bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibition of cancer stem cells with TACH101, a first-in-class inhibitor of KDM4 histone lysine demethylase.
Authors: Perabo Frank , Chandhasin Chandtip , Dang Van , Del Rosario Joselyn , Chen Young K , Filvaroff Ellen , Stafford Jeffrey , Quake Stephen , Clarke Michael F.
Published: June 2022

e15105

Background: Cancer stem cells (CSCs) are believed to be responsible for both therapy resistance and metastasis. Until now, these resistant CSCs have not been well-characterized, and potential treatments targeting these cells have yet to be identified. Epigenetic modifiers, such as KDM4 histone demethylase, have been shown to play an important role in CSC renewal and maintenance. TACH101 is a novel, first-in-class pan inhibitor of KDM4 that has promising pre-clinical and pharmacologic properties as a possible cancer therapeutic. Methods: Effects of TACH101 on CSC population were evaluated in the colorectal cancer SU60 xenograft model. Mice engrafted with SU60 cells were treated with TACH101 or vehicle. The day after the last dose, tumors from each group were dissociated into single cells and used to perform (1) flow cytometry analysis of the tumorigenic cell population using markers CD44 and EpCAM, (2) single cell gene expression analysis using quantitative reverse transcription polymerase chain reaction (RT-qPCR), and (3) functional tumorigenicity assays (limiting dilution assays). Results: TACH101 administration reduced SU60 tumor growth by 62% compared to vehicle-treated mice (p < 0.0005). Flow cytometry analysis of SU60 tumor cells showed the proportion of cells with cancer stem cell features (CD44HighEpCAM+) was 2.5-fold lower in TACH101-treated mice as compared to vehicle-treated animals. Single cell gene expression analysis followed by hierarchical clustering based on expression of immature and mature cell markers showed that TACH101-treated tumors had a significant reduction in the proportion of progenitor-like cells (p = 0.01) and an increase in number of both intermediate-like and differentiated-like cells although the increase was not significant (p = 0.07). In limiting dilution assay experiments, result showed that tumors were bigger/grew faster in animals receiving tumor cells derived from vehicle-treated animals compared to TACH101-treated animals. Furthermore, TACH101 was shown to reduce the number of tumor-initiating cancer stem cells by 4.4-fold. Further evaluation of TACH101 across additional xenograft models including esophageal, gastric, breast, and lymphoma showed tumor growth inhibition of up to 100%. TACH101 demonstrated favorable cell permeability, good oral bioavailability, and high metabolic stability. Toxicity studies in rats and dogs identified potential target tissues and provided safety guidance for the use of TACH101 in human trials. Conclusions: TACH101 inhibited proliferation of and tumor initiation by CSCs. As therapy resistance and metastatic dissemination are grave consequences of CSC activity, TACH101 provides a novel approach to eradicating this population and shows broad applicability as a potential therapeutic agent. Preparations to advance TACH101 into clinical trials are underway.
An AI-based, automated workflow for identification and scoring of invasive tumors in Ki-67 stained breast cancer specimens.
Authors: Patel Bhavika , Allen Stephanie , Talwalkar Sameer S. , Mehra Navi , Thagaard Jeppe , Ramsing Thomas W. , Overgaard Agnete , Caldara Jeni
Published: June 2022

e15108

Background: Understanding the rate of tumor cell growth in breast cancer specimens may be indicative of disease aggressiveness, a tumor characteristic which can be used to make an informed treatment decision. The nuclear protein Ki-67 is increased in cells as they prepare to divide or proliferate and is therefore widely used as a proliferation marker for tumor progression. This degree of tumor cell proliferation, or the proliferative index, is commonly detailed in pathology reports shared with the patient care team. Methods: In this study, we utilized the Ki-67 [K2] immunohistochemistry (IHC) assay to stain 10 breast cancer specimens. Stained slides were imaged using the AT2 scanner (Leica Biosystems, Buffalo Grove, IL) and analyzed using the Visiopharm Image Analysis platform. Results: Previous efforts to assess Ki-67 positivity utilizing image analysis have relied on the use of a secondary stain or manual effort by the pathologist to exclude non-invasive tumor regions. These antiquated methods are costly to the lab as they require additional materials or valuable pathologist time. Our novel image analysis approach utilizes artificial intelligence (AI) to automatically denote non-invasive verses invasive tumor regions, which can then be used to quantify the Ki-67 proliferative index. Conclusions: This valuable tool will allow for greater accuracy, cost-savings, and time efficiency when analyzing breast cancer samples compared to traditional methods.
The pattern of KRAS mutations in non-small cell lung cancer (NSCLC): A retrospective study from south-eastern Georgia.
Authors: Matosz Sabrina , Elzaidy Mostafa , Abdel Karim Nagla Fawzy
Published: June 2022

e15110

Background: Carcinogenic Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation is a common oncogenic mutation found in lung cancer. It is a gain-of-function mutation that is the most commonly mutated oncogene in NSCLC; occurs in about 30% of all lung adenocarcinomas. A lot of progress has been made in targeted therapies against other oncogenic drivers, such as EGFR, HER2, MET, BRAF mutations. However, KRAS mutant lung cancer is still very difficult to manage and options are limited. Most recently, K-ras G12C has a newly approved novel targeted therapy. Different KRAS mutations may also represent different outcomes. Multiple studies have been looking into mutant KRAS and investigating it in the clinical relevance in lung cancer. Here we characterize a cohort of KRAS subtypes in all tumor types of lung cancer from south-eastern Georgia. Methods: This is a retrospective study that evaluated patients with K-ras mutant lung cancer from Augusta, Georgia geographical area. Samples were obtained from May 15th, 2015 to January 4th, 2022 and patients with KRAS mutant lung cancers were identified via Guardant platform. Results: In our cohort of patients, a total of 622 patients were evaluated in which 531 patients had a lung cancer diagnoses. Of those 531 patients, 383 had lung adenocarcinoma, 109 lung squamous cell, 34 NSCLC, 3 small cell, 1 lung carcinoid, and 1 large cell lung carcinoma. Of the 531 lung cancer patients, 14 (2.6%) patients expressed KRAS mutation with 12 (3.1%) patients expressing KRAS with lung adenocarcinoma. NRAS was expressed separately in 2 patients and HRAS was expressed separately in 1 patient. Our cohort of patients with K-ras mutant NSCLC had TP53 co-mutation in 78 (14%), MSI-High mutation in 60 (11%) patients, and EGFR mutation in 23 (4.3%) patients. The most common KRAS subtype in lung adenocarcinoma was G12V (42%), G12C (42%), and Y64D (8.3%). Two patients were unable to identify the type of the K-ras mutation. In addition, 92% of the carriers for KRAS mutation in lung adenocarcinoma were males. Its been noted that G12C mutation is the most common; however, in south-east Georgia, G12V is as common as G12C. Conclusions: KRAS mutation subtypes have distinct genomic landscape which requires further assessment to guide future therapeutic development. In the geographical area of Augusta, Georgia, KRAS subtype G12V is as common as G12C.
Identification of biomarker associated with Trop2 expression in breast cancer: Potential implication for targeted therapy.
Authors: Liao Ning , Lai Jianguo , Luo Yuting , Qi Xiaofang , Li Cheukfai
Published: June 2022

e15120

Background: Trop2 has been confirmed to enhance tumor proliferation, metastasis and invasion in various epithelial tumors. Breast cancer (BC) patients with high Trop2 protein expression have better prognosis and objective response rates. Thus, this study aimed to explore potential biomarker associated with Trop2 protein expression in BC. Methods: BC patients with complete clinical parameters were enrolled, including age, estrogen receptor (ER) status, progesterone receptor (PR) status, human epithelial growth factor receptor 2 (HER2 status), molecular subtype, Ki67 status, T stage, N stage, TNM stage, PD-L1 and Trop2 protein expression level. Univariate and multivariate ordinal logistic regression analyses were performed to identify the independent factor for Trop2 protein expression level. Immunohistochemical analysis was conducted to detect the protein expression level of Trop2 in BC. Kaplan–Meier analysis and the log-rank test were executed to assess the survival difference between low- and high- gene expression level of Trop2. Results: A total of 65 BC patients from the Guangdong Provincial People’s Hospital were included. Based on the univariate and multivariate ordinal logistic regression analyses, Ki67 status was the only independent factor for Trop2 protein expression level (P < 0.05). This finding revealed that BC patients with higher Ki67 status may harbor higher Trop2 protein expression level. According to cBioPortal database, the mutation rate of Trop2 was 2.1% and mutation type was amplification. BC patients with low Trop2 gene expression level had significantly greater survival prognosis (P < 0.05). Conclusions: We performed the comprehensive analysis of the Trop2 in BC patients. It has the potential to guide individualized targeted treatment in BC patients.
MiRNAs hsa-miR-30a-5p and hsa-miR-99b-5p regulate chemokine-mediated immune response in colorectal cancer.
Authors: Kit Oleg I. , Pushkin Anton A. , Gvaldin Dmitry Yu. , Novikova Inna A. , Timoshkina Natalya N. , Soldatkina Natalya V. , Gevorkyan Yuriy A. , Petrov Dmitriy S. , Kolesnikov Vladimir E. , Savchenko Dmitriy A. , Tolmakh Roman E. , Dashkov Andrey V. , Katelnitskaya Oksana V. , Ilchenko Sergei A. , Dzhenkova Elena A. , Kolesnikov Evgeniy N. , Maksimov Aleksey Yu. , Shaposhnikov Aleksandr V.
Published: June 2022

e15500

Background: The immune response plays a key role in the oncogenesis of colorectal cancer. The heterogeneity of the tumor environment determines the need for immunogenetic profiling to identify associations with the implementation of tumor-specific immune responses in colorectal cancer. The purpose of our study was to describe the expression profiles of miRNAs and genes involved in the regulation of the immune response in colorectal cancer. Methods: The study included 18 patients (median age 66 years) diagnosed with colorectal cancer who were treated at the National Medical Research Centre for Oncology in 2018-2019. Total RNA was isolated using TRIzol (Thermo Fisher, USA) followed by treatment with DNase 1 (ThermoFisher, USA). Sequencing of RNA samples was performed using two approaches: AmpliSeq for Illumina Immune Response Panel (Illumina, USA) and TruSeq Small RNA Library Prep Kit -Set A (Illumina, USA) according to the manufacturer's instructions on a NextSeq 550 device (llumina, USA). Results: The study revealed 168 differentially expressed genes and 46 differentially expressed miRNAs (p < 0.05). 29 miRNA-mRNA pairs were identified. It has been established that the key signaling mechanism involved in the regulation of the tumor-specific immune response is chemokine signaling pathway (hsa04062). Expression of the CXCL1 and CXCL10 genes encoding the chemokines of the same name is increased in tumor cells (logFC = 1.51, p = 0.006 and logFC = 2.67, p < 0.001, respectively). At the same time, the level of hsa-miR-30a-5p and hsa-miR-99b-5p, which negatively regulate the expression of CXCL1 and CXCL10, is decreased (logFC = -2.26, p < 0.001 and logFC = -1.57, p < 0.001). Conclusions: Activation of expression CXCL1 and CXCL10 with simultaneous loss of negative regulators hsa-miR-30a-5p and hsa-miR-99b-5p was determined in colorectal tumors by NGS-sequencing, which seems promising for the development of personalized therapy, based on the immunogenetic features of colon tumors.
Immunological microenvironment in colon cancer patients with different phenotypes of cancer stem cells.
Authors: Zlatnik Elena Yu , Novikova Inna A. , Ulianova Elena P. , Bondarenko Elena S. , Gevorkyan Yuriy A. , Soldatkina Natalya V. , Petrov Dmitriy S. , Kolesnikov Vladimir E. , Savchenko Dmitriy A. , Tolmakh Roman E. , Dashkov Andrey V. , Katelnitskaya Oksana V. , Ilchenko Sergei A. , Dzhenkova Elena A. , Snezhko Aleksandr V. , Kolesnikov Evgeniy N. , Shaposhnikov Aleksandr V. , Kit Oleg I. , Maksimov Aleksey Yu.
Published: June 2022

e15503

Background: The purpose of this study was to analyze the effect of the CD44+ and CD133+ co-expression in cancer stem cells (CSCs) on lymphocytic microenvironment of colon cancer (CC). Methods: 200 CC patients received surgery as the first stage of treatment. The percentage of CSCs with the expression of CD44+ and/or CD133+ markers was studied in the tumor homogenates by flow cytometry, as well as some indicators of local immunity (CD3+, CD4+, CD8+, T regs (CD4+CD25+CD127dim), CD19+, PD-1, PD-L1, Th0, Tm, CD16/56+ and immunophenotypic characteristics of tumor cells (PD-L1, MHC-ABC). Results: Gradation depending on the absence or presence of co-expression of CSC markers on tumor cells allowed identification of 11 statistically significant differences out of 17 studied parameters of tumor cells and their lymphocytic microenvironment. Co-expression of CSC markers was accompanied by higher percentage of T regs (7.3±0.4 versus 5.3±0.5%), together with lower levels of CD4+ cells. At the same time, a higher content of the total number of T-lymphocytes was noted due to CD8+ with an increase in the percentage of memory T cells and a decline in naive T lymphocytes within this subpopulation. In addition, the co-expression of CSC markers was accompanied by a lower content of PD-L1 (34.3±3.0 vs. 42.9±2.5%) on lymphocytes and its higher content on tumor cells (10.6±1.5 vs. 4.1±0.8%), while the PD-1 expression on lymphocytes was higher (38.4±3.7 versus 22.3±2.9%). The presence of CD44+CD133+ CSCs was also accompanied by lower percentage of tumor cells expressing MHC class I (60.4±4.9 vs. 79.3±7.6%), which characterized the inhibition of recognition processes, and increased levels of CD8+, perhaps, should be considered as compensatory. Conclusions: The lymphocytic microenvironment of CC in the presence of CSCs with the CD44+CD133+ immunophenotype seems to be more immunosuppressive, according to the increase in the local content of T regs and the decrease in MHC-ABC expression. Higher expression of PD-L1 on tumor cells and PD-1 on lymphocytes allows activation of the PD-1/PD-L1 interaction, which enhances the immunosuppressive and growth-stimulating properties of the tumor microenvironment, but at the same time, makes tumor cells adequate targets for immunotherapy with immune checkpoint inhibitors.
A colorectal biomarker think tank collaborative: Devising solutions for patients, caregivers, and cancer care teams.
Authors: Newcomer Kim , Goodman Andrea , Fathi Negeen , Shoeb Abdullah
Published: June 2022

e15507

Background: Colorectal cancer is the third-most commonly diagnosed cancer and the second-leading cause of cancer death in men and women combined in the United States. With more than a dozen known mutations in colorectal cancer, and growing knowledge about different efficacy of drug options dependent on biomarker status, biomarker testing and results can aid in more effective and lifesaving treatment planning specifically for the unique characteristics of each individual’s tumor. However, biomarker testing in colorectal cancer remains low, and the Colorectal Cancer Alliance aims to increase knowledge and awareness of testing among patients and their care teams. Methods: In 2019, the Alliance distributed an online survey to assess patient, survivor, and caregiver knowledge and understanding of biomarker testing. The results identified patient confusion, suboptimal biomarker testing rates, and critical aspects of patients' medical treatment plan. To further understand identified gaps, the Alliance recruited a diverse set of patients and caregivers at various stages of colorectal cancer for a focus group in 2021 to explore understanding around biomarkers, treatment pathways, biomarker testing decisions, and gaps around current testing and re-testing processes. Working with an expert Advisory Committee, the Alliance utilized findings from the survey and focus group to plan a 2021 Summit focused on identifying solutions for known barriers. Results: Summit participants discussed innovative and evidence-based solutions focused on three audiences: patients, caregivers, and cancer care team members, to close some of the gaps identified previously. Patient solutions focused on cancer field-wide collaborations to create standard language and health literacy standards for biomarkers and testing that allow for clear, transparent notes, patient engagement, and shared decision making. Caregiver solutions focused on elevating the caregiver role as an advocate through updated telehealth infrastructure that allows for caregiver support in the journey. Cancer care team solutions focused on utilizing continuing medical education (CME) courses to create standard health literacy standards, become better advocates for biomarker testing, and create multidisciplinary discussion opportunities between health professionals. Conclusions: Patients and caregivers are overwhelmed by the complexity and variety of treatment options. It is critical that we put swift, collaborative solutions in place with efforts to improve resources, shared language, infrastructure, and advocacy to empower cancer care teams, patients and caregivers alike. We aim to increase knowledge of and access to guideline-concordant biomarker testing, so that patients, caregivers, and cancer care teams can make informed treatment decisions accordingly, and understand the choices and discussions at each step.
Ultra-deep sequencing with unique molecular identifier(UMI) for detection of ctDNA by fragment profiling using machine learning.
Authors: Yukai Hu , Nan Hu , Rui Liao , Bing Wang , Xiaohong Duan , Chunyan Yang , Lifen Wang , Wan Qianhui , Pei Zhihua , Qiming Zhou , Wang Dongliang
Published: June 2022

e15508

Background: Liquid biopsy has been well known for its potential in cancer detection, non-invasive tumor genotyping and disease surveillance. However, ctDNA levels are low in the early stages of monitoring and postoperative progression of most tumors, which makes detection and analysis of ctDNA quite complicated. Methods: In our study, fixed-sequence UMI double-ended sequencing with a 1123-gene panel was used both on blood samples from 200 healthy donors and tissue-plasma samples from 1000 colorectal cancer (CRC) patients. First, GATK mutation detection was performed on tissue and plasma samples from 700 CRC patients to obtain trustable positive mutation sites in DBSNP138 database, meanwhile Samtools MPileUP analysis was performed on 200 healthy samples to obtain negative sites at low frequencies below 1%. Then, six features were extracted from the supporting variation sequences for the two above types of loci: IS (insert size), VBQ (variation base quality), MRBQ (mean read base quality), PIR (position in read), MQ (mapping quality) and R1&R2 (read 1 and read 2 of the paired-end sequencing). All the above data were used to establish the training set model; after that, SNV background noise was modeled by SVM and optimized through five-fold cross-validation. Last, plasma samples from 300 CRC patients were used as a validation set to verify the accuracy of the model. Results: The test set of 300 CRC patients was used to verify the accuracy of the model, in which， the effectiveness of VAF mutation frequency above 0.2% was 95%, and above 0.02% was 80% in plasma. Conclusions: We established a specific method based on UMI two-terminal capture with machine learning modeling, which was significantly superior to any available method in eliminating noise background errors and filtering false-positive low-frequency mutation.
Prediction value of TRIM29 on immunotherapy in colorectal cancer.
Authors: Han Jing , Zhang Xue , Fan Zhisong , Wang Long , Feng Li , Li Dan , Zuo Jing , Wang Yudong , Zhou Xinliang , Liu Jiayin
Published: June 2022

e15533

Background: Our previous study have found that TRIM29 expressed higher in right colon cancer than left colon cancer and rectal cancer.But the main functions of TRIM29 was not fully clarified.Bioinformatics can be used for exploring the biological function of a gene.So we further explored the molecular mechanism by using bioinformatics analysis.The results showed that TRIM29 correlated to immune dysfunction.Mismatch repair deficient(dMMR) is closely related to the efficacy of immunotherapy in colorectal cancer.We also used GEO data to explore the relationship between TRIM29 and dMMR.At last, clinical pathological data were used to explore the relationship between TRIM29 and tumor lymphocyte infiltration. Methods: At first, bioinformatics analysis was used to further explore the molecular mechanism of TRIM29.Hub genes correlated with TRIM29 and Reactome/KEGG Pathway of the hub genes were identified and performed using String database(http://string.embl.de/).TISIDB(http://cis.hku.hk/TISIDB/) was utilized to analyse the correlations between TRIM29 expression and tumor infiltrating lymphocytes, immunomodulator and chemokine.Then GEO public data including 583 sample size was download and used to confirm the correlation ship between TRIM29 expressed and pMMR/dMMR status.At last, HE sections of the 227 CRC patients were collected to explore the connection between TRIM29 and tumor infiltrating lymphocytes. Results: Functional annotations and immune activity analysis showed TRIM29 is related to tumor infiltrating lymphocytes and due to immune dysfunction in colorectal patients.For tumor infiltrating lymphocytes analyzing, elevated TRIM29 was significantly associated with Act_DC, iDC,monocyte, NK,NKT, pDC, Tcm_CD4, Tcm_CD8, Tem_CD8 and Th1 cell infltration in colorectal ( P< 0.05), leading to a general increase in immune infiltration.For chemokines analyzing,elevated TRIM29 was significantly associated with high expression of CXCR1,CXCR2 and CXCR4( P< 0.05).For immunostimulators analyzing,TRIM29 over-expression was significantly associated with C10orf54, CD70, CD276, HHLA2 and ICOSLG, causing immune imbalance( P< 0.05).For immunoinhibitors analyzing, elevated TRIM29 expression was significantly associated with PD-L1, LGALS9, PD-1, PVRL2,TGFBR1,TIGIT and VTCN1( P< 0.05).The HE results revealed that high TRIM29 protein expression was correlated with high tumor-infiltrating lymphocytes ( P= 0.0053).GSE39582 data analyzing results showed that dMMR patients expressed higher TRIM29 level than dMMR patients( P= 0.0014). Conclusions: High TRIM29 expression is related to tumor infiltrating lymphocytes and due to immune dysfunction in colorectal patients.Elevated TRIM29 expression up regulating immune checkpoint molecules after immune stimulation to avoid immune damage.TRIM29 may serve as a new biomarker for immunotherapy.
An Immune-metabolic signature (IMMETCOLS) identifies three clusters in mCRC with different immune-phenotype distribution and potential clinical implications.
Authors: Archilla Ivan , Pedrosa Leire , Garcia de Herreros Marta , Fernandez-Mañas Laia , Esposito Francis , Jares Pedro , Figueras Carolina , López Sandra , Oliveres Helena , Foguet Carles , Cascante Marta , Maurel Joan , Cuatrecasas Miriam
Published: June 2022

e15534

Background: The overall response rate following immune check-point blockade (ICB) is < 5% in microsatellite stable (MSS) advanced colorectal cancer (mCRC), and between 30-35% in MSI mCRC. We here evaluate the relationship between our immune-metabolic signature (IMMETCOLS) distribution (cluster (IMC) 1; mesenchymal glycolytic, IMC 2; epithelial-non glycolytic and IMC 3; epithelial mitochondrial oxidative) with immune phenotypes (inflamed (IF), immune-excluded (IE) and immune-desert (ID)) in MSS and MSI mCRC patients (pts). Methods: We have analyzed IMMETCOLS in a retrospective cohort of 128 mCRC pts enriched with MSI-H and BRAF genotype using the nCounter platform (Nanostring Technologies, US). Immune phenotypes were evaluated by immunohistochemistry using 7 immune markers (CD68, CD163, CD8, CD3, FOXP3, PD-L1 and PD1) in a subset of 47 mCRC pts (27 MSS and 20 MSI), in TMAs containing 4 cores from the center of the tumor (CT) and invasive front (IF). The number of stained immune cells was counted using a computerized image analysis system, and PD-L1 was evaluated using CPS score (< 1 vs > 1). Patients having a CD3 cell count below 572 cells/mm2 and a CD8 density below 175 cells/mm2 in IF or CT were considered as ID. (Halama Nils, 2011). CD3 density was also semi-quantitatively estimated in peritumoral stroma and intra-tumoral (range 1-4), defining as IE those cases with a difference > 1 between the two regions in both IF and CT (Brooks JM, 2019). Results: Cluster distribution was similar between MSI (IMC1-40%, IMC2-20% and IMC-40%) and MSS (IMC1-34%, IMC2-24%, IMC3-43%) pts. Patients with high LDH levels (> 1.5ULN) were enriched with IMC3 phenotype (p < 0.0001). MSI have increased CD3 (p = 0.002), CD68 (p = 0.002) and CD163 (p = 0.001) in CT than MSS patients. IMC1 pts had increased CD163/CD68 ratio in CT (p = 0.004). 75% of MSI pts were IE and 25% IF. 55% of MSS pts were IE, 38% ID and 7% IF. IMMETCOLS/ immune-phenotype distribution was: IMC1 (16% ID/ 84% IE), IMC2 (12% ID/ 63% IE/ 25% IF) and IMC3 (35%ID/ 47% IE/ 18% IF). PD1 immuno-expression > 1% (IF and CT) and PD-L1 positivity was observed in 38%, 30% and 28% of pts respectively. There were no differences in PD-L1 (CPS) and PD1 expression between MSS and MSI tumors. Inflamed tumors show higher PD-L1 expression compared with IE and ID immune-phenotypes (p = 0.014). PD1 > 1% expression at IF was significatively lower in IMC1 vs IMC2 and IMC3 tumors (p = 0.032). Conclusions: IMC1 subtype is associated with low PD1 expression, high CD163/CD68 ratio and IE phenotype even in MSI-H mCRC patients. Therefore, IMMETCOLS testing would be of value to identify MSI mCRC pts that do not benefit to ICB therapy.
Study of the effectiveness of chemotherapy in patients with colorectal cancer depending on the location of the metastatic lesion.
Authors: Kamishov Sergey Viktorovich , Niyozova Shakhnoza Khamoidinovna
Published: June 2022

e15540

Background: The reason for the increased interest in the chemotherapeutic treatment of metastatic colorectal cancer (CRC) is the steady increase in the incidence of this oncological pathology, as well as the high incidence of neglect of the tumor process in a significant proportion of patients in the absence of improvement in long-term treatment results. Methods: In 84 patients with metastatic CRC (mCRC), the clinical effect and toxicity of the FOLFOX4 and CAPOX regimens were studied. In 51 (60.7%) patients, multiple metastases in various organs were most common, in 18 (21.4%) - solitary, and only in 15 (17.9%) patients - solitary. Among the examined patients, men accounted for 46 (54.7%), women - 38 (45.2%). The average age of men was 57.2+0.2 years, women 65.4+0.4 years. Patients underwent 2-4 courses of treatment, after which the effect of PCT was evaluated according to the REGIST scale (2009). Results: Out of 84 patients with mCRC who received 2-4 courses of palliative chemotherapy according to the FOLFOX4 and CAPOX regimens, complete regression of the process was observed in 14 (16.7%) patients, partial regression in 34 (40.5%) patients, stabilization of the process in 19 (22.6%) and in 17 (20.2%) progression of the disease was revealed. At the same time, the highest objective response rate (PR + FR) was with metastases in the liver - 16 (76.1%) and lungs - 12 (63.1%). Of the 3 patients with brain metastases, stabilization was noted in 2 cases and progression of the process in 1 case. With combined distant metastases (lungs + liver and lungs + bones), there were 2-3 times more patients who were not sensitive to therapy than those who were sensitive. With combined distant metastases (lungs + liver and lungs + bones), there were 2-3 times more patients who did not respond to therapy than those who were sensitive to treatment. The “treatment sensitive” group included 48 (57.1%) patients with complete and partial regression. The “treatment-resistant” group consisted of 36 (42.9%) patients with progression and stabilization of the disease. Conclusions: The highest objective response rate (PR+FR) in patients with mCRC was with metastases in the liver - 16 (76.1%) and lungs - 12 (63.1%). The comparatively better results in metastatic lesions of the liver and lungs are obviously associated with a more developed blood supply to these organs, which leads to a better supply of chemotherapy drugs and the effectiveness of treatment. At the same time, the combination of localization of CRC metastatic lesions in various organs significantly worsens the results of treatment.
Clinical and molecular characterization of fusion genes in colorectal cancer.
Authors: Karan Canan , Tan Elaine , Sarfraz Humaira , Walko Christine Marie , Kim Richard D. , Knepper Todd C , Sahin Ibrahim Halil
Published: June 2022

e15568

Background: Next-generation sequencing (NGS) based molecular profiling technologies have revealed several oncogenic fusion genes that are actionable with small molecule inhibitors leading to practice change, particularly in lung cancer. The molecular and clinical characteristics of these gene fusions are not well defined in colorectal cancer patients (CRC). In this study, we aimed to define clinical and molecular characteristics of fusion genes in patients with CRC who underwent molecular profiling. Methods: Molecular characteristics of tissue confirmed 917 CRC patients were retrieved from the Moffit Cancer Center Clinical Genomics Action Committee database. Patients’ demographic and clinicopathological features and treatment history were collected from the database. All fusion genes were shown by hybridization-based NGS computational algorithms that determined cancer‐related genes, including single‐nucleotide variations, indels, microsatellite instability (MSI) status. Results: Among a total of 917 patients, 24 patients with CRC (2.6%) were found to have at least one fusion gene with a total number of 26 pathogenic fusions. The gene fusions are shown in Table. The most common, potentially targetable, fusion genes in our cohort were (1) RET fusions 0.5% (5/917), (2) ALK fusions 0.4% (4/917), (3) ROS1 fusions 0.2% (2/917), (4) NTRK1 fusion 0.1% (1/917), (5) NRG1 fusion 0.1% (1/917). Fusion genes were more common in MSI-H CRC (N = 27), and 3 (11.1%) patients with MSI-H CRC were found to have fusion genes [(RET (2) and NTRK(1)]. Fusion genes were present in both RAS wild-type (54%; 13/24) and RAS mutant (46%; 11/24) tumors. Most patients were older than 50 years (75%, 18/24) and had left-sided tumor (61.1%) tumor. Conclusions: Fusion genes are rare events in CRC. While fusion genes seem to be more prevalent in MSI-H CRC, RAS status does not correlate with the frequency of fusion genes. Actionable RET and ALK/ROS gene fusion are more common than NTRK fusion genes in this cohort of CRC patients.[Table: see text]
Characterization of NTRK alterations in metastatic colorectal cancer.
Authors: Karan Canan , Tan Elaine , Sarfraz Humaira , Walko Christine Marie , Kim Richard D. , Knepper Todd C , Sahin Ibrahim Halil
Published: June 2022

e15569

Background: Increased molecular profiling ability has resulted in the recognition of important actionable genes that can be used to direct targeted therapies in colorectal cancers (CRC). Neurotrophin receptor tyrosine kinase (NTRK) gene fusions are one of these molecular alterations that are potentially actionable with novel targeted therapeutics. However, other biologically pathogenic NTRK alterations, including point mutations, are not yet actionable in CRC. This study aimed to characterize NTRK alterations, including fusions in metastatic CRC patients. Methods: Molecular characteristics of 917 patients with CRC were collected from the Moffitt Cancer Center Clinical Genomics Action Committee database. Demographic, clinicopathological, and molecular data and treatment history were abstracted from electronic medical records. Mutations with potential oncogenic activity are considered “potentially pathogenic”, while alterations with proven oncogenic activity such as fusions are considered “pathogenic”. Results: There were 917 patients with CRC from November 2013 to December 2021, and 77 of them had NTRK alterations excluding synonymous mutations (8.3%, 77/917). Six patients had potentially pathogenic NTRK alterations, including one NTRK rearrangement (0.6%, 7/917); however, only 1 patient had an actionable pathogenic NTRK1 fusion (0.1%, 1/917), while the others (70) were a variant of unknown significance (VUS). The majority of NTRK alterations were missense mutations (92%; 71/77). The NTRK1 fusion partner was LMNA and occurred in the setting of an MSI-H tumor (3.7%; 1/27). Among patients with pathogenic and potentially pathogenic alterations (N = 7), there was only 1(14%) patient who had low tumor mutation burden (TMB) (< 10 mut/MB). Most patients were older than 50 years (70.1%, 54/77) and male (58.4%, 45/77). Thirty-six patients (46..7%) had right-sided tumor, while 41 patients (53.2%) left-sided. Across all NTRK alterations cohort, MSI-H was found in 10.3% (7/77), and POLE/POLD1 pathogenic mutations were seen in 6.4% (5/77) patients. Conclusions: NTRK gene fusion is a relatively rare event (< 1%) in CRC, including the MSI-H subtype. The majority of NTRK alterations in CRC are VUS, and they are not actionable, and they tend to be seen in the tumors with high TMB (TMB > 10). Hypermutator tumors cause frequent VUS alterations in the NTRK gene with unknown clinical relevance.
Concurrent TP53 mutations and association with outcomes within the SMAD4 mutated subgroup of metastatic colorectal cancer.
Authors: Wang Chongkai , Sandhu Jaideep Singh , Tsao Amber , Fakih Marwan
Published: June 2022

e15578

Background: SMAD4 mutations have been associated with poor prognosis in patients with metastatic colorectal cancer. However, results have been inconsistent between studies. This study aimed to determine the impact of coexisting mutations with SMAD4 on overall survival (OS) in patients with metastatic colorectal cancer. Methods: This is a retrospective, single institute study. Patients with metastatic colorectal cancer treated at City of Hope between 2013 and 2020 and with available Clinical Laboratory Improvement Amendment (CLIA) certified next-generation tumor sequencing (NGS) results were included. Overall survival was measured from the date of diagnosis of metastatic colorectal cancer. Differences in OS between groups were compared using Kaplan–Meier curves, with p-values calculated via log-rank test. Both univariate and multivariate Cox regression models were applied to estimate the hazard ratios and confidence intervals of survival based on mutation status and other clinical factors. Results: 433 patients with metastatic colorectal cancer were identified. SMAD4 mutation was found in 16.2% (70/433) of tumors. A systemic univariate and multivariate survival analysis model including age, gender, sidedness of primary tumor, RAS, BRAFV600E, APC, TP53 and SMAD4 status showed SMAD4 mutation alone was not associated with worse prognosis (multivariate HR = 1.25, 95% CI 0.90-1.73, p = 0.18). We then investigated SMAD4 mutation in combination with each of the top 4 most frequently associated oncogenes or tumor suppressor genes ( TP53-80%, n = 56; APC- 59%, n = 41; RAS-54%, n = 38; BRAFV600E-11%, n = 8) as a predictive biomarker of survival in patients with metastatic colorectal cancer. Coexisting mutations in SMAD4 and TP53 were significantly associated with worse overall survival (multivariate HR = 2.51, 95% CI 1.46-4.30, p = 0.001). The median overall survival of patients with coexisting SMAD4 and TP53 mutation was 24.2 months compared to 42.2 months for the rest of the population (p = 0.002). Conclusions: SMAD4 mutation status alone is not sufficient for predicting poor prognosis in patients with metastatic colorectal cancer. Coexisting mutations in SMAD4 and TP53 were significantly associated with worse overall survival in patients with metastatic colorectal cancer.
Real-world outcomes among patients with metastatic colorectal cancer treated first line with bevacizumab-awwb.
Authors: Jin Ran , Ogbomo Adesuwa S. , Accortt Neil A. , Lal Lincy S. , Bishi Geetanjali , Sandschafer Darcie , Goldschmidt Jerome H.
Published: June 2022

e15581

Background: Bevacizumab-awwb (MVASI) was the first FDA-approved biosimilar to Avastin (reference product, RP). Real-world data on effectiveness and safety remain limited and may help address barriers to utilization. Methods: Adult patients who had a confirmed diagnosis of metastatic colorectal cancer (mCRC) (initial presentation on or after 1 January 2018) and initiated bevacizumab-awwb between 19 July 2019 and 30 April 2020 were identified in the ConcertAI Definitive Oncology EMR Dataset. A retrospective medical chart review was conducted to evaluate patient clinical characteristics and outcome data. The current analysis focused on the subset of patients who initiated first-line (1L) bevacizumab-awwb containing therapy (with no prior use of RP) to evaluate incidence of events of interest (EOIs) (Table) and overall survival (OS) probability using Kaplan-Meier analysis. Patients were followed from the initiation of 1L therapy until death, end of record, or end of study period (June 2021), whichever occurred first. Results: A total of 129 patients who initiated bevacizumab-awwb as 1L treatment in combination with chemotherapy were included in this analysis. Majority of patients (78.3%) were treated at clinical oncology practices in a community setting (median age: 60.5 years, 53.5% male). 34.9% of patients had non-metastatic disease (stage of I/II/III) at the initial diagnosis and 38.8% had undergone surgical resection. Median duration of available follow-up data was 10.7 (range: 0.69-22.4) months. During the study period, 100 out of 129 patients had disease progression of which 46 patients had a record of death. The Kaplan-Meier analysis showed that 12-month OS probability was 71.4% (95% CI: 61.0%-79.5%). During treatment with bevacizumab-awwb, 20 EOIs were reported in 18 patients (14.0%). Distribution of events and their management are presented in the Table. None of these EOIs resulted in death. Conclusions: Biosimilar bevacizumab-awwb appeared to be well tolerated, with observed EOIs being manageable, and 12-month OS probability of > 70% for treating patients with mCRC in the real-world setting.[Table: see text]
Total neoadjuvant treatment approach and carcinoembryonic antigen level in locally advanced rectal cancer.
Authors: Sethi Ashish , Abel Stephen , Wegner Rodney E. , Renz Paul , Kirichenko Alexander V. , Wagner Patrick , McCormik James , Finley Gene Grant , Raj Moses S.
Published: June 2022

e15595

Background: Total Neoadjuvant therapy (TNT) has gained acceptance in the treatment of locally advanced rectal cancer, although the optimal sequencing of therapy chemoradiation (CRT) followed by consolidation chemotherapy (cChT) or induction chemotherapy followed by chemoradiation (iChT), remains a subject of ongoing debate. The effect of TNT sequencing and carcinoembryonic antigen (CEA) level on progression free survival (PFS) is uncertain. We conducted a retrospective analysis to examine these issues. Methods: Patients (n = 44) with locally advanced rectal cancer from June 2016 to December 2020 were reviewed. CEA level was compared against the primary outcome of response to TNT approaches. We categorized patients into 3 groups based on pre-TNT and post-TNT (i.e. pre-surgical) CEA: normal CEAPRE/normal CEAPOST, elevated CEA PRE/normal CEA POST, elevated CEA PRE/elevated CEA POST. 3-Year PFS was calculated using Kaplan-Meier method. Univariable and multivariable logistic regression analyses identified characteristics predictive of PFS and clinicopathologic variables associated with TNT sequencing. Results: The study cohort had a median age of 61 years and was predominantly male (70%) and Caucasian (94%). Pre-treatment stage was either II (27%) or III (72%), with the majority (65%) undergoing iChT. Downstaging occurred in 42/44 (95%). Baseline CEA was elevated in 40.9% of patients. On multivariable, logistic regression variable associated with receipt of CRT followed by cChT included: Age > 61 years clinical T4 disease and lack of T downstaging (p < 0.05 for all).There was no difference in 3-year PFS between patients receiving iChT versus patients receiving cChT (p = 0.53). When patients were stratified according to pretreatment CEA level, no difference in 3 year PFS were noted (p = 0.46). On multivariable analysis, lack of nodal downstaging following neoadjuvant treatment was associated with higher likelihood of progression (p = 0.02). Similarly, pretreatment CEA > 4.25 ng/ml (p = 0.08) and failure of CEA to decrease by >2 ng/ml following TNT (p = 0.07) trended toward higher likelihood of progression. Conclusions: Neither TNT sequencing, nor baseline CEA predicted the PFS although the power of our study was limited. Lack of nodal downstaging was identified as a predictor of worse PFS. Further areas of study should include plasma-based assays to quantitate circulating tumor DNA and next generation sequencing to assess prognosis with different sequencing of TNT.
Outcomes in high-grade neuroendocrine carcinomas (HG-NEC) of the gastrointestinal (GI) tract with modern therapies.
Authors: Belmont Erika , Paydary Koosha , Liao Chih-Yi , Polite Blase N. , Kindler Hedy L. , Setia Namrata , Shergill Ardaman
Published: June 2022

e15609

Background: HG-NEC of the GI tract are rare and aggressive neoplasms with poor prognosis. Approximately 37.5% of extra-pulmonary NEC are of the GI origin and are most commonly located in esophagus, stomach, pancreas and colon (1,2). Median survival of 7.5 months, with range of 5.7 months to 25.1 months has been reported (2). However, data regarding response to immunotherapy, as well as response to molecularly directed therapies are sparse. In this study, we conducted a retrospective review of GI tract HG-NEC with objective to assess role of modern diagnostics and therapies in clinical outcomes. Methods: We identified 14 patients with GI tract HG-NEC who received care at University of Chicago Medical Center (UCMC). Electronic medical records were reviewed for disease stage, treatments and clinical course. We reviewed available next generation sequencing (NGS) and circulating tumor DNA (ct-DNA) test results. In this cohort, UCMC’s NGS panel: Oncoplus was available and Guardant 360 results were reviewed for liquid biopsy. Results: In our initial review, site of origin included right side of colon (46%), left sided colon (46%), and anus/anorectal (15%). Median overall survival (mOS) ranged from 1.3 months to 81.3 months, and notably the median response to chemo-immunotherapy (IO) was 7.9 months (table 1). Notably one patient received maintenance therapy with immunotherapy alone with progression of disease (POD) in 3 weeks. Six patients had NGS results of which three (50%) had therapeutic targetable alterations (Table). Two patients had liquid biopsy done, of which one had targetable alterations and the other had no tumor related alterations detected. Of the two patients with targetable lesions, one patient has received targeted therapy with POD in 1.2 months and median OS 8.8 months; the other is in the process of initiating targeted therapy. Conclusions: To our knowledge, this is the first report to show a response to combination chemo-immunotherapy and targeted therapies in HG-NEC of GI tract. We are collaborating with other institutions to collate outcomes to similar therapy approaches in this patient cohort. With our study, we hope to inform future therapies and innovation in this important disease.
Different gene mutations among gastric cancer patients with MSS and MSI-H types in China.
Authors: Zheng Jianyong , Du Kunli , Ren Guangming , Xie Zhenyu , Li Ruikai , Zheng Gaozan , Feng Fan , Duan Weiming , Huang Depei , Zhang Hushan
Published: June 2022

e16018

Background: Gastric cancer is one of the leading causes of cancer-related deaths worldwide, although the incidence has gradually decreased in many Western countries. The status of microsatellites is an important biomarker of gastric cancer immunotherapy, but not all patients with MSI-H have excellent curative effect. Therefore, this study of the molecular background of MSS and MSI-H, which is helpful for the development of gastric cancer immunotherapy in Chinese patients. Methods: The formalin-fixed paraffin-embedded (FFPE) tissues of 6603 patients with CRC who have underwent next-generation sequencing (NGS) from Jan, 2019 to Apr, 2021 in 3DMed Clinical Laboratory Inc. were investigated in this study. These patients are still being followed up. Statistical analysis was performed using Microsoft Office Excel (2013). Results: 7.0% (139/1997) patients with MSI-H status, MSI-H and MSS tumors showed striking gene mutation differences. Among the 10 genes with the highest mutation rate, TP53 ERBB2 CDH1 PIK3CA mutations appear in both MSI-H and MSS patients. But the mutation rates of these genes vary greatly (32.3% VS 53.7%, 19.4% VS 13.0%,12.2% VS 8.2%, 34.5% VS 8.2%, respectively). Among the top 10 mutated genes, ARID1 (70.5%), mutation with the highest rate is only mutated in MSI-H patients. There are other gene mutations, including KMT2C (68.3%), RNF43 (59.7%), TGFBR2 (58.3%), RNF43 (34.5%), MSH3 (46.8%), RAD50(41.0%), MSH6(31.7%), ATR (30.2％), which have hugely higher mutation rates than MSS patients. It is worth noting that the mutation rate of TP53, BCL2L11, CYP2C19, MYC, CCNE1 and UGT1A1 in MSS patients is absolutely higher than that in MSI-H. Conclusions: There are completely differences in gene mutations between MSI-H and MSS gastric cancer patients in the Chinese population, especially TP53, ERBB2, CDH1, PIK3CA KMT2C, RNF43, TGFBR2, RNF43, MSH3, RAD50, MSH6 and ATR, which are of great significance for accurate patient stratification and treatment.