Xiaoyan Jiang

Tyrosine kinase inhibitor (TKI) therapies have been introduced into clinical practice with remarkable effects on chronic myeloid leukemia (CML). However, early relapse, acquired drug resistance and persistence of leukemic stem cells (LSCs) remain problematic. Improved treatments specifically targeting key molecular elements active in CML LSCs are needed. One candidate is the oncoprotein AHI-1 (Abelson helper integration site-1), which is highly deregulated in LSCs. It harbors two key domains, SH3 and WD40-repeat, which are known important mediators of protein-protein interactions. An AHI-1-mediated protein complex containing BCR-ABL and JAK2 has been shown to modulate transforming activity and TKI-response/resistance of CML LSCs. In this study, I investigated the functional roles of the AHI-1 SH3 domain in regulation of cellular resistance of primitive CML cells to TKIs. I showed that deletion of the SH3 domain of Ahi-1 significantly enhanced apoptotic response of BCR-ABL⁺ cells to TKIs compared to cells expressing full-length Ahi-1. I solved the crystal structure of the AHI-1 SH3 domain and identified several unique features, providing potential target sites for designing specific drugs. Using immunoprecipitation/mass spectrometry, I identified a novel protein interaction between AHI-1 and Dynamin-2 (DNM2), a GTPase, through the AHI-1 SH3 domain. I showed that DNM2 expression was significantly upregulated in CML stem/progenitor cells compared to normal bone marrow cells. I also determined that the AHI-1 SH3 domain and the proline rich domain of DNM2 were mainly responsible for their interaction. Most importantly, I identified a novel protein complex in CML cells, containing BCR-ABL, AHI-1 and DNM2. Furthermore, I demonstrated an oncogenic role of DNM2 in primitive CML cells by showing that knockdown of DNM2 greatly impaired the survival of CML stem/progenitor cells and sensitized them to TKI treatments. Lastly, I illustrated that DNM2 might be involved in deregulation of endocytosis, ROS production and autophagy in TKI-insensitive CML stem/progenitor cells. This study detailed the identification and characterization of the newly-identified BCR-ABL-AHI-1-DNM2 protein complex and described the oncogenic functions of DNM2 in primitive CML cells. It further suggested that targeting DNM2 may facilitate eradication of LSCs as a new treatment option in CML.

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The identification of BCR-ABL1 as the key molecular event in chronic myeloid leukemia (CML) has revolutionized treatment opportunities for early phase patients. Imatinib mesylate (IM) and other ABL1 tyrosine kinase inhibitors (TKIs) have been introduced into the clinic with remarkable effects. However, initial and acquired resistance, relapse and in particular, the persistence of CML stem cells upon TKI therapy represent critical challenges and warrant the identification of predictive biomarkers and novel, distinct targets for improved treatment strategies. In this work, I investigated how CML stem and progenitor cells survive TKI therapy through intrinsic and bone marrow (BM) niche-associated mechanisms. I revealed that the core autophagy protease ATG4B, and the focal adhesion protein and serine/threonine kinase Integrin-linked kinase (ILK) play crucial roles in CML, and that they can be successfully targeted with small molecule inhibitors. By comparing the expression of various core autophagy genes and proteins, ATG4B was identified as potential biomarker in CML to predict IM-responders versus IM-nonresponders prior to the initiation of therapy. Furthermore, my studies illustrated that deregulation of ATG4B is critical to autophagy, survival and growth of CML stem and progenitor cells. Inhibition or suppression of ATG4B decreased CML cell viability significantly and sensitized leukemic cells to TKI treatment highlighting ATG4B as a novel target in CML. ILK was identified as a differentially expressed gene between CD34⁺ CML patient cells and healthy donors by RNA-sequencing (RNA-seq) analysis, and the importance of the ILK protein and its kinase functions in mediating TKI responses and resistance in CML stem and progenitor cells was demonstrated by ILK inhibitor (QLT0267) and ILK suppression studies. Moreover, various in vitro and in vivo assays showed that the simultaneous kinase inhibition of ILK and BCR-ABL1 is effective in targeting both leukemic stem and progenitor cells, including quiescent CML cells, and in the presence of stromal cells of the BM microenvironment that make TKI monotherapies ineffective. Overall, these studies provide the first evidence of the importance of ATG4B and ILK in CML, and their potential as novel therapeutic targets for improved combination treatments with TKIs to specifically eliminate CML stem and progenitor cells.

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Cutaneous T-cell lymphoma (CTCL) is a group of lymphoproliferative disorders consisting of two main subtypes: mycosis fungoides (MF) and Sézary syndrome (SS). Due to the lack of robust histological markers, it remains a challenge to establish an accurate diagnosis and offer long term prognostication for CTCL. In addition, the molecular pathogenesis of CTCL is only partially understood. Previously our group discovered that early stage MF skin biopsies contained ectopic expression of TOX gene, which is essential for the early development of CD4⁺ T cells but normally is switched off in mature CD4⁺ T cells in the peripheral tissues. The objectives of my thesis research are to evaluate if TOX can be used to improve CTCL diagnosis and prognostication, and to characterize the functional role of TOX in the pathogenesis of CTCL.Using skin biopsies and clinical databases from Vancouver, Beijing and Boston, I confirmed that TOX expression levels were significantly upregulated in the full spectrum of MF and in SS. In addition, as a diagnostic marker, high TOX expression levels differentiated CTCL from non-CTCL controls with good sensitivity and specificity. Furthermore, as a prognostic marker, high TOX mRNA levels correlated with increased risks of disease progression and disease-specific mortality in MF, and increased risks of disease-specific mortality in SS.I also investigated the functional role of TOX in CTCL pathogenesis using multiple CTCL cell lines and a mouse xenograft model. TOX knockdown in three CTCL cell lines led to markedly increased apoptosis, reduced cell proliferation, and impaired tumorigenic ability. These effects were partially mediated by increased expression of two cell cycle regulators, CDKN1B and CDKN1C. In addition, transcriptome analysis between TOX-suppressed cells and control CTCL cells uncovered additional potential molecules downstream of TOX, such as tumor suppressors FOXO3 and HBP1.Our results provide strong evidence that aberrant activation of TOX can serve as a diagnostic and prognostic biomarker for CTCL. Further, we demonstrated that TOX plays a crucial oncogenic role in CTCL pathogenesis, partially through regulating transcription of CDKN1B, CDKN1C and other downstream genes. Therefore TOX and/or its downstream genes may be promising therapeutic targets for CTCL.

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Chronic myeloid leukemia (CML) has long served as a paradigm for new insights into the cellular origin, pathogenesis and treatment of human cancers. ABL tyrosine kinase inhibitor (TKI) therapies have had remarkable effects on treatment of early phase CML. However, TKI monotherapies are not curative, and initial and acquired TKI resistance remain clinically challenging. Particularly, CML stem/progenitor cells are insensitive to TKIs. Therefore, novel treatments and predictive biomarkers are clearly needed. In this work, I studied the biological effects of dual BCR-ABL and JAK2 suppressions on TKI-nonresponder stem/progenitor cells, and identified and characterized novel microRNA (miRNA) biomarkers in these cells. I examined the biological effects of a new JAK2 inhibitor, BMS-911543, in combination with TKIs on CD34⁺ CML cells from IM-nonresponders. I demonstrated that combination therapy significantly reduces JAK2/STAT5 and CRKL activities, induces apoptosis, inhibits colony growth, and eliminates leukemic stem cells in vitro, while sparing healthy counterparts. I further showed that oral BMS-911543 combined with dasatinib is more effective in eliminating leukemic cells in an aggressive mouse model of BCR-ABL⁺ human leukemia. Next, I identified differentially expressed miRNAs in CD34⁺ CML cells using RNA-seq analysis, and validated the results in additional samples using high-throughput qPCR. Potential miRNA target genes were also identified by integrating miRNA expression profiles with gene expression profiles using strand-specific RNA-seq. These studies revealed that expression of miR-185 is significantly reduced in CD34⁺ CML cells from TKI-nonresponders compared to TKI-responders. Restoration of miR-185 expression by lentiviral transduction in CD34⁺ TKI-nonresponder cells significantly impairs survival of these cells and sensitizes them to TKI treatment in vitro and in vivo. Additionally, I validated the target genes of miR-185 to rationalize its roles in CML. Lastly, I demonstrated that the expression levels of several miRNAs, including miR185, were restored in patients treated with nilotinib, suggesting their potential as biomarkers to predict clinical response to TKI therapies.These studies have uncovered the biological significance of JAK2 and miR-185 in regulation of the properties of drug-insensitive CML stem/progenitor cells, and their potential as therapeutic targets for improved treatments with TKIs especially in patients at risk of developing TKI resistance.

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Cutaneous T-cell lymphomas (CTCLs) represent a group of lymphoproliferative disorders characterized by homing of malignant T-cells to the skin’s surface. There are two main types of CTCL: Mycosis Fungoides (MF) and Sezary Syndrome (SS). We have demonstrated that expression of the Abelson helper integration site-1 (AHI-1) oncogene is significantly increased in CD4⁺CD7- cells from SS patients. Bridging integrator 1 (BIN1) has been identified by microarray analysis of CTCL cells as a candidate gene involved in AHI-1-mediated lymphomagenesis. Interestingly, BIN1expression is significantly reduced in SS patient samples. However, the role of BIN1 and its molecular connection to AHI-1 in lymphomagenesis remains unexplored. I extensively investigated the role of key BIN1 isoforms in primary and CTCL cell line model systems both in vitro and in vivo. I demonstrated that overexpression/restored expression of BIN1 isoforms has strong anti-proliferative and pro-apoptotic roles in CTCL cells in vitro, and significantly inhibits the tumorigenic activity of these cells in vivo. The pro-apoptotic role of BIN1 in CTCL cells occurs through downregulation of c-FLIP, a critical inhibitor of Fas/FasL-mediated apoptosis. I also observed significant reduction and increase in BIN1 and c-FLIP transcripts in primary CTCL samples, respectively. Interestingly, high BIN1 and low c-FLIP transcripts correlated with better survival rate in SS patients. Thus, BIN1 deficiency may play an important role in CTCL pathogenesis by causing apoptosis resistance.Furthermore, I explored potential mechanisms by which AHI-1 leads to downregulation of BIN1, by (1) examining if AHI-1 physically interacts with BIN1; and (2) determining if AHI-1 alters transcription of BIN1 by changing the methylation status of the BIN1 promoter. These experiments did not yield direct evidence of these two potential mechanisms of AHI-1’s role in BIN1 suppression. Thus, the mechanism by which AHI-1 regulates BIN1 remains unknown. Nevertheless, several potential BIN1 interacting proteins were uncovered in CTCL cells, including α/β-tubulin and β-actin. Overall, this study provides the first evidence of strong tumor suppressor activity of BIN1 in CTCL. It points to the loss of BIN1 and subsequent upregulation of c-FLIP as an important mechanism to induce apoptosis resistance in CTCL cells, and identifies BIN1 and c-FLIP as potential CTCL therapeutic targets.

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