Formalin-fixed Paraffin-embedded Specimens Research Articles

Correlation of microscopic tumor extension with tumor microenvironment in esophageal cancer patients.

In the era of image-guided adaptive radiotherapy, definition of the clinical target volume (CTV) is achallenge in various solid tumors, including esophageal cancer (EC). Many tumor microenvironmental factors, e.g., tumor cell proliferation or cancer stem cells, are hypothesized to be involved in microscopic tumor extension (MTE). Therefore, this study assessed the expression of FAK, ILK, CD44, HIF-1α, and Ki67 in EC patients after neoadjuvant radiochemotherapy followed by tumor resection (NRCHT+R) and correlated these markers with the MTE. Formalin-fixed paraffin-embedded tumor resection specimens of ten EC patients were analyzed using multiplex immunofluorescence staining. Since gold fiducial markers had been endoscopically implanted at the proximal and distal tumor borders prior to NRCHT+R, correlation of the markers with the MTE was feasible. In tumor resection specimens of EC patients, the overall percentages of FAK+, CD44+, HIF-1α+, and Ki67+ cells were higher in tumor nests than in the tumor stroma, with the outcome for Ki67+ cells reaching statistical significance (p < 0.001). Conversely, expression of ILK+ cells was higher in tumor stroma, albeit not statistically significantly. In three patients, MTE beyond the fiducial markers was found, reaching up to 31 mm. Our findings indicate that the overall expression of FAK, HIF-1α, Ki67, and CD44 was higher in tumor nests, whereas that of ILK was higher in tumor stroma. Differences in the TME between patients with residual tumor cells in the original CTV compared to those without were not found. Thus, there is insufficient evidence that the TME influences the required CTV margin on an individual patient basis. BO-EK-148042017 and BO-EK-177042022 on 20.06.2022, DRKS00011886, https://drks.de/search/de/trial/DRKS00011886 .

Abstract PO3-01-09: Results of a prospective observational study evaluating the impact of the Prosigna assay on neoadjuvant treatment decision-making in patients with early-stage HR+/HER2- breast cancer

Abstract Background. Prosigna (PAM50) is an FDA-approved prognostic test that measures the expression of 50 classifier genes in breast cancer tissue samples. It provides intrinsic subtyping, which classifies the biology of an individual patient's tumor, as well as a risk of recurrence (ROR) score that predicts the probability of distant recurrence over 10 years. Currently, the Prosigna assay is only approved for use in postoperative specimens. Given studies demonstrating that Prosigna can identify tumors that are more likely to benefit from chemotherapy, this decision-impact study sought to evaluate whether the assay could influence physicians' choices and patients' confidence in the neoadjuvant treatment plan. Methods. This prospective observational study was conducted at a single institution and included patients with HR+/HER2- breast cancer measuring ≥ 0.5 cm, any nodal status, who were deemed candidates for neoadjuvant systemic treatment based on physician’s choice. Formalin-fixed paraffin-embedded core biopsy specimens were centrally analyzed using Prosigna. Patients' tumors were classified according to intrinsic tumor subtype (Luminal A, Luminal B, HER2-enriched, Basal-like) and ROR score (low, intermediate, or high). Physicians and patients were surveyed before and after performing Prosigna, regarding neoadjuvant therapy recommendations. The primary endpoint was assessment of the effect of Prosigna on oncologists' treatment recommendations and the actual treatment received (neoadjuvant hormonal therapy [NAHT], neoadjuvant chemotherapy [NACT], or upfront surgery). Secondary endpoints included determining whether treatment changes were based on ROR score, intrinsic subtype, or both, as well as assessing physicians' and patients' confidence in the treatment plan. Results. A total of 54 patients were enrolled in the study between March 2019 and April 2023. The distribution of intrinsic tumor subtypes was as follows: 15 patients (28%) had a Luminal A subtype, 34 (63%) had a Luminal B subtype, 3 (6%) had a HER2-enriched subtype, and 2 (4%) had a Basal-like subtype. Thirty-three patients (61%) were classified as ROR-low, 11 (20%) as ROR-intermediate, and 10 (19%) as ROR-high. Out of the 43 patients who had both pre- and post-assay survey results available, a change in the treatment decision was observed in 28% of cases. Specifically, 14% of patients transitioned from NAHT to NACT, 7% from NACT to NAHT, and 5% from NACT to upfront surgery, as shown in the Table. Treatment changes were based on the ROR score, intrinsic subtype, and both in 33%, 3%, and 64% of cases, respectively. Overall, 45% of physicians experienced an increase in confidence for the treatment plan after Prosigna testing, while 16% reported a decrease and 39% maintained the same level of confidence. Sixty-two percent of patients experienced a reduction in anxiety about treatment. Associations of ROR score and intrinsic subtypes will be presented at the meeting. Conclusion. Prosigna performed on presurgical core biopsies influenced oncologists' treatment recommendations regarding neoadjuvant treatment and reduced patient anxiety about treatment among patients with early-stage HR+/HER2- breast cancer. Table. Neoadjuvant treatment recommendations before and after Prosigna assay, overall and according to nodal status. Data are presented as frequencies (%). Abbreviations: NACT, neoadjuvant chemotherapy; NAHT, neoadjuvant hormonal therapy. Citation Format: Chiara Corti, Xiangying Chu, Pedro Exman, Danielle Kline, Nolan Priedigkeit, Nabihah Tayob, Erica Mayer, Adrienne Waks, Melissa Hughes, Antonio Giordano, Giuseppe Curigliano, Nancy Lin, Tari King, Rinath Jeselsohn, Deborah Dillon, Elizabeth Mittendorf, Sara Tolaney. Results of a prospective observational study evaluating the impact of the Prosigna assay on neoadjuvant treatment decision-making in patients with early-stage HR+/HER2- breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-01-09.

Abstract PO4-25-10: Towards personalized medicine for DCIS - the role of hormone receptors, HER2, and Ki67 status in high-grade DCIS

Abstract Objective: This study aimed to investigate the molecular details in breast ductal carcinoma in situ (DCIS). Expression status of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and Ki67 were investigated among luminal A (LumA), luminal B HER2-negative (LumB HER2-), luminal B HER2-positive (LumB HER2+), HER2-enriched, and triple-negative (TPN), subtypes of DCIS. Materials &amp; Methods: The study comprised formalin-fixed paraffin-embedded (FFPE) specimens of 357 DCIS grade 3 cases diagnosed between 1996 – 2018. Routine diagnostic immunohistochemical (IHC) staining were performed. DCIS cases were classified as LumA, LumB HER2-, LumB HER2+, HER2-enriched or TPN, according to the 2013 St. Gallen guidelines, which is used for molecular subtyping of invasive breast carcinoma (IBC). Each subtype was sorted into three subcategories: “pure” meaning those without an invasive component; “w/invasive” meaning those with an invasive component; and “all” meaning the entire group of the given subtype. Furthermore, ER and PR-receptor expression was registered for LumA, LumB HER2- and LumB HER2+ cases as intervals. The distribution of Ki67 was analyzed within each subtype. For some analyses, we combined the LumA and LumB HER2- subtypes into one entire group. The inter-observer variability of Ki67 was calculated by setting a cut-off value of 20% (2013 St. Gallen). A cohort (n = 47) of DCIS cases with a median Ki67 value of 18% was selected. Ki67 was calculated by analyzing 200 DCIS cells in two separate hotspots. Cohen's Kappa coefficient was calculated based on these data. HER2 (IHC) was scored based on ASCO/CAP guidelines established for routine diagnostic work-up for IBC. 16 equivocal cases (2+) were further investigated using dual SISH. Results: 98% of “all” cases of the LumA subtype showed an ER ≥ 50%. PR expression ≥ 50% was found in 91% of cases in this subtype. The incidence of ER-receptor at a cut-off ≥ 50% in the LumA subtype was significantly higher than that in the LumB HER2- and LumB HER2+ subtypes (p &amp;lt; 0.0001, Chi-square). In contrast, there was a statistically significant reduction in ER-receptor expression at a cut-off &amp;lt; 10% in LumA compared to the latter subtypes. The proportion of cases with PR-receptors with a cut-off of &amp;lt; 20% showed significant differences between LumA, LumB HER2- and LumB HER2+ subtypes (1.6%; 47% and 37%, respectively). There was also a significantly higher proportion of PR-receptor ≥ 50% cases among the LumA subtype. We found a significant association between PR &amp;lt; 20% and HER2 (3+) in luminal subtypes (p &amp;lt; 0.0004, Fisher's exact). There was no significant difference in ER/PR expression in “pure” cases of luminal subtypes of DCIS versus those with an invasive component (p = 0.1831, Chi-square). The Ki67 in the entire population (n = 357) varied from &amp;lt; 1% to &amp;gt; 80%. The mean and median were around 20% in those subtypes whose classifications were not depended on Ki67. There was a significant difference in the distribution of Ki67 when cases of LumA “all” and those of LumB HER2- “all” were combined as one entire group and were compared to LumB HER2+ “all” and HER2-enriched “all” (p-adjusted &amp;lt; 0.0001, Kruskal Wallis). The assessment of Ki67 among different observers showed a Cohen's kappa coefficient of 0.29 – 0.31 (fair agreement). We compared the HER2 (IHC) 0, 1+ and 2+ score among LumA and LumB HER2- subtypes and did not find a statically significant difference, when the “pure” and “w/invasive” were compared (p = 0.603, Chi-square). Conclusions: Ki67 was highly variable in DCIS grade 3. Inter-observer agreement was (as expected) suboptimal, and the cut-off at 20% defined by the 2013 St Gallen guidelines for IBC is not reliable for the distinction of LumA and LumB HER2 subtypes of DCIS. The LumB subtype of DCIS is heterogeneous with considerable variability among the four IHC markers used in the present study. A low PR is strongly associated with HER2 (3+), in luminal subtypes (p &amp;lt; 0.0004, Fisher's exact). Citation Format: Hossein Schandiz, Lorant Farkas, Daehoon Park, Solveig Norheim Andersen, Jürgen Geisler, Torill Sauer. Towards personalized medicine for DCIS - the role of hormone receptors, HER2, and Ki67 status in high-grade DCIS [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-25-10.

Proteomic profiling of FFPE specimens: Discovery of HNRNPA2/B1 and STT3B as biomarkers for determining formalin fixation durations

Recent advancements in proteomics technologies using formalin-fixed paraffin-embedded (FFPE) samples have significantly advanced biomarker discovery. Yet, the effects of varying sample preparation protocols on proteomic analyses remain poorly understood. We analyzed mouse liver FFPE samples that varied in fixatives, fixation duration, and storage temperature using LC/MS. We found that variations in fixation duration significantly affected the abundance of specific proteins, showing that HNRNPA2/B1 demonstrated a significant decrease in abundance in samples fixed for long periods, whereas STT3B exhibited a significant increase in abundance in samples fixed for long periods. These findings were supported by immunohistochemical analysis across liver, spleen, and lung tissues, demonstrating a significant decrease in the nuclear staining of HNRNPA2/B1 in long-term AF-fixed FFPE samples, and an increase in cytoplasmic staining of STT3B in long-period NBF-fixed liver and lung tissues, and granular staining in all long-term AF-fixed FFPE tissue types. Similar trends were observed in the long-period fixed HeLa cells. These results demonstrate that fixation duration critically affects the proteomic integrity of FFPE samples, emphasizing the urgent need for standardized fixation protocols to ensure consistent and reliable proteomic data. SignificanceThe quality of formalin-fixed, paraffin-embedded (FFPE) samples is primarily influenced by the fixation and storage conditions. However, previous studies have mainly focused on their impact on nucleic acids. and the extent to which different fixation conditions affect changes in proteins has not been evaluated. In addition, to our knowledge, proteomic research focusing on differences in formalin fixation conditions has not yet been conducted. Here, we analyzed FFPE samples with different formalin fixation and storage conditions using liquid chromatography/mass spectrometry (LC/MS) and evaluated the impact of different fixation conditions on protein variations. Our study unequivocally established formalin fixation time as a critical determinant of protein variation in FFPE specimens and successfully identified HNRNPA2/B1 and STT3B as potential biomarkers for predicting formalin quality for the first time. The study findings open new avenues for quality assessment in biomedical research and diagnostics.

Evaluation of the Role of Oral Microbes in Pathogenesis of Oral Lichen Planus

ABSTRACT Background: The pathophysiology and etiology of oral lichen planus (OLP) are still unknown, despite the fact that the condition’s progression has been connected to a T-cell-based immune response. Research has focused on variables, such as oral bacteria, that may cause an autoimmune reaction with conflicting results. Aim: This study was conducted to evaluate the role of oral microorganisms in the pathogenesis of OLP. Materials and Methods: In this study, 82 formalin-fixed paraffin-embedded specimens of histopathologically confirmed cases of OLP and 20 such specimens of normal healthy subjects were obtained. Immunohistochemistry was carried out for the identification of microorganisms. Results: Candida albicans was observed in 47.12% of OLP cases and 9.43% of healthy controls. Helicobacter pylori was discovered in 45.21% of OLP cases and 13.46% of healthy controls. Periodontopathogenic bacteria was found in 33.14% of OLP cases and 13.45% of healthy controls. Human papillomavirus (HPV)-16 was noticed in 38.12% of OLP cases and 11.24% in the control group. HPV-18 was found in 32.43% of OLP patients and 11.43% in the control group. Mycoplasma salivarium was found in 46.47% of OLP patients and 6.45% in control. Conclusion: It was observed that several microorganisms like H. pylori, C. albicans, M. salivarium, periodontopathogenic bacteria, HPV-16, and HPV-18 were found to be related to OLP.

CORRELATION OF TUMOR MARKERS HER2 NEU ER PR AND KI 67 IN BREAST CANCER PATIENTS

: Every year, more than a million women are diagnosed with breast cancer, and over 700.000 of them have positive for hormone receptors (FIR). The expression of key markers, such as ER and PP, and clinical circumstances show specific biological traits. Risk factors may have a role in the development of some hormone receptor-positive breast cancers. Objective: The objective of this study was to investigate the correlations between key tumor markers, including HER2, ER, PR, ALP, and KI67, in hormone receptor-positive breast cancers. Methods: Tumour tissue samples were collected for histopathology (10% neutral buffered Formalin-fixed paraffin-embedded tissue specimens) during Trucut biopsy or mastectomy at the oncology department of a tertiary care hospital in Karachi from October 2022 to July 2023. Tissues were analyzed under a light microscope for tumor hormone receptors at a tertiary care hospital in Karachi.  Results: There were several significant correlations observed between HER 2 NUE, KI 67, ER, and PR. Specifically, a weak negative correlation was noted between HER 2 NUE and KI 67, while weak positive correlations were observed between HER 2 NUE and both ER and PR. Additionally, a weak positive correlation was found between ER and HER 2 NUE, PR, and KI 67, and a weak positive correlation existed between PR and ER, HER 2 NUE, and KI 67. Finally, KI 67 displayed a weak positive correlation with HER 2 NUE, PR, and ER. Conclusions: Her two nurses, ER, ALP, KI 67, and breastfeeding, are significantly and directly related. PR is not significantly related to other mentioned tumor markers.

Enhancing Specific Fluorescence In Situ Hybridization with Quantum Dots for Single-Molecule RNA Imaging in Formalin-Fixed Paraffin-Embedded Tumor Tissues.

Single-molecule fluorescence in situ hybridization (smFISH) represents a promising approach for the quantitative analysis of nucleic acid biomarkers in clinical tissue samples. However, low signal intensity and high background noise are complications that arise from diagnostic pathology when performed with smFISH-based RNA imaging in formalin-fixed paraffin-embedded (FFPE) tissue specimens. Moreover, the associated complex procedures can produce uncertain results and poor image quality. Herein, by combining the high specificity of split DNA probes with the high signal readout of ZnCdSe/ZnS quantum dot (QD) labeling, we introduce QD split-FISH, a high-brightness smFISH technology, to quantify the expression of mRNA in both cell lines and clinical FFPE tissue samples of breast cancer and lung squamous carcinoma. Owing to its high signal-to-noise ratio, QD split-FISH is a fast, inexpensive, and sensitive method for quantifying mRNA expression in FFPE tumor tissues, making it suitable for biomarker imaging and diagnostic pathology.

Abstract 562: Frequent copy number gain of MCL1 is a therapeutic target for osteosarcoma

Abstract Osteosarcoma (OS) is the most common primary malignant bone tumor that predominantly occurs in children, adolescents, and young adults. The treatment for OS that combines surgery with chemotherapy, which consists of a four-drug combination of adriamycin (DOX), cisplatin (CDDP), high-dose methotrexate (MTX), and ifosfamide, was established in 1970s, and it is still used as a standard therapy. Oncogenic driver mutations and fusion genes common to OS have not been identified, which is one of the reasons for the lack of success in drug development for OS. Herein, to explore the characteristic vulnerability in OS, molecular targeted drugs were screened against OS cell lines and patient-derived cells; obatoclax, a pan-BH3 mimetic, and a concomitant drug that enhances obatoclax-induced apoptosis, OSI906, a dual inhibitor of IGF1R and IR, were found. Fluorescence in situ hybridization (FISH) analysis revealed that copy number gains of MCL1, an antiapoptotic Bcl-2 family protein, were observed in 46.3% of formalin-fixed paraffin-embedded (FFPE) specimens from patients with OS (N = 41) and in 45.5% of OS cell lines (N = 11), thereby causing vulnerability to BH3 mimetics. IHC staining also revealed high expression of Mcl-1 protein in specimens with MCL1-amplification in FISH analysis. Pharmacological or genetic inhibition of Mcl-1 induced potent apoptosis in MCL1-amplified OS cells, which was enhanced by the co-inhibition with Bcl-xL. Moreover, chromosome 1q21.2-3, where MCL1 is located, contains several IGF1R/PI3K pathway-related genes, including PIP5K1A, TARS2, OUTD7B, and ENSA, whose copy numbers were also increased in MCL1-amplified OS cells, suggesting that 1q21.2-3-amplified OS cells readily activate downstream pathways via IGF1R. IGF signaling activation in 1q21.2-3-amplified OS cells negated the obatoclax-induced apoptosis, which was overcome by OSI906 treatment. Combined obatoclax and OSI906 administration remarkably suppressed MCL1-amplified OS tumor growth in the xenograft mouse model and resulted in tumor regression; however, none of the treatments reduced tumor growth of OS without MCL1 amplification. These results suggest that combining obatoclax with OSI906 could be a potential therapeutic intervention for 1q21.2-3-amplified OS, and that prior stratification of OS based on the 1q21.2-3 amplification status would be important for the success of this combination therapy. Thus, we elucidated the mechanism of action of drugs and their potential as a novel therapeutic strategy for approximately 50% of patients with OS. Moreover, a FISH analysis that can detect copy number gains of MCL1 in FFPE specimens from patients with OS was established to stratify patients eligible for this therapy. Citation Format: Satoshi Takagi, Ryohei Katayama. Frequent copy number gain of MCL1 is a therapeutic target for osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 562.

Abstract 2266: Detection of androgen receptor splice variants from clinical sequencing

Abstract Background: Androgen receptor splice variant-7 (AR-v7) has been widely studied as a biomarker of resistance to AR-targeted therapy in castration-resistant prostate cancer (CRPC). Various methods have been used to detect AR-v7 in CRPC specimens, including next generation sequencing (NGS) technology. However, NGS technologies applied in clinical sequencing have focused on using blood or fresh-frozen CRPC tissue specimens. There is not yet an AR-v7 detection system tailored to formalin-fixed paraffin-embedded (FFPE) tissue specimens commonly used for clinical sequencing in hospitals. Methods: In this respect, we propose a novel approach to identify AR-v7 in targeted RNA sequencing (RNA-seq) data derived from FFPE specimens. This approach can identify, in addition to AR-v7, all constitutively active AR splice variants (AR-Vs) that are co-expressed with AR-v7. In short, our two-step approach first gathers soft-clipped or divided reads that are adjacent to the splicing sites of AR-Vs and then yields the number of splitting reads that support the existence of AR-Vs. Next, the algorithm selects the paired-end reads whose one side and the other side are mapped to the preceding and following exons, respectively. The final number of spanning reads are calculated following to the removal of low-quality reads. Results: We validated the proposed approach using two large-scale, independent RNA-seq datasets of prostate cancer (PC) samples: 111 samples from Seoul National University Hospital (SNUH) and 558 samples from The Cancer Genome Atlas (TCGA) dataset. The majority of both datasets were localized PC tumors, especially in the SNUH dataset, where localized PC accounted for 91% of the total. Overall, our approach successfully identified samples with putative AR-Vs, including AR-v7, AR-v3, and AR-v9. Statistical analyses of 111 SNUH PC patients suggested potential detection threshold in clinical sequencing settings (at least 200 split reads). In the SNUH dataset, the AR-v7 positive group, which included 5 patients (5%) with values above the threshold, shared the following characteristics: higher AR-v7/full length AR expression levels, AR amplification and co-expression with AR-v3/AR-v9. AR-v7 positivity was experimentally validated by Sanger sequencing. The similar pattern was also found in the analysis of TCGA dataset. Conclusions: These results demonstrate that the detection system can successfully identify AR-v7 positivity not only for metastatic PC but also for patients with localized PC through clinical sequencing. We expect that the further in-depth analyses including larger samples and clinical outcomes can discover clinical applicability of AR-v7. Citation Format: Suhyun Hwangbo, Sungyoung Lee, Sheehyun Kim, Hongseok Yun. Detection of androgen receptor splice variants from clinical sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2266.

Abstract 2275: Reducing artifactual somatic variant calls from formalin-fixed paraffin-embedded specimens by using DEEPOMICS FFPE, a bioinformatic approach based on deep neural networks

Abstract Formalin-fixed, paraffin-embedded (FFPE) tissue specimens are routinely used in pathological diagnosis. However, formalin induced artificial mutations make it challenging to accurately analyze next-generation sequencing data. Existing FFPE filtering tools tend to categorize all low-frequency variants as artifacts, making it difficult to identify true variants with low allele frequencies, compromising analysis of tumors with low tumor cell content. To address this issue, we developed DEEPOMICS FFPE, an AI model designed to distinguish true variants from artifacts. We gathered paired exome genome sequencing data from both fresh frozen and FFPE samples of 24 tumors from public sources. These data were used to train and validate the model, with a split of 70% for training and 30% for validation. The deep neural network model, comprising three hidden layers, was trained using input features derived from the outputs of the MuTect2 caller. We employed the SHapley Additive exPlanations algorithm to identify relevant features, and then fine-tuned them based on the training outcomes. We assessed the performance of the final DEEPOMICS FFPE model in comparison to existing models (MuTect filter, FFPolish, and SOBDetector) using well-defined test datasets. Our findings revealed 43 distinguishing characteristics for FFPE artifacts. Refining the quantification of these characteristics resulted in improved model performance. DEEPOMICS FFPE successfully filtered out 99.6% of artifacts while retaining 85.2% of true variants, achieving an F1-score of 87.8 in the validation dataset, surpassing the performance of existing tools. Furthermore, the model demonstrated consistent performance even for variants with low allele frequencies, exhibiting a specificity of 0.998, suggesting its capability to identify subclonal variants. Future enhancement of the model will include the ability to use other variant callers and analysis of whole genome sequencing data. This newly developed tool has potential applications in designing capture panels for personalized circulating tumor DNA assays and identifying candidate neoepitopes for personalized vaccine development. DEEPOMICS FFPE is freely accessible for research purposes on the web at http://deepomics.co.kr/ffpe. Citation Format: Dong-hyuk Heo, Inyoung Kim, Heejae Seo, Seong-Gwang Kim, Minji Kim, Jiin Park, Hongsil Park, Seungmo Kang, Juhee Kim, Soonmyung Paik, Seong-Eui Hong. Reducing artifactual somatic variant calls from formalin-fixed paraffin-embedded specimens by using DEEPOMICS FFPE, a bioinformatic approach based on deep neural networks [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2275.

Abstract 5183: Retrospective analysis of CCNG1 expression in tumors, a novel biomarker in development for partnering with DRG-101, a tumor targeted retrovector encoding a CCNG1 inhibitor gene

Abstract Background: CCNG1, a non-canonical cyclin, is a novel biomarker in development for partnering with DRG-101 (DeltaRex-G), a tumor targeted retrovector encoding a CCNG1 inhibitor gene. Expanded access using DRG-101 is currently open for an intermediate-size population of advanced pancreatic cancer, sarcoma and carcinoma of breast (NCT04091295). Therefore, it is important to identify patients who might respond favorably to DRG-101 gene therapy. Previously, we reported that CCNG1 expression is enhanced in sarcoma tumors (Ann Oncol 34, 1980P, 2023). In this report, we have expanded the analysis to 137 patients with all cancer types and describe patients with known CCNG1 expression levels who have been treated with DRG-101. Methods: Archived formalin-fixed paraffin-embedded (FFPE) tumor specimens (n=137) from patients who were followed at the Sarcoma Oncology Research Center were collected, processed, and subjected to RNA sequencing. Briefly, RNA-seq libraries were sequenced to generate 50 million reads, aligned using Kallisto v0.42.4 to GENCODE v23 transcripts with default parameters. Only protein-coding, IGH/K/L- and TCR-related transcripts were retained for downstream processing, resulting in 20,062 protein-coding genes. Gene expression levels in patients of the reference cohorts are categorized as low/medium/high, defined by Low = &amp;lt; 17%; Medium-high = 50%-83%; Medium-low = 17%-49%; High = &amp;gt;83%. Results: Seventy women and sixty-seven men, ranging in age from 16 to 87 years, were studied. All tumors showed enhanced CCNG1 expression. Thirty (22%) tumors exhibited high CCNG1 expression, 53 (39%) showed medium-high CCNG1 expression, 48 (35%) displayed medium-low CCNG1 expression, and six (4%) had low CCNG1 expression. One hundred (73%) patients had metastatic disease, and 37 (27%) had localized disease. There was no correlation between CCNG1 expression and disease stage. As a result of these findings, the FDA-CBER authorized the use of DRG-101 in an Expanded Access program as platform therapy upon which one or more FDA approved cancer drugs/immunotherapies may be added. Historically, one patient with metastatic pancreatic cancer, one with early stage, HR+ HER2+ invasive breast cancer and one with early stage triple negative breast cancer are alive 15, 3 and 2.5 years in sustained remission with DRG-101 therapy, and had 24%, 23% and 74% CCNG1 tumor expression levels respectively. Five patients with advanced pancreatic cancer, sarcoma and breast cancer and known CCNG1 expression levels are currently being treated with DRG-101. Conclusions:(1) 100% of tumors tested showed enhanced CCNG1 expression at varying levels, and (2) the use of DRG-101 in combination with FDA approved cancer drugs/immunotherapies is on-going for an intermediate size population of advanced pancreatic cancer, sarcoma and carcinoma of breast. Citation Format: Nadezhda Omelchenko, Vaishali Kumar, Samantha Jeffrey, Grace Haroun, Don Brigham, William H. Isacoff, Sant Chawla. Retrospective analysis of CCNG1 expression in tumors, a novel biomarker in development for partnering with DRG-101, a tumor targeted retrovector encoding a CCNG1 inhibitor gene [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5183.

Abstract 3652: Spatial transcriptomic study of the tumor microenvironment in HNSCC

Abstract Background: The complex and dynamic nature of the tumor-immune microenvironment (TME) presents challenges for identification of robust and predictive biomarkers in immuno-oncology (IO). Standard multiplex immunohistochemistry (mIHC) or multiplex immuno-fluorescent assays (mIF) allow for the phenotyping on the cellular level but are limited by the number of markers available and the detection systems. Gene expression or next generation sequencing (NGS) platforms provide high-plex bulk data sets about the TME, but the spatial context of the tumor and immune cell interactions is lost. The NanoString GeoMx® Digital Spatial Profiler (DSP) combines spatial context, utilizing fluorescent morphological markers, with molecular profiling capabilities. This combination allows for the quantitative analysis of high-plex analyte abundance which can be traced back to a region of interest within a sample, providing biological inference in the region of interest. Methods: Formalin-fixed paraffin-embedded (FFPE) specimens from HNSCC patients were cut in 5µm sections for all analyses. Whole section tissue analysis was previously performed utilizing the NanoString nCounter® PanCancer IO 360™ Panel. Tumor inflammation signatures (TIS), an 18-gene signature measuring the adaptive immune response within tumors, was generated for each specimen and categorized each as immune-hot or immune-cold based on predefined parameters. Four specimens were selected based on their TIS score and two sets of cut sections were processed by either Labcorp lab in Morrisville, NC or Nanostring lab in Seattle, WA for precision evaluation, using the GeoMx Human Whole Transcriptome Atlas (WTA) panel (18,000 genes) with the NanoString GeoMx digital spatial profiling technology. The TME regions of interest (ROI) were identified using a set of morphology markers consisting of panCK, CD45 and Syto13; 12 ROIs were selected from each sectioned tumor material. The same ROIs were selected at the two testing sites with matching tissue location and morphology characters. Results: GeoMx WTA panel provided an unbiased view of 18,000 protein-coding genes at specific TME regions. These counts were successfully mapped to the 12 ROIs on the tissue. A pseudo-TIS score was generated using the same 18 gene signature from the WTA panel for each ROI. The pseudo-TIS scores from ROIs from the four specimens showed consistency with the specimen-wise TIS score, yet variations were observed across different TME/ROI within each specimen. Whole transcriptome expression results showed high correlation between the two testing sites, providing confidence in the reproducibility of the technology. High resolution fluorescent staining images were able to be fed to downstream quantitative digital analysis to generate complementary spatial data. Citation Format: Caitlin Schroyer, Shanshan Zhou. Spatial transcriptomic study of the tumor microenvironment in HNSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3652.

Abstract 1134: Dissecting pancreatic cancer tumor-immune microenvironment crosstalk using spatial transcriptomics

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) often fails to respond to immune therapies due to various factors, including the role of Epithelial to Mesenchymal Transition (EMT) plasticity in conferring broad resistance to diverse therapies. However, the relationship between cancer cell heterogeneity and the tumor immune microenvironment remains unclear. To address this, we utilized single cell RNA-seq and spatial transcriptomics to uncover the landscape of these cell-cell interactions in human PDAC. Here, we applied to specimens from a clinical trial testing Losartan, an indirect TGF-beta inhibitor with FOLFIRINOX chemotherapy and nivolumab (anti-PD1) in a randomized multi-institutional clinical trial for PDAC (NCT03563248). Methods: Using the NanoString GeoMx Digital Spatial Profiler, we selected multiple regions of interest in formalin-fixed paraffin-embedded (FFPE) human PDAC specimens. Immunofluorescent antibody-guided isolation of RNA and protein from cancer cells (pan-cytokeratin), cancer-associated fibroblasts (alpha-SMA), and immune cells (CD45) were performed. Utilizing the whole transcriptome assay (WTA; 18,000+ protein-coding genes) and a new IO Proteome Atlas (IPA; 500+ plex proteins), we ventured to understand the relationship between tumor cells and the surrounding microenvironment. Results: PDAC cells, CAFs, and immune cells were successfully characterized using NanoString GeoMx in clinical trial specimens. Analysis revealed associations between cancer cell plasticity, TGF-beta signaling mesenchymal subtypes in PDAC cells. These TGF-beta enriched mesenchymal PDAC cells were enriched in Arm 1 (FOLFIRINOX) compared to Arm 2 (FOLFIRINOX+losartan). Immune deconvolution analysis identified variations in immune infiltrates, showing an anti-correlation between macrophages and T-cells. The IPA analysis revealed lower MHC I protein levels in short compared to long term survivors in Arm 3. Conclusions: Spatial transcriptomics and proteomics reveal insights into the spatial relationship between PDAC tumor cell EMT plasticity, CAFs, and immune infiltrates. This enables the discovery of novel immune response biomarkers and potential therapeutic avenues to target tumor and microenvironment interactions. Trial Registration: DF/HCC protocol 18-179: Losartan and Nivolumab in Combination With FOLFIRINOX and SBRT in Localized Pancreatic Cancer. NCT03563248 Ethics Approval: All studies presented were approved by the Dana-Farber/Harvard Cancer Center IRB protocols 18-179. Citation Format: Amaya Pankaj, Michael J. Raabe, Bidish K. Patel, Evan R. Lang, Joshua R. Kocher, Katherine H. Xu, Linda T. Nieman, William L. Hwang, Alec C. Kimmelman, David P. Ryan, Theodore S. Hong, Martin J. Aryee, David T. Ting. Dissecting pancreatic cancer tumor-immune microenvironment crosstalk using spatial transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1134.

Abstract 5659: Origin of synchronous or metachronous multiple pancreatic cancers

Abstract [Introduction] The majority of patients with pancreatic cancer are inoperable at the time of diagnosis and even those cases with successful tumor resection for early-stage tumors frequently had second tumors within the remaining pancreas shortly after the surgery, contributing to a poor clinical outcome. Additionally, synchronous multiple pancreatic cancers have been frequently documented. One of the long-standing issues about such synchronous and/or metachronous multiple pancreatic cancers is their clonal origins. This study is designed to elucidate the origin of multiple pancreatic cancers through an unbiased detection of somatic mutations in primary and metachronous cancers, along with adjacent precursor lesions. [Methods] Serially obtained formalin-fixed paraffin-embedded surgical specimens from 20 patients who had undergone curative surgery for an early-stage pancreatic cancer were subjected to laser microdissection for the enrichment of tumor and precancerous lesions, from which DNA was extracted and analyzed for somatic mutations using whole-exome sequencing (WES) with matched normal DNA. The investigation into the shared and private mutations across different samples aimed to unveil the clonal evolution history of these lesions. [Results] We analyzed 20 patients with multiple pancreatic cancers of 2 metachronous and synchronous, 16 metachronous, and 2 synchronous tumors. In metachronous cases, all patients exhibited margin-negative pathology for the primary cancer, with a median interval of 38.9 months (ranging from 7 to 85 months) between the initial and second surgery. In addition, a total of 20 pancreatic intraepithelial neoplasia (PanIN) from 5 of these cases were analyzed. We identified a median of 66 (range: 31-232) and 20 (14-42) somatic mutations in cancer and PanIN lesions, respectively. None of the patients have known pathogenic germline variants. All samples had one or more driver mutations. In most cases (N=19), sharing many somatic mutations, multiple tumors had a common clonal origin. In another synchronous case, the synchronous tumors shared only one mutation, suggesting that they were clonally independent tumors. By contrast, none of the mutations other than hotspot KRAS mutations were shared between precursor and cancer lesions. While multiple independent clones were observed in precancerous lesions, most of multiple cancers originated from a common ancestor. Moreover, negative pathology of the margins at the initial surgery suggested that those multiple lesions arose from distant dissemination or metastasis, rather than contiguous, intraductal invasion. [Conclusions] In conclusion, our study suggests that even in early pancreatic cancer, dissemination within the pancreas may occur, contributing to the development of synchronous and metachronous cancers. Citation Format: Tomonori Hirano, Nobuyuki Kakiuchi, Yasuhide Takeuchi, Takayuki Anazawa, Kazuyuki Nagai, Toshihiko Masui, Sachiko Minamiguchi, Hironori Haga, Takeshi Tanaka, Atsuhiro Masuda, Yuzo Kodama, Norimitsu Uza, Hiroshi Seno, Satoru Miyano, Hiroko Tanaka, Seishi Ogawa. Origin of synchronous or metachronous multiple pancreatic cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5659.

Pathology Laboratory Archives: Conservation Quality of Nucleic Acids and Proteins for NSCLC Molecular Testing.

In the molecular era, proper archival conditions within pathology laboratories are crucial, especially for formalin-fixed paraffin-embedded (FFPE) tissue specimens retrieved years after the original diagnosis. Indeed, improper preservation can impact the integrity of nucleic acids and protein antigens. This study evaluates the quality status of stored FFPE blocks using multilevel omics approaches. FFPE blocks from 45 Non-Small Cell Lung Carcinoma (NSCLC) cases were analyzed. The blocks were collected from six different pathology archives across Italy with distinct environmental characteristics. Nucleic acids' quantity and quality, as well as protein antigens, were assessed using various techniques, including MALDI-MSI. RNA was quantitatively higher, but more fragmented, compared to DNA. DNA quantity and quality were suitable for molecular analyses in 94.4% and 62.3% of samples, respectively. RNA quantity was adequate across all samples, but it was optimal only in 22.3% of cases. DNA quality started to deteriorate after 6-8 years, whereas RNA quality diminished only after 10 years of storage. These data might suggest a particular DNA susceptibility to FFPE blocks conservation. Immunohistochemical intensity decreased significantly after 6-8 years of storage, and MALDI-MSI analysis revealed that younger tissue blocks contained more unique proteomic signals than the older ones. This study emphasizes the importance of proper FFPE archiving conditions for molecular analyses. Governance should prioritize attention to pathology archives to ensure quality preservation and optimize predictive testing. By elucidating the nuances of FFPE block storage, this research paves the way for enhanced molecular diagnostics and therapeutic insights regarding oncology and beyond.

Abstract 7005: Distinct DNA methylation patterns between early-onset and average-onset colorectal cancer patients

Abstract Objective: Early onset colorectal cancer (EO CRC) is rising at an alarming rate. While average onset colorectal cancer (AO CRC) affects patients mostly above 65 years of age, EO CRC affects patients under 50 years of age, disproportionately affecting males from low-income communities and racial/ethnic minorities. Chronic inflammation has been identified as a strong contributor to pathogenesis. We hypothesize that methylation of DNA may serve as a potential mechanism associated with chronic inflammation that contributes to the etiology differentially between EO and AO CRC. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue specimens from four AO and EO CRC patients each were retrieved from the Tissue Repository. Paraffin curls containing tumor and adjacent normal tissues were generated from appropriate EO and AO CRC patient tissues. The Qiagen GeneRead DNA FFPE genomic DNA kit was then used to extract the DNA from the paraffin curls. Illumina Methylation EPIC v2.0 kit was used to evaluate DNA methylation (DNAm) patterns after the restoration process from deamination in the fixed/embedded sample using the Uracil-N-Glycosylase enzyme. Unreliable and non-specific probes were removed before statistical analysis for differentially methylated CpG sites. Age acceleration for each tissue was calculated by comparing the estimated DNAm age with chronological age using the Horvath approach. Results: A clear clustering of DNAm patterns by age of onset were observed for both normal and tumor tissues. However, there was no difference when comparing tumor and normal tissues after multiple corrections. Four-way ANCOVA adjusting for race, gender, BMI, and tissue type suggested that age onset was the most significant factor. We also found that age acceleration in EO CRC tissue is greater than in AO CRC. After applying Bonferroni correction, significant differentially methylated regions (DMRs) were found in the promoter and the gene body of SNTB1, NFATC3, SLC25A24, RABGAP1L, WDSUB1, WWOX, SELB, SLC28A3, and PPP6R2 in EO CRC patients when compared to AO CRC. SNTB1 regulates colorectal cancer progression and stemness, while NFATC3 has been associated with inflammation and cancer. Conclusions: The preliminary results from this study showed a significant difference in the DNAm profile of FFPE samples between AO and EO CRC. The finding suggests that epigenetics may play a role in the etiology of CRC, potentially involved in the chronic inflammation pathway. The analysis of a larger patient number is underway to strengthen these findings. Citation Format: L. Joseph Su, Ping-Ching Hsu, Aniruddha Rathod, Yulun Liu, Jacopo Ferruzzi, Syed Kazmi, Emina Huang. Distinct DNA methylation patterns between early-onset and average-onset colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7005.

Abstract 6127: Characterization of germline and somatic homologous recombination deficiency features in high-grade serous ovarian cancer among Black individuals

Abstract Background: Approximately 50% of high-grade serous ovarian carcinomas (HGSOC) are homologous recombination deficient (HRD). HRD is associated with increased T-cell infiltration and improved survival. This study aimed to describe the distribution of HRD features and cytotoxic T-cell infiltration by gene expression subtype among Black HGSOC cases. Methods: We included Black HGSOC cases from the African American Cancer Epidemiology Study and the North Carolina Ovarian Cancer Study. We used RNASeq data to assign gene expression subtypes (n=160), and whole exome sequencing data from matched blood and tumor formalin-fixed paraffin-embedded specimens (n=206) to characterize HRD features. We defined HRD features as (1) germline variants and somatic mutations in HRD genes, and (2) HRD-associated signatures (SBS3 and ID6) that we obtained from de novo mutational signature analysis for single-base pair substitution, insertion, and deletion. We estimated the proportion of intratumoral cytotoxic T cells using multiplex immunofluorescence (n=125). Results: The subtype distribution in our study was 39% immunoreactive, 29% mesenchymal 27% proliferative, and 4% differentiated. Germline variants and somatic mutations in any HRD gene were observed in 27% and 23% of cases, respectively, and at least one of these was observed in 42% of cases. Pathogenic germline variants and somatic mutations were observed in 7% and 3% of cases, respectively. The prevalence of germline or somatic variants by gene was 16% for BRCA1, 14% for BRCA2, 11% for ATM, 5% for RAD51, and 2% each for BRIP1, PALB2, and BARD1. We observed a COSMIC HRD signature in 43% of cases, with 25% SBS3 only, 5% ID6 only, and 13% with both signatures. The prevalence of any HRD gene variant or signature was higher in immunoreactive cases (52% and 59%, respectively) than in mesenchymal (28% and 43%) or proliferative (44% and 28%) cases. Germline HRD variants were more common in the proliferative subtype (44%) compared with immunoreactive (25%) and mesenchymal (17%). In contrast, somatic HRD mutations were more common in the immunoreactive subtype (33%), compared with proliferative (16%) and mesenchymal (15%). This was due to a higher occurrence of BRCA1 somatic mutations in the immunoreactive subtype (25%) compared with proliferative (9%) and mesenchymal (8%). A higher proportion of cytotoxic T-cells (≥1% vs &amp;lt;1%) was also observed in the immunoreactive subtype (44%) compared with mesenchymal (31%) and proliferative (11%). Conclusion: We observed differences in the distribution of HRD features and cytotoxic T-cells by gene expression subtype. In particular, in the immunoreactive subtype, the most common gene expression subtype in Black HGSOC cases, we observed a higher occurrence of any HRD feature, somatic BRCA1 mutations, and cytotoxic T cell infiltration than in any of the other gene expression subtypes. Citation Format: Katherine Lawson-Michod, Mollie E. Barnard, Natalie Davidson, Lindsay J. Collin, Courtney Johnson, Lucas A. Salas, Casey Greene, Jeffrey R. Marks, Lauren Peres, Joellen M. Schildkraut, Jennifer A. Doherty. Characterization of germline and somatic homologous recombination deficiency features in high-grade serous ovarian cancer among Black individuals [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6127.

Mass Spectrometry-Based Method to Measure Aflatoxin B1 DNA Adducts in Formalin-Fixed Paraffin-Embedded Tissues.

Aflatoxin B1 (AFB1) is a potent human liver carcinogen produced by certain molds, particularly Aspergillus flavus and Aspergillus parasiticus, which contaminate peanuts, corn, rice, cottonseed, and ground and tree nuts, principally in warm and humid climates. AFB1 undergoes bioactivation in the liver to produce AFB1-exo-8,9-epoxide, which forms the covalently bound cationic AFB1-N7-guanine (AFB1-N7-Gua) DNA adduct. This adduct is unstable and undergoes base-catalyzed opening of the guanine imidazolium ring to form two ring-opened diastereomeric 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy-aflatoxin B1 (AFB1-FapyGua) adducts. The AFB1 formamidopyrimidine (Fapy) adducts induce G → T transversion mutations and are likely responsible for the carcinogenic effects of AFB1. Quantitative liquid chromatography-mass spectrometry (LC-MS) methods have shown that AFB1-N7-Gua is eliminated in rodent and human urine, whereas ring-opened AFB1-FapyGua adducts persist in rodent liver. However, fresh frozen biopsy tissues are seldom available for biomonitoring AFB1 DNA adducts in humans, impeding research advances in this potent liver carcinogen. In contrast, formalin-fixed paraffin-embedded (FFPE) specimens used for histopathological analysis are often accessible for molecular studies. However, ensuring nucleic acid quality presents a challenge due to incomplete reversal of formalin-mediated DNA cross-links, which can preclude accurate quantitative measurements of DNA adducts. In this study, employing ion trap or high-resolution accurate Orbitrap mass spectrometry, we demonstrate that ring-opened AFB1-FapyGua adducts formed in AFB1-exposed newborn mice are stable to the formalin fixation and DNA de-cross-linking retrieval processes. The AFB1-FapyGua adducts can be detected at levels comparable to those in a match of fresh frozen liver. Orbitrap MS2 measurements can detect AFB1-FapyGua at a quantification limit of 4.0 adducts per 108 bases when only 0.8 μg of DNA is assayed on the column. Thus, our breakthrough DNA retrieval technology can be adapted to screen for AFB1 DNA adducts in FFPE human liver specimens from cohorts at risk of this potent liver carcinogen.

Clinical and molecular characteristics of Jordanian oropharyngeal cancer patients according to P16 expression: a retrospective study and a report of a novel biomarker.

The purpose of this study was to assess the clinicopathological features of oropharyngeal cancer patients in Jordan based on their HPV status. Sixty-nine biopsies from two hospitals were included. Tissue microarrays were prepared from formalin-fixed paraffin-embedded (FFPE) specimens andstained with antibodies for CDKN2A/P16, EGFR, PI3K, PTEN, AKT, pS473AKT, PS2mTOR, and TIMAP. The cohort was divided according to P16 expression. Chi-square test and survival analyses were employed to evaluate the variations among the study variables and determine the prognostic factors, respectively. P16 expression was found in 55.1% of patients; however, there was no significant association between P16 expression and the patients' clinicopathological features. The Kaplan-Meier test revealed that smoking in P16-positive group and younger age (< 58years) negatively impacted disease-free survival (DFS) (P = 0.04 and P = 0.003, respectively). Multivariate Cox regression test indicated that smoking, age, PI3K, and AKT were negative predictors of DFS (P = 0.021, P = 0.002, P = 0.021, and P = 0.009, respectively), while TIMAP was a positive predictor (P = 0.045). Elevated P16 expression is found in more than half of the patients' specimens. DFS is negatively affected by younger age and the combined effect of smoking and P16 overexpression. TIMAP is overexpressed in P16-positive oropharyngeal cancer, and it is a favorable predictor of DFS.

CUL4A Ubiquitin Ligase Is an Independent Predictor of Overall Survival in Pancreatic Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with dismal prognosis. Genomic instability due to defects in cell-cycle regulation/mitosis or deficient DNA-damage repair is a major driver of PDAC progression with clinical relevance. Deregulation of licensing of DNA replication leads to DNA damage and genomic instability, predisposing cells to malignant transformation. While overexpression of DNA replication-licensing factors has been reported in several human cancer types, their role in PDAC remains largely unknown. We aimed here to examine the expression and prognostic significance of the DNA replication-licensing factors chromatin licensing and DNA replication factor 1 (CDT1), cell-division cycle 6 (CDC6), minichromosome maintenance complex component 7 (MCM7) and also of the ubiquitin ligase regulator of CDT1, cullin 4A (CUL4A), in PDAC. Expression levels of CUL4, CDT1, CDC6 and MCM7 were evaluated by immunohistochemistry in 76 formalin-fixed paraffin-embedded specimens of PDAC patients in relation to DNA-damage response marker H2AX, clinicopathological parameters and survival. We also conducted bioinformatics analysis of data from online available databases to corroborate our findings. CUL4A and DNA replication-licensing factors were overexpressed in patients with PDAC and expression of CDT1 positively correlated with H2AX. Expression of CUL4A and CDT1 positively correlated with lymph node metastasis. Importantly, elevated CUL4A expression was associated with reduced overall survival and was an independent indicator of poor prognosis on multivariate analysis. Our findings implicate CUL4A, CDT1, CDC6 and MCM7 in PDAC progression and identify CUL4A as an independent prognostic factor for this disease.