A phase I study of GPC3 targeted CAR-T cell therapy in advanced GPC3-expressing hepatocellular carcinoma (HCC)

TPS624

Background: The mortality of hepatocellular carcinoma (HCC) is increasing worldwide, but outcome of systemic treatments in advanced HCC is suboptimal. Adoptive T-cell transfer therapy represents a promising field that exploits the ability of T-cells to recognize and eliminate their target. Targeting the tumor-associated antigen glypican- 3 (GPC3) through chimeric antigen receptors (CAR) engineered T cells is a mechanistically rational novel treatment for advanced HCC. This study aims to determine the dose and early signals of GPC3 targeted (CAR)-T cells in advanced GPC3 expressing HCC (NCT05003895). Methods: This phase I first in human dose escalation trial will study the safety and feasibility of CAR (hYP7)- T cells in advanced HCC patients expressing GPC3. Eligibility criteria includes advanced HCC, not candidates for curative interventions, progressed on first line systemic treatment, tumor GPC3 positivity of ³ 25% by IHC, Child-Pugh Class A, ³1 measurable lesion, ECOG 0 or 1, adequate organ and marrow function. ParticipantsÕ T cells collected through leukapheresis will be transduced with a lentivirus encoding the CAR construct to generate CAR expressing T cells. Patients receive a conditioning chemotherapy regimen of cyclophosphamide and fludarabine prior to the infusion of the GPC3 directed CAR-T cells (Table). The trial has a 4-level modified Fibonacci dose escalation with a minimum of 3 patients at each level and a 28-day interval between the first three patients. Response will be assessed by imaging every two months during the first year. Patients undergo close monitoring with safety assessments during the first year and are followed for life. The primary objective is to determine the MTD, DLT, safety and feasibility of anti-GPC3 CAR expressing T- cells in patients with GPC3-expressing advanced HCC. Secondary objectives include best overall response and overall survival. Exploratory objectives are multiple and include studies to evaluate the persistence and peak levels of anti-GPC3 CAR-T cells after infusion. Recruitment began in December 2021 and the two patients at dose level -1 has been treated; the planned sample size is 38 patients. Table 1 Dose Level Anti-GPC3 CAR-T Cyclophosphamide (mg/m2) Fludarabine (mg/m2) Level -1 0.3x106 CAR-T per kg bw 200 30 Level 1 0.3x106 CAR-T per kg bw 300 30 Level 2 1x106 CAR-T per kg bw 300 30 Level 3 3x106 CAR-T per kg bw 300 30. Clinical trial information: NCT05003895 .

Clinical features and long-term outcomes of patients with colonic oligopolyposis of unknown etiology

BACKGROUND

Colonic adenomatous polyposis of unknown etiology (CPUE) is an adenomatous polyposis phenotype that resembles Familial Adenomatous Polyposis (FAP) even though no germline pathogenic variant is identified.

AIM

We sought to better characterize the clinical features and outcomes in a cohort of CPUE patients.

METHODS

This is a retrospective case series of patients 18 years old or older with aden-omatous oligopolyposis (between 10-100 adenomas) and negative genetic testing, identified through the Hereditary Gastrointestinal Cancer Database at Massachusetts General Hospital, a tertiary academic referral center. A retrospective chart review was performed with a focus on demographics, alcohol and tobacco use, medication use, familial malignancy and polyp burden, genetic testing information, endoscopic surveillance data including the corresponding histopathology, colonic and extracolonic malignancies, mortality events, and their etiology. Spearman correlation and Pearson Chi-square test (or Fisher's exact test) were used for continuous and categorical variables respectively.

RESULTS

CPUE patients were primarily male (69%) and presented for genetic counseling at 63.7 years. Only 2 patients (2.9%) reported a first-degree relative with polyposis. During an average surveillance period of 12.3 years, 0.5 colonoscopies per year were performed. Patients developed 2.3 new adenomas per year. 4 (5.7%) were diagnosed with colorectal cancer (CRC) at a mean age of 66 years, and 3 were diagnosed prior to the onset of oligopolyposis. 7 (10%) required colectomy due to advanced dysplasia or polyp burden. With respect to upper gastrointestinal manifestations, 1 patient had a gastric adenoma, but there were no cases of gastric or small bowel polyposis. During surveillance, 10 (14%) patients died at a mean age of 72, and none were due to CRC.

CONCLUSION

CPUE is distinct from familial adenomatous polyposis (FAP) syndrome and the use of FAP surveillance guidelines may result in unnecessarily frequent upper and lower endoscopies.

Effectiveness and cost effectiveness of palliative care interventions in people with chronic heart failure and their caregivers: a systematic review

BACKGROUND

Chronic heart failure is a common condition, and its prevalence is expected to rise significantly over the next two decades. Research demonstrates the increasing multidimensional needs of patients and caregivers. However, access to palliative care services for this population has remained poor. This systematic review was to provide an evidence synthesis of the effectiveness and cost-effectiveness of palliative care interventions for people with chronic heart failure and their caregivers.

METHODS

Relevant publications were identified via electronic searches of MEDLINE, Embase, PsychInfo, CINAHL, CENTRAL and HMIC from inception to June 2019. Grey literature databases, reference list, and citations of key review articles were also searched. Quality was assessed using the Revised Cochrane Risk of Bias Tool.

RESULTS

Of the 2083 records, 18 studies were identified including 17 having randomised controlled trial (RCT) designs and one mixed methods study with an RCT component. There was significant heterogeneity in study settings, control groups, interventions delivered, and outcome measures used. The most commonly assessed outcome measures were functional status (n = 9), psychological symptoms (n = 9), disease-specific quality of life (n = 9), and physical symptom control (n = 8). The outcome measures with the greatest evidence for benefit included general and disease-specific quality of life, psychological symptom control, satisfaction with care, physical symptom control, medical utilisation, and caregiver burden. Moreover, the methodological quality of these studies was mixed, with only four having an overall low risk of bias and the remaining studies either demonstrating high risk of bias (n = 10) or showing some concerns (n = 4) due to small sample sizes and poor retention. Only two studies reported on economic costs. Both found statistically significant results showing the intervention group to be more cost effective than the control group, but the quality of both studies was at high risk of bias.

CONCLUSIONS

This review supports the role of palliative care interventions in patients with chronic heart failure and their caregivers across various outcomes, particularly quality of life and psychological wellbeing. Due to the highly heterogeneous nature of palliative care interventions, it is not possible to provide definitive recommendations as to what guise palliative care interventions should take to best support the complex care of this population. Considerable future research, particularly focusing on quality of care after death and the caregiver population, is warranted.

P-272 Automatic Tracking of the ICSI procedure using Deep Learning

Study question

Can deep learning be used to detect and track spermatozoa and the different parts of an ICSI procedure?

Summary answer

Deep learning can be used as a tool to assist and organize the contents of an ICSI procedure.

What is known already

Sperm tracking has been a topic of research and practice for many years, especially in the context of computer-aided sperm analysis (CASA). Recent studies have proposed using deep learning algorithms to track spermatozoa for spermatozoon selection in human and animal samples. One critical part of performing ICSI involves the selection of the “best” spermatozoon for injection, but other parts of the procedure may also be of importance. However, as far as we know, tracking using deep learning has not been applied to the ICSI procedure, where detecting instruments and the oocyte could also be helpful in post-analysis and training.

Study design, size, duration

The study was performed using three anonymized videos of the ICSI procedure. The frames of the videos were manually annotated by data scientists and verified by an embryologist. The annotations were bounding boxes around specific parts of the ICSI procedure, including sperm, pipettes, and the oocyte. We trained a YOLOv5 model on the collected data, where two videos were used for training and one video for validation.

Participants/materials, setting, methods

The videos of the ICSI procedure were captured at 200x magnification with a DeltaPix camera at Fertilitetssenteret in Oslo, Norway. ICSI was performed using a Nikon ECLIPSE TE2000-S microscope connected with Eppendorf TransferMan 4m micromanipulators. The spermatozoa were immobilised in 5 µl Polyvinylpyrrolidone (PVP; CooperSurgical). The videos had a resolution of 1920x1080 and were resized to 640x640 before being processed by the YOLOv5 model. The data will be made public in a later study.

Main results and the role of chance

Mean average precision (mAP) with the threshold of 0.5 (mAP@.5) is the main quantitative parameter measured in the YOLOv5 model. All the experiments were performed using three-fold cross-validation, where we present the average metrics calculated over the three folds. Overall, the method showed an average mAP@.5 of 0.50 across all predicted classes, which means that the method can track the different components with good accuracy. Looking closer at the individual classes, we see that instruments like the holding pipette and ICSI pipette are detected with high accuracy with a mAP@.5 of 0.87 and 0.94, respectively. The oocyte is also easily tracked with a mAP@.5 of 0.92. The first polar body is well detected with a mAP@.5 of 0.65. The model has issues detecting and tracking individual sperm (both outside and within the pipette), where the method achieved a mAP@.5 of 0.46 for tracking sperm outside the pipette and 0.03 for the sperm inside the pipette. The low score of detecting the sperm in the pipette can be explained by the often unclear visibility of the sperm through the pipette and the low number of training samples.

Limitations, reasons for caution

The limited sample size makes the generalizability of the method difficult to determine. A more extensive evaluation is necessary. Moreover, as the currency study focuses on tracking, patient information and clinical outcome were not included in the analysis.

Wider implications of the findings

Deep learning has the potential to aid embryologists to perform successful ICSI through tracking and detection of spermatozoa, pipettes, and the oocyte. This could potentially lead to better internal quality control and teaching possibilities, and hopefully better results.

Trial registration number

not applicable

Toward a better understanding of the experience of patients with moderate penetrance breast cancer gene pathogenic/likely pathogenic variants: A focus on ATM and CHEK2

This study explored the experiences of patients with pathogenic or likely pathogenic variants in the moderate penetrance breast cancer genes, ATM and CHEK2. There were 139 eligible female patients who received genetic counseling at the Massachusetts General Hospital Center for Cancer Risk Assessment (MGH CCRA) from 2014 to 2018. They were sent surveys assessing their understanding of the clinical significance of their genetic test results, adherence to medical management recommendations, dissemination of genetic test results to relatives, and informational resource needs. In total, 66 surveys were returned with a response rate of 47.5%. Most participants reported understanding the clinical implications of their genetic test results and adhering to medical management recommendations. Although 20.3% found it upsetting, nearly all participants shared their genetic test results with relatives. When asked about resource needs, 54.5% reported seeking out additional resources. Our ATM/CHEK2 sample appears to have a good understanding of the personal and familial implications of their genetic test results but may benefit from additional resources. It is unclear whether similar results would be found in patients who do not receive genetic counseling from a board-certified genetic counselor, and this should be examined. This study is one of the first to assess the experiences and needs of the moderate risk population.

Cardiac radiotherapy induces electrical conduction reprogramming in the absence of transmural fibrosis

Cardiac radiotherapy (RT) may be effective in treating heart failure (HF) patients with refractory ventricular tachycardia (VT). The previously proposed mechanism of radiation-induced fibrosis does not explain the rapidity and magnitude with which VT reduction occurs clinically. Here, we demonstrate in hearts from RT patients that radiation does not achieve transmural fibrosis within the timeframe of VT reduction. Electrophysiologic assessment of irradiated murine hearts reveals a persistent supraphysiologic electrical phenotype, mediated by increases in NaV1.5 and Cx43. By sequencing and transgenic approaches, we identify Notch signaling as a mechanistic contributor to NaV1.5 upregulation after RT. Clinically, RT was associated with increased NaV1.5 expression in 1 of 1 explanted heart. On electrocardiogram (ECG), post-RT QRS durations were shortened in 13 of 19 patients and lengthened in 5 patients. Collectively, this study provides evidence for radiation-induced reprogramming of cardiac conduction as a potential treatment strategy for arrhythmia management in VT patients.

Development and Pilot Test of a Culturally Relevant Toolkit to Enhance Advance Care Planning With Chinese American Patients

BACKGROUND

First-generation Chinese American patients have low engagement in advance care planning (ACP). Among the causes may be clinician uncertainty about traditional cultural values.

AIM

Based on a survey identifying barriers to ACP among older ethnic Chinese American patients, we created a toolkit to support clinicians in culturally relevant ACP practices and conducted a pilot test to evaluate usability, acceptability, and preliminary outcomes.

DESIGN/SETTING/PARTICIPANTS

The toolkit includes culturally relevant information and an ACP guideline with a prompt list of questions. Six clinicians (three physicians, two nurse practitioners, and one physician assistant) in two New York City-based practices piloted the toolkit through discussions with 66 patients.

RESULTS

Patients' age averaged 70.2 years (SD=12.4); 56.1% were women. Almost two-thirds had not finished high school and 53.0% spoke only Cantonese. More than three-quarters (78.8%) did not understand the purpose of ACP before the discussion. During the discussion, 58 patients (87.9%) completed a new proxy naming a health care agent, 21 (31.8%) requested a nonhospital DNR order, and two (3%) completed a living will. Topics discussed included treatment preferences (discussed with 80.3% of patients); health care values (77.3%); treatment decisions (72.7%); goals of care (68.2%), and hospice (1.5%). Five of the six clinicians expressed satisfaction ("very" or "somewhat") with the toolkit, four were "very" comfortable using it, and three stated that it helped them "a lot" with effective discussions.

CONCLUSIONS

An ACP toolkit may facilitate culturally relevant ACP discussions by increasing clinician competency and patient engagement. Further studies of this approach are needed.

Prevalence of Psychological Symptoms in Community-Dwelling Chinese American Patients with Chronic Cancer Pain

Cancer is common among older Chinese American immigrants. Psychological distress may be associated with cancer pain, yet prior studies have not examined this relationship. We conducted a secondary analysis of 514 Chinese Americans with cancer-related pain. Patients completed validated questionnaires, including the Chinese Health Questionnaire-12 (CHQ-12). Analyses evaluated associations among sociodemographics, acculturation, psychological distress, and pain variables. Most patients had low acculturation and socioeconomic levels. Overall, 51.9% of patients reported moderate-severe psychological distress, 35.8% reported worst pain intensity ≥7/10 over the previous week and 41.2% had high pain-related distress. Higher CHQ-12 scores were associated with younger age (β = -0.13); lower educational level (β = -0.12); birthplace in China (β = -0.18); lack of a caregiver (β = -0.10); higher worst pain intensity (β = 0.15); and higher pain-related distress (β = 0.28; all p < 0.05; R² = 0.23). Chinese American cancer patients with chronic pain experience high psychological distress, which is associated with pain characteristics and other social factors.

Attitudes and Beliefs Toward Advance Care Planning Among Underserved Chinese-American Immigrants

CONTEXT

Many in the rapidly growing Chinese-American population are non-English-speaking and medically underserved, and few engage in advance care planning (ACP). Evaluating culturally-determined factors that may inhibit ACP can inform programs designed to increase ACP engagement.

OBJECTIVES

To describe attitudes and beliefs concerning ACP in older, non-English-speaking Chinese Americans in a medically-underserved urban region.

METHODS

Patients were consecutively recruited from a primary care practice in New York City to participate in a cross-sectional survey. Attitudes and beliefs were measured using an ACP Survey Tool and the validated Traditional Chinese Death Beliefs measure. Exploratory analyses evaluated associations between these two measures and between each measure and sociodemographics, primary dialect, acculturation (using the Suinn-Lew Asian Self Identity Acculturation Scale), and health status (using the Short Form-8 Health Survey).

RESULTS

Patients (n = 179) were 68.2 years on average; 55.9% were women, and 81.0% were non-English speaking (42.8% Cantonese, 15.2% Mandarin, 19.3% Toisanese, and 19.3% Fuzhounese). Most had low acculturation (mean 1.7/5.0) and highly-rated physical and mental health (mean 70.1/100 and 81.5/100, respectively). Few patients (15.1%) had an advance directive and 56.8% were unfamiliar with any type; 74.4% were willing to complete one in the future. Thirty-two percent "agreed" that "talking about death in the presence of a dying person would accelerate death". The analyses revealed no significant associations.

CONCLUSION

These Chinese-American older adults had low acculturation and very limited knowledge of, or engagement in, ACP. Factors that may predict culturally-determined attitudes and beliefs about ACP were not identified. Further research can inform efforts to improve ACP engagement in this population.

Palliative Care and the Management of Common Distressing Symptoms in Advanced Cancer: Pain, Breathlessness, Nausea and Vomiting, and Fatigue

Good symptom management in oncology is associated with improved patient and family quality of life, greater treatment compliance, and may even offer survival advantages. With population growth and aging, the proportion of patients with multiple symptoms—both related and unrelated to their cancer—is anticipated to increase, supporting calls for a more routine and integrated approach to symptom management. This article presents a summary of the literature for the use of symptom assessment tools and reviews the management of four common and distressing symptoms commonly experienced by people with advanced cancer: pain, breathlessness, nausea and vomiting, and fatigue. We also discuss the role of palliative care in supporting a holistic approach to symptom management throughout the cancer trajectory.

Predictors of Rehospitalization in Post-Acute Rehabilitation among Different Ethnic Groups

OBJECTIVES

Previous research has shown that ethnicity may play a role in increased risk for hospital readmission during a post-acute rehabilitation care (PARC) stay. However, little is known about risk factors influencing discharge status from PARC settings among different ethnic groups. Hence, the aim of our study was to investigate the relationship of individual characteristics (eg, sex, neighborhood quality) and health behavior (use of rehabilitation services) with rehospitalization across ethnic groups of older adult patients who received post-acute rehabilitation for a cardiovascular disease at a skilled nursing facility (SNF).

DESIGN

Retrospective study with data extraction from electronic medical records (EMRs) at admission and discharge.

SETTING

SNF.

PARTICIPANTS

The sample consisted of 520 post-acute rehabilitation patients (96 Hispanics, 172 African Americans, and 252 Whites) 60 years or older with an admitting condition of a circulatory-related disease.

MEASUREMENTS

Sociodemographic and health-related variables, and discharge status (rehospitalized or home).

RESULTS

For the Hispanic sample, lower community quality was associated with a greater likelihood of being rehospitalized. For African Americans, having no social support, higher levels of admission functional dependency, and shorter length of stay were significantly associated with a higher likelihood of being rehospitalized. For the group of White participants, the following variables emerged as risk factors for rehospitalization: being male, lower admission cognitive functioning, higher levels of admission depressive symptomatology, and shorter length of stay.

CONCLUSIONS/IMPLICATIONS

Individual characteristics and health behaviors that are risk factors for rehospitalization during a post-acute stay vary across ethnic groups. Hence, the study provides insights for PARC clinicians into specific patient characteristics to be aware of as risk factors for less optimal patient outcomes.

Evaluation of the self-directed format of Walk With Ease in patients with systemic lupus erythematosus: the Walk-SLE Pilot Study

OBJECTIVE

To conduct a proof-of-concept pilot evaluation of the self-directed format of Walk With Ease (WWE), a 6-week walking program developed for adults with arthritis, in patients with systemic lupus erythematosus (SLE).

METHODS

This was a single arm, 6-week pre- and post-evaluation of the self-directed WWE program to assess feasibility, tolerability, safety, acceptability, and effectiveness. Adult patients with physician-diagnosed SLE were recruited to participate during regularly scheduled visits to an academic rheumatology clinic. Self-reported outcomes of pain, stiffness, and fatigue were assessed by visual analog scales (VAS) and the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-fatigue) scale at baseline and at completion of the 6-week program. Patients also completed a satisfaction survey at the end of the program. Multivariate linear regression models were used to calculate mean changes between baseline and 6-week follow-up scores, adjusting for covariates. Mean change scores were used to estimate effect sizes (ES).

RESULTS

At 6 weeks, 48 of the 75 recruited participants completed the WWE program. Participants experienced modest improvements in stiffness and fatigue (ES = 0.12 and ES = 0.23, respectively, for VAS scores; ES = 0.16 for FACIT-fatigue score) following the intervention. The majority of participants reported satisfaction with the program (98%) and benefitted from the workbook (96%).

CONCLUSIONS

The self-directed format of WWE appears to reduce stiffness and fatigue in patients with SLE. It also seems to be a feasible and acceptable exercise program to patients with SLE. Larger studies are needed to confirm these findings.

Transient Notch Activation Induces Long-Term Gene Expression Changes Leading to Sick Sinus Syndrome in Mice

RATIONALE

Notch signaling programs cardiac conduction during development, and in the adult ventricle, injury-induced Notch reactivation initiates global transcriptional and epigenetic changes.

OBJECTIVE

To determine whether Notch reactivation may stably alter atrial ion channel gene expression and arrhythmia inducibility.

METHODS AND RESULTS

To model an injury response and determine the effects of Notch signaling on atrial electrophysiology, we transiently activate Notch signaling within adult myocardium using a doxycycline-inducible genetic system (inducible Notch intracellular domain [iNICD]). Significant heart rate slowing and frequent sinus pauses are observed in iNICD mice when compared with controls. iNICD mice have structurally normal atria and preserved sinus node architecture, but expression of key transcriptional regulators of sinus node and atrial conduction, including Nkx2-5 (NK2 homeobox 5), Tbx3, and Tbx5 are dysregulated. To determine whether the induced electrical changes are stable, we transiently activated Notch followed by a prolonged washout period and observed that, in addition to decreased heart rate, atrial conduction velocity is persistently slower than control. Consistent with conduction slowing, genes encoding molecular determinants of atrial conduction velocity, including Scn5a (Nav1.5) and Gja5 (connexin 40), are persistently downregulated long after a transient Notch pulse. Consistent with the reduction in Scn5a transcript, Notch induces global changes in the atrial action potential, including a reduced dV_m/dt_max. In addition, programmed electrical stimulation near the murine pulmonary vein demonstrates increased susceptibility to atrial arrhythmias in mice where Notch has been transiently activated. Taken together, these results suggest that transient Notch activation persistently alters ion channel gene expression and atrial electrophysiology and predisposes to an arrhythmogenic substrate.

CONCLUSIONS

Our data provide evidence that Notch signaling regulates transcription factor and ion channel gene expression within adult atrial myocardium. Notch reactivation induces electrical changes, resulting in sinus bradycardia, sinus pauses, and a susceptibility to atrial arrhythmias, which contribute to a phenotype resembling sick sinus syndrome.

Challenges Experienced at Age 100: Findings From the Fordham Centenarian Study

This article examines the challenges experienced by very old individuals and their consequences for well-being and mental health. In order to capture unique issues experienced in very old age, 75 participants of the population-based Fordham Centenarian Study answered open-ended questions on everyday challenges. Theme-based coding was then used to categorize and quantify responses. The challenges mentioned most often were challenges faced in the functional (e.g., physical health/activities of daily living restrictions, mobility, sensory impairment), psychological (e.g., loss of well-liked activity, dependency, negative emotions, death), and social (e.g., family loss) life domains. Functional challenges were negatively associated with aging satisfaction and positively associated with loneliness. Psychological challenges were positively linked to aging satisfaction. Social challenges were marginally related to loneliness. Notably, challenges were not related to depression. In conclusion, the challenges experienced in very old age are multidimensional and multifaceted, unique in nature, and have differential relations to mental health. Functional, psychological, and social challenges affect very old individuals' lives and therefore need to be better understood and addressed. Given their consequences, it is imperative for policy makers to develop an awareness for the different types of challenges faced by centenarians, as there may be unique policy implications related to each.

Notch-Mediated Epigenetic Regulation of Voltage-Gated Potassium Currents

RATIONALE

Ventricular arrhythmias often arise from the Purkinje-myocyte junction and are a leading cause of sudden cardiac death. Notch activation reprograms cardiac myocytes to an induced Purkinje-like state characterized by prolonged action potential duration and expression of Purkinje-enriched genes.

OBJECTIVE

To understand the mechanism by which canonical Notch signaling causes action potential prolongation.

METHODS AND RESULTS

We find that endogenous Purkinje cells have reduced peak K⁺ current, I_to, and I_K,slow when compared with ventricular myocytes. Consistent with partial reprogramming toward a Purkinje-like phenotype, Notch activation decreases peak outward K⁺ current density, as well as the outward K⁺ current components I_to,f and I_K,_slow. Gene expression studies in Notch-activated ventricles demonstrate upregulation of Purkinje-enriched genes Contactin-2 and Scn5a and downregulation of K⁺ channel subunit genes that contribute to I_to,f and I_K,slow. In contrast, inactivation of Notch signaling results in increased cell size commensurate with increased K⁺ current amplitudes and mimics physiological hypertrophy. Notch-induced changes in K⁺ current density are regulated at least in part via transcriptional changes. Chromatin immunoprecipitation demonstrates dynamic RBP-J (recombination signal binding protein for immunoglobulin kappa J region) binding and loss of active histone marks on K⁺ channel subunit promoters with Notch activation, and similar transcriptional and epigenetic changes occur in a heart failure model. Interestingly, there is a differential response in Notch target gene expression and cellular electrophysiology in left versus right ventricular cardiac myocytes.

CONCLUSIONS

In summary, these findings demonstrate a novel mechanism for regulation of voltage-gated potassium currents in the setting of cardiac pathology and may provide a novel target for arrhythmia drug design.

Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs

BACKGROUND

Mutations or alterations in expression of the 5' nucleotidase gene family can lead to altered responses to treatment with nucleoside analogs. While investigating leukemia susceptibility genes, we discovered a very rare p.L254P NT5C1A missense variant in the substrate recognition motif. Given the paucity of cellular drug response data from the NT5C1A germline variation, we characterized p.L254P and eight rare variants of NT5C1A from genomic databases.

MATERIALS AND METHODS

Through lentiviral infection, we created HEK293 cell lines that stably overexpress wild-type NT5C1A, p.L254P, or eight NT5C1A variants reported in the National Heart Lung and Blood Institute Exome Variant Server (one truncating and seven missense). IC50 values were determined by cytotoxicity assays after exposure to chemotherapeutic nucleoside analogs (cladribine, gemcitabine, 5-fluorouracil). In addition, we used structure-based homology modeling to generate a three-dimensional model for the C-terminal region of NT5C1A.

RESULTS

The p.R180X (truncating), p.A214T, and p.L254P missense changes were the only variants that significantly impaired protein function across all nucleotide analogs tested (>5-fold difference vs. wild-type; P<0.05). Several of the remaining variants individually showed differential effects (both more and less resistant) across the analogs tested. The homology model provided a structural framework to understand the impact of NT5C1A mutants on catalysis and drug processing. The model predicted active site residues within NT5C1A motif III and we experimentally confirmed that p.K314 (not p.K320) is required for NT5C1A activity.

CONCLUSION

We characterized germline variation and predicted protein structures of NT5C1A. Individual missense changes showed considerable variation in response to the different nucleoside analogs tested, which may impact patients' responses to treatment.

Differential responses of two wetland graminoids to high ammonium at different pH values

Enhanced soil ammonium (NH4+) concentrations in wetlands often lead to graminoid dominance, but species composition is highly variable. Although NH4+ is readily taken up as a nutrient, several wetland species are known to be sensitive to high NH4+ concentrations or even suffer toxicity, particularly at low soil pH. More knowledge about differential graminoid responses to high NH4+ availability in relation to soil pH can help to better understand vegetation changes. The responses of two wetland graminoids, Juncus acutiflorus and Carex disticha, to high (2 mmol·l(-1) ) versus control (20 μmol·l(-1) ) NH4+ concentrations were tested in a controlled hydroponic set up, at two pH values (4 and 6). A high NH4+ concentration did not change total biomass for these species at either pH, but increased C allocation to shoots and increased P uptake, leading to K and Ca limitation, depending on pH treatment. More than 50% of N taken up by C. disticha was invested in N-rich amino acids with decreasing C:N ratio, but only 10% for J. acutiflorus. Although both species appeared to be well adapted to high NH4+ loadings in the short term, C. disticha showed higher classic detoxifying responses that are early warning indicators for decreased tolerance in the long term. In general, the efficient aboveground biomass allocation, P uptake and N detoxification explain the competitive strength of wetland graminoids at the expense of overall biodiversity at high NH4+ loading. In addition, differential responses to enhanced NH4+ affect interspecific competition among graminoids and lead to a shift in vegetation composition.

Examining the Positivity Effect in Autobiographical Memory Across Adulthood

The positivity effect in memory is characterized by enhanced memory for emotionally positive information or decreased memory for emotionally negative information with increased age. The goals of the current study were to (a) examine the positivity effect in autobiographical memory using instructions that limited experimental constraints, (b) examine the relationship between memory valence and subjective well-being, and (c) examine the relationship between age and other memory characteristics across adulthood. In the current study, 281 individuals between the ages of 18 and 94 (Mage=53.14, SD=17.04) completed a modified Memory Experiences Questionnaire using online survey methods. Participants answered questions about emotional valence and other phenomenological characteristics regarding two memories, including any specific memory of their choosing and a personally meaningful memory. Results indicated that memory valence was unrelated to age, thus failing to provide evidence for the positivity effect. However, memory valence was found to be a significant predictor of life satisfaction. Age moderated the relationship between memory valence and subjective well-being but did so differently across the two memories. Age was also associated with increased vividness, coherence, sensory detail, time clarity, and a first-person perspective for the personally meaningful memory.

Abstract A8: Functional analysis of genomic variants identified through whole exome sequencing of pediatric lymphocytic leukemia kindreds

The underlying genetic basis of many childhood cancers remains largely unknown, which places a significant focus on the discovery and understanding of cancer susceptibility genes. Even genetic predisposition of the most common childhood cancer, acute lymphocytic leukemia (ALL), remains poorly understood. Our research focuses on the identification of novel high risk cancer susceptibility genes through the use of next generation sequencing methods, bioinformatics tools, and functional assays. We are analyzing a small cohort of ethnically diverse families with at least two first-degree relatives with childhood ALL or lymphoma transmitting in an autosomal dominant manner. Whole exome sequencing was performed on affected individuals' normal lymphoblasts and tumor samples when available. In one particular Hispanic kindred, sequencing generated a list of over 1500 heterozygous missense variants shared among three affected individuals. Filtering out common variants found in databases such as dbSNP, reduced this list by 95% and filtering variants seen in a whole exome sequenced intrafamilial control narrowed down the list to 33 potential rare heterozygous cancer susceptibility variants. In order to select which rare variants to analyze by functional methods, various bioinformatics tools were utilized. Variants leading to the change of a conserved amino acid were given a higher priority. In addition, variants had to be predicted to be damaging or deleterious to protein structure or function by 3 out of 4 algorithms. These bioinformatics analyses left us with 8 candidate variant genes (PIK3R4, SUPT3H, NT5C1A, TRPM4, PRKAG3, C6orf136, GLT25D1, and LPIN2). All of these rare variants were retained in tumors from affected family members, but there was no evidence for second hits. RNA-seq data assessing expression in hematopoietic cell populations from murine bone marrow has been a valuable tool to select genes from this variant list for further analysis. Variants that are potential inactivating mutations in genes robustly expressed in murine bone marrow, such as PIK3R4, are prioritized for knock down in murine bone marrow transplantation studies. The p.M239V variant is located in the serine/threonine kinase domain of PIK3R4. PIK3R4 is needed to regulate and activate PIK3C3, which is involved in vesicle trafficking, autophagy, and nutrient sensing. We are currently developing a novel murine model in which we harvest the bone marrow from 5-FU treated CD45.2 mice. Harvested bone marrow is then transduced with murine stem cell virus (MSCV) retroviral vectors expressing GFP and miRNAi to target the knock down of our gene of interest (GOI). The transduced bone marrow is then transplanted into CD45.1 recipient mice that have had their bone marrow ablated by radiation. These mice are then observed for signs of leukemia and their blood is collected at different time points to detect any alterations in hematopoiesis caused by the knockdown of the GOI. Alternatively, if an activating mutation is predicted of a candidate gene, we can use the MSCV retroviral system to overexpress the mutant cDNA in donor bone marrow transplanted into a recipient mouse. Within our larger cohort of ALL kindreds, none of these 8 variants are present, which demonstrates genetic heterogeneity of familial childhood leukemia. Determining the underlying genetic cause of childhood cancers will require collaborative studies across many cancer centers along with multiple model systems for functional analysis.

Citation Format: Jason Saliba, Ryan Zabriskie, Bradford Powell, Stephanie Hicks, Marek Kimmel, Hannah Cheung, Deborah Ritter, Donna M. Muzny, Jeffrey G. Reid, David A. Wheeler, Richard A. Gibbs, Sharon E. Plon. Functional analysis of genomic variants identified through whole exome sequencing of pediatric lymphocytic leukemia kindreds. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A8.

Prognostic factors associated with decreased survival in patients with acinic cell carcinoma

IMPORTANCE

Acinic cell carcinoma is a rare salivary neoplasm that is generally associated with a good prognosis, although a subset of patients develops local and distant recurrences. Given the rarity of the disease, factors to identify patients at risk for recurrences or decreased survival are not clearly defined.

OBJECTIVES

To identify clinicopathologic factors associated with adverse survival in patients with acinic cell carcinoma and to assess the effect of local, regional, and distant recurrences on survival.

DESIGN, SETTING, AND PARTICIPANTS

Retrospective medical record review in a tertiary care cancer center of 155 patients treated for acinic cell carcinoma from January 1990 through February 2013.

MAIN OUTCOMES AND MEASURES

Primary outcomes evaluated were overall and disease-free survival. The end points assessed were age at diagnosis, sex, size of primary tumor, presence of positive surgical margins, postoperative radiation therapy, and development of local, regional, or distant recurrences.

RESULTS

The median survival was 28.5 years, with 13 patients (8.4%) dying of their disease. Women (n = 104) were affected twice as often as men (n = 51) but had an improved survival (P < .001). Patients diagnosed as having acinic cell carcinoma before or at the age of 45 years had an improved survival (P = .02) compared with their elder counterparts, a finding that was independent of sex. Neoplasms larger than 3 cm at presentation were associated with a decreased overall survival compared with smaller lesions (P = .02). The development of distant metastases was most associated with death from the disease (odds ratio, 49.90; 95% CI, 6.49-2246.30; P < .001) compared with local and regional recurrences.

CONCLUSIONS AND RELEVANCE

Although patients with acinic cell carcinoma generally have a favorable prognosis, we have identified several factors associated with decreased survival, including male sex, age older than 45 years, neoplasms larger than 3 cm, and the development of a distant recurrence. These results suggest that maximizing local and regional control for this disease can offer substantial benefit when no distant disease is detectable.

Type II diabetes increases mitochondrial DNA mutations in the left ventricle of the Goto-Kakizaki diabetic rat

Mitochondrial dysfunction has a significant role in the development of diabetic cardiomyopathy. Mitochondrial oxidant stress has been accepted as the singular cause of mitochondrial DNA (mtDNA) damage as an underlying cause of mitochondrial dysfunction. However, separate from a direct effect on mtDNA integrity, diabetic-induced increases in oxidant stress alter mitochondrial topoisomerase function to propagate mtDNA mutations as a contributor to mitochondrial dysfunction. Both glucose-challenged neonatal cardiomyocytes and the diabetic Goto-Kakizaki (GK) rat were studied. In both the GK left ventricle (LV) and in cardiomyocytes, chronically elevated glucose presentation induced a significant increase in mtDNA damage that was accompanied by decreased mitochondrial function. TTGE analysis revealed a number of base pair substitutions in the 3' end of COX3 from GK LV mtDNA that significantly altered the protein sequence. Mitochondrial topoisomerase DNA cleavage activity in isolated mitochondria was significantly increased in the GK LV compared with Wistar controls. Both hydroxycamptothecin, a topoisomerase type 1 inhibitor, and doxorubicin, a topoisomerase type 2 inhibitor, significantly exacerbated the DNA cleavage activity of isolated mitochondrial extracts indicating the presence of multiple functional topoisomerases in the mitochondria. Mitochondrial topoisomerase function was significantly altered in the presence of H2O2 suggesting that separate from a direct effect on mtDNA, oxidant stress mediated type II diabetes-induced alterations of mitochondrial topoisomerase function. These findings are significant in that the activation/inhibition state of the mitochondrial topoisomerases will have important consequences for mtDNA integrity and the well being of the diabetic myocardium.

Small molecule inhibitors of phospholipase C from a novel high-throughput screen

Phospholipase C (PLC) isozymes are important signaling molecules, but few small molecule modulators are available to pharmacologically regulate their function. With the goal of developing a general approach for identification of novel PLC inhibitors, we developed a high-throughput assay based on the fluorogenic substrate reporter WH-15. The assay is highly sensitive and reproducible: screening a chemical library of 6280 compounds identified three novel PLC inhibitors that exhibited potent activities in two separate assay formats with purified PLC isozymes in vitro. Two of the three inhibitors also inhibited G protein-coupled receptor-stimulated PLC activity in intact cell systems. These results demonstrate the power of the high-throughput assay for screening large collections of small molecules to identify novel PLC modulators. Potent and selective modulators of PLCs will ultimately be useful for dissecting the roles of PLCs in cellular processes, as well as provide lead compounds for the development of drugs to treat diseases arising from aberrant phospholipase activity.

An S/T-Q cluster domain census unveils new putative targets under Tel1/Mec1 control

Background

The cellular response to DNA damage is immediate and highly coordinated in order to maintain genome integrity and proper cell division. During the DNA damage response (DDR), the sensor kinases Tel1 and Mec1 in Saccharomyces cerevisiae and ATM and ATR in human, phosphorylate multiple mediators which activate effector proteins to initiate cell cycle checkpoints and DNA repair. A subset of kinase substrates are recognized by the S/T-Q cluster domain (SCD), which contains motifs of serine (S) or threonine (T) followed by a glutamine (Q). However, the full repertoire of proteins and pathways controlled by Tel1 and Mec1 is unknown.

Results

To identify all putative SCD-containing proteins, we analyzed the distribution of S/T-Q motifs within verified Tel1/Mec1 targets and arrived at a unifying SCD definition of at least 3 S/T-Q within a stretch of 50 residues. This new SCD definition was used in a custom bioinformatics pipeline to generate a census of SCD-containing proteins in both yeast and human. In yeast, 436 proteins were identified, a significantly larger number of hits than were expected by chance. These SCD-containing proteins did not distribute equally across GO-ontology terms, but were significantly enriched for those involved in processes related to the DDR. We also found a significant enrichment of proteins involved in telophase and cytokinesis, protein transport and endocytosis suggesting possible novel Tel1/Mec1 targets in these pathways. In the human proteome, a wide range of similar proteins were identified, including homologs of some SCD-containing proteins found in yeast. This list also included high concentrations of proteins in the Mediator, spindle pole body/centrosome and actin cytoskeleton complexes.

Conclusions

Using a bioinformatic approach, we have generated a census of SCD-containing proteins that are involved not only in known DDR pathways but several other pathways under Tel1/Mec1 control suggesting new putative targets for these kinases.

Abstract 5113: Functional analysis of genomic variants identified through whole exome sequencing for susceptibility to lymphocytic leukemia

The underlying genetic basis of many childhood cancers remains largely unknown, which places a significant focus on the discovery and understanding of cancer susceptibility genes. Our research is focused on the identification of novel high risk childhood cancer susceptibility genes through next generation sequencing methods and functional assays. One kindred contained four individuals diagnosed during childhood with lymphocytic leukemia or lymphoma transmitted in an autosomal dominant pattern of inheritance. Whole exome sequencing was performed on the constitutional DNA of three of the patients diagnosed with childhood cancer and one non-transmitting parent as an internal control. This analysis resulted in over 1000 unique single nucleotide variant (SNV) sites shared among the three affected family members. Of these SNVs, greater than 95% were found in control databases and excluded. Also, any variant found in the non-transmitting parent was eliminated. Systematic bioinformatics analysis resulted in a short list of seven missense SNVs predicted to be functionally important. Within this list is the missense mutation of a conserved residue (L254P) of Human Cytosolic 5′ Nucleotidase (NT5C1A). NT5C1A has a role in nucleoside metabolism as this protein primarily catalyzes the production of adenosine through the dephosphorylation of AMP. Adenosine metabolism is essential for lymphocyte maturation and viability, making NT5C1A an attractive leukemia susceptibility candidate to pursue further through functional genomic assays. Prior studies have shown that overexpression of wild type NT5C1A in HEK293 cells improves cell survival after treatment with purine and pyrimidine analogs also used in leukemia treatment. We created multiple HEK293 cell lines that stably overexpress either the NT5C1A wild type or L254P mutant protein. These cells were tested for quantitative changes in NT5C1A mediated cytotoxicity to the nucleoside analogs, Cladribine and Gemcitabine. We have replicated the prior findings in cells overexpressing wild type NT5C1A and demonstrated that resistance is dependent on the amount of exogenous NT5C1A protein expressed. Importantly, overexpression of the L254P protein is deficient in mediating resistance to these analogs, which is consistent with this novel variant interfering with NT5C1A activity. This finding has led us to hypothesize that the L254P mutation leads to a reduction in protein function, most likely through reduced substrate binding, which may increase AMP levels in early lymphocytes and predispose to tumorigenesis. Future directions include experiments to determine the L254P protein's substrate binding affinity and activity and the introduction of the mutation into murine leukemia models as well as analysis of L254P as a pharmacogenetic variant.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5113. doi:1538-7445.AM2012-5113

Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed

Multiple algorithms are used to predict the impact of missense mutations on protein structure and function using algorithm-generated sequence alignments or manually curated alignments. We compared the accuracy with native alignment of SIFT, Align-GVGD, PolyPhen-2, and Xvar when generating functionality predictions of well-characterized missense mutations (n = 267) within the BRCA1, MSH2, MLH1, and TP53 genes. We also evaluated the impact of the alignment employed on predictions from these algorithms (except Xvar) when supplied the same four alignments including alignments automatically generated by (1) SIFT, (2) Polyphen-2, (3) Uniprot, and (4) a manually curated alignment tuned for Align-GVGD. Alignments differ in sequence composition and evolutionary depth. Data-based receiver operating characteristic curves employing the native alignment for each algorithm result in area under the curve of 78-79% for all four algorithms. Predictions from the PolyPhen-2 algorithm were least dependent on the alignment employed. In contrast, Align-GVGD predicts all variants neutral when provided alignments with a large number of sequences. Of note, algorithms make different predictions of variants even when provided the same alignment and do not necessarily perform best using their own alignment. Thus, researchers should consider optimizing both the algorithm and sequence alignment employed in missense prediction.

Maturity-onset diabetes of the young (MODY): how many cases are we missing?

AIMS/HYPOTHESIS

Maturity-onset diabetes of the young is frequently misdiagnosed as type 1 or type 2 diabetes. A correct diagnosis of MODY is important for determining treatment, but can only be confirmed by molecular genetic testing. We aimed to compare the regional distribution of confirmed MODY cases in the UK and to estimate the minimum prevalence.

METHODS

UK referrals for genetic testing in 2,072 probands and 1,280 relatives between 1996 and 2009 were examined by region, country and test result. Referral rate and prevalence were calculated using UK Census 2001 figures.

RESULTS

MODY was confirmed in 1,177 (35%) patients, with HNF1A (52%) and GCK mutations (32%) being most frequent in probands confirmed with MODY. There was considerable regional variation in proband referral rates (from <20 per million in Wales and Northern Ireland to >50 per million for South West England and Scotland) and patients diagnosed with MODY (5.3 per million in Northern Ireland, 48.9 per million in South West England). Referral rates and confirmed cases were highly correlated (r = 0.96, p < 0.0001). The minimum prevalence of MODY was estimated to be 108 cases per million.

CONCLUSIONS/INTERPRETATION

Assuming this minimal prevalence throughout the UK then >80% of MODY is not diagnosed by molecular testing. The marked regional variation in the prevalence of confirmed MODY directly results from differences in referral rates. This could reflect variation in awareness of MODY or unequal access to genetic testing. Increased referral for diagnostic testing is required if the majority of MODY patients are to have the genetic diagnosis necessary for optimal treatment.

Conformational diversity of short DNA duplex

Two 25 base-pair cDNA strands are encapsulated within an optically trapped nanodroplet, and we observe the kinetics of their hybridization in dynamic equilibrium via single-molecule fluorescence resonance energy transfer (FRET) as a function of temperature and of the solution's NaCl concentration. We have observed the duplex unfolding and refolding, and we have observed quasistable partially unfolded states under low salinity conditions. Furthermore, our measurements reveal that, even in conditions under which the duplex is stable, it undergoes conformational fluctuations in solution.

The effects of plant traits and phylogeny on soil-to-plant transfer of 99Tc

Assessments of the behaviour of (99)Tc in terrestrial environments necessitate predicting soil-to-plant transfer. An experiment with 116 plant taxa showed that (99)Tc transfer to plants was positively related to plant dry weight but negatively related to % dry matter and age at exposure. Activities of (99)Tc analysed by hierarchical ANOVA coded with an angiosperm phylogeny revealed significant effects, with 55% of the variance between species explained at the Ordinal level and above. Monocots had significantly lower transfer of (99)Tc than Eudicots, within which Caryophyllales > Solanales > Malvales > Brassicales > Asterales > Fabales. There was a significant phylogenetic signal in soil-to-plant transfer of (99)Tc. This phylogenetic signal is used to suggest that, for example, a nominal Tc Transfer Factor of 5 could be adjusted to 2.3 for Monocots and 5.3 for Eudicots.