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Journal articles on the topic 'Tumor cell computation'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

Ryser, Marc D., Byung-Hoon Min, Kimberly D. Siegmund, and Darryl Shibata. "Spatial mutation patterns as markers of early colorectal tumor cell mobility." Proceedings of the National Academy of Sciences 115, no. 22 (2018): 5774–79. http://dx.doi.org/10.1073/pnas.1716552115.

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A growing body of evidence suggests that a subset of human cancers grows as single clonal expansions. In such a nearly neutral evolution scenario, it is possible to infer the early ancestral tree of a full-grown tumor. We hypothesized that early tree reconstruction can provide insights into the mobility phenotypes of tumor cells during their first few cell divisions. We explored this hypothesis by means of a computational multiscale model of tumor expansion incorporating the glandular structure of colorectal tumors. After calibrating the model to multiregional and single gland data from 19 hum

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Bernardis, Alessia, Marco Bullo, Luca Giovanni Campana, et al. "Electric field computation and measurements in the electroporation of inhomogeneous samples." Open Physics 15, no. 1 (2017): 790–96. http://dx.doi.org/10.1515/phys-2017-0092.

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AbstractIn clinical treatments of a class of tumors,e.g. skin tumors, the drug uptake of tumor tissue is helped by means of a pulsed electric field, which permeabilizes the cell membranes. This technique, which is called electroporation, exploits the conductivity of the tissues: however, the tumor tissue could be characterized by inhomogeneous areas, eventually causing a non-uniform distribution of current. In this paper, the authors propose a field model to predict the effect of tissue inhomogeneity, which can affect the current density distribution. In particular, finite-element simulations,

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Eddy, James A., Vésteinn Thorsson, Andrew E. Lamb, et al. "CRI iAtlas: an interactive portal for immuno-oncology research." F1000Research 9 (August 24, 2020): 1028. http://dx.doi.org/10.12688/f1000research.25141.1.

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The Cancer Research Institute (CRI) iAtlas is an interactive web platform for data exploration and discovery in the context of tumors and their interactions with the immune microenvironment. iAtlas allows researchers to study immune response characterizations and patterns for individual tumor types, tumor subtypes, and immune subtypes. iAtlas supports computation and visualization of correlations and statistics among features related to the tumor microenvironment, cell composition, immune expression signatures, tumor mutation burden, cancer driver mutations, adaptive cell clonality, patient su

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Neeru Saxena. "Ensemble XMOB Approach for Brain Tumor Detection Based on Feature Extraction." Tuijin Jishu/Journal of Propulsion Technology 45, no. 03 (2024): 593–607. http://dx.doi.org/10.52783/tjjpt.v45.i03.7253.

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Brain tumors are a serious health threat in adults. These fast-growing abnormal cell masses disrupt normal brain function. Doctors use various imaging techniques to identify the specific type, size, and location of brain tumors in patients. Accurately identifying and classifying brain tumors is crucial for understanding how they develop and progress. Magnetic Resonance Imaging (MRI), a well-established medical imaging technique, plays a vital role in this process by assisting radiologists in investigating the location of the tumor. Previous models frequently encounter a compromise between accu

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Zhang, Bing, and Michal Bassani-Sternberg. "Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery." Journal for ImmunoTherapy of Cancer 11, no. 10 (2023): e007073. http://dx.doi.org/10.1136/jitc-2023-007073.

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Identification of tumor antigens presented by the human leucocyte antigen (HLA) molecules is essential for the design of effective and safe cancer immunotherapies that rely on T cell recognition and killing of tumor cells. Mass spectrometry (MS)-based immunopeptidomics enables high-throughput, direct identification of HLA-bound peptides from a variety of cell lines, tumor tissues, and healthy tissues. It involves immunoaffinity purification of HLA complexes followed by MS profiling of the extracted peptides using data-dependent acquisition, data-independent acquisition, or targeted approaches.

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Bloom, Alexander B., and Muhammad H. Zaman. "Influence of the microenvironment on cell fate determination and migration." Physiological Genomics 46, no. 9 (2014): 309–14. http://dx.doi.org/10.1152/physiolgenomics.00170.2013.

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Several critical cell functions are influenced not only by internal cellular machinery but also by external mechanical and biochemical cues from the surrounding microenvironment. Slight changes to the microenvironment can result in dramatic changes to the cell's phenotype; for example, a change in the nutrients or pH of a tumor microenvironment can result in increased tumor metastasis. While cellular fate and the regulators of cell fate have been studied in detail for several decades now, our understanding of the extracellular regulators remains qualitative and far from comprehensive. In this

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Trusov, P. V., N. V. Zaitseva, and V. М. Chigvintsev. "Predicting a risk of tumor evolution considering regulatory mechanisms of the body and angiogenesis." Health Risk Analysis, no. 4 (December 2023): 134–45. http://dx.doi.org/10.21668/health.risk/2023.4.13.eng.

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Adverse environmental and lifestyle factors produce considerable effects on occurrence of cancerous tumors, both directly and indirectly through impaired functionality of the body protection mechanisms. Investigation of these effects has practical significance for risk assessment and development of effective cancer preventive strategies. Mathematical modeling is an eligible method for considering complex multicomponent interactions between elements of various systems involved in tumor growth. This article presents an approach to assessing risks of cancerous tumors by using a created predictive

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Trusov, P. V., N. V. Zaitseva, and V. М. Chigvintsev. "Predicting a risk of tumor evolution considering regulatory mechanisms of the body and angiogenesis." Health Risk Analysis, no. 4 (December 2023): 134–45. http://dx.doi.org/10.21668/health.risk/2023.4.13.

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Adverse environmental and lifestyle factors produce considerable effects on occurrence of cancerous tumors, both directly and indirectly through impaired functionality of the body protection mechanisms. Investigation of these effects has practical significance for risk assessment and development of effective cancer preventive strategies. Mathematical modeling is an eligible method for considering complex multicomponent interactions between elements of various systems involved in tumor growth. This article presents an approach to assessing risks of cancerous tumors by using a created predictive

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Satomi, Kaishi, Ryo Nishikawa, Masao Matsutani, Koichi Ichimura, and Hirokazu Takami. "PATH-42. PROGNOSTIC FACTORS OF CNS GERM CELL TUMORS; MOLECULAR AND HISTOPATHOLOGICAL ANALYSES ON 154 CASES FROM THE IGCT CONSORTIUM." Neuro-Oncology 23, Supplement_6 (2021): vi124—vi125. http://dx.doi.org/10.1093/neuonc/noab196.494.

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Abstract BACKGROUND Germ cell tumors (GCTs) preferentially occurs in pediatric and young adult age groups. Chemo- and radiation therapies cause long-term sequelae in their later lives. We searched for clinical and histopathological features to predict the prognosis and affect treatment response, with a future goal of treatment stratification. METHODS A total of 154 GCT cases were included in the analysis. Total of 114 germinoma cases underwent measurement of tumor cell content on H-E specimen, and 82 GCT cases underwent 450K methylation analysis. 12p gain was determined on methylation-based co

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Takami, Hirokazu, Kaishi Satomi, Kohei Fukuoka, et al. "BOT-3 Prognostic Factors of CNS Germ Cell Tumors; Molecular and Histopathological Analyses on 154 Cases from the iGCT Consortium." Neuro-Oncology Advances 3, Supplement_6 (2021): vi8—vi9. http://dx.doi.org/10.1093/noajnl/vdab159.031.

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Abstract Background: Germ cell tumors (GCTs) preferentially occurs in pediatric and young adult age groups. Chemo- and radiation therapies cause long-term sequelae in their later lives. We searched for clinical and histopathological features to predict the prognosis and affect treatment response, with a future goal of treatment stratification.Methods: A total of 154 GCT cases were included in the analysis. Total of 114 germinoma cases underwent measurement of tumor cell content on H-E specimen, and 82 GCT cases underwent 450K methylation analysis. 12p gain was determined on methylation-based c

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Anderson, Hannah, Gregory P. Takacs, Christian Kreiger, et al. "209 A CTS Team Approach to Modeling Migration and Suppression of CCR2+/CX3CR1+ Myeloid Cells in Glioblastoma." Journal of Clinical and Translational Science 6, s1 (2022): 32. http://dx.doi.org/10.1017/cts.2022.111.

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OBJECTIVES/GOALS: Evaluate the migration and immune suppressive functions of CCR2+/CX3CR1+ myeloid-derived suppressor cells (MDSCs). Integrate experimental data and biologically relevant mathematical models of infiltrating MDSCs in the context of glioblastoma (GBM). METHODS/STUDY POPULATION: CCR2+/CX3CR1+ cells were enriched from bone marrow obtained from CCR2(+/RFP)/CX3CR1(+/GFP) glioma-bearing mice to evaluate their immune-suppressive phenotype and ability to migrate to CCL2 and CCL7. Fluorescent imaging and quantification were performed on a range of tumor sizes to acquire vasculature, tumo

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Liu, Zichao, Xiaofei Song, Jiang He, et al. "Abstract 1143: Dissection of melanoma and cutaneous lymphoma spatial molecular architecture by multimodal single-cell and spatial transcriptomics with generative AI." Cancer Research 84, no. 6_Supplement (2024): 1143. http://dx.doi.org/10.1158/1538-7445.am2024-1143.

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Abstract Advances in single-cell multiomic technologies have revolutionized our understanding of how heterogeneous cell types and cell states shape the tumor microenvironment (TME). However, dissociated single cell profiling lacks spatial context. To resolve the organization, cell-cell communication, and granular structures in the TME, new single-cell spatial transcriptomic (ST) characterizations are needed. Here, we dissected the spatial molecular architecture of the melanoma (30 tumors, 30 patients) and transformed cutaneous T-cell lymphoma (tCTCL, 12 tumors, 6 patients) TMEs by Multiplexed

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Wesseling, Pieter, Carlo Vermeulen, Marc Pages-Gallego, et al. "INNV-36. ULTRA-FAST DEEP-LEARNED CNS TUMOR CLASSIFICATION USING NANOPORE-SEQUENCING DURING SURGERY." Neuro-Oncology 25, Supplement_5 (2023): v164—v165. http://dx.doi.org/10.1093/neuonc/noad179.0625.

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Abstract BACKGROUND Preoperative imaging and intraoperative histological analysis provide important guidance during CNS tumor surgery but are not always precise enough. Also, the diagnosis of CNS tumors increasingly requires a combination of morphological and molecular analysis. Illumina DNA methylation array analysis provides information on hundreds of thousands of methylation sites genome-wide but is relatively time-consuming and expensive. Nanopore sequencing enables real-time generation of an increasingly precise methylation profile. AIM: To exploit the potential of nanopore sequencing as

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McFall, Thomas, Jolene K. Diedrich, Meron Mengistu, et al. "A systems mechanism for KRAS mutant allele–specific responses to targeted therapy." Science Signaling 12, no. 600 (2019): eaaw8288. http://dx.doi.org/10.1126/scisignal.aaw8288.

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Cancer treatment decisions are increasingly guided by which specific genes are mutated within each patient’s tumor. For example, agents inhibiting the epidermal growth factor receptor (EGFR) benefit many colorectal cancer (CRC) patients, with the general exception of those whose tumor includes a KRAS mutation. However, among the various KRAS mutations, that which encodes the G13D mutant protein (KRASG13D) behaves differently; for unknown reasons, KRASG13D CRC patients benefit from the EGFR-blocking antibody cetuximab. Controversy surrounds this observation, because it contradicts the well-esta

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Pan, Weiling, Hui Wang, Fangfei Qi, et al. "Abstract C130: Discovery and characterization of an MTA-cooperative and brain-penetrant PRMT5 inhibitor." Molecular Cancer Therapeutics 22, no. 12_Supplement (2023): C130. http://dx.doi.org/10.1158/1535-7163.targ-23-c130.

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Abstract Introduction: MTAP is homozygous deleted in ~50% in glioblastoma and many other cancers. PRMT5*MTA inhibition has been shown to be synthetic lethal with MTAP deletion. First generation PRMT5 inhibitors could not distinguish between PRMT5*MTA or PRMT5 alone, thus limited by their shallow therapeutic windows in clinical use. Development of selective PRMT5*MTA inhibitors may improve not only safety but also therapeutic efficacy. Leveraging advanced computation-aided structural analysis and medicinal chemistry design, we have discovered a potent and selective MTA-cooperative and brain-pen

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Vukojicic, Nevena, Aleksandar Danicic, Zelia Worman, et al. "Abstract 2075: Highly customizable multi-sample single cell RNA-Seq pipeline on the CGC." Cancer Research 83, no. 7_Supplement (2023): 2075. http://dx.doi.org/10.1158/1538-7445.am2023-2075.

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Abstract Single-cell (sc) transcriptomics has revolutionized our understanding of the biological characteristics and dynamics of cancer development. It can help us identify rare cell subpopulations and understand mechanisms associated with tumor genesis, progression, and response to therapy. The most important step in the analyses of any scRNA-seq dataset is subpopulation identification, usually performed via unsupervised clustering, followed by gene marker identification. We created a highly customizable workflow for sc data analysis, implemented in Common Workflow Language (CWL) on the Cance

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Tripodi, Lorella, Emanuele Sasso, Sara Feola, et al. "Systems Biology Approaches for the Improvement of Oncolytic Virus-Based Immunotherapies." Cancers 15, no. 4 (2023): 1297. http://dx.doi.org/10.3390/cancers15041297.

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Oncolytic virus (OV)-based immunotherapy is mainly dependent on establishing an efficient cell-mediated antitumor immunity. OV-mediated antitumor immunity elicits a renewed antitumor reactivity, stimulating a T-cell response against tumor-associated antigens (TAAs) and recruiting natural killer cells within the tumor microenvironment (TME). Despite the fact that OVs are unspecific cancer vaccine platforms, to further enhance antitumor immunity, it is crucial to identify the potentially immunogenic T-cell restricted TAAs, the main key orchestrators in evoking a specific and durable cytotoxic T-

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Liu, Jian-Guo, Min Tang, Li Wang, and Zhennan Zhou. "Analysis and computation of some tumor growth models with nutrient: From cell density models to free boundary dynamics." Discrete & Continuous Dynamical Systems - B 24, no. 7 (2019): 3011–35. http://dx.doi.org/10.3934/dcdsb.2018297.

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D'Antongiovanni, Vanessa, Serena Martinelli, Susan Richter, et al. "The microenvironment induces collective migration in SDHB-silenced mouse pheochromocytoma spheroids." Endocrine-Related Cancer 24, no. 10 (2017): 555–64. http://dx.doi.org/10.1530/erc-17-0212.

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Pheochromocytomas (Pheos) and paragangliomas (PGLs) are neuroendocrine tumors. Approximately 30–40% of Pheos/PGLs are due to germline mutations in one of the susceptibility genes, including those encoding the succinate dehydrogenase subunits A-D (SDHA-D). Up to 2/3 of patients affected bySDHBmutated Pheo/PGL develop metastatic disease with no successful cure at present. Here, for the first time, we evaluated the effects ofSDHBsilencing in a three dimension (3D) culture using spheroids of a mouse Pheo cell line silenced or not (wild type/wt/control) for the SDHB subunit. We investigated the rol

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Liu, Francine, Andrew Zhai, Ozge Yoluk, et al. "Abstract PO5-27-05: Computational design and validation of a novel peptide-drug conjugate for treatment of triple negative breast cancer." Cancer Research 84, no. 9_Supplement (2024): PO5–27–05—PO5–27–05. http://dx.doi.org/10.1158/1538-7445.sabcs23-po5-27-05.

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Abstract Sortilin (SORT1) is a member of the vacuolar protein sorting 10 protein (Vps10p) family that functions as a receptor regulating peptide and protein trafficking between the plasma membrane, lysosomes, and trans-golgi network. As a cell surface receptor, SORT1 is able to mediate efficient endocytosis of extracellular ligands to the lysosomal compartment. Numerous reports have identified enriched SORT1 expression in a variety of tumor types, including triple-negative breast cancer (TNBC), a subtype of breast cancer associated with aggressive clinical behavior and poor disease outcomes. W

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Oon, Ming Liang, Jing Quan Lim, Bernett Lee, et al. "T-Cell Lymphoma Clonality by Copy Number Variation Analysis of T-Cell Receptor Genes." Cancers 13, no. 2 (2021): 340. http://dx.doi.org/10.3390/cancers13020340.

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T-cell lymphomas arise from a single neoplastic clone and exhibit identical patterns of deletions in T-cell receptor (TCR) genes. Whole genome sequencing (WGS) data represent a treasure trove of information for the development of novel clinical applications. However, the use of WGS to identify clonal T-cell proliferations has not been systematically studied. In this study, based on WGS data, we identified monoclonal rearrangements (MRs) of T-cell receptors (TCR) genes using a novel segmentation algorithm and copy number computation. We evaluated the feasibility of this technique as a marker of

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Soloff, Adam C., Rebecca A. Stanton, Nicholas M. Radio, et al. "Neuropilin-2 Isoforms Regulate Distinct Functions of Tumor-associated Macrophages in Breast Cancer." Journal of Immunology 202, no. 1_Supplement (2019): 187.23. http://dx.doi.org/10.4049/jimmunol.202.supp.187.23.

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Abstract Introduction Neuropilins are neural guidance molecules which contribute to tissue development. We have shown that the two isoforms of neuropilin-2 endow opposing functionality to tumor cells due to distinct signaling pathways, with Nrp2b promoting metastatic behavior. Due to the role of macrophages (Mθ) in organogenesis and metastasis, we examine the role of Nrp2 isoforms in these cells. Methods Stable shRNA knockdown of Nrp2a or Nrp2b in Raw264.7 Mθ were generated. Phagocytosis, cytokine production, and migration were assessed in knockdowns in response to stimuli (TGFβ, HGF, VEGF, IL

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Bryan, Cassie M., Gabriel J. Rocklin, Matthew J. Bick, et al. "Computational design of a synthetic PD-1 agonist." Proceedings of the National Academy of Sciences 118, no. 29 (2021): e2102164118. http://dx.doi.org/10.1073/pnas.2102164118.

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Programmed cell death protein-1 (PD-1) expressed on activated T cells inhibits T cell function and proliferation to prevent an excessive immune response, and disease can result if this delicate balance is shifted in either direction. Tumor cells often take advantage of this pathway by overexpressing the PD-1 ligand PD-L1 to evade destruction by the immune system. Alternatively, if there is a decrease in function of the PD-1 pathway, unchecked activation of the immune system and autoimmunity can result. Using a combination of computation and experiment, we designed a hyperstable 40-residue mini

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Kirson, Eilon David, Moshe Giladi, Rosa S. Schneiderman, et al. "Effect of tumor-treating fields on DNA repair in cancer cell lines." Journal of Clinical Oncology 31, no. 15_suppl (2013): e22138-e22138. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e22138.

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e22138 Background: TTFields Therapy is an antimitotic treatment modality approved by FDA for the treatment of patients with recurrent glioblastoma (GBM). TTFields act by disruption of spindle microtubule arrangement during metaphase and interference with cytokinesis during anaphase and telophase. These effects are the result of rotation of charged and/or polar macromolecules in the direction of the applied antimitotic fields. We hypothesized that the negatively charged, double stranded DNA fragments induced by ionizing radiation (RT) or ultraviolet light (UV) undergo similar rotation. Double s

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Yu, Jin-Hai, Dong-Xiang Wu, Zhi-Pu Yu, et al. "New e:b-Friedo-Hopane Type Triterpenoids from Euphorbia peplus with Simiarendiol Possessing Significant Cytostatic Activity against HeLa Cells by Induction of Apoptosis and S/G2 Cell Cycle Arrest." Molecules 24, no. 17 (2019): 3106. http://dx.doi.org/10.3390/molecules24173106.

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Seven rare e:b-friedo-hopane-type triterpenoids including four new (1–4) and three known (5–7) ones with 5 being first reported as a natural product, together with five other known triterpenoids (8–12), were isolated from the nonpolar fractions of the ethanolic extract of Euphorbia peplus. Structural assignments for these compounds were based on spectroscopic analyses and quantum chemical computation method. The structural variations for the C-21 isopropyl group, including dehydrogenation (1 and 3) and hydroxylation at C-22 (simiarendiol, 2), were the first cases among e:b-friedo-hopane-type t

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Ying, Haiyan, Wenqun Xin, Haibing Deng, et al. "Abstract LB317: Discovery and characterization of a next-generation FGFR inhibitor overcoming FGFR resistant mutations." Cancer Research 83, no. 8_Supplement (2023): LB317. http://dx.doi.org/10.1158/1538-7445.am2023-lb317.

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Abstract Introduction: FGFRs play important roles in cancer development and inhibition of FGFR could disrupt tumor cell proliferation and growth. Four selective FGFR inhibitors have been approved (erdafitinib, pemigatinib, infigratinib, and futibatinib) and several others are in clinical development. Unfortunately upon treatment with these first-generation FGFR inhibitors, acquired resistance often develops and is frequently associated with the emergence of secondary FGFR2/3 kinase domain mutations. Therefore, selectively targeting FGFR2/3 as well as their resistant mutations may render a seco

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Emadi, Ali, Tomasz Lipniacki, Andre Levchenko, and Ali Abdi. "Single-Cell Measurements and Modeling and Computation of Decision-Making Errors in a Molecular Signaling System with Two Output Molecules." Biology 12, no. 12 (2023): 1461. http://dx.doi.org/10.3390/biology12121461.

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A cell constantly receives signals and takes different fates accordingly. Given the uncertainty rendered by signal transduction noise, a cell may incorrectly perceive these signals. It may mistakenly behave as if there is a signal, although there is none, or may miss the presence of a signal that actually exists. In this paper, we consider a signaling system with two outputs, and introduce and develop methods to model and compute key cell decision-making parameters based on the two outputs and in response to the input signal. In the considered system, the tumor necrosis factor (TNF) regulates

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Wu, Ran, Puwei Yuan, Yang Xie, et al. "Abstract 1871: Discovery and characterization of NXV01c, an EGFR × cMET bispecific nanobody drug conjugate with potent anti-tumor activity." Cancer Research 84, no. 6_Supplement (2024): 1871. http://dx.doi.org/10.1158/1538-7445.am2024-1871.

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Abstract EGFR and cMET are proven cancer targets co-expressed in diverse tumor types. EGFR × cMET bispecific antibody has been approved for the treatment of NSCLC, supporting a simultaneous targeting strategy. In addition to this dual targeting benefit, bispecific antibody drug conjugates (ADCs) targeting EGFR and cMET have also been developed to further improve anti-tumor activity and tissue selectivity. Sufficient target affinity, good cellular internalization and high tumor infiltration are critical for an ADC to mediate therapeutic activity. To this end, we developed the first EGFR × cMET

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Sade, Hadassah, Ansh Kapil, Philipp Wortmann, et al. "Abstract 468: Quantitative assessment of IHC using computational pathology allows superior patient selection for biomarker-informed patients." Cancer Research 82, no. 12_Supplement (2022): 468. http://dx.doi.org/10.1158/1538-7445.am2022-468.

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Abstract Many targeted cancer therapies rely on biomarkers, which are assessed by standard pathologist scoring of immunohistochemically stained tissue. However, this process is subjective, semi-quantitative and does not assess expression heterogeneity. A quantitative method to measure IHC markers might therefore significantly improve patient selection particularly of proteins expressed at low levels. To address these challenges, we have developed the Quantitative Continuous Scoring (QCS) that deploys the power of fully supervised Deep Learning (DL) algorithms to provide objective and continuou

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Gopalan, Vishaka, and Sridhar Hannenhalli. "Abstract LB275: Transcriptomic reversal analysis yields cytokines and drugs mediating tumor microenvironmental reprogramming during cancer progression and therapy response." Cancer Research 83, no. 8_Supplement (2023): LB275. http://dx.doi.org/10.1158/1538-7445.am2023-lb275.

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Abstract Recent computational work links therapy response to a drug based on the drug’s ability to reverse a tumor’s transcriptome towards a healthy state. This idea of reversal has been used to mine databases of cell-line transcriptional responses against drug libraries to prioritize anti-cancer drugs. However, there are two key shortcomings in these approaches: (1) though cytokines and their receptors are proposed as modulators of therapy response, there is no reversal-based method to prioritize cytokines as potential drugs or targets, and (2) responses of microenvironmental cell types to dr

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Zhang, Yongxian, Mingming Zhang, Baowei Zhao, et al. "Abstract B151: Discovery and characterization of a novel small molecule brain penetrant PD-L1 inhibitor." Molecular Cancer Therapeutics 22, no. 12_Supplement (2023): B151. http://dx.doi.org/10.1158/1535-7163.targ-23-b151.

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Abstract Introduction: Immunotherapy has revolutionized cancer treatment in the last decade. Several monoclonal PD-1 and PD-L1 antibodies have been approved for treating various cancers. Small molecule PD-L1 inhibitors with brain-penetrating ability may have potential to overcome the limitations of antibodies and bring benefit for patients with intracranial tumors. Leveraging advanced computation-aided structural analysis and medicinal chemistry design, we have successfully discovered an innovative orally available small molecule PD-L1 inhibitor ABSK044. In preclinical experiments, this compou

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Devi, Gayathri R., Dorababu Sannareddy, Alexandra Bennion, et al. "Abstract P3-08-06: Monitoring Lymphovascular Invasion and Tumor Growth of Inflammatory Breast Cancer in a Murine Lymphatic Reporter Window Chamber Model." Cancer Research 83, no. 5_Supplement (2023): P3–08–06—P3–08–06. http://dx.doi.org/10.1158/1538-7445.sabcs22-p3-08-06.

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Abstract Background: Lymphovascular invasion (LVI) is a major route of metastatic dissemination and recent studies indicate its value as an independent prognostic indicator for advanced breast, colorectal, squamous cell, prostate, brain cancers. LVI is a clinicopathological hallmark of inflammatory breast cancer (IBC), an understudied and most lethal breast cancer. IBC is often misdiagnosed due to an absence of a solid mass and its unique presentation of diffuse tumor cell clusters/emboli in the dermal lymphatics. Widely used mammary tumor implantation models coupled with bioluminescence or fl

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Gustavson, Mark, Markus Schick, Ansh Kapil, Anatoliy Shumilov, Carl Barrett, and Hadassah Sade. "Abstract PO4-26-01: Computational pathology: Revolutionizing diagnostics and clearing the way for precision medicine." Cancer Research 84, no. 9_Supplement (2024): PO4–26–01—PO4–26–01. http://dx.doi.org/10.1158/1538-7445.sabcs23-po4-26-01.

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Abstract While targeted cancer therapies often rely on subjective and semi-quantitative visual assessment of protein biomarkers by pathologists through immunohistochemically stained tissue, the transformative force of computational pathology is reshaping healthcare by unleashing unprecedented diagnostic accuracy and unlocking personalized treatments. In recent years, we have established a large integrated computational pathology unit to foster collaboration between interdisciplinary teams of computer scientists, pathologists, molecular biologists, and data scientists. This integration of cutti

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R, Usha, and Perumal K. "A modified fractal texture image analysis based on grayscale morphology for multi-model views in MR Brain." Indonesian Journal of Electrical Engineering and Computer Science 21, no. 1 (2021): 154–63. https://doi.org/10.11591/ijeecs.v21.i1.pp154-163.

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This paper presents a modified fractal texture feature analysis with the use of grayscale image morphology for automatic image classification of different views in MR brain images into normal and abnormal. This main contribution of this approach is a reduction of the total number of a threshold value, and the number of image decomposition, in which only the number of extract threshold value two or three are enough for tumor region extraction compared to four or more is required in the previous method of SFTA (segmentation based fractal texture analysis). This is achieved by preprocessing of hi

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Lee, Alexander, Yang Pan, Aaron Mochizuki, et al. "IMMU-02. NEOANTIGENS ARISING FROM ALTERNATIVE SPLICING EVENTS MAY BE TARGETED BY TUMOR INFILTRATING LYMPHOCYTES IN GLIOBLASTOMAS." Neuro-Oncology 21, Supplement_6 (2019): vi118—vi119. http://dx.doi.org/10.1093/neuonc/noz175.496.

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Abstract INTRODUCTION Alternative splicing, the cellular process that converts premature mRNA to mature mRNA and allows for single genes to produce multiple protein products, is frequently dysregulated in many cancers, including glioblastoma. However, along with non-synonymous mutations in the DNA, altered splicing mechanisms in cancers may produce novel antigens (so-called neoantigens) that distinguish cancer cells from healthy cells and can thus be targeted by the immune system. METHODS We developed a new computation pipeline (IRIS – Isoform peptides from RNA splicing for Immunotherapy targe

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van Bree, Elise, Carmen Rubio Alarcón, Soufyan Lakbir, et al. "Abstract A020: Structural variants in the pathogenesis of colorectal cancer: The elephant in the room." Cancer Research 82, no. 23_Supplement_1 (2022): A020. http://dx.doi.org/10.1158/1538-7445.crc22-a020.

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Abstract Background: Cancer is caused by somatic DNA alterations, comprising single/small nucleotide variants (SNVs), somatic copy number alterations (SCNAs) and chromosomal rearrangement structural variants (SVs). We previously demonstrated that SVs are recurrently identified in hundreds of genes and are highly prevalent in common fragile site genes, e.g., in MACROD2 in &gt;40% of colorectal cancers (CRCs). However, computational methods that discriminate SV-driver from SV-passenger events are lacking and laboratory methods to detect SVs at nucleotide resolution from routinely obtained fo

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Sun, Jijia, Baocheng Liu, Ruirui Wang, Ying Yuan, Jianying Wang, and Lei Zhang. "Computation-Based Discovery of Potential Targets for Rheumatoid Arthritis and Related Molecular Screening and Mechanism Analysis of Traditional Chinese Medicine." Disease Markers 2022 (June 4, 2022): 1–19. http://dx.doi.org/10.1155/2022/1905077.

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This study is aimed at screening potential therapeutic ingredients in traditional Chinese medicine (TCM) and identifying the key rheumatoid arthritis (RA) targets using computational simulations. Data for TCM-active ingredients with clear pharmacological effects were collected. Absorption, distribution, metabolism, excretion, and toxicity were evaluated. Potential RA targets were identified using the Gene Expression Omnibus (GEO) database, protein–protein interaction network, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and potential TCM ingredients using Auto

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Kode, Jyoti, Jitendra Maharana, K. Nirmal Kumar, et al. "Abstract 4222: Phenstatin based indole linked chalcone compound 9a exhibits anti-oral cancer activity through regulating NLRP3 inflammasome innate immune pathway." Cancer Research 82, no. 12_Supplement (2022): 4222. http://dx.doi.org/10.1158/1538-7445.am2022-4222.

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Abstract Oral cancer is the sixth most prevalent malignancy in the world and oral squamous cell carcinoma accounts for majority of all oral malignancies. Upregulated NLRP3 inflammasome innate immune pathway is of importance to tumor development. Current efforts are being focused on identifying small molecules that exhibit anti-cancer activity as inflammasome pathway inhibitors. Our previously published work on phenstatin based indole linked chalcone scaffold 9a with 1-methyl, 2- and 3-methoxy substituents in the aromatic ring revealed 9a as an anti-oral cancer compound. 9a was found to act thr

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Pérez, Liliana, John E. Kerrigan, Xiaojin Li, and Huizhou Fan. "Substitution of methionine 435 with leucine, isoleucine, and serine in tumor necrosis factor alpha converting enzyme inactivates ectodomain shedding activity." Biochemistry and Cell Biology 85, no. 1 (2007): 141–49. http://dx.doi.org/10.1139/o06-179.

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Tumor necrosis factor alpha (TNF-α) converting enzyme (TACE) is a zinc metalloprotease that has emerged as a general sheddase, which is responsible for ectodomain release of numerous membrane proteins, including the proinflammatory cytokine TNF-α, the leukocyte adhesin l-selectin and epidermal growth factor receptor ligand-transforming growth factor α (TGF-α), and related family members. Structurally, TACE belongs to a large clan of proteases, designated the metzincins, because TACE possesses a conserved methionine (Met435), frequently referred to as the met-turn residue, in its active site. A

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Pannellini, Tania, Fabio Iannelli, Valentina Tabanelli, et al. "Abstract 2525: Translating clinically validated antibodies into a multiplexed immunofluorescent panel for the spatial profiling of lymphoid malignancies." Cancer Research 85, no. 8_Supplement_1 (2025): 2525. https://doi.org/10.1158/1538-7445.am2025-2525.

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Abstract Lymphoid malignancies present significant diagnostic challenges due to overlapping immunophenotypic features between tumor cells and reactive background cells, complicating the distinction between indolent lymphomas and benign lymph node hyperplasia [Nicolae A, Hemato, 2024, DOI:10.3390/hemato5030026]. Moreover, some Hodgkin lymphoma (HL) subtypes, such as lymphocyte-rich (LRHL) and nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) and certain variants of diffuse large B-cell lymphoma (DLBCL), exhibit similar phenotypic profiles despite having different therapeutic implications

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Luo, Yangkun, Lu Li, Gang Yin, and Jin Yi Lang. "Predicting tumor mutational burden in head and neck squamous cell carcinoma based on CT imaging features: A TCGA/TCIA study." Journal of Clinical Oncology 38, no. 15_suppl (2020): e15254-e15254. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e15254.

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e15254 Background: Immunotherapy has substantially changed the therapeutic strategies for cancers. Unfortunately, only 20–50% of patients with advanced solid tumours respond to treatment. There is therefore a need for the development of methods to identify patients who are most likely to respond to immunotherapy. Tumor mutation burden (TMB) have been served as the most prevalent biomarkers to predict immunotherapy response. This study was designed to investigate the ability of radiomics to predict TMB status in patients with head and neck squamous cell carcinoma (HNSCC). Methods: TMB values we

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Andersson, Natalie, Adriana Mañas Nuñez, Kristina Aaltonen, et al. "Abstract PR001: Deciphering clonal evolution under chemotherapy in high-risk neuroblastoma using patient derived models." Cancer Research 82, no. 10_Supplement (2022): PR001. http://dx.doi.org/10.1158/1538-7445.evodyn22-pr001.

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Abstract Neuroblastoma is a pediatric tumor originating from the developing sympathetic nervous system, most often arising in the adrenal medulla in children below 5 years of age. After diagnosis, children with high-risk neuroblastoma are treated with COJEC, which is an aggressive chemotherapeutic treatment protocol encompassing five different chemotherapeutic agents. This is followed by surgical resection of the remaining tumor tissue. The aim of this project was to decipher how the subclonal landscape in the tumor changes during treatment with COJEC. To do this, three different patient deriv

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Esmail, Abdullah, Jian Guan, Jiaqiong Xu, et al. "Prognostic value of molecular response via ctDNA measurement in predicating response of systemic therapy in patients with advanced solid cancer." Journal of Clinical Oncology 40, no. 16_suppl (2022): e13001-e13001. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e13001.

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e13001 Background: Molecular profiling of cancer can guide treatment decision, monitor response and predict clinical outcome in the era of precision medicine and individualized treatment. Emerging evidence has suggested that ctDNA change correlates with treatment response and predates radiological relapse. Thus, we aim to provide real-world data regarding the dynamic changes of ctDNA level measured via Guardant 360 Response in advanced solid cancer correlates with clinical outcome. Methods: We retrospectively reviewed data of patients with advanced solid cancer and had at least 2 timepoints of

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Kashyap, Abhishek, Dimpy Rani, Suresh Kumar, and Shailendra Bhatt. "Design and Computational Evaluation of New Carbamate Derivatives for the Inhibition of Monoacylglycerol Lipase Enzyme by using Docking." International Journal of Pharmaceutical Sciences and Drug Research 15, no. 05 (2023): 665–74. http://dx.doi.org/10.25004/ijpsdr.2023.150515.

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Different disorders and physiological process have been found to be associated with monoacylglycerol lipase enzyme in humans, like pain, inflammation, and neurodegenerative diseases also. The enzyme is a 33 KDa in weight and a type of serine hydrolase enzyme in nature. The presence of enzyme has been reported in both central and peripheral nervous systems and has show its importance as a key signalling factor in endocannabinoid signalling network system. The enzyme has also reported as source of free fatty acid provider for the cancer cell and tumor growth and their proliferation. In prolifera

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Ying, Haiyan, Nannan Zhang, Haibing Deng, et al. "Abstract LB328: Discovery & characterization of a next-generation FGFR4 inhibitor overcoming resistant mutations." Cancer Research 83, no. 8_Supplement (2023): LB328. http://dx.doi.org/10.1158/1538-7445.am2023-lb328.

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Abstract Introduction: Aberrant activation of FGF19-FGFR4 signaling pathway plays an essential role in the tumorigenesis of Hepatocellular carcinoma (HCC) and FGFR4 inhibitors have shown preliminary efficacy in recent clinical trials for patients with FGF19 overexpression. However, the observed responses only lasted a few months before tumors relapse. Acquired FGFR4 resistant mutations were found in ~30% of FGFR4 inhibitor responsive patients. Similar FGFR4 mutations haven also been found de novo in about 7-10% of Rhabdomyosarcoma (RMS) and ER-treated invasive lobular carcinoma patients. First

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Andor, Noemi, Jill Barnholtz-Sloan, and Hanlee Ji. "COMP-01. MODELING THE EVOLUTION OF PLOIDY IN A RESOURCE RESTRICTED ENVIRONMENT." Neuro-Oncology 21, Supplement_6 (2019): vi61. http://dx.doi.org/10.1093/neuonc/noz175.244.

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Abstract Progression of lower-grade gliomas (LGG) to glioblastoma (GBM) is accompanied by a phenotypic switch to an invasive cell phenotype. Converging evidence from colorectal-, breast-, and lung-cancers, suggests a strong enrichment of high ploidy cells among metastatic lesions as compared to the primary. Even in normal development: trophoblast giant cells are responsible for invading the placenta during embryogenesis and these cells often have tens of copies of the genome. We formulate a mechanistic Grow-or-go model that postulates higher energy demands of high-ploidy cells as driver of inv

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Cheng, Da-Chuan, Jen-Hong Chi, Shih-Neng Yang, and Shing-Hong Liu. "Organ Contouring for Lung Cancer Patients with a Seed Generation Scheme and Random Walks." Sensors 20, no. 17 (2020): 4823. http://dx.doi.org/10.3390/s20174823.

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In this study, we proposed a semi-automated and interactive scheme for organ contouring in radiotherapy planning for patients with non-small cell lung cancers. Several organs were contoured, including the lungs, airway, heart, spinal cord, body, and gross tumor volume (GTV). We proposed some schemes to automatically generate and vanish the seeds of the random walks (RW) algorithm. We considered 25 lung cancer patients, whose computed tomography (CT) images were obtained from the China Medical University Hospital (CMUH) in Taichung, Taiwan. The manual contours made by clinical oncologists were

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Wu, Wen-Lian, Taishan Hu, Zhilin Deng, et al. "Abstract 1808: Discovery of highly selective novel MTA-cooperative PRMT5 inhibitors for the treatment of cancers." Cancer Research 84, no. 6_Supplement (2024): 1808. http://dx.doi.org/10.1158/1538-7445.am2024-1808.

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Abstract Protein arginine methyltransferase 5 (PRMT5), a type II PRMT catalyzing the formation of symmetric dimethylation of arginine residues on histone and non-histone proteins, regulates many biological pathways in mammalian cells, including cell growth and differentiation. Methylthioadenosine phosphorylase (MTAP) is required for the methionine salvage pathway, deletion of MTAP leads to the accumulation of inhibitory PRMT5 cofactor methylthioadenosine (MTA). MTAP gene is adjacent to and frequently co-deleted with CDKN2A gene, the most commonly deleted tumor suppressor gene in human cancers.

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Marron, Thomas, Julia Kodysh, Alex Rubinsteyn, et al. "289 PGV-001: a phase 1 trial of a personalized neoantigen peptide vaccine for the treatment of malignancies in the adjuvant setting." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A316. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0289.

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BackgroundThe efficacy of T cell directed immunotherapies relies on adequate priming of T cells to tumor-specific neoantigens, which some studies have augmented with synthetic neoantigen vaccines. This is the first report of a personalized genomic vaccine (PGV-001) in multiple histologies in the adjuvant setting.MethodsTumor and germline RNA and DNA were sequenced, and neoantigen peptides were selected using our OpenVax custom computation pipeline that identifies and ranks mutant sequences by a combination of predicted MHC-I binding affinity and neoantigen abundance within tumor. Up to 10 pept

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Montierth, Matthew, Yujie Jiang, Kaixian Yu, et al. "Abstract 7153: Subclonal mutation load predicts survival and response to immunotherapy in cancers with low to moderate TMB." Cancer Research 85, no. 8_Supplement_1 (2025): 7153. https://doi.org/10.1158/1538-7445.am2025-7153.

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Abstract Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment, yet current biomarkers like tumor mutation burden (TMB) and mismatch repair deficiency identify responders in only a small fraction of patients, particularly in low-to-moderate TMB cancers. This is critical as the majority of cancer patients (ex. approximately 90% of TCGA) have TMB&lt;10, the FDA-approved threshold for ICI therapy. As such, there is need to identify biomarkers to predict immunotherapy response in these currently overlooked patients.We developed CliPP, a novel statistical machine learning appr

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