bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcome of concurrent treatment with a-CTLA4 and metronidazole in murine model of colon adenocarcinoma.
Authors: Medik Yusra B. , Zhou Yifan , Kahn Laura M. , Patel Bhakti , Babcock Rachel L. , Chrisikos Taylor T. , Wan Xianxiu , Dyevoich Allison , Ajami Nadim J. , Wargo Jennifer Ann , Watowich Stephanie S. 
Published: June 2021

e14566 Background: Immune checkpoint blockade (ICB) therapy transformed clinical oncology by inducing durable responses and increasing survival rates in many types of cancers. However, ICB is effective in only in a subset of patients. Recent studies delineated the role of gut microbiome as both a biomarker and a therapeutic in ICB responsiveness. We aimed to increase understanding of the microbiome-immune system axis in ICB therapy by using antibiotics to knock out certain components of gut microbiome. Methods: We treated MC38 colon adenocarcinoma-bearing mice with a widely-used antibiotic, metronidazole, that is effective against anaerobic and protozoal infections including Clostridioides difficile – a major mediator of colitis. Metronidazole was administered via oral gavage or mixed in drinking water before and after tumor injections. Mice received twice weekly treatment with a-CTLA4 ICB. Results: Metronidazole treatment alone slowed the growth rate of MC38 tumors, consistent with the current literature regarding colon cancer murine models. When metronidazole treatment was combined with a-CTLA4 therapy, we found ̃90% complete tumor regression. In the metronidazole and a-CTLA4 combination group, we also observed an increase in the number of CD103+ type 1 conventional dendritic cells (cDC1s) in colon lamina propria, which suggests enhanced antigen sampling from lumen. Also, in the mesenteric lymph nodes (mLN), we detected upregulation of CD80 and CD86 co-stimulatory molecule expression on CX3CR1+ antigen presenting cells. Multiplex analysis of colon cytokines and colon pathology evaluation was comparable among groups, which implies a non-inflammatory environment in colon. Analysis of tumor-draining lymph nodes eight days after tumor injections showed higher expression of CD86 on CD103+ cDC1s implying superior anti-tumor immunity. 16S rRNA gene sequencing analysis of fecal samples revealed loss of Lachnospiraceae and enrichment of Bifidobacteriaceae and Sutterellaceae families in metronidazole-treated mice. Conclusions: Shifting microbiome composition with metronidazole treatment elicits a favorable anti-tumor immune response to a-CTLA4 treatment in murine colon adenocarcinoma.
125I seed combined with DCS loaded with tumor antigen to convert irradiated liver cancer into effective in situ vaccine.
Authors: Zeng Peng 
Published: June 2021

e14573 Background: With unique feature of self-immune tolerance and high radio-sensitivity, hepatocellular carcinoma (HCC) can gradually develop undesired effects. Iodine-125 (125I) seed, as a source of internal radiation therapy, may have a favorable adaptability and immunostimulation. In this study, we investigated whether 125I seeds can stimulate local tumor infiltrating lymphocytes (TILs) and whether a combination of 125I seeds and dendritic cells (DCs) loaded with tumor antigen (Ag+DCs) can enhance both local tumor control and abscopal effect in murine subcutaneous tumor models. The related mechanism of anti-tumor immune response was also explored. Methods: H22/Hepa1-6 HCC cells were examined for radiosensitivity and immunosensitivity. Cell apoptosis and expression of MHC-I (major histocompatibility complex class I) and PD-L1 (programmed death-ligand 1) were detected before and after irradiation. The tumor cells were injected subcutaneously as primary and abscopal tumor. Bone marrow-derived dendritic cells (BM-DCs) were induced from mouse bone marrow cells and incubated with tumor cell lysate. 125I seeds were implanted into the primary tumors, followed by intratumoral injection of Ag+DCs and intraperitoneal injection of αPD1 antibody (αPD1-ab). DC migration was detected by transwell chambers in vitro and CFSE (carboxyfluorescein succinimidyl ester)-labeled DCs in vivo. DC maturation was tested by flow cytometry. Analyses of tumor growth and survival rates were performed in vitro, and that of, TILs, T-cell proliferation, cytotoxicity test, immunostimulatory cytokines release, and immunological memory were performed in vivo. In situ vaccine and abscopal effect were verified in orthotopic mouse models of liver cancer and lung metastatic tumor. Results: 125I seeds alone could induce TILs and activate cytotoxic T cells (CTLs), but these effects were limited. The combination treatment of 125I seeds with Ag+DC administration inhibited primary tumor growth and significantly prolonged survival time in association with a significant increase in T-cell proliferation and interferon-γ release. In addition, triple-combination treatment with αPD1-ab amplified these responses, leading to significant regression of primary and metastatic tumors and successful stimulation of immunological memory. Conclusions: 125I seeds can safely activate anti-tumor immune response.125I seeds combined with Ag+DC administration is able to convert irradiated liver cancer into effective in situ vaccine. Furthermore, triple-combination therapy of 125I seeds, Ag+DC, and αPD1-ab can be a promising approach to activate systemic anti-tumor immunity, which is a potential novel individualized therapy for patients with solid cancers.
Exploration of the TMB and hypermutation landscape in Chinese pan-cancer patient by next-generation sequencing.
Authors: Wang Shuo , Xu Jiasheng , Sun Jian , Wei Deng , Zhang Xinsheng , Wang Danhua , Ma Tonghui 
Published: June 2021

e14575 Background: Among a variety of malignant tumors, the level of the patient's TMB was currently an important criterion for clinical judgment whether to adopt immunotherapy. Hypermutation could produce many nearby mutation sites at the same time, which seriously damages genetic material and may cause cancer. Therefore, performing TMB detection on cancer patients and understanding the occurrence of hypermutation in pan-cancer patients will help clinical researchers to further understand the disease characteristics of cancer patients and helped the choice of treatment methods. Previously, TMB and Hypermutation had been tested and studied in pan-cancer patients in the United States and Europe, but rare research was reported in China. In this study, we explored the TMB and hypermutation landscape in Chinese pan-cancer patient by next-generation sequencing. Methods: A total of 8,361 cancer patients from multiple cancer hospitals and research centers in China were included in the study. We sequenced 8,361 Chinese cancer patients from 8 cancer types using the oncopanscan product of Genetron Health Co., Ltd. and calculated the tumor mutation burden of the patients. We separately analyzed the tumor mutation burden of patients in 8 cancer types and analyzed the relationship between the occurrence of hypermutation and the patient's age and gender. Results: The results showed that in pan-cancer, hypermutation patients accounted for 16.97%, and ultrahypermutation patients accounted for 0.78%. Among them, patients with lung cancer have the highest proportion of hypermutation, reaching 27.72%, and patients with colorectal cancer have the highest proportion of ultrahypermutation, reaching 2.86%. Correlation analysis between TMB and age and gender was carried out on 8336 patients. The results showed that in the patients with intrahepatic bile duct cancer, the proportion of men and women was the same. Among the other cancer types, hypermutation patients were more male, and the proportion of men with liver cancer was the largest, with 90 percent. We further explored the correlation between the TMB of pan-cancer patients and the patient’s age, and found that in gastric cancer, liver cancer, and melanoma, the older patients have higher TMB; however, the younger the patients in brain cancer, the higher the TMB ( P<0.05). Conclusions: In this study, we explored the TMB and hypermutation landscape in Chinese pan-Cancer patient for the first time. We found that among Chinese cancer patients, lung cancer patients have the highest proportion of hypermutation. In a variety of cancers, hypermutation patients account for a higher proportion of men, and the older the patient, the higher the TMB.
A micro-organosphere potency assay for adoptive T-cell therapy.
Authors: Natesh Naveen , Ding Shengli , Sanati Golshid , Hsu Shiaowen David , Antonia Scott Joseph , Shen Xiling 
Published: June 2021

e15027 Background: Lung cancer is the leading cause of death worldwide. Metastatic lung cancer patients often relapse or grow refractory to chemotherapy, radiotherapy, and checkpoint inhibitors. Adoptive T cell therapy (ACT) has been garnering more attention due to longitudinal complete responses. Tumor resections from patients harbor tumor-infiltrating lymphocytes (TILs) which can be cultured ex vivo and assessed for tumor reactivity before infusion. This generally follows a patient lymphodepletion regimen which allows the transferred T cells an optimal environment to proliferate and survive in the patient. TIL ACT can produce complete responses – rarely ever observed using traditional onco-therapy – in metastatic melanoma patients. However, while TILs specific to the neo-antigens expressed by tumor cells can be expanded ex vivo, this observed specificity is low in the clinic. Researchers have attempted to solve this by priming ex vivo expanded T cells with antigen-presenting cells previously pulsed with peptides representative of the neo-antigen repertoire of the matched tumor, but have rarely observed complete responses, likely due to current biomarkers for T cell activity poorly predicting anti-tumor cytotoxicity. To date there has been no acceptable potency assay for manufactured TILs, a requirement by the FDA for approval to use them in the clinic. Thus, the need to assess potency of ex vivo engineered T-cells against matched tumor cells is evident. Methods: We have developed a novel diagnostic immune-oncology (IO) pipeline, which uses a membrane-microfluidic platform to culture patient-derived tumor micro-organospheres (MOs) in extracellular matrix droplets. MOs can be rapidly established following patient tumor sample acquisition through biopsies or resection, and preserve the stromal cell populations in the original tumor microenvironment, as characterized by both flow cytometry and single-cell RNA-seq. An automated imaging assay was further established to robustly quantify the amount of immune-induced apoptosis of tumor cells in the MOs by patient-matched TILs, which is highly specific and yields minimal background. Results: We find that this method is not only amenable to high-throughput microscopy, but the larger surface-area-to-volume ratio of micro-organospheres also allows greater TIL infiltration and interaction with tumor cells. The resulting highly-sensitive assay requires far fewer input immune and tumor cells to achieve robust, clinical grade sensitivity response, making it the first clinically feasible assay for testing personalized TIL potency. Conclusions: The MO IO technology is currently being used for assessing clinical efficacy of manufactured TIL products for an upcoming ACT trial for non-small cell lung cancer patients. This technology also provides a companion to TIL ACT, CAR T therapy, and other immunotherapies, for which the ability to predict clinical potency is generally lacking.
Pharmacologic characterization of TACH101, a first-in-class KDM4 inhibitor for development as a cancer therapeutic.
Authors: Yoo Sanghee , Chandhasin Chandtip , Del Rosario Joselyn , Chen Young K , Stafford Jeffrey , Perabo Frank , Clarke Michael F. 
Published: June 2021

e15067 Background: The histone Lysine (K) Demethylase 4 family, KDM4 family, is involved in nuclear functions such as programming development, activation or repression of transcription, timing and control of the cell cycle, and initiating DNA replication and repair through chromatin remodeling. Overexpression of KDM4 leading to mistakes in post-translational histone modification has been associated with many cancer types and is being investigated as a potential therapeutic drug target. TACH101 is a novel potent and small molecule inhibitor of the KDM4 family. It demonstrated strong efficacy in multiple cancer types in vitro and in vivo and favorable pharmacokinetics (PK) and safety profiles in preclinical models. Methods: The target interaction properties of TACH101 were evaluated using purified enzymes for biochemical, biophysical, and inhibition mechanism studies. For PK parameter measurements, Sprague-Dawley rats and Beagle dogs were used for intravenous or oral administration of TACH101. Hepatocytes or liver microsomes were used to measure cytochrome P450 (CYP) inhibition and induction studies. Cell lines expressing cardiac channels were used for radioligand displacement assays and patch clamping. Results: Biochemical, biophysical, and inhibition mechanism studies using purified enzymes showed TACH101 is a reversible, alpha-KG (co-factor) competitive, and slow-binding inhibitor with IC50 values less than 100 nM. Pharmacologic studies showed plasma protein binding of TACH101 to be ≥99% bound in mouse, rat, dog, and human. TACH101 appeared to be selective in off-target panel assays of receptors, ion channels and transporters. TACH101 did not show any significant binding displacement activity against cardiac ion channels or any effect on hERG in CHO cells using manual patch clamp techniques. In rats and dogs, TACH101 exhibited low systemic clearance, a moderate volume of distribution in rats and dogs, linear exposure profiles with a terminal half-life (̃ 6-hour) and high bioavailability (46-100%). In repeated dose studies in rats and dogs, mean Cmax and AUC values increased in a dose-related manner over the dose range evaluated. There was no significant impact of food on systemic exposure in dogs. TACH101 did not show inhibition or induction of CYP enzymes tested. Conclusions: TACH101 is a potent KDM4 specific inhibitor without significant off-target activity in in vitro and in vivo studies. It did not show inhibition or induction of CYP enzymes suggesting low probability of CYP mediated drug-drug interaction. The exposure from oral administration in rats and dogs was dose proportional and was not significantly affected by food intake in dogs. Given the favorable target activity, PK properties and safety profile, a Phase 1 study is being planned to advance TACH101 for patients with advanced cancer.
AcornHRD: A novel tool to identify homologous recombination deficiency events in whole genome sequencing data.
Authors: Liu Kai , Hao Xueyu , Zhang Mengmeng , Li Mingwei , Wang Wang , Zhang Xinhao , Guo Jing , Wang Huina , Lou Feng , Cao Shanbo 
Published: June 2021

e15078 Background: Recently, homologous recombination deficiency (HRD) scores are associated with the efficacy of Poly‐(ADP‐Ribose)‐Polymerase (PARP) inhibition and platinum-based chemotherapy in a variety of cancers. Evaluating HRD level in patients with cancers is becoming far more important and influential, so far, there is no standard method to be used in clinical. In this study, we developed an algorithm to detect HRD from next-generation sequencing (NGS) for finding additional patients may potentially benefit from target therapy. Methods: Forty-eight patients were enrolled, including breast cancer, ovarian cancer, prostatic cancer. Fifteen cell lines with breast cancer and endometrial carcinoma were collected from Cobioer biosciences co., LTD. Forty-eight Formalin-fixed, paraffin embedded (FFPE) samples and 15 cell lines were performed by DNA extracting. We developed an HRD score algorithm, termed as AcornHRD algorithm. HRD score was analyzed by whole-genome sequencing, and GATK mutect2 software was used to detect BRCA1/2mutation by deep sequencing. Results: BRCA1/2 deleterious mutations were observed in 20 patients (41.7%). HRD was explained by deficiencies in 17 patients (85.0%) with BRCA mutation, whereas eight HRD-high tumors were non- BRCA related (28.6%). Among BRCA wild-type patients, the corresponding percentage of HRD positive patients in breast cancer, ovarian cancer and prostate cancer were 36.3%, 37.5% and 11.1%, respectively. Similar results were also verified in the cell line datasets. The findings showed that 100% (3/3) BRCA1/2 deficient cell lines are also HRD-high. Furthermore, HRD scores were highly correlated with standard results in the cell line datasets. Conclusions: We here report the NGS-based HRD scores to distinguish similarly well between BRCA mutant and BRCA wild-type cases in a cohort of Chinese population. AcornHRD scores were highly associated with BRCA1/2 deficiency. AcornHRD algorithm can be a useful tool to detect HRD events in clinical settings.
Genomic aberrations in African American patients with solid tumors: A comparative institutional study.
Authors: Shah Manan , Lee Michelle Jeung-Eun , Hong Nicholas , Kollepara Sri Lakshmi Sudha , Lillard James , Oprea Gabriela , Jain Sanjay R. 
Published: June 2021

e15086 Background: Genomic mutations play an important role in cancer pathogenesis and can be used as targeted agents for treatment. Cancer related biomarkers in body fluids and tissues are being used to identify specific target genes. They also help in predictive and prognostic assessment related to the disease. Various platforms like guardant 360, foundation act, oncotype are commercially available. Specific genomic aberrations have enhanced the field of Precision Medicine in individualizing treatment protocols. Methods: Prospective data was collected from 45 African American patients at our institution using the commercially available Genomic Enabled Medicine ExTra cancer panel (Ashion Analytics). Sample include 18 types of cancer (10 breast, 9 colorectal, 5 endometrium, 4 prostate, 3 uterine, 2 cervical, 1 pancreas, 1 gallbladder, 1 melanoma, 1 larynx, 1 gastric, 1 carcinoid, 1 carcinosarcoma, 1 lymphoma, 1 ovary, 1 bladder, 1 thyroid). Both tumor and normal DNA were collected from year 2019 through 2020. For comparison, clinical and genomic, The Cancer Genome Atlas (TCGA) data for 1,065 African American adults with solid tumors were downloaded from the NCI Genome Data Common portal. The two data sets were eventually compared for identifying common genetic mutations and possible new targets for cancer management. Results: Of the 45 patients, 38 patients (84%) had at least one genomic alteration, and 38 known driver mutations were identified. Their median age was 56 years (range, 37 – 94). TP53 mutations were most common, identified in 44% of patients versus 37% in African Americans in TCGA. PIK3CA and KRAS mutations were next most common (22% and 20%, respectively) compared to TCGA African American samples (13% and 12%, respectively). The most frequent mutations on PIK3C were H1047R in 4 patients (8.8%), followed by E545K in 3 patients (6.6%). Oncogenic mutations were observed in APC, PTEN, ARID1A, FBXW7, NF1, PIK3R1, RNF43, ATM, CCNE1. Conclusions: In our study, we found higher prevalence of oncogenic driver gene mutations (including TP53, PIK3CA, KRAS, APC, PTEN, ARID1A) in African American cancer patients compared to TCGA African American cancer patients. It is important to note that high percentage of our patients had actionable oncogenic drivers that may be useful in treatment decision-making. Our aim is to continue to build on our database on African American patients for identifying specific and common gene mutations to enhance development of targeted agents.
Association of PIK3CA, PTCH1, FGF6, and NRAS mutations with venous thromboembolism in advanced lung and gastrointestinal cancer.
Authors: Maharaj Satish , Bhandari Shruti , Wu Xiaoyong , Abhyankar Anuja , Zetter Daniel , Rai Shesh , Rojan Adam , Chesney Jason Alan , Sharma Vivek R. 
Published: June 2021

e15087 Background: Venous thromboembolism (VTE) in patients with gastrointestinal (GI) and non‐small cell lung cancer (NSCLC) is common and increases morbidity and mortality. In advanced GI and NSCLC, molecular subtyping has increased use of next-generation sequencing (NGS). The association between tumor mutation profile and VTE risk remains undetermined. Methods: We conducted a retrospective cohort study of consecutive GI/NSCLC patients from 2014-2019 with NGS and follow‐up at Brown Cancer Center. The NGS platform detected substitutions, indels, copy number alterations and select rearrangements in 324 genes. Patients with thrombophilia, anticoagulation use or >1 malignancy were excluded. VTE was defined as deep vein thrombosis, pulmonary embolism or visceral vein thrombosis within 6 months prior to diagnosis or any time after. For statistical analysis SAS 9.5 was used with significance at alpha=0.05. Multinomial logistic regression was performed, in which the log odds of VTE was modeled as a linear combination of the genes. Odds ratios and 95% confidence intervals for VTE were generated. Results: A total of 364 patients were reviewed; after exclusions 326 patients were included comprising Stage III/IV NSCLC (58%), metastatic colorectal (33%) and other metastatic GI cancers - gastric, duodenal, esophageal, pancreatic and cholangiocarcinoma (9%). Approximately half (53%) were males with mean age of 59.1 yrs and 76.4% current/former smokers. There was a low level of microsatellite instability (0.9%). VTE occurred in 75 patients (23%) during a mean follow‐up of 24.5 months. Only 1 patient had surgery within 90 days prior to VTE. Of 248 genes mutated in the VTE group, 9 were more prevalent compared to those without VTE (Table). Statistical analysis showed PIK3CA, PTCH1, FGF6, and NRAS mutations significantly increased odds of VTE, with PIK3CA the most prevalent of these (Table). Conclusions: Patients with PIK3CA, PTCH1, FGF6 and NRAS mutations had significantly higher VTE risk. These tumor mutations and associated pathways may provide novel insight into risk stratification, prevention and targeted treatment of VTE in cancer. [Table: see text]