bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma-informed minimal residual disease (MRD) assay: A multicenter prospective study in Japanese patients with stage II colorectal cancer.
Authors: Oki Eiji , Ando Koji , Hisamatsu Yuichi , Nakanishi Ryota , Nakaji Yu , Kudou Kensuke , Kusumoto Tetsuya , Kagawa Yoshinori , Ung Weng Chit , Niiro Hayato , Tada Sachiyo , Hirose Takashi 
Published: January 2022

161 Background: ̃80% of stage II colorectal cancer (CRC) can be cured by surgery alone. However, adjuvant chemotherapy is recommended for patients with high risk features such as bowel obstruction, < 12 lymph nodes examined and T4 tumors. Traditional pathological grading and biomarkers such as carcinoembryonic antigen has limited sensitivity. Several reports indicated circulating tumor DNA (ctDNA) may represent a promising prognostic factor to assess MRD as a factor for prediction of recurrence after surgery. Here, we present a proof-of-concept study for the development of a novel plasma-based highly sensitive Next Generation Sequencing (NGS) panel using SafeSEQ technology in operable CRC Japanese patients. Methods: This multicenter prospective study recruited patients diagnosed as operable clinical stage II CRC (n = 46) with pre- and post- (4̃6 weeks) operative plasma samples collected between Nov, 2019 and Jan, 2021. ctDNA were extracted and a 14-gene NGS panel was used to analyze single nucleotide variants (SNVs) and Indels covered by gene-specific amplicons. MRD variant was defined as same variant detected in both pre- and post- operative plasma samples. Tissue NGS by a 500-gene panel was also performed in a small number of tissue samples (n = 5) to compare the concordance of plasma and tissue variants. Results: Pre- and post-operative ctDNA status of 46 patients were analyzed. ctDNA positive was observed in 69.6% (32/46, 95%CI 55.2, 81.0) pre- and 34.8% (16/46, 95%CI 22.7, 49.3) post- samples. AKT1, CTNNB1, NRAS, POLE and PPP2R1A mutation were not detected in this study. TP53 mutation was most frequently detected in both pre- (22/46) and post- (11/46) samples, whereas APC mutation was ranked 2nd in pre- (15/46) but none in post- samples. A combined 96 variants were detected in all samples, in which 76 of them were < 0.5% mutant allele frequency (MAF). MRD variants were detected in 17.4% (8/46, 95%CI 8.82, 30.99) post- samples. Evaluation of positive percentage agreement between tissue and pre- plasma samples in three patients show that a total 7 variants detected in plasma, and 3 of them were detected in tissue samples. Conclusions: This study assesses the feasibility of a plasma-informed NGS panel by evaluating pre- and post- operative plasma samples. The presence of variants with < 0.5% MAF detected in this study indicate a highly sensitive method is required for accurate MRD detection. Further observation is required to explore the relationship between MRD variant and clinical outcome such as 2-year progression-free survival.
Spatially resolved transcriptomics deconvolutes histological prognostic subgroups in patients with colorectal cancer and synchronous liver metastases.
Authors: Wood Colin , Leslie Holly , Legrini Assya , Melissourgou-Syka Lydia , Pennel Kathryn AF , Edwards Joanne , Steele Colin William , Jamieson Nigel Balfour 
Published: January 2022

165 Background: Up to 50% of patients with Colorectal Cancer (CRC) will metastasise to the liver (CRLM). KRAS-mt liver metastases particularly when co-mutated with TP53 are associated with poor prognosis. We have used the Glasgow Microenvironment Score (GMS), a histological score performed on H+E slides utilising immune and stromal components of the microenvironment to robustly stratify outcome in primary CRC. The aim of the current study was firstly to determine the utility of GMS in metastatic CRC and secondly to employ the NanostringTM GeoMx Digital Spatial Profiler (DSP), a state-of-the art analysis platform enabling spatial transcriptomic characterisation while maintaining tumour microenvironment (TME) topographical features, to interrogate the functional biology underlying the GMS. Methods: FFPE specimens from primary and metastatic lesions from 44 patients undergoing synchronous resection of CRLM underwent GMS, IHC and panel genomic assessment. Primary endpoints were recurrence-free survival (RFS) and cancer-specific survival (CSS). In addition to bulk transcriptomic assessment, 4 matched pairs from the cohort were selected for GeoMx analysis: 2 samples were GMS0 (high-immune) and 2 were GMS1 (low-immune) with an equal distribution of KRASmt and wt. After multiplex IF staining (PanCK, CD45, DAPI, αSMA), 48 regions of interest were selected and Cancer Transcriptome Atlas Transcriptomic outputs (2000 genes) were analysed using Pathway enrichment analysis with immune deconvolution of the transcriptome performed. Results: GMS0 (high-immune) was associated with improved RFS (p=0.0048) and CSS (p=0.0012) remaining an independent predictor of survival on multivariate analysis (HR 2.90, 95% C.I 1.18-7.16 P=0.021). GMS0 lesions were enriched for adaptive immune (NES=2.20 p.adj<0.0005) and IL-10 (NES=1.9 p.adj<0.0005) pathways specifically at the invasive edge. In contrast, a poor prognostic KRAS/TP53 lesion demonstrated profound immunosuppression, upregulated NOTCH signalling (NES=2.13 p.adj<0.0005) and neutrophil degranulation (NES=1.99 p.adj<0.0005). Topographical Immune-cell deconvolution demonstrated significantly higher populations of CD4 (p=0.05) and CD8 (p=0.0003) cells in GMS0 leading edges. Conclusions: We have demonstrated that spatial transcriptomic analysis using the Nanostring GeoMx tool can reveal potential novel mechanisms underlying biologically relevant histological and mutational subgroups (KRAS-mt) of CRC, providing potential therapeutic targets requiring further investigation. Future studies will apply this technology to pre and post treatment biopsy samples.
Reproducibility of lymphocyte-to-monocyte ratio (LMR), neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) in patients with locally advanced rectal cancer.
Authors: Gawiński Cieszymierz 
Published: January 2022

166 Background: Rectal cancer constitutes over one-third of all colorectal cancers (CRC) and is one of the leading cause of cancer-related death in developed countries. Treatment modalities applied in locally advanced tumors differ substantially among research centers. In order to identify high-risk patients and better adjust the therapy new markers are needed. Systemic inflammatory response (SIR) markers such as LMR, NLR and PLR have been proved highly prognostic in many malignancies, including CRC; however, they lack proper validation. In our study we assessed the reproducibility of LMR, NLR and PLR. Methods: Sixty patients with locally advanced rectal cancer treated in Maria-Sklodowska Curie National Institute of Oncology in Warsaw, Poland between 08.2017 and 12.2020 were prospectively enrolled in the study. Three consecutive blood morphology tests of each patient within a median period of 21 days were obtained before start of the treatment. Results: LMR, NLR and PLR calculated at two time-points were correlated with the coefficient of 0.776, 0.696 and 0.751 (p < 0.005 in all measurements), respectively. Patients were divided into LMR, NLR, PLR-high and low groups. If LMR at the first test was out of the range of 2.2-3.0 (+/- 0.4 from the cut-off) the risk of misclassification in the second measurement defined as an affiliation to a different (high or low) group than initially was 5.0% (95% CI 1.0-13.9%). In case of NLR, when outside of the range of 2.5-3.5 (+/- 0.5) it was 8.3% (95% CI 2.8-18.4%) and PLR outside of the range of 125-175 (+/- 25) 10.0% (95% CI 3.8-20.5%). Mean percentage change between the third and the first measurement of lymphocytes, monocytes, neutrophils and platelets count ranged from -5.59% to 4.76% and the standard error from 2.0 to 3.9. Conclusions: In conclusion SIR markers are reproducible, easily obtained biomarkers with potential application in clinical practice.
Age-associated mutations in RAS-mutated versus RAS-nonmutated metastatic colorectal cancer.
Authors: Kundranda Madappa N. , Kemkes Ariane C. , Routh Josh , De La O Jean-Paul , Evans Mark C. , Flannery Cynthia A. , Hall David W. , Therala Nishitha , Turner Michelle , Thakkar Snehal Govind 
Published: January 2022

171 Background: Mutational profiling is recommended for selecting targeted therapy for metastatic colorectal cancer (mCRC). Evidence suggests that among patients with mutations in one of three RAS genes who underwent resection of liver metastasis, those with early onset mCRC had worse outcomes compared to those with late onset mCRC. The goal of this study was to explore whether other mutated genes in mCRC exhibit an association between age and wild type versus mutant RAS status. Methods: Between October 2018 and October 2020, 974 tumor samples from patients with mCRC were identified. Samples meeting requirements were profiled with the Oncotype MAP Pan-Cancer Tissue test, which sequences 257 genes from tumor tissue, including all 3 RAS genes ( HRAS, KRAS, NRAS). Using the Oncotype MAP assay, single base variants, indels, copy number alterations and structural variants/fusions were identified. Tumor mutational burden (TMB) and microsatellite instability (MSI) were also determined. To identify genes for which there was an association between age group (patients ≤50 years vs >50 years) and RAS status we used Fisher’s Exact Test. Results: Of the 974 samples, 840 met minimum tumor tissue requirements for DNA sequencing (3mm2 and 15% tumor cellularity). Of these, 759 samples were successfully sequenced for NGS. Median turnaround time from the date of sample accessioning to the date of laboratory report was 5 days (interquartile range, IQR, 4-6 days). TMB varied from 0-227 mutations per megabase (median 6, IQR 4-8), and was high (≥10 mut/Mb) in 117 samples (15%). Of 775 specimens processed for MSI, 714 could be measured and approximately 7% were MSI-high. A total of 496 RAS variants were identified, of which 391 were pathogenic, likely pathogenic, or variants of unknown significance (349 KRAS, 34 NRAS, 8 HRAS). Of the 27 genes with at least 78 mutations in the data set, there was an association between RAS status and patient age for mutations at SMAD4, ABCC1, and RICTOR (Fisher’s Exact test, P < 0.05). For all three, mutations at these genes are relatively more prevalent in samples from young RAS wild type patients compared to young RAS mutant patients (Table). Conclusions: The Oncotype MAP Pan-Cancer Tissue test identified numerous genomic changes in mCRC samples. There appears to be an association between age group and RAS status for three mutated genes, SMAD4, ABCC1, and RICTOR. The clinical implication is unclear and warrants further investigation with outcomes data.[Table: see text]
Rapid point of care NGS in colorectal cancer.
Authors: Raskin William , Cheema Parneet , Perdrizet Kirstin , Iafolla Marco , Dudani Shaan , Sheffield Brandon 
Published: January 2022

172 Background: Next generation sequencing (NGS) is the laboratory cornerstone of precision oncology treatment. In advanced colorectal cancer (CRC), current guidelines recommend testing RAS, BRAF and MMR biomarkers as standard of care. The added value of comprehensive genomic profiling is so far unclear. Traditional NGS operations are complicated, requiring specialized equipment and personnel. In many jurisdictions, cancer patients are treated in publicly-funded community hospitals, where NGS is not typically utilized and access to testing via send-out services is associated with lengthy turnaround times. Here, we have validated and implemented one of the world's first "point of care" NGS services. Our early experience on NGS implementation and impact in CRC patients is described. Methods: All NGS studies were performed using the Oncomine Precision Assay (OPA) on the genexus integrated sequencer. NGS was performed at the request of the treating physician. All NGS was performed in a local community pathology lab by histotechnologists, simultaneously responsible for IHC testing (such as MMR) and interpreted by anatomic pathologists in conjunction with routine diagnostic pathology services. Retrospective chart review was performed for all patients undergoing sequencing studies and key data, including turnaround time and NGS findings were extracted from the electronic medical record for analysis. Results: A total of 51 cases with CRC were tested using point of care NGS from November 2020-August 2021, initiated by treating physicians. The median turnaround time for results was 3 days. Oncogenic driver events were identified in 46 (90%) cases, including canonical mutations in KRAS, NRAS and BRAF (Table). Actionable mutations were identified in 13 (25%) samples that would not have been identified with single-gene testing. Conclusions: Here, we show that comprehensive NGS can reveal occult resistance mechanisms to standard therapy and identify actionable biomarkers in a substantial proportion of patients with CRC. NGS added valuable information compared to guideline-recommended testing standards. Our study demonstrates that local testing can have rapid turnaround times. To our knowledge, this is the first report of “point of care” NGS in CRC. Further follow up is needed to explore the utility of these expanded roles for NGS testing. [Table: see text]
Metastatic bulk to predict subclonal heterogeneity by ctDNA in RAS/RAF-wildtype colorectal cancer.
Authors: Kratz Jeremy D. , Lubner Sam Joseph , LoConte Noelle K. , Patel Monica Arun , Uboha Nataliya Volodymyrivna , Lesnik Dyan M. , Ahmed Sara , Kelley Michael J. , Lemmon Kayla , Bassetti Michael Frederick , Sanger Cristina , Deming Dustin A. 
Published: January 2022

186 Background: Distinct molecular subgroups of colorectal cancer (CRC) have been afforded with use of next-generation sequencing (NGS) as standard in clinical practice for advanced disease. We have previously demonstrated that disease bulk predicts clinical resistance to EGFR inhibition in RAS/RAF-wildtype (WT) CRC. We hypothesized bulky disease would predict advanced subclonal heterogeneity by circulating tumor DNA (ctDNA) in RAS/RAFWT CRC. Methods: Following IRB-approval, a retrospective review of molecular profiles in advanced CRC (n = 965) were compiled from the Veteran Administration’s (VA) National Precision Oncology Program (NPOP) and University of Wisconsin Precision Medicine Molecular Tumor Board (MTB). Disease bulk was defined as the longest diameter of metastatic disease or short axis for advanced lymphadenopathy. Molecular profiling was performed using commercially available platforms including Strata Oncology (MTB) and FoundationOne (NPOP). Bulky was compared as categorical (> 35 cm) and continuous variable against the count of pathologic variants. Results: The population was largely representative of advanced CRC with alterations in TP53 (80.5%), KRAS (44.8%), PIK3CA (22.0%) and BRAF (12.8%). Veterans had increased frequency of alterations in PIK3CA (22.7% v. 13.0%, p < 0.02) and BRAF (13.3% v. 6.9%, p < 0.05). There was no difference in metastatic bulk at the time of NGS for tissue biopsy between MTB and NPOP populations (t = 0.80). Disease bulk did not predict the number of pathologic variants from tissue sampling in RAS/RAFWT CRC (n = 96, t = 0.24). RAS/RAFMT cancers had increased frequency of subclonal alterations by ctDNA (9.1±4.0) v. RAS/RAFWT (4.5±3.4, p < 0.0001). Using ctDNA, bulky disease in RAS/RAFMT CRC was not predictive of increased pathologic variants (8.8±3.5 v. 9.5±4.8, t = 0.62). Bulky disease (> 35mm) in RAS/RAFWT CRC predicted increased subclonal variants (6.2±3.6 v. 3.5±2.9, p < 0.02). As a continuous variable, disease bulk predicted the number of pathologic variants in RAS/RAFWT CRC (R = 0.51). Conclusions: These data indicate that metastatic bulk is a predictor of subclonal heterogeneity by ctDNA in RAS/RAFWT CRC. Molecular profiling of tissue alone did not predict differences in subclonal heterogeneity when stratified by disease bulk in RAS/RAFWT CRC. Limited subclonal heterogeneity in non-bulky cancers support ongoing prospective investigations to select non-bulky cancers for early incorporation of anti-EGFR inhibition (NCT04587128).
Next generation sequencing (NGS) to identify relapsed gastrointestinal (GI) solid tumor patients with human leukocyte antigen (HLA) loss of heterozygosity (LOH) for future logic-gated CAR T therapy to reduce on target off tumor toxicity.
Authors: Hecht J. Randolph Randolph , Kopetz Scott , Patel Sandip Pravin , Welling Theodore , Morelli Maria Pia , Borad Mitesh J. , Molina Julian R. , Kirtane Kedar , Lin Yi , Fan-Port Michelle , Mardiros Armen , Beutner Karl , Lozac'hmeur Ariane , Lau Denise , Liechty Kirstin B. , Vong Judy , Ng Eric , Maloney David G. , Go William Y. , Simeone Diane M. 
Published: January 2022

190 Background: Metastatic colorectal (CRC), pancreatic (PANC), and gastroesophageal (GE) cancers are the leading causes of GI cancer–related mortality (5-yr survival rate, 14%, 3% and ̃5-6%, respectively). T-cell immunotherapy targeting GI-associated tumor antigens has been attempted, but efficacy has been constrained by on-target off-tumor toxicity, limiting the therapeutic window. The Tmod (TM) platform is an AND-NOT logic-gated CAR T modular system, versions of which have a CEA- or MSLN-targeting CAR activator and a separate HLA-A*02-targeting blocker receptor to protect normal cells. Tmod CAR T exploits HLA LOH, common in GI malignancies (10-33% in primary solid tumors [TCGA]) and can kill tumor cells without harming healthy cells in vitro and in vivo. However, the prevalence of HLA LOH across GI tumors is unknown in the real-world setting. We utilized the Tempus xT oncology NGS database of patients with multiple GI tumors. From a standard-of-care NGS assay, GI cancer patients can be readily identified for HLA LOH and future treatment with Tmod CAR T therapy. Methods: The occurrence of HLA LOH in GI tumors of 1439 patients was assessed using paired germline and somatic DNA sequencing using a research assay [6]. CRC, PANC and GE patients with ≥ stage 3 were then extracted, and rates of HLA LOH were identified (ie, whether loss occurred across high-frequency HLA-A alleles). In addition, mutations in KRAS and BRAF, as well as MSI status were stratified to determine any association with HLA-A LOH. Results: HLA-A LOH was detected in 830 (17.3%) of all solid tumor records, and a similar proportion when all GI cancer records were analyzed (17.0%). For GI subtypes, these values ranged from 13.5% to 23.1% (Table). No high-frequency HLA-A allele (A*01, A*02, A*03, A*11) was more likely to be lost. Clinical biomarkers ( KRAS, BRAF and MSI status) were not associated with HLA-LOH. Conclusions: The frequency of HLA LOH among advanced solid tumor cancers in this dataset is 17.3%, with a range of 13.5-23% between CRC, PANC and GE. The HLA LOH frequency observed in these GI tumors is consistent with that in primary tumors from TCGA, which also used germline-matched and tumor samples. Clinical biomarkers were not associated with HLA LOH. Tempus NGS was able to identify HLA LOH, which can be used for Tmod CAR T therapy to an enhanced therapeutic window. Identification of these patients in BASECAMP-1 (NCT04981119) will enable novel Tmod CAR T therapy. [Table: see text]
Prognostic effect of RAS/BRAF mutations in patients (pts) with metastatic colorectal cancer (mCRC).
Authors: Abid Haisam , Szabo Aniko , Taylor Bradley W. , Shreenivas Aditya V. , Chakrabarti Sakti , Kamgar Mandana , Thomas James P. , George Ben 
Published: January 2022

191 Background: Somatic alterations in KRAS and BRAF have prognostic as well as predictive impact in pts with mCRC; however, the differential impact of various somatic alterations in these genes need further characterization. We analyzed the prognostic impact of specific somatic mutations in K RAS and BRAF in mCRC pts. Methods: We retrospectively reviewed the electronic medical records of pts with mCRC at our institution who underwent comprehensive genomic profiling (CGP) utilizing the Foundation One assay. Prevalence of genetic alterations was estimated using proportions and compared between groups using a chi-squared test. Patients were followed for survival from metastatic diagnosis until death or last follow-up, with left truncation at the time of CGP. Kaplan-Meier estimates were used to estimate overall survival, and groups were compared using a Cox-regression based likelihood ratio test. Results: 192 pts were identified - median age at diagnosis was 55 years, 62% (119/192) presented with metachronous metastatic disease, and 28% (54/192) had a rectal primary. Somatic mutations in KRAS were found in 49% (95/192) pts, and 53% (50/95) had a left sided primary (p = 0.3). Majority of the KRAS mutations localized to codon 12 (72/95 -76%), KRAS G12C comprised 12% (11/95). Median Overall Survival (mOS) of KRAS mutated pts was 3.0 years compared to 3.5 years for KRAS wild type (WT) pts (p = 0.5). Median OS of pts with different KRAS mutations were as follows: codon 12 mutations (excluding G12C) - 2.7 years; KRAS G12C – 5.2 years; non-codon 12 KRAS mutations - 4.8 years. BRAF mutations were identified in 7.8% (15/192) pts, and 67% (10/15) had a right sided primary (p = 0.062). BRAF V600E represented the most common alteration in BRAF – 87% (13/15). Patients with BRAF mutation had a mOS of 1.8 years compared to 3.1 years for BRAF WT pts (p = 0.2). Median OS of pts with different BRAF mutations were as follows: BRAF V600E – 1.8 years and BRAF non V600E - 2.1 years (p = 0.4). Conclusions: The numerically higher mOS in pts with KRAS G12C and non-codon 12 KRAS mutations merit further biologic characterization with functional assays. Individualized therapeutic strategies must be conceptualized for mCRC pts with specific RAS/BRAF mutations, considering their widely disparate prognosis and putative downstream signaling mechanisms. Dynamic molecular simulation to understand conformational changes in proteins associated with specific mutations will be pivotal to optimizing precision therapeutic strategies.