Windber Research Institute

Abstract Background: Liquid biopsies using blood provide a less invasive method for cancer detection and treatment assessment compared to conventional tissue biopsies. The plasma proteome involves secreted proteins from various organs and tissues, making it a prime candidate for extensive biomarker discovery. However, the vast dynamic range of protein abundance in plasma presents a challenge. In this study, we employed a highly sensitive aptamer-based assay to explore plasma proteins associated with breast cancer (BC). Methods: The subjects were enrolled and specimens were collected through the Clinical Breast Care Project using IRB-approved protocols. We analyzed 260 heparinized plasma samples from breast cancer patients at primary diagnosis, prior to neoadjuvant chemotherapy and excisional surgery. Patients with stage IV, prior DCIS, synchronous breast cancer, or relapse within 6 months were excluded. SomaScan Assay 7k (Somalogic Inc, USA) using 7289 aptamers for human proteins was performed. The association of each clinicopathologic feature of the cohort with plasma protein expression was evaluated using linear regression. The clinical features with notable effect size were further subjected to differential expression analysis using Limma with matched samples followed by pathway analysis using Ingenuity Pathway Analysis (IPA) tool. Results: The protein expression levels were significantly (FDR < 0.05) associated with age, race and stage groups. Differential expression using matched subsets identified 359 significant (FDR < 0.05, |FC| > 1.2) differentially expressed proteins (DEPs) between old (>60 years, n = 44) and young (<40 years, n = 44), and 184 between Caucasian (n = 67) and African American (n = 67) sample groups. We utilized data from Peptide Atlas, and existing literature on normal aging and established cancer biomarkers to contextualize the significant proteins. Pathways significantly (p val < 0.05, |z score| > 2) upregulated in the old group included immune response (cytokine signaling, neutrophil degranulation etc.) and tumor related (PAK, SNARE signaling etc.) pathways. Pathways identified in young were PPAR, DHCR4 signaling, and LXR/RXR activation. For the race group, there were 11 significant pathways upregulated in Caucasians that included FAK and S100 family signaling. For the higher (n = 62) and lower (n = 62) stage comparison, there were 127 significant DEPs (p val < 0.01, |FC| > 1.2) with several cancer-related signaling pathways upregulated in higher stage group (VEGF, SCF-KIT etc.). To explore potential markers of relapse, we conducted a subgroup analysis within the higher-stage cohort, comparing patients who relapsed (n = 30) to those who did not (n = 30) that identified 24 significant DEPs (p < 0.05, |FC| > 1.2) LASSO regression with leave-one-out cross-validation (LOOCV) resulted in a predictive model comprising 18 proteins, achieving a classification accuracy of 0.92. Conclusion: This study identified plasma proteins associated with age group, race and tumor stage in breast cancer patients. These findings indicate that BC related plasma protein expression differs across age and racial groups, a factor to consider in drug target development. We also identified 18 proteins that are potential markers for BC relapse. The identified proteins need to be validated in samples of large cohort. Disclaimer: The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions, or policies of Uniformed Services University of the Health Sciences (USUHS), the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., the Department of Defense (DoD) or the Departments of the Army, Navy, or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. government. Citation Format: A. Praveen Kumar, P. Raj-Kumar, J. Liu, B. Deyarmin, B. Mostoller, C. Larson, H. Blackburn, D. Teeter, K. Miller, M. Johnson, M. Russo, L. Fantacone-Campbell, J. Hooke, C. Shriver, H. Hu, A. Kovatich, X. Lin. Association of clinicopathologic features with plasma protein expression in primary invasive breast cancer patients [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 PS2-10-05.

There have been few studies on the relationship between chronic inflammatory diseases and breast cancer outcome. We evaluated the relationship between chronic inflammatory diseases and survival among breast cancer patients in the U.S. military health system (MHS), a universal healthcare system. The study used the Military Cancer Epidemiology database (MilCanEpi), which linked databases from the Department of War's Central Cancer Registry (CCR) and the Military Health System (MHS) Data Repository (MDR). A total of 33 chronic inflammatory diseases were identified. A time-dependent Cox proportional hazard regression model was used to estimate hazard ratios (HRs) and 95% confidence intervals (95% CIs) of death associated with chronic inflammatory diseases while adjusting for potential confounders. The final data included 14,258 patients with histologically confirmed primary breast cancer. Among them, 7883 had a diagnosis of chronic inflammatory diseases at or after breast cancer and 6375 had no diagnosis at any time in the data. A diagnosis of chronic inflammatory diseases was independently associated with a significantly increased risk of all-cause death after adjustment for confounders (adjusted HR = 1.76, 95% CI = 1.56-1.98). Notably, the increased risk of death associated with the inflammatory diseases persisted among stage-IV patients who usually died of breast cancer. The association was also observed regardless of age, comorbidity, hormone receptor status, timing of disease diagnosis relative to breast cancer diagnosis, or other characteristics. Chronic inflammation, characterized by chronic inflammatory diseases, was independently associated with increased all-cause death among breast cancer patients in MHS. Future research with cancer-specific death as the outcome is warranted.

In 2020, BLOODPAC recommended 11 pre-analytical minimal technical data elements for collection and submission of liquid biopsy data to public databases. This article expands on that work by recommending 22 clinical context and 10 patient context data elements. These elements, essential for liquid biopsy data submitted to repositories like the BLOODPAC Data Commons, cover tumor characteristics, disease progression, and patient demographics, supporting biomarker validation, research, and clinical trials.

Adults with chronic kidney disease (CKD) tend to be extremely sedentary. We investigated the feasibility and acceptability of a sedentary-reducing intervention for adults with CKD. The intervention utilized telephone-delivered coaching and a consumer wearable device to support participants to reduce their sedentary time. The mean age of participants in the sample was 60.5 years; 72% were women, and 83% had CKD Stage 3. At baseline, participants spent 73% of their waking time sedentary. Inter vention phone call attendance was 100%, study retention was 82%, and the intervention was rated as enjoyable (9.1/10). A telephone-delivered, sedentary-reducing intervention is feasible and acceptable in adults with CKD. Future work is needed investigating the efficacy of sedentary-reducing interventions for adults with CKD.

Introduction:Breast cancer mortality rates are 40% higher in non-Hispanic Blacks (NHBs) than in non-Hispanic White (NHWs) in the United States. All women treated within the Murtha Cancer Center at Walter Reed National Military Medical Center (MCC/WRNMMC) have health insurance and are provided multidisciplinary health care. Pathological factors and outcomes of NHBs and NHWs treated within the MCC/WRNMMC were evaluated to determine whether equal-access health care reduces disparate phenotypes and survival between the racial groups.Methods:Between 2001 and 2018, 368 NHB and 819 NHW women were diagnosed with breast cancer at MCC/WRNMMC. Differences between NHBs and NHWs in epidemiological and pathological characteristics were evaluated. Overall and breast cancer-specific 5- and 10-year survival rates were compared between races.Results:Compared with NHWs, NHBs were significantly more likely to have a body mass index ≥30 kg/m2, to be unmarried, to have tumors of higher grade, later stage, with lymph node metastases, and to be hormone receptor negative (HR−)/human epidermal growth factor receptor 2 positive (HER2+) or triple negative. After adjustment for demographic factors, NHBs remained significantly more likely to have tumors diagnosed at a higher grade and later stage, and to be HR−/HER2+ or triple negative. Neither 5- nor 10-year overall or breast cancer-specific survival differed significantly between the racial groups after adjusting for demographic and pathological variables.Discussion:Despite having tumors with less favorable pathological characteristics, overall and disease-free survival disparities were not observed for NHBs treated at MCC/WRNMMC. These data suggest that survival disparities of NHBs with breast cancer can be diminished with provision of quality care.

Abstract Background: For breast cancer patients undergoing lumpectomy, margin status remains an important risk factor for local recurrence. Positive margins mandate re-excision, and some patients may require multiple resections and mastectomy to obtain negative margins. In this study, association of various clinicopathologic factors with positive surgical margins for primary invasive breast cancer was assessed using both public and in-house datasets. Method: The datasets were obtained from The Cancer Genome Atlas-Breast Cancer (TCGA-BC) and Clinical Breast Care Project (CBCP). The proportion of positive to negative margins in both TCGA-BC (3.86%, 38/984) and CBCP (3.78%, 15/397) was similar. The role of each clinicopathologic factor for margin prediction was evaluated using logistic regression, Fisher’s exact test and Cox proportional hazards models. Results: The univariable and multivariable logistic regression using both TCGA-BC and CBCP data sets showed that higher tumor stage, tumor size and positive lymph nodes significantly contributed (p < 0.05) to positive surgical margins. In agreement with the results of logistic regression, Fisher’s exact test also showed the association of tumor stage with margin status. Furthermore, PAM50 subtype normal-like was significantly associated (p = 0.044) with positive margins while Her2 subtype was close to significance (p= 0.062) in TCGA-BC. However, they were not significant in the multivariable model. In addition, young patients also showed close significance to positive margins (p = 0.054) in the multivariable model. The bivariable cox hazards model demonstrated that margin status along with PAM50 subtype significantly associated with progression of the disease in TCGA-BC. On the other hand, margin status along with stage or TNM (T:Tumor size, N: Lymph Node Status, M: Metastasis) was insignificant. This shows that margin status was surrogate to tumor stage or TNM. Conclusion: This characterization study showed that chances of obtaining positive margins increases with higher tumor stage, tumor size and positive lymph nodes. Subtype and age also trended to affect margin status. If validated in a dataset of a larger number of cases with positive margin, our results may provide an additional perspective of how the margin status is associated with the clinical outcome of breast cancer patients which may further impact care provider’s decision making for re-excisions. Disclaimer: The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of USUHS, HJF, the DoD or the Departments of the Army, Navy or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Anupama Praveen Kumar, Diego Vicente, Praveen Kumar Raj Kumar, Jianfang Liu, Brenda Deyarmin, Brad Mostoller, Albert J. Kovatich, Jeffrey A. Hooke, Leigh Fantacone-Campbell, Xiaoying Lin, Craig D. Shriver, Hai Hu. Clinicopathologic factors associated with surgical margins in primary invasive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3363.

Abstract Introduction: The treatment methods and response vary among different cancer types that can result in different cancer recurrent rate and clinical outcomes, within and between cancer types. Here we performed a comprehensive analysis on TCGA (The Cancer Genome Atlas) treatment data over 22 cancer types, to explore the efficacy of cancer treatments, the recurrent rates of each cancer type, and their associated underlying molecular mechanism. Methods: TCGA treatment data for 22 cancer types was downloaded from TCGA data portal, and processed. Treatment response rate and recurrent rate across different cancer types were compared. Survival analysis was performed between patients who achieved complete response after first course of treatment (CRAFCT) with those who did not. RNAseq data analyses were further performed to identify significant genes associated with CRAFCT vs without CRAFCT to find the underlying molecular reasons of treatment efficacy. Results: Treatment responses after first course of treatment were compared for 22 cancer types. Cancer types were classified based on the rate of CRAFCT into 3 categories: high (>80%), median (50%-80%), and low (<50%); There were 12 cancer types with high complete response rate, 8 with median complete response rate, and 2 with low complete response rate. Cancer recurrent rates were further classified as high (>25%), median (10%-25%), and low (<10%) to check how the complete response rates affect the recurrent rate. After achieving CRAFCT, we found that cancers having high response rate can have low, median and high recurrent rate, while cancers having median or low response rate can have median and high recurrent rate. Patients who achieved CRAFCT had a much better overall survival than patients who didn’t across all 22 cancer types. Significantly expressed genes associated with treatment efficacy were identified and compared across 18 out of 22 cancer types. 6 genes were shared over 4 cancer types, 87 genes were shared over 3 cancer types. Finally, gene and cancer type networks were constructed to demonstrate the connections of cancer types, genes, and relationships of cancer types and genes. Conclusion: Cancer treatment therapy and therapy regimens were either cancer-specific or shared across cancer types; different cancer types had different treatment response rate which might result in different cancer recurrent rate; treatment related gene-cancer networks were constructed across cancer types which could be targeted for clinical and therapeutic applications to drive new drug development for multiple cancer types. The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views, opinions or policies of the USUHS, HJF, the DoD or the Departments of the Army, Navy, or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Jianfang Liu, Peter T. Hu, Praveen-Kumar Raj-Kumar, Anupama Praveen-Kumar, Xiaoying Lin, Craig D. Shriver, Hai Hu. Association of treatment response, recurrence and underlying molecular mechanism for over 22 TCGA cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5411.

Abstract Purpose: Identification of women with hereditary forms of cancer allows for use of precision medicine approaches to improve survival. Non-Hispanic Black (NHB) women in the US general population are less likely to undergo genetic testing or utilize risk-reducing strategies. Whether these disparities exist within the equal-access military healthcare system of the Department of Defense is not known. Methods: Genetic test information and surgical procedures were extracted for all NHB and Non-Hispanic Whites (NHW) with invasive breast cancer who were diagnosed and treated at the Murtha Cancer Center at Walter Reed National Military Medical Center and enrolled in the Clinical Breast Care Project. National Comprehensive Cancer Network criteria from the year of diagnosis were assessed for all patients. Data were analyzed using chi-square analysis with p<0.05 defining significance. Results: NHB were significantly (p=0.009) more likely to meet criteria for genetic testing compared to NHW, however, test uptake did not differ significantly between populations (p=0.292). Pathogenic variant frequency (p=0.597), prophylactic mastectomy (p=0.915) and oophorectomy (p=0.076) did not differ significantly between populations. Conclusion: These data demonstrate that when barriers, such as cost and lack of insurance barriers were removed, NHB were as willing to pursue testing and risk-reducing strategies as their NHW counterparts. Increasing the availability of testing and clinical management for NHB with hereditary forms of cancer may help reduce disparate survival seen in the US general population. The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of Uniformed Services University of the Health Sciences (USUHS), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., the Department of Defense (DoD) or the Departments of the Army, Navy, or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Rachel Ellsworth, Ashlee Vargason, Clesson Turner, Craig Shriver. Genetic testing in non-Hispanic Black women with breast cancer treated within an equal-access healthcare system [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-14-04.

Abstract Introduction: Breast cancer (BC) is the second most common cause of cancer death among women in the USA. Recent proteogenomic studies of human BC have identified many potential therapeutic biomarkers for the most common types of BC. Here, we strive to comprehensively understand the proteogenomic landscape of difficult-to-treat breast cancer (DTBC) tumors. Methods: 118 primary breast tumors, with a focus on DTBC patients, were selected from the IRB-approved protocol. The study cohort included 30 triple negative, 16 HER2+, 16 Luminal A, 39 Luminal B1, and 17 Luminal B2 selected by immunohistochemistry. Breast tumors were embedded in OCT (Optimum Cutting Temperature) and processed by laser microdissection (LMD) to remove non-tumorous tissue. DNA, RNA, and protein were simultaneously extracted from each tumor using the illustra triplePrep kit. Paired-end RNA sequencing and whole genome sequencing (WGS) were performed for 118 and 100 tumors, respectively, using the Illumina HiSeq platform. Quantitative global proteomics and phosphoproteomic analyses were performed on 113 and 50 tumors, respectively, using isobaric TMT 6-plex labeling with the “universal reference” strategy. Results: Unlike other BC cohorts, our WGS cohort had an almost equal number of Estrogen(ER)+ (55.6%) and ER- (44.4%) cases, which gave us a nominally higher percentage TP53 (57%) and lower PIK3CA (32%) non-silent somatic mutation. Similar to previous reports, GATA3 was mutated in 13% of only ER+ cases. Unlike a recent report on proteomics clustering of bulk-processed tumors, our data show that a stromal-enriched cluster was not mixed with all subtypes but a majority of Luminal A (LumA) subtype, probably because LMD excluded stromal components in other tumor subtypes. Consensus clustering of proteomics data separated intrinsic Her2 patients with outcome differences. Her2 patients associated with the Basal-enriched proteome cluster had better survival than those associated with the LumA-enriched proteome cluster. Previously reported marker PGK1, a predictor for poor survival in BC, was upregulated in Her2 tumors associated with the LumA-enriched proteome cluster. The clustering of phosphoproteomics data separated intrinsic Basal patients into groups with and without relapse. We identified 3 and 18 genes with upregulated kinase activities in the relapse-free and relapsed Basal patients, respectively. In conclusion, this study provides a high-quality proteogenomic resource for DTBC investigation and identifies potential molecular markers for predicting outcomes for patients with less responsive tumors. The views expressed in this abstract are solely of the authors and do not reflect the official policy of the Departments of Army/Navy/Air Force, DoD, USUHS, HJF. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Praveen-Kumar Raj-Kumar, Tao Liu, Lori A. Sturtz, Albert J. Kovatich, Marina A. Gritsenko, Vladislav A. Petyuk, Brenda Deyarmin, Jianfang Liu, Anupama Praveen-Kumar, Jason E. McDermott, Anil K. Shukla, Ronald J. Moore, Matthew E. Monroe, Bobbie-Jo M. Webb-Robertson, Jeffrey A. Hooke, Leigh Fantacone-Campbell, Leonid Kvecher, Jennifer Kane, Jennifer Melley, Stella Somiari, Stephen C. Benz, Justin Golovato, Shahrooz Rabizadeh, Patrick Soon-Shiong, Richard D. Smith, Richard J. Mural, Karin D. Rodland, Craig D. Shriver, Zhaoyu Li, Hai Hu. Proteogenomics of laser microdissected difficult-to-treat breast cancers identifies Basal and Her2 patients associated with outcome differences [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2172.

Abstract In this chapter, an effort has been made to give an overview of the aerodynamic loading on structures due to non-synoptic wind events, mainly tornadoes and downbursts. A brief description of the provisions in the building codes and standards for non-synoptic wind loads is presented. Current state of the art in simulating non-synoptic wind systems to obtain wind loads on structures is also discussed. The primary focus is buildings, bridges, and transmission lines in the discussion of the aerodynamic loading on structures. Finally, some insights are given on how future research in evaluating non-synoptic wind loads on structures might unfold.