Supplementary Figure from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

2025-11-26

Supplementary Figure from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

Data from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

2025-11-26

<div>AbstractBackground:<p>High-risk human papillomavirus (hrHPV) testing is utilized in primary cervical cancer screening, generally along with cytology, to triage abnormalities to colposcopy. Most screening-based hrHPV testing involves pooled detection of any hrHPV or of HPV16/18. Cervical neoplasia progression risks based on extended hrHPV genotyping—particularly non-16/18 hrHPV types—are not well characterized. HPV genotype-specific incidence of high-grade cervical intraepithelial neoplasia or more severe (CIN2+) following an abnormal screening result was examined.</p>Methods:<p>We assessed a US-based prospective, multiracial, clinical cohort of 343 colposcopy patients with normal histology (<i>n</i> = 226) or CIN1 (<i>n</i> = 117). Baseline cervical samples underwent HPV DNA genotyping, and participants were followed up to 5 years. Genotype-specific CIN2+ incidence rates (IR) were estimated with accelerated failure time models. Five-year CIN2+ risks were estimated nonparametrically for hierarchical hrHPV risk groups (HPV16; else HPV18/45; else HPV31/33/35/52/58; else HPV39/51/56/59/68).</p>Results:<p>At enrollment, median participant age was 30.1 years; most (63%) were hrHPV-positive. Over follow-up, 24 participants progressed to CIN2+ (7.0%). CIN2+ IR among hrHPV-positive participants was 3.4/1,000 person-months. CIN2+ IRs were highest for HPV16 (8.3), HPV33 (7.8), and HPV58 (4.9). Five-year CIN2+ risk was higher for HPV16 (0.34) compared with HPV18/45 (0.12), HPV31/33/35/52/58 (0.12), and HPV39/51/56/59/68 (0.16) (<i>P</i> = 0.05).</p>Conclusions:<p>Non-16/18 hrHPV types are associated with differential CIN2+ progression rates. HPV16, 33, and 58 exhibited the highest rates over 5 years. HPV risk groups warrant further investigation in diverse US populations.</p>Impact:<p>These novel data assessing extended HPV genotyping in a diverse clinical cohort can inform future directions to improve screening practices in the general population.</p></div>

Supplementary Table from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

2025-11-26

Supplementary Table from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

Abstract A022-PR005: CDK8 Inhibition Releases the Muscle Differentiation Block in Fusion-Driven Alveolar Rhabdomyosarcoma

Cancer Research · 2025-09-25

Abstract Functional and chemical genomic approaches, such as the Broad Institute’s Cancer Dependency Map and PRISM (Profiling Relative Inhibition Simultaneously in Mixtures) chemical screening, have revolutionized the identification of context-specific genetic dependencies and therapeutic vulnerabilities across diverse cancer types. These datasets empower the identification of therapeutic strategies in cancers with limited actionable mutations. Alveolar rhabdomyosarcoma (aRMS), a pediatric cancer driven by a hard-to-target fusion oncoprotein, PAX3::FOXO1, typically expresses no immediately actionable mutations. Using aRMS as a disease model, we utilized the Broad Institute’s Cancer Dependency Map dataset, coupled with single-sample gene set enrichment analysis (ssGSEA), to systematically assess protein complex dependencies in aRMS. We nominated the Mediator complex and further identified CDK8, a member of the Mediator kinase module, as a clinically actionable target in aRMS. Other members of the Mediator kinase module, including CCNC, MED12, and MED13, are also essential to aRMS proliferation. In addition, in aRMS cell lines, there was a positive correlation (R=0.68) between the CDK8 gene-effect score and the effect of the CDK8 inhibitor, BI-1347, in the PRISM screening. We validated that both genetic loss of CDK8 and kinase inhibition by CDK8 small molecule inhibitors impaired aRMS cell line growth in vitro and induced evidence of myogenic differentiation. Our in vivo studies demonstrated that the clinical grade CDK8 inhibitor SEL-120-34A decreased aRMS cell line xenograft tumor growth. Functional genomic screens also serve as powerful tools to understand the mechanisms of small molecule inhibitors and to identify resistance and sensitizer mechanisms. We thus performed an unbiased genome-scale CRISPR-Cas9 screen with the CDK8 inhibitor BI-1347 in aRMS. We determined that the maximal anti-tumor activity of the CDK8 inhibitor requires the presence of the SAGA complex, particularly the SAGA HAT module. We further identified SIX4 as a key transcription factor mediating CDK8 inhibitor-induced transcriptional activation of myogenic differentiation genes. In addition, we revealed that the maximal activity of BI-1347 requires the presence of the Mediator kinase module, suggesting a trapping-related mechanism in addition to kinase enzymatic inhibition. Accordingly, we found that CDK8 inhibition increased the binding of components of the Mediator kinase module and SIX4 and TADA2B at enhancers of terminal muscle differentiation-related genes, such as VGLL2, SEMA3D, MYL1, leading to their transcriptional activation, as shown by PRO-seq analyses. These findings provide a framework for uncovering therapeutic targets using network-based analysis of functional genomic screens, and for studying the small molecular inhibitor mechanisms. In aRMS, CDK8 inhibition is a differentiation-inducing therapeutic strategy. Citation Format: Susu Zhang, Kathleen Engel, Assil Fahs, Clare Malone, Kenneth Ross, Marissa Just, Brian Guedes, Diyana Granum, Kristianne M Oristian, Alexander Kovach, Gabriela Alexe, Giulia Digiovanni, Leen Barbar, Rex Bentley, Christian Cerda-Smith, Ozgun Le Roux, Elizabeth Mendes, Seth P Zimmerman, Matthew Rees, Jennifer Roth, Jack F Shern, Kris C Wood, Christopher M Counter, Corinne M Linardic, Kimberly Stegmaier. CDK8 Inhibition Releases the Muscle Differentiation Block in Fusion-Driven Alveolar Rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2):Abstract nr A022-PR005.

Automation of fluorescent in situ hybridization (FISH) leading to cost savings and consistent high-quality results

Journal of Clinical Pathology · 2025-09-17 · 1 citations

AIMS: Despite continually improving guidelines, human epidermal growth factor receptor 2 (HER2) testing for breast and gastro-oesophageal carcinoma continues to be a technical challenge in clinical laboratories. Manual HER2 fluorescence in situ hybridisation (FISH) testing is labour-intensive and prone to inter-run and interoperator variability. We aimed to adopt and validate a Leica BOND-III automated staining platform for HER2 FISH testing. METHODS: We recently validated the Leica BOND-III automated staining platform for HER2 FISH testing and compared it to our previous manual FISH (Agilent HER2 IQFISH pharmDx) methodology using 77 breast cancer cases and 8 gastric cancer cases. RESULTS: Using the automated Leica BOND-III automated staining platform, we achieved 0.95 sensitivity and 0.97 specificity in HER2 FISH testing for breast cancer cases and 1.0 sensitivity and specificity for gastric carcinoma cases. There was a 98% concordance rate between results of automated testing versus our previous manual method. The automated staining platform decreased technical hands-on time significantly while also reducing overall supply costs for the laboratory. CONCLUSIONS: We were able to implement and validate the automated Leica BOND-III staining platform seamlessly into a complex laboratory for HER2 FISH testing that has overall significantly decreased hands-on time by technologists and supply costs. Automated Leica BOND-III HER2 FISH staining results were highly concordant with our previous manual FISH method in both breast cancer and gastric cancer cases.

Supplementary Table from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

2025-11-26

Supplementary Table from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

Supplementary Table from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

2025-11-26

Supplementary Table from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

Supplementary Figure from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

2025-11-26

Supplementary Figure from Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

CDK8 Inhibition Releases the Muscle Differentiation Block in Fusion-driven Alveolar Rhabdomyosarcoma

bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-18

ABSTRACT Alveolar rhabdomyosarcoma (aRMS) is a fusion-driven pediatric cancer with poor survival and limited therapeutic options. To uncover novel vulnerabilities, we employed complex-based analysis of the DepMap functional genomic data, identifying CDK8 as a dependency in aRMS. Both CDK8 knockout and pharmacologic inhibition impaired tumor cell growth and induced myogenic differentiation in vitro and in vivo . Compared to genetic loss, CDK8 inhibition induced more dynamic transcriptional changes. With a genome-scale CRISPR-Cas9 drug modifier screen, we determined that the maximal anti-tumor activity of the CDK8 inhibitor requires the presence of the Mediator kinase module and transcriptional cooperation with the SAGA complex. We further identified SIX4 as a key transcription factor mediating CDK8 inhibitor-induced transcriptional activation of myogenic differentiation genes and tumor cell proliferation. These findings suggest a distinct gain-of-function mechanism of the CDK8 inhibitor and establish a strong rationale for CDK8 inhibition as a differentiation-inducing therapeutic strategy in aRMS. STATEMENT OF SIGNIFICANCE We provide a framework for uncovering therapeutic targets by network-based analysis of functional genomic screens. We identify CDK8 as a druggable target in aRMS and determine that CDK8 inhibition drives myogenic differentiation and impairs tumor progression via a collaborative mechanism involving the Mediator kinase module, SAGA complex, and SIX4.

Standardized Pathologic Reporting for Phyllodes Tumors: Where are We after 3 Years?

Annals of Surgical Oncology · 2025-12-10