bluuebunny/crossref_metadata_2025 huggingface dataset:
HTG transcriptome panel (HTP): An accurate and robust tool for transcriptome-wide gene expression profiling.
Authors: Jaramillo Melba C. , Reinholz Greg , Rounseville Matthew , LaRoche Dominic , Kankipati Vidya
Published: June 2022

e15063

Background: Analysis of transcriptome-wide gene expression has the potential to provide insights into biological pathways and molecular mechanisms that regulate disease progression and treatment response. RNA-Seq is considered the gold standard for transcriptome analysis; however, it may not perform well with older, archival formalin-fixed paraffin embedded (FFPE) tissues or low-quality/low-quantity RNA. To help researchers overcome these challenges, HTG Molecular Diagnostics developed a Research Use Only, extraction-free, targeted human transcriptome panel with an automated, proprietary web-based data analysis pipeline that provides fast, accurate, and repeatable quantitative gene expression data for 19,398 protein-coding mRNA targets from lysed FFPE tissue samples or extracted RNA (eRNA). Methods: Panel precision was evaluated by Lin’s Concordance Correlation Coefficient (Lc) using FFPE tissue lysates and eRNA from FFPE and fresh frozen tissues, including FFPE blocks that were older than ten years. The accuracy of the HTP to perform differential expression analysis was assessed by comparing it to RNA-Seq using FFPE samples from different cancer indications. The agreement of the log fold changes between the two platforms was measured by Pearson Correlation Coefficient (Pc). Additionally, a cohort of 83 breast cancer FFPE samples, that had also been evaluated for estrogen (ER) and progesterone (PR) receptor expression by immunohistochemistry (IHC), were used to determine the correlation between HTP gene expression and orthogonal IHC data. Results: The precision of the panel measured by Lc, ranged from 0.90-0.94 across multiple operators, instruments, lots, and processing days, demonstrating that the HTP is a precise and robust panel. In addition, HTP is a competitive alternate to RNA-seq (estimated log-fold changes, Pc = 0.83 between the platforms). Archival samples demonstrated high repeatability (Pc > 0.9) with sample pass rates of 100% for HTP, which further confirms panel’s robust performance. Furthermore, the HTP gene expression results correlated with the IHC markers for ER (Pc = 0.92) and PR (Pc = 0.88) receptor status in a cohort of 83 breast cancer samples, which highlights the potential of the panel to replace IHC staining while providing expression data on thousands of additional genes. Conclusions: The results demonstrate the HTP is a powerful tool for comprehensive gene expression analysis that addresses several key limitations of RNA-Seq. The HTP is precise, accurate, user-friendly (avoids extraction-bias, fewer steps, automated data analysis), and efficient (quicker, requires lower amounts of sample, works well with samples of low quality and archival samples). Collectively, the data demonstrate HTP has the potential to be used for biomarker discovery and the development of clinical solutions.
Retrospective study on the safety and efficacy of pyrotinib in the treatment of HER2-positive non-breast advanced solid tumors.
Authors: Wang Jianzheng , Zhang Baiwen , Cheng Xiaojiao , Li Qingli , Lv Huifang , Nie Caiyun , Chen Beibei , Xu Weifeng , Zhao Jing , He Yunduan , Tu Shuiping , Chen Xiaobing
Published: June 2022

e15064

Background: Human epidermal growth factor receptor 2 (HER2) is a member of the ErbB family and a key oncogene in solid tumors. Pyrotinib has been approved for the treatment of HER2-positive, recurrent or metastatic breast cancer. However, there are very few clinical studies on pyrotinib in other HER2-positive solid tumors. Therefore, more clinical evidence is urgently needed to guide pyrotinib-based therapy in HER2-positive non-breast advanced solid tumors. Methods: We retrospectively analyzed HER2-positive non-breast advanced solid tumors patients with HER2 amplification or mutations who were treated with pyrotinib-based therapy in Henan Cancer Hospital between July 1, 2019 and December 2, 2021. In this study, 25 eligible patients were included with 16 patients with lung cancer, 6 with gastric cancer, 2 with colorectal cancer and 1 with cholangiocarcinoma. The primary end point was progression-free survival (PFS). Results: The median PFS and overall survival (OS) were 188 days (95% CI: 83–NA days) and 250 days (95% CI: 188–NA days), respectively. 16 patients with lung cancer and 6 patients with gastric cancer had a median PFS of 204 days (95% CI: 55–NA days) and 142 days (95% CI: 83–NA days), respectively. The median OS was 366 days (95% CI: 248–NA days) in patients with lung cancer and 179 days (95% CI: 90–NA days) in patients with gastric cancer. Patients receiving > 3 lines of therapies had a numerically lower median PFS and OS than those receiving≤ 3 lines of treatments (PFS:188 vs 204 days, p=0.92; OS:188 vs 366 days, P = 0.43). All 25 patients were available for efficacy evaluation. The objective response rate (ORR) was 24% and disease control rate (DCR) was 68%. The ORR for lung cancer was 25% and for gastric cancer was 16.7%. In addition, the DCR for lung cancer was 62.5% and for gastric cancer was 66.7%. Moreover, patients receiving≤3 lines of treatments had a numerically higher ORR and DCR than those receiving >3 lines of treatment (ORR:35.7% vs 9.1%,p=0.18; DCR:71.4% vs 63.6%, P＞0.99). The most common treatment-related adverse events (TRAEs) were diarrhea (84%), but only 3 (12%) patients reported grade 3 diarrhea which could be well controlled. Conclusions: These results indicated that pyrotinib-based therapy exhibited good anti-tumor activity and acceptable safety profile in HER2-positive non-breast advanced solid tumors. This retrospective study is a pilot study aimed at promoting larger-scale studies to further clarify the safety and efficacy of pyrotinib in the treatment of non-breast solid tumors. Keywords: pyrotinib, HER2-positive, solid tumor, retrospective study, advanced solid tumors.
Influence of albumin and methotrexate clearance on high-dose methotrexate-induced mucositis.
Authors: Taylor Zachary L. , Miller Tamara P. , DeGroote Nicholas , Pommert Lauren , Awoniyi Oluwafunbi , Board Sarah , Poweleit Ethan , Kastner Samuel , Ugboh Ngozi , Joshi Vivek , Ambrosino Nicholas , Weisnicht Allison , Hsiao Heidi , Bernhardt Brooke , Schafer Eric Scott , O'Brien Maureen Megan , Castellino Sharon M. , Ramsey Laura
Published: June 2022

e15081

Background: Methotrexate (MTX) is a cornerstone of therapy for several types of cancer. HDMTX-induced mucositis can impact quality of life and delay subsequent chemotherapy. Objective: The objective of this study was to understand the factors increasing risk for mucositis in patients receiving HDMTX in a multicenter cohort. Methods: A multi-center retrospective study collected data on pediatric and young adult patients ages 0-32 years at diagnosis who received at least one dose of HDMTX (>500 mg/m2) at Children’s Healthcare of Atlanta or Cincinnati Children’s Hospital Medical Center from January 2010 through December 2020. Demographic and clinical variables were manually abstracted, while medications and lab values were electronically pulled from the electronic medical record. Common Terminology Criteria for Adverse Events v5 was used to identify the presence and grade of mucositis after HDMTX administration. Institutional review board approval was obtained at each site. Chi-square and t-tests, as appropriate, were calculated using GraphPad Prism v9. MTX concentrations were fit to a published pharmacokinetic model to estimate clearance using NONMEM. Results: The cohort is described in Table. The rate of mucositis was highest after the first HDMTX administration (54.6%), when the MTX clearance is slowest (30.1%<10 L/hr/1.73m2 and albumin was lowest (14.3%<2.5g/dL). Mucositis was significantly more likely in patients with hypoalbuminemia and in patients with MTX clearance <10 L/hr/1.73m2 (OR 1.75 (CI: 1.503 to 2.028), p<0.0001 and OR 1.43 (CI: 1.236 to 1.653), p<0.0001, respectively). Conclusions: Mucositis after administration of HDMTX is common, with 72% of patients experiencing at least grade 1 mucositis and a third of HDMTX administrations leading to mucositis. Chart abstraction is ongoing at a third hospital to increase the sample size, particularly those of Hispanic/Latino ethnicity, in order to investigate differences by race and ethnicity. In addition, current analyses are evaluating the impact of changes in supportive care on HDMTX-induced mucositis and other adverse events. The results of this study will demonstrate who is at highest risk for adverse events so supportive care can be tailored during this potentially toxic chemotherapy.[Table: see text]
Real-world analysis of BRAF inhibitors with patients positive for BRAF V600E mutations diagnosed with rare tumors.
Authors: Peelay Zoya , Patil Vijay Maruti , Noronha Vanita , Pathak Shruti , Menon Nandini Sharrel , Prabhash Kumar
Published: June 2022

e15085

Background: BRAF mutation is seen in multiple cancers and BRAF inhibitors have a tumor agnostic nature. However there is very limited real world data for BRAF inhibitors and hence we have performed this analysis. Methods: In Tata Memorial Hospital, the medical oncology solid unit 2 maintains a prospective database of all patients who undergo molecular testing. A query was raised from this database and 17 patients were identified who were BRAF mutant positive. The demographic details of these patients, the previous treatment details, the therapy received by these patients, the response to the therapy, the date of progression and the date of death was recorded. Descriptive statistics were performed and Kaplan-Meier analysis was used to estimate the progression-free survival (PFS) and overall survival (OS). Results: In all the 17 patients the mutation was BRAF V600E.The median age of the patients was 58 years (16-77). The m:f ratio was 13:4. The Eastern Cooperative Oncology Group (ECOG) performance status (PS) was 0-1 in 9 patients (52.9%) and 2-3 in 8 patients (47.1%). The primary sites included in the analysis were lung cancer in 8 (47.1), glioma in 3 (17.7), thyroid in 2 (11.8%) and one each of parotid, melanoma, esophagus, thymoma. BRAF inhibitors could be provided in 9 patients (52.9%) and its was dabrafenib-trametinib in 8 patients and vemurafenib then dabrafenib-trametinib in 1 patient. The median progression free survival was 203 days (95% CI 25.1-380.9) and overall survival was 220 days (95% CI 49.8-408.2) . Conclusions: The real world data suggests that the efficacy of BRAF inhibitors seems to be lower than that seen in pivotal studies. The reasons for which is unknown.
Precision medicine: Novel PI3K inhibitor as cancer treatment.
Authors: Hutchings Kasen Reed , Beck Patrick , Qiu Rebecca , Bui Vincent , Sheng Zhi
Published: June 2022

e15093

Background: Phosphoinositide 3-kinase (PI3K) is an attractive anti-cancer drug target due to its promotion of cell growth and proliferation; however, available pan-PI3K inhibitors currently lack specificity, leading to excessive drug toxicity and adverse effects. Selectide-18 is a novel PI3K inhibitor that targets PI3K’s catalytic subunit p110β, resulting in reduced viability of cancer cells. The p110β subunit is the most prominent PI3K subunit in many chemoresistant tumors. Previous research has revealed a unique 18-residue long motif within the C2 domain of p110β. This motif is not found in other catalytic subunits (p110α, p110δ, or p110γ), making it a promising drug target. Selectide-18 is a memetic peptide drug modeled after this motif and has been shown to effectively inhibit p110β binding without affecting other isoforms, separating it from currently available pan-PI3K inhibitors. While Selectide-18 has been successful in inhibiting PI3K in previous studies, it has poor cell permeability due to its large size. Previous findings have revealed functional redundancies among Selectide-18’s residues. This study aims to remove these redundancies and determine the optimal formulation of Selectide-18 through in silico analysis. Methods: An in silico protocol was developed to determine the optimal formulation of Selectide-18. By utilizing the PEP-FOLD server, 455 peptide models were created using 91 unique fragments of the Selectide-18 amino acid sequence ranging in size from 6 to 17 residues. Physical conformation of each model was compared to wild-type Selectide-18 using root-mean-square deviation data collected using PyMOL and UCSF Chimera software. Computational docking through AutoDock Vina was performed to test the binding affinity of each model to the active site of regulatory subunit p85α. The distance between each drug and the active site was measured with UCSF Chimera’s distance function. Finally, ClusPro docking of drug-bound p85α/p110β was compared to wild-type p85α/p110β, as well as non-truncated Selectide-18-bound p85α/p110β. Statistical significance was determined using a Student's t-test. Results: Select truncated models demonstrated physical confirmation (RMSD = 0.024), binding affinity (-8.74 kcal/mol), and simulated inhibitory capabilities comparable to Selectide-18. A specific group of variants comprised of 9 amino acids (9 residue_6K-14Q) had the shortest formulation without significant declines in binding affinity. Conclusions: Selectide-18 is a selective PI3K inhibitor that can be optimized by removing functionally redundant amino acids. A 9-residue variant ranging from amino acids 6Lys to 14Gln showed the most promise and will be used in future studies to reformulate Selectide-18. Being half the size of Selectide-18, this optimized drug is anticipated to have improved cell permeability without sacrificing inhibitory function.
The development of APS03118, a potent next-generation RET inhibitor for treating RET-inhibitor-resistant patients.
Authors: Subbiah Vivek , Zhong Jun , Lu Ying , Liu Yongbo , Chen Minchun , Chen Xiaohu , Wang Hao , Zhu John , Lu Shun , Drilon Alexander E.
Published: June 2022

e15107

Background: Oncogenic RET is an actionable target across a variety of cancers. Selective RET inhibitors selpercatinib and pralsetinib were recently approved by the FDA and EMA for patients with RET-dependent NSCLC and thyroid cancers. The solvent front mutations (SFMs) RET G810C/S/R have been identified as mechanisms of acquired resistance to both drugs. APS03118 is a novel next-generation RET inhibitor which is potent against a range of RET fusions and mutations including both SFMs and gatekeeper mutations. Methods: The selectivity, anti-RET activity, and intracranial efficacy of APS03118 were confirmed in vitro and in vivo in a variety of RET-dependent tumor models. Results: APS03118 was highly selective against a panel of 468 kinases and demonstrated 130-fold selectivity over VEGFR-2. In enzymatic assays, APS03118 showed low nanomolar potency against wild type RET and 25 RET mutations/fusions, including the inhibition of RET G810R/C/S (IC50 0.04-5 nM) and RET V804M/L/E (IC50 0.04-1 nM). APS03118 inhibited RET phosphorylation (IC50 < 15 nM) in Ba/F3 engineered RET cells (WT, G810R, V804M, M918T). In cell proliferation assays, APS03118 potently inhibited the proliferation of KIF5B-RET Ba/F3 (WT, V804M, V804L, M918T), CCDC6-RET Ba/F3 (WT, V804M, S904F), LC2/ad (CCDC6-RET), TT (RET C634W) (IC50 < 10nM); Ba/F3 RET G810R and G810S IC50 (8-65 nM). APS03118 demonstrated marked anti-tumor efficacy in vivo in RET-driven cell-derived (Ba/F3 KIF5B-RET, V804M, TT (C634W)) and patient-derived (KIF5B-RET, CCDC6-RET, CCDC6-RET V804M) xenograft tumor models at 10 mg/kg (TGI 87-108%). Tumors completely subsided in CCDC6-RET orthotopic brain model with a 100% survival rate. In the Ba/F3 KIF5B-RET G810R xenograft model, APS03118 30 mg/kg showed 90% TGI and was well tolerated, and RET G810 mutations often drive clinical progression on current RET inhibitors. The pharmacokinetic/pharmacodynamic relationship of APS03118 in Ba/F3 KIF5B-RET G810R and WT xenograft tumor model was investigated, and the sustained decrease of the phosphorylated RET were observed at 30 mg/kg with the plasma exposure exceed cell IC90. Conclusions: APS03118 is a novel highly selective next-generation RET inhibitor that possesses potent in vitro and in vivo activity against a diverse range of RET alterations, including SFMs-mediated resistance. APS03118 has received IND approval and Fast Track Designation from FDA, and a first-in-human phase 1 trial for patients with RET-driven solid tumors with activating RET alterations is planned for 2022.
Pan-Cancer analysis of the mutation frequency of genes in DDR pathway in Chinese population.
Authors: Zhang Zhe , Li Zhuoqi
Published: June 2022

e15109

Background: The DNA damage repair (DDR) pathway is of vital importance to maintain human genomic stability. And the variation of DDR pathway related genes is closely related to tumorigenesis, tumor progression and therapeutic response. In order to comprehensively study the mutation status of DDR pathway related genes in human cancers, we evaluated the genomic features of Chinese pan-cancer patients and investigated the mutation frequency of genes in DDR pathway. Methods: A total of 5018 patients consisting of more than 22 cancer types were enrolled in this study. Utilizing target next-generation sequencing (NGS) platform, genomic profiling of 599 cancer-related genes was performed on tumor tissue or blood samples. And many DDR pathway related genes are included and detected mutations such as TP53, BRCA2, BRCA1, ATM, BLM, FANCA, POLE and so on. Results: We observed 91.23% (4578/5018) of cases harbored at least one alteration of the DDR pathway genes. The mutation frequency ranges from 71.88% to 100.00% among the 22 cancer types. Among them the DDR gene mutation frequency of lymphoma, esophagus and esophagogastric junction cancer and endometrial cancer are all 100%, and mutation frequency of bowel cancer, hepatobiliary cancer, melanoma, breast cancer, esophageal cancer, gastric cancer and central nervous system cancer are also more than 90% respectively. The highest mutation rate gene is a well-known tumor suppressor gene TP53, which mutated in 2650 patients and the mutation rate is 52.81%. And it primarily mutated in esophageal cancer, with a mutation rate of 81.43%. Besides the mutation rate of TP53 in gastric cancer, bowel cancer, breast cancer, ovarian cancer, pancreatic cancer, bladder cancer and hepatobiliary cancer are all more than 50%. Followed by is BRCA2 gene, which is also a tumor suppressor gene and the mutation rate is 16.04%. Next is ATM, BLM and FANCA, the mutation rate of which is 11.68%, 11.12% and 8.97% respectively. Conclusions: We find a unique genomic feature of DDR pathway in the comprehensively analysis of the mutation profile of the Chinese pan-cancer patients, which may provide potential therapeutic targets in the future.
Mapping the epidemiologic characteristics of cancer patients with NTRK gene fusions: A real-world analysis of the Cerner Enviza Eletronic Health Records (EHR) database.
Authors: Vikis Haris G. , Clark Otavio , Furegato Martina , Vavroch Nathan , Purinton Stacey , Haskell Tom , Boshears Tasha
Published: June 2022

e15123

Background: Fusions in neurotrophic-tropomyosin receptor kinase (NTRK) genes occur in a vast array of tumors and are among the most important genetic alterations in cancer patients. Their presence warrants the use of specific agnostic therapy (AT) with TRK inhibitors Larotrectinib (L) and Entrectinib (E). AT is associated with high levels of tumor response rate in patients showing NTRKgenetic alterations. This mutation is rare and the epidemiologic profile and clinical characteristics of NTRK positive patients are not completely clear. Methods: Our aim was to identify and describe the characteristics of patients with NTRK fusions in a large EHR database. De-identified records of NTRK positive oncologic patients were retrieved from Cerner-Enviza EHR, a healthcare provider network with 100 different providers across the USA, between November 2018 to August 2021. Data extracted were primary tumor, gender, age, and treatment received. Results: We identified 123 patients with NTRK alterations. Major primary tumor locations are described in the table. Males were 56% of the population, median age at diagnosis was 59 years, 36% of the patients were treated with E and 64% with L. Conclusions: In this sample, NTRK mutations were more common in patients with Lung Cancer and Soft Tissue tumors. The median age at diagnosis was 59 years.[Table: see text]
Insights into mutational differences between upper tract urothelial carcinoma and urothelial carcinoma of the bladder.
Authors: Chen Yuanlei , Lu Zeyi , Wang Fangqin , Luo Yijie , Xu Liwei
Published: June 2022

e15125

Background: Upper tract urothelial carcinoma (UTUC) is histologically similar to bladder urothelial carcinoma (BUC), yet several clinical, biological and molecular features are unique to UTUC. UTUC may have unique genomic factors compared to BUC, while major knowledge gaps remain in our understanding of the biology and genomic landscape of UTUC. Methods: We retrospectively sequenced tumor samples and matched germline DNA using targeted next-generation sequencing methods and analyzed at least 642 cancer-associated genes. The cohort included 35 UTUC patients and 36 BUC patients. Results: Among all cases, KMT2D and TP53 were the most common mutations (account for 66% and 75% in UTUC and BUC, respectively). The most frequently mutated genes in UTUC were KMT2D (37%), TP53 (29%), ELF3 (26%), FGFR3 (23%), ASXL1 (20%), DKN2A (20%), DKN2B (17%), REBBP (17%), MT3B (17%), GNAS (17%) and PIK3CA (17%). The most frequently mutated genes in BUC were KMT2D (36%), TP53 (39%), MUC17 (14%), ARID1A (22%), GNAS (19%), RB1 (19%), BCL6 (19%), E2F3 (19%), EIF4A2 (19%) and FGF3 (19%). However significant differences in the prevalence of mutations in individual genes were observed. FGFR3 (23% vs. 8%) and ELF3 (26% vs. 11%) were more frequently altered, whereas RB1 (6% vs. 19%), E2F3 (3% vs. 19%) and BCL6 (3% vs. 19%) were less frequently altered in UTUC (P < 0.05). FGFR3 mutations have been shown to be oncogenic and RB1 inactivation has been associated with genomic instability in urothelial cancer in previous researches, which represent potential therapeutic targets. Conclusions: Â UTUC and UCB exhibit significant differences in the prevalence of genomic landscape and carcinogenesis. A comprehensive understanding of the biology of UTUC and UCB is needed to identify new drug targets in order to improve clinical outcomes.
Integrated analysis of genomic alterations of Chinese lung adenocarcinoma with micropapillary component.
Authors: Wang Yongjie , Yang Ronghua , Wang Dong , Zhang Shanshan , Xuan Yunpeng , Li Peng , Wang Lingjie , Che Shuyu , Han Minghui , Yu Yi
Published: June 2022

e15130

Background: Lung adenocarcinoma (LADC) with micropapillary component (MPC) is a special pathological subtype of LADC, which poses higher invasive with poor prognosis, regardless of proportion of MPC. The effectiveness of molecular targeted therapy in MPC-LADC patients is still being explored without sufficient clinical evidence. Herein, we comprehensive analyzed the genetic alterations of MPC-LADC in order to find effective potential drug-target genes and guide new therapeutic strategies. Methods: We enrolled 31 MPC-LADC patients at Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University from January 2019 to December 2020, and also randomly selected 89 non-MPC-LADC patients as a reference cohort. FFPE or fresh tumors and matched blood samples were performed for NGS-based target panel detection of at least 420 genes (range 420-638 genes), and we analyzed the genomic alterations of the genes with intersection in the above panels sequencing. Results: In our MPC-LADC cohort, the proportion of micropapillary component in 31 tumors were: 5 cases with MPC < 5%, 13 cases with MPC 5% - 20%, 10 cases with MPC ≥20% and other 3 cases unclear. The most frequently mutant genes were EGFR (61.3%, 19/31), TP53 (41.9%, 13/31), ALK (19.4%, 6/31), CTNNB1 (16.1%, 5/31), KRAS (12.9%, 4/31) and SMAD4 (12.9%, 4/31). Moreover, 90.3% (28/31) patients harbored genomic alterations in RTK/RAS/MAPK pathway, 54.8% (17/31) in cell-cycle pathway, 38.7% (12/31) in Wnt pathway, and 19.4% (6/31) in PI3K/AKT/mTOR pathway. Notably, the median age of patients with ALK fusions were younger than wild-type patients (53 vs 60 years, p < 0.05). Patients with KRAS mutations had larger tumor sizes than wild-type patients (Median: 3.4 vs 2.2 cm, p < 0.05), and their lesions are more prone to vascular invasion (p < 0.05). Compared with the reference group of non-MPC-LADC patients, three mutant genes were significantly enriched in MPC-LADC group, namely, CTNNB1 (16.1% vs 1.1%, p < 0.01), ALK (16.1% vs 2.2%, p < 0.05) and SMAD4 (12.9% vs 2.2%, p < 0.05). Finally, we obtained the date of micropapillary lung adenocarcinoma in Memorial Sloan-Kettering Cancer Center (MSK) from cBioPortal database, and survival outcome analysis displayed that EGFR mutations were significantly associated with poor overall survival (OS) (p < 0.05). Conclusions: In this study, we comprehensive revealed the genomic alterations of Chinese MPC-LADC patients and their association with clinicopathological characteristic. Several MPC-enriched genes including EGFR, ALK, KRAS, CTNNB1 and SMAD4 were identified which may be potential genetic drivers of micropapillary lung tumors and could help us to reveal distinct therapeutic avenues of MPC-LADC.
Utilization of nano-hmC-seal technology to detect epigenetic signatures of peritoneal metastasis in cell-free DNA (cfDNA) in patients with colorectal and high-grade appendiceal cancer.
Authors: Dhiman Ankit , Malina Yuri , Gao Lu , West-Szymanski Diana , Rivas Marco , Cui Xiao-Long , Witmer Hunter D. D. , Berger Yaniv , Ulrich Leah , Dougherty Urszula , Kwesi Akushika , Zhang Wei , He Chuan , Bissonnette Marc , Turaga Kiran
Published: June 2022

e15510

Background: Peritoneal metastases from lower GI tumors are common and cause significant morbidity. Assays of circulating-tumor DNA (ctDNA) to identify peritoneal recurrence after curative-surgical intent are limited due to the low abundance of DNA shed by these tumors, especially mucinous tumors. We demonstrate for the first time an ultra-sensitive test to detect biomarkers modified by the epigenetic mark 5-hydroxymethylcytosine (5hmC) in human cfDNA utilizing nano-hmC seal technology to identify patients with peritoneal metastases (PM) after curative-intent resection. Methods: Patients treated with curative intent resection of colorectal (CRC) and high-grade appendiceal (HGA) cancers underwent prospective plasma collection. Peritoneal disease was documented by direct visual inspection (laparoscopy/laparotomy). Plasma samples were analysed using nano-hmC-seal technique to obtain 5hmC signatures. Genome-wide differential analysis was used to identify significant 5hmC- differentially modified gene body regions (p-value < 0.01 and log-fold change > 10%). Functional annotation analysis was performed to further characterize differentially 5hmC -modified genes noted on multivariate logistic models. Results: Of 64 patients included in the study (CRC = 26; HGA = 38), 47 (73%) were PM+. The median DNA extracted per sample was 23.5 ng (IQR: 15.8-38.3), and no sample failed sequencing criteria. After genome-wide analysis, 39 gene body regions were identified as differentially 5hmC-modified, and 14 genes remained significant after multivariate adjustment. The signatures for PM+ patients were distinguishable from PM- patients using hierarchical clustering and principal component analyses. Functional annotation analysis based on the 14 genes point to alterations in immune and microbiome-related pathways in PM+ group (Table). Conclusions: We report for the first time the detection of peritoneal metastasis in cfDNA from human lower GI cancers using nano-5hmC seal epigenomic technology. This technology could be exploited to detect recurrences in tumors that shed very low levels of cfDNA. This signature is being validated in a prospective clinical trial (NCT 04157322).[Table: see text]
Survival analysis of patients with early and standard onset colorectal cancer: A single center study.
Authors: Patel Dhruv , Martins Maia Catarina , Lyudmer Michael , Tolu Seda , Chergui Adel , Patel Riya Jayesh , Kim So Yeon , Gali Radhika , Acuna Villaorduna Ana , Goel Sanjay
Published: June 2022

e15512

Background: While more aggressive clinical/pathological features have been consistently described in between patients with early-onset (EO) and standard-onset (SO) colorectal cancer (CRC), survival data have been conflicting. While some studies report better survival rates for EO-CRC; others found that outcomes among groups are not different. In a prior study, using the Surveillance, Epidemiology and End Results (SEER), we reported that cancer-related survival did not differ between EO-CRC and SO-CRC; however, a main limitation was the lack of molecular status and treatment details among groups. This study aims to compare the survival of EO-CRC and SO-CRC patients at Montefiore Medical Center. Methods: Retrospective cohort among 690 patients diagnosed with metastatic colorectal cancer (CRC) at Montefiore Medical Center between 2010 and 2018. Patients were identified using the software Clinical Looking Glass and charts were reviewed manually to gather information about demographics (race/ethnicity defined as Non-Hispanic White [NHW], Non-Hispanic Black [NHB] and Hispanic [H], gender, comorbidity index, calculated using the Charlson comorbidity score), clinicopathological features (grade, tumor sidedness, K-ras mutation) and treatment-related characteristics (metastatectomy, lines of chemotherapy and use of biologics). EO-CRC was defined as CRC diagnosis before age 50 and SO-CRC as CRC diagnosed at 50 years or older. Overall survival was compared between EO-CRC and SO-CRC using Kaplan Meier and Cox regression analyses. Stata v15.1 was used for statistical analysis. Results: Of 690 patients with CRC, 139 (20.1%) had EO-CRC and 551 (79.9%) had SO-CRC. Participants with EO-CRC had a higher frequency of poorly-differentiated tumors (35.5% vs. 23.8%, p = 0.02), a lower comorbidity index (6 vs. 7, p < 0.001). and a higher use of biologics (70.5% vs. 60.8%, p = 0.03) compared to SO-CRC. K-ras mutation was available for 377 (54.5%) of cases and did not differ among groups (45.9% vs. 45.9%, p = 0.99). In a model adjusted for race/ethnicity, gender, comorbidity index, sidedness, use of biologics and metastatectomy, there was no difference in mortality among groups (HR:0.9, 95%CI: 0.58 – 1.43, p = 0.68). This result remained unchanged in a model restricted to patients with available K-ras-status (n = 75), adjusted for all these variables. Conclusions: Despite more aggressive clinical/pathological features in patients with EO-CRC, survival does not differ compared to SO-CRC.
Diagnostic accuracy of the CxPREVENTIVE Colon model for early detection of colorectal cancer.
Authors: Calleja Sergio J , Patiño Édgar C
Published: June 2022

e15518

Background: Despite different available methods for colorectal cancer (CRC) screening and their proven benefits, morbidity, and mortality of this malignancy are still high, partly due to technical limitations and low compliance with screening. The aim of the present study was to assess the diagnostic accuracy for early detection of CRC using a modeling algorithm based on multiple blood and urine biomarkers. Methods: In this retrospective cohort study, clinical and blood and urine markers-based algorithms with predefined cutoff values were applied to a generally healthy asymptomatic outpatient cohort of adults aged 50 years or older undergoing colonoscopy and histopathology for routine colorectal cancer screening. We used a modeling algorithm based on two different frameworks (Multiple Biomarkers Disease Activity Algorithm MBDAA [Bioprognos], and Artificial Intelligence Recursive Algorithm AIRA [Mintlot] both in Barcelona, Spain). Both algorithms compute information from a wide number of analytes, tumor markers (AFP, CA 19.9, CA 72.4, CA 125, CEA, Cyr61, NGAL, EGFR and 8-OHdG), and additional clinical data (age, weight, height, and BMI). MBDAA includes Barcelona Criteria (four criteria to correctly interpret the cause of the increase in tumor markers, benign or malignant, defined by the Spanish Society of Clinical Biochemistry and Molecular Pathology, Commission of Biological Markers of Cancer). To assess the association between the modelling algorithm and downstream diagnosis we used logistic regression to compute receiver operating characteristic curves (ROC). Exact binomial confidence limits were calculated to test accuracy, sensitivity, and specificity. Results: 221 people (median age 63 yr. [IQR 49-77]; 107 [49%] women and 114 [51%] men) who underwent colonoscopy at the Juan Ramón Jiménez Hospital (Huelva, Spain), were included in this analysis. Based on colonoscopy and histopathologic findings, CRC was diagnosed in 45 (20%) patients, colonic polyposis in 56 (25%), inflammatory bowel disease in 37 (17%), and absence of pathological findings (control group) was seen in 83 (38%). The diagnostic intervention for CRC yielded an area under the curve (AUC) of 1 among the entire specimen set, accuracy 1 (95% CI 0.996,1), Se 1 (0.988, 1) and Sp 1 (0.997, 1). Besides, the algorithm also performed very well in the identification of polyps with an accuracy 1 (95% CI, 0.967 to 1), Se of 1 (0.991, 1) and of Sp 1 (0.996, 1), as well in the diagnosis of inflammatory bowel disease with an accuracy of 1 (0.968 to 1), Se of 1 (0.986, 1) and Sp of 1 (0.997, 1). Conclusions: Using colonoscopy as a gold standard, our data suggest that an innovative newly designed non-invasive blood and urine-based biomarker algorithm CxPREVENTIVE Colon may provide a timely diagnosis of CRC with very high accuracy. Our findings warrant further investigation, and we are planning large-scale (n 10,000), fully powered study to inform clinical practice.
A RAS-independent biomarker panel pedicts response to MEK-inhibitors in colorectal cancer.
Authors: Pfohl Ulrike , Loskutov Jürgen , Bashir Sanum , Kühn Ralf , Templin Markus , Mamlouk Soulafa , Belanov Sergei , Vetter Marcus , Reinhard Christoph , Wedeken Lena , Regenbrecht Christian RA
Published: June 2022

e15524

Background: Biomarker discovery and development are essential for stratifying cancer patients in order to improve treatment outcomes. In colorectal cancer (CRC), mutations in the TGF-β/BMP pathway, especially in the SMAD4 gene have been correlated with decreased overall survival and are suspected to modulate drug sensitivity on the cellular level, hence SMAD4 mutations are worthwile targets for novel targeted therapy aproaches. Methods: In the present study, we uncover the mechanistic role of a loss-of-function mutation in SMAD4 in syngeneic patient-derived organoids (PDOs). CRISPR-engineered SMAD4R361H PDOs were subjected to a comparative drug screening, RNA-Sequencing and multiplex protein profiling analysis (DigiWest®). We have confirmed the response towards MEK inhibition of the initial model in an additional set of 62 PDOs with known mutational status. Results: We show that acquisition of SMAD4 loss-of-function mutations renders PDOs sensitive to MEK-inhibitors. Further, an activation of the TGF-β/BMP signaling pathway, specifically of the BMP branch was observed in SMAD4wt PDOs; indicating that BMP signaling is likely responsible for the resistance towards MEK inhibition. It is plausible that functional loss of SMAD4 and thus loss of BMP signaling renders SMAD4 mutated tumors more sensitive to MEK-inhibitors. By looking at additional genes involved in TGF-β/BMP signaling that are frequently mutated in CRC, we identified the novel gene mutational SFAB-signature ( SMAD4, FBXW7, ARID1A, or BMPR2), when at least one pathogenic mutation is present in these genes. The frequency of SFAB in CRC patient cohort (TCGA, n = 594) was comparable to the frequency of SFAB in our PDOs. For PDOs with SFAB-signature, we found up to 95% and 70% significant positive prediction for cobimetinib and selumetinib, respectively and also up to 70% positive prediction for trametinib. Thus, the SFAB-signature predicts response to MEK inhibition in PDOs with a very high confidence. We further investigated whether the RAS status of CRC PDOs does predict sensitivity to MEK inhibition. The RAS status alone and in combination with SFAB-signature failed to yield better prediction sensitivity to MEK-inhibitors. Conclusions: The present study is a significant step forward to more personalized treatment regimens for CRC patients by early inclusion of MEK-inhibitors. The SFAB-signature should be put to clinical testing as a RAS-independent biomarker for stratification of patients providing a valuable alternative treatment option against CRC, thus ensuring that all patients receive effective and specific therapies as early as possible.
Modifiable and non-modifiable risk factors associated with early-onset colorectal cancer: Analysis of the National Health Interview Survey.
Authors: Kang Hyeun Ah , Zhang Yahan
Published: June 2022

e15528

Background: The incidence of early-onset colorectal cancer (EO-CRC), colorectal cancer (CRC) diagnosed in individuals younger than 50 years, is rapidly increasing in the United States. However, risk factors for EO-CRC are poorly understood. Identifying potential risk factors using population-based health data is critical to identify at-risk populations and develop cost-effective screening guidelines and other prevention strategies. This study aimed to identify potential modifiable and non-modifiable risk factors associated with EO-CRC. Methods: This cross-sectional study used data from 2004-2018 National Health Interview Survey (NHIS), a nationally representative health information of US population collected through personal household interviews. Individuals who were at an age of 18-49 years and had a history of CRC diagnosis at the time of the interview were identified as patients with EO-CRC, and their demographic, clinical, and behavioral characteristics were compared with those of non-cancer young adult (18-49 years) population. In addition, their non-age-related characteristics (gender, race/ethnicity, region, and body mass index [BMI]) were compared with those of individuals who were diagnosed with CRC at age 50 or older (late-onset CRC; LO-CRC). For both comparisons, bivariate and multivariable logistic regression (proc surveylogistic) analyses were performed. Results: We identified 156 patients with EO-CRC (weighted: 105,300; 46.4% female; mean age = 41.8 [SE = 0.69]), 204,846 with non-cancer (weighted: 126,257,662; 50.7% female; mean age = 33.6 [SE = 0.05]), and 1,972 with LO-CRC (weighted: 920,231; 48.6% female; mean age = 72.6 [SE = 0.28]). Results from the comparison between patients with EO-CRC and non-cancer population showed that higher odds of having EO-CRC were associated with older age (Odds Ratio [OR] = 1.11; 95% CI = 1.08–1.14), living in Midwest (vs. South; OR = 1.64, 95% CI = 1.06 – 2.55), and history of alcohol consumption (vs. lifetime abstainer; OR = 2.09, 95% CI = 1.01 – 4.36). Lower odds of having EO-CRC were associated with being Hispanic or Asian (vs. non-Hispanic White; OR = 0.43, 95% CI = 0.22 – 0.84 and OR = 0.38, 95% CI = 0.16 – 0.92, respectively) and doing vigorous physical activity (vs. no activity; OR = 0.34; 95% CI = 0.21 – 0.55). Gender, BMI, diabetes, and smoking were not significantly different between the two groups. Compared with patients with LO-CRC, those with EO-CRC were more likely to be Hispanic (vs. non-Hispanic White; OR = 2.21, 95% CI = 1.14 – 4.31) and live in Midwest (vs. South; OR = 1.62, 95% CI = 1.02 – 2.58). Gender and BMI were not significantly different between the two groups. Conclusions: In this cross-sectional population-based study, we identified potential modifiable (alcohol consumption and physical activity) and non-modifiable (age, race/ethnicity, and region) risk factors associated with EO-CRC.
Identifying potential glycoproteomic biomarkers for diagnosis of colorectal cancer (CRC).
Authors: Lindpaintner Klaus , Desai Khushbu , Xu Gege , Rice Rachel , Castellanos Alyn , Serie Danie , Mitchell Alan
Published: June 2022

e15529

Background: Excluding skin cancers, colorectal cancer is the third most common cancer diagnosed in both men and women in the United States. Colorectal cancer (CRC) affects men and women of all racial and ethnic groups and is most often found in people who are 50 years old or older. To aid diagnosis and improve screening for CRC, this study focuses on identifying glycoprotein biomarkers using blood serum. Methods: Novel methods including liquid-chromatography/mass-spectrometry (LC-MS) with in-house peak integration software PB-Net were used to identify glycoprotein biomarkers by analyzing blood serum. Samples were sourced from different biorepositories including 245 CRC, 38 adenoma and 196 healthy controls. The data were split into 75% training and 25% hold-out test set for multivariable predictions. Statistical analysis was performed on normalized data to identify potential biomarkers differentiating adenoma and different stages of CRC samples from the healthy controls. Results: There were 419 significantly differentially expressed glycopeptides/peptides from comparisons between CRC and adenoma samples against the healthy control samples with an FDR < 0.05. A subset of these biomarkers were assessed, generating a 21-biomarker multivariable classifier model. We observed a test set AUC of 0.926, and the sensitivity for all stages of CRC was 90% (87% early stage, 92% late stage). Notably, sensitivity for adenomas was 79%, a large improvement upon the state of the art in adenoma diagnosis. Conclusions: Identification of these key glycopeptides/peptides in blood serum could prove to be a promising non-invasive diagnostic tool that can help improve screening and aid in early detection of advanced adenomas and CRC.
Deep neural networks and association with inpatient survival for patients admitted to the hospital with colon cancer undergoing open colectomy.
Authors: Baig Aqsa , Khawaja Uzzam Ahmed , Khan Ayesha Liaquat , Khalil Mohammad Hamza , Ali Syed Musadiq , Qaudri Syed Abdul-Qader , Tariq Tooba , Irfan Furqan Bin , Ahmed Fahad Shabbir
Published: June 2022

e15537

Background: During hospitalization for colectomy patients with colon cancer may be at risk for mortality due to several reasons including underlying cancer, other comorbidities or age. Our aim was to develop a machine learning algorithm to predict end of admission mortality in patients undergoing colectomy for their cancer. We hypothesized that machine learning could be applied to patients undergoing open colectomy as part of their colon cancer treatment. Methods: All adult patients (> 18 years) for the National in-patient Services (NIS) database 2014 was used to develop our algorithm. We extracted all patients with a diagnosis of cancer using the ICD-9 codes and all patients that underwent colectomy. We conducted a multivariate analysis to look at the risk factors that dictate mortality in these patients. We also developed a linear regression model and a deep learning algorithm to predict mortality in these patients. Results: We identified a total of 4120 patients that underwent open colectomy with colon cancer in the NIS 2014. We observed that several clinical and lab-based parameters were statistically significant for multivariate analyses while others were not. With most significant being all patients refined diagnosis related groups (APRDRG) risk mortality (HR = 6.20, 95%CI = 4.10-9.36), APRDRG severity (HR = 4.78, 95%CI = 3.27-7.00), chronic anemia (HR = 0.61, 95%CI = 0.40-0.94), coagulation disorders (HR = 2.32, 95%CI = 1.31-4.10), chronic electrolytes disorders (HR = 2.12, 95%CI = 1.39-3.24), neurological disorders (HR = 1.92, 95%CI = 1.11-3.32), underweight (low BMI) (HR = 2.40, 95%CI = 1.05-5.48), Hyperkalemia (HR = 2.40, 95%CI = 1.28-4.50), Acidosis (HR = 4.04, 95%CI = 2.64-6.19). In the machine learning analysis, we found out that our proposed DNN outperformed the RF with test set accuracy of 91.1%, sensitivity of 88.5%, specificity 91.2%, PPV of 24.7, NPV of 99.5% and AUROC of 0.968 [95%CI = 0.08-.014]. Conclusions: Our novel DNN model outperformed RF classifier models. The model is easy to implement, user friendly and with good accuracy. However, further external validation of the model is required.
Natural distribution of genomic alterations correlated with the resistance to KRASG12C inhibitor in Chinese colorectal cancer.
Authors: He Ke , Chen Yuerong , Liu Fei , Li Liheng , Wu Chaosheng , Lv Xiu , Liu Xinyi
Published: June 2022

e15550

Background: KRAS inhibitors exhibited promising efficacy as systemic therapy in KRAS G12C-mutant colorectal cancers (CRC) lately. Recent studies have revealed a number of genomic alterations related to acquired resistance to this type of drugs. The discovered resistant gene mutations include: 1. Novel acquired secondary KRAS mutations within the adagrasib-binding pocket such as Y96C, H95D/Q/R, R68S, 2. Activating mutations in genes ( KRAS, BRAF, MAP2K1) MAPK signaling pathway, 3. Oncogenic fusions involving ALK, RET, BRAF, RAF1, and FGFR3, 4. Gene amplifications in KRAS, MET, MYC. Although found as acquired resistance mechanism to KRAS inhibitors, these genomic alterations might be primary or secondary in the setting of other type of therapies. Characterizing the natural distribution of these genomic alterations in cancer patients would contribute to clarifying the application potential of KRAS inhibitors. We herein performed a large-sample size analysis in Chinese colorectal cancer. Methods: A total of 9385 early-stage, late-stage, treated or treatment-naive CRC were included in this analysis. Calling of single nucleotide variants (SNV), copy number variants (CNV), insertion/deletions (indels), fusions and evaluation of tumor mutational burden (TMB) were performed using a wide panel next-generation sequencing (NGS) testing. Results: 43.4% (4069/9385) cases were KRAS-mutant in this cohort. KRAS G12C account for 5.8% (236/4069) in all KRAS-mutant CRC, and 15.7% (37/236) were harbored the above resistance genomic alterations. Fifteen KRAS G12C-mutant CRC were detected to have activating MAPK mutations, including G12D/V (n = 6), G13D (n = 3), Q61H (n = 6), NRAS Q61K (n = 3), MAP2K1 K57T (n = 3), and BRAF V600E (n = 4). Ten KRAS G12C-mutant CRC were detected to have oncogenic fusions, including TGFBR2- CACNA1D (n = 3), TPM4- ALK (n = 1), FGFR3- TACC3 (n = 1), ETV6- SNRPC (n = 1), KAZN- PAX7 (n = 1), NRG1- TTC12 (n = 1), TCF7L2- EWSR1 (n = 1) and ERBB2 arrangement (n = 2). It is noteworthy that a single case was with 5 gene arrangement events in 17q ( ERBB2- ZPBP2, IKZF3- ERBB2, PGAP3- ERBB2, RARA- ERBB2, RARA- GRB7). Thirteen KRAS G12C-mutant CRC were detected to have amplifications in KRAS (n = 5), MYC (n = 5) and MET (n = 4) genes. TP53 (81%), APC (65%) and PIK3CA (32%) were the utmost frequent somatic mutational genes in this subgroup of CRC. In addition, all cases were microsatellite stable (MSS). Tumors harboring fusion variants showed relatively high TMB level in this cohort. Conclusions: Our analysis results indicate about 15% KRAS G12C-mutant Chinese CRC were probable resistant to KRASG12C inhibitor. One-third of these patients had co-existed oncogenic fusions and higher TMB levels, suggesting possibilities for other therapeutic choices.