Citations

Abstract We are interested in artificial gene regulation by exploiting principles learned from lactose repressor (lacI) control of the Escherichia coli lac operon through the formation of tight DNA loops on the order of 100–200 base pairs. We previously showed that appropriately designed DNA target-programmable Transcription Activator-Like Effector dimer (TALED) proteins can produce DNA-looping-dependent gene repression comparable to lacI. Here, we demonstrate regulation of such switches by the principle of controlled repressor autoinhibition. Thus, TALEDs are inhibited by controlled cyclization, dependent on small molecules. Cyclized TALEDs poorly participate in DNA looping. We fit DNA loop length-dependent data with an established thermodynamic model to quantitate these effects. We further demonstrate the ability of small molecules to induce gene expression using this system in actively growing E. coli cells. The resulting designed systems demonstrate regulated gene expression by DNA looping, emulating the lac system but with entirely different molecular components.

Abstract Rationale Acute cellular rejection (ACR) within first-year post-lung transplantation has important implications for prognosis. Calcineurin inhibitors (CNI), including tacrolimus or cyclosporine, along with cell cycle inhibitors (CCI) and steroids, remain the standard immunosuppression regimen post-transplant. Although tacrolimus is used as the primary CNI, target therapeutic levels vary across recipients due to adverse effects and tolerability, sometimes requiring switching over to Cyclosporine. We hypothesized that ACR within the first year is associated with switching CNI from Tacrolimus to Cyclosporine. Methods We performed a cross-sectional study of 255 adult lung transplant recipients between June 2019 to November 2024 at Mayo Clinic, Florida. Demographics, induction regimens, CNI type and their levels (average low and high levels) were compared between the 2 groups. The institutional maintenance immunosuppression regimen is Tacrolimus, Mycophenolate Mofetil (MMF) and prednisone, but could be switched to Cyclosporine if the previous regimen is not tolerated. The primary outcome was ACR <1 year diagnosed based on biopsy and/or clinical criteria. Comparisons between groups were performed using Chi-Square test for categorical variables and t-test or Wilcoxon Rank sum test for continuous variables. Multivariable regression analysis was performed with ACR <1 year as the outcome to adjust for the confounders. Results Our cohort included 255 lung transplant recipients with median age of 63 years, 61% Male, 84% Caucasians, 88% bilateral lung transplant (Further details elucidated in Table 1). A total of 173 (67%) out of 255 patients had ACR <1 year. The group with ACR < 1 year had higher proportion of Interstitial Lung Disease (ILD) (81% vs 68%, p = 0.044), use of Basiliximab for induction (70% vs 55%, p = 0.018), and cyclosporine instead of tacrolimus (23% vs 11%, p = 0.027). Group with ACR <1 year also had higher Antibody Mediated Rejection (AMR) < 1year (15% vs 6.1%, p = 0.041) and higher CLAD (BOS 0p-3: 43% vs 25.6%, p = 0.033) compared to the group without ACR < 1 year (Table 1.1). Multivariate regression analysis showed ILD (adjusted odds ratio, aOR 2.84, 95% CI 1.31 - 6.27, p = 0.008) and use of cyclosporine (aOR 2.55, 95% CI 1.07 - 6.78, p = 0.034) as independent predictors of ACR < 1 year (Table 2). Conclusions The presence of ACR < 1 year was associated with the use of Cyclosporine over Tacrolimus as a maintenance regimen. Also, ACR < 1year was associated with higher AMR and CLAD. Further prospective studies are needed to study this long-term given its significant prognostic implications. This abstract is funded by: Not Applicable

ABSTRACT Objective Identifying and addressing pediatric hearing loss is critical to supporting a child's development. School‐based hearing screening is a mainstay of timely identification of hearing loss. The objectives of this study were to characterize the current hearing screening practices in public, charter, and private elementary schools in Minnesota. Methods This was a cross‐sectional survey with data collected between March and June 2023. Surveys assessed the presence of standardized hearing screening processes and compliance with American Academy of Audiology (AAA) or Minnesota Department of Health (MDH) guidelines. Results About 146 public schools, 43 charter schools, and 60 private schools met inclusion criteria and responded to the survey. There was a statistically significant difference in the rate of standardized screening between school types ( χ 2 = 18.06; p < 0.001). Only 10.44% ( n = 26) of schools completed hearing screenings per AAA guidelines, and even fewer, 4.82% ( n = 12), completed hearing screenings according to MDH guidelines. The odds of screening per AAA or MDH guidelines were 3.50 times higher in charter schools compared to public schools (95% CI: 1.14, 10.73) and 4.61 times higher in private schools compared to public schools (95% CI: 1.73, 12.26). Conclusion There is a lack of standardization in hearing screening processes in Minnesota elementary schools. Adherence to screening per AAA or MDH recommendations is low in all types of elementary schools. Charter and private schools were more likely than public schools to screen per AAA or MDH guidelines. Overall, our data demonstrate an opportunity for improvement in school‐based hearing screening. Level of Evidence N/A.

Summary Longitudinal plasma cell-free DNA profiling from the phase 3 Alliance A031201 trial revealed divergent resistance trajectories in metastatic castration-resistant prostate cancer. Rapid progressors harbored non–androgen receptor (AR) alterations suggesting intrinsic resistance, whereas delayed progressors showed progressive AR amplifications, structural rearrangements, and extrachromosomal DNA–associated evolution. These findings support biomarker-guided strategies targeting AR-dependent and AR-independent disease states. See related article by Valentín López et al., p. 2413

Abstract A short diagnosis-to-treatment interval independently predicts inferior outcomes in follicular lymphoma. Using international discovery and validation cohorts, we demonstrate its prognostic value beyond established prognostic indices, with implications for risk stratification, clinical trial design, and interpretation.

Abstract Introduction: Long intergenic noncoding RNAs (lincRNAs) and circular (circ) RNAs have been shown to play key roles in carcinogenesis and tumor progression. Urine represents a promising source of tumor-reflective signals shed directly from the urothelial microenvironment in bladder cancer (BC) patients. Here, we evaluate the urine cell-free (cf) RNA transcriptome in a cohort of 50 patients with localized BC. Methods: A total of 50 localized BC patients and 24 healthy adults were enrolled. Pre-operative urine (collected on the day of radical cystectomy) was processed to isolate cfRNA from urine supernatant. Libraries were prepared using an Illumina tagmentation-based RNA enrichment workflow and sequenced to 100M paired-end reads per sample on a NovaSeq X. FASTQ files were concatenated per sample and QC-checked with RNA-SeQC and Samtools. Reads were aligned to GRCh38/hg38 with STAR, and gene counts were generated using Feature Counts. Linear differential expression analysis (DEA) was performed with DESeq2. For discovery we used random halves of TCGA-BLCA and healthy urine cfRNA samples, alongside a second DEA with random halves of urine BC cfRNA vs. controls; overlapping upregulated genes were validated in the remaining samples. For circular (circ) RNAs, annotations from MiOncoCirc were used; junctions with ≥5 supporting reads were retained, and DEA was conducted with edgeR. Results: In this study, the median age was 68 years, and 80% (40/50) were male. Among the cohort, 66% (33/50) had muscle-invasive bladder cancer (MIBC), of whom 54% received neoadjuvant chemotherapy. Differential expression analysis of TCGA-BLCA tumors and BC urine cfRNA, identified 27 genes commonly upregulated, with 23 of the 27 shared genes strikingly being long intergenic noncoding RNAs (lincRNAs). These BC/urine-specific lincRNAs—including LINC00930, LINC01004, DLG5-AS1, APTR, PSORS1C3, and SERPINB9P1—have known roles in proliferation, EMT, metabolism, and immune signaling. Outside of lincRNAs, tumor-reflective coding transcripts in BC/urine were enriched for autophagy, driven by MAP1LC3B2.TCGA-BLCA survival analysis showed that LINC00930 and PSORS1C3 were associated with worse overall survival. Expanding beyond linear RNA sequences, analysis of urine circRNAs from BC patients revealed a strong cancer-specific dysregulation pattern, with 77 circRNAs significantly upregulated compared with healthy controls. Upregulated urine circRNAs arose from host genes involved in BC-relevant pathways, including invasion (DOCK1, ARHGAP5), autophagy/ER stress (VMP1, ERN1), and luminal differentiation (GRHL2, ESRP1). Conclusion: Cell-free RNA profiling reveals a distinct transcriptomic signature including differential lincRNA- and circRNA-driven autophagy, EMT, proliferation, metabolic, differentiation, and immune signaling programs in the urine of bladder cancer patients. Citation Format: Pradeep Chauhan, Li Lin, Irfan Alahi, Jessica Linford, Lilli J. Greiner, Ayesha Hashmi, Anushka Viswanathan, Nathan Colon, Faridi Qaium, Peter K. Harris, John Sheng, Jacob J. Orme, Eric H. Kim, Zachary L. Smith, Woodson Smelser, Christopher A. Maher, Aadel A. Chaudhuri. Urine cell-free RNA captures tumor-reflective long intergenic noncoding and circular RNA programs in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1133.

Abstract Glioblastoma (GBM) is an aggressive, high-grade glioma with a near-universally fatal prognosis. Therapeutic failure is often attributed to the highly selective blood brain barrier (BBB), the diffuse infiltrative nature of the tumor, and the marked intratumoral heterogeneity of GBM. Although antibody drug conjugates ADCs have shown promise for high grade gliomas such as GBM, efficacy is limited by ADC size. Aptamers—short, synthetic, single-stranded DNA or RNA molecules—can be ∼6-fold lower in molecular weight than IgG antibodies and have the potential to cross the intact BBB. Unlike other nucleic acid-based therapies, aptamer function arises from three-dimensional shape rather than genetic coding. Here we aim to replace the targeting component of the ADC paradigm with a DNA aptamer, thus creating an aptamer-drug conjugate (ApDC). We employed in vivo SELEX using an orthotopic patient-derived xenograft (PDX) GBM mouse model and a vast (∼100 trillion 80-mer sequences) ApDC library. We report the results from this first in vivo ApDC selection of its kind. We characterize target tissue binding ex vivo , cell association, biodistribution, and pharmacokinetics from this selection. This study exemplifies an unbiased approach to a problem that rational design has yet to overcome, offering a new direction for GBM therapeutic development.

Abstract Background: The diagnosis and treatment of breast cancer impose a significant psychological burden, which can include suicidal ideation. However, data from conflict-affected regions like Syria are scarce. This study aimed to determine the prevalence of suicidal thoughts and identify associated risk factors among Syrian patients with breast cancer. Methodology: An institution-based cross-sectional study was conducted at Al-Biruni University Hospital in Damascus, Syria. Between April and August 2025, a total of 319 breast cancer patients undergoing chemotherapy were recruited. Data were collected through structured face-to-face interviews and reviews of medical records. Standardized instruments included the Patient Health Questionnaire-2 (PHQ-2), the Multidimensional Scale of Perceived Social Support (MSPSS), and the Columbia-Suicide Severity Rating Scale (C-SSRS). Statistical analyses were used to identify factors associated with suicidal ideation. Results: The overall prevalence of suicidal ideation was 8.2%. Suicidal thoughts were significantly associated with depression (p=0.0014), anxiety (p&lt;0.001), and low perceived family support (p=0.0293). Key clinical predictors included advanced disease stage (p=0.0275), metastatic disease (p=0.0251), and severe pain (p=0.0011). A higher prevalence was also noted in patients who had not undergone surgery (p=0.0057). Significant sociodemographic factors included being divorced (p=0.0117) and residency location (p=0.0039). Among those experiencing suicidal ideation, a small but significant portion progressed toward action, with approximately 5.2% to 5.6% reporting they had worked out details of a plan or had some intention of acting on their thoughts. Regarding deterrents, religious beliefs were the most common reason cited for not attempting suicide (58%), followed by personal reasons (46%). Conclusion: Suicidal ideation is a significant concern among Syrian breast cancer patients, strongly associated with psychological distress, advanced disease, severe pain, and specific sociodemographic vulnerabilities. These findings highlight the critical need to integrate mental health screening and targeted psychosocial support into routine oncological care, especially for high-risk individuals in this vulnerable population. Citation Format: A. Al-Bitar, M. Doyya, N. Battah, S. Achkar, F. Nahhat, M. Saifo. Suicidal Ideation and the Role of Social Support Among Breast Cancer Patients in Syria [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS5-12-30.

Abstract Background: In conflict zones like Syria, accessing cancer care presents immense challenges. However, there is a critical lack of data on the specific barriers patients face. This study aimed to document these obstacles for breast cancer patients in Syria following 14 years of civil war. We surveyed patients presenting for cancer care to better understand the challenges they faced. Methods: This cross-sectional study included adult patients with a confirmed breast cancer diagnosis presenting to Al-Bairouni University Hospital for care. Data was collected through face-to-face interviews using a structured questionnaire adapted for the Syrian context. The survey covered six key areas: Demographic & Clinical, Healthcare System Barriers, Financial Barriers, Geographic & Security barriers, Reasons for Diagnostic Delays, and Psychosocial Impact. Multivariate analysis via logistic regression was conducted to determine which responses were associated with a higher odds ratio (OR) of having a late-stage (III/IV) cancer diagnosis. Results: A total of 109 patients diagnosed with breast cancer were enrolled. The mean age was 51.4 years (±15.2 SD). Advanced diagnostics (CT/MRI/biopsy) and radiation therapy were inaccessible for 58% (n=63) and 63% (n=69) of patients. Systemic therapy drugs were "rarely" or "never" available for 33% (n=36) of patients, and 14% (n=15) reported waiting over three months for an appointment. The costs of medications "greatly" or "very greatly" impacted 86% (n=94) of patients. Over two-thirds of patients reported that essential pain control medications (e.g., morphine) were "rarely" or "never" available (66%, n=72). Nearly two-thirds (67%, n =73) reported that security concerns "greatly" or "somewhat" affected their ability to access treatment. An overwhelming 89% (n=97) of patients reported a negative psychological impact from their treatment course. Patient responses associated with a higher OR of late-stage cancer diagnosis are present in Table 1. Conclusions: Breast cancer patients in Syria confront overwhelming systemic, financial, and security barriers that compromise their care and contribute to advanced diagnoses. The findings highlight a profound humanitarian crisis and underscore the urgent need for targeted public health and aid interventions to support cancer care in conflict settings. Citation Format: A. Al-Bitar, A. Kouli, F. Nahhat, M. Saifo. Systemic Barriers to Breast Cancer Care in Conflict-Affected Syria [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS5-11-14.

809 Background: Barriers to necessary care can pose a significant burden on patients with cancer, even more so in places of conflict. Following a devastating 14-year war in Syria, there is limited data published on access to cancer care and the impact that barriers to management have on our patients. We surveyed patients presenting for cancer care to better understand the challenges they faced. Methods: This cross-sectional study included adult patients with a confirmed gastrointestinal (GI) cancer diagnosis presenting to Al-Bairouni University Hospital for care. Data was collected through face-to-face interviews using a structured questionnaire adapted for the Syrian context. The survey covered six key areas: Demographic & Clinical, Healthcare System Barriers, Financial Barriers, Geographic & Security Barriers, Reasons for Diagnostic Delays, and Psychosocial Impact. Multivariate analysis via logistic regression was conducted to determine which responses were associated with a higher odds ratio (OR) of having a late-stage (III/IV) cancer diagnosis. Results: A total of 122 patients diagnosed with a GI cancer were enrolled. The mean age was 57.4 years (±11.2 SD), with a male predominance (68%, n=83). Advanced diagnostics (CT/MRI/biopsy) and radiation therapy were inaccessible for 55% (n =67) and 61% (n =74) of patients, respectively. Systemic therapy drugs were "rarely" or "never" available for 35% (n=43) of patients, and 12% (n=15) reported waiting over three months for an appointment. The costs of medications "greatly" or "very greatly" impacted 88% (n=107) of patients. Over two-thirds of patients reported that essential pain control medications (e.g., morphine) were "rarely" or "never" available (68%, n=83). Nearly two-thirds (65%, n =79) reported that security concerns "greatly" or "somewhat" affected their ability to access treatment. An overwhelming 87% (n=106) of patients reported a negative psychological impact from their treatment course. Patient responses associated with a higher OR of late-stage cancer diagnosis are present in the table. Conclusions: Patients in Syria with GI cancers face profound systemic, financial, geographic, and psychosocial challenges throughout their care journey. More than half were diagnosed at advanced stages, with diagnostic delays strongly linked to prolonged waiting times and financial strain. Financial toxicity was highly evident, resulting in treatment compromise and asset liquidation. This data should serve as a reference for future public health and humanitarian efforts in the region. Factors associated with late-stage (III/IV) diagnosis of GI malignancies (multivariate logistic regression). Variable Adjusted Odds Ratio (aOR) 95% Confidence Interval p-value Waiting Time First Oncology appointment >1 month 3.10 1.45 - 6.62 0.003 * Unemployed due to cancer 2.85 1.20 - 6.78 0.018 * Sold Assets to Finance Care 2.40 1.10 - 5.25 0.028 * *Statistically significant at p < 0.05.