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Consensus Guideline for the Management of Gastric Cancer with Synchronous Peritoneal Metastases medRxiv. Oncol. Pub Date : 2024-04-21 PSM Writing Group, PSM Consortium Group, Kiran K Turaga
Background Gastric cancer with synchronous peritoneal metastases (GCPM) is a debilitating disease with limited treatment options. This manuscript describes an update of the 2018 Chicago Consensus Guidelines addressing the management of GCPM in line with most recent evidence.
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The role of pulmonary metastasectomy (PM) for non-primary lung cancer: Umbrella review of meta-analyses medRxiv. Oncol. Pub Date : 2024-04-20 Wongi Woo, Brandon Park, Awranoos Ahadi, Liam il-young Chung, Chan Mi Jung, Ankit Bharat, Young Kwang Chae
Introduction Due to heterogeneous characteristics of primary cancers, the efficacy of pulmonary metastasectomy(PM) in non-primary lung cancers has not been investigated other than colorectal cancers. This study aims to investigate the clinical outcomes of PM for non-primary lung cancer.
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Multiparametric MRI Along with Machine Learning Informs on Molecular Underpinnings, Prognosis, and Treatment Response in Pediatric Low-Grade Glioma medRxiv. Oncol. Pub Date : 2024-04-19 Anahita Fathi Kazerooni, Adam Kraya, Komal S. Rathi, Meen Chul Kim, Arastoo Vossough, Nastaran Khalili, Ariana Familiar, Deep Gandhi, Neda Khalili, Varun Kesherwani, Debanjan Haldar, Hannah Anderson, Run Jin, Aria Mahtabfar, Sina Bagheri, Yiran Guo, Qi Li, Xiaoyan Huang, Yuankun Zhu, Alex Sickler, Matthew R. Lueder, Saksham Phul, Mateusz Koptyra, Phillip B. Storm, Jeffrey B. Ware, Yuanquan Song, Christos
In this study, we present a comprehensive radiogenomic analysis of pediatric low-grade gliomas (pLGGs), combining treatment-naïve multiparametric MRI and RNA sequencing. We identified three immunological clusters using XCell enrichment scores, highlighting an ‘immune-hot’ group correlating with poorer prognosis, suggesting potential benefits from immunotherapies. A radiomic signature predicting immunological
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Computational flow cytometry immunophenotyping at diagnosis is unable to predict relapse in childhood B-cell Acute Lymphoblastic Leukemia medRxiv. Oncol. Pub Date : 2024-04-19 Álvaro Martínez-Rubio, Salvador Chulián, Ana Niño-López, Rocío Picón-González, Juan F. Rodríguez Gutiérrez, Eva Gálvez de la Villa, Teresa Caballero Velázquez, Águeda Molinos Quintana, Ana Castillo Robleda, Manuel Ramírez Orellana, María Victoria Martínez Sánchez, Alfredo Minguela Puras, José Luis Fuster Soler, Cristina Blázquez Goñi, Víctor M. Pérez-García, María Rosa
B-cell Acute Lymphoblastic Leukemia is the most prevalent form of childhood cancer, with approximately 15% of patients undergoing relapse after initial treatment. Further advancements depend on novel therapies and more precise risk stratification criteria. In the context of computational flow cytometry and machine learning, this paper aims to explore the potential prognostic value of flow cytometry
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Prophylactic Para Aortic Irradiation vs Pelvic Radiotherapy in Pelvic node-positive Carcinoma Cervix in the setting of concurrent chemoradiation: A phase II Open-label Multi centric Randomized Controlled Trial (PRO-PARA) medRxiv. Oncol. Pub Date : 2024-04-19 Tapesh Bhattacharyya, Santam Chakraborty, Bhavana Rai, Shirley Lewis, Srinivas Gowda, Anurupa Mahata, Samar Mandal, Gaurav Trivedi, Sreekripa Rao, Sarath Shyan
Background EMBRACE and Retro EMBRACE studies have shown that excellent local control and pelvic control could be achieved with concurrent chemoradiation and MRI-based brachytherapy in carcinoma cervix. Now para aortic nodal failure and distant metastasis are the predominant modes of failure. Paraaortic nodal failure rates are higher in pelvic node-positive cases as compared to pelvic node-negative
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How many microbial species are there in human tumor and normal tissues? medRxiv. Oncol. Pub Date : 2024-04-19 Zhanshan (Sam) Ma
The study of tissue microbiomes is a recent endeavor in human microbiome research, particularly in the area of blood microbiomes. This is primarily due to their low biomass, which presents inadvertent operational contamination as a significant experimental obstacle. The critical role of the tissue microbiomes in cancer development has brought this topic to the forefront of cancer research. However
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Incorporating Real-World Clinico-Genomic Insights to Inform Diversity Enrollment Targets in Oncology Trials medRxiv. Oncol. Pub Date : 2024-04-19 Francisco M. De La Vega, Yannick Pouliot, Brooke Rhead
The passage of the US Food and Drug Administration (FDA) Omnibus Reform Act of 2022 underscores a national commitment to enhancing diversity in clinical trials. This commitment recognizes not only the ethical imperative of inclusivity but also the practical necessity to ensure the safety and efficacy of medications across all demographic groups. Particularly for Phase 3 and pivotal clinical trials
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MPN Transformation Is Characterized By Heterogeneous Shifts In Lineage Character Resulting In Both HSC-Like And More Differentiated Lineage Signatures medRxiv. Oncol. Pub Date : 2024-04-19 Kamal Menghrajani, Deepika Dilip, Noushin Farnoud, Chris Famulare, Erin McGovern, Maria Sirenko, John Mascarenhas, Heidi Kosiorek, Ronald Hoffman, Ross Levine, Richard Koche, Raajit Rampal, Jacob Glass
Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs) have a propensity to transform to an accelerated or blast phase (MPN-AP/BP). The resulting disease has clinically similar manifestations to Acute Myeloid Leukemia (AML) but worse clinical outcomes. Here we present the first comprehensive description of the transcriptomic characteristics of MPN-AP/BP. Our analysis incorporates data
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Adiposity, metabolites and endometrial cancer risk: Mendelian randomization and Observational analyses medRxiv. Oncol. Pub Date : 2024-04-19 Matthew A Lee, Vanessa Y. Tan, Dimitri J Pournaras, Sabrina Wang, Laure Dossus, Marc J. Gunter, Kaitlin H. Wade, Laura J. Corbin, Nicholas J. Timpson
Introduction Increased and excess adiposity is associated with increased risk of endometrial cancer (EC) and both of these are associated with circulating metabolite profiles. However, how metabolites relate to the adiposity-EC relationship remains unclear.
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Pan-cancer proteogenomic landscape of whole-genome doubling reveals putative therapeutic targets in various cancer types medRxiv. Oncol. Pub Date : 2024-04-18 Eunhyong Chang, Hee Sang Hwang, Kyu Jin Song, Kwoneel Kim, Min-Sik Kim, Se Jin Jang, Kwang Pyo Kim, Sungyong You, Joon-Yong An
Background Whole-genome doubling (WGD) is prevalent in cancer and drives tumor development and chromosomal instability. Driver mutations in mitotic cell cycle genes and cell cycle upregulation have been reported as the major molecular underpinnings of WGD tumors. However, the underlying genomic signatures and regulatory networks involved in gene transcription and kinase phosphorylation remain unclear
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Integrating bulk and single-cell RNA sequencing reveals SH3D21 promotes hepatocellular carcinoma progression by activating the PI3K/AKT/mTOR pathway medRxiv. Oncol. Pub Date : 2024-04-16 Wangxia Tong, Tao Lu, Li Liu, Rong Liu, Jibing Chen, Ning Luo
As a novel genetic biomarker, the potential role of SH3D21 in hepatocellular carcinoma remains unclear. Here, we decipher the expression and function of SH3D21 in human hepatocellular carcinoma. The expression level and clinical significance of SH3D21 in hepatocellular carcinoma patients, the relationship between SH3D21 and the features of tumor microenvironment (TME) and role of SH3D21 in promoting
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Bridge Capture Permits Cost-Efficient, Rapid and Sensitive Molecular Precision Diagnostics medRxiv. Oncol. Pub Date : 2024-04-15 Simona Adamusová, Anttoni Korkiakoski, Tatu Hirvonen, Anna Musku, Tuula Rantasalo, Nea Laine, Jukka Laine, Juuso Blomster, Juha-Pekka Pursiheimo, Manu Tamminen
Liquid biopsies are gaining popularity as a less invasive alternative to tissue biopsies that have been the mainstay of cancer diagnostics to date. Recently, the quantification of mutations in circulating tumor DNA (ctDNA) by next-generation sequencing (NGS) has been gaining popularity. Targeted NGS approaches are preferable in ctDNA analysis as they provide greater sequencing depth and affordability
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Detection of Microsatellite Instability in Colorectal Cancer Tissue and Plasma samples using a new Multiplex Droplet Digital PCR kit medRxiv. Oncol. Pub Date : 2024-04-15 Camille Evrard, Kariman Chaba, Justine Abdelli, Simon Garinet, Helene Blons, Aziz Zaanan, Jean-Baptiste Bachet, Leonor Benhaim, Claire Mulot, Audrey Didelot, Delphine Le Corre, Jerianne Lukban, Jennifer Yin, Adam Corner, Mai Ho, Valérie Taly, David Tougeron, Pierre Laurent-Puig
Management of colorectal cancer (CRC) patients relies on the accurate determination of microsatellite instability (MSI) status. MSI status can have an influence on therapy decisions centered on immune checkpoint inhibitors. In this study a novel droplet digital PCR (ddPCR) kit for MSI status determination was validated across 2 separate CRC patient cohorts: 102 tumor samples from the ALGECOLS cohort
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Folate receptor alpha protein expression in ovarian serous cystadenocarcinoma tumors of The Cancer Genome Atlas: exploration beyond single-agent therapy medRxiv. Oncol. Pub Date : 2024-04-14 Christianne Persenaire, Benjamin G. Bitler, Bradley R. Corr
Epithelial ovarian cancer (EOC) can be highly lethal, with limited therapeutic options for patients with non-homologous recombination deficient (HRD) disease. Folate receptor alpha (FOLR1/FRα)-targeting agents have shown promise both alone and in combination with available therapies, but the relationship of FRα to other treatment-driving biomarkers is unknown. The Cancer Genome Atlas (TCGA) was queried
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Evaluation of Artificial Intelligence (AI)-based in silico tools for variant classification in clinically actionable NSCLC variants medRxiv. Oncol. Pub Date : 2024-04-14 Eugene Kim, Samantha E Duarte, Emma Yu, Ilene Hong, Grace Lee, Young Kwang Chae
Introduction/Background Genetic variants beyond FDA-approved drug targets are often identified in non-small cell lung cancer (NSCLC) patients. Although the performances of in silico tools in predicting variant pathogenicity have been analyzed in previous studies, they have not been analyzed for actionable targets of FDA-approved therapies for NSCLC. The aim of this study is to compare the performance
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Identification of ovarian high-grade endometrioid-type tumors through multi-omics analysis: JGOG3025-TR2 study medRxiv. Oncol. Pub Date : 2024-04-13 Shiro Takamatsu, R. Tyler Hillman, Kosuke Yoshihara, Tsukasa Baba, Muneaki Shimada, Hiroshi Yoshida, Hiroaki Kajiyama, Katsutoshi Oda, Masaki Mandai, Aikou Okamoto, Takayuki Enomoto, Noriomi Matsumura
Objective There is considerable interobserver variability in the differential diagnosis between ovarian high-grade endometrioid carcinoma (HGEC) and ovarian high-grade serous carcinoma (HGSC) due to their histopathological similarities. While the association between homologous recombination deficiency (HRD) and platinum sensitivity and PARP inhibitors is well established in HGSC, the molecular characteristics
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Consensus Guideline for the Management of Malignant Gastrointestinal Obstruction in Patients with Peritoneal Surface Malignancies medRxiv. Oncol. Pub Date : 2024-04-13 PSM Writing Group, PSM Consortium Group, Kiran K. Turaga
Background Malignant gastrointestinal obstruction (MGIO), a frequent complication of peritoneal surface malignancies (PSM), often portends a poor prognosis. The lack of high-quality evidence on optimal management strategies necessitated a national consensus to address this clinical problem.
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Consensus Guideline for the Management of Patients with Peritoneal Mesothelioma medRxiv. Oncol. Pub Date : 2024-04-13 PSM Writing Group, PSM Consortium Group, Kiran K Turaga
Background Treatment of peritoneal mesothelioma (PeM) poses significant challenges owing to its rare incidence, heterogeneity and limited clinical evidence. This manuscript describes results from a national consensus aimed at addressing management of PeM.
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Consensus Guideline for the Management of Peritoneal Metastases in Patients with Neuroendocrine Neoplasms medRxiv. Oncol. Pub Date : 2024-04-13 Kiran Turaga
Background Neuroendocrine neoplasms (NEN) with peritoneal metastases (PM) represent a complex clinical challenge due to low incidence and heterogeneous phenotypes. This manuscript describes the results of a national consensus aimed at addressing clinical management of patients with NEN-PMs.
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Conditional Survival and Nomogram for Elderly Non-Metastatic Colon Cancer Patients Following Colectomy medRxiv. Oncol. Pub Date : 2024-04-12 Yadong Gao, Huimin Wang, Yi Zhang, Jing Zhao, Sujuan Feng, Jianwei Qiu
Background This study aimed to evaluate the conditional survival (CS) of elderly patients with non-metastatic colon cancer who underwent colectomy and build conditional nomograms that can accommodate varying survival periods and estimate survival rates.
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Deep generative AI models analyzing circulating orphan non-coding RNAs enable accurate detection of early-stage non-small cell lung cancer medRxiv. Oncol. Pub Date : 2024-04-12 Mehran Karimzadeh, Amir Momen-Roknabadi, Taylor B. Cavazos, Yuqi Fang, Nae-Chyun Chen, Michael Multhaup, Jennifer Yen, Jeremy Ku, Jieyang Wang, Xuan Zhao, Philip Murzynowski, Kathleen Wang, Rose Hanna, Alice Huang, Diana Corti, Dang Nguyen, Ti Lam, Seda Kilinc, Patrick Arensdorf, Kimberly H. Chau, Anna Hartwig, Lisa Fish, Helen Li, Babak Behsaz, Olivier Elemento, James Zou, Fereydoun Hormozdiari, Babak
Liquid biopsies have the potential to revolutionize cancer care through non-invasive early detection of tumors, when the disease can be more effectively managed and cured. Developing a robust liquid biopsy test requires collecting high-dimensional data from a large number of blood samples across heterogeneous groups of patients. We propose that the generative capability of variational auto-encoders
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Consensus guideline for the management of patients with appendiceal tumors Part 1: Appendiceal tumors without peritoneal involvement medRxiv. Oncol. Pub Date : 2024-04-12 PSM Appendiceal Tumor Writing Group, PSM Consortium Group, Kiran K Turaga
Background Appendiceal tumors comprise a heterogeneous group of tumors which may be localized or disseminate throughout the peritoneum. Limited high quality clinical data exists and many practices have been extrapolated from colorectal cancer without validation in appendiceal cohorts. Many controversies exist regarding their treatment, and practices vary widely between centers and care settings. A
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Optimized patient-specific immune checkpoint inhibitors therapy for cancer treatment based on tumor immune microenvironment modeling medRxiv. Oncol. Pub Date : 2024-04-10 Yao Yao, Frank Youhua Chen, Qingpeng Zhang
Objective Enhancing patient response to immune checkpoint inhibitors (ICIs) is crucial in cancer immunotherapy. We aim to create a data-driven mathematical model of the tumor immune microenvironment (TIME) and utilize deep reinforcement learning (DRL) to optimize patient-specific ICI therapy combined with chemotherapy (ICC).
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Establishing the Automatic Identification of Clinical Trial Cohorts from Electronic Health Records by Matching Normalized Eligibility Criteria and Patient Clinical Characteristics medRxiv. Oncol. Pub Date : 2024-04-09 K. Lee, Y. Mai, Z. Liu, K. Raja, M. K. Higashi, T. Jun, M. Ma, T. Wang, L. Ai, E. Calay, W. Oh, E. Schadt, X. Wang
The use of electronic health records (EHRs) holds the potential to enhance clinical trial activities. However, the identification of eligible patients within EHRs presents considerable challenges. In this study, we developed a pipeline for phenotyping eligibility criteria, enabling the identification of patients from EHRs with clinical characteristics that match those criteria. We utilized clinical
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Health Utility Adjusted Survival: a Composite Endpoint for Clinical Trial Designs medRxiv. Oncol. Pub Date : 2024-04-09 Yangqing Deng, John R. de Almeida, Wei Xu
Many randomized trials have used overall survival as the primary endpoint for establishing non-inferiority of one treatment compared to another. However, if a treatment is non-inferior to another treatment in terms of overall survival, clinicians may be interested in further exploring which treatment results in better health utility scores for patients. Examining health utility in a secondary analysis
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Real World Predictors of Response and 24-month survival in high-grade TP53-mutated Myeloid Neoplasms medRxiv. Oncol. Pub Date : 2024-04-09 Amandeep Kaur, Alexandra E. Rojek, Emily Symes, Anand A. Patel, Mariam Nawas, Jay L. Patel, Payal Sojitra, Barina Aqil, Madina Sukhanova, Megan E. McNerney, Leo Wu, Aibek Akmatbekov, Jeremy Segal, Melissa Tjota, Sandeep Gurbuxani, Jason X. Cheng, Su-Yeon Yeon, Harini V. Ravisankar, Carrie Fitzpatrick, Angela Lager, Michael W. Drazer, Caner Saygin, Pankhuri Wanjari, Panagiotis Katsonis, Olivier Lichtarge
Current therapies for high-grade TP53-mutated myeloid neoplasms (≥ 10% blasts) do not offer a meaningful survival benefit except allogeneic stem cell transplantation in the minority who achieve a complete response to first line therapy (CR1). To identify reliable pre-therapy predictors of complete response to first-line therapy (CR1) and outcomes, we assembled a cohort of 238 individuals with TP53-mutated
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Consensus Guidelines for the Management of Peritoneal Surface Malignancies: Introduction and Methodology medRxiv. Oncol. Pub Date : 2024-04-09 PSM Writing Group, PSM Consortium Group, Kiran K. Turaga
Introduction The management of peritoneal surface malignancies (PSM) remains a challenge, characterized by limited high-level evidence and reliance on expert opinions. This paper outlines the methodology used in the development of clinical management pathways for PSM.
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An atlas of causal and mechanistic drivers of interpatient heterogeneity in glioma medRxiv. Oncol. Pub Date : 2024-04-07 Serdar Turkarslan, Yu He, Parvinder Hothi, Carl Murie, Abran Nicolas, Kavya Kannan, James H Park, Min Pan, Alaa Awawda, Zachariah D Cole, Mark A Shapiro, Timothy J Stuhlmiller, Hwahyung Lee, Anoop P Patel, Charles Cobbs, Nitin S Baliga
Grade IV glioma, formerly known as glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor, and its treatment remains challenging in part due to extensive interpatient heterogeneity in disease driving mechanisms and lack of prognostic and predictive biomarkers. Using mechanistic inference of node-edge relationship (MINER), we have analyzed multiomics profiles from 516 patients
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Dysregulation of lncRNA MALAT1 Contributes to Lung Cancer in African Americans by modulating the tumor immune microenvironment medRxiv. Oncol. Pub Date : 2024-04-06 Jin Li, Pushpa Dhilipkannah, Van K Holden, Ashutosh Sachdeva, Nevins W Todd, Feng Jiang
African American (AA) populations present with notably higher incidence and mortality rates from lung cancer in comparison to other racial groups. Here, we elucidate the contribution of long non-coding RNAs (lncRNAs) in the racial disparities and their potential clinical applications in both diagnosis and therapeutic strategies. AA patients had elevated plasma levels of MALAT1 and PVT1 compared with
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Genetic Risk, Health-Associated Lifestyle, and Risk of Early-onset Total Cancer and Breast Cancer medRxiv. Oncol. Pub Date : 2024-04-06 Yin Zhang, Sara Lindström, Peter Kraft, Yuxi Liu
Importance Early-onset cancer (diagnosed under 50 years of age) is associated with aggressive disease characteristics and its rising incidence is a global concern. The association between healthy lifestyle and early-onset cancer and whether it varies by common genetic variants is unknown.
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Cardiovascular events associated with CDK4/6 inhibitors based on randomized controlled trials or cohort trials: a safety meta-analysis medRxiv. Oncol. Pub Date : 2024-04-04 Chengrong Zhang, Guoshuang Shen, Shengmei Li, Fei Ma, Huihui Li, Yuyao Tang, YongXin Li, Zhoujuan Li, Zijun Zhu, Tianlei Qiu, Zhilin Liu, Yi Zhao, Shifeng Huang, Fuxing Zhao, Fanzhen Kong, Jiuda Zhao
Background CDK4/6 inhibitors is highly valued, but the incidence of cardiovascular events (CVAEs) associated with CDK4/6 inhibitors is not clear.
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Individualized dynamic risk assessment for multiple myeloma medRxiv. Oncol. Pub Date : 2024-04-03 Carl Murie, Serdar Turkarslan, Anoop Patel, David G. Coffey, Pamela S. Becker, Nitin S. Baliga
Background Individualized treatment decisions for patients with multiple myeloma (MM) requires accurate risk stratification that takes into account patient-specific consequences of genetic abnormalities and tumor microenvironment on disease outcome and therapy responsiveness.
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Effectiveness of Non-Pharmacological Interventions to Improve Cognition in Cancer: A Protocol for an Overview of Systematic Reviews medRxiv. Oncol. Pub Date : 2024-04-03 Darren Haywood, Ashley M. Henneghan, Evan Dauer MclinPsych, Sherry Vasan, Oscar Y. Franco-Rocha, Helen Wilding, Nicolas H. Hart
Many cancer survivors, including those with a current or previous diagnosis of cancer, experience cancer-related cognitive impairments (CRCI). CRCI can impact their ability to think quickly, clearly, make decisions and perform daily actions. There have been a variety of non-pharmacological interventions developed and trialed with the aim of reducing CRCI or mitigating its impact. The aim of this work
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Personalized Rescheduling of Adaptive Organ-at-Risk-Sparing Radiation Therapy for Head and Neck Cancer under Re-planning Resource Constraints: A Novel Application of Markov Decision Processes medRxiv. Oncol. Pub Date : 2024-04-02 Fatemeh Nosrat, Cem Dede, Lucas B. McCullum, Raul Garcia, Abdallah S. R. Mohamed, Jacob G. Scott, James E. Bates, Brigid A. McDonald, Kareem A. Wahid, Mohamed A. Naser, Renjie He, Amy C. Moreno, Lisanne V. van Dijk, Kristy K. Brock, Jolien Heukelom, Seyedmohammadhossein Hosseinian, Mehdi Hemmati, Andrew J. Schaefer, Clifton D. Fuller, the Rice/MD Anderson Center for Operations Research in Cancer (CORC)
Objective The objective of this study was to determine personalized optimal timing for re-planning in adaptive organ-at-risk-sparing radiation therapy under limited re-planning resources in patients with head and neck cancer (HNC).
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An Evidenced-Based Prior for Estimating the Treatment Effect of Phase III Randomized Trials in Oncology medRxiv. Oncol. Pub Date : 2024-04-01 Alexander D. Sherry, Pavlos Msaouel, Gabrielle S. Kupferman, Timothy A. Lin, Joseph Abi Jaoude, Ramez Kouzy, Zachary R. McCaw, Ethan B. Ludmir, Erik van Zwet
Purpose The primary results of phase III oncology trials may be challenging to interpret, given that such results are generally based on meeting P-value thresholds. The probability of whether a treatment is beneficial, although a more intuitive summary of the results, is not provided by most trials. In this study, we developed and released a user-friendly tool that calculates the probability that a
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Circulating biomarkers of kidney tumors in TSC (tuberous sclerosis complex) patients medRxiv. Oncol. Pub Date : 2024-04-01 Varvara I. Rubtsova, Yujin Chun, Joohwan Kim, Cuauhtemoc B. Ramirez, Sunhee Jung, Elizabeth Cassidy, Gabrielle Rushing, Dean J. Aguiar, Wei Ling Lau, Rebecca S. Ahdoot, Moyra Smith, Sang-Guk Lee, Cholsoon Jang, Gina Lee
Patients with tuberous sclerosis complex (TSC) develop an array of multi-organ disease manifestations, with angiomyolipomas (AML) and cysts in the kidneys being one of the most common and deadly. Early and regular AML/cyst detection and monitoring are vital in lowering TSC patient morbidity and mortality. However, current standard of care for imaging-based methods are not designed for rapid screening
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LOMIA-T: A Transformer-based LOngitudinal Medical Image Analysis framework for predicting treatment response of esophageal cancer medRxiv. Oncol. Pub Date : 2024-03-30 Yuchen Sun, Kunwei Li, Duanduan Chen, Yi Hu, Shuaitong Zhang
Deep learning models based on medical images have made significant strides in predicting treatment outcomes. However, previous methods have primarily concentrated on single time-point images, neglecting the temporal dynamics and changes inherent in longitudinal medical images. Thus, we propose a Transformer-based longitudinal image analysis framework (LOMIA-T) to contrast and fuse latent representations
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Sulfated N-glycans Upregulation in Sera Predicts Early-Stage Breast Cancer in Patients medRxiv. Oncol. Pub Date : 2024-03-28 Dereje G. Feleke, Bryan M. Montalban, Solomon T. Gizaw, Hiroshi Hinou
Alterations in sulfated glycans are associated with several pathological conditions, including cancer. However, analysis of sulfated glycans poses challenges, making the investigation of sulfated glycan profiles a topic of significant interest in the search for novel biomarkers for early BC detection. We used a glycoblotting-based sulphoglycomics workflow to examine sulfated N-glycans present in the
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Differential Non-Coding RNA Profiles for Lung Cancer Early Detection in African and White Americans medRxiv. Oncol. Pub Date : 2024-03-29 Lu Gao, Pushpa Dhilipkannah, Van K Holden, Janaki Deepak, Ashutosh Sachdeva, Nevins W Todd, Sanford A Stass, Feng Jiang
Introduction Lung cancer leads in cancer-related deaths. Disparities are observed in lung cancer rates, with African Americans (AAs) experiencing disproportionately higher incidence and mortality compared to other ethnic groups. Non-coding RNAs (ncRNAs) play crucial roles in lung tumorigenesis. Our objective was to identify ncRNA biomarkers associated with the racial disparity in lung cancer.
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The applications of circulating cell-free DNA for oral squamous cell carcinoma patients as non-invasive diagnostics of structural variants, fusions and oncoviruses medRxiv. Oncol. Pub Date : 2024-03-26 Mahua Bhattacharya, Dan Yaniv, Eyal Yosefof, Sharon Tzelnick, Rajesh Detroja, Dylan P. D’Souza, Gidi Baum, Aviram Mizrachi, Gideon Bachar, Milana Frenkel Morgenstern
Circulating cell-free DNA (cfDNA) has been widely used as a prognostic marker for different cancers. In this study, we used cfDNA from oral squamous cell carcinoma (OSCC) patients to study various correlation factors that could improve the disease early-stage diagnostics and/or prognosis. We found that OSCC patient cfDNA concentration can serve as an indicator of tumor stage, malignancy, and survival
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The Burden of Cancer and Pre-cancerous Conditions Among Transgender Individuals in a Large Healthcare Network medRxiv. Oncol. Pub Date : 2024-03-26 shuang Yang, Yongqiu Li, Christopher Wheldon, Mattia Prosperi, Thomas George, Elizabeth Shenkman, Fei Wang, Jiang Bian, Yi Guo
The current study aimed to examine the prevalence of and risk factors for cancer and pre-cancerous conditions, comparing transgender and cisgender individuals, using 2012-2023 electronic health record data from a large healthcare system. We identified 2,745 transgender individuals using a previously validated computable phenotype and 54,900 matched cisgender individuals. We calculated the prevalence
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Immune-oncology-microbiome axis may result in AKP or anti-AKP effects in intratumor microbiomes medRxiv. Oncol. Pub Date : 2024-03-26 Zhanshan (Sam) Ma
An emerging consensus regarding the triangle relationship between tumor, immune cells, and microbiomes is the immune-oncology-microbiome (IOM) axis, which stipulates that microbiomes can act as a discrete enabling (or disabling) characteristic that broadly influence the acquisition of certain hallmarks of cancer, i.e., a set of functional capabilities acquired by human cells during carcinogenesis and
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FIS103, a Novel SULT1A1-dependent Prodrug, Demonstrates Potent Antitumor Activity in Renal Cell Carcinoma medRxiv. Oncol. Pub Date : 2024-03-26 Ross A. Hamilton, Uksha Saini, Mai Tran, Christopher J. Foley, Pooja Enagala, Leniher C. Chibas, Disha Chatterjee, Stephanie P. Vega, Dev Chatterjee, Atul Varadhachary
Intra-tumoral heterogeneity has been shaping the field of precision medicine for cancer patients ever since its emergence. Prodrugs, which require activation by tumor associated enzymes (TAEs), are a rapidly emerging approach for targeted therapeutics. SULT1A1, a sulfotransferase enzyme and TAE, is over-expressed in about 5-15% of cancer patients including breast, prostate and renal cell carcinoma
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Evaluating soluble Axl as a biomarker for glioblastoma: a pilot study medRxiv. Oncol. Pub Date : 2024-03-26 Daniel Raymond, Melanie Fukui, Samuel Zwernik, Amin Kassam, Richard Rovin, Parvez Akhtar
With current imaging, discriminating tumor progression from treatment effect following immunotherapy or oncolytic virotherapy of glioblastoma (GBM) is challenging. A blood based diagnostic biomarker would therefore be helpful. Axl is a receptor tyrosine kinase that is highly expressed by many cancers including GBM. Axl expression is regulated through enzymatic cleavage of its extracellular domain.
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Clinical Retrospective Analysis: Higher Rates of Gene Mutations in the Microsatellite Stable (MSS) Population of Colorectal Cancer medRxiv. Oncol. Pub Date : 2024-03-25 Xionglin Liu, Wei Mao, Yuan Zhou, Haiping Pei
Abstract With the increasing incidence of colorectal cancer, understanding different subgroups, such as the microsatellite stable (MSS) population, is crucial. Our study aimed to explore the unique characteristics and underlying genetic and epigenetic features of the microsatellite stable (MSS) population within colorectal cancer. Using 325 samples, we compared MSS with other microsatellite statuses
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Detecting microbiome species unique or enriched in 20+ cancer types and building cancer microbiome heterogeneity networks medRxiv. Oncol. Pub Date : 2024-03-24 Zhanshan (Sam) Ma, Lianwei Li, Jiandong Mei
It is postulated that tumor tissue microbiome is one of the enabling characteristics that either promote or suppress cancer cells and tumors to acquire certain hallmarks (functional traits) of cancers, which highlights their critical importance to carcinogenesis, cancer progression and therapy responses. However, characterizing the tumor microbiomes is extremely challenging because of their low biomass
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Clinical activity of Mitogen-Activated Protein Kinase (MAPK) inhibitors in patients with MAP2K1 (MEK1)-mutated metastatic cancers medRxiv. Oncol. Pub Date : 2024-03-24 Matthew Dankner, Emmanuelle Rousselle, Sarah Petrecca, Francois Fabi, Alexander Nowakowski, Anna-Maria Lazaratos, Charles Vincent Rajadurai, Andrew J.B Stein, David Bian, Peter Tai, Alicia Belaiche, Meredith Li, Andrea Quaiattini, Nicola Normanno, Maria Arcila, Arielle Elkrief, Douglas B Johnson, Marc Ladanyi, April Rose
PURPOSE: MAP2K1/MEK1 mutations are potentially actionable drivers in cancer. MAP2K1 mutations have been functionally classified into three groups according to their dependency on upstream RAS/RAF signaling. However, the clinical efficacy of MAPK pathway inhibitors (MAPKi) for MAP2K1 mutant tumors is not well defined. We sought to characterize the genomic and clinical landscape of MAP2K1 mutant tumors
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Overview of prognostic factors in adult glioma; a 10-year experience at a single institution medRxiv. Oncol. Pub Date : 2024-03-24 Amir Barzegar Behrooz, Hadi Darzi Ramandi, Hamid Latifi Navid, Payam Peymani, Rahil Tarharoudi, Nasrin Momeni, Mohammad Mehdi Sabaghpour Azarian, Sherif Eltonsy, Ahmad Pour-Rashidi, Saeid Ghavami
Objective: The most prevalent central nervous system (CNS) neoplasm arising from glial cells is glioma, which diffusely invades brain tissue. Among gliomas, Glioblastoma (GBM) is a glioma of the highest grade and associated with a grim prognosis, with a median overall survival of 15 months with and 3-4 months without therapy. We examined how clinical variables and molecular profiles may have affected
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Equalizing prognostic disparities in stage III KRAS-mutant NSCLC: addition of durvalumab to combined chemoradiotherapy improves survival medRxiv. Oncol. Pub Date : 2024-03-22 Ella A Eklund, Mathilda Orgard, Delice Wallin, Sama I Sayin, Henrik Fagman, Sukanya Raghavan, Levent M Akyurek, Jan Nyman, Clotilde Wiel, Andreas Hallqvist, Volkan I Sayin
Introduction: Stage III non-small cell lung cancer (NSCLC) is heterogeneous and identification of subgroups with differential responses is crucial to optimize treatment. Addition of durvalumab to concurrent chemoradiotherapy (cCRT) has previously been shown to improve survival outcomes. Meanwhile, subgroups harboring KRAS mutations have been shown to have worse prognosis. We investigated whether KRAS
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Combined assessment of KRAS mutational status and tumor size has no impact on prognosis in early-stage non-small cell lung cancer medRxiv. Oncol. Pub Date : 2024-03-21 Ella A Eklund, Ali Mourad, Clotilde Wiel, Sama I Sayin, Henrik Fagman, Andreas Hallqvist, Volkan I Sayin
Background: KRAS mutation status, stage and tumor size at the time of diagnosis are well-established independent prognostic factors in non-small cell lung cancer (NSCLC). Here, we investigate the prognostic value of combining survival data on KRAS mutation status and tumor size in early-stage NSCLC. Methods: We studied the combined impact of KRAS mutational status and tumor size on overall survival
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Hand-Crafted Quantitative Radiomic Analysis of Computed Tomography Scans Using Machine and Deep Learning Techniques Accurately Predicts Histological Subtypes of Non-Small Cell Lung Cancer medRxiv. Oncol. Pub Date : 2024-03-21 Suhrud Panchawagh
Background: Non-small cell lung cancer (NSCLC) histological subtypes impact treatment decisions. While pre-surgical histopathological examination is ideal, it's not always possible. CT radiomic analysis shows promise to predict NSCLC histological subtypes. Objective: To use CT scan radiomic analysis from NSCLC-Radiomics data to predict NSCLC histological subtypes using machine learning and deep learning
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BC-Predict: Mining of signal biomarkers and multilevel validation of cascade classifier for early-stage breast cancer subtyping and prognosis medRxiv. Oncol. Pub Date : 2024-03-20 Sangeetha Muthamilselvan, Ashok Palaniappan
Disease heterogeneity is the hallmark of breast cancer, which remains a scourge and the most common malignancy among women. With a steep increase in breast cancer morbidity and mortality, there exists a critical need for effective early-stage theragnostic and prognostic biomarkers. This would help in patient stratification and optimal treatment selection towards better disease management. In this study
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Machine learning and biological validation identify sphingolipids as potential mediators of paclitaxel-induced neuropathy in cancer patients medRxiv. Oncol. Pub Date : 2024-03-20 Jörn Lötsch, Khayal Gasimli, Sebastian Malkusch, Lisa Hahnefeld, Carlo Angioni, Yannick Schreiber, Sandra Trautmann, Saskia Wedel, Dominique Thomas, Nerea Ferreiros Bouzas, Christian Brandts, Benjamin Schnappauf, Christine Solbach, Gerd Geisslinger, Marco Sisignano
Background: Chemotherapy-induced peripheral neuropathy (CIPN) is a serious therapy-limiting side effect of commonly used anticancer drugs. Previous studies suggest that lipids may play a role in CIPN. Therefore, the present study aimed to identify the particular types of lipids that are regulated as a consequence of paclitaxel administration and may be associated with the occurrence of post-therapeutic
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The Landscape of RAD51D in Chinese Ovarian Cancer Patients: Prevalence, Correlation with HRD Score, and Correlation with Efficacy medRxiv. Oncol. Pub Date : 2024-03-20 Tianqi Sun, Mengpei Zhang, Xinyun Xu, Yiming Liang, Jinghong Chen, Qingli Li, Jing Zeng, Zhe Li, Yu Dong, Rutie Yin
Human genome is continuously threatened by endogenous and exogeneous sources of DNA damage, DNA damage repair (DDR) mechanisms are vital for genome instability and cancer prevention. Homologous recombination repair (HRR) is one of the most important DDR mechanisms because of its high-fidelity. BRCA1/2 have long been the best characterized HRR genes, but other non-BRCA1/2 HRR genes should not be overlooked
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Domain-specific LLM Development and Evaluation -- A Case-study for Prostate Cancer medRxiv. Oncol. Pub Date : 2024-03-19 Amara Tariq, Man Luo, Aisha Urooj, Avisha Das, Jiwoong Jeong, Shubham Trivedi, Bhavik Patel, Imon Banerjee
In this work, we present our strategy for developing domain-specific large language models which cover the vocabulary of the target domain and train on reliable sources of clinical information. Prostate cancer was chosen as a use-case for this study. We collected more than 1.8 million clinical notes and radiology and pathology reports for 15341 patients treated for prostate cancer in Mayo Clinic across
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Tumor and pan-tumor diversity and heterogeneity of cancer tissue microbiomes: a medical ecology analysis across 32 cancer types medRxiv. Oncol. Pub Date : 2024-03-19 Zhanshan (Sam) Ma
Diversity and heterogeneity are hallmarks of any ecosystems including cancer ecosystems. Tumor heterogeneities have been a hot spot in cancer research because of their critical roles in promoting clonal evolution and metastasis of cancer cells and in influencing cancer progression and therapy efficacy. Cancer tissue microbiome as part of tumor microenvironment can influence tumor heterogeneities both
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Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits medRxiv. Oncol. Pub Date : 2024-03-18 Sukoluhle Dube, Sharefa Al-Mannai, Li Liu, Sara Tomei, Apryl Sanchez, William Mifsud, Davide Bedognetti, Wouter R.L. Hendrickx, Christophe Michel Raynaud
Background: FFPE tissue samples are commonly used in biomedical research and are a valuable source for next-generation sequencing in oncology, however, extracting RNA from these samples can be difficult the quantity and quality achieved can impact the downstream analysis. This study compared the effectiveness of seven different commercially available RNA extraction kits specifically designed for use
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Estimating the selection pressure of tumor growth on tumor tissue microbiomes medRxiv. Oncol. Pub Date : 2024-03-18 Lianwei Li, Zhanshan (Sam) Ma
Background: The relationships between tumor and its microbiome are still puzzling, with possible bidirectional interactions. Tumor microbiomes may suppress or stimulate tumor growth on the one hand; on the other hand, tumor growth may exert selection pressure on its microbiomes. There is not any consensus on the mode and/or extension of the bidirectional interactions. The objective of this study is
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Cytokine release syndrome after treatment with immune checkpoint inhibitors: an observational cohort study of 2672 patients from Karolinska University Hospital in Sweden medRxiv. Oncol. Pub Date : 2024-03-16 Osama Hamida, Frans Karlsson, Andreas Lundqvist, Marco Gerling, Lisa L Liu
Immune checkpoint inhibitors (ICIs) are linked to diverse immune-related adverse events (irAEs). Rare irAEs surface first in clinical practice. Here, we systematically studied the rare irAE, cytokine-release syndrome (CRS), in a cohort of 2672 patients treated with ICIs at Karolinska University Hospital in Stockholm, Sweden. We find that the risk of ICI-induced CRS, defined as fever, negative microbiological
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Radiotherapy combined with EGFR-TKIs for stage III EGFR-Mutated lung cancer: A retrospective cohort study medRxiv. Oncol. Pub Date : 2024-03-15 Liu Gang, LIU GANG, WEI YUAN, GAN LANGGE, GAN MEI, ZHENG QINGPING, HUANG JING
The present study aimed to evaluate the efficacy and safety of combining thoracic RT with epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors(TKIs) in managing stage III lung cancer with EGFR mutation. Cases of patients with stage III EGFR-mutant lung cancer who received thoracic RT between December 2014 and December 2022 from multiple hospitals including The People's Hospital of Laibin