Biology subjects

Tan, T. Z.

Publications and source records attributed to Tan, T. Z..

11 recordsLinked to original sources

bioRxiv2026

FOXA1 preserves cell polarity and restrains lysosome biogenesis in non-small cell lung adenocarcinoma

BackgroundThis study investigates the role of the pioneer transcription factor FOXA1 as a master gene in sustaining epithelial cell polarization in early-stage lung adenocarcinoma. The partial loss of FOXA1 is explored to determine if it will affect plasticity and progression of lung adenocarcinoma. The study also addresses the transcriptional circuitry that links polarity defects to lysosome homeostasis. MethodsA multiomics approach was used to define the status of the chromatin in epithelial and mesenchymal states of A549 adenocarcinoma cells obtained with a newly synthetized TGF-{beta} receptor inhibitor or TGF-{beta} respectively. The study leveraged ATAC-seq, RNA sequencing, Cut&Tag sequencing of FOXA1 and histone marks profiling. The functional impact of FOXA1 was examined by partial silencing in vitro and by heterozygous FOXA1 deletion in a KrasG12D mouse model. Three-dimensional organoid culture, high-resolution electron microscopy, spatial transcriptomics and multiplex immunohistochemistry assessed carcinoma cell polarity, proliferation, the tumor microenvironment and organelle content. Group differences were evaluated with two-tailed t tests or one-way analysis of variance. ResultsFOXA1 binding and expression were highest in cells harboring an epithelial phenotype. In mouse KrasG12D LUAD tumors FOXA1 marked polarized, CDH1-positive cells; heterozygous loss diminished CDH1, disrupted apical-basal architecture, lowered organoid-forming efficiency and remodeled the immune microenvironment. Spatial transcriptomics and ultrastructural analyses showed that FOXA1-deficient carcinoma cells accumulated lysosomes, down-regulated vesicle fusion genes of the SNARE family and activated the lysosomal CLEAR gene network. FOXA1 occupied enhancers of lysosome-associated genes and competed with the transcription factor TFE3, thereby suppressing transcription of cathepsin B and cathepsin C and restricting lysosome biogenesis. ConclusionsFOXA1 is a central regulator that preserves epithelial cell polarity and limits lysosome formation in lung adenocarcinoma. Targeting the FOXA1-TFE3-lysosome axis may affect tumor plasticity and provide new therapeutic opportunities.

cancer biology↗

bioRxiv2024

Spatial Transcriptomic Profiling Of Advanced Ovarian Clear Cell Carcinoma Reveals Intra-Tumor Heterogeneity In Epithelial-Mesenchymal Gradient

Intratumoral heterogeneity is intrinsically comprised of molecular alterations of tumor cells and extrinsically from interconnections with microenvironments. This study explores the spatial heterogeneity of ovarian clear cell carcinoma (OCCC), a rare cancer with significance to East Asian women. We profile 21 primary-metastatic tumor pairs in a discovery cohort and 16 tumors in two validation cohorts using spatial transcriptomic (ST) platforms. Our integrative analysis revealed an inverse relationship between OXPHOS and inflammation along the EMT gradient. OCCC cells undergoing partial EMT have metabolic shifts and lose LCN2 expression, possibly via concomitant down-regulation of SOX9. Conversely, LCN2 expression correlated with OXPHOS-enriched tumor signature, low EMT, and better outcomes in OCCC. Single-cell ST profiling using CosMx further identifies nine spatially distinct cancer cell populations including the LCN2-high cancer subclone with a high epithelial score. SOX9 induction could partially restore epithelial-ness in LCN2-low cells suggesting that plasticity in OCCC is achieved via transcriptional reprogramming. Our findings provide further insights into epithelial-mesenchymal plasticity and the adaptive interactions between cancer cells and their microenvironments in OCCC.

cancer biology↗

bioRxiv2023

Spatial profiling of ovarian clear cell carcinoma reveals immune-hot features

IntroductionOCCC has high incidence in Asia with frequent occurrence at early stage but without sufficient data on molecular stratification for high-risk patients. Recently, immune-hot features have been proposed as an indicator for poor prognosis for early-stage OCCC. Specific patterns of intra-tumoral heterogeneity (ITH) associated with immune-hot features need to be defined. MethodsFormalin-fixed paraffine embedded (FFPE) tumor sections from 10 early-stage OCCC patients were included. Digital Spatial Profiling (DSP) of 18 protein targets was conducted by using the nanoString GeoMx system to profile selected regions of interest (ROIs) based on the reference H&E staining morphology. Areas of illumination (AOIs) were defined according to ROI segmentation by the fluorescence signals of visualization markers pan-cytokeratin (PanCK), CD45, or DNA. ResultsUnsupervised hierarchical clustering of 252 AOIs from 229 ROIs showed that PanCK segments expressed different combinations of immune markers suggestive of immune mimicry features. Three immune-hot clusters were identified: granzyme B high (C1-a), immune signal high (C1-b) and immune-like cells (C1-c); two immune-cold clusters were identified: fibronectin-high (C2-a) and signal-cold (C2-b). Immune cells around C1-b and C1-c PanCK+ AOIs were tumor infiltrating immune cells (TIIs) with higher expression of CD68, while those around C1-a, C2-a and C2-b PanCK+ AOIs were non-TIIs with higher expression of SMA. C1-c and C2-a PanCK+ AOIs were associated with OCCC recurrence. TIIs had higher frequencies in C1-b and C1-c PanCK+ AOIs and were associated with OCCC recurrence. Correlating with morphology, tumor samples with recurrence showed higher frequency of papillary pattern. Plus, ROIs with papillary pattern had extremely high frequency of PanCK segments of C1-c feature, higher frequency of TIIs, and macrophage lineage immune mimicry with high intensity of CD68. ConclusionsSpatial profiling of early-stage OCCC tumors revealed that immune mimicry of tumor cells, the presence of TIIs, and papillary pattern in morphology were associated with recurrence.

cancer biology↗

bioRxiv2022

Cancer Cells in all EMT States Lack Rigidity Sensing Depletion of Different Tumor Suppressors Causes Loss of Rigidity Sensing in Cancer Cells

Cancer cells have many different behaviors from epithelial to mesenchymal forms. We report here that 36 distinct tumor cell lines regardless of EMT form or other features lack the ability to sense rigidity and will grow on soft surfaces. In the majority of lines, cells were missing at least one protein needed for rigidity sensing (primarily tropomyosin2.1 (Tpm2.1) but also PTPN12, FilaminA (FLNA), and myosinIIA) while all had high levels of Tpm3. In the few cases where the major rigidity sensing components were present, those tumor cells were not able to sense rigidity. Thus, we suggest that tumor cells can lose the ability to sense rigidity by many different means and that the loss of rigidity sensing is sufficient to cause the transformed phenotype that enables targeted treatments.

cancer biology↗

bioRxiv2021

Case study: Digital spatial profiling of metastatic clear cell carcinoma reveals intra-tumor heterogeneity in epithelial-mesenchymal gradient.

Intrinsic intra-tumor heterogeneity (ITH) has been linked to worse patient outcomes. The development of spatial profiling technology has enabled the deciphering of ITH with multiple analysis readouts. Advanced ovarian clear cell carcinoma (OCCC), known to harbor ITH, is chemoresistant, poor prognostic, and possesses distinct molecular and histological characteristics. However, detailed spatial information of the nature of ITH within OCCC remains unclear. Here, we utilized the NanoString Digital spatial profiling (DSP) GeoMx platform to perform multiplex protein expression analysis on tumor samples of primary and colonic metastatic sites from one advanced OCCC patient. The spatial resolution revealed the existence of an epithelial-mesenchymal (EM) gradient within the metastatic tumor but not the primary tumor, and similar EM gradient was not observed within the primary tumor. The EM gradient exhibited a distinct pattern from the periphery to the core of the metastatic tumor. Compared to tumor cells at the primary site, there was an intermediate zone in between the tumor periphery and the tumor core in the colonic metastasis with differential expression patterns of pan-cytokeratin (PanCK), fibronectin (FN), smooth muscle actin (SMA), neural cell adhesion molecule (NCAM), integrin alpha X (ITGAX), and Ki-67. Our study provides the first spatially resolved in situ evidence of intermediate or hybrid EM states within the tumor samples of similar morphology. This not only demonstrates the promising applications of spatial profiling in precision medicine but also provides an unprecedented view of the EM gradient during the progression of cancer such as OCCC.

cancer biology↗

bioRxiv2020

TRAF4 inhibits bladder cancer progression by promoting BMP/SMAD signalling pathway

Bladder cancer is one of the most prevalent cancer types in the world, frequently exhibiting invasion and metastasis and therefore associated with poor prognosis. It is a progressive disease with high recurrence rates even after surgery, which calls for the urgent need for early intervention and diagnosis. The E3 ubiquitin ligase TNF Receptor Associated Factor 4 (TRAF4) has been largely implicated as a tumour-promoting element in a wide range of cancers. Over-expression and amplification of this gene product has been a common observation in breast and other metastatic tumours. In contrast, we observed that expression of TRAF4 negatively correlated with overall patient survival. Moreover, its expression was repressed at epigenetic levels in aggressive bladder cancer cells. We also describe an ERK kinase phosphorylation site on TRAF4 that inhibits its stability and localization to plasma membrane in such cells. Furthermore, knockdown of TRAF4 in epithelial bladder cancer cell lines leads to gain of mesenchymal genes and a loss of epithelial integrity. Reciprocally, stable over-expression of TRAF4 in mesenchymal cells leads to decreased migratory and invasive properties. Transcriptomic analysis upon TRAF4 mis-expression in bladder cancer cell lines revealed that higher TRAF4 expression enhanced BMP/SMAD and dampened NF-{kappa}B signalling pathways. Importantly, this notion was confirmed in bladder cancer patient material. Mechanistically, we showed that TRAF4 targets the E3 ubiquitin ligase SMURF1, a negative regulator of BMP/SMAD signalling, for proteasomal degradation in bladder cancer cells. We show that genetic and pharmacological inhibition of SMURF1 or its function inhibited migration of aggressive (mesenchymal) bladder cancer cells.

cancer biology↗

bioRxiv2020

Primary platinum resistance and immune exclusion in ovarian carcinomas with high expression of the homologous recombination mediator RAD51

BackgroundHomologous recombination deficiency (HRD) in ovarian cancer confers increased sensitivity to Poly-ADP-Ribose-Polymerase (PARP) inhibitors and platinum. The homologous recombination (HR) mediator RAD51, however, is commonly overexpressed, potentially driving unregulated HR. Due to non-quantitative measurements and heterogeneous cohorts, the clinical relevance of RAD51 expression in ovarian cancer is unclear. MethodsFluorescent immunohistochemistry and multispectral imaging were used to quantitate RAD51 expression, in relation to other markers, in independent cohorts of ovarian carcinomas from British Columbia Cancer (BCC n=284) and the phase III SCOTROC4 trial (n=268). Independent cohorts (TCGA n=566, GSE9891 n=267, GSE26712 n=185 and GSE3149 n=146) were used for mRNA expression and immune infiltration analyses. ResultsRAD51-High tumours had shorter progression-free and overall survival compared to RAD51-Low cases in both BCC and SCOTROC4. The negative prognostic significance of high RAD51 was primarily evident in cases classified "HRD negative" by the Myriad genomic scar assay. Unexpectedly, overexpression of RAD51 in ovarian cancer cell lines did not affect sensitivity to platinum or PARP inhibitors, but modified the expression of immune-regulatory genes. Accordingly, tumours with high RAD51 mRNA showed consistent changes in immunomodulatory transcripts across four independent ovarian cancer cohorts. In-situ multiplexed imaging confirmed that high RAD51 tumours correlated with tumour exclusion of cytotoxic-T-cells, possibly explaining their poor outcomes after chemotherapy. ConclusionsHigh RAD51 expression, in conjunction with a HRD score <42, identifies a subgroup of EOC cases with platinum resistance and an immune excluded tumour microenvironment. Tumours with high RAD51 may require alternate or additional adjuvant therapeutic strategies to overcome immune exclusion. Statement of Translational RelevanceHomologous recombination deficiency (HRD) in ovarian cancer confers increased sensitivity to Poly-ADP-Ribose-Polymerase (PARP) inhibitors and platinum. Currently, methods to identify patients who do poorly on first-line platinum based chemotherapy in ovarian cancer represent an unmet clinical need. In this report we show that RAD51 expression can identify patients with primary platinum resistance in two large cohorts, including a unique phase-III trial of carboplatin as adjuvant monotherapy. The clinical relevance of a positive genomic scar HRD score, a biomarker for assessing HRD status, in predicting benefit to PARP inhibitors has been established following recent phase 3 trials in first line and 2nd line maintenance treatment of ovarian cancer. Our findings suggest that HRD negative ovarian tumours may be further stratified by RAD51 expression status in the context of platinum sensitivity, and may serve to guide future trials of HRD targeted agents.

cancer biology↗

bioRxiv2019

Integrative analysis and machine learning based characterization of single circulating tumor cells

We collated publicly available single-cell expression profiles of circulating tumor cells (CTCs) and showed that CTCs across cancers lie on a near-perfect continuum of epithelial to mesenchymal (EMT) transition. Integrative analysis of CTC transcriptomes also highlighted the inverse gene expression pattern between PD-L1 and MHC, which is implicated in cancer immunotherapy. We used the CTCs expression profiles in tandem with publicly available peripheral blood mononuclear cell (PBMC) transcriptomes to train a classifier that accurately recognizes CTCs of diverse phenotype. Further, we used this classifier to validate circulating breast tumor cells captured using a newly developed microfluidic systems for label-free enrichment of CTCs.

genomics↗

bioRxiv2019

Single-cell analysis of EphA clustering phenotypes to probe cancer cell heterogeneity

Eph receptors, a family of receptor tyrosine kinases, play a crutial role in the assembly and maintenance of healthy tissues. Dysfunction in Eph signaling are causally and correlatively associated with cancer progression. In breast cancer cells, dysregulated Eph signaling has been largely linked to alterations in receptor clustering abilities. In the present study, we implemented a single-cell assay and a scoring scheme to systematically probe the spatial organization of activated EphA receptor in carcinoma cells of different origin. Using this assay, we found that cancer cells retained EphA clustering phenotype upon cell division for several generations and degree of clustering reported for population as well as single-cell migration potential. Finally, using patient-derived cancer cell lines, we probed the evolution of EphA signalling in cancer cell populations that underwent metastatic transformation and acquisition of drug resistance. Taken together, our simple and scalable approach provides a reliable quantitation of EphA associated gene expression and phenotypes in multiple carcinomas and can assay the heterogeneity of cancer cell populations in a cost- and time-effective manner.

cancer biology↗

bioRxiv2017

DNA methylation profiling of breast cancer cell lines along the epithelial mesenchymal spectrum - implications for the choice of circulating tumour DNA methylation markers

Epithelial-mesenchymal plasticity (EMP) is a dynamic process whereby epithelial carcinoma cells reversibly acquire morphological and invasive characteristics typical of mesenchymal cells, which facilitates metastasis. Understanding the methylation differences between epithelial and mesenchymal states may assist in the identification of optimal DNA methylation biomarkers for the blood-based monitoring of cancer. Methylation-sensitive high-resolution melting (MS-HRM) was used to examine the promoter methylation status of a panel of established and novel markers in a range of breast cancer cell lines spanning the epithelial-mesenchymal spectrum. Pyrosequencing was used to validate the MSHRM results. The results indicate an overall distinction in methylation between epithelial and mesenchymal phenotypes. The mesenchymal expression markers VIM, DKK3 and CRABP1 were methylated in the majority of epithelial breast cancer cell lines while methylation of the epithelial expression markers GRHL2, MIR200C and CDH1 was restricted to mesenchymal cell lines. We also examined EMP association of several methylation markers that have been used to assess minimal residual disease. Markers such as AKR1B1 and APC methylation proved to be selective for epithelial breast cell lines, however RASSF1A, RAR{beta}, TWIST1 and SFRP2 methylation was seen in both epithelial and mesenchymal cell lines, supporting their suitability for a multi-marker panel.

cancer biology↗

bioRxiv2017

TGH: Trans-Generational Hormesis And The Inheritance Of Aging Resistance

Animals respond to dietary changes by adapting their metabolism to available nutrients through insulin and insulin-like growth factor signalling. Restricting calorie intake generally extends life and health span, but Drosophila fed non-ideal sugars such as galactose are stressed and have shorter life spans. Here, we report that although these flies have shorter life spans, their offspring show significant life extension if switched to a normal sugar (glucose) diet. We define this as TGH or trans-generational hormesis, a beneficial effect that comes from a mild stress. We trace the effects to changes in stress responses in parents, ROS production, effects on lipid metabolism, and changes in chromatin and gene expression. We find that this mechanism is similar to what happens to the long lived Indy mutants on normal food, but surprisingly find that Indy is required for life span extension for galactose fed flies. Indy mutant flies grown on galactose do not live longer as do their siblings grown on glucose, rather overexpression of Indy rescues lifespan for galactose reared flies. We define a process where sugar metabolism can generate epigenetic changes that are inherited by offspring, providing a mechanism for how transgenerational nutrient sensitivities are passed on.

biochemistry↗