bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel orally bioavailable small molecular ENPP1 inhibitor (OC-1) for cancer immunotherapy.
Authors: Chen Jiyun , Pujala Brahmam , Gupta Ashu , Ansaria Amantullah , Khana Farha , Lee Elbert , Chakravarty Sarvajit 
Published: June 2023

e15136 Background: Ectonucleotide pyrophosphatase/phosphodiesterase I (ENPP1) is a type II transmembrane glycoprotein with nucleotide pyrophosphatase and phosphodiesterase enzymatic activities. Inhibiting ENPP1 activity has emerged as an attractive approach in cancer immunotherapy, based on two distinct mechanisms. One mechanism is the stabilization of cyclic GMP–AMP (2’3’-cGAMP), which binds to stimulator of IFN genes (STING) and functions as an endogenous second messenger to activate the innate immune system; the other is the lowering of adenosine concentrations in the tumor microenvironment. ENPP1 inhibitors have shown promising monotherapy activity and synergy with various targeted therapies in preclinical models. Methods: OC-1 was characterized, for activity and selectivity, in the following in vitro assays: a luminescence-based enzymatic assay; cell proliferation assays; selectivity assays against 15 phosphodiesterases (PDE) based on inhibition of enzymatic activity; and a cytokine release assay in human THP cells and mouse splenocytes looking at changes in IFN-β/CXCL10. Oral bioavailability of OC-1 in mice and rats was studied following oral gavage. Plasma exposures were quantified using standard LC/MS/MS methods. In vivo tumor growth inhibition (TGI) of OC-1 was evaluated in syngeneic mouse tumor models (CT26 and MC38), as monotherapy and in combination with an anti-PD1 antibody. OC-1 was dosed orally in all in-vivo models. Results: We have discovered a novel small molecule inhibitor of ENPP1, OC-1, with a Ki value less than 10 nM in an ENPP1 enzymatic assay. Increase in gene expression of IFN-β and CXCL10/IP10 was observed in OC-1-treated THP1 cells. No inhibition in cell proliferation in various cancer lines was seen up to the highest concentration tested (30 µM). OC-1 was also selective against 15 PDEs with IC50 > 30 µM. The mean oral bioavailability of OC-1 was 72% and 63% in mice and rats, respectively. OC-1 showed single agent activity (20 – 40% TGI) and combination activity of approximately 75% TGI when it was combined with an anti-PD-1 antibody in in vivo efficacy studies with no impact on body weight. Conclusions: In summary, OC-1 is an orally bioavailable ENPP1 inhibitor with promising anti-tumor activity in preclinical models. Its physicochemical properties make it a suitable candidate for clinical investigation.
Clinical and genomic characteristics between DDR germline and somatic mutations in pan-cancer.
Authors: Li Yanchun , Sun Tingting , Zhang Qin , Qi Chuang 
Published: June 2023

e15139 Background: The defects DNA-damage repair (DDR) genes would drive tumor formation and are associated with increased genomic instability and tumor mutational burden (TMB) in cancer. Although, alterations of DDR genes are common in tumor, the differences between the germline and somatic alterations are poorly characterized. Methods: The DNA sequencing data of 540 genes from 6174 pan-cancer patients were retrospectively collected and 276 DDR genes were analyzed. The variations were annotated as pathogenic (P), likely pathogenic (LP), and nonpathogenic (NP) according to ACMG (American College of Medical Genetics) guideline. The patients were divided into 3 groups: DDR-germline (P&LP germline variants, N = 766), DDR-somatic group (only P&LP somatic variants, N = 2923) and non-DDR group (NP variants, N = 2485). Results: In pan-cancer, 12.41% patients have germline DDR gene mutations, of which tumors with high germline mutation frequency include ovarian cancer (27/102, 26.47%), glioma (22/136, 16.18%), breast cancer (25/159, 15.72%), genitourinary cancer (17/114, 14.91%), biliary tract cancer (42/284, 14.79%), pancreatic cancer (28/193, 14.51%), colorectal cancer (95/727, 13.07%), head-neck tumors (11/85, 12.94%) and esophagus cancer (16/124, 12.90%). Meanwhile, 47.34% patients have somatic DDR gene mutations, of which tumors with high somatic mutation frequency include esophagus cancer (89/124, 71.77%), colorectal cancer (488/727, 67.13%), endometrial cancer (49/73, 67.12%), head-neck tumors (50/85, 58.82%), pancreatic cancer (111/193, 57.51%), gastric carcinoma (233/415, 56.14%), ovarian cancer (53/102, 51.96%) and biliary tract cancer (138/284, 48.59%). The most commonly germline alterations were found in TP53 (33%), PTEN (14%) and BRCA2 (14%), while in the somatic mutations, TP53 (52%) showed the highest frequency, PTEN (9%) and MSH3 (8%) followed. In pairwise comparisons of the three groups’ actionable mutations, DDR-somatic group was more likely to have alterations in TP53 (OR = 5.68), AKT3 (OR = 5.81) and APC (OR = 1.42) compared with DDR-germline group. Taken non-DDR group as reference, mutations in TP53 (OR = 5.09), PTEN (OR = 7.65), BRCA2 (OR = 5.32) were more common in DDR-germline group, but TP53 (OR = 28.90), PTEN (OR = 7.73), APC (OR = 2.68) in DDR-somatic group. The tumor mutational burden (TMB) was statistically different among the three groups (p < 2.22e−16). The DDR-somatic group exhibits the highest median TMB (5.68) compared with 1.42 in DDR-germline and 2.13 in non-DDR group. Conclusions: The differences in the mutation profile between the DDR-germline and DDR-somatic groups and the distinct actionable genes may indicate the different target-therapy choices. Besides, DDR-somatic group exhibited the highest TMB, which might indicate patients with somatic DDR alterations may better benefit from the immunotherapy.
Clinical characterization of MYC family proto-oncogene amplification in solid tumors from Chinese patients.
Authors: Liu Zhiliang , Han Tiantian , Kong Rongrong , Guo Didi , Wang Mengjuan , Dong Yuwei , Chen Siqi , Fan Jiawen , Deng Wanglong , Ding Ran , Bu Fanfeng 
Published: June 2023

e15140 Background: The dysregulation of the MYC family oncogenes ( c-MYC, MYCN and MYCL) play critical roles in tumorigenesis, prognosis and immune escape. MYC inactivation can result in sustained tumour regression and many therapeutic agents that directly target MYC are under development. MYC signaling is associated with tumor cell PD-L1, overall immune cell infiltration. Herein, we explore MYC family proto-oncogene amplification profiles and clinical characterization in chinese solid tumors. Methods: This research comprehensively characterized gene mutations by next-generation sequencing (NGS) in 23990 chinese solid tumors tissues to reveal the prevalence of MYC family proto-oncogene amplification(MYC AMP) and the association with Tumor mutational burden(TMB) and microsatellite instability(MSI). Results: The prevalence of MYC AMP (copy number, CN≥5) in the cohort was 2.1% (504/23,990), in which ovarian cancer (7.6%, 22/289) showed the highest prevalence, followed by breast cancer (6.1%, 26/429), esophagus cancer (5.9%, 17/287). Only one glioma patient(pt) carried co-amplification of MYCN and c-MYC. In 504 MYC AMP pts, c-MYC AMP accounted for 93.7%(472/504), MYCN and MYCL AMP accounted for 6.5%(33/504) in total. The CN was significantly higher in MYCN and MYCL AMP pts than c-MYC AMP pts (22.9 vs 7.6, p < 0.0001). MSI-H showed a lower detection rate in MYC AMP pts other than Non-MYC AMP pts (0% vs 1.2%, p < 0.05). The proportion of TMB-L in MYC AMP pts was similar to Non-MYC AMP pts (90.9% vs. 90.1%, p > 0.05). Conclusions: In totally, 2.1% of chinese solid tumor pts had MYC high level AMP, mainly c-MYC Amp. The CN was higer in MYCN/ MYCL AMP pts than c-MYC AMP pts. In addition, MYC AMP pts tended to have MSS and TMB-L, suggesting that MYC may be a novel target for tumor immunotherapy. MYC inhibitor combines with immunotherapy may be an important direction for the treatment of MYC AMP pts.
Impact of overfixation on actionable biomarkers and checkpoint inhibitor (CKI) targets with immunohistochemistry (IHC) in a patient population with non-small cell lung cancer (NSCLC).
Authors: Gérus-Durand Marie , Gaspo Rania , Tsao Ming Sound , Jean Alexandra , Sallette Jérôme , Burrer Renaud , Finan Amanda 
Published: June 2023

e15144 Background: The treatment of patients with advanced NSCLC has become reliant on tissue specimens and biomarkers to help guide appropriate treatment options. Currently, there are numerous lung cancer biomarker-defined patient subgroups, with evidence showing that fixation conditions may alter their expression on FFPE specimens, but little evidence on the ensemble of targetable biomarkers and CKI targets. Methods: We assessed 30 adult patients with primary NSCLC tumors. 25 specimens were properly fixed with neutral 10% formalin using gentle agitation for 24-48 hours, whereas 5 specimens were over-fixed (52-108 hours). We examined expression of actionable and exploratory biomarkers ALK, ROS1, BRAF, EGFR, c-Met, panTRK, HER2 and MEK1. We also examined CKI targets such as PDL1, CD3/CD8, CD3/CD8/FoxP3, PD1, CD3/CD8/PD1. We performed IHC on all slides which were scored by a thoracic pathologist per standard clinical practice. Descriptive statistics were applied to further explore the impact of overfixation on IHC results. Results: Results are shown in the table below. Patients had an average age of 64, were mostly male (22/30) with adenocarcinoma histology (21/30). Specimens were collected in compliance with local rules and regulations and tumor staging was from IB-IV. For the 5 overfixed specimens, multiplex PD-L1 was less expressed when compared to the normally fixed specimens. We also surprisingly observed that cMet and HER2 had stronger expression with overfixed tissue. All other targets had no differences observed in this small patient population. Conclusions: Overfixation of NSCLC FFPE had little to no detrimental impact on most targetable biomarkers, except multiplex PD-L1. We also observed that cMet and HER2 had a slightly stronger expression level with overfixed tissue. As we do not have a reference of the overfixed samples fixed from 24-48 hrs, we cannot be assured that the differences in expression levels are not inherent to the sample itself and independent of fixation time. Additional tests of the same sample fixed over different periods will help to identify the true cause. We propose a consistent approach on tissue fixation time and process as the ensemble of preanalytical conditions is critical in ensuring proper biomarker characterization and validation with IHC. [Table: see text]
Use of CLIA accredited multi-omic platforms to correlate clinical significance of WES/WTS testing with functional protein/phosphoprotein drug target activity.
Authors: Elsey Rachel , Meissner Tobias , Mueller Claudius , Corgiat Brian , Davis Justin B , Hattum Crystal , Spanos William Charles , Starks David , Solomon Benjamin Maurice , Petricoin Emanuel , Lee John H. , Williams Casey B. 
Published: June 2023

e15150 Background: Targeted cancer therapies almost exclusively disrupt protein function and phosphorylation, but genomics-based biomarkers underpin the vast majority of oncology molecular profiling. The reverse phase protein array (RPPA) technology has been used in the clinical setting to identify potential drug targets and to monitor the effects of treatment on protein expression and phosphorylation. Here, we investigated the Theralink RPPA assay, a highly sensitive CAP/CLIA accredited protein/phosphoprotein profiling technology, across a pan-tumor cohort of 188 samples which had undergone whole exome sequencing and transcriptomics. Methods: Using the Theralink RPPA assay, 32 key protein and phosphoprotein cancer therapy targets were quantified from formalin-fixed, laser capture microdissected (LCM) tumor epithelium across a pan-tumor cohort of 188 cancer cases. All samples had concomitant CLIA-based whole exome and whole transcriptome analysis performed. Most of these tumors were head and neck cancer (34%), uterine cancer (23%), and ovarian/fallopian tube cancer (17%), with the remaining 26% made up of various cancer types, including skin, breast, lung, brain, and other cancers. Results: Of the pan-tumor cohort, 95% of cases had at least one actionable protein target identified, compared to 86% of cases with clinically relevant genomic alterations. Altered genes and Theralink RPPA assay protein targets were broadly classified into 10 biological pathways. The pathway most frequently identified as actionable via Theralink’s RPPA assay was HER-family protein signaling (85% of cases) with concurrent genomic alterations in HER-family genes found for 9% of cases. In contrast, mTOR signaling was found to be the most frequent clinically relevant genomically altered pathway (48% of cases). When using a clinical breast cancer reference for HER2 protein/phosphorylation levels that is guiding HER2-targeted therapy in the unamplified setting, actionable total and phospho-HER2 levels were found in 82% of the pan-tumor cases, overlapping with ERBB2 genomic alterations in 4% of cases. The gene found to be altered the most was TP53 (101 cases; 54%), which was not part of the targeted Theralink RPPA assay. Conclusions: Our data suggest that quantification of key cancer proteins and phosphoproteins using RPPA extend the identification of actionable drug targets beyond what was found with WES/WTS testing alone. Especially the quantification of total and phospho-HER2 identified a significant pan-tumor subpopulation that may benefit from HER2-targeted therapies, including trastuzumab deruxtecan (T-Dxd).
Multi-omics study of the genomic features and clinical characteristics of hepatic sarcomatoid carcinoma located at different sites.
Authors: Li Yanchun , Guo Wei , Mo Mengjun , Li Yangcan , He Qingqing , Lian Baofeng , Shi Xiaoliang , Lin Guomin , Pang Fei 
Published: June 2023

e15153 Background: Hepatic sarcomatoid carcinoma (HSC) is a rare and highly malignant tumor, which accounts for less than 2% of hepatic carcinoma. HSC can occur in the liver (Sarcomatoid hepatocellular carcinoma, SHCC) or in the intrahepatic bile duct (Sarcomatoid intrahepatic cholangiocarcinoma, SiCCA). We aimed to compare the clinical characteristics and genomic features between SHCC and SiCCA. Methods: In this study, we recruited 20 patients who were pathologically diagnosed with HSC from January 2018 to February 2021 in Hunan Provincial People’s Hospital. Whole exome sequencing and PD-L1 expression detected by immunohistochemistry were performed on the qualified tissue samples obtained from18 (14 with SHCC and 4 with SiCCA) of the enrolled patients. Tests were performed in OrigiMed, a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Fisher test was used to determine the association between two categorical variables, and P< 0.05 was considered statistically significant. Results: A total of 15 cases of SHCC and 5 cases of SiCCA were enrolled in this study, with median age of 59 years old (ranged from 34 to 75 years old). Among them, 15 (75%) were diagnosed as AJCC stage III-IV. Compared with SiCCA, we observed a significant higher proportion of undifferentiated samples in SHCC ( P< 0.001) (Table 1). The most commonly mutated genes of HSC included TP53 (64% in SHCC and 75% in SiCCA) and TTN (43% in SHCC and 100% in SiCCA). The most commonly mutated genes in SHCC also included TERT (43%), CCDC168 (36%), and LATS1 (36%), and that in SiCCA also included CDKN2A (50%), KRAS (50%), and CDKN2B (50%). All these genes were mainly enriched in cell cycle and ERBB pathway. In addition, amplifications of HYDIN, C4A, LRRC37A and deletions of CDKN2A, NTRK2, NTRK3, NRG1, PAX3, OR4K5, TPP2 and KRTAP4-6 were detected in the SHCC cohort, and amplifications of ZDHHC11, PMS2 and deletions of NRG1 and CDKN2A were detected in the SiCCA cohort. We also assessed TMB and PD-L1 status among these two cohorts. We found that 86% (12/14) of SHCC and 100% (4/4) of SiCCA had TMB of lower than 10 mutations/Mb. The expression of PD-L1 was positive (CPS > = 1) in 86% (12/14) of SHCC and 75% (3/4) of SiCCA. Conclusions: We are the first to discover the significant differences in tumor differentiation between SHCC and SiCCA. We also profiled the mutational characteristics, TMB status, and PD-L1 status of HSC, shedding light on the precision medicine of HSC. [Table: see text]
Pattern of CD8+ tissue resident memory T cells between local recurrence and distant metastasis in nasopharyngeal carcinoma.
Authors: Kam Ngar Woon , Lau Cho Yiu , Lai Syrus Pak Hei , Che Chi Ming , Lee Victor Ho-Fun 
Published: June 2023

e15161 Background: CD8+ T lymphocytes are believed to be the major anti-tumor immune subsets. Consequently, most cancer immunotherapeutic approaches seek to amplify cytotoxic T lymphocytes specific to malignant cells. A recently identified subpopulation of memory CD8+ T cells, named tissue-resident memory T (Trm) cells, persists in non-lymphoid tissues, including solid tumors. This T-cell subset is considered an independent memory T-cell lineage with cytotoxic features. However, their function, spatial location and influence on disease-related outcomes (local recurrence [LR], distant metastasis [DM] in nasopharyngeal carcinoma (NPC), a disease entity characterized by substantial immune infiltrate, remain poorly understood. We aim to close this gap through investigation on the abundance and spatial localization of CD8+ Trm in relation to tumor site (primary or recurrence [LR and DM]). Methods: This retrospective cohort analysis based on 20 NPC patient samples: primary (initial diagnosis; [I; n = 19], recurrence ([LR; n = 14] and [DM; n = 10]). We accessed the spatial localization in tumor tissues within tissue-segmented classifications of either cancer islands (pan-cytokeratin–positive [CK+] areas) or stromal areas (CK– areas). Tumor infiltrating lymphocytes (TILs) among patients from I, LR and DM group was quantified through multiplexed 5-colour opal staining using biomarkers against CD8, CD103, IL17, CK plus DAPI (nuclear cell counterstain). Results: While total CD8+ TILs (total tumor) as well as their spatially localized cell densities (tumor islet [TI] vs. tumor stroma [TS]) did not show any significant changes among I, LR and DM patient groups, a higher proportion of CD8+ TILs in the TI co-express the CD103 molecule, an indication of CD8+ Trm (CD103+CD8+) infiltration (mean CD103+CD8+/CD8+ in TI: 32.1% in I group, 44.8% in LR group, 46.0% in DM group; mean CD103+CD8+/CD8+ in TS: 19.0% in I group, 26.2% in LR group 26.2% in DM group). Notably, we observed that such augmentation only reached statistically significant within TI from patient in LR group (p = 0.0451). Furthermore, we found that CD8+ Trm in the LR group expressed higher level of cytokine IL-17, which was ~2.1-fold (p = 0.0788) and 3.6-fold upregulated (p = 0.0285) as compared to I and DM, respectively. Conclusions: Cancer islet–localized CD8+ TILs are composed of CD103+ Trms, which make up nearly 45% the total CD8+ T cell population within LR tumors of NPC patients, highlighting spatial localization of CD103+CD8+ Trms as a key phenotype of CD8+ TIL subset. The CD8+ Trm expressed with increased IL17 suggests that enrichment of this T-cell subset might exerts cytotoxic functions. Our results demonstrate that CD8+ Trm had a greater likelihood as an indicator of LR risk for NPC patients and help identify patient cohorts likely to benefit from immunotherapy.
Comprehensive multigene profiling impact on clinical decisions in patients with advanced cancers: A multicenter, retrospective analysis.
Authors: Kuznetsova Olesya , Ivanov Maxim , Tryakin Alexey , Lebedeva Alexandra , Ignatova Ekaterina , Fedyanin Mikhail 
Published: June 2023

e15163 Background: Comprehensive molecular profiling (CMP) via next generation sequencing (NGS) is currently applied in clinical practice and has enabled the detection of biomarkers of response to targeted treatment. Given the lack of the data about optimal range of analyzed alterations, the clinical usefulness of CMP has not been established. To address the challenges in incorporating genomics in treatment of oncology patients, we conducted a retrospective study. Methods: Preliminary analysis of NGS reports and clinical data of patients with advanced solid tumors was performed. CMP was conducted in 261 cancer patients (non-small cell lung cancer - 30,6%, colorectal cancer - 24,8%, pancreatic cancer - 7,4%, breast cancer- 6,2%; 59,3% were female, median number of prior systemic treatment lines was 2 (0-12)). In the present study, tumor molecular profile analysis was performed using 160 - 400 gene NGS panels, containing the majority of clinically significant genes for cancer treatment selection. We assessed the percentage of patients who were recommended to receive molecularly-matched therapy (MMT) after CMP, immunotherapy (IT) distribution of recommended therapies according to ESCAT tiers, median progression-free survival (PFS) – ratio ( = PFS after CMP / PFS before CMP, PFS2/PFS1), median PFS2. Results: MMT after CMP was recommended for 55 (21,1%) patients. ESCAT tiers could be assessed in 48 MMT patients (87%). For 31% of patients, administered therapy was considered as ESCAT I tier recommendation (data on mPFS2/1, mPFS2 not available). ESCAT tiers II, III, IV and IT administration were considered in 31, 8, 8 and 22% of patients respectively (detailed data is presented in Table 1). Most commonly altered genes were TP53 (53%), RAS (29%), APC (18%), CDKN2A/B (16%), PIK3CA(14%), NF1 (10%), BRCA1/2 (9%). Positive predictive factors for MMT after CMP were MSI-high status (HR 0,13, 95% CI 0,03 - 0,67), presence of EGFR alteration (HR 0,32, 95% CI 0,12 - 0,86). Presence of RAS mutation was considered a negative predictive factor (HR 2,78, 1,07 - 7,26). Conclusions: Available NGS panels offer a wide range of analyzed alterations that are not feasible in clinical practice. Most of the alterations that can cause impact on treatment plan can be detected with other methods than NGS. Further studies are needed to determine optimal range of alterations depending on tumor site. [Table: see text]