Yasir, Saba

ABSTRACT Imaging mass spectrometry has made significant advancements in recent years owing to its ability to study the spatial localization and abundance of proteins, peptides, lipids, glycans, metabolites, and drugs. In this study, we employed an imaging mass spectrometry‐based workflow called MALDI‐IHC, which uses antibodies conjugated with photocleavable mass‐tags, to investigate the detection of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) along with pan‐cytokeratin in formalin‐fixed paraffin‐embedded (FFPE) sections from cases with breast cancer. The expression of ER, PR, and HER2 was consistent with the clinical diagnosis based on conventional immunohistochemistry, lacking signal in triple‐negative cases and concordant signals in the cases that were classified as ER+/PR+/HER2+, ER+/PR+/HER2−, and ER−/PR−/HER2+ groups, respectively. In addition, the potential utility of a seconday antibody‐based MALDI‐IHC approach for HER2 expression was evaluated. In agreement with immunohistochemistry results, HER2 expression co‐localized within tumor regions in a HER2+ breast cancer case, while no expression was observed in a HER2− case. Collectively, these results highlight the potential of imaging mass spectrometry‐based MALDI‐IHC workflow for multiplexed detection of proteins in clinically relevant tissue sections.

Abstract Introduction: Patients with ER+/HER2- breast cancer associated with germline pathogenic variants (PVs) in BRCA1, BRCA2 and CHEK2 exhibit distinct clinicopathological features compared to sporadic cases. However, the optimal endocrine therapy strategies for these patients remain undefined. The Breast Cancer Index (BCI) is a validated gene expression-based signature that stratifies patients based on the risk of overall (0-10 years) and late (post-5 years) distant recurrence and predicts the likelihood of benefit from extended endocrine therapy (EET) in early-stage, HR+ breast cancer. Here we utilize BCI to investigate endocrine sensitivity and the predicted EET benefit in a cohort of ER+/HER2- breast cancer patients with BRCA1, BRCA2 and CHEK2 PVs. Methods: BRCA1, BRCA2 and CHEK2 PV carriers with ER+/HER2- breast cancer diagnosed at Mayo Clinic between 1996 and 2024 at Mayo Clinic were identified from a registry tracking germline test result. For comparison, we utilized the BCI Registry, a prospective, multi-institutional tumor registry of patients with early-stage ER+/HER2- breast cancer undergoing BCI testing, regardless of germline PV status. The analysis was restricted to women with invasive, early-stage locoregional breast cancer and available pre-treatment tumor specimens. BCI testing was performed by RT-PCR blinded to clinical outcome. BCI prognostic and BCI predictive categories were compared between the Mayo Clinic germline PV cohort and the BCI Registry using descriptive statistics and Fisher’s exact test. Results: The final analysis included 123 PVcarriers (BRCA1: 36; BRCA2: 40; CHEK2: 47) from the MayoClinic cohort and 2,563 women from the BCI Registry. The proportion of patientsdiagnosed before age 50 was higher among PV carriers—52.8% in BRCA1,50.0% in BRCA2, and 21.3% in CHEK2—compared to 7.0% in the BCIRegistry. PV carriers were also more likely to be premenopausal andnode-positive at diagnosis. Based on BCI score, a significant higher proportionof BRCA1 (75.0%, p=0.002) andBRCA2 (70.0%, p=0.01) PV carriers wereclassified as high risk, compared to 48.5% of patients in the BCI Registry, butno significant difference was seen for CHEK2 PV carriers (46.8%,p=0.88). A significantly higher proportion of BRCA1 PV carriers werepredicted to benefit from EET compared to the BCI Registry cohort (77.8% vs.33.9%, p<0.001), whereas no significant differences in BCI Predictivecategories were observed for BRCA2 or CHEK2 PV carriers. Overall,compared to breast cancer cases in the BCI registry, a significant differencein the distribution of the combined BCI prognostic and predictive categorieswas noted for BRCA1 (p<0.001)and BRCA2 (p=0.02) PV carriers,but not for CHEK2 PV carriers (p=0.66). In particular, BRCA1 andBRCA2 PV carriers were enriched for high-risk tumors with a high likelihoodof EET benefit (66.7% and 37.5%, respectively vs 25.1%, p<0.001 and p=0.02),whereas only a small non-significant increase was observed for CHEK2 PVcarriers (29.8% vs 25.1%, p=0.66) compared to breast cancer cases in the BCIRegistry. Conclusions: Genomicclassification by BCI reveals distinct patterns of endocrine sensitivity andpredicted EET benefit among germline PV carriers, particularly in BRCA1and BRCA2 PV carriers. These findings warrant further investigation andmay inform personalized endocrine therapy strategies for women with germlinePV-associated ER+/HER2- breast cancer. Citation Format: S. Yadav, B. O'Neal, S. Yasir, N. Siuliukina, A. Karki, Y. Zhang, A. K. Anderson, K. Treuner, M. P. Goetz, F. J. Couch. Endocrine Sensitivity and Predicted Benefit of Extended Endocrine Therapy based on Breast Cancer Index (BCI) in BRCA1, BRCA2 and CHEK2 Pathogenic Variant Carriers with ER+/HER2- Breast Cancer [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 PS2-08-25.

Abstract Introduction/Objective Microglandular adenosis (MGA) of the breast is an uncommon lesion characterized by a benign course. However atypical MGA (AMGA) and MGA-associated carcinoma have been described, suggesting that MGA may represent a non-obligate precursor of carcinoma. We report five cases of MGA-associated breast carcinoma and describe the key pathological features of this entity. Methods/Case Report Five cases of MGA-associated breast carcinoma were identified. Clinical data, histologic and immunohistochemical characteristics were reviewed and analyzed. Results All cases involved women with ages ranging 48 to 75 with a median of 70. Four of five cases demonstrated invasive carcinoma, while one case showed ductal carcinoma in-situ (DCIS). Invasive carcinomas encompassed various histologic types: metaplastic carcinoma with chondromyxoid matrix production (2 cases), invasive carcinoma with secretory features (1 case), and invasive carcinoma of no special type (ductal) (1 case). A morphologic transition from MGA to AMGA to carcinoma was observed in all cases. S100 was consistently positive in all cases. Myoepithelial markers demonstrated the absence of myoepithelial cells in the invasive carcinoma as well as MGA / AMGA component. Conclusion This series highlights the histologic spectrum and key diagnostic features of MGA-associated carcinoma. Awareness of this entity is crucial for appropriate diagnosis and clinical management.

Abstract Background: Germline Pathogenic Variants (PVs) in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are known to increase breast cancer (BCa) risk, but the effect of these PVs on tumor biology is not well-understood. Ki-67 is an established prognostic marker in hormone receptor (HR) positive breast cancer but the distribution of Ki-67 in breast cancer associated with germline PVs is not known. Methods: The study included patients with loco-regional (Stage I-III) HR-positive (ER+ or PR+), HER2-negative invasive ductal or lobular breast cancer evaluated at Mayo Clinic for curative intent treatment between 2012 and 2021. PV carrier status was ascertained in more than two-thirds of cases from germline whole exome sequencing (Regeneron) of patients who participated in a prospective registry at Mayo Clinic. Additional PV carriers were identified through a review of the results of clinical germline genetic testing in electronic medical records aided by natural language processing. Clinically performed Ki-67 values were abstracted from electronic medical records and analyzed as continuous and categorical variables (low: < 20% vs. high: ≥20%). Throughout the timeline of the study, a consistent method for assessment of Ki-67 was utilized at Mayo Clinic, Rochester: Immunohistochemical staining of the Ki-67 antigen in formalin-fixed paraffin-embedded tissue was performed using MIB-1 clone, the scanned slides were reviewed by a technologist and traced areas further analyzed for Ki-67 using Aperio Software. Patients who received neoadjuvant therapy prior to the assessment of Ki-67, with metastatic disease at diagnosis, with PVs in two or more genes of interest, or unknown germline PV or Ki-67 status were excluded from the analysis. Multiple primary tumors in the same patient diagnosed within one year of each other were analyzed independently. The control (non-carrier) group included randomly selected patients from the prospective registry who tested negative for PVs in the five genes over the same time period. Ki-67 values were compared between germline PV carriers and non-carriers in a multivariable logistic regression analysis adjusting for sex, race, age at diagnosis, stage at presentation, and histology of the tumor. Results: A total of 113 HR+/HER2- tumors from 111 PV carriers (ATM: 27, BRCA1: 24, BRCA2: 28, CHEK2: 22, and PALB2:12) along with 431 HR+/HER2- tumors from 422 randomly selected non-carriers were evaluated. The majority (>95%) of patients were non-Hispanic White. Germline PV carriers in each gene were diagnosed at a significantly younger age (P< 0.05) compared to non-carriers. The median Ki-67 value was 12 (Range: 1 to 93) for non-carriers, 16 (Range: 0 to 79) for ATM, 31 (Range: 4 to 86) for BRCA1, 30 (Range: 6 to 80) for BRCA2, 13 (Range: 1 to 38) for CHEK2, and 20 (Range: 3 to 46) for PALB2 PV carriers. In multivariable analysis, compared to non-carriers, we observed significantly higher odds of a high Ki67 value (≥20%) for tumors arising from germline PV carriers in BRCA1 (Odds Ratio (OR): 7.3, 95%CI: 2.3 – 23.3, p< 0.001), BRCA2 (OR: 3.0, 95%CI: 1.2 – 7.4, p=0.02) and PALB2 (OR: 3.9, 95%CI: 1.1 – 14.5, p=0.04). No such relationship was observed with either ATM (OR: 1.1, 95%CI: 0.4 – 2.9, p=0.81) or CHEK2 (OR: 0.8, 95%CI: 0.3 – 2.2, p=0.63). Conclusion: This study reveals that HR+/HER2- tumors in BRCA1, BRCA2, and PALB2 PV carriers have a significantly higher Ki-67 expression compared to non-carriers. These findings have implications for understanding prognosis and endocrine response PV with HR+ breast cancer. Further exploration of the relationships between Ki67 and germline PV status is necessary to personalize systemic therapy options in germline PV carriers. Acknowledgments: Thank you to Regeneron Genetics Center. The study was funded in part by the NIH Specialized Program of Research Excellence in Breast Cancer [P50CA116201] to Mayo Clinic, Mayo Clinic Department of Oncology Small Grants Program, and the Paul Calabresi Program at Mayo Clinic Citation Format: Robert Scheel, Grace Choong, Tara Rao, Nicholas Boddicker, Chunling Hu, Jie Na, Vinod Kaggal, Sean Murphy, Karthik Giridhar, Saba Yasir, Matthew Goetz, Fergus Couch, Siddhartha Yadav. Ki-67 Expression in Breast Cancer associated with ATM, BRCA1, BRCA2, CHEK2 and PALB2 Pathogenic Variants [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 PO5-08-07.

Abstract Patching whole slide images (WSIs) is an important task in computational pathology. While most of the are designed to classify or detect the presence of pathological lesions in a WSI, the confounding role and redundant nature of normal histology are generally overlooked. In this paper, we propose and validate the concept of an “atlas of normal tissue” solely using samples of WSIs obtained from normal biopsies. Such atlases can be employed to eliminate normal fragments of tissue samples and hence increase the representativeness the remaining patches. We tested our proposed method by establishing a normal atlas using 107 normal skin WSIs and demonstrated how established search engines like Yottixel can be improved. We used 553 WSIs of cutaneous squamous cell carcinoma to demonstrate the advantage. We also validated our method applied to an external dataset of 451 breast WSIs. The number of selected WSI patches was reduced by 30% to 50% after utilizing the proposed normal atlas while maintaining the same indexing and search performance in leave-one-patient-out validation for both datasets. We show that the proposed concept of establishing and using a normal atlas shows promise for unsupervised selection of the most representative patches of the abnormal WSI patches.

Subtyping hepatic adenomas is important for patient management due to differing complication risks. Immunohistochemical staining with C-reactive protein (CRP) and serum amyloid-A (SAA) is widely accepted as a surrogate for molecular classification to identify inflammatory hepatocellular adenomas. Limited data, however, has been published on how these 2 stains compare for sensitivity. We conducted a large, multicenter, retrospective study to examine the sensitivity and staining characteristics of CRP and SAA in inflammatory hepatic adenomas, with focal nodular hyperplasia (FNHs) as a control group. Inflammatory adenomas were identified in 133 patients (average age 37 years, 109 were female). In all, 69.9% of cases were resection specimens and 90.2% of all cases showed positive staining for both CRP and SAA; 10 (7.5%) were positive for CRP only and 3 (2.3%) were positive for SAA only. CRP was more sensitive than SAA (97.74% vs. 92.48%, P-value = 0.0961) and showed more extensive and intense staining, with a significantly higher modified H-score (P<0.001). Focal nodular hyperplasia can also show positive CRP and SAA staining but with a lower modified H-score (P<0.0001). Based on beta-catenin and glutamine synthetase staining, 26 of inflammatory adenomas also had beta-catenin activation (19.5%). All 3 cases with positive SAA and negative CRP staining were beta-catenin activated. In contrast, the proportion of cases that were CRP positive and SAA negative was similar regardless of beta-catenin activation. The data affirms the strategy of using both CRP and SAA immunostains for hepatic adenoma subtyping and raises the awareness of the highly variable nature of SAA staining characteristics.

Hepatic angiosarcomas are aggressive malignant tumors of the liver with variable morphology. One of the rare morphologies is that of the sinusoidal growth pattern, which is challenging to diagnose because of its subtle imaging and morphologic findings. This retrospective study characterizes the clinical, histologic, and immunohistochemical features of sinusoidal hepatic angiosarcomas. Thirteen cases were included in the study, comprising 12 (92.3%) needle core biopsies and 1 wedge biopsy; one of the needle biopsies also had a subsequent resection specimen available for review. Multiple biopsies were needed to make the diagnosis in 4 cases. At least moderate sinusoidal dilatation was seen in 53.8% of cases. Increased cellularity within the sinusoids was seen at both low-power and high-power magnification (69.2% and 84.6%, respectively). Cytologic atypia ranged from mild to marked. Multinucleated tumor cells were present in most cases (10/13 cases) but were often sparse. Mitotic activity was identified in 5/13 cases. ERG immunostains were more reliable than CD31 and CD34 in identifying the tumor cells. Ki-67 proliferative index ranged from 5% to 30%. p53 immunostains were available in 9 cases and c-MYC in 7 cases; they were positive in 62.5% and 33.3% of cases, respectively and had a mutually exclusive staining pattern. In summary, this rare pattern of hepatic angiosarcoma is challenging to diagnose but has distinctive morphologic findings that can be supplemented with immunostains to establish the diagnosis.

Newer radiotherapy techniques, such as stereotactic body radiation, have been increasingly used as part of the treatment of cholangiocarcinomas, particularly as a bridge to liver transplantation. Although conformal, these high-dose therapies result in tissue injury in the peritumoral liver tissue. This retrospective study characterized the morphologic changes in the liver after stereotactic body radiation in a series of liver explant specimens with perihilar cholangiocarcinoma. The morphologic changes in the irradiated zone were compared against the nonirradiated background liver parenchyma to control for chemotherapy-related changes. Of the 21 cases studied, 16 patients (76.2%) had underlying primary sclerosing cholangitis, and 13 patients (61.9%) had advanced liver fibrosis. The average duration between completion of radiotherapy and liver transplantation was 33.4 weeks (range: 6.29 to 67.7). Twelve patients (57.1%) had no residual tumor in the liver. The most frequent histologic changes in the peritumoral irradiated liver tissue were sinusoidal congestion (100%), sinusoidal edematous stroma (100%), and hepatocellular atrophy (100%), followed by partial/complete occlusion of central veins (76.2%), sinusoidal cellular infiltrates (76.2%), and hepatocyte dropout (66.7%). The findings in the radiated areas were more extensive than in the background liver (P<0.01). Sinusoidal edematous stroma was striking and dominated the histologic findings in some cases. Over time, there was less sinusoidal congestion but more hepatocyte dropout (rs=−0.54, P=0.012 and rs=0.64, P=0.002, respectively). Uncommon findings, such as foam cell arteriopathy in the liver hilum, were also observed. In summary, postradiation liver specimens have distinctive morphologic findings.