University Of Tx Md Anderson Can Ctr

NIH Research Projects · FY 2025 · 2021-02

PROJECT SUMMARY Lung adenocarcinoma (LUAD) is the most common cancer diagnosed in lifetime smokers of whom there are more than 90 million in the United States. Smokers with LUAD frequently (more than 25%) harbor somatic activating mutations in the Kras oncogene. Kras-mutant LUAD (KM-LUAD) displays very poor clinical outcome and inferior response to therapy. Despite the urgent need of new strategies for early treatment of this fatal disease, we still do not understand targetable changes that promote onset of KM-LUAD. Using a human- relevant genetically engineered mouse model comprised of tobacco exposure and high somatic mutation burdens including driver Kras variants, features that constitute a perfect storm for LUAD pathogenesis in humans, we identified significant progressive changes in gut microbiome composition that were coexistent with reduced levels of gut and circulating bacterial metabolites and closely associated with evolution of KM-LUAD. Similar microbial phenotypes were observed in mice exposed to combustible cigarette smoke (CCS). We further found in lungs of the mice up-regulation of pro-tumor inflammatory cues including activation of the IL-6 /STAT3 pathway which we have previously shown to promote KM-LUAD development by immune reprogramming. Also, we noted that lipocalin 2 (LCN2), a host defense antimicrobial protein that is released from cells during microbiome imbalance, was markedly progressively up-regulated in normal airway cells prior to onset of Kras-mutant preneoplasias and LUADs. Genetic deletion of Lcn2 in these mice markedly increased KM-LUAD development concomitant with global changes in the gut microbiome and heightened pro-tumor lung inflammation. Despite these insights, the interplay between the host microbiome and key immune responses in the pathogenesis of KM-LUAD are poorly understood. We hypothesize that the host microbiome (derived from the gut and possibly the lung) promotes tobacco-associated KM-LUAD development through activation of the IL-6/STAT3 pathway and changes in systemic and lung immune contexture. We will address our hypothesis using the following three aims. In Aim 1, using sequencing, metagenomics, as well as bacterial metabolite and immune profiling approaches, we will discern evolving microbiome changes that are functionally linked to tobacco carcinogen- and CCS-associated KM-LUAD development as well as probe downstream systemic and local (in lung) immunomodulatory effects including those on the pro-tumor IL- 6/STAT3 pathway. In Aim 2, we will determine the role of host antimicrobial and immunomodulatory cues mediated by LCN2 induction in KM-LUAD pathogenesis. In Aim 3, we will investigate chemopreventive and early therapeutic effects of microbiome intervention, alone or in combination with immunotherapy, against KM- LUAD. At the conclusion of our studies, we will have shed light on uncharted host processes in the evolution of KM-LUAD, paved the way for identification of new targets to guide chemoprevention and early detection of this fatal disease in smokers and contributed novel models for studying LUAD pathogenesis.

NIH Research Projects · FY 2025 · 2021-02

Project Summary Alzheimer's disease (AD) is a major health concern defined by pathologic changes in the brain that coincide with altered behavior and cognitive function. Animal models have advanced our understanding of AD, but these models artificially induce neuropathy to simulate the human disease. For instance, while amyloid- beta (Aβ) deposition occurs in most mammals, tau-positive neurofibrillary tangles (NFT) have only been identified in a few nonhuman species studied to date. Our research team recently discovered that chimpanzees, one of our closest genetic relatives, naturally develop both Aβ plaques and NFT, the pathological hallmarks of AD. In addition to AD pathology, elderly chimpanzees also develop cerebral amyloid angiopathy (CAA), a neurovascular condition found in 80% of AD patients associated with cognitive decline. Therefore, additional studies in chimpanzees could shed new light on the etiology of AD and CAA, leading to potentially new directions for therapeutic interventions. The overall goals of the proposed studies are to further examine the pathologic, epigenetic, and cognitive characteristics of aging, CAA, and AD in chimpanzees. In Aim 1, we will perform comprehensive pathologic analyses aimed at quantifying biomarkers of CAA and AD, including Aβ40 and Aβ42 plaque and vessel volumes, NFT density, pericyte and smooth muscle cell vessel volumes, neuron and synapse densities, and mitochondrial dysfunction. The collective neuropathologic measures will be examined in a sample of chimpanzees for which antemortem cognitive data is available, and the main focus will be determining which pathologic markers best predict individual variation in cognition. Moreover, we will test the correlation of AD and CAA pathologies with inflammatory processes, such as microglial activation and astrogliosis. In Aim 2, we will quantify epigenetic age in the chimpanzee population and evaluate whether chimpanzees with CAA or AD lesions demonstrate accelerated epigenetic aging in the brain relative to apes without pathology. We also will determine if epigenetic age is a better predictor than chronological age of changes in cognition, region-specific gray matter volume, and white matter integrity and connectivity. Finally, though previous studies have found cross-sectional age differences in cognition in chimpanzees, we will determine whether chimpanzees show longitudinal changes in cognition and whether any age-related loss in performance predicts the subsequent expression of AD pathology in this proposal. All biomaterials and cognitive data obtained in the proposed studies will be added to the National Chimpanzee Brain Resource and made publicly available to the scientific community through a web portal. The proposed studies, in their entirety, will fill an important gap in our knowledge about the comparative biology of aging and disease in chimpanzees and may provide critical translational insight into how those processes contribute to the progression of CAA and AD in humans. This information will provide crucial direction for future translational studies using rodent and nonhuman primate models.

NIH Research Projects · FY 2025 · 2021-02

ABSTRACT. Genomic deletions of major tumor suppressor genes are frequent events in cancer yet presently remain therapeutically unactionable for the purpose of precision oncology. Our lab has pioneered an innovative therapeutic paradigm known as collateral lethality, whereby genes neighboring a TSG locus encoding a key housekeeping enzyme are coincidentally deleted. We discovered that the metabolic vulnerabilities arising from such collateral deletions may be therapeutically exploited through inhibition of the enzyme’s redundant isoform. Emblematic of this framework are cancers harboring homozygous deletion of the glycolytic enzyme Enolase 1 (ENO1). As glycolysis is an essential bioenergetic process, ENO1-homozygous deleted cancers are entirely reliant on the ENO2 to perform glycolysis and ensure the cellular viability. Inhibition of ENO2 selectively kills ENO1-homozygous deleted the cancers while leaving normal tissues unperturbed. To pharmacologically act on this vulnerability, our lab has developed an ENO2-preferred inhibitor, HEX. As testament to the strong therapeutic viability of collateral lethality, we have shown that HEX is capable of completely eradicating ENO1- homzoygous deleted intracranial orthotopic models of glioblastoma in mice at concentrations well-tolerated in non-human primates. Such robust anti-neoplastic effects are unprecedented in the context of glioblastoma and speak to the power of the collateral lethality approach. One critique of the focus of collateral lethality is its scope: in the case of ENO1-deletions, only a small percentage of patients would be able to benefit. To broaden the therapeutic reach of collateral lethality, this proposal will focus on targeting ENO1-heterozygous deleted cancers, which comprise ~20% of all human cancers. This will be accomplished by adding tumor subtype-specific pro- drug moieties onto HEX to improve its delivery. While ENO1-heterozygous deleted cancers are deficient in total Enolase, they are not nearly as depleted as ENO1-homozygous deleted cancers are. As HEX is a negatively charged molecule, tumor-subtype specific pro-drug attachment onto HEX will not only enhance its cell permeability but will also improve its tumor specificity. Together, these two traits will enable drug dosing at lower concentrations to afford a therapeutic window sufficiently large to treat ENO1-heterozygous deleted cancers without the perturbing normal tissues. Overall, this proposal leverages the concept of rational pro-drug design to improve the specific of our core ENO2 inhibitor so that we may widen the therapeutic reach of collateral lethality.

NIH Research Projects · FY 2025 · 2021-02

SUMMARY / ABSTRACT With current treatment options, the five-year survival rate of patients with glioblastoma (GBM) is only 5%. Oncolytic viruses are promising treatments against solid tumors, including malignant gliomas. In a phase I clinical trial evaluating Delta-24-RGD, an oncolytic adenovirus characterized in our laboratory, 20% of recurrent GBM patients receiving the virus achieved a durable response, surviving more than 3 years from the time of treatment, suggesting the existence of a subgroup of patients who would respond to adenoviral treatments. The clinical trial also showed that the efficacy of Delta-24-RGD was due to not only direct tumor cell oncolysis, but also indirect activation of anti-tumor immune responses, a paradigm-shifting finding that radically repositions virotherapy as a type of immunotherapy. Therefore, understanding the interplay between the oncolytic effects of adenoviruses and the viral-mediated anti-glioma immune activation is critical in determining how to increase the efficacy of these promising agents. Our group generated and preclinically characterized an immune agonist-armed version of Delta-24-RGD, named Delta-24-RGDOX, which expresses the T-cell activator OX40L, which will be soon translated to the clinical setting. In this project, we aim to amplify the effect of Delta-24-RGDOX with the administration of inhibitors of the factors that maintain the immunosuppression characteristic of gliomas. Because indoleamine-2,3-dioxgenase (IDO) expression increases significantly after virus infection, we are particularly interested in developing strategies to downmodulate IDO during virotherapy. The catabolism of tryptophan by IDO has important metabolic effects in glioma cells. In addition, the metabolites of tryptophan, including kynurenine (Kyn), activate the aryl hydrocarbon receptor (AhR) that induces Treg differentiation and CD8+ T-cell dysfunction. The central hypothesis of this study is that therapy consisting of Delta-24-RGDOX in combination with IDO and AhR inhibitors will stimulate a cytotoxic immune effect and inhibit the suppressive immune response against the tumor cells, thereby providing a potential effective novel treatment for malignant gliomas. To test this hypothesis, we propose three aims: Specific Aim 1: Examine the activation of the IDO-Kyn-AhR pathway during the infection of gliomas with Delta-24-RGDOX oncolytic adenovirus; Specific Aim 2: Identify the metabolic and immune modifications in the tumor microenvironment produced by the inhibition of the IDO-Kyn-AhR pathway in gliomas treated with Delta-24- RGDOX; and Specific Aim 3: Test the combination of Delta-24-RGDOX and IDO/AhR inhibitors in pre- clinically relevant models of gliomas. This project is the next step in achieving our long-term goal of legitimizing viro-immunotherapy as standard treatment for malignant gliomas.

NIH Research Projects · FY 2025 · 2021-02

PROJECT SUMMARY/ABSTRACT Targeting the immune system to destroy cancer cells using immunotherapy has rapidly emerged as a promising avenue for treating cancer, and has resulted in robust clinical responses in a subset of patients. While the initial success stories have provided proof of concept that the immune system can be harnessed to treat cancer, the majority of patients do not achieve long lasting or even initial benefit, highlighting the need to better understand the barriers to successfully using the immune system to eliminate cancer cells. The focus of this proposal is non- small cell lung cancer (NSCLC), which has only shown 20-40% of patients having an objective response to immune based therapies to date. A major obstacle to improving current immunotherapies in lung cancer is a lack of understanding of the overarching T cell response during tumorigenesis. Indeed, few studies have been able to longitudinally dissect the CD8 T cell response in a physiological time frame in the native lung microenvironment. Previous work has identified a population of less dysfunctional T cells in the tumor that express the transcription factor T cell factor 1 (TCF-1), and it is this population that is thought to mediate productive anti-tumor responses. However, how to generate these cells when they are lacking, the developmental trajectories of these cells during tumorigenesis, and how to best target these cells for therapeutic purposes remain unclear. The goal of this project is to address these critical questions surrounding the TCF-1+ subset of anti-tumor CD8 T cells using an autochthonous mouse model of lung adenocarcinoma that recapitulates both the time scale and anatomical progression of human NSCLC. Utilizing cutting edge methodologies and techniques, including single cell RNA sequencing, parabiosis and proximity labeling, we will define the ontogeny, differentiation, function, and determinants that dictate the fate of responding anti-tumor TCF-1+ CD8 T cells. In Aim 1, we will build on our preliminary data demonstrating heterogeneity within the TCF- 1+ CD8 T cell compartment by elucidating functionality and transcriptional status of anti-tumor CD8 T cell populations. We will compare the transcriptomic data we generate in Aim 1 to existing human single cell RNA sequencing to determine the relevance of the CD8 T cell states we identify in our model. In Aim 2 we will determine the role of tumor-T cell interactions in T cell phenotype and fate using a proximity labeling system to identify CD8 T cells that have recently interacted with tumor cells. In Aim 3, we will define the relationship of lymph node and lung TCF-1+ CD8 T cells, and will attempt to therapeutically harness anti-tumor CD8 T cells within the dLN to seed more TCF-1+ CD8 T cells into the tumor. Taken together, our aims are positioned to redefine our understanding of the anti-tumor CD8 T cell response and potentially identify new therapeutic avenues to treat cancer.

NIH Research Projects · FY 2025 · 2021-02

Project Summary The lack of specific targets for the treatment of triple-negative breast cancer (TNBC) is a major challenge, as many TNBCs do not respond to cytotoxic chemotherapies. Immune checkpoint blockade (ICB) has yielded promising results in both advanced and early-stage TNBC and is expected to substantially improve the overall prognosis of patients with this disease. However, since TNBC is not inherently immunogenic, it is important to identify patients who would benefit most from immunotherapy and to identify agents that can prime the tumor microenvironment to enhance the therapeutic effects. TNBC is known to exhibit high levels of replication stress, which occurs when the DNA replication machinery encounters obstacles that impede the replication process. In normal cells, replication stress activates the replication stress response (RSR) to maintain genome integrity. Defective RSR allows cells with high replication stress to survive and proliferate. Recently, we have identified a gene signature that represents defects in RSR (RSRD). We found this RSRD signature to be highly enriched in TNBC cells. Furthermore, RSRD-high TNBC cells accumulate cytoplasmic DNA and induce STING-dependent cytokine production, which is required for the effectiveness of ICB. Intriguingly, the RSRD signature score correlates perfectly with the response of TNBC to ICB in syngeneic mouse models, and it accurately predicts ICB response across 5 low–mutation-burden tumor lineages. All these intriguing findings support the hypotheses that RSRD may act as a key determinant of ICB outcomes in low–mutation-burden cancers, including TNBC, and that RSRD-enhancing drugs may sensitize ICB-resistant TNBC to immunotherapy. These hypotheses will be tested via 3 specific aims. (1) To determine how the immune microenvironment is modified in RSR-defective TNBC. We will use a highly multiplexed imaging mass cytometry panel to determine how RSRD remodels the immune microenvironment of TNBC and induces susceptibility to ICB. In addition, we will manipulate the RSR status in TNBC cells to assess the relationship between RSR defects and immunotherapy response. (2) To identify causative drivers of RSRD-high–mediated ICB responsiveness in TNBC. Our preliminary studies suggest that RSR defects may drive immunotherapy response through accumulation of immunostimulatory cytosolic single-stranded DNA (ssDNA). We will, therefore, seek to manipulate the cytosolic ssDNA level in TNBC models to determine whether cytosolic ssDNA is indeed a causative driver of ICB responsiveness in TNBC. In addition, to understand why our RSRD gene signature predicts response to ICB in TNBC, we will apply an in vivo CRISPR screen to determine what transcriptional changes contained within our RSRD gene signature cause this response. (3) To develop novel combination therapy to convert RSRD-low TNBC to RSRD-high to improve their response to ICB. Using cutting-edge systems and bioinformatics approaches, we have identified many potential RSRD-inducing agents. We will assess the 6 most promising candidates and identify the best candidate compound that can effectively sensitize RSRD-low TNBC to ICB.

NIH Research Projects · FY 2025 · 2020-12

PROJECT SUMMARY Chronic pain is a serious condition which is produced and maintained by a variety of different mechanisms, many of which remain poorly understood This has led to difficulties in providing effective treatments. One key mechanism underlying chronic pain conditions, such as nociplastic pain, is central sensitization in which plastic changes at the level of the spinal cord contribute to and maintain hypernociception. To add further complexity, we have found that different mechanisms underlie the acute, transition, and chronic phases of central sensitization in our model of nociplastic pain. In order to better understand, and therefore successfully treat, chronic pain conditions, the mechanisms underlying these three phases, as well as resolution of chronic pain, must be elucidated. Already, I have shown that excitation of capsaicin-sensitive afferents attenuates the response of sGABAn to low-intensity synaptic stimulation. Furthermore, I have shown that spinal microglia and inflammation mediate the chronic phase of central sensitization underlying a nociplastic pain state. In the F99 phase of the proposed project, I will further characterize the neuronal circuitry underlying the acute and maintenance phases of central sensitization, focusing on 1) how nociceptor activation and subsequent release of reactive oxygen species impair Aβ-fiber-evoked sGABAn activation in the acute phase, 2) whether such impairment allows low-threshold afferent inputs to activate spinal microglia to drive the transition phase, and 3) if reactive microglia and inflammatory mediators maintain the impairment in the chronic phase. In the K00 phase, I will move to a prominent pain research laboratory to investigate the mechanisms by which pro-resolution lipid mediators, such as resolvins, are dysregulated in pain conditions, and their effect on nociceptive circuitry. Additionally, I will investigate how resolvins and the circuitry which they effect may be manipulated to convert chronic pain back to resolving pain. Overall, the proposed project will provide key understanding of the chronification and resolution of nociceptive neural circuit sensitization. These will ultimately reveal new therapeutic targets, allowing for the development of better pain treatments.

NIH Research Projects · FY 2026 · 2020-12

ABSTRACT Estrogen receptor-positive (ER+)/HER2-negative breast cancer represents 70% of all breast cancer cases. Surgery and adjuvant/neo-adjuvant endocrine therapy (ET) are mainstays of treatment in early stage disease. However, some patients receiving ET for early stage ER-positive breast cancer only have a partial reduction in their risk of recurrence and mortality, and those with advanced breast cancer (ABC) either progress shortly after initiating therapy (intrinsic resistance), or ultimately experience progression over time (acquired resistance). CDK4/6 inhibitors (CDK4/6is) with ET are currently considered standard of care for patients with advanced ER +/HER2 negative breast cancer. A key feature of CDK4/6 inhibition is the cell cycle inhibitory response it elicits through induction of senescence, which can be escaped resulting in cells readily re-entering the cell cycle as soon as drug is withdrawn. Senescent cells secrete interleukins, inflammatory cytokines, and growth factors, which comprise the senescence-associated secretory phenotype (SASP) that affects surrounding cells and promotes tumor growth. The most prominent SASP cytokine is interleukin-6 (IL-6), which is associated with metastasis, tumor aggressiveness and decreased survival. IL-6 activates STAT3, which is associated with a more aggressive phenotype and resistance to many therapies [chemotherapy, targeted therapy, and immune checkpoint inhibitor therapy]. We developed CDK4/6i (i.e. palbociclib) resistant breast tumor cell line models and their molecular analysis showed that resistant cells adapt to palbociclib treatment by upregulation of IL-6 and activation of STAT3 (phosphorylation of STAT3 on Y705, pY-STAT3). Treatment of the resistant cells with an oral, small-molecule inhibitor of STAT3 (TTI-101) decreased cell viability by >25-fold and resulted in decreased levels of pY-STAT3 with concomitant decreases in (i) stem-like (CD44high/CD24low) population, (ii) primary and secondary mammosphere formation, (iii) the EMT pathway. Furthermore, TTI-101 treatment of mice bearing patient derived xenografts (PDX) that express a similar gene expression signature as palbociclib-resistant cell lines resulted in a marked decrease in tumor volume, prolonged tumor-free survival and downregulation of serum IL-6 levels. We hypothesize that inhibition of IL-6 and/or STAT3 can reverse acquired CDK4/6i resistance in vivo transgenic and PDX models and in patients who have progressed on CDK4/6i based therapy. We propose a coordinated mechanistic, preclinical and early phase clinical testing strategy to develop biomarker-qualified therapy for the clinical need to overcome CDK4/6i resistance. To address these goals we will 1): Determine the mechanism of IL-6 induction by long term CDK4/6 inhibition in vivo and the impact of IL-6 on tumorigenesis in transgenic mouse models; 2) Conduct pre-clinical trials in palbociclib resistant PDX and transgenic mouse models to determine if inhibition of STAT3 and IL-6 can improve the survival of mice with CDK4/6i resistant tumors; and 3) Perform a Phase IB/II clinical trial of adding TTI-101 to standard of care palbociclib and aromatase inhibitor upon progression.

NIH Research Projects · FY 2025 · 2020-12

Project Summary Ferroptosis is an iron-dependent form of nonapoptotic cell death that is induced by excessive lipid peroxidation. Previous studies by us and others identified ferroptosis as a natural tumor suppression mechanism and showed that ferroptosis inactivation, like apoptosis inactivation, contributes to tumor development. Recently, we and others also showed that radiotherapy (RT) can potently induce ferroptosis and suggested that ferroptosis inducers (FINs) can be used in RT to overcome radioresistance. However, the underlying mechanisms of ferroptosis in radioresistance and the exact cancer or genetic contexts in which to target ferroptosis in RT still remain largely unexplored. This application aims to determine the mechanisms by which ferroptosis inactivation contributes to radioresistance in KEAP1-mutant lung cancer cells and to assess the combination of RT and FINs in treating KEAP1-mutant lung cancers. KEAP1 is commonly mutated in lung cancer, and KEAP1-mutant lung cancers are resistant to RT. KEAP1 mutation or deficiency in lung cancer stabilizes NRF2 and promotes an NRF2-mediated antioxidant response. Our recent publication and new preliminary data support our central hypotheses that (i) KEAP1 deficiency promotes radioresistance largely through inhibiting ferroptosis, and KEAP1 regulates ferroptosis through NRF2 transcriptional targets SLC7A11 and other unidentified downstream targets; and (ii) combining RT and FINs that inactivate SLC7A11 (or other potential ferroptosis inhibitors identified from our studies) is an effective therapeutic strategy to overcome radioresistance in KEAP1-mutant lung cancers without causing significant damage in normal tissues. To test our hypotheses, we will pursue the following specific aims: Specific Aim 1: To determine the mechanisms by which KEAP1 regulates ferroptosis and radioresistance in lung cancer cells. Specific Aim 2. To determine the effectiveness of combining FINs with RT for treating KEAP1-mutant lung cancer. Our proposed studies are expected to identify novel mechanisms of ferroptosis and radioresistance and to identify effective new therapeutic strategies to overcome radioresistance in lung cancer treatment. Our proposed studies will have a significant impact on both our understanding of the fundamental mechanisms of ferroptosis and radiation biology and our ability to target ferroptosis-related radioresistance in cancer treatment.

NIH Research Projects · FY 2025 · 2020-12

Project Summary: RUNX1 is the DNA-binding subunit of the core binding factor (CBF) complex and a master-regulator transcription factor, which is involved in normal and malignant hematopoiesis. Somatic, heterozygous RUNX1 mutations commonly occur in Myelodysplastic Syndrome (MDS) (10%), as well as in secondary (s) or de novo AML (~10%). Germline mutations in RUNX1 cause the highly penetrant (~40%) autosomal dominant, Familial Platelet Disorder (FPD), which can evolve into myeloid malignancy (FPD-MM). Majority of mutant (mt) RUNX1 behave mostly as loss of function mutations, conferring relative therapy-resistance and poorer survival in patients with AML. Consequently, there is a strong unmet need to develop novel therapies for AML expressing somatic or germline mtRUNX1. Our preliminary studies have demonstrated for the first time that shRNA- mediated knockdown of RUNX1 (mutant and wild-type) or disruption of its binding to CBFβ induces greater lethality in AML progenitor cells (HPCs) expressing mtRUNX1 compared to wild-type (wt) RUNX1. We also found that the +24kb enhancer (eR1) within the intragenic super-enhancer (SE) of RUNX1 regulates its transcription in AML cells. The chromatin reader BET (Bromodomain Extra-terminal) protein (BETP) BRD4 promotes transcription of RUNX1 and its targets. BRD4 degradation or eviction from chromatin, or gene-editing of the +24kb RUNX1 eR1, induces lethality in AML cells. By determining and utilizing the mRNA signature from RUNX1-depleted (by shRNA) AML cells, we queried, through LINCS1000-CMap (Connectivity Mapping) analysis, for expression mimickers (EMs). We identified novel EMs that repress RUNX1 and its targets and induce significantly more apoptosis of AML cells expressing mtRUNX1 versus wtRUNX1. Therefore, the hypothesis motivating our studies is that knocking down of levels of RUNX1 and its targets will induce lethality not only in AML blasts expressing somatic mtRUNX1 but also in FPD/MM HPCs expressing germline mtRUNX1. The specific aims of studies proposed are: AIM 1: To determine impact on active enhancers, transcriptome and pre-clinical in vitro and in vivo efficacy of BETP antagonist along with its co-repression of RUNX1, BCL2 and CDK6, alone or in combination with BCL2 or CDK6 inhibitor, in AML blasts and patient- derived xenograft (PDX) models expressing somatic mutant RUNX1. Additionally, we will evaluate pre-clinical efficacy of co-targeting CRISPR-Cas9 screen-discovered top ‘druggable’ dependencies along with BETP antagonist against AML blasts expressing somatic mtRUNX1. AIM 2: To elucidate pre-clinical in vitro and in vivo efficacy of the EMs homoharringtonine (omacetaxine) or fedratinib alone and in combination with BETP antagonists against patient-derived AML blasts and PDX models expressing somatic mtRUNX1. AIM 3: To determine pre-clinical in vitro and in vivo efficacy of selected EMs that repress RUNX1 and its targets against patient-derived HPCs from FPD-MM expressing germline mtRUNX1 and other somatic co-mutations versus HPCs from RUNX1-FPD expressing only germline mtRUNX1.

NIH Research Projects · FY 2025 · 2020-12

Project Summary Diffuse large B-cell lymphoma (DLBCL) is the most common form lymphoma and is conventionally treated with a combination of chemotherapeutics with the anti-CD20 antibody, Rituximab. Although more than half of patients can be cured with this approach, the remainder have a dire prognosis with a short survival. Despite the variability in patient outcome, there are currently no routinely utilized molecular biomarkers that can be employed for risk stratification or to direct a specific therapy. That is, precision medicine does not currently exist for DLBCL. We have identified a genetic alteration on the q-arm of chromosome 18 (18q) that is associated with an aggressive subtype of DLBCL, and defined the TCF4 and BCL2 genes as critical targets at this locus. The BCL2 gene encodes an important oncogene that prevents cell death, and can be targeted with the inhibitor Venetoclax. The TCF4 gene encodes a transcription factor protein that we have found to drive key malignant properties of lymphoma, such as promoting the expression of the MYC oncogene and the B-cell receptor. In addition, we have defined a way to eliminate TCF4 expression using a novel type of protein-degrader molecules that are directed towards BET proteins. This therefore provides an exciting rational therapeutic avenue for targeting TCF4. We hypothesize that combining this with an inhibitor of BCL2 will target both genes that are activated by 18q alterations, and provide a precision medicine approach for treating this aggressive subset of DLBCL. Here, we are proposing to investigate the function of 18q alterations in DLBCL and validate the mechanism by which we believe this genetic event leads to lymphoma. We will also perform pre-clinical investigation of combinations of BET and BCL2 inhibitors for the specific therapeutic targeting of 18q alterations. Together, this work will advance our understanding of DLBCL disease biology and may lead to advances in precision medicine for this disease.

NIH Research Projects · FY 2024 · 2020-09

PROJECT SUMMARY/ABSTRACT Chronic pain and the addictive effects of opioids used to control pain are major health problems affecting millions of Americans. Validation of novel targets for the safe treatment of chronic pain is urgently needed. We identified peptidase inhibitor 16 (PI16) as a novel regulator of chronic pain in an unbiased RNA seq screen. PI16 is a putative peptidase inhibitor that has not been studied in the context of pain. We showed that male and female Pi16-/- mice are protected against mechanical allodynia in the spared nerve injury (SNI) and paclitaxel models of neuropathic pain. Along the neuraxis, PI16 is only detectable in fibroblasts around peripheral nerves (perineurium), and in the meninges of dorsal root ganglia (DRG), spinal cord, and brain, but not in neurons, glia or leukocytes. . PI16 levels in perineurial and DRG meningeal fibroblasts increase during neuropathic pain. The overall objective of this project is to validate PI16 as a novel target for the treatment of chronic pain using mouse models and human tissues of neuropathy patients and controls and to identify the underlying mechanisms. Our central hypothesis is that increased PI16 secretion by DRG meningeal and perineurial fibroblasts promotes chronic pain by increasing blood nerve barrier (BNB) permeability and leukocyte trafficking into nerve and DRG. The significance is in the validation of PI16 as a novel, potentially druggable, regulator of chronic pain and the discovery of fibroblasts as key regulators of chronic pain. We propose the following three specific aims: 1. Validate the key role of PI16 in chronic pain. In two independent laboratories, we will test the hypothesis that genetic deletion of Pi16 in male and female mice protects against chronic pain in well-established models of chronic pain. 2. Investigate expression and regulation of PI16 in fibroblasts around mouse DRG and mouse and human peripheral nerves. The hypothesis is that PI16 production by fibroblasts in DRG meninges and perineurium is increased via a TGFβ− and Epac1-mediated pathway to promote chronic pain. We will use tissues from the neuraxis in mouse pain model and nerves from humans with neuropathic pain. 3. Determine the contribution of PI16 to blood nerve barrier integrity in mouse pain models and in a human in vitro model. Using a model of the human BNB, we will test the hypothesis that PI16 increases BNB permeability and leukocyte transmigration. Using co-immuno-precipitation and mass spectrometry we will identify novel PI16 targets. This proposal is conceptually innovative because successful completion will validate PI16 as a novel key regulator of neuropathic and inflammatory pain and establish a novel role of perineurial fibroblasts in regulating BNB function with major consequences for chronic pain. The expected findings are significant because they will advance our fundamental understanding of cellular and molecular mechanisms that contribute to chronic pain and will identify a novel target for treatment of pain that is not expressed in the brain, and therefore is unlikely to lead to addiction.

NIH Research Projects · FY 2024 · 2020-09

PROJECT SUMMARY/ABSTRACT: Quantitative PET Imaging of Hepatocellular Carcinoma Clinical decisions regarding the treatment of patients with hepatocellular carcinoma (HCC) remain largely guided by conventional, anatomical imaging modalities. These methods, namely magnetic resonance imaging (MRI) and x-ray computed tomography (CT), provide little information about the cellular and molecular underpinnings of individual tumors. HCC is the most common primary tumor of the liver and represents a major healthcare challenge in the United States (US) and elsewhere. The American Cancer Society estimates diagnosis of greater than 42,000 new cases of liver cancer in the US this year. In contrast to cancers more frequently diagnosed in the US and for which precision cancer medicine is routinely employed, such as colon or breast, incidence of liver cancer and liver cancer-associated deaths are both increasing. Improved tools to detect HCC at early, potentially curable stages, and tools to predict future tumor behavior are urgently needed. Molecular imaging with positron emission tomography (PET) is uniquely poised to provide those tools, yet novel tracers are required. The sensitivity of routine 18F-FDG PET, the most commonly utilized approach in clinical oncology, is limited in HCC, and other tracers that exhibit greater potential, such as 11C-acetate, suffer technical limitations that prevent their broad clinical use. The overarching goal of this application is to clinically evaluate an innovative PET imaging tracer that has the potential to personalize decision making in the care of patients with HCC. We propose to conduct the first quantitative imaging clinical trial of (S)-4-(3-[18F]fluoropropyl)-L-glutamic acid (18F-FSPG) PET in the setting of HCC. As an emerging PET tracer reflecting tumor glutamate transport, 18F-FSPG PET has shown clinical safety and efficacy in multiple tumor settings, including breast, lung, and brain cancer. Our preliminary data in a pilot cohort of Vanderbilt patients, as well as a pilot clinical study conducted in Asia (n = 5), suggest the feasibility of using 18F-FSPG PET to improve the detection of HCCs even among cirrhosis, a comorbidity that diminishes the effectiveness of conventional imaging approaches. Our study has three Specific Aims. In patients undergoing surgery for treatment of HCC, we will (1) evaluate the relationship between 18F-FSPG PET, pathology and cancer metabolism; (2) compare 18F-FSPG PET with standard-of-care (SOC) diagnostic imaging in patients with HCC and benign liver lesions; and (3) compare uptake of 18F-FSPG with 11C-acetate and 18F-FDG in HCC and background liver. This study has the potential to establish a new role for non-invasive molecular imaging in the delivery of individualized cancer care for patients with HCC.

NIH Research Projects · FY 2025 · 2020-09

Abstract The incidence of pancreatic adenocarcinoma (PDAC) is steadily increasing while most treatment modalities remain ineffective. Therefore, it would not be a surprise to learn that PDAC is one of the top-4 causes of cancer- related mortality. What is most striking about this malignancy is that even if detected at early stages, outcomes remain poor. It is well known that pancreatic cancer is characterized by an immunosuppressive environment, already found surrounding premalignant lesions or pancreatic intraepithelial neoplasia (PanIN), which has been postulated as one of the main reasons for the lack of response to most therapies. However, the regulatory signals that precede and support the development of this suppressive TME are not well characterized. The objective of this grant extension is to characterize the gut cellular compartments and mechanisms implicated in the intestinal IL-17 signaling dependent regulation of the gut microbiome and tumor growth and potential avenues to reverse it through immune checkpoint blockade and microbial interventions. Our laboratory found that IL- 17-secreting immune cells play an important role in promoting pancreatic tumorigenesis in genetically engineered mouse (GEMM) models of pancreatic cancer. Further, we revealed IL-17-IL-17RA signaling specific to the gut epithelium plays a key role in modulating tumor growth through microbial regulation. We now plan to characterize the cellular compartment within the intestinal epithelium responsible for modulating IL-17/IL-17RA mechanisms. GEMM models with specific IL-17RA deletion in Intestinal Stem Cells and Secretory Progenitor cells will be used to assess the cellular compartment regulating IL-17 effects (Aim 4). Finally, we have recently found that mice with global elimination of B7H4 presented higher CD8+ T cells pancreatic infiltration and, when using therapeutic antibodies blocking B7H4 in combination with aPD1 immunotherapy in PDAC orthotopic models, a strong immune remodeling occurred. We now plan to definitively address the therapeutic effect of B7H4 inhibition alone and in combination with immune checkpoint blockade in PDAC (Aim 5). Achieving our goals will not only help us better understand immunological as well as microbial mechanisms implicated in pancreatic tumorigenesis but will also result in practical novel interventions with either monoclonal antibodies, narrow spectrum antibiotics or microbial transplants that would have a direct impact in preventing and/or treating this deadly disease.

NIH Research Projects · FY 2024 · 2020-09

Project Summary/Abstract PTEN is one of the most frequently inactivated tumor suppressor genes across all cancer types. The loss of PTEN activates PI3K/AKT, which inhibits GSK3β, thereby stabilizing Myc and contributing to oncogenesis. Myc recruits histone acetyltransferases to increase chromatin accessibility of target genes involved in both cell proliferation and apoptosis. Among these histone acetyltransferases, the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex preferentially acetylates histone H3 lysine 9 and histone H4 lysine 16 to activate gene expression. A pan-cancer analysis of mutually exclusive gene inactivation patterns identified a previously uncharacterized long non-coding RNA (lncRNA) as synthetic essential in the context of PTEN deficient cancer. Preliminary studies suggest that this lncRNA inhibits SAGA-mediated histone acetylation, thereby inhibiting Myc transactivation of target genes. PTEN and lncRNA double-knockout SF-763 glioma cells showed Myc pathway enrichment, impaired cell viability, and pronounced aneuploidy, which was not observed in wild-type or single knockout cell lines. We hypothesize that inhibition of SAGA-mediated acetylation by this lncRNA inhibits Myc transactivation of pro-apoptotic target genes and Myc-driven endoreduplication, thereby promoting cancer survival. This proposal will investigate the potential of targeting the poorly studied non-coding genome for cancer treatment, advance our knowledge of the role of histone acetylation on cancer genomic stability (widely targeted using genotoxic drugs and radiotherapy), and describe a novel mechanism for the regulation of Myc's dual functions in proliferation and apoptosis. We will verify lncRNA expression in cell lines from various cancer types and in clinical samples to validate the pan-cancer relevance and translational potential of this study, respectively. Annexin V and caspase 3/7 assays will be used to assess the hypothesis of Myc-driven apoptosis. Endoreduplication will also be probed using BrdU incorporation into colcemid-arrested cells. Chromatin isolation by RNA purification and chromatin immunoprecipitation sequencing will be used to demonstrate how the lncRNA inhibits histone acetylation by SAGA. To assess the role of the lncRNA in vivo, we will functionally validate its putative mouse homolog and generate a genetically engineered mouse model to characterize its effects on tumor development. The lncRNA knockout allele will be bred into a Qki;Pten;Trp53 glioblastoma mouse model to assess the effects of lncRNA suppression in the context of Pten deletion. The training plan will address gaps in the applicant's research and clinical abilities, ensuring that he can successfully complete the proposed work and preparing him for the next stage of his career. The training will be completed in Dr. Ronald DePinho's lab at MD Anderson, where the applicant will have access to the resources, facilities, and, most importantly, colleagues that will nurture his continuing development and growth into a physician-scientist.

NIH Research Projects · FY 2024 · 2020-09

Abstract The development of a high-throughput biotechnology highly relies on relevant computational methods for systematic optimization and data analysis. On the other hand, the development of bioinformatics methods requires in-depth understanding of the biological systems and the experimental protocols. The long-term goal of our lab is to develop computational methods that can be seamlessly integrated with high-throughput experiments to address biological questions, with a focus on transcriptional and epigenetic regulations. Understanding protein functions is a fundamental aim in biology. The recent advances of CRISPR screening techniques have enabled functional studies of proteins in a high-throughput manner, leading to novel discoveries beyond the capacity of traditional methods. During the next five years, our short-term goal is to develop solutions to boost the utilization of high-throughput CRISPR screens for protein functional analysis. To achieve this goal, we propose three research topics: 1) Prediction of sgRNA knockout effects for improved sgRNA library design in CRSIPR screens. This will address the bioinformatics needs in the design of CRISPR screens; 2) Protein domain analysis using CRISPR tiling-sgRNA screens. This will lead to innovative solutions for the studies of protein domain and structure. 3) Inference of transcriptional regulatory networks from CRISPR screen and -omic data. This will lead to the development of new methodology to address an open problem involving protein-protein interactions and regulations of transcription factors and epigenetic regulators. Collectively, the proposed project will contribute new methods to enrich the toolbox for protein functional analysis, and will provide novel insights into the fields of transcriptional and epigenetic regulations.

NIH Research Projects · FY 2025 · 2020-09

PROJECT SUMMARY/ABSTRACT Although concurrent chemoradiation (CRT) improves the overall survival for head and neck cancer (HNC) patients, it is associated with debilitating toxicities (e.g., mucositis, dysphagia, and fatigue), which may lead to increased healthcare utilization (e.g., emergency department (ED) visits, feeding tube (FT) placements) during and after treatment. In light of the extremely high treatment-related burden, HNC patients need extensive and persistent care and support from their families. Patients' family caregivers are their most important and valued source of support and care; yet, caregiving is physically and emotionally taxing. In fact, family caregivers report high rates of psychological distress, fatigue, and sleep disturbances, which may not only compromise their own quality of life but also the quality of care they are able to provide to the patient. Therefore, evidence-based, dyadic supportive care programs targeting both patient and caregiver outcomes are urgently needed. To address critical knowledge gaps and build upon our pilot work, we propose an efficacy trial of a 6-week dyadic yoga (DY) intervention targeting patient health utilization and caregiver QOL outcomes. The proposed research will randomly assign patient-caregiver dyads to either a dyadic yoga (DY) or usual care (UC) control group. To increase accessibility, the intervention will be delivered via video-conferencing following our pilot- tested procedures. Patients and caregivers will be assessed at baseline (prior to randomization and starting CRT) and then again, at the end of treatment and 1, 3, and 6 months later. During the treatment period, we will assess patients and caregivers' symptoms on a weekly basis. At the 3-month follow-up assessment, we will also collect qualitative samples to further understand participants' experiences. We will integrate data from institutional records with self-report measures to evaluate efficacy, estimate costs and assess the cost- effectiveness of the DY intervention relative to UC for both patients and caregivers. Based on our exciting pilot findings, we propose a mediational model hypothesizing that the intervention will impact patient and caregiver outcomes via improved symptom burden, objective physical function, and relationship well-being and reduced pharmacological management using quantitative and qualitative methods. Thus, this innovative and scientifically rigorous design will address imperative hypotheses that are highly relevant to the clinical care of a vulnerable patient-caregiver population. The knowledge gained from this randomized controlled trial will advance the science of behavioral medicine, and, ultimately, inform the clinical care of a vulnerable and understudied population. .

NIH Research Projects · FY 2024 · 2020-09

Project Summary/Abstract Primary and metastatic central nervous system tumors (CNS) are associated with a high degree of morbidity and mortality. There is a need for new and more effective strategies for diagnosing, treating and monitoring patients with primary and metastatic CNS tumors. Methodologies that address the need for molecular information that is required for the use of precision medicine and targeted therapies, in patients with CNS tumors, are limited. A liquid biopsy assay will facilitate early molecular characterization and monitoring of patients with CNS tumors and will revolutionize patient management. Studies have shown that blood is not a suitable fluid for the detection of tumor-derived biomarkers in patients with CNS malignancies. In contrast, cerebrospinal fluid (CSF), due to its proximity to the brain parenchyma, is a source of informative biomarkers (e.g., circulating tumor DNA (ctDNA) and metabolites). We hypothesize that it is possible to perform pre- operative molecular characterization and monitoring of patients with CNS tumors by analyzing ctDNA and metabolites in the CSF. Moreover, our prediction is that the levels of these biomarkers will correlate with tumor burden. We anticipate that quantification of these biomarkers in the CSF will facilitate monitoring patients with CNS cancer for tumor recurrence and response to therapies. Our preliminary experiments show that we can isolate ctDNA from small volumes of CSF and detect mutations by next generation sequencing (NGS) and droplet digital PCR (ddPCR), at a mutant allele frequency of 0.25% and 0.1%, respectively. We have also identified tumor-specific metabolic signatures in the CSF, and our data shows higher levels of D-2- hydroglyglutarate in the CSF of patients with CNS tumors harboring an IDH1/IDH2 mutation. We propose to pursue two specific aims to develop a CSF-liquid biopsy assay: (1) Validation of a next generation sequencing (NGS) assay to quantify tumor DNA in CSF; (2) To perform metabolomic analysis of ~125 tumor-derived metabolites in CSF. This multi-platform approach will allow comparisons of sensitivity and specificity among various methodologies and cross correlation of results between platforms. Volumetric analysis of CNS lesions in MRI will allow us to evaluate the potential of each biomarker for quantifying CNS tumor burden. We anticipate that these studies will culminate in the clinical implementation of a liquid biopsy assay to facilitate diagnosis and the use of targeted therapies in adult of pediatric patients with primary or metastatic CNS tumors.

NIH Research Projects · FY 2024 · 2020-09

Project Summary/Abstract Flow Cytometry, Mass Cytometry, Cell Sorting, and Imaging are essential tools for a wide range of methodologies aimed at understanding complex single cell proteomic and genomic cancer research. The instrumentation involved is large, complex, and can be difficult to maintain and operate. As such, a targeted core facility is critical for a Comprehensive Cancer Center such as MD Anderson. The FCCIF, est. 1982, provides these services. Since the last CCSG renewal (2012) 404 cancer center members from all 16 cancer center programs have used the facility and produced 604 publications. Many of the hot topics in cancer biology currently stem from immune cell interaction with the tumor cell; immunephenotyping is an in demand field of research that requiring a unique high plex assay. This requires a specialized imaging or cytometry approach and the FCCIF has specifically acquired two different platforms because of their diversity and flexibility. These platforms are the Vectra Multispectral imaging system and the CyTOF (suspension and imaging) Mass Cytometers. The FCCIF provides a common source of state-of-the-art expertise and technical skills to support the varied research efforts of MD Anderson investigators. The FCCIF provides a comprehensive service to all of the institutional investigators regardless of prior expertise. Dr. Jared K. Burks (author of this R50, co-Director of the FCCIF-NC) provides critical services including: 1) education, 2) consultation on needed technological approach, 3) training on equipment use, analytics, and proper experimental design. I identify and acquire novel technologies for use by MDACC investigators and I provide support in a manner to ensure success and mitigate pitfalls. I am expected to develop new strategies and technologies to meet the research needs of our faculty. A few examples of what I have currently been working on is the Vectra Polaris Multispectral Microscope, Helios and Hyperion Suspension and Imaging CyTOFs. The Polaris has operated on average 13.5 hours per day for the last year. The CyTOFs are reporting 5090% growth since the last CCSG renewal. These results stem from mitigating the pitfalls, making the technologies approachable and affordable, and supporting the researchers throughout the process all the way to publication. Collaborations, both academic and industry, have resulted to develop or test novel applications. The models we have created to support these technologies have and will continue to be shared with others operating the technologies. We are highly involved with both developing and standardizing new technologies for use at MD Anderson and with our facilities and researchers implementing them worldwide.

NIH Research Projects · FY 2024 · 2020-09

PROJECT SUMMARY/ABSTRACT Our proposal is in keeping with the objectives of the RFA to continue the excellent ongoing studies of the consortium (CPDPC) to study the relationship between Chronic Pancreatitis (CP), Diabetes (DM) and Pancreatic Cancer (PDAC). The Principal Investigators of this proposal (Drs. Chari and Maitra, both currently based at UT MD Anderson Cancer Center, UTMDACC) have played key and substantial roles in the first cycle of the CPDPC. First, they have served as co-leaders of the DM-PDAC working group, which has been responsible for the design and conduct of the ongoing NOD study, which was inspired by a series of seminal observations made by Dr. Chari in the 2000s. Second, Dr. Maitra has served as Co-PI of the Data Management and Coordination Center (DMCC) of the CPDPC, which provides him with extensive familiarity with the inner workings of data management and oversight required for accrual to NOD and other prospective cohorts. Third, Dr. Chari was previously the site Co-PI of Mayo Clinic site, which has contributed to all aspects of CPDPC in the last cycle. From the experience of the past 4.5 years, it is clear that successful recruitment of subjects to these studies requires a mix of tertiary care hospitals (for PROCEED and DETECT cohorts), combined with access to large primary care healthcare systems with integrated electronic medical record systems, information technology (IT) support and infrastructure (for the NOD study). To this end, an Alliance of Texas and Louisiana investigators and institutions overseen by the PIs at UTMDACC will recruit to ongoing CPDPC cohort studies. In addition, we propose 6 ancillary studies that are ideally suited for performance by a collaborative consortium and significantly advance our understanding of the interconnected pathologies of CP, PDAC and DM. In accordance with the RFA, the Specific Aims of our proposal are to: Aim 1 a) Recruit subjects for PROCEED study: This will occur at the University of Texas Health Sciences Center, Houston (UTHSC-H) and Memorial Hermann Health System, both large volume gastroenterology practices that are well positioned to recruit patients for the PROCEED Study. b) Recruit subjects for the DETECT study: The UTHSC-H will recruit patients for DETECT study c) Recruit subjects for the NOD Study: The recruitment will occur through the Ochsner Clinic, Louisiana, a large, integrated primary health system in Louisiana, which is also highly enriched for underrepresented minority population of African Americans, who are known to harbor a preponderance of both DM and PDAC. Aim 2) Perform a series of innovative ancillary studies to examine the association among CP, DM and PDAC: 6 such studies are outlined in this proposal.

NIH Research Projects · FY 2024 · 2020-09

PROJECT SUMMARY Small cell lung cancer (SCLC) is an aggressive malignancy characterized by rapid onset of chemoresistance and poor clinical outcomes. Recent advances in immunotherapy have changed the standard of care for SCLC for the first time in over 30 years. Dr. Allison Stewart (Resarch Specialist) and Dr. Lauren Byers (Unit Director) in the Department of Thoracic Head and Neck Medical Oncology at University of Texas M.D. Anderson Cancer Center aim to address major, unmet needs in SCLC, including development of novel therapeutic targets, investigation of approaches to enhance response to immunotherapy, and the study of heterogeneity and its contribution to drug resistance. Mechanisms underlying treatment-resistance remain obscure due to scarcity of tissue samples from relapsed patients. To address this deficiency, Dr. Stewart has led efforts to establish novel SCLC models and analyze serial blood and tumor biopsies from patients using innovative genomic, transcriptomic, and proteomic assays to study mechanisms driving treatment resistance to chemotherapy, immunotherapy, or targeted therapies in SCLC. Patient liquid biopsies are non-invasive, facilitate both serial and post-relapse tissue sampling and contain sufficient circulating tumor cells (CTCs) for generation of CTC-derived xenograft (CDX) models of SCLC, as well as for direct single-cell transcriptional profiling. CDXs mirror patient disease by expression of SCLC markers, sites of metastatic disease and platinum response. Intratumoral heterogeneity (ITH) of SCLC and its contribution to clinical outcomes has not been fully characterized. To investigate ITH, single-cell analyses (including single-cell RNAseq) were performed on novel platinum-sensitive and -resistant SCLC CDX models, as well as longitudinal analyses of CDX models and patient CTCs over the course of therapy. Dr. Stewart has demonstrated that refractory SCLC is characterized by increased heterogeneity and the development of multiple, disparate resistant cell populations within the same patient. In order to address the scarcity of SCLC tissue samples, especially paired and post-relapse samples, Dr. Byers has spearheaded an effort to integrate serial tissue acquisition into the design of all SCLC- focused clinical trials at MDACC. Dr. Stewart's goal is to coordinate a SCLC platform by working with multi-disciplinary teams, including a clinical team (identify and consent patients), a laboratory processing team (process/bank specimens, as well as generate animal models), an experimental analysis team (perform experiments with CTCs, tumor specimens and animal models) and a bioinformatics team (scientific analysis) to establish a repository of SCLC specimens for understanding treatment resistance and developing methods to recognize patient response.

NIH Research Projects · FY 2024 · 2020-09

As a recognized leader in cancer research,1 MD Anderson Cancer Center is uniquely positioned to train and support the career development of the next generation of cancer researchers. We will do so via early intervention programs that foster sustained interest in cancer research in students with limited research experience. Since 2011, we have directed a summer undergraduate training program encompassing 345 trainees (from 2011-2018). Significantly, outcomes for research limited trainees in our program are indistinguishable; research limited, and non-limited alumni are enrolled in or have completed STEM bachelor’s (98.8% vs 98.1%) and doctoral (both 67.1%) degrees and are retained in STEM education or workforce (98.3% vs 98.6%, respectively). Built upon these successes, we have designed a comprehensive cancer research training program for high school and undergraduates with limited exposure to cancer research via the R25 YES initiative. In our focused program, we address major barriers in the pursuit and success in STEM, including limited 1) research experience, 2) career path knowledge, and 3) scientific identity formation and exposure to science; 4) underdeveloped professionalism and communication skills; 5) inadequate research, educational, and career mentoring; and 6) barriers in the graduate application process. Our proposed UPWARDS Training Program (Undergraduate Students Working Towards Research in Science) has 3 tracks: full-time, 12-week summer research for 1) high-schoolers and 2) undergraduates and 3) part-time, 40-week research for undergraduates. Within each track, we propose the following aims to address the aforementioned barriers: Aim 1) Employ focused recruitment and holistic strategies for program involvement and deliver didactic learning and hands-on cancer research experiences through a cadre of outstanding mentoring faculty. Aim 2) Develop and deliver individualized mentoring, career exploration, and professional development that stimulates graduate education and cancer research career pursuit. Aim 3) Educate and inspire communities, young generations in the STEM pipeline, and the families and support systems of our students through training, STEM outreach, and hands-on engagement. We will encourage our trainees to lead and encourage their communities and younger generations through hands-on STEM outreach activities and design and delivery of community education. Aim 4) Implement and maintain a rigorous assessment program with continual appraisal and enactment of novel, evidence-driven best practices derived from these efforts. Lastly, we commit to disseminating our findings and best practices via peer-reviewed publications. Through the UPWARDS Program, we will build upon our prior experiences and best practices to launch a cancer research training program specifically designed to fit the needs of research limited trainees in our local community and nationally. We anticipate our efforts will effectively increase the STEM educational pipeline and cancer research workforce.

NIH Research Projects · FY 2025 · 2020-09

PROJECT SUMMARY Older smokers suffer disproportionately from smoking-related disease, particularly lung cancer, and smoking prevalence among older smokers has not declined as steeply as that of younger smokers. The majority of risk results from the chronic inhalation of combusted cigarette (CC) smoke. However, older smokers are often more unwilling or unable to quit smoking than younger smokers, which suggests that they might benefit from switching to potentially less harmful nicotine products. Recent studies, as well as statements from the FDA, suggest that electronic cigarettes (ECs), may be less harmful than CCs. However, it is unknown how ECs would be used in this population, in a real-world setting, and whether or not such use would provide a safer alternative to CC smoking. This project will evaluate changes in product use, acceptability, reinforcement, symptoms of nicotine dependence, and biomarkers of inflammation, oxidative stress, and metabolism in smokers at high risk of lung cancer as they switch from CCs to ECs. Participants (n=330) will be smokers who meet criteria for high risk of lung cancer, who are uninterested in quitting smoking, but who are interested trying ECs and changing CC consumption. Participants will be randomly assigned to one of 2 conditions, EC or usual brand (UB) CC, for 6 months (26 weeks). Those assigned to the EC condition will sample and choose from among 4 EC flavors. All participants will be strongly encouraged to quit CC smoking at the end of the study if they have not already, and will be offered free standard treatment (NRT and counseling) in our clinic, if interested. We will address the following specific aims: (1) To characterize the effects of switching from CCs to ECs on product use, product acceptability, and reinforcement among adult daily CC smokers at high risk for lung cancer; (2) To characterize the effects of switching from CCs to ECs on biomarkers of inflammation and oxidative stress among adult daily CC smokers at high risk for lung cancer; (3) To characterize metabolomic changes that result from switching from CCs to ECs among CC smokers at high risk for lung cancer; (4) To characterize which factors moderate or mediate the effects of switching from CCs to ECs among CC smokers at high risk for lung cancer. This project is significant because it will inform regulatory science and public health policy about the potential harms and benefits of switching from CCs to ECs in older adult smokers at greatest risk for lung cancer who are uninterested in quitting CC smoking. This project is innovative because it will be among the first to focus exclusively on this high risk group and to evaluate the harms and benefits the effect of switching from CCs to ECs using a prospective clinical trial, that accesses the risks and benefits of switching across multiple domains, including behavior, addiction, and health outcomes.

NIH Research Projects · FY 2024 · 2020-09

Opioid use disorder (OUD) has been declared as a public health emergency in the United States. Data from the Centers for Disease Control and Prevention indicate a fivefold increase in the number of deaths due to opioids from 1999 to 2016. Neuroimaging is a powerful tool in understanding the neurocircuitry and physiology of OUD in order to target treatments for patients suffering from this disorder. This K23 application presents a training program for a board-certified clinical medical physicist, who specializes in magnetic resonance imaging (MRI), in order to receive training in the neuroscience of substance use disorders and to become an independent investigator. The goals set in this application will build on the candidate’s imaging physics background by (1) developing a foundational knowledge of brain function and neurocircuitry in substance use disorders in order to design, optimize, and interpret advanced neuroimaging techniques for addiction research; (2) acquiring training in professional development to become an independent investigator, mentor and educator; and (3) receiving additional training in the responsible and ethical conduct of scientific research. The overall training program will involve a research study focused on (1) brain effective connectivity (i.e., directional connectivity) of neural circuits in OUD, and (2) magnetic resonance spectroscopic quantification of neurotransmitters related to these circuits. In this proposed work, we will employ fMRI-based dynamic causal modeling of effective connectivity with guided expertise from mentors in order to identify neurocircuits underlying drug craving and attentional bias to dug cues. In addition, we will use MR spectroscopy to investigate the neurotransmitters gamma-aminobutyric acid (GABA) and glutamate in OUD and their relation to drug craving and attentional bias, and to explore the association of these neurotransmitters with brain effective connectivity.

NIH Research Projects · FY 2024 · 2020-09

Summary The integrated hypothesis of this Program proposal is that age-associated cellular and molecular features of the mouse thymus microenvironment, mirrored by similar features in the human thymus, play a major role in shaping the distinct functional potential of T cells that emigrate from the thymus during the perinatal versus juvenile periods. Currently, there is little information in mice, and even less in humans, on changes in the composition and function of thymic epithelial cells (TECs), hematopoietic antigen presenting cells (HAPCs), and other stromal cell subsets during this transition. Given that T cells with effector and regulatory functions are vital for newborn health, the Program research objectives are to: 1) identify changes in the composition and organization of TECs, HAPCs and other thymus stromal cells over the perinatal to juvenile transition in both mice and humans; 2) map transcriptional changes in these cellular subsets that regulate their proliferation, differentiation, function and cross-talk; and 3) determine how such changes impact the ability of the perinatal thymic environment to generate T cells with distinct functional capabilities. The Program is structured to use scRNA-seq and multiplex imaging to collaboratively identify candidate cell populations and molecular mechanisms underlying functionally significant changes in mouse and human thymus microenvironments across the perinatal to juvenile transition. In the discovery phase, RPs will generate scRNA- seq datasets of TECs (RP1), stromal cells (RP2) and HAPCs (RP3) from mouse and human (Core C) thymus. These datasets will be analyzed by Core B to identify cellular and molecular candidates. In the prioritization phase, RPs will determine which candidates are conserved across species with Core B. RPs will then collaborate to use multiplex imaging to visualize changes in location and/or interactions of these candidates during the transition that may mediate important biological functions. Both species conservation and imaging results will provide a rationale to prioritize cell subsets and molecular pathways for functional testing. In the testing phase, each RP will assess novel, as well as previously identified candidates, for functional significance according to Project specific goals. Collectively, these parallel scRNA-seq and imaging experiments in the three RPs will synergize to: 1) identify changes in the transcriptional profiles, cellular composition and organization of the thymus microenvironment over the perinatal to juvenile transition in both mice and humans; and 2) enable us to test which changes regulate proliferation, differentiation, and function of these subsets across the transition with downstream consequences for perinatal immune function. Program components are: RP1 (Richie): Molecular mechanisms controlling TEC dynamics and lineage hierarchies in the perinatal thymus RP2 (Manley): The role of Foxn1 in controlling the transition from thymus expansion to homeostasis RP3 (Ehrlich): Differential contribution of thymic APCs to central tolerance during the perinatal to adult transition Core A (Richie): Admin. Core; Core B (Yi): Bioinformatics/Biostats Core; Core C: (Hale) Human Thymus Core