bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thomson Effect, Leg Design, Heat Interaction, and Material Impacts on Segmented Thermoelectric Cooler: Insights From Three-Dimensional Simulation
Authors: Mani Aakash , Sarkar Jahar 
Published: February 2025

Abstract
Thermoelectric coolers (TECs) have emerged as promising cooling solutions; however, their relatively low coefficient of performance (COP) remains challenging. Hence, to better understand the factors influencing TEC efficiency and to guide the design of more effective systems, a three-dimensional numerical model is developed. It includes temperature-dependent thermoelectric properties (Thomson effect) and convective–radiative heat interactions. This study explores the TEC performance by analyzing various leg configurations, such as segmented and non-segmented legs, with constant and variable cross section using different material compositions to maximize the cooling effect and COP. Cylindrical legs outperformed conventional square legs, offering a 3% increase in COP and 2.5% in cooling effect. The non-segmented legs emphasize the need for condition-specific material selection, while segmented legs show up to 6.3% higher COP and 5.5% better cooling effect at lower currents, with performance declining at higher currents. A larger temperature lift between the hot and cold sides reduces TEC efficiency. The material-specific segmented leg length ratio can be optimized for maximum performance. A uniform circular leg cross section is more effective than a variable one. Incorporating the temperature-dependent material properties and the Thomson effect in the model significantly increases the TEC performance (up to 30%). Similarly, considering convective–radiative heat interaction in the model increases the performance (about 10%). These two inclusions enhance the accuracy of performance prediction of the model used in this study. These findings provide valuable insights for designing TECs according to application and operating conditions.
Sleep‐Breath–Related Characteristics in Males With Chronic Rhinosinusitis
Authors: Xue Wenjun , Zhang Qianqian , Wu Xiaolin , Zhu Huaming , Li Xinyi , Feng Yunhai , Ye Haibo 
Published: February 2025

Background: Patients with chronic rhinosinusitis (CRS) often exhibit sleep impairments that are closely associated with obstructive sleep apnea (OSA). However, objective evaluations of sleep quality in inpatients with CRS are lacking. This study explored the sleep‐breath–related characteristics of CRS patients without nasal polyps (CRSsNP).Methods: In this cross‐sectional single‐center study, we recruited 147 adult male inpatients diagnosed with CRSsNP between March 2019 and April 2020. OSA was diagnosed using standard PSG. The patients were classified into two groups based on the apnea–hypopnea index: CRSsNP with OSA and CRSsNP without OSA groups. Demographic features and sleep parameters were evaluated and compared between the groups.Results: Inpatients with CRSsNP were at high risk of OSA (61.2%). Interestingly, the oxygen desaturation index (ODI), sleep efficiency (SE), and wake duration showed no differences between the CRSsNP with OSA and CRSsNP without OSA patients. The CRSsNP with OSA group exhibited a higher prevalence of obesity, slept for less time, was more easily aroused, and exhibited higher SE and larger CT90 scores during sleep (p < 0.05) compared to the CRSsNP without OSA group. Linear regression analysis revealed that the average SpO2 value (β = 1.182; p = 0.036) and ODI (β = 0.818; p < 0.001) remained significantly associated with OSA in CRS patients even after adjusting for age and body mass index.Conclusions: Male inpatients with CRSsNP exhibited a high prevalence of OSA. CRSsNP patients evidenced severe hypoxia and exhibited more awakenings during sleep.
Kinome-Focused CRISPR-Cas9 Screens in African Ancestry Patient-Derived Breast Cancer Organoids Identify Essential Kinases and Synergy of EGFR and FGFR1 Inhibition
Authors: Madorsky Rowdo Florencia P. , Martini Rachel , Ackermann Sarah E. , Tang Colin P. , Tranquille Marvel , Irizarry Adriana , Us Ilkay , Alawa Omar , Moyer Jenna E. , Sigouros Michael , Nguyen John , Al Assaad Majd , Cheng Esther , Ginter Paula S. , Manohar Jyothi , Stonaker Brian , Boateng Richard , Oppong Joseph K. , Adjei Ernest K. , Awuah Baffour , Kyei Ishmael , Aitpillah Francis S. , Adinku Michael O. , Ankomah Kwasi , Osei-Bonsu Ernest B. , Gyan Kofi K. , Hoda Syed , Newman Lisa , Mosquera Juan Miguel , Sboner Andrea , Elemento Olivier , Dow Lukas E. , Davis Melissa B. , Martin M. Laura 
Published: February 2025

Abstract
Precision medicine approaches to cancer treatment aim to exploit genomic alterations that are specific to individual patients to tailor therapeutic strategies. Yet, some targetable genes and pathways are essential for tumor cell viability even in the absence of direct genomic alterations. In underrepresented populations, the mutational landscape and determinants of response to existing therapies are poorly characterized because of limited inclusion in clinical trials and studies. One way to reveal tumor essential genes is with genetic screens. Most screens are conducted on cell lines that bear little resemblance to patient tumors, after years of culture under nonphysiologic conditions. To address this problem, we aimed to develop a CRISPR screening pipeline in three-dimensionally grown patient-derived tumor organoid (PDTO) models. A breast cancer PDTO biobank that focused on underrepresented populations, including West African patients, was established and used to conduct a negative-selection kinome-focused CRISPR screen to identify kinases essential for organoid growth and potential targets for combination therapy with EGFR or MEK inhibitors. The screen identified several previously unidentified kinase targets, and the combination of FGFR1 and EGFR inhibitors synergized to block organoid proliferation. Together, these data demonstrate the feasibility of CRISPR-based genetic screens in patient-derived tumor models, including PDTOs from underrepresented patients with cancer, and identify targets for cancer therapy.
Significance: Generation of a breast cancer patient-derived tumor organoid biobank focused on underrepresented populations enabled kinome-focused CRISPR screening that identified essential kinases and potential targets for combination therapy with EGFR or MEK inhibitors.
See related commentary by Trembath and Spanheimer, p. 407
Abstract A008: Epigenetic dynamics in KMT2A-amplified leukemia
Authors: Ogino Jayme , Liu Yang , Yang Wentao , Sukhanova Madina , Li Sheng , Dou Yali 
Published: February 2025

Abstract
The lysine methyltransferase KMT2A/MLL1 plays a crucial role in normal development and hematopoiesis. Rearrangement of KMT2A results in the formation of a KMT2A fusion protein with aberrant activity, which is a well-characterized driver of leukemogenesis and is therapeutically targetable. In contrast to the widely studied KMT2A translocation, the molecular consequences of other KMT2A alterations, including KMT2A amplification, remain unknown. KMT2A amplification is detected in highly aggressive and treatment-resistant myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). It strongly associates with TP53 mutations and complex karyotypes. Unlike KMT2A rearrangement, KMT2A amplification is reported mostly in patients older than 65 and treated with alkylating agents. Here, we conducted a comprehensive molecular analysis of KMT2A-amplified MDS/AML by long-read nanopore sequencing. We have revealed the unique epigenetic landscape, including DNA methylation, histone modification, and chromatin accessibility, associated with KMT2A amplification. We also explored the potential of targeting KMT2A or KMT2A-medicated pathways to block leukemogenesis. These results provide a foundation for targeting the KMT2A complex in KMT2A-amplified disease, representing a promising first step toward treating MDS/AML associated with KMT2A amplification.
Citation Format: Jayme Ogino, Yang Liu, Wentao Yang, Madina Sukhanova, Sheng Li, Yali Dou. Epigenetic dynamics in KMT2A-amplified leukemia [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr A008.
Abstract B004: Promoter methylation gains in aging and cancer are independent of replication
Authors: Thursby Sara-Jayne , Jin Zhicheng , Patel Nibedita , Tao Yong , Bhandari Yuba , Petkovich Daniel , Lu Shangzhi , Yang Lijing , Wang Tza-Huei , Pisanic Thomas R. , Baylin Stephen B , Easwaran Hariharan 
Published: February 2025

Abstract
DNA methylation alterations are observed across multiple cancers, occurring early during tumor initiation. However, evolution and drivers of these changes remain poorly understood and difficult to assess at the clonal level. Consequently, we developed a method for profiling genome-wide DNA methylation from low DNA amounts and applied it to the organoid model of BRAFV600E oncogene-induced colon cancer (CC) tumorigenesis. Single organoid clones, derived from single stem cells, were profiled every month for 5 months to map nucleotide-level dynamic heterogeneity in methylation changes. Uninduced control organoids exhibit a pattern of epigenetic drift leading towards clonal convergence not until 5 months. Whereas BRAFV600E-induced organoids exhibit a step-wise divergence throughout the different time points, likely explained by progressive clonal takeovers. The methylation changes in BRAFV600E induced organoids are explained by the age-in-culture associated methylation changes; especially BRAFV600E did not induce epigenetic changes, as previously thought. The CpG sites affected in the control and BRAFV600E comparison were not shared but mapped to the same genomic elements, indicating common drivers of methylation changes regardless of oncogene. Investigation of promoter CpG-island methylation gains revealed that they are decoupled from replication. External validation in other pre-cancerous and CC datasets, and experimental cell line data sets, show that methylation gains at regulatory elements are a function of “biological aging” and independent of replication or cell division cycles. Our studies provide new insights into the early epigenetic changes involved in BRAFV600E driven carcinogenesis rooted in the age-dependent drivers of epigenetic alterations.
Citation Format: Sara-Jayne Thursby, Zhicheng Jin, Nibedita Patel, Yong Tao, Yuba Bhandari, Daniel Petkovich, Shangzhi Lu, Lijing Yang, Tza-Huei Wang, Thomas R. Pisanic II, Stephen B Baylin, Hariharan Easwaran. Promoter methylation gains in aging and cancer are independent of replication [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr B004.
Abstract B005: The functional role of transposable element-oncogene chimeric transcript during cancer progression
Authors: Saintilnord Wesley N , Wu Yixin , Liang Yonghao , Wang Ting 
Published: February 2025

Abstract
Nearly half of the human genome is composed of transposable elements (TEs), which were once considered “junk” DNA due in part to their repetitive and non-coding characteristics. However, TEs are now emerging as important regulators of gene activity, especially when they escape typical epigenetic silencing mechanisms like DNA methylation and histone modifications. When activated, TEs can contribute sequences that are exploited as disruptors of genomic stability or novel gene regulatory elements, making them important factors in both development and disease, including cancer. In cancer, these previously silenced elements can act as alternative promoters of oncogenes, leading to the production of TE-chimeric transcripts in a process called “onco-exaptation”. While these oncoexaptation events are reported to be widespread across many cancers, only a few TE-chimeric transcripts have been validated as active contributors to cancer progression. Additionally, it remains unclear whether these TE-chimeric transcripts are merely a consequence of the inherent genomic instability in cancer or whether they can initiate cancer. To address these gaps, we designed a cDNA overexpression library incorporating our previously identified pan-cancer TE-chimeric transcript candidates. This library is used in early passage (EP) BJ fibroblast, a cell line known for its transformation potential in the well-established Weinberg transformation model, which allows us to systematically investigate these onco-exaptation events during cancer progression. Our initial analyses indicate that most TE-chimeric oncogenes are not expressed in EP fibroblast, but are activated in subsequent transformation stages following hTERT, SV40 and HRas induction, underscoring the model viability. We are currently using this model to distinguish TE-chimeric transcripts that act as drivers (TE-chimeric oncogenes) from those requiring previous vulnerabilities, such as telomere inactivation by hTERT or p53 and Rb inactivation by SV40. Ultimately, this work will identify novel biomarkers and therapeutic targets, enhance insights into gene regulation, and provide opportunities for early detection and intervention. These findings have the potential to improve cancer treatment and patient outcomes.
Citation Format: Wesley N Saintilnord, Yixin Wu, Yonghao Liang, Ting Wang. The functional role of transposable element-oncogene chimeric transcript during cancer progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr B005.
Abstract B010: Concurrent analysis of multiple methylated CpG sites using multiplex MethyLight assay for epithelial ovarian cancer detection
Authors: Bisht Deepa , Sachan Manisha 
Published: February 2025

Abstract
Objective: Epithelial ovarian cancer (EOC), a heterogeneous and aggressive gynaecologic malignancy, remains a leading cause of cancer-related death due to the lack of reliable, sensitive, and specific early diagnostic biomarkers. Methods: This study employed a cost-effective, CpG site-specific Amplification Refractory Mutation System PCR (ARMS-PCR) to assess the methylation frequency of six diagnostically potent CpG sites (cg18878992, cg00480298, cg029572270, cg10636246, cg10061138, and cg12910797) in 45 EOC samples and 25 normal controls. Methylation patterns (methylated, unmethylated, partially methylated) were confirmed through image analysis and Combined Bisulfite Restriction Analysis (COBRA). Three top methylated CpG sites were chosen to form two biomarker panels, which were subsequently tested for diagnostic efficiency. Furthermore, a TaqMan-based quantitative PCR (MethyLight) assay was developed, integrating the three most hypermethylated CpG sites (cg02957270, cg00480298, and cg10061138) in a triplex format. Results: ARMS-PCR revealed the diagnostic potential of two hypermethylated CpG sites (cg02957270, cg10061138) and one hypomethylated site (cg10061138). The sensitivity of the singleplex and multiplex panels reached 80%, 73.3%, and 82.3%, respectively. The MethyLight assay demonstrated an enhanced sensitivity of 86% and specificity of 92% for the multiplex panel (cg02957270 and cg00480298) along with control col2A1. ROC curve analysis revealed AUC values of 0.96, 0.91, and 0.84 for the singleplex assays and 0.97 for the multiplex panel. While ARMS-PCR showed limited correlation with clinicopathological characteristics, significant associations were found in the MethyLight assay (p &lt; 0.05). Conclusions: This discovery opens a new frontier in DNA methylation research, suggesting the potential to harness clinically relevant, independent CpG sites, in hypermethylated state for the development of novel biomarkers.
Citation Format: Deepa Bisht, Manisha Sachan. Concurrent analysis of multiple methylated CpG sites using multiplex MethyLight assay for epithelial ovarian cancer detection [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr B010.
Abstract B015: Collection and purification of microgram amounts of cfDNA from urine for methylation analysis
Authors: Taub Floyd , Ray Lindsey , Neff Charles Preston , Barstis Elijah , Henry Charles , Arnold Kirsten 
Published: February 2025

Abstract
Background: DNA methylation studies often require relatively large amounts of DNA, typically methods suggest hundreds of nanograms to a microgram per assay. While this is easy to obtain if genomic DNA (gDNA) is used, preforming similar studies on circulating cell free DNA (cfDNA) may be difficult. Plasma, especially that from normal individuals needed for comparison, may yield only 10 ng to 20 ng per ml. Thus, experimental designs involving multiple repeat analysis of the same specimen, or applying different complementary methylation methods to one specimen, may be limited by the amount of cfDNA in a blood sample. It is known that urine contains cfDNA, but reports on the amount vary from very low to being comparable to blood; the conflicting data may be due in part to the low yield some methods of isolation have reported to have when the DNA is small. Hypothesis: We postulated that a system which filtered hundreds of mls of urine and captured the DNA based on charge rather than absorption to silica, could capture adequate amounts of cfDNA from urine for repeat studies. Results: Initially, filtering large amounts of urine was problematic due to clogging. A system of stacked filters was devised. The method uses 200- 250 ml size syringes and 5 cm filter cartridges. It allows full voids, in fact up to 1 liter, to be filtered. The urine is first collected in a measuring cup containing preservatives, it is immediately filtered. This is simple enough to be done by a patient at home. The first of the stacked filters, collects urothelial and other cells that may be used to analyze gDNA; it also clarifies the urine sufficiently to pass through a second lower pore size filter modified to be highly positively charged. On average, a 150 ml void provides 2100 nanograms of cfDNA. The binding to the filter is sufficiently strong that DNases cannot bind or digest the DNA. Thus, the DNA is stable in the cartridge for four days and allows for shipping without special handling. The in-lab purification consists of separating the filters, then washing the cfDNA trapping filter, followed by elution of the DNA. It takes under 10 minutes and results in purified DNA that is suitable for downstream analysis. Conclusions: Microgram amounts of cfDNA can be easily extracted from urine to facilitate initial analyses sufficient for statistically robust studies and banking of specimens for future testing.
Citation Format: Floyd Taub, Lindsey Ray, Charles Preston Neff, Elijah Barstis, Charles Henry, Kirsten Arnold. Collection and purification of microgram amounts of cfDNA from urine for methylation analysis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr B015.
Abstract B026: NEBNext® enzymatic solutions for DNA methylation profiling at picogram scale
Authors: panchapakesa Vaishnavi , Ponnaluri Chaithanya , Evanich Daniel , Campbell Matthew , Blum Laura , Langhorst Bradley , Williams Louise 
Published: February 2025

Abstract
DNA methylation is an important epigenetic regulator of gene expression. 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) play distinct roles in epigenetic regulation, however the ability to distinguish between 5mC and 5hmC is often lost as they are frequently read as a combined signal in traditional sequencing approaches. NEBNext Enzymatic Methyl-seq v2 (EM-seq v2) and NEBNext Enzymatic 5hmC-seq (E5hmC-seq) are enzymatic approaches used to investigate cytosine methylation. EM-seq v2 detects both 5mC and 5hmC whereas E5hmC-seq detects only 5hmC. The first step for each method protects either 5mC and/or 5hmC from deamination by APOBEC enzyme. Cytosines are deaminated to uracil in EM-seq v2 whereas for E5hmC-seq, 5mC and cytosine bases are converted to thymine and uracil respectively. Using a subtractive data analysis approach, whereby E5hmC-seq data is subtracted from EM-seq data, the locations of 5mC and 5hmC can be decoupled at single base resolution. EM-seq v2 libraries and E5hmC-seq libraries were prepared using 0.1 ng to 200 ng of genomic DNA. Both methods leave DNA intact and result in superior sequencing libraries with longer insert sizes, lower duplication rates and minimal GC bias as well as accurately detecting methylation down to 0.1 ng DNA. These methods are streamlined due to reduced library preparation time as well as the removal of a cleanup step. Coverage of genomic features such as CpG islands and enhancers, for both methods were maintained to 1 ng but dropped as expected with the 0.1 ng inputs. EM-seq v2 and E5hmC-seq provides consistent methylation metrics for inputs ranging from 0.1 ng to 200 ng. EM-seq v2 and E5hmC-seq libraries provide accurate measurements across inputs from 0.1 ng – 200 ng with expected methylation, insert sizes and minimal GC bias. In addition, combining E5hmC-seq and EM-seq data to discriminate between 5mC and 5hmC will provide key insights into the role of these cytosine modifications in development and disease.
Citation Format: Vaishnavi panchapakesa, Chaithanya Ponnaluri, Daniel Evanich, Matthew Campbell, Laura Blum, Bradley Langhorst, Louise Williams. NEBNext® enzymatic solutions for DNA methylation profiling at picogram scale [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr B026.
Abstract IA022: Harnessing epigenetic profiles in MDS for the development of predictive biomarkers
Authors: Figueroa Maria E 
Published: February 2025

Abstract
While significant progress has been made in understanding the genetic landscape of MDS, less is known about the epigenetic makeup of this disease and how this may impact biology and response to azacitidine (AZA). To address this, we performed genomic, epigenomic, and transcriptomic analyses on CD34+ cells from a multicenter cohort of 94 intermediate or higher-risk MDS patients treated with AZA who had documented responses. DNA methylation (DNAme) by ERRBS, gene expression (GE) by RNA-seq, mutational profiling, and detailed clinical, cytogenetic, and laboratory data were documented. Supervised and unsupervised analyses revealed that aberrant DNAme in MDS is not distributed randomly but rather is highly correlated with disease phenotypes, capturing clinically relevant heterogeneity, beyond what is identified by methodologies used in the past that focused solely on promoter regions. Moreover, this epigenetic information can be harnessed for the development of robust biomarkers predictive of AZA response and integrative approaches combining clinical, mutation, GE and DNAme data can further improve the predictive performance of these biomarkers, with an AUC score=0.94.
Citation Format: Maria E Figueroa. Harnessing epigenetic profiles in MDS for the development of predictive biomarkers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr IA022