Citations

Abstract The two most common lung cancer subtypes are adenocarcinoma (ADC) and squamous cell carcinoma (SCC). Even though both subtypes are epithelial in origin, it is now clear that tumor associated fibroblasts (TAFs) are key regulators of tumor progression and response to therapies. Nintedanib is an antifibrotic drug that targets the tumor stroma and has been clinically approved to treat lung ADC patients owing to the therapeutic benefits exhibited by this drug selectively in ADC (but not in SCC) in the LUME-1 cinical trial. We have implicated recently both ADC-TAFs and ADC cancer cells in the selective effects of nintedanib in ADC, since this drug reduced the growth and invasion induction elicited by the secretome of TGF-β-activated ADC-TAFs on a panel of ADC cells, whereas such reduction was not observed in SCC-TAFs. However, the key molecules involved in the aberrant TAF-carcinoma crosstalk in ADC remain unknown. TIMP-1 is a multifunctional protein that has been associated with poor prognosis in lung cancer and is downregulated by nintedanib in a bleomycin model of pulmonary fibrosis. Our preliminary results revealed that the TIMP-1 receptor CD63 is overexpressed in ADC patients compared to SCC. Therefore, our working hypothesis was that nintedanib reduces ADC cells growth and invasion by abrogating the TAF-carcinoma crosstalk driven by TIMP-1 and CD63.To test this hypothesis, we used primary TAFs obtained with the patient informed consent, and using protocols approved by the Ethics Committee of the Hospital Clinic. TGF-β1-activated ADC-TAFs and SCC-TAFs were treated with nintedanib, and their secreted TIMP-1 was determined by ELISA. Two high-CD63 cell lines (H1437 and H23) were used in some experiments, and siRNA was used to knock-down either TIMP-1 in TAFs or CD63 in cancer cellsOur in vitro results showed that the secretion of TIMP-1 was significantly larger in ADC-TAFs compared to SCC-TAFs. Likewise, nintedanib elicited a higher TIMP-1 downregulation in ADC-TAFs compared SCC-TAFs. Of note, TIMP-1 and CD63 were both implicated in the pro-tumorigenic crosstalk, since knocking-down TIMP-1 in ADC-TAFs or CD63 in ADC cells was sufficient to abrogate the growth and invasion enhancement elicited by the secretome of TAFs. Moreover, CD63 was necessary to enhance the invasion of ADC cells upon stimulation with recombinant TIMP-1. In addition, we found that knocking-down TIMP-1 in ADC-TAFs was sufficient to compromise the inhibitory effects of nintedanib on the growth and invasion enhancement elicited by the secretome of TAFs on ADC cells. Collectively, our results support a novel TAF-carcinoma crosstalk driven by TIMP-1 and CD63 in lung ADC, and support that such heterotypic crosstalk may underlie the aberrant tumor-promoting effects of ADC-TAFs that are selectively downregulated by nintedanib. Citation Format: Paula Duch, Natalia Díaz-Valdivia, Marta Gabasa, Rafael Ikemori, Marselina Arshakyan, Frank Hillberg, Noemí Reguart, Derek Radisky, Jordi Alcaraz. Stromal TIMP-1 drives tumor progression in lung adenocarcinoma through CD63 interaction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3167.

Abstract Large cell carcinoma (LCC) is an aggressive lung cancer subtype with poor prognosis and no targeted therapies. We previously reported that tumor-associated fibroblasts (TAFs) derived from LCC tumors exhibit premature senescence, and coculture of pulmonary fibroblasts with LCC cell lines selectively induces fibroblast senescence, which in turn drives LCC cell growth and invasion. Here we report that MMP1 is overexpressed specifically in LCC cell lines. Notably, silencing MMP1 expression in LCC cancer cell lines using shRNA revealed that MMP1 expression by LCC cells is necessary for induction of fibroblast senescence in coculture experiments with normal pulmonary fibroblasts, as revealed by the analysis of a panel of standard senescence markers, including β-galactosidase (SA-βgal) staining, permanent growth arrest and expression of senescence-associated secretory factors. Injecting control (shScr) or shMMP1 LCC cells into immunodeficient nude mice revealed that tumor growth, tumor take and cancer cell dissemination to the lung were reduced in shMMP1 H460 tumors compared to control tumors. We also observed fewer senescent fibroblasts in tumors from shMMP1 H460 cells using Sentragor staining, which allows identification of senescent cells in paraffin embedded tissues. Moreover, we found that recombinant active MMP1 in combination with TGF-β1 were sufficient to induce normal fibroblast senescence. In terms of the potential underlying mechanisms, treatment with the antioxidant n-acetyl cysteine (NAC) significantly attenuated the increase in SA-βgal+ fibroblasts elicited by co-stimulation with rMMP1 and TGF-β1, and its corresponding conditioned medium elicited a significantly lower growth and invasion in LCC cancer cells, revealing the oxidative stress implication in fibroblast senescence induction and associated pro-tumorigenic secretome. In summary, our results establish a new role for MMP1 in cancer and support that LCC cells elicit a tumor-supporting niche through the aberrant secretion of MMP1 and TGF-β1 to induce senescence in adjacent fibroblasts. Furthermore, we implicate oxidative stress in MMP1/TGF-β1-induced TAF senescence and support a novel therapeutic strategy in LCC based on targeting senescent TAFs. Citation Format: Marta Gabasa, Evette S. Radisky, Rafael Ikemori, Giulia Bertolini, Marselina Arshakyan, Alexandra Hockla, Paula Duch, Ornella Rondinone, Alejandro Llorente, Maria Maqueda, Alexandre Perera, Noemí Reguart, Luca Roz, Derek C. Radisky, Jordi Alcaraz. MMP1 and TGF-β1 cooperate to drive tumor progression in large cell carcinoma of the lung through fibroblast senescence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2515.

Abstract Benign breast disease (BBD) is an established risk factor for development of breast cancer (BC). However, little is known about the prevalence of somatic genetic alterations at the time of BBD diagnosis and relationship to subsequent BC. To characterize DNA variants in BBD and investigate association with BC risk, we isolated DNA from formalin-fixed paraffin-embedded (FFPE) BBD biopsies and assessed mutations using a panel of 93 breast cancer predisposition genes (Qiagen GeneRead). The study set consisted of 120 BBD patients from three age-matched groups defined based on 16 years of BC follow-up: BBD-controls (cancer-free after 16 years), BBD-ER+, or BBD-ER- breast cancer (within 16 years). Bioinformatics quality checks included comparisons of paired fresh-frozen and FFPE replicates to reduce false variant calls induced by FFPE artifacts. Gene-level variant burden differences among study groups were assessed using 12 statistical approaches, adjusted for patient age, year of biopsy, and histology. To investigate possible immune implications of increased variant burden, extent of leukocytes in the BBD biopsies was assessed using CD45 immunohistochemistry. To assess variant profile changes during the progression from BBD to BC, we also performed targeted sequencing of 12 BBD-matched subsequent tumor samples (six ER+ and six ER-) developed within 5 years of BBD diagnosis. Gene-level association results showed consistently skewed distributions suggesting a higher variant burden in BBD controls: among the top 10 genes associated with case-status (p<0.05), all had BC-risk odds ratio estimates less than 1.0. Immune infiltrates, assessed by CD45 H-scores, were positively associated with overall variant burden (r=0.42, p=0.0031), and noticeably higher in cancer-free controls (r=0.50, p=0.005). Comparison of mutation variants in 12 BBD cases that developed cancer within 5 years of diagnosis and their subsequent tumors revealed that more than half of the non-SNP variants were shared between the BBD and the subsequent tumor (54.6%), whereas less than one quarter were unique to the tumor (20.6%) or unique to the BBD (24.9%). Through BBD-BC paired variant analysis, three subjects were found with newly emergent clones uniquely appearing in the tumors and four subjects had loss of clones in the tumor that were present in the BBD. These results show that somatic variant burden is lower in patients with BBD that progress to BC, mutation profiles of BC progression are heterogeneous, and BBD tissues with reduced variant burden also show reduced immune infiltrate. This implicates a potential protective role for immune activation in BBD. Future directions will define the characteristics of the potentially protective immune response and its role in variant heterogeneity in a larger sample set, integrated with paired RNA sequencing to better understand the pathways involved and the relationship to immune infiltration. Citation Format: Stacey J. Winham, Julie M. Cunningham, Yuanhang Liu, Aditya V. Bhagwate, Ethan P. Heinzen, Samantha J. McDonough, Melody L. Stallings-Mann, Robert A. Vierkant, Jodi M. Carter, Mark E. Sherman, Derek C. Radisky, Amy C. Degnim, Chen Wang. Somatic variant burdenin benign breast disease and association with risk of subsequent breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2274.

Serine protease inhibitors of the Kunitz‐bovine pancreatic trypsin inhibitor (BPTI) family, such as tissue factor pathway inhibitor‐1 Kunitz domain 1 ( KD1 TFPI1) and amyloid precursor protein inhibitor (APPI), are biological regulators of proteolysis and serve as important scaffolds for developing therapeutics. Mesotrypsin is a unique human protease with cancer‐promoting properties which rapidly cleaves and inactivates serine protease inhibitors; because of this, it is a challenging therapeutic target and an excellent model for developing therapeutic inhibitors with improved proteolytic resistance. We hypothesize that stabilization of the Kunitz inhibitor binding loop by disulfide bond anchoring to the scaffold can reduce proteolytic susceptibility and improve binding efficacy. Here we have engineered a new disulfide bond into both KD1 TFPI1 and an APPI variant previously engineered for mesotrypsin affinity. The new disulfide bond anchors the binding loop to the scaffold, resulting in reduced mesotrypsin proteolytic cleavage by 17‐fold and 3‐fold, respectively. To gain insight into the structural basis for improved proteolytic stability, we crystallized mutant KD1 TFPI1 and APPI with mesotrypsin and solved these novel structures. We then performed all‐atom molecular dynamics simulations using these mesotrypsin‐mutant inhibitor complexes compared to models lacking the engineered disulfide bond. Our simulation results support our hypothesis that the cause of decreased proteolysis rates is dampened conformational fluctuations in the binding loop and minimized motion at the enzyme‐inhibitor interface. We also performed simulations using unbound inhibitors to show that stabilization of the binding loop to states similar to the bound configuration correlates with stronger binding affinity. Our disulfide engineering approach is potentially a useful tool in biopharmaceutical development for mesotrypsin, other serine proteases, and possibly for other enzyme targets. Support or Funding Information NIH grant R01CA154387 to E.S.R., European Research Council grant 336041 to N.P., US‐Israel Binational Science Foundation grant BSF2015134 to E.S.R. and N.P. Xray diffraction data were measured at the Berkeley Center for Structural Biology at the Advanced Light Source and at the European Synchrotron Radiation Facility. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Matrix metalloproteinases (MMPs) play a pivotal role in progression of several diseases including cancer and fibrosis, which makes these enzymes promising targets for developing protein therapeutics. The challenge in using MMP inhibitors as drugs in MMP‐associated diseases is lack of high selectivity toward specific target MMPs. Therefore, development of selective MMP inhibitors is a critical goal. Tissue inhibitors of metalloproteinases (TIMPs), as natural MMP inhibitors, offer ideal scaffolds for engineering highly selective MMP‐targeted therapeutics. We have previously shown a key role for MMP‐3 in the pathogenesis of pulmonary fibrosis. TIMP‐1 is a natural MMP‐3 inhibitor with picomolar affinity; it also binds to other MMPs with a spectrum of affinities. Engineering of TIMP‐1 for more selective inhibition of MMP‐3 may provide protein therapeutics with applications in treating lung fibrosis. I have used directed evolution and yeast surface display toward development of selective MMP‐3‐targeted biologic agents through protein engineering of TIMP‐1. I have screened a library of TIMP‐1 mutants generated by random mutagenesis of residues comprising the MMP‐interacting loops of TIMP‐1 to select for enhanced MMP‐3 binding on the yeast surface. Diversified residues have been chosen based on structural studies of TIMP‐1/MMP‐3 interactions. TIMP‐1 mutants isolated after rounds of Fluorescent‐Activated Cell Sorting (FACS) showed substantial improvement in MMP‐3 binding compared to the wild‐type TIMP‐1, both in the surface display context and in enzyme inhibition studies using soluble purified proteins. I have also developed a counter‐selection strategy to screen TIMP‐1 mutants that bind selectively to MMP‐3 in the presence of MMP‐10, an MMP with the greatest sequence and structural similarity to MMP‐3. The isolated TIMP‐1 mutants after five rounds of competitive screening showed up to 20‐fold improvement in binding selectivity, highlighting the significant potential of this approach for development of inhibitors with single‐MMP selectivity. In ongoing studies, I have identified some of the key TIMP‐1 mutations responsible for improvements in MMP‐3 affinity and selectivity. I have co‐crystallized one of the top affinity mutants with the catalytic domain of MMP‐3, and have obtained synchrotron diffraction data at a resolution of 2.2 Å; efforts to solve this crystal structure are underway. I anticipate that this structure will offer insights into the structural basis for improvements in selectivity, and will help to guide future library design for refinement of my directed evolution methodology for generating selective engineered TIMPs. This work provides a promising and innovative strategy to develop protein therapeutics based on natural enzyme inhibitors, critically improving selectivity to eliminate offtarget effects. Support or Funding Information This project is funded through two grants from Department of Defense (DoD) (ID # W81XWH‐16‐2‐003015), and National Institute of Health (NIH) (R21CA205471). This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

There is evidence in the literature that many serine proteases, as typified by thrombin, possess an autoinhibitory loop (AIL) that controls substrate access to the active site. The presence of an AIL has not been documented in trypsins. Mesotrypsin is a human trypsin implicated in tumor cell invasiveness for pancreatic and other cancers. However, it is a challenging therapeutic target because of high structural similarity to other trypsin‐like serine proteases, typically lower affinity for inhibitors compared to related serine proteases, and unique ability to cleave proteinaceous serine protease inhibitors. We have recently solved a high‐resolution crystal structure of unbound mesotrypsin which revealed that residues 215‐220 partially occluded the substrate binding site. Comparison of this new structure with previous inhibitor‐bound crystal structures of mesotrypsin demonstrate the conformational transition of the AIL between closed and open states. These two conformational states were investigated with molecular dynamics simulations to discern the dynamical behavior of the AIL in different conformations. The AIL has increased local dynamics in the closed position, as well as a larger number of conformational clusters; this suggests there is a more well‐defined open state ready to accept substrate, while there are a dynamic variety of closed states that preclude substrate binding to various extents. Additionally, we identified novel binding sites that are exposed by the conformational shift of the AIL to the closed state. We have conducted initial in silico screening for compounds predicted to bind preferentially to the AIL closed (but not open) structure and stabilize the closed conformation. These efforts have resulted in more than 40 compounds as initial hits. Exploiting the AIL as a novel allosteric binding site represents a new mechanism for targeting mesotrypsin and preventing its protumorigenic function.

Tissue inhibitors of metalloproteinases (TIMPs) are natural inhibitors of matrix metalloproteinases (MMPs), enzymes known for contributions to diseases including cancer and fibrosis. The TIMP N‐terminal domain, regarded as the “inhibitory domain”, has been the center of attention both for understanding natural regulation of MMPs by TIMPs, and for developing protein‐based MMP inhibitors for therapeutic applications. The role of the TIMP C‐terminal domain in MMP inhibition has not been well studied. I have used directed evolution via yeast surface display for protein engineering of full‐length human TIMP‐1 toward development of MMP‐3‐targeted ultra‐binders. TIMP‐1 variants with up to 10‐fold improvement in MMP‐3 binding (compared to WT‐TIMP‐1) were isolated after six rounds of library screening using fluorescence‐activated cell sorting (FACS). Analysis of individual and paired mutations from the selected TIMP‐1 variants revealed a cooperative effect between distant mutations on the N‐ and C‐terminal TIMP domains, positioned on opposite sides of the interaction interface with MMP‐3. I have co‐crystallized two TIMP‐1 variants containing single and composite mutations in complex with the catalytic domain of MMP‐3 and solved the X‐ray crystal structures of these complexes. The protein structures reveal substantial conformational changes in the TIMP‐1 binding interfaces near the two cooperative mutations. Affinity appears to be strengthened by tighter cinching of a reciprocal tyrosine clasp formed between the N‐terminal loop of TIMP‐1 and the proximal MMP3 interface, and adoption of an alpha‐helical conformation by a segment of the TIMP‐1 C‐terminal domain, resulting in stabilized interactions between the two TIMP‐1 domains and improved hydrophobic interactions between TIMP‐1 and MMP‐3. Our protein engineering and structural studies provide novel insight into the cooperative function of N‐ and C‐terminal TIMP domains and the significance of peripheral TIMP epitopes in MMP recognition. Our results further point to new approaches for design of TIMP‐based protein therapeutics with improved affinity and selectivity. Support or Funding Information This work was supported by grants DOD W81XWH‐16‐2‐0030, and NIH R21 CA205471. Diffraction data were measured at the Berkeley National Synchrotron Light Source. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

COVID-19 is a devastating respiratory and inflammatory illness caused by a new coronavirus that is rapidly spreading throughout the human population. Over the past 12 months, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has already infected over 160 million (>20% located in United States) and killed more than 3.3 million people around the world (>20% deaths in USA). As we face one of the most challenging times in our recent history, there is an urgent need to identify drug candidates that can attack SARS-CoV-2 on multiple fronts. We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors—S/Ace2, Tmprss2, Cathepsins L and K, and Mpro—to prevent binding, membrane fusion and replication of the virus, respectively. All together, we generated an ensemble of structural conformations that increase high-quality docking outcomes to screen over >6 million compounds including all FDA-approved drugs, drugs under clinical trial (>3000) and an additional >30 million selected chemotypes from fragment libraries. Our results yielded an initial set of 350 high-value compounds from both new and FDA-approved compounds that can now be tested experimentally in appropriate biological model systems. We anticipate that our results will initiate screening campaigns and accelerate the discovery of COVID-19 treatments.