Deep Learning based HEp-2 Image Classification: A Comprehensive Review

Classification of HEp-2 cell patterns plays a significant role in the indirect immunofluorescence test for identifying autoimmune diseases in the human body. Many automatic HEp-2 cell classification methods have been proposed in recent years, amongst which deep learning based methods have shown impressive performance. This paper provides a comprehensive review of the existing deep learning based HEp-2 cell image classification methods. These methods perform HEp-2 image classification at two levels, namely, cell-level and specimen-level. Both levels are covered in this review. At each level, the methods are organized with a deep network usage based taxonomy. The core idea, notable achievements, and key strengths and weaknesses of each method are critically analyzed. Furthermore, a concise review of the existing HEp-2 datasets that are commonly used in the literature is given. The paper ends with a discussion on novel opportunities and future research directions in this field. It is hoped that this paper would provide readers with a thorough reference of this novel, challenging, and thriving field.Comment: Published in Medical Image Analysi

In vitro expanded human CD4+CD25+ regulatory T cells suppress effector T cell proliferation.

Regulatory T cells (Tregs) have been shown to be critical in the balance between autoimmunity and tolerance and have been implicated in several human autoimmune diseases. However, the small number of Tregs in peripheral blood limits their therapeutic potential. Therefore, we developed a protocol that would allow for the expansion of Tregs while retaining their suppressive activity. We isolated CD4+CD25 hi cells from human peripheral blood and expanded them in vitro in the presence of anti-CD3 and anti-CD28 magnetic Xcyte Dynabeads and high concentrations of exogenous Interleukin (IL)-2. Tregs were effectively expanded up to 200-fold while maintaining surface expression of CD25 and other markers of Tregs: CD62L, HLA-DR, CCR6, and FOXP3. The expanded Tregs suppressed proliferation and cytokine secretion of responder PBMCs in co-cultures stimulated with anti-CD3 or alloantigen. Treg expansion is a critical first step before consideration of Tregs as a therapeutic intervention in patients with autoimmune or graft-versus-host disease

An automatic image based single dilution method for end point titre quantitation of antinuclear antibodies tests using HEp-2 cells

Indirect Immunofluorescence (IIF) on Human epithelial (HEp-2) cells test has been the golden standard for identifying the presence of Anti-Nuclear Antibodies (ANA) due to its high sensitivity and the large range of antigens that can be detected. Furthermore, IIF ANA test allows the positive sample strength (sample end point titre) to be reported. Despite its advantages, the IIF ANA test needs to be performed manually, and therefore it is perceived as an expensive and laborious process. This also applies to determining the strength of positive samples (end point titre) which traditionally is done by serially diluting the specimen. In this paper, we present an image-based method which is able to automatically determine the end point titre of positive samples based only on a single screening dilution. This can be done by simulating the manual titration process using a mathematical model of the exposure-density curve. Technically, a new Image Titration Endpoint (ITE) unit based on the model is introduced. Each specimen image is then measured in terms of this unit. Finally, the end point titre for the specimen is determined through a standard curve which specifies the end point titre given an ITE unit. This process is fully automated which would give an advantage over the current digital titration methods. The overall endpoint titre agreement between the proposed approach and the manual serial dilution method in the evaluation of 134 positive samples was 100%. This high agreement demonstrates that the proposed approach is suitable for routine ANA IIF testing in the clinical settings

Interplay between inflammation, autoimmunity and regeneration in the NOD mouse model of type 1 diabetes and Sjogren’s Syndrome.

PhDA continuous process of tissue remodelling and regeneration is a fundamental feature of the homeostatic response of the target organ of several autoimmune diseases. In type 1 diabetes (T1D) the β cell mass is in a constant process of death and renewal in order to regenerate the islets damaged by the autoimmune process. The relationship linking inflammation and regeneration during autoimmunity remains elusive. Reg genes, a multigene family discovered using cDNA libraries derived from rat regenerating islets, have been suggested to play an important role in epithelial regeneration not only in the pancreas but also in the salivary glands (SG) of Sjogren’s Syndrome (SS) during autoimmune sialoadenitis. Both in patients and animal models of T1D and SS, the chronic inflammatory/autoimmune process is heterogeneous and display high immunological variability. In particular, in a sizeable subset of cases, inflammatory lesions display ectopic lymphoid structures (ELS) characterised by T/B cell segregation, follicular dendritic cells networks and differentiation of germinal center B cells. However, there is limited evidence on the cellular and molecular mechanisms underlying ELS formation and their contribution to autoimmunity in the pancreas during autoimmune insulitis and in SG during autoimmune sialoadenitis. In this PhD project, I used the NOD mouse model of T1D and SS in order to investigate i) the cellular and molecular mechanisms regulating ELS formation, ii) the functionality of ELS in supporting in situ autoreactive B cell differentiation and iii) the relationship between formation of ELS and the expression of REG genes. In this work I showed that ELS formation was preceded by local up-regulation of lymphotoxins (LTαβ) and lymphoid chemokines CXCL13 and CCL19 and that, once formed, ELS were fully functional in promoting autoreactive B cell activation. Importantly, inhibition of the LT-β pathway prevented the formation of ELS and B cell autoimmunity. Finally, I showed that the expression pattern of Reg genes was strictly related to the development of inflammatory infiltrates in NOD 7 mice and that Reg proteins were target of the autoimmune process itself, as shown by the development of anti-Reg1 antibodies in patients with T1D. Overall, these results suggest that the processes of destruction and regeneration occurring in chronic autoimmune/inflammatory diseases are strongly interdependent whereby autoimmunity may be further enhanced by the attempt to regenerate