bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical validation of OriMIRACLE S, a personalized and tumor-informed approach to minimal residual disease surveillance.
Authors: Li Zhendong , Zhao Weirong , Gan Yanhui , Zheng Xin , Yao Jicheng , Li Feng , Wang Weifeng 
Published: June 2022

e15013 Background: The presence of minimal residual disease (MRD) after curative-intent therapies in solid tumors is recognized as a risk factor for relapse. Glycoprotein-based tumor markers lack sensitivity and specificity for clinical application. Circulating tumor DNA (ctDNA) based MRD detection which can identify disease relapse ahead of radiological imaging has shown promising performance. The objective of this study was to develop and validate OriMIRACLE S (Minimal Residual Circulating Nucleic Acid Longitudinal Detection in Solid Tumor), a highly sensitive and specific tumor-informed assay for MRD detection via plasma cell-free DNA. Methods: Tumor-specific somatic single nucleotide variants (SNVs) were identified by whole exome sequencing of tumor tissue and matched germline DNA. Clonal SNVs were selected by OriSelector algorithm for patient-specific multiplex PCR-based NGS assay for MRD tracking. The limit of detection (LOD), specificity, sensitivity, repeatability, and reproducibility of this assay were determined experimentally with a series of standard references and in silico. Standard references were developed as following for assessing assay performance. The somatic variant references were two commercialized standards each containing five positive sites at variant allele frequency [VAF] of 0.1% and 1%, and a wild type sample. The single nucleotide polymorphism (SNP) references were made by blending three gDNA samples (160 sites) with gDNA samples without these SNPs to VAFs of 0%, 0.005%, 0.01%, 0.02%, 0.05% and 0.1%. And cfDNA references were made by titrating the clinical cfDNA mixture from five patients containing 31 positive sites with mononucleosomal HEK293 DNA to VAFs of 0.01-0.3% and 0.1-3%. Results: Site level sensitivity of ctDNA samples were 68.8% to 100% with 10 to 50ng input ctDNA (3,000 to 15,000 haploid genome equivalents). Site level reproducibility and repeatability were 98.0% and 97.0% using somatic variant references, respectively. The detection of three positive sites was sufficient to achieve a nearly 100% overall sample level sensitivity and specificity (6,000 haploid genome equivalents of gDNA samples) determined either by calculating a binomial probability or in silico with customized panels have 21 to 30 variants. The LOD of this assay was as low as 0.01% with the algorithm of OriCleverClover which could filter process and sequencing-related artifacts. Conclusions: OriMIRACLE S has been analytically validated as a highly sensitive and specific method to detect low quantities of ctDNA in plasma. The low limit of detection at a VAF of only 0.01% with low DNA input. OriMIRACLE S has wide-ranging potential applications in the clinical setting and drug development in a real-world scenario.
Large-scale whole-genome sequencing identifies genetic alterations in circulating hepatocellular carcinoma cells.
Authors: Zhou Zhihang , Xu Tao , Zou Heng , Yang Zihan , Yang Mengsu 
Published: June 2022

e15019 Background:Hepatocellular carcinoma (HCC) is one of the most lethal malignancies. Most of the patients have large tumor burden, vascular invasion, or metastasis at initial diagnosis. Liver biopsy is usually inaccessible in HCC patients due to the high risk of hemorrhage and tumor dissemination. Circulating tumor cells (CTCs) are malignant cells shed from the tumor tissue into the blood or lymphatic vessel. The fact that CTCs are live tumor cells makes them distinct from any of the existing cancer biomarkers. The biophysical property-based enrichment methods make downstream process easier as the isolated CTCs are not tagged with antibodies and the cell viability can be largely remained. Our objective is to isolate CTCs using a novel inertial focusing-base microfluidic device (CTC-100) and determine both their clinical value and the genomic features. Methods: We enriched and isolated CTCs in 155 HCC patients, 51 cirrhosis patients and 10 healthy donors. These patients were enrolled from Sep, 2020 to Feb, 2022 in the Second Affiliated Hospital of Chongqing Medical University (Chongqing, China). This method enriches CTCs according to the cell size and is label-free. The enriched CTCs are then validated via immunostaining. The CD45-EpCAM+DAPI+ cells with size larger than 15μm are considered as epithelial CTCs, and CD45-EpCAM-DAPI+ cells are considered mesenchymal. The CTCs were then micromanipulated from the slide and the pooled CTCs from each patient were then subjected to MALBAC whole genome amplification and whole genome sequencing, which has been finished in CTCs from 12 patients receiving surgery and 4 without tumor biopsy. The other samples are under processing. Results: Our data revealed that the number of total CTCs or mesenchymal CTCs were significantly higher in HCC patients than that in cirrhosis or healthy donors. The detection rate of CTC in HCC patients was 100%. The EpCAMpositive CTCs accounted only for 16.6% (298/1798) of the total CTCs. Moreover, the number of CTCs was positively associated with macrovessel invasion and tumor size (P < 0.01). Most of the mutated genes in CTC samples were accordant with corresponding cancer tissues. We have detected 24 CTC-specific mutated genes, including FBXL22, USP3, MIR1827, S100A1. We then figure out the frequently mutated genes in CTC samples. Finally, we cluster the SNVs in CTCs according to clinicopathological parameters including macrovessel invasion, distant metastasis, tumor size. The results showed that part of the mutated genes might be associated with tumor invasion or metastasis. Conclusions: The novel microfluidic platform can efficiently detect CTCs in HCC patients. CTC number is associated with macrovessel invasion and tumor size. Finally, the SNV but not CNV in CTC samples is tightly consistent with that in tumor tissue. We also find out some CTC-specific mutated genes that might be involved in HCC metastasis. Clinical trial information: ChiCTR2100051584.
Genomic profile by liquid biopsy of Peruvian patients with lung cancer.
Authors: Galvez-Nino Marco , Roque Perez Katia , Castro Melanie Wendy , Ruiz Rossana , Valdivieso Natalia , Coanqui Ofelia , Olivera Hurtado de Mendoza Mivael , Amorin Edgar , Mas Luis 
Published: June 2022

e15027 Background: The optimal treatment of advanced NSCLC patients is currently led by genomic profiling with the goal of detecting actionable mutations with an approved targeted therapy. However, tissue DNA samples are not always available to perform this assays. In this context, liquid biopsy has emerged as a valuable tool for providing the best treatment option. Methods: Retrospective study held at Instituto Nacional de Enfermedades Neoplasicas (INEN), Lima - Peru, between January 2019 and September 2021 to assess the genomic profile of 190 newly diagnosed advanced NSCLC patients through liquid biopsy. Blood samples were profiled with the FoundationOne Liquid Biopsy assay. We describe frequency of pathogenic and targetable genetic alterations, as well as the survival outcomes. Genomic and clinical data were recorded from clinical files. Results: The median age was 63 years (26-90), 66.3% were women, 15.3% smokers, 26.3% had exposure to biomass, 22.6% had a first-degree family history of cancer. The most frequent histological type was adenocarcinoma (86.8%). Regarding genomic profile, 183 patients (96.3%) had at least one pathogenic genetic alteration, the most frequent altered genes were TP53 (54.7%), EGFR (50.5%), DNMT3A (17.9%), KRAS (9.5%) and NF1 (6.8%). 116 patients (61%) had a targetable mutation: EGFR Ex19del/ins (27.4%), EGFR L858R/L861Q (17.9%), ALK rearrangements (5.8%), BRAF V600E (3.2%), RET fusions (1.6%), METex14 skipping (1.6%), KRAS G12C (1.6%), ROS 1 (1.1%), and NTRK (0.5%). Of these, 71 patients (65.5%) were able to access target therapy. For the latter, estimated median PFS and OS were 14.0 months (9.3 – 18.6) and 17.8 months (8.2 – 27.4), respectively. Conclusions: Peruvian NSCLC patients represent a population with a high frequency of pathogenic and targetable mutations, being EGFR mutations and ALK rearrangements the most prevalent ones. Despite limited access, a great proportion of patients received target therapy, achieving remarkable survival.
Assessment of tumour infiltrating subpopulations and pathological complete response using multiplex immunohistochemistry and digital pathology in early HER2+ breast cancer.
Authors: Hurley Camille , Lacroix Laetitia , Sheehan Katherine , Lucas Mairi , Buckley Rachel , Blümel Anna , Toomey Sinead , Hennessy Bryan T. , Crown John , Sautes-Fridman Catherine , O'Connor Darran 
Published: June 2022

e15041 Background: The treatment of HER2+ breast cancer (BC) has improved substantially with the use of targeted therapies, and patients achieving pathological complete response (pCR) following neoadjuvant therapy have significantly improved disease free survival. However, there is currently no way to determine which patients are most likely to respond to neoadjuvant HER2-targeting treatment. Growing evidence indicates tumour infiltrating lymphocytes influence HER2+ BC outcome. We hypothesize that a deeper investigation of the immune landscape of HER2+ patient tumours may improve patient stratification and identify an immune profile associated with pCR. Methods: 3plex immunohistochemistry panels identifying immune cell subpopulations and tertiary lymphoid structures were applied to HER2+ BC tumors (pre-treatment N=19, post-treatment N=9) of patients of the neoadjuvant TCHL clinical trial (NCT01485926), who received HER2-targeting therapy. Quantitative analysis of CD3+, CD20+, DC-Lamp+, CD4+, and CD8+ immune cells on multi-labelled whole-slide images of TCHL tumor sections was performed using artificial intelligence image analysis models. Patient-specific densities of each cell type in tumor regions were determined to facilitate assessment of pre-treatment differences in target immune subpopulations in complete, partial, and non-responders. Results: Statistical analysis demonstrated a trend for higher densities of each immune subpopulation in pre-treatment biopsies of pCR vs. non-pCR patients. Patient categorisation based on median threshold demonstrated patients achieving pCR are more frequently high for each immune cell type assessed, while non-pCR patients are more frequently in the low category. Investigation of association of pre-treatment immune infiltrate with clinicopathological features demonstrated trends for higher levels of T-cell infiltration in later stage and hormone receptor negative patients. Conclusions: Multiplex IHC is an optimal technique for the concurrent assessment of multiple target markers in patient tissue, which can be quantitatively analyzed in a high throughput manner using AI models. The findings of this preliminary study support recent evidence regarding the role of tumor infiltrating immune cells in HER2+ BC outcome and warrant further investigation in a larger cohort.
Comparison of 3 PCR-based assays for microsatellite instability detection in formalin-fixed paraffin-embedded tissues of patients with colorectal cancer.
Authors: Yang Jun , Zhang Biao , Guan Wenyan , Pu Xiaohong , Miao Shuying , Fan Zhiwen , He Lu 
Published: June 2022

e15042 Background: Routine assessment of microsatellite instability (MSI) status in colorectal cancer (CRC) patients can help with initial screening for Lynch syndrome, prediction of tumor prognosis and selection of patients for immunotherapy. Immunohistochemistry (IHC) and PCR-based approaches represent the current clinical laboratory standard for the evaluation of MSI status. Both Bethesda and Promega marker panels have been used widely in the world and the Bethesda panel and the six mononucleotides panel (NR21/BAT25/NR24/NR27/MONO27/BAT26) have been approved by the National Medical Products Administration (NMPA) in China. The Idylla MSI Test, a fully automated system based on real-time PCR, which incorporates 7 novel MSI loci (ACVR2A/BTBD7/DIDO1/MRE11/RYR3/SEC31A/SULF2) can perform MSI analysis within 150min using 1-3 tissue slides. The aim of this study was to evaluate the performance of the three 3 PCR-based assays for MSI detection including Idylla MSI Test, Bethesda and that six mononucleotides panel. Methods: One hundred and fifty-three formalin-fixed paraffin-embedded (FFPE) tumor tissues from patients with CRC were collected and their MSI status were analyzed using 3 PCR-based assays, respectively, i.e. the Idylla MSI, “2B3D” NCI panel and the six mononucleotides panel. All samples were previously evaluated by IHC method. Results: In the all 153 patients, IHC identified 27 cases to be MMR-deficient (dMMR), and 126 to be MMR-proficient (pMMR). Using IHC as a reference, the Idylla MSI had a higher consistency that showed overall agreement, sensitivity and specificity as 93.46%, 92.89% and 93.65%, respectively, while the corresponding values of the six mononucleotides panel were 84.31%, 92.59% and 82.54% respectively, and the “2B3D” NCI panel showed a sensitivity of 92.16%, a specificity of 88.89% and an overall concordance of 92.86%. The PCR-based approaches identified 11 more MSI-H cases than IHC while 22 dMMR cases identified by IHC were detected by all the 3 assays, 2 dMMR by 2 assays, 1 dMMR by one assay only and 1 dMMR by neither assays above. Moreover, the Idylla MSI showed advantages in ease of use, turnaround time (TAT) and small dose of tissue input. Conclusions: Our findings support that the Idylla MSI assay provides a rapid, reliable, and ease-to-use solution to MSI detection in Chinese CRC patients with high sensitivity and specificity. The inconsistent cases between IHC and PCR-based approaches need a further analysis.
Discovery of potent, orally active KIF18A inhibitors targeting CIN-high cancer cells.
Authors: Zhang Rumin , Cogan Derek , Eng Christina , Phillips Aaron , Carty Marysol Chu , Feinberg Tamar , Verma Akanksha , Tourdot Richard , Swiston Albert , Bettigole Sarah , Drutman Scott , Su Michael 
Published: June 2022

e15046 Background: KIF18A is a kinesin assisting chromosome congression and alignment during mitosis. It is nonessential in normal, euploid cell division but essential for a subset of aneuploid cancer cells with high chromosomal instability (CIN-high). KIF18A knockdown in these cells leads to mitotic arrest, cytostasis and cell death. As a result, KIF18A is an attractive anticancer target. Methods: Volastra drug discovery efforts identified and validated KIF18A as a promising target using genetic knockdown and pharmacological inhibition with a tool compound. High-throughput screening identified an ATP-noncompetitive hit that was optimized for potency, selectivity, and pharmacokinetic properties. Breadth of efficacy studies against a panel of cancer cell lines were used to formulate responder hypotheses and aid in patient selection. Mechanistic profiling and cell fate determination upon KIF18A inhibition was used to identify target engagement and clinical response biomarkers. Results: Our lead candidates bind to KIF18A with sub-nM potency and exhibit long (̃2 days) drug-target residence time. They are ATP and microtubule uncompetitive. They are highly selective for KIF18A and have no known off-target effects on related kinesins and in an in vitro safety screen. They are orally bioavailable in preclinical species, well tolerated and demonstrate tumor regression in mouse xenograft models. In contrast to many agents that disrupt the mitotic machinery, KIF18A inhibition does not impact growth of proliferating normal cells. Breadth of efficacy studies performed on a large panel of human cancer cell lines reveal sensitivity to KIF18A inhibitors across multiple tumor types including high-grade serous ovarian, as well as subtypes of breast and lung cancer. Conclusions: Volastra’s research efforts have culminated in the discovery of orally active, highly potent, selective, and efficacious KIF18A inhibitors as development candidates.
Development of heterobifunctional proteomimetic polymers for delivery of MYC inhibitory peptides and targeted MYC degradation.
Authors: Truica Mihai Ioan , Wang Max Mu , Gattis Brayley , Abdulkadir Sarki , Gianneschi Nathan 
Published: June 2022

e15049 Background: The c-Myc(Myc) oncogene plays critical roles in tumorigenesis and therapeutic resistance, being dysregulated in up to 70% of all human cancers. Heterodimerization with the closely related bHLH-LZ protein Max is required for oncogenic transformation, yet the development of small molecule inhibitors has been challenging since disordered Myc and Max monomers lack suitable binding pockets, while the Myc-Max interface is flat and extensive. Myc inhibitory peptides derived from the first helix (H1) of the bHLH-LZ region have overcome the limited binding affinity of small molecules. However, poor cellular penetrance and extremely limited bioavailability have precluded clinical translation of peptide-based approaches. Aim: To address and improve the limitations and low potential for clinical translation of Myc inhibitory peptides via a versatile peptide delivery platform. This novel platform technology is referred to as the Protein-Like Polymer (PLP) and it is based on packaging peptides together as high-density brush polymers. Methods: We generated H1-PLPs using ring-opening metathesis polymerization and characterized them using HPLC, LC-MS, NMR, and GPC. We also explored the potential of PLPs to be designed as heterobifunctional compounds by copolymerizing with secondary side chain peptides (nuclear localization sequences and degron sequence). For biological studies, immunofluorescence and confocal microscopy were used to assess cellular penetration; cellular viability assays coupled with use of both cellular (isogenic pairs, Myc-dependent and independent lines) and biochemical (scrambled H1 sequence, homopolymers, monomeric peptides) controls were used to assess tumor antiproliferative effects and Myc-based selectivity of response. Myc target engagement was assessed via immunoprecipitation assays and dual-reporter luciferase-based assays. Results: Our studies show that heterobifunctional PLPs employing H1 peptide and a degron sequence are cell-penetrating and co-localize with Myc in the nucleus. They display antiproliferative effects with submicromolar IC50 values in a Myc-dependent manner. The PLPs lead to Myc/Max complex disruption, promote significant levels of Myc degradation and prevent binding of Myc/Max heterodimers to the Myc/Max consensus canonical DNA binding site. Selectivity studies reveal that antiproliferative effects are dependent on intact H1 sequence. Animal studies using transplanted Myc-CaP model, which mimics the clinical course of human castration resistant prostate cancer are ongoing. Conclusions: We present a novel peptide delivery platform that addresses the challenges inherent to peptide delivery approaches. The presented work demonstrates the feasibility of this platform in delivering Myc inhibitory peptides and provides rationale for further in vivo studies in Myc-dependent tumor models.
Systems biology basis of permanent tumor regression with normal tissue protection: Experimentally validated signaling pathway framework.
Authors: Kumari Bindu , Sakode Chandrasekhar , Raghavendran L. , Roy Prasun Kumar 
Published: June 2022

e15066 Background: Clinicians generally deal with malignant tumors in progression phase only, but there is a reverse complimentary process, namely permanent spontaneous regression of tumors, a well-known phenomenon occurring across human populations at 22%-46% rate (Scandinavian and Wisconsin Screening Registries: 0.33 million and 2.95 million populace respectively; Lancet Oncol.12: 1118-24, 2011; J.Nat.Cancer.Inst.36: 37-47, 2006). Probing such a phenomenon can illuminate how one can induce a permanent regression process on human tumors therapeutically. Here we develop a systems biology approach for this process, that we validate by experimental findings. Methods: Mathematical System Biology Formulation: For permanent tumor regression, we develop a coupled differential equations-based cell kinetic analysis, keeping normal tissue protected. Thereby, we mathematically model the temporal variation of the level of three essential tumor-lysis components: DNA replication-blockade, Antitumor Lymphocyte, Cytokine interleukin-2. Experimental Investigation: We investigate the temporal process of spontaneous tumor regression of melanoma (in Liebechov pigs) and analyze the microarray signal using IPA platform Gene expression signature: Using IPA analysis, we find the signaling pathways associated with the permanent tumor regression. Results: Mathematical System Biology Formulation: We find the temporal behavior of tumor-lysis components are: (1) DNA replication-blockade activation: Unimodal inverted U function (2) Antitumor Lymphocyte activation: Bimodal M function; (3) Interleukin-2 activation as Stationary step function. Experimental findings: Our microarray analysis gives temporal pattern of gene-expression levels corresponding to above three components: G2/M DNA damage checkpoint regulation (genes CCNB1, CDC2), Chemokine signaling activation - Interleukin 2 ( GRB2, PIK3CG), T Lymphocyte Receptor Signaling (CCR5, PRF1). These three temporal components respectively show Unimodal, Bimodal, and Stationary activation. Validation: We show that the three mathematically-derived temporal activation functions are well corroborated by corresponding experimental temporal pathway activation data (Smirnov-Kolmogorov statistical test satisfied; α = 5%). Conclusions: A novel tri-phasic activation of three antitumor signaling pathways (DNA blockade, Interleukin 2, Cytotoxic T cell) can permanently regress melanoma tumor in the experimental setting if the pathways are activated at different time points and not simultaneously; These temporally orchestrated patterns are much different from conventional chemotherapy/ immunotherapy protocols where the temporal activations are simultaneous and empirically chosen. Optimal temporal profiling of administration of antitumor agents is thus crucial from a therapeutic standpoint.