Biology subjects

Suneja, G.

Publications and source records attributed to Suneja, G..

3 recordsLinked to original sources

bioRxiv2025

Comparison of QuPath and HALO platforms for analysis of the tumor microenvironment in prostate cancer

QuPath, an open-source digital pathology platform, has gained widespread use for image analysis in biomedical research since its release in 2016. However, its reproducibility and reliability compared to commercial software, such as HALO, requires further validation, particularly for multiplex immunofluorescence (mIF) analysis. In this study, we performed a direct comparison of QuPath and HALO using a mIF-stained prostate cancer tissue microarray (TMA) inclusive of 192 unique cores. We evaluated performance across three key analytical modules: immune cell phenotyping, tumor infiltration with immune cells, and nearest neighbor analysis. Furthermore, we integrated QuPath with CytoMap, an open-source spatial analysis tool, to perform unsupervised clustering of immune cell infiltration--a feature not available in HALO. Our results demonstrated high concordance between two platforms, with correlation coefficients exceeding 0.89 for immune cell density, distance and pattern of cell organization in tumor microenvironment (TME). A neighborhood analysis using CytoMap was further performed and provided a more detailed spatial analysis of immune cell distribution across different prostate cancer grades. A significant increase of CD103+ T cell infiltration into TME was observed in prostate cancer, which might be associated with the expression level of its ligand (E-cadherin) in the tumor region. In conclusion, our findings validate QuPath as a robust and reproducible alternative to commercial platforms for fluorescence-based digital pathology. By demonstrating QuPaths capability to perform high-quality quantitative analysis with additional flexibility for integration with external tools, our study underscores its potential for advancing tumor microenvironment research in translational oncology.

pathology↗

bioRxiv2025

Population analysis and immunologic landscape of melanoma in people living with HIV

PurposeTo dissect the clinical and immunological features of people living with HIV (PLWH) diagnosed with melanoma, who have consistently shown worse outcomes than HIV-negative individuals (PLw/oH) with the same cancer. Experimental DesignWe analyzed electronic health records from 1,087 PLWH and 394,437 PLw/oH with melanoma. Demographic and clinical characteristics were compared. Spatial immune transcriptomics (72 immune-related genes) was performed on melanoma tumor samples (n=11), with downstream validation using multiplex immunofluorescence (n=15 PLWH, n=14 PLw/oH). ResultsPLWH were diagnosed at a younger age, had greater representation of Hispanic and Black individuals, and showed reduced survival. They also had a markedly increased risk of brain metastases. PLWH experienced significant delays in initiating immune checkpoint inhibitor (ICI) therapy and had worse post-ICI survival, even after balancing covariates. Spatial transcriptomics revealed a more immunosuppressive tumor microenvironment in PLWH, with increased transcription of immune checkpoints (PD1, LAG3) and reduced antigen-presentation markers (HLA-DRB, B2M), with distinct spatial distributions in tumors and surrounding microenvironments. Multiplex immunofluorescence demonstrated features of an exhausted CD8 T cell compartment, including enrichment of PD1intLAG3- and PD1intLAG3 subpopulations, and a significant accumulation of myeloid-derived suppressor cells (CD11b HLA-DR- CD33). ConclusionsMelanoma in PLWH is associated with distinct clinical and immunological features, including delayed ICI treatment, reduced survival, and an immunosuppressive microenvironment with exhausted CD8 T cells and expanded myeloid-derived suppressor cells. These findings suggest that chronic HIV infection may impair antitumor immunity in melanoma. Targeting the pathways identified here may improve therapeutic responses and outcomes in this population. Statement of translational relevanceThis study reveals critical barriers to effective melanoma treatment in people living with HIV (PLWH). Despite receiving immune checkpoint inhibitors (ICIs), PLWH face delayed therapy initiation, a greater likelihood of brain metastases, and significantly higher long-term mortality, even after adjusting for demographic covariates. Transcriptional immune profiling further uncovers a tumor microenvironment enriched in immunosuppressive myeloid-derived suppressor cells and CD8 T cell populations with features of exhaustion. These findings suggest that poorer outcomes in PLWH stem not only from delayed care, but also from distinct targetable mechanisms of immune dysfunction. For example, strategies to reverse MDSC accumulation in the tumor or tailored ICI regimens could enhance immune responsiveness and improve treatment efficiency. By defining the clinical and immunological features of this population, this work highlights opportunities for precision immunotherapy tailored to PLWH with melanoma, with direct implications for improving survival and reducing disparities.

cancer biology↗

bioRxiv2019

A Novel, Versatile Speculum-free Callascope for Clinical Examination and Self-Visualization of the Cervix

BackgroundInvasive cervical cancer is preventable, yet affects 500,000 women worldwide each year, and over half these women die. Barriers to cervical cancer screening include lack of awareness of cervical cancer and the cervix, fear of the speculum, and lack of women-centric technologies. We developed a low-cost ([~]$50), cervix-imaging device called the Callascope, which comprises an imaging component, camera and inserter that eliminates the need for a speculum and enables self-insertion. We sought to assess the quality of physicians images of the cervix using the Callascope versus the speculum in live patients and study womens willingness to independently use the Callascope to image their cervix.\n\nMethodsWe conducted two main studies: (1) a clinical study in which a physician imaged the cervix of patients using both the speculum and Callascope in a 2x2 crossover design; and (2) home-based self-cervix imaging with the Callascope.\n\nResultsParticipants of the clinical study (n=28) and home study (n=12) all indicated greater comfort and an overall preference for the Callascope over the speculum. The clinical study data indicated that the Callascope enabled similar visualization compared to the speculum while significantly improving patient experience. With physician insertion and manipulation, the Callascope enabled cervix visualization for 82% of participants. In the home-study, 83% of participants were able to visualize their cervix with the Callascope on the first try and 100% after multiple attempts.\n\nConclusionThe Callascope is more comfortable and provides similar visualization to the speculum. The Callascope can be used by medical providers for clinical exams while also enabling home self-screening for cervical cancer and promoting a better understanding of ones cervix to increase awareness of cervical screening needs. The Callascope may increase cervical cancer screening rates through reducing barriers including cost, discomfort, lack of awareness and stigma.

clinical trials↗