tbuckley/cabot-search huggingface dataset:
Ultra-short circulating tumor DNA (usctDNA): A new paradigm for ctDNA liquid biopsy.
Authors: David T. Wong, Fang Wei, Chien-Chung Lin, Wei-Lun Huang, Cheuk Ying Tang, Hua-Jun He, Yong Kim, Feng Li
Journal: Journal of Clinical Oncology (2024)

e20510 Background: Mononucleosomal ctDNA (mnctDNA, 157-bp, double-stranded) spearheads liquid biopsy (LB) for cancer detection, treatment and clinical care. The bottleneck of mnctDNA LB are low copy number of ctDNA and limit of detection of platform technologies. Recent discovery of ultra-short ctDNA (usctDNA, 52-54 nt, single-stranded) that harbors somatic mutations prompted us to explore the quantification and stoichiometry of usctDNA to mnctDNA in plasma and saliva of NSCLC patients. Methods: Paired plasma and saliva from 20 advanced NSCLC patients with tissue genotyped positive for L858R were processed for cfDNA extraction and quantification with Qubit and Tape Station. Digital PCR assays targeting L858R somatic mutation to generate amplicons of 57-bp (usctDNA) and 100-bp (mnctDNA) were performed by UCLA and independently by NIST. Results: Results in Table 1 revealed that three findings of usctDNA that will have potential to impact ctDNA liquid biopsy. First, the somatic mutation (L858R) is present in usctDNA. Second, The stoichiometric ratio of usctDNA to mnctDNA is similar in plasma and saliva at 1.6X. For the wild-type counterpart, the ratio is 1.1X for plasma and 0.6X for saliva. Third, the copy number of usctDNA and mnctDNA in saliva to plasma is 7.8X and 7.7X. Conclusions: Detection of tumor-associated/specific EGFR L858R somatic mutations in uscfDNA is translationally impactful, adding 1.6X of the ctDNA targets for molecular detection, effectively cumulating 2.6X of total ctDNA targets, permitting earlier cancer detection, treatment monitoring and therapy prognostication. The finding that saliva harbors 7X of the us- and mnctDNA further raises the prospect of advancing saliva ctDNA liquid biopsy for NSCLC detection as it may effectively allow 15.5X (7.8X+7.7X) ability to detect malignancy-associated ctDNA. [Table: see text]
Elucidating the role of RBM10 in brain metastasis of EGFR19del lung adenocarcinoma.
Authors: Yan Yu, Gang Xu, Dexin Jia
Journal: Journal of Clinical Oncology (2024)

e20501 Background: The EGFR mutation was detected in 66.3% of Asian patients with lung adenocarcinoma. Among these mutations, EGFR 19del exhibited the highest sensitivity and best response. However, it is worth noting that patients with EGFR 19del have a high cumulative incidence of brain metastases, which contributes significantly to treatment failure. Based on previous WES analysis of primary lung cancer cases and their corresponding brain metastases, RBM10 co-mutation was observed in four out of ten cases with EGFR 19del mutation, leading to decreased expression levels of RBM10. These findings suggest a potential role for RBM10 in modulating the development of brain metastases in patients with EGFR 19del lung cancer. Methods: To investigate the role of RBM10 in brain metastasis, we performed RNA-seq on the PC9 cell line to identify metabolic pathways and genes associated with RBM10 and brain metastasis. Additionally, the brain metastasis model was established by injecting PC9 cells into the left ventricle of nude mice, and the ability of PC9 cells to form brain metastases after knocking down RBM10 was confirmed through two rounds of in vivo screening using the PC9 cell line. Lipidomics analysis further validated that RBM10 affects key metabolite production. Clip-seq and RNA-seq were employed to analyze how RBM10 regulates sphingolipid metabolism. Finally, we identified key targets affecting blood-brain barrier function within the sphingolipid metabolism pathway and verified their ability to inhibit brain metastasis using both in vitro and in vivo models. Results: RNA-seq results demonstrated the regulatory role of RBM10 in the sphingolipid metabolism pathway, specifically in GALC regulation. In vitro and in vivo models revealed an enhanced brain metastasis ability of the PC9shRBM10 group. Lipidomics analysis revealed that the knockdown of RBM10 resulted in a reduction in ceramide and an elevation in SPH. Integrated RNA-seq and Clip-seq analyses demonstrated that the splicing regulation on GALC was attenuated upon RBM10 knockdown, leading to an increase in GALC expression. Furthermore, this perturbation enhanced the downstream sphingosine-1-phosphate signalling axis (SPH-SK1/2-S1P), consequently promoting increased S1P production and elevated blood-brain barrier permeability. Finally, fingolimod, an S1P inhibitor, was employed to validate its efficacy in inhibiting brain metastasis; moreover, a combination therapy comprising osimertinib and fingolimod exhibited superior capacity for suppressing brain metastasis. Conclusions: This study aims to elucidate the regulatory mechanism underlying the impact of RBM10 on sphingolipid metabolism in brain metastasis of EGFR 19del lung adenocarcinoma, to identify novel therapeutic targets for preventing brain metastasis in patients exhibiting EGFR 19del lung adenocarcinoma with low RBM10 expression.
Associations of early adverse events with clinical outcomes in patients with NSCLC treated with EGFR tyrosine kinase inhibitors.
Authors: Fang-Ju Lin, Wen-Yen Lin, Chi-Chuan Wang, Jin-Yuan Shih
Journal: Journal of Clinical Oncology (2024)

e20551 Background: Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR TKIs) constitute the primary treatment modality for EGFR-mutant non-small cell lung cancer (NSCLC). While efficacious, EGFR TKIs are associated with adverse events (AEs) like dermatologic toxicities, diarrhea, and stomatitis. This study examined the prognostic implications of these on-target AEs in NSCLC patients receiving EGFR TKI therapy. Methods: A retrospective cohort study was conducted, encompassing advanced NSCLC patients treated with first-line EGFR TKIs within two distinct healthcare delivery systems in Taiwan between June 2011 and December 2019. Patients were stratified by TKI type, and those who had received AE reliever medications within 180 days prior to EGFR TKI initiation were excluded. We examined correlations between AEs and key endpoints: time to next treatment (TTNT) and overall survival (OS). To minimize immortal time bias, a landmark analysis at 60 days post-treatment initiation was utilized. On-target AEs were identified based on the issuance of at least two prescriptions for AE management on different dates within this period. Multivariable Cox proportional hazards models were utilized to evaluate the association between AEs and clinical endpoints, and a random-effects meta-analysis was performed to combine findings from both institutions. Results: Our analysis included 1,605 patients on gefitinib, 848 on erlotinib, and 1,236 on afatinib. Despite potential variations in AE reporting due to prescribing behaviors, the incidence of AE within the first 60 days of treatment was highest for afatinib, particularly with diarrhea (76.7%) and stomatitis (14.9%), followed by erlotinib with notable skin reactions (49.4%). Gefitinib showed the lowest incidence rates across all examined AEs. Of note, afatinib-treated patients who experienced diarrhea within the initial 60 days demonstrated a statistically significant extension in OS (HR 0.75, 95% CI 0.60-0.92). No significant prognostic link was found for other AEs in afatinib users or any AEs among users of gefitinib and erlotinib. Sensitivity analyses, incorporating modified AE definitions, corroborated these outcomes. Conclusions: Identifying AEs via prescription records for symptom relief poses methodological challenges and introduces uncertainty. Nevertheless, the occurrence of diarrhea within the first 60 days of therapy emerged as a significant predictor of enhanced OS in EGFR-mutant NSCLC patients receiving afatinib. This finding suggests a potential prognostic implication. The correlation was not evident in patients treated with first-line gefitinib or erlotinib.
Effect of NIR-II on cancer nanocomposite vaccines for lymph node targeted delivery and enhanced immunotherapy.
Authors: HaiYu Zhou, YuCheng Huang, Bin Xu, HengLiang Hou
Journal: Journal of Clinical Oncology (2024)

e20506 Background: Cancervaccines have become one of the hot areas of research in recent years. However, different types of tumors and the tumor tissue itself are heterogeneous. Some cancervaccines contain a single epitope and have weak immunogenicity. The antigen-presenting cells cannot adequately absorb and present the antigen peptide contained in the vaccine. As a result, the body fails to elicit an effective immune response, which greatly limits the therapeutic effect of the cancervaccine. In situ cancervaccines composed of antigens and adjuvants are a promising cancer treatment modality; however, convenient manufacturing of vaccines in vivo and their efficient delivery to lymph nodes (LNs) remain a significant challenge. In this study, we outline a facile approach to simultaneously achieve in situ programming of vaccines via two synergistic nanomedicines to generate robust immune responses. Methods: We first prepared two synergistic nanocomposite systems: Gold nanorods, amphiphilic polymer polyphosphate mPEG- b-PHEP encapsulating the immune adjuvant R848, and nanoparticles doped with cationic liposomes DOTAP. Two nanomedicines were characterized and the efficacy of the nanovaccine was verified at the Cellular Experiments. At the animal level, the lymph node targeting of the nanoparticles was demonstrated through IVIS. We also constructed distant model and lung metastasis model to verify the nanovaccine's effect on enhancing systemic immunotherapy. Results: We used amphiphilic polymer polyphosphate mPEG- b-PHEP to encapsulate TLR7/8 agonist R848 to obtain VNP R848 nanoparticles. Gold nanorods (~ 100nm) can produce a strong photothermal effect mediated by NIR-II, killing tumor cells and releasing abundant antigens at the same time. The small size of VNPR848 (~ 30nm) is beneficial to the enrichment of lymph nodes. After capturing the antigens produced by photothermal, nanoparticles will be targeted and delivered to the tumor draining lymph nodes together with R848, and will be effectively absorbed by DC cells. This in situ tumor vaccine with the ability of targeted delivery of lymph nodes can trigger a strong anti-tumor immune response. This therapy can completely inhibit distant tumors in some mice and produce a long-term immune memory effect on NSCLC metastasis. Conclusions: We propose a simple personalized in situ cancervaccine strategy, which uses nanotechnology to remove tumors in situ and release antigens. Antigens and immune adjuvants are simultaneously delivered to the draining lymph nodes to initiate the antigen presentation function of DC cells, resulting in an anti-tumor immune response to inhibit tumor recurrence and metastasis. The nano-vaccine based on powerful therapeutic effect provides an attractive technology for in situ programming of personalized cancervaccine and an effective strategy for the development of cancervaccine.
Outcomes in STK11-, KEAP1-, and KRAS-mutant lung squamous cell carcinoma (LSCC) with use of immune checkpoint inhibitors (ICIs).
Authors: Julian A. A. Marin-Acevedo, Justin Wang Shi, Yan Han, Mya Tran, Ahmad Karkash, Weston He, Misty Dawn Shields, Nasser H. Hanna
Journal: Journal of Clinical Oncology (2024)

e20504 Background: Studies have suggested that STK11, KEAP1, and KRAS mutations impact response to ICIs in individuals with lung adenocarcinoma. The effect of these mutations in LSCC is unknown. Methods: We conducted a retrospective analysis from January 1, 2018 through December 31, 2023 evaluating individuals seen in the Indiana University Health System with STK11, KEAP1, or KRAS-mutant advanced LSCC treated with ICI-based therapy. Demographic information and baseline PD-L1 levels were collected. Response to therapy was assessed using standardized real-world criteria. Progression-free survival (PFS) was calculated using the Kaplan-Meier method and compared using a log-rank test. Results: Thirty-one of 316 evaluable patients with LSCC had a mutation in KEAP1, STK11, or KRAS. Twenty-one of those individuals had advanced disease treated with ICIs. Nine of 21 had tumors harboring KEAP1 and/or STK11, 10 had tumors harboring KRAS, and 2 had KRAS + STK11-mutant tumors. The median age was 67 years, 71% (15/21) were male, 86% (18/21) were White, 83% (15/18) had PD-L1 levels ≥1%, and 81% (17/21) were evaluable for response including 11 treated with ICIs + chemotherapy and 6 who received ICIs alone. The overall response rate (ORR) was 65% with 5 individuals having progressive disease (PD), 1 with stable disease (SD), and 11 exhibiting partial response (PR). Those receiving ICIs + chemotherapy had an ORR of 73% (3 PD, 8 PR). The ORR was 50% (2 PD, 1 SD, 3 PR) in the cohort treated with ICIs alone. Among those with KEAP1 and/or STK11 mutations, the ORR was 43% (4 PD, 3 PR). The ORR was 88% for the KRAS-mutant cohort (1 SD, 7 PR) and 50% in the KRAS + STK11 subgroup (1 PD, 1PR). The median PFS was 6.4 months for the entire population, 6.0 months for those treated with ICIs + chemotherapy, and 8.1 months for those receiving ICIs alone. Although the cohort size was limited, individuals with KRAS mutations appeared to have improved PFS compared to those with STK11, KEAP1, or KRAS + STK11 mutations treated with ICI-based therapy (Table 1). Conclusions: STK11, KEAP1, and KRAS mutations impact response to ICIs in individuals with LSCC. There was a trend toward improved ORR and PFS in those with KRAS-mutant LSCC treated with ICI-based therapy compared to those with STK11, KEAP1, or KRAS + STK11-mutations. [Table: see text]
Effect of strong programmed cell death ligand-1 (PD-L1) expressions on clinical outcomes in advanced non-small cell lung cancer treated with third-generation epidermal growth factor receptor-tyrosine kinase inhibitors.
Authors: Jiling Niu, Xuquan Jing, Qinhao Xu, Haoyu Liu, Yaru Tian, Zhengqiang Yang, Hui Zhu, Yulan Sun
Journal: Journal of Clinical Oncology (2024)

e20500 Background: Third-generation tyrosine kinase inhibitors (TKIs) are the standard treatment for advanced epidermal growth factor receptor (EGFR) mutation-positive lung adenocarcinoma. In first/second generation EGFR-TKIs, strong programmed death ligand 1 (PD-L1) expression contributes to primary resistance, significantly affecting patient prognosis. Despite this, the relationship between PD-L1 expression levels and third-generation TKIs remains unclear. Methods: This retrospective cohort study reviewed patients with advanced NSCLC who received third-generation EGFR-TKIs as first-line systemic therapy at the Shandong Cancer Hospital between March 2019 and June 2022. The EGFR status of the patients was assessed using amplification refractory mutation system fluorescence quantitative polymerase chain reaction, and the PD-L1 expression level was evaluated using Dako 22 C3 immunohistochemical staining. The Kaplan–Meier method was used for survival analysis. The log-rank test was used to compare differences in survival curves between the two groups. Results: Overall, 150 patients were included in this study. PD-L1 expression was negative (PD-L1 tumor proportion score &lt; 1%) in 89 cases, weak (1–49%) in 42 cases, and strong (≥50%) in 19 cases. The median follow-up period for the entire cohort was 22.12 months (median progression-free survival [mPFS]: 24.33 months); the median overall survival was not reached. mPFS for patients with negative, weak, and strong PD-L1 expressions was 23.60, 26.12, and 16.60 months, respectively. The mPFS for strong PD-L1 expression was significantly shorter than that for with weak PD-L1 expression but was not associated with negativity, particularly in the 19DEL and 21L858R subgroups. PFS was significantly shorter in patients with strong PD-L1 expression in both subgroups (19DEL and 21L858R) than in those with weak PD-L1 expression. Conclusions: Strong PD-L1 expression in tumor cells influenced the clinical outcomes of patients with advanced NSCLC treated with third-generation EGFR-TKIs. Stronger PD-L1 expression in TKI-treated patients with advanced first-line EGFR-mutated NSCLC was associated with worse PFS.
Genetic characteristics of cerebrospinal fluid-derived circulating tumor DNA in brain metastases of lung adenocarcinoma.
Authors: Rongjie Tao, Hui Zhang, Shaohua Xu, Tao Li, Xiaoyong Tang, Jiayan Wu, Xuejiao Sun, Chunmei Zhang, Hong Shangguan
Journal: Journal of Clinical Oncology (2024)

e20503 Background: Brain metastases (BM), encompassing parenchymal metastases (PM) and leptomeningeal metastases (LM), are a common and fatal complication of advanced lung adenocarcinoma (LUAD). However, the genomic disparities between PM and LM, as determined by cerebrospinal fluid (CSF)-derived circulating tumor DNA (ctDNA), and its clinical utility as a liquid biopsy medium remain unclear. Methods: We conducted a retrospective study involving 33 patients diagnosed with BM from LUAD, comprising 16 cases with PM and 17 cases with LM, at Shandong Cancer Hospital between March 2018 and June 2021. CSF and matched peripheral blood lymphocyte samples were collected from all patients, and plasma samples were collected from 25 of them. Genomic profiles of CSF and plasma in patients with PM and LM were compared. CSF-ctDNA, plasma-ctDNA, and DNA from matched peripheral blood lymphocytes underwent next-generation sequencing (NGS) based on a 769 cancer-related gene panel. Results: A total of 363 mutations were detected in CSF-ctDNA, with 90.9% (30/33) of all LUAD patients with PM or LM showing mutations. EGFR mutations were the most common, occurring in PM samples from 56.3% (9/16) of patients and in LM samples from 76.5% (13/17) of patients, followed by other frequently mutated driver genes, including TP53 in 19 (57.6%) patients, MLH1 in 9 (27.3%) patients, and KMT2C in 8 (24.2%). Notably, EGFR 19del was more prevalent as a driver mutation in patients with LM compared to those with PM in our study, particularly the p.E746_A750del mutated subtype. Furthermore, the frequency of mutations in the mismatch repair (MMR) pathway was significantly higher in patients with LM than in those with PM. Additionally, CSF exhibited a more comprehensive profile of driver genomic mutations than matched plasma in patients with any form of BM, accompanied by a higher variation burden and detection of druggable mutations. Conclusions: CSF-ctDNA sequencing revealed distinct genomic patterns in patients with BM, particularly in LM, and could potentially enhance the management of BM patients compared to plasma.
PLWH and lung cancer: A single cancer center experience in Philadelphia, PA.
Authors: Andrew Bernstein, Garrett Melby, Matthew Tucker, Julia Palecki, Zoe Begun, Ting Ting Zhan, Ida Micaily
Journal: Journal of Clinical Oncology (2024)

e20502 Background: Lung cancer has been identified as the leading cause of cancer-related deaths in people living with HIV (PLWH), and disproportionately affects this population independently of smoking status and CD4 count. At the Sidney Kimmel Cancer Center (SKCC) at Jefferson Health, we serve a uniquely underserved patient population of PLWH. As PLWH were categorically excluded from most lung cancer clinical trials, we aim to study the clinical course of our patients with HIV and lung cancer. Methods: A retrospective review of 36 patients within SKCC at Jefferson Health in Philadelphia, PA from 2016 to 2023 were obtained utilizing ICD codes for lung cancer and HIV. Patients who were found to have HIV after their lung cancer diagnosis were excluded. Patient demographics, viral status, antiviral therapy, lung cancer stage, histology, molecular and fusion status, PD-L1 status, form of cancer-directed therapy, date of progression, last date of treatment, and date of death were recorded. Results: Of our 36 patients, 24 (66.7%) were male, and 20 (55.6%) racially identified as Black. 27 patients had NSCLC (20 with adenocarcinoma, 7 with squamous cell carcinoma), and 3 had SCLC. 24 (66.7%) patients had an undetectable viral load at the time of diagnosis and 35 (97.2%) were on antiviral therapy. 32 of 36 patients (88.9%) had advanced stage at the time of diagnosis; 11 had stage III disease (30.6%), and 21 (58.3%) had stage IV disease. Only 4 patients (11.1%) were diagnosed with stage I disease. The mean age of patients at diagnosis was 61.6 years (+/- 8.7 years). Of 18 patients with molecular testing performed, 4 had a KRAS mutation (22.2%) and 1 (5.6%) had a targetable EGFR mutation. Of 16 patients with PD-L1 testing, 7 (43.8%) had 0% expression, 8 (50%) had 1-49% expression, and 1 patient (6.2%) had PD-L1 expression &gt; 50%. The OS among this cohort was 1.3 years (95% CI: 0.8-3.8 years). Conclusions: Our cohort of patients demonstrated more advanced disease at presentation, a younger mean age at diagnosis and poor OS. These trends exist despite the majority of these patients having an undetectable HIV viral load at the time of diagnosis in the setting of ongoing antiviral therapy, indicating a potential relationship between even well-controlled HIV and aggressive lung cancer that warrants further exploration.
Cardiotoxicity in tumor-bearing mice receving thoracic radiation plus tumor radiation and PD-1 inhibitor therapy.
Authors: Yao Liu, Shengfa Su
Journal: Journal of Clinical Oncology (2024)

e20509 Background: At present, most preclinical studies explore the cardiotoxicity caused by radiotherapy combined with Anti-PD1s in tumor-free mice. we assessed the overall cardiotoxicity of radiotherapy combined with Anti-PD1, the possibility that blocking HMGB1 does not affect the anti-tumor effect, and the possibility that radiotherapy combined with Anti-PD1 reduces heart damage in tumor-bearing mice. Methods: 25 tumor-bearing C57BL/6 mice on both hind limbs were treated with anti-PD1 or PBS or Anti-HMGB1 with or without thoracic irradiation 20gy and right hind limb tumor 8gy×3F irradiation. HE staining was used to observe the cardiac structure and morphological changes. Flow cytometry was used to observe the distribution of CD3+, CD4+, CD8+T cells in cardiac and peripheral blood. Cardiac function was examined by echocardiography. The expression of myocardial injury marker LDH in peripheral blood was detected by Elisa. Results: Five group was established:A = Control;B = anti-PD1,C = RT,D = RT+Anti-PD1,E = RT+Anti-PD1+Anti-HMGB1.HE showed the myocardial injury in A(without any treatment) was the most severe,and and B and D was slightly severe than C group, administration of Anti-HMGB1 partially attenuated myocardial injury in D. Elisa showed the LDH of A was highest, B were consistent with D in LDH expression, RT was lower. Cardiac function showed no difference in ejection fraction and fractional shortening in five groups. Peripheral blood flow cytometry showed the absolute counts of CD3+T-cell and cd8+T cells were greatest in B group, followed by A, C, D, and E groups. Absolute CD4+ T cell values were highest in the B. The results of myocardial tissue infiltrating lymphocytes showed that the absolute CD3+T-cell and cd8+T cells counts were biggest in the B group, followed by A, C, D, and Egroups. Absolute CD4+T cell counts were highest in B group. C, D had the best anti-tumor effect, and the use of Anti-HMGB1 partially attenuated the cardiac injury caused by D group. Conclusions: (1)Without any treatment, the cancer cachexia induced by tumor will cause serious damage to myocardial. (2) The overall cardiotoxicity of radiotherapy combined with Anti-PD1 group was only slightly increased compared to RT or anti-PD1 alone. Maybe radiotherapy killed part of the Anti-PD1-activated lymphocytes, only resulting in a slight increase in cardiac infiltrating lymphocytes. Anti-HMGB1 maintain the anti-tumor effect of RT+Anti-PD1 and partially attenuated the cardiac damage. [Table: see text]