DigitalCommons@The Texas Medical Center
Not a member yet
41791 research outputs found
Sort by
Dietary Lipids Induce PPARd and BCL6 to Repress Macrophage Il-23 Induction After Intestinal Injury and LPS Exposure
No full textUnresolved tissue damage is a common feature of Inflammatory Bowel Disease (IBD) that facilitates disease progression. Here, we showed that high animal fat diets (HFD), an environmental risk factor associated with IBD pathogenesis, suppress intestinal macrophage production of critical tissue repair responses after damage. This includes reduced IL-23 production, which drives downstream production of IL-22, which is needed for barrier repair. Indicating that dietary lipids interfere with responses to microbial molecules needed to induce barrier protective functions, we found oleic acid could directly suppress macrophage Il23a induction after lipopolysaccharide (LPS) treatment. Deleting the lipid transporter CD36 on macrophages restored the Il23a and Il22 response, reducing intestinal damage in HFD-fed DSS-treated mice. We found that CD36-mediated intracellular lipid accumulation, mainly oleic acid, in macrophages leads to peroxisome proliferator-activated receptor delta (PPARδ) release of the transcriptional repressor protein B-cell lymphoma 6 (BCL6). BCL6 suppresses Il23a transcription in microbe-exposed macrophages. The studies suggest dietary lipid modulation of the macrophage PPARδ/BCL6 transcriptional repressor complex is a key mechanism of fat-associated defects in intestinal damage repair and immune dysregulation. Overall, our findings provide new insights into dietary lipid contribution to intestinal disease progression and identify new potential therapeutic targets to decrease diet-associated risk for IBD
Culture-Independent Meta-Pangenomics Enabled by Long-Read Metagenomics Reveals Associations With Pediatric Undernutrition
No full textThe human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies
Mouse Metastable Epialleles Are Extremely Rare
No full textMetastable epialleles (MEs) are genomic loci at which epigenetic marks are established stochastically during early embryonic development and maintained during subsequent differentiation and throughout life, leading to stable epigenetic and phenotypic variation among genetically identical individuals. Although MEs were first described in mice over 20 years ago, the extent of epigenetic metastability in the mouse genome remains unknown. We present the first unbiased genome-wide screen for MEs in mice. Using deep whole-genome bisulfite sequencing across tissues derived from the three embryonic germ layers in isogenic C57BL/6J mice, we identified only 29 MEs, precisely localizing them and documenting their rarity. Consistent with recent findings, we found no effects of maternal dietary methyl donor supplementation on ME methylation in the offspring, challenging previous assertions that MEs generally exhibit developmental plasticity. Most but not all MEs are associated with intracisternal A-particle (IAP) elements, tending to localize to the 5\u27 end of the IAP. Additionally, we discovered autosomal regions at which systemic interindividual variation in DNA methylation is associated with sex, providing insights into sex-associated epigenetic development that apparently precedes sexual differentiation. Our findings indicate that expression of transcription factors, including CCCTC-binding factor (CTCF) and specific KRAB zinc finger proteins during early embryonic development, plays a key role in orchestrating stochastic establishment and/or maintenance of DNA methylation at metastable transposable elements. Overall, these findings advance our understanding of the genomic determinants of epigenetic metastability and suggest that interindividual epigenetic variation at MEs is unlikely to be a major determinant of phenotypic variation among isogenic mice
Il-12-Producing Cytokine Factories Induce Precursor Exhausted T Cells and Elimination of Primary and Metastatic Tumors
No full textBackground: Curative responses to immunotherapy require the generation of robust systemic immunity with limited toxicity. Recruitment of T cell populations such as precursor exhausted T cells (Tpex) from lymphoid tissues to tumors is a hallmark of effective treatment. However, the ability to efficiently induce this recruitment is lacking in current immunotherapy approaches. Furthermore, systemic administration of immunotherapies frequently results in dose-limiting toxicities, yielding an inadequate therapeutic window for eliciting durable responses.
Methods: In this investigation, we evaluated the safety and antitumor efficacy of locally administered interleukin 12 (IL-12) using a clinically translatable cytokine delivery platform (NCT05538624) to identify Tpex recruitment capabilities at tolerable cytokine doses.
Results: We show IL-12 cytokine factories can effectively treat a broad spectrum of cancer types. Single-cell RNA sequencing data suggests that the antitumor efficacy seen in our studies was due to retinal pigmented epithelial cells-mIL12 treatment inducing differentiation of Tpex cells within the tumor microenvironment. When administered in combination with checkpoint therapy, IL-12 cytokine factory treatment generated systemic abscopal immunity, preventing subcutaneous tumor outgrowth in 8/9 mice with colorectal cancer and lung metastasis in mice with melanoma. Furthermore, this platform was well tolerated in a non-human primate without signs of toxicity.
Conclusions: Our new immunotherapy approach provides a robust strategy for inducing Tpex recruitment and systemic immunity against a range of solid peritoneal malignancies, many incurable with current immunotherapy strategies. Notably, these features were achieved using IL-12, and by leveraging our technology, we avoided the toxicities that have prevented the translation of IL-12 to the clinic. Our findings provide a strong rationale for the clinical development of IL-12 cytokine factories
Resilience and Vulnerabilities of Tumor Cells under Purine Shortage Stress
No full textPurpose: Purine metabolism is a promising therapeutic target in cancer; however, how cancer cells respond to purine shortage, particularly their adaptation and vulnerabilities, remains unclear.
Experimental design: Using the recently developed purine shortage-inducing prodrug DRP-104 and genetic approaches, we investigated the responses in prostate, lung, and glioma cancer models.
Results: We demonstrate that when de novo purine biosynthesis is compromised, cancer cells employ microtubules to assemble purinosomes, multiprotein complexes of de novo purine biosynthesis enzymes that enhance purine biosynthesis efficiency. Although this process enables tumor cells to adapt to purine shortage stress, it also renders them more susceptible to the microtubule-stabilizing chemotherapeutic drug docetaxel. Furthermore, we show that although cancer cells primarily rely on de novo purine biosynthesis, they also exploit methylthioadenosine phosphorylase (MTAP)-mediated purine salvage as a crucial alternative source of purine supply, especially under purine shortage stress. In support of this finding, combining DRP-104 with an MTAP inhibitor significantly enhances tumor suppression in prostate cancer models in vivo. Finally, despite the resilience of the purine supply machinery, purine shortage-stressed tumor cells exhibit increased DNA damage and activation of the cGAS-STING pathway, which may contribute to impaired immunoevasion and provide a molecular basis of the previously observed DRP-104-induced antitumor immunity.
Conclusions: Together, these findings reveal purinosome assembly and purine salvage as key mechanisms of cancer cell adaptation and resilience to purine shortage while identifying microtubules, MTAP, and immunoevasion deficits as therapeutic vulnerabilities
Promotion of HIV Clearance by Sensitization of HIV Reservoirs to Cell Death
No full textIntroduction: HIV integrates its proviral DNA into the host genome to establish persistent infection. To promote HIV clearance, we have designed an approach for selective elimination of host cells harboring replication-competent HIV (SECH), through inhibition of autophagy and anti-apoptotic molecules during viral reactivation. SECH approach can clear HIV-infected cells in approximately 50% humanized mice. However, the mechanisms for the resistance of reservoirs to depletion in mice with failure in HIV clearance are unclear.
Methods: We have performed single cell transcriptome analyses of HIV-infected T cells that escaped the treatments, in order to identify cellular pathways that could be targeted to facilitate the deletion of refractory HIV reservoirs.
Results: By single cell RNA sequencing analyses of T cell reservoirs resistant to SECH treatments, we found increases in pro-survival autophagy and glycolysis. Moreover, these resistant reservoirs expressed more epigenetic modifiers that repress HIV gene expression, while targeting such epigenetic repression promoted cell death in HIV-infected cells.
Discussion: Our results indicate that T cell reservoirs refractory to depletion maintain a delicate balance between low levels of HIV gene expression and evasion of cell death. This study suggests that targeting epigenetic repression of HIV is critical for the depletion of the viral reservoirs
Nrf2 Hyperactivation as a Driver of Radiotherapy Resistance and Suppressed Antitumor Immunity in Head and Neck Squamous Cell Carcinoma
No full textPurpose: Alterations in the KEAP1/NFE2L2 (NRF2)/CUL3 pathway occur in ∼20% of human head and neck squamous cell carcinomas (HNSCC) and are associated with resistance to standard-of-care therapy. However, this pathway\u27s role in radiotherapy resistance in HNSCC has not been well studied.
Experimental design: We generated genetically engineered mouse models and developed primary murine cancer cell lines harboring mutations commonly observed in human HNSCC, including inducible activation of PIK3CA and deletion of Trp53, with or without Keap1 loss. Primary tumors were initiated via 4-hydroxytamoxifen injection ± the tobacco carcinogen benzo[a]pyrene (BAP) into the oral buccal mucosa. Tumors were analyzed by Western blotting, IHC, and RNA sequencing and subjected to fractionated radiotherapy to investigate the role of the KEAP1/NRF2 pathway in radioresistance and modulation of the tumor-immune microenvironment.
Results: BAP exposure accelerated primary tumor formation within 1 month, with histologic analysis confirming invasive squamous cell carcinoma, validated by cytokeratin and differentiation marker expression. Primary cell lines derived from Keap1-haploinsufficient tumors exhibited upregulation of NRF2 target genes and a radioresistant phenotype, which was reversed after Nrf2 knockdown in vitro. Bulk RNA sequencing revealed that Keap1 haploinsufficiency correlated with NRF2 pathway activation, increased myeloid infiltration, and enhanced angiogenic signatures. In vivo, Keap1 haploinsufficiency promoted accelerated tumor growth and decreased survival. Finally, using fractionated radiotherapy, we showed that Keap1-haploinsufficient primary tumors were significantly more radioresistant than Keap1-proficient tumors, regardless of BAP exposure.
Conclusions: These data demonstrate that Keap1 haploinsufficiency in HNSCC is linked to unfavorable tumor-immune microenvironment, aggressive growth, and a radioresistant phenotype
Barriers and Timely Postoperative Radiation Therapy in Head and Neck Cancer
No full textImportance: Initiation of postoperative radiation therapy (PORT) within 6 weeks of surgery is associated with improved outcomes among patients with head and neck squamous cell carcinoma. However, the relationship of barriers to care with timely PORT is unknown.
Objective: To categorize barriers to timely PORT, evaluate the association of barriers to care with initiation of timely PORT, and describe the primary reason for delay among patients without timely PORT.
Design, setting, and participants: This prospective cohort study at a US academic medical center included adults with head and neck squamous cell carcinoma undergoing curative-intent surgery with an indication for PORT. Patients were recruited for the study from May 19, 2020, to November 6, 2023.
Main outcomes and measures: The primary outcome was initiation of timely PORT, defined as starting radiation therapy within 6 weeks of surgery. Barriers to PORT were prospectively collected via patient self-report and the electronic health record. Among patients who did not start PORT within 6 weeks of surgery, the primary reason for delay was defined as the singular barrier category that most directly led to the delay.
Results: Among 78 patients (mean [SD] age, 61.5 [10.8] years; 54 males [69.2%]), 32 patients (41%) initiated PORT within 6 weeks of surgery, and 46 patients (59%) did not initiate PORT within 6 weeks of surgery. Each additional barrier was associated with a decreased odds of initiating timely PORT (adjusted odds ratio, 0.81 [95% CI, 0.63-1.01]); patients with 5 or more barriers had a 76% reduction in the odds of starting PORT within 6 weeks of surgery relative to those with 0 to 2 barriers (adjusted odds ratio, 0.24 [95 CI%, 0.06-0.84]) on multivariable analysis. When analyzed by barrier category, patients with a perioperative adverse effects-related barrier were less likely to initiate timely PORT than patients without a perioperative adverse effects barrier (adjusted odds ratio, 0.17 [95% CI, 0.04-0.66]) on multivariable analysis. Among patients without timely PORT, the most common primary reason for delay was a barrier related to poor care coordination (19/46 [41.3%]).
Conclusions and relevance: In this prospective cohort study, patients with a greater number of barriers and those with a barrier related to the perioperative adverse effects category were less likely to initiate timely PORT. Among patients without timely PORT, the most common primary reason for delay was a barrier related to poor care coordination. Efforts to improve timely PORT should focus on decreasing the number of barriers, improving surgical quality, and enhancing care coordination
Virus-Specific T-Cell Therapy for the Management of Viral Infections in the Immunocompromised
No full textBackground: Immunocompromised individuals are at major risk for severe infectious complications. This is particularly relevant in the context of allogeneic hematopoietic stem cell transplantation (allo-HCT) - a treatment modality that has proven curative for a range of malignant and nonmalignant hematological diseases. However, transplant-associated immune suppression leaves patients susceptible to infectious complications from viruses such as cytomegalovirus (CMV), adenovirus (AdV), Epstein-Barr virus (EBV), and BK virus (BKV). While pharmacological agents are available to prevent and/or treat some of these viruses, they can be associated with significant toxicities and are often ineffective. To circumvent these issues, several groups have explored the clinical potential of adoptively transferred virus-specific T cells (VSTs) to prevent/treat virus-associated complications after allo-HCT or solid organ transplantation (SOT) and this review will provide an overview of these endeavors.
Summary: This review will focus on the progress that has been made over the past 30 years in the field of nonengineered VST manufacturing technologies and will summarize the clinical experience with VSTs, primarily in the posttransplant setting.
Key messages: Over the last 3 decades, adoptively transferred VSTs - both HCT donor and third party-derived - have been tested in numerous single and multicenter clinical trials and have unequivocally proven to be safe and associated with clinical activity
Nerve-to-Cancer Transfer of Mitochondria During Cancer Metastasis
No full textThe nervous system has a pivotal role in cancer biology, and pathological investigations have linked intratumoural nerve density to metastasis1. However, the precise impact of cancer-associated neurons and the communication channels at the nerve–cancer interface remain poorly understood. Previous cancer denervation models in rodents and humans have highlighted robust cancer dependency on nerves, but the underlying mechanisms that drive nerve-mediated cancer aggressivity remain unknown2,3. Here we show that cancer-associated neurons enhance cancer metabolic plasticity by transferring mitochondria to cancer cells. Breast cancer denervation and nerve–cancer coculture models confirmed that neurons significantly improve tumour energetics. Neurons cocultured with cancer cells undergo metabolic reprogramming, resulting in increased mitochondrial mass and subsequent transfer of mitochondria to adjacent cancer cells. To precisely track the fate of recipient cells, we developed MitoTRACER, a reporter of cell-to-cell mitochondrial transfer that permanently labels recipient cancer cells and their progeny. Lineage tracing and fate mapping of cancer cells acquiring neuronal mitochondria in primary tumours revealed their selective enrichment at metastatic sites following dissemination. Collectively, our data highlight the enhanced metastatic capabilities of cancer cells that receive mitochondria from neurons in primary tumours, shedding new light on how the nervous system supports cancer metabolism and metastatic dissemination