Shoari, Alireza

Matrix metalloproteinases (MMPs) have long been recognized as key mediators of tumor invasion and metastasis due to their capacity to degrade extracellular matrix components. However, clinical failure of broad-spectrum MMP inhibitors has revealed a more complex and context-dependent role for these proteases in cancer. Among them, macrophage metalloelastase, MMP-12, has emerged as a particularly intriguing enzyme with both tumor-promoting and tumor-suppressive functions. Predominantly expressed by tumor-associated macrophages, MMP-12 occupies a unique position at the interface of proteolysis, inflammation, and immune regulation within the tumor microenvironment. Accumulating evidence from experimental models and clinical studies demonstrates that MMP-12 can exert potent anti-tumorigenic effects, primarily through inhibition of angiogenesis. Mechanistically, MMP-12 generates angiostatin and other anti-angiogenic fragments, suppresses vascular endothelial growth factor signaling, and reduces tumor vascularization, thereby limiting tumor growth and metastatic expansion. In several cancer types, including lung, colorectal, and hepatocellular carcinoma, elevated MMP-12 expression has been associated with reduced tumor progression and improved patient outcomes. Conversely, MMP-12 can also promote tumor progression through extracellular matrix remodeling, facilitation of invasion, and modulation of inflammatory pathways, particularly in environments characterized by chronic inflammation or immunosuppressive macrophage phenotypes. These seemingly contradictory roles are governed by multiple context-dependent factors, including macrophage polarization, tumor type, disease stage, and microenvironmental cues such as hypoxia and cytokine signaling. In this review, we comprehensively examine the molecular regulation, functional mechanisms, and clinical relevance of MMP-12 in cancer. We highlight the dualistic nature of MMP-12 activity and discuss its implications for therapeutic strategies, emphasizing the need for selective and context-aware targeting approaches rather than broad inhibition of MMP activity.

Current treatments for choroidal neovascularization (CNV) and its associated subretinal fibrosis (SRF), major causes of vision loss, are limited by the need for frequent intravitreal injections and the emergence of drug resistance. This study evaluated the safety and efficacy of the intravitreal administration of engineered humanized anti-vascular endothelial growth factor Nanobodies, including a wild-type Nanobody (WHNb) and two mutated variants (MHNb136 and MHNb256), in a rat model of laser-induced CNV and associated SRF. Safety was assessed through in vivo electrophysiological and histopathological analyses following intravitreal injection of Nanobodies at doses of 12.5, 25, 50, and 100 µg. Efficacy was evaluated in rat models of laser-induced CNV and SRF using double immunohistochemistry for isolectin B4 and anti-collagen type I on sclerochoroidal flat mounts. Mean CNV and SRF areas in Nanobody-treated groups were compared with those in bevacizumab-treated and sham control groups. None of the Nanobodies showed retinal toxicity in safety assessments. Compared with bevacizumab, MHNb136 and MHNb256 reduced the CNV area by 1.72-fold and 1.8-fold, respectively (both p < 0.0001), whereas WHNb showed an effect nearly identical to that of bevacizumab. In addition, 12.5 µg MHNb136 and 100 µg MHNb256 reduced the SRF area by 1.3-fold (p = 0.047) and 1.6-fold (p = 0.0007), respectively, relative to bevacizumab. For CNV reduction, 12.5 µg MHNb136 was comparable to 25 µg MHNb256; both outperformed bevacizumab. For SRF reduction, 12.5 µg MHNb136 was more effective than bevacizumab and comparable to 100 µg MHNb256. These findings suggest that 12.5 µg MHNb136 may represent a cost-effective bioengineered Nanobody candidate for future clinical studies.

Abstract Matrix metalloproteinases (MMPs) are key regulators of tumor progression, invasion, and metastasis; however, clinical efforts to inhibit MMPs have largely failed due to a lack of selectivity and unintended suppression of protective family members. In triple-negative breast cancer (TNBC), MMP-9 (gelatinase B) is strongly associated with tumor aggressiveness, extracellular matrix remodeling, and metastatic dissemination. In contrast, MMP-8 has been shown to exert anti-tumorigenic effects in breast cancer by limiting inflammation and suppressing metastasis. This functional divergence underscores the importance of selectively targeting MMP-9 while preserving MMP-8 activity as a rational therapeutic strategy in TNBC. To address this challenge, we engineered variants of the endogenous MMP inhibitor tissue inhibitor of metalloproteinases-1 (TIMP-1) with enhanced selectivity for MMP-9 over MMP-8. A yeast surface display library of human TIMP-1 was constructed and screened using fluorescence-activated cell sorting through iterative rounds of positive selection for recombinant MMP-9, followed by competitive counter-selection against MMP-8 to eliminate off-target binders. This strategy enabled enrichment of TIMP-1 variants with improved specificity for MMP-9 compared with wild-type TIMP-1. Several TIMP-1 variants exhibited enhanced binding and inhibitory selectivity toward MMP-9, with TIMP-1-C6.2 emerging as the most promising candidate. TIMP-1-C6.2 preferentially inhibited MMP-9 with a Ki of 0.3 ± 0.04 nM, while demonstrating substantially weaker inhibition of MMP-8 (Ki = 6.8 ± 0.27 nM), corresponding to an approximately 23-fold selectivity for MMP-9. Importantly, functional evaluation in Matrigel invasion assays using MDA-MB-231 TNBC cells revealed that TIMP-1-C6.2 significantly enhanced inhibition of tumor cell invasion compared with wild-type TIMP-1 in a dose-dependent manner (p &lt; 0.0001). This improved anti-invasive activity reflects refined target selectivity rather than a generalized increase in inhibitory potency. Collectively, these findings demonstrate that selective engineering of TIMP-based inhibitors can overcome a central limitation of MMP-targeted therapies by suppressing pro-tumorigenic MMP-9 while sparing anti-tumorigenic MMP-8. This work provides a strong foundation for the development of selective MMP-9 inhibitors with improved safety and therapeutic potential for TNBC and other MMP-driven cancers. Citation Format: Alireza Shoari, Alexandra Hockla, Mathew A. Coban, Ella E. Aitchison, Alexandra M. Dimesa, Evette S. Radisky. Protein engineering of selective MMP-9 inhibitors reveals a therapeutic strategy for triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(8_Suppl):Abstract nr LB233.

Liver cancer, also known as hepatocellular carcinoma (HCC), remains a major global health concern, with high mortality driven by late-stage diagnosis, limited treatment efficacy, and frequent therapeutic resistance. Matrix metalloproteinases (MMPs), a large family of zinc-dependent endopeptidases, are central to the biological processes that drive liver tumor initiation and progression. By degrading and reorganizing extracellular matrix components, MMPs facilitate tumor expansion, tissue invasion, and metastatic dissemination. In addition, these enzymes regulate the availability of growth factors, cytokines, and chemokines, thereby influencing angiogenesis, inflammation, immune cell recruitment, and the development of an immunosuppressive tumor microenvironment. Aberrant expression or activity of multiple MMP family members is consistently associated with aggressive clinicopathologic features, including vascular invasion, increased metastatic potential, and reduced patient survival, highlighting their promise as prognostic markers and actionable therapeutic targets. Past attempts to modulate MMP activity were hindered by broad inhibition profiles and dose-limiting toxicities, underscoring the need for improved specificity and delivery strategies. Recent advances in molecular design, biologics engineering, and nanotechnology have revitalized interest in MMP targeting by enabling more selective, context-dependent modulation of proteolytic activity. Preclinical studies demonstrate that carefully tuned MMP inhibition can limit tumor invasion, enhance anti-angiogenic responses, and potentially improve the efficacy of existing systemic therapies, including immuno-oncology agents. This review synthesizes current knowledge on the multifaceted roles of MMPs in HCC pathobiology and evaluates emerging therapeutic strategies that may finally unlock the clinical potential of targeting these proteases.

Matrix metalloproteinases (MMPs) are secreted and cell membrane‐associated enzymes that remodel the extracellular matrix (ECM) and cleave extracellular proteins to promote tumor invasion, angiogenesis, immune evasion, and many other aspects of cancer progression. Among this family, the gelatinases MMP‐2 and MMP‐9, specialized for cleaving collagen IV, are tightly linked to metastatic progression in breast cancer and adverse clinical outcomes. Here, we summarize gelatinase biochemistry and regulation, including zymogen activation, TIMP control, cell‐surface trafficking and tethering, and receptor‐mediated clearance, and explain how crosstalk between ECM and proteases amplifies invasion and metastatic seeding. We then review therapeutic strategies in two parts: direct inhibition and indirect pathway modulation. Direct approaches emphasize selective small molecules (thiirane mechanism‐based inhibitors, allosteric blockers of pro‐MMP‐9 activation) and protein biologics (monoclonal antibodies, nanobodies, engineered TIMPs). Indirect strategies target upstream signals that drive MMP‐2/‐9, including MAPK/AP‐1, PI3K/Akt/mTOR, NF‐κB, EGFR/JAK/STAT, and nuclear receptor and Nrf2/HO‐1 programs, with agents that curb invasion, angiogenesis, and metastasis in breast cancer models. Together, these advances define a maturing toolkit for precise gelatinase control and support prospective evaluation in rational combinations to restrain metastatic progression in high‐risk breast cancer.

Breast cancer is the most prevalent cancer among women and is challenging to diagnose and treat due to its diverse subtypes and stages. Precision medicine aims to improve early detection, prognosis, and treatment planning by identifying new clinical biomarkers. The review emphasizes the importance of using cutting-edge technology and artificial intelligence (AI) to identify new biomarkers associated with epithelial–mesenchymal transition (EMT). During EMT, epithelial cells transform into a mesenchymal state, a process driven by genetic and epigenetic alterations that facilitate cancer progression. The review discusses how statistical analysis and machine learning methods applied to multi-omics data facilitate the discovery of novel EMT-related biomarkers, thereby advancing therapeutic strategies. This conclusion is supported by numerous clinical and preclinical studies on breast cancer.

Cancer continues to be a leading cause of global mortality, necessitating innovative therapeutic strategies to address its complexity and heterogeneity. Protein engineering has emerged as a transformative approach in developing cancer biotherapeutics, enabling the creation of highly specific, potent, and adaptable treatments. This paper provides a comprehensive review of the state-of-the-art in protein engineering, highlighting key techniques such as directed evolution, rational design, and hybrid approaches that underpin the development of monoclonal antibodies, bispecific antibodies, and novel fusion proteins. Case studies of FDA-approved therapies, including engineered monoclonal antibodies like trastuzumab and bispecific T-cell engagers such as blinatumomab, are discussed to illustrate the impact of these advancements. Furthermore, emerging trends, including AI-driven protein design and synthetic biology applications, are explored alongside their potential to revolutionize future cancer treatments. Challenges such as immunogenicity, stability, and scalability are critically evaluated, offering insights into potential solutions and future research directions. By synthesizing advancements in protein science and oncology, this paper aims to guide researchers and clinicians in harnessing the full potential of engineered proteins for cancer therapy.

Abstract Tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors that regulate the function and activity of matrix metalloproteinases (MMPs), enzymes that are known for their involvement in cancer progression. MMP-9, also known as gelatinase B, plays a crucial role in tumorigenesis of several cancers including triple negative breast cancer (TNBC); tumor cell-produced MMP-9 promotes malignant progression and metastasis of basal-like TNBC. Here, we have used full-length TIMP-1 as a scaffold for engineering inhibitors that bind with higher selectivity to MMP-9, for potential therapeutic applications. We previously developed a yeast surface display library of human TIMP-1, with diversity incorporated at 17 residues within five loops; mutation burden was tuned to 3-5 mutations per clone. Here, we have screened the TIMP-1 library for affinity toward recombinant MMP-9 by using fluorescence-activated cell sorting (FACS). Yeast cells were incubated with an incrementally decreasing concentration of biotinylated MMP-9 (400 nM to 25 nM) in successive rounds of sorting. Samples were analyzed using flow cytometry and highest affinity populations were selected using FACS. Among the TIMP-1 variants with highest enrichment, we identified the TIMP-1-C15 variant that showed 12-fold enhanced binding with improved selectivity toward MMP-9 compared with wild type TIMP-1 (WT TIMP-1). We next expressed and purified soluble recombinant TIMP-1-C15 and conducted inhibition studies using a fluorogenic substrate to evaluate inhibitory potency towards MMP-9 activity. These experiments showed that TIMP-1-C15 inhibits MMP-9 activity with an inhibition constant (Ki) of 0.61 nM, more than 5-fold stronger than WT TIMP-1; these studies also corroborated the improved selectivity towards MMP-9 over other MMPs. Additionally, we further evaluated the functional impact of the TIMP-1-C15 variant on cancer cell invasiveness using TNBC cell lines in cellular invasion assays. The TIMP-1-C15 variant markedly reduced the invasive capabilities of TNBC cells to a greater extent than WT TIMP-1. Currently, we are working to isolate additional TIMP-1 variants from our library that exhibit enhanced selectivity for MMP-9, with MMP-8 included in the sorting process as a competitive target to ensure specificity. Selective inhibition of MMP-9 over MMP-8 is particularly important in breast cancer therapy, as MMP-8 has been shown to have anti-tumorigenic properties, and its inhibition could counteract therapeutic efforts aimed at reducing cancer invasiveness. Our findings suggest that engineered TIMP-1 variants could serve as potent inhibitors of MMP-9, offering a novel approach to reducing the invasiveness of breast cancer cells and potentially limiting the progression of metastatic disease. Citation Format: Alireza Shoari, Alexandra Hockla, Mathew A. Coban, Alexandra M. Dimesa, Derek C. Radisky, Evette S. Radisky. Engineered TIMP-1 for selective MMP-9 inhibition: A novel strategy to suppress breast cancer invasiveness [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5115.

Matrix metalloproteinases (MMPs) are a family of zinc-dependent proteolytic enzymes that are crucial for the remodeling of the extracellular matrix, a process that is often co-opted by cancers, including brain tumors, to facilitate growth, invasion, and metastasis. In gliomas, MMPs contribute to a complex interplay involving tumor proliferation, angiogenesis, and immune modulation, thereby influencing tumor progression and patient prognosis. This review provides a comprehensive analysis of the roles of various MMPs in different types of gliomas, from highly malignant gliomas to metastatic lesions. Emphasis is placed on how the dysregulation of MMPs impacts tumor behavior, the association between specific MMPs and the tumor grade, and their potential as biomarkers for diagnosis and prognosis. Additionally, the current therapeutic approaches targeting MMP activity are discussed, exploring both their challenges and future potential. By synthesizing recent findings, this paper aims to clarify the broad significance of MMPs in gliomas and propose avenues for translational research that could enhance treatment strategies and clinical outcomes.

Proteases play a pivotal role in cancer progression, facilitating processes such as extracellular matrix degradation, angiogenesis, and metastasis. Consequently, protease inhibitors have emerged as promising therapeutic agents in oncology. This review provides a comprehensive overview of the mechanisms by which protease inhibitors modulate cancer biology, categorizing inhibitors by their target protease classes, including matrix metalloproteinases, cysteine proteases, and serine proteases. We discuss the therapeutic potential of both synthetic and natural protease inhibitors, highlighting their applications in preclinical and clinical settings. Furthermore, challenges such as specificity, toxicity, and resistance mechanisms are addressed, alongside strategies to overcome these limitations through innovative drug designs and combination therapies. The future of protease inhibitors in cancer treatment lies in precision medicine, leveraging proteomic profiling to tailor therapies to individual tumors. This review underscores the importance of ongoing research and the development of novel approaches to harness protease inhibitors effectively for cancer management.