IFN-alpha Research Articles

3-Fucosyllactose-mediated modulation of immune response against virus infection

Viral pathogens, particularly influenza and SARS-CoV-2, pose a significant global health challenge. Given the immunomodulatory properties of human milk oligosaccharides, in particular 2′-fucosyllactose and 3-fucosyllactose (3-FL), we investigated their dietary supplementation effects on antiviral responses in mouse models. This study revealed distinct immune modulations induced by 3-FL. RNA-sequencing data showed that 3-FL increased the expression of interferon receptors, such as Interferon Alpha and Beta Receptor (IFNAR) and Interferon Gamma Receptor (IFNGR), while simultaneously downregulating interferons and interferon-stimulated genes, an effect not observed with 2′-fucosyllactose supplementation. Such modulation enhanced antiviral responses in both cell culture and animal models while attenuating pre-emptive inflammatory responses. Nitric oxide concentrations in 3-FL-supplemented A549 cells and mouse lung tissues were elevated exclusively upon infection, reaching 5.8- and 1.9-fold increases over control groups, respectively. In addition, 3-FL promoted leukocyte infiltration into the site of infection upon viral challenge. 3-FL supplementation provided protective efficacy against lethal influenza challenge in mice. The demonstrated antiviral efficacy spanned multiple influenza strains and extended to SARS-CoV-2. In conclusion, 3-FL is a unique immunomodulator that helps protect the host from viral infection while suppressing inflammation prior to infection.

Production of Recombinant Human Interferon alpha 2b (rhIFN?-2b) in genetically engineered strain of Bacillus subtilis

Interferon alpha 2b (IFN?-2b) is a critical therapeutic protein with immunomodulatory properties, widely used in the treatment of various diseases, including viral infections and cancer. This study presents a comprehensive methodology for the cloning and characterization of the IFN?-2b gene, including the identification of point mutations, followed by expression in Bacillus subtilis. The research begins with gene isolation, primer design, RNA extraction, cDNA synthesis, and PCR amplification. Cloning into a T/A vector and subsequent sequencing reveal point mutations within the gene. The transformed construct is expressed in Bacillus subtilis, and the resulting protein is analyzed using SDS-PAGE. The identification of point mutations and successful protein expression in Bacillus subtilis. This study provides valuable insights into the IFN?-2b gene and its potential applications.

P096 Pathway directionality across different immune cell lineages contributes to methotrexate response in juvenile idiopathic arthritis

Abstract Background/Aims Juvenile idiopathic arthritis (JIA) is the most common autoimmune rheumatic disease in children with methotrexate (MTX) as the first line treatment. However, about 50% of JIA patients will not respond well to MTX yet still experience drug side effects. Early prediction to MTX treatment response would be beneficial for patients and families to avoid incurring unnecessary MTX side effects and ongoing uncontrolled inflammation: such validated tools or biomarkers are currently not available. Methods Transcriptional analysis was performed on peripheral blood mononuclear cells (PBMC) from pre-MTX-treated JIA patients (n = 97) of all ILAR JIA subtypes, excluding systemic JIA. RNAseq was performed on total PBMC and sorted immune cell populations: CD4+ T cells, CD8+ T cells, CD19+ B cells, and CD14+ monocytes. Clinical data collected at the time of sampling (baseline) and at the follow-up time (between 3-12 months) were used to define outcomes, measured as change in active joint count (AJC), change in Physician VAS (PhysVAS), and change in cJADAS10. After batch normalisation with ComBat-seq, differential gene expression (DGE) analysis was performed using limma-voom with age, sex, ethnicity, and steroid status included as covariates. Log2 fold changes were utilised to rank genes to implement gene set enrichment analysis (GSEA) by fgsea. Results DGE analysis showed minimal significant differentially expressed (DE) genes that passed 5% false discovery rate (FDR). The greatest number of significant DE genes were observed in CD14+ monocytes, where baseline expression of 13 genes were significantly associated with change in PhysVAS. As alterations of gene expression for a heterogeneous disease such as JIA can be subtle and correlated between genes, GSEA was performed to investigate expression changes at pathway level. Using MSigDb Hallmark pathways, GSEA showed interferon-related and tumor-necrosis-factor pathways as significantly associated with MTX response in all cell types (5% FDR). However, the directionality (up/down regulation) differed between cell lineages, suggesting pathways divergence between T cell and non-T cell lineages. For example, in interferon gamma pathway, up-regulation associated with poor treatment response in T-cells and down-regulation in non-T cells. Preliminary analysis of the leading edge genes of the interferon gamma pathway in the non-T cell lineages showed that many of the genes are driven by interferon alpha, whilst within CD4+ and CD8+ T cells the majority of the leading edge genes are specific to interferon gamma. Conclusion Different directionality of pathways that might be relevant to JIA response to treatment with MTX is observed in different mononuclear cell lineages. This could potentially explain the difficulties of finding biomarkers which correlate with response to treatment from whole blood or PBMC. Shared genes across different interferon-related pathways also suggest that interaction between interferon pathways might be driving the different direction of interferon pathway expression in different cell lineages. Disclosure M. Kartawinata: None. W. Lin: None. B. Jebson: None. K. O'Brien: None. E. Ralph: None. R. Restuadi: None. G.T. Hall: None. S. Castellano: None. C. Wallace: None. L.R. Wedderburn: Grants/research support; LRW Declares in kind contributions to CLUSTER by AbbVie, GSK, UCB, Sobi and Pfizer inc and non renumerated collaborations with Lilly and Novartis.

OA01 Cluster medicine: the role of genetics for identifying shared biological pathways between rheumatoid arthritis and common comorbidities for targeting treatments

Abstract Background/Aims Rheumatoid arthritis (RA) is a chronic inflammatory disorder associated with significant pain and disability, as well as increased risk of comorbidities. These comorbidities, such as coronary artery disease, stroke, heart failure and type 2 diabetes, often form predictable clusters highlighting the importance of common disease mechanisms. Identifying these clusters, and the underlying shared mechanisms, is key to the concept of cluster medicine which aims to take a more systemic approach to treating comorbidity. It is hypothesised that inflammatory processes in RA promote the pathogenesis of these comorbid diseases, which typically occur at an earlier stage of life than in the general population. However, few studies have investigated the degree of shared genetic susceptibility implicated across these traits. The present study aimed to identify and characterise pleiotropic loci and shared biological pathways involved in the pathogenesis of RA and cardiometabolic disorders. Methods European-only GWAS summary statistics were collected for RA (seropositive, seronegative, and overall) and seven cardiometabolic traits, including ischemic stroke, any stroke, heart failure, coronary artery disease, hypertension, atrial fibrillation, and type 2 diabetes. Cross-trait linkage disequilibrium score regression was employed to estimate the degree of genetic correlation (rg) between all pairs of traits. Subset-based meta-analysis was performed using the R package ASSET to identify pleiotropic single nucleotide polymorphisms (SNPs). Pleiotropic SNPs were assigned to genes based on positional and eQTL mapping. Prioritised genes were tested for over-representation in functional categories and biological pathways in gene sets obtained from MsigDB and WikiPathways using the hypergeometric test loci. Gene mapping and enrichment analyses were conducted in FUMA. Results RA showed significant positive genetic correlation with all cardiometabolic traits, with the seronegative subtype showing greater correlation than the seropositive subtype. Correlations between RA and cardiometabolic phenotypes ranged from 0.11 - 0.38, the strongest of which was between seronegative RA and heart failure (rg = 0.38, P = 2.6e-07). A total of 67 lead SNPs were identified as potentially pleiotropic. Pleiotropic SNPs were mapped to genes including IL6R, PTPN11, ATXN2, PLCL1 and SOX6. Pathway enrichment analyses revealed that mapped genes were primarily involved in inflammatory signalling pathways, involving interleukins, TNF-α and interferon (gamma and alpha) response. Conclusion This study provides evidence for pleiotropy across RA and cardiometabolic traits, whereby inherited genetic variants predispose to aberrant cytokine signalling, thus conferring risk to multiple diseases where inflammation is a key driver of pathogenesis. Disclosure M. Stoves: None. M. Soomro: None. S. Zhao: None. D. Plant: None. A. Barton: None. J. Bowes: None.

Molecular characterization of the evolution of premalignant lesions in the upper aerodigestive tract.

Early relapse and development of metastatic disease are some of the primary reasons for the poor prognosis of patients with head and neck squamous cell carcinoma (HNSCC). HNSCC is a heterogeneous disease which may develop in large premalignant fields of genetically altered cells. Yet knowing which individuals will progress and develop clinically significant cancers during their lifetimes remains one of the most important challenges of reducing HNSCC morbidity and mortality. To further elucidate the molecular mechanisms, we performed a focused analysis of the genome and immune microenvironment from multiple, matched normal squamous tissue, premalignant lesions, as well as primary and recurrent tumors from seven patients with p16-negative HNSCC. We performed targeted panel Next Generation Sequencing (161 genes) to analyze somatic variants from sequentially collected, matched formalin-fixed paraffin-embedded tissue (normal, premalignant, HNSCC) from two patients. These samples plus samples from five additional patients were analyzed with the Nanostring PanCancer Immune Panel. In addition, we performed shallow whole genome sequencing (0.5x coverage on average) on samples from three of these patients. Patients were, apart from one case, primarily treated with curative-intent surgery, and received subsequent adjuvant treatment, if indicated. The most frequently mutated genes were TP53 and NOTCH1. Other mutated genes included NOTCH3 and CDKN2A, among others. A significant number of mutations were private to dysplasia and invasive carcinoma, respectively, however, almost 20% were shared between them. Increasing genomic instability was observed when comparing histologically normal squamous mucosa with higher levels of dysplasia. High-grade dysplasia showed similarly rearranged genomes as invasive carcinoma. Pathways related to interferon alpha and gamma response were upregulated even in moderate dysplastic lesions with increasing expression in higher grades of dysplasia and carcinoma. SPINK5, a known tumor suppressor gene in HNSCC, was already downregulated in low-grade dysplastic lesions, indicating an early deactivation in the evolution of the disease. Genomic alterations as well as aberrant immune gene expression can be observed early in the evolution of tumors of the upper aerodigestive tract, highlighting the potential for targeting early mechanisms of disease progression.

Study on the correlation between DPP9 rs2109069 and IFNAR2 rs2236757 polymorphisms with COVID-19 mortality

Understanding the complex mechanisms of the immune system in dealing with the COVID-19 infection, which is probably related to the polymorphism in cytokine and chemokine genes, can explain the pro-inflammatory condition of patients. Therefore, in this study, the relationship between the frequency of single nucleotide polymorphisms in the two pro-inflammatory genes dipeptidylpeptidase 9 (DPP9) and interferon alpha and beta receptor subunit 2 (IFNAR2) and the severity of COVID-19 was assessed. This study involved 954 COVID-19 patients, including 528 recovered and 426 deceased patients. To investigate the polymorphisms of IFNAR2 rs2236757 and DPP9 rs2109069, we used the polymerase chain reaction with the restriction fragment length polymorphism assay. The results showed that IFNAR2 rs2236757 A allele is related to the reduced severity of the disease, whereas the incidence of DPP9 rs2109069 A allele was higher among the deceased than recovered individuals. On the other hand, in people carrying the G allele in the DPP9 gene polymorphism and the allele A in the IFNR2 gene polymorphism, the improvement of the disease was significantly higher. In conclusion, the results showed that IFNAR2 rs2236757 A allele is related to the decrease in the severity of the disease, while the frequency of DPP9 rs2109069 A allele was higher in deceased people than in recovered people. This shows the important role of genes related to inflammatory responses as well as the role of genetic variants of these genes in the severity of COVID-19.

Enhancing NSCLC recurrence prediction with PET/CT habitat imaging, ctDNA, and integrative radiogenomics-blood insights

While we recognize the prognostic importance of clinicopathological measures and circulating tumor DNA (ctDNA), the independent contribution of quantitative image markers to prognosis in non-small cell lung cancer (NSCLC) remains underexplored. In our multi-institutional study of 394 NSCLC patients, we utilize pre-treatment computed tomography (CT) and 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) to establish a habitat imaging framework for assessing regional heterogeneity within individual tumors. This framework identifies three PET/CT subtypes, which maintain prognostic value after adjusting for clinicopathologic risk factors including tumor volume. Additionally, these subtypes complement ctDNA in predicting disease recurrence. Radiogenomics analysis unveil the molecular underpinnings of these imaging subtypes, highlighting downregulation in interferon alpha and gamma pathways in the high-risk subtype. In summary, our study demonstrates that these habitat imaging subtypes effectively stratify NSCLC patients based on their risk levels for disease recurrence after initial curative surgery or radiotherapy, providing valuable insights for personalized treatment approaches.

Use of Recombinant Human Interferon Alpha in felines infected with FeLV

Abstract. The feline leukemia virus (FeLV) is a retrovirus that belongs to the genus Gammaretrovirus and exclusively affects felids. The virus carries the reverse transcriptase enzyme, which integrates into the host's DNA permanently, leading to different clinical conditions. The main complications caused by FeLV are hematopoietic neoplasms, immune-mediated disorders, neurological alterations and immunosuppression, among other ailments. The disease has no effective treatment, but antiviral and immunomodulatory drugs are still under trial. Using Recombinant Human Interferon Alpha has shown to be helpful in reducing clinical symptoms and controlling opportunistic infections, increasing the quality and life expectancy of cats infected with FeLV. Retroviruses are among the main causes of death in domestic cats. The lack of knowledge about the disease among guardians and growing cat population in Brazil are helping to increase the number of FeLV cases. Although the disease lacks a universal veterinary medical protocol, there are new studies and information available that can help to treat infected animals, improving their quality of life and expectancy and, in some cases, potentially eliminating the virus. This fact clashes with another reality: outdated professionals who are not familiar with the guidelines for Feline Retrovirus Testing and Management from the AAFP (American Association of Feline Practitioners), an international entity that since 1971 has been working to improve feline health by providing evidence-based guidelines for veterinary practices. Population growth and diseases that exclusively affect the species also highlight the need to include a deeper understanding of feline health in the curricula of undergraduate courses, preparing these future professionals to meet the demand for updated veterinarians with sufficient knowledge to care for the species.

Genetic variants in ATP2B2 as risk factors for mortality in patients unrelated but not associated with families with severe COVID-19

IntroductionThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus Disease 2019 (COVID-19). The disease has a wide range of clinical manifestations, from asymptomatic to severe. Ancestral contribution, sex, immune response, and genetic factors influence the presentation of the disease. The objective of the present study was to validate these genetic variants in patients with severe COVID-19 who died and in survivor patients. Methods: Single nucleotide variants (SNVs) in six genes: ATPase plasma membrane Ca2+ transporting 2 (ATP2B2), transmembrane serine protease 2 (TMPRSS2), dedicator of cytokinesis 2 (DOCK2), (interferon alpha and beta receptor subunit 2) IFNAR2, tumor necrosis factor receptor superfamily, member 1A (TNFRSF1A), and tumor necrosis factor receptor superfamily, member 1B (TNFRSF1B), were explored in two groups: the first consisted of severe COVID-19-related patients (familial cases from 58 families, n = 130), and the second group of unrelated severe COVID-19 patients (n = 1045). In each study group, death was evaluated as the outcome. ResultsIn non-related patients with severe COVID-19, carriers of GG genotype (rs2289274) in the ATP2B2 gene showed a high-risk probability of non-surviving (OR = 1.43). Survival analysis to 75 days indicates that carriers of GG have a higher risk than GA or AA genotypes (p = 0.0059). The haplotype GG (rs2289273-rs2289274) in ATP2B2 was found to be associated with a high risk of death in severe non-related COVID-19 patients. No significant associations were found between severe COVID-19-related patients and SNVs in ATP2B2, TMPRSS2, DOCK2, IFNAR2, TNFRSF1A, or TNFRSF1B. ConclusionsUnrelated patients with severe COVID-19 that carry the GG genotype (rs2289274) in ATP2B2 showed a high death risk. Survival analysis to 75 days indicates that carriers of GG have a higher risk of non-survival compared to GA or AA genotypes.

Results of Response-Guided Therapy with Pegylated Interferon Alpha 2a in Chronic Hepatitis B and D.

Pegylated interferon alpha 2a continues to be used for the treatment of chronic hepatitis D. The reported on-treatment virologic response varies between 17 and 47%, with relapses in more than 50% of these patients. No stopping rules have been defined, and the duration of the treatment is not clearly established, but it should be between 48 and 96 weeks. In total, 76 patients with compensated liver disease treated with peg-interferon according to the Romanian National protocol for the treatment of hepatitis D were retrospectively included. The duration of treatment was up to 96 weeks, with the following stopping rules: less than a 2 log HDV RNA decrease by week 24 and less than a 1 log decrease every 6 months afterwards. Six months after stopping the treatment, it can be restarted for unlimited cycles. The inclusion criteria were aged above 18, HBs Ag-positive, HDV RNA detectable, ALT above ULN and/or liver fibrosis at least F1 at liver biopsy, or Fibrotest and/or Fibroscan higher than 7 KPa and/or inflammation at least A1 at liver biopsy or Fibrotest. We monitored our patients for a total period of 4 years (including those that repeated the cycle). After the first 6 months of treatment, 27 patients (35.5%) had a greater than 2 log HDV RNA decrease, 19 of them achieving undetectable HDV RNA. Seventeen patients (22.3%) had undetectable HDV RNA 24 weeks after stopping 96 weeks of treatment, and none relapsed in the following 2 years. Of these 17 patients, 6 were cirrhotic, and 4 had F3. Undetectable HDV RNA at 24 weeks was the only parameter that predicted a long-term suppression of HDV RNA. In 49 patients, the treatment was stopped after 6 months according to protocol, but it was restarted 6 months later. Five of these patients finished a 48-week course of treatment; none achieved undetectable HDV RNA. During the first course of therapy, 45 patients had at least one moderate adverse reaction to treatment. In one patient, the treatment was stopped due to a serious adverse event (osteomyelitis). Treatment doses had to be reduced in 29 patients. The virologic response at week 24 can select the patients who will benefit from continuing the treatment from those who should be changed to another type of medication when available.

An immune-competent human gut microphysiological system enables inflammation-modulation by Faecalibacterium prausnitzii

Crosstalk of microbes with human gut epithelia and immune cells is crucial for gut health. However, there is no existing system for a long-term co-culture of human innate immune cells with epithelium and oxygen-intolerant commensal microbes, hindering the understanding of microbe-immune interactions in a controlled manner. Here, we established a gut epithelium-microbe-immune (GuMI) microphysiological system to maintain the long-term continuous co-culture of Faecalibacterium prausnitzii/Faecalibacterium duncaniae with colonic epithelium, antigen-presenting cells (APCs, herein dendritic cells and macrophages), and CD4+ naive T cells circulating underneath the colonic epithelium. In GuMI-APC condition, multiplex cytokine assays suggested that APCs contribute to the elevated level of cytokines and chemokines secreted into both apical and basolateral compartments compared to GuMI condition that lacks APC. In GuMI-APC with F. prausnitzii (GuMI-APC-FP), F. prausnitzii increased the transcription of pro-inflammatory genes such as toll-like receptor 1 (TLR1) and interferon alpha 1 (IFNA1) in the colonic epithelium, without a significant effect on cytokine secretion, compared to the GuMI-APC without bacteria (GuMI-APC-NB). In contrast, in the presence of CD4+ naive T cells (GuMI-APCT-FP), TLR1, IFNA1, and IDO1 transcription levels decreased with a simultaneous increase in F. prausnitzii-induced secretion of pro-inflammatory cytokines (e.g., IL8) compared to GuMI-APC-FP that lacks T cells. These results highlight the contribution of individual innate immune cells in regulating the immune response triggered by the gut commensal F. prausnitzii. The integration of defined populations of immune cells in the gut microphysiological system demonstrated the usefulness of GuMI physiomimetic platform to study microbe-epithelial-immune interactions in healthy and disease conditions.

Abstract 2882: Investigating mechanisms of radioresistance in TYK2 knockout head and neck cancer cells

Abstract Radiation therapy is the primary form of treatment of head and neck squamous cell carcinoma (HNSCC). However, more than half of patients experience disease progression with standard of care treatment. To investigate novel therapeutic targets, a CRISPR screen was done to identify genes that are associated with radioresistance. The screening results indicated that JAK1 and TYK2 knockout (KO) resulted in radioresistance in HNSCC. Preliminary data suggests that loss of JAK1 causes an enhanced G2/M arrest phenotype and enhanced genome stability that contribute to radioresistance. To investigate whether TYK2 KO caused changes to the cell cycle and genome stability as observed in JAK1 KO, Western blots, cell cycle assays, and micronuclei staining experiments were performed. Cal27, a HNSCC cell line, was used. Cal27 cells were transduced with a non-targeting control (NT2) guide RNA (gRNA) or two different gRNAs targeting TYK2 to generate TYK2 KO cells. Western Blot analysis was performed to determine changes in signaling upon TYK2 KO. Additional conditions included radiation and treatments with Interferon gamma, Interferon alpha and Interleukin-6 to activate the canonical JAK-STAT pathways. Overall, there were minimal changes in downstream signaling between the treatments and the knockouts. Cell cycle analysis via flow cytometry revealed no changes between the NT2 and TYK2 KO cells, potentially corroborating signaling results. Forty percent of TYK2 KO cells were arrested at the G2/M checkpoint at 8 hrs and 24 hrs after radiation treatment, but twenty percent returned to the G1 phase at 24 hrs. This indicates that loss of TYK2 is not responsible for cell cycle arrest. Lastly, micronuclei formation was observed to measure genomic instability. Twenty thousand Cal27 NT2 and TYK2 KO cells were seeded. They were allowed to incubate for 48 hrs before treatment with 4 Gy. Micronuclei staining revealed minimal differences between NT2 and TYK2 KO cell lines, although there were significant differences between the control and the radiation groups. Overall, radioresistance by TYK2 KO is not caused by changes in cell cycle or genomic instability as demonstrated with JAK1 KO. To understand how TYK2 is causing radioresistance in HNSCC, next steps would be to see if there are changes in proliferation. If MTT assays demonstrate significant changes, downstream signaling in growth pathways will be measured. If there is no increased proliferation, we will examine changes in DNA damage repair. Citation Format: Nicole Mayerli Constante, Vanessa Kelley, Joseph Contessa. Investigating mechanisms of radioresistance in TYK2 knockout head and neck cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2882.

Abstract 4213: Multiplex digital spatial profiling of proteins and RNA in MC38 mouse colorectal cancer syngeneic model

Abstract Introduction Characterization of the tumor microenvironment (TME) has become an essential step for the understanding of the complexity of cell interactions and the discovery of biomarkers for prediction and prognosis of immunotherapy response1. The NanoString GeoMx® Digital Spatial Profiler (DSP) technology includes the ability to quantitatively assess RNA and protein levels as well as sample multiple user-defined regions of interest, specifically focused on defining heterogeneity and TME interactions2. This technology has been widely used to identify biomarkers in clinical surgical specimens, but its applications in preclinical models are still needed. MC38 colorectal cancer syngeneic model is one of the most utilized models for assessing anti-cancer immunotherapies. In this study, we present the spatial profiling of proteins and RNA on MC38 model treated with anti-PD-1 through GeoMx® DSP technology. Methods GeoMx protein panel was used to detect the target protein expression differential in tumor-rich region and immune-rich region within MC38 subcutaneous tumor sections treated. Mice were treated with vehicle or anti-PD-1 (10mg/kg, BIW x 4 doses, ip). Whole Transcriptome Atlas (WTA) was employed, and then a comprehensive assessment of the data and comparison was performed. Results Two morphology markers, CD45 and PanCK, were used to separate tumor-rich region and immune-rich region. The GeoMx® protein data showed that the abundance of VISTA in tumor-rich region differed significantly (log2(fold-change) = 0.67, p < 0.01) in anti-PD-1 group compared to vehicle group. While in immuno-rich region, GITR was significantly altered (log2(fold-change) = 0.79, p < 0.05) in anti-PD-1 group (TGI value = 50.39%). From WTA data, we observed the upregulation of 839 genes, while 1048 genes were downregulated in immuno-rich region in anti-PD-1 group compared with vehicle group (p < 0.05). For tumor-rich regions, 550 genes were upregulated while 782 genes were downregulated in anti-PD-1 group versus vehicle group (p < 0.05). From the gene set enrichment analysis, we found that interferon alpha and interferon gamma, which are related to tumor immunity and immunotherapy response, were upregulated in anti-PD-1 group. Conclusion Both the differential expressing genes and proteins in TME of MC38 syngeneic models treated with anti-PD-1 could be well detected by GeoMx® DSP, which has the potential to provide insightful data for use in biomarker discovery in preclinical cancer models. References Charmsaz S, Collins DM, Perry AS, Prencipe M. Novel Strategies for Cancer Treatment: Highlights From the 55th IACR Annual Conference. Cancers (Basel) 2019; 11(8). Toki MI, et al. High-plex predictive marker discovery for melanoma immunotherapy-treated patients using digital spatial profiling. Clin. Cancer Res. 2019;25:5503-5512. Citation Format: Meihui Chen, Hengyuan Liu, Xiaolong Tu, Sheng Guo, Xiaobo Chen. Multiplex digital spatial profiling of proteins and RNA in MC38 mouse colorectal cancer syngeneic model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4213.

Abstract 6842: The effect of intra-tumoral Candida albicans on host gene expression

Abstract The gut and tumor microbiome have been shown to affect tumorigenesis, tumor immune infiltration, and response to traditional cancer therapeutics such as radiation therapy. Further, specific microbe-cancer relationships have been established. One such microbe is Candida albicans, which has been identified within several gastrointestinal cancers and is associated with an increased risk of metastases and decreased overall survival. By completing RNA-sequencing on murine rectal tumors colonized with C. albicans, we can better understand whether intratumoral changes in gene expression exist based on colonization of specific microbes. This study utilizes gut-to-tumor translocation and whole transcriptome analysis for a discovery-based approach to identify the effects of C. albicans on the host tumor. We established a rectal tumor model with C57BL/6 mice using MC38 rectal cancer cells subcutaneously injected on the right flank, local radiation to the tumor (standard-of-care for rectal cancer), and gavage with either C. albicans (Ca) or PBS. Fungal presence within tumors was validated by staining with calcofluor white and subsequently, tumors were sent for bulk RNA-sequencing to determine differences in gene expression using DeSeq2 and a gene set enrichment analysis (GSEA). In unsupervised analysis of gene expression differences between PBS-gavaged and Ca-gavaged with bulk RNA sequencing, tumors gavaged with C. albicans possessed unique gene expression and pathway analysis when compared to PBS-gavaged mice. Global differential gene expression showed 1,947 genes upregulated in Ca gavage and 593 genes upregulated in the PBS gavage (p < 0.05). C. albicans colonized tumors showed decreased expression in gene pathways relating to immune activation (interferon alpha response, IL-6 and STAT3 signaling), p53 expression, DNA repair, oxidative phosphorylation, NOTCH signaling, and apoptosis. We subsequently used a network-based approach to identify the most important genes driving the differences in the tumors, calculating the degree, closeness, and betweenness centralities. Several microbes have been regarded as potential contributors to decreased treatment response and survival in rectal cancer. In the case of tumors colonized with C. albicans, bulk RNA-sequencing indicates down regulation of gene pathways related to cell proliferation, immune activation, and DNA maintenance. Down regulation of gene pathways related to cell cycle control and arrest suggests that intratumoral colonization of C. albicans may causally affect tumorigenesis. Decreases in immune signaling in tumors suggest a potentially causal role of C. albicans immune suppression. These results highlight initial steps to understand how intratumoral C. albicans may be affecting rectal cancer progression and treatment response and serve as a technique to allow better insight to individual microbial impact on tumors. Citation Format: Alexander Loncar, Dennis Grencewicz, Rebecca Hoyd, Aaditya Pallerla, Nyelia Williams, Martin Benej, Yogita Mehra, Shiva Jahanbakhshi, Matthew Anderson, Nicholas Denko, Daniel Spakowicz. The effect of intra-tumoral Candida albicans on host gene expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6842.

Abstract 2809: Bifidobacterium species BB_003 identified through metatranscriptomic analysis with experimentally validated antitumor actions

Abstract Introduction & Objectives: A host's microbiome influences both gene expression and phenotype. Whole transcriptome sequencing (WTS) provides information about the microbiome in addition to gene expression. This research probes the correlation between microbial abundance, host gene transcription, and therapeutic efficacy, pinpointing a beneficial microbial strain and its mechanism of action. Materials & Methods: Bladder tissue biopsies from NMIBC patients underwent WTS and subsequent bioinformatic analysis. After in silico evaluation, in vitro assays including WST, quantitative PCR, and immune cell profiling were performed on mouse splenocytes. These assays were followed by in vivo assessment in both subcutaneous and orthotopic murine tumor models. Results: Among 59 biopsies, non-recurrence correlated with heightened presence of Lactococcus species LC_001 and Bifidobacterium species BB_003. Notably, BB_003 was associated with an extended recurrence-free survival (RFS). Gene set enrichment analysis (GSEA) implicated BB_003 in mediating a pro-inflammatory cascade, accentuating macrophages and interferons. In vitro WST assays showed the antitumor potential of BB_003_β, characterized by upregulated pro-inflammatory gene transcription. This strain increased effector CD8 T cells and M2 macrophages. In vivo, direct live BB_003_β introduction into subcutaneous tumors curtailed tumor proliferation. An increase in effector CD8 T cell populations within tumors and elevated cDC1 and M1 macrophage counts in tumor-draining lymph nodes were observed. Intravesical administration of live bacteria markedly decreased bladder weight, amplifying interferon alpha and beta gene expressions compared to controls. Conclusions: According to this study, BB_003_β inhibits tumor growth and is involved in immune response. Our study confirmed the antitumor properties of BB_003_β and suggested that cytokine and immune cell stimulation play a key role in its mechanism of action. Augmented insights warrant further exploration, particularly in synergy with intravesical BCG treatment. Citation Format: Xuan-Mei Piao, Kyungchan Min, Young Joon Byun, Chuang-Ming Zheng, Seon-Kyu Kim, Seong-Hwan Park, Sungmin Moon, Kyeong Kim, Ho Won Kang, Won Tae Kim, Seok Joong Yun, Hansoo Park. Bifidobacterium species BB_003 identified through metatranscriptomic analysis with experimentally validated antitumor actions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2809.

Abstract 5660: Gene expression signatures from FFPE to predict recurrent metastatic nasopharyngeal cancer

Abstract Nasopharyngeal cancer (NPC) is an EBV-driven epithelial cancer endemic to Southeast Asia, Southern China and the Middle East. Accurate profiling of the gene expression of NPC has been challenging because of its intense inflammatory infiltrate, as well as the 3 - 4mm size of biopsies limiting the amount of available material. Here we present a large cohort of 339 micro-dissected gene expression libraries from formalin-fixed paraffin-embedded (FFPE) biopsies from NPC patients treated at the National University Health System, Singapore, as well as healthy controls. NPC tumors from patients who subsequently developed recurrent or metastatic disease (Group A), and patients who did not develop recurrent or metastatic disease (Group B) were profiled. Tumor epithelial and microenvironment compartments were separately obtained using laser-capture microdissection, followed by library preparation performed for RNA-Seq using an in-house specialised technique. Gene signatures for NPC tumor epithelial and microenvironment content were used to validate the purity of gene expression libraries. Our preliminary analysis revealed that primary, pre-treatment tumors from patients who subsequently developed recurrence (Group A) showed downregulation of processes related to interferon gamma and interferon alpha response (p-adj <0.001 for both), while processes related to epithelial-mesenchymal transition (p-adj < 0.05) were enriched compared to patients who remained healthy (Group B). In contrast to primary tumors, recurrent tumors in Group A were enriched for cellular respiration including oxidative phosphorylation (p-adj < 0.0001). Our approach highlights the utility of whole transcriptome profiling from small quantities of archival FFPE material. The gene signatures identified from the primary tumors of high-risk patients are biologically relevant and have the potential to be used in precision medicine to guide additional targeted intervention. Citation Format: Joshua K. Tay, Wei Keat Teo, Joseph W. Foley, Luvita Suryani, Bing Cheng Wu, Chor Hiang Siow, Kwok Seng Loh. Gene expression signatures from FFPE to predict recurrent metastatic nasopharyngeal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5660.

Abstract 355: BCLxL inhibition enhances copanlisib response in colorectal cancer

Abstract Background: Anti-apoptotic signaling, including through BCLxL, is a potential mechanism of resistance to PI3K inhibition in PIK3CA mutant cancers. We have previously demonstrated enhanced activity of PI3K inhibition in combination with BCLxL inhibition in PIK3CA mutated colorectal cancer (CRC) models. Here we examine the potential impact of BCLxL expression in PIK3CA mutant CRCs and the mechanism of treatment response with the combination of copanlisib and navitoclax. Methods: PIK3CA mutant CRCs were identified within TCGA colorectal adenocarcinoma data set and two cohorts were generated based on BCL2L1 (gene that encodes protein BCLxL) expression. Differentially expressed genes and gene set enrichment analysis were performed. CRC cell lines SW48 and SW48PK (Horizon Discovery, SW48 with a PIK3CAH1047R/+ mutation) were treated with copanlisib (copan) (1-100 nM) and navitoclax (250 nM). Immunoblotting was performed quantified using ImageJ to evaluate PI3K and apoptotic signaling. Flow cytometry using annexin V and propidium iodide (PI) was performed as a measure of apoptosis. Immunohistochemistry (IHC) using Ki67 was performed as a measure of cell proliferation on SW48PK xenografts and quantified as percent positive nuclei at 40x field of view (FOV). Results: Two datasets comprised of PIK3CA mutant CRC patients with either high or low BCL2L1 expression containing 39 and 47 patients, respectively, were used in the TGCA analysis. There was no difference in age, gender, or staging between these two datasets. An increase in DNA repair (false discovery rate q-value= 0.034) and interferon alpha signaling pathways (q= 0.022) was seen in PIK3CA mutant and high BCL2L1 expression compared to PIK3CA mutant and low BCL2L1 expression patients. PIK3CA mutant patients with low expression of BCL2L1 had a greater disease-free and overall survival (p= 0.037 and p= 0.042, respectively). Combination of copan and navitoclax treatment of the SW48 and SW48PK cell lines resulted in a reduction in activated ribosomal protein S6 (pRPS6) as compared with control or navitoclax alone at both 6 and 24. Cleaved PARP increased in SW48PK cells treated with 100 nM copan plus navitoclax versus control at both 6 and 24 hour timepoints (p= 0.03, p= 0.049). SW48 and SW48PK cells that were treated with copan and navitoclax for 24 hours had an increase in annexin v, a marker for apoptosis, compared to cells treated with control or single agents. In SW48PK xenografts, a significant reduction in Ki67 percent positive nuclei was seen in combination compared to control (median percent positive nuclei: 20.5, control: 33.2, p<0.001). Conclusions: High BCLxL expression is a sign of poor prognosis for PIK3CA mutant CRC. Inhibiting BCLxL can enhance the sensitivity of PI3K inhibition in PIK3CA mutant cancers and deserves further investigation clinically. Citation Format: Alexa E. Schmitz, Rebecca A. DeStefanis, Alyssa K. DeZeeuw, Autumn M. Olson, Anna L. Lippert, Kennedy J. Maduscha, Katherine A. Johnson, Sean Kraus, Cheri A. Pasch, Dustin A. Deming. BCLxL inhibition enhances copanlisib response in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 355.

Abstract 2040: Targeting MUS81 endonuclease to enhance chemo-immunotherapy response in head and neck squamous cell carcinoma

Abstract Background: In advanced head and neck squamous cell carcinoma (HNSCC), immune checkpoint inhibitors are only effective in 15-20% of cases. Defects in replication stress response represent a promising avenue for enhancing the therapeutic efficacy of immunotherapy through DNA damage and the release of immunostimulatory DNA. MUS81, a DNA structure-specific endonuclease involved in resolving replication stress, is upregulated in many cancer types including HNSCC, and MUS81-associated cytosolic DNA is implicated in triggering cGAS-STING mediated innate immunity. The objectives of this study were to assess the impact of targeting MUS81 on HNSCC cell sensitivity to cisplatin, and investigate its role in enhancing immunotherapy response in HNSCC, through the cell viability and cell cycle analysis, differential gene expression, and DNA release within small extracellular vesicles (exosomes). Methods and Results: We used HNSCC cell lines and patient-derived organoids (PDOs) to investigate the consequences of CRISPR/Cas9-mediated MUS81 knockout (KO). We demonstrated that MUS81 KO increased HNSCC cell sensitivity to cisplatin, inducing a G2/M cell cycle arrest. Transcriptomic analysis of differentially expressed genes (DEG) in MUS81 KO vs control cells highlighted upregulation of ANXA6 (tumor suppressor gene encoding for Annexin A6), MACROH2A2 (involved in the quiescent phenotype acquisition of malignant HNSCC cells) and CDA (encoding for cytidine deaminase, implicated in replication stress). MUS81 KO was also associated with downregulation of LCP1 (encoding for lymphocyte cytosolic protein 1, upregulated in oral cancer and controlling cellular proliferation, invasiveness, and migratory activities). Gene Set Enrichment Analysis (GSEA) of RNA-seq data, revealed positive enrichment in MUS81 KO cells treated with cisplatin in genes involved in the hallmark interferon alpha (Normalized Enrichment Score (NES) 3.03, p-value < 0.001) and interferon gamma (NES 2.83, p- value < 0.001) pathways, indicative of innate and adaptive immune responses. Additionally, the pathway of hallmark inflammatory response was positively enriched (NES 2.22, p < 0.001). In addition, cisplatin treatment in MUS81 KO was associated with notable alterations in the concentration and length of exosomal DNA, with implications for immune response modulation within the tumor microenvironment. Conclusions: Our study underscores the potential significance of MUS81 as a novel therapeutic target in HNSCC. In addition to sensitizing HNSCC cells to chemotherapeutic agents, targeting MUS81 may influence the dynamics of the tumor microenvironment, thereby enhancing the prospects of immunotherapy in this context. Further in-depth investigations are imperative to validate these observations and facilitate the development of innovative therapeutic strategies tailored to targeting MUS81 in HNSCC. Citation Format: Ali Abdulnabi Suwaidan, Anna Pasto, Caitlin McCarthy, Teng Pan, Jinhai Deng, Luigi Dolcetti, Giovanna Alfano, Rami Mustapha, James Monypenny, Martin Forster, Tony Ng. Targeting MUS81 endonuclease to enhance chemo-immunotherapy response in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2040.

Abstract 6870: Immunological aging in triple negative breast cancer leads to a chronic interferon phenotype and immune cell exhaustion that impedes response to therapy

Abstract Age is the biggest risk factor for developing most forms of cancer, and understanding how age impacts cancer progression is critical to improving responses to therapy. As we age immune function declines suggesting that therapeutic responses, particularly to immunotherapies, will also change with age. Early clinical trial data suggests that there are age-associated responses to immunotherapies. Clinical trials, however, are not designed to reflect patient chronological and immunological ages - over 50% of breast cancer patients are over the age of 60, yet less than 25% of patients in clinical trials are in this age range. Here, we utilize a preclinical mouse model of immunological aging to understand how aging impacts immune responses to triple-negative breast cancer (TNBC). Immunologically young (8 weeks old) and aged (~12 months old) FVB mice were orthotopically injected with syngeneic Met1 TNBC cells. We previously established that this preclinical model mimics human immunological aging and enables us to better understand how age impacts disease progression and therapeutic responses. Once tumors became palpable, mice were treated with paclitaxel or vehicle control and/or anti-PDL1 to mimic first-line therapeutic strategies. Tumors grew significantly faster in young control mice compared to aged, but young mice had a more robust response to therapy. Notably, only young mice had a significant benefit of combo therapy (paclitaxel + anti-PDL1) over monotherapy alone. Tumors in aged mice had significantly more infiltration of CD8+ cytotoxic T cells and FOXP3+ inhibitory T-regulatory cells compared to young control mice, yet only tumors in young mice exhibited an increase in T cell infiltration with chemo or immunotherapy. Depletion of either CD8+ or CD4+ T cells in immune-competent FVB mice both led to a complete loss of age-associated differences in tumor growth. RNA sequencing analysis indicated that the infiltrating T cells in aged mice may be exhausted due to a chronic interferon phenotype, as indicated by enrichments of interferon alpha, interferon gamma, and IL2 signaling pathways, as well as expression of RIPK1, TNFa, and the immune exhaustion markers PD1, CTLA4, TIM3, and LAG3. Analysis of published single cell RNAseq data indicated the same interferon response pathways enriched with age in human TNBC, particularly in the T cell compartment. Our findings show that the aging immune microenvironment significantly impacts tumor progression and that a chronic interferon phenotype with age may lead to T cell exhaustion and impaired therapeutic responses. This work suggests that targeting interferon signaling may lead to improved therapeutic responses. Together these findings demonstrate how immunological aging can impact disease progression and response to therapy and highlight the importance of developing age-stratified treatment strategies. Citation Format: Milos Spasic, Adrienne Parsons, Gregory Goreczny, Qiuchen Guo, Abigail Recko, Elizabeth Mittendorf, Peter van Galen, Sandra McAllister. Immunological aging in triple negative breast cancer leads to a chronic interferon phenotype and immune cell exhaustion that impedes response to therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6870.

Abstract 1282: Gavage with Candida albicans leads to fungal colonization of colorectal tumors and decreased response to radiotherapy

Abstract The host microbiome in the gut and tumors have been shown to affect tumor growth and therapeutic response in cancer. Furthermore, the presence of specific fungal taxa are associated with tumor hypoxia, tumor progression, therapeutic response, and clinical outcomes in colorectal cancer (CRC). Preliminary data from our group found that the presence of Candida species increased tumor hypoxia and decreased overall survival in CRC. However, whether intratumoral Candida drive, support, or simply inhabit tumors with poor prognoses remains unclear. Here, we investigate a casual role for Candida albicans in tumor progression and therapy response using a syngeneic mouse model of microsatellite-instability high (MSI-H) colorectal cancer. We subcutaneously implanted MC38 colorectal cancer cells into C57BL/6 mice and then orally gavaged these mice with C. albicans, Saccharomyces cerevisiae, or PBS. The site of tumor formation was locally irradiated once (7.5 Gy), and growth of the tumor was measured over time. Differences in tumor volume were assessed by longitudinal mixed-effect models. Tumor sections were stained for fungi using calcofluor white (CFW) and underwent bulk RNA sequencing to detect differential gene expression, which were interpreted using gene set enrichment analysis (GSEA). Mice gavaged with C. albicans showed decreased response to radiation compared to mice gavaged with either S. cerevisiae (p<0.05) or PBS (p<0.001). Additionally, hyphae were observed in murine tumors gavaged with C. albicans, suggesting translocation of gavaged C. albicans from the gut to tumors. Further, tumors from mice gavaged with C. albicans displayed unique gene expression profiles, including decreased interferon alpha and IL-6 and STAT3 signaling, decreased oxidative phosphorylation, and decreased apoptosis-related gene expression. Here, we show that C. albicans may confer resistance to radiation therapy and affects immune and cancer cell activity in the MC38 (MSI-H) syngeneic in vivo model of colorectal cancer. Further, we show that hyphal fungi can be visualized in heterotopic murine tumors from our C. albicans gavage condition. These data establish that fungi can translocate from the gut to distal tumor sites, and that upon translocation, changes in gene expression and therapy response are observed. Future directions will explore the mechanism by which these effects occur and whether these findings can be leveraged to improve radiotherapy outcomes. Citation Format: Dennis J. Grencewicz, Alexander Loncar, Rebecca Hoyd, Aaditya Pallerla, Nyelia Williams, Martin Benej, McKenzie Kreamer, Yogita Mehra, Shiva Jahanbakhshi, Matthew Anderson, Nicholas Denko, Daniel Spakowicz. Gavage with Candida albicans leads to fungal colonization of colorectal tumors and decreased response to radiotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1282.