Medical image registration using unsupervised deep neural network: A scoping literature review

In medicine, image registration is vital in image-guided interventions and other clinical applications. However, it is a difficult subject to be addressed which by the advent of machine learning, there have been considerable progress in algorithmic performance has recently been achieved for medical image registration in this area. The implementation of deep neural networks provides an opportunity for some medical applications such as conducting image registration in less time with high accuracy, playing a key role in countering tumors during the operation. The current study presents a comprehensive scoping review on the state-of-the-art literature of medical image registration studies based on unsupervised deep neural networks is conducted, encompassing all the related studies published in this field to this date. Here, we have tried to summarize the latest developments and applications of unsupervised deep learning-based registration methods in the medical field. Fundamental and main concepts, techniques, statistical analysis from different viewpoints, novelties, and future directions are elaborately discussed and conveyed in the current comprehensive scoping review. Besides, this review hopes to help those active readers, who are riveted by this field, achieve deep insight into this exciting field

Characterising the novel MYB-TYK2 fusion gene in high-risk acute lymphoblastic leukaemia: oncogenic potential, effective therapeutic strategies and in vitro modelling of drug resistance mechanisms

A growing number of TYK2 activating alterations have been detected in acute lymphoblastic leukaemia (ALL) patients, including the MYB-TYK2 fusion gene. MYB-TYK2 was identified in a high risk (HR) Ph- ALL case and is associated with poor outcome. The transforming and leukaemogenic potential of activating TYK2 alterations, including those of MYB-TYK2, requires clarification in the ALL setting. Tyk2 is a member of the JAK family of tyrosine kinases and similar to JAK fusions, may result in activation of JAK/STAT signalling, and potentially be amenable to JAK inhibitor (JAKi) therapy. In depth characterisation of the underlying mechanisms resulting in leukaemogenesis are warranted and will inform drug response and targetability potential. Moreover, since the development of clinical resistance to targeted therapies such as JAKi, broad investigation of effective small molecule inhibitors (SMIs) is essential. Exploration of the possible modes of drug resistance following long-term treatment and importantly, how to circumvent resistance development, will provide alternative therapies for JAKi resistance in TYK2-altered patients. Hence, this study aimed to 1) identify and characterise the mechanisms of oncogenicity and activated downstream signalling pathways in MYB-TYK2 harbouring cells, 2) assess the efficacy of targeted therapeutics against MYB-TYK2 altered disease and 3) determine the possible mechanisms of resistance to candidate therapy via in vitro models to inform alternative therapeutic approaches to overcome possible disease persistence and resistance. In vitro and in vivo models were used to comprehensively model MYB-TYK2-altered disease. Depending on the downstream experiments, either cytokine-dependent Ba/F3 pro-B cells, Arf-/- pre-B primary mouse cells or NIH-3T3 cells, were retrovirally transduced with the MYB-TYK2 fusion gene isolated from an ALL patient. The targetability of the MYB-TYK2 fusion gene was investigated via high throughput screen (HTS) of 3088 cytotoxic and targeted compounds with further validation of candidates in pre-clinical models. Resistance modelling of the candidate JAKi cerdulatinib was achieved by gradual exposure of cells expressing the MYB-TYK2 fusion gene to increasing concentrations of cerdulatinib over several months. This study elucidated the transformative ability and functional significance of the MYB-TYK2 fusion gene to induce B-ALL in vivo. Results demonstrated the constitutive activation of JAK/STAT signalling due to expression of the MYB-TYK2 fusion gene. HTS identified the HDACi, vorinostat and the HSP90i, tanespimycin as effective targeted therapeutics against cells harbouring the MYB-TYK2 fusion gene in vitro. In addition, the sensitivity of the MYB-TYK2 fusion gene was established to the novel JAKi, cerdulatinib. Both vorinostat and cerdulatinib demonstrated anti-leukaemic effects in pre-clinical in vivo models of the MYB-TYK2 altered disease, resulting in a significantly reduced leukaemic burden. Further investigations into resistance following long-term exposure to cerdulatinib, indicated the likelihood of resistance to cerdulatinib therapy. Results suggested a persistent JAK/STAT activation despite Tyk2 inhibition via possible heterodimer formation with Jak1 and thus, Myb-Tyk2 trans-phosphorylation. This persistent signalling, however, was successfully reversed by HDACi treatment. Overall, the findings presented in this thesis demonstrate, for the first time, the driving potential of TYK2 activating alterations. Through robust modelling and rigorous testing of effective SMIs, this study identified novel therapeutic strategies using vorinostat and cerdulatinib against MYB-TYK2-altered disease. These results provide strong evidence for re-purposing of these drugs as an addition to a chemotherapy backbone for treatment of this highly aggressive subtype of B-ALL. Further insights into the resistance profile in response to cerdulatinib, as well as incorporation of targeted therapeutics to overcome this resistance, will assist high-risk patients in a clinical setting. These findings contribute to precision medicine approaches and will ultimately improve outcome and long-term survival for patients harbouring activating TYK2 alterations.Thesis (Ph.D.) -- University of Adelaide, Adelaide Medical School, 202

Folate modulates guanine-quadruplex frequency and DNA damage in Werner syndrome

Guanine-quadruplexes (G4) are stable tetra-stranded DNA structures that may cause DNA replication stress and inhibit gene expression. Defects in unwinding these structures by DNA helicases may result in telomere shortening and DNA damage. Furthermore, due to mutations in WRN helicase genes in Werner syndrome, G4 motifs are likely to be key elements in the expression of premature aging phenotypes. The methylation of DNA plays a significant role in the stability and occurrence of G4. Thus, G4 frequency and DNA methylation mechanisms may be affected by excesses or deficiencies in methyl donors such as folate. B-Lymphocytes from Werner patients (n = 5) and healthy individuals (n = 5) were cultured in RPMI medium under condition of folate deficiency (20 nM) or sufficiency (200 nM) for 14 days. Cells were fixed on microscope slides for immunofluorescent staining to measure G4 frequency and γH2AX (a marker of DNA strand breaks) intensity, using automated quantitative imaging fluorescent microscopy. There was a significant increase (p < 0.05) in G4 levels in Werner syndrome patients compared to healthy controls. Werner and control cells grown in 20 nM folate media also showed significant increases in G4 (p < 0.001) and γH2AX (p < 0.01) signals compared with the same cells grown in 200 nM folate. Control cells grown in 20 nM folate also showed a significant reduction in DNA methylation levels (P < 0.05). The results of this study suggest that the occurrence of DNA G4 structures can be modulated in vitro via nutrients with important roles in methylation.Paniz Tavakoli Shirazi, Wayne Richard Leifert, Michael Felix Fenech, Maxime Françoi

The first report about in vitro differentiation of menstrual blood stem cells into keratinocyte-like cells

Introduction: Recently, some characteristic of menstrual blood stem cells (MensScs) such as non-invasive accessibility, refreshing & high proliferation capability have impelled scientists to take advantages of these cells for cell therapy of different diseases including skin disorders. In this study, we evaluated the transdifferentiation capability of MenSCs into keratinocyte. Methods: The isolated stem cells from menstrual blood samples were characterized and subsequently co-cultured with seeded human keratinocytes on trans-wells up to 2 weeks. Thereafter, expression of keratinocyte markers such as Involucrin (IVL), Cytokeratin 14 (K14) and P63 was assessed in differentiated cells in reference to undifferentiated cells using immunofluorescent staining and Real-time PCR. Results: Based on given analysis, the isolated MenSCs exhibited typical expression of keratinocyte markers at mRNA and protein levels. The immunocytochemistry staining showed that the differentiated MenSCs could express P63, K14 and IVL protein. Moreover, the expression levels of P63, K14 and IVL mRNA significantly up regulated in differentiated MenSCs compared to undifferentiated cells (6.59 , 11, 2.94 fold, respectively, P=0.001 for all the three markers). Conclusion: Our result demonstrated that MenSCs can develop to keratinocytes. The development of the method for efficient differentiation of MensScs into keratinocyte lineage will enable us to access the massive source of epithelial cells for treatment and healing purposes. But the future studies are required to found out applicability of these cells for clinical trial of skin diseases. Keywords: Menstrual blood stem cell, keratinocyte, differentiatio

Constitutive JAK/STAT signaling is the primary mechanism of resistance to JAKi in TYK2-rearranged acute lymphoblastic leukemia

Activating TYK2-rearrangements have recently been identified and implicated in the leukemogenesis of high-risk acute lymphoblastic leukemia (HR-ALL) cases. Pre-clinical studies indicated the JAK/TYK2 inhibitor (JAKi), cerdulatinib, as a promising therapeutic against TYK2-rearranged ALL, attenuating the constitutive JAK/STAT signaling resulting from the TYK2 fusion protein. However, following a period of clinical efficacy, JAKi resistance often occurs resulting in relapse. In this study, we modeled potential mechanisms of JAKi resistance in TYK2-rearranged ALL cells in vitro in order to recapitulate possible clinical scenarios and provide a rationale for alternative therapies. Cerdulatinib resistant B-cells, driven by the MYB-TYK2 fusion oncogene, were generated by long-term exposure to the drug. Sustained treatment of MYB-TYK2-rearranged ALL cells with cerdulatinib led to enhanced and persistent JAK/STAT signaling, co-occurring with JAK1 overexpression. Hyperactivation of JAK/STAT signaling and JAK1 overexpression was reversible as cerdulatinib withdrawal resulted in re-sensitization to the drug. Importantly, histone deacetylase inhibitor (HDACi) therapies were efficacious against cerdulatinib-resistant cells demonstrating a potential alternative therapy for use in TYK2-rearranged B-ALL patients who have lost response to JAKi treatment regimens.Paniz Tavakoli Shirazi, Laura N.Eadie, Elyse C.Page, Susan L.Heatley, John B.Bruning, Deborah L.Whit

Modeling of human intervertebral disc annulus fibrosus with complex multi-fiber networks

Collagen fibers within the annulus fibrosus (AF) lamellae are unidirectionally aligned with alternating orientations between adjacent layers. AF constitutive models often combine two adjacent lamellae into a single equivalent layer containing two fiber networks with a crisscross pattern. Additionally, AF models overlook the inter‐lamellar matrix (ILM) as well as elastic fiber networks in between lamellae. We developed a nonhomogenous micromechanical model as well as two coarser homogenous hyperelastic and microplane models of the human AF, and compared their performances against measurements (tissue level uniaxial and biaxial tests as well as whole disc experiments) and seven published hyperelastic models. The micromechanical model had a realistic non-homogenous distribution of collagen fiber networks within each lamella and elastic fiber network in the ILM. For small matrix linear moduli (10%) due to the elastic fiber network. However, at moduli >0.2 MPa, the effects of the elastic fiber network on differences in stress-strain responses at different directions disappeared (<10%). Variations in sample geometry and boundary conditions (due to uncertainty) markedly affected stress-strain responses of the tissue in uniaxial and biaxial tests (up to 16 times). In tissue level tests, therefore, simulations should represent testing conditions (e.g., boundary conditions, specimen geometry, preloads) as closely as possible. Stress/strain fields estimated from the single equivalent layer approach (conventional method) yielded different results from those predicted by the anatomically more accurate apparoach (i.e., layerwise). In addition, in a disc under a compressive force (symmetric loading), asymmetric stress-strain distributions were computed when using a layerwise simulation. Although all developed and selected published AF models predicted gross compression-displacement responses of the whole disc within the range of measured data, some showed excessively stiff or compliant responses under tissue-level uniaxial/biaxial tests. This study emphasizes, when constructing and validating constitutive models of AF, the importance of the proper simulation of individual lamellae as distinct layers, and testing parameters (sample geometric dimensions/loading/boundary conditions)