Discovering Synergistic Compounds with BYL-719 in PI3K Overactivated Basal-like PDXs

Basal-like triple-negative breast cancer (TNBC) tumor cells are difficult to eliminate due to resistance mechanisms that promote survival. While this breast cancer subtype has low PIK3CA mutation rates when compared to estrogen receptor-positive (ER+) breast cancers, most basal-like TNBCs have an overactive PI3K pathway due to gene amplification or high gene expression. BYL-719 is a PIK3CA inhibitor that has been found to have low drug-drug interactions, which increases the likelihood that it could be useful for combinatorial therapy. Alpelisib (BYL-719) with fulvestrant was recently approved for treating ER+ breast cancer patients whose cancer had developed resistance to ER-targeting therapy. In these studies, a set of basal-like patient-derived xenograft (PDX) models was transcriptionally defined with bulk and single-cell RNA-sequencing and clinically actionable mutation profiles defined with Oncomine mutational profiling. This information was overlaid onto therapeutic drug screening results. BYL-719-based, synergistic two-drug combinations were identified with 20 different compounds, including everolimus, afatinib, and dronedarone, which were also found to be effective at minimizing tumor growth. These data support the use of these drug combinations towards cancers with activating PIK3CA mutations/gene amplifications or PTEN deficient/PI3K overactive pathways.

Abstract P1-13-23: Carboplatin resistance-associated changes in the 3D chromatin landscape of a triple-negative breast cancer Patient-Derived Xenograft

Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2Mb) interactions, chromatin looping, formation of topologically associating domains (TAD), chromatin state switching into a more active state, and amplification of ATP-binding cassette (ABC) transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.

Citation Format: Mikhail Dozmorov, Maggie Marshall, Narmeen Rashid, Jacqueline Grible, Aaron D. Valentine, Amy Olex, Kavita Murthy, Abhijit Chakraborty, Joaquin Reyna, Daniela Salgado Figueroa, Da-Inn Lee, Brittany Baur, Sushmita Roy, Ferhat Ay, Chuck Harrell. Carboplatin resistance-associated changes in the 3D chromatin landscape of a triple-negative breast cancer Patient-Derived Xenograft [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-13-23.

Transcriptomic changes underlying EGFR inhibitor resistance in human and mouse models of basal-like breast cancer

The goals of this study were to identify transcriptomic changes that arise in basal-like breast cancer cells during the development of resistance to epidermal growth factor receptor inhibitors (EGFRi) and to identify drugs that are cytotoxic once EGFRi resistance occurs. Human patient-derived xenografts (PDXs) were grown in immunodeficient mice and treated with a set of EGFRi; the EGFRi erlotinib was selected for more expansive in vivo studies. Single-cell RNA sequencing was performed on mammary tumors from the basal-like PDX WHIM2 that was treated with vehicle or erlotinib for 9 weeks. The PDX was then subjected to long-term erlotinib treatment in vivo. Through serial passaging, an erlotinib-resistant subline of WHIM2 was generated. Bulk RNA-sequencing was performed on parental and erlotinib-resistant tumors. In vitro high-throughput drug screening with > 500 clinically used compounds was performed on parental and erlotinib-resistant cells. Previously published bulk gene expression microarray data from MMTV-Wnt1 tumors were contrasted with the WHIM2 PDX data. Erlotinib effectively inhibited WHIM2 tumor growth for approximately 4 weeks. Compared to untreated cells, single-cell RNA sequencing revealed that a greater proportion of erlotinib-treated cells were in the G1 phase of the cell cycle. Comparison of WHIM2 and MMTV-Wnt1 gene expression data revealed a set of 38 overlapping genes that were differentially expressed in the erlotinib-resistant WHIM2 and MMTV-Wnt1 tumors. Comparison of all three data types revealed five genes that were upregulated across all erlotinib-resistant samples: IL19, KLK7, LCN2, SAA1, and SAA2. Of these five genes, LCN2 was most abundantly expressed in triple-negative breast cancers, and its knockdown restored erlotinib sensitivity in vitro. Despite transcriptomic differences, parental and erlotinib-resistant WHIM2 displayed similar responses to the majority of drugs assessed for cytotoxicity in vitro. This study identified transcriptomic changes arising in erlotinib-resistant basal-like breast cancer. These data could be used to identify a biomarker or develop a gene signature predictive of patient response to EGFRi. Future studies should explore the predictive capacity of these gene signatures as well as how LCN2 contributes to the development of EGFRi resistance.

Trace Amine-Associated Receptor 1 Trafficking to Cilia of Thyroid Epithelial Cells

Trace amine-associated receptor 1 (rodent Taar1/human TAAR1) is a G protein-coupled receptor that is mainly recognized for its functions in neuromodulation. Previous in vitro studies suggested that Taar1 may signal from intracellular compartments. However, we have shown Taar1 to localize apically and on ciliary extensions in rodent thyrocytes, suggesting that at least in the thyroid, Taar1 may signal from the cilia at the apical plasma membrane domain of thyrocytes in situ, where it is exposed to the content of the follicle lumen containing putative Taar1 ligands. This study was designed to explore mouse Taar1 (mTaar1) trafficking, heterologously expressed in human and rat thyroid cell lines in order to establish an in vitro system in which Taar1 signaling from the cell surface can be studied in future. The results showed that chimeric mTaar1-EGFP traffics to the apical cell surface and localizes particularly to spherical structures of polarized thyroid cells, procilia, and primary cilia upon serum-starvation. Moreover, mTaar1-EGFP appears to form high molecular mass forms, possibly homodimers and tetramers, in stably expressing human thyroid cell lines. However, only monomeric mTaar1-EGFP was cell surface biotinylated in polarized human thyrocytes. In polarized rat thyrocytes, mTaar1-EGFP is retained in the endoplasmic reticulum, while cilia were reached by mTaar1-EGFP transiently co-expressed in combination with an HA-tagged construct of the related mTaar5. We conclude that Taar1 trafficking to cilia depends on their integrity. The results further suggest that an in vitro cell model was established that recapitulates Taar1 trafficking in thyrocytes in situ, in principle, and will enable studying Taar1 signaling in future, thus extending our general understanding of its potential significance for thyroid autoregulation.

A prospective study of the incidence and open-label treatment of interferon-induced major depressive disorder in patients with hepatitis C

Interferon (IFN) therapy has been associated with the development of Major Depressive Disorder (MDD) when given to patients with hepatitis C (HCV). The incidence, time course, risk factors, and treatment of IFN-induced MDD are poorly understood. The objectives of the present study were to determine the incidence of IFN-induced MDD, as well as to determine the efficacy of open-label antidepressant treatment, in particular selective serotonin reuptake inhibitors (SSRIs) for IFN-induced MDD. Thirty-nine HCV patients on IFN therapy were monitored weekly using the Beck Depression Inventory (BDI). Those who became depressed were treated with citalopram, a SSRI antidepressant. Main outcome measures included the incidence of IFN-induced MDD, as well as response rates to antidepressants in those patients who developed IFN-induced MDD. Our results showed that 13 of 39 patients (33%) developed IFN-induced MDD. There were no differences in age, gender, past history of MDD, or substance use between those who became depressed and those who did not. However, there were significantly fewer African American patients in the depressed group. Patients who developed IFN-induced MDD were on IFN therapy for an average of 12.1 weeks prior to the development of MDD. Eleven of 13 patients (85%) were responsive to antidepressant treatment. We conclude that IFN-induced MDD is common in HCV patients. Health care providers should follow IFN-treated HCV patients for the development of MDD, particularly between the 2nd and 5th months of IFN therapy. SSRIs, in particular citalopram, are an effective treatment for IFN-induced depression in HCV patients.

Cognitive and mood disturbance as causes and symptoms of fatigue in cancer patients

Fatigue, cognitive dysfunction, and depression are very common in cancer patients. A relationship among the three entities is recognized but poorly understood. Factors that contribute to this poor understanding are the subjective nature of the symptoms, multiple potential causes, and a lack of reliable assessment tools. An understanding of fatigue in cancer patients may benefit from studies of chronic fatigue syndrome (CFS) and other nonmalignant diseases indicating that cognitive impairment varies with physical and mental fatigue, and that symptoms of depression experienced by patients with physical illnesses and primary mood disorders are qualitatively different. The multidimensional nature of fatigue suggests that interventions should be patient-specific. They could be related to lifestyle or involve the use of specific behavioral or pharmacologic therapies. As is the case with depression and cognitive disorders, targeted interventions against cancer-related fatigue will benefit from a better understanding of its potential biologic causes. Consideration of cognitive dysfunction and depression complicates the understanding of cancer-related fatigue; however, it provides opportunities to assist patients who must deal with this serious problem.

Methylphenidate therapy improves cognition, mood, and function of brain tumor patients

PURPOSE

Patients with malignant glioma develop progressive neurobehavioral deficits over the course of their illness. These are caused both by the effects of the disease and the effects of radiation and chemotherapy. We sought to determine whether methylphenidate treatment would improve these patients' neurobehavioral functioning despite their expected neurologic deterioration.

PATIENTS AND METHODS

Thirty patients with primary brain tumors underwent neuropsychologic assessment before and during treatment with methylphenidate. Ability to function in activities of daily living and magnetic resonance imaging (MRI) findings were also documented. Patients were assessed on 10, 20, and 30 mg of methylphenidate twice daily.

RESULTS

Significant improvements in cognitive function were observed on the 10-mg twice-daily dose. Functional improvements included improved gait, increased stamina and motivation to perform activities, and in one case, increased bladder control. Adverse effects were minimal and immediately resolved when treatment was discontinued. There was no increase in seizure frequency and the majority of patients on glucocorticoid therapy were able to decrease their dose. Gains in cognitive function and ability to perform activities were observed in the setting of progressive neurologic injury documented by MRI in half of the subjects.

CONCLUSION

This study demonstrated improved patient function in the setting of a progressive neurologic illness. Methylphenidate should be more widely considered as adjuvant brain tumor therapy.

Mood and cognitive side effects of interferon-alpha therapy

The central nervous system side effects associated with interferon-alpha (IFN-alpha) therapy, including depression and cognitive changes, can compromise otherwise effective immunotherapy. The term "depression" has multiple meanings ranging from a feeling of sadness to a neuropsychiatric disorder with defined diagnostic criteria. A syndrome of mood disturbance with memory impairment, cognitive slowing, and impaired executive function is common with IFN-alpha therapy and is consistent with mild subcortical dementia. Cognitive deficits and mood disorder may occur independently, and in some cases depression is a reactive phenomenon. Risk factors for development of IFN-alpha neurotoxicity include duration of treatment, high-dose therapy, and prior cranial irradiation or neurologic illness. Past or current psychiatric illness also may put the patient at risk. Subtypes of major depression are associated with neuroendocrine and neurochemical alterations that are consistent with the observed activities of IFN-alpha. This may provide insight into the etiology of IFN-alpha neurotoxicity, as well as possible interventions. Assessment of the neuropsychiatric status of patients treated with IFN-alpha should be a standard of care. Possible pharmacologic interventions to decrease the neurotoxicity associated with IFN-alpha therapy include antidepressants, psychostimulants, and opioid antagonists. Preliminary clinical and research experience suggests that it is possible to effectively palliate IFN-alpha toxicity.

Manic episodes in two patients treated with interferon alpha

The authors report the assessment of 2 patients on interferon alpha (IFN-alpha) therapy for chronic myelogenous leukemia who developed manic symptoms long after IFN-alpha therapy had been initiated. These cases suggest that chronic IFN-alpha therapy may be associated with vulnerability for developing overt psychiatric symptoms, particularly in cases where the patient is experiencing psychosocial stress, and that the current definition of persistent adverse effects of IFN-alpha should be broadened to include the occurrence of manic episodes.

A retrospective study of the psychiatric management and outcome of delirium in the cancer patient

This report describes the evaluation and treatment of delirium in the cancer patient in a major comprehensive cancer center. Ninety consecutive cases of delirium seen by the inpatient psychiatry consultation/liaison service were analyzed in a retrospective fashion to evaluate demographic information, alcohol use, central nervous system disease, coexisting medical disease, and past psychiatric history. Delirium cases were divided into hyperalert, hypoalert, and mixed subtypes. For these three subtypes, medication profiles including dose of medication, duration of delirium, outcome, and the venue where the delirium began were also evaluated. The hyperalert subtype of delirium was the commonest type observed (71%) and had the shortest duration (P < 0.0001) and best outcome (P < 0.001). The patients with a hyperalert delirium subtype were treated with the least amount of haloperidol (P < 0.0001). Patients were delirious for longer when the delirium began in the intensive-care units (P < 0.04). In general, patients who received no haloperidol experienced delirium of longer duration (P < 0.02) than those receiving haloperidol. Since the data represent patients who were referred for psychiatric treatment, this may explain the increased number of hyperalert deliriums and, therefore, the generalizability of the results is limited. Delirium in the cancer patient is particularly problematic given the coexisting medical problems these patients experience. Because the outcome of delirium is better when the duration is shorter, it is important for clinicians to be sensitive to early symptoms so that treatment can be implemented faster, leading to less morbidity and mortality.

Pattern of neurobehavioral deficits associated with interferon alfa therapy for leukemia

We evaluated the neuropsychological and personality profiles of 25 patients with chronic myelogenous leukemia treated with interferon alfa (IFN-alpha). This group of persons performed well below expectation on tests of cognitive speed, verbal memory, and executive functions. Personality changes included depression, increased somatic concern, and stress reactions. A control group of leukemia patients not treated with IFN-alpha had significantly better cognitive speed and mood. The pattern of cognitive and personality changes in patients receiving IFN-alpha is highly suggestive of frontal-subcortical brain dysfunction.

Studies with [11C]alprazolam: an agonist for the benzodiazepine receptor

We have built a system for the synthesis of high specific activity carbon-11 alprazolam (Xanax), a high affinity agonist for the benzodiazepine receptor. The system produces 30-40 mCi of the compound with a specific activity of > 12,000 Ci per millimole. Using this compound we have performed PET studies on 6 normal subjects and studied the cerebral influx and efflux of the compound. The uptake in the brain was low, approx. 1% of the administered dose. However, the levels of the compound in the circulation at early time points are heavily affected by the specific activity of the tracer, i.e. when pharmacologically active doses are used as blocking doses the concentration of radioactive material is higher in the circulation and more material enters the brain. We attribute this to a depot effect where the compound is trapped in saturatable sites in an organ, probably the lungs, and is slowly released over time. In the presence of blocking doses of agonist, the compound washes out of the brain more quickly suggesting that some blockade of the receptors is occurring. However, the pharmacological activity of the compound does not permit the administration of enough material to ensure complete receptor blockade. The compound shows definite signs of acting as a receptor binding ligand but the unusual pharmacokinetics complicate the interpretation of the data.

Methylphenidate in the treatment of neurobehavioral slowing associated with cancer and cancer treatment

Psychostimulants used in the treatment of psychiatric conditions, including depression, alleviate some of the observed psychomotor retardation. We describe 3 patients with impairments of arousal and psychomotor speed secondary to tumor-related organic brain dysfunction who benefited from stimulant therapy.

Treatment of neurotoxic side effects of interferon-alpha with naltrexone

Interferon-alpha (IFN-alpha) has potential dose-limiting neurotoxic side effects when used in cancer therapy. The nature of this neurotoxicity is speculative, and there is no definitive treatment. Because animal studies suggest that IFN-alpha acts at opioid receptor sites, we gave naltrexone, a long-acting opioid antagonist, to 9 patients who had hematological malignancies and who suffered from IFN-alpha side effects. Seven of these patients experienced complete or moderate relief of side effects. Five of the patients tested before and during naltrexone treatment showed improvement of cognitive functioning. Two patients could not tolerate naltrexone side effects. This study suggests an intervention against IFN-alpha side effects and provides support for the role of opioid receptor interaction in IFN-alpha neurotoxicity.

Reversible neurotoxicity of interleukin-2 and tumor necrosis factor: correlation of SPECT with neuropsychological testing

A 41-year-old man developed subacute neurotoxicity associated with interleukin-2 and tumor necrosis factor therapy for metastatic renal cell carcinoma. Cognitive deficits revealed on neuropsychological testing and frontal lobe perfusion deficits revealed on SPECT resolved after 1 month. Findings suggest possible neuroanatomic and physiologic substrates of cytokine neurotoxicity.

A community approach to the prevention of dental disease in the children of developing countries

Even in developed Western countries the ready availability of sophisticated restorative dentistry has been relatively unsuccessful in reducing the prevalence of dental disease. It is therefore totally wrong to seek to impose a similar structure of dental care in the developing countries with their shortages of wealth, communications and trained personnel. Instead, the emphasis must be on education and the application of preventive methods by relatively simply trained personnel working with the support and under the guidance of a few fully trained dentists. The establishment of a dental service in the developing countries must contain the following three elements. First, the undertaking of a nationwide survey of the prevalence of dental disease. Next the establishment of training schools in each ethnic area where dental surgeons, dental therapists and dental assistants can be recruited and trained. Lastly, the recruitment and training of local instructors in dental health to work in their own schools, villages and districts, concerned with the supervision of oral hygiene, fluoride mouthrinsing and diet. This scheme is based on the principle of self help through locally recruited and trained personnel and the encouragement of community pride in positive dental health.