented here suggest that thymocytes may regulate GKLF transcriptionally in the cortical epithelium at the developmental check-point controlled by TCR beta gene rearrangement. Furthermore, GKLF expression in hematopoietic stroma might suggest the thus far uncharacterised participation of this factor in hematopoiesis.

Small GTPases in lymphocyte biology: Rho proteins take center stage

Almost a decade ago, the small GTPase Ras was shown to be activated in response to antigen receptor triggering in T cells. Since then, Ras has been further characterized as a central molecule for the regulation of signal transduction pathways in lymphocytes. However, over the last couple of years, its exclusive role in lymphocyte biology has been challenged by the emergence of its relatives of the Rho family. Today it is well established that Rho GTPases act as unique molecular switches at several critical checkpoints in lymphocyte development and function. Additionally, a new and critical concept in GTPase signaling has taken shape over the last couple of years in that small GTPases are able to regulate quite diverse cellular processes in the immune response by linking to multiple biochemical effector pathways.

Modulation of stress-induced murine lymphoid tissue involution by age, sex and strain: role of bone marrow

C57BL/6 and Balb C male and female mice of various ages were stressed by immobilization for 1 h/day (1, 2, 3, 5, 8, 11 or 14 consecutive days). The animals were then killed for determination of total body weight and the weights of the thymus, spleen and axillary lymph nodes. In addition, the total number of cells in the thymus and the proportion of lymphoid cells in the bone marrow cell population was defined. The effects of stress were modulated by age, sex and strain. Stress-induced involution of the thymus was generally more pronounced in older animals, while for the spleen was the opposite. Involution of the thymus was higher in males than in females, but there were no marked differences between the sexes in the response of the spleen. In general C57BL/6 mice were more sensitive to stress than Balb C mice. However, for the involution induced by stress on lymph nodes there were not a clear trend with age, sex or strain. In male and female mice of all ages and both strains, stress led to statistically significant reductions in the absolute number of cells inside the thymus and spleen and in the proportion of lymphoid cells in the bone marrow.

Calcium-dependent nitric oxide synthase activity in rat thymocytes

We examined the conversion of L-[3H]arginine to L-[3H]citrulline in lysate from rat thymocytes, which was dependent on Ca2+ and cofactors (FAD, BH4, NADPH). Removal of Ca2+ of the medium, reduced the total L-[3H]citrulline formation by about 97%. The L-[3H]citrulline formation was completely inhibited by the NO synthase inhibitors, NG-nitro-L-arginine and NG-monomethyl-L-arginine, with values for IC50 of 1.2 microM and 19.4 microM, respectively. In intact thymocytes, the L-[3H]citrulline formation was dependent on the intracellular Ca2+ ([Ca2+]i) concentration. Increasing the extracellular free-Ca2+ concentration up to 1.5 mM, was accompanied by an increase in [Ca2+]i inside the thymocytes and there was a parallel increase in the intracellular L-[3H]citrulline formation, which reached a maximal value of 371.2 nM of [Ca2+]i. Addition of NG-nitro-L-arginine to the medium, completely inhibited the formation of L-[3H]citrulline. The immunolabeling study revealed that 15% of the thymocytes isolated from rat thymus constitutively expressed the endothelial isoform of NO synthase.

GTPases in antigen receptor signalling

Immunological interest in small GTPases has focused for some years almost exclusively on the role of Ras in promoting lymphocyte activation and development. A new concept in this field is that GTPases are linked to multiple biochemical effector signalling pathways and are consequently able to regulate diverse cellular processes. It is also now recognised that GTPases other than Ras regulate lymphocyte biology. Rap 1 has been suggested as a negative regulator of lymphocyte responses and Rho GTPases are important components of signalling pathways used by antigen receptors and by costimulatory, cytokine and chemokine receptors to regulate the immune response.

A combination of stem cell factor and granulocyte colony-stimulating factor enhances the growth of human progenitor B cells supported by murine stromal cell line MS-5

We have developed a long-term culture system using the murine bone marrow stromal cells MS-5 to support the growth of progenitor B cells with CD34-, CD10+, CD19+, and cytoplasmic mu chain (C mu)-negative surface phenotype from human CD34+ cells purified from umbilical cord blood (CB). When 10(3) CD34+ cells/well were seeded on MS-5 stromal cells at the beginning of culture in the absence of exogenously added cytokines, progenitor B cells first appeared after 14 days, and the maximal cell production was achieved during the 6th week of culture. Intriguingly, the addition of recombinant human stem cell factor (rhSCF) and granulocyte colony-stimulating factor (rhG-CSF), but not rhIL-7, strikingly enhanced the growth of progenitor B cells from CB CD34+ population cultured on MS-5 stromal cells. The culture of progenitor B cells could be maintained until the 6th week of culture when some cells were revealed to have a C mu phenotype, and a small number of cells had immunoglobulin mu chain on their cell surface in the presence of both rhSCF and rhG-CSF. When CD34+ cells were cultured physically separated from the stromal layer by membrane, supportive effects of MS-5 stromal cells for the growth of progenitor B cells were not observed. These results suggest that the present culture system could generate progenitor B cells to proliferate from CB CD34+ cells, that some of these progenitor B cells could differentiate into immature B cells in conjunction with rhSCF and rhG-CSF, and that a species-cross-reactive membrane-bound factor(s), which stimulates early human B lymphopoiesis, may exist in MS-5 stromal cells. Further studies are required to investigate the mechanism how rhG-CSF acts on progenitor B cells to allow their proliferation and differentiation.