Serial Collection Research Articles

BIOM-61. CSF CTDNA ANALYSIS OF PATIENTS WITH DIFFUSE GLIOMAS REVEALS DIAGNOSTIC MOLECULAR ALTERATIONS

Abstract There is a critical need for better strategies to diagnose and monitor patients with diffuse gliomas. Liquid biopsies are less invasive than tissue biopsies and are amenable to serial collection at multiple timepoints. However, analysis of circulating tumor DNA (ctDNA) in cerebrospinal fluid (CSF) in patients with diffuse gliomas remains underutilized in clinical practice due to technical challenges and a scarcity of studies demonstrating clinical utility. We evaluated ctDNA in 49 CSF samples from patients with various types of diffuse gliomas with a next generation sequencing (NGS) panel interrogating 613 cancer-related genes. Cell-free DNA concentration obtained from CSF (0.4-5mL) ranged from 0.009 to 60ng/µL. Input DNA concentration ranged from 0.12-30ng. Mutations were detected in 29/49 (59.2%) samples including 22/49 (44.9%) with single nucleotide changes, 14/49 (28.6%) with copy number changes, and 1 fusion (2.0%). The majority of samples without mutations detected (n=20) had suboptimal DNA input (<30ng): 17/20 (85%). We identified diagnostic alterations in CSF including mutations in IDH1 (3/5 IDH-mutant gliomas), TERTp and EGFR amplification (7/34 glioblastomas), H3-3A (4/6 pediatric high-grade gliomas). Some of these mutations, in combination with other clinical parameters, allowed us to identify specific CNS tumor types based on the 2021 WHO classification of CNS tumors, resulting in the reclassification of 2 patients. Matched tumor tissue sequencing results were available for 23/49 (46.9%) patients and the results showed good concordance with CSF ctDNA analysis. In summary, our results suggest that the NGS analysis of CSF-ctDNA can provide clinically relevant information in patients with diffuse gliomas.

The Oswestry Disability Index in Elective Single level Lumbar Fusion: Is 3 month follow up enough?

BackgroundProspective, longitudinal collection of patient reported outcomes (PRO) has become an essential metric in orthopedics. Despite the utility of PROs, data collection presents a significant challenge to the healthcare system. There is a need to better understand if serial data collection over a 1 to 2 year postoperative period is truly warranted. The purpose of this study was to determine if continued PRO collection after 3 months postop is needed in patients that underwent lumbar fusion. MethodsThis retrospective study utilized 239 patients that underwent an elective single level lumbar fusion between April 1, 2020 and February 1, 2023. Changes in the Oswestry Disability Index (ODI) scores over a one year period were assessed for all patients. Patients were placed into one of three study groups, those that improved by 10 points, those that worsened by 10 points, and those that did not change (score change less than 10 points in either direction). Movement between study groups, the minimal clinical important difference (MCID), and patient satisfaction were analyzed for each patient. ResultsImprovement between preoperative and the 3 month postoperative evaluations was noted for most patients. There was limited change in scores after 3 months. Patients in the improved group continued to improve through 1 year post-operative. Patients in the worsened group continued to decline by 1 year postoperative. Patients in the no change group demonstrated the highest potential to change groups. ConclusionsPatients with substantial improvement or worsening at 3 months have a low likelihood of substantial clinical change thereafter. This subset of patients may not need further evaluation with PROs, but those in the worsened group may benefit from other interventions to potentially alter their course.

Safety and immunogenicity of a delayed booster dose of the rVSVΔG-ZEBOV-GP vaccine for prevention of Ebola virus disease: a multicentre, open-label, phase 2 randomised controlled trial

rVSVΔG-ZEBOV-GP is the first approved vaccine with clinical efficacy against Ebola virus disease. Although a seroprotective threshold has not been defined for those at occupational risk of exposure, the current vaccine strategy is to attain a sustained high level of antibody titres. The aim of this trial was to explore the effects of delayed boosting upon both the height and duration of antibody titres following primary immunisation. In this open-label phase 2 randomised controlled trial, we compared antibody titres at month 36in participants who had received a homologous booster dose at month 18following primary immunisation with those who had received no booster. From Oct 25, 2016, to Jan 29, 2020, healthy adults aged 18years or older deemed at occupational risk of exposure to Ebola virus due to laboratory work, clinical duties, or travel to an active endemic region were recruited from four hospital clinics in the USA and one hospital clinic in Canada and received primary vaccination with 2×107 plaque-forming unit per mL of VSVΔG-ZEBOV-GP. 18months later, individuals who consented and were still eligible were randomly assigned 1:1 to receive either a homologous booster dose or no booster. Study visits for safety and serial blood collections for antibody titres were done on enrolled participants at months 0, 1, 3, 6, 12, 18, 19, 24, 30, and 36. Through July, 2021, a web-based application was used for randomisation, including assignments with schedules for each of the five sites using mixed permuted blocks. The trial was not masked to participants or site staff. The primary endpoint was a comparison of geometric mean titres (GMTs) of anti-Ebola virus glycoprotein IgG antibody at month 36 (ie, 18months after randomisation) for all randomly assigned participants who completed the 36months of follow-up (primary analysis cohort). Investigators were aware of antibody titres from baseline (enrolment) through month 18but were masked to summary data by randomisation group after month 18. This study is registered with ClinicalTrials.gov (NCT02788227). Of the 248participants who enrolled and received their primary immunisation, 114proceeded to the randomisation step at month 18. The two randomisation groups were balanced: 57participants (24 [42%] of whom were female; median age was 42years [IQR 35-50]) were randomly assigned to the booster group and 57 (24 [42%] of whom were female; median age was 42years [IQR 36-51]) to the no-booster group. Of those randomly assigned, 92participants (45 in the booster group and 47in the no-booster group) completed 36months of follow-up. At 18months after primary immunisation, GMTs in the no-booster group increased from a baseline of 10ELISA units (EU)/mL (95% CI 7-14) to 1451EU/mL (1118-1882); GMTs in the booster group increased from 9EU/mL (6-16) to 1769EU/mL (1348-2321). At month 19, GMTs were 31 408EU/mL (23 181-42 554) for the booster group and 1406EU/mL (1078-1833) for the no-booster group; at month 36, GMTs were 10 146EU/mL (7960-12 933) for the booster group and 1240EU/mL (984-1563) for the no-booster group. Accordingly, the geometric mean ratio (GMR) of antibody titres had increased almost 21-fold more in the booster versus no-booster group at 1month after booster administration (GMR 20·6; 95% CI 18·2-23·0; p<0·0001) and was still over 7-fold higher at month 36 (GMR 7·8; 95% CI 5·5-10·2; p<0·0001). Consistent with previous reports of this vaccine's side-effects, transient mono-articular or oligo-articular arthritis was diagnosed in 18 (9%) of 207primary vaccination recipients; after randomisation, arthritis was diagnosed in one (2%)of 57participants in the no-booster group. No new cases of arthritis developed after booster administration. Four serious adverse events occurred following randomisation: one (epistaxis) in the booster group and three (gastrointestinal haemorrhage, prostate cancer, and tachyarrhythmia) in the no-booster group. None of the serious adverse events was judged attributable to the booster vaccination assignment. In addition to no new safety concerns and in marked contrast to earlier trials evaluating short-term boosting, delaying a rVSVΔG-ZEBOV-GP booster until month 18resulted in an increase in GMT that remained several-fold above the no-booster group GMT for at least 18months. These findings could have implications for defining the optimal timing of booster doses as pre-exposure prophylaxis in populations at ongoing risk for Ebola virus exposure. The Division of Intramural Research and the Division of Clinical Research of the National Institute of Allergyand Infectious Diseases at the US National Institutes of Health, Canadian Immunization Research Network through the Public Health Agency of Canada, Canadian Institutes of Health Research, and the US Defense Threat Reduction Agency.

Clinical Effects and Pharmacokinetic Profile of Intramuscular Dexmedetomidine (10 μg/kg) in Cats.

This study investigated the pharmacokinetic profile of and pharmacodynamic response to dexmedetomidine administered intramuscularly (IM) at a dose of 10 μg/kg in healthy cats. Nine adult cats were evaluated before and after administration of the drug, with serial collections of plasma samples. Dexmedetomidine induced deep sedation, with a rapid onset of action and a duration of one hour, reaching a peak between 20 and 30 min after administration. The half-life (T½) was 70.2 ± 48 min, with a maximum concentration (Cmax) of 2.2 ± 1.9 ng/mL and time to reach maximum concentration (Tmax) of 26.4 ± 19.8 min. The area under the curve (AUC) was 167.1 ± 149.1 ng/mL*min, with a volume of distribution (Vd) of 2159.9 ± 3237.8 mL/kg and clearance (Cl) of 25.8 ± 33.0 mL/min/kg. There was a reduction in heart rate (HR) and respiratory rate (RR) in relation to the baseline, with a slight decrease in systolic (SBP), diastolic (DBP), and mean (MAP) blood pressure in the first hour. Blood glucose increased after 60 min. Dexmedetomidine proved to be effective and safe, with rapid absorption, metabolization, and elimination, promoting good sedation with minimal adverse effects after IM administration in healthy cats.

Comparative Ocular Pharmacokinetics of Dexamethasone Implants in Rabbits.

Purpose: Dexamethasone eye implant has been used to treat macular edema and non-infectious uveitis. To date, its ocular pharmacokinetics are not fully characterized, and the development of generic preparations is in progress, as the patent of the original brand expires soon. Therefore, this work was designed to 1) determine the time course of vitreous dexamethasone concentrations following intravitreal implantation in rabbits and 2) explore the alternative use of NDF-SI01 from a pharmacokinetic point of view compared to Ozurdex®, which is currentlyused in the market. Methods: Ozurdex® and NDF-SI01 were implanted into the right and left eyes of the rabbit, respectively. A serial vitreous collection was performed to minimize the sacrifice of animals, and dexamethasone concentrations were measured by HP LC-MS/MS. Results: After implantation, dexamethasone concentration reaches the maximum concentration (3.1 μg/mL) in 19.5 days and decreases with a half-life of 40.3 h. AUC and clearance are 683.9 μg·h/mL and 1.29 mL/h, respectively. There is no significant difference in pharmacokinetic parameters between NDF-SI01 and Ozurdex®. The overall patterns of the cumulative release of both implants are similar. Conclusions: NDF-SI01 could alternate Ozurdex® in clinics based on the in vivo comparative pharmacokinetic study and in vitro dissolution test.

Workflow and Framework for Collecting and Implementing Point-of-Care Ultrasound Data in the Management of Heart Failure Patients.

Management and prevention of acute decompensated heart failure remain highly prevalent and challenging medical conditions. Incorporation of Point-of-Care Ultrasound (POCUS) as an adjunctive tool for assessing volume status and treatment response has shown significant promise. POCUS can be used for imaging internal anatomic structures serially and capturing these images for comparison and measurement over time. This protocol describes a scalable and standardized methodology for the serial assessment of the inferior vena cava (IVC). The methodology includes serial image collection, measurement, and presentation in the electronic medical record. A workflow for POCUS-acquired images of the IVC was created to capture the images and measure the diameter in a discrete data field for direct comparison over time and in response to clinical management. The protocol also includes the assessment of the presence or absence of pleural effusion as discrete data in the standardized workflow. By integrating POCUS into heart failure management, clinicians can improve patient outcomes through more precise and timely adjustments in treatment.

Baseline Lung Allograft Dysfunction After Bilateral Lung Transplantation Is Associated With an Increased Risk of Death: Results From a Multicenter Cohort Study.

A prior single-center, retrospective cohort study identified baseline lung allograft dysfunction (BLAD) as a risk factor for death in bilateral lung transplant recipients. In this multicenter prospective cohort study, we test the association of BLAD with death in bilateral lung transplant recipients, identify clinical risk factors for BLAD, and assess its association with allograft injury on the molecular level. This multicenter, prospective cohort study included 173 bilateral lung transplant recipients that underwent serial pulmonary function testing and plasma collection for donor-derived cell-free DNA at prespecified time points. BLAD was defined as failure to achieve ≥80% predicted for both forced expiratory volume in 1 s and forced vital capacity after lung transplant, on 2 consecutive measurements at least 3 mo apart. BLAD was associated with increased risk of death (hazard ratio, 1.97; 95% confidence interval [CI], 1.05-3.69; P = 0.03) but not chronic lung allograft dysfunction alone (hazard ratio, 1.60; 95% CI, 0.87-2.95; P = 0.13). Recipient obesity (odds ratio, 1.69; 95% CI, 1.15-2.80; P = 0.04) and donor age (odds ratio, 1.03; 95% CI, 1.02-1.05; P = 0.004) increased the risk of developing BLAD. Patients with BLAD did not demonstrate higher log10(donor-derived cell-free DNA) levels compared with no BLAD (slope [SE]: -0.0095 [0.0007] versus -0.0109 [0.0007]; P = 0.15). BLAD is associated with an increased risk of death following lung transplantation, representing an important posttransplant outcome with valuable prognostic significance; however, early allograft specific injury on the molecular level does not increase the risk of BLAD, supporting further mechanistic insight into disease pathophysiology.

Aedes aegypti Knockdown Resistance Mutations and Dengue Virus Infection in Haiti.

Haiti is home to approximately 11 million people and has a high incidence of vector-borne disease, including more than 70,000 cases of dengue per year. Vector control is difficult in Haiti and adulticide spray of malathion is the main method of control employed during the outbreak of disease although pyrethroids are used in both bed net campaigns and in widely available aerosol cans for personal use. However, limited pathogen or insecticide resistance surveillance data are available for making operational decisions. In this study, we assessed Aedes aegypti from serial surveillance collections from 3 locations for the presence of dengue virus serotypes 1-3 (DENV1-3) by polymerase chain reaction and assessed, by melt curve analysis, samples from 10 locations in 2 departments for the presence of two mutations (V1016I and F1534C), that in combination, are linked to strong pyrethroid insecticide resistance. Only one of the 32 tested pools was positive for the presence of dengue virus. The two knockdown resistance (kdr) mutations were present in all locations. The 1016I mutation frequency varied from 0.29 to 0.91 and was in all sites lower than the 0.58-1.00 frequency of the 1534C mutation. We also observed that the genotype homozygous for both mutations (IICC), which has been linked to strong pyrethroid resistance, varied from 13 to 86% in each population. Notably, 3 locations - Ti Cousin and Christianville in Ouest department and Camp Coq in Nord department had more than 30% of the tested population without the presence of kdr mutations. These results indicate that the kdr markers of pyrethroid resistance are present in Haiti, at high frequency in several locations and, based on previous studies linking kdr genotypes and phenotypic resistance, that operational interventions with pyrethroids are not likely to be as effective as expected.

Trouble with the curve: the 90-9-1 rule to measure volitional participation inequalities among Royal Canadian Mounted Police cadets during training.

The Royal Canadian Mounted Police (RCMP) Study includes longitudinal multimodal assessments of RCMP cadets from pre-training (i.e., starting the Cadet Training Program [CTP]) to post-deployment and for five years thereafter. The data allow for investigating the multidimensionality of volitional participation in digital health data collection frameworks within serial data collection platforms and the impact of participation inequalities by classifying cadets using the 90-9-1 rule. By classifying cadets as Lurkers, Contributors, and Superusers formally described by the 90-9-1 rule, where 90% of actors do not participate, 9% seldom contribute, and 1% contribute substantially allows for the assessing of relationships between participation inequalities in self-monitoring behaviors as well as whether mental health disorder symptoms at pre-training (i.e., starting the CTP) were associated with subsequent participation. Participants were asked to complete a Full Assessment prior to their training at CTP, as well as short daily surveys throughout their training. Participation frequency was described using a process where participants were rank ordered by the number of daily surveys completed and classified into one of three categories. Full assessment surveys completed prior to their training at CTP included screening tools for generalized anxiety disorder (GAD), major depressive disorder (MDD), posttraumatic stress disorder (PTSD), alcohol use disorder (AUD), and panic disorder (PD). The Kruskal-Wallis H test was used to assess differences in participation rates between mental health disorder symptom screening groups for each measure at pre-training, and Spearman's Rho was used to test for associations amongst self-reported Full Assessment screening tool responses and the number of daily surveys completed during CTP. There were 18557 daily survey records collected from 772 participants. The rank-ordering of cadets by the number of daily surveys completed produced three categories in line with the 90-9-1 rule: Superusers who were the top 1% of cadets (n=8) and produced 6.4% of all recordings; Contributors who were the next 9% of cadets (n=68) and produced 49.2% of the recordings; and Lurkers who were the next 90% of cadets (n=695) and produced 44.4% of daily survey recordings. Lurkers had the largest proportion of positive screens for self-reported mental health disorders at pre-training. The creation of highly individualized, population-based mental health injury programs has been limited by an incomplete understanding of the causal relationships between protective factors and mental health. Disproportionate rates of disengagement from persons who screen positive for mental health disorders further compounds the difficulty in understanding the relationships between training programs and mental health. The current results suggest persons with mental health challenges may be less likely to engage in some forms of proactive mental health training. The current results also provide useful information about participation, adherence, and engagement that can be used to inform evidence-based paradigm shifts in health-related data collection in occupational populations.

Programmed Death Ligand 1 Expression in Circulating Tumor Cells as a Predictor and Monitor of Response to Atezolizumab plus Bevacizumab Treatment in Patients with Hepatocellular Carcinoma.

There remains no reliable biomarker of therapeutic efficacy in hepatocellular carcinoma (HCC) for the PD-L1 inhibitor atezolizumab and bevacizumab (Atezo/Bev). Circulating tumor cells (CTCs) enable the serial collection of living tumor cells. Pre-treatment and serial CTC gene expression changes and tumor histology were evaluated to identify predictors of response to Atezo/Bev. Peripheral blood from 22 patients with HCC treated with Atezo/Bev and 24 patients treated with lenvatinib was serially collected. The RNA expression in CTCs was analyzed using qRT-PCR. Higher PD-L1 expression in pre-treatment CTCs was associated with response and improved prognosis with Atezo/Bev treatment, but not with lenvatinib. There was no correlation between PD-L1 expression in CTCs and that in liver tumor biopsy specimens scored using imaging software. Furthermore, PD-L1 RNA expression in CTCs was dynamically altered by Atezo/Bev, decreasing during effective response and increasing upon progression. CTC-derived RNA collected during Atezo/Bev indicates that patients with higher PD-L1 expression in CTCs at baseline were 3.9 times more responsive to treatment. Therefore, PD-L1 RNA levels in CTCs are an accurate response predictor and may be a monitorable biomarker that changes dynamically to reflect the response during Atezo/Bev treatment.

Abstract PO2-14-04: Circulating tumor DNA after neoadjuvant chemotherapy is a better prognostic test than Residual Cancer Burden in patients with triple negative breast cancer and residual tumor

Abstract Background The presence of residual tumor at surgery (non-pathological complete response or non-pCR) occurs in about half of TNBCs treated with neoadjuvant chemotherapy (NAC) signals chemoresistance. Although the addition of further adjuvant chemotherapy (Capecitabine/Xeloda) significantly improves RFS in these patients, the majority of patients nevertheless have a good prognosis, and thus may not require adjuvant Capecitabine. One of the best prognostic biomarkers in these patients is Residual Cancer Burden (RCB), which relies on the pathological examination of the residual tumor bed and lymph nodes obtained at surgery. Circulating tumor DNA (ctDNA) is a plasma-based biomarker, which has been shown to accurately detect minimal residual disease in breast cancer. We have previously shown that detection of ctDNA after NAC but before surgery in patients with non-pCR signals very poor prognosis, while non-detectable ctDNA is associated with an excellent prognosis. We now compare ctDNA to RCB score in TNBC patients with non-pCR. Methods In the multicenter TRICIA study, 44 TNBC patients with non-pCR after NAC in 5 hospital centers had consented to serial plasma collection prior to and after surgery. RCB score was calculated from pathology records. Whole exome sequencing (WES) was performed on DNA extracted from primary tumor biopsies or residual tumors at surgery to identify tumor-specific mutations (5 variants/patient). Digital droplet PCR (ddPCR) assays were developed for these mutations and tests were run in an academic hospital setting. Patients with at least one detectable mutation were considered ctDNA positive for a given time point. The detection of ctDNA was correlated with relapse-free survival (RFS). Results: The median follow up was 40 months. 19 of the 44 patients relapsed within 2 years after surgery. Detection of ctDNA at the end of NAC but before surgery (T1) was correlated with very poor RFS (H.R. = 0.15, p&amp;lt; 0.0001 (95% CI = 0.067-0.35)). 14/15 patients (93%) without detectable ctDNA did not recur, while 76% of patients with detectable ctDNA relapsed. The RCB score distribution was as follows: 7 RCB1, 21 RCB2 and 16 RCB3. According to RCB score, 1/7 RCB1, 11/21 RCB2 and 11/16 RCB3 patients relapsed. All but one of the relapsed patients had detectable ctDNA in at least one timepoint. All 11 RCB3 patients that relapsed had detectable ctDNA while none of the 5 RCB3 patients without relapse had detectable ctDNA. The one RCB1 patient with detectable ctDNA also relapsed. In cox regression analysis, the lack of ctDNA detection was significantly associated with excellent RFS in RCB2 (HR=0.16, p=0.003, (95% CI=0.05-.53)) and RCB3 groups (HR=0.10, p=0.0005, 95% CI= 0.03-.36). Conclusion ctDNA testing using ddPCR in an academic hospital-based setting at the post-NAC time point identifies an excellent prognostic group in TNBC patients with non-pCR and can discriminate very good from very poor prognosis in both RCB2 and RCB3 score subgroups. The detection of ctDNA may be superior to RCB scores in assessing prognosis in patients with non-pCR. Citation Format: Mark Basik, Talia Roseshter, Anna Klemantovich, Luca Cavallone, Adriana Aguilar-Mahecha, Josiane Lafleur, Cathy Lan, Oluwadara Elebute, Sarah Jenna, Jean-Francois Boileau, Manuela Pelmus. Circulating tumor DNA after neoadjuvant chemotherapy is a better prognostic test than Residual Cancer Burden in patients with triple negative breast cancer and residual tumor [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 PO2-14-04.

Abstract PO3-06-12: Targeting Fatty Acid Synthase in Brain Metastatic Triple-negative Breast Cancer

Abstract Introduction: Treating triple-negative breast cancer (TNBC) is challenging due to the lack of clearly defined and targetable biomarkers, and treatment options become increasingly limited with TNBC brain metastases (BM). Since the brain microenvironment has relatively low lipid availability, breast cancer cells that colonize the brain increase their reliance on the endogenous biosynthesis of fatty acids. This reveals a potential metabolic vulnerability that can be targeted, and fatty acid synthase (FASN) inhibition has been shown to decrease breast cancer cell invasion in preclinical models. Methods: In our study, we utilized the TNBC cell line MDA-MB-231-Luc/GFP, its brain-seeking subclone, MDA-MB-231-BR-GFP, and two novel cell lines generated from patient-derived organoids obtained from serial collection of brain-metastatic TNBC resections from the same patient, denoted PDO-BC25 and PDO-BC25-2. Cell lines were screened with FASN inhibitors as single agents vs. combined with SN-38 (topoisomerase I inhibitor) and synergy was assessed by the Chou-Talalay method. To characterize signaling changes with FASN inhibition and identify any off-target signaling, we used a Nanostring metabolic pathways nCounter panel to perform differential expression analysis on cells treated with the FASN inhibitor, TVB-2640, vs. vehicle control across the four cell lines. This panel detects the expression of 768 metabolism-related genes. We used 4 biological replicates per sample and the Benjamini-Hochberg statistical method to control for the false discovery rate after performing a t-test to calculate P-values. In addition, we performed spheroid outgrowth assays to identify any phenotypic impacts of FASN inhibition on spheroid outgrowth. Results: Combinatory drug screening between FASN inhibitors and SN-38 revealed synergy in MDA-MB-231-BR-GFP, PDO-BC25, and PDO-BC25-2, but not in the parental MDA-MB-231-Luc/GFP. The Nanostring nCounter metabolic pathways panel identified direct target engagement where FASN, SCD, and the transcription factor SREBP1 were significantly upregulated in the cells treated with TVB-2640 compared to vehicle control (P-adjusted &amp;lt; 0.05). Other upregulated genes were related to the pentose phosphate pathway, nucleotide salvage and synthesis, reactive oxygen species response, amino acid synthesis and transport, and autophagy. Genes that were down-regulated are involved in cell cycle progression, deoxynucleotide synthesis, DNA damage repair, fatty acid oxidation, and cytokine and chemokine signaling. Moreover, despite no decrease in cell viability, TVB-2640 alone was able to slow the outgrowth and invasion of Matrigel-embedded spheroids in a spheroid outgrowth assay. Conclusions: In our study, we have shown that the combination of SN-38 and FASN inhibitors is synergistic in the TNBC brain-seeking cell lines, and that FASN inhibition alone causes on-target transcriptome-level changes and a decrease in spheroid invasion. Next, we plan on testing the brain-metastatic potential of these cell lines in the presence and absence of a FASN inhibitor using an organ-on-chip microfluidic device developed by our lab that mimics the blood-brain barrier, to identify if this strategy has a potential role in prevention of brain metastases. Further studies to refine the molecular basis of the mechanism of action of the combination are underway. Citation Format: Habib Serhan, Liwei Bao, Xu Cheng, Matthew Soellner, Sofia Merajver, Aki Morikawa, Nathan Merrill. Targeting Fatty Acid Synthase in Brain 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 PO3-06-12.

Abstract PO2-13-11: High circulating tumor DNA (ctDNA) concentration was associated with shorter progression free survival in patients with metastatic breast cancer

Abstract Background: Metastatic breast cancer can be classified into different subtypes depending on hormone receptor (HR) and HER2 status. The subtype can change during tumor progression, and repeated biopsy is needed to deliver the most appropriate treatment every time a new lesion is found. It is not always possible to get a new biopsy from metastatic sites, and therefore liquid biopsy using circulating tumor DNA (ctDNA) is suggested as an alternative method to replace conventional biopsy. Methods: We performed a prospective serial collection of 65 ctDNA samples from 17 patients with metastatic breast cancer (mBC) at Seoul National University Hospital from October 2020 to March 2022. We used IMBdx AlphaLiquid®100 method to detect the genetic changes and analyzed the correlation with clinical outcomes. Results: Median age was 45 (range 32 – 62). Fifteen patients (88.2%) were relapsed mBC and most of the patients (14/17: 82.4%) were HR-positive and HER2-negative. Most of the patients had their ctDNA examined at baseline and at the time of maximal response and/or at progression. Fifteen patients (88.2%) received systemic therapy including hormone therapy, anti-HER2 therapy, and cytotoxic chemotherapy. Eight patients (47.1%) were on the first-line treatment for mBC, and 7 patients (41.2%) were on the second or later lines for mBC at the time of baseline sampling. The concentration of ctDNA and the sum of mutated allelic frequency was calculated for each sample. The ctDNA concentration ranged from 0.71 to 1386.00 ng/mL, and the median value was 5.37 ng/mL. We dichotomized these samples into two groups, with ctDNA concentration either higher or lower than the median value. Then we analyzed progression free survival (PFS) of each group. Patients with higher ctDNA concentration showed shorter PFS (7 mo. vs. not reached, p&amp;lt; 0.001). The sum of mutated allelic frequency ranged from 0.00% to 223.46% and the median value was 6.36%. Patients with higher mutated allelic frequency showed shorter PFS (6 mo. vs. 22 mo., p&amp;lt; 0.001). In addition, the PFS was significantly worse in patients who had mutated PIK3CA (5 mo vs. 22 mo, p&amp;lt; 0.001). The patients with mutated TP53 also showed shorter PFS (6 mo vs. 17 mo, p&amp;lt; 0.001) in univariate analysis. High estrogen receptor positivity in immunohistochemistry was correlated with lower mutated allelic frequency in ctDNA (p=0.003) but had no impact on the concentration of ctDNA (p=0.165). The concentration of ctDNA differed by metastatic sites. Patients with metastases to bones (p=0.007), liver (p&amp;lt; 0.001), soft tissue or lymph nodes (p=0.002) were more likely to have higher concentrations of ctDNA, while patients with brain metastases had significantly lower ctDNA concentration (p=0.006). When the sum of mutated allelic frequency of ctDNA and metastatic sites was analyzed, bone (p=0.001), liver (p&amp;lt; 0.001), and soft tissue or lymph node (p&amp;lt; 0.001) metastases had a positive correlation, while brain had negative correlation (p=0.017). Lung or pleural metastases had no significant correlation with ctDNA, neither concentration (p=0.271) nor mutated allelic frequency (p=0.965). Conclusion: Patients with mBC with higher concentrations of ctDNA or higher mutated allelic frequency of ctDNA at baseline showed significantly shorter PFS. PIK3CAmt and TP53mt detected by liquid biopsy could be used as a poor prognostic biomarkers for mBC patients. Citation Format: Hanbaek Yi, Tae-Yong Kim, Myung Geun Song, Hwang-Phill Kim, Tae-You Kim, Jinyong Kim, Dae-Won Lee, Kyung-Hun Lee, Seock-Ah Im. High circulating tumor DNA (ctDNA) concentration was associated with shorter progression free survival in patients with metastatic 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 PO2-13-11.

Evaluation of a human peripheral blood NK humanized hIL-15 mouse model lacking murine Fc gamma receptors

Abstract Fc gamma receptors (FcγRs) on residual murine immune cells can interact with human IgG-based therapeutics and confound preclinical results. This is critical for therapeutics with human NK cell mediated antibody-dependent cellular cytotoxicity (ADCC) as their primary mode of action. We compared humanization, kinetics, and persistence of NK cell reconstitution in human IL-15-expressing mice with or without FcγRs using intraperitoneal (IP) or intravenous (IV) administration of cells from multiple donors. Methods: Negatively selected human NK cells were engrafted into hIL-15 NOG or FcResolv™ hIL-15 NOG (FcγR knockout) with identical protocols. Human reconstitution, immune profile and persistence was evaluated via serial blood sampling and terminal collections for blood, spleen, and bone marrow. Results: Human NK cell reconstitution and persistence was equivalent between strains. There was a significant difference in the overall chimerism in IV vs. IP administration (IV &amp;gt; IP). There was no significant difference in % body weight, body condition scores, morbidity or mortality across study duration. NK cell persistence and kinetics were consistent between strains, administration, and donors, with a peak at 4-5 WPE and persistence to 12+ WPE in the blood. The dominant circulating NK phenotype was CD56+CD16+. Conclusions: huNK-engrafted hIL-15 NOG and FcResolv hIL-15 NOG mice provide a 12+ week study window, with equivalent reconstitution, immune profiling and kinetics.

Venipuncture Site Influences Blood-drop Volume in C57BL/6 Mice.

Many experiments require the collection of serial blood samples from mice. However, the size of mice limits the volume of blood that can be safely collected as a survival procedure. In IACUC protocols, investigators may report the amount of blood they collect from mice as a number of drops. Many institutions, including ours, use an anecdotal conversion factor (1drop of mouse blood = 25μL) to ensure that blood-collection volumes are compliant with institutional guidelines. To our knowledge, previous work has not experimentally determined the volume of a drop of mouse blood. In this 10-wk crossover experiment, 2 phlebotomists bled 30 C57BL/6J mice from 3 sites (facial, saphenous, and tail) using one or 2 different needle gauge sizes per site. Male and female mice were weighed weekly and divided among 5 groups (n = 6): left and right tail vein, left and right saphenous vein, and facial vein. A single blood drop from each site was weighed, and the volume of each drop was calculated using the average blood density determined from 8 mice terminally bled at the end of the study. Venipuncture site and side significantly influenced blood-drop weight and thus calculated volume. Facial vein puncture produced the largest drop volume (mean: 21.7μL), followed by the saphenous vein (mean: 9.97μL) and tail vein (mean: 4.96μL). Collection from the facial vein was associated with more hemorrhage and morbidity. Left-sided venipuncture was associated with slightly larger-volume blood drops, though the effect size of side was small. The results of this study may be useful in more accurately estimating blood loss via conversion of drops to volume. Our data indicate that blood collection from saphenous and tail veins minimizes blood loss relative to facial vein puncture and may optimize both serial collection of small-volume blood samples and animal welfare.

Genomic spectrum of actionable alterations in serial cell free DNA (cfDNA) analysis of patients with metastatic breast cancer

We aimed to study the incidence and genomic spectrum of actionable alterations (AA) detected in serial cfDNA collections from patients with metastatic breast cancer (MBC). Patients with MBC who underwent plasma-based cfDNA testing (Guardant360®) between 2015 and 2021 at an academic institution were included. For patients with serial draws, new pathogenic alterations in each draw were classified as actionable alterations (AA) if they met ESCAT I or II criteria of the ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT). A total of 344 patients with hormone receptor-positive (HR+)/HER2-negative (HER2-) MBC, 95 patients with triple-negative (TN) MBC and 42 patients with HER2-positive (HER2 + ) MBC had a baseline (BL) cfDNA draw. Of these, 139 HR+/HER2-, 33 TN and 13 HER2+ patients underwent subsequent cfDNA draws. In the HR+/HER2- cohort, the proportion of patients with new AA decreased from 63% at BL to 27–33% in the 2nd-4th draws (p < 0.0001). While some of the new AA in subsequent draws from patients with HR+/HER2- MBC were new actionable variants in the same genes that were known to be altered in previous draws, 10-24% of patients had new AA in previously unaltered genes. The incidence of new AA also decreased with subsequent draws in the TN and HER2+ cohorts (TN: 25% to 0–9%, HER2 + : 38% to 14–15%). While the incidence of new AA in serial cfDNA decreased with subsequent draws across all MBC subtypes, new alterations with a potential impact on treatment selection continued to emerge, particularly for patients with HR+/HER2- MBC.

Abstract 1010: Feasibility of serial microbiome collection in a multi-site neoadjuvant pancreatic cancer clinical trial allowing for a diverse patient population

Abstract Background: Pancreatic cancer portends a very poor prognosis. It is the third leading cause of cancer deaths in the United States. African Americans have a 50- 90% increased incidence of pancreatic cancer in comparison to other racial groups. 20% of patients present with operable disease and will have a median overall survival of 2.5 years if able to undergo surgical resection. There is a desperate need to discover novel ways of treating pancreatic cancer. Understanding of the microbiome may be informative to overcoming chemotherapy resistance, toxicity and improving outcomes and disparities. The aim of this study is to (1) identify changes in the microbiota during neoadjuvant treatment of pancreatic ductal adenocarcinoma that correlate with treatment response and (2) identify changes in the microbiota during neoadjuvant treatment of pancreatic ductal adenocarcinoma that correlate with treatment toxicity in a diverse patient population. Methods: Patients with resectable or borderline resectable pancreatic cancer who are enrolled in a multi-site clinical trial (NCT03483038) receiving neoadjuvant NEO-Nali-IRI (oxaliplatin, liposomal irinotecan and 5- FU) followed by surgical resection were asked to provide serial microbiome collections of saliva, urine (collected in clinic), and stool with a dietary log during the following four (or five) time points: at baseline, mid-therapy (after C4), at completion of chemotherapy (after C8), after radiation if applicable, and at 4-6 weeks post-operative. Participants were given stool collection kits during clinic visits for home sample acquisition. All stool samples were mailed to the University of Florida Health Cancer Center Microbiome Biorepository. Demographics, stage, medical history and concurrent medications including antimicrobics and probiotics, chemotherapy dose-reductions, delays, discontinuations, adverse events, safety adverse events, attribution of causality, and hospitalizations were obtained. Outcomes include imaging response using RECIST criteria, CA 19-9 trend, development of metastatic disease, and the ability to proceed to definitive surgical resection. DNA will be extracted from stool and analyzed using 16S rRNA sequencing methods to determine signatures and alpha/beta biodiversity. Descriptive statistics and correlative analysis will be reported. Continuous and categorical variables will be compared with Student’s t-test and Chi-squared test. Multiple groups will be compared by ANOVA. Kaplan-Meier logistic regression will be performed to compare outcomes between the different microbiota groupings. Conclusion: Serial microbiome collection from a multi-site clinical trial is feasible during neoadjuvant chemotherapy for pancreatic cancer and can increase the diversity of the sample population. Citation Format: Sherise Rogers, Ryan Thomas, Ibrahim Nassour, Ilyas Sahin, Brian Ramnaraign, Karen Russell, Steven Hughes, Kathryn Hitchcock, Omar Kayaleh, Anita Turk, Maisey Ratcliff, Thomas George. Feasibility of serial microbiome collection in a multi-site neoadjuvant pancreatic cancer clinical trial allowing for a diverse patient population [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 1010.

Abstract 3660: Plasma cell free DNA hydroxymethylation profiling reveals anti-PD1 treatment response and resistance biology in non-small cell lung cancer

Abstract Background: Treatment with immune checkpoint inhibitors (ICIs) targeting programmed death-1 (PD-1) can yield durable anti-tumor responses, yet not all patients respond to ICIs. Current approaches to select patients who may benefit from anti-PD-1 treatment are insufficient. 5-hydroxymethylation (5hmC) analysis of plasma-derived cell free DNA (cfDNA) presents a novel non-invasive approach for identification of therapy response biomarkers which can tackle challenges associated with tumor biopsies such as tumor heterogeneity and serial sample collection. Methods: 151 blood samples were collected from 31 non-small cell lung cancer (NSCLC) patients before therapy start and at multiple timepoints whilst on therapy. Blood samples were processed to obtain plasma-derived cfDNA, followed by enrichment of 5hmC-containing cfDNA fragments through biotinylation via a two-step chemistry and binding to streptavidin coated beads. 5hmC-enriched cfDNA and whole genome libraries were prepared in parallel and sequenced to obtain whole hydroxymethylome and whole genome plasma profiles, respectively. Results: Comparison of on-treatment timepoint to matched pre-treatment samples from same patients revealed that anti-PD-1 treatment induced distinct changes in plasma cfDNA 5hmC profiles of responders, as judged by RECIST, relative to non-responders. In responders, 5hmC accumulated over genes involved in immune activation such as IFNγ and IFNα response, inflammatory response, and TNFα signaling, whereas in non-responders 5hmC increased over epithelial to mesenchymal transition genes. The Molecular Response to anti-PD-1 treatment, as measured by 5hmC changes in plasma cfDNA profiles were observed early, starting with the first cycle of treatment. Comparison of pre-treatment plasma samples revealed that anti-PD-1 treatment response- and resistance-associated genes can be captured by 5hmC profiling of plasma-derived cfDNA. Conclusions: These results demonstrate that 5hmC profiling can identify response and resistance associated biological pathways in plasma samples, offering a novel method for non-invasive prediction and monitoring of immunotherapy response in NSCLC. Citation Format: Gulfem D. Guler, Yuhong Ning, Ceyda Coruh, Tierney Phillips, Maryam Nabiyouni, Kyle Hazen, Aaron Scott, Wayne Volkmuth, Samuel Levy. Plasma cell free DNA hydroxymethylation profiling reveals anti-PD1 treatment response and resistance biology in non-small cell lung cancer [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 3660.

Abstract 7630: Therapeutic relevance of systemic immune status to treatment effects of abemaciclib

Abstract Background: The addition of a CDK4/6 inhibitor (CDK4/6i) on endocrine therapies (ET) has been currently a standard treatment for hormone receptor (HR)-positive HER2-negative metastatic breast cancers (MBCs). Especially abemaciclib has been implicated in multiple mechanisms of action including cell cycle arrest, senescence. In addition, immunomodulatory effects have been suggested but are not yet clear. The aim of the study was to investigate the clinical relevance of abemaciclib to systemic immune status by examining the status of peripheral immune cells in patients with MBC who received abemaciclib plus ET. Methods: Patients with MBC who were treated with abemaciclib plus ET in our hospital were included in this study. Response was evaluated by RECIST 1.1. Peripheral blood at the initiation of abemaciclib treatment, 4 weeks, 12 weeks and 24weeks after abemaciclib treatment initiation were analyzed using mass cytometry by time of flight (CyTOF). Changes of cellular densities of each immune cell and survival by immune cell density were analyzed without calculating p values because of small sample number. Results: Twenty patients were enrolled, among whom 14 and 6 received an aromatase inhibitor and fulvestrant, respectively, as concomitant ET. 7 premenopausal patients received an LH-RH analogue. The analysis of serial blood collection showed an increase in CD8-positive T cell density by 12.5% and conversely a decrease in monocyte density by 52.3% at 4 weeks after treatment initiation. In responders (N = 10), an increase of the ratio between CD8-positive T cell density and Treg density (CD8/Treg) at 4 weeks after the treatment initiation were observed (65.2%), while not in non-responders (7.3%). In the analysis of the blood samples at the treatment initiation, lower Treg density and lower NK density at treatment initiation indicated longer PFS than the counterparts (median PFS for Treg: low, not reached; high, 8.8 months; for NK: low, not reached; high, 8.8 months). Conclusion: An increase of CD8/Treg at 4 weeks after the treatment initiation was associated with a good response in patients with HR-positive HER2-negative MBC treated with abemaciclib plus ET. Our results suggest an association between systemic immune status and clinical outcome in MBC patients who received abemaciclib plus ET treatment. A larger study is needed to validate the results. Citation Format: Takayuki Ueno, Shigehisa Kitano, Takayuki Kobayashi, Makiko Yamashita, Fumikata Hara, Yukinori Ozaki, Meiko Nishimura, Toshimi Takano, Naoko Toriguchi, Tsutomu Kawaguchi. Therapeutic relevance of systemic immune status to treatment effects of abemaciclib [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 7630.

A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst

With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.