Biology subjects

Lee, J. M.

Publications and source records attributed to Lee, J. M..

At least 19 recordsLinked to original sources

bioRxiv2026

FORGE-KI: A Modular Framework for Endogenous Knock-In Engineering Across HDR and PITCh/MMEJ Repair Pathways

Targeted knock-in technologies have enabled precise insertion of reporters, affinity tags, degrons, and other functional payloads into endogenous genomic loci. Over the past decade, a diverse collection of genome engineering strategies has emerged, including approaches based on homology-directed repair (HDR), microhomology-mediated end joining (MMEJ), homology-mediated end joining (HMEJ), and related methodologies. While these advances have greatly expanded the capabilities of endogenous genome engineering, they have also increased the complexity of donor design, assembly, and validation. Here, we describe FORGE-KI (Functional Oncology Research Genetic Engineering - Knock in), a pathway-matched design workflow for endogenous knock-in engineering that aligns the assembly strategy with the underlying repair mechanism. For large-cargo insertions, we use a modular five-component framework that separates gene-specific targeting arms from reusable functional modules, allowing rapid assembly of HDR donor constructs targeting AHR, IRF1, and FOSL1 from a shared reagent collection. For MMEJ/PITCh applications, where short targeting elements permit rapid fabrication, we developed a streamlined one-step pipeline in which the entire donor and selection payload is synthesized as a single continuous fragment for direct cloning, compressing the design-to-reagent cycle time. This MMEJ workflow is paired with a dual-promoter nuclease vector (pForge-KI-MMEJ-Cas9-DualGuide) that drives the PITCh-release and locus-specific guides from distinct promoters, a design intended to reduce the repeated-promoter instability associated with some dual-guide vectors. We also established a standardized workflow for donor assembly, generation of knock-in cell populations, molecular validation, and selectable-cassette removal, and we demonstrate it by generating a functional, selection-marker-free, cytokine-inducible IRF1 HDR reporter line and an inducible IRF1 PITCh/MMEJ reporter pool with confirmed junction enrichment. In parallel, we developed forgeKI, an R package that automates C-terminal reporter knock-in design across both HDR and PITCh/MMEJ repair pathways, including guide selection, target-biology validation, targeting-arm design, domestication, donor-assembly planning, and generation of synthesis-ready constructs. Together, the reagents and software provide a practical system for endogenous knock-in engineering that supports multiple payloads, selection strategies, and repair pathways within a shared donor organization. Rather than replacing existing knock-in technologies, this framework provides a modular foundation for incorporating, extending, and automating the published knock-in methods.

molecular biology↗

bioRxiv2026

LEO1 loss promotes ER stress-adapted migration and cholesterol dependency in colorectal cancer

The RNA polymerase-associated factor 1 complex (PAF1C) is an evolutionarily conserved transcription elongation complex that regulates RNA polymerase II-mediated transcription and chromatin modification. LEO1, a core subunit of PAF1C, has been implicated in developmental gene regulation, WNT signaling, and leukemogenesis; however, its role in solid tumor progression remains poorly understood. In this study, we found that although LEO1 expression is generally elevated in colorectal cancer (CRC), its expression is reduced in stage IV tumors and is associated with poor clinical outcomes. To investigate its function, we established LEO1 -deficient HCT116 cell line and performed transcriptomic analyses. Loss of LEO1 suppressed epithelial differentiation and developmental gene programs while inducing cell cycle delay. Despite these changes, LEO1-deficient cells exhibited aggressive phenotypes, including enlarged nuclei and increased expression of migration-associated genes, which were further enhanced under glucose deprivation. Motif analysis identified FOXM1 as a key regulator of these migration-related genes. Mechanistically, LEO1 deficiency promoted accelerated transcriptional activation of GRP78, a central regulator of endoplasmic reticulum (ER) stress adaptation. GRP78 was required for survival under ER stress conditions, and its inhibition suppressed both migration and migration-associated gene expression. In addition, transcriptomic analyses revealed upregulation of cholesterol metabolism-related genes in LEO1-deficient cells. Consistently, treatment with the HMG-CoA reductase inhibitor atorvastatin selectively impaired their survival, indicating cholesterol metabolic dependency. Collectively, these findings demonstrate that LEO1 loss promotes ER stress-adapted migration and cholesterol metabolic dependency in CRC, suggesting that these pathways may represent therapeutic vulnerabilities in metastatic LEO1-low CRC.

cancer biology↗

bioRxiv2026

ORBIT: Orthogonal Rotation for Biological Inter-species Transfer

MotivationCross-species gene embeddings are central to transferring functional annotations between species. A recent method demonstrated that species-specific STRING (PPI) network embeddings can be aligned across 1322 eukaryotes with autoencoders (FedCoder), but this approach is computationally expensive, depends on careful hyperparameter selection, leaves substantial room for improvement in cross-species retrieval quality, and has not been demonstrated on coexpression networks. ResultsWe introduce an alignment pipeline for cross-species coexpression network embeddings based on orthogonal Procrustes rotation. Species-specific Node2Vec embeddings of coexpression networks are aligned to a shared space using ortholog anchors from OrthoFinder, solved in closed form via Singular Value Decomposition (SVD). Applied to 153 plant species and 5.7 million genes, Procrustes alignment achieves four-fold higher cross-species Spearman correlation and consistently higher retrieval metrics than the SPACE autoencoder, while leaving within-species coexpression structure invariant (preservation ratio 1.000 against the unaligned baseline). The full alignment completes in under three minutes on a single CPU, and on downstream tasks, Procrustes embeddings improve within-species GO term prediction and outperform SPACE for cross-species GO transfer. Procrustes and sequence embeddings remain complementary for biological-process prediction, consistent with observations from SPACE. AvailabilityCode for producing the embeddings is made available at https://github.com/pwissenberg/orbit.

bioinformatics↗

bioRxiv2025

Human Norovirus NS7 Protein Activates Canonical Inflammasome Pathways via NLRP6 in Intestinal Epithelial Cells

Human norovirus (HNoV) is a leading cause of acute gastroenteritis, yet the mechanisms by which it interfaces with host innate immunity remain elusive. Here, we demonstrate that the HNoV NS7 protein, an RNA-dependent RNA polymerase, acts as a direct activator of canonical inflammasomes. Using reconstituted cell systems and human intestinal enteroids (HIEs), we found that NS7 interacts with both NLRP3 and NLRP6, promoting ASC speck formation, caspase-1 cleavage, and secretion of IL-1{beta} and IL-18. HNoV infection of HIEs recapitulated these events, including gasdermin D processing and robust IL-18 release. Importantly, CRISPR/Cas9-mediated NLRP6 deficiency abrogated inflammasome activation and markedly enhanced viral replication, underscoring the essential role of NLRP6 in epithelial antiviral defense. These findings identify NS7 as a novel inflammasome activator and establish NLRP6 as a key determinant of innate immune control of HNoV. Our study highlights inflammasome signaling as a potential therapeutic target for norovirus infection. Author summaryIn this study, we used human intestinal organoid models to explore how norovirus infection triggers a specific immune response known as inflammasome, which helps protect the gut from viral invaders. We focused on a viral protein called NS7 and discovered that it directly activates two types of inflammasome sensors, NLRP3 and NLRP6. We found that NLRP6, which is abundant in the gut lining, is especially important for detecting norovirus and launching an immune response. When we removed NLRP6 from intestinal cells, the virus was able to replicate more easily, and normal immune activation was lost. Our results reveal that norovirus uses its NS7 protein to interact with the bodys immune machinery in the intestine, and that NLRP6 plays a key role in controlling infection. This work highlights a new way in which the gut senses and responds to norovirus and may help guide future efforts to develop treatments that target these immune pathways.

immunology↗

bioRxiv2025

Compositional and Functional Profiling of the Gut Microbiome in Sarcoidosis

BackgroundSarcoidosis is a chronic inflammatory disease characterized by systematic granuloma formation, predominantly in the lungs. One leading hypothesis posits that prolonged exposure to microbial antigens may trigger chronic and dysregulated inflammation. Prior studies have examined the lung microbiota of sarcoidosis patients, but the role of the gut microbiota along the gut-immune axis remains largely unexplored. We elucidate the community composition and function of the gut microbiome in sarcoidosis. MethodsSubjects diagnosed with sarcoidosis (n=37) were recruited and matched with healthy control subjects (n=37). Stool samples were collected from sarcoidosis patients for metagenomic sequencing, followed by taxonomic classification and functional annotation as KEGG Orthology (KO) pathways. Differential analysis between sarcoidosis and control cohorts was performed using both standard and compositional approaches. ResultsSarcoidosis microbiomes exhibited similar alpha diversity but significantly different beta diversity from control microbiomes (p<0.05). At the phylum level, the proportion of Actinobacteria and Firmicutes expanded whereas Bacteroides and Verrucomicrobia proportionally shrunk in sarcoidosis gut microbiomes compared to healthy control ones. At the species level, 1,495 species were significantly more abundant and 279 less abundant in sarcoidosis compared to controls (FDR<0.05). Of these, 13 species demonstrated greater intergroup than intragroup variation (effect size>1), including microbes previously detected in the lungs and granulomas of sarcoidosis. Functional profiling revealed 409 KO pathways that were significantly underrepresented in sarcoidosis compared to control (FDR<0.05), of which 79 met an effect size > 1. These include pathways in amino acid and energy metabolism as well as HIF-1 signaling. ConclusionsOur findings highlight the potential role of gut microbiome composition and function in inflammatory processes that are associated with granuloma formation in sarcoidosis and warrant further investigation into gut hyperoxia-driven dysbiosis.

microbiology↗

bioRxiv2025

Astrocytic MAOB-GABA axis as a molecular brake on repair following spinal cord injury

Neuroregeneration and remyelination rarely occur in the adult mammalian brain and spinal cord following central nervous system (CNS) injury. The glial scar has been proposed as a major contributor to this failure in the regenerative process. However, its underlying molecular and cellular mechanisms remain unclear. Here, we report that monoamine oxidase B (MAOB)-dependent excessive GABA release from reactive astrocytes suppresses CNS repair system by reducing BDNF and TrkB expression in severe spinal cord injury (SCI) animal models. Genetic deletion of MAOB in a mouse SCI model promotes both functional and tissue recovery. Notably, the selective MAOB inhibitor, KDS2010, facilitates recovery and regeneration by disinhibiting the BDNF-TrkB axis in a rat SCI model. Its dose-dependent effects were further validated in a monkey SCI model. Moreover, KDS2010 demonstrates a tolerable safety profile and dose-proportional pharmacokinetics in healthy humans during a phase 1 clinical trial. Our findings identify the astrocytic MAOB-GABA axis as a crucial molecular and cellular brake on CNS repair system following SCI and highlight translational potential of KDS2010 as a promising therapeutic candidate for SCI treatment.

neuroscience↗

bioRxiv2025

A Chk1-Sp1-CD59 axis of the DNA damage response impedes rituximab-mediated complement-dependent cytotoxicity

The DNA damage response (DDR) is a central regulator of cancer cell fate, coordinating both pro-death and pro-survival pathways in response to genotoxic stress. Here, we reveal an unexpected role for the DDR at the cell surface, in mediating immune evasion from complement-dependent cytotoxicity (CDC), an innate immune mechanism exploited by therapeutic monoclonal antibodies (mAbs). In the context of diffuse large B-cell lymphoma (DLBCL), where the anti-CD20 mAb rituximab utilizes CDC, we show that genotoxic chemotherapy induces expression of membrane-bound complement regulatory proteins (mCRPs) CD46, CD55, and CD59, thereby reducing CDC sensitivity and compromising rituximab activity. In this setting, CD59 emerged as the dominant DDR-induced inhibitor of complement-mediated killing. A high-throughput kinase inhibitor screen identified checkpoint kinase 1 (Chk1) as a critical mediator of this response. Mechanistically, DNA damage activates Chk1, enhancing CD59 transcription via an Sp1-bound promoter. Co-immunoprecipitation mass spectrometry revealed a Chk1 dependent remodelling of Sp1-associated complexes to a transcriptionally active state with recruitment of the histone acetyltransferase KAT2A. These findings expand the role of the DDR in immune resistance at the tumor cell surface, and highlight a negative interaction between chemotherapy and monoclonal antibodies that may require sequential administration or targeting of the Chk1- Sp1-CD59 axis. SignificanceThe DNA Damage Response upregulates complement-protective proteins, extending its role in modulating immune evasion at the cell surface, with direct implications for combinations of chemotherapy and monoclonal antibodies widely used in cancer.

cancer biology↗

bioRxiv2024

Toxicity of extracellular cGAMP and its analogs to T cells is due to SLC7A1-mediated import

STING agonists are promising innate immune therapies and can synergize with adaptive immune checkpoint blockade therapies for cancer treatment, but their effectiveness is limited by the toxicity to activated T cells. An important class of STING agonists are analogs of the endogenous STING agonist, cGAMP, and while transporters for these small molecules are known in some cell types, how they enter and kill T cells remains unknown. Here, we identify the cationic amino acid transporter SLC7A1 as the dominant transporter of cGAMP and its analogs in activated primary mouse and human T cells. T cells upregulate this transporter upon activation and rapid proliferation to meet their high metabolic demand, but this comes at the cost of enabling increased transport and toxicity of cGAMP. To circumvent the essentiality of SLC7A1 to proliferating T cells, we found that the residues responsible for cGAMP transport are separate from the arginine binding pocket allowing us to perturb cGAMP transport and STING-activation mediated killing without impacting arginine transport. These results suggest that SLC7A1 is a potential target for alleviating T cell toxicity associated with cGAMP and its analogs.

immunology↗

bioRxiv2024

Next generation APOBEC3 inhibitors: Optimally designed for potency and nuclease stability

APOBEC3 (or A3) enzymes have emerged as potential therapeutic targets due to their role in introducing heterogeneity in viruses and cancer, often leading to drug resistance. Inhibiting these enzymes has remained elusive as initial phosphodiester (PO) linked DNA based inhibitors lack stability and potency. We have enhanced both potency and nuclease stability, of 2'-deoxy-zebularine (dZ), substrate-based oligonucleotide inhibitors for two critical A3s: A3A and A3G. While replacing the phosphate backbone with phosphorothioate (PS) linkages increased nuclease stability, fully PS-modified inhibitors lost potency (1.4-3.7 fold) due to the structural constraints of the active site. For both enzymes, mixed PO/PS backbones enhanced potency (2.3-9.2 fold), while also vastly improving nuclease resistance. We also strategically introduced 2'-fluoro sugar modifications, creating the first nanomolar inhibitor of A3G-CTD2. With hairpin-structured inhibitors containing optimized PS patterns and LNA sugar modifications, we characterize the first single-digit nanomolar inhibitor targeting A3A. These extremely potent A3A inhibitors, were highly resistant to nuclease degradation in serum stability assays. Overall, our optimally designed A3 oligonucleotide inhibitors show improved potency and stability, compared to previous attempts to inhibit these critical enzymes, opening the door to realize the therapeutic potential of A3 inhibition.

biochemistry↗

bioRxiv2024

A Third COVID-19 Vaccine Dose in Kidney Transplant Recipients Induces Antibody Response to Vaccine and Omicron Variants but Shows Limited Ig Subclass Switching

Solid organ transplant recipients (SOTRs) suffer more frequent and more severe infections due to their compromised immune responses resulting from immunosuppressive treatments designed to prevent organ rejection. Pharmacological immunosuppression can adversely affect immune responses to vaccination. A cohort of kidney transplant recipients (KTRs) received their third dose of ancestral, monovalent COVID-19 vaccine in the context of a clinical trial and antibody responses to the vaccine strain, as well as to Omicron variants BA.1 and BA.5 were investigated and compared with healthy controls. Total IgG and live virus neutralizing antibody titers were reduced in KTRs compared to controls for all variants. KTRs displayed altered IgG subclass switching, with significantly lower IgG3 antibodies. Responses in KTRs were also very heterogeneous, with some individuals showing strong responses but a significant number showing no Omicron-specific neutralizing antibodies. Taken together, immune responses after COVID-19 vaccination in KTRs were not only lower than healthy controls but highly variable, indicating that simply increasing the number of vaccine doses alone may not be sufficient to provide greater protection in this population. ImportanceThis study addresses the challenges faced by kidney transplant recipients (KTRs) in mounting effective immune responses against COVID-19. By evaluating the antibody responses to a third dose of monovalent mRNA COVID-19 vaccine and its effectiveness against Omicron subvariants (BA.1 and BA.5), this study reveals significant reductions in both binding and neutralizing antibodies in KTRs compared to healthy controls. The research highlights altered IgG subclass switching and heterogeneous responses within the KTR population. Reduced recognition of variants, coupled with differences in IgG subclasses, decreases both the quality and quantity of protective antibodies after vaccination in KTRs. These findings underscore the need for tailored vaccination strategies for immunosuppressed populations such as KTRs. Alternative formulations and doses of COVID-19 vaccines should be considered for people with severely compromised immune systems, as more frequent vaccinations may not significantly improve the response, especially regarding neutralizing antibodies.

immunology↗

bioRxiv2024

Clonal spheroids capture functional and genetic heterogeneity of head and neck cancer

Head and neck cancer squamous cell carcinoma (HNSCC) cells exhibit both structural and functional diversity, making them valuable models for understanding tumor heterogeneity at clinical levels. In this study, we generated single-cell-derived spheroids (SCDS) from HNSCC cell lines and patient tumor cells using scaffold- and non-scaffold-based methods to assess this variability. A distinct structural variability among these SCDS, categorized as hypo- and hyperproliferative spheroids based on size, was observed. Hyperproliferative spheroids demonstrated heightened proliferative and tumorigenic potential and increased sensitivity to cisplatin and radiation, while hypoproliferative spheroids exhibited enhanced migratory capabilities. Single-cell RNA sequencing (scRNA-seq) of hypo- and hyperproliferative spheroids provided insights into the transcriptional landscape of HNSCC cells, validating the observed structural and functional heterogeneities within primary tumors. These functionally and genetically characterized spheroids offer valuable tools for the development of next-generation therapeutics. Statement of SignificanceEstablishment and characterization of single-cell-derived spheroids from head and neck cancer cells, employing scaffold and non-scaffold materials, demonstrate functional and genetic heterogeneity. Single-cell analysis reveals correlations between genetic diversity and spheroid functionality. These characterized spheroids offer potential for advancing therapeutics development.

cancer biology↗

bioRxiv2024

Characterization of high affinity IgM and IgG monoclonal antibodies against norovirus variants GII.4 and GII.17

Human norovirus, a leading cause of viral gastroenteritis, results in significant global health and economic burden, requiring sensitive and accurate diagnosis and effective therapeutics and vaccines. In this study, we immunized mice with the virus like capsid particles of GII.4, a mainstream strain, and GII.17, a modern strain that began to circulate in 2014, and used hybridoma technology to generate hybridoma cells that produce norovirus-binding antibodies against GII.4 and GII.17, respectively. Selection of these hybridoma cells yielded monoclonal IgG and IgM antibodies against these strains. Characterization of these antibodies revealed that avidity effect by multivalent binding is necessary for IgM to bind to norovirus at high efficiency, while IgG achieve high affinity even by monovalent binding. Surface plasmon resonance and ELISA data suggest that the high density of antigen protrusion domain in the norovirus capsid, containing approximately protomers, facilitates IgM to bind to norovirus capsid with high efficiency.

biochemistry↗

bioRxiv2024

Parallel comparison reveals conservation and re-wiring of abiotic stress response networks across three plant species

Abiotic stresses trigger significant alterations in plant morphology, yield, and nutrient composition. To counter these stresses, plants have developed strategies involving gene expression adjustments, impacting their growth and development to ensure survival and reproduction. Although transcriptomic studies have extensively examined stress responses, our understanding of their conservation remains limited. We conducted a comprehensive study on the effects of 24 different environmental and nutrient conditions on the growth yield of three hydroponically grown leafy crops (cai xin, lettuce, and spinach). This research identified optimal conditions for maximizing yield and vitamin content and pinpointed conditions that induce abiotic stress. Our findings highlight the substantial impact of stress on various plant functions, with photosynthesis playing a pivotal role in vitamin content regulation. A detailed comparative analysis of gene expression across these crops revealed conserved gene sets potentially crucial for abiotic stress response. Furthermore, we introduced a novel method that merges regression and genomics to construct reliable gene regulatory networks for stress response. Despite significant conservation of these networks among the studied crops, their key transcription factors showed limited similarity to those in Arabidopsis thaliana, suggesting notable functional divergence. To give easy access to the data and comparative transcriptomic tools, we established StressPlantTools, an public online database (https://stress.sbs.ntu.edu.sg/), facilitating further research into stress-responsive genes.

plant biology↗

bioRxiv2024

Direct delivery of stabilized Cas-embedded base editors achieves efficient and accurate editing of clinically relevant targets

Over the last 5 years, cytosine base editors (CBEs) have emerged as a promising therapeutic tool for specific editing of single nucleotide variants and disrupting specific genes associated with disease. Despite this promise, the currently available CBEs have the significant liabilities of off-target and bystander editing activities, in part due to the mechanism by which they are delivered, causing limitations in their potential applications. In this study we engineeredhighly stabilized Cas-embedded CBEs (sCE_CBEs) that integrate several recent advances, andthat are highly expressible and soluble for direct delivery into cells as ribonucleoprotein (RNP) complexes. Our resulting sCE_CBE RNP complexes efficiently and specifically target TC dinucleotides with minimal off-target or bystander mutations. Additional uracil glycosylase inhibitor (UGI) protein in trans further increased C-to-T editing efficiency and target purity in a dose-dependent manner, minimizing indel formation to untreated levels. A single electroporation was sufficient to effectively edit the therapeutically relevant locus for sickle cell disease in hematopoietic stem and progenitor cells (HSPC) in a dose dependent manner without cellular toxicity. Significantly, these sCE_CBE RNPs permitted for the transplantation of edited HSPCs confirming highly efficient editing in engrafting hematopoietic stem cells in mice. The success of the designed sCBE editors, with improved solubility and enhanced on-target editing, demonstrates promising agents for cytosine base editing at other disease-related sites in HSPCs and other cell types.

biochemistry↗

bioRxiv2024

Oncogenic KRASG12D extrinsically induces an immunosuppressive microenvironment in lung adenocarcinoma

Withdrawal StatementThis manuscript has been withdrawn by the authors due to a dispute over co-first authorship that is currently being arbitrated by the medical school at our institution. Therefore, the authors do not wish this work to be cited as reference for the project. Upon completion of the arbitration process, we will take steps to revert the current withdrawn status. If you have any questions, please contact the corresponding author.

cancer biology↗

bioRxiv2023

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

ABSTRACTHuman influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population, and how this heterogeneity affects virus evolution. Here we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of the A/Hong Kong/45/2019 (H3N2) and A/Perth/16/2009 (H3N2) strains affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that fixed in influenza variants after 2020 cause the greatest escape from sera from younger individuals. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups, and suggest approaches to understand how this heterogeneous selection shapes viral evolution.

microbiology↗

bioRxiv2023

Addressing the dNTP bottleneck restricting prime editing activity

Prime editing efficiency is modest in cells that are quiescent or slowly proliferating where intracellular dNTP levels are tightly regulated. MMLV-reverse transcriptase - the prime editor polymerase subunit - requires high intracellular dNTPs levels for efficient polymerization. We report that prime editing efficiency in primary cells and in vivo is increased by mutations that enhance the enzymatic properties of MMLV-reverse transcriptase and can be further complemented by targeting SAMHD1 for degradation.

biochemistry↗

bioRxiv2023

Modeling Molecular Pathogenesis of Idiopathic Pulmonary Fibrosis-Associated Lung Cancer in Mice

Idiopathic Pulmonary Fibrosis (IPF) is characterized by progressive, often fatal loss of lung function due to overactive collagen production and tissue scarring. IPF patients have a sevenfold-increased risk of developing lung cancer. The COVID-19 pandemic has increased the number of patients with lung diseases, and infection can worsen prognoses for those with chronic lung diseases and disease-associated cancer. Understanding the molecular pathogenesis of IPF-associated lung cancer is imperative for identifying diagnostic biomarkers and targeted therapies that will facilitate prevention of IPF and progression to lung cancer. To understand how IPF-associated fibroblast activation, matrix remodeling, epithelial-mesenchymal transition, and immune modulation influences lung cancer predisposition, we developed a mouse model to recapitulate the molecular pathogenesis of pulmonary fibrosis-associated lung cancer using the bleomycin and the Lewis Lung Carcinoma models. Models of pulmonary fibrosis, particularly bleomycin-induced fibrosis, do not recapitulate all aspects of human disease; however, to simplify nomenclature, we refer to our bleomycin-induced fibrosis model as IPF. We demonstrate that development of pulmonary fibrosis-associated lung cancer is linked to increased recruitment or reprogramming of tumor-associated macrophages and a unique gene signature that supports an immune-suppressive microenvironment through secreted factors. Not surprisingly, pre-existing fibrosis provides a pre-metastatic niche and results in augmented tumor growth. Tumors associated with bleomycin-induced fibrosis are characterized by an epithelial-to-mesenchymal transition characterized by dramatic loss of cytokeratin expression. ImplicationsWe provide new therapeutic targets that may aid the characterization of tumors associated with lung diseases and development of treatment paradigms for lung cancer patients with pre-existing pulmonary diseases.

cancer biology↗