bluuebunny/crossref_metadata_2025 huggingface dataset:
MATRIX plasma-in-plasma contrived samples assessment and detection of MRD using the Personalis NeXT Personal assay.
Authors: Labrousse Paul
Published: June 2023

e15056

Background: Detection of circulating tumor DNA (ctDNA) has been shown to correlate with clinical outcome of oncology patients. Molecular residual disease (MRD) profiling by ctDNA is being rapidly deployed. Current tumor-informed MRD tests assess a relatively small number of personalised variants, placing limits on their detection sensitivity and ultimately leading to false-negative results due to insufficient assay limit of detection (LOD). Here we report a performance evaluation of the Personalis NeXT Personal tumor-informed MRD assay, using a novel design for contrived samples that are highly commutable to clinical samples, enabling robust assessment of these emerging MRD assays. Methods: Our novel samples were built from commercially acquired matched tumor and plasma samples, across different indications. The cancer plasma was diluted into a background of healthy donor plasma to create the 72 plasma-in-plasma samples in each study (total of 144). Personalis performed WGS on the matched solid tumor and normal samples from each patient. ~1800 somatic variants were selected for each patient. A personalized panel was designed and used to enrich for the selected targets in the individual plasma samples. An aggregated positive variant score was evaluated to determine the presence of ctDNA in each plasma sample. Results: MATRIX 1 panels averaged 1863 variants (range: 1818 to 1888) selected for MRD tracking. With 152 clinically relevant variants and additional assay components, an average of 2206 variants were assessed per patient. MATRIX 2 panels averaged 1836 variants (range: 1819 to 1867) selected for MRD tracking. With 2130 clinically relevant variants they averaged 4094 variants assessed per patient. In the MATRIX 1 study, tumor signal was detected in all analyzed samples, including 9 samples at 0.002% tumor plasma dilution, with an assay sensitivity of 100%. The MATRIX 2 study showed tumor signal detected in 14 of 16 samples at 0.001% tumor plasma dilution. The 2 false negatives were reported at the 0.001% tumor plasma dilution. Thus, the assay sensitivity was 87.5% at the lowest dilution (0.001%) and 96.8% overall. Conclusions: The MATRIX plasma-in-plasma approach is a robust option for assessing the sensitivity of MRD assays to low levels of ctDNA. This approach addresses all parts of an MRD assay for both the plasma and tumor/normal tissues, and is the closest thing to real clinical samples while allowing direct interrogation of sensitivity. Additionally, it allows assessment of any genomic or epigenomic biological feature. The Personalis NeXT Personal assay shows ultra-high sensitivity with reproducible data down to the 1-3 PPM range, and expansion of the personalized panel fixed clinical content allows tracking of more driver and resistance mutations with no impact to the MRD sensitivity.
Diagnostic utility of next generation sequencing for somatic variants in cancer: A seven year cumulative cohort.
Authors: Boga Ibrahim , Sonmezler Ozge , Rencuzogullari Cagla , Mujde Cem , Tug Bozdogan Sevcan , Bisgin Atil
Published: June 2023

e15060

Background: Next generation sequencing (NGS) makes it possible to identify the specific molecular biomarkers to define patient eligibility for targeted therapies via multigene panels. Since then, even though the interpretation of data is complex and not all tumors have genomic alterations within actionable genes, using somatic sequencing for cancer patients becomes a daily routine in clinical oncology. Thus, here we present the data derived from our experience in NGS testing of different cancer patients and biological samples over the course of 7 years in our genetic diagnosis center. Methods: The cohort was consisted of total 5511 cases. While 2590 (46.99%) of them were formalin fixed paraffin embedded (FFPE) tissues, 2906 (52.73%) were liquid biopsies and 15 (0.27%) were other types of biological samples. Total of 15 different cancers were classified (Table 1) and were sequenced using 3 different multigene NGS panels (additional Table 1, BRCAs’ testing for breast/ovarian cancer is not included). NGS was performed via GeneReader NGS System (Qiagen, Germany). Bioinformatics analyzes and variant classification were performed using QCI-Analyze and QCI-Interpret interfaces. Results: As a result, the cases of 93.36% (n = 5145) among all samples were successfully sequenced. The lung cancer group was the most frequent with 47.96% (n = 2643 patients), followed by 491 (%8.9) colorectal 288 (5.23%) and breast cancer patients respectively, while 781 cases (14.17%) grouped as other including many rare cancers. Overall positivity rate was 42.57% (n = 2346) and 366 samples (6.64%) were not sufficient enough to be sequenced. The distribution of positivity rates in relation to cancer type and biological samples used were listed in Table 1. Classification and diagnosis of all tested cases, specimens and Tier 1-2 variants included in this cohort are available on the Additional Table 2. Conclusions: This report is a comprehensive review of the aggregate data across the entire cohort of cancer patients referred to a genetics diagnosis center. While our findings highlight the importance of NGS testing in the somatic setting for cancer patients, also these data stress the importance of diagnosis, biological sample types tested and test results. [Table: see text]
Expanding the spectrum of neoplasms harboring EWSR1:CREM fusion as detected by a real-world clinical genomics platform.
Authors: Campoverde Leticia , Evans Mark Gordon , Elliott Andrew , Camacho Felipe , Adler Jeremy , Oberley Matthew James , Sledge George W. , Rosenberg Andrew E. , Trent Jonathan C.
Published: June 2023

e15061

Background: Malignancies with various well-defined phenotypes and prognoses have been shown to possess gene fusions between Ewing Sarcoma Breakpoint Region 1 ( EWSR1) and one of the CREB family genes, specifically CREB1 and ATF1. However, less is known about neoplasms that harbor EWSR1:CREM rearrangements, which are thought to result in constitutive activation of CREM and subsequent dysregulation of oncogenes, such as BCL-2 family genes, EGFR1, and cyclins. EWSR1:CREM fusion has been identified in rare cases of angiomatoid fibrous histiocytoma, clear cell sarcoma, hyalinizing clear cell carcinoma of the head and neck, and intracranial myxoid mesenchymal tumor. Our study represents the largest to date and seeks to expand and further define the diversity of tumor subtypes that possess EWSR1:CREM fusions. Methods: Detection of EWSR1:CREM rearrangements by whole transcriptome sequencing was performed for > 240,000 neoplasms submitted to Caris Life Sciences (Phoenix, AZ). Histological review of the identified tumors was performed by two board-certified pathologists (MGE, AER). Treatment and outcome information were collected, where available. Results: An EWSR1:CREM fusion was detected in 18 cases, which included one intracranial myxoid mesenchymal tumor, one mesothelioma, four hyalinizing clear cell carcinomas of the head and neck, two clear cell sarcomas, two small round and spindle cell sarcomas, and eight histologically malignant tumors having an epithelioid morphology. While the latter were in keeping with a disease entity recently reported in the medical literature (epithelioid neoplasm with predilection for mesothelial-lined cavities), several of these cases demonstrated unexpected neuroendocrine differentiation and were found at unusual sites, including the kidney, uterus, and cervical spine. Moreover, three cases had the features of squamous cell carcinoma. Surgical resection was performed in all patients, and pazopanib was utilized in two round and spindle cell sarcoma cases. This medication was shown radiographically to produce a partial response at 19 months and stable disease at 26 months, respectively, in heavily pretreated patients. Conclusions: By detecting an EWSR1:CREM rearrangement, molecular testing may aid in the diagnosis of a variety of rare tumor types, including a poorly understood malignant epithelioid neoplasm that arises in a variety of anatomic sites including mesothelial-lined cavities. Tumors harboring this fusion may ultimately be susceptible to treatment with tyrosine kinase inhibitor targeted therapy.
Comprehensive clinical tumor RNA sequencing for children with cancer.
Authors: Vaske Olena Morozova , van den Bout Anouk , McCabe Molly , Echandia-Monroe Kathryn , Beale Holly , Kephart Ellen T. , Learned Katrina , Draper Jolene , Lyle Geoff , Bjork Isabel , Devine Patrick
Published: June 2023

e15067

Background: Cancer is the number one cause of death by disease for children in the United States. The underlying cause for most childhood cancers is unknown and unlike most adult cancers, childhood cancers harbor fewer coding mutations compared to adult cancers and are often driven by epigenetic deregulation. The functional impact of both genetic and epigenetic abnormalities can be detected from the analysis of tumor RNA. While tumor RNA profiling has entered several clinical trials, it is not utilized comprehensively and there is limited availability of clinical-grade RNA-Seq assays. We have published preliminary evidence of the utility of using research tumor RNA information in the pediatric oncology clinic. The next step is to develop an RNA-Seq assay that identifies gene fusions, expressed mutations, and important gene expression abnormalities in pediatric tumors. Methods: To validate our RNA-Seq assay pipeline, we have started with fusion detection and compared our results with a CLIA-validated DNA-based assay. We used RNA-Seq data generated from three fusion-positive cell lines to define the minimum of Mapped, Exonic, Non-Duplicate (MEND) reads necessary to accurately identify known fusions. Results: We found that the fusion, which has moderate expression (above 3 log2(TPM+1)), was consistently detectable in subsets containing at least 1 million MEND reads (Table). We next evaluated the precision of this finding. The fusion was detected in each of 21 additional subsets of 2 million MEND reads with replacement, but in only 71% of 21 subsets of 1 million MEND reads. In RNA-Seq data generated from tumor samples preserved with FFPE, we compared our RNA-based fusion findings with structural variants detected with the DNA-based gene panel test UCSF 500. Seven positive results were concordant, and one negative result was concordant. Two negative findings were positive by UCSF 500. Evaluation of these discordant results is ongoing, but the expression data indicates that the RNA result for one, a TMPRSS-ERG fusion, is accurate. To incorporate gene expression into our assay, we assessed the precision of gene expression measurements. In a preliminary dataset of three technical replicates, we found that the 95% confidence interval of expression values greater than 3 log2(TPM+1) is 4.5% of the measured value. Comprehensive clinical validation of our protocol will involve additional previously-characterized cancer samples. Conclusions: In summary, these data establish and validate key analytical parameters necessary for successful implementation of RNA-Seq analysis in the pediatric oncology clinic and advance our ultimate goal of bringing the most innovative molecular diagnostic methods to every child with cancer. [Table: see text]
Approaches and data needed for real-world evaluation of multicancer early detection tests.
Authors: Tunis Sean , Parmar Mahesh K. B. , Burris Howard A. , LeBeau Michelle M. , Kessler Larry
Published: June 2023

e15069

Background: The MCED Consortium is a group of volunteers, advisors, and companies from the US and the UK spanning a wide range of expertise in biomarker evaluation and implementation, with a special focus on clinical practice, health equity, and communication. The development of Multi Cancer Early Detection (MCED) markers may herald a new approach to screening and detection of multiple cancers at one time via various biological assays. Methods: The Consortium is developing recommendations for the evaluation of test utility, appropriate population targets for screening or early detection, downstream actions in health systems, issues of health equity, and communication challenges related to this new, potentially revolutionary generation of tests. While randomized controlled trials with cancer-specific endpoints have been the gold standard for the evaluation of cancer screening tests for decades, and have successfully shown effectiveness of breast, colorectal, cervical and lung cancer screening, there are compelling reasons not to rely entirely on those approaches to guide the evaluation and clinical use of MCEDs. Results: A large number of MCED products are likely to reach the market well before trials with mortality endpoints can be completed. The release of tests in clinical practice in the US via the laboratory-developed-test pathway means data could be available many years before data is available from trials. The MCED Consortium proposes approaches for the structure, systematic collection of real-world data that will complement such trials. This includes adopting shared definitions of RWD & RWE, definition of core data elements to be collected from all patients undergoing MCED testing, and the need for collaboration strategies across test developers, health systems, payers, clinicians, and others. Conclusions: We will present a framework for learning from clinical experience through data collection that will move MCEDs forward in the context of sensible clinical practice.
Molecular characteristics of KRAS mutations in Chinese patients with cancer.
Authors: Yan Hui , Li Mengmeng , Luo Ningning , Qi Yingxue , Sun Tingting , Qi Chuang
Published: June 2023

e15070

Background: Sotorasib, the first KRAS G12C inhibitor, has been approved for the treatment of non-small cell lung cancer (NSCLC) patients with KRAS G12C mutation-positive. Understanding the molecular characteristics of KRAS in Chinese patients with cancer is imperative, which is conducive to screening the beneficiary groups. Here, we focus on the molecular characterization of KRAS in NSCLC, colorectal cancer (CRC), pancreatic cancer (PC), and gastric cancer (GC). Methods: This study enrolled 17,775 pan-cancer patients detected by next-generation sequencing (NGS) from June 2021 to February 2022, in which NSCLC, CRC, PC and GC were 48.67% (8651/17775), 10.87% (1933/17775), 1.92% (342/17775) and 5.37% (955/17775), respectively. Results: The KRAS mutation rate in pan-cancer is 16.28% (2893/17775). In NSCLC, CRC, PC and GC cohorts, the mutation rates of KRAS were 13.28% (1149/8651), 50.34% (973/1933), 66.67% (228/342) and 7.64% (73/955), respectively. In NSCLC cohort, 1274 KRAS mutations were detected, and the subtypes were concentrated in G12C (346;27.16%), G12D (205;16.10%), G12V (194;15.23%), G12A (86;6.75) and Q61H (57;4.47%). In CRC cohort, 1094 KRAS mutations were detected. The subtypes were mainly distributed in G12D (350;31.40%), G13D (184;16.82%), G12V (180;16.45%), A146P (66;6.03%) and G12C (49;4.48%). In PC cohort, 251 KRAS mutations were detected, and the subtypes were concentrated in G12D (109;43.43%), G12V (70;27.89%), G12R (32;12.75%), G12C (9;3.59%) and Q61H (9;3.59%). In GC cohort, 82 KRAS mutations were detected. The subtypes of these mutations were concentrated in G12D (23;28.05%), G13D (12;14.63%), Q61H (7;8.54%), G12V (5;6.10%) and Q61R (5;6.10%). Conclusions: In NSCLC, CRC, PC and GC cohorts, K RAS mutations were concentrated in exon 2, accounting for 78.41% (999/1274), 81.63% (893/1094), 91.63% (230/251) and 64.63% (53/82), respectively. In NSCLC cohort, KRAS G12C was the molecular subtype with the highest mutation rate. However, in other cohorts, KRAS G12D was the predominant molecular subtype. G12D mutation will become the next research hotspot, and the breakthrough will help to further expand the beneficiary population of KRAS mutations.
The analysis of BRAF fusions characteristics in Chinese solid tumor patients.
Authors: Ma Fang , Zhao Yaping , Wang Chenxi , Han Tiantian , Ding Ran , Deng Wanglong , Bu Fanfeng
Published: June 2023

e15073

Background: BRAF encodes a RAF kinase, which signal downstream of RAS and activate the MAPK pathway, and has emerged as a major oncogenic driver and a potential therapy target. BRAF V600E base substitution is an approved target for the BRAF inhibitors in solid tumors. BRAF gene fusions represent a different mechanism of BRAF activation. BRAF fusions have shown responses to MEK inhibitors and non-specific RAF inhibitors (eg, sorafenib) in Melanoma (NCCN). We sought to analysis of BRAF fusions characteristics in Chinese solid tumor patients to explore the possibility of therapeutic intervention in solid tumors. Methods: We comprehensively characterized BRAF fusions from next-generation sequencing (NGS) data from May 2019 to January 2023 in 80083 various solid tumors. Considering the characteristics of the receptor tyrosine kinase, we focused on the BRAF fusions which contain the kinase domain. Results: A total of 164 unique cases (70.1% (115/164) glioma and 29.9% (49/164) non-glioma with BRAF fusions) were identified. The non-glioma cohort consisted up mainly lung tumors (49%, 24/49), colorectal tumors (18.4%, 9/49), pancreatic tumors (10.2%,5/49), melanoma (9.2%, 4/49) and biliary tumors (4.1%, 2/49). In the glioma cohort, the median age of the 115 patients was 12 with a range of 0–66; 43 (37.4%) of the patients were female and 72 (62.6%) were male. On the other hand, the median age was 64 with a range of 33–82; 23 (46.9%) of the patients were female and 26 (53.10%) were male in the non-glioma cohort. In the glioma cohort, 82.4% of the partners were KIAA1549. However, the most common fusion partners were AGK (14.04%), TRIM24(14.0%), SND1(12.28%), TPK1(8.77%) in the non-glioma cohort. These BRAF fusions comprised 49 unique 5′ fusion partners, of which 51% (25) were known and 49.0% (24) were novel. 14 novel partners were TMEM176B, HMBOX1, SEMA3E, LOC441204, PDE4D, DENND2A, STIM1, TNS3, PRRC2B, BCR, MET, COL4A3BP, TPM4, ZBTB16 and 10 novel partners were intergenic region. 130 patients with BRAF fusions could be evaluated for concurrent mutations. Of interest is that no KRAS and BRAF V600E mutations were identified in the 130 cases. Conclusions: BRAF fusions were detected in 0.2% (164/80083) of Chinese solid tumor patients. 70.1% of BRAF fusion positive cases were diagnosed with glioma and 29.9% were diagnosed with non-glioma. 14 novel BRAF fusion partners were discovered. BRAF fusion is an important driver genomic alteration and occur in a mutually exclusive pattern with other activating mutations in the MAP kinase signaling pathway. BRAF fusion targeted therapies should be further explored in solid tumors.
CDK4/6 inhibitors and cardiovascular toxicity: Real-world evidence.
Authors: Fiste Oraianthi , Liontos Michael , Gavriatopoulou Maria , Dimitrakakis Constantine , Evangelou George , Nikolaidou Vasiliki , Kotteas Elias A. , Syrigos Kostas N. , Dimopoulos Meletios A. , Zagouri Flora
Published: June 2023

e15074

Background: Cyclin-dependent kinases 4/6 inhibitors (CDK4/6i) have fundamentally transformed the therapeutic landscape of hormone receptor-positive and human epidermal growth factor receptor 2 (HER2) negative breast cancer, either as monotherapy (abemaciclib) or combined with classic endocrine therapy (ribociclib, abemaciclib, and palbociclib). However, evidence regarding treatment-related cardiovascular complications, beyond the context of clinical trials, remains scarce. Methods: We retrospectively explored the FDA Adverse Events Reporting System (FAERS) to gain insight into both frequency and spectrum of cardiovascular toxicities of these novel targeted agents in real-world setting. Results: For the period January 2018 - September 2022, a total of 90,999 adverse events (AEs) in patients under CDK4/6i have been reported, with 2,739 (3.01%) and 5,176 (5.69%) records being submitted as cardiac and vascular events, respectively. The incidence of these AEs was higher in the case of ribociclib, with arrhythmia representing the main cardiac complication (512 cases), followed by palpitations (120 cases), and acute coronary syndrome (115 cases). Interestingly, there was only one report of QT prolongation; of note, ribociclib has labeling guidance for QTc assessment. Hypertension/hypertensive crisis (302 cases), flushing (251 cases), and thrombotic events (226 cases) -with the exception of pulmonary embolism which was categorized as respiratory AE- comprised the foremost vascular toxicities associated with ribociclib. Conclusions: FAERS displays a public, post-market safety evaluation database with reports from healthcare professionals as well as consumers, yet it may include duplicates, inaccurate information, and fails to confirm causal relationship between the AEs and the medicinal product. In the light of CDK4/6i long-term usage, pharmacovigilance studies are warranted to elucidate their potential cardiovascular hazard. [Table: see text]
The genomic landscape of adolescent and young adult (AYA) malignancies using DNA and RNA-based next generation sequencing.
Authors: Lustberg Maryam B. , Kaneva Kristiyana , Teslow Emily , Mauer Elizabeth , Federman Noah , Eisfeld Ann-Kathrin
Published: June 2023

e15091

Background: Survival for adolescents and young adult (AYA) cancer patients (defined as age 15-39 years by the NCI) has not improved compared to survival outcomes in pediatric and older adult patients. Several factors contribute to the outcomes disparity, including lack of access to novel treatments. Currently, only a fraction of AYA cancer patients receive advanced genomic testing. Herein, we aim to characterize the molecular landscape of AYA cancers. Methods: De-identified records of 2,706 AYA patients diagnosed with solid tumors and hematologic malignancies who received Tempus xT next-generation sequencing (NGS) were identified. The prevalence of pathogenic/likely pathogenic (P/LP) single-nucleotide variants (SNVs), insertions/deletions (indels), fusions, and copy number alterations were assessed to describe the somatic landscape. Tumor biomarkers, such as microsatellite instability (MSI) and tumor-mutational burden (TMB) were also analyzed. Results: The cohort consisted of 2,706 AYA patients diagnosed with: central nervous system (N = 779), breast cancer (N = 700), bone and soft tissue sarcomas (N = 226), hematologic (N = 198), and gastrointestinal (GI) (N = 803) malignancies. Among 407 high-grade gliomas (HGG WHO Grade 3 & 4), variants in TP53 167 (41%), 136 (33%) IDH1, 125 (31%) ATRX, and 48 (12%) TERT were seen. Among the 82 patients with low-grade glioma (LGG, WHO Grade 1 & 2), 42 (51%) had a variant in IDH1, 40 (49%) TP53, and 35 (43%) ATRX. Among 269 patients with HR+ HER2- breast cancer, 82 (30%) had variants in TP53, 66 (25%) PIK3CA, 46 (17%) GATA3, 43 (16%) FGFR1 and 34 (13%) in ESR1. In triple-negative breast cancers (TNBC), 95 (77%) had a variant in TP53, and 9 (7.3%) in BRCA1. In ewing sarcomas (N = 36), 28 (78%) patients had a fusion with EWSR1, with TP53, STAG2, FGFR2, and RET altered in 2 (5.6%) patients. Within osteosarcomas (N = 46), 12 (26%) patients had a variant in TP53 and 9 (20%) in RB1 . In the AML subgroup (N = 34), WT1 was altered in 5 (15%) and FLT3 in 4 (12%) cases. Finally, in the GI cohort (806), 22 (5%) cases were MSI-H. Within colorectal cancer patients (N = 446), 247 (55%) patients had a variant in TP53, 150 (34%) in KRAS, 64 (14%) in PIK3CA, and several with NRG1 (8, 1.8%) and NTRK (3, 0.7%) fusions. Conclusions: We describe the somatic landscape of common malignancies in one of the largest AYA datasets. Additional analyses will focus on how this landscape differs from non-AYA age groups.
A novel anti-HER2 monoclonal antibody IAH0968 in HER2-positive, heavily pretreated solid tumors: Results from a phase Ⅰa/Ⅰb, first-in-human, open-label, single-center study.
Authors: Song Na , Teng Yuee , Teng Zan , Shi Jing , Jin Bo , Qu Jinglei , Zhang Lingyun , Yu Ping , Zhao Lei , Wang Jin , Li Aodi , Tong Linlin , Liu Yunpeng , Qu Xiujuan
Published: June 2023

e15098

Background: IAH0968 is an afucosylated anti-epidermal growth factor receptor 2 (HER2) monoclonal antibody which possessing the same binding properties to HER2 as trastuzumab and improving antibody-dependent cellular cytotoxicity (ADCC) activity and superior anti-tumor efficacy. We present results from patients with advanced HER2 positive malignant solid tumors including trastuzumab resistant and ineffective patients to establish the recommended dose of IAH0968 for phase II trials, as well as to investigate the safety, tolerability, pharmacokinetics (PK) and preliminary clinical activity of the drug. Methods: This was a single institution investigator-initiated phaseⅠa/Ⅰb study, using 3+3 design. The primary endpoint was safety, tolerability and preliminary clinical activity. Secondary endpoints included PK, recommended phase II dose, and anti-drug antibody (ADA). PK detection used ELISA to quantitatively determine blood drug concentration of IAH0968. Results: Eighteen pts were evaluable for safety and fifteen pts were suitable for efficacy analysis. The primary cancer sites included breast (8/18), colon (3/18), stomach (2/18), rectum (2/18), biliary tract (2/18), and pancreas (1/18). Median age was 54.2±9.7, ECOG 1/2 = 17/1, and 72.2% received anti-HER2 therapy in prior lines. Doses escalation were 6mg/kg (N = 3), 10mg/kg (N = 6), 15mg/kg (N = 5), and tolerable up to 20mg/kg (N = 4). Only one DLT was found at dosage 10mg/kg, and no MTD was reached. No ADA against IAH0968 was detected. The main PK parameters included mean T1/2 for doses 6~20 mg/kg ranging from 105 to 118 hours. The volume of distribution (Vz-obs) ranged from 4110.16 mL to 5395.64 mL. EC50 of ADCC activity of IAH0968 was 17.75~63.25 ×10-3 µg/mL. All grade treatment-related adverse events (TRAEs) occurred in 100% of pts, including grade 3 in 16.7%, and grade 4 in 5.6% of pts. The most common grade 3 TRAEs were hypokalemia (5.6%), arrhythmia (5.6%), QTC interval extension (5.6%), and infusion reaction (5.6%). The grade 4 TRAE was arrhythmia (5.6%). No serious TRAE or G5 were reported. 22.2% of pts had a TRAE leading to dose adjustment and 16.7% leading to discontinuation of IAH0968. After a median follow-up of 56.5 days (range, 0-479), objective response rate (ORR) was 13.3% (2/15), disease control rate (DCR) was 53.3% (8/15), and median progression-free survival (PFS) was 57.5 days (range, 42-236), with 4/15 responses ongoing. Conclusions: In heavily pretreated metastatic pts with HER2 positive, IAH0968 demonstrated promising clinical activity and tolerable safety profiles. IAH0968 will be further assessed in Phase Ⅱ study in combination treatment. Clinical trial information: NCT04934514 .
MELK and Del-1 as druggable targets in TNBC.
Authors: Lee In Hee , Lee Soo Jung , Kang Byeongju , Lee Jeeyeon , Park Ho Yong , Park Ji-young , Park Jee-Young Nora , Chae Yee Soo
Published: June 2023

e15100

Background: In our previous study, the researchers found that Del-1 was a promising predictive marker for breast cancer. However, the Del-1 downstream targets and biological effectors remain unknown and undruggable in breast cancer. We used RNA-seq to analyze the transcriptome and investigate the mechanism of Del-1 in regulating the course of breast cancer to uncover a druggable target. Methods: To evaluate the expression levels of Del-1 and MELK, mRNA levels in several breast cancer cell lines were analyzed. Due to the heterogeneity of TNBC, eight different TNBC cell lines were analyzed (BT20, TNBC; MDA-MB-468, basal-like 1; HCC-1806, basal-like 2; DU4475, Immunomodulatory; BT549, mesenchymal-like; MDA-MB-231, mesenchymal stem-like; HS578T, mesenchymal stem-like; MDA-MB-453, TNBC Luminal androgen receptor). Total RNA was isolated using RNAiso Plus (TaKaRa, Otsu, Shiga, Japan). Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit. High-throughput sequencing was performed as paired-end 100 sequencing using NovaSeq 6000 (Illumina, Inc., USA). OTS167 was treated for inhibition of MELK. The effects of MELK on cell proliferation and invasion were determined using MTT and Matrigel Transwell assays. To further investigate the relationship between DEL-1 and MELK, the researchers performed dual inhibition of DEL-1 & MELK. Results: Del-1 and MELK expression were significantly increased in TNBC cell lines compared to luminal or HER 2 positive breast cancer cell lines. Expression of Del-1 and MELK was dramatically enhanced in MB 468, HCC-1806, and MB 231 TNBC cell lines. Three TNBC cell lines were transfected with Del-1-specific siRNA to examine the effect of Del-1 downregulation on breast cancer. Del-1 knockdown HCC-1806 & MDA-MB 231 cells significantly decreased MELK expression, suggesting the possible relation between Del-1 and MELK. OTS 167, a MELK inhibitor, significantly inhibits breast cell proliferation and promotes cell apoptosis (MBA-MB-468, p < 0.001). Furthermore, when the OTS 167 was treated, the cell viability decreased as the dose of the MELK inhibitor increased, and the degree was the greatest in MBA-MB 468, basal-like 1 TNBC cell line. To further investigate the relationship between DEL-1 and MELK, the researchers inhibited DEL-1 and then MELK in MTT assay. Dual inhibition significantly reduced cell viability in MDA-MB468 and MDA-MB 231 cell lines, with the basal-like 1 cell lines showing the most significant effect. Conclusions: In this study, we sought to investigate the association between De1-1 and MELK in TNBC cell lines and tumor tissue. We found that MELK is downstream of del-1 and is a promising target, especially in the basal-like 1 subtype. Further research is warranted.
Retrospective evaluation of erlotinib and gefitinib used in the military health system from the perspective of drug-drug interactions.
Authors: Shou Karen J , Luong Thu-Lan T. , Powers Chelsea N. , Reinhardt Brian J. , McAnulty Mike J. , Weina Peter J.
Published: June 2023

e15108

Background: Erlotinib and gefitinib are epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) approved primarily for non-small cell lung cancer treatment, with pharmaceutical drug-drug interactions (DDIs) that are vague and poorly understood. Previous studies show that concomitant use of EGFR-TKIs with fluoxetine or losartan results in inhibition of both fluoxetine and losartan. Since DDIs can cause significant clinical ramifications, drugs that may interact with erlotinib or gefitinib must be identified. Methods: Data review was performed by Military Health System (MHS) data experts with data provided by the Joint Pathology Center (JPC) from the Department of Defense (DoD) Cancer Registry, the comprehensive ambulatory/professional encounter record (CAPER) and the pharmacy data transaction service (PDTS). Patients treated for cancer were identified, and the CAPER database was used to identify comorbidities. The PDTS database identified prescription drugs filled during erlotinib/gefitinib use, for all cancers. Patients were sorted into subgroups, (1) completed treatment (erlotinib or gefitinib was the last drug that patients completed, without recorded side effects), or (2) discontinued treatment (patients were treated with erlotinib or gefitinib but had recorded side effects and/or switched treatment). PDTS data and retrospective analysis of encounter notes, were used to sort medications into those that were taken before or after (“.”, “,”, “/”, or space between drugs) and those that were taken at the same time (“+”, “-/+”, or “and” between drugs). Results: 348 patients had diagnosis data, with 234 patients having completed treatment and 114 patients having discontinued treatment. Patients who discontinued treatment were diagnosed with more health issues than patients who completed treatment. A total of 258 patients had pharmacy data filled for erlotinib (240 patients) or gefitinib (18 patients). Of these, 177 patients completed treatment and 81 patients discontinued treatment. Patients in the completed treatment group filled 1 to 75 drugs, median range 11-20 drugs. Patients in the discontinued treatment group filled 3 to 103 drugs, median range 31-40 drugs. Patients who discontinued treatment filled more drugs than patients who completed treatment. The 20 most filled drugs, associated with side effects during erlotinib or gefitinib usage and the specific associated side effects were identified. Conclusions: This review cannot conclude that any drug resulted in erlotinib or gefitinib discontinuation. However, associations between top filled drugs and side effects have been made. Proof of concept in vitro laboratory testing should be done with these identified drugs, to confirm mechanistic interactions that may lead to clinical effects.
Characterization of drug and non-drug interactions in patients treated in medical oncology.
Authors: Ghomari Yacine-Abdallah , Guendouz Souaad , Soumeyya Ghomari
Published: June 2023

e15110

Background: Oncology patients frequently get multiple medications, including herbal supplements and medicines (chemotherapy, supportive care, comorbidities drugs, self-medication). This might pose a serious risk for drug interactions (DI) and non-drug interactions (NDI), which could endanger the patient's health. Our aims are to characterize the interactions, describe the risks to the patient they pose, and suggest a course of action to be followed. Methods: To make a pharmaceutical validation of chemotherapy prescriptions, this prospective study—the first of its kind at the national level—was carried out at the level of the Medical Oncology Department of CHU-Tlemcen from November 2021 to February 2022. It included patients treated on an outpatient basis who were receiving chemotherapy and/or targeted therapy. Following a medication reconciliation interview, patients from our sample who are being treated for one or more comorbidities are chosen in order to detect DIs using two French platforms (Vidal, Theriaque) and one Anglo-Saxon platform (Drugs). Hedrine was utilized to detect NDIs. Results: A total of 76 patients were enrolled for chemotherapy pharmaceutical validation. 36 (47%) of them were interviewed (median age = 61 years [42-86], sex ratio = 0,2), had at least one comorbidity treatment and 16 patients (45%) had breast cancer. The most frequently used protocols were anthracyclines (10 patients; 28%), anthracycline-taxanes (5 patients; 14%), capecitabine (5 patients; 14%), and capecitabine-oxaliplatin (3 patients; 8%). Seven patients (19%) used herbal supplements, primarily black seed ( Nigella sativa L.). Forty different interactions were listed for Vidal (23 precautions for use, 18 to be considered), 4 involved a chemotherapy drug. Forty-seven interactions with Theriaque (7 new interactions that Vidal missed, including 5 undesirable associations due to the use of ethanol as an excipient with a notable effect), 8 were due to a chemotherapy drug. On Drugs, 102 interactions were observed (4 serious, 90 moderated, and 8 minor), 38 involved a chemotherapeutic agent. Most interactions necessitated clinical and/or biological patient monitoring. In terms of NDIs, Hedrine indicates possible interactions by cross-referencing the effects of different plants on the organism with those of drugs, without giving any indication of the level of risk, what to do in case of risk. This makes interpretation difficult and requires expert opinion to guide action. No serious events were reported in the study. Conclusions: It is worthwhile to continue the pharmaceutical interview, especially for those most at risk for drug interactions, i.e., the elderly and/or patients on multiple medications. To widen the scope of interaction detection, it should be carried out prior to the recommendation of chemotherapy and refreshed when a patient's protocol changes utilizing at least one French and one Anglo-Saxon database.
Continuous dosing of AUM001 with cyclical gemcitabine/nab-paclitaxel to maintain the tumor growth kinetics in KPC xenograft model.
Authors: Chowbay Balram , Leong Wai Fook , Lee Sze Sing , Lim Jyue Yuan , Vidergar Romana , Tai Wai Meng David , Biswas Subhra Kumar
Published: June 2023

e15112

Background: PDAC is a highly desmoplastic and aggressive disease with limited therapeutic options and poor 5-year survival outcome. Gemcitabine (GEM) plus nab-paclitaxel (nPTX) is widely used as a first line treatment for PDAC but advancement for greater improvement on efficacy is still warranted. Dysregulated mRNA translation of pro-tumorigenic genes has contributed to the proliferative and metastatic nature of PDAC. Targeting oncogenic mRNA translation via MNK-coupled phosphorylation of eIF4E could serve as a target for inhibition to synergize chemotherapy. AUM001 is a novel MNK1/MNK2 inhibitor undergoing clinical trials in various solid tumors. We hypothesize that combination of AUM001 with GEM-nPTX would have synergistic effect in modulating the tumor growth kinetics and maintaining the tumor in a stable state. Methods: PDAC KPC cells were subcutaneously implanted into BL6 mice and randomized into five treatment groups once tumor volumes of 60-80mm3 were reached. Saline (control), GEM-nPTX were administered intraperitoneally on days 1, 4 and 8 while AUM001 was given orally on a daily basis for 8 days. The combination of GEM-nPTX and AUM001 were administered at similar doses and frequency. AUM001 was given for another 3 weeks in the continuous dosing group. Body weight and tumor volume were measured thrice weekly. Immunohistochemistry staining was performed on FFPE sections for Ki67, angiogenesis and stromal markers. Apoptosis was analyzed by Annexin V-propidium iodide flow cytometric assay. P < 0.05 was considered as statistically significant. Results: GEM-nPTX and AUM001 (GPA) or GEM-nPTX (GP) alone resulted in approximately 30% reduction in relative tumor volume. The continuous dosing of AUM001 (GPAc) after the cessation of chemotherapy showed a marked 55% decline in relative tumor volume ( P= 0.0079) compared to GPA. The phosphorylation of EIF4E (target of MNK1/2) and Myc expression were significantly inhibited in GPAc vs GPA groups at end of observation (EOO) (P < 0.05). VEGFA expression at EOO was found to be suppressed in GPAc compared to GPA group ( P= 0.0159) with no difference in MVD ( P> 0.05). Greater fraction of apoptotic cells was detected in GPAc at EOO ( P= 0.055) than GPA ( P> 0.999) when referenced to GP group. Conclusions: This study demonstrated that continuous dosing of AUM001 with cyclical GEM-nPTX is well-tolerated and confers good anti-tumor effect. Pharmacodynamic analysis also suggests that AUM001 may potentiate the reduction in pro-tumorigenic protein expression. This is the first study depicting the continuous dosing of AUM001 after cessation of chemotherapy could help to maintain the tumor state, facilitating its possible use in clinics as maintenance therapy in PDAC.
Preclinical evaluation of novel HER3-targeting radioconjugates for the imaging and treatment of HER3-expressing cancers.
Authors: Beckford Vera Denis , Li Jason , Xu Le-Cun , Lewis Debbie , Chin Amanda , Brodin Patrik , Chen Mary , Roy Monideepa , Kotanides Helen
Published: June 2023

e15114

Background: HER3 overexpression in tumors is associated with poor survival and is implicated in drug resistance mechanisms of HER1 (EGFR) and HER2 targeted therapies. Although antibodies against HER3 have been developed and evaluated in clinical trials, no HER3 targeted therapy has been approved, underscoring the unmet need for novel HER3 therapeutic approaches. We hypothesized that HER3 radioligand targeted therapies could provide enhanced therapeutic efficacy against HER3-positive cancers through the energy deposited by alpha or beta emitting radionuclides in tumor cells. Here we describe the development and preclinical evaluation of novel anti-HER3 antibody radioconjugates (ARCs), 225Ac-HER3 and 177Lu-HER3, using the alpha-emitting Actinium-225 (225Ac) and beta-emitting Lutetium-177 (177Lu) radioisotopes, respectively. Methods: ARCs were prepared by radiolabeling HER3 antibody with 225Ac or 177Lu using S-2-(4-Isothiocyanatobenzyl)-1,4,7,10-tetraazacyclododecane tetraacetic acid (p-SCN-Bn-DOTA) to yield 225Ac or 177Lu-HER3-ARCs. DOTA modified antibodies were characterized by HPLC and MALDI-TOF and HER3-ARCs were fully characterized by instant thin-layer chromatography (iTLC) and HPLC. The in vitro binding properties of the HER3-ARCs were evaluated using HER3 recombinant proteins and cells expressing HER3 in ELISA and flow cytometry. The in vivo pharmacological properties of the HER3-ARCs were evaluated by molecular imaging using Zirconium-89 (89Zr) Positron Emission Tomography (PET), biodistribution and antitumor efficacy studies. Results: HER3 antibody was successfully modified with p-SCN-Bn-DOTA to yield a conjugate with approximately 8 DOTAs per antibody molecule. Results from the in vitro binding assays of ARCs to either HER3 human recombinant protein or cells expressing HER3 demonstrated similar binding properties of 225Ac-HER3 and 177Lu-HER3 to unmodified HER3 antibody. The biodistribution study in NCI-H1975 tumor bearing mice showed that both 225Ac-HER3 and 177Lu-HER3-ARCs specifically accumulate in HER3-expressing tumors relative to other tissues. In agreement with the biodistribution studies, PET images revealed specific uptake of 89Zr-HER3 in NCI-H1975 tumors. Furthermore, 225Ac and 177Lu-HER3-ARCs showed significantly more potent NCI-H1975 tumor growth inhibition compared to controls. Conclusions: Our findings suggest that a HER3 targeted radiotherapy approach can enhance therapeutic response and overcome the limitations of previously explored HER3 targeted drug modalities. Thus, further preclinical evaluation of 225Ac-HER3 and 177Lu-HER3 is warranted, including in settings of tumor drug resistance, which can provide the basis for investigating HER3-ARCs as an effective treatment approach in future clinical trials.
A novel 89Zr-a-PD-1 immuno-PET-CT may improve pseudoprogression detection in a lung cancer murine model receiving immunotherapy.
Authors: Puyalto Calvo Ander , Rodríguez-Remírez María , Lopez Ines , Iribarren Fabiola , Torregrosa Maria , Simon Jon Ander , Ecay Marga , Collantes Maria , Vilalta Anna , Francisco-Cruz Alejandro , Solorzano Jose Luis , Peñuelas Ivan , Ajona Daniel , Gil-Bazo Ignacio
Published: June 2023

e15116

Background: Immune checkpoint inhibitors (ICIs) have revolutionized lung cancer treatment improving survival outcomes of non-small cell lung cancer (NSCLC) patients. Response assessment of patients on ICIs treatment represents a challenge since an increase in tumor size or the appearance of new lesions might not reflect true disease progression (P) but pseudoprogression (PP), which has been reported in a range of 3-6% in NSCLC. Conventional 18F-FDG-PET scans do not accurately discriminate P from PP. We have recently reported the efficacy of a combined blockade of PD-1 and ID1 in NSCLC mouse model. We aimed to evaluate a novel 89Zr-labelled radiotracer for micro mPET-CT to detect PP in a NSCLC murine model. Methods: Syngeneic subcutaneous tumors were generated using LLC cells (with constitutive expression of ID1 or ID1-silenced) in C57BL6J and in ID1-deficient mice, treated with PBS or with a commercially available monoclonal antibody against PD-1 (a-PD-1) (RPM1-14, 300 mg, IP, on days 7, 10 and 14). Tumor growth and response to ID1-PD-1 blockade, was measured by 18F-FDG uptake. Additionally, PP was measured labelling the anti-PD-1 with 89Zr (89Zr-a-PD-1) and analyzing 89Zr uptake at day 15, 17 and 20. Tumor microenvironment was analyzed with immunohistochemistry, multiplex immunofluorescence and quantification of relative expression of interleukins by RT-PCR. Results: 18F-FDG uptake did not show significant differences between groups, underestimating the real metabolic response induced by the treatment. However, 89Zr-mPET-CT showed a significantly higher 89Zr uptake when ID1 was inhibited in both, tumor cells and tumor micro-environment and mice were treated with a-PD-1 (p = 0.0075). The analysis of the tumor tissues in those animals by immunohistochemistry and multiplex immunofluorescence disclosed an increase in immune T CD8+ cells infiltration, being responsible for the antitumor response observed and correlating with 89Zr signal. Moreover, the analysis of interleukins expression showed that tumors with ID1 inhibition in the tumor micro-environment presented an upregulation of pro-inflammatory interleukins, favoring T- cell infiltration. Conclusions: ID1 inhibition in tumor cells and in tumor micro-environment combined with PD-1 blockade enhanced immune cell infiltration through pro-inflammatory interleukins upregulation. 89Zr-a-PD-1 immuno-PET-CT may improve PP detection in a NSCLC murine model receiving immunotherapy.
Antitumor activity of AX-0085, a novel AXL kinase inhibitor: Analysis of apoptotic cell death in triple-negative breast cancer cells.
Authors: Choi Myeong Jun , Woo SangHyeon , Kim DongHa , Janardhan Keshav Karapurkar , Yoon SungIl , Park Young Jun , Kim Jaesang , Jang Jun Young , Han Byung Woo , Suresh Ramakrishna , Kim Kye-Seong
Published: June 2023

e15120

Background: Triple-negative breast cancer (TNBC) is insensitive to targeted therapies due to the negative expression of human epidermal growth factor receptor-2, estrogen receptor and progesterone receptor. TNBC cells express higher levels of AXL more often than other breast cancer subtypes. The receptor tyrosine kinase AXL plays a role in survival, invasion, migration, epithelial-mesenchymal transition (EMT), metastasis, resistance, and immune suppression in cancer cells including in TNBC. Thus, AXL is a promising therapeutic target for the treatment of TNBC, and we developed a new small-molecule AXL inhibitor, AX-0085. Methods: The interaction mechanism between AX-0085 and AXL was studied by molecular dynamic simulations, cell-based kinase assay, and western blotting in TNBC cells. We investigated the anti-tumor activity of AX-0085 on the AXL-dependent pro-tumorigenic properties such as cell proliferation, invasion, migration, EMT, and immune suppression (PD-L1 expression) in TNBC cell lines and investigated in vivo efficacy of AX-0085 with the 4T1 xenograft model. Results: In the molecular dynamic simulations, estimated binding energy of AX-0085 and cabozantinib to AXL was -10.1Kcal/mol and -8.1Kcal/mol, respectively. AX-0085 was made a hydrogen bond with catalytically important residue Lys567 and blocked the activation of AXL by inhibiting the salt bridge with Lys567-Glu585. AX-0085 (IC50: 4.4nM for AXL kinase in cell-based kinase assay) was one of the most potent AXL inhibitors. AX-0085 showed a high antitumor activity against all TNBC subtypes and was a more potent anti-proliferative activity than other kinase inhibitors in MDA-MB-231 cell line. AX-0085 effectively blocked the activation of AXL in TNBC and further inhibited AXL-dependent pro-tumorigenic events such as cell proliferation, invasion, migration, EMT, and PD-L1 expression in TNBC cell. AX-0085 induced cell cycle arrest at G1 phase and suppressed the expression of CDK2 and Cyclin E in TNBC. AX-0085 promoted apoptotic cell death by up-regulating cleaved caspase-9 and down-regulating Bcl-2 in TNBC. Pharmacological investigation showed that the AX-0085 treated tumors displayed a dose-dependent reduction in volume and weight of the tumors in the 4T1 mouse xenograft. Conclusions: Our results demonstrated that AX-0085 selectively blocks AXL activation which confers an effective therapeutic value in the treatment of TNBC. Currently, AX-0085 is undergoing non-clinical trials.