bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk and predictors of ipilimumab-associated cardiac adverse events among patients treated for melanoma: A national cohort analysis.
Authors: Labban Muhieddine , Adib Elio , Langbein Bjoern , Chen Xi , Nguyen David-Dan , Cole Alexander P , Lipsitz Stuart R. , Sun Maxine , Trinh Quoc-Dien
Published: June 2022

e14592

Background: Ipilimumab is a CTLA-4 inhibitor widely used to treat advanced melanoma. While ipilimumab-induced cardiac immune-related adverse events (irAE) have been reported, there is a paucity of data from large cohorts. We investigated the risk and predictors of ipilimumab-associated cardiac irAE in a national cohort of patients with cutaneous melanoma. Methods: Using SEER-Medicare linked data, we compared the risk of cardiac irAE between patients treated with ipilimumab with or without concomitant treatment for cutaneous melanoma and controls not treated with ipilimumab following a primary diagnosis of cutaneous melanoma. We excluded patients ≤65 years and patients with cardiac comorbidities diagnosed within one year prior to the initiation of melanoma treatment. The primary endpoint was the incidence of at least one cardiac irAE after ipilimumab initiation including acute pericarditis, myocarditis, cardiomyopathy, conduction disorders, cardiac dysthymias, acute heart failure, and takotsubo syndrome. To estimate the risk of cardiac irAE, we conducted a multivariable competing-risk analysis adjusting for death of any cause within one year of treatment as a competing event. Then, we constructed a stepwise logistic regression to assess the predictors of having at least one cardiac irAE within one year of ipilimumab initiation. Subgroup analysis was conducted among patients who received ipilimumab only. The models were adjusted for patient demographics, disease stage, Charlson comorbidity index (CCI), history of hypertension, autoimmune disease, end stage renal disease (ESRD), chronic anticoagulant, and steroid use. Results: The cohort included 715 patients treated with ipilimumab and 22,070 controls. In the ipilimumab arm, 23.4% had metastatic disease, 9.5% had a history of autoimmune disease, and 2.2% had CCI≥2. The incidence rates of cardiac irAE among patients who received ipilimumab and among the control group were 23.3 and 13.6 per 1,000 person-years, respectively. We found that patients who received ipilimumab had a higher risk of cardiac irAE compared to controls (adjusted hazard ratio 1.87; 95%CI 1.50-2.32; p < 0.001). In addition to ipilimumab treatment, other predictors of cardiac irAE included male gender, older age, patients with metastatic disease, history of autoimmune disease, hypertension, ESRD, anticoagulant use, and CCI≥2. The predictors of cardiac irAE were also consistent in the subgroup analysis of patients who received ipilimumab only. Conclusions: Patients who received ipilimumab with or without concomitant treatment for cutaneous melanoma had a higher risk for cardiac irAE. Predictors of cardiac irAE help tailor therapy according to patients’ risk profiles.
Proteogenomic detection of circulating biomarkers for clinical oncology.
Authors: Quan Qimin , Ritchey Joshua , Wilkinson Joe , Kaiser Alaina , Geanacopoulos John , Boyce John
Published: June 2022

e15010

Background: Circulating biomarkers have the potential to detect cancer in its earliest stages and monitor patients in remission. The integration of proteogenomics in circulating biomarkers may transform the molecular diagnostics of cancer and accelerate basic and clinical oncology research. Proteomics bridges the gaps of functional information lost due to post-transcriptional and post-translational modifications in a genomic approach. A recent study showed that adding just 8 protein biomarkers to a panel of circulating DNA biomarkers increased the diagnostic accuracy up to 98% sensitivity and 99% specificity. However, the proteogenomic approach normally requires the use of multiple different assay technologies and laboratory workflows, including mass spectrometry. Methods: MosaicNeedles are densely integrated nanoneedle sensors fabricated on a planar substrate that integrates proteogenomic analysis in one platform. 94,000 sensors with more than 2 billion total nanoneedles can be integrated on to a standard SBS plate, which can be configured into 96, 384 or 1536 well format. Each sensor contains an array of nanoneedles, dedicated to detecting one analyte of interest. All nanoneedles comprising the same sensor are functionalized with the same capture probes. The capture probe can be either an antibody for protein detection or an oligonucleotide with a specific target sequence to a DNA fragment, mRNA, or miRNA of interest. Results: At low analyte concentration, the binding of proteins to the nanoneedles follows a Poisson distribution. Therefore, statistically, no more than one molecule is bound per nanoneedle. A further addition of aptamers or antibodies will form a sandwich complex with the target analyte. Since each of the nanoneedles has an intrinsic optical resonance spectrum and will red-shift as the sandwich complex forms on its surface, the number of analytes can be quantitated by simply counting the number of nanoneedles that display a color change. At high analyte concentration, each nanoneedle has more than one analyte, so the number of analytes can be calculated by averaging the spectrum shifts of all nanoneedles. This combined single molecule counting (digital) and spectrum shift (analog) analysis allows the platform to detect both high abundance and low abundance protein analytes in one reaction. A 10,000-plex study can be achieved with a total of 2.5 billion nanoneedles on a 50mm by 50mm consumable. In this consumable, a 2,000-plex proteome and 8,000 cell-free DNA fragments can be detected. Conclusions: A full proteogenomic quantification can be performed on the NanoMosaic platform in one reaction with high sensitivity and large dynamic range. It simplifies the workflow and allows users to integrate proteomic and genomic information to discover new circulating biomarkers.
How circulating cancer cells disguise: The role of platelets.
Authors: Schott Dorothea , Pizon Monika , Pachmann Ulrich A. , Schill Erika , Pachmann Katharina
Published: June 2022

e15011

Background: Solid tumors are notorious for their ability to form lethal metastases, sometimes several decades following initial cancer diagnosis. Development of distant metastases is a result of the primary tumor shedding cells that travel via lymphatics and the blood to distant sites where they can form metastases. Platelets are known to specifically enhance tumor cells’ survival in the bloodstream by as yet poorly understood mechanisms. To study the interplay of platelets with circulating tumor cells, we implemented our published approach to label both circulating epithelial tumor cells and platelets. Methods: Blood samples were collected from 86 non-metastatic breast cancer patients avoiding fixation and processed at 4 time points following blood collection using the maintrac approach. Samples were additionally stained with anti-CD36 antibody to visualize platelets. Results: Typically, we observed at 0h post-blood draw platelet aggregates strictly attached to single cells that did not stain with anti-EpCAM antibody. These clogged unstained cells were, by far, outnumbered by surrounding white blood cells with no platelets attached. After keeping blood samples at room temperature for 24h a completely different picture became apparent: there were still cells detectable with platelets attached to them but the underlying cell now became accessible to the anti-EpCAM antibody leading to green fluorescence staining. CETCs were detected in 94% patients on day 1 post-blood draw. The increase in single platelets in the background could be a sign that after 24h, platelets detach from CETCs. At 72 h following initial blood drawing, platelets had almost completely disappeared from the cell surface. Numbers of EpCAM-positive cells remained stable between days 1 and 3. No CETCs were observed in 2 individuals with no cancer diagnosis, neither on day zero, nor on day 1. Conclusions: Our results suggest that platelets play a key role in masking circulating tumor cells. Masking may explain the difficulties in detection of these cells and prevention of their elimination by the immune system. Our unmasking approach detects sufficient numbers of circulating tumor cells to monitor the effect on blood tumor cells of different therapeutic measures, thus contributing to improved systemic therapies for cancer.
Using nucleosome levels, copy number alterations, and DNA methylation to profile disease state through liquid biopsy.
Authors: Harrison Sarah , Poplawski Shane G. , Orlanski Shari , Wei Melvin , Atteberry Brandi , Berman Benjamin P. , Kelly Terry
Published: June 2022

e15014

Background: Nucleosomes are the repeating unit of chromatin that contain important signals for proper genomic function and transcriptional activity. Upon cell death, chromatin is fragmented, and nucleosomes are released into circulation and thus, detectable in liquid biopsy. Cell death naturally occurs over time and increases in a variety of diseases resulting in elevated levels of circulating nucleosomes and the genetic and epigenetic signatures they carry. These signatures contain important information about the cells from which they were derived, as well as the reason for them being in circulation. Methods: We measured circulating nucleosome levels, using Volition’s Nu.Q H3.1 sandwich ELISA across a healthy cohort spanning 40-85 years of age as well as patients whom had been diagnosed with Non-Hodgkin's Lymphoma (NHL), some of which were untreated and others that had undergone treatment. Additionally, to demonstrate that the correlation between nucleosome (Nu.Q) levels and copy number alterations is specific to cancer, we assessed the genomic integrity of an NHL sample with a Nu.Q level of 744 ng/ml and a sepsis sample with Nu.Q level of 3,281 ng/ml using low coverage Oxford Nanopore whole genome sequencing to identify genomic amplifications and deletions. We further used cell type specific methylation patterns to identify the cell of origin of cfDNA in each sample. Results: Importantly, we found no significant correlation between nucleosome level and age in our healthy cohort (R2= 0.0004; 40-49: N = 10, mean = 39 ng/ml; 50-59: N = 10, mean = 18 ng/ml; 60-69: N = 10, mean = 35 ng/ml; 70-79: N = 15, mean = 34 ng/ml; 80-85: N = 5, mean = 32 ng/ml). We did however find elevated nucleosome levels in untreated NHL patients (N = 4, mean 646 ng/ml) and that nucleosome levels in NHL patients that had undergone treatment were reduced (N = 29, mean = 180 ng/ml). Using copy number changes, we found that the fraction of cfDNA estimated to be derived from the tumor in the NHL sample was 54% and were able to detect amplifications in chromosomes 10, 11 and 18 and deletions in chromosomes 1, 8, 17, 18 and 23, whereas we found no copy number alterations present in the cfDNA sample derived from a sepsis patient and a tumor fraction of 0. Furthermore, using cell type specific methylation patterns to deconvolute the data we found that a large fraction of the cfDNA in the NHL sample was derived from B-cells consistent with the NHL sample being of B-cell origin whereas we determined that the cell of origin of the cfDNA in the sepsis sample was Neutrophils. Conclusions: This data shows that nucleosome levels, as measured by Nu.Q, can be used in conjunction with shallow sequencing and DNA methylation profiles to define tumor fraction and cell of origin in liquid biopsy.
High-multiplexing quantitative CodePlex proteomic profiling of platelets in triple-negative breast cancer (TNBC) patients and healthy subjects.
Authors: Han Edward Xu , Gu Sean , Steinle Matthew , Gu Vivian , Tyagi Tarun , Mackay Sean , Hwa John , Zhou Jing
Published: June 2022

e15017

Background: Platelets play significant roles in inflammation, immune regulation, and intracellular communication processes involved in tumor pathogenesis. Aberrant platelet activation has been associated with tumor progression and metastasis, however, cancer patient platelet deep profiling remains underutilized. New tools are needed for rapid high throughput quantification of potential altered platelet secretome in cancer patients. Such technology may provide novel insights into impactful cancer-associated biomarkers. Methods: We have developed a high throughput multiplexed proteomic technology to profile platelet cytokine content and releasates and performed a pilot study in healthy patients versus triple negative breast cancer (TNBC). Macrochambers of the CodePlex chip were pre-patterned with a 23-plex antibody IsoPlexis Human Adaptive Immune Panel: GM-CSF, Granzyme B, IFN-g, IL-10, IL-13, IL-15, IL-17A, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IP-10, MCP-1, MIP-1a, MIP-1b, perforin, sCD137, TGF-b1, TNF-a, TNF-b. 2% BSA/PBS was used as background control. The chips are loaded into an IsoLight automation system, releasates measured by fluorescence ELISA, and analysis performed by IsoSpeak software. In a pilot study to test feasibility, platelets were meticulously harvested from triple negative breast cancer patients (n=2) and healthy controls (n=2) and stimulated for 30 minutes (ADP or TRAP-6) to promote cytokine release. Both the supernatants and platelet lysates were then loaded on CodePlex chips and analyzed. Results: The methodology of bulk proteomic measurements has previously been validated in a variety of biofluids such as serum/plasma, cerebrospinal fluid, tracheal washes, and cell culture supernatants. Freshly isolated platelets activated by TRAP6 generally released more cytokines than those activated by ADP stimulation in both healthy controls and disease samples. Interestingly, platelet releasates in supernatants from TNBC patients demonstrated increased pro-tumor IL-8 and IL-9, and reduced antitumor IFN-g compared to healthy controls. Higher levels of IL-8 and IL-9 and minimal IFN-g were detected at similar activation concentrations, in platelet lysates from both healthy and TNBC platelets. This suggests that TNBC may alter platelet content and/or activation. Increased numbers are being performed to validate these initial results. Conclusions: From this small pilot study, multiplexing quantitative proteomic analysis is potentially useful in detecting differential cytokine profile in platelet releasates and lysate contents between TNBC patients and healthy controls. Quantifying the platelet proteomes in cancer patients using high throughput proteomics may provide valuable insights to dissect cancer-platelet crosstalk and potential pathogenesis mechanisms.
Comprehensive genomic profiling: Insights into diagnostic value and treatment strategy.
Authors: Shiller Michelle , Zhang Haiying , Yin Lihui , Mukherjee Sandeep , Coldren Christopher , Mennel Robert Gary , Konduri Kartik , Wood David , Chandra Pranil
Published: June 2022

e15028

Background: The clinical application of next-generation sequencing (NGS) has continued to advance precision oncology by enabling the identification of biomarkers that may predict potential response to targeted therapy, yet the benefit of tissue-based NGS to patient care is not solely confined to this narrow application. Not uncommonly, NGS can reveal genomic characteristics of the tumor that may be inconsistent with initial pathology review and clinical presentation. When this occurs, these genomic insights along with other clinical and diagnostic findings may be utilized to reconsider the initial diagnosis and seek to explore alternative diagnostic explanations that may be more consistent with the genomic findings. Methods: Patient diagnoses and clinical data were reviewed and compared against NGS results to determine if the genomic profile was consistent with and supports the initial diagnosis. If the genomic profile of the tumor was found to be inconsistent with the initial diagnosis, a secondary review of the case was initiated. Out of a cohort of >2,500 patient cases, notable examples of cases were identified that highlight the impact of NGS findings on the diagnostic classification of the tumor. Genomic profiling was conducted utilizing PathGroup’s molecular pathology-directed tumor profiling solution, Endeavor, which is powered by the FDA-cleared PGDx elio tissue complete test. Results: Among the identified patient cases where initial pathological diagnosis was altered following review of NGS results, several examples include 1) a sarcoma case being re-classified as melanoma, 2) a lung lesion initially diagnosed as NSCLC that was metastatic basal cell carcinoma and 3) a cancer of unknown primary that was determined to be a cholangiocarcinoma. Treating oncologists were kept apprised of all diagnostic findings and modifications to either the initial diagnosis or to the tumor classification which led to an altered treatment strategy in each case. Conclusions: NGS can be broadly applied throughout the cancer care continuum, with a new perspective on its potential value diagnostically. In these cases, re-evaluation and subsequent re-classification led to treatment strategy shifts that are more specific to the patient’s tumor type. These findings provide critical real-world evidence that supports the value of broad genomic profiling in complex cancer cases, especially when the genomic findings are inconsistent with the initial diagnosis, or the diagnosis is unclear.
Identification of clinically actionable biomarkers via routine comprehensive genomic profiling across a large community health system.
Authors: Weerasinghe Roshanthi K. , Meng Ryan , Dowdell Alexa K. , Bapat Bela , Vita Ann , Schroeder Brock , Stein Alisha , Harold Lauren , Schmidt Mark , Chang Shu-Ching , Ward Thomas , Wagner Josiah , Piotrowski Stanley , Febbo Phillip G. , Bifulco Carlo Bruno , Piening Brian
Published: June 2022

e15035

Background: Precision therapies and immunotherapies have revolutionized cancer care, with novel genomic biomarker-associated therapies being introduced into clinical practice rapidly. We assessed the utility of comprehensive genomic profiling (CGP)-based testing for identifying biomarkers associated with approved therapies, and therapies in precision medicine basket clinical trials (CT) across a large cohort of advanced cancer patients in the Providence health system. Methods: Advanced cancer patients were tested utilizing the Providence CGP workflow between 2019-2021. Clinical actionability was assessed for CGP and compared with results from an in silico 50-gene panel based on a previously utilized lab-developed test at Providence. Clinical actionability was assessed based on OncoKB and alterations were assigned as: FDA recognized (Level 1), standard of care (Level 2), FDA approved/investigational drug in another indication or having compelling clinical evidence (Level 3). CT matching was assessed based on enrollment criteria for ASCO-TAPUR, NCI-MATCH and My Pathway CTs at time of testing. Pooled electronic medical record and genomic data were curated and standardized. Results: Of the 3,218 advanced cancer patients tested with CGP, 52% were female, 80% were white, and median age was 67 years. Across 31 tumor types, the most commonly tested were lung (26%), bowel/colon (16%), and breast (9%). Overall, 48% of patients tested with CGP harbored at least one actionable biomarker (OncoKB Levels1/2/3). Clinical actionability was significantly higher in the CGP cohort compared to the in silico cohort based on presence of at least one Level 1 biomarker (45% vs. 19%, p < 0.001). CGP cohort had higher proportion of patients with multiple/co-occurring Level 1 biomarkers compared to in silico cohort (20% vs. 9%, p < 0.001). Of the most prevalent tumor types, 57% lung, 94% bowel/colon, and 37% breast had Level 1 alterations with CGP testing. Notably, 49% of CGP cohort vs. 23% in silico cohort (p < 0.001) harbored a biomarker matching to one or more arms of the three basket CTs. Conclusions: CGP and small panel testing can both identify patients eligible for approved therapies and/or basket CTs with CGP having significantly higher clinical actionability and CT eligibility. We expect value of CGP to increase as biomarker actionability transforms clinical practice.
Utility and timeliness of somatic genetic testing for patients enrolled in the molecular screening and therapeutics (MoST) study at Princess Alexandra Hospital (PAH).
Authors: Watson Benjamin , Arneil Melissa , Leo Paul , O'Byrne Kenneth John , Atkinson Victoria
Published: June 2022

e15039

Background: Next generation sequencing (NGS) technologies are increasingly employed to deliver optimal precision therapy for patients with cancer. The Molecular Screening and Therapeutics (MoST) study led by Prof David Thomas, Garvan Institute, Sydney, Australia, was established to identify patients for enrolment into clinical trials and for targeted or immune therapies not routinely indicated for their illness, specifically focusing on those with rare or neglected malignancies or with more common malignancies that had completed standard therapy. Methods: 111 patients were enrolled at the PAH between 1/5/2020 and 31/5/2021. Of these the results of the first 100 patients with complete medical records and sufficient tissue for NGS analysis are reported. Sources included electronic medical record, cancer state-wide database and the Molecular Tumor Board reports. The NGS Illumina TSO500 platform was employed for genetic testing. Determining utility of the results/reports included analyzing the proportion of patients with clinically relevant mutations detected, treatment recommendations, clinical trial recommendations and clinical trial enrolments. The timeframe from enrolment to results/recommendations conveyed to the patient was recorded. Demographic data was collected at enrolment. The final date of data collection was 31/12/2021, ensuring a minimum of six months follow-up. Local ethical regulations were complied with. Results: The study included 51 men and 49 women, ECOG 0-1, median age 57 years (range 21 – 84 years). Gastrointestinal malignancies were the most common, 31 patients, followed by sarcoma, 16, and breast cancer, 14. At enrolment, 64 patients were receiving chemotherapy, with the lines of treatments received ranging from 0 – 7, mean of 2.6. Mutations were detected in the following number of specimens: Tier 1A - 21, Tier 2C - 27, Tier 2D - 69 and Tier 3 - 69. High tumor mutational burden, defined as >10Muts/Mb, was present in 12 specimens and potential germline mutations were detected in 22 patients. There were 34 treatment recommendations and 27 clinical trial recommendations with 14 patients enrolled in clinical trials. The mean timeframe from enrolment to the result of testing being conveyed to the patient was 85.1 days. The overall median survival was 9.72 months. Conclusions: Results demonstrate that somatic genetic testing generates clinical trial, treatment and genetics health recommendations for a significant number of patients with 1:7 being recruited into clinical trials. Median length of time between recruitment and delivery of results to the patient was almost 3 months, which will improve through streamlining of clinical and logistical processes and advances in testing technologies, ensuring timely results for clinicians and their patients.
Comprehensive genomic and clinical analysis of cancer of unknown primary site in Chinese patients.
Authors: Xue Hongsheng , Yuan Shaohua , Chen Hui , Zhang Yuman , Wang Aodi , Mei Lei , Wang Liwei , Dong Xiaowei , Wang Kai
Published: June 2022

e15071

Background: Cancer of unknown primary (CUP) comprises 2-5% of all diagnosed cancers worldwide and is one of most common cause of death. Deep understanding of CUP plays an imported role in improving the disease diagnoses and finding the primary sites. In this study, our data revealed the genomic and clinical features of CUP in Chinese patients. Methods: FFPE samples and matched peripheral blood were collected for NGS based 450 cancer genes panel assay. Somatic variants were analyzed following CAP/CLIA-certificated workflows, including Single Nucleotide Variant (SNV), Copy Number Variation (CNV), large insertion and deletions (Lindel) and gene rearrangements. MSI status and TMB were also acquired by an NGS algorithm in house. PD-L1 status was analyzed by IHC. Results: Of the 264 CUP patients, 54.2% were male and median age was 61 years old (range, 2-88 years old). The median value of TMB was 4.6 muts/Mb (range, 0-61.2). Only 1 patient was found MSI-H status with the TMB value of 61.2 muts/Mb. In addition, 23.9% and 28.4% of the CUP patients presented PDL1 positive (> 1%) and PDL1 negative respectively, with others unavailable. In the patients of available stage status, they were all advanced stage (stage ≥ III). Top metastatic sites were lymphaden (17.8%), liver(15.9%) and bone (15.5%). TP53 was the most common mutated gene (62.1%), followed by KRAS (22.3%), CDKN2A (15.9%), TERT (10.2%), EGFR (9.8%) and PIK3CA (9.8%). In the alterations of KRAS, G12D, G12V and G12C were occupied 32.2%, 28.8% and 8.4% respectively. Among the alterations of EGFR, 38.5% were L858R and 19.2% were 19del. Besides, amplification of MYC (4.9%) and 11q13 (5.3%) obviously appeared in our data. Fusion/Rearrangements of ALK and ROS1 accounted for 0.8% and 1.1% respectively . The gene alterations of tyrosine kinase were found in 48.4% of CUP patients such as ALK, BRAF, EGFR, FGFR1/2/3/4, RET, ROS1 and so on. PI3K−Akt signaling pathway and MAPK signaling pathway were the most significantly pathways (fdr < 0.001) enriched in our data. A CUP patient with positive PDL1 and high TMB achieved a 9-month PFS after treatment of TP chemotherapy and immunotherapy. Conclusions: In this study, we revealed comprehensive genomic and clinical features of cancer of unknown primary site in Chinese patients. It shows promise to identify the origin anatomic site of tumor while targeted therapeutic approaches to improve outcomes.
D3S-001, a highly potent, selective, and differentiated covalent inhibitor of KRAS G12C: Human dose prediction and first‐in‐human (FIH) trial design.
Authors: Lu Jingtao , Zhang Jing , Zheng Zhiqiang , Chen Cheng , Wang Jia , Chen Janet , Lu Jiang , Rui Haopeng , Wang Allison , Chen Zhi Jian
Published: June 2022

e15087

Background: Effective inhibition of G12C mutated KRAS is believed to be critical for anti-tumor efficacy in KRAS-driven cancers. D3S-001 is a potent and highly differentiated KRAS G12C inhibitor, which demonstrates rapid and near complete target inhibition and strong anti-tumor activity in preclinical cell line and animal models [Preclinical characterization of D3S-001, a highly potent, selective, and differentiated covalent inhibitor of KRAS G12C, ASCO 2022 Abstract #378099]. The current study utilizes pharmacokinetic (PK) modeling to predict the extent of KRAS G12C target inhibition at the proposed clinical dose range. Methods: Allometric scaling and non-linear fixed effect modeling were used to predict human PK profiles from DMPK data in animals. Human in vivo target inhibition was calculated based on human PK predictions, free drug fraction and results from in vitro target engagement assay. A First-in-Human (FIH) study was designed to investigate D3S-001 monotherapy in subjects with advanced solid tumors having a KRAS G12C mutation. Six dose escalation cohorts will be investigated, starting from 50mg QD. Results: Based on a GLP toxicology study in dogs, the highest non-severely toxic dose (HNSTD) was determined to be 20 mg/kg/day. Per ICH S9, a 20 mg/kg/day dose in dog supports a FIH starting dose of 110 mg. To ensure an additional safety margin, a lower starting dose of 50 mg was proposed. At 50 mg QD, the predicted human exposure (Cmax 60 nM, Caverage 49 nM, Ctrough 31 nM) is expected to achieve ̃70% target inhibition at 2 hours after dosing. In NCI-H358 mouse xenograft model, this exposure is associated with 94% tumor growth inhibition (TGI). Safety margins based on Cmax and AUC comparing to dog HNSTD are 17-fold and 9-fold, respectively. At 100 mg QD, the predicted human exposure (Cmax 120 nM, Caverage 98 nM, Ctrough 63 nM) is expected to achieve ̃95% target inhibition. This exposure is associated with tumor regression of 72% in the NCI-H358 mouse xenograft model. At dose levels higher than 100 mg QD, predicted human exposures are expected to consistently achieve >95% target inhibition starting 1 hour after dosing. These exposures are associated with deeper levels of tumor regression of 97%. Moreover, even at 400 mg QD, predicted human plasma concentrations are still below dog plasma concentration of 443 nM, Caverage at HNSTD. Conclusions: D3S-001 is predicted to achieve rapid and consistently efficacious KRAS G12C target inhibition in humans at proposed clinical dose range. This high degree of KRAS G12C inhibition over the dosing interval may translate into greater clinical benefit to patients with KRAS G12C mutations comparing with other clinical-stage KRAS G12C inhibitors. Clinical data from the FIH study will be evaluated and compared to preclinical predictions.
Selective inhibition of METTL3 enhanced anticancer activity via targeting the c-Myc pathway.
Authors: Arumugam Paramasivam , Jayaseelan Vijayashree Priyadharsini
Published: June 2022

e15089

Background: Methyltransferase-like 3 (METTL3) is a master regulator enzyme in the N6-methyladenosine (m6A) methyltransferase system, that not only plays a crucial role in cancer but has become a promising therapeutic target for the same. This study was aimed to discover molecular mechanisms underlying the potential anticancer effects of a novel and selective METTL3 inhibitor named STM2457 against oral squamous cell carcinoma (OSCC). Methods: OSCC patient-derived organoids (PDOs) and the corresponding 2D cell lines were established from the patients who have increased expression of METTL3 and c-Myc. The pharmacological activity of STM2457 was extensively studied with organoids and primary OSCC cells. Cell proliferation, wound healing and colony formation assays were used to detect STM2457 anticancer activity in vitro. Patient-Derived tumor Xenograft (PDX) model of OSCC was used to detect STM2457 anticancer activity in vivo. m6A level of mRNA was measured by an m6A-RNA methylation quantification kit. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to screen the target genes of METTL3. RNA stability assay was used to detect the half-lives of METTL3 target genes. Real-time quantitative PCR was used for gene expression and western blot was used for protein expression analysis. Results: We found that STM2457 treatment exerted potential anticancer activity in PDOs and primary OSCC cells. MeRIP-seq revealed that c-Myc was the downstream gene of METTL3. Functionally, knockdown or pharmacological inhibition of METTL3 by STM2457 reduced stability and expression of c-Myc. This eventually, results in significant attenuation of migration, invasion, tumorsphere formation, and colony formation abilities of OSCC cells. Moreover, STM2457-treated OSCC cells showed reduced tumorigenic activity in vivo. Furthermore, STM2457 treatment reduced m6A level in PDOs and OSCC cells by blocking METTL3 activity thereby elucidating the importance of personalized approach for effective cancer treatment. Conclusions: Altogether, the revelation of anticancer effect of STM2457 exerted by blocking of METTL3-c-Myc signaling pathway opens novel avenues into the field of epitranscriptomics.
FAT4 mutation as a potential predictive biomarker for immunotherapy combined with anti-angiogenic therapy in MSS metastatic colorectal cancer.
Authors: Chen Mifen , Zhang Qi , Chen Hui , Wang Zhenghang , Xu Ting , QI Changsong , Chen Shiqing , Zhao Xiaochen , Bai Yuezong , Peng Zhi , Wang Xicheng , Zhang Xiaotian , Gong Jifang , Shen Lin , Li Jian
Published: June 2022

e15504

Background: Microsatellite stable (MSS) metastatic colorectal cancer (CRC) lacks effective treatments and has a poor prognosis. The aim of this study was to identify patients who could benefit from immunotherapy combined with anti-angiogenic therapy. Exploration of predictive biomarkers could help to maximize the clinical benefits. Methods: In total, FFPE tissues samples before immunotherapy combined with anti-angiogenic therapy of 21 patients were successfully tested for tumor microenvironments (TMEs) by multiple immunofluorescence, of which 11 of them were successfully detected by 733-gene NGS panel in a CLIA-certified laboratory. The correlation between gene variations and clinical durable benefit (DCB: PR, or SD≥6 months), PFS and TMEs were analyzed by Fisher's test, K-M survival curve analysis and Mann Whitney analysis respectively. Results: Significant difference was detected between FAT4 mutation (FAT4-MUT) and FAT4 wildtype (FAT4-WT) regarding DCB (100%, 4/4 vs 17%, 1/7, P = 0.0152) and progress-free survival (median PFS, 13.8 months vs 2.8 months, LogRank P = 0.003). There was no significant difference in TMB level between DCB and NDB (SD＜6 months, or PD) groups (12 mut/Mb vs 6 mut/Mb, P = 0.0823) or between FAT4-MUT and FAT4-WT (11 mut/Mb vs 6 mut/Mb, P = 0.3697). TMEs analyses revealed that the CD3+CD4+ T cell proportion was tended to be higher in FAT4-MUT (0.7% vs 0.3%, P = 0.054). Further TIMER2.0 data showed FAT4-MUT was significantly associated with higher Immune infiltration of four immune cells, including CD4+ T cell in both colon and rectal adenocarcinoma, CD8+ central memory T cell, B cell, and Macrophage in colon adenocarcinoma. Conclusions: Our findings indicated that FAT4 mutation serves as a potential novel biomarker correlated with a better response to immunotherapy combined with anti-angiogenic therapy in MSS metastatic CRC, which may be related to the activation of CD4 T cell infiltration. However, these need to be validated by further cohort expansion.
Recurrence risk stratification model for patients with stage I-III colorectal cancer based on clinicopathological and postoperative ctDNA predictors.
Authors: Gu Jin , Lei Fuming , Wang Xiaodong , Chen Hui , Huang Wensheng , He Xiaomang , Hong Yuming , Zeng Qingmin , Wang Yanzhao , Gao Qingkun , Yuan Zheping , Niu Pengfei , Huang Dandan , Gao Zhaoya , Ding Changming , Zhai Zhichao , An Ke , Chen Shiqing , Zhao Xiaochen , Bai Yuezong
Published: June 2022

e15511

Background: The aim of this study was to propose a new kind of recurrence risk classification and further establish a prognostic model for resected stage I-III colorectal cancer (CRC). Methods: From 2017 to 2020, 142 patients diagnosed with stage I-III CRC at Peking University Shougang Hospital were recruited for this study. Tissues and paired white blood cells were analyzed with a 733-gene NGS panel, and peripheral plasma obtained 7-10 days after surgery was analyzed with a 127-gene ultra-deep target panel in a CLIA-certified laboratory. The relationship between the postoperative ctDNA status, clinicopathological features and recurrence-free survival (RFS) was identified by log-rank test and Cox regression analysis. Results: In total, 108 patients successfully completed both tissue and postoperative plasma NGS tests, of which 17 patients were postoperatively positive for ctDNA (tumor-informed, ≥1 somatic mutation). Postoperative ctDNA positivity was independently associated with poorer RFS (HR = 8.4, P < 0.0001). Postoperative recurrence rates were significantly higher in ctDNA-positive patients than ctDNA-negative patients (76.5% vs 16.5%, P < 0.0001). Univariate analysis showed that, in addition to ctDNA status, stage, vascular invasion, neural invasion, and preoperative CEA were all significantly associated with worse RFS (P < 0.05). Furthermore, in a COX regression model, the contribution of these clinicopathological factors to RFS has been adjusted. The model showed good discrimination [the concordance index (c-index): 0.811] of recurrence. Clinically high-risk groups according to clinicopathological risk model had significantly poorer RFS than low-risk groups (HR = 10.6, P < 0.001). In the clinicopathological high-risk group, ctDNA-positive patients can still further differentiate the higher risk of recurrence (HR = 3.7, P = 0.0012). There were similar trends in the clinicopathological low-risk group (HR = 6.1, P = 0.066). Combining the clinicopathological model and ctDNA, patients with either clinicopathological high-risk or ctDNA-positive had a significantly poorer RFS, compared with both clinicopathological low-risk and ctDNA-negative (HR = 12.9, P < 0.0001). Conclusions: Postoperative ctDNA can independently predict the risk of recurrence in stage I-III CRC. Combining clinicopathological factors and ctDNA showed superiority for recurrence risk stratification over either alone. This recurrence risk stratification model may serve as a useful clinical tool to help clinicians determine individualized treatment plans for stage I-III CRC patients. However, the model still needs further external cohort validation.
Racial parity in rectal cancer treatment and outcomes within an integrated healthcare system.
Authors: Kwak Hyunjee V. , Hsu Diana S. , Chae Andrew , Douaiher Jeffrey , Chang Ching-Kuo
Published: June 2022

e15538

Background: This study evaluates survival outcomes of rectal adenocarcinoma patients treated at a large, integrated health system and whether there are differences in survival based on race. Methods: We conducted a retrospective study of patients at Kaiser Permanente Northern California (KPNC) who were treated between 2010-2019. Self-reported racial ethnic groups included Caucasian, African American, Hispanic, Asian, and Other. Kaplan Meier and Cox regression analyses were used to evaluate differences in race, age, stage, and treatment utilization in relation to overall survival. Results: A total of 3,589 patients were diagnosed with rectal adenocarcinoma from 2010-2019. There was a significant difference between race groups in stage at the time of diagnosis (p < .001) with more African Americans having localized disease (58.4%) compared to Hispanics (45.5%). Overall survival was longest for African American at 70.9 months but shortest for Hispanic at 60.6 months (p = 0.007). Hispanic patients were more likely to be male, younger, and with nodal disease. Conclusions: This study identified racial parity in survival outcomes for rectal cancer patients who were treated at a large, integrated healthcare system where patients have equal access to care. Improvement in outreach and screening should be tailored to the ethnic groups at higher risk for earlier age and more advanced disease at presentation.
A single center phase 2 study of anti-PD-1 antibody plus bevacizumab and FOLFIRI as second-line treatment for patients with MSI-H metastatic colorectal cancer.
Authors: Li Hongli , Ning Tao , Zhang Le , Ge Shaohua , Yang Yuchong , Bai Ming , Wang Xia , Ji Zhi , Liu Rui , Deng Ting , Ba Yi
Published: June 2022

e15541

Background: The therapeutic efficacy of second-line chemotherapy for metastatic colorectal cancer (mCRC) is low. Immunotherapy is suitable for MSI-H mCRC, but the efficacy of single-drug immunotherapy is still unsatisfactory. We investigated to combine immunotherapy with bevacizumab and FOLFIRI as second-line treatment for these patients. Methods: This single center exploratory phase 2 study enrolled adults patient with histologically confirmed metastatic colorecal adenocarcinoma, who were failure of oxaliplatin-based chemotherapy as first-line therapy. Patients receive FOLFIRI (iritecan 180mg/m2, leucovorin 400mg/m2, fluorouracil 400mg/m2 bolus, fluorouracil 2400mg/m2 46-48 hours), anti-PD-1 antibody (Nivolumab 240mg, or Pembromab 200mg, or Terriprizumab 240mg), and bevacizumab (5mg/kg). Maintenance therapy was allowed using PD-1, bevacizumab and/or fluorouracil. An-PD-1 antibody is given for up to 24 months. Results: Between November 29,2018 and January 15, 2021, a tolal of 8 patients were enrolled in our study. There were 3 femles and 5 males, and the median age was 39.5 years old. Among 8 patients who were evaluated, complete resonse (CR) was obtained in 3 cases, partial response (PR) was observed in 3 cases, and stable disease (SD) in 2 cases. Objective response rate was 75%, and disease control rate was 100%. The median PFS and the median overal survival have not yet been reached. The most common adverse events (AE) were alopecia (87.5%), nausea (75%), vomit (50%), hypothyroidism (50%), leukopenia (37.5%), hypertension (25%) and proteinuria (25%). Most of the AEs were grade 1 or 2, and the most common grade 3 or 4 treatment-related AE was hypertension (25%). Conclusions: Anti-PD-1 antibody plus bevacizumab and FOLFIRI demonstrated promising activity as second-line treatment for patients with MSI-H metastatic colorectal cancer. Clinical trial information: NCT05035381.
Immune landscape of colorectal cancer lung metastasis.
Authors: Lee Song-Yi , An Minae , Lee Jeeyun
Published: June 2022

e15542

Background: Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related death worldwide. What makes CRC treatment a challenge is synchronous or metachronous recurrence at distant organs; metastasis. Approximately half of CRC patients develop metastases in the course of the disease and the most prevalent metastatic site is liver, followed by lung and peritoneum. A 5-year survival rate metastatic CRC is much poorer than that of patients with regional and localized CRC. Methods: From 2019 to 2020, 9 metastatic CRC patients who had recurrence to lung oligo-metastases were enrolled. These patients were eligible for lung metastatectomy of curative intent. The surgically resected lung metastases were collected and whole exome sequencing/RNA sequencing,10x chromium single cell RNA sequencing analysis were performed. The purpose of this study was to uncover distinctive tumor microrenvironment (TME) of the lung metastases from CRC, we compared these results with those from public available primary CRC data. Results: We successfully analyzed all 9 metastatic lung samples. Compared to primary CRC, we found that lung metastasis had more immune-suppressive TMEs, represented by downregulation of TCR signaling, innate/adaptive immune system and antigen presentation. In addition, there were higher expression levels of immune checkpoint molecules, such as PD-1, LAG-3 and TIGIT in metastatic lung samples when compared to primary colon cancer public database. Macrophage polarization of lung metastases toward alternatively activated M2 subset, rather than classically activated M1 subset, resulting in low M1/M2 ratio, was also thought to attribute to immune suppressive environments of the lung metastases and successful colonization of primary tumors. Conclusions: This study identified different TMEs of lung metastasis specimens from primary CRCs. Our study underscores the importance of the tumor microenvironment and the anatomic location of the tumor cells for optimized immunotherapeutic strategies.
Impact of perioperative chemotherapy on survival outcome of advanced colorectal cancer patients treated with cytoreduction and hyperthermic intraperitoneal chemotherapy: A retrospective study.
Authors: Elsamany Shereef Ahmed , Alzahrani Saleh , Alzahrani Abdulaziz , Bukhari Ammar , Arbaein Amr , Hassanin Fayza , Elkhatib Hani
Published: June 2022

e15570

Background: Colorectal cancer (CRC) with peritoneal carcinomatosis (PC) is generally associated with poor prognosis. The present study aims to assess potential value of perioperative systemic chemotherapy in patients treated with cytoreductive surgery with HIPEC (CRS/HIPEC) in a single institute in Saudi Arabia. Methods: We included CRC with PC who underwent CRS/ HIPEC from January 2012 till December 2019. Different clinicopathological, treatment-related factors and dates of relapse/death, were retrospectively assessed. We checked the distribution of these factors in addition to survival outcome in those who received perioperative chemotherapy vs. none. Results: We recruited 127 eligible patients (79 patients [62.2%] received systemic chemotherapy). Patients with no perioperative chemotherapy were more likely to have grade 1 tumours (62.5% vs. 25.3%, p < 0.0001), mucinous adenocarcinoma (41.7% vs. 12.7%, p = 0.002), normal CEA ≤5 ng/dl (70.2% vs. 47.4%, p = 0.016) and peritoneal-only metastasis (66.7% vs. 45.6%, p = 0.021). Median PFS and OS were 34 and 62.2 months, respectively. Patients with no perioperative systemic chemotherapy had significantly better PFS and OS (median PFS: not reached vs. 19 months, HR = 0.29, 95% CI = 0.15-0.59, p < 0.0001, OS :HR = 4.3, 95% CI 1.3-14.3, p = 0.009). After adjustment of different prognostic factors, there was no significance difference in OS between the two groups (HR = 3.8, 95% CI = 0.98-14.71, p = 0.053), while PFS was still significantly better in the no chemotherapy group (HR = 2.52, 95% CI = 1.13-5.63, p = 0.024). Conclusions: CRS/HIPEC provided favourable survival outcome in our study cohort especially in patients with more favourable prognostic features. No survival benefit with perioperative chemotherapy could be demonstrated.
Toripalimab with Fruquintinib as the third-line treatment for refractory advanced metastatic colorectal cancer: Results of a single-arm, single-center, prospective, phase II clinical study.
Authors: Ma Shoucheng , Chen Rui , Hou Xiaoming , Duan Lin , Li Chunmei , Yang Tianning , Ling Xiaoling , Zhao Da
Published: June 2022

e15573

Background: The most effective treatment of immune checkpoint inhibitors (ICIs) is restricted in microsatellite instability (MSI-H) subsets of advanced colorectal cancer, but MSI-H only accounts for 4-5% among them. Currently, Fruquintinib/ Regorafenib is the standard third-line treatment for metastatic colorectal cancer (mCRC) with microsatellite stable (MSS), which efficacy remains limited in pre-clinical trials. According to the published literature, ICIs has little efficacy in the treatment of refractory advanced mCRC patients with MSS. However, there may be a good synergistic mechanism in the combination of ICIs and anti-VEGFR drugs, which can improve the tumor microenvironment (TME). Our study aimed to evaluate the efficacy and safety of Fruquintinib plus Toripalimab as third-line treatment for refractory advanced mCRC. Methods: This was a single-arm, single-center, phase II clinical trial with 30 patients. Pts received toripalimab (240mg, i.v., Q3W), combined with Fruquintinib (5mg, p.o., 3 weeks on/ 1 week off) until the disease progresses/unacceptable toxicity or receiving the above two drugs as maintenance treatment. The primary endpoint was objective response rate (ORR); the secondary endpoints were disease control rate (DCR), 1-year progression-free survival (PFS) rate, overall survival (OS) and safety. Results: As of Feb 5, 2022, 24 mCRC pts (female: 29.2%, median age: 52.1 years) with ECOG PS ≤ 2 who failed to at least 2 previous lines of therapy containing fluoropyrimidine, oxaliplatin or irinotecan combined with Bevacizumab or Cetuximab were enrolled. The ORR was 16.7% (95% CI：59.7%-94.8%). The DCR was 54.1%, including 4 patients with PR and 9 patients with SD, respectively. 16 patients were alive and the study treatments for 6 patients were still ongoing. Median PFS was 6.0 months (95% CI：3.511-12.489), the 1-year PFS rate was 18%; median OS was 8.0 months (95% CI：1.452-10.548). Overall, 24 pts were enrolled for safety analysis, The most frequent treatment related adverse events were fatigue (50%), hepatocyte dysfunction (36.3%), hypertension (29.1%) and abdominal pain (27.0%). 6 patients (25%) experienced grade 3/4 TRAE (including hypertension, liver enzyme elevation, and immune-associated pneumonia). No treatment-related death was reported. TRAEs leading to either Fruquintinib or Toripalimab discontinuation occurred in 3 (12.5%) pts each. Conclusions: Fruquintinib plus Toripalimab showed certain efficacy and favorable safety profile in refractory advanced mCRC with MSS. It may provide a new choice for mCRC patients who are receiving third-line treatment. The results supported ongoing combined treatment in mCRC patients with MSS and more data will being updated subsequently. Clinical trial information: ChiCTR2000028965.