A novel humanized mouse model recapitulates the unique TME found in patients with HIV-associated NSCLC

Revue des Maladies Respiratoires Actualités

IntroductionLes déterminants de sensibilité et de résistance aux inhibiteurs des points de contrôle immunitaires (ICIs) sont mal compris. Une machinerie de présentation antigénique (MPA) HLA de classe-I intacte est nécessaire pour la reconnaissance de l’antigène tumoral par les lymphocytes T CD8. Des perturbations dans la MPA peuvent entraîner une résistance aux ICIs. Le CCP est composé de plusieurs protéines chaperons situées dans le réticulum endoplasmique dans lequel Tapasin (Tap), Calreticulin (CalR) et ERp57 jouent des rôles majeurs. Le CCP permet une sélection et un chargement optimaux des peptides sur la chaîne lourde HLA de classe-I et est essentiel pour une présentation adéquate des complexes peptide-HLA à la surface cellulaire. Nous avons étudié la fréquence et l’impact clinique des altérations du CCP dans les cellules cancéreuses dans le CBNPC.MéthodesAfin de mesurer de …

Journal of Thoracic Oncology

IntroductionPatients with metastatic EGFR-mutant NSCLC inevitably have disease progression while on tyrosine kinase inhibitor (TKI) therapy. Co-occurring tumor suppressor gene (TSG) alterations have been associated with poor outcomes, however, detailed analyses of their impact on patient outcomes are limited.MethodsPatients with EGFR-mutant NSCLC treated with EGFR TKIs who had tumor genomic profiling were included. Alterations in TP53 and five additional TSGs (RB1, NF1, ARID1A, BRCA1, and PTEN) were used to stratify the cohort into the following three subgroups: patients with tumors harboring a TP53 mutation plus a mutation in at least one additional TSG (TP53mut/TSGmut), those having a TP53 mutation without additional TSG mutations (TP53mut/TSGwt), and those with TP53wt. Patient characteristics and clinical outcomes were assessed in two independent cohorts.ResultsA total of 101 …

Journal of the American Statistical Association

In this article, we study high-dimensional multivariate logistic regression models in which a common set of covariates is used to predict multiple binary outcomes simultaneously. Our work is primarily motivated from many biomedical studies with correlated multiple responses such as the cancer cell-line encyclopedia project. We assume that the underlying regression coefficient matrix is simultaneously low-rank and row-wise sparse. We propose an intuitively appealing selection and estimation framework based on marginal model likelihood, and we develop an efficient computational algorithm for inference. We establish a novel high-dimensional theory for this nonlinear multivariate regression. Our theory is general, allowing for potential correlations between the binary responses. We propose a new type of nuclear norm penalty using the smooth clipped absolute deviation, filling the gap in the related non-convex …

Genetically modified non-human animals expressing human EPO from the animal genome are provided. Also provided are methods for making non-human animals expressing human EPO from the non-human animal genome, and methods for using non-human animals expressing human EPO from the non-human animal genome. These animals and methods find many uses in the art, including, for example, in modeling human erythropoiesis and erythrocyte function; in modeling human pathogen infection of erythrocytes; in in vivo screens for agents that modulate erythropoiesis and/or erythrocyte function, eg in a healthy or a diseased state; in in vivo screens for agents that are toxic to erythrocytes or erythrocyte progenitors; in in vivo screens for agents that prevent against, mitigate, or reverse the toxic effects of toxic agents on erythrocytes or erythrocyte progenitors; in in vivo screens of erythrocytes or erythrocyte …

Nature Communications

Epithelial barrier dysfunction and crypt destruction are hallmarks of inflammatory bowel disease (IBD). Intestinal stem cells (ISCs) residing in the crypts play a crucial role in the continuous self-renewal and rapid recovery of intestinal epithelial cells (IECs). However, how ISCs are dysregulated in IBD remains poorly understood. Here, we observe reduced DHX9 protein levels in IBD patients, and mice with conditional DHX9 depletion in the intestinal epithelium (Dhx9ΔIEC) exhibit an increased susceptibility to experimental colitis. Notably, Dhx9ΔIEC mice display a significant reduction in the numbers of ISCs and Paneth cells. Further investigation using ISC-specific or Paneth cell-specific Dhx9-deficient mice demonstrates the involvement of ISC-expressed DHX9 in maintaining epithelial homeostasis. Mechanistically, DHX9 deficiency leads to abnormal R-loop accumulation, resulting in genomic instability and the …

bioRxiv

Various Foundation Models (FMs) have been built based on the pre-training and fine-tuning framework to analyze single-cell data with different degrees of success. In this manuscript, we propose a method named scELMo (Single-cell Embedding from Language Models), to analyze single cell data that utilizes Large Language Models (LLMs) as a generator for both the description of metadata information and the embeddings for such descriptions. We combine the embeddings from LLMs with the raw data under the zero-shot learning framework to further extend its function by using the fine-tuning framework to handle different tasks. We demonstrate that scELMo is capable of cell clustering, batch effect correction, and cell-type annotation without training a new model. Moreover, the fine-tuning framework of scELMo can help with more challenging tasks including in-silico treatment analysis or modeling perturbation …

With the development of next-generation sequencing technology, de novo variants (DNVs) with deleterious effects can be identified and investigated for their effects on birth defects such as congenital heart disease (CHD). However, statistical power is still limited for such studies because of the small sample size due to the high cost of recruiting and sequencing samples and the low occurrence of DNVs. DNV analysis is further complicated by genetic heterogeneity across diseased individuals. Therefore, it is critical to jointly analyze DNVs with other types of genomic/biological information to improve statistical power to identify genes associated with birth defects. In this review, we discuss the general workflow, recent developments in statistical methods, and future directions for DNV analysis.

Nucleic Acids Research

High throughput sequencing of B cell receptors (BCRs) is increasingly applied to study the immense diversity of antibodies. Learning biologically meaningful embeddings of BCR sequences is beneficial for predictive modeling. Several embedding methods have been developed for BCRs, but no direct performance benchmarking exists. Moreover, the impact of the input sequence length and paired-chain information on the prediction remains to be explored. We evaluated the performance of multiple embedding models to predict BCR sequence properties and receptor specificity. Despite the differences in model architectures, most embeddings effectively capture BCR sequence properties and specificity. BCR-specific embeddings slightly outperform general protein language models in predicting specificity. In addition, incorporating full-length heavy chains and paired light chain sequences improves the …

JCI insight

The central nervous system HIV reservoir is incompletely understood and is a major barrier to HIV cure. We profiled people with HIV (PWH) and uninfected controls through single-cell transcriptomic and T cell receptor (TCR) sequencing to understand the dynamics of HIV persistence in the CNS. In PWH on ART, we found that most participants had single cells containing HIV-1 RNA, which was found predominantly in CD4 central memory T cells, in both cerebrospinal fluid (CSF) and blood. HIV-1 RNA–containing cells were found more frequently in CSF than blood, indicating a higher burden of reservoir cells in the CNS than blood for some PWH. Most CD4 T cell clones containing infected cells were compartment specific, while some (22%) — including rare clones with members of the clone containing detectable HIV RNA in both blood and CSF — were found in both CSF and blood. These results suggest that infected T cells trafficked between tissue compartments and that maintenance and expansion of infected T cell clones contributed to the CNS reservoir in PWH on ART.

Metabolites

Pregnancy at an advanced maternal age is considered a risk factor for adverse maternal, fetal, and neonatal outcomes. Here we investigated whether maternal age could be associated with differences in the blood levels of newborn screening (NBS) markers for inborn metabolic disorders on the Recommended Universal Screening Panel (RUSP). Population-level NBS data from screen-negative singleton infants were examined, which included blood metabolic markers and covariates such as age at blood collection, birth weight, gestational age, infant sex, parent-reported ethnicity, and maternal age at delivery. Marker levels were compared between maternal age groups (age range: 1544 years) using effect size analyses, which controlled for differences in group sizes and potential confounding from other covariates. We found that 13% of the markers had maternal age-related differences, including newborn metabolites with either increased (Tetradecanoylcarnitine [C14], Palmitoylcarnitine [C16], Stearoylcarnitine [C18], Oleoylcarnitine [C18:1], Malonylcarnitine [C3DC]) or decreased (3-Hydroxyisovalerylcarnitine [C5OH]) levels at an advanced maternal age (≥35 years, absolute Cohen’s d > 0.2). The increased C3DC levels in this group correlated with a higher false-positive rate in newborn screening for malonic acidemia (p-value < 0.001), while no significant difference in screening performance was seen for the other markers. Maternal age is associated with inborn metabolic differences and should be considered together with other clinical variables in genetic disease screening.

bioRxiv

Drug synergy prediction is a challenging and important task in the treatment of complex diseases including cancer. In this manuscript, we present a novel Foundation Model, known as BAITSAO, for tasks related to drug synergy prediction with a unified pipeline to handle different datasets. We construct the training datasets for BAITSAO based on the context-enriched embeddings from Large Language Models for the initial representation of drugs and cell lines. After demonstrating the relevance of these embeddings, we pre-train BAITSAO with a large-scale drug synergy database under a multi-task learning framework with rigorous selections of tasks. We demonstrate the superiority of the model architecture and the pre-trained strategies of BAITSAO over other methods through comprehensive benchmark analysis. Moreover, we investigate the sensitivity of BAITSAO and illustrate its unique functions including new drug discoveries, drug combinations-gene interaction, and multi-drug synergy predictions.

JAMA psychiatry

ImportanceMany psychiatric outcomes share a common etiologic pathway reflecting behavioral disinhibition, generally referred to as externalizing (EXT) disorders. Recent genome-wide association studies (GWASs) have demonstrated the overlap between EXT disorders and important aspects of veterans’ health, such as suicide-related behaviors and substance use disorders (SUDs).ObjectiveTo explore correlates of risk for EXT disorders within the Veterans Health Administration (VA) Million Veteran Program (MVP).Design, Setting, and ParticipantsA series of phenome-wide association studies (PheWASs) of polygenic risk scores (PGSs) for EXT disorders was conducted using electronic health records. First, ancestry-specific PheWASs of EXT PGSs were conducted in the African, European, and Hispanic or Latin American ancestries. Next, a conditional PheWAS, covarying for PGSs of comorbid psychiatric …

Nature

Interleukin-10 (IL-10) is a key anti-inflammatory cytokine that can limit immune cell activation and cytokine production in innate immune cell types. Loss of IL-10 signalling results in life-threatening inflammatory bowel disease in humans and mice—however, the exact mechanism by which IL-10 signalling subdues inflammation remains unclear, , –. Here we find that increased saturated very long chain (VLC) ceramides are critical for the heightened inflammatory gene expression that is a hallmark of IL-10 deficiency. Accordingly, genetic deletion of ceramide synthase 2 (encoded by Cers2), the enzyme responsible for VLC ceramide production, limited the exacerbated inflammatory gene expression programme associated with IL-10 deficiency both in vitro and in vivo. The accumulation of saturated VLC ceramides was regulated by a decrease in metabolic flux through the de novo mono-unsaturated fatty acid synthesis …

Parasites & Vectors

BackgroundAlthough whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health.MethodsWe designed a SNP chip for Ae. albopictus …

bioRxiv

Spatially resolved transcriptomics or proteomics data have the potential to contribute fundamental insights into the mechanisms underlying physiologic and pathological processes. However, analysis of these data capable of relating spatial information, multiplexed markers, and their observed phenotypes remains technically challenging. To analyze these relationships, we developed SORBET, a deep learning framework that leverages recent advances in graph neural networks (GNN). We apply SORBET to predict tissue phenotypes, such as response to immunotherapy, across different disease processes and different technologies including both spatial proteomics and transcriptomics methods. Our results show that SORBET accurately learns biologically meaningful relationships across distinct tissue structures and data acquisition methods. Furthermore, we demonstrate that SORBET facilitates understanding of the spatially-resolved biological mechanisms underlying the inferred phenotypes. In sum, our method facilitates mapping between the rich spatial and marker information acquired from spatial `omics technologies to emergent biological phenotypes. Moreover, we provide novel techniques for identifying the biological processes that comprise the predicted phenotypes.

Journal of Human Genetics

Identification of pleiotropy at the single nucleotide polymorphism (SNP) level provides valuable insights into shared genetic signals among phenotypes. One approach to study these signals is through mediation analysis, which dissects the total effect of a SNP on the outcome into a direct effect and an indirect effect through a mediator. However, estimated effects from mediation analysis can be confounded by the genetic correlation between phenotypes, leading to inaccurate results. To address this confounding effect in the context of genetic mediation analysis, we propose a restricted-maximum-likelihood (REML)-based mediation analysis framework called REML-mediation, which can be applied to either individual-level or summary statistics data. Simulations demonstrated that REML-mediation provides unbiased estimates of the true cross-trait causal effect, assuming certain assumptions, albeit with a slightly …

Nature Biotechnology

Single-cell RNA sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typically rely on constructing cell pseudotime through cell trajectory inference. However, the presence of concurrent gene processes in the same group of cells and technical noise can obscure the true progression of the processes studied. To address this challenge, we present GeneTrajectory, an approach that identifies trajectories of genes rather than trajectories of cells. Specifically, optimal transport distances are calculated between gene distributions across the cell–cell graph to extract gene programs and define their gene pseudotemporal order. Here we demonstrate that GeneTrajectory accurately extracts progressive gene dynamics in myeloid lineage maturation. Moreover, we show that GeneTrajectory …

Nature Biotechnology

Single-cell RNA sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typically rely on constructing cell pseudotime through cell trajectory inference. However, the presence of concurrent gene processes in the same group of cells and technical noise can obscure the true progression of the processes studied. To address this challenge, we present GeneTrajectory, an approach that identifies trajectories of genes rather than trajectories of cells. Specifically, optimal transport distances are calculated between gene distributions across the cell–cell graph to extract gene programs and define their gene pseudotemporal order. Here we demonstrate that GeneTrajectory accurately extracts progressive gene dynamics in myeloid lineage maturation. Moreover, we show that GeneTrajectory …

Statistica Sinica

We study the high-dimensional asymptotic behavior of inferences based on summary statistics that are widely used in genome-wide association studies (GWAS) under model misspecification. The high dimensionality is in the sense that the number of single-nucleotide polymorphisms (SNPs) under consideration may be much larger than the sample size. The model misspecification is in the sense that the number of causal SNPs may be much smaller than the total number of SNPs under consideration. Specifically, we establish two parameters of genetic interest, namely, the consistency and asymptotic normality of the estimators of the heritability and genetic covariance. Our theoretical results are supported by the findings of empirical studies involving simulated and real data.

bioRxiv

With continuous progress of single-cell chromatin accessibility profiling techniques, scATAC-seq has become more commonly used in investigating regulatory genomic regions and their involvement in developmental, evolutionary, and disease-related processes. At the same time, accurate cell type annotation plays a crucial role in comprehending the cellular makeup of complex tissues and uncovering novel cell types. Unfortunately, the majority of existing methods primarily focus on label transfer within scRNA-seq datasets and only a limited number of approaches have been specifically developed for transferring labels from scRNA-seq to scATAC-seq data. Moreover, many methods have been published for the joint embedding of data from the two modalities, which can be used for label transfer by adding a classifier trained on the latent space. Given these available methods, this study presents a comprehensive benchmarking study evaluating 27 computational tools for scATAC-seq label annotations through tasks involving single-cell RNA and ATAC data from various human and mouse tissues. We found that when high quality paired data were available to transfer labels across unpaired data, Bridge and GLUE were the best performers; otherwise, bindSC and GLUE achieved the highest prediction accuracy overall. All these methods were able to use peak-level information instead of purely relying on the gene activities from scATAC-seq. Furthermore, we found that data imbalance, cross-omics dissimilarity on common cell types, data binarization, and the introduction of semi-supervised strategy usually had negative impacts on model …

Cancer Research

INTRODUCTION: Black women are 41% more likely to die from breast cancer compared to White women yet remain underrepresented in clinical trials and population studies. We have previously shown a higher proportion of Black women with HR+HER2- tumors further classify as Basal-Type compared with White women, using BluePrint molecular subtyping. Other studies have demonstrated higher 3-year recurrence rates in patients with BluePrint Basal-Type tumors compared to Luminal-Type. To determine whether the increased frequency of HR+/Basal-Type tumors impacts long-term outcomes in this cohort, we compared 3-year outcomes with BluePrint and the risk of distant recurrence signature, MammaPrint (MP), between Black and White women with HR+HER2- breast cancer. We also evaluated the association of MP and BluePrint with 10-year outcomes in a subset of Black women. METHODS: This study …

Cancer Research

The pancreatic ductal adenocarcinoma (PDAC) microenvironment is populated by distinct subtypes of cancer-associated fibroblasts (CAFs), including myofibroblastic CAFs (myCAFs) that synthesize and remodel the stromal matrix and inflammatory CAFs (iCAFs) that secrete cytokines and growth factors. Subpopulations of CAFs reside in regions of tumor hypoxia, which may play a role in determining CAF behaviors. We tested the hypothesis that iCAFs preferentially drive ductal cell epithelial-mesenchymal transition (EMT), which promotes PDAC chemoresistance, and that hypoxia promotes the iCAF phenotype. Cell-cell communication analysis using publicly available single-cell RNA sequencing (scRNA-seq) data of human tumors indicated that iCAFs secrete growth factors predicted to promote ductal cell EMT. This inference was confirmed in experiments showing that PDAC cells exhibit stronger EMT in …

Cancer Research

Epithelial-mesenchymal transition (EMT) is a developmental process that is aberrantly activated in cancers such as pancreatic ductal adenocarcinoma (PDAC) to promote disease progression and chemoresistance. EMT occurs heterogeneously among PDAC ductal cells, which frustrates efforts to identify the underlying signaling regulatory mechanisms. We hypothesize that cell-to-cell variation in the activities of specific signaling pathways explains EMT heterogeneity. To test this, we developed a workflow integrating: 1) iterative indirect immunofluorescence imaging (4i) to quantify the activities of up to seven purported EMT-regulating pathways with single-cell resolution and 2) a multivariate mutual information computational model to predict the pathways that are most informative of the EMT phenotype. In cultured PDAC cells, EMT was induced by treating cells with growth factors present in the tumor …

Cancer Research

The tumor microenvironment in pancreatic ductal adenocarcinoma (PDAC) plays a key role in tumor progression and response to therapy. The dense PDAC stroma causes hypovascularity, which leads to hypoxia. Here, we showed that hypoxia drives long-lasting epithelial-mesenchymal transition (EMT) in PDAC primarily through a positive-feedback histone methylation-MAPK signaling axis. Transformed cells preferentially underwent EMT in hypoxic tumor regions in multiple model systems. Hypoxia drove a cell-autonomous EMT in PDAC cells which, unlike EMT in response to growth factors, could last for weeks. Furthermore, hypoxia reduced histone demethylase KDM2A activity, suppressed PP2 family phosphatase expression, and activated MAPKs to post-translationally stabilize histone methyltransferase NSD2, leading to an H3K36me2-dependent EMT in which hypoxia-inducible factors played only a …

Cancer Research

Despite the considerable success of immune checkpoint therapies targeting T cells, a sizable proportion of patients experience resistance or relapse due to the immunosuppressive nature of the tumor microenvironment. Myeloid cells, a major component that suppresses effector lymphocytes, have emerged as an alternative and promising therapeutic target. However, there is a deep lack of widely accessible immunological models capable of representing the intricate three-way interaction between tumor cells, T cells, and myeloid cells. To address this need, we conducted a comprehensive protein profiling of human tumor and immune cell lines available at ATCC for various established and novel immune checkpoint molecules. Cell lines with high endogenous expression of the immune checkpoint proteins, such as programmed death-ligand 1 and 2 (PD-L1 and PD-L2), cluster of differentiation 155 (CD155), B7 …

Cancer Research

Monosomy 7 (-7) or del(7q) are recurrent in high-risk myeloid neoplasms, including up to 50% of myeloid neoplasms arising after prior exposure to chemotherapy and/or radiation. Although putative chromosome 7 tumor suppressor genes have been identified, the effects of combinatorial 7q gene loss remain unclear. A barrier to understanding the pathogenesis of -7/del(7q) is the challenge of modeling aneuploidy in animal models. To address this knowledge gap, we established an in vivo model of del(7q) clonal hematopoiesis and drug resistance using multiplex CRISPR-Cas9 to simultaneously target four 7q genes (Cux1, Ezh2, Kmt2c, and Kmt2e) in murine hematopoietic stem cells. After chemotherapy exposure, we observe significant myeloid expansion of clones edited for both Cux1 and Ezh2. Compared to the transcriptomes of control or single gene edited cells, Cux1;Ezh2-deficient cells fail to induce DNA …

Cancer Research

We have developed multiple novel preclinical syngeneic triple negative breast cancer(TNBC) genetically engineered mouse (GEM) models, which have been characterized genomically and with respect to their immune microenvironments. By integrating the immunological characterization of murine syngeneic mammary tumor models with analyses of human breast cancer datasets, we have demonstrated a relationship between EMT and myeloid cells, specifically tumor-associated macrophages (TAMs). We also have leveraged our syngeneic GEM models to define the response to immune checkpoint blockade therapy (ICBT) with emphasis on the myeloid cell environment. We have used our GEM models to test single agent drugs along with standard-of-care therapies for appropriate durations. Finally, we have tested these treatment regimens on established metastases with sufficient tumor burdens. Specifically …

Cancer Research

Background: Increased macrophage infiltration and elevated levels of Epithelial to Mesenchymal Transition (EMT) gene signatures are associated with a poor outcome following neo-adjuvant chemotherapy in patients with triple negative breast cancer (TNBC). Further, metastatic disease with overall the poorest survival rates has a cold tumor immune microenvironment (TIME), especially in lung and liver metastases. Interestingly, an abundance of macrophages are observed at these metastatic sites. We have extensively characterized multiple preclinical syngeneic Trp53-/- tumor models that have extensive Tumor Associated Macrophage (TAM) infiltration. These tumor models transcriptionally resemble “claudin-low”, “basal-like” and “luminal-like” breast cancers. From these models the “claudin-low” closely phenocopy the high EMT/TAM subtype observed in patients. Objective: Accordingly, we asked if SNDX …

Cancer Research

Background: The mammary gland exhibits extensive proliferative and differentiation potential throughout development. Wnt signaling has been recognized as a crucial player in multiple stages of mammary gland development, including mammary placode specification, gland branching morphogenesis, stem cell maintenance, and alveolar development. In our laboratory, prior research has revealed the importance of the β-catenin-independent noncanonical Wnt receptor, Ror2, in branching morphogenesis, cell differentiation, and actin-cytoskeletal dynamics within the mammary epithelium. However, the specific roles of Ror2 in the myoepithelial and luminal cell compartments have yet to be fully elucidated. Methods and Results: In this study, we investigated the functional role of Ror2 in these two distinct cell populations by developing mouse models with lineage-specific deletion of Ror2 in myoepithelial versus …

Cancer Research

Triple-negative breast cancer (TNBC) is a biologically heterogeneous and clinically important breast cancer subtype because if considered a distinct disease, TNBC would rank as the 5th leading cause of cancer deaths in women. TNBC patients resistant to standard-of-care therapies have poor survival. Tumor-associated immune cells such as neutrophils and macrophages can display a pro-tumoral phenotype and contribute to therapy resistance. Epigenetic enzymes have been shown to reprogram both the tumor cells and tumor-associated immune cells. Thus, targeting epigenetic enzymes is a potential strategy to improve the response of TNBC to standard-of-care therapies. Previously, our laboratory performed an epigenetic drug screen and identified several epigenetic inhibitors. We selected IACS-70654, a novel selective p300/CBP BRD inhibitor, to be the primary focus of this study. We determined the effects …

Cancer Research

Introduction: Efforts to overcome resistance to immune checkpoint inhibition (ICI) are paramount, and novel combination strategies are in development. Image-guided percutaneous cryoablation is an established minimally invasive oncologic treatment that has demonstrated immune modulatory effects. We hypothesized that cryoablation may prime the tumor microenvironment (TME) through direct modulation of the tumor, thereby generating an anti-tumor response in ICI refractory tumors. Methods: In this non-randomized phase II single-center study, subjects with unresectable melanoma progressing on ICI underwent cryoablation of an enlarging metastasis, and ICI was continued for a minimum of two additional cycles. The primary endpoint was safety and feasibility, with objective response rate (ORR) and disease control rate (DCR) in non-ablated lesions a key secondary endpoint. To better understand the …

Cancer Research

Background: Rhabdomyosarcoma (RMS) is an aggressive pediatric solid tumor with poor survival and new targeted therapies are needed. Aims: Using an integrative proteogenomic quantitative approach, we sought to identify candidate immunotherapeutic targets then validate top targets in RMS preclinical models. Methods: We first performed plasma membrane enrichment followed by mass spectrometry (MS) to define the surfaceome of 7 fusion-positive (FP) and 14 fusion-negative (FN) RMS patient-derived xenograft models. Surface proteins were scored by IMMUNOTAR, our custom pipeline which extracts and integrates quantitative features from diverse proteogenomic and annotation datasets to provide a score for each protein, using mean-average-precision for score optimization. Cell surface expression of IMMUNOTAR-prioritized proteins was validated using flow cytometry, focusing on targets with …

Cancer Research

Background: More than 60,000 U.S. adults are diagnosed with non-muscle invasive bladder cancer (NMIBC) each year. These patients are recommended to undergo surveillance via repeated cystoscopies. However, the ideal frequency of post-diagnostic cystoscopy surveillance remains unknown, and efforts are underway to de-escalate surveillance given uncertainty regarding its effect on mortality. We therefore aimed to compare the effectiveness of different post-diagnostic cystoscopy surveillance strategies on bladder cancer specific mortality. Methods: We used observational data from the Surveillance, Epidemiology, and End Results (SEER)-Medicare linkage to emulate a target trial, i.e., a hypothetical, pragmatic randomized trial that would answer our causal question. Eligible individuals were aged 66 years or older, diagnosed with NMIBC (Ta, Tis, or T1) classified as urothelial carcinoma between January 1 …

Cancer Research

Introduction: Randomized trials have shown that physical activity can improve quality of life (QOL) among individuals with cancer. In the absence of a randomized trial of adequate size and follow-up to comprehensively evaluate this relationship for prostate cancer, we aim to emulate a target trial of guideline-based physical activity strategies and 6-year physical QOL. Methods: We will use observational data on individuals in the Health Professionals Follow-up Study diagnosed with nonmetastatic prostate cancer between 2010-2016 and free of conditions that could preclude following current physical activity recommendations at baseline (first post-diagnostic questionnaire). The physical activity strategies of interest are (1) engage in ≥150 minutes of moderate activity, or ≥75 minutes of vigorous activity per week, or an equivalent combination (i.e., ≥7.5 metabolic equivalent of task [MET]-hours/week of vigorous or …

Cancer Research

Introduction: Social support is associated with improved cancer survivorship, but literature on its association with prostate cancer specific physical and psychosocial quality of life (QoL) is lacking. We investigated the associations of social support with physical and psychosocial QoL in individuals with prostate cancer in HPFS. Methods: We included 1,692 men (ages 61-95 years, mean: 71 years) diagnosed with non-metastatic prostate cancer between 2008 and 2016. Social support was measured by the Berkman-Syme Social Network Index (SNI) (a composite measure of marital status, sociability, membership in religious groups or other community organizations: socially isolated, moderately isolated, moderately integrated, socially integrated) and marital status (married, not married). Physical (measured by EPIC-CP: bowel function, urinary incontinence, urinary irritation/obstruction, sexual function, vitality/hormonal …

Cancer Research

Metastasis of cancer cells to vital organs remains the leading cause of cancer related deaths, emphasizing a strong need for actionable targets in advanced stage cancer. To address this, we study novel dysregulated mitochondrial signaling mechanisms that cells utilize to metastasize. Here, we focus on how outer mitochondrial membrane protein—Mitochondrial Rho GTPase 2 (MIRO2)—promotes tumor cell invasion and metastasis. Our previous work identified higher MIRO2 mRNA expression in cancer vs. normal patient samples in a multitude of cancer types, which correlated with worse patient outcomes. Furthermore, we demonstrated that MIRO2 was critical for prostate cancer cell growth and survival in vitro and in vivo. However, it remains unknown if MIRO2 only affects primary tumor growth or if this protein is important throughout tumor progression. Using siRNA mediated knockdown (KD) of MIRO2 we find …

Cancer Research

Medulloblastoma is one of the most common malignant brain tumors of children, and 30% of medulloblastomas are driven by gain-of-function genetic lesions in the Sonic Hedgehog (SHH) signaling pathway. EYA1, a haloacid dehalogenase phosphatase and transcription factor, is critical for tumorigenesis and proliferation of SHH medulloblastoma (SHH-MB). Benzarone and benzbromarone have been identified as allosteric inhibitors of EYA proteins. Using benzarone as a point of departure, we developed a panel of 35 derivatives and tested them in SHH-MB. Among these compounds, DS-1–38 functioned as an EYA antagonist and opposed SHH signaling. DS-1–38 inhibited SHH-MB growth in vitro and in vivo, showed excellent brain penetrance, and increased the lifespan of genetically engineered mice predisposed to fatal SHH-MB. These data suggest that EYA inhibitors represent promising …

Cancer Research

Checkpoint inhibitors have achieved durable responses and long-lasting immunologic memory in cancer patients. However, the initial and acquired resistance remains an unsolved problem. It’s urgent to learn the molecular mechanisms causing resistance. microRNAs (miRNAs) are short transcripts that regulate many pathophysiological processes. Here, we investigated the miRNAs expression changes after GVAX combined with monoclonal PD-1 antibody treatment in the murine melanoma B16F10 tumors and identified microRNAs down-regulated in responsive tumors. Deletion of this family member in three different syngeneic mouse tumors did not affect their in vitro nor in vivo proliferation but sensitized anti-PD1 immunotherapy. The miRNA deletion with anti-PD1 therapy increased total CD45+ leukocyte infiltration with all types of hematopoietic cells except macrophages. Both tumor bulk RNA sequencing and …

Cancer Research

In human lung adenocarcinoma that carry Epidermal Growth Factor Receptor (EGFR) sensitizing mutations, targeting the EGFR pathway with the use of EGFR tyrosine kinase inhibitors (EGFR-TKIs) has emerged as a promising therapeutic strategy providing initial clinical benefit to many patients. Unfortunately, resistance to EGFR-TKIs eventually develops leading to disease progression. In addition to genetic mutations, transcriptional and epigenetic mediated changes in gene expression remain an important mechanism contributing to EGFR-TKI resistance. Here, we report a novel function of the transcriptional corepressor Transducin-Like Enhancer of Split-1 (TLE1) in mediating EGFR-TKI resistance in EGFR mutant LUAD cells through its survival promoting gene transcriptional program. In EGFR mutant, EGFR TKI sensitive LUAD cells, sole activation of the TLE1 nuclear function attenuates EGFR TKI sensitivity …

Cancer Research

Introduction: While inverse associations have been reported in epidemiologic studies of breast feeding and ovarian cancer risk, little is known about the biologic pathways impacted by breastfeeding that leads to risk reduction. Therefore, we aimed to identify individual metabolites and pathways associated with breastfeeding among parous women in the Nurses’ Health Study (NHS) (n=7,111) and NHSII (n=2,793), and ultimately develop a breastfeeding metabolite score to quantify the association of this score with ovarian cancer risk using a nested case control study within NHS/NHSII (n=504 cases and controls). Methods: To identify individual metabolites associated with breastfeeding, we conducted a cross-sectional analysis using data from all nested studies of metabolites and various disease outcomes (e.g., ovarian cancer, type 2 diabetes, stroke) within the NHS/NHSII. Liquid chromatography tandem mass …