Cancer Research Institute

Background Next-generation sequencing (NGS) testing in patients with metastatic non-small cell lung cancer (mNSCLC) identifies actionable driver oncogenes (ADO) and targeted treatment (TT). Potential inequities were evaluated in NGS testing and TT in patients with mNSCLC. Patients and methods This retrospective study used a nationwide electronic health record–derived deidentified database for patients ≥18 years diagnosed with mNSCLC between 4/2018 and 4/2024, ≥2 recorded visits, and follow-up ≥90 days post diagnosis. For TT, patients must have received NGS testing before first-line (1L) treatment and harbored ≥1 1L ADO. Results A total of 15 392 patients with mNSCLC were included: 66% with commercial insurance, 16% with Medicare, 12% with other, 4% with Medicaid, and 3% with other government insurance. Patients with commercial insurance had significantly higher odds of receiving NGS testing vs Medicare, Medicaid, or other insurance. While patient characteristics varied across insurances, the effect of insurance type on NGS testing did not differ by race/ethnicity, age, or socioeconomic status (SES). Site of care was a significant effect modifier, with increased odds of NGS testing for community vs academic settings for commercial, Medicare, and other insurance and decreased odds for Medicaid. When all patients received NGS testing, significantly lower odds of receiving TT occurred for patients with SES 2 vs SES 1 (lowest); higher odds occurred for Asian vs white patients. Conclusion Insurance is a key contributor to inequity in NGS testing. When all patients received NGS testing, equity was achieved in patients receiving TT, except those with lower SES, who potentially did not qualify for Medicaid.

Palmitic acid (PA), being the most prevalent free fatty acid in the human, holds significant implications as a risk factor for atherosclerosis (AS) due to its ability to induce physiological dysfunction in endothelial cells (ECs). Endothelial cell-specific molecule 1 (ESM1), has been identified as a marker for activated ECs. Nevertheless, the mechanisms underlying ESM1-induced endothelial cell proliferation remain elusive. The expression of ESM1, ANGPTL4 and autophagy related protein were confirmed by western blot. Proliferation ability was tested by MTT and EdU. Lipids level was confirmed by Oil red staining. Autophagic flux was confirmed by Monodansylcadaverine (MDC) staining and pCMV-mCherry-GFP-LC3B fluorescence staining assay. The mouse model of AS was used to observe the effect of PA on the ESM1-ANGPTL4-autophagy signaling axis. This study elucidates ESM1-ANGPTL4 axis in maintaining proliferation of ECs and lipid reprogramming. Furthermore, it has been observed that PA has the ability to stimulate EC to autonomously increase the expression of ESM1, which in turn can counteract the detrimental effects of PA on ECs. Conversely, when ESM1 is suppressed, the damaging effects of PA on ECs are exacerbated. Mechanistically, our findings indicate that ESM1 facilitates EC proliferation and lipids homeostasis by up-regulating autophagy through ANGPTL4. This effect of ESM1 on ECs can be attenuated by ATG7 inhibiting. Additionally, the serum levels of ESM1 were found to be elevated in AS mice. ESM1 was found to enhance ECs proliferation and mitigate endothelial cell injury induced by PA through the upregulation of autophagy. This mechanism potentially serves as a protective factor against atherosclerosis progression.

Premature ovarian insufficiency (POI), defined by early loss of ovarian activity before the age of 40 years, is the leading cause of infertility and systematic aging in women, posing a public health challenge worldwide. However, its molecular etiology and therapeutic options are still lacking. Here, leucine‐rich repeat containing 4 (LRRC4) is identified as a critical regulator of folliculogenesis expressed in granulosa cells (GCs), which contributes to ovarian reserve maintenance. LRRC4 deficiency triggers defective oocyte maturation and excessive follicular atresia through inhibition of GC differentiation and ultimately leads to POI. Mechanistically, LRRC4 balances mitochondrial fission and fusion to inhibit excessive mitophagy by promoting the K48‐linked ubiquitination degradation of Yes‐associated protein (YAP), thereby maintaining the metabolic homeostasis of mitochondrial aerobic respiration and glycolysis. Importantly, targeting LRRC4 normalized follicular development and ovarian function in POI model mice. In conclusion, these data reveal the novel pathogenesis of POI and suggest that LRRC4 is a potential target for the diagnosis and treatment of POI.

Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with poor clinical outcome. There is a dire need for the development of new targeted therapies for TNBC. Midkine (MDK), a multifunctional cytokine/growth factor, functions as an oncoprotein and its expression is elevated in various cancers. The absence of small molecule inhibitors targeting MDK represents a significant knowledge gap for translation. In this study, we identified HBS-101 as a potent MDK-inhibitor with high specificity. Our modeling studies revealed that the interaction of HBS-101 with MDK is primarily driven by hydrophobic forces, and this interaction disrupted MDK’s binding to its endogenous receptors. Microscale thermophoresis (MST), cellular thermal shift assay (CETSA) and biotin pulldown studies confirmed the direct interaction of HBS-101 with MDK. Therapeutically, HBS-101 treatment significantly reduced cell viability (IC50 0.3-2.8 µM), clonogenic survival, invasiveness, and increased apoptosis. The underlying mechanism of HBS-101 involves suppression of Akt/mTOR, STAT3, and NF-B pathways. Importantly, HBS-101 exhibits distinct pharmacologic advantages, including oral bioavailability, blood-brain-barrier penetration, and in vivo stability. Histologically, up to a dose of 10 mg/kg showed no observable organ toxicity and had no effect on the mice's body weight. Dose range studies identified 5 mg/kg as the minimal effective dose, achieving more than 50% tumor reduction. HBS-101 treatment led to a significant reduction in the growth of TNBC patient-derived xenograft tumors in vivo and markedly reduced TNBC brain-metastatic-tumor growth and prolonged mice survival. Collectively, our studies identified a first-in-class MDK inhibitor, HBS-101, that can be used to treat MDK-driven cancers.

Sleep disturbance is a common symptom experienced by approximately 70% of breast cancer survivors and persists after the conclusion of chemotherapy. This study aimed to quantify the circadian disruption of the core body temperature (CBT) rhythm and its correlation with sleep disturbance following chemotherapy. In a sample of 25 breast cancer survivors, CBT was measured using an ingestible thermometer pill to calculate the relative amplitude (RA) prior to chemotherapy. The Pittsburgh Sleep Quality Index (PSQI) was employed to assess global sleep quality at three time points: prior to the commencement of chemotherapy, at 1 month (T1) and 9 months (T2) following the conclusion of chemotherapy. Subjective and objective sleep latency (SL s and SL o ) were measured using the PSQI and actigraphy, respectively. The lower RA group exhibited higher intradaily variability of CBT and a higher average temperature of the lowest 5‐h period in comparison to the higher RA group. The lower RA group exhibited lower global sleep quality than the higher RA group at both time points (T1 and T2). SL s in the lower RA group were significantly longer compared to the higher RA group at both time points. Furthermore, the discrepancy in SL (∆SL s –SL o ) demonstrated a notable between‐group difference at both time points. The findings of this study suggest that breast cancer survivors with pronounced circadian disruption of the CBT rhythm prior to chemotherapy are more prone to sleep disturbances following chemotherapy. Additionally, prolonged SL s may be a contributing factor to their poor sleep quality. Trial Registration: clinicaltrials.gov : NCT04364347

Background Cancer screening is an important prevention tool shown to improve cancer morbidity and mortality. Primary care professionals (PCPs) can play an important role in facilitating cancer screening and addressing barriers. Our aim was to learn from PCPs that see a high proportion of patients experiencing marginalization and that have high screening rates in their practices (high performers) to identify key barriers and enablers to addressing cancer screening with this patient population. Methods This was a qualitative descriptive study conducted using the principles of ‘design thinking’ to engage PCPs who are high performers in order to understand key barriers and enablers to cancer screening. An interview guide informed by the Systems Model of Clinical Preventive Care was used to collect data. Participants eligible for this study included both physicians and nurse practitioners working in Ontario in a variety of settings including solo and team-based practice models. All interviews were audio-recorded, transcribed verbatim and checked for quality assurance. Transcripts were coded by two independent members of the research team using deductive content analysis. The data were mapped onto the Systems Model of Clinical Preventive Care domains and presented in a narrative summary. Results We interviewed a total of 22 PCPs of which 54.5% were women and just over half (54.5%) were White. Most participants worked in a team-based primary care model. Our results suggest that a number of strategies can support high screening rates among those experiencing marginalization including interprofessional team-based collaborative practice, culturally competent and trauma-informed care, and adaptive approaches to overcome barriers such as improving the ease, access, and acceptability of the screening test. Conclusion Addressing cancer screening with patients experiencing marginalization requires a multi-pronged approach to care to facilitate screening. Team-based models of care may have more infrastructure and supports in place to support PCPs in addressing cancer screening with patients experiencing marginalization. Lastly, providers and teams need to work in a supportive clinical context that allows for innovation to address system barriers to promote and enable screening for those who are structurally marginalized.

The interplay between tumor cells and the microenvironment significantly influences cancer progression. Here, we report a significant role of the transcription factor FOXM1 in shaping the tumor immune landscape. Single-cell sequencing reveals that tumor-intrinsic FOXM1 creates an immune-suppressive tumor microenvironment by inhibiting expression of stress ligands (including ULBP1) on cancer cells, thereby blocking NKG2D-NKG2DL interactions critical for priming natural killer- and T cell-mediated cytotoxicity of cancer cells. FOXM1 suppresses ULBP1 expression by epigenetically silencing the DNA-sensing protein STING using a DNMT1-UHRF1 complex, which in turn inhibits the unfolded protein response protein CHOP from activating ULBP1. Importantly, cancer patients with higher levels of FOXM1 and DNMT1, and lower levels of STING and ULBP1, have worse survival and are less responsive to immunotherapy. Collectively, our findings provide key insight into how a tumor-intrinsic transcription factor epigenetically shapes the tumor immune microenvironment, with strong implications for refining existing and designing new cancer immunotherapies.

The human placenta is the composite of multiple cell types, each which contributes uniquely to placental function. Small non-coding RNAs (sncRNAs) are regulators of gene expression and can be cell-specific. The sncRNA transcriptome of individual placental cell types has not yet been investigated due to difficulties in their procurement and isolation. Using a custom sequencing method, we explored the expression of seven sncRNA species (miRNA, piRNA, rRNA, scaRNA, snRNA, snoRNA, tRNA) from whole chorionic villi and four major sample-matched FACS-sorted cell type (cytotrophoblast, stromal, endothelial, Hofbauer) samples from 9 first trimester and 17 term placentas. After normalization for technical variables, samples clustered primarily by cell type lineage. No sncRNAs were uniquely expressed by cell type, however, mean expression differed by cell type for 115 sncRNAs. Known placentally-expressed sncRNAs showed differing expression by cell type and trimester. Expression of few sncRNAs varied by sex. Lastly, sample-matched sncRNA expression and DNA methylation correlation was not significant, although high correlation (> R² ± 0.6) was observed for some sncRNA-CpG pairs. This study represents the first exploration of the sncRNA transcriptome of bulk placental villi and placental cell types, informing about the expression and regulatory patterns underlying human placental development.

Human leukocyte antigen (HLA) molecules are pivotal in guiding human adaptive immune responses through their presentation of peptide ligands, collectively known as the immunopeptidome. This process is central to the development of cancer immunotherapies, such as vaccines and T-cell therapies. Profiling the immunopeptidome from plasma and other biofluids has gained increasing traction, as it offers a minimally invasive approach for monitoring disease states and immune responses toward cancer therapy. Here we present the second iteration of SAPrIm, a refined immunopeptidomics tool optimized for soluble HLA analysis. It can process up to 12 samples per batch within a day. In this plasma-focused iteration, we identified approximately 1,200 to 4,000 immunopeptides from 100 µL to 1 mL of plasma, demonstrating high reproducibility across technical replicates, biological replicates, and inter-day analyses. This robust reproducibility highlights the method’s strong potential for reliable relative quantification of immunopeptides in plasma-based studies. This workflow is positioned to advance the field of immunopeptidomics by enabling efficient plasma-based comparative analyses and mid-size cohort studies.

Cancer cells are capable of surviving, proliferating, and invading or migrating within hypoxic environments by regulating various adaptive mechanisms. Due to the activation of oncogenes and the inactivation of tumor suppressor genes, and relative deficiencies in oxygen and nutrients, cancer cells demonstrate elevated production of reactive oxygen species (ROS), primarily sourced from NADPH oxidases (NOX family). A key aspect of the reorientation of tumor cell metabolism is the combating of cellular oxidative stress through the promotion of antioxidant molecule synthesis to counteract ROS production. Given that most cancers experience hypoxia and that NOX is closely linked to numerous redox‐dependent signaling pathways, the expression and function of NOX are altered in various malignancies. Therefore, this review summarizes the characteristics of NOX family members, their influence on tumor proliferation, invasion, and migration, the role of NOX in promoting tumor angiogenesis, the impact of NOX on the function of immune cells within the tumor microenvironment, and the potential of targeting NOX in tumor therapy. This aims to offer a fresh viewpoint on a comprehensive understanding of the functions of NOX family members.

Sialidases in Akkermansia muciniphila are pivotal for mucin degradation, enabling energy acquisition, modulating gut microbiota balance, and influencing host health. However, their structural and functional mechanisms remain poorly characterized. This study resolved the magnesium-bound crystal structure of Amuc_1547, revealing a six-bladed β-propeller fold linked to a carbohydrate-binding module (CBM)-like β-sandwich domain. Structural characterization identified a conserved S-x-D-x-G-x-x-W motif, a unique metal-binding pocket coordinated by residues Glu289, Glu299, and Asp300, and a putative carbohydrate substrate-binding pocket within the CBM-like domain. Enzymatic assays confirmed the functional relevance of these structural elements and demonstrated that both metal ions and glycans significantly enhance enzymatic activity. Molecular docking, dynamics simulations, and enzyme kinetics analysis identified critical residue substitutions involved in sialic acid substrate binding and catalysis: Gln367 replaces an arginine in the classical Arg-triplet, while Gln350 and His349 replace the nucleophilic tyrosine. These substitutions collectively mediate substrate binding, nucleophilic attack, and transition state stabilization, distinguishing the catalytic mechanism of Amuc_1547 from other six-bladed β-propeller sialidases. Additionally, comparative analysis of the four A. muciniphila sialidases highlights sequence divergence and domain architecture variations, suggesting niche-specific roles in gut microenvironments. Our work not only deciphers the structural basis of metal-dependent substrate recognition in Amuc_1547 but also advances our understanding of the adaptation of A. muciniphila to gut niches, offering a blueprint for leveraging sialidase-driven mucin metabolism in microbiota-targeted therapies.

Meticulous lymph node 6 station (LN#6) dissection is mandatory in pylorus-preserving gastrectomy (PPG), but can increase the risk of complications, such as postoperative delayed gastric emptying. With analyzing lymphatic spread patterns based on cross-sectional tumor location, we planned to predict the surgical burden of LN#6 dissection, balancing oncological safety and risk of postoperative complications. We included consecutive PPG cases at Seoul National University Hospital (2007–2017) to assess the incidence, 5-year survival rate (5YSR), and 3-year recurrence-free survival (3RFS) of LN#6 metastasis. Cox regression analyzed the impact of LN#6 metastasis itself on 5YSR and 3RFS. The effect of tumor location among gastric middle-third tumors on LN#6 metastasis was evaluated. The therapeutic indices (TI) of LN#6 based on tumor location were calculated. Among 1070 PPG patients, 5YSR and 3RFS were 97.0% and 98.9%. LN#6 metastasis was found in 11 patients (1.03%), with 3 recurrences observed among them (3/11, 0.28%). LN#6 metastasis itself did not significantly affect 5YSR (p = 0.266) or 3RFS (p = 0.075). Tumor location showed a significant association for LN#6 metastasis (p = 0.015), with low body greater curvature (LB-GC) showing the highest prevalence (5/11, 45.45%). TI of LN#6 for LB-GC tumors was 3.76, while TI for low body lesser curvature (LB-LC) and midbody lesser curvature (MB-LC) tumors was 0.0. LN#6 metastasis is infrequent and does not affect 5YSR or 3RFS in PPG patients. Tumors in LB-GC demonstrated a higher tendency for lymphatic spread to LN#6, while those in lesser curvature demonstrated a lower spread, suggesting a reduced surgical burden for lesser curvature tumors. This study evaluated LN#6 metastasis in 1070 PPG patients, demonstrating low incidence and favorable oncological outcomes, supporting tailored LN#6 dissection for lesser curvature tumors to minimize complications without compromising safety.

Caerin peptides exhibit a dual role in cancer treatment by directly killing cancer cells and modulating the tumour microenvironment to enhance anti-tumour immunity. This study investigates the mechanisms underlying caerin 1.1/1.9-induced acute cell death in epithelial cancer cells and explores their therapeutic potential. HeLa, A549, and Huh-7 cancer cell lines were treated with caerin 1.1/1.9 peptides. Morphological observations, flow cytometry, lactate dehydrogenase (LDH) release, and IL-18 secretion assays revealed the occurrence of pyroptosis following treatment. Specifically, a 1-h treatment with caerin 1.1/1.9 induced pyroptosis in HeLa, A549, and Huh-7 cells, characterised by cell swelling, membrane bubbling, and the release of IL-18 and LDH. Western blotting confirmed the upregulation of pyroptosis markers, including caspase-3, cleaved caspase-3, and GSDME-N fragments. These findings highlight the significant role of caerin peptides in inducing acute pyroptosis, a form of programmed cell death that enhances the immunogenicity of dying cancer cells, thus potentially improving the effectiveness of immunotherapies. This research underscores the therapeutic potential of caerin 1.1/1.9 peptides in cancer treatment, providing a foundation for developing new anti-cancer strategies that leverage both direct cytotoxic effects and immune modulation to achieve more effective and sustained anti-tumour responses.

Patient-derived xenograft (PDX) models are widely used in cancer research. Genomic andtranscriptomic profiling of PDXs are inevitably contaminated by sequencing reads originated frommouse cells. Here, we examine the impact of mouse read contamination on RNA sequencing(RNAseq), Whole Exome Sequencing (WES), and Whole Genome Sequencing (WGS) data of 21 PDXs.We also systematically benchmark the performance of 12 computational protocols for removingmouse reads from PDXs. We find that mouse read contamination increases expression of immune andstromal related genes, and inflates the number of somatic mutations. However, detection of genefusions and copy number alterations is minimally affected by mouse read contamination. Using goldstandard datasets, we find that pseudo-alignment protocols often demonstrate better predictionperformance and computing efficiency. The best performing tool is a relatively new tool Xengsort. Ourresults emphasize the importance of removing mouse reads from PDXs and the need to adopt newtools in PDX genomic studies.