tbuckley/cabot-search huggingface dataset:
Abstract 2469: Enhancing pathology workflows with chemical imaging and AI-driven generative models
Authors: Kianoush Falahkheirkhah, Sudipta Mukherjee, John Cheville, Rohit Bhargava
Journal: Cancer Research (2025)

Abstract Histopathology has been a cornerstone of biomedical tissue assessment for decades, involving a labor-intensive and multi-step process that includes biopsy, gross examination, sampling, and subsequent tissue processing into snap-frozen or formalin-fixed paraffin-embedded (FFPE) blocks. These blocks are then sectioned, stained, and examined microscopically to diagnose and grade tissues. Despite its effectiveness, the traditional workflow is time-consuming, resource-intensive, and reliant on chemical dyes and expert interpretation. Recently, innovative chemical imaging techniques, such as Stimulated Raman Scattering (SRS) microscopy, have begun to redefine this field by enabling direct measurement of the molecular composition of tissues, thereby bypassing conventional tissue processing and staining protocols. This study demonstrates the integration of SRS microscopy into pathology workflows to rapidly acquire high-resolution chemical data from minimally processed fresh-frozen tissues. Unlike traditional methods that rely on thin-sectioned slides, this approach collects data from intact thick tissues using "optical sectioning, " enabling the generation of three-dimensional datasets across multiple planes. These chemical images are processed through a generative adversarial network (GAN) pipeline to produce virtual hematoxylin and eosin (H&amp;E) images that are visually and diagnostically comparable to traditionally stained specimens. Furthermore, the generative model is extended to simulate the morphology and staining patterns of FFPE-processed tissues, offering a versatile tool for creating archival-quality images. This method significantly enhances diagnostic capabilities by preserving lipids and small molecules that are often lost during conventional processing. Within minutes, it generates high-quality stained images that demonstrated high inter-pathologist agreement in tissue grading, proving diagnostically reliable for clinical use. We evaluate our approach through a comprehensive survey of pathologists, assessing its diagnostic utility and reliability. Our results demonstrate that the generated images are comparable in quality to real histological images, showing no discernible inferiority in diagnostic utility. In prostate pathology, the integration of SRS microscopy and AI significantly streamlines traditional workflows, reducing complexity and processing time while preserving diagnostic precision. Citation Format: Kianoush Falahkheirkhah, Sudipta Mukherjee, John Cheville, Rohit Bhargava. Enhancing pathology workflows with chemical imaging and AI-driven generative models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2469.
Abstract 1455: Impact of ZFHX3 loss on endometrial cancer progression
Authors: Areebah Qazi, Sophia Agrusa, Swornalata Pukhrambam, Juveria Ali, Sanjeev Ganesh, Jessica Back, Mike R. Wilson
Journal: Cancer Research (2025)

Abstract Endometrial cancer (EC) is the sixth most common cancer among women and ranks as the leading type of gynecological cancer. Although EC is often diagnosed early, current treatment plans significantly limit fertility-sparing options, posing challenges for younger patients. This research focuses on the role of the gene ZFHX3 (ATBF1) to understand its effects on the advancement of endometrial cancer. In order to investigate this, we first transfected 12Z-ESR1 epithelial endometrial cells with ZFHX3 siRNA to create transient gene knockdowns. Following cell collection, western blotting was performed to measure ZFHX3 protein expression levels. Furthermore, we used CRISPR Cas9 plasmid guides tagged with GFP to establish more stable knockdowns. After bacterial transformation, we utilized flow cytometry to sort GFP-expressing cells and confirm successful gene editing. Subsequent western blots were conducted to validate which guide were successful in creating an efficient knockdown of ZFHX3. In vivo studies complemented these cellular experiments. We dissected the uteri of mice with ZFHX3 homozygous and ZFHX3/Pten heterozygous knockdowns. Analysis through H&amp;E staining allowed us to quantify the number of endometrial glands. Our findings revealed that ZFHX3 loss disrupts progesterone signaling, a critical regulator of endometrial function, and leads to increased cell proliferation, which may drive tumor growth. These results highlight ZFHX3 as a potential target for therapeutic strategies aimed at balancing fertility preservation and inhibiting the progression of cancer. Citation Format: Areebah Qazi, Sophia Agrusa, Swornalata Pukhrambam, Juveria Ali, Sanjeev Ganesh, Jessica Back, Mike R. Wilson. Impact of ZFHX3 loss on endometrial cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1455.
Abstract 5276: Comprehensive spatial mapping uncovers immune ecotypes linked to tumor heterogeneity in HCC lung metastasis
Authors: Jinghan Zhu, Guangzhen Cai, Bin Guo, Xiaoping Chen, Huilan Zhang, Hong Zhu, Wanguang Zhang
Journal: Cancer Research (2025)

Abstract Tumor immune microenvironment (TME) heterogeneity, shaped by diverse immune and stromal cells, significantly influences tumor metastasis, yet the specific immune ecotypes involved and their relationship to intra-tumor heterogeneity remain unclear. In this study, we present a comprehensive spatial and cellular multi-omics analysis of 44 primary and 54 lung metastatic lesions from 34 HCC patients. By integrating public single-cell RNA sequencing data from 187, 290 tumor cells across 146 HCC cases, we define HCC cellular states and uncover their organization in high-dimensional spatial expression profiles from paired HCC primary and metastatic lung lesions. Our integrated analysis, incorporating data with three independent cohorts, uncovers three pro-metastatic modules—Cell cycle(G2/M), Cellular Stress and Hypoxia —that contribute to early HCC lung metastasis. Notably, the first two modules are specific to lung metastasis, while the latter one is common across all extrahepatic organs. We show how tumor cells with distinct modules interact with various immune cell types, facilitating metastasis through different mechanisms. Additionally, these tumor cells form multi-layered structures of varying sizes, with specific state pairs preferentially clustering across multiple scales, all within a 55 µm limit. In vivo studies further reveal that interactions between G2/M-high tumor cells and Angio-macrophages and T3-neutrophils accelerate lung dissemination. Treatment with the G2/M inhibitor paclitaxel effectively disrupts this process, reducing metastasis. These findings provide critical insights into how tumor cell heterogeneity reshapes the TME to drive metastasis, underscoring the importance of spatially informed features for personalized cancer therapies. Our work emphasizes the potential of tailored strategies to prevent and manage metastasis based on tumor-immune interactions. Citation Format: Jinghan Zhu, Guangzhen Cai, Bin Guo, Xiaoping Chen, Huilan Zhang, Hong Zhu, Wanguang Zhang. Comprehensive spatial mapping uncovers immune ecotypes linked to tumor heterogeneity in HCC lung metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5276.
Abstract 2642: High expression of N-acetyl transferase 9 in cholangiocarcinoma and its possible role in tumor progression
Authors: Tamara Hoteit, Harlan P. Jones, Pankaj Chaudhary
Journal: Cancer Research (2025)

Abstract Cholangiocarcinoma (CCA) is a rare and aggressive subtype of liver cancer known for its limited number of biomarkers and its resistance to anticancer drugs, leading to difficulty in its early detection. The five-year survival rate for CCA varies between 2% and 24%, depending on factors such as the severity of the cancer, the presence of metastasis, and the timing of diagnosis. Currently, surgery is the most effective treatment option, but only under certain criteria, such as early cancer detection and absence of metastasis. N-terminal acetylation is an epigenetic modification that plays an important role in the regulation of cellular growth and function. This process is modulated by the enzyme N-acetyl transferase (NAT), which is involved in various functions, such as protein stability, membrane targeting, gene silencing, and drug resistance. These functions can regulate cell cycle progression, cell proliferation, and energy metabolism, all of which are key characteristics of cancer. NAT9, a subset of NATs, has abundant transcripts in breast, ovarian, and endometrial cancers; however, its role and expression in CCA have not been studied. In this study, we aimed to assess the expression, role, and function of NAT9 in CCA progression and metastasis using cell lines and patient tissue samples. According to The Cancer Genome Atlas (TCGA) database, NAT9 is overexpressed in patients with CCA, and its expression increases with the increase in the grade of CCA. NAT9 was also overexpressed in CCA cell lines and patient tissue samples compared to their normal and non-cancerous counterparts at both RNA and protein levels. In vitro, NAT9 knockdown experiments showed that NAT9 plays a role in CCA cellular proliferation and migration. These findings suggest that NAT9 plays a critical role in the development and progression of CCA. Citation Format: Tamara Hoteit, Harlan P. Jones, Pankaj Chaudhary. High expression of N-acetyl transferase 9 in cholangiocarcinoma and its possible role in tumor progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2642.
Abstract 1710: Advancing HER2-targeted ADC drug discovery through resistant cell line generation and cancer cell panel analysis
Authors: Lili Chai, Taotao Cao, Xue Yang, Wei Liu, Zhengtai Li, Xiaojian Wang, Tj (Tiejun) Bing
Journal: Cancer Research (2025)

Abstract Antibody-drug conjugates (ADCs) represent a cutting-edge class of targeted cancer therapeutics, seamlessly integrating the high specificity of monoclonal antibodies with the cytotoxic power of chemotherapy agents. This strategic union facilitates the precise delivery of a potent cytotoxic payload to HER2-expressing cancer cells, where HER2 is a well-established therapeutic target. Despite the promising efficacy of HER2-directed ADCs in treating HER2-positive breast cancer, the emergence of resistance in tumor cells poses a significant obstacle to their therapeutic potential. The present study is designed to meticulously assess the anti-tumor efficacy of HER2-targeted ADCs across a diverse panel of cancer cell lines exhibiting varying levels of HER2 expression. Furthermore, to delve into the complexities of resistance, we have developed in vitro models of resistance by subjecting cells to cyclical exposure to DS-8201, a leading HER2-targeted ADC, and its payload, Dxd. Our findings reveal a pronounced inhibitory effect of HER2-targeted ADCs on HER2-positive cancer cell lines, underscoring their selective cytotoxicity. A critical insight from our research is the observation of a significant reduction in HER2 protein levels in cell lines that have developed resistance. This decrease is hypothesized to be a key factor in the resistance mechanism, potentially by limiting the availability of the target for ADC binding. The elucidation of these resistance mechanisms is pivotal, as it informs the strategic development of next-generation HER2-targeted therapies. By addressing the issue of resistance, we aim to enhance the efficacy of HER2-targeted treatments and ultimately improve patient outcomes in the battle against breast cancer. Citation Format: Lili Chai, Taotao Cao, Xue Yang, Wei Liu, Zhengtai Li, Xiaojian Wang, Tj (Tiejun) Bing. Advancing HER2-targeted ADC drug discovery through resistant cell line generation and cancer cell panel analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1710.
Abstract 5254: Multi-plexed spatial interaction analysis of the tumor microenvironment in head and neck cancers
Authors: Vahid Yaghoubi Naei, Sara Bodbin, Habib Sadeghirad, Rafael Tubelleza, James Monkman, Agata Wicher, Subham Basu, Arutha Kulasinghe
Journal: Cancer Research (2025)

Abstract Head and neck cancers are the 7th most common cancer type globally accounting for over 900, 000 cases annually. With increasing numbers of systemic and targeted therapies, including immune checkpoint inhibitors (ICI), it has become increasingly important to understand the complex tumour microenvironment (TME) milieu dictating clinical responses to therapy. In this study, we profiled 40 whole slide, head and neck cancer tissues from patients prior to ICI therapy and profiled the TME for spatial interactions using the NaveniPlex in situ proximity ligation assay (isPLA, Navinci ). Using the Leica BOND RX, formalin-fixed, paraffin-embedded (FFPE) tissue sections were prepared by baking, deparaffinization, and epitope unmasking. Staining was then carried out using the NaveniPlex isPLA technology on the Leica BOND RX instrument. To assess interactions between PD1/PD-L1, CD8/MHCI, and CD3+ T cells, three pairs of Navenibodies were employed simultaneously. Briefly, the NaveniPlex isPLA protocol involves tissue blocking, followed by incubation with primary Navenibodies, ligation, and rolling circle amplification (RCA). Each Navenibody pair generates a distinct RCA product. The RCA products for PD1/PD-L1, CD8/MHCI, and CD3+ T cells were visualized using oligonucleotides conjugated to Atto647N, Atto550, and AlexaFluor488, respectively.Our spatial interaction analysis for PD1/PDL1, CD8/MHCI and CD3+ T-cells showed distinct TME interactions associated with responders and non-responders to ICI therapy. Interactions mapped with cellular phenotypes revealed the cellular neighbourhoods and communities at which these interactions may be useful prognostically. Taken together, this study provides a methodological framework to profile pre-ICI treatment tissues to identify spatial interactions associated with clinical endpoints. Citation Format: Vahid Yaghoubi Naei, Sara Bodbin, Habib Sadeghirad, Rafael Tubelleza, James Monkman, Agata Wicher, Subham Basu, Arutha Kulasinghe. Multi-plexed spatial interaction analysis of the tumor microenvironment in head and neck cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5254.
Abstract 5154: Modeling luminal urothelial carcinoma in the bladder and the upper tract
Authors: Dongbo Xu, Kyle Wieczorek, Li Wang, Yali Zhang, Jianmin Wang, Bo Xu, David W. Goodrich, Ahmed A. Hussein, Khurshid Guru, Qiang Li
Journal: Cancer Research (2025)

Abstract Introduction: Pan-urothelial carcinoma (panUCC) involves synchronous or metachronous urothelial carcinoma of the bladder (UCB) and upper tract urothelial carcinoma (UTUC). We sought to model panUCC using a triple knockout (TKO: Trp53; Rb1; Pten) genetically engineered mouse model (GEMM). Methods: Using a urothelium-specific Uroplakin 2-Cre ERT2 (Upk2-CreERT2), we generated novel TKO mice (Upk2-Cre ERT2; Trp53f/f; Rb1f/f; Ptenf/f). The mice were monitored for hematuria, urine retention, tumor formation, and survival. PCR primers were designed to amplify the genes after recombination. Tumor histology and metastasis were examined by hematoxylin and eosin (HE) and immunohistochemistry (IHC). The subtype of tumors was classified using luminal (Upk3, CK8, GATA-3) and basal markers (CK5, p63), and a neuroendocrine marker (synaptophysin, Syp). Results: Upk2-CreERT2; TKO mice (n = 34, 18 males and 16 females) developed non-muscle invasive urothelial carcinoma tumors located in the bladder and/or the renal pelvis/ureter with a median survival of 294 days. PCR results validated Trp53/Rb1/Pten mutations in UC tumors. Mice with UCB or mixed UCB/UTUC tumors exhibited a longer survival compared to mice with UTUC only [median survival 393 days (n = 7) VS 278 days (n = 27), P = 0.006]. No obvious evidence of distant metastases was detected. IHC of both UCB and UTUC tumors demonstrated luminal UC tumors with strong expression of luminal markers (Upk3, CK8, GATA-3) and no expression of basal and neuroendocrine markers (CK5, p63, and Syp). Conclusion: We developed a novel TKO GEMM that faithfully recapitulates human panUCC. This GEMM provides a useful tool for investigating the molecular and therapeutic differences between UCB and UTUC tumors. Funding: This research work was supported in part by NIH Grants, K08CA252161(Li, Q), P30CA016056 (NCI Cancer Center Core Support Grant), and the Roswell Park Alliance Foundation. Citation Format: Dongbo Xu, Kyle Wieczorek, Li Wang, Yali Zhang, Jianmin Wang, Bo Xu, David W. Goodrich, Ahmed A. Hussein, Khurshid Guru, Qiang Li. Modeling luminal urothelial carcinoma in the bladder and the upper tract [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5154.
Abstract 1491: ATM, CHEK2 and BLM mutant prostate cancers do not have high homologous recombination deficiency scores
Authors: Ekaterina Sh. Kuligina, Aglaya G. Iyevleva, Anna P. Sokolenko, Svetlana N. Aleksakhina, Maria V. Syomina, Ekaterina A. Otradnova, Evgeny N. Imyanitov
Journal: Cancer Research (2025)

Background: Homologous recombination deficiency (HRD) resulting from inactivating mutations in the BRCA1 and BRCA2 genes promotes increased chromosomal instability and renders tumor cells susceptible to platinum derivatives and PARP inhibitors. Hereditary and/or somatic mutations in BRCA2, ATM, CHEK2 and other loci involved in homologous recombination DNA repair (HRR) have been reported in up to 25% of metastatic prostate cancer (PC) cases. The contribution of alterations in HRR-related genes beyond BRCA1/2 to homologous recombination deficiency remains largely unknown. The aim of the current study was to compare the HRD scores in prostate tumors with alterations in different HRR genes. Methods: HRD scores were determined as the sum of genomic loss of heterozygosity (LOH), large-scale state transition (LST) and telomeric allelic imbalance (TAI) scores by targeted NGS using HiSNP Ultra Panel v1.0 (Nanodigmbio, China) in two PC groups. The first group consisted of 58 PC cases with germline or somatic mutations in any of 34 HRR genes, while the second group included 214 cases without HRR mutations. The cut-off for the presence of homologous recombination deficiency was set as an HRD score ≥ 42. Results: HRD was observed more frequently in PCs with HRR mutations (9/58, 16%) than in cases without detectable HRR alterations (10/214, 5%, p = 0.008). In the HRR-mutated subgroup, high HRD scores were found in cases with BRCA2 (n = 4), ATM (n = 2), CDK12, NBN and FANCM mutations. The median HRD scores in PCs with mutations in BRCA2 (n = 9), ATM (n = 12), CHEK2 (n =8), NBN (n = 3), FANCM (n = 3), BRCA1 (n = 3), BLM (n = 3) were 41, 22.5, 7.5, 3, 10, 6, and 3, respectively. The comparison of HRD scores between BRCA2-mutant cases and ATM- (p = 0.046), CHEK2- (p = 0.005), or BLM-mutant PCs (p = 0.042) reached statistical significance. The presence of somatic TP53 mutations was associated with a higher degree of chromosomal instability and elevated HRD scores (p = 0.0001). Conclusions: A high HRD score is observed in a noticeable proportion of prostate tumors lacking mutations in the HRR genes. Prostate cancer cases with alterations in ATM, CHEK2, BLM, and possibly also NBN, FANCM genes are unlikely to have severe HRD. This work has been supported by the Russian Science Foundation (grant number 23-15-00262). Citation Format: Ekaterina Sh. Kuligina, Aglaya G. Iyevleva, Anna P. Sokolenko, Svetlana N. Aleksakhina, Maria V. Syomina, Ekaterina A. Otradnova, Evgeny N. Imyanitov. ATM, CHEK2 and BLM mutant prostate cancers do not have high homologous recombination deficiency scores [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1491.
Abstract 1236: Immune competent 3D pancreatic adenocarcinoma (PDAC)-on-chip model for preclinical drug discovery
Authors: Alina Deipenbrock, Ben Eric Wilmes, Kyra Moustakas, Irene Esposito, Thomas Sommermann, Martin Raasch, Nicole Teusch
Journal: Cancer Research (2025)

Abstract Representing the most common malignancy of the pancreas, pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer type with a five-year survival rate of less than 13%. To date, targeted treatment regiments are not available, leaving only cytotoxic chemotherapy with gemcitabine or FOLFIRINOX as the first-line-treatment for patients who are ineligible for surgical resection. One factor which contributes to the lack of efficient treatment options is the presence of a highly fibrotic and immunosuppressive tumor microenvironment (TME), mainly consisting of cancer associated fibroblasts (CAF) and tumor associated macrophages (TAM). Furthermore, effective treatments require drug candidates to pass the endothelium into the tumor. This barrier is not addressed in most in vitro models traditionally used in drug screening. Thus, novel PDAC models reflecting, the cellular heterogeneity within the TME including a vascular linkage will be essential to find efficacious treatment strategies. Using the Dynamic42 biochip platform, which allows dynamic culturing of cells in three channels each separated by porous membranes, we generated a fit-for-purpose 3D model of human PDAC. The model combines a perfused vasculature with an underlying tumor tissue consisting of tumor spheroids with a CAF hull embedded into an extracellular matrix (ECM). We first used this PDAC-on-chip model as a proof-of-principle to deliver small molecule drug candidates via a vasculature to the 3D spheroids. As one example, we identified vorinostat, a histone deacetylase inhibitor already approved for cutaneous T cell lymphoma, significantly reducing PDAC spheroid viability in a dose dependent manner without impacting the vascular integrity. We further expanded the PDAC-on-chip model by introducing peripheral blood mononuclear cells (PBMC)-derived monocytes. We show that monocytes applied through the vasculature invade through the endothelial barrier and migrate into CAF rich areas, where they differentiate to M2-like macrophages upregulating CD163 and loosing CD86 and HLA-DR expression. We now use this system to study T cell invasion, as well as direct vascularization of PDAC tumors. Citation Format: Alina Deipenbrock, Ben Eric Wilmes, Kyra Moustakas, Irene Esposito, Thomas Sommermann, Martin Raasch, Nicole Teusch. Immune competent 3D pancreatic adenocarcinoma (PDAC)-on-chip model for preclinical drug discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1236.