Biology subjects

Huang, R. Y.-J.

Publications and source records attributed to Huang, R. Y.-J..

7 recordsLinked to original sources

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↗

bioRxiv2024

Inter- and intra-tumor heterogeneous immune presentation in primary uterine carcinosarcoma determined by digital spatial profiling

Uterine carcinosarcoma (UCS) is a rare gynecologic cancer with unfavorable prognosis. Its biphasic histologic components are known to associated with outcomes. Dissecting the tumor heterogeneity within UCS is crucial to discover molecular biomarkers for patient stratification. The aim of this study was to utilize spatial profiling technology to analyze immune presentation in different histological components within UCS tumors. The study included 23 UCS patients whose tumor sections were subjected to nanoString GeoMx Digital Spatial Profiling (DSP) to profile 30 immune-related proteins in 491 segments. We identified distinct cluster-labeled subtypes showing varied immune marker expressions. The immune presentations within the carcinoma and sarcoma components showed significant differences. Markers indicating M2 macrophages (CD45+CD163+) and epithelial-mesenchymal transition (EMT) (SMA, fibronectin) were highly expressed in the sarcoma components. The immune presentation subtypes within each histological component also differed between patients with recurrence in 5 years and without recurrence over 5 years. The cluster-labeled subtype with high Neutrophil/PMN-MDSC marker expression (CD66b) was associated with longer survival, whereas the subtype with high NK cell marker expressions (CD56) was linked to poor prognosis. Our result suggested that immune features within the carcinoma component of UCS tumors would determine patient outcomes and should be considered as a strategy for patient stratification.

immunology↗

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↗

bioRxiv2023

Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature

ObjectivesSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus infection in pregnancy is associated with higher incidence of placental dysfunction, referred to by a few studies as a "preeclampsia-like syndrome". However, the mechanisms underpinning SARS-CoV-2-induced placental malfunction are still unclear. Here, we investigated whether the transcriptional architecture of the placenta is altered in response to SARS-CoV-2 infection. MethodsWe utilized whole-transcriptome, digital spatial profiling, to examine gene expression patterns in placental tissues from participants who contracted SARS-CoV-2 in the third trimester of their pregnancy (n=7) and those collected prior to the start of the coronavirus disease 2019 (COVID-19) pandemic (n=9). ResultsThrough comprehensive spatial transcriptomic analyses of the trophoblast and villous core stromal cell subpopulations in the placenta, we identified signatures associated with hypoxia and placental dysfunction during SARS-CoV-2 infection in pregnancy. Notably, genes associated with vasodilation (NOS3), oxidative stress (GDF15, CRH), and preeclampsia (FLT1, EGFR, KISS1, PAPPA2), were enriched with SARS-CoV-2. Pathways related to increased nutrient uptake, vascular tension, hypertension, and inflammation, were also enriched in SARS-CoV-2 samples compared to uninfected controls. ConclusionsOur findings demonstrate the utility of spatially resolved transcriptomic analysis in defining the underlying pathogenic mechanisms of SARS-CoV-2 in pregnancy, particularly its role in placental dysfunction. Furthermore, this study highlights the significance of digital spatial profiling in mapping the intricate crosstalk between trophoblasts and villous core stromal cells, thus shedding light on pathways associated with placental dysfunction in pregnancies with SARS-CoV-2 infection. Graphical abstractIn this study, using spatial digital profiling transcriptomic approaches, we demonstrate that SARS-CoV-2 infection in pregnancy disrupts optimal placental function by altering the genomic architecture of trophoblasts and villous core stromal cells.

developmental 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

A Method to sort heterogenous cell populations based on migration in 2D and 3D environments

Whereas phenotypic assays such as Boyden chambers and wound healing assays can easily be employed to characterize the migratory potential of cells at the population level, few methods exist that can sort subpopulations of cells based on their migratory behaviour from an initial heterogeneous pool. In this paper, we present an approach to sort migratory cancer and immune cells based on their spontaneous migration in 2D and 3D microenvironments. Using this method, which is easy to implement and readily scalable, millions of live cells can be sorted based on their migratory characteristics and then subjected to downstream genomic, molecular and functional tests. We reveal that enrichment of the most migratory cytotoxic T lymphocytes yields a pool of cells with enhanced cytotoxicity against cancer cells. This new functional sorting method opens new avenues for the precise characterization of the mechanisms underlying hitherto unexplained heterogeneities in migratory phenotypes within a cell population, and for the targeted enrichment of the most potent migratory leukocytes in immunotherapies.

cell biology↗

bioRxiv2018

Actin cytoskeleton self-organization in single epithelial cells and fibroblasts under isotropic confinement

We systematically investigated the principles of actin cytoskeleton self-organization in two cell types, fibroblasts and epitheliocytes, by confining isolated cells on isotropic adhesive islands of varying size. In fibroblasts, we previously described that an initially circular pattern of circumferential actin dynamically evolves into a radial pattern of actin bundles that spontaneously transforms into a chiral pattern, before finally producing parallel linear stress fibres. We now show that progression from circular to chiral actin patterns depends on cell projected area and rarely occurs on small islands. Epitheliocytes however, did not exhibit succession through all the actin patterns described above even on large islands. Upon confinement, the actin cytoskeleton in non-keratinocyte epitheliocytes is arrested at the circular stage, while in keratinocytes it can progress as far as the radial pattern but still cannot break symmetry. Epithelial-mesenchymal transition pushed actin cytoskeleton development from circular towards radial patterns but remains insufficient to cause chirality. Surprisingly, small doses of G-actin sequestering drug, latrunculin A, induced chiral swirling in keratinocytes. During this swirling, keratin filaments follow actin and also demonstrate chiral swirling movement. Elimination of the keratin network by genetic silencing of Type II keratins, however, did not affect the self-organization of the actin cytoskeleton.

cell biology↗