Biology subjects

Lou, E.

Publications and source records attributed to Lou, E..

14 recordsLinked to original sources

bioRxiv2026

Explaining and predicting pseudoprogression in immunotherapythrough joint modeling of immune infiltration and ctDNA dynamics

Pseudoprogression in response to immune checkpoint inhibitor (ICI) therapy can be a complex challenge during treatment response evaluation. Erroneous classification of progression may result in stopping effective treatment for patients, while delayed confirmation of progression can prolong an ineffective treatment course. We develop a mechanistic mathematical model of tumor-immune dynamics under ICI treatment in which observed tumor volume includes contributions from both tumor burden and immune infiltration. We show analytically how pseudoprogression can arise from increased immune infiltration and proliferation as well as continued tumor growth during the ``ramp-up" phase. The model also incorporates circulating tumor DNA (ctDNA) dynamics, which we demonstrate are able to closely fit existing longitudinal tumor and ctDNA data and extract realistic parameter ranges to generate representative in silico data. Using model-generated cohorts, we train a random forest (RF) classifier using longitudinal tumor and ctDNA measurements to distinguish pseudoprogression and true progression, and demonstrate that it improves response classification relative to the Response Evaluation Criteria in Solid Tumors (RECIST 1.1) and provides classification earlier than the immunotherapy-specific iRECIST, even in the presence of tumor measurement noise. This work predicts that paired longitudinal tumor-ctDNA measurements may enable earlier discrimination of true progression from pseudoprogression, and motivates collection of imaging and ctDNA data synchronously during ICI therapy, especially in the setting of suspected disease progression.

cancer biology↗

bioRxiv2026

Modeling CISH-KO TIL therapy: T-cell persistence and endogenous competition determine response in gastrointestinal cancer

BackgroundTumor-infiltrating lymphocyte (TIL) therapies have shown promise in murine models; however, early-phase clinical trials reveal substantial heterogeneity in treatment response across patients. Elucidating the biological drivers of this variability is critical for improving patient selection and therapeutic design. MethodsWe developed a mechanistic mathematical model of Cish-inactivated TIL therapy capturing interactions among tumor cells, endogenous TILs, and infused CISH-KO (Cish gene knockout) T-cells. The model was calibrated to longitudinal tumor size data from two murine studies and also fitted to clinical data from a first-in-human phase 1 trial enrolling 22 and treating 12 patients with metastatic gastrointestinal cancers (27 independently tracked tumor lesions). We used the calibrated model to identify patient-level determinants of response and to simulate combination and fractionation treatment strategies in silico. FindingsFour mechanistically distinct parameters emerged as dominant determinants of therapeutic outcome: CISH-KO T-cell persistence (r = 0.827, p < 10-4) was the single strongest predictor of therapeutic failure; other major determinants included endogenous T-cell proliferation rate (r = 0.648, p < 10-4) , CISH-KO T-cell killing rate, and intrinsic tumor growth rate. In silico simulations predicted that the addition of anti-PD-1 checkpoint blockade to standard-dose CISH-KO TIL therapy achieved comparable or superior tumor control relative to dose doubling, while maintaining lower peak T-cell level. Additionally, fractionating the same total dose across multiple delayed infusions further improved predicted tumor control by prolonging CISH-KO T-cell persistence, again without raising peak effector burden. InterpretationThe efficacy of current CISH-KO TIL protocols is influenced not only by the cytotoxic potency of infused T-cells, but also by their persistence within the tumor microenvironment and competitive pressure from the reconstituting host immune compartment. These findings support strategies that enhance the functional efficiency and prolong the availability of infused T-cells--such as concurrent PD-1 blockade or fractionated dosing of the same total cell product--rather than dose escalation alone and identify CISH-KO T-cell persistence and endogenous immune competition as actionable targets for improving TIL-based immunotherapies.

Cancer Biology↗

bioRxiv2025

The transcriptional regulatory circuit as a driver and therapeutic target in CML blast crisis

Patients with blast crisis in chronic myeloid leukemia (CML) exhibit an extremely poor prognosis, with median survival of only a few months and limited therapeutic options. Dysregulated transcriptional regulation plays a pivotal role in driving blast crisis progression. In this study, we performed histone modification and transcriptomic high-throughput sequencing on bone marrow cells derived from chronic and blast-phase CML patients, identifying a CML blast-specific transcriptional regulatory circuit comprising MEF2C, MYB, MEIS1, and ZEB2. These transcription factors (TFs) form protein complexes that co-bind to shared enhancers or promoters, reciprocally enhancing each others transcriptional activity and that of their downstream targets. Mechanistically, this circuit synergistically reprograms chromatin accessibility and transcriptional landscapes in blast cells, parallel activation of purine metabolism and Rho GTPase signaling pathways which exhibit functional crosstalk. Functional validation demonstrated that silencing components of this circuit or its downstream core targets significantly suppressed CML blast progression in vitro and in vivo. Notably, mebendazole (MBZ), a clinically approved inhibitor targeting MYB protein stability, recapitulated these inhibitory effects. Our findings establish the MEF2C-MYB-MEIS1-ZEB2 transcriptional circuit as a central driver of CML blast crisis and position MBZ as a high-potential translational strategy for targeting this lethal phase of the disease. Key PointsO_LIMEF2C, MYB, MEIS1, and ZEB2 form the CML blast-crisis transcriptional circuit, synergistically reprogramming chromatin and transcription. C_LIO_LIMebendazole inhibits CML blast progression by impairing the circuit, offering a rapid translational strategy for this lethal phase. C_LI

cancer biology↗

bioRxiv2025

Targeting Neutrophil Extracellular Traps to inhibit Colon Cancer Tumor Necrosis and Metastasis

Necrosis, conventionally thought of as a passive consequence of aggressive tumor growth, is associated with poor prognosis in colorectal cancer (CRC). We recently discovered that necrosis can be caused by neutrophils and neutrophil extracellular traps (NETs) aggregates driving vascular occlusion within the tumor vasculature in models of breast cancer. Here, we evaluated the role of NETs in inducing necrosis and metastasis in CRC. We found that the numbers of neutrophils primed to form NETs were elevated in the circulation of patients with CRC as compared to controls. CD177Low neutrophils were also elevated, and they showed reduced extravasation capacity with intact ability to form NETs. The extent of necrosis correlated with metastasis (stage IV disease), independent of tumor size, in our human cohort. In both human and murine CRC tumors, necrotic regions were characterized by neutrophil infiltration and NET accumulation, and NET aggregates were observed in the vasculature next to the necrotic regions. Single cell RNA sequencing and spatial transcriptomic analysis of human CRC and liver metastases revealed that necrotic tumors activate pathways associated with increased metastatic potential, including epithelial-to-mesenchymal-transition. Using a mouse model of DNA mismatch repair proficient CRC, we found neutrophil infiltration and NETs increased with tumor progression. Genetic or pharmacological inhibition of NET formation decreased necrosis and metastasis, and importantly enhanced chemotherapy efficacy. Altogether, our findings show that NET formation in human CRC is a key feature of tumor necrosis, that it is associated with metastasis, and further suggest that preventing NET formation may offer clinical benefits to CRC patients.

cancer biology↗

bioRxiv2025

CISH, a novel intracellular immune checkpoint, in comparison and combination to existing and emerging cancer immune checkpoints

Over the past decade, Immuno-Oncology has largely focused on blocking inhibitory surface receptors like PD-1 to enhance T cell anti-tumor activity. However, intracellular immune checkpoints such as CISH, which function independently of tumor-expressed ligands, offer powerful and previously untapped therapeutic potential. As a downstream regulator of TCR signaling, CISH controls T cell activation, expansion, and neoantigen reactivity. Though historically considered undruggable, recent advances in CRISPR engineering have enabled functional interrogation of these targets. We demonstrate that CISH deletion enhances T cell activation and anti-cancer functions more effectively than other emerging intracellular checkpoints. In CAR-T cells, CISH inactivation significantly increased sensitivity to tumor antigen, enabling robust recognition and killing even at low antigen levels, conditions that often lead to treatment failure with conventional T cell therapies, mirroring antigen escape scenarios seen in solid tumors. Our findings further validate CISH as a potent and druggable intracellular checkpoint capable of boosting anti-tumor T cell responses across diverse cancer types, independent of PD-L1 status. The underlying mechanisms of CISH inhibition may help explain the positive outcomes reported in recent clinical studies of this approach in solid tumor immunotherapy.

cancer biology↗

bioRxiv2024

Early ctDNA kinetics as a dynamic biomarker of cancer treatment response

Circulating tumor DNA assays are promising tools for the prediction of cancer treatment response. Here, we build a framework for the design of ctDNA biomarkers of therapy response that incorporate variations in ctDNA dynamics driven by specific treatment mechanisms. We develop mathematical models of ctDNA kinetics driven by tumor response to several therapy classes, and utilize them to simulate randomized virtual patient cohorts to test candidate biomarkers. Using this approach, we propose specific biomarkers, based on ctDNA longitudinal features, for targeted therapy, chemotherapy and radiation therapy. We evaluate and demonstrate the efficacy of these biomarkers in predicting treatment response within a randomized virtual patient cohort dataset. These biomarkers are based on novel proposals for ctDNA sampling protocols, consisting of frequent sampling within a compact time window surrounding therapy initiation - which we hypothesize to hold valuable prognostic information on longer-term treatment response. This study highlights a need for tailoring ctDNA sampling protocols and interpretation methodology to specific biological mechanisms of therapy response, and it provides a novel modeling and simulation framework for doing so. In addition, it highlights the potential of ctDNA assays for making early, rapid predictions of treatment response within the first days or weeks of treatment, and generates hypotheses for further clinical testing.

cancer biology↗

bioRxiv2023

Clinical Significance of the Stromatic Component in Ovarian Cancer: Quantity Over Quality in Outcome Prediction

BackgroundThe tumor stroma is composed of a complex network of non-cancerous cells and extracellular matrix elements that collectively are crucial for cancer progression and treatment response. Within the realm of ovarian cancer, the expression of the stromal gene cluster has been linked to poorer progression-free and overall survival rates. However, in the age of precision medicine and genome sequencing, the notion that the simple measurement of tumor-stroma proportion alone can serve as a biomarker for clinical outcome is a topic that continues to generate controversy and provoke discussion. Our current study reveals that it is the quantity of stroma, rather than its quality, that serves as a clinically significant indicator of patient outcome in ovarian cancer. MethodsThis study leveraged the High-Grade-Serous-Carcinoma (HGSC) cohort of the publicly accessible Cancer Genome Atlas Program (TCGA) along with an independent cohort comprising HGSC clinical specimens in diagnostic and Tissue Microarray formats. Our objective was to investigate the correlation between the Tumor-Stroma-Proportion (TSP) and progression-free survival (PFS), overall survival (OS), and response to chemotherapy. We assessed these associations using H&E-stained slides and tissue microarrays. Our analysis employed semi-parametric models that accounted for age, metastases, and residual disease as controlling factors. ResultsWe found that high TSP (>50% stroma) was associated with significantly shorter progression-free survival (PFS) (p=0.016) and overall survival (OS) (p=0.006). Tumors from patients with chemoresistant tumors were twice as likely to have high TSP as compared to tumors from chemosensitive patients (p=0.012). In tissue microarrays, high TSP was again associated with significantly shorter PFS (p=0.044) and OS (p=0.0001), further confirming our findings. The Area Under the ROC curve for the model predicting platinum was estimated at 0.7644. ConclusionsIn HGSC, TSP was a consistent and reproducible marker of clinical outcome measures, including PFS, OS, and platinum chemoresistance. Assessment of TSP as a predictive biomarker that can be easily implemented and integrated into prospective clinical trial design and adapted to identify, at time of initial diagnosis, patients who are least likely to benefit long-term from conventional platinum-based cytotoxic chemotherapy treatment.

pathology↗

bioRxiv2022

Treatment with Tumor-Treating Fields (TTFields) Suppresses Intercellular Tunneling Nanotube Formation In Vitro and Upregulates Immuno-Oncologic Biomarkers In Vivo in Malignant Mesothelioma

Intercellular communication is critical for the development of invasive cancers. Multiple forms of intercellular communication have been well characterized, involving diffusible soluble factors or contact-dependent channels for immediately adjacent cells. Over the past 1-2 decades, the emergence of a unique form of F-actin-based cellular protrusion known as tunneling nanotubes (TNTs) has filled the niche of long-range cell-contact dependent intercellular communication that facilitates cell growth, differentiation, and in the case of invasive cancer phenotypes, a more chemoresistant phenotype. The cellular machinery of TNT-mediated transport is an area of active investigation, and microtubules have been implicated in this process as they are in other membranous protrusions. Tumor-Treating Fields (TTFields) therapy is a novel therapeutic strategy in clinical use for patients with advanced cancers, based on the principle of using low-intensity alternating electric fields to disrupt microtubules in cancer cells undergoing mitosis. Other mechanisms of action have also been demonstrated. In this study, we investigated the effects of TTFields on TNTs in malignant pleural mesothelioma (MPM) in vitro and also on the spatial transcriptomic landscape in vivo. We found that applying TTFields at 1.0 V/cm significantly suppressed TNT formation in a biphasic MPM cell line (MSTO-211H), but not in sarcomatoid MPM (VAMT). At these parameters, TTFields significantly reduced cell count in MSTO-211H, but did not significantly alter intercellular transport of mitochondria via intact TNTs. To understand how TTFields may impact expression of genes with known involvement to TNT formation and overall tumor growth, we performed spatial genomic assessment of TTFields-treated tumors from an in vivo animal model of MPM, and detected upregulation of immuno-oncologic biomarkers with simultaneous downregulation of pathways associated with cell hyperproliferation, invasion, and other critical regulators of oncogenic growth. Several molecular classes and pathways coincide with markers that we and others have found to be differentially expressed in cancer cell TNTs, including MPM specifically. In this study, we report novel cellular and molecular effects of TTFields in relation to tumor communication networks enabled by TNTs and related molecular pathways. These results position TNTs as potential therapeutic targets for TTFields-directed cancer treatment strategies; and also identify the ability of TTFields to potentially remodel the tumor microenvironment, thus enhancing response to immunotherapeutic drugs.

cancer biology↗

bioRxiv2021

GLS1 is a Protective Factor Rather than a Molecular Target in ARID1A-Mutated Ovarian Clear Cell Carcinoma

Targeting glutamine metabolism has emerged as a novel therapeutic strategy for several human cancers, including ovarian cancer. The primary target of this approach is the kidney isoform of glutaminase, glutaminase 1 (GLS1), a key enzyme in glutamine metabolism that is overexpressed in several human cancers. A first-in-class inhibitor of GLS1, called CB839 (Telaglenastat), has been investigated in several clinical trials, with promising results. The first clinical trial of CB839 in platinum-resistant ovarian cancer patients is forthcoming. ARID1A-mutated ovarian clear cell carcinoma (OCCC) is a relatively indolent and chemoresistant ovarian cancer histotype. In OCCC-derived cells in vitro and mouse models, loss of ARID1A leads to upregulation of GLS1. Thus, targeting of GLS1 with CB839 has been suggested as a targeted approach for OCCC patients with tumors harboring ARID1A-mutations. Here, we investigated whether GLS1 is differentially expressed between OCCC patients whose tumors are ARID1A positive and patients whose tumors are ARID1A negative. In clinical specimens of OCCC, we found that GLS1 overexpression was not correlated with ARID1A loss. In addition, GLS1 overexpression was associated with better clinical outcomes. Our findings suggest that GLS1 expression in OCCC may be a protective factor and that caution should be taken when considering the use of CB839 to treat OCCC patients.

cancer biology↗

bioRxiv2021

Genetic editing of CISH enhances T cell effector programs independently of immune checkpoint cell surface ligand expression

PD-1 acts as a negative regulator of T cell-mediated immune responses in the setting of persistent antigen expression, including cancer and chronic pathogen infections. Antibody-mediated blockade of the PD-1/PD-L1 axis benefits a subset of patients with highly immunogenic malignancies; however, many patients fail to respond due to a requirement for expression of the cell surface ligand PD-L1 within the tumor microenvironment. CISH is a member of a new class of intra-cellular immune checkpoint molecules that function downstream of the T cell receptor to regulate antigen-specific effector functions, including reactivity to cancer neoantigens. Herein, we employed multiplex CRISPR editing of primary human T cells to systematically compare the function of CISH deletion relative to PDCD1 (the gene encoding PD-1) and/or VSIG9 (the gene encoding TIGIT) in a model of neoantigen-mediated cancer cell cytolysis. PD-1 and TIGIT disruption enhanced cytolytic activity exclusively in the setting of high PD-L1 expression. In contrast, CISH inactivation enhanced antigen-specific cytolysis of tumor cells regardless of PD-L1 expression, including outperforming PD-1 and TIGIT disruption even in the presence of high PD-L1 tumor cells. Furthermore, we observed a synergistic increase in tumor cell killing when CISH and PD-1 or TIGIT are inactivated in combination, supporting the notion that these immune checkpoints regulate non-redundant pathways of T cell activation. Together, these data demonstrate that the intra-cellular immune checkpoint protein CISH can potentially enhance anti-tumor responses against a broad range of cancer types regardless of PD-L1 biomarker status.

cancer biology↗

bioRxiv2019

RAS Internal Tandem Duplication Disrupts GAP-binding to Activate Oncogenic Signaling

Molecular testing of oncogenic RAS mutations in colorectal cancer (CRC) have led to increased identification of mutations in patients with CRC. NRAS-mutated CRC has not been well characterized because it is less common (<6%) than KRAS mutations. Here, we report a novel 10 amino acid internal tandem duplication (ITD) in NRAS, which disrupts the switch II domain, in a patient with widely disseminated CRC. Hotspot next generation sequencing of a brain metastasis identified the NRAS ITD and a TP53 missense mutation (p.P275F). Whole exome sequencing of the primary tumor and two metastatic lesions (lung and brain) confirmed that the NRAS ITD and TP53 mutation were conserved between the primary tumor and both metastatic tumors, and identified an additional pathogenic mutation in CSMD1 (a tumor suppressor gene). Structural biology and biochemical analyses demonstrated that the NRAS ITD prevented binding to GAP protein, leading to sustained RAS activation, increased interaction with RAF, and downstream MAPK activation. Additionally, we provide the first crystal structure of the RAS ITD. In conclusion, these studies indicate that the NRAS ITD was the probable primary driver mutation of this aggressive CRC. Identical or biologically similar ITDs in NRAS and KRAS may be rare drivers of CRC and other aggressive malignancies.

molecular biology↗

bioRxiv2019

Tumor-draining lymph nodes resection and chemotherapy have diverse impacts on cancer immunotherapies

Immunotherapies are used as adjuvant therapies for cancers. However, knowledge of how traditional cancer treatments affect immunotherapies is limited. Using mouse models, we demonstrate that tumor-draining lymph nodes (TdLNs) are critical for tumor antigen-specific T-cell response. However, removing TdLNs concurrently with established primary tumors did not affect the immune checkpoint blockade (ICB) response on localized secondary tumor due to immunotolerance in TdLNs and distribution of antigen-specific T cells in peripheral lymphatic organs. Notably, treatment response improved with sequential administration of 5-fluorouracil (5-FU) and ICB compared to concurrent administration of ICB with 5-FU. Immune profiling revealed that using 5-FU as induction treatment increased tumor visibility to immune cells, decreased immunosuppressive cells in the tumor microenvironment, and limited chemotherapy-induced T-cell depletion. We show that the effect of traditional cytotoxic treatment, not TdLNs, influences immunotherapy response in localized secondary tumors. We postulate essential considerations for successful immunotherapy strategies in clinical conditions. Graphic abstractThe effects of tumor-draining lymph nodes (TdLNs) resection and a combination of cytotoxic chemotherapy on immune checkpoint blockade therapies are evaluated in this study. TdLNs resection was adverse in eliciting an antitumor immune response in early-stage tumors, but not in late-stage tumors. Further, sequential treatments with cytotoxic chemotherapy and immunotherapy showed better tumor control compared to concurrent combinatorial treatments.

cancer biology↗

bioRxiv2019

UNC-45A is preferentially expressed in epithelial cells and binds to and co-localizes with interphase MTs

UNC-45A is a ubiquitously expressed protein highly conserved throughout evolution. Most of what we currently know about UNC-45A pertains to its role as a regulator of the actomyosin system. However, emerging studies from both our and other laboratories support a role of UNC-45A outside of actomyosin regulation. This includes studies showing that UNC-45A: regulates gene transcription, co-localizes and biochemically co-fractionates with gamma tubulin and regulates centrosomal positioning, is found in the same subcellular fractions where MT-associated proteins are, and is a mitotic spindle-associated protein with MT destabilizing activity in absence of the actomyosin system.\n\nHere, we extended our previous findings and show that UNC45A is variably expressed across a spectrum of cell lines with the highest level being found in HeLa cells and in ovarian cancer cells inherently paclitaxel-resistant. Furthermore, we show that UNC-45A is preferentially expressed in epithelial cells, localizes to mitotic spindles in clinical tumor specimens of cancer and co-localizes and co-fractionates with MTs in interphase cells independent of actin or myosin.\n\nIn sum, we report alteration of UNC45A localization in the setting of chemotherapeutic treatment of cells with paclitaxel, and localization of UNC45A to MTs both in vitro and in vivo. These findings will be important to ongoing and future studies in the field that further identify the important role of UNC45A in cancer and other cellular processes.

cell biology↗

bioRxiv2018

Real time monitoring of transtibial elevated vacuum prostheses: a case series on socket air pressure

Elevated vacuum is a prosthetic suspension method used to reduce slippage between the prosthetic socket and the residual limb. Evaluation of the effectiveness of these systems is limited due to a lack of correlation to actual socket air pressure, particularly during unconstrained movements. This may explain some of the variability in functional outcomes reported in the literature. We developed a light-weight portable socket measurement system to quantify internal socket air pressure, temperature, and acceleration. We implemented the system onto the sockets of three transtibial prosthesis users with mechanical elevated vacuum pumps. Participants completed five functional tasks with and without the vacuum pumps actively connected, including the 2-Minute Walk test, 5-Times Sit-to-Stand test, 4-Square Step test, L-Test, and Figure-8 test. Results demonstrated that the use of elevated vacuum pumps produced different gait profiles and pressure ranges for each user, with significant differences between pump conditions. Two of the participants demonstrated substantially lower air pressure (higher vacuum) over time while the pump was active compared to inactive. The minimum air pressure measured at the completion of the 2-Minute Walk test was -34.6 {+/-} 7.7 kPa, which is not as low as pressures reported in literature during benchtop experiments. One participant did not show substantial changes in pressure over time for either pump condition. Functional task performance was not significantly different between pump conditions. Correlation with accelerometer readings allowed air pressure data to be aligned with the gait cycle; peak positive pressures occurred just following initial contact of the foot in early stance, and the most negative pressures (vacuum) were observed throughout swing. This study has demonstrated the use of a portable data logging tool that may serve the clinical and research communities to quantify the operation of elevated vacuum systems, and better understand the variability of mechanical pump operation and overall system performance.

bioengineering↗