bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating the various predictive values of TP53 mutations for response to immune checkpoint inhibitors (ICIs) in different solid tumors.
Authors: Li Xiaoguang , Zhang Xin , Niu Yanling , Ma Tonghui
Published: June 2022

e14581

Background: TP53, a well-known tumor suppressor gene that encodes p53.The mutations of TP53 have been shown to be associated with higher tumor mutation burden (TMB). And patients with TP53 mutations are more likely to benefit from ICIs therapy. Previous studies have shown that TMB has divergent predictive value for response to ICIs therapy in different cancer types. We hypothesized that the associations between TP53 mutations and ICIs efficacy are also varied in different solid tumors. Therefore, we explored the prediction values of TP53 mutations in some cancer types. Methods: The ICIs treatment cohort from the Memorial Sloan Kettering Cancer Center (MSKCC) was selected to analyze the association of TP53 mutations with ICIs efficacy. The patients were classified into two groups: TP53 mutation (Mut) and wildtype (WT). Overall survival (OS) after ICIs therapy was estimated with the Kaplan-Meier method. Results: In MSKCC pan-cancer dataset, patients with TP53 mutations had significantly shorter median OS after ICIs therapy (14.00 vs 23.00 months, P < 0.0001), indicating that TP53 mutations were associated with worse immunotherapy outcome. Then we analyzed the predictive roles in each cancer type. Notably, we found the associations of TP53 mutations with longer median OS in bladder cancer (27.00 vs 14.00 months, P = 0.0359). However, the associations between TP53 mutations and ICIs efficacy were not observed in breast cancer, esophagogastric cancer, glioma, head and neck cancer, melanoma, non-small cell lung cancer and renal cell carcinoma. We found the associations of TP53 mutations with shorter median OS in colorectal cancer (13.00 vs 34.00 months, P = 0.0368). Furthermore, the data showed that the median TMB was significantly lower in the Mut group for colorectal cancer (17.63 vs 35.98 muts/Mb, P = 0.0086) and higher in the Mut group for bladder cancer (14.25 vs 10.81 muts/Mb, P = 0.1588). Conclusions: Although TP53 mutations were associated with better ICIs efficacy in previous studies, the prolonged OS was only found in the Mut group for bladder cancer. Although TP53 mutations were associated with worse ICIs efficacy for all the enrolled patients, the poor outcome was only found in the Mut group for colorectal cancer. These data suggested that TP53 mutations may be a useful predictor for ICIs efficacy in these two types of cancer.
Genomic characterization of immune checkpoint inhibitor resistance genes and hyperprogression genes in advanced solid tumors.
Authors: Xu Libin , Zhang Ge , Mu Tianhao , Wang Zhizheng
Published: June 2022

e14582

Background: Immune checkpoint inhibitors have been widely used in the systematic treatment of various advanced solid tumors, but they show poor efficacy or lead to hyperprogression in some patients. Some studies reported that EGFR mutations, ALK fusion, interferon pathway or Wnt signal pathway gene mutations might reduce the efficacy of immunotherapy and lead to tumor hyperprogression. The aim of this study was to determine the frequency of gene variations associated with immunotherapy resistance or hyperprogression in advanced solid tumors. Methods: The tumor tissues or blood samples of 111 patients with advanced solid tumors were collected. The tumor tissues were sequenced by targeted next-generation sequencing (55 genes, Illumina novaseq 6000), MSI (PCR) and PD-L1 detection (IHC). Blood cfdna was extracted and sequenced by targeted next-generation sequencing (55 genes, Illumina novaseq 6000). Results: A total of 111 patients with advanced solid tumors were included in the study, including 34 patients with colorectal cancer, 27 patients with hepatobiliary tumors, 18 patients with gastric cancer, 15 patients with urothelial carcinoma, and 17 patients with other solid tumors. Among the 82 samples tested for MSI, there were 77 cases of MSS (93.9%), 1 case of MSI-L (1.2%), and 4 cases of MSI-H (4.9%). 44 samples were tested for PD-L1 expression. 33 (75%) had PD-L1 expression < 1%, and 11 (25%) had PD-L1 expression greater than 1% but less than 49%. Among the genes related to immunotherapy, the mutations of genes related to cell growth or cell cycle regulation (EGFR, ALK, CDKN2A and CCND1) accounted for 3 (2.7%), 5 (4.5%), 12 (10.8%) and 5 (4.5%), respectively. The mutation of antigen presentation related gene (B2M) accounted for 3 (2.7%). The mutations of interferon signaling pathway related genes (JAK1, JAK2, JAK3 and IFNGR1) accounted for 2 (1.8%), 5 (4.5%), 1 (0.9%) and 1 (0.9%), respectively. The mutations in Wnt signaling pathway related genes (APC, AXIN1, CTNNB1) accounted for 41 (36.9%), 5 (4.5%) and 7 (6.3%). The mutations of tumor suppressor genes (PTEN, STK11 and PTPN2) accounted for 9 (8.1%), 1 (0.9%) and 3 (2.7%). Mutations in other genes (APLNR, DNMT3a, MDM2) accounted for 1 (0.9%), 6 (5.4%) and 7 (6.3%). Conclusions: Our study shows that in patients with advanced solid tumors, there are multiple gene variants related to drug resistance or hyperprogression of tumor immune checkpoint inhibitor treatment, suggesting that it may be the reason for the difference in the efficacy of immunotherapy. It is necessary to further study the efficacy of immunotherapy in patients with different gene mutations and the combination of immune checkpoint inhibitors for patients with different pathway mutations.
Radiologic features of immune checkpoint inhibitor-related nephritis with clinical correlation in biopsy-proven cases.
Authors: Awiwi Muhammad , Abudayyeh Ala , Abdel-Wahab Noha , Diab Adi , Gjoni Migena , Xu Guofan , Vikram Raghu , Elsayes Khaled M.
Published: June 2022

e14585

Background: Radiologic findings associated with biopsy proven immune checkpoint inhibitor (ICI) related nephritis have not been described. The objective of this study is to describe the radiologic features of immunotherapy related nephritis on computerized tomography (CT) and positron emission tomography (PET). A secondary objective is to investigate the association of these radiologic features with renal outcomes. Methods: A retrospective review of all biopsy proven ICI-related nephritis between February 2017 and April 2021 was performed and 34 patients were identified. CT and PET-CT scans before the initiation of immune checkpoint inhibitors (baseline), at nephritis and after resolution of nephritis were reviewed. Total kidney volume, renal parenchymal SUVmax, renal pelvis SUVmax and blood pool SUVmean were obtained. Results: The total kidney volume was significantly higher at nephritis compared to baseline (464.7±96.8 mL vs. 371.7±187.7 mL; p < 0.001). Fifteen patients (44.1%) had > 30% increase in total kidney volume at nephritis. A > 30% increase in total kidney volume was associated with significantly higher renal toxicity grade (p = 0.007), higher peak creatinine level (p = 0.004) and more aggressive medical treatment (p = 0.011). New/increasing perinephric fat stranding was noted in 10 patients (29.4%) at nephritis. Among 8 patients with contrast-enhanced CT at nephritis, 1 patient (12.5%) developed bilateral wedge-shaped hypoenhancing cortical lesions that healed with focal scarring on subsequent scans. On PET-CT, the renal parenchymal SUVmax-to-blood pool SUVmean ratio was significantly higher at nephritis compared to baseline (2.13 vs. 1.68; p = 0.035). The renal pelvis SUVmax-to-blood pool SUVmean ratio was significantly lower at nephritis compered to baseline (3.47 vs. 8.22; p = 0.011). Conclusions: Bilateral increase in kidney size, new/increasing perinephric stranding and bilateral wedge-shaped hypoenhancing cortical lesions can occur in immunotherapy-related nephritis. On PET-CT, diffuse bilateral increase in radiotracer uptake throughout the renal cortex and decrease in radiotracer activity in the renal pelvis can be seen. A > 30% increase in total kidney volume was associated with significantly higher renal toxicity grade and more aggressive medical treatment in a subset of patients. Acknowledgment: National Institute of Health K01 Award (N.A.: K01AI163412).
Correlation of BRAF genomic alterations with higher mutation burden and predictive response to immune checkpoint inhibitors among human malignancies.
Authors: Kuan Feng-Che , Shi Chung-Sheng , Lin Meng-Hung
Published: June 2022

e14589

Background: The treatment of BRAF-mutated melanoma leads the evolution of management in BRAF-mutated human malignancies from targeted agents to immune checkpoint inhibition. The correlation between BRAF genomic alterations and mutation burden is not well-studied as well as its prognostic role and predictive role to immune checkpoint inhibitors. Methods: Three Public genomic database (AACR GENIE v.11 [N = 119,058], MSKCC pan-cancer [10,080], MSKCC ICI [1,608]) were retrieved from cBioPortal ( https://www.cbioportal.org ). Raw data of cancer types, BRAF status, mutation counts (MC), exposure to immune checkpoints inhibitors (ICIs), and survival were analyzed. Violin plots were used to compare the distribution of MC among BRAF-altered and -wild tumors, and the Kaplan-Meier method was used to estimate survival rates. Statistical significance was set at a two-sided P < 0.05. Results: BRAF genomic alterations exist in 7,361 (6.2%, AACR GENIE v.11), 560 (5.6%, MSKCC pan-cancer) and 165 patients (10.3%, MSKCC ICI). There are 4,851 (4.1%), 357 (3.6%), and 312 (19.4%) patients with melanoma in these database, respectively. AACR GENIE v.11 includes the other two MSKCC databases, and 10.7% (N = 1,074) patients in MSKCC pan-cancer databases are also cases in MSKCC ICI. The median MCs were 7/Mb and 4/Mb, with interquartile ranges of 1 to 1,467 and 1 to 821 in the BRAF-altered and -wild tumors in AACR GENIE v.11. In this three databases, the distribution of MC was different between the BRAF-altered and -wild tumors (p < 0.001). In MSKCC pan-cancer cohort, the median overall survival in BRAF-altered and -wild tumors are 22.8 vs. 26.3 months (logrank p = 0.005). In MSKCC ICI cohort, the median overall survival of BRAF-altered and -wild tumors are 47.0 vs. 17.0 months (logrank p < 0.001). Conclusions: BRAF genomic alterations are associated with higher mutation counts, represent a poor prognostic factor and positively predictive to immune checkpoint inhibition among human malignancies.
Personalized multimodality therapy with immune checkpoint inhibitors, chemotherapy, and targeted treatment (ICTriplex) in advanced/refractory cancer.
Authors: Salem Philip A. , Jabboury Khaled W. , McCallum William G.B. , Stenoien Randall A. , Wheeler Thomas M.
Published: June 2022

e14590

Background: Advanced/refractory malignancies are associated with poor prognosis and their treatment remains a major challenge. The combination of immune checkpoint inhibitors (ICI) and chemotherapy (CT) has been shown in some cancers to be superior to chemotherapy alone. In our treatment program (ICTriplex), targeted therapy (TT) was added to this combination for the treatment of these diseases, as these three approaches have convergent efficacy but divergent toxicity. Our initial data was previously reported in ASCO 2019 (abstract e14254) and ASCO 2020 (abstract e15150). Methods: Treatment was highly personalized and was tailored to the individual patient depending on diagnosis, prior therapy, and genomic profiling. Between April 2016 and January 2022, 41 patients with advanced malignancies were treated. The median age was 59 years (range 17-78). 24 patients were female. The Median Eastern Cooperative Oncology Group Performance Status was 2 (range 0-4). Tumor types included; lung (10), pancreas (7), colorectal (4), cholangiocarcinoma (3), breast (3), ovarian (2), Glioblastoma (2), cervical (2), sarcoma (2), melanoma (2), Hodgkin’s (1), gallbladder (1), thymoma (1), and gastric (1). PDL-1 status was positive in 10, negative in 16 and unknown in 15. 32 patients received prior therapy. Of these, 9 received ICI, 14 received TT, and 31 received chemotherapy for a median of 2 regimens (range 1-11). In ICTriplex, the ICIs used were Pembrolizumab in 14, Nivolumab in 12, and Atezolizumab in 7. 8 patients received dual ICI with ipilimumab. Combination chemotherapy including platinum was used in 21 patients, taxanes in 17, and gemcitabine in 24. TT included 18 agents with erlotinib in 9 and bevacizumab in 8. Response was evaluated by both PET/CT and CT scans. A complete response was achieved when all metabolic activity had resolved. Results: A complete response (CR) was achieved in 19 patients (46.3%), and a partial response (PR) in 16 (39%), with a total response rate of 85.3%. All but 2 patients had response. Of the 10 patients with lung cancer, 7 had CR, and 3 of them had a duration of response of more than 30 months. Also, 3 of the complete responders with brain metastases achieved intracranial CR by MRI without radiation. 2 patients with pancreatic cancer had a response duration of more than 30 months. Regarding side effects, 2 patients died of pulmonary complications possibly due to treatment. There were no other unexpected side effects. Conclusions: ICTriplex therapy is highly effective in advanced/refractory cancer and therefore should be considered when standard therapy fails, as well as for patients for whom standard therapy is not available.
Exosome in ascites can be a potential therapeutic target for gastric cancer with malignant ascites.
Authors: Hyung Sujin , Ko Jihoon , Kim Seung , Kang Won Ki , Lee Jeeyun ,   Samsung Medical Center Group
Published: June 2022

e15008

Background: Recently, exosomes widely distributed in body fluids, including blood, urine, saliva, and ascites, serve as an essential biomarker in cancers. Exosomes are considered as a cargo of potential oncogenic protein such as MET during cancer progression. Methods: Exosomes from the malignant ascites (exoAscites) of four patients with stage IV gastric cancers (GCs) were isolated by different serial centrifugation steps (300 g, 2000 g, 10,000 g, and 110,000 g at 4). After ultracentrifugation, nanoparticle tracking analysis, western blotting, and immunocytochemistry were performed for characterization of the exoAscites. Results: In this study, we enrolled 4 patients with malignant ascites which needed to be drained for symptom control. In all 4 patients, we successfully isolated highly concentrated exosomes in 50 ml of ascites (range, 55108 – 260 108exosomes/ml). (pt#1, 140108 particles/ml; pt#2, 138 108, pt#3, 55.6 108; pt#4, 260 108 exosomes/ml). In twopatients with MET amplification (METamp) in tumor specimens, exoAscites retrieved from the ascites harbored cMET protein in exosomes. In addition, the in-vitro cancer microenvironment model showed that tropism of exoAscitesharboring cMET oncogenic protein had the potential to induce cancer progression (EpCAM immunofluorescent intensity value; a 2.4-fold increase compared to control). In this model, the cancer invasiveness and angiogenesis were significantly enhanced by treatment with exoAscites with over time. (2.4-(EpCAM immunofluorescent intensity) and 3.6-(CD31 immunofluorescent intensity) fold increase, respectively). Furthermore, the cancer invasiveness was substantially increased as the exosome concentration increased from 0, 101, 103, 105, 107 exosome particles/ml. Cancer invasiveness measured by EpCAM immunofluorescent intensity was significantly decreased upon exosiMET treatment in MET amplified GC cells when compared to the control. Conclusions: For the first time, we demonstrated that exosomes from malignant ascites carry MET protein in their exosomes. Exosomes may be early mediators of cancer spread in GC.
Development of blood components samples collection as a source for new biomarkers search in multiple myeloma.
Authors: Gnennaya Nadezhda V. , Kit Oleg I. , Filippova Svetlana Yu , Sitkovskaya Anastasia O. , Mezhevova Irina V. , Shamova Tatiana V. , Timofeeva Sofia V. , Novikova Inna A. , Lysenko Irina B. , Nikolaeva Nadezhda V. , Samaneva Natalia Yu. , Gaysultanova Yakha S. , Kamaeva Inna A. , Tishina Anna V. , Pushkareva Tatiana F. , Kapuza Elena A.
Published: June 2022

e15009

Background: Multiple myeloma (MM) is a B-cell malignancy resulting from the abnormal proliferation of neoplastic plasma cells that produce monoclonal immunoglobulin (Ig). The high variability of the course of this disease, its genetic clonal heterogeneity, is due to chromosomal deletions, chromosomal hyperploidy involving an odd number of chromosomes, as well as genetic aberrations, such as rearrangement of the Ig heavy chain gene loci. Since the available biomarkers do not take into account this feature of MM, there is a need to develop more advanced biomarkers that will more accurately predict the course of the disease and response to treatment. Methods: The collection of MM samples included biological samples obtained from patients over 18 years of age with a diagnosis of MM, who received treatment in the National Medical Research Center of Oncology since 2019. Only patients who signed an informed consent for the use of their biomaterial for scientific purposes were included in the project. The material was collected according to the developed algorithm of clinical information and biological material collection, sample preparation, quality control and storage in the cryostorage of the National Medical Research Centre for Oncology of the Ministry of Health of Russia (Rostov-on-Don). Results: As of December 23, 2021, collection consists of 387 samples of whole blood, serum, plasma and mononuclear cells obtained from 42 MM patients of both sexes, whose average age was 59.7 ± 1.49 (±SD) years. Each patient was assigned a unique identification number. Freezing of the obtained samples occurred in accordance with the low-temperature storage protocol. Registration, accounting and certification of the material were carried out in a specialized database for recording and storing information about biological samples. Conclusions: The identification of MM biomarkers is important for increasing the sensitivity of molecular monitoring, which makes it possible to stratify patients into risk groups for early relapses and treatment resistance development. Thanks to the accumulated experience, the Biobank of the National Medical Research Centre for Oncology of the Ministry of Health of Russia serves as a valuable resource for providing research in the development of new predictive molecular markers.
Performance and clinical utility of homologous recombination deficiency (HRD) determined by genome-wide loss of heterozygosity (LOH).
Authors: Li Chien-Feng , Chen Shu-Jen , Tan Kien Thiam , Tse Ka-Po , Wang Woei-Fuh
Published: June 2022

e15025

Background: Homologous recombination deficiency (HRD) status plays an important role in identifying patients with ovarian cancer likely to benefit from Poly (ADP-ribose) polymerase inhibitor (PARPi) and platinum-based chemotherapies. Methods: ACTHRD is an NGS-based assay was designed to determine the homologous recombination deficiency (HRD) status based on the extent of genome-wide loss of heterozygosity (gLOH) and the detection of BRCA1/2 genes alteration. More than that, ACTHRD also assesses the mutational status of 22 homologous recombination repair (HRR) genes. We evaluated the performance and clinical utility of the ACTHRD and compared it with the FDA-approved companion test myChoice CDx. Results: Of the 36 specimens assayed, 24 were determined to be HRD, and 10 were determined to be homologous recombination repair proficient (HRP). The results showed high concordance with myChoice CDx with 100% positive percent agreement (PPA) and 90.91% negative percent agreement (NPA) in the HRD status estimation. Except one case showed HRD in the ACTHRD but showed homologous recombination proficiency (HRP) in the comparator panel. This patient responded to platinum-based chemotherapy and remained disease-free for up to 56 months. One BRCA1/2 wild-type patient was identified as HRD by myChoice CDx but not eligible for ACTHRD test due to low tumor cellularity experienced refractory 13 months after the initiation of the treatment. We further found that ovarian cancer patients identified as HRD by ACTHRD had significantly prolonged progression-free survival (PFS) after being treated with platinum-containing chemotherapies, regardless of BRCA1/2 mutational status. Conclusions: The ACTHRD assay provides high accuracy for identifying deleterious BRCA1/2 alterations and determining the HRD status of ovarian cancers. The analytical robustness of the test has been validated and indicates its suitability for clinical use. Notably, the prognosis data demonstrates that ACTHRD can predict eligible patients for platinum-based chemotherapy and may also be sensitive to PARPi treatment.
Bedside to benchtop translational development: Targeting the S1P/ceramide axis may alleviate symptoms of chemical induced peripheral neuropathy.
Authors: Takigiku Ray , Wesolowski Robert , Rixe Olivier , Morris John Charles , Yilmaz Emrullah , Villano John L. , Muller Carolyn , Curry Richard Charles , Puduvalli Vinay K. , Wise-Draper Trisha Michel , Wolfe Darren , Tapolsky Gilles
Published: June 2022

e15045

Background: Chemical Induced Peripheral Neuropathy (CIPN) is a debilitating and serious side-effect associated with many chemotherapeutic treatments. Often, CIPN is a dose-limiting toxicity, and its effects can be long-lasting in some patients. The pathology of CIPN is thought to involve not only cytotoxicity of neuronal cells, but also inflammation and immune responses. Hence, it is not surprising that the sphingolipid sphingosine-1-phosphate (S1P) is thought to be a key contributor to CIPN. Methods: BXQ-350, a nanovesicle comprised of recombinantly expressed Saposin C and dioleoylphosphatidylserine, has broad anticancer activity. It modulates sphingolipid metabolism and signaling, lowers S1P and increases pro-apoptotic ceramides, and induces an anti-tumoral immune response. BXQ-350 was investigated in a Phase 1 dose-escalation safety study of all-comer cancer patients with advanced solid malignancies, including high grade gliomas ( NCT02859857 )*. Multiple secondary parameters were included to characterize BXQ-350’s pharmacokinetics, efficacy profile and to elucidate potential biomarkers. Results: Interestingly, several patients with established CIPN spontaneously reported improvement of their neuropathy-related symptoms following BXQ-350 administration. Plasma samples from those patients revealed changes in circulating levels of sphingolipids and cytokines, including reduction of circulating levels of S1P and of IL-6, IL-8, cytokines, following BXQ-350 dosing. These properties of BXQ-350 were subsequently investigated in a murine oxaliplatin-CIPN preclinical model; results showed a dose-dependent prevention/resolution of CIPN, which also correlated with decreasing systemic S1P levels. Additional plasma based CIPN specific biomarkers were investigated, and preclinical results suggest that BXQ-350 may also favorably inhibit specific immune cells that favor CPIN. Conclusions: These preclinical and clinical observations related to CIPN, coupled with the fact that BXQ-350 acts synergistically with many chemotherapies and radiation, warrant further its investigation into preventing or improving CIPN related symptoms in cancer patients. Clinical trial information: 02859857.
3D Jones-maxtrix scanning of polycrystalline films of blood plasma in the diagnosis of pathological conditions of human organs.
Authors: Tryfonyuk Liliya , Dubolazov Alexandr , Ushenko Yuriy , Soltys Irina , Pavlukovich Natalia , Ushenko Oleksandr
Published: June 2022

e15053

Background: This work is devoted to the development and experimental verification of a new method of three-dimensional matrix mapping of anisotropic properties of optically thin layers of polycrystalline films of blood plasma of biological tissues for express diagnostics and differentiation of histological sections of a prostate tumor. Methods: Biological samples. Three representative groups of polycrystalline blood plasma films were formed: 1 group consisted of blood plasma samples of polycrystalline adenoma; Group 2 consisted ofpolycrystalline adenocarcinoma, blood plasma samples are moderately differentiated (3+3 on the Gleason scale); Group 3 consisted ofpolycrystalline adenocarcinoma, blood plasma samples are poorly differentiated (4+4 on the Gleason scale). Results: The results obtained can be associated with changes in the ratio between the concentrations of albumin and globulin proteins in the blood plasma from patients with prostate tumors. It is known that malignant processes are accompanied by an increase in the concentration of optically active globulin molecules. Due to this, there is an increase in the magnitude and range of scatter in the magnitude of circular birefringence of samples of polycrystalline blood plasma films from patients with adenocarcinoma (3 + 3) and adenocarcinoma (4 + 4) in comparison with similar maps of blood plasma from patients with benign adenoma. On the contrary, due to a decrease in the concentration of albumin molecules, the values of linear birefringence of blood plasma films from patients with malignant prostate tumors decrease. Conclusions: The method of 3D Jones matrix mapping of blood plasma layers with digital holographic reconstruction of layered maps of linear and circular birefringence is analytically substantiated. The operational characteristics (sensitivity, specificity and balanced accuracy) that demonstrate the diagnostic power of 3D Jones matrix mapping of biological layers. The use of the algorithm for tomographic reproduction of linear birefringence maps provided high accuracy in differentiating benign and malignant conditions of the prostate tissue.[Table: see text]
Anticancer effects of PARP1 hyperactivation by a decoy oligodeoxynucleotide in vitro and in vivo.
Authors: Jdey Wael , Doizelet Chloe , Galassi Claudia , Zandanel Christelle , Trochon-Joseph Veronique , Hayes Vincent , Lienafa Marie-Christine , Petroni Giulia , Galluzzi Lorenzo
Published: June 2022

e15060

Background: Poly (ADP-ribose) polymerase (PARP) inhibitors mediate significant anticancer effects against homologous recombination defective (HRD) tumors but have limited efficacy against homologous recombination proficient (HRP) neoplasms. Moreover, HRD tumors often become resistant to PARP inhibitors during treatment, constituting a major limitation to the clinical use of these agents. Here, we describe the metabolic, antineoplastic and immunomodulatory effects of a first-in-class oligodeoxynucleotide that operates as a PARP1 decoy (OX413), resulting in constitutive hyperactivation of PARP1 and consequent exhaustion of the DNA damage response. Methods: OX413-induced PARP trapping and hyperactivation, NAD+ consumption and cell cytotoxicity were monitored using (HRP and HRD) breast, ovarian or prostate cancer cells as well as normal fibroblasts and leukocytes. DNA repair abrogation was monitored by analyzing repair protein recruitment to damage sites. Accumulation of cytoplasmic DNA fragments was monitored after DNA staining and microscopy analysis. Effects on the innate immune response was assessed by following STING pathway activation and T-cell mediated anti-tumor cytotoxicity. In a mouse xenograft model of breast cancer, OX413-induced PARP activation and tumor infiltration by immune cells were analyzed ex-vivo by flow cytometry. Antitumor efficacy of OX413 alone or combined to a PD1 blocker was assessed in MPA/DMBA-driven HR+ HER2- mouse mammary carcinomas. Results: At odds with conventional PARP inhibitors, OX413 bound to and hyperactivated PARP1 with high affinity and in a dose-dependent manner, resulting in elevated cytotoxicity in multiple cancer (but not normal) cells irrespective of HR status. OX413 impaired DNA repair due to PARP trapping and rapid NAD+ consumption, leading to the accumulation of cytoplasmic chromatin fragments (CCFs). Consistent with this, OX413 triggered activation of the CGAS/STING pathway, CCL5 secretion and potentiation of tumor-targeting T cell responses. PARP1 engagement and STING activation were corroborated in vivo in EMT6 mouse mammary carcinomas, correlating with anticancer effects coupled to tumor infiltration by innate and adaptive immune cells. In MPA/DMBA-driven tumors, OX413 mediated considerable anticancer effects that could be exacerbated by PD1 inhibition. Conclusions: Our results provide preclinical rationale for using OX413 to trigger metabolic exhaustion in cancer cells and initiate inflammatory responses that can be actioned by immune checkpoint inhibitors in patients bearing HRD as well as HRP tumors.
Translational modeling for patients with RAS mutant tumors: Profiling the dual-MEK inhibitor IMM-1-104 in a humanized 3D assay.
Authors: Hall Brett , Nair Praveen , Fowler Kevin , Axel Amy , Kolitz Sarah , Funt Jason , Barrett Scott , Zeskind Benjamin , King Peter J.
Published: June 2022

e15084

Background: Elevated RAS-RAF-MEK-ERK (MAPK pathway) signaling is observed in over half of all solid human tumors, and mutations in RAS or RAF account for a large fraction. Given MEK’s unique position in the MAPK cascade, it remains an attractive target in cancer. However, FDA-registered MEK inhibitors are susceptible to pathway reactivation events that limit their use to RAF mutant disease and cause on-target toxicities stemming from chronic target engagement. IMM-1-104 is a novel, allosteric dual-MEK inhibitor designed for better applicability to RAS mutant tumors by preventing MEK reactivation. Endowed with a short plasma half-life, IMM-1-104 promotes deep cyclic inhibition with a near-zero drug trough, affording normal cells a chance to recover between doses. Methods: We characterized IMM-1-104’s pharmacologic activity across 52 tumor cell lines that spanned 11 distinct tumor types in a humanized, ECM-based 3D tumor growth assay (3D-TGA). The 3D-TGA has better predicted in vivo tumor responses versus 2D culture and more accurately reflects human tumor biology. Tumor models were categorized based on in vivo drug PK limits as sensitive to IMM-1-104 (EC50 < 1uM), intermediate (1uM≤EC50≤10uM and ≥25% inhibition at 10uM) or resistant otherwise. Models were evaluated by whole exome sequencing, along with RNA sequencing in the 3D context, to profile determinants of sensitivity and resistance and to prioritize patient populations most likely to respond to IMM-1-104. Results: Models sensitive to IMM-1-104 were enriched for MAPK driver mutations, consistent with pathway addiction. We reasoned that activation of parallel compensatory pathways that can reduce reliance on MAPK signaling may increase the likelihood of resistance to IMM-1-104. Pathways and genes suspected of contributing to resistance helped refine signatures based on 3D-TGA outcome data. Models with a MAPK driver mutation and compensatory mutations such as PIK3CA or PTEN deletion were more likely to show intermediate response than those with a greater addiction to MAPK drivers. Models lacking a clear MAPK driver mutation but harboring other putative resistance alterations were more likely to be resistant in the 3D-TGA. Conclusions: To better understand the relevance of tumor model responses in the 3D-TGA relative to RAS mutant patient populations, we computationally compared tumor model data to patient somatic alterations, identified in the public resource GENIE, which has cataloged the molecular profiles of over 100,000 cancer patients. Based on model-to-patient molecular mapping, we identified biomarker-defined subsets of sensitive KRAS mutant lung and colorectal models. The most broadly sensitive patient-aligned models in the 3D assay were KRAS mutant pancreatic cancer and NRAS mutant melanoma patients, supporting the inclusion of such patients in planned clinical studies of IMM-1-104.
Drugging the undruggable-targeting P53: A comparative analysis of APR-246 and coti-2 in human tumor primary culture explants.
Authors: Nagourney Adam Jeremiah , Evans Steven Scott , Duesberg Max Serge , D'Amora Paulo , Bernard Paula J. , Francisco Eric , Nagourney Robert Alan
Published: June 2022

e15092

Background: The TP53 tumor suppressor is the most commonly mutated gene in human cancer. P53 protein comprised of 393 amino acids functions as a tetramer with the loss of function mutations concentrated in “hotspots” that often affect DNA binding domains. APR-246 and COTI-2 are novel small molecules that are under clinical investigation for the treatment of P53 mutated cancers. APR, a quinuclidine binds to P53 cysteine residues altering the functional conformation while COTI is a thio-semicarbazone, found active in P53 mutant tumors using a novel computational platform. As the mechanisms of action may differ we undertook a comparative analysis of these compounds in 3D human tumor explants derived from surgical specimens. Methods: Ex Vivo Analyses of Programmed Cell Death (EVA/PCD) (D’Amora, P et al Gyn. Oncol. 2021) was applied to 236 human tumor primary culture explants isolated from surgical specimens. After disaggregation, micro-spheroids, isolated by precise density centrifugation were exposed to APR, COTI and other agents for 72-96 hours. Drug-induced cell death was measured by delayed-loss-of-membrane integrity and ATP content (luciferase). Dose response curves were interpolated to LC50 values. Synergy analysis used the method of Chou & Talalay. Correlation coefficients used Pearson moment. Results: APR and COTI reveal the highest activity in hematologic neoplasms. Solid tumor activity patterns diverged with COTI active in gynecologic malignancies and NSCLC and moderately active in breast and colorectal while APR is active in colorectal but less active in breast and NSCLC. Pearson moments for COTI vs APR revealed an R value = 0.146 (NS). COTI activity correlated with Nitrogen Mustard and Alpelisib (PIK3CA) while APR activity correlated with Doxorubicin and Everolimus. COTI combinations focused upon ovarian cancers identified synergy in 25% and antagonism in 18%. Conclusions: P53’s function as the “guardian of the genome” is consistent with our findings that many cytotoxic and targeted agents that induce cell death reveal correlations with APR and COTI. While APR affects the structural conformation of P53, COTI may function downstream via oxidative, metabolic or other stress responses. The correlation coefficient for APR vs COTI at 0.146 (NS) suggests distinct mechanisms of action. This is supported by different disease-specific-profiles and correlations with other drugs. COTI synergy in ovarian cancers, the target of current clinical trials at 25% is below expectations. With differing disease specificities, selecting between these and related agents to optimize clinical outcomes may require a more granular examination of cellular mechanisms of response and resistance. Primary culture analyses offer insights into drug mechanisms of action, combinatorial potential and have the capacity to improve patient selection.
Antitumor activity of KIN-2787, a next-generation pan-RAF inhibitor, in combination with MEK inhibition in preclinical models of human NRAS mutant melanoma.
Authors: Miller Nichol , Wang Tim Sen , Lee Catherine , Severson Paul , Ke Eugene , Kobayashi Ken , Williams Richard Thomas
Published: June 2022

e15099

Background: NRAS mutations which activate MAPK signaling represent oncogenic driver alterations in approximately 20% melanoma cases in the US. NRAS mutant melanomas are uniquely dependent upon CRAF rather than BRAF for activation of downstream MEK/ERK signaling. In BRAF mutant melanoma, approved RAF-targeted therapies are commonly used in combination with a MEK inhibitor which provides clinical benefit by inhibition of two targets within the oncogenic MAPK signaling pathway. Emerging data with pan-RAF inhibitors in early clinical development suggests benefit with and without combined MEK inhibition, yet no approved targeted therapy exists for NRAS mutant melanoma patients. KIN-2787 is a novel, orally available pan-RAF inhibitor designed to be effective in RAF-dependent cancers, regardless of isoform. Methods: Kinome profiling was evaluated by radiometric enzyme assay at Reaction Biology across 688 kinases (including wild type, atypical, and mutant). Cellular activity was assessed by suppression of downstream MAPK pathway signaling and cell growth inhibition in human tumor cell lines. Combination cell growth inhibition studies were performed in 9x5 dose matrices with KIN-2787 and binimetinib, respectively. Extended cell growth inhibition effects were assessed by Incucyte imaging. In vivo KIN-2787 and combination efficacy was evaluated in NRAS mutant xenograft models. Results: Kinome profiling of KIN-2787 revealed exquisite selectivity with only 2 of 669 non-RAF family kinases inhibited > 75% at 1 M KIN-2787 and retained ̃10x and 70x selectivity window against those two kinases, DDR1 and p38b, respectively, relative to RAF kinases. We previously reported KIN-2787 activity across BRAF, NRAS, and KRAS mutant tumor cell lines with greatest sensitivity in Class II and III dimer-driven BRAF models. Here, we evaluated NRAS mutant, BRAF WT melanoma for combination potential with binimetinib. Melanoma tumor cell lines bearing NRAS hotspot mutations demonstrated synergistic benefit with KIN-2787 combined with binimetinib. Daily KIN-2787 plus binimetinib treatment in NRAS mutant melanoma xenograft models resulted in significant tumor growth inhibition benefit relative to either agent alone and was associated with added MAPK pathway biomarker suppression. Conclusions: KIN-2787 is a highly selective, potent, next-generation, pan-RAF inhibitor with activity across BRAF and RAS mutant human tumor cell models. Preclinical in vitro and in vivo studies using KIN-2787 in combination with binimetinib demonstrated significant combination benefit in NRAS mutant melanoma models. Taken together with its unique selectively, these data support use of KIN-2787 in combination therapy in this patient segment. A Phase 1/1b dose escalation and expansion clinical trial evaluating the safety and efficacy of KIN-2787 is ongoing (NCT04913285).
The landscape of KDM5A mutations and hotspots in Chinese patients with solid tumors.
Authors: Li Ke , He Zhe
Published: June 2022

e15115

Background: As a kind of histone modification enzyme, Lysine-specific demethylase can eliminate di- and tri-methyl groups from lysine 4 of histone. A growing number of shreds of evidence demonstrate that the disfunction of KDM5A relates closely to the initiation and progression of various diseases, particularly cancers, including but not limited to breast cancer, prostate cancer, glioblastoma, etc. However, research on the mutation spectrum of KDM5A in Chinese cancer patients is lacking. Methods: Ranging from Jan 14, 2020, to Oct 25, 2021, genomic DNA extracted from 5419 blood or tissue samples involving more than 22 solid tumors types were analyzed by NGS assay to investigate the landscape of KDM5A mutations and hotspots. Results: KDM5A somatic mutations existed in approximately 6.50% of all samples and almost all kinds of screened cancer types, among which, endometrial cancer comes first with the highest mutational frequency up to 21.05%, followed by the esophagus and esophagogastric junction cancer (18.18%) and bladder cancer (12.50%). Further analysis was conducted to explore mutational hotspots in KDM5A. Although almost 150 mutation sites existing in KDM5A had been identified in our research, the most prominent mutational hotspots are G1200, T30, M766, occupying 19.63%, 17.51%, and 6.37% of all SNV and Indel KDM5A mutations, respectively. Conclusions: Our study partially disclosed the panorama of the KDM5A mutational landscape in Chinese patients with solid tumors for the first time. Further studies with larger samples and populations are much needed to enhance our understanding of this enzyme in cancer biology.
Tissue-based next generation sequencing (NGS) testing in solid tumors: A single-center experience in Malaysia.
Authors: Ahmad Azura Rozila , Toh Yi Long , Tan William , Wahid Mohamed Ibrahim A.
Published: June 2022

e15121

Background: There is an increased appreciation for precision oncology in which clinicians are utilizing NGS testing to guide treatment selection and to identify resistance mutations. This study aims to identify clinically significant biomarkers in prospectively collected FFPE tumor tissue specimens. Genomic testing of molecular alterations was conducted using an in-house 50-gene hotspot APEX panel (MiRXES). Herein, we report a single center experience with targeted NGS panel testing in solid tumors. Methods: The analyzed cohort consisted of 75 clinical samples submitted for molecular testing over a 3-month period from Beacon Hospital, Malaysia (October to December 2021). The identified variants were tiered according to AMP/ASCO/CAP guidelines, in which actionable targets are defined as being able to be matched with existing FDA-approved drugs, including off-label prescriptions. Results: Among the samples received, 85.3% of samples passed quality control requirements for SNV/Indels and amplifications. Majority of the tumor types were categorized under colorectal cancer (20.3%), NSCLC (18.7%), followed by breast cancer (13.6%). Of the samples successfully sequenced, actionable targets were identified in 76.2% of patients, with Tier I variants [such as EGFR exon19del (6), EGFR exon20insertion (1), ERBB2 amp (5), KRAS G12C (3), KRAS G12D (1), KRAS G12V(1), KRAS G12F (1) KRAS G13D (1), PIK3CA H1047R (1), MET exon 14 skipping (1) and NRAS Q61H (1)) being identified in 20 patients. When stratified across tumor types, actionability rates were found to differ, with 100.0%, 83.3% and 81.8%, of tested tissues samples yielding results informing treatment selection or resistance mutations for breast, colorectal and NSCLC respectively. Based on APEX-tissue testing, the median number of actionable genes identified was 2 (IQR: 0 – 3) while the mean time from sampling to report was 4.7 days. Conclusions: This study shows the clinical utility and feasibility of targeted panel testing in cancer types of breast, colorectal and NSCLC. With fast turnaround time of 4 working days, this ensures timely access to treatment for patients.
Analysis of ROS1 fusions in nonlung solid tumors.
Authors: Yan Dong , Xu Mengxiang , Wang Weiran , Han Yushuai , Zhu Jianhua , Ma Tonghui
Published: June 2022

e15124

Background: Somatic chromosomal fusions involving ROS1 produce chimeric proteins that drive tumorigenesis and progression. Currently, ROS1-directed tyrosine kinase inhibitors (TKIs) are effective treatments for advanced non-small cell lung cancer (NSCLC) patients (pts) with ROS1 fusions. Except for NSCLC, Glioblastoma and spitzoid neoplasms, ROS1 fusions have been rarely reported in other cancers. Therefore, clarifying the patterns and frequency of ROS1 fusions in multi-cancer may help pts benefit from ROS1 inhibit therapy. Methods: To characterize the ROS1-fusion patterns in Chinese pts, we retrospectively analyzed the next-generation sequencing (NGS) data of 11,740 pts from 2017 to 2021. Results: In this study, a total of 12 ROS1 fusions were identified in this Chinese nonlung solid tumors cohort (12/11,740). Among them, the ROS1-fusion positive rate is 0.037% in colonrectal cancer pts (2/5,467), 0.13% in stomach cancer pts (3/2,268), 0.11% in liver cancer pts (2/1,774), 0.19% in kidney cancer pts (1/540), 0.21% in pancreatic cancer pts (2/966) and 0.28% in sarcoma pts (2/725). Particularly, we observed the coexistence of CD80- ROS1 and Intergenic- ROS1 in the same kidney cancer pt. Among ROS1 fusions described in this cohort, the frequency of known partners was 16.67%, and the frequency of unreported partners was 83.33%. Compared with NSCLC (1%̃2%), the ROS1 fusions are less frequent in the nonlung solid tumors (≤0.3%), and fusion partners are mostly unreported, which means that the efficacy of ROS1 TKIs in these solid tumor pts may be different from that in lung cancer. Therefore, more attention and in-depth research are needed in ROS1 fusion positive nonlung solid tumors, which have a low incidence and few cases, so as to bring clinical benefits to more pts. Conclusions: Through NGS, we identified ROS1 fusion patterns in non-lung solid tumors, most of which fusion partners are unreported, expanding the range of ROS1 fusions documented in tumors and providing potential for ROS1 TKIs in multiple tumors.[Table: see text]
Features of chromosome instability in Chinese early-onset colorectal cancers.
Authors: Zhou Xiangwu , Chen Guijin , Zhuo Jinchun , Liu Xinyi , Gao Haixin , Yi Quanwang , Huang Mengli
Published: June 2022

e15519

Background: In recent years, the etiology and molecular mechanism of early-onset colorectal cancers (EOCRC) has evoking more and more attention. Previous studies suggested that EOCRC had unique somatic mutational characteristics, such as frequent mutations in genes of WNT signaling pathway. However, the features of chromosome instability in this particular subgroup of colorectal cancer remain unclear. Somatic copy number alteration (SCNA) is the main manifestation of chromosome instability. We performed a systematic analysis in regard to SCNAs in a large cohort of Chinese colorectal. Since the microsatellite instable (MSI-H) cancers rarely occurred SCNAs, only microsatellite stable (MSS) patients were included. Methods: A total of 1696 Chinese MSS CRC patients diagnosed in 2018-2020 were included. Early-onset were defined as patients diagnosed under 50 year-olds and the others were late-onset (LO). Genomic alterations and SCNAs were elucidated in all patients’ tumor specimen using next-generation sequencing (NGS) testing. Results: All patients were stratified as EOCRC (n = 439) and LOCRC (n = 1214). 3.87% EOCRC harbored germline cancer susceptibility genes (mainly APC and ATM) mutations while in the LOCRC counterpart the proportion was only 2.06% (mainly MUTYH and BRCA2). Of note, MYC amplification was detected in 71.43% EOCRC with copy-number gain and presented a trend to correlated with APC germline mutations (Fisher’s exact test, p-value = 0.07). In the other CRC (n = 1654) with no germline cancer susceptibility genes, genomic amplifications were detected in 831 (50.2%) cases. The frequency of 8q and 13q amplification were equal in EOCRC and LOCRC. However, EOCRC had higher proportion of 8p and 17q amplification, lower proportion of 20q amplification than LOCRC. Moreover, a higher ratio of EOCRC had high-level amplifications, mainly concentrated in 17q ( ERBB2, CDK12 and RARA) and 13q ( FLT3, CDK8 and FLT1), than LOCRC (23.7% vs 19.1%). Other high-level amplified genes include MYC, CCND2 and EGFR. EGFR high-level amplifications occurred more in EOCRC than LOCRC (13.5 % 2.6%), while CCND2 high-level amplifications were only detected in LOCRC. Gene copy number losses were detected in 195 (11.8%) cases. Loss of SMAD4, CDKN2A, CDKN2B, MAP2K4, PTEN and AMER1 genes were most recurrent. The incidence of SMAD4 (43.1% vs 22.9%), CDKN2B (11.8% vs 6.2%), MAP2K4 (7.8% vs 4.2%) gene losses were higher in EOCRC while the incidence of PTEN (13.9% vs 7.8%) and SMAD3 (6.9% vs 1.9%) gene losses were higher in LOCRC. Conclusions: EOCRC present different SCNA characteristics from LOCRC, including unique focal amplifications, distinct recurrent genes with copy number losses, and more high-level amplifications events mainly distributed in 17q and 13q. It can be reasonably speculated that MYC gene gain was a critical event correlated with familial mutations in EOCRC.