Biology subjects

Pham, J. H.

Publications and source records attributed to Pham, J. H..

6 recordsLinked to original sources

bioRxiv2026

Identification of TM4SF1 as a novel tumor-associated antigen in biliary tract cancers targetable by CAR-T cell therapy

Background & Aims: Biliary tract cancers (BTCs) are a rare set of genetically heterogenous and aggressive malignancies associated with delayed presentation and poor prognosis. Thus, there is an unmet clinical need for the development of novel therapeutic strategies. Identification of uniquely expressed cell-surface, tumor-associated antigens (TAAs) holds promise in epithelial tumors more generally, as they can serve as ligands for a variety of therapeutics, including CAR-T cell therapy. However, TAA identification in BTCs has been limited by expression in normal liver tissue. Here, we aim to characterize the cell-surface protein transmembrane 4 L six family member 1 (TM4SF1) as a potential BTC TAA targetable by CAR-T therapy. Methods: TM4SF1 expression in BTC relative to normal hepatic/biliary tissue was characterized at the mRNA level by analyzing TCGA datasets and at the protein level by immunohistochemistry of archival primary BTC tissue. Anti-TM4SF1 CAR-T cells were evaluated through in vitro coculture assays against human-derived BTC cell lines and in a cell line-derived xenograft (CDX) model. Results: We find TM4SF1 is significantly upregulated in BTC relative to normal hepatic/biliary tissue and across BTC anatomical subtypes at the mRNA and protein level. To validate TM4SF1 as a targetable TAA in BTC, we show anti-TM4SF1 CAR-T cells demonstrate robust growth inhibition of BTC cell lines in vitro and significant anti-tumor activity against a CDX in vivo. Conclusions: Together, our data provides support for TM4SF1 as a promising TAA in BTCs that can be used for the rational development of targeted therapeutic modalities, including CAR-T cells, in a patient population with significant unmet need.

cancer biology↗

bioRxiv2026

A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis

Prostate cancer encompasses a spectrum of disease states driven by complex cellular heterogeneity. To delineate the transcriptional programs underlying lineage plasticity and metastasis, we constructed a comprehensive single-cell atlas of 128 patients, spanning localized, castration-resistant, and metastatic disease. Lineage plasticity was prevalent in localized disease, with subsets of tumor cells adopting distinct basal-like and club-like states. Luminal-like cancer cells also displayed extensive lineage infidelity, defined not by a binary loss of identity but by the combinatorial erosion of luminal gene modules associated with higher grade and stage. In the metastatic setting, gene program association analysis (GPAS) identified a broad induction of cell-cycle gene modules across organ sites as well as an induction of organ-specific gene modules, including osteomimetic signaling in bone, neuro-migratory genes in brain, and erythroid-like transitions in liver. Neuroendocrine prostate cancers (NEPCs) were not monolithic but defined by combinations of NE-associated gene modules including a novel HES6 program. Notably, these modules were detected at intermediate levels in localized samples, suggesting molecular plasticity precedes histological transformation. We also developed a refined NE signature that could distinguish NEPC tumors more accurately than previously published signatures. Within the tumor microenvironment (TME), we observed an elevation of pro-inflammatory Th17 T-cells in African American patients and identified a rare Schwann cell population. Finally, we present PCformer, a transformer-based foundation model trained on >500,000 cells to automate cell-state classification. Together, this comprehensive atlas demonstrates the complex nature of gene modules underlying lineage infidelity and plasticity in cancer cells and highlights distinct immune and stromal populations within the tumor ecosystem.

genomics↗

bioRxiv2025

3D Contractile and Remodeling Behaviors of Functionally Normal and Prolapsed Human Mitral Valve Interstitial Cells

Mitral valve prolapse (MVP) can lead to heart failure, arrhythmia, and death. The only treatments available for MVP are replacement or repair; alternative therapies remain elusive due to lack of knowledge of the underlying pathological processes. The goal of the present study was thus to explore how MVP affects human mitral valve interstitial cell (hMVICs) extracellular matrix (ECM) remodeling and basal contractility characteristics. Isolated MVP and physiologically normal hMVICs were embedded in poly(ethylene) glycolbased hydrogels containing fluorescent fiducial markers and 3D traction force microscopy via inverse modeling was employed to determine the local change in hMVIC hydrogels due to enzymatic degradation and collagen deposition. Results indicated pronounced hydrogel softening occurred generally further from the hMVICs, whereas stiffening occurred in close proximity to hMVICs due to collagen deposition as verified by collagen-staining. MVP hMVICs induced greater hydrogel stiffening and less degradation than normal hMVICs. Interestingly, even though MVP hMVICs had higher basal contractile displacements, their corresponding traction forces and hydrogel strain energy densities were significantly lower than those of normal hMVICs. These findings elucidate, for the first time, that MVP hMVICs have significantly altered biophysical contractile and ECM remodeling behaviors compared to normal hMVICs. Simple SummaryWhen a mitral heart valve gets thick, stiffened, and degraded, it can flip backwards (prolapse), causing blood to flow the wrong way. This can cause heart failure, arrhythmia, or even death. The only treatment for mitral valve prolapse (MVP) is surgery. To pave the way for a medication, this study aimed to understand how cells that maintain the mitral valve, mitral valve interstitial cells (MVICs), act on their surrounding tissue. The mechanical properties of the MVICs were tested, including how much they contract and how much they pull on their surroundings. Also, the mechanical properties that the MVICs place on their surroundings were tested, like how much they stiffen and degrade the tissue and how much energy is stored in the tissue as the MVICs contract. Compared to normal MVICs, we found that MVP MVICs stiffen their surroundings more and degrade their surroundings less. We also found that even though MVP MVICs contract more than normal MVICs, the energy that they place on their surroundings is less than that of normal MVICs, indicating that MVP MVICs are less mechanically effective. This is the first time that this ineffectiveness has been seen and may be key to targeting MVP with future medications.

cell biology↗

bioRxiv2025

A New Computational Inverse Modeling Approach for Cellular Traction Force Microscopy that Accounts for Hydrogel Compressibility

We have recently documented significant compressible behaviors in hydrogels implemented in 3D traction force microscopy (TFM). Therefore, here we have developed a new computational pipeline that accounts for this observation. Additionally, the new method accurately recovers large ranges and spatial heterogeneity of hydrogel moduli induced by cellular remodeling associated with enhanced extracellular matrix secretion and MMP-degradation. The algorithm sought best fit of the 3D displacement field with a multi-stage approach, wherein the Tikhonov regularization parameter in L-BFGS was progressively lowered. Forward simulations were performed in FEniCS, with gradients computed with FEniCS-adjoint and MOOLA to weight degrees of freedom according to hydrogel volume affected. Once developed, we conducted a series of synthetic test cases applying actual cell geometries, experimentally-matched compressibility, and realistic displacements with experimental noise levels. Employing an incompressible material model resulted in predicted moduli with over 415% mean relative error and predicted strain energies 5-fold greater than the prescribed values. Moreover, errors in predicted traction forces were amplified by a factor of 10. Thus, accounting for hydrogel compressibility was critical for accurate hydrogel moduli and strain energy recovery. To demonstrate the utility of our approach, we applied it to TFM data of human mitral valve interstitial cells embedded in PEG hydrogels with pre-altered moduli of 54 Pa. We determined that J [isin] [0.45, 1.66] and local hydrogel moduli exhibited large variations, 3.6 Pa to 2.4 MPa. This study underscores the need for correct handling of hydrogel compressibility for accurate estimation of local hydrogel moduli and traction forces.

bioengineering↗

bioRxiv2023

RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4

Microsatellite instability high (MSI-H) tumors are malignant tumors that, despite harboring a high mutational burden, often have intact TP53. One of the most frequent mutations in MSI-H tumors is a frameshift mutation in RPL22, a ribosomal protein. Here, we identified RPL22 as a modulator of MDM4 splicing through an alternative splicing switch in exon 6. RPL22 loss increases MDM4 exon 6 inclusion, cell proliferation, and augments resistance to the MDM inhibitor Nutlin-3a. RPL22 represses expression of its paralog, RPL22L1, by mediating the splicing of a cryptic exon corresponding to a truncated transcript. Therefore, damaging mutations in RPL22 drive oncogenic MDM4 induction and reveal a common splicing circuit in MSI-H tumors that may inform therapeutic targeting of the MDM4-p53 axis and oncogenic RPL22L1 induction.

cancer biology↗

bioRxiv2019

Spreading depolarization and repolarization during cardiac arrest as an ultra-early marker of neurological recovery in a preclinical model

Spreading depolarization (SD) accompanies numerous neurological conditions, including migraine, stroke, and traumatic brain injury. There is significant interest in understanding the relationship between SD and neuronal injury. However, characteristics underlying SD and repolarization (RP) induced by global cerebral ischemia (e.g., cardiac arrest (CA)) and reperfusion are not well understood. Quantifying features of SD and RP during CA and cardiopulmonary resuscitation (CPR) may provide important metrics for diagnosis and prognosis of neurological injury from hypoxia-ischemia. We characterized SD and RP in a rodent model of asphyxial CA+CPR using a multimodal platform including electrocorticography (ECoG) and optical imaging. We detected SD and RP by (1) alternating current (AC), (2) direct current (DC), and (3) optical imaging of spreading ischemia, spreading edema, and vasoconstriction. Earlier SD (r=-0.80; p<0.001) and earlier RP (r=-0.71, p<0.001) were associated with better neurological recovery after 24hrs. SD+RP onset times predicted good vs poor neurological recovery with 82% sensitivity and 91% specificity. To our knowledge, this is the first preclinical study to link SD and RP characteristics with neurological recovery post-CA. These data suggest that SD and RP may be ultra-early, real-time prognostic markers of post-CA outcome, meriting further investigation into translational implications during global cerebral ischemia.

neuroscience↗