Life Sciences Commons^™

Deformable Motion Compensation In Interventional Cone-Beam Ct With A Context-Aware Learned Autofocus Metric, Heyuan Huang, Yixuan Liu, Jeffrey H Siewerdsen, Alexander Lu, Yicheng Hu, Mathias Unberath, Alejandro Sisniega

Faculty, Staff and Student Publications

Purpose: Interventional Cone-Beam CT (CBCT) offers 3D visualization of soft-tissue and vascular anatomy, enabling 3D guidance of abdominal interventions. However, its long acquisition time makes CBCT susceptible to patient motion. Image-based autofocus offers a suitable platform for compensation of deformable motion in CBCT, but it relies on handcrafted motion metrics based on first-order image properties and that lack awareness of the underlying anatomy. This work proposes a data-driven approach to motion quantification via a learned, context-aware, deformable metric, VIFDL , that quantifies the amount of motion degradation as well as the realism of the structural anatomical content in the image. …

International Consensus Guidelines For The Definition, Detection, And Interpretation Of Autophagy-Dependent Ferroptosis, Xin Chen, Andrey S Tsvetkov, Han-Ming Shen, Ciro Isidoro, Nicholas T Ktistakis, Werner J H Koopman, Lorenzo Galluzzi, Shouqing Luo, Daqian Xu, Wei Gu, Olivier Peulen, Qian Cai, David C Rubinsztein, Jen-Tsan Chi, Donna D Zhang, Changfeng Li, Shinya Toyokuni, Jinbao Liu, Jong-Lyel Roh, Enyong Dai, Gabor Juhasz, Wei Liu, Jianhua Zhang, Minghua Yang, Jiao Liu, Ling-Qiang Zhu, Weiping Zou, Mauro Piacentini, Wen-Xing Ding, Zhenyu Yue, Yangchun Xie, Morten Petersen, David A Gewirtz, Michael A Mandell, Charleen T Chu, Debasish Sinha, Eftekhar Eftekharpour, Boris Zhivotovsky, Sébastien Besteiro, Dmitry I Gabrilovich, Do-Hyung Kim, Valerian E Kagan, Hülya Bayir, Guang-Chao Chen, Scott Ayton, Jan D Lünemann, Masaaki Komatsu, Stefan Krautwald, Ben Loos, Eric H Baehrecke, Jiayi Wang, Jon D Lane, Junichi Sadoshima, Wan Seok Yang, Minghui Gao, Christian Münz, Michael Thumm, Martin Kampmann, Di Yu, Marta M Lipinski, Jace W Jones, Xuejun Jiang, Herbert J Zeh, Rui Kang, Daniel J Klionsky, Guido Kroemer, Daolin Tang

Faculty, Staff and Student Publications

Macroautophagy/autophagy is a complex degradation process with a dual role in cell death that is influenced by the cell types that are involved and the stressors they are exposed to. Ferroptosis is an iron-dependent oxidative form of cell death characterized by unrestricted lipid peroxidation in the context of heterogeneous and plastic mechanisms. Recent studies have shed light on the involvement of specific types of autophagy (e.g. ferritinophagy, lipophagy, and clockophagy) in initiating or executing ferroptotic cell death through the selective degradation of anti-injury proteins or organelles. Conversely, other forms of selective autophagy (e.g. reticulophagy and lysophagy) enhance the cellular defense …

Omicsmic: A Comprehensive Benchmarking Platform For Robust Comparison Of Imputation Methods In Mass Spectrometry-Based Omics Data, Weiqiang Lin, Jiadong Ji, Kuan-Jui Su, Chuan Qiu, Qing Tian, Zhe Luo, Hui Shen, Hongwen Deng

Faculty, Staff and Student Publications

Mass spectrometry is a powerful and widely used tool for generating proteomics, lipidomics and metabolomics profiles, which is pivotal for elucidating biological processes and identifying biomarkers. However, missing values in mass spectrometry-based omics data may pose a critical challenge for the comprehensive identification of biomarkers and elucidation of the biological processes underlying human complex disorders. To alleviate this issue, various imputation methods for mass spectrometry-based omics data have been developed. However, a comprehensive comparison of these imputation methods is still lacking, and researchers are frequently confronted with a multitude of options without a clear rationale for method selection. To address …

Prospective Performance Of The Iwg-2023 Criteria And Ipss-M In A Phase 2 Trial Of Guadecitabine For Higher-Risk Mds Or Cmml, Samuel Urrutia, Prithviraj Bose, Yesid Alvarado, Gautam Borthakur, Farhad Ravandi, Naveen Pemmaraju, Koichi Takahashi, Tapan Kadia, Courtney Dinardo, Steven Kornblau, Rashmi Kanagal-Shamanna, Xuelin Huang, Kristy Bodden, Hagop Kantarjian, Guillermo Garcia-Manero

Faculty, Staff and Student Publications

Guadecitabine (SGI-110) is a dinucleotide form of decitabine that has been studied in myelodysplastic syndrome (MDS) and acute myeloid leukemia. Here, we present the results of a single-center phase 2 trial of this agent for patients with higher-risk MDS or chronic myelomonocytic leukemia (CMML). Guadecitabine was administered at a dose of 60 mg/m2 subcutaneously for 5 days. Of 100 enrolled patients, 82% had MDS. The median age was 69 years, and International Prognostic Scoring System (IPSS) was intermediate-2 in 78% and high in 14%. Thirty-eight percent had complex cytogenetics, and 32% had TP53 mut . By the International Working Group …

Us Filipino Adults Have Elevated Prevalence Of Hypertension Across The Adult Lifespan: Findings From A Cross-Sectional Electronic Health Record Study, Nancy P Gordon, Irvin C Lien, Jamal S Rana, Joan C Lo

Faculty, Staff and Student Publications

INTRODUCTION: The prevalence of hypertension increases with age and differs by race and ethnicity. Among U.S. Asian adults, prevalence is higher for Filipino adults than for other major Asian subgroups, but whether this disparity exists across the adult lifespan is unknown. This study examined hypertension prevalence by age decade, comparing Filipino adults with South Asian, Chinese, Black, Hispanic, and White adults.

METHODS: This cross-sectional study used 2015-2016 electronic health record data from a Northern California integrated healthcare delivery system for 1,839,603 adults aged 30-79 years, including 128,124 Filipino adults. Hypertension was defined by diagnosis codes. Sex-specific prevalence was calculated by …

Determination Of Quality Of Life-Related Health Utilities For Surgical Complications In Ovarian Cancer, Rudy S Suidan, Charlotte C Sun, Amy K Schneider, Karen H Lu, Sharon H Giordano

Faculty, Staff and Student Publications

Objective: To assess the health state utilities of ovarian cancer patients, clinicians, and non-cancer controls regarding surgical complications in ovarian cancer.

Methods: Utilities for 14 surgical complications were assessed from patients with recently diagnosed or recurrent ovarian cancer, clinicians, and non-cancer controls using the visual analog scale (VAS) and time trade-off (TTO) methods. Health state utilities were converted to a 0-to-1 scale, where 0 represents the least favorable outcome and 1 represents the most favorable outcome.

Results: Fifty patients, 50 clinicians, and 50 controls participated. Median VAS scores were lower than TTO scores across all groups (p < 0.01). Patients viewed 'bleeding requiring transfusion' most favorably (VAS utility 0.75), followed in order by less favorable utility scores for hernia, thromboembolism, pleural effusion, abscess, ileus/bowel obstruction, wound infection, bowel obstruction requiring surgery, anastomotic leak requiring drain, temporary ostomy, anastomotic leak requiring surgery, genito-urinary fistula, permanent ostomy, and genito-intestinal fistula (VAS utility 0.2). Overall, clinicians perceived complications more favorably than patients by VAS (overall utility score 0.49 vs 0.43, p < 0.01), but not by the TTO. There were no differences in overall utility scores between patients and controls. Patients who had not experienced certain surgical complications had less favorable scores than patients who did (utility score for ostomy = 0.2 for patients without ostomy vs. 0.7 for patients with ostomy, p = 0.02).

Conclusions: This study …

Genome-Wide Interaction Study Of Dietary Intake Of Fibre, Fruits, And Vegetables With Risk Of Colorectal Cancer, Nikos Papadimitriou, Andre Kim, Eric S Kawaguchi, John Morrison, Virginia Diez-Obrero, Sonja I Berndt, Stephanie A Bien, D Timothy Bishop, Emmanouil Bouras, Hermann Brenner, Daniel D Buchanan, Peter T Campbell, Robert Carreras-Torres, Andrew T Chan, Jenny Chang-Claude, David V Conti, Matthew A Devall, Niki Dimou, David A Drew, Stephen B Gruber, Tabitha A Harrison, Michael Hoffmeister, Jeroen R Huyghe, Amit D Joshi, Temitope O Keku, Anshul Kundaje, Sébastien Küry, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Brigid M Lynch, Victor Moreno, Christina C Newton, Mireia Obón-Santacana, Jennifer Ose, Andrew J Pellatt, Anita R Peoples, Elizabeth A Platz, Conghui Qu, Gad Rennert, Edward Ruiz-Narvaez, Anna Shcherbina, Mariana C Stern, Yu-Ru Su, Duncan C Thomas, Claire E Thomas, Yu Tian, Konstantinos K Tsilidis, Cornelia M Ulrich, Caroline Y Um, Kala Visvanathan, Jun Wang, Emily White, Michael O Woods, Stephanie L Schmit, Finlay Macrae, John D Potter, John L Hopper, Ulrike Peters, Neil Murphy, Li Hsu, Marc J Gunter, W James Gauderman

Faculty, Staff and Student Publications

Background: Consumption of fibre, fruits and vegetables have been linked with lower colorectal cancer (CRC) risk. A genome-wide gene-environment (G × E) analysis was performed to test whether genetic variants modify these associations.

Methods: A pooled sample of 45 studies including up to 69,734 participants (cases: 29,896; controls: 39,838) of European ancestry were included. To identify G × E interactions, we used the traditional 1--degree-of-freedom (DF) G × E test and to improve power a 2-step procedure and a 3DF joint test that investigates the association between a genetic variant and dietary exposure, CRC risk and G × E interaction …

Predictive Capacity Of Immune-Related Adverse Events And Cytokine Profiling In Neoadjuvant Immune Checkpoint Inhibitor Trials For Head And Neck Squamous Cell Carcinoma\, Angela E Alnemri, Sruti Tekumalla, Annie E Moroco, Ioannis Vathiotis, Madalina Tuluc, Tingting Zhan, Joseph M Curry, Athanassios Argiris, Alban Linnenbach, Andrew P South, Larry A Harshyne, Jennifer M Johnson, Adam J Luginbuhl

Faculty, Staff and Student Publications

OBJECTIVES: Certain low-level immune-related adverse events (irAEs) have been associated with survival benefits in patients with various solid tumors on immune checkpoint inhibitors (ICIs). We aimed to investigate the association between irAEs and response to neoadjuvant ICIs in patients with head and neck squamous cell carcinoma (HNSCC) and to identify differences in circulating cytokine levels based on irAE status.

METHODS: This was a retrospective cohort study including three neoadjuvant clinical trials from July 2017 to January 2022: NCT03238365 (nivolumab ± tadalafil), NCT03854032 (nivolumab ± BMS986205), NCT03618654 (durvalumab ± metformin). The presence and type of irAEs, pathologic treatment response, and survival …

Immune Checkpoint Blockade Resistance In Lung Cancer: Emerging Mechanisms And Therapeutic Opportunities, Jessica M Konen, Haoyi Wu, Don L Gibbons

Faculty, Staff and Student Publications

Immune checkpoint blockade (ICB) therapy works by inhibiting suppressive checkpoints that become upregulated after T cell activation, like PD-1/PD-L1 and CTLA-4. While the initial FDA approvals of ICB have revolutionized cancer therapies and fueled a burgeoning immuno-oncology field, more recent clinical development of new agents has been slow. Here, focusing on lung cancer, we review the latest research uncovering tumor cell intrinsic and extrinsic ICB resistance mechanisms as major hurdles to treatment efficacy and clinical progress. These include genomic and non-genomic tumor cell alterations, along with host and microenvironmental factors like the microbiome, metabolite accumulation, and hypoxia. Together, these factors …

From Pre-Clinical To Translational Brain Metastasis Research: Current Challenges And Emerging Opportunities, Emilija Aleksandrovic, Siyuan Zhang, Dihua Yu

Faculty, Staff and Student Publications

Brain metastasis, characterized by poor clinical outcomes, is a devastating disease. Despite significant mechanistic and therapeutic advances in recent years, pivotal improvements in clinical interventions have remained elusive. The heterogeneous nature of the primary tumor of origin, complications in drug delivery across the blood-brain barrier, and the distinct microenvironment collectively pose formidable clinical challenges in developing new treatments for patients with brain metastasis. Although current preclinical models have deepened our basic understanding of the disease, much of the existing research on brain metastasis has employed a reductionist approach. This approach, which often relies on either in vitro systems or in …

A Phase I Study Of Tak-659 And Paclitaxel In Patients With Taxane-Refractory Advanced Solid Tumors, M A Gouda, J Shunyakova, A Naing, E Dumbrava, D S Hong, P Yang, Y Liang, J Peng, D Karp, A M Tsimberidou, J Rodon, T A Yap, S A Piha-Paul, F Meric-Bernstam, S Fu

Faculty, Staff and Student Publications

BACKGROUND: Paclitaxel resistance limits durability of response in patients with initial clinical benefit. Overexpression of spleen tyrosine kinase (SYK) has been proposed as a possible resistance mechanism. This phase I trial evaluated the safety and preliminary activity of the SYK inhibitor TAK-659 combined with paclitaxel in patients with advanced taxane-refractory solid tumors.

PATIENTS AND METHODS: Patients with advanced solid tumors and prior progression on taxane-based therapy received intravenous infusion of paclitaxel on days 1, 8, and 15 plus oral TAK-659 daily in 28-day cycles. The dose-escalation phase included six cohorts treated at different dose levels; the dose-expansion phase included patients …

Positron Emission Tomography In Oncology And Environmental Science, Samantha Delaney

Dissertations, Theses, and Capstone Projects

The last half century has played witness to the onset of molecular imaging for the clinical assessment of physiological targets. While several medical imaging modalities allow for the visualization of the functional and anatomical properties of humans and living systems, few offer accurate quantitation and the ability to detect biochemical processes with low-administered drug mass doses. This limits how physicians and scientists may diagnose and treat medical issues, such as cancer, disease, and foreign agents.

A promising alternative to extant invasive procedures and suboptimal imaging modalities to assess the nature of a biological environment is the use of positron emission …

Listening For Lemurs: Translating Black-And-White Ruffed Lemur (Varecia Variegata) Vocalizations Into Conservation Insights Through Acoustic Monitoring, Carly H. Batist

Dissertations, Theses, and Capstone Projects

The field of bioacoustic monitoring has undergone a significant evolution in recent years, driven by technological innovations that have revolutionized how researchers study animal vocalizations. Traditionally, bioacoustics was rooted in active acoustic monitoring (AAM), involving human observers using recorders in the field to study animal sounds and understand species' vocal communication. However, the emergence of passive acoustic monitoring (PAM) has introduced a new complementary approach, utilizing specialized recorders placed in ecosystems to autonomously capture sounds at wide spatial and temporal scales. My dissertation adopts a translational approach to bioacoustic monitoring, integrating both AAM and PAM techniques to study and survey …

Systematics And Comparative Genomics Of The Petaluridae (Odonata: Anisoptera), Ethan R. Tolman

Dissertations, Theses, and Capstone Projects

The Anisoptera (Insecta: Odonata), or dragonflies exhibit diverse life histories and diversification patterns, with the family Petaluridae standing out as particularly unique. Comprising only 11 extant species, all of which inhabit increasingly threatened fen habitats, Petaluridae are known for their longevity, which can exceed five years, semi-terrestrial lifestyle, and remarkable physical size, ranking among the largest insects on Earth. Despite the evolutionary peculiarities of this family, no previous genomic studies have investigated the Petaluridae. This work presents two high-quality genome sequences and a targeted enrichment dataset to explore the chromosome architecture of Petaluridae, identifies genomic adaptations associated with their distinctive …

High Mdmx (Mdm4) In Mutant P53 Expressing Breast Cancer Cells Activates The Cxcl12-Cxcr4 Metastasis Signaling Axis, Rusia H. Lee

Dissertations, Theses, and Capstone Projects

The metastasis-promoting G-protein coupled receptor (GPCR) CXCR4 is activated by the cytokine CXCL12 (also known as SDF-1) to promote metastasis through CXCR4 upregulation. High CXCR4-expressing cancer cells utilize CXCL12, the exclusive endogenous ligand of CXCR4, to intravasate into the blood as circulating tumor cells (CTCs) which then extravasate to distant metastatic sites. We previously determined the oncogenes, Mouse Double Minute 2 and 4 (MDM2 and MDM4, also known as MDMX), drive TNBC metastasis and positively correlate with high expression of CXCR4. Interestingly, this upregulation of CXCR4 was only observed in primary tumor cells grown in the tumor microenvironment …

Machine-Learning Qsar-Based Novel Drug Identification To Inhibit Retinoblastoma Extracellular Vesicle Release And Metastatic Signaling, Kunhui Huang

Dissertations, Theses, and Capstone Projects

Extracellular vesicles (EVs) are lipid-enclosed particles that are generated by most types of cells and have been identified as an important mechanism for cell communication aside from cell direct contact. EVs contain a variety of functional macromolecules including proteins, lipids, RNA, which can be transferred from the host cells to target cells at a distance. The molecular pathways of EV biogenesis have been studied intensely in recent decades and the process involves several key genes and proteins. Cancer cell released EVs target distant tissues and upregulate signals that are attractive to cancer cell homing, playing a role in tumor progression …

Flanker Task Performance In Young And Older Adults: A Behavioral And Erp Study, Fatima Medrano

Dissertations, Theses, and Capstone Projects

Research suggests that as we get older, executive function abilities decline (Hasher & Zacks, 1988; Salthouse, 1996). One affected ability is that of inhibitory control, which aids in monitoring our responses to non-target stimuli or information. Current research on inhibition reveals inconsistencies across studies. Monitoring brain responses during the Flanker (used to measure inhibitory control) task may add valuable insight into the processes underlying group differences behaviorally, by studying the N200 and P300 event-related potentials which have been associated with inhibitory control processes. This study investigated whether there are differences between older and younger adults in inhibitory control and whether …

Integrating In Vitro And In Silico Approaches To Gain Insight Into The Mechanism Of Amyloid Fibrillogenesis, Marvin M. Bilog

Dissertations, Theses, and Capstone Projects

Amyloid fibril formation, the hallmark of numerous amyloid-related diseases, has been the subject of a vast number of scientific studies due to its pathological implications. Since the fibrillization process exhibits a certain level of intricacy, its investigation requires a multidisciplinary approach that integrates both experimental and computational methods. In vitro techniques involve biophysical assays and imaging tools for characterizing the structural and kinetic aspects of amyloid fibril formation. In parallel, in silico techniques offer programs for predicting atomistic details and behaviors of amyloidogenic proteins and peptides at the nanoscale level. Serum amyloid A (SAA), human islet amyloid polypeptide (hIAPP), and …

Cross-Linguistic Differences In Neural Encoding And Processing Of Stop Consonants: The Impact Of Language Experience On Attention Allocation, Aline Dos Santos Oliveira

Dissertations, Theses, and Capstone Projects

This study aims to examine the intricate relationship between language experience and the neural processing of stop consonant speech sounds. Previous research has shown minimal differences in amplitudes and latencies of cortical Auditory Evoked Potentials (AEPs) to speech sounds across listeners from various language backgrounds. It is only towards the later latencies (around the P2 peak at 200 ms), that there have been suggestions of cross-linguistic differences. In addition, a recent study, observed an AEP difference between monolinguals and bilinguals when processing speech, specifically an "Nd effect”. The Nd effect, which is an increased negativity of the AEP is proposed …

Germline Predisposition In Hematologic Malignancies: Testing, Management, And Implications, Lucy A Godley, Courtney D Dinardo, Kelly Bolton

Faculty, Staff and Student Publications

Although numerous barriers for clinical germline cancer predisposition testing exist, the increasing recognition of deleterious germline DNA variants contributing to myeloid malignancy risk is yielding steady improvements in referrals for testing and testing availability. Many germline predisposition alleles are common in populations, and the increasing number of recognized disorders makes inherited myeloid malignancy risk an entity worthy of consideration for all patients regardless of age at diagnosis. Germline testing is facilitated by obtaining DNA from cultured skin fibroblasts or hair bulbs, and cascade testing is easily performed via buccal swab, saliva, or blood. Increasingly as diagnostic criteria and clinical management …

Response To: Comment On "Effects Of A Pragmatic Home-Based Exercise Program Concurrent With Neoadjuvant Therapy On Physical Function Of Patients With Pancreatic Cancer: The Pancfit Randomized Clinical Trial", An T Ngo-Huang, Nathan H Parker, Keri L Schadler, Matthew H G Katz

Faculty, Staff and Student Publications

No abstract provided.

Clinical Features And Genomic Epidemiology Of Bloodstream Infections Due To Enterococcal Species Other Than Enterococcus Faecalis Or E Faecium In Patients With Cancer, Dierdre B Axell-House, Patrycja A Ashley, Stephanie L Egge, Truc T Tran, Claudia Pedroza, An Q Dinh, Pranoti V Sahasrabhojane, William R Miller, Samuel A Shelburne, Blake M Hanson, Cesar A Arias

Faculty, Staff and Student Publications

BACKGROUND: Non–Enterococcus faecium, non–E. faecalis (NFF) enterococci are a heterogeneous group of clinically pathogenic enterococci that include species with intrinsic low-level vancomycin resistance. Patients with cancer are at increased risk for bacteremia with NFF enterococci, but their clinical and molecular epidemiology have not been extensively described.

METHODS: We conducted a retrospective review of all patients (n = 70) with NFF bacteremia from 2016 to 2022 at a major cancer center. The main outcomes assessed were 30-day mortality, microbiological failure (positive blood cultures for ≥4 days), and recurrence of bacteremia (positive blood cultureclearance). Whole-genome sequencing was performed on all …

Prostein Expression On Circulating Tumor Cells As A Prognostic Marker In Metastatic Castration-Resistant Prostate Cancer, Zhenchao Zhang, Rui Luo, William K Kelly, Joshua Chen, Shane Donahue, Nathan R Handley, Miranda L Tsang, Felix J Kim, Ronald Myers, Grace Lu-Yao, Jian Gu, Jianqing Lin, Bingshan Li, Chun Wang, Hushan Yang

Faculty, Staff and Student Publications

Background: Identification of emerging molecular biomarkers on circulating tumor cells (CTCs) represents an attractive feature of liquid biopsy that facilitates precision and tailored medicine in the management of metastatic castration-resistant prostate cancer (mCRPC). Prostein is an androgen-regulated transmembrane protein with high prostate specificity. Prostein-positive circulating tumor cell (CTC) was recently suggested to have diagnostic potential; however, no study has been conducted to evaluate its prognostic value in mCRPC.

Methods: CTCs from mCRPC patients were enumerated using the CellSearch System. Prostein-positive CTCs were identified by immunostaining results. The relationships between prostein expression on CTCs and PSA response rate, PSA progression-free survival …

Utilization Of Biologic Disease-Modifying Antirheumatic Therapy In Patients With Rheumatoid Arthritis And Recently Diagnosed Breast Cancer, Juan I Ruiz, Xiudong Lei, Chi-Fang Wu, Hui Zhao, Sharon H Giordano, Maria E Suarez-Almazor

Faculty, Staff and Student Publications

Objective: Biologic disease-modifying antirheumatic drugs (bDMARDs) are immunosuppressants, and there have been concerns that they might impact tumor immunity in patients with cancer with rheumatoid arthritis (RA). The purpose of this study was to describe the utilization trends of bDMARD in patients with RA after breast cancer (BC) diagnosis.

Methods: We performed a retrospective cohort study of adults with RA and BC (2008 onward) from Optum's de-identified Clinformatics® Data Mart Database (CDM); the Surveillance, Epidemiology, and End Results Program (SEER) Medicare; and the Texas Cancer Registry (TCR) Medicare databases. We evaluated bDMARD utilization trends during the first three years after …

Cardiovascular Disease In Childhood, Adolescent, And Young Adult Cancer Survivors: The Impact Of Family History Of Premature Heart Disease, Amy M Berkman, Clark R Andersen, Andrew P Landstrom, Michelle A T Hildebrandt, Susan C Gilchrist

Faculty, Staff and Student Publications

No abstract provided.

A Bayesian Quasi-Likelihood Design For Identifying The Minimum Effective Dose And Maximum Utility Dose In Dose-Ranging Studies, Feng Tian, Ruitao Lin, Li Wang, Ying Yuan

Faculty, Staff and Student Publications

Most existing dose-ranging study designs focus on assessing the dose-efficacy relationship and identifying the minimum effective dose. There is an increasing interest in optimizing the dose based on the benefit-risk tradeoff. We propose a Bayesian quasi-likelihood dose-ranging design that jointly considers safety and efficacy to simultaneously identify the minimum effective dose and the maximum utility dose to optimize the benefit-risk tradeoff. The binary toxicity endpoint is modeled using a beta-binomial model. The efficacy endpoint is modeled using the quasi-likelihood approach to accommodate various types of data (e.g. binary, ordinal or continuous) without imposing any parametric assumptions on the dose-response curve. …

Statistical And Practical Considerations In Planning And Conduct Of Dose-Optimization Trials, Ying Yuan, Heng Zhou, Suyu Liu

Faculty, Staff and Student Publications

The U.S. Food and Drug Administration launched Project Optimus with the aim of shifting the paradigm of dose-finding and selection toward identifying the optimal biological dose that offers the best balance between benefit and risk, rather than the maximum tolerated dose. However, achieving dose optimization is a challenging task that involves a variety of factors and is considerably more complicated than identifying the maximum tolerated dose, both in terms of design and implementation. This article provides a comprehensive review of various design strategies for dose-optimization trials, including phase 1/2 and 2/3 designs, and highlights their respective advantages and disadvantages. In …

Cascade Genetic Testing: An Underutilized Pathway To Equitable Cancer Care?, Roni Nitecki Wilke, Erica M Bednar, Sara Pirzadeh-Miller, Sayoni Lahiri, Isabel C Scarinci, Melissa K Frey, J Alejandro Rauh-Hain

Faculty, Staff and Student Publications

The Precision Medicine Initiative was launched upon the potential of genomic information to tailor medical care. Cascade genetic testing represents a powerful application of precision medicine and involves the process of familial diffusion or the "cascade" of genomic risk information. When an individual (proband) is found to carry a cancer-associated germline pathogenic mutation, the information should be cascaded or shared with at-risk relatives. First degree relatives have a 50% likelihood of carrying the same cancer-associated mutation. This process of cascade testing offers at-risk relatives the opportunity for genetic testing and, for those who also carry the cancer-associated mutation, genetically targeted …

A Prismatic View Of The Epigenetic-Metabolic Regulatory Axis In Breast Cancer Therapy Resistance, Chandrima Das, Apoorva Bhattacharya, Swagata Adhikari, Atanu Mondal, Payel Mondal, Siddhartha Roy, Kamlesh K Yadav, John A Tainer, Tej K Pandita

Faculty, Staff and Student Publications

Epigenetic regulation established during development to maintain patterns of transcriptional expression and silencing for metabolism and other fundamental cell processes can be reprogrammed in cancer, providing a molecular mechanism for persistent alterations in phenotype. Metabolic deregulation and reprogramming are thus an emerging hallmark of cancer with opportunities for molecular classification as a critical preliminary step for precision therapeutic intervention. Yet, acquisition of therapy resistance against most conventional treatment regimens coupled with tumor relapse, continue to pose unsolved problems for precision healthcare, as exemplified in breast cancer where existing data informs both cancer genotype and phenotype. Furthermore, epigenetic reprograming of the …

Mortality In Recipients Of Allogeneic Haematopoietic Cell Transplantation In The Era Of Cytomegalovirus Primary Prophylaxis: A Single-Centre Retrospective Experience, Anthony Febres-Aldana, Fareed Khawaja, Oscar Morado-Aramburo, Terri Lynn Shigle, Gabriela Rondon, Amy Spallone, Jeremy Ramdial, Amin Alousi, Richard Champlin, George Chen, May Daher, Katayoun Rezvani, Ella J Ariza-Heredia, Elizabeth J Shpall, Roy F Chemaly

Faculty, Staff and Student Publications

Objectives: Allogeneic haematopoietic cell transplant (allo-HCT) recipients who are cytomegalovirus (CMV)-seronegative have better post-transplant outcomes than CMV-seropositive recipients. Letermovir (LTV) is approved for CMV primary prophylaxis in adults who are CMV-seropositive after allo-HCT, and its use is associated with improved long-term post-transplant outcomes. We analysed whether LTV has affected the relationship between CMV serostatus and post-transplant outcomes.

Methods: We conducted a retrospective single-centre cohort study of allo-HCT recipients, stratified according to donor (D) and recipient (R). CMV serostatus and the use of LTV: D-/R-, R+/LTV-, and R+/LTV+. Outcomes measured were all-cause and non-relapse mortality, clinically significant CMV infection, graft-versus-host disease, …