bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variant allelic fraction of driver mutations predicts success of genomic methylation classification in CNS tumors.
Authors: Jamshidi Pouya , McCord Matthew , Lukas Rimas Vincas , Santana-Santos Lucas , Jennings Lawrence , Horbinski Craig M. 
Published: June 2022

e14035 Background: Whole genome CpG DNA methylation profiling is proving to be an extremely valuable tool in the diagnostic and prognostic classification of central nervous system (CNS) tumors, and is especially adept at discriminating between very different tumors, or tumor subtypes, that are histologically similar. However, like any bulk assay, reliability of methylation-based classification depends on sufficient tumor cellularity, as admixed nonneoplastic elements (e.g., neurons, glial cells, inflammatory cells) have their own unique methylation profiles, and thus can skew the results. Currently, it is recommended that at least 70% of the analyzed specimen be tumor; however, this is based on subjective estimates from light microscopy. Many neoplastic entities have well-known driver mutations that occur in virtually 100% of tumor cells, and next-generation sequencing (NGS) assays can detect those mutations and report their relative amounts in the form of Variant Allelic Fraction (VAF). Since NGS and methylation profiling are now frequently being done on the same tumor block, we sought to determine whether driver mutation VAF affects the accuracy of methylation profiling, and whether VAF can help establish more rigorous cutoffs for quality assurance. Methods: Using NGS and Infinium Epic850K methylation arrays, we evaluated 62 CNS neoplasms representing a range of entities, including TERT promoter-mutant glioblastoma, IDH-mutant astrocytoma, IDH-mutant oligodendroglioma, SHH-driven medulloblastoma, and CTNNB1-driven adamantinomatous craniopharyngioma. Results: VAFs of each driver mutation ranged between 1-60%. Forty-four of 62 cases (71%) had a methylation classification score ≥0.9, the most widely accepted cutoff for a successful result. A fit-of-mixture analysis via CutoffFinder (PMID: 23251644) suggested that the optimal VAF cutoff is 21%. Forty-one of 46 (89%) cases with a VAF of 21% or higher had a methylation classification score ≥0.9, whereas only 3/16 (19%) at or below 21% were classifiable with methylation profiling ( P< 0.0001 by Fisher’s exact test). Nonlinear regression of VAF versus methylation score by least squares fit produced R2= 0.54, with sum of squares = 2.0. Conclusions: These data indicate that VAF can serve as a useful predictor of classification success via methylation profiling, and should be taken into account when interpreting methylation profiling results.
Dose-dependent efficacy of bevacizumab in recurrent glioblastoma.
Authors: Melhem Jawad , Tahir Ali , Calabrese Eirena , Granovskaya Inga , Atenafu Eshetu G. , Sahgal Arjun , Lim-Fat Mary Jane , Perry James R. 
Published: June 2022

e14042 Background: Bevacizumab (bev), at a standard dose of 10 mg/kg every 2 weeks is associated with prolonged progression free survival (PFS) but no improvement in overall survival (OS) in recurrent glioblastoma (rGBM). While there are reports of lower dose regimens of bev being better tolerated and effective in rGBM, this has not been studied in comparison to a standard dose of bev. The main aim of this study is to report on the dose-dependent efficacy of bev by comparing PFS and OS in rGBM patients receiving standard dose (SD) vs lower dose (LD) of bev. Methods: A single-center retrospective study of patients with rGBM started on bev between 2015 – 2020 was performed. Clinical and treatment data including bev dose regimen (SD [10 mg/kg every 2 weeks] vs LD [5 mg/kg every 2-3 weeks or 10 mg/kg every 3 weeks]) received at the time of rGBM diagnosis were captured. Overall survival (OS) and progression-free survival (PFS) on bev were compared between the two groups using the Kaplan-Meier product-limit method. Log-rank test was used to compare potential predictive factors. Cox regression model was performed for multivariable analysis of OS and PFS. Results: A total of 96 patients were included with a median follow-up duration of 6.84 months (range 1.12-50.63 months) from date of the first infusion. The LD group consisted of 55/96 patients (57 %) and the age in the LD group was significantly older than the SD group (62 vs 54 years p = 0.009). There was no significant difference in MGMT status between the 2 groups (p = 0.73). Eight patients received lomustine with bev (3 from the standard and 5 from the low dose group). The LD group had prolonged OS (10.23 months versus 6.28 months; p-value = 0.0010) and PFS (5.89 months versus 3.22 months; p-value = 0.0112). Multivariable analysis including dose of bev, extent of resection, gender and age revealed that standard dose of bev, subtotal resection and female sex were associated with worse OS. Eleven patients in the SD group vs 15 patients in the LD group reported an adverse event related to bev. Conclusions: In this study we demonstrate that a reduced dose of bev (5 mg every 2-3 weeks) prolonged both the OS and PFS compared to a standard dose of 10 mg/kg every 2 weeks. This may represent a better and more cost-effective option for patients with rGBM in need of salvage therapy.
Urinary potassium and association with methotrexate (MTX) elimination delay in patients with primary central nervous system lymphoma (PCNSL).
Authors: Harlay Vincent , Boucard Celine , Petrirena Gregorio , Barrie Maryline , Campello Chantal , Autran Didier , Gouton Etienne , Chinot Olivier L. , Tabouret Emeline 
Published: June 2022

e14045 Background: First-line treatment of PCNSL consists in a polychemotherapy based on high-dose MTX with hyperhydratation until MTX elimination. Renal toxicity remains frequent with pejorative impact on renal function and patient survival. Our objective was to determine urinary predictive factors of MTX elimination delay. Methods: Patients with PCNSL followed in our institution were prospectively recruited from December 2020 to May 2021. Daily serum and urinary creatinine and ionogram were collected from the day before MTX administration until elimination. Patients characteristics, biological data and MTX concentration were recorded. Normal elimination time was defined by MTX ≤ 0.05 at 72 hours. Results: We collected data from 64 MTX cycles corresponding to 20 patients. Median age was 71 years (range, 33 - 86) and median Karnofsky Performance Status (KPS) was 70. Forty-four percent of cycles were full dose (3500 mg/m2). Median urinary osmolarities one day before, the day and 24 hours after MTX administration were 325 mOsm (range, 62 - 542), 316 mOsm (range, 58 - 671) and 291 mOsm (range, 56 - 554), respectively. Median time for MTX elimination was 94.7 hours (range, 47 - 205). Only one patient needed to receive MTX antidote (glucarpidase). The factors significantly associated with MTX elimination time were age (p < 0.001), KPS (p < 0.001) and urinary K+ concentration at 24 hours post MTX administration (u-K+) (p = 0.008). Using ROC curve analyses, we determine optimal cutoffs for age (80 years, p < 0.001, AUC = 0.825), KPS (70, p < 0.001, AUC = 0.808) and u-K+ (17.2 mmol/L, p = 0.008 AUC = 0.712). This u-K+ cutoff presented with a specificity of 81% and a sensibility of 60%. Focusing on patients aged < 80 years (52 cycles / 64), we confirmed that both KPS (p = 0.022) and u-K+ (p = 0.027) were significantly correlated with MTX elimination time by multivariate analysis. Then, we derived a 3-factors score including 5 subgroups: 1) aged ≥ 80 (N = 12); 2) age < 80, KPS < 70 and high u-K+ (N = 11); 3) age < 80, KPS < 70 and low u-K+ (N = 6); 4) age < 80, KPS ≥ 70 and high u-K+ (N = 8); 5) age < 80, KPS≥70 and low u-K+ (N = 21). The median times for MTX elimination were 112, 96, 95, 82 and 72 hours respectively. The normal elimination rates in each subgroup were 17%, 0%, 17%, 37% and 71% respectively. Conclusions: Age, KPS and u-K+ were correlated with MTX elimination time. We derived a predictive score based on these items that could be used in routine to anticipate MTX elimination delay and to potentially prevent the risk of renal toxicity. These results need to be prospectively confirmed in a larger cohort.
Prognostic value of beta 2-microglobulinin (β2MG) in cerebrospinal fluid (CSF) in primary central nervous system lymphoma (PCNSL).
Authors: Bertucci Alexandre , Boucard Celine , Harlay Vincent , Chinot Olivier L. , Tabouret Emeline 
Published: June 2022

e14047 Background: Prognosis and response assessment are crucial to guide PCNSL patient therapeutic management. β2MG is a well-known prognostic factor of systemic lymphoma but its prognostic value in PCNSL remains uncertain. Objective is to evaluate the prognostic value of β2MG in CSF in PCNSL patients. Methods: We prospectively analyzed the CSF β2MG concentration in all newly PCNSL patients referred to our institution between March 2014 and November 2021 for whom lumbar punction was allowed. β2MG analysis was performed at diagnosis before the first treatment administration, after 2 and 4 treatment cycles. The clinical, radiological, histological, biological and treatment data were retrospectively collected. Results: Thirty-six patients were included with a median age of 71.8 (range 42.5 – 85.3). All patients presented with DLBCL CD20+ lymphoma. Median KPS was 70 (range, 30 – 100). Median dose of prednisone at diagnosis was 60 mg (range, 0 – 1000). Thirty-two patients (88.9%) received polychemotherapy with high-dose methotrexate as first line treatment. In CSF, median β2MG was 3.55 mg/L (range, 0.88 – 19.24), median IL10 was 35.0 pg/mL (range, 3.0 – 2843) and median IL6 was 22.1 pg/mL (range, 2.0 – 120). Only 14% and 16% of patients presented with normal CSF and blood β2MG rate at diagnosis, respectively. Five patients presented with meningitis involvement. CSF β2MG was independent from blood β2MG (p = 0.861), from CSF IL10 (p = 0.379), from CSF IL6 (p = 0.479) and from blood LDH (p = 0.685). Complete, partial responses or progressive disease were observed in 18 (54.5%), 10 (30.3%) and 5 (15.2%) patients respectively. CSF β2MG concentration tended to be correlated to patient response (p = 0.129). The rates of complete response were 65% and 44% for low (< median) and high (> median) CSF β2MG rates, respectively. At last follow-up, 17 patients (47%) had relapsed, and 11 patients (31%) died. Median progression-free survival (PFS) and overall survival (OS) were 21.2 months (95%CI: 5.9 – 36.4) and 47.6 months (95%CI not estimable due to the low number of events), respectively. In univariate analysis, low KPS and high CSF β2MG were associated with poor PFS (p = 0.002 and p = 0.008, respectively) with no detectable impact of blood β2MG. CSF IL10 and IL6 were not associated with patient outcome. In multivariate analysis high CSF β2MG tended to remain associated with worse PFS (p = 0.087, HR: 2.784, 95%CI: 0.862 – 8.987). In responder patients, CSF β2MG was significantly decreased at 4 months after first line treatment initiation (p = 0.005). Conclusions: CSF β2MG may exhibit a prognostic value in PCNSL patients. These results need to be validated in a larger prospective study.
Utilization of immortalized B cells to identify SDCBP as a novel therapeutic target in ovarian carcinoma.
Authors: Handley Katelyn , Mehta Sumit , Martin Alexandra , Biswas Subir , Maharaj Kamira Karen , Mine Jessica A. , Cortina Carla , Nagy Mate , Sprenger Kimberly , Mandal Gunjan , Innamarato Patrick , Powers John Joseph , Harro Carly M. , Chaurio Ricardo A. , Anadon Carmen M. , Pinilla-Ibarz Javier , Shahzad Mian M. , Flores Idhaliz , Conejo-Garcia Jose 
Published: June 2022

e14507 Background: We hypothesized that tumor-infiltrating B cells in endometriosis and endometriosis-associated ovarian cancer can be used to identify novel, targetable antigen domains to inhibit the progression of ovarian carcinomas. We aimed to identify targets that are spontaneously recognized by B-cell-derived antibodies within ovarian clear cell carcinoma (CCC), endometrioid carcinoma (EC), and endometriosis and to determine the preclinical anti-cancer efficacy of a candidate antibody that recognizes the extracellular domain of an identified target. Methods: B cells from freshly dissociated CCC (n = 2), EC (n = 2), and endometriomas (n = 2) were isolated, activated, and EBV-immortalized. Antibodies were purified from B cell supernatants and used for screening in a proteome array. Targets were prioritized based on accessibility (transmembrane or secreted proteins), expression in endometriosis and cancer, and concurrent IgA and IgG responses. Tumor-promoting syndecan binding protein (SDCBP) was identified and SDCBP-reactive B cells were FACS-sorted and subjected to single cell B cell receptor sequencing to determine the variable heavy and light chain sequences of enriched clonotypes. We then generated a recombinant IgG4 antibody targeting SDCBP with the dominant VH/VL matching sequences. Immunoblots and qPCR were performed to assess SDCBP expression in ovarian cancer cell lines and tumor samples. In vivo studies compared anti-tumor potential of the α-SDCBP IgG4 with controls using immunodeficient mouse models of human CCC and high-grade serous ovarian carcinoma (HGSOC). Results: Nine accessible proteins were detected by both IgA and IgG in all samples, including SDCBP. SDCBP is expressed in ovarian cancer cell lines and tumor samples of multiple histologies, including CCC, EC, and HGSOC. Administration of α-SDCBP IgG4 in TOV21G (CCC) tumor-bearing mice significantly decreased tumor volume compared to non-antigen-specific irrelevant IgG4 (iIgG4, p = 0.002) and vehicle (0.001), and correspondingly trended toward decreased tumor weight compared to vehicle (p = 0.06). Likewise, administration of α-SDCBP IgG4 in OVCAR3 (HGSOC) tumor-bearing mice significantly decreased tumor volume compared to iIgG4 (p = 0.03) and trended toward decreased tumor weight (p = 0.06). Conclusions: An α-SDCBP IgG4 has demonstrated anti-tumor efficacy in SDCBP+ CCC and HGSOC, and SDCBP-targeted therapy for endometriosis and associated malignant conditions, as well as HGSOC, warrants further investigation.
The landscape of ACVR2A mutations in Chinese solid tumor patients.
Authors: Li Xin , Ren Yaoyao , Li Caifeng , Luo Cui , Ma Juan , Bian Zhengying , Ge Minghui , Lu Guanghua , Ding Ran , Bu Fanfeng 
Published: June 2022

e14523 Background: ACVR2A (activin A receptor type 2A) encodes a receptor that mediates the functions of activins, and it contains two polyadenine (A8) microsatellite loci, which are located in exon 3 and exon 10. Recent studies have shown that ACVR2A mutant was associated with microsatellite instability-high (MSI-H) and high tumor mutational burden(TMB-H) in gastrointestinal cancers. However, this association remains unclear in other solid tumors. Methods: We retrospectively analyzed the ACVR2A mutations from comprehensive 539-gene profiling of 10434 Chinese patients with pan-cancer. Somatic mutations in tumor tissue were assessed. We screened out ACVR2A mutations, calculated the mutation frequency, TMB in different types of cancer. Results: ACVR2A mutants were detected in 340 (2.9%) samples. The top 5 frequently cancers were colorectal cancer (98, 28.8%), lung carcinoma (68, 20%), hepatocellular carcinoma (64, 18.8%), gastric cancer (48, 14.1%) and biliary tract cancers (19, 5.6%). And 12.7% were other cancers (e.g., pancreatic cancer, small bowel adenocarcinoma, brain cancer). ACVR2A variants included truncation (50%), splicing site variant (9.0%), and other mutant types(41.1%). Truncation was the most common type, recurring in a few hot spots (K437Rfs*5/ K437Rfs*19, D96Tfs*54/ D96Rfs*4, V433del, R438Efs*19). The TMB in ACVR2A mutation group was significantly higher than that in ACVR2A wild-type group (p < 0.001). In addition, TMB ≥10 muts/Mb was seen in 76.7% tumors with ACVR2A truncation or splicing site mutant(INACT) and 20.6% tumors with other mutant types(VUS)(p = 0.002). The median TMB of INACT group and VUS group was 35.46 muts/Mb (0.74-344.12) and 6.62 muts/Mb(0.5-598.53), respectively. Conclusions: We analyzed the distribution of ACVR2A mutants in Chinese patients with solid tumors. Our data shows that ACVR2A truncation or splice site mutant type is significantly associated with TMB-H, and this may be potential molecular marker of immunotherapy.
Correlation of circulating tumor cells as a positive interventional biomarker in cancer patients.
Authors: Khandare Jayant , Aland Gourishankar , Jayant Sreeja , Chakraborti Pratim , D'Souza Alain , Kadam Avinash , Birari-Gawande Poonam , Bendale Yogesh Narayan 
Published: June 2022

e14527 Background: Circulating Tumor Cells (CTC) is a predictive biomarker for accounting disease progression and for minimal residual disease (MRD). Effect of conventional anticancer therapy on CTC count is well documented, however there is paucity of data related to effect of CAM based modality on CTC count in cancer patients. This study provides a preliminary observation about the effect of Ayurveda therapy on CTC count. Methods: The retrospective study involved stratification of 72 cancer patients undergoing cancer and maintenance treatment in a non-conventional, Ayurveda cancer treatment in India. For monitoring of prognosis in cancer patients, CTC count was assesed in patients attending Rasayu Cancer clinic. 17 cancer types, namely, breast cancer, cervix and ovarian cancer, bladder, lung, Head and neck squamous carcinoma, follicular thyroid, diffuse B-cell lymphoma, Hodgkin’s and non-Hodgkin’s, colorectal, Hepatocellular, stomach with abdominal metastasis, metastatic prostate cancer, SCC with lung and skeletal metastasis etc. Total 33 (46%) males and 39 (54.1%) female patients of various types and stages were analyzed for the presence of CTCs retrospectively. CTCs were isolated and renumerated from 1.5 ml of patient’s blood sample using OncoDiscover Liquid Biopsy Technology platform enriched with anti-EpCAM antibody immunomagnetic kit, approved by Drug Controller General of India (DCGI). CTCs were confirmed for cytokeratin+ 18 (CK18), DAPI+ and CD45-. Subsequently CTCs were imaged using Zeiss Axio Observer 7 fluorescence microscope. In 28 patients (50%), CTC was accounted for at both pre and post treatment in duration of 3-6 months. 28 patients were assessed for quality of life measured by FACT-G questionnaire. The outcome was quantified for clinico-pathological parameters; age / gender, cancer types, and CTC distribution. Results: The mean and median CTC distribution was observed to be 15.34 and 12.5, respectively. 8% patients showed the absence of any CTCs (6 subjects (1 male and 5 females). While 32 males (96%) and 34 females (87%) showed presence of CTCs. The correlation coefficient of CTC presence in male and female was significant 0.4799 (p < 0.05). The Ayurveda Rasayana therapy showed significant reduction in post interventional CTC count (-3.94±1.2) (P=0.02). In addition, this group of patients also showed significant improvement in health-related quality of life as measured by the FACT-G questionnaire (P<0.05). Conclusions: CTC is a validated predictive biomarker for accounting minimal residual disease, both in pre and post cancer treatments. The enumeration of CTCs represents an effective prognostic biomarker in assessing the disease progression. Reduction in CTC count was seen to be associated with improvement in health-related quality of life (QoL) which needs to be investigated further to establish correlation.
Isoflavonoid-based therapeutics to remodel immunologically cold tumors in nasopharyngeal carcinoma.
Authors: Kam Ngar Woon , Laczka Olivier , Hung Desmond , Li Xiang , Dai Wei , Tsao George , Lee Victor Ho-Fun , Kwong Dora Lai Wan 
Published: June 2022

e14534 Background: Nasopharyngeal carcinoma (NPC) is endemic in Southern China and is well-known to be heavily infiltrated by lymphocytes and constitute a unique but poorly defined tumor microenvironment. We aimed at delineating and defining the contribution of idronoxil (IDX), a synthetic flavonoid derivative, in restoring sensitivity to apoptosis and potentially modulating the immune microenvironment of NPC. Methods: Using multiplexed staining, we measured the levels of ENOX2 (IDX’s target), CD8 (cytotoxic T cell) and pan-cytokeratin (tumor marker) in 86 NPC patients’ cancerous specimens in tissue microarray format. NPC tissue bulk RNA-Seq and affymetrix microarray public datasets were gathered to examine ENOX2 significance. Interaction between ENOX2-expressing tumor cell lines (C17 and NPC43) and T cells were also studied. In vivo, antitumor effects of IDX on the growth of NPC43+ve tumors in nude mice and humanized mice were studied. Results: We performed median density as cut-off and tumors can be classified as hot or cold. 68.6% “cold”-phenotype tumors were observed in our cohort and the top 20% patients with highly positive ENOX2-expresing tumor cells showed lower number of CD8 infiltrates. Publicly dataset showed that highly expressed ENOX2 group associated with poorer prognosis (log-rank test p = 0.041). In vitro, we observed increased migration of T cells towards cancer cells when tumor cells were pre-treated with the combination of IDX and cisplatin (IDX+Cis) compared with monotherapy (IDX or cis alone) or untreated. We also observed increased susceptibility of tumor cells to T cell cytotoxicity when both IDX and Cis were added. In nude mice, IDX+Cis significantly decreased the tumor growth compared to saline-treated group. In humanized mice, upon treatment, we found 1.69-fold (p = 0.039) more CD3+ T cells in the tumor than in the blood when compared to control group. In humanized mice, the ratio between human T cell levels in tumor and blood was increased by the IDX+Cis compared to control group (1.67-fold, p = 0.01 by t-test). Conclusions: Distinct immunospatial profiles could be associated with clinicopathologic characteristics. The ability of IDX to modulate T cell populations indicates the potential of IDX to enhance the efficacy of current chemotherapy treatments in NPC by upregulating cellular trafficking toward tumor.[Table: see text]