Khazaie, Khashayarsha

Abstract Maternal obesity has been epidemiologically linked to an increased risk of sporadic colorectal cancer (CRC) in offspring, the third most prevalent cancer worldwide. This association underscores the lasting influence of early-life exposures on long-term health and disease susceptibility. Intestinal stem cells (ISCs), the long-lived cells that sustain epithelial renewal and often serve as the origin of intestinal cancers, are thought to play a central role in mediating this elevated cancer risk. However, how maternal obesity shapes the early-life programming and maturation of ISCs in their offspring remains poorly understood. Using mouse models of diet-induced obesity, we show that offspring exposed to a maternal high-fat Western diet (HFD) during pre- and postnatal development exhibit increased colonic proliferation, enhanced stem cell self-renewal, and a hypermetabolic state that persists into adulthood, even after dietary normalization. Alongside changes in stem cell properties, we observe a significant shift in epithelial cell composition, characterized by an increase in cells of secretory lineage at the expense of absorptive enterocytes, and these changes endure into adult life. Additionally, these changes are accompanied by an increased tumor burden in the loss of Apc heterozygosity model. Our data indicate that IL-17a, a pro-inflammatory cytokine, is critical in mediating these changes. Specifically, receptor IL-17RA/C expression is significantly upregulated in ISCs and secretory cells in maternal HFD-exposed offspring. Administration of IL-17a to intestinal organoids demonstrates sufficiency by mimicking the maternal obesogenic phenotype, indicating that immune-epithelial interactions influence ISC function and may be a driver of durable molecular patterning. These findings emphasize the long-term consequences of maternal HFD exposure on intestinal stem cell activity and epithelial composition, and possibly contribute to a higher risk of CRC in offspring later in life. Citation Format: Gourab Lahiri, Karla Mullen, Yesenia B. Millan, Swathi Sankar, Dominic R. Saiz, Thomas H. McDermott, Madeline Blatt, Abhigyan Shukla, Khashayarsha Khazaie, Miyeko D. Mana. Maternal obesity reprograms intestinal stem cells to elevate colorectal cancer risk in offspring [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 841.

Abstract The circadian clock imposes a critical yet incompletely understood layer of regulation on adaptive immunity. T helper 17 (Th17) antimicrobial immune responses including expression of IL-17A by lamina propria CD4⁺ T cells, exhibit diurnal variation and are sensitive to circadian disruption. While the core circadian regulators CLOCK and BMAL1 canonically function as a heterodimer to drive rhythmic gene expression, emerging evidence suggests they may have distinct regulatory roles. Here we integrated ChIP-seq, ATAC-seq, and RNA-seq analyses in naïve CD4⁺ T cells to reveal that the CLOCK-BMAL1 complex controls circadian and metabolic programs through promoter binding, whereas exclusive CLOCK binding at promoters, together with CLOCK-BMAL1 binding at enhancers, regulates immune-associated genes. Using the mutant CLOCKΔ19, which lacks the transactivation domain, we observed disrupted circadian transcription and globally reduced chromatin accessibility, alongside increased accessibility at Th17-associated loci that their altered temporal regulation. Functionally, ClockΔ19 produces β-catenin stabilization in T cells, pronounced expansion of RORγt⁺ CD4⁺ T cells and Treg cells, impaired Treg suppression of Th17 responses, heightened Th17 responses, and reduced IFN-γ production during viral infection. Collectively, these findings define BMAL1 dependent and independent CLOCK functions that program naïve CD4⁺ T cell fate, restrain Th17 differentiation, and preserve immune homeostasis.

ABSTRACT Maternal obesity is associated with increased risk of sporadic colorectal cancer (CRC) in offspring, suggesting that early-life environmental exposures durably shape disease susceptibility. Intestinal stem cells (ISCs), long-lived drivers of epithelial renewal and tumor initiation, are well poised to mediate this effect; however, how maternal obesity influences ISC programming during development remains poorly understood. Using mouse models of diet-induced obesity, we show that exposure to a maternal high-fat Western diet (mHFD) during pre- and postnatal development stably programs colonic ISCs. Offspring exhibit increased ISC proliferation, enhanced self-renewal, a hypermetabolic state, and altered epithelial lineage composition that persists into adulthood despite dietary normalization. These changes are accompanied by increased tumor burden following loss of Apc heterozygosity. Mechanistically, we identify the pro-inflammatory cytokine IL-17A as a key extrinsic driver and PPARd/a nuclear receptors as intrinsic mediators of the mHFD phenotype, revealing an immune-epithelial axis that programs ISC function during early life. Together, our findings demonstrate that maternal metabolic environments durably enhance stem cell fitness, providing a mechanistic link between developmental exposure and adult disease risk.

Early-onset colorectal cancer (EOCRC) in people < 50 years of age has been rising globally, yet its causes remain unknown. Emerging evidence suggests that environmental factors, including exposure to micro-and nanoplastics (MNPs), may contribute to colorectal carcinogenesis. MNPs can enter the gastrointestinal tract through ingestion, translocate across the epithelial barrier via endocytosis or paracellular pathways, and interact directly with epithelial and immune cells. Once internalized, they may generate events associated with tumor initiation including oxidative stress, disruption of membrane integrity, pro-inflammatory signaling, and disruption of genomic and epigenomic stability. Patient-derived colorectal organoids offer a physiologically relevant and scalable 3D model that closely mimics the cellular architecture and genetic landscape of primary tumors. We highlight how organoid models can be leveraged to study the impact of MNPs on the key processes of inflammation, DNA damage, senescence, and epigenetic modifications. Furthermore, we discuss the application of organoid-based systems to model EOCRC driven by environmental exposures, including the integration of organoid platforms with high-throughput assays, omics profiling, and microfluidics to better capture MNP-induced pathogenic mechanisms. Altogether, colorectal organoids provide a powerful bridge between environmental plastic exposure and EOCRC etiology, offering a tractable platform to identify mechanistic pathways and potential biomarkers of early disease.

Abstract Mutations in non-coding regulatory elements are increasingly recognized as critical drivers of cancer development and progression. Among these, structural alterations such as duplications of super-enhancers (SEs), large clusters of enhancers that regulate key oncogenes, have emerged as significant contributors to oncogenesis. In T-cell acute lymphoblastic leukemia (T-ALL), a particularly aggressive hematologic malignancy, SE duplications have been identified in approximately 5% of human cases. These duplications frequently involve a non-coding region located approximately 1.3 megabases downstream of the Myc oncogene, a region known as N-Me. Despite the growing recognition of the role of SE duplications in T-ALL, functional studies to determine their molecular origins and contributions to leukemogenesis have been limited, largely due to the absence of suitable and genetically tractable preclinical models. This gap in knowledge hinders both our understanding of disease pathogenesis and our ability to design targeted therapeutic interventions. Here, we report the generation and characterization of a novel genetically engineered mouse model of T-ALL that spontaneously develops oncogenic SE duplications at the Myc locus. This model offers the first spontaneous in vivo system to investigate the origin, regulation, and oncogenic function of SE duplications. This model was created by conditionally stabilizing β-catenin in CD4⁺CD8⁺ double-positive (DP) thymocytes in combination with targeted deletion of the transcription factor HEB. This combination is sufficient to drive the development of aggressive T-cell leukemias that consistently harbor duplications of the N-Me super-enhancer. This finding recapitulates the genomic alteration observed in a subset of human T-ALL and provides a unique platform for mechanistic studies. We further demonstrate that the molecular events leading to SE duplication and oncogenic Myc activation unfold in a stepwise manner. At the preleukemic stage, stabilization of β-catenin alone is sufficient to enhance recruitment of HEB to the N-Me region. The simultaneous loss of HEB greatly increased chromatin accessibility at the N-Me enhancer. This altered chromatin landscape permits aberrant binding of transcription factors including TCF-1, which plays a critical role in T-cell development and leads to N-Me SE activation associated with significant three-dimensional chromatin reorganization. Chromosome conformation analyses in the leukemic cells reveal the formation of a novel chromatin loop that brings the activated N-Me SE into close spatial proximity with the Myc promoter, enabling oncogenic Myc transcription. These findings uncover a novel mechanistic pathway by which β-catenin and HEB interact to reshape the enhancer landscape and three-dimensional chromatin architecture, ultimately promoting SE duplication and aberrant Myc expression in T-ALL. β-catenin appears to play a dual role, first facilitating HEB recruitment under physiological conditions and then, upon HEB loss, permitting the reprogramming of enhancer activity through chromatin opening and ectopic transcription factor binding. Our data suggest that the cooperative interplay between signaling pathways and transcriptional regulators at enhancer elements can initiate structural genomic changes that drive malignancy. This work provides a long-sought preclinical model that faithfully mirrors key features of human T-ALL. Our findings open new avenues for understanding how non-coding regulatory mutations arise and exert oncogenic effects and have the potential to provide insights that may extend beyond T-ALL to other cancers driven by enhancer dysregulation. Moreover, by revealing molecular intermediates such as β-catenin, HEB, and TCF-1 in the regulation of enhancer activity, our findings identify potential therapeutic targets to disrupt the oncogenic enhancer-promoter interactions that underlie Myc-driven leukemogenesis.

Abstract Oral commensals such as Parvimonas micra are increasingly implicated in sporadic colorectal cancer (CRC). Several findings support an emerging notion that alterations in host DNA methylation constitute a mechanism by which P. micra adapts to the host microenvironment and contributes to pathogenic processes. However, multiple limitations hinder definitive conclusions, including the correlative nature of the human studies and the absence of human microbiota in mouse models. Here, we investigated how a complex human microbiome influences the adaptation and oncogenic potential of P. micra in a spontaneous mouse model of polyposis. Adult mice, following antibiotic conditioning, received fecal microbiota transplants (FMT) from a healthy human donor, with or without supplementation of P. micra. P. micra caused significant reshaping of the gut microbial community and altered co-occurrence network structures, which however largely recovered within 21 days post FMT. Despite the transient nature of these changes, P. micra caused a marked increase in both the number and invasive potential of intestinal polyps. Epigenomic profiling of polyp crypts revealed global DNA hypomethylation alongside gene-specific hypermethylation, accompanied by transcriptional changes in key oncogenic pathways. Affected pathways included Wnt signaling, epithelial-to-mesenchymal transition, circadian rhythm regulation, and host–microbe interactions. These findings demonstrate that P. micra exerts a profound influence on microbial ecology, host epigenetic programming, and tumorigenesis in a genetically predisposed host, highlighting its role as a microbial driver of intestinal carcinogenesis.

Objective How tumour-adherent microbiome can influence outcomes in patients with colorectal cancer (CRC). Methods and analysis CRC tissues (n=97) were analysed using RNAseq, whole exome sequencing (WES) and 16 r sRNA sequencing. Inflammatory/immune cells were quantified by immunohistochemistry in mice and human tissues. Patient outcomes were analysed according to virulent bacteria and gene RNA levels in tumour tissues. We performed faecal microbiota transfer (FMT) in germ-free mice using presurgery stool samples from nine patients with sporadic CRC. Changes in gene mutations and DNA methylation in the colonic mucosa were measured and compared with those in mice receiving FMT from nine healthy individuals. Immune cells in the tumour tissues of donor and mouse recipients were compared. Results FMT from CRC donors led to preferential DNA demethylation, but specific host genes, including pleckstrin homology domain and leucine-rich repeat protein phosphatase 1 (PHLPP1), were hypermethylated compared with FMT from healthy donors. CRC faecal samples showed elevated levels of virulent bacteria, reduced levels of commensals and triggered colon inflammation in mice. Notably, PHLPP1 was downregulated in CRC tumours, and its expression varied in accordance with other CRC cardinal genes (n=137, as identified in the scientific literature to be involved in colon carcinogenesis), and was most pronounced in inflammatory bowel disease associated CRC. Tumours with reduced PHLPP1 expression are more inflammatory and correspond to patients with a higher relative abundance of adherent virulent bacteria and poorer outcomes. Conclusion The composition of CRC tumour-adherent bacteria predicts epigenetic modifications and altered expression of cardinal CRC genes such as PHLPP1. PHLPP1 downregulation characterises patients with CRC with inflammatory tumours and poor survival outcomes.

Abstract Purpose: Intratumoral injection of Clostridium novyi-nontoxic (C. novyi-NT), lacking alpha-toxin, germinates and subsequently replicates in the tumor hypoxic regions, causing cell lysis and inflammation. This phase Ib study investigated the safety and synergistic effects of pembrolizumab and C. novyi-NT in advanced solid tumors. Patients and Methods: Patients with injectable solid tumors received one intratumoral C. novyi-NT injection (day 8) across four dose cohorts (3 × 104 to 100 × 104 spores) with pembrolizumab (200 mg intravenously every 3 weeks, day 0–24 months). Sixteen patients were enrolled with a median age of 62.5 years, and the most common tumor types were breast cancer and melanoma. Results: The combination therapy demonstrated a manageable safety profile, with one grade 3 dose-limiting toxicity of abscess formation and the remainder of treatment-related adverse events in ≥10% of patients being grade 1 or 2 injection site reaction (25%), pyrexia (19%), pruritus (13%), leukopenia (13%), and anemia (13%). The maximum tolerated dose was determined to be pembrolizumab intravenously at 200 mg every 3 weeks and a single dose of 100 × 104C.novyi-NT spores intratumorally on day 8. The confirmed overall objective response rate of 25% was observed among four patients with nonkeratinizing undifferentiated nasopharyngeal squamous carcinoma, human papilloma virus–positive squamous cell carcinoma of the base of the tongue, vulvar melanoma, and chordoma. Among these patients, we obtained three partial responses and one complete response. The median duration of the response was 10.93 months, and stable disease was observed in 69% of patients. Conclusions: This study highlights the potential of the C. novyi-NT and pembrolizumab combination as a promising therapeutic strategy for treatment-refractory solid tumors.

Summary Background Colorectal cancer (CRC) results from the accumulation of mutations and epigenetic changes in gut epithelial cells likely due to gut microbiota dysbiosis. However, limited research has been done to explore the link between host tumour dysbiosis and disease outcome. Methods The mechanisms influencing outcomes of 97 colorectal cancer (CRC) patients, including 13 with Lynch syndrome, 20 with inflammatory bowel disease (IBD), and 64 sporadic cases, were analyzed using a multiomics approach. These patients were categorized into two groups: “disease-free/stable disease” and “progression disease” survival outcomes. The analysis included tumor adherent microbiota composition (16S rRNA), somatic gene mutations (WES), gene expression (RNAseq), immune markers (RNAscope), and immune infiltrate cells (immunohistochemistry). Results IBD-CRC patients had worse outcomes than those with Lynch or sporadic CRC, regardless of TNM staging or treatment. Symbiotic bacteria like Lactococcus lactis were significantly reduced in IBD-CRC tissues. Patient outcomes were influenced by the abundance of virulent ( Escherichia coli ) relative to beneficial bacteria ( Lactococcus lactis ). Although no significant increase in deleterious somatic mutations was found in IBD-CRC. 16sRNA revealed increased virulent- and decreased anti-inflammatory symbiotic-bacteria correlating with the upregulation of oncogenes and downregulation of anti-oncogenes like PHLPP1. The multiplex in situ hybridization of CD8, IFNγ and PHLPP1 an anti-oncogene revealed significant decrease of immune cells with detectable PHLPP1 expression in IBD-CRC tumour tissues as compared to sporadic CRCs. Conclusion The poor outcomes in IBD-CRC patients are likely due to gut dysbiosis and immune cell alterations, possibly triggered by microbiota-related epigenetic pathways. What You Need to Know BACKGROUND AND CONTEXT Colorectal cancer (CRC) is associated with gut microbiota dysbiosis. Inflammatory bowel disease-related CRC (IBD-CRC) is classified as an environment-related condition. NEW FINDINGS In relation with patient outcomes, tumour tissues from three types of CRC (Sporadic-, IBD-, and Lynch syndrome-CRC) were analyzed using a multiomic approach. This included examining tissue adherent virulent bacteria, gene analyses, and quantifying immune cell infiltration in the mucosa. IBD-CRC patients had the worst outcomes, associated with the down regulation of PHLPP1 gene, virulent/symbiotic imbalance, and immune response failure. LIMITATIONS Lack of animal experiments using FMT of fresh stool from IBD-CRC patients. CLINICAL AND TRANSLATIONAL RESEARCH RELEVANCE Among the different types of CRC, IBD-CRC patients showed a greater imbalance between harmful and beneficial bacteria, along with immune response failure. Lay summary This study compares the pathological and clinical characteristics of patients with colorectal cancer (CRC) across three distinct etiologies: sporadic CRC, inflammatory bowel disease (IBD)-associated CRC, and Lynch syndrome-associated CRC (LS-CRC). Distinct differences in tumor-adherent microbiota, gene expression and immune response profiles were observed. Notably, IBD-CRC patients demonstrated the poorest prognosis depending on microbe-host gene interaction highlighting potential biomarkers for disease prognosis and treatment strategies.

Abstract Endometriosis (EMS) is a prevalent systemic disorder impacting 10% of women of reproductive age, characterized by the growth of endometrial-like tissue outside the uterine cavity, chronic inflammation, and fibrosis, leading to pain, infertility, and organ dysfunction. Despite its widespread occurrence, the pathogenesis of EMS remains elusive, and current treatments are inadequate, with recurrence post-surgery being a significant issue. Notably, EMS displays features reminiscent of malignancy, including genetic mutations and clonal cell proliferation. The presence of tertiary lymphoid structures (TLSs) within lesions indicates a potential role of immune dysfunction in disease progression. This study aims to explore immune mechanisms underlying EMS through three specific aims: 1) Analyzing cellular, molecular, and spatial characteristics of T and B cell interactions; 2) Defining the functional phenotype of immune cells involved; and 3) Investigating the B cell antigen receptor repertoire and the specificity of locally produced antibodies. Techniques such as single-cell RNA sequencing, spatial transcriptomics, and multiplex immunofluorescence, are employed. The outcomes provide insights into immune contributions to EMS pathology and guide the development of novel diagnostic and therapeutic strategies. Citation Format: Ariana F Rahman, Khashayarsha Khazaie, Elika Javaheri, Yohannes Woldeamanuel. Characterizing immune dysregulation and tertiary lymphoid structures in endometriosis: Pathogenic insights and therapeutic implications [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B081.