Diversity Of Immune Repertoire Research Articles

An Engineered Mouse Model That Generates a Diverse Repertoire of Endogenous, High-Affinity Common Light Chain Antibodies.

Bispecific antibodies have gained increasing popularity as therapeutics as they enable novel activities that cannot be achieved with monospecific antibodies. Some of the most popular bispecific formats are molecules in which two Fab arms with different antigen specificities are combined into one IgG-like molecule. One way to produce these bispecific molecules requires the discovery of antibodies against the two antigens of interest that share a common light chain. Here, we present the generation and characterization of a common light chain mouse model, in which the endogenous IGKJ cluster is replaced with a prearranged, modified murine IGKV10-96/IGKJ1 segment. We demonstrate that genetic modification does not impact B-cell development. Upon immunization with ovalbumin, the animals generate an antibody repertoire with VH gene segment usage of a similar diversity to wildtype mice, while the light chain diversity is restricted to antibodies derived from the prearranged IGKV10-96/IGKJ1 germline. We further show that the clonotype diversity of the common light chain immune repertoire matches the diversity of immune repertoire isolated from wildtype mice. Finally, the common light chain anti-ovalbumin antibodies have only slightly lower affinities than antibodies isolated from wildtype mice, demonstrating the suitability of these animals for antibody discovery for bispecific antibody generation.

Comprehensive characterization and database construction of immune repertoire in the largest Chinese glioma cohort

Immune receptor repertoire is valuable for developing immunotherapeutic interventions, but remains poorly understood across glioma subtypes including IDH wild type, IDH mutation without 1p/19q codeletion (IDHmut-noncodel) and IDH mutation with 1p/19q codeletion (IDHmut-codel). We assembled over 320,000 TCR/BCR clonotypes from the largest glioma cohort of 913 RNA sequencing samples in the Chinese population, finding that immune repertoire diversity was more prominent in the IDH wild type (the most aggressive glioma). Fewer clonotypes were shared within each glioma subtype, indicating high heterogeneity of the immune repertoire. The TRA-CDR3 was longer in private than in public clonotypes in IDH wild type. CDR3 variable motifs had higher proportions of hydrophobic residues in private than in public clonotypes, suggesting private CDR3 sequences have greater potential for tumor antigen recognition. Finally, we developed GTABdb, a web-based database designed for hosting, exploring, visualizing, and analyzing glioma immune repertoire. Our study will facilitate developing glioma immunotherapy.

Retracted: Correlation of IgH-CDR3 Immune Repertoire Diversity Test in Peripheral Blood of Neuromyelitis Spectrum Diseases.

[This retracts the article DOI: 10.1155/2022/6790145.].

Influence of Radiation Fractionation on Immune Repertoire Diversity in Solid Tumor Patients

Radiation (RT)-induced lymphopenia (RIL) occurs in up to 75% of patients undergoing RT and is associated with worse tumor control and survival across a spectrum of solid tumors. Patients undergoing hypofractionated RT are at lower risk of RIL compared with patients treated with more prolonged RT courses. However, it is unknown whether immune repertoire diversity is similarly affected by fractionation scheme in patients undergoing RT. This prospective study analyzed RT-induced changes in immune repertoire diversity in patients treated with conventionally (CFRT) vs hypofractionated RT (HFRT). RNA-based T and B cell receptor sequencing was performed on peripheral lymphocytes collected prospectively before RT and within 4 weeks of the last RT fraction from 23 patients (18 men, 5 women, median age 67 y) with primary solid tumors undergoing CFRT (≤3 Gy/day x ≥10 days, n = 13) or HFRT (≥5 Gy/day x ≤5 days, n = 10). Absolute lymphocyte counts (ALC; cells/μL) were obtained from clinical laboratory data. The number of unique CDR3 receptors (uCDR3) and Shannon entropy were used to monitor changes in T (TCR Vβ) and B (BCR IgH) receptor diversity. ALC decreased after RT in 90% (20/22) of patients (mean pre-RT ALC 1830 vs 1040 post-RT, p <0.001). Mean % ALC loss was greater in CFRT vs HFRT patients (44.3 vs. 35.2%). After RT, entropy in IgH and Vβ decreased in 18/23 (78%) and 17/23 (74%) patients, respectively; uCDR3 in IgH and Vβ decreased in 14/23 (61%) and 15/23 (65%). Among patients with concordant decreases in ALC and uCDR3, a moderate correlation between magnitude of ALC loss and uCDR3 levels in the T-cell receptor Vβ was observed (r = 0.64, p = 0.02). For both receptor species studied (IgH and Vβ), HFRT patients were more likely to have an increase in either entropy or uCDR3 in the face of decreased ALC (36 vs 15%, X2 p = 0.03). Furthermore, while decreases in entropy were observed among the CFRT patients for both IgH (median entropy 10.4 vs 9.4, p = 0.06) and Vβ (9.7 vs 8.1, p = 0.02), entropy did not significantly change following RT in the HFRT patients (IgH 10.6 vs 10.4, p = 0.74 and Vβ 10.9 vs 10.8, p = 0.24). RT-induced changes in immune repertoire diversity are variably reflected in the peripheral ALC. Both HFRT and CFRT depleted circulating lymphocytes, but patients undergoing HFRT were more likely to experience increases in T and B cell diversity metrics despite lymphopenia. It is therefore possible that relative sparing of repertoire diversity among patients undergoing HFRT could increase the likelihood of tumor antigen recognition by peripheral blood lymphocytes. As immune repertoire diversity is associated with the likelihood of response to immunotherapy, these findings also have implications for RT-immunotherapy combinations. Further study is required to understand the relationship between RT exposure to circulating lymphocyte populations and immune repertoire diversity.

Overexpression of CD73 is associated with recurrence and poor prognosis of gingivobuccal oral cancer as revealed by transcriptome and deep immune profiling of paired tumor and margin tissues.

For various cancers, differences in response to treatment and subsequent survival period have been reported to be associated with variation in immune contextures. We sought to identify whether such association exists in respect of gingivobuccal oral cancer. We performed deep immune profiling of tumor and margin tissues collected from 46 treatment naïve, Human Papillomavirus (HPV) negative, patients. Each patient was followed for 24 months and prognosis (recurrence/death) noted. Key findings were validated by comparing with TCGA-HNSC cohort data. About 28% of patients showed poor post-treatment prognosis. These patients exhibited a high probability of recurrence even within 1 year and death within 2 years. There was restricted immune cell infiltration in tumor, but not in margin, among these patients. Reduced expression of eight immune-related genes (IRGs) (NT5E, THRA, RBP1, TLR4, ITGA6, BMPR1B, ITGAV, SSTR1) in tumor strongly predicted better quality of prognosis, both in our patient cohort and in TCGA-HNSC cohort. Tumors of patients with better prognosis were associated with (a) lower CD73+ cells with concomitant lower expression level of NT5E/CD73, (b) higher proportions of CD4+ and CD8+ T cells, B cells, NK cells, M1 macrophages, (c) higher %Granzyme+ cells, (d) higher TCR and BCR repertoire diversities. CD73 expression in tumor was associated with low CD8+ and CD4+ T cells, low immune repertoire diversity, and advanced cancer stage. High infiltration of anti-tumor immune cells in both tumors and margins results in good prognosis, while in patients with minimal infiltration in tumors in spite of high infiltration in margins results in poor prognosis. Targeted CD73 immune-checkpoint inhibition may improve clinical outcome.

Bispecific PD1-IL2v and anti-PD-L1 break tumor immunity resistance by enhancing stem-like tumor-reactive CD8+ T cells and reprogramming macrophages

Immunotherapies have shown remarkable, albeit tumor-selective, therapeutic benefits in the clinic. Most patients respond transiently at best, highlighting the importance of understanding mechanisms underlying resistance. Herein, we evaluated the effects of the engineered immunocytokine PD1-IL2v in a mouse model of de novo pancreatic neuroendocrine cancer that is resistant to checkpoint and other immunotherapies. PD1-IL2v utilizes anti-PD-1 as a targeting moiety fused to an immuno-stimulatory IL-2 cytokine variant (IL2v) to precisely deliver IL2v to PD-1+ Tcells in the tumor microenvironment. PD1-IL2v elicited substantial infiltration by stem-like CD8+ Tcells, resulting in tumor regression and enhanced survival in mice. Combining anti-PD-L1 with PD1-IL2v sustained the response phase, improving therapeutic efficacy both by reprogramming immunosuppressive tumor-associated macrophages and enhancing Tcell receptor (TCR) immune repertoire diversity. These data provide a rationale for clinical trials to evaluate the combination therapy of PD1-IL2v and anti-PD-L1, particularly in immunotherapy-resistant tumors infiltrated with PD-1+ stem-like Tcells.

Correlation of IgH-CDR3 Immune Repertoire Diversity Test in Peripheral Blood of Neuromyelitis Spectrum Diseases.

Neuroretinitis spectrum disorder (NMOSD) is generally regarded as an acute or subacute inflammatory demyelinating disease of the central nervous system, mainly involving the optic nerve and spinal cord, mediated by humoral immunity. To address these questions, this work established an immunomic library of the heavy chain complementarity determinant 3 (gHI-CDR3) of peripheral blood lymphocyte B cell receptors. The library was established in patients with a spectrum of neurosyphilis-retinitis disorders. Six NMOSD patients and six healthy volunteers were recruited, and the NMOSD group was divided into an early-onset group and a stable group according to treatment conditions. The IgH-CDR3 gene fragment cultured in vitro was amplified by multiplex PCR technology, and the gene was sequenced by the second-generation high-throughput sequencing technology, and the statistical analysis was carried out by the method without reference. The quantity, type, and diversity of IgH-CDR3 in peripheral blood B lymphocytes of NMOSD patients were significantly lower than those of normal group (P > 0.05); the variation of IgH-CDR3 sequence in the initial stage of treatment was higher than that in the stable stage (P > 0.05); the replication frequency of the characteristic gene “CASSICLGSGCGGYYYGMDVW” was significantly increased in patients at the initial stage of NMOSD treatment (P < 0.05). The conclusion was that the gene expression and gene expression analysis of NMOSD patients could accurately judge the condition of NMOSD patients, evaluate their efficacy, and provide new molecular targets and new theoretical basis for clinical application.

Immune repertoire and evolutionary trajectory analysis in the development of diabetic nephropathy.

Diabetic nephropathy (DN) is the leading cause of death and the greatest risk to the lives of people with advanced diabetes. Yet, the molecular mechanisms underlying its development and progression remain unknown. In this research, we studied the primary pathways driving DN using transcriptome sequencing and immune repertoire analysis. Firstly, we found that the diversity and abundance of the immune repertoire in late DN were significantly increased, while there was no significant change in early DN. Furthermore, B cell-mediated antibody responses may be the leading cause of DN progression. By analyzing master regulators, we found the key DN-driving transcription factors. In the late stage of DN, immune cells, fibroblasts, and epithelial cells were abundant, but other stromal cells were few. Early DN kidneys had a higher tissue stemness score than normal and advanced DN kidneys. We showed that DN progression involves proximal tubular metabolic reprogramming and stemness restoration using Monocle3. Through WGCNA, we found that co-expression modules that regulate DN progression and immune repertoire diversity mainly regulate immune-related signaling pathways. In addition, we also found that early DN had apparent activation of immune-related signaling pathways mainly enriched in immune cells. Finally, we found that activation of fibroblasts is typical of early DN. These results provide a research basis for further exploring the molecular biology and cellular mechanisms of the occurrence and development of DN and provide a theoretical basis for the prevention and treatment of DN.

Aging T cell Immunity to Conserved Viral Epitopes

Abstract Although seasonal vaccination is widely accessible, its efficacy is inconsistent. Older individuals, in particular, tend to have difficulty mounting adequate immunity to infection. A possible reason for this struggle may be due to high mutagenesis in influenza hemagglutinin (HA), the major component of vaccines. Since older individuals possess diminished immune repertoire diversity compared to younger individuals, large sweeps in the viral proteome can be devastating. Unlike the antibody response, which primarily targets mutagenic surface proteins like HA; however, the T cell response can target more conserved regions of the viral proteome. Vaccines designed to stimulate T cells may thus provide greater protection in older individuals. To better understand the T cell repertoire in relation to the conserved regions of the viral proteome, we have predicted highly conserved viral T cell epitopes from various influenza strains and used our next-generation sequencing based method, TetTCR-seq HD, to pair T cell receptor (TCR) sequence, antigen specificity, transcriptome, and surface protein expression at the single cell level. In addition to novel antigen discovery, our high dimensional data have revealed the presence of immunity toward highly conserved influenza epitopes in older and younger individuals. Additionally, although age appears to decrease TCR repertoire and antigenic diversity, other factors such as immunodominance toward other viral epitopes, such as human cytomegalovirus, interestingly have a greater impact on the influenza-specific repertoire and phenotype. Our data ultimately indicate that healthy individuals harbor a reservoir of influenza-specific T cells that may be targetable by vaccines.

ImSpectR - R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data.

SummaryAn effective immune system is characterized by a diverse immune repertoire. There is a strong demand for accurate and quantitative methods to assess the diversity of the immune repertoire for various (pre-)clinical applications, including the diagnosis and prognosis of primary immune deficiencies, or to assess the response to therapy. Current strategies for immune diversity assessment generally comprise the visual inspection of the length distribution of rearranged T- and B-cell receptors. Visual inspections, however, are prone to subjective assessments and thus lead to biases. Here, we introduce ImSpectR, a unified approach to quantify immunodiversity using either spectratype, repertoire sequencing or single cell RNA sequencing data. ImSpectR scores various types of deviations from the expected length distribution and integrates these into one measure, allowing for robust quantitative comparisons of immune diversity across individuals or conditions.Availability and implementationR-package is available for download on GitHub at https://github.com/martijn-cordes/ImSpectR.Supplementary information Supplementary data are available at Bioinformatics online.

TCR immune repertoire characteristics of patients with drug-induced liver injury due to Polygonum multiflorum preparations

To explore the immune status of patients with drug-induced liver injury caused by Polygonum multiflorum preparations,and analyze their immune characteristics. Case-control design was used to collect the cases of drug-induced liver injury caused by P. multiflorum preparations through key specialized surveillance. Five matching factors,namely type of P. multiflorum preparations,gender,age,basic diseases and concomitant medication were controlled. According to the ratio of 1 ∶ 1,cases of patients who took P. multiflorum preparations but with no liver injury were monitored at prospective hospitals. The demographic information,disease information,medication information and laboratory examination information of the two groups were recorded,and venous blood was collected. The gene sequence was detected by high-throughput sequencing technology,and the characteristics of TCR immune repertoire of the two groups were analyzed. A total of 46 pairs of patients were enrolled in the study. The results showed significant differences in the number of CDR3 and clone species,the length of amino acid sequence in CDR3 region,the abundance of V gene and J gene,the cross-linking of V-J gene and the diversity of immune repertoire between patients with drug-induced liver injury and patients without liver injury. The immunohistochemical diversity and high-frequency V-J cross-linking characteristics of patients with liver injury caused by P. multiflorum preparations were found,which provided a reference for screening out drug users to reduce the occurrence of liver injury caused by P. multiflorum preparations.

1163P - Study on treatment of stage IV solid tumors with mutant neoantigen specific T cells

Background: As an important tumor immunotherapy, the specificity and efficiency of PD1 inhibitor is not yet satisfactory. The treatment of solid tumor with mutant neoantigen specific T (MNaS-T) cells developed in this study is an adoptive cell therapy which is specific for each patient. The aim is to explore the difference in safety and efficacy between MNaS-T cells and PD1 inhibitors, and to evaluate the charateristic of immune repertoire (IR) as predictive biomarker.Table: 1163PDemographic and clinical characteristics of 22 patientsCharacteristicMNaS-T cells plus PD1 inhibitors plus BSC (N = 11)PD1 inhibitors plus BSC (N = 11)Disease Progression (N=4)No Disease Progression (N=7)Total (N = 11)Age--no.(%)<604 (100)5 (71.4)9 (81.8)6 (54.5) > =6002 (28.6)2 (18.2)5 (45.5)Sex--no.(%)Male3 (75)3 (42.9)6 (54.5)8 (72.7)Female1 (25)4 (57.1)5 (45.5)3 (27.3)Previous treatments--no.Chemotherapy471111Targeted therapy471111ECOG--no.(%)0000011676≥23145Stage--no.IV471111Peripheral IR Diversity--mean (SD)EvennessBaseline0.01 (0.01)0.07 (0.08)0.05 (0.07)1st cycle0.05 (0.05)0.06 (0.07)0.05 (0.06)1st cycle / Baseline3.29 (2.09)0.85 (0.44)1.74 (1.71)ClonalityBaseline0.32 (0.09)0.25 (0.18)0.27 (0.15)1st cycle0.25 (0.12)0.27 (0.16)0.26 (0.14)1st cycle / Baseline0.76 (0.18)1.2 (0.27)1.04 (0.32) Open table in a new tab Methods: A total number of 11 patients with advanced solid tumors who failed after multiline treatments were recruited. They were treated with MNaS-T cells, PD1 inhibitors and BSC; other 11 patients were treated with PD1 inhibitors and BSC as control. Peripheral blood was collected at baseline and per cycle (21-28d) respectively. Multiple PCR and NGS on TCR beta chain was used to detect IR. Results: PFS of two groups had a statistical significance (P < 0.05), suggesting MNaS-T cells prolong patients' PFS. The safety was analyzed from routine blood urine stool test, coagulation function, liver and kidney function. There was no significant difference at baseline (P > 0.05). Compared with C group, total protein and albumin in T group had a transient decrease in 3rd, 4th and 5th follow-up respectively (P < 0.05), however, It can be recovered autonomously before 6th cycle. Evenness index and Clonality indexe were examined to illuminate the diversity and clonality of IR seperately. Compared to baseline, T cell repertoir of disease-progression patients and no-disease-progression patients after 1st cycle showed significantly different changes: Evenness 3.29 vs 0.85, P = 0.013; Clonality 0.76 vs 1.20, P = 0.015. Elevated Clonality may indicate amplification of tumor specific T cells which could recognize mutant neoantigen specifically. Conclusions: The combined immunotherapy of MNaS-T cells and PD1 inhibitors is more effective than PD1 inhibitor alone in prolonging the PFS, and has a good safety. IR Clonality change shows its potential as a predictive biomarker. Legal entity responsible for the study: J. Shunchang. Funding: Has not received any funding. Disclosure: All authors have declared no conflicts of interest.

Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires.

Recent studies have revealed that immune repertoires contain a substantial fraction of public clones, which may be defined as Ab or TCR clonal sequences shared across individuals. It has remained unclear whether public clones possess predictable sequence features that differentiate them from private clones, which are believed to be generated largely stochastically. This knowledge gap represents a lack of insight into the shaping of immune repertoire diversity. Leveraging a machine learning approach capable of capturing the high-dimensional compositional information of each clonal sequence (defined by CDR3), we detected predictive public clone and private clone-specific immunogenomic differences concentrated in CDR3's N1-D-N2 region, which allowed the prediction of public and private status with 80% accuracy in humans and mice. Our results unexpectedly demonstrate that public, as well as private, clones possess predictable high-dimensional immunogenomic features. Our support vector machine model could be trained effectively on large published datasets (3 million clonal sequences) and was sufficiently robust for public clone prediction across individuals and studies prepared with different library preparation and high-throughput sequencing protocols. In summary, we have uncovered the existence of high-dimensional immunogenomic rules that shape immune repertoire diversity in a predictable fashion. Our approach may pave the way for the construction of a comprehensive atlas of public mouse and human immune repertoires with potential applications in rational vaccine design and immunotherapeutics.

Advances in research and application of immune repertoire analysis in hematological malignancies

The diversity of immune repertoire (IR) is closely related to immune function and tumors derived from B or T lymphocytes. In recent years, the development of next generation sequencing has greatly promoted the progression and application of IR analysis. The research of IR has become a new hotspot of the American Society of Hematology Annual Meeting in 2016. Relevant reports in this meeting will be reviewed together with advances in research and application of IR analysis in hematological malignancies in recent years. Key words: Immune repertoire; Immunoglobulin; T-cell receptor; Hematological malignancies; American Society of Hematology Annual Meeting

Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients.

Specific changes in immune repertoires at genetic level responding to the lethal H7N9 virus are still poorly understood. We performed deep sequencing on the T and B cells from patients recently infected with H7N9 to explore the correlation between clinical outcomes and immune repertoire alterations. T and B cell repertoires display highly dynamic yet distinct clonotype alterations. During infection, T cell beta chain repertoire continues to contract while the diversity of immunoglobulin heavy chain repertoire recovers. Patient recovery is correlated to the diversity of T cell and B cell repertoires in different ways – higher B cell diversity and lower T cell diversity are found in survivors. The sequences clonally related to known antibodies with binding affinity to H7 hemagglutinin could be identified from survivors. These findings suggest that utilizing deep sequencing may improve prognostication during influenza infection and could help in development of antibody discovery methodologies for the treatment of virus infection.

Abstract 4362: T cell repertoire diversification is associated with immune related toxicities following immune checkpoint inhibition in metastatic cancer patients

Abstract Immune checkpoint inhibitors can induce clinical responses to a broad range of tumor types by presumably enhancing T cell responses against the tumor. These treatments are also associated with certain side effects that are also thought to be immune mediated (termed immune-related adverse events, or IRAEs). The mechanism by which IRAEs occur, and biomarkers that may predict IRAE development, are unknown. In prior work (Cha et al. Sci Transl Med 2014), we demonstrated that treating metastatic cancer patients with checkpoint inhibitors blocking CTLA-4 can lead to T cell repertoire diversification. However, we found that prolonged survival was not associated with the induction of high frequency clonotypes, but rather the maintenance of a pre-existing T cell response. Here, we examined whether treatment-induced TCR diversification is related to another clinical outcome: the development of IRAEs. We find that IRAEs are specifically associated with a more diverse T cell repertoire and with an increase in the number of T cell clonotypes, including the generation of de novo clones. This broadening of the circulating T cell repertoire occurred early with treatment, preceding the development of IRAEs. While IRAE patients demonstrate markedly greater diversity in their CD4+ T cells, they demonstrate a greater degree of change in clonal frequencies in their CD8+ T cells after ipilimumab, which may have key implications in the pathogenic mechanism of IRAE development. Finally, clinical response to checkpoint blockade is also associated with increased diversity. These results indicate that immune repertoire diversity following immune checkpoint inhibition can be both detrimental and beneficial to patients with metastatic cancer. Citation Format: David Y. Oh, Jason Cham, Li Zhang, Grant Fong, Mark Klinger, Malek Faham, Lawrence Fong. T cell repertoire diversification is associated with immune related toxicities following immune checkpoint inhibition in metastatic cancer patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4362.

Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples.

The diversity of an organism's B- and T-cell repertoires is both clinically important and a key measure of immunological complexity. However, diversity is hard to estimate by current methods, because of inherent uncertainty in the number of B- and T-cell clones that will be missing from a blood or tissue sample by chance (the missing-species problem), inevitable sampling bias, and experimental noise. To solve this problem, we developed Recon, a modified maximum-likelihood method that outputs the overall diversity of a repertoire from measurements on a sample. Recon outputs accurate, robust estimates by any of a vast set of complementary diversity measures, including species richness and entropy, at fractional repertoire coverage. It also outputs error bars and power tables, allowing robust comparisons of diversity between individuals and over time. We apply Recon to in silico and experimental immune-repertoire sequencing data sets as proof of principle for measuring diversity in large, complex systems.

The potential role of the circadian rhythm in immune repertoire formation and pathogenesis of immune disorders

The incidence of immune disorders such as autoimmunity and hypersensitivity reactions has been increasing in industrialized countries recently . Although some hypotheses based on epidemiological studies have been proposed to evaluate this increase among the immune disorder cases such as “Hygiene Hypothesis”, the underlying mechanism is not clear yet. It has been well studied that impairments in immune repertoire, total diversity among the antigenic receptors such as B cell receptor, T cell receptor and antibodies, may be causative factors of several immune disorders. Although genetic aspects of these immune disorders are well established, elucidating the responsible mutations in the genes encoding the molecules having key role in the formation of immune repertoire, we still lack knowledge on what kind of environmental factors take role in the pathogenesis of these diseases. Establishment of the diversity of immune repertoire depends on the recruitment of V(D)J re-arrangement which is basically Non-Homologous End Joining (NHEJ), one of the DNA repair mechanisms, mediated pathway. Circadian rhythm which DNA repair mechanisms may have effects on V(D)J recombination through NHEJ pathway especially in the early stages of life when immune repertoire is formed. The proteins recruited in the circadian regulation of the cells and regulation of DNA repair mechanisms such as Per1, Cry1, Parp-1 ve Tim are candidate molecules which may regulate V(D)J rearrangement. We suggested in our hypothesis that a novel molecular pathways linking circadian rhythm to immune system functioning and environmental factors disrupting circadian rhythm may have potential role in the pathogenesis of several immune disorders through epigenetic control of V(D)J recombination.

A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status

BackgroundLymphocyte receptor repertoires are continually shaped throughout the lifetime of an individual in response to environmental and pathogenic exposure. Thus, they may serve as a fingerprint of an individual’s ongoing immunological status (e.g., healthy, infected, vaccinated), with far-reaching implications for immunodiagnostics applications. The advent of high-throughput immune repertoire sequencing now enables the interrogation of immune repertoire diversity in an unprecedented and quantitative manner. However, steadily increasing sequencing depth has revealed that immune repertoires vary greatly among individuals in their composition; correspondingly, it has been reported that there are few shared sequences indicative of immunological status ('public clones'). Disconcertingly, this means that the wealth of information gained from repertoire sequencing remains largely unused for determining the current status of immune responses, thereby hampering the implementation of immune-repertoire-based diagnostics.MethodsHere, we introduce a bioinformatics repertoire-profiling framework that possesses the advantage of capturing the diversity and distribution of entire immune repertoires, as opposed to singular public clones. The framework relies on Hill-based diversity profiles composed of a continuum of single diversity indices, which enable the quantification of the extent of immunological information contained in immune repertoires.ResultsWe coupled diversity profiles with unsupervised (hierarchical clustering) and supervised (support vector machine and feature selection) machine learning approaches in order to correlate patients’ immunological statuses with their B- and T-cell repertoire data. We could predict with high accuracy (greater than or equal to 80 %) a wide range of immunological statuses such as healthy, transplantation recipient, and lymphoid cancer, suggesting as a proof of principle that diversity profiling can recover a large amount of immunodiagnostic fingerprints from immune repertoire data. Our framework is highly scalable as it easily allowed for the analysis of 1000 simulated immune repertoires; this exceeds the size of published immune repertoire datasets by one to two orders of magnitude.ConclusionsOur framework offers the possibility to advance immune-repertoire-based fingerprinting, which may in the future enable a systems immunogenomics approach for vaccine profiling and the accurate and early detection of disease and infection.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0169-8) contains supplementary material, which is available to authorized users.

Unraveling the repertoire in Wiskott-Aldrich syndrome.

OPINION article Front. Immunol., 27 October 2014Sec. Primary Immunodeficiencies Volume 5 - 2014 | https://doi.org/10.3389/fimmu.2014.00539