bluuebunny/crossref_metadata_2025 huggingface dataset:
Local progenitor cells shape the neoplastic vasculature and promote brain tumor growth.
Authors: Kälin Roland , Cai Linzhi , Zhao Dongxu , Zhang Huabin , Zhang Wenlong , Kirchleitner Sabrina , Siller Sebastian , Enard Wolfgang , Schiemann Matthias , Andrä Immanuel , Giachino Claudio , Taylor Verdon , Synowitz Michael , Tonn Joerg , Baumgarten Louisa von , Hellmann Ines , Glass Rainer
Published: June 2021

e14044

Background: Aggressive brain tumors like glioblastoma depend on support by their local environment. While the role of tumor-associated myeloid cells on glioblastoma progression is well-documented, we have only partial knowledge of the pathological impact of glioblastoma -parenchymal progenitor cells. Methods: We investigated the glioblastoma microenvironment with transgenic lineage-tracing models ( nestin-creER2, R26-tdTomato and sox2-creER2,R26-tdTomato), intravital imaging, single-cell transcriptomics, immunofluorescence and flow-cytometry as well as histopathology and characterized a previously unknown tumor-associated progenitor cell. In functional experiments, we studied the knockout of the transcription factor SOX2 in these tumor-associated cells. Results: Lineage-traced cells from mouse glioblastoma were obtained by flow-cytometry and single cell transcriptomes compared to established gene expression data from brain tumor parenchymal cells. The traced tumor-associated cells had a transcriptomic profile largely resembling myeloid cells and expressed microglia-/macrophage-markers on the protein-level. However, transgenic models and bone-marrow chimera revealed that the traced cells were clearly distinct from microglia or macrophages. The traced tumor associated cells with a myeloid expression profile derived from a SOX2-dependent progenitor cell. Consequently, conditional Sox2-knockout ablated the entire myeloid-like cell population. Remarkably, this tumor-associated cell population had a large impact on disease-progression causing significant reduction of glioblastoma –vascularization to 53%, changing vascular function and leading to a decrease in tumor volume to 42% as compared to controls. The myeloid-like progenitor cells were identified in human brain tumors by immunofluorescence and in scRNA-seq data. Conclusions: We identified a previously unacknowledged population of tumor-associated progenitor cells with a myeloid-like expression profile that transiently appeared during glioblastoma growth. These progenitors have strong impact on glioblastoma progression and point towards a new and promising therapeutic target in order to support anti-angiogenic regimen in glioblastoma.
Activating chimeric receptor on IL-15 armored NK cells to improve in vitro and in vivo tumor response within the liver following regional delivery.
Authors: Tan Joanne , Guha Prajna , Wadsworth Sarah , Ghosh Chandra C. , Chai Louis F. , Katz Steven C. , Trager James
Published: June 2021

e14517

Background: Colorectal cancer liver metastases (CRCLM) are a major source of morbidity and mortality. Historically, curative therapy has been limited to surgical resection, but only a small fraction of patients are eligible. Cellular immunotherapy has shown promise in hematologic cancers, but challenges to solid tumor therapy remain, including lymphocyte trafficking, elevated interstitial fluid pressures, and immunosuppression. Regional intravascular infusion is a non-surgical, minimally invasive procedure commonly used in liver cancer to deliver therapeutics, which can be augmented by Pressure Enabled Drug Delivery (PEDD). We hypothesized that utilizing established regional delivery strategies to administer natural killer (NK) cells engineered to express a natural killer group 2, member D (NKG2D) activating chimeric receptor and membrane bound IL-15 (CAR NKG2D cells) could increase anti-tumor activity against liver cancer. Methods: In vitro cytotoxicity of CAR NKG2D NK cells was determined in co-culture systems. CRCLM-bearing NSG mice were treated with either CAR NKG2D, non-transduced NK cells (NT-NK), or vehicle via portal vein (PV) for regional PEDD or tail vein (TV) for systemic delivery (SD). Tumor burden was measured via tumor bioluminescence. Mann-Whitney tests were performed for statistical comparisons. Correlation of NKG2D ligand expression in tissue and serum was measured by CODEX and Luminex. Results: Multiple NKG2D ligands are highly expressed in hepatocellular and colorectal carcinoma cell lines (HCC and CRC respectively). As such, these cells lines are highly susceptible to NKG2D-mediated cytotoxicity. CAR NKG2D NK cells were 3- to 4-fold more potent in vitro than NT-NK cells against multiple HCC and CRC cell lines, including those bearing Ras pathway mutations. Using a mouse model of locoregional delivery under high pressure (10 mL/minute), we show that significant tumor reduction (p < 0.05) is only achieved when CAR NKG2D NK cells, but not vehicle or NT-NK cells, were delivered via PV and not via TV. Recovery of CAR NKG2D NK cells in hepatic tissues was on average 2-fold higher after administration via PV than that observed after TV delivery (p = 0.0001). PV delivery of NT-NK cells did not result in appreciable liver engraftment or tumor growth inhibition. Conclusions: CAR NKG2D NK cells demonstrate enhanced in vitro and in vivo cytotoxicity against CRC and HCC cell lines. Significant tumor control using regional delivery in initial studies support continued clinical development. NKX101 is an investigational agent comprised of CAR NKG2D NK cells being evaluated in a phase 1 clinical study for treatment of relapsed/refractory acute myeloid leukemia or higher risk myelodysplastic syndrome. Studies are ongoing to understand NKX101 kinetics, role of delivery pressure, and activity in combination in preclinical models of CRCLM.
A pan-cancer profiling of somatic mutations and tumor microenvironment to reveal mutation dependent immunophenotypic signature differences in KRAS.
Authors: McDaniel Lee , Abbott Charles , Pyke Rachel , Levy Eric , Zhang Simo V. , Wang Jing , McClory Rena , Chen Richard , Boyle Sean Michael
Published: June 2021

e14526

Background: The ubiquity of tumor genotyping has identified hundreds of clinically actionable somatic mutations such as KRAS mutations predicting anti-EGFR response in colorectal cancer. Here, we describe an integrative pan-cancer study leveraging the Personalis NeXT Platform across 13 tumor types to reveal a broad portrait of clinically relevant mutations across 36 genes. Given the ascendance of tumor immunotherapy, there is an urgent need to better elucidate associations between clinically relevant gene mutations, patient demographics, and tumor immunobiology. Methods: Paired tumor-normals (n > 450) were sequenced on the Personalis NeXT Platform, a diagnostic platform which simultaneously profiles tumor and immune microenvironments via exome and transcriptome sequencing. Samples were evaluated for the presence of KRAS variants at the G12, G13, and Q61 positions, requiring a minor allele frequency of more than 2%. Additionally, more than 200 clinically relevant amino acid changes were considered across 36 genes. DNA sequencing data was harnessed to profile MSI status, oncovirus status, HLA allele-specific LOH, SNVs, and neoantigens. RNA sequencing data furnished profiles for gene expression, TILs, TCR, BCR, and immune signatures. Statistical tests compared both the presence of clinically relevant mutations, and specific amino acid changes, to each of these DNA and RNA derived features. Results: Immunogenomic analysis with the Personalis NeXT Platform identified KRAS mutations at the G12, G13, and Q61 positions in 6 of the 13 tumor types, including bladder, CRC, liver, NSCLC, pancreatic, and uterine cancers, consistent with known KRAS allelic incidence. 11 different KRAS amino acid substitutions were identified in this cohort, including G12(A/C/D/R/S/V), G13(C/D), and Q61(H/K/L), with 14% of samples positive for KRAS variants across our pan-cancer cohort, including malignancies not associated with KRAS. Immune signatures, including TCRB clones, mutational burden, and TILs signatures demonstrated variability in a KRAS allele-dependent manner. Pancreatic cancers demonstrated a statistically significant increase in macrophage enrichment score (p < 0.001) in KRAS-mutant tumors. Conclusions: Utilizing the Personalis NeXT Platform, our analysis characterized the tumor microenvironment of over 460 samples across 13 tumor types, 36 genes, and over 200 clinically relevant amino acid substitutions. This comprehensive characterization demonstrated significant differences in immune cell signatures in pancreatic cancer, suggestive of an association between the presence of KRAS mutations and immune cell infiltrate composition.
Investigating the impact of immune related adverse events, glucocorticoids use and immunotherapy interruption on long-term survival outcomes.
Authors: Lafayolle de la Bruyère Charline , Peron Julien , Souquet Pierre Jean
Published: June 2021

e14551

Background: It remains unclear whether immune related adverse events (irAEs) and glucocorticoids use could impact long term-outcomes in patients treated for solid tumors with immune checkpoint inhibitors (ICI). Methods: All patients treated with a single-agent ICI for any advanced cancer were included in this retrospective multicentric study. Objectives were to assess the impact of grade 3+ irAEs, glucocorticoids use and interruption of immunotherapy on progression free survival (PFS) and overall survival (OS). Data collection was performed retrospectively using a standardized data collection form. Adverse events were categorized as irAEs based on the judgement of the treating physicians, based on the common Terminology Criteria for Adverse Events, version 4.0. Only grade 3 and more irAEs were considered in this study. As irAEs might happen late during the follow-up and progression event or death might happen early, an immortal-time bias might occur as patients responding to ICI will receive the ICI and then be exposed to irAE for a longer period of time. The first occurrence of an irAE was then included in Cox models, as a time-varying covariate. Similar methods were used to evaluate the impact of glucocorticoids introduction or ICI interruption. Results: In this 828 patients’ cohort, 78 patients presented at least one grade 3+ irAE. The first occurrence of grade 3+ irAEs had no significant impact on PFS (HR 0,94; 95%CI 0.7-1.26; p = 0,70) or OS (HR 0.82; 95%CI 0.6-1,12; p = 0,21). 65% of patients with anti CTLA4 and 55% of patients with anti PD(L)1 requested glucocorticoids, which was associated with a significant shorter PFS (adjusted HR 3.0; 95%CI 1.6-5.4; p = 0.00040) and a trend toward shorter OS. Grade 3+ irAEs led to interruption of the ICI in 82 % of patients, which was associated with a significant shorter PFS (adjusted HR 3.5; 95%CI 1.7-6.0; p < 0.00043) and shorter OS (HR 4.5; 95%CI 1.7-12.1; p = 0.0027). The use of glucocorticoids was statistically associated with immunotherapy interruption. Conclusions: In our population of patients treated with single agent ICI, grade 3+ irAEs did not impact long-term outcomes. However, the need for glucocorticoids and the interruption of immunotherapy resulted in poorer long-term outcomes. The impact of grade 3+ irAEs reported in other studies might then be explained by the management of the irAEs.
CARG-2020, an oncolytic artificial virus co-delivering three immunomodulators, to regress and cure established tumors in mice.
Authors: Almassian Bijan , Madina Bhaskara R , Chen Ju , Krady Marie M , Ma Xianyong , Yarovinsky Timur O , Nakaar Valerian , Wang Kepeng
Published: June 2021

e14560

Background: Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in humans. Treatment of late-stage CRC remains ineffective, even with the use of latest immunotherapies. Oncolytic viruses have shown limited use for the treatment of cancers, and further improvement of these agents with immune-modulating activities may prove crucial for patients with CRC and other malignancies. To this end, we developed CARG-2020 as an artificial virus for infectious diseases and immuno-oncology (AVIDIO) that employs virus-like vesicles (VLV). VLVs, which are membrane-encapsulated RNA replicons, are oncolytic and can deliver multiple genes resulting in the modulation of several independent immune pathways. Methods: The AVIDIO platform is comprised of in vitro evolved RNA-dependent RNA polymerase from an alphavirus, Semliki Forest virus, and envelope glycoproteins from vesicular stomatitis virus, which together form VLVs. Unarmed or empty vector (VLV), VLV armed with IL-12 (VLV-IL-12) and a VLV that simultaneously expresses IL-12, a dominant-negative form of IL-17 receptor A (dn-1L17RA) and shRNAs targeting PD-L1 (CARG-2020), were given intratumorally to test their therapeutic potential against established (500-600mm3) MC38 tumors in mice. We used tumor growth measurements and analyses of tumor-infiltrating cells after consecutive treatments with these agents to monitor their antitumor and immunomodulatory activities, respectively. Results: Both VLV-IL-12 and CARG-2020 regressed the tumors to undetectable levels in most mice harboring syngeneic MC38 tumors when given intratumorally. CARG-2020, carrying IL-12, dn-IL17RA and PD-L1 shRNA, exerts broader spectrum of immuno-responses and higher number of complete response rates compared with VLV-IL-12. Treatment of primary tumors with VLV-IL-12 or CARG-2020 also significantly repressed the growth of secondary tumors on the other flank of mouse’s body, suggesting an effective systemic immunity elicited by these two agents against the same type of tumors. In addition to the marked local and systemic activation of Th1 cells and CD8+ T cells by both vectors, CARG-2020 also downregulated PD-L1 expression in tumors, and suppressed expression of IL-17A-activated chemokines CXCL1 and CXCL2 that are known to promote cancer development and therapy resistance. Conclusions: As an oncolytic RNA replicon, AVIDIO platform-derived CARG-2020 encodes IL-12, dn-IL-17RA and PD-L1 shRNAs which are expressed concurrently within the same vector. CARG-2020 modulates IL-12, IL-17RA and PD-L1 signaling, and exerts broad immune modulation in tumor microenvironment. Treatment with CARG-2020 eliminates the majority of grafted large tumors in mice, and is effective against both primary and distal tumors. Based on this impressive efficacy results, further development of CARG-2020 in colorectal patients is warranted.
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]
The imprecise promise of the Precision Medicine Initiative (PMI): Where we got it wrong and how can we fix it?
Authors: Clinton Natasha , Patel Kashyap B.
Published: June 2021

e15102

Background: Over the last several years, science has taken strides in how we understand and treat cancer. We have learned that each person’s cancer is unique, in part because it is influenced by a patient’s biological characteristics, environmental exposures, lifestyle and epigenetic influence. There is excitement about the potential of PMI to transform healthcare delivery and improve population health. Targeted therapies developed based on specific mutations can result in improved outcomes and reduced toxicities. Limited knowledge of cancer biology and the genomic underpinnings of cancer in racial and ethnic minorities diminishes the potential of PMI. Previous efforts of obtaining biospecimens from institutional or local biobanks presents a challenge of inadequate representation of racial and ethnic diversity. This can result in exacerbation in the therapies efficaciousness. Methods: Numerous research studies have surfaced indicating that PMI has resulted in widening racial and ethnic health care disparities since state-of-the art diagnostic and treatment options are unequally distributed across the entire cancer population. A literature review highlighted the racial inequalities and disparities. Results: A report examining the racial diversity of samples in TCGA found that whites were overrepresented in the U.S. population while Asian and Hispanic patients were underrepresented at a 5 percent frequency. In the BATTLE study, 82 percent of participants were white, and only 6% were African American (AA). The NCI-MATCH trial preliminary numbers show that AAs accounted for about 10 percent of patients. Therefore, it should not be assumed that the response rates or clinical effectiveness of the therapeutics tested in these trials will generalize to all racial and ethnic groups. The underrepresentation of racial and ethnic minorities in cancer clinical trials and prevention research, along with the documented challenges to enrolling these individuals into studies pose a barrier for the implementation of precision medicine in these populations. Collectively, these challenges can slow the pace of medical innovation, decrease the generalizability of research findings, lead to incorrect interpretations, and limit our full understanding of precision medicine. Conclusions: It is imperative we develop solutions to solve for issues identified related to precision medicine testing and treatment development. We have developed a framework to address disparities in PMI through community-based initiatives. A two-step solution could be considered to address this unmet need. Through the development of a registry and biospecimen banking as well as just in time trials that include pharmacogenomics, we can follow the patient journey to identify unique characteristics by race and/or socioeconomic status to begin solving for the disparities across the population.
Association of the anorectal microbiome and patient-reported gastrointestinal outcomes in patients with anal cancer.
Authors: Kouzy Ramez , Lin Daniel , El Alam Molly Blue , Abi Jaoude Joseph , Smith Grace L. , Koay Eugene Jon , Minsky Bruce D. , Das Prajnan , Holliday Emma B. , Klopp Ann , Taniguchi Cullen M. , Colbert Lauren Elizabeth
Published: June 2021

e15504

Background: Among patients with anal cancer undergoing chemoradiotherapy, the association between the microbiome and toxicity is not well documented. We sought to quantify the gastrointestinal-related patient-reported outcomes (PROs) and local microbiome profiles of patients with anal cancer receiving chemoradiotherapy in order to check for potential profiles that can help in predicting toxicity during treatment. Methods: We prospectively followed patients with non-metastatic squamous cell carcinoma of the anal canal who received definitive chemoradiotherapy. Anorectal swab samples were collected before treatment initiation and at 4 subsequent timepoints. Consequently, PROs were collected using the bowel subdomain of the Expanded Prostate Cancer Index Composite (EPIC). Samples were sequenced using 16S rRNA of the V4 region. Sequence reads were grouped by amplicon sequence variants (ASV’s) representative of unique bacterial species. We then used Linear discriminant analysis Effect Size (LEfSe) with an effect size of 4 to identify taxa at baseline that were differentially enriched in patients with high vs. low toxicity by end of treatment. We compared the EPIC scores with the relative abundance of species identified in the LEfSe using a paired Wilcoxon test. Results: The study included 22 patients (18 women and 4 men), whose median age was 59 years. Most patients were Stage III (59%) with negative HIV status (94%). The majority of patients (91%) received standard of care chemoradiotherapy. Overall toxicity was the highest at week 5 of treatment. At all individual time points, alpha diversity of the microbiome did not correlate with patient-reported GI function, additionally overall baseline diversity was not predictive of eventual GI outcomes. The LEfSe identified that patients with low patient reported toxicity at week 5 had higher of abundance of Selenomonas at baseline, while patients with higher toxicity had high abundance of baseline Actinobacteria, Peptoniphilus, Clostridiales , and Clostridia. When comparing the relative abundance of bacterial species among patients with high and low toxicities, patients with higher relative abundance of Clostridia and Actinobacteria had significantly higher toxicity (p = 0.03). Conclusions: Certain microbiome profiles at baseline are associated with anal cancer patients’ gastrointestinal-related PROs during chemoradiation. Our data provide novel avenues to study the potential uses of the local microbiome as a biomarker in predicting treatment toxicities in anal cancer.
Peripheral blood levels of tumor-infiltrating lymphocytes (TILs) and circulating tumor cells (CTCs) in patients with colorectal cancer.
Authors: Novikova Inna A. , Kit Oleg I. , Zlatnik Elena Yu. , Sitkovskaya Anastasia O. , Shulgina Oksana G. , Ulianova Elena P. , Gevorkyan Yuriy A. , Soldatkina Natalya V. , Kolesnikov Vladimir E. , Aleksandrovich Maksim K. , Dashkov Andrey V. , Poluektov Sergey I. , Kaymakchi Dmitry O. , Mirzoyan Ellada A. , Pavlov Vladislav K. , Dzhenkova Elena A. , Shaposhnikov Aleksandr V. , Vereshchak Maksim A. , Katelnitskaya Oksana V. , Savchenko Dmitriy A.
Published: June 2021

e15510

Background: Tumor is a structure where malignant cells interact, among others, with cells of the adaptive and innate immune systems largely determining the tumor microenvironment. The role of TILs in the disease prognosis has been shown. The amount of CTCs is one of the factors that significantly affect the risk and rate of metastasis. The purpose of the study was to assess an association between TILs and CTCs in the peripheral blood of patients with various stages of colorectal cancer (CRC). Methods: The study included 299 patients (aged 42-86 years, mean age 64.2±1.7) with stage II-IV CRC T1-4N0-2M0-1. TILs were identified in tumor material after standard histological processing. Lymphocytes were counted per 100 epithelial cells in 5 fields of view at a magnification of x400; the result was expressed as a percentage ( < 5% weak, 5-30% moderate, >30% strong). The numbers of CTCs were measured in the peripheral blood using the Veridex CellSearch system (Janssen), taking into account the expression of epithelial cell adhesion markers EpCAM, cytokeratins 8,18,19 and absence of the CD45 expression. The blood sample was evaluated according to the following criteria: 0 CTCs, 1-3 CTCs, and more than 3 CTCs. Statistical analysis of results was performed in the Statistica 13.0 program (StatSoftInc., USA). Results: Weak lymphocytic infiltration was detected in 32.8%, moderate - in 48.1%, strong - in 19.1% of cases. CTCs were detected in 62.9% cases (in 188 of 299 patients). The percentages of patients with 1-3 CTCs and with >3 CTCs were equal - 50% (94 of 188). CTCs were not registered in 37.1% cases (111 of 299). The absence of CTCs was noted equally often in moderate and strong lymphocytic infiltration – 43.7% and 43.8%. The presence of tumor cells in the peripheral blood was most often detected in weak lymphocytic infiltration, being 1.4 times more frequent than in moderate and strong infiltration (76.5% vs. 56.3% and 56.2%) (p = 0.019, c2= 11.890). Conclusions: The study demonstrated a significant relationship between the level of CTCs and the intensity of lymphocytic infiltration in the tumor (p≤0.05), which can be used as a new prognostic approach.
A retrospective study of local hepatic artery infusion chemotherapy combined with regorafenib in the treatment of advanced colorectal cancer with predominant liver metastases.
Authors: Cao Guang , Zhu Xu , Yang Renjie , Chen Hui , Wang Xiaodong , Liang Xu
Published: June 2021

e15563

Background: The hepatic arterial infusion chemotherapy (HAIC) as a second/third-line therapy has resulted in promising clinical outcomes for unresectable liver metastatic colorectal cancer (CRC). HAIC combined with regorafenib has not been reported for advanced CRC patients with predominant liver metastases. This retrospective study explored the benefits and tolerability in advanced hepatic metastatic CRC patients who received HAIC combined with regorafenib after failure of standard systemic chemotherapy. Methods: This retrospective study collected and analyzed 47 patients treated with HAIC in combination with regorafenib after standard systemic oxaliplatin and/or irinotecan in combination with Bevacizumab or Cetuximab between Jan 2017 and Jun 2020 at the Beijing cancer hospitals in China. Regorafenib was taken for 3 weeks every 4-week cycles and mostly taken 5-7 days before or after the first HAIC. The overall survival (OS), progression-free survival (PFS), objective response rate (ORR), disease control rate (DCR), and adverse events (AEs) were observed. Results: Among these 47 patients, 32(68%) were males. The median age was 61 (range: 29-75) . The median follow-up was 22.2 months (range:3.7-50.7 months). Before receiving HAIC in combination with regorafenib, 34 (72.3%) patients had previously received ≥ 2 prior lines of systemic therapy and 37 (78.7%) patients had previously received targeted biological treatment (anti-VEGF or anti-EGFR, or both).These patients underwent HAIC for a median of 4 sessions (range2--8,). The starting doses of regorafenib were 40 mg/d (n = 1, 2.13%), 80 mg/d (n = 11, 23.43%), 120 mg/d (n = 2, 4.26%), and 160 mg/d (n = 23, 48.94%). The median OS was 22.2 months. The median PFS was 10.8 (95% CI: 9.0-13.7) months. The ORR was 51.3% and DCR was 100% among 39 patients whose tumor responses were evaluated in the liver. The ORR was 13.8% and DCR was 48.3% among 29 patients whose tumor responses were evaluated outside the liver. Toxicity profile of regorafenib was as expected, with common AE were hand-foot skin reaction (12.77%), fatigue (6.38%), vomiting (6.38%), and decreased appetite (6.38%). The most common grade 3 and 4 adverse events were hand-foot skin reaction (4.26%), hypertension (2.13%), diarrhea (2.13%), and stomachache (2.13%). Only 2 patients stopped regorafenib due to AEs. Conclusions: This real-world study demonstrated that regorafenib combined with HAIC was beneficial and tolerable in advanced CRC patients with liver metastases whose disease had progressed after standard systemic therapy. It also indicated a new promising treatment strategy for late stage CRC. Additional prospective and large-scale studies are required for further confirmation. Key words: hepatic artery infusion chemotherapy; regorafenib; colorectal cancer