bluuebunny/crossref_metadata_2025 huggingface dataset:
A prospective non-randomized phase I trial of dendritic cell–based cryoimmunotherapy combined with checkpoint inhibitors in mCRPC.
Authors: Thomsen Liv Cecilie Vestrheim , Honoré Alfred , Gjertsen Bjorn T. , Børretzen Astrid , Reisæter Lars Anders , Almås Bjarte , Helle Svein Inge , Førde Kristina , Biermann Martin , Azeem Waqas , Gabriel Benjamin , Knappskog Stian , Halvorsen Ole Johan , Akslen Lars , Pantel Klaus , Riethdorf Sabine , Øyan Anne Margrete , Kalland Karl-Henning , Beisland Christian
Published: June 2023

e14708

Background: Despite improvements, metastatic castration-resistant prostate cancer (mCRPC) still has dismal overall survival (OS). We treated 18 mCRPC patients with dendritic cell (DC)-based cryoimmunotherapy (CryoIT) as monotherapy or combined with checkpoint inhibitors to determine safety and immune response. Methods: mCRPC patients were biopsied before cryoablation, and subsequently injected intratumorally with autologous immature DCs. DC doses were escalated in a 3+3 design (n=9) followed by dose expansion combined with either ipilimumab (n=6) or pembrolizumab (n=3). The disease burden was assessed by PSA values, iRECISTv1.1 (PET/CT, MRI and bone scintigraphy at baseline, 14, 22 and 46 weeks) and circulating tumor cells (CTC; CellSearch). Immune response was monitored by ultradeep T-cell receptor sequencing. Results: The patients had aggressive cancer, with ISUP grade group 4 and 5 in 72% (13/18) at diagnosis and in 100% at inclusion. At baseline, higher ALP correlated with higher regulatory T cells (p=0.047), FoxP3+/CD3+ratios (p=0.014) and FoxP3+/CD8+ratios (p=0.004) in tissues. Median OS and progression-free survival (PFS) were 40.7 and 10.5 months, respectively. Of the 8 patients alive 43 to 85 months post-CryoIT, 7 had progressed and received other treatment. Early decreases in PSA (p=0.002) and LDH (p=0.01) levels 6 weeks after CryoIT indicated better outcomes at 22 weeks. Longer OS correlated with lower tissue ratios of CD4+/CD3+cells (p=0.002) and CD4+/CD8+cells (p=0.007). All patients with increased numbers of new T-cell clonotypes after CryoIT and CTC at the pretreatment level of 1-4 cells/ 7.5 mL blood changed to negative during follow-up up to 72 weeks. Conclusions: CryoIT demonstrates non-inferior OS and PFS compared to other mCRPC trials, and therapy response was suggested by decreased CTCs and induction of new T-cell clonotypes post-CryoIT. Lower CD4+cell fractions of lymphocytes in the TME indicate better OS after CryoIT. CryoIT appears not to decrease effects of post-treatment recurrence therapies. Clinical trial information: NCT02423928 . [Table: see text]
Importance of patient related outcomes in diagnosing fatigue related to immunotherapy treatment in patients with lung cancer: A real life study.
Authors: Almodovar Maria-Teresa , Picado Mariana , Gaspar Carina
Published: June 2023

e14709

Background: Lung cancer is a common cancer with a dismal prognosis that was improved with treatment with check-point inhibitors (CPI). Fatigue is the most frequent adverse event of CPI, often undervalued by physicians. Patient report outcomes may be a key to overcome underdiagnose of fatigue. Methods: The aim of this study is to identify whether the assessment Non-Small Cell Lung Cancer (NSCLC) patients report when answering the BFI questionnaire of fatigue is consistent with the one recorded by the clinical team at the pneumology consultation the during treatment with immunotherapy in monotherapy or in combination with chemotherapy. A prospective observational study was carried out during 8 months. The research was conducted through the collection of medical records from the patients clinical files and the application of the Brief Fatigue Inventory questionnaire before each one of the 4 treatment cycles. This questionnaire was validated and linguistically translated into Portuguese and assesses the severity and functional impact of fatigue in cancer patients. A 95% confidence interval was considered. Results: The 31 patients, 26 male (84%) and 5 female (16%) with a mean age of 68.5 years. The mean value of the BFI score before the first treatment, as well as in the following 3 evaluations, was higher for the participants who presented symptoms of asthenia/tiredness/fatigue recorded in the clinical files at the consultation and lower for those who did not. However, the differences were not statistically significant (pre 1st treatment - p=0.299, pre 2nd treatment - p=0.125, pre 3rd treatment - p=0.103 and pre 4th treatment - p=0.954). By comparing the BFI score with medical records, we found that fatigue remained underreported at the consultation in different assessment times (71% of sample participants were not identified as having fatigue at the 1st assessment time; 60% at the pre 2nd treatment visit; 54% at the pre 3rd treatment visit and 40% at the pre 4th treatment visit). Conclusions: In the present study, the BFI questionnaire allowed us to identify and stratify fatigue, showing greater sensitivity when compared to the medical records of the consultation alone.
Management of immune related adverse events through electronic multidisciplinary consultation: Five years of experience from Peking Union Medical College Hospital.
Authors: Liu Xiaoyan , Shi Yuequan , Zhang Dongming , Chen Minjiang , Xu Yan , Zhao Jing , Zhong Wei , Wang Mengzhao
Published: June 2023

e14712

Background: The increasing occurrence of immune-related adverse events (irAEs) pose a growing challenge for patients receiving immunotherapy. We sought to evaluate the utility of telemedicine in improving access to the multidisciplinary service and to provide a comprehensive overview of practical issues in the diagnosis and management of irAEs. Methods: A virtual multidisciplinary service dedicated to the diagnosis and management of irAEs was launched in July 2018. Data were collected using a digital referral system. Results: Data were collected from 1 July 2018 to 30 June 2022. After excluding 11 consultations that were lost to follow-up or had incomplete medical records, 278 consultations were included in this study. 187 consultations related to the diagnosis and management of irAEs; 68 related to the management of irAEs; 23 related to the suitability of immunotherapy. The diagnosis of irAE was ruled out in 23% (43/187) of cases. The differential diagnosis included overlapping toxicity attributed to concurrent use of targeted therapy or chemotherapy (n = 16), comorbidities (n = 11), infection (n = 10), and cancer progression (n = 6). A diagnosis of irAE was confirmed in 206 cases. Of these, 131 cases were single organ/system irAEs and 75 cases were multiple organ/system irAEs. 83% of these were grade 3-4. The most common confirmed irAEs were interstitial lung disease (n = 45), diarrhoea/colitis (n = 41), liver dysfunction (n = 38) and myocarditis (n = 33). Initiation of corticosteroids was recommended in 100% (138/138) of treatment-naïve patients. The most commonly recommended corticosteroid dose was 1-4 mg/kg/d (n = 83, 45%). Corticosteroid dose adjustment was recommended in 90% (61/68) of treated patients, including dose escalation (n = 19), dose re-escalation or prolonged tapering (n = 30), and rapid tapering (n = 12). Cardiovascular, pulmonary, rheumatic and hepatic irAEs were the top four irAEs requiring immunosuppression in addition to corticosteroids. Intravenous immunoglobulin (n = 108), tocilizumab (n = 51), mycophenolate mofetil (n = 41), and infliximab (n = 21) were the four most commonly recommended immunosuppressants. Consultation recommendations were followed in 87% (166/191) of cases. Clinical improvement was observed in 83% (137/166) of cases. Conclusions: This study demonstrated the feasibility of the electronic multidisciplinary consultation in the diagnosis and management of irAEs. Common challenges in the diagnosis of irAEs were identified, mainly the differential diagnosis of non-immune toxicity, infection, cancer progression, or comorbidities. Awareness of differential diagnosis should also be raised in patients suspected of irAE flare. The use of corticosteroids and additional immunosuppressants needs to be further investigated.
The impact of clinical equations on carboplatin dosing: A systematic review to determine appropriate dosing of carboplatin in adult cancer patients.
Authors: Leiva Maya , Yamauchi Sabrine
Published: June 2023

e15005

Background: The Calvert formula is used to estimate the carboplatin dose needed to achieve the desired Area Under the Curve (AUC) despite little consensus on which estimated Glomerular Filtration Rate (eGFR) equation best reflects renal clearance. Cockcroft-Gault (CG) is often used when calculating estimated Creatinine Clearance (CrCl) for the Calvert formula. Equations like Modification of Diet in Renal Disease or CKD-EPI (based on serum creatinine (SrCr) or cystatin C), take into account parameters such as race, gender, weight. We compared several publications to determine the most effective dosing strategy for carboplatin. Methods: Utilizing PubMed, 19 articles were found with the keywords “carboplatin, dosing, eGFR, measure GFR, creatinine clearance, muscle mass.” Our inclusion criteria consisted of being published within the last 10 years, included carboplatin dosing, and evaluated either measured GFR, measured CrCl, carboplatin clearance or toxicities caused by carboplatin. Studies not meeting these parameters were excluded. Of the 19 articles, 11 articles were identified regarding the accuracy of eGFR and its effects on carboplatin dosing and/or dose limiting toxicities. An extensive literature review of each article was used to find a consensus among the clinical equations used in carboplatin dosing. Results: There remains no consensus on the most accurate eGFR equation. Eight studies evaluated accuracy of varying equations in estimating GFR, creatinine clearance or carboplatin clearance. Two studies created new equations (one measuring GFR and the other measuring CrCl) and compared them to current equations for accuracy. Ultimately, only two studies were in agreement that CKD-EPI was the most viable option when GFR uses SrCr. Based on four studies, CG is an inadequate measurement of eGFR. CG ranked low due to a high mean percent error when compared to measured GFR, indicating a larger discrepancy between measured GFR and the estimated value of CG, as compared to other equations. Three of the studies evaluated for a correlation in skeletal muscle mass and hematological toxicities, indicating that changes in muscle mass could correlate with hematological toxicities. One small study developed a new equation based on muscle mass and SrCr and showed positive results for accuracy when compared to measure CrCl. Conclusions: Although a definitive equation to estimate renal clearance could not be established, equations like CG have limited accuracy due to race, weight, age, and gender. The single study that utilized muscle mass demonstrated the most promise and presents a better option for patients, particularly when muscle mass changes over time. Other studies illustrated that muscle mass is significantly correlated with carboplatin toxicity and should be considered for future studies to determine the safest method for dosing carboplatin.
A phase 1, multi-center, open-label, dose-escalation and dose expansion study of CBP-1018, a bi-ligand-drug conjugate, in patients with heavily treated advanced solid tumors.
Authors: Li Kaiwen , Wu Junyan , Ye Suiwen , Liu Yanqiong , Huang Hao , Fan Fan , Lai Yiming , Zhuang Suili , Zhou Liyan , Huang Robert , Teng Yan , Chai Xiaoyan , Shi Yehui , Huang Hai
Published: June 2023

e15007

Kaiwen Li and Junyan Wu contributed equally to this work. Yehui Shi and Hai Huang are the corresponding authors.

Background: Prostate-specific membrane antigen (PSMA) or folate hydrolase 1 (FOLH1) is highly expressed on prostate cancer and folate receptor α (FRα) overexpressed in various malignant tissues which both related to tumor invasiveness. CBP-1018 is a first-in-class bi-ligand-drug conjugate targeting both PSMA and FRα with monomethyl auristatin E (MMAE) as payload. Methods: This phase 1 study included both a dose-escalation and expansion stage. In the dose-escalation stage, an accelerated titration was conducted in single patient at 0.03mg/kg followed by an i3+3 design for dose levels (DLs) ≥ 0.06 mg/kg, Q2W in a 4-week cycle. This stage mainly enrolled patients (pts) with metastatic castration resistant prostate cancer (mCRPC) received a median 3.5 prior lines of treatment. The primary objectives were to evaluate the safety and tolerability, determine dose limiting toxicity (DLT) and maximum tolerated dose (MTD). Additionally, pharmacokinetics (PK) and preliminary efficacy will also be evaluated. Results: As of 24 Nov 2022, 14 pts (12 mCRPC, 1 bladder cancer and 1 ureteral carcinoma) were enrolled at 5 DLs (1 pt at 0.03 mg/kg, 3 pts each at 0.06, 0.08, 0.10 mg/kg, 4 pts at 0.12 mg/kg). No DLTs or drug-related deaths were observed. For 9 pts (64.3%) experienced treatment-related adverse events (TRAEs) ≥ grade 3, most common were neutrophil decrease (35.7%), WBC decrease (28.6%), lymphocyte decrease (14.3%), elevated GGT (14.3%) and hypertriglyceridaemia (14.3%). Among 10 efficacy evaluable pts with mCRPC, 3 SD were observed at DLs of 0.08, 0.10, and 0.12mg/kg, 4 non-PD at 0.06, 0.10, and 0.12 mg/kg, and 3 PD at 0.06 and 0.08 mg/kg. Decrease of prostate-specific antigen (PSA) was detected in 3 pts at 0.10 mg/kg. Overall median PFS was 7.2 months (95%CI, 1.7-9.3) and not reached in mCRPC pts. For PK profile of CBP-1018 and free MMAE, t1/2z was ranged 0.54-1.15 h and 40.28-57.27 h, respectively, no accumulation of both substances after multiple doses. Conclusions: CBP-1018 was well-tolerated at DLs of 0.03-0.12 mg/kg Q2W with no DLTs. Multiple SD were observed at DLs of 0.08-0.12 mg/kg, conferred a promising preliminary antitumor activity in pts with mCRPC. MTD was not reached and dose-escalation to establish the RP2D is continuing. Clinical trial information: NCT04928612 .
Development of a CUB domain-containing protein 1 (CDCP1)-targeting antibody-drug conjugate for triple-negative and metastatic breast cancer.
Authors: Gough Madeline , Kwah Kayden , He Yaowu , Snell Cameron Edward , Hooper John D. , Kryza Thomas
Published: June 2023

e15012

Background: CUB-domain containing- protein 1 (CDCP1) is a transmembrane receptor involved in the progression of several cancers. Recent studies demonstrate that CDCP1 is a rational target for the development of innovative targeted therapies for cancer including theranostics agents and antibody-drug conjugates. Methods: To determine the therapeutic potential of CDCP1 in breast cancer, we investigated its expression in multiple cohorts of breast cancer tissues by immunohistochemistry, as well as in various preclinical models including cell lines, primary cells and patient-derived xenografts using flow cytometry, western blot and immunofluorescence staining. Then, we evaluated the capacity of the CDCP1-targeting chimeric antibody ch10D7 to specifically accumulate in breast cancer lesions in in vivo preclinical models including patient-derived xenografts and breast cancer metastasis models. Finally, we determined the efficacy of the ch10D7-MMAE antibody-drug conjugate to kill breast cancer cells in vitro and breast tumours ex-vivo and in vivo. Results: The CDCP1 receptor is expressed at targetable level in a significant proportion of breast cancer cases with high/intermediate expression detected in ~30% of localized ER-positive cases, ~50% of metastatic ER-positive cases and > 70% of Triple-negative or HER2-positive cases. Similar proportion of expression was detected in cellular models. We demonstrated that ch10D7 antibody labelled with the radionucleotide Zircodium-89 specifically accumulates in breast cancer lesions in vivo allowing the detection of mammary-fat pad implanted patient-derived xenografts and of breast cancer metastasis by PET/CT imaging. Finally, we confirmed that the ch10D7-MMAE antibody-drug conjugate is very efficient at inducing cell death in vitro as well as controlling primary tumour and metastatic tumour burden in pre-clinical models, conferring a significant survival advantage compared to classical therapy. Conclusions: Our work demonstrates that CDCP1 is a potential target to detect and limit the progression of breast tumours in both the primary and metastatic disease setting, particularly in triple-negative and HER2-positive breast cancer subtypes. Furthermore, we show that biomolecules specifically recognising this receptor are promising therapeutic agents which could improve survival of patients.
Impact of panel size on minimum residual disease (MRD) assay performance.
Authors: Battey Christopher Jon , Acevedo Ashley , LaBella Matt , Ganesh Sangita , Patel Ravi , Trettin Kyle , Buser Elise , Xu Nafei , Gould Genevieve M. , Muzzey Dale
Published: June 2023

e15022

Background: Sequencing circulating tumor DNA is a promising method for monitoring cancer treatment response and detecting recurrence, but sensitivity at the low tumor fractions typical of early-stage, post-treatment, and early recurrent tumors is limited by the small number of variants targeted in commercially available assays. Methods: We developed a tumor-informed minimum residual disease (MRD) assay using tumor-normal whole-genome sequencing (WGS) followed by interrogation of select somatic variants in cell-free DNA (cfDNA). We describe theoretical limits on panel designability as a function of tumor purity and sequencing depth using simulations and a discovery cohort of 31 patient samples. cfDNA assay performance was tested by creating serial dilutions of patient plasma before somatic enrichment and sequencing. Simulations and in-silico downsampling of target sites were used to test sensitivity as a function of panel size. A bioinformatics pipeline incorporating somatic calling, copy number inference, error assessment, and tumor-fraction estimation was developed to analyze results. Results: Across a range of tissues, tumor-normal WGS identified from hundreds to tens of thousands of somatic variants to inform an MRD capture panel. 97% of samples tested returned at least 300 high-confidence somatic variants, and targeted sequencing demonstrated over 95% positive predictive value in somatic variant calls. In cfDNA dilution experiments, we observed > 99% sensitivity at a tumor fraction of 0.01%. Expanding the panel size from 16 to 300 target variants increased sensitivity at 0.005% tumor fraction from approximately 20% to > 95%. Our tumor fraction model returned accurate quantification down to the parts per hundred thousand (0.001%) range, even when only a single tumor molecule could be observed at each target site. Conclusions: Increasing the number of targeted variants in an MRD assay increases sensitivity at low tumor fractions, and WGS-driven panel design ensures a sufficient number of interrogated variants while minimizing the failure rate due to panel designability. High sensitivity MRD has the potential to enable earlier recurrence detection while also giving researchers and clinicians new tools for monitoring patient treatment responses.
Candidates for early detection: Effect of pluripotent very small embryonic-like stem cells (VSELs) to transform into cancer stem cells (CSCs) and candidacy for early detection of cancer in a liquid biopsy.
Authors: Tripathi Ashish , Pansare Kshama , Jha Nitu , Bhartiya Deepa , Ranade Anantbhushan , Joshi Deepa , Tripathi Anish
Published: June 2023

e15024

Background: Prevailing somatic mutation theory (SMT) is mired with several paradoxes and still there is no clarity on how cancer initiates. No distinct pattern of somatic driver mutations specific to cancers affecting solid tissues has yet emerged even after massive NGS studies since 2007. Rather than cancer being a genetic disease, we postulate that endogenous, tissue-resident VSELs get transformed into CSCs to initiate cancer. Under normal conditions, VSELs along with tissue-specific progenitors work in a subtle manner to maintain life-long homeostasis in adult tissues. VSELs express steroid and gonadotropin hormone receptors, are directly vulnerable to environmental insults, and their dysfunction initiates various pathologies, including cancer. Recent mice studies have shown that environmental insults resulted in global hypomethylation, genomic instability and loss of imprinting (LOI) at IGF2/H19 loci that transformed quiescent VSELs into CSCs. Unlike VSELs, CSCs undergo excessive self-renewal, acquire bad-luck mutations during clonal expansion and oncogene activation to initiate cancers, and can also further mobilize to distant sites to cause metastasis. A 1000-sample clinical study based on OCT-4A expression by qRT-PCR suggested that CSCs that get mobilized from affected organs can serve as potential novel candidates for early detection of cancer through liquid biopsy. Methods: CSCs were enriched from the peripheral blood using our proprietary technology. They were enumerated by flow cytometry. VSELs undergo epigenetic changes and LOI to transform into CSCs. TaqMan based qRT-PCR was carried out to study OCT-4A and ALDH-1 positive CSCs and IGF2 expression to monitor LOI at the IGF2/H19 loci. LOI of IGF2 is commonly associated with initiation and also progression of multiple cancers and is also responsible for pushing VSELs out of quiescence and enter the cell cycle as CSCs. Results: Increased numbers of CSCs (epigenetically altered VSELs) were detected in peripheral blood samples of cancer subjects compared to normal subjects (p < 0.0001) by flow cytometry studies. The median absolute count of circulatory VSELs/CSCs was 190 per ml (IQR: 105-295) in normal subjects and 690 per ml (IQR: 370-1265) in cancer subjects. The qRT-PCR study conducted on 100 subjects showed increased expression of OCT-4A, IGF2 and ALDH1 genes in cancer compared to non-cancer subjects. Conclusions: Early detection of cancer by evaluating circulating tumor cells (CTCs) or tumor DNA (ctDNA) holds promise, but their scarce nature and mobilization in late stages only when tumor is > 3 mm in size, are major limitations for widespread translation. Circulating VSELs/CSCs in peripheral blood are evidently promising candidates to screen and classify subjects for cancer absence, likely risk, or presence.
An in-house testing for detection of homologous recombination repair deficiency (HRD) in patients with solid tumors.
Authors: Tan Shuguang , Guo Weifeng , Cai Bin , Mu Tianhao , Liu Ming , Wang Zhouyang , Zhou Yanqing , Yin Yan
Published: June 2023

e15025

Background: HRD is associated with sensitivity towards PARP inhibitors (PARPi) in various cancer types, such as ovarian cancer, breast cancer, pancreatic cancer, and prostate cancer, and its determination is used as a biomarker for therapy decision making. HRD leads to the larger genome alterations, called “genomic scars“, which comprise loss of heterozygosity (LOH), telomeric allelic imbalance (TAI) and large scale state transitions(LST). The detection of SNPs is capable of measuring chromosomal abnormalities including genomic scars as mentioned above. Methods: Using a panel targeting more than 50,000 SNPs that evenly spaced across the entire human genome and the next generation sequencing technique, we developed an in-house testing for HRD detection, namely HRD score, which was computed by combining the measurements of large genomic defects including LOH, TAI, and LST. Then, we detected 44 ovarian cancer patients without BRCA1/2 mutations and 14 ovarian cancer patients harboring BRCA1/2 mutations to explore the application possibility of HRD score 42 as the threshold for HRD patients. Furthermore, we studied the HRD score distribution of 494 solid tumor patients. Results: For the 44 ovarian cancer patients without BRCA mutation, 50% (22/44) of them had the HRD score greater than 42. For the 14 ovarian cancer patients harboring BRCA1/2 mutations, 100%(14/14) of them had the HRD score greater than 42. For the 494 solid tumor patients, 38.66% (191/494) of them had the HRD score greater than 42. Conclusions: For this in-house HRD testing, the percentage of ovarian cancer patients without BRCA mutation who had HRD score greater than 42 was consistent with former report. Besides, the HRD score of all the 14 ovarian cancer patients harboring BRCA1/2 mutations were greater than 42, which was consistent with the facts. Therefore, it seems applicable to define the patients with HRD score greater than 42 as HRD positive. In addition, there is a wide range of demands for comprehensive implementation of HRD testing for other tumor entities.
Comparison of cfDNA content in different cancer types with different extraction methods.
Authors: Zhang Wenlong , Zhao Yanan , Li Jun , Cong Dan , Zhou Di , Yang Yang , Bai Yuansong , Mu Tianhao , Liu Ming , Yin Yan , Chen Shifu , Liu Yuanyuan
Published: June 2023

e15026

Background: ctDNA liquid biopsy technology has been widely used in the whole course of cancer management, from early screening and early diagnosis of tumors to tumor monitoring and medication guidance. However, the performances of ctDNA as a biomarker in these scenarios are different among different cancer types. One possible reason is that different types of cancer release different amounts of ctDNA or cfDNA, therefore, we explored the cfDNA levels in different cancer types in this study. Methods: We collected 15913 peripheral blood samples from 14686 cancer patients with different clinicopathologies, 256 patients with pulmonary nodules, and 971 healthy people. We isolated their plasma and extracted the cfDNA using QIAamp Circulating Nucleic Acid Kit, Apostle MiniMax cfDNA Extraction Kit or HaploX magnetic bead method cfDNA extraction kit. We calculated the average concentration of cfDNA (ng/ml) for different groups. Results: The number of samples of cervical cancer, liver cancer, glioma, colon cancer, prostate cancer, nasopharyngeal carcinoma, gallbladder carcinoma, melanoma, cholangiocarcinoma, colorectal cancer, breast cancer, gastric cancer, endometrial carcinoma, lung cancer, urothelial carcinoma, rectal cancer, ovarian cancer, healthy people, and pulmonary nodule patients are 93, 469, 113, 277, 139, 76, 89, 132, 171, 4010, 407, 547, 68, 7750, 46, 203, 96, 971 and 256, respectively. The cfDNA level of corresponding groups are 88.07, 79.51, 75.57, 63.58, 61.37, 59.09, 57.59, 57.16, 42.67, 34.73, 31.75, 31.37, 31.33, 29.84, 28.72, 28.69, 23.83, 17.82 and 12.54 ng/ml, respectively. The main groups are shown in the table below. Conclusions: The cfDNA concentrations of healthy people or pulmonary nodule patients were significantly lower than that of tumor patients, and there were also significant differences between different types of cancer. What's interesting, the cfDNA concentrations of lung cancer patients, pulmonary nodule patients and healthy people were quite different. What’s more, there were differences between Colon cancer and Rectal cancer patients. So, the cfDNA concentration maybe a good dimention to be used in early cancer screening and tracing of tumor types. [Table: see text]
Detecting variation of clonal hematopoiesis using machine-learning in liquid biopsy.
Authors: Zhang Yiqun , Pei Zhihua , Zhao Yuting , Hu Yifan , Li Zhencong , Wang Dongliang , Zhou Qiming
Published: June 2023

e15027

Background: Tumor‐derived DNA released to the plasma of cancer patients which could be captured and detected by ultra-deep sequencing. NGS provides the technical probability of somatic mutations detection from circulating cell‐free DNA (cfDNA) in plasma samples, while clonal hematopoiesis (CH) mutations affect the accuracy of liquid biopsy for clinical diagnosis or choice of drug and tracing of minimal residual disease (MRD). CH mutation screening of cfDNA samples still an unsolved issue, herein we propose a method that based on multi-variable tree model which screen the CH mutation effectively. Methods: We sequenced 1992 cfDNA (raw depth 35000x) and matched peripheral blood lymphocyte (PBL, raw depth 2000x) samples by 1123 genes target capture sequencing from cohorts which include 962 non-small cell lung cancers (NSCLC), 631 gastric cancers (GC), 379 other non-hematological cancers and 40 healthy normal control. First, we compared the coherence patterns of cfDNA-PBL between CH genes (ASXL1, DNMT3A, TET2) hotspot mutation and tumor associated mutation (EGFR L858R T790M, KRAS G12D G13D, TP53 R43H R141H). Next, we labeled canonical mutations by: point mutation and indels; top frequent tumor genes (from cbioportal collected TCGA cancers); published frequent CH genes; known hotspots and unknown significance genes. Furthermore, hotspot tumor mutation and hotspot CH mutations and other mutations were labeled. kNN classify all mutation to labeled mutations groups, and decided the next steps tree model’s node thresholds build a classify tree model screen the confident CH and somatic mutations. Finally, we validated 6 TP53 CH mutation from healthy normal control by ddPCR. Results: Previous published imbalance test model: 'fisher test p.value > 0.5 & 0.5 < OR < 1.5' only covered 23.2%, 26.9%, 17.5% top 10 hotspot CH mutations (ASXL1, DNMT3A, TET2) correspondingly, while 0.75 quantiles both g_VAF and t_VAF less than 1% and alter reads count less than 20. In terms of tumor associated mutations only 3/155,6/123,7/108,7/71,323/998,16/189 exceed the imbalance test models threshold, especially L858R with median t_VAF 3.4% and t_alter_count 60. Population frequency distribution of CH and tumor genes mutation were different significantly (median 0.776% and 0.569%; p.value < 1.44e-05, F-test). After assign hotspot and CH mutations classify by kNN, The tree model screened 42.9% and 83.6% CH mutations in cancer and healthy normal samples respectively. TP53 were common both in tumor and CH mutation ambiguously, tree model screened 6 TP53 CH mutation (c.12G > A, R43H, G113D, R70C, c.16C > T, A80T) from normal plasma sample all validated by ddPCR. Conclusions: CH mutations were ubiquitous in plasma sample and abundance pattern different from common tumor mutations significantly. CH mutation could be screened by optimal condition assembled decision trees effectively.
Analysis of cell-free DNA (cfDNA) fragmentomes and prediction scores across distinct molecular subtypes.
Authors: Schuurbiers Milou , Leal Alessandro , Aghamirzaie Delasa , Chesnick Bryan , Peters Erica , Wu Tony , Jakubowski Debbie , Tom Jennifer , Dracopoli Nicholas C. , Bach Peter B. , Scharpf Robert B. , Velculescu Victor E. , Monkhorst Kim , van den Broek Daan , van den Heuvel Michel
Published: June 2023

e15029

Background: Liquid biopsies have the advantage of being convenient in collecting tumor-derived DNA for clinical use. Genome-wide analysis of cell-free DNA (cfDNA) fragmentomes has emerged as a promising approach to detect lung cancer based on the examination of sequencing features other than actionable mutations. Here we report initial analyses of the DELFI (DNA evaluation of fragments for early interception) technology in patients enrolled in the Dutch Lung Cancer Early Molecular Assessment (LEMA) trial (NCT02894853), a prospective, observational, and multicenter study, to evaluate fragmentation patterns in genotyped blood samples with actionable alterations irrespective of disease stage and histology subtype. Methods: Plasma samples from 576 patients with an established diagnosis of lung cancer but awaiting the start of definitive treatment were processed and examined using low-coverage whole-genome sequencing. A lasso model that incorporated genome-wide fragmentation profiles was trained on an internal Delfi Diagnostics cohort and used to generate patient-specific DELFI scores for participants in LEMA. Results: Enrollees comprised 531 individuals with non-small cell lung cancer, 38 with small-cell lung cancer, and 7 with unknown lung cancer type. Most patients were diagnosed with late-stage disease (28% stage I, 10% stage II, 26% stage III, and 36% stage IV). Current smokers (N = 238; 41%) and former smokers (N = 295, 51%) outnumbered never smokers (N = 43; 8%). Analysis showed a stepwise increase of the DELFI scores from T1 to T4 and N0 to N1-3 disease, associating aberrant fragmentation profiles with the overall tumor burden. Small-cell carcinomas and squamous cell carcinomas presented with higher DELFI scores than adenocarcinomas ( p< 1e-7, generalized linear model). Patients without a smoking history had similar scores to those who had a previous history of smoking. When adjusted for stage, mutation status in ALK, BRAF, EGFR, ERBB2, KRAS, MET, RET, and ROS were not associated with DELFI scores ( p= 0.5, likelihood ratio test). Similarly, PD-L1 staining did not significantly affect DELFI scores when a 1% cutoff was applied to cases with PD-L1 staining data ( p= 0.07, generalized linear model). Conclusions: Our results reveal that DELFI scores increase stepwise with stage and are higher in small-cell and squamous cell carcinomas. The LEMA study reinforces the potential usefulness of genome-wide cfDNA fragmentation profiling as a liquid biopsy approach for identifying patients with lung cancer regardless of smoking status, somatic driver mutation, and PD-L1 expression scores.
Bi-directional interaction and predictive potential of inflammatory and oxidative stress-related biomarkers in patients with non-small cell lung cancer.
Authors: Nikolovski Srdjan , Jaradeh Mark , Siddiqui Fakiha , Walenga Jeanine , Jeske Walter , Fareed Jawed , Vigneswaran Wickii T.
Published: June 2023

e15030

Background: Interplay between oxidative stress and inflammation play major role in the development and progression of various malignancies. As one of the most common and the deadliest malignancy, lung cancer has a prominent vicious cycle of oxidative stress and immune response. The aim of this study is to examine the inter-relationship between basic oxidative stress and inflammation-related plasma biomarkers in patients with non-small cell lung cancer (NSCLC) undergoing surgical resection procedure. Methods: After obtaining informed consent, pre-operative plasma levels of alpha-fetoprotein, nitrotyrosine, urokinase-type plasminogen activator, and myeloperoxidase (MPO) as oxidative stress-related biomarkers were determined in 49 patients with diagnosed NSCLC. In the same patient group, plasma levels of interleukin (IL)-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, vascular endothelial growth factor (VEGF), interferon gamma, tumor necrosis factor alpha (TNF-α), monocyte chemoattractant protein-1 (MCP-1), and epidermal growth factor were also evaluated. Control samples were obtained from 34 healthy individuals. Plasma biomarkers were determined by enzyme-linked immunosorbent assay. Applicable statistical methods were used to analyze the data. Results: Positive correlation was observed between MPO and levels of the following inflammation-related biomarkers: IL-6 (r = 0.397, p = 0.007), VEGF (r = 0.494, p = 0.001), TNF-α (r = 0.348, p = 0.019), and MCP-1 (r = 0.377, p = 0.011). Biomarkers showing significance in correlation analysis were further analyzed by linear logistic regression in order to determine presence and strength of causality in each direction (oxidative stress to inflammation and inflammation to oxidative stress). IL-6 and VEGF were observed as a predictors of MPO levels (B = 0.334, p = 0.031, and B = 0.391, p = 0.039, respectively). Furthermore, causality was observed in the opposite direction as well. MPO levels were shown as a slightly better predictor of both IL-6 and VEGF plasma levels (B = 0.349, p = 0.007, and B = 0.433, p = 0.001, respectively), but also as a predictor of TNF-α and MCP-1 levels (B = 0.193, p = 0.019, and B = 0.217, p = 0.011, respectively). Conclusions: Conclusion: These studies showed a strong correlation between measured oxidative stress-related and inflammatory biomarkers. Furthermore, these observations underscore the importance of oxidative stress in the pathogenesis of lung cancer.
C-reactive protein in solid tumors: Clinically meaningful change and prognosis.
Authors: Lasheen Wael , Walsh Declan
Published: June 2023

e15036

Background: C-Reactive Protein (CRP) has been associated with overall survival (OS) in both solid and hematologic malignancies. CRP is used alone or in conjunction with other variables e.g., albumin to create prognostic scores, yet use in clinical practice is limited. One barrier is the lack of guidelines quantifying clinically relevant changes. The aim of this study was to determine important changes in CRP and any association with OS. Methods: This was a retrospective cohort study of electronic medical record data. Subjects were included if they had a solid tumor, ≥2 CRP measurements post diagnosis, ≥7 days apart, age ≥18. They were divided into Baseline High CRP (HCRP≥10 mg/L), and Baseline Normal CRP (NCRP < 10 mg/L) groups and analyzed separately. Median (range) and counts (%) were reported. Variables compared with parametric or nonparametric tests. CRP change (∆ = (2nd CRP-1st CRP)/1st CRP) cut-off points were determined by Receiver Operator Curves or dividing groups into tertiles for sensitivity and specificity. We report the Kaplan-Meier survival plots and Cox Proportional Hazard Survival Models. Results: 4931 solid tumors were identified with CRP values; 1473 ≥2 CRP at least one week apart. N = 943 HCRP; N = 530 NCRP. HCRP were more likely to have gastrointestinal cancers, high white blood cell count, liver disease, metastatic disease, undergone surgery. NCRP were more likely breast or skin cancer, female, higher BMI, longer OS. 50% ↓ or 2-fold ↑ in CRP from baseline were statistically relevant cut-off points. In HCRP, estimated OS for ≥50% and < 50% ↓ in CRP was, mean (SE), 87(2) and 81(4) months respectively; a six-month difference. In NCRP, estimated OS for ≥2 and < 2-fold ↑ was 90(3) and 105(3) respectively; a fifteen-month difference. In the COX models, ≥ 50% CRP ↓ in HCRP was associated with 40% lower mortality risk; ≥ 2x CRP ↑ in NCRP was associated with 2-fold ↑ mortality risk. Conclusions: CRP level changes with cut-off points of either a 50% reduction or a 2-fold ↑ from baseline correlated with better and worse OS respectively, during follow up of solid tumors. This was both statistically and clinically important. CRP has the characteristics of an ideal tumor biomarker. This could aid in disease prognostication and impact treatment decision making in routine clinical practice. [Table: see text]
Implementing liquid biopsy in rural cancer care when tissue is insufficient for molecular testing: Retrospective review.
Authors: Singh Jaswinder , Singh Siraj , Singh Gina J. , Nagaich Amitoj
Published: June 2023

e15039

Background: Liquid biopsy is a promising and minimally invasive genetic test examining plasma circulating tumor DNA. Coupled with the rapidly developing next-generation sequencing (NGS) technologies, it holds the potential for implementation in selecting signal-matched therapeutic options. Analysis of tumor cell free DNA, or liquid biopsy, is emerging as a useful adjunct to tissue biopsies in advanced solid tumors. These tests may reduce the need for repeating invasive biopsies, and may be performed serially with minimal risk to patients. Many a times solid tumor biopsies are not sufficient enough to run next generation sequencing and hence the need for repeat biopsies. The purpose of our study is to document how liquid biopsies are being used in a large, diverse community based practice in rural Missouri where travel to tertiary care center for repeat biopsies is not easy and how often the results were able to demonstrate yield of finding FDA approved therapeutic options or clinical trials for these patients. Methods: A retrospective chart review was conducted on adult patients with advanced solid tumors whose tumors were not sufficient enough to be tested for next generation sequencing and hence tested with Guardant360 assay, between December 2015 and December 2022. A total of 515 patients were referred for testing by 4 oncologists from within a five satellite rural community cancer centers. Results: The majority of patients were tested upfront for molecular marker evaluation, in either newly diagnosed advanced cancer patients, or in recurrent patients without enough tissue for testing. 66 out of 515 patients (12.8 %) were not found to have any tumor alterations on liquid biopsy. A total of 16 histological types were tested among 449 patients with lung ( n = 177; (39.42% ),breast cancer ( n = 58; 12.9 %) and colorectal ( n = 135; 30 % ); cancers being the most common types of the 16 histological subtypes. Of those with positive test results (n = 449 ), 56 (12.4%) patients had ≥ 1 FDA approved, target-matched therapeutic opportunity. Similarly, 329 patients (73%) had ≥ 1 target-matched therapeutic opportunity, outside current indications. Lastly, when no FDA-approved target-matched therapy was available results from liquid biopsy testing offered signal-based clinical trial opportunity in all 449 patients. Conclusions: Implementation of NGS-based liquid biopsy testing is feasible within a community rural oncology practice. In the era of precision oncology, such assays have the potential to expedite the efforts towards target-matched therapies and signal-based clinical trial opportunities especially when there is problem of lack of accessibility and affordability of repeat biopsies is a problem.
Cancer signature ensemble integrating cfDNA methylation, copy number, and fragmentomic patterns for multi-cancer early detection.
Authors: Kim Su Yeon , Jeong Seongmun , Lee Wookjae , Jeon Yujin , Kim Yong-Jin , Park Seowoo , Go Dayoung , Lee Sanghoo , Woo Hyun Goo , Yoon Jung-Ki , Park Young Sik , Kim Young Tae , Lee Se-Hoon , Kim Kwang Hyun , Lim Yoojoo , Song Sang-Hyun , Kim Jin-Soo , Kim Hwang-Phill , Bang Duhee , Kim Tae-You
Published: June 2023

e15040

Background: The use of cfDNA sequencing has demonstrated great potential for cancer screening; particularly, methylation signatures, copy number variations, and fragmentomic profiles have proven to be effective for identifying early cancer signals. However, most large-scale studies have only focused on either targeted methylation sites or whole-genome sequencing, limiting comprehensive analysis that integrates both epigenetic and genetic signatures. In this study, we present a platform for multi-cancer early detection that enables simultaneous analysis of whole-genome methylation, copy number, and fragmentomic patterns of cfDNA in a single assay. Methods: For a total of 950 plasma samples (361 healthy controls and 107 colon, 113 liver, 238 lung, and 131 prostate cancer) and 239 tissue samples, whole-genome methylation sequencing data were generated. Machine learning was conducted for multiple feature types engineered from cfDNA samples, and independent test performance was assessed. Results: A multi-feature cancer signature ensemble (CSE) classifier, integrating all features, outperformed single-feature classifiers. At 95.2% specificity, the cancer detection sensitivity with methylation, copy number, and fragmentomic models were 77.2% [CI 72-82], 61.4% [CI 56-67], and 60.5% [CI 55-66], respectively; but it was significantly increased to 87.7% [CI 84-91] with CSE ( p-value < 0.0001). For tracing the tissue of origin, CSE enhanced the accuracy beyond the methylation classifier, from 74.7% [CI 69-80] to 77.5% [CI 72-82]. Conclusions: This work proves the utility of a signature ensemble integrating epigenetic and genetic information for accurate cancer detection.
Analysis of survival outcomes in patients with non–small-cell lung cancer with mutations in STK11/LKB1 receiving chemoimmunotherapy.
Authors: Kim Diana , Elsey Rachel , Meissner Tobias , Sun Yuliang , Xu Bing , Hattum Crystal , Solomon Benjamin Maurice , Lee John H. , Williams Casey B.
Published: June 2023

e15043

Background: Many patients with non-small-cell lung cancer (NSCLC) do not benefit from first-line treatment with immune checkpoint inhibitors (ICI) alone or in combination with chemotherapy due to resistance or toxicity. In NSCLC, significant research has been undertaken to provide prognostic markers for single agent immune checkpoint inhibitor therapy. Co-alterations in TP53, STK11/LKB1 and KRAS have a low reported prevalence in NSCLC, however, potentially may represent a distinct molecular subtype of NSCLC that conveys primary resistance to single-agent ICI. Data continues to accumulate regarding resistance mechanisms to ICI, but limited data exists exploring these alterations and the corresponding survival outcomes in patients that receive chemoimmunotherapy. The primary objective of this study was to assess the association between alterations and co-alterations in STK11/LKB1 and survival outcomes in patients with NSCLC receiving chemo-immunotherapy. Methods: This was a retrospective study of patients ≥18 years old who had completed NGS testing and had a diagnosis of non-small-cell lung cancer that received chemoimmunotherapy from January 2016 to November 2022. NGS reports were reviewed to assess the status of STK11/LKB1, KRAS, KEAP1, and TP53 alterations. Additional markers assessed were PD-L1 status, TPS, CPS, TMB, and MSI if available. Results: Sixty-five patients were identified who had received chemoimmunotherapy for NSCLC, had NGS testing results, and were considered to be evaluable for retrospective review. Four patients were identified with co-altered KRAS, STK11, and TP53, and this alone was not significant for PFS (p= 0.48) or OS (p = 0.52) compared to patients without the alterations, however patients with the co-alterations and a positive PD-L1 showed an improvement in PFS (p =0.053). Patients with altered STK11, including those classified as VUS, had a poorer OS (p = 0.088). Our analysis also showed that PD-L1 negative patients had poorer OS (p = 0.088). Conclusions: The addition of chemotherapy to ICI may overcome resistance previously described in NSCLC patients with co-alterations in KRAS, STK11, and TP53, who received single-agent ICI and these genomic findings should not deter from the use of chemoimmunotherapy based on our limited experience. Patients with alterations in STK11 did have poorer outcomes overall, which is in line with previously published data describing STK11 as a poor prognostic marker in NSCLC. STK11 alterations have previously been described to be associated with PD-L1 negativity which may explain, at least in part, the poorer responses in the STK11 mutated subgroup.