Chinten James Lim: Associate Professor at Department of Pediatrics, UBC Faculty of Medicine

Associate Professor

Faculty of Medicine

Research Classification

Cancer progression and metastasis

Solid cancer tumours

Hematological tumours

Research Interests

tumour cell biology

mechanisms of drug resistance

integrin cell adhesion and migration

tumour microenvironment

pediatric oncology

Relevant Thesis-Based Degree Programs

View all programs

Affiliations to Research Centres, Institutes & Clusters

BC Children's Hospital Research Institute

Research Options

I am available and interested in collaborations (e.g. clusters, grants).

I am interested in and conduct interdisciplinary research.

I am interested in working with undergraduate students on research projects.

Open All

Research Methodology

cellular biochemistry

single cell imaging

FRET

TIRF

live cell microscopy

Flow cytometry

chorioallantoic membrane

patient derived xenografts

Recruitment

Looking to recruit:

Master's students

Doctoral students

Desired start dates: Any time / year round

Potential research project areas:

Integrin cell adhesion in chemotherapeutic resistance. Targeted drug susceptibilities. Tumour microenvironment. Immunogenic cell death. Pediatric oncology.

Other options:

I support public scholarship, e.g. through the Public Scholars Initiative, and am available to supervise students and Postdocs interested in collaborating with external partners as part of their research.

I support experiential learning experiences, such as internships and work placements, for my graduate students and Postdocs.

I am open to hosting Visiting International Research Students (non-degree, up to 12 months).

Complete these steps before you reach out to a faculty member!

Check requirements

Familiarize yourself with program requirements. You want to learn as much as possible from the information available to you before you reach out to a faculty member. Be sure to visit the graduate degree program listing and program-specific websites.
Check whether the program requires you to seek commitment from a supervisor prior to submitting an application. For some programs this is an essential step while others match successful applicants with faculty members within the first year of study. This is either indicated in the program profile under "Admission Information & Requirements" - "Prepare Application" - "Supervision" or on the program website.

Focus your search

Identify specific faculty members who are conducting research in your specific area of interest.
Establish that your research interests align with the faculty member’s research interests.
- Read up on the faculty members in the program and the research being conducted in the department.
- Familiarize yourself with their work, read their recent publications and past theses/dissertations that they supervised. Be certain that their research is indeed what you are hoping to study.

Make a good impression

Compose an error-free and grammatically correct email addressed to your specifically targeted faculty member, and remember to use their correct titles.
- Do not send non-specific, mass emails to everyone in the department hoping for a match.
- Address the faculty members by name. Your contact should be genuine rather than generic.
Include a brief outline of your academic background, why you are interested in working with the faculty member, and what experience you could bring to the department. The supervision enquiry form guides you with targeted questions. Ensure to craft compelling answers to these questions.
Highlight your achievements and why you are a top student. Faculty members receive dozens of requests from prospective students and you may have less than 30 seconds to pique someone’s interest.
Demonstrate that you are familiar with their research:
- Convey the specific ways you are a good fit for the program.
- Convey the specific ways the program/lab/faculty member is a good fit for the research you are interested in/already conducting.
Be enthusiastic, but don’t overdo it.

Attend an information session

G+PS regularly provides virtual sessions that focus on admission requirements and procedures and tips how to improve your application.

ADVICE AND INSIGHTS FROM UBC FACULTY ON REACHING OUT TO SUPERVISORS

These videos contain some general advice from faculty across UBC on finding and reaching out to a potential thesis supervisor.

Supervision Enquiry

If you have reviewed some of this faculty member's publications, understand their research interests and have reviewed the admission requirements, you may .

Graduate Student Supervision

Doctoral Student Supervision

Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.

Autocrine and paracrine signaling contributes to acquired chemotherapeutic resistance in Group 3 medulloblastoma (2022)

Group 3 medulloblastoma (MB) is the most aggressive type of MB with the least favourable outcome. Although enhanced STAT3 signaling is implicated in acquired chemoresistance of multiple cancers, a role for STAT3 in MB chemoresistance is not known. Here, I evaluated if IL-6/STAT3 signaling contributes to acquired chemoresistance in Group 3 MB. Group 3 MB cells that are initially chemosensitive were rendered chemoresistant either by incremental drug selection, or by conditioning with IL-6 family cytokines. IL-6 cytokines robustly stimulated the activation of JAK/STAT3 activity, and the chemoresistant variants exhibited increased STAT3 phosphorylation when transiently treated or conditioned with IL-6. Abrogation of STAT3 or IL6R expression in the chemoresistant cells successfully restored the chemosensitivity, highlighting the requirement of IL-6/STAT3 signaling in acquired chemoresistance. MB cells rendered chemoresistant following IL-6 conditioning secreted high levels of IL-6, indicating that an IL-6 autocrine feedback loop forms an important stimulus able to sustain enhanced STAT3 signaling. Furthermore, IL-6 secreted by chemoresistant cells also stimulated phosphorylated STAT3 in treatment-naïve chemosensitive cells, suggesting acquired chemoresistance may be propagated through the tumour microenvironment via a paracrine mechanism. I postulated that immune cells in the TME could initiate paracrine cytokine signaling. Indeed, microglia co-cultured with MB cells secreted cytokines, including IL-6, that phosphorylated STAT3 and enhanced MB chemoresistance. Unexpectedly, IL6R-/- MB cells co-cultured with microglia also exhibited enhanced STAT3 phosphorylation and chemoresistance, suggesting involvement of cytokines in addition to IL-6. I then demonstrated that IL-6 family cytokines effectively induced STAT3 phosphorylation and chemoresistance. Gp130 encodes the common β subunit for the IL-6 family cytokine receptors required for activating JAK/STAT3 signaling. Abrogation of gp130 expression in MB effectively blocked STAT3 signaling and IL-6 cytokine mediated chemoresistance. Furthermore, combination chemotherapy that included inhibitors targeting gp130, JAKs or STAT3 effectively circumvented IL-6 mediated chemoresistance in Group 3 MB. Analysis of multi-layered GEO databases of MB unveiled certain gene expression changes in the IL-6/STAT3 signaling axis that correlated with poor outcomes associated with Group 3 MB. Overall, elucidation of the role of IL-6/STAT3 signaling in cell survival and acquired chemoresistance revealed strategies for molecular targeted therapies to combat chemoresistance in Group 3 MB.

View record

Alpha-integrin expression and function modify chemoresistance and immunogenicity of acute lymphoblastic leukemia (2017)

The overall survival rate for pediatric Acute Lymphoblastic Leukemia (ALL) is >85%, achieved mainly via multi-agent chemotherapy. However, therapeutic options remain limited for those experiencing relapse, thus understanding the causes for treatment failures remains an important priority. In this thesis, I investigate the underlying mechanisms that allow leukemic cells to escape chemotherapy. Specifically, I evaluate how integrin-mediated cell adhesion promotes tumor cell survival by increased pro-survival signaling, enhanced resistance to chemotherapeutics, and decreased presentation of immunogenic cell death (ICD) markers. I show that T-lymphoblast adhesion via α4β1-integrin promotes chemoresistance to doxorubicin-induced apoptosis. Expression of α4δ, a tail-truncated α4-integrin with GFFKR as the cytoplasmic motif, promotes chemoresistance in a manner independent of integrin-mediated adhesion. The adhesion-independent chemoresistance is reproduced by expression of Tacδ, a non-integrin transmembrane receptor fused to the cytosolic GFFKR motif. Additionally, the GFFKR motif-mediated chemoresistance is associated with enhanced Akt activation, Ca²⁺ influx, and drug efflux. GFFKR is a conserved motif found in α-integrins and previously shown to interact with calreticulin, a calcium-binding endoplasmic reticulum chaperone protein. I found that α4-calreticulin interaction was enhanced by cell adhesion, while α4δ-calreticulin interaction occurred in an adhesion-independent manner. Since cell surface calreticulin is a pro-phagocytic marker for cells undergoing ICD, the impact of integrin function on surface calreticulin in lymphoblasts treated with ICD-inducing agents was evaluated. Engagement of integrins via adhesion, or expression of the minimal GFFKR motif as α4δ or Tacδ, was sufficient to reduce the levels of surface calreticulin. Furthermore, surface calreticulin was also reduced for cells co-treated with a β1-integrin activating antibody. The resulting integrin-mediated decrease in surface calreticulin significantly reduced engulfment of the target lymphoblasts by macrophages. Calreticulin expression in lymphoblasts was nullified to assess its role in integrin-mediated chemoresistance. Chemosensitivity was partially restored in calreticulin-null Tacδ cells under non-adherent conditions, and in calreticulin-null wildtype cells under adherent conditions. The affect was partly attributed to calreticulin’s role as a regulator of Ca²⁺ influx and drug efflux. Calreticulin was also implicated as a mediator of cytokine-dependent STAT proliferative signaling. This thesis provides evidence for integrin function and cell adhesion as a physiological pro-survival mediator for T-lymphoblasts.

View record

Master's Student Supervision

Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.

The role of cytosolic calreticulin in the promotion of oncogenic signaling in acute lymphoblastic leukemia (2022)

Acute lymphoblastic leukemia (ALL), a malignancy of the bone marrow that is mainly caused by the uncontrolled proliferation of B- or T-lymphoblasts, is the most common form of pediatric cancer in Canada. Pediatric ALL is currently highly treatable due to advances in contemporary risk-directed ALL chemotherapy. However, some patients will be unresponsive to treatment and prognosis remains poor for patients undergoing relapse. Adverse side effects from drug toxicity used in chemotherapy also remain a major challenge. Recently, the lectin chaperones calreticulin (CALR) and calnexin (CANX), along with their co-chaperone, PDIA3, are increasingly implicated in the biological processes of various human cancers, along with their main role of facilitating protein folding in the endoplasmic reticulum (ER). Here, I investigated the role of CALR and PDIA3 in the promotion of pro-survival JAK/STAT signaling in human T-lymphoblasts. Previously, PDIA3 was found to be required for CALR localization in the cytosol. I generated CALR-/- and PDIA3-/- T-lymphoblasts using CRISPR-Cas9 to assess the effects of deficiency in total and cytosolic CALR on JAK/STAT signaling. CALR-/- and PDIA3-/- cells exhibited reduction in STAT3 phosphorylation compared to wildtype cells. This suggested that cytosolic CALR played a role in the regulation of STAT3 phosphorylation. Unexpectedly, I found that STAT5b mRNA was reduced in CALR-/- and PDIA3-/- Jurkat T-lymphoblasts, leading to an observed deficiency in STAT5 protein expression. This further emphasized the biological significance of CALR and PDIA3 in their extra-ER functions. To assess the clinical significance of CALR, CANX and PDIA3 expression in ALL, I analyzed publicly available transcriptome databases of pediatric ALL, which revealed the potential clinical utility of CALR and CANX mRNA expression in diagnostic tumour samples as biomarkers for predicting treatment response. Elevated CALR and CANX was correlated with the presence of minimal residual diseases (MRD) at the end of induction treatment in T-ALL and B-ALL respectively. As MRD remains a powerful prognostic indicator for risk stratification, the linkage between diagnostic tumour CALR and CANX mRNA expression and MRD status may provide important insights in treatment response for physicians at the time of diagnosis.

View record

The role of calreticulin in cell adhesion (2019)

Acute lymphoblastic leukemia (ALL) is the most commonly diagnosed childhood cancer in Canada. Even though childhood ALL has a high overall survival rate, therapeutic options remain limited for those experiencing relapse; therefore, understanding the causes for treatment failure is vital. Adhesion of leukemic cells to bone marrow and the extracellular matrix provides chemotherapy protection to ALL, leading to drug resistance. In this thesis, I investigated the involvement of an endoplasmic reticulum (ER) chaperone, calreticulin (CRT), in integrin mediated cell adhesion. I show that integrin-mediated adhesion of Jurkat T-lymphoblasts is disrupted in CRT-/- cells, and CRT re-expression restores the wildtype phenotype. To determine the requirement of cytosolic CRT for integrin-mediated cell adhesion, I used ERp57-/- cells, previously characterized to express no CRT in the extra-ER compartment. Interestingly, ERp57-/- cells have decreased adhesion compared to wildtype cells, indicating the involvement of cytosolic CRT in integrin-mediated cell adhesion.To evaluate the requirement of LRP1 as a surface receptor for CRT during immunogenic cell death (ICD), I utilized CRISPR-Cas9 technology to generate LRP1-/- lymphoblasts. I show that drug-treated stimulation of surface CRT presentation is lost in LRP1-/- cells, a result consistent with LRP1 as a cis-acting receptor for CRT during ICD. I utilized CRT-/- HEK cells expressing various CRT constructs that are localized in different cellular compartments. All constructs successfully rescued the adhesion defect of CRT-/- cells. Furthermore, I found that mutant variants of CRT that lack the C-terminal KDEL ER retention motif were proteolytically truncated, and that the N-terminal truncated fragment can be detected on the cell surface.

View record

Role of SDF-1/CXCR4 Signaling in Regulation of PKA Activity During Cell Migration (2014)

Cell migration plays an important role in development and the immune system, and the signaling pathways governing this process are regulated in a spatial and temporal manner. One important signaling molecule is cAMP-dependent Protein Kinase (PKA), which has been shown to be a key regulator of migration. In migrating cells, PKA activity exists in a gradient that is highest at the leading edge, where it phosphorylates proteins that promote migration. Although the functions of PKA in migration have been identified, upstream regulators of PKA-mediated cell migration have yet to be defined. A candidate for regulation of PKA during migration is the chemokine receptor CXCR4, which has been shown to induce cell migration and signal through PKA-phosphorylatable proteins upon ligation with stromal derived factor-1 (SDF-1). I have created a novel CXCR4 deficient Jurkat cell line, JC4, and show that Jurkat cell migration towards SDF-1 is CXCR4-dependent. As well, we show through biochemical studies that the SDF-1/CXCR4 signaling pathway is an upstream regulator of PKA activation in CHO-CXCR4 cells, J774 macrophages, and Jurkat T-cells. Furthermore, the SDF-1/CXCR4 signaling pathway is an upstream regulator of PKA activation in migrating cells. This is supported by the observation that there is a CXCR4-dependent increase in PKA-phosphorylated substrates at the periphery of J774 macrophages and protrusions of Jurkat T-cells upon SDF-1 stimulation. Furthermore, SDF-1/CXCR4 signaling establishes a PKA activity gradient in migrating Jurkat cells that is highest at the leading edge. These studies define a regulatory role for the SDF-1/CXCR4 signaling pathway in promoting PKA-mediated cell migration.

View record

Steam Pre-Treatment and Leaching for the Production of High-Quality Oil Palm Residue Pellets (2014)

It is estimated that about 26 million metric tons of oil palm oil residues are produced annually in Malaysia. The oil palm residues contain high ash content, high alkali metals and low lignin content. Ash and alkali metals lead to slagging in a combustion reactor and fouling of surfaces in convective tubes of heat exchangers. Low lignin content leads to disintegration of pellets during pellet handling and storage. This research thesis investigated the pelletization performance and the ash reduction on Empty Fruit Bunches (EFB) and Palm Kernel Shell (PKS) of oil palm residues by two different pre-treatment processes: steam explosion and water leaching. Steam explosion for increasing binding ability was performed by reacting EFB/PKS with saturated steam ranging from 120 to 220℃ for 5 minutes in a batch reactor. Water leaching for reducing the ash and alkali metals of EFB and PKS was investigated by immersing the samples in water from 25 to 55℃. The immersion time ranged from instantaneous to 240 minutes. Single pellets were made from water treated and steam treated samples. A significant ash reduction from 5.47 to 2.47 % was found for the EFB pellet due to water leaching. A slight reduction of pellet’s porosity and a significant reduction in ash content suggested that water leaching may be used to improve the quality of EFB as a biofuel. On the other hand, pre-treatment processes were not necessary for PKS, considering low binding ability and no ash reduction after pre-treatments. Kinetic models of EFB and PKS leaching were developed. A mass balance of cross flow process was investigated for evaluating the number of stages for a continuous leaching system of EFB and PKS. The techno-economic analysis showed that the additional leaching process costs $25.75 per tonne in a pellet making line.

View record

The Role of Interactions between 4N1K and CD47 on Integrin Activation and Integrin-Mediated Cell Adhesion (2014)

Integrins are heterodimeric, cell-surface receptors that play a role in adhesion and chemoresistance. Integrins can be found in one of two states: an inactivated state where integrin-mediated adhesion is not supported, or in an activated state where integrin-mediated adhesion is possible. CD47 is a cell surface receptor that is said to regulate integrin functions by interacting with integrins and regulating their activation state. A thrombospondin C-terminal motif, RFYVVMWK, has been found to be responsible for cell adhesion and was subsequently shown to be specific for CD47. The 10-mer peptide derived from this sequence, 4N1K, has since been used as the prototypic ligand for CD47 and this interaction has been shown to decrease integrin-mediated adhesion and induce cell aggregation and apoptosis. However, the role of the 4N1K/CD47/integrin axis in chemoresistance has not been investigated. My thesis investigated the consequences of CD47 ligation by 4N1K on integrin-mediated functions.I found that the 4N1K peptide induces binding of a variety of antibodies, including non-specific control antibodies, to the surface of cells. In addition, cells that were deficient in CD47 expression were able to bind substrate-immobilized 4N1K as efficiently as their CD47-expressing parental cells. 4N1K was also found to block cell adhesion and induce cell aggregation in a manner that was independent on CD47 expression. These results suggest that 4N1K may produce artifacts in assays that use antibodies as reporters of integrin activation due to its hyper-adhesive nature, resulting in 4N1K binding to a variety of Ig-containing proteins, such as antibodies and cell-surface proteins. In addition, non-specific binding of 4N1K on cell surfaces and homotypic 4N1K interactions appear to be responsible for many of the observed phenotypes on cell adhesion and aggregation, and may explain the reported CD47-independent effects of 4N1K. As such, I propose that the 4N1K peptide not be used as a ligand to assess the role of thrombospondin/ CD47 interactions on cell functions, since the non-specific adherent nature of 4N1K could lead to erroneous interpretations of experimental data.

View record

Studies on encapsulation of pelletized biomass (2013)

Hygroscopicity and dust generation are among major challenges to the safe and cost effective use of wood pellets. Wood pellets can rot and disintegrate during storage due to the moisture adsorption from humid environment. In British Columbia, pellets are transported by rail from inland manufacturing plants to a shipping port and stored in silos. At the ports, pellets are loaded from the silo on to the ocean vessel for transport to overseas. Loading is stopped during rain because wood pellets disintegrate when they come into contact with water. The lost revenue from loading shutdown during rain can be large. Furthermore, breakage of wood pellets during handling and storage causes dustiness. Dust and fines may cause adverse health effect, fire, and explosion in storage and silos. Encapsulation of wood pellets with a hydrophobic membrane or surface modification can be a good way to increase water repellent capacity of wood pellets, and avoid dust generation. In this research, commercial wood pellets were coated with a wax solution, linseed oil, cellulose acetate, canola oil, etc. The treated pellets were either dipped in water or exposed to humid environment. The results showed that the investigated liquid coatings increased the durability of wood pellets in water. However, the tested liquid coatings did not decrease water vapor adsorption of pellets significantly. Surface treatments with O₂ etching and CF₄ plasma were applied to render wood pellets hydrophobic. It was demonstrated that CF₄ plasma treatment increased water repellency of wood pellets while O₂ etching without CF₄ deposition step made pellets more hydrophilic. Surface modification with O₂ etching combined with CF₄ deposition created the most hydrophobic surface when pellets were dipped in water. However this combined plasma treatment did not decrease water vapor adsorption from humid environment.

View record