Pockaj, Barbara A.

Abstract BACKGROUND: The amplification of genes PDL-1, PDL-2, and JAK2 on chromosome 9p24, known as the PDJ amplicon, has been identified in 15% of triple negative breast cancer (TNBC) and is associated with tumor infiltrating lymphocytes and elevated JAK2 mRNA, suggesting a coordinated inflammatory response in TNBC. Adding pembrolizumab to chemotherapy in KEYNOTE trials 355 and 522 has validated the use of PD-1 blockade in TNBC and redefined the standard of care. Despite preclinical data suggesting a role for targeting the IL- 6/JAK2/STAT3 pathway, the JAK1/JAK2 inhibitor ruxolitinib has not shown efficacy as a single Agent in breast cancer. This is the first phase I clinical trial evaluating the combination of pembrolizumab and ruxolitinib in the treatment of metastatic TNBC. METHODS: We conducted a phase I clinical trial with accrual from 2018 to 2023 at Mayo Clinic Arizona. Patients (n=12) received 200 mg of IV pembrolizumab per cycle (every 3 weeks) with 3+3 dose escalation of oral ruxolitinib twice a day (dose level 0: 10 mg PO BID, level 1: 15 mg PO BID, level 2: 20 mg PO BID). The primary endpoint was to determine the maximum tolerated dose (MTD) of ruxolitinib and secondary endpoints were treatment safety and efficacy. Clinical response was assessed by computed tomography of the chest, abdomen, and pelvis every 3 cycles. PD-L1 expression in tumor was measured by immunohistochemistry (IHC). The effect of the combined therapies on T and B cell populations were assessed by flow cytometry and antibody profiling of 695 tumor antigens and 8 viral antigens by nucleic acid protein programmable array. RESULTS: Twelve female patients with chemotherapy refractory metastatic TNBC were treated on study. All received 200 mg IV pembrolizumab every cycle. Due to rapid disease progression of three patients early after treatment initiation, eligibility was restricted to prohibit patients with extensive pulmonary disease or elevated LDH. Those patients were excluded from efficacy or correlative analysis. The most common toxicities were transaminitis (n=12), anemia/leukopenia (n=12), and fatigue (n=9). The majority of adverse events were grade 1 and occurred at dose level 2. There were 5 adverse events grade 3 or higher: respiratory or thoracic complications (n=3), hypertension (n=1), and abdominal pain (n=1), but MTD was not established. The median number of cycles was 4 for each dose level (range n=2.0-9.0) and the median time to progression was 3 months (range n=1.4-6.3). No patient had tumor response by RECIST v1.1 criteria and there was no association of disease stability with PD-L1 tumor expression by IHC. Circulating antibodies to tumor antigens remained stable, and viral-specific antibodies mildly decreased by month 2 in all patients at dose levels 0 and 1. Of the 7 patients reactive to TRIM21 autoantibodies, 2 patients had a transient increase at 2 months. CONCLUSIONS: The combination of pembrolizumab with ruxolitinib was well tolerated at all dose levels, and the number but not the severity of adverse events increased with higher ruxolitinib dose. Two of six patients in dose level 0 and 1 had stable disease for six months on treatment, suggesting that the lower dose levels of ruxolitinib (i.e. 10 mg PO BID) may have more activity in combination with pembrolizumab. Citation Format: Anelia Kassi, Jacqueline Carmona, Sarah M. Green, Heidi Kosiorek, Michael T. Barrett, Barbara A. Pockaj, Donald Northfelt, Karen S. Anderson. Phase I trial of combination pembrolizumab and ruxolitinib in metastatic triple negative 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 PO1-18-07.

Abstract We demonstrate development and technical validation of a novel approach for analysis of plasma circulating-tumor DNA (ctDNA) for residual disease detection and monitoring that offers improvements over existing technologies. ctDNA in blood can be leveraged to monitor treatment response, detect cancer recurrence, and inform treatment decisions for cancer patients. However, accurate detection and quantification of ctDNA is technically challenging due to low concentration of plasma DNA, especially in the adjuvant setting. Most current assays rely on interrogating multiple patient-specific point mutations to achieve exquisite limits of detection but struggle with polymerase errors, sequencing artifacts and limited conversion of input DNA. To overcome these challenges, we developed an approach called Structural Variant Enrichment and Normalization (SVEN) that targets patient-specific genomic rearrangements to achieve sensitive detection and quantification of plasma ctDNA. This method leverages intrinsic features of tumor-derived structural variants (SVs) to improve enrichment and confidence of detection at low tumor fraction through multiplexed PCR and amplicon-based next generation sequencing. To evaluate the assay, we performed whole genome sequencing of DNA from two breast cancer cell lines, as well as matched FFPE tumor and buffy coat samples from 21 early-stage breast cancer patients. We identified consensus SVs, and designed multiplexed SV-specific primers for each subject. We then conducted PCR amplification of cell-free DNA followed by sequencing, amplicon identification, and quantification. Analytical validation was conducted using 284 replicates of cell line dilutions from 1% to 0.003%, and 5 to 40 ng of input. We developed multiplexed assays targeting 25 and 32 SVs across two cell lines, and 3 - 43 SVs across breast cancer patients (median 23 per patient). 91% and 42% of PCR targets were successfully validated for cell lines and FFPE samples respectively. Cell line dilutions demonstrated a sensitivity of 89% at 0.003% tumor fraction with 10 ng input or more. Tumor fractions measured using SVEN agreed with known values (R2 = 0.989). Application of validated panels to patient plasma samples and tumor/germline dilutions is ongoing. SVEN is a novel approach for tumor-guided ctDNA detection and quantification with potential relevance for residual disease detection. On-going studies are investigating the performance of this approach for ctDNA detection in patients with early and locally advanced breast cancer treated with neoadjuvant therapy. Citation Format: Bradon R. McDonald, Kirsten L. Dennison, Amanda L. Schussman, Stephanie M. McGregor, Barbara A. Pockaj, Muhammed Murtaza. Personalized minimal residual disease detection using tumor-derived structural variants in cell-free DNA [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 2416.

Background: There is limited research on the impact of revisional surgery after breast reconstruction on patient experience and postoperative quality of life (QoL). Methods: Patients undergoing mastectomy with immediate implant-based or autologous free-flap breast reconstruction from 2008 to 2020 were reviewed. These patients were categorized by revisions (0–1, 2–3, and 4+) and surveyed on QoL metrics using BREAST-Q and Was It Worth It? (WIWI) questionnaires. BREAST-Q QoL, satisfaction, and WIWI metrics between revision groups were evaluated. Results: Among 252 patients, a total of 150 patients (60%) underwent zero to one revisions, 72 patients (28%) underwent two to three revisions, and 30 patients (12%) underwent four or more revisions. Median follow-up was 6 years (range, 1–11 years). BREAST-Q satisfaction among patients with four or more revisions was significantly lower ( P = 0.03), while core QoL domains (chest physical, psychosocial, and sexual well-being) did not significantly differ. Analysis of unplanned reoperations due to complications and breast satisfaction showed no significant difference in QoL scores between groups ( P = 0.08). Regarding WIWI QoL metrics, four or more revisions were associated with a higher rate of worse QoL ( P = 0.035) and worse overall experience ( P = 0.001). Most patients in all revision groups felt it was worthwhile to undergo breast reconstruction (86%), would choose breast reconstruction again (83%), and would recommend breast reconstruction to others (79%). Conclusions: Overall, a majority of patients undergoing revisions after breast reconstruction still have a worthwhile experience. Although reoperations after breast reconstruction do not significantly impact long-term BREAST-Q QoL domains, patients undergoing four or more revisions have significantly lower breast satisfaction, worse QoL, and a postoperative experience worse than expected.

BACKGROUND: Although the overall psychosocial benefits and body image gains of postmastectomy breast reconstruction are well-established, there is limited information on how postoperative complications affect patient quality of life (QOL). STUDY DESIGN: A single-institution cross-sectional survey analysis was performed on patients who underwent postmastectomy breast reconstruction between 2008 and 2020. QOL was assessed using the BREAST-Q and the Was It Worth It questionnaires. The results were compared among patients who had major complications, minor complications, and no complications. Responses were compared using 1-way ANOVA and chi-square tests as appropriate. RESULTS: A total of 568 patients met inclusion criteria, and 244 patients responded (43% response rate). Most patients did not have any complications (n = 128; 52%), 41 had minor complications (17%), and 75 had major complications (31%). There were no differences in any of the BREAST-Q well-being metrics based on degree of complication. Across all 3 groups, patients reported that surgery was worthwhile (n = 212; 88%), they would choose reconstruction again (n = 203; 85%), and they would recommend it to a friend (n = 196; 82%). Overall, 77% reported that their overall experience either met or exceeded expectations, and 88% of patients had unchanged or improved overall QOL. CONCLUSIONS: Our study demonstrates that QOL and well-being are not negatively impacted by postoperative complications. Although patients who had no complications had an overall more positive experience, nearly two-thirds of all patients, no matter the degree of complication, stated that their overall experience either met or exceeded their expectations.

Genome-wide fragmentation patterns in cell-free DNA (cfDNA) in plasma are strongly influenced by cellular origin due to variation in chromatin accessibility across cell types. Such differences between healthy and cancer cells provide the opportunity for development of novel cancer diagnostics. Here, we investigated whether analysis of cfDNA fragment end positions and their surrounding DNA sequences reveals the presence of tumor-derived DNA in blood. We performed genome-wide analysis of cfDNA from 521 samples and analyzed sequencing data from an additional 2147 samples, including healthy individuals and patients with 11 different cancer types. We developed a metric based on genome-wide differences in fragment positioning, weighted by fragment length and GC content [information-weighted fraction of aberrant fragments (iwFAF)]. We observed that iwFAF strongly correlated with tumor fraction, was higher for DNA fragments carrying somatic mutations, and was higher within genomic regions affected by copy number amplifications. We also calculated sample-level means of nucleotide frequencies observed at genomic positions spanning fragment ends. Using a combination of iwFAF and nine nucleotide frequencies from three positions surrounding fragment ends, we developed a machine learning model to differentiate healthy individuals from patients with cancer. We observed an area under the receiver operative characteristic curve (AUC) of 0.91 for detection of cancer at any stage and an AUC of 0.87 for detection of stage I cancer. Our findings remained robust with as few as 1 million fragments analyzed per sample, demonstrating that analysis of fragment ends can become a cost-effective and accessible approach for cancer detection and monitoring.

We report the occurrence of a refractory infection caused by the “rapidly growing” nontuberculous mycobacterium, Mycobacterium fortuitum, after incisional hernia repair using synthetic mesh. The patient had previously undergone three herniorrhaphies incorporating polypropylene mesh. Multiple surgical debridements were required, along with complete removal of all the mesh, to eradicate the infection. Prolonged antimicrobial therapy with sulfamethoxazole, an agent active against the patient's isolate, was also used. Although this atypical mycobacterium has been reported to cause a variety of infections, including many types of periprosthetic infections, this case represents successful treatment of M. fortuitum infecting abdominal wall mesh.

Abstract Purpose Accurately predicting the clinical breast cancer subtypes could be extremely helpful for radiologists, pathologists, surgeons, and clinicians and inform future treatment prediction algorithms. Therefore, we evaluate and compare the accuracy of radiomic features extracted from contrast enhanced mammography (CEM) and magnetic resonance imaging (MRI) scans to make predictions to subtypes of breast cancer. Methods This HIPAA-compliant prospective single institution study was approved by the local institutional review board with written informed consent. Women with breast tumors 2 cm or larger underwent dynamic contrast-enhanced MRI and/or CEM for surgical staging. Semi-manual regions of interest were drawn by radiologist using Cancer Imaging Phenomics Toolkit (CaPTk). Radiomic features were obtained using PyRadiomics and MR- and CEM- based classification models were built on a low-dimensional representation of the features obtained via kernel principal component analysis. We subscribed to an ensemble tree-based learning approach called extremely randomized trees (ERT) to predict cancer subtypes captured via immunohistochemistry markers. Results For MRI analysis, 124 women with newly diagnosed breast cancer were included in the analysis comprising 49 HR+HER2-, 37 HR+HER2+, 11 HR-HER2+, and 27 HR-HER2- cases. For CEM analysis, models were built using data from 170 female patients including 74 HR+HER2-, 41 HR+HER2+, 14 HR-HER2+, and 43 HR-HER2-. CEM based model resulted in accuracies of 55%, 72%, 88%, and 71% respectively for HR+HER2-, HR+HER2+, HR-HER2+, and HR-HER2- whereas MRI based model alone led to accuracies of 54%, 62%, 89%, and 76% respectively for HR+HER2-, HR+HER2+, HR-HER2+, and HR-HER2-. Conclusions Radiomic features extracted from CEM and MR were strong predictors of breast cancer subtypes with CEM-based radiomic features performing slightly better, though not statistically significantly better (p = 0.82), than its MRI counterpart.

AbstractBackgroundWe hypothesized full‐thickness chest wall resection (FTCWR) with advanced surgical techniques and modern systemic therapy is safe, provides local control, and good overall survival.MethodsRetrospective review of FTCWR (including rib or part of sternum) for breast cancer between 2000 and 2020. Primary endpoints included 90‐day morbidities and all‐cause mortality. Secondary endpoints were loco‐regional and distant recurrence, DFS and overall survival (OS).ResultsA total of 35 patients met the criteria. 34 FTCWR were for recurrence and the median time to chest wall recurrence was 6 years. Tumor subtype was triple‐negative in 51% and the remainder HR+ Her2−. 58% were palliative resections. FTCWR included rib(s) in 89% and portion of sternum in 57%; 94% required reconstruction and 80% were R0 resections. There were no 90‐day mortalities. Overall morbidity was 10/35(28%). 17(49%) patients received neoadjuvant systemic therapy for their recurrence and three received neoadjuvant radiation. Adjuvant treatment included chemotherapy (8), endocrine therapy (3), and both (8). Ten patients (28%) received adjuvant radiation. The Median follow‐up was 31 months and there were 6 (17%) loco‐regional and 7 (20%) distant recurrences. OS was 86% and 67% at 1 and 3 years, respectively.ConclusionFTCWR was associated with low morbidity, mortality, recurrence rates, and good OS. Selective FTCWR is safe and has acceptable short‐term survival rates.