bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the ability of Idylla EGFR to differentiate result of ARMS EGFR in gray area and identify rare mutation variants.
Authors: Qiu Tian , Zhang Fanshuang , Zheng Bo , Junling Li , Ying Jianming
Published: June 2022

e15033

Background: Molecular testing involving Epidermal growth factor receptor ( EGFR) mutations is recommended for patients with non-small cell lung cancer (NSCLC), especially with lung adenocarcinoma, and is nowadays an essential element of precision medicine. Although amplification-refractory mutation system (ARMS) is one of the most commonly used methods for EGFR mutation detection, it can only detect variants in known gene loci and give indistinct results in gray area occasionally, which may be caused by the input of poor DNA quality or low-abundance variants. Idylla EGFR assay can detect 51 EGFR mutations directly from formalin-fixed, paraffin-embedded (FFPE) samples within 2.5 hours with < 2 minutes of hands-on time, without manual data analysis need, whose accurate and robust have been proven among Caucasian and Chinese patients. But the assay’s ability to detect EGFR mutation in low abundance which may lead the result of ARMS EGFR in gray area or rare variants has never been evaluated. Methods: FFPE samples were retrospectively collected from 98 lung cancer patients followed by EGFR testing using the Idylla system, which were also previously assessed with ARMS-PCR. Forty-six of them were in gray area by ARMS-PCR of EGFR and need to be retested by ARMS-PCR or validated by the third method. In another 52 cases, no mutations were found by ARMS-PCR of EGFR, but mutations were found by next-generation sequencing (NGS). The ability of Idylla EGFR to detect cases with result in gray area and rare variants were analyzed. Results: In 46 cases with result in gray area by ARMS-PCR of EGFR, after retesting or validation by the third method, 37 of them had the same result with Idylla mutation test, with an overall concordance of 80.4%. Idylla EGFR test missed 8 mutational cases (22/30), identified 1 mutational case in addition (15/16). Except 2 cases with higher CQ value than 29, which means the poor DNA quality or low quantity input, low mutational abundance maybe the main reason for no mutation identified by Idylla EGFR test. In 52 cases with rare EGFR variants, Idylla EGFR test identified 9 mutational cases, while 4/9 mutational variants beyond the scope of Idylla EGFR test, 2 20ins, 1 L858R and 1 19del. Five of the 9 mutational cases, Idylla test detected 5 different 19dels. The variants of all the 52 cases beyond the scope of ARMS-PCR of EGFR, and ARMS-PCR of EGFR didn’t find mutation. Conclusions: The Idylla system provides a rapid and accurate ability to differentiate result of ARMS-PCR of EGFR in gray area and identify more rare mutation variants which may decrease the repeat testing or validation. But the ability of NGS to find more actionable variants is still important.
Reducing pre-analytical sample QC failure rates for cancer molecular genetic assays with SLIMamp technology.
Authors: Fink Lynn , Waring Paul Michael , Jaradi Binny , Stone Nathan , Anderson Lisa , Leo Paul , Marshall Mhairi , Ellis Jonathan , O'byrne Kenneth
Published: June 2022

e15034

Background: Identification of somatic variants in cancer by high-throughput sequencing has become common clinical practice largely because many of these variants may be predictive biomarkers for targeted therapies. However, there can be high sample QC failure rates for some assays (sometimes up to 40%), preventing the return of results that may affect patient treatment decisions. Pillar Biosciences has incorporated their patented SLIMamp technology into commercially available cancer NGS testing kits with the claim that these kits can successfully interrogate challenging formalin-fixed paraffin-embedded tissue (FFPET) samples with low tumor purity, poor DNA quality, and/or low input DNA, resulting in a high sample QC pass rate. The aim of this study was to substantiate that claim using Pillar’s amplicon-based oncoReveal Solid Tumor Panel. Methods: We acquired 48 tumor samples that had failed one or more pre-analytical QC sample parameters for whole exome sequencing (WES) from ATGC’s ISO15189 accredited diagnostic genomics laboratory. XING Genomic Services performed an exploratory data analysis using our pre-analytical QC assays to characterise the samples and then sequenced the samples in our ISO15189 accredited laboratory using the validated oncoReveal Solid Tumor Panel. Results: We were able to achieve high sequencing coverage (>3000X) for all 48 samples and explored the determinants of sample “success”. We were able to generate clinical reports for 45 samples (94%), of which 38 (79%) contained clinically actionable or significant variants that would not have otherwise been identified. Ten samples had a higher number of total variant calls with over-representation of C>T transitions representing stochastically-amplified, formalin-induced artefacts in samples with very low input template DNA. Of these, 7 cases had reportable variants and 3 were deemed unreportable. We demonstrated that DNA integrity is the major determinant of success even in samples with low input DNA or low tumor purity and were able to further refine pre-analytical and post-analytical QC metrics to better identify samples with poor quality DNA that can be sequenced reliably. Conclusions: In this study, we showed that the Pillar Biosciences oncoReveal Solid Tumor Panel, which uses SLIMam technology, was able to generate reliable, interpretable results for 94% of samples that failed pre-analytical QC for WES, substantiating Pillar’s claim.
Clinical utility of a molecular tumor board (MTB) in a community oncology practice.
Authors: Amatruda Thomas , Malisetti Nithya , Hirst Jeff , Vadnais Malia , Katipamula-Malisetti Rajini
Published: June 2022

e15038

Background: We convened a molecular tumor board in an oncology specialty practice of 60 oncologists. Monthly meetings were held remotely, with participation of molecular oncology experts from Caris Life Sciences. Cases were selected for MTB by CLS or clinicians, largely from patients whose genomic testing results did not suggest level 1 guideline therapy options. Methods: We reviewed the clinical value of the genomic test results. To measure the impact of the MTB on patient care, we reviewed a sample of cases with a database instrument. Results: Over calendar year 2021, 491 genomic tests were reported by CLS. These tests involved whole exome and whole transcriptome analysis of microdissected tumor samples. 151 tests showed no association with approved therapy on initial report. In addition to the reported analysis of mutations and fusions, supplemental data concerning emerging biomarkers such as deletions, homologous repair deficiency, and gene expression was provided by CLS for MTB discussion. Between May 2020 and February 2021, 47 cases were presented, representing 19 different diagnoses. 17 cases were reviewed in detail. In 88% of cases (15/17) a recommendation was made by the group. These included suggestions for standard therapy, on sequencing of therapies, on genetic counseling and testing for inherited mutations, and on clinical trial opportunities for emerging biomarker guided therapeutics. In 35% of cases (6/17), the tumor board presentation had an impact on care. In 17% of cases (6/17), we suggested germline genetic testing for patient or family. In 23% of cases (4/17), patient treatment was changed based on discussion. In 9 cases, recommendations were not acted on, because patients deteriorated, remained stable, or chose other therapies. Many patients were presented after multiple lines of treatment or at a time of declining clinical status, which limited the clinical impact of MTB discussion. Evaluation of inherited mutations in patients and family members were difficult to complete when care was dispersed across multiple health systems. Conclusions: The MTB provided valuable updates on new molecular findings and targeted therapies. Incorporation of tumor genomic testing and MTB discussion at an earlier point in the clinical care continuum could improve overall patient outcomes. Challenges in the structure and utility of the conference will be discussed.
A novel molecular subtype of hepatocellular carcinoma based on the tumor purity and tumor microenvironment-related polygenic risk scores.
Authors: Lin Yan , Liang Rong , Gao Xing , He Ziqin , Lu Lu , Luo Min , Li Qian , Wang Xiaobo , Li Yongqiang , Wu Guobin , Luo Xiaoling , Ye Jiazhou
Published: June 2022

e15040

Background: The molecular classification of hepatocellular carcinoma (HCC) plays a vital role in the management of precision therapy. Several molecular classification systems, mainly focusing on the tumor cells, were developed according to distinct omics features of HCC. Heterogeneous tumor microenvironment (TME) in HCC is recognized as a crucial part of inter-tumor heterogeneity. Few molecular classifications of HCC have so far taken into account both the related molecules of tumor cells and TME. Methods: Wefirstly identified the tumor purity (TP)-related and TME-related genes in the differentially expressed genes in HCC using GSE14520 data set, and separately constructed the TP-related and TME-related polygenic risk score (PRS). Secondly, according to the TP-related and TME-related PRSs, we proposed the TP-TME risk classification which was validated in two external data sets from The Cancer Genome Atlas Program and International Cancer Genome Consortium database. We also performed functional enrichment and drug repositioning analysis to reveal the potential biological heterogeneity among different subtypes. Results: The three TP-TME risk subtypes of HCC had significantly different prognosis and biological characteristics. The TP-TME low risk subtype had the best prognosis and was characterized by well-differentiated, the TP-TME high risk subtype had the worst prognosis and was characterized by aberrant activation of TGFβ and WNT pathways, and the TP-TME high risk subtype had the moderate prognosis and was characterized by exhibited activated MYC targets and proliferation-related gene sets. We also found that these three TP-TME risk subtypes may respond differently to immunotherapy (e.g., immune checkpoint inhibitors and chimeric antigen receptor-modified T cells) or other drug therapies. Conclusions: By combining separately constructed TP-related PRS and TME-related PRS, we proposed and validated a novel molecular classification system, the TP-TME risk subtyping system, to divide patients with HCC into three subtypes with distinct biological characteristics and prognosis. These findings highlight the significant clinical implications of the TP-TME risk subtyping system and provide potential personalized immunotherapy strategies for patients with HCC.
Detection of multiple types of cancer driver mutations using targeted RNA sequencing in NSCLC.
Authors: Hong Yuanyuan , Wang Xiaoqing , Mu Weina , Zeng Xuexia , Su Lin , Lin Xiaojing , Zhang Zhuo , Zhang Qi , Chen Weizhi
Published: June 2022

e15043

Background: DNA NGS sequencing has been widely used as a companion diagnostic method for matching NSCLC patients with appropriate personalized target therapy. RNA-based NGS has been proved to be valuable in detecting fusion and exon skipping mutations and therefore recommended by NCCN guidelines for these mutation types. It would be helpful to have a diagnostic method that suits different types of clinically actionable mutations in a single tube. Methods: We developed an RNA-based hybridization panel targeting actionable driver oncogenes in solid tumors. Experimental and bioinformatics pipelines were optimized for detection of fusion, SNV and indel mutations, as well as gene expression quantification. Reference materials were used for analytical validation of the panel, and 1253 FFPE samples from NSCLC patients were analyzed by DNA panel sequencing and RNA panel sequencing in parallel to assess the performance of the RNA panel in detection of multiple types of clinically actionable mutations. Results: Analytical validation showed a detection specificity of 100.0% for SNVs and fusions. The targeted RNA panel achieved a 1.45-3.15 copies/ng limit of detection (LOD) for SNVs and a 0.21-6.48 copies/ng LOD for fusions. Gene expression analysis revealed a correlation greater than 0.9 between the RNA-seq and targeted RNA panel results. Among 1253 NSCLC FFPE samples, multiple mutation types were called at both DNA and RNA levels and compared between the two assays. Twenty-one fusion and six METex14 skipping events were only detected by the RNA panel. The positive percent agreement (PPA) and positive prediction value (PPV) were 98.08% and 98.62% for targetable SNVs and 98.15% and 99.38% for targetable Indels, respectively. We also explored the relationship of RNA expression with gene copy number and protein expression. The RPKM (reads per kilobase per million mapped reads) of EGFR transcripts exhibited a linear relationship with copy number, whereas MET gene expression seemed to be regulated in a more complexed manner. In IHC analysis, all MET IHC 3+ samples had significantly higher RPKM levels than samples with MET IHC level of 2+/1+. Conclusions: Parallel DNA and RNA systematic analysis demonstrated the accuracy and robustness of the RNA sequencing panel for detection of multiple types of clinically actionable mutations. The simplified experimental workflow, lowered cost and sample consumption, along with the superior performance in simultaneous detection of multiple types of mutations will make RNA panel sequencing an effective method in clinical testing for NSCLC.
A phase 1, safety and dose escalation study of BXQ-350, a nanovesicle formulation of saposin c, a modulator of sphingolipid metabolism, in patients with advanced solid malignancies.
Authors: Curry Richard Charles , Rixe Olivier , Morris John Charles , Wesolowski Robert , Yilmaz Emrullah , Villano John L. , Muller Carolyn , Wise-Draper Trisha Michel , Noonan Anne M. , Puduvalli Vinay K. , Tapolsky Gilles , Takigiku Ray
Published: June 2022

e15059

Background: Bexion recently completed an all-comer Phase 1 clinical study of BXQ-350 in patients with advanced solid tumors including high grade gliomas to evaluate the safety profile and to determine the maximum tolerated- or biologically effective dose. BXQ-350 is a nanovesicle comprised of recombinantly expressed Saposin C (SapC) and dioleoylphosphatidylserine. SapC, a human protein encoded by the Psap gene, is an allosteric activator of several enzymes involved sphingolipid metabolism. Sphingolipids are bioactive signaling molecules implicated in multiple cellular processes including apoptosis and immune stimulation/inhibition. In nonclinical studies, BXQ-350 evidences broad anticancer activity, selectively inducing apoptosis of cancer cells by modulating sphingolipids (ceramides/S1P), and BXQ-350 acts synergistically with multiple classes of anticancer agents and treatments. Methods: In the trial (NTC02859857), performed at four US sites, BXQ-350 was administered intravenously for a minimum of 6 cycles over 28 weeks at escalating doses from 0.7 mg/kg up to 2.4 mg/kg. Multiple secondary parameters were included to characterize its pharmacokinetics, efficacy profile and identify potential biomarkers. Results: Results indicate that: i) BXQ-350 was safe and well-tolerated as no DLT was observed and an MTD was not reached; ii) treatment related adverse events leading to discontinuation were typical for this patient population and disease related; iii)* biomarker analyses suggest positive modulation of sphingolipid metabolism and stimulation of the immune system; iv)* surprisingly, some patients noted improvement of existing peripheral neuropathies. RANO or RECIST ver 1.1 criteria were used to evaluate tumor response: 13 patients reached Cycle 6 restaging (17% ORR); 8 patients (11.0% of evaluable patients) demonstrated progression free survival over more than 6 months; and 2 patients (a GBM and CRC patient) are still on study after 5 years. * subject of separate abstracts. Conclusions: In conclusion, BXQ-350 is a first-in-human and first-in-class novel biologic whose Phase 1 results suggest that it may have clinical utility either as a monotherapy or when combined with other targeted agents. Clinical trial information: 028559857.
The landscape of NRG1 fusions based on NGS in Chinese solid tumor patients.
Authors: Yuan Shaohua , Chen Hui , Wang Liwei , Dong Xiaowei , Wang Aodi , Wang Kai
Published: June 2022

e15073

Background: Neuregulin 1 gene ( NRG1) fusions are oncogenic in various tumor types and represent an emerging potential therapeutic target. In the previous reports, NRG1 fusions are overall rare (0.12%) in the Western population, being seen most frequently in NSCLCs. The incidence of NRG1 fusions in a variety of solid tumors based on NGS has been explored limitedly in Chinese patients. Methods: FFPE samples and matched peripheral blood were collected for NGS based 450 cancer genes panel assay and RNA panel assay.Somatic variants were analyzed following CAP/CLIA-certificated workflows, including Single Nucleotide Variant (SNV), Copy Number Variation (CNV), large insertion and deletions (Lindel) and gene rearrangements. Results: A total of 47 patients harboring NRG1 fusions and four of them were detected in RNA level. Non-small cell lung cancer (NSCLC) was the most common cancer type with the incidence of 0.19% (25/13089). The followed cancer types were bone sarcoma, breast carcinoma, pancreatic adenocarcinoma and colorectal carcinoma with the frequency of 0.30% (3/973), 0.16% (3/1850), 0.14% (3/2098) and 0.07% (3/4344) respectively. CD74 (10.1%), SLC34A2 (10.1%) and WRN (4.3%) represented the most common NRG1 fusion partners, other known partners contained CDH1, HMBOX1, ADAM5 and UNC5D. In total, 76.6% of the partners were novel partners, and the most common break points of NRG1 were intron5 and intron1. The 47 NRG1 fusion patients evenly distributed in female (49%) and male (51%), and 44.7% were at advanced stage (stage ≥ III). The median age was 57 years old (range, 8-86 years old) and the median TMB was 3.3 muts/Mb (range, 0-30.5). TP53 (48.9%), CDKN2A (14.9%) and ERBB2/FGFR1/MUC16/SMAD4 (12.8%) were the most common co-occurred mutated gene. In the alterations of ERBB2, 50% were amplifications and 2 patients were breast carcinoma. Only one patient showed ALK fusion and one showed FGFR1 fusion. Among all patients, 8.5% included p.G12X mutation of KRAS and 10.6% included alterations of EGFR with two L858R and two 19del mutations. Conclusions: This study revealed NRG1 fusions in approximately 0.19% of Chinese NSCLC tumor pts and presented the frequency of same common tumors. Also the genomic and clinical feature were analysed. NGS panel sequencing and OrigiFus algorithm showed the advantage of detecting NRG1 fusion and providing structure information of partners which could potentially guide more precise treatment options.
A deep learning approach to discover cyclin-dependent kinases 12 (CDK12) inhibitors in breast cancer.
Authors: Wen Tingyu , Li Lixi , Li Yiqun , Wang Jun , Gao Peng , Xie Guotong , Ma Fei
Published: June 2022

e15086

Background: Although anti-HER2 tyrosine kinase inhibitors (TKIs) have significantly prolonged survival and improved prognosis in HER2-positive breast cancer patients, resistance is a constant obstacle leading to TKIs treatment failure and tumor progression. Our previous research shows dual inhibition of HER2/CDK12 will prominently benefit the outcomes of patients with HER2-positive breast cancer by sensitizing the tumors to anti-HER2 TKIs treatment. Unfortunately, there is no high selective CDK12 inhibitor in clinical. This study sought to accelerate the CDK12 inhibitor discovery by a deep learning approach. Methods: We developed a large-scale self-supervised graph neural network to learn 11 million unlabelled compounds for molecular representation. And the model was trained with 233,823 kinase domain sequences by drug-target interaction datasets from the BindingDB database. Then, this transformer architecture was used to predict potential CDK12 inhibitors. The candidate hits compounds with diverse skeletons were divided into 50 clusters by clustering analysis. The representative hits with high transform scores and rational binding mode in each cluster were detected in the homogeneous time-resolved fluorescence CDK12 kinase assay. Candidate clusters with half-maximal inhibitory concentrations (IC50) lower than 200 nM were selected into expanded validation and kinase selective panel detection. xCELLigence RTCA system was adopted to monitor cell growth and sensitivity of breast cancer cells to CDK12 inhibitors in a real-time manner. Results: Our predictive transfer learning model yielded satisfactory predictions on various targets including CDK12. We screened a total of 4,527,236 compounds and recommended 50 clusters of potential CDK12 inhibitors for further enzyme activity detection. The IC50 of seven cluster representative compounds is lower than 10 uM. Expanded screening of 500 compounds in these clusters discovered a lot of hits with highly CDK12 selective inhibition. Half of the new compounds are showed promising proliferation inhibition in breast cancer cell lines. Conclusions: Our study provides a highly efficient and end-to-end deep learning approach to discover highly selective CDK12 inhibitors in breast cancer.
The landscape of RAS mutations and hotspots in Chinese patients with solid tumors.
Authors: Li Mei , Li Han
Published: June 2022

e15114

Background: As one of the most commonly oncogene, RAS mutations ( HRAS, NRAS, KRAS) have been confirmed closely related to the tumorgenesis and proliferation of solid tumors.Yet a comprehensive analysis of RAS mutations and hotspots in Pan-Cancers of Chinese is lacking. Herein, we firstly report the RAS mutation frequency and hotspots features based on a Chinese pan-cancers database, aiming to evaluate the correlation between RAS mutation status and the clinical implication of human cancers. Methods: This was a retrospective study in patients with solid tumors performed NGS panel based on tissue or blood samples in ChosenMed. A cohort of 5420 samples consisting of 22 solid tumor types from Chinese was analyzed to exhibit the landscape of RAS mutations and hotspots. Results: According to our database, the total mutation frequency of KRAS, NRAS, and HRAS was 17.34% (940/5429) in 22 tumor types, of which pancreatic cancer, bowel cancer and endometrial eancer occurred more commonly (with mutation frequencies of 64.04%, 46.07%, and 26.32%, respectively). The RAS mutation hotspots mainly consisted of G12, G13, and Q61, which exhibited preference in each RAS isoforms. For KRAS, G12 mutation site occupied 76.99% (619/804) of all mutations, and mutations at Q61 accounted for 52.83% (28/53) of NRAS mutations. Lastly, HRAS mutations at above three sites presented lowest proportion of 16.83% (17/101). Conclusions: This study firstly reports the RAS mutation characters in pan-cancers based on the Chinese database, which has provided RAS hotspots details for helping to screen more tumor patients who are sensitive to RAS inhibitors. Also, further investigation should be performed for the development of RAS-targeting drugs.
The landscape of NFE2L2 alteration in Chinese solid tumor patients.
Authors: Xian Xiuying , Li Chunhai , Meng Hong , Wang Lixin , Liu Chuang , Meng Fanfan , Li Ling
Published: June 2022

e15126

Background: NFE2L2 encodes a transcription factor which is a member of a small family of basic leucine zipper (bZIP) proteins. NFE2L2 variations were detected in many tumors, such as lung cancer, esophageal cancer, renal cell carcinoma and other cancer types. The landscape of NFE2L2 gene in solid tumors of Chinese population has not been descripted. Methods: 3193 normal-paired samples from patients with solid tumors were analyzed using hybridization capture-based next generation sequencing, and alterations including single base substitution, short and long insertion/deletions, copy number variations, gene fusions and rearrangements. Results: NFE2L2 gene was altered in 2.0% (65 of 3193) of all solid tumors. The frequency of NFE2L2 variations was assessed in multiple cancer types, including lung cancer (33/1109), liver cancer (10/206), colorectal cancer (6/391), stomach cancer (3/227), cervical cancer (3/112), esophageal cancer (3/53), and other cancer types. A total of 54 variations of NFE2L2 were found, mainly in exon 2 (26/54), exon 5 (11/54), exon 3 (4/54) and exon 4 (2/54), no variation in exon 1. NFE2L2 D16G, D21H, R34_S40del, V36_E45del, F37_E45del, R42P, L48P, K53Tfs*2, L62P, E67Q and L76_E78delinsQ in exon 2 have not been reported before. In addition, we identified copy number amplifications of NFE2L2 in four patients, including three lung squamous cell carcinomas and one cervical squamous cell carcinoma patients. Furthermore, in our cohort, NFE2L2 mutation carriers also owned other actionable or driver mutation, the most frequent one was TP53 (71%), followed by PIK3CA (34%), MLL2 (28%), CDKN2A (31%), and ATR (25%). Analysis of co-mutation correlation of NFE2L2 showed that NFE2L2 variation was correlated with ATR, ACVR1B, TERC and Sox2 ( p<0.001). TERC and SOX2 were mainly copy number amplification at chromosome 3q36, and there is higher amplification frequency at 3q36 in squamous cell carcinoma. In TCGA cohort, the patients with NFE2L2 variations and 3q36 amplification had a longer median survival than those group without 3q36 amplification (63.59 vs 32.04 months, p = 0.0459). Conclusions: NFE2L2 deleterious mutations are highly diverse and present at low to moderate frequencies across many cancers. Our results revealed the potential targeted therapeutic strategies and prognostic analysis among NFE2L2 population with solid tumors should be considered in further study.
A pancancer analysis of KRAS alterations in Chinese population.
Authors: Hou Yan , Lou Luyan , Zhang Yanrui , Zhang Yun , Liang Xiayuan , Lou Feng , Cao Shanbo , Wang Huina
Published: June 2022

e15127

Background: Kirsten rat sarcoma viral oncogene homologue (KRAS) is the most frequently mutated oncogene in human cancers. Sotorasib (AMG 510) has shown promising anticancer activity in patients with heavily pre-treated KRAS p.G12C mutant solid tumors. Here, we provide an overview of genomic diversity of KRAS alterations in a large cohort of Chinese patients. Methods: Molecular profiles of 16,654 tumor specimens were obtained using gene-panel target-capture next-generation sequencing, and classified based on the presence and subtypes of KRAS mutation. Tumor mutation burdens (TMB) were calculated using an Acornmed panel with 808 cancer-related genes. Results: In total,15.04% (2505/16654) of pan-cancer patients harbored RAS mutations, and 13.58% (2262/16654) patients carried KRAS mutations in the current study. Five main subtypes of KRAS mutation were detected including G12D (642, 28.38%), G12V (392, 17.33%), G12C (354, 15.65%), G13 (220, 9.73%), G12A (101, 4.47%). In our cohort, the highest KRAS G12C mutation frequency tumor type was lung cancer (12.33%) followed by colorectal cancer (1.99%), which is comparable with the previously published data. Among all patients with KRAS G12C mutation, 77.40% (274/354) of the patients were male and 22.60% (80/354) were female. Tumor mutation burdens (TMB) were calculated for 151 samples of all the 352 KRAS G12C mutation samples. The median TMB was 10.15 mut/Mb with 50.99%≥10 mut/Mb and 14.57%≥20 mut/Mb. However, according to the results of CodeBreaK 100 exploratory analysis at the 2021 ASCO annual meeting, among all patients with KRAS G12C mutation, 17.86% of the patients had ≥ 10 mut /Mb, which was defined as TMB-high. Therefore, it can be found that the TMB of domestic and foreign patients is different. Conclusions: Genomic alterations in KRAS are widespread among Chinese pan-cancer patients. Results of CodeBreaK 100 exploratory analysis presented at the 2021 ASCO Annual Meeting showed no significant difference (40% vs 42%) in objective response rates between TMB high (≥ 10 mut/Mb) and TMB low (< 10 mut/Mb). Based on our data, the threshold of TMB high in the Chinese population should be higher. The molecular marker exploration of AMG 510 efficacy in the Chinese population needs to be further carried out and confirmed.
Characterization of mutational signatures of homologous recombination deficiency (HRD) in Chinese breast cancer.
Authors: Liu Xiao , Li Mingwei , Lou Feng , Cao Shanbo , Wang Huina
Published: June 2022

e15129

Background: Homologous recombination deficiency (HRD) is a common molecular characteristic of genomic instability and has been proved to be an important biomarker for personalized therapy decisions and stratified management in breast cancer. In this study, we explored the mutational features of HRD tumors identified by HRD score in Chinese breast cancer. Methods: Tumor tissue DNA from 68 breast cancer patients was isolated and sequenced by next-generation sequencing (NGS) technologies with AcornMed 808-genes panel. HRD score was calculated as an unweighted sum of loss of heterozygosity (LOH) score, telomeric allelic imbalance (TAI) score and large-scale state transition (LST) score by AcornHRD algorithm, and mutations in 39 homologous recombination (HR) related genes including BRCA1/2 were identified for each case. Results: Based on the mutation alternation profiles from our cohort, somatic BRCA1/2 mutations were present in 15 patients (22.1%) while 29 patients (42.6%) harbored one or more mutations in HR-related genes excluding BRCA1/2. Germline mutations of BRCA1/2 and other HR-related genes occurred in 11.8% and 4.4% of cases detected, respectively.In our cohort, the median HRD score was 40 (range from 3 to 92). Sixty-eight cases were divided into HRD-high or HRD-low group based on a cut-off value of ≥ 42 or < 42, with HRD-high group accounting for approximately 47% of our cohort, indicating the combination with HRD score yielded an increment of 26.5% in coverage of HRD within BRCA1/2 wildtype cases. The HRD-high group covered 82.4% of the BRCA-mutated cases and also showed higher mutation level of BRCA1/2-excluded HR genes than HRD-low group (p = 0.001). Prevalence of mutations in a total of 12 genes, including BRCA1(31.3% vs 5.6%, p = 0.009) and NBN (25% vs 5.6%, p = 0.038), were significant difference between HRD-high and HRD-low group. Besides, Cosmic Signature 1 (spontaneous deamination of 5-methylcytosine) and 5 (unknown) were existed in both groups, whereas Signature 6 (defective DNA mismatch repair) was only discovered in HRD-high group. Compared with HRD-low ones, copy number variations ratio was higher in HRD-high group (p = 0.031). Meanwhile, the patients with ERBB2 amplification (HER2+) showed a lower level of HRD score than HER2- ones. Conclusions: This study comprehensively delineated the genetic characteristics of HRD tumors, which suggests that HRD status marked by HRD score is strongly associated with BRCA1/2 and HR-related genes mutation as well as other genomic instability signatures, thus indicating its predictive value as a promising biomarker for DNA repair deficiency related drugs or therapies in Chinese breast cancer.
Clinical and genomic characteristics of lung cancer concomitant chronic obstructive pulmonary disease (COPD).
Authors: Ma Hongxia , Zhang Qian , Duan Qianqian , Zhang Qin , Tan Yuan , Sun Tingting , Qi Chuang
Published: June 2022

e15131

Background: Lung cancer and chronic obstructive pulmonary disease (COPD) often coexist. Lots of clinical and genomic descriptions related lung cancer have been investigated. However, the clinical and genomics characteristics of lung cancer coexisting COPD are still unclear. Herein, we explored the clinical characteristics and somatic mutational landscape of lung cancer coexisting COPD (COPD-LC) and compared with non-COPD Lung cancer (non-COPD-LC). Methods: We retrospectively collected total COPD-LC and non-COPD-LC patients who performed next generation sequencing (NGS) simultaneously from The Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University during December 2018 to August 2021. And collected COPD-LC data from TCGA to further analysis. COPD was defined as incompletely reversible airflow obstruction associated with post-bronchodilator forced expiratory volume in one second (FEV1) and its ratio to forced vital capacity (FEV1/FVC) < 0.7. Results: Of the 139 patients enrolled in the study, 51 were categorized as COPD and 88 as non-COPD. In our clinical cohort, compared with non-COPD-LC, amount of male gender, older age and smoking patients were significantly higher than non-COPD in term of clinical data (all P < 0.01). As for somatic mutation in our cohort, compared with non-COPD-LC, COPD-LC had higher mutation frequency of LRP1B (43% vs 9%, P = 0.001), EPHA5 (24% vs 1%, P = 0.002), PRKDC (14% vs 1%, P = 0.039) and PREX2 (14% vs 0%, P = 0.012), which had relationship with improved tumor immunity. Immunotherapy biomarker of PD-L1 positive expression (62.5% vs 52.0%, P = 0.397) and TMB (P = 0.004) also were higher in COPD group. Whereas, COPD-LC had lower frequency of EGFR (19% vs 50%, P = 0.013). And survival analysis showed in EGFR mutant patients with targeted therapy, COPD-LC had worse PFS than non-COPD-LC (HR = 3.52, 95%CI: 1.27-9.80, P = 0.01). TCGA cohort mutation data differed from the results of our cohort. In addition, RNA data from TCGA indicated COPD-LC increased tumor immunity. Conclusions: In our research, COPD-LC had unique clinical and molecular features. High PD-L1 expression and TMB indicated these patients may benefit from immunotherapy. Notably, mutation difference between Chinese and TCGA cohort and COPD-LC immunotherapy efficacy need prospective further study.
Distribution features of genomic amplifications in microsatellite stable Chinese colorectal cancer.
Authors: Yang Zhenhuai , Li Guanning , Yang Junjie , Yang Zetian , Geng Yi , Shi Zhenjun , Liu Xinyi , Huang Mengli
Published: June 2022

e15509

Background: Genomic amplification is key mutational events in microsatellite stable (MSS) colorectal cancer (CRC). A distinctive amplification region of CRC is Chr20q. It was revealed by several investigations the most recurrent amplified band in CRC and often co-exist with Chr8q. However, there is very little data to describe the characteristics of chromosome co-exist amplifications in CRC. We did an exploratory analysis in this issue in a large size of Chinese CRC. Methods: A total of 1977 CRC with detected genomic amplifications were included in this analysis. Calling of single nucleotide variants (SNV), copy number variants (CNV), insertion/deletions (indels), fusions were performed using a wide panel next-generation sequencing (NGS) testing. Amplifications were stratified as high-level, moderate-level and low-level according to the number of copies (cut-off: 20, 8 copies). Results: Nine chromosome arm were detected amplified in more than 10% cases in this cohort. Chr20q (65.9%), Chr13q (57.1%) and Chr8q (34.3%) were the most frequent. Chr17q and Chr12q had more high-level amplifications than other chromosome arms with ratio of 54.9% and 33.7%, respectively. In contrast, Chr20q and ChrX substantially had low-level amplifications. 36.2% (715/1977) cases had amplifications on more than two chromosome arms (median 2, range 2-7). In patients (92%) with 2-4 co-current amplified chromosome arms, the most frequent co-amplified patterns were Chr20q-Chr13q (20%) and Chr20q-Chr8q (15%). Most patients among this subgroup had more than three amplified genes in Chr20q while only one amplified gene in Chr8q. In patients (8%) with 5-7 co-current amplified chromosome arms, the most frequent amplified regions were Chr20q, Chr8q and Chr7q, and more than 60% cases harbored Chr20q-Chr8q. Interestingly, these patients mainly had multiple amplified genes in Chr8q and only one amplified gene in Chr20q, in the contrary to the patients with 2-4 co-current amplified chromosome arms. In addition, high-level focal amplifications in Chr17q and Chr12q participated equally to the amplifications with other chromosome arms. Conclusions: Our analysis results suggested the heterogeneity of Chr20q co-amplifications patterns in CRC. Amplifications in Chr20q and Chr8q may play distinct critical roles in the tumorigenesis of CRC. High-level amplifications were, on the other hand, independent of their driven process.
The prognostic impact of intramural invasion in patients undergoing surgery for non-metastatic colon cancer.
Authors: Ozer Leyla , Şenocak Taşçi Elif , Mutlu Arda Ulaş , Piyade Betul , Ramoğlu Nur , Ajredini Mırac , Gurleyik Damla , Çeçen Recep , Dinçer Sena Nur , Musevitoglu Turan , Erdamar Çetin Ayşe Sibel , Yildiz Ibrahim , Aytac Erman
Published: June 2022

e15516

Background: The invasion of extramural veins is an independent predictor of poor outcome in colorectal cancer whereas the significance of intramural component of venous as well as lymphatic and perineural invasion is less clear. We aimed to search the prognostic impact of these invasion patterns and their association with various clinicopathological variables. Methods: All patients undergone surgery for colon cancer between December 2014 and December 2020 were analyzed retrospectively and patients with stage II and III disease were enrolled. The patients were divided into four categories as no invasion, intramural invasion only, extramural invasion only or both (intramural and extramural) for vascular invasion (VI), lymphatic invasion (LI) and perineural invasion (PNI). 5-year disease-free (DFS) and overall-survival (OS) were the primary outcomes. Results: 626 patients were included (47.1% stage II patients). There was no significant difference between the presence of ‘intramural only’ venous (DFS, 87.2 vs 88.4% p = 0.84; OS, 88.3 vs 90.7% p = 0.90), lymphatic (DFS, 89.5 vs 85.1%, p = 0.13; OS, 89.5 vs 89.4%, p = 0.9) and perineural invasion (DFS, 89.1 vs 80.9%, p = 0.26; OS, 90.6 vs 84.8%, p = 0.12) compared to ‘no invasion’ in terms of DFS and OS. Invasion of both intramural and extramural compartments for each of these parameters demonstrated poor survival. Presence of exclusively extramural venous and perineural invasion without intramural invasion had adverse effect on DFS (87.2 vs 78.7%, p = 0.036, 89.1 vs 80.9%, p = 0.044, respectively) but not OS (88.3 vs 89.3%, p = 0.78, 90.6 vs 83.8%, p = 0.215, respectively). Tumor sidedness did not have impact on the depth and rate of lymphatic invasion however right-sided and dMMR tumors exhibited less venous and perineural invasion (24.7 vs 33.9% p = 0.007; 34.5 vs 41.5% p = 0.034 and 13.5 vs 33.5% p < 0.001; 25 vs 41.4% p = 0.004, respectively). The ratio of stage III patients with venous, lymphatic and perineural invasion was consistently higher when compared with stage II patients (for LI 69.8 vs 39.7% vs p < 0.001; for VI 36.9 vs 22.7% p < 0.001; for PNI 51.4 vs 24.4% p < 0.001). Low grade tumors exhibited less LI and PNI when compared with high grade tumors (for LI 53.2 vs. 71.3% p = 0.004, for PNI 37.1 vs. 48.3% p = 0.031) however there was no significant difference for venous invasion rates among two groups. Conclusions: Presence of merely intramural component of invasion may not be considered a synonym for lymphovascular invasion which is supposed to be a high-risk factor for systemic recurrence.
Homologous recombination pathway alternations in relation to prognosis of MSS/pMMR colorectal cancer patients treated with immune checkpoint inhibitors (ICIs).
Authors: Liu Xing , Fu Zhichao
Published: June 2022

e15517

Background: Colorectal cancer is a common malignant tumor in the gastrointestinal tract and represents the third deadliest cancer worldwide. Recently, the advent of immune checkpoint inhibitors (ICIs) has provided significant survival benefit for colorectal cancer(CRC) patients with MSI-H/dMMR. However, the majority of MSS/pMMR CRC patients show poorly durable responses of immunotherapy, and more proper predictive biomarker is required to guiding immunotherapy treatment for these CRC cancer patients. The purpose of the present study was to explore the role of Homologous recombination (HR) pathway alternations in predicting the prognosis of MSS/pMMR CRC patients treated with ICIs. Methods: All data of patients undergoing immunotherapy were obtained from the cBioPortal database (https://www. cbioportal.org), which include genomic sequencing datasets and clinical data for eight diverse cancers from MSKCC, and RNAseq data and clincial data for CRC from International Cancer Genome Consortium (TCGA). Results: In the MSKCC cohort, HR mutation was analyzed by univariate Cox regression in nine different cancers, the analysis performed revealed HR mutation were associated with a better prognosis of colcrectal cancer (p = 0.003; HR, 0.24; 95%Cl, 0.09-0.62) and melanoma (p = 0.042; HR,0.66; 95% Cl, 0.09-0.62), with no significant correlations in other cancers. By doing survival analysis of the CRC patients without MSI-H/dMMR status by Kaplan–Meier (KM) method. The results showed that the OS of the patients with HR-MT was signifcantly longer than that of patients with HR-WT (P = 0.0029), and no significance association has been identified between Tumor Mutational Burden (TMB) and overall prognosis of patients without MSI-H/dMMR. Notably, in TCGA CRC dataset, we found TMB and Neoantigens were significantly higher in HR-MT patients than that of HR-WT patients(p < 0.0001), and a higher-level expression of CD8 T cell were also observed in the HR-MT patients patients in TCGA dataset (p = 0.036). Conclusions: Our study results showed that HR-mutation is a favorable prognostic factor in these CRC patients with MSS/pMMR, which can be used as a potential biomarker for predicting the immunotherapy efficacy of these patients.
The role of ACAA2 in colorectal caner patient with active glucose metabolism.
Authors: Yuan Yitao , Liu Tianshu , Liu Mengling , Gan Lu
Published: June 2022

e15522

Background: colorectal cancer(CRC) is third in incidence and mortality in worldwide with a 5-year survival rate is 65%. CRC patients(pts) with active glucose metabolism have a worse outcome. Molecular biological mechanisms in this subgroup have not been well uncovered. Here we identified ACAA2 has a significant prognostic role in CRC pts and more down-regulated in those with higher standardized uptake value(SUV). Then we focused on its functions and mechanisms behind it. Methods: Clinical and transcriptional data of pts with CRC obtained from GSE39582 dataset (n = 510) and a Zhongsh an Hospital Fudan University Cohort(ZHFUC) with CRC diagnosed at 6/2015-12/2018 were collected (n = 441). The ACAA2 protein expression of ZHFUC was evaluated by immunohistochemistry staining. Metabolic activity was evaluated by SUV. Overall survival (OS) was analyzed via Kaplan-Meier Curves with Log-rank test and multivariable Cox regression. Silencing (KD) and over-expression (OE) of ACAA2 were performed in CRC cells, respectively(KD: HCT116;RKO and OE: DLD1;RKO). The effect of ACAA2 was tested through CCK8, colony formation assays, cell cycle assays, seahorse for glucose metabolism and subcutaneous xenograft models. The potential mechanism under ACAA2 contribution was explored by RNA sequencing and western blot. Results: ACAA2 of ZHFUC was down-regulated in CRC compared to normal tissues. Pts divided into ACAA2 high (n = 226) and low (n = 215) with an evenly distribution in their clinicopathological features.Of 143 pts with available PETCT imaging took as a SUV-related group), 78 were identified as ACAA2 high and 65 were low. In comparison to ACAA2 high ones, pts in ACAA2 low showed an higher SUV (p < 0.05) and a significantly worse OS (total pts: p = 0.012; SUV-related group:p = 0.024; median OS is not reached). The multivariate analysis showed that ACAA2 low was independently associated with inferior OS [total pts: HR 1.99(95%CI: 1.2 ¨C 3.2), p < 0.001; SUV-related group: HR 2.51(95%CI: 1.1 ¨C 5.7), p =< 0.05]. Over-expression ACAA2 inhibited tumor growth both in vitro and in vivo, and lower glucose metabolism and arrested G0/G1 cell cycle were observed in HCT116-OE cells, while reversed effects in RKO-KD cells. gene expression profiling analysis and consistent results in western blot highlighted the role of AKT signaling pathway in those contributions of ACAA2. A AKT inhibitor could suppress cell proliferation causing by silencing ACAA2 both in vitro and in vivo. Conclusions: while ACAA2 expression was an independent prognostic factor for CRC pts. And those of them with an active glucose metabolism had a lower ACAA2 expression. The silencing and over-expression of ACAA2 expression in CRC cell lines promoted and inhibited cell proliferation and tumor growth in vitro and in vivo, oppositely. ACAA2 expression levels might classified a subtype of CRC pts, who might benefit from AKT inhibitors treatment.
Necroptosis-related lncRNA biomarkers for colon cancer prognosis and the associations with the immune landscape.
Authors: Wang Tao , Xu Shaohua , Wang Qian , Xiao Shanshan ,   Hangzhou Repugene Technology Co,.Ltd
Published: June 2022

e15525

Background: Necroptosis is a regulated caspases-independent cell death involved in colon cancer development and antitumor activity. lncRNAs are widely considered as biomarkers in various diseases. In this study, we identified prognosis biomarkers using necroptosis-related lncRNAs, and predict immunotherapeutic responses for colon cancer. Methods: A total of 453 colon cancer (CRC) patients (480 normal and 41 tumor samples) were enrolled in this study. The RNA expression dataset were obtained from The Cancer Genome Atlas (TCGA-COAD). They were randomly grouped as training set and validation set(7:3 ratio). Necroptosis-related lncRNAs were identified using Pearson’s correlation analysis with 67 necroptosis-related genes previously reported. Stepwise Cox regression and LASSO algorithm were performed to construct the prognostic risk score model. The overall survival (OS) difference between the high- and low-risk groups(cutoff using median risk score) was compared using Kaplan-Meier statistics. Furthermore, we evaluated the associations between the identified lncRNAs and the immune-related phenotypes including tumor micro-environment (TME) scores calculated by ESTIMATE, immune cell infiltration estimated by CIBERSORT, chemotherapeutics sensitivity predicted by pRRophetic and immune checkpoint expression,etc. Results: A total of 1926 necroptosis-related lncRNAs were identified and four lncRNAs (LINC02753, AC073283, AC010973, AP003555) were found to be correlated with 10 differential expressed necroptosis-related genes. The identified four lncRNAs were used to construct the prognostic model. The identified biomarkers was found to significantly correlate with worse prognosis in TCGA cohort (Train set: HR = 4.65, 95%CI = 2.42-8.93, P < 0.001; Validation set: HR = 3.06, 95%CI = 1.32-7.12, P = 0.006; Whole set: HR = 4.04, 95%CI = 2.41-6.76, P < 0.001) and was found to be independent to clinicopathological parameters. In addition, the lower TME scores suggested the lower infiltration of non-tumor cells in high-risk group and eight drugs were predicted to be more effective in high-risk group (i.e., PAC-1, AS601245). Further immune-related analysis revealed that the infiltrating immune cells including B cells, CD4 T cells, resting NK cells, M1 macrophages, monocytes, were all significantly different between the two groups. Moreover, TNF superfamily members (i.e., TNFSF14/15/25) were found to be substantially increased in high-risk group, which was considered as a type of important immune checkpoint molecule and participates in the initiation and regulation of necroptosis. Conclusions: The identified 4-lncRNA signature based on necroptosis showed potential prognosis value in CRC patients. The results can also help to guide immunotherapy and clinical research with TNFSF inhibitors for colon cancer patients with further experimental and clinical validation.