bluuebunny/crossref_metadata_2025 huggingface dataset:
Advanced imaging to assess longitudinal vascular changes in brain metastases treated with checkpoint inhibition.
Authors: Kim Albert Eusik , Chang Ken , Emblem Kyrre E. , Kalpathy-Cramer Jayashree , Lee Eudocia Quant , Lin Nancy U. , Tolaney Sara M. , Nayak Lakshmi , Chukwueke Ugonma Nnenna , Oh Kevin S. , Shih Helen Alice , White Michael , Lawrence Don P. , Moy Beverly , Cohen Justine Vanessa , Giobbie-Hurder Anita , Cahill Daniel P. , Sullivan Ryan J. , Brastianos Priscilla Kaliopi , Gerstner Elizabeth Robins
Published: June 2021

3059

Background: Immune checkpoint inhibitors (ICI) have recently been shown to be effective for brain metastases (BM) in melanoma and lung cancer. Several studies demonstrate that 20-50% of BM patients respond to ICI. The reasons behind this wide variability in treatment response is not clear. Therefore, using physiologic imaging, we seek to identify the longitudinal biological changes exerted on BM as a result of ICI administration. Methods: Given the importance of aberrant tumor vasculature in cancer proliferation, we have focused on assessing changes in vascular physiology. We analyzed standard post-contrast and dynamic susceptibility contrast (DSC) MRI to identify characteristic vascular signatures as part of an ongoing Phase 2 study of pembrolizumab for patients with untreated or progressive, previously treated BM from any histology. Tumor volume measurements were calculated by summating all enhancing voxels. As per modified RECIST and RANO criteria for immunotherapy, volumetric increase of > 40% was defined as progressive disease (PD), a decrease of > 60% as partial response (PR), and stable disease (SD) as between -60% and +40%. Results: 35 patients, out of the total cohort of 60, have undergone DSC-MRI analysis. Histologies include 15 with breast cancer, 6 with non-small cell lung cancer, 4 with melanoma, and 10 with other cancers. At baseline, the total number of BM was 1-50+ per patient. Based on summing the entire enhancing intracranial disease burden, best volumetric responses for the 35 evaluable patients include 4 PR, 12 SD, and 19 PD. Thus far, we found that ICI-resistant BM had a 50% increase in cerebral blood flow (CBF), 105% increase in cerebral blood volume (CBV), a 15% increase in mean transit time (MTT), and an 80% increase in vessel caliber at 6 weeks post-treatment. On the other hand, ICI-responsive BM had no change in CBF, a 33% increase in CBV, a 10% decrease in MTT, and no change in vessel caliber. Ongoing analysis to uncover additional vascular changes (e.g. tumor oxygenation, vessel size index) within BM to ICI are pending. Conclusions: Our data provides evidence that effective ICI for BM is associated with unique intra-tumoral vascular physiology. With final analysis, we will uncover other facets of vascular physiology that correlate with ICI response, and may reveal mechanisms of response/resistance within tumors to ICI.
Comprehensive molecular profiling of advanced cancers in a real-world setting using an ultrasensitive amplicon-based next-generation sequencing (NGS) liquid biopsy assay.
Authors: Poh Jonathan , Ngeow Kao Chin , Pek Michelle , Tan Daniel , Lim Jing Shan , Choudhury Yukti
Published: June 2021

3062

Background: Molecular profiling of circulating tumor DNA (ctDNA) by NGS has demonstrated the value of liquid biopsy in informing treatment decisions and monitoring disease progression in cancer patients. Here we report results from the real-world clinical application of an ultrasensitive amplicon-based NGS liquid biopsy assay for advanced cancers. Methods: Plasma cell-free DNA (cfDNA) from 1,338 consecutive samples (51.3% lung, 15.6% breast, 8.4% colorectal, 26.8% from 18 other cancer types; 86.3% of cancer samples were metastatic) underwent real-world testing in a Singapore-based, CAP-accredited, CLIA-certified laboratory from Jan 2018 – Nov 2020. Genomic alterations were analyzed using an amplicon-based NGS assay that detects alterations in 80 cancer-related genes, microsatellite instability (MSI) and cancer-causing viruses, with previously validated cfDNA detection limits of 0.1% variant allele frequency (VAF) for SNPs and indels, 5% tumor fraction, and 2 IU/mL plasma, respectively. Results: ctDNA was successfully detected in 70.0% of cancer samples (76.3% from metastatic and 24.7% from localized tumors) for a total of 977 unique variants. Across ctDNA-positive samples the median VAF was 1.4%, and 8.5% of all reported variants had VAFs between 0.01 – 0.09%. The most frequently altered genes were TP53 (48.8%), EGFR (36.9%), KRAS (17.4%), PIK3CA (15.3%), and APC (9.5%). In ctDNA-positive lung cancer, 74.6% of samples (66.5% EGFR+) harbored ≥1 actionable target, with 29.9% of patients treated with a first- or second-generation EGFR tyrosine kinase inhibitor harboring an EGFR T790M resistance mutation. Among breast cancers, ESR1 or PIK3CA alterations predicting drug resistance/response were detected in 44.2% of HR+ cases. In colorectal cancer, alterations implicated in anti-EGFR resistance ( NRAS, KRAS, BRAF, ERBB2) were found in 50.0% of samples. Profiling of cfDNA also enabled cancer monitoring, even among cancers with low genetic biomarker prevalence. 50% of nasopharyngeal cancer samples were Epstein-Barr virus-positive while 35.7% of liver cancer samples were Hepatitis B virus-positive, enabling an additional yield of 14.3% and 7.1% respectively, over ctDNA detection. cfDNA profiling of cancers of unknown primary origins informed potential tumor origins via the detection of tumor type-specific alterations such as mutations in AR, ESR1, GNAS, EGFR genes, viral biomarkers, and MSI. Conclusions: The use of a comprehensive pan-cancer liquid biopsy panel with rational inclusion of actionable and driver genes resulted in detection of ctDNA in the vast majority of clinical cases processed routinely. These findings support the utility of ultrasensitive amplicon-based NGS liquid biopsy assays in probing cancer drug sensitivity/resistance, tumor burden monitoring, and molecular characterization of tumors.
Improving differential diagnosis of pulmonary large cell neuroendocrine carcinoma (LCNEC) and small cell lung cancer via a transcriptomic, biological pathway-based ridge regression model.
Authors: Hong Jun , Hou Likun , Zhang Wei , Dong Zhengwei , Huang Zhan , Yuan Wuzhou , Zhang Lei , Wu Chunyan
Published: June 2021

3065

Background: In clinics, it can be challenging to make correct diagnosis of LCNEC, Small cell lung cancer (SCLC), if tissues, like needle biopsies, are insufficient or morphology was poorly preserved. In this study, a reliable classifier was constructed based on transcriptome data and machine learning (Ridge regression) to improve the diagnostic accuracy for LCNEC and SCLC. Methods: RNA-Seq data obtained from 3 public cohorts were collected as training set, including 60 NSCLC cases from The Cancer Genome Atlas (TCGA), 66 LCNEC cases from Julie George et al., Nature Communications 2018, and 33 SCLC cases from Julie George et al., Nature 2015. Another 80 NSCLC, 30 LCNEC and 15 SCLC cases published by Martin Peifer et al., Nature Genetics 2012 were used as validation set. Additionally, RNA-Seq data of 27 borderline samples which were hard to make diagnosis based on histology and Immunohistochemistry were used to test the accuracy of the prediction model. Results: 13,959 genes mapped to 186 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were included. Gene Set Variation Analysis (GSVA) algorithm was used to enrich and score each KEGG pathway. A prediction model based on GSVA score of each pathway was constructed via Ridge regression. This GSVA Score Model achieved ROC-AUC 0.949 and concordant rate of 0.75 for the entire prediction efficiency. Of the 27 borderline samples which were hard to make confirmed diagnosis, 17/27 (63.0%) were predicted as LCNEC, 7/27 were predicted as SCLC, and the remainder were predicted as NSCLC. While only 8 (29.6%) cases with LCNEC were diagnosed by pathologists, which was significantly lower than the results predicted by the model. Furthermore, cases with model predicted LCNEC had a significant longer disease-free survival than that with model predicted SCLC (median DFS,59 months for LCNEC vs 5 months for SCLC, p = 0.0043), which was in parallel with currently known prognostic difference of these two types of neuroendocrine tumors. Conclusions: This GSVA algorithm-based prediction model was able to make accurate diagnosis of LCNEC and SCLC. And it may provide valuable information for clinics to choose optimal therapeutic approach for patients with pulmonary neuroendocrine tumors.[Table: see text]
TP53 and CHEK2 germline mutations in malignant solid tumors.
Authors: Zhang Zhiye , Wu Yaqing , Luo Ningning , Zhang Qin , Han Tiantian , Bu Xuesong , Shuai Qin , Qi Yingxue
Published: June 2021

3119

Background: Li-Fraumeni syndrome (LFS, OMIM #151623) is an autosomal dominant cancer predisposition syndrome. Typical LFS tumors comprise adrenocortical carcinomas, sarcoma, breast cancer and central nervous system tumors. LFS is also associated with an increased risk of a multitude of other common types of cancer, such as prostate cancer, lung cancer, gastric cancer, colorectal cancer, ovarian cancer, melanoma, etc. TP53 germline mutations are the most common gene with LFS. Germline mutations of CHEK2 have been identified as another predisposing gene and associated with a range of cancer types. However, the pattern of TP53 and CHEK2 germline mutations in malignant tumors remains unknown. Methods: We identified 8535 malignant solid tumors patients without selecting age or family history in a retrospective cohort. Germline mutations were categorized based on ACMG (American College of Medical Genetics and Genomics) guidelines in pathogenicity. The patients were divided into three groups, P group (with pathogenic mutations), LP group (with likely-pathogenic mutations) and Non_P group (neither pathogenic nor likely-pathogenic mutation). Statistical significance was defined as P-value less than 0.05. Results: A total of 461 (461/8535) patients carried TP53 or CHEK2 germline mutations were identified, in which 15 patients with pathogenic mutations and 17 patients with likely-pathogenic mutations. One patient with lung cancer in LP group carried TP53 homozygous mutation ( p. Ser215Ile), and the remaining 31 patients all carried heterozygous mutations. Among these 31 carriers, 16 (51.6%) carried nonsense or missense mutations (10 for nonsense and 6 for missense mutations). 3 patients in the P group carried CHEK2 p. Y139* (one liver cancer patient and two lung cancer patients) were identified. The median age of group P, LP and Non_P was 55 (39 for TP53, 61 for CHEK2), 63 (52 for TP53, 66 for CHEK2) and 59, respectively. Somatic mutation analysis found no significant difference in tumor mutation burden (TMB) among three groups. The SNV/INDEL mutation frequency of LRP1B in the P or LP group was significantly lower than the Non_P group. Conclusions: Our data showed that 0.375% (32/8535) malignant solid tumor patients carried TP53 (16/8535) or CHEK2 (16/8535) germline pathogenic or likely-pathogenic mutations. The relationship between germline mutations and cancer susceptibility will be studied in the future.[Table: see text]
Analysis of the MOSAIC correlative cancer database integrating molecular cancer classification and tumor profiling to identify targeted treatment options for metastatic cancer.
Authors: Ma Li , Treuner Kai , Wong Jenna , Spigel David R. , Schnabel Catherine A. , Greco F Anthony
Published: June 2021

3121

Background: Unless tumor type and genetic alterations can be identified, metastatic cancer patients with unknown or uncertain diagnoses may be limited to empiric chemotherapy. The 92-gene assay (CancerTYPE ID) is a validated gene expression classifier of 50 tumor types and subtypes for patients with cancer of unknown primary (CUP) or ambiguous diagnoses. Multimodal molecular biomarker testing by next-generation sequencing (NGS), tumor mutational burden (TMB), fluorescent in situ hybridization (FISH), microsatellite instability (MSI), and immunohistochemistry (IHC) can identify genetic targets. A database integrating tumor typing with biomarker analysis in metastatic cases was utilized to identify the most prevalent genetic alterations by tumor type. Methods: MOSAIC (Molecular Synergy to Advance Individualized Cancer Care) is an IRB-approved database of cases with CancerTYPE ID testing plus multimodal biomarker testing. The current study determined molecular tumor type followed by molecular profiling by NGS for up to 323 genes, (NeoTYPE profiles, Neogenomics). Results: Tumor type was determined in 1992 of 2151 cases (92.7%), comprised of 27 different tumor types. 72% of cases were comprised of the 7 tumor types shown in the table,which also shows the frequency of the 10 most commonly mutated genes by tumor type. Bolded are genes with actionable genetic mutations for which FDA-approved therapies are not currently indicated in the identified tumor type. Conclusions: Precise targeted treatment for many patients with CUP or ambiguous diagnoses requires accurate diagnosis of the cancer origin combined with multimodal molecular testing to identify actionable genetic alterations in the appropriate cellular context. Future studies will evaluate additional biomarker profiles, including TMB, FISH, MSI, and IHC for cases in the MOSAIC database.[Table: see text]
Temporal and spatial topography of cell proliferation in cancer.
Authors: Kabraji Sheheryar Kairas , Gaglia Giorgio , Argyropoulou Danae , Dai Yang , Wang Shu , Bergholz Johann , Coy Shannon , Lin Jia-Ren , Jeselsohn Rinath , Metzger Otto , Winer Eric P. , Dillon Deborah , Zhao Jean , Sorger Peter , Santagata Sandro
Published: June 2021

3122

Background: Tumors are complex ecosystems where exogenous and endogenous cues are integrated to either stimulate or inhibit cancer cell proliferation. However, the nature of these complex cell cycle states, their spatial organization, response to perturbation, and implications for clinical outcomes, are poorly characterized in tumor tissues. Methods: We used multiplexed tissue imaging to develop a robust classifier of proliferation, the multivariate proliferation index (MPI), using 513 unique tumors across five cancer types. Next, we used dimensionality reduction analysis to assess how the patterns of cell cycle protein expression in tumors were altered in response to perturbation. Results: The MPI outperforms single markers, like Ki67, when classifying proliferative index across diverse tumor types and reveals the proliferative architecture of tumors in situ. We find that proliferative and non-proliferative cancer cells are organized across microscopic (cell-to-cell) and macroscopic (tissue-level) scales. Both domains are reshaped by therapy, and local clusters of proliferative and non-proliferative tumor cells preferentially neighbor distinct tumor-infiltrating immune cells. We further phenotyped non-proliferating cancer cells using markers of quiescent cancer cells, cancer stem cells, and dormant cancer cells. We found that these types of non-proliferating cancer cells can occupy distinct regions within the same primary tumor. In high-dimensional marker space, populations of proliferative cancer cells express canonical patterns of cell cycle protein markers, a property we refer to as “cell cycle coherence”. Untreated tumors exist in a continuum of coherence states, ranging from optimal coherence, akin to freely cycling cells in culture, to reduced coherence characterized by either cell cycle polarization or non-canonical marker expression. Coherence can be stereotypically altered by induction and abrogation of mitogen signaling in a HER2-driven model of breast cancer. Cell cycle coherence is modulated by neoadjuvant therapy in patients with localized breast cancer, and coherence is associated with disease-free survival after adjuvant therapy in patients with colorectal cancer, mesothelioma and glioblastoma. Conclusions: The MPI robustly defines proliferating and non-proliferating cells in tissues, with immediate implications for clinical practice and research. The coherence metrics capture the diversity of post-treatment cell cycle states directly in clinical samples, a fundamental step in advancing precision medicine. More broadly, replacing binary metrics with multivariate traits provides a quantitative framework to study temporal processes from fixed static images and to investigate the rich spatial biology of human cancers.
Frequency of longitudinal changes in TP53 mutation status from gene sequencing of serial tumor biopsies from a large cohort of cancer patients.
Authors: Annis D. Allen Allen , Pavlick Dean C. , Frampton Garrett M. , Albacker Lee A. , Vukovic Vojislav M. , Aivado Manuel
Published: June 2021

3124

Background: The p53 pathway is one of the most important in cancer biology, with mutation of the TP53 gene that encodes the p53 tumor suppressor protein observed in ≈50% of all cancers. We evaluated the frequency of changes in TP53 mutation status in a large cohort of serial tumor biopsies. Methods: From a database of >200,000 next-generation gene sequencing results we identified 16,592 samples arising from repeat biopsies from 7840 patients (pts), average 2.12 per pt, 1007 pts with ≥3, max 11; over an interval up to 234 months (mos), average 11.0 mos. TP53 mutations with known or unknown significance in successive biopsies and changes in assignment from TP53-Wild-Type (WT) to Mutant (Mut), or Mut to WT, were evaluated vs. cancer type and time between biopsies. Results: Table: N (%) of samples vs. change in TP53 status from previous biopsy vs. mos from initial biopsy in all samples (7840 initial + 8752 successive, 46% TP53-Mut) and the three most represented cancers: non-small cell lung cancer (NSCLC, 1189 initial + 1268 successive, 60% Mut), breast (947 initial + 993 successive, 55% Mut), multiple myeloma (MM, 578 initial + 981 successive, 18% Mut). Conclusions: Changes in TP53 status were rare (<10% of samples). Differences may occur in serial biopsy samples for pathophysiological reasons, e.g., a mutant clone becoming dominant and/or heterogeneity at different tumor biopsy sites, or analytical differences in biopsy tumor content or assay sensitivity between samples. In this analysis, WT-to-Mut changes were more frequent (5.9%) than Mut-to-WT changes (3.3%), suggesting a small selection pressure for TP53 alterations later in oncogenesis and indicating that these alterations are truncal. Mut-to-WT changes are not readily explained physiologically and may suggest these infrequent changes are mostly due to sampling or analytical variability, and genuine changes in TP53 mutation status are quite rare.[Table: see text]
The value of defining molecular resistance in patients with progressive EGFR and ALK-driven lung cancer in a public system.
Authors: Barron Carly C. , Stockley Tracy , Law Jennifer H. , Shabir Muqdas , Fernandes Roxanne , Zhang Tong , Le Lisa W. , Tsao Ming Sound , Kamel-Reid Suzanne , Pal Prodipto , Cabanero Michael , Schwock Joerg , Ko Hyangmi , Liu Geoffrey , Bradbury Penelope Ann , Sacher Adrian G. , Shepherd Frances A. , Leighl Natasha B. , Perdrizet Kirstin
Published: June 2021

3126

Background: Repeat molecular profiling, except to detect EGFR T790M, is not routinely performed in Canadian patients with lung cancer progressing on EGFR tyrosine kinase inhibitors (TKIs). We performed genomic profiling on post-progression biopsies in patients with stage IV non-small cell lung cancer (NSCLC) and known EGFR/ ALK aberrations treated with TKIs to identify resistance mechanisms, evaluate options for subsequent treatment, and to assess clinical trial eligibility and costs. Methods: From Feb 2018-Aug 2020, post-progression tumour biopsies from consenting patients at a major cancer centre underwent genomic profiling (ThermoFisher OCA v3.0 including hotspots, fusions, and copy number variations in 161 cancer-associated genes). Outcomes of interest were the identification of resistance mutations, actionable targets, clinical trial eligibility (per clinicaltrials.gov), and costs. Results: Thirty-two patients consented to the study. Most, 84% (n = 27), had successful testing completed while 16% (n = 5) had insufficient tissue. Median age of the cohort was 56 yrs, 59% (n = 16) were female, 74% (n = 20) were never-smokers, 81% (n = 22) had ECOG performance status 0-1, and 67% (n = 18) were Asian. The majority, 81% (n = 22) had EGFR mutated NSCLC, and had progressed on EGFR TKIs (15 with previously identified T790M had progressed on osimertinib), and 19% (n = 5) had ALK fusions. Patients had received a median of 2 prior lines of targeted therapy prior to re-biopsy (IQR 1.5,3). One patient had evidence of small cell transformation and associated TP53 and RB1 mutations, 11% (n = 3) had acquired EGFR C797S mutations, and 11% (n = 3) had acquired ALK resistance point mutations (G1202R n = 2, I1171N n = 1). Genomic profiling identified additional actionable targets in 19% of patients (n = 5: MET exon 14 skip mutation n = 1, MET amplification n = 2, BRAF V600E n = 2). Overall, 33% (n = 9) patients had management-changing resistance mechanisms identified (small cell transformation n = 1, actionable targets n = 5, ALK inhibitor resistance = 3). New clinical trial options based on genomic profiling results were identified for 67% (n = 18) of patients. Incremental costs for repeat genomic profiling were approximately $880 CAD per case. Conclusions: Molecular profiling upon development of resistance to targeted therapy in our cohort revealed actionable resistance mechanisms for over a third of patients and clinical trial options for 67%. These incremental benefits for patients highlight the importance of routine molecular profiling in the setting of acquired TKI resistance in lung cancer.
Clinically advanced pelvic squamous cell carcinomas (pSCC) in men and women: A comprehensive genomic profiling (CGP) study.
Authors: Spiess Philippe E. , Grivas Petros , Mata Douglas A. , Bratslavsky Gennady , Jacob Joseph M , Necchi Andrea , Danziger Natalie , Lin Douglas I. , Decker Brennan , Sokol Ethan , Huang Richard S.P. , Ross Jeffrey S.
Published: June 2021

3130

Background: Given that the clinical manifestations, disease course, and treatment options for pSCC differ between tumor types, we performed CGP to examine possible genomic differences. Methods: 1,741 clinically advanced pSCCs including 230 penile (penSCC), 17 male urethral (murthSCC), 125 male anal (manSCC), 7 female urethral (furthSCC), 263 vulvar (vulSCC), 822 cervical (crvSCC), and 277 female anal SCCs (fanSCC) underwent hybrid capture-based CGP to evaluate all classes of genomic alterations (GAs). Tumor mutational burden (TMB) was determined on up to 1.1 Mb of sequenced DNA and microsatellite instability (MSI) was determined on up to 114 loci. PD-L1 expression was determined by IHC (Dako 22C3). Results: HPV-16/18 detection was lowest in murthSCC and vulSCC and highest in manSCC, fanSCC, and crvSCC. TP53 GAs were inversely associated with HPV status. PIK3CA GA frequency varied (22-43%). DNA-damage response (DDR) GAs (e.g., BRCA1/2, ATM, others) were low ( < 1-3%) throughout. Cell-cycle GAs were most frequent in external cases (penSCC, furthSCC, vulSCC). MTOR pathway GAs ( PTEN, FBXW7) were the most frequently identified “actionable” GAs. FGFR3 GA were present in >5% of murthSCC, crvSCC, and fanSCC; other receptor-tyrosine kinase (RTK) targeted options were 1% in BRAF/ ERBB2. NOTCH1 GAs were present in > 15% of penSCC and vulvSCC. TMB ≥10 mut/Mb was >15% in manSCC, fanSCC, and crvSCC. PD-L1 low expression was > 25% in all pSCC except crvSCC and high expression was > 18% in all pSCC except urthSCC and manSCC. Conclusions: Despite similar histology, pSCC differ widely in GAs and HPV status. PIK3CA is the most frequent “targetable” GA followed by MTOR pathway and cell cycle; RTK targets are extremely rare. PARP inhibitor options appear low given the infrequent finding of DDR GAs. Anti-PD(L)1 could be considered in a number of cases based on TMB>10 mut/Mb and PD-L1 expression.[Table: see text]
Cancer and COVID-19: A proposed mechanism with therapeutic interventions.
Authors: Leyfman Yan , Emmanuel Nancy , Tentler Aleksey , Cappelli Jared , Erick Timothy K , Sharma Pushpa , Park Chandler H.
Published: June 2021

3135

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel betacoronavirus that causes the respiratory illness coronavirus disease 2019 (COVID-19). COVID-19 ranges in severity from an asymptomatic viral infection to life-threatening cases of pneumonia, acute respiratory distress syndrome (ARDS), multi-organ damage and sepsis. Cancer patients are at an increased risk of severe SARS-CoV-2 infection due to their immunocompromised status. We propose a mechanism by which SARS-CoV-2 infection causes multiple organ damage through IL-6-mediated inflammation and hypoxia-induced cellular metabolic alterations leading to cell death. Hypoxia is also induced by malignancy due to alterations in metabolism, resulting in greater IL-6 secretion. Methods: To highlight the possible effect of active cancer on the likelihood of hypoxia in COVID-19, we analyzed the correlation between cancer status and the severity of COVID-19 from the COVID-19 and Cancer Consortium data registry. For cancer status, we looked at progressive cancer and remission of cancer only -- those being the two extremes of presence and absence of uncontrolled cancer. Similar to prior studies, the severity of COVID-19 was used as an indication of hypoxia. Results: We observed a 24% positive deviation between expected and actual number of patients with actively progressing cancer who had hypoxic COVID-19 (moderate to severe), and a 26.9% negative deviation between expected and actual number of patients with active cancer who had no hypoxia with COVID-19 (p<0.0001). Conversely, for patients with cancer in remission, there was only a +5.8% and -5.1% deviation between expected and actual number of patients who did not have hypoxia and who had hypoxia, respectively. Conclusions: These results suggest that in the presence of poorly controlled malignancy, there is an increased likelihood of hypoxia in patients with COVID-19, thereby exacerbating downstream cytokine release syndrome and contributing to prolonged systemic inflammatory injury. Appreciating this pathway, future therapies can be developed to target the pathogenesis of both diseases and prevent progression, as seen with mesenchymal stem cells, which demonstrated a 91% overall survival and 100% survival in patients younger than 85 years old at one month after a single treatment.[Table: see text]
Genome-wide cfDNA fragmentation in patients with cancer and other diseases.
Authors: Carey Jacob , Jones Sian , Leal Alessandro , Chesnick Bryan , Butler Denise , Rongione Michael , Scharpf Robert B. , Johansen Julia S. , Velculescu Victor E. , Dracopoli Nicholas C
Published: June 2021

3136

Background: Genome-wide cfDNA fragmentation patterns have previously been demonstrated to distinguish with high sensitivity and specificity between plasma samples from individuals with and without cancer. Methods: To further evaluate cfDNA fragmentation as a blood-based screening test for cancer, we have evaluated these genomic features in patients with and without cancer who have been diagnosed with other common comorbidities. For this study, we have used low coverage (1-2x) whole genome sequencing to analyze plasma samples from 412 patients referred to an advanced diagnostic center due to unexplained signs and symptoms associated with cancer. Results: Seventy-seven of these patients were ultimately diagnosed with one of sixteen different solid cancers, 68 with cardiovascular disease, 48 with diabetes, as well as other comorbidities. We used the DELFI approach (DNA evaluation of fragments for early interception) to measure the cfDNA fragmentation in plasma from all 412 patients included in the study using a cross-validated machine learning model. Patients with cancer could be distinguished from non-cancer individuals with high sensitivity and specificity (AUC = 0.92), including for common cancers such as colorectal and lung cancer. Conclusions: These data support the hypothesis that abnormal cfDNA fragmentation is a consequence of unregulated mitoses in cancer cells and can be distinguished from fragmentation patterns of individuals with co-morbidities.
Germline polymorphisms in genes maintaining replication fork to predict the efficacy of oxaliplatin and irinotecan in metastatic colorectal cancer (mCRC) patients enrolled in MAVERICC trial.
Authors: Arai Hiroyuki , Xiao Yi , Wang Jingyuan , Battaglin Francesca , Kawanishi Natsuko , Jayachandran Priya , Soni Shivani , Wu Zhang , Mancao Christoph , Salhia Bodour , Mumenthaler Shannon M. , Millstein Joshua , Lenz Heinz-Josef
Published: June 2021

3139

Background: Protection of replication forks is critical for the survival of cancer cells. Chemotherapeutic drugs such as oxaliplatin and irinotecan can impede the progression of replication forks by inducing DNA lesions, which cause fork collapse and generate double-strand breaks. We hypothesized that functional genetic variants in genes involved in the maintenance of replication forks may predict the efficacy of cytotoxic drugs in mCRC patients. Methods: We analyzed genomic and clinical data from MAVERICC, a phase II trial which compared mFOLFOX6 and FOLFIRI in combination with bevacizumab in untreated mCRC patients. Genomic DNA extracted from blood samples was genotyped using an OncoArray (Illumina, Inc., San Diego, CA, USA). Candidate six missense single nucleotide polymorphisms (SNPs) ( SLFN11 rs9898983, SLFN11 rs12453150, RPA1 rs5030749, MCM3 rs2230240, TIMELESS rs2291739, and TIMELESS rs774047) were tested for association with progression-free survival (PFS) and overall survival (OS), using Cox proportional hazards model. To confirm the predictive value, the treatment-by-SNP interaction was tested. Results: A total of 324 patients were available for the SNP analyses (mFOLFOX6 plus bevacizumab arm [OHP arm]: n = 161; FOLFIRI plus bevacizumab arm [IRI arm]: n = 163). In the OHP arm, univariable analysis showed a significantly better PFS in patients with G/G genotype of TIMELESS rs2291739 compared to those with any A allele, and in patients with T/T genotype of TIMELESS rs774047 compared to those with any C allele. However, neither of these SNP’s associations were confirmed by multivariable analysis: TIMELESS rs2291739 (any A allele vs G/G, hazard ratio [HR] = 0.60, 95% confidence interval [CI] = 0.31–1.17, p = 0.12) and TIMELESS rs774047 (any C allele vs T/T, HR = 0.74, 95% CI = 0.41–1.36, p = 0.33). In the IRI arm, univariable analysis showed a significantly worse OS in patients with G/G genotype of TIMELESS rs2291739 compared to those with any A allele, and in patients with T/T genotype of TIMELESS rs774047 compared to those with any C allele. Multivariable analysis confirmed the significant associations in these SNPs: TIMELESS rs2291739 (any A allele vs G/G, HR = 3.06, 95% CI = 1.49–6.25, p < 0.01) and TIMELESS rs774047 (any C allele vs T/T, HR = 2.95, 95% CI = 1.43–6.08, p < 0.01). Treatment-by-SNP interaction test confirmed the significant predictive value of both SNPs, both on PFS and OS. Conclusions: Germline polymorphisms in the TIMELESS gene involved in the protection of replication forks may predict efficacy of oxaliplatin and irinotecan in mCRC patients. Our novel findings warrant further validation studies.
Maintenance therapy with 5-fluoruracil/leucovorin (5FU/LV) plus panitumumab (pmab) or 5FU/LV alone in RAS wildtype (WT) metastatic colorectal cancer (mCRC) - the PANAMA trial (AIO KRK 0212).
Authors: Modest Dominik Paul , Karthaus Meinolf , Frühauf Stefan , Graeven Ullrich , Müller Lothar , Koenig Alexander , Von Weikersthal Ludwig Fischer , Caca Karel , Kretzschmar Albrecht , Goekkurt Eray , Haas Siegfried , Kurreck Annika , Stahler Arndt , Heinemann Volker , Held Swantje , Jarosch Armin , Horst David , Kasper Stefan , Stintzing Sebastian , Trarbach Tanja
Published: June 2021

3503

Background: Planned discontinuation or stop-and-go use of oxaliplatin are established strategies in the systemic therapy of mCRC. Consequently, and irrespective of antibody use, 5FU/LV represents the standard backbone of most maintenance strategies. Unlike VEGF-targeted substances, there is limited evidence that EGFR-antibodies add efficacy to 5FU/LV maintenance in RAS wildtype ( RAS WT) mCRC patients. Methods: Following induction therapy with six cycles of 5FU/LV, oxaliplatin (FOLFOX) and pmab, the trial randomized maintenance therapy with 5FU/LV plus pmab vs. 5FU/LV alone in a 1:1 fashion in patients (pts) with RAS WT mCRC. The primary endpoint was PFS (progression-free survival: time from randomization until progression or death). With 218 events needed for PFS, the trial was designed to demonstrate superiority of the 5FU/LV+ pmab arm vs. 5FU/LV alone with a hazard ratio (HR) of 0.75, power of 80% and a significance level of 10%. Secondary endpoints included overall survival (OS), objective response to induction- and maintenance therapy as well as quality of life. The trial is registered with ClinicalTrials.gov, NCT01991873. Results: The full analysis set consists of 248 pts (125 pts 5FU/LV + pmab and 123 pts 5FU/LV) who were randomized and received maintenance therapy. Median age was 66 vs. 65 years, male patients were 69.6% vs. 63.4%, ECOG 0 was 56.8% vs. 60.2% in the respective trial arms (5FU/LV+ pmab vs. 5FU/LV). At data cut-off, with 218 events, PFS of maintenance therapy was improved with 5FU/LV+ pmab vs. 5FU/LV alone (8.8 (80% CI 7.6-10.2) months vs. 5.7 (80% CI 5.6-6.0) months, HR 0.72 (80%CI 0.60-0.85), p = 0.014). OS (event rate 54.4%) numerically favoured the 5FU/LV+ pmab arm (28.7 (95% CI 25.4-39.1) months) as compared to 5FU/LV alone (25.7 (95% CI 22.2-28.2) months), HR 0.84 (95% CI 0.60-1.18). Conclusion: In RAS WT mCRC, maintenance therapy with 5FU/LV+ pmab appears to be superior to 5FU/LV alone and should be regarded as standard of care maintenance regimen following induction therapy with FOLFOX plus pmab. Clinical trial information: NCT01991873.
Phase II trial of neoadjuvant mFOLFOX 6 with panitumumab (P) in T3 rectal cancer with clear mesorectal fascia (MRF) and KRAS, NRAS, BRAF, PI3KCA wild type (4WT). GEMCAD 1601 PIER trial.
Authors: Fernandez-Martos Carlos , Pericay Carles , Maurel Joan , Virgili Ana , Capdevila Jaume , Gallego Javier , Vera Ruth , Rodriguez-Salas Nuria , Losa Ferran , Valladares Manuel , Vivancos Ana , Ayuso Juan , Maas Monique , Martínez Fernando , Melian Marcos , García de Albéniz Xabier
Published: June 2021

3512

Background: Patients with advanced colorectal cancer with 4WT tumors achieve increased response rates with chemotherapy and anti-EGFR therapy as compared with chemotherapy alone. In clinically staged (c) T3 rectal cancer neoadjuvant oxaliplatin/fluoropyrimidine combination has shown to induce encouraging pathological complete response (pCR). We hypothesize that combining FOLFOX and P could improve outcomes in 4WT tumors. Methods: PIER was an investigator-initiated phase II, single-arm, multicentre clinical trial to evaluate the safety and efficacy of neoadjuvant mFOLFOX6 with P in pts < 75-y, with 4WT rectal cancer of the middle third staged as T3 by centrally-reviewed magnetic resonance imaging (MRI) and clear MRF, who were candidate for a R0 resection with sphincter preservation surgery. Pts received 6 cycles and underwent re-staging with MRI and sigmoidoscopy. Pts without progression underwent total mesorectal excision 4 weeks after the last cycle. Patients with progression were treated with pre-op chemoradiotherapy. The primary endpoint was pCR. The study followed a 2-Stage Simon’s MiniMax design (P0 of 16%, P1 of 35%, alpha and beta of 0.1). The target sample size was 35 patients and if 9 or more achieved a pCR, the results would be compatible with efficacy. We present primary and early secondary endpoints. Results: Between 9/2017 and 6/2020, 90 patients were screened (56 excluded; 42 were excluded due to mutations, 12 were excluded due to discrepancies with central review of radiology) of whom 34 were enrolled. In the ITT population a pCR was observed in 11 pts (32.3%; [95% CI 17.39-50.53]) and a near-complete pathological response (Mandard 1+2) was observed 17 pts (52.9%). Clinical complete or near complete response was achieved in 50% and there were no progressions. R0 resection rate and pathological circumferential resection margin neg- were 100%. Full compliance with induction was 88%. Neoadjuvant G3/4 toxicity occurred in 54% and was consistent with FOLFOX/P safety profile. G3/4 postoperative related toxicity was 19% with one reoperation. Conclusions: The study met the threshold for efficacy. mFOLFOX6 with P as neoadjuvant therapy can be effective and safe without unexpected toxicities in mrT3, clear MRF and 4WT rectal cancer and resulted in a higher rate of pCR compared with our previous series (GEMCAD 0801; The Oncologist 2014) in a similar molecular-unselected population. This study was funded by Amgen S.A. Clinical trial information: NCT03000374.
Use of circulating tumor DNA in colorectal cancer patients to assess tumor burden and response to therapy: An observational study.
Authors: Symonds Erin L. , Pedersen Susanne Kartin , Yeo Bernita Hui Li , Al Naji Hiba , Byrne Susan E. , Roy Amitesh Chandra , Young Graeme P.
Published: June 2021

3528

Background: Residual disease after treatment for colorectal cancer (CRC) poses a risk for recurrence but imaging and CEA are limited in their capacity to detect residual disease. A simple test is needed for assessing treatment response. This study determined whether levels of methylated BCAT1/IKZF1 DNA in blood correlate with tumor burden and whether post-treatment levels inform efficacy of different treatments for CRC. Methods: Patients with primary CRC had blood collected prior to treatment (n = 282, 59.9% males, median age 68.5y). Cell free DNA (cfDNA) was extracted from plasma and assayed for methylation in BCAT1 and IKZF1. Detection of methylation in either gene deemed a sample positive; levels were expressed as %methylation (average methylation/average cfDNA). Positive patients had additional samples collected post-treatment for early stage CRC (surgery, n = 31), advanced/metastatic CRC (surgery + adjuvant chemotherapy, n = 15), and rectal cancer (neoadjuvant therapy, surgery +/- chemotherapy, n = 6), or following mid-therapy suspension of treatment in advanced CRC (n = 24). Tumor size was expressed as the maximum diameter of the primary (assessed surgically or by MRI). Results: Pretreatment results increased with CRC stage. Positivity by stage was: I, 23.7% (14/59); II, 62.1% (54/87); III, 68.6% (70/102); IV, 85.3% (29/34). Level by stage: I, 0.0%; II, 0.06%; III, 0.07%; IV, 4.07%, p < 0.001). Pretreatment levels correlated significantly with tumor size (r = 0.372, p < 0.001). Post-treatment blood was collected a median 2.4mo (IQR 1.7-3.9) after therapy completion. Positivity decreased after completing treatment (Table), with 88.4% of cases (46/52) becoming ctDNA negative. All cases with complete treatment had a reduction in biomarker levels, whereas in those with incomplete therapy, 54.5% (12/22) remained positive and the pre- and post-treatment levels were not significantly different. Of those positive after treatment, 13 had a further blood sample: 8 had become ctDNA negative and all but one remained disease free. Five remained positive and all had further suspected or confirmed disease. Conclusions: Levels of methylated BCAT1 and IKZF1 DNA in blood correlated with tumor burden; levels became undetectable in the majority of patients following completion of planned curative intent treatment. The methylated ctDNA blood test aids monitoring of responses to therapy and identification of those cases with residual cancer who might benefit from ongoing therapy.[Table: see text]
The impact of colorectal cancer screening on incidence and stage IV disease in the Netherlands.
Authors: Krul Myrtle F , Elferink Marloes AG , Kok Niels FM , Dekker Evelien , Lansdorp-Vogelaar Iris , Meijer Gerrit A. , Nagtegaal Iris D , Ruers Theo JM , van Leerdam Monique E , Kuhlmann Koert FD
Published: June 2021

3531

Background: Population-based screening for colorectal cancer (CRC) aims to decrease incidence and mortality due to precancerous polyp removal, early detection and early treatment of CRC. In the Netherlands, phased introduction of a biennial fecal immunochemical hemoglobin test started in 2014 for individuals aged 55-75. This evaluation of the national data focuses on the initial effect of CRC screening on incidence and stage distribution and the impact on stage IV disease. Methods: All CRC patients diagnosed in the Netherlands between 2009 and 2018 were selected from the Netherlands Cancer Registry (NCR). Patients were linked to the Dutch national pathology registry (PALGA) to identify screen-detected tumors. Results: The NCR identified 137,717 CRC patients between 2009 and 2018. The incidence within screening age (55-75 yr) of all CRC stages showed an initial peak after introduction of screening in 2014, followed by a continuous decrease for all stages. CRC incidence outside the screening age did not show these explicit changes between 2009 and 2018. In 2018, the incidence of stage IV CRC within screening age was lower than the level at the start of the screening program. Stage distribution within screening age shifted towards earlier stages in the screening period (2014-2018) compared to the period before screening (2009-2012) (stage I: 31% vs. 18%, stage II: 22% vs. 26%, stage III: 29% vs. 31%, Stage IV: 18% vs. 25%, respectively). In the period 2014-2018 and within screening age, the ratio of screen-detected and symptom-detected tumors was highest in stage I (47%:53%) and lowest in stage IV (9%:91%). Screen-detected compared to symptom-detected stage IV patients diagnosed in the period 2014-2018 and within screening age had more frequently single organ metastases (74.5% vs 57.4%, p < 0.001), higher resection rate of the primary tumor (57.5% vs. 41.3%; p < 0.001) and higher local treatment rate of metastases (40.0% vs. 23.4% p < 0.001). The median overall survival of screen-detected stage IV patients was significantly longer than that of symptom-detected stage IV patients (31.0 months (95% CI: 27.7 – 34.3) vs. 15.0 months (95% CI: 14.5 – 15.5), p < 0.001). Conclusions: The initial results of the introduction of CRC screening in the Netherlands showed a favorable trend on CRC incidence and stage distribution. Screen-detected patients with stage IV disease had less extensive disease, resulting in better treatment options and improved survival.
A model combing an immune-related genes signature and an extracellular matrix-related genes signature in predicting prognosis of left- and right-sided colon cancer.
Authors: Zhong Min-Er , Cai Du , Fan Dejun , Wang Wei , Li Cheng-Hang , Huang Ze-Ping , Zhu Qiqi , Lv Min-Yi , Hu Chuling , Wu Xiaojian , Gao Feng
Published: June 2021

3533

Background: Primary tumor sidedness has been found to be prognostic in colorectal cancer (CRC), with right-sided colon cancer (RCC) having a worse survival than left-sided tumors (LCC), even after controlling for known negative prognostic factors. Our previous proteomic study identified differences in protein profiles between LCC and RCC. Immune-related proteins were found to be up-regulated in LCC while the differentially expressed proteins in RCC were mainly enriched in extracellular matrix-related proteins. Herein we aim to construct a prognostic prediction model for LCC and RCC patients by using immune-related genes (IRGs) and extracellular matrix-related genes (ECMGs). Methods: A total of 1,868 CRC patients with complete follow-up data from 1 training cohort (n = 562) and 3 independent validation cohorts (n = 622, n = 403, n = 281, respectively) were enrolled in our study. Tumors located in the splenic flexure, descending colon, sigmoid colon, and rectum are defined as LCC. In contrast, tumors located in the region from the hepatic flexure to the cecum are defined as RCC. The Least Absolute Shrinkage and Selection Operator (LASSO) algorithm was used to construct the multi-gene signatures. Univariate and multivariate analyses were used to test the prognostic value of these models. Results: Our biomarker discovery effort identified a 9-gene IRGs signature that significantly associated with poor DFS for LCC (HR = 3.46, 95%CI = 2.38-5.01, P < 0.001) and a 21-gene ECMGs signature associated with prognosis for RCC (HR = 4.53, 95%CI = 2.84-7.22, P < 0.001). For LCC, the IRGs signature was significantly correlated with worse prognosis in three independent validation cohort (Validation-1 cohort: HR = 2.08, 95%CI = 1.41-3.09, P < 0.001; Validation-2 cohort: HR = 2.19, 95%CI = 1.26-3.81, P = 0.004; Validation-3 cohort: HR = 2.94, 95%CI = 1.53-5.63, P < 0.001). Similarly, the ECMGs signature also robustly predicted survival for RCC in three independent validation (Validation-1 cohort: HR = 1.86, 95%CI = 1.22-2.83, P = 0.003; Validation-2 cohort: HR = 1.96, 95%CI = 1.18-3.26, P = 0.008; Validation-3 cohort: HR = 2.8, 95%CI = 1.27-6.17, P = 0.007). When compared with Oncotype DX, we found IRGs achieved an improved survival correlation in LCC (C-index, validation-3 cohort: 0.75 vs 0.64) and ECMGs got a better survival correlation in RCC (C-index, validation-3 cohort: 0.74 vs 0.58). Conclusions: Combing a 9-gene IRGs signature for LCC and a 21-gene ECMGs signature for RCC, we established a prognostic model that can robustly stratify CRC patients into high- and low- risk groups of tumor recurrence and predict prognosis.
Genetic variants involved in the cGAS-STING pathway to predict outcome in patients (pts) with metastatic colorectal cancer (mCRC): Data from FIRE-3 and TRIBE trials.
Authors: Wang Jingyuan , Xiao Yi , Loupakis Fotios , Stintzing Sebastian , Arai Hiroyuki , Battaglin Francesca , Kawanishi Natsuko , Jayachandran Priya , Soni Shivani , Zhang Wu , Mancao Christoph , Cremolini Chiara , Heinemann Volker , Falcone Alfredo , Millstein Joshua , Lenz Heinz-Josef
Published: June 2021

3535

Background: The intracellular DNA sensor stimulator of interferon genes (STING) plays a vital role in anti-tumor immune responses by recognition of self-DNA from tumors and by-products of genomic instability. Activation of STING was reported to enhance cetuximab mediated natural killer cell activation and dendritic cell maturation. Previous reports suggested that polymorphisms of cGAS-STING can affect innate immune response. Therefore, we hypothesized that genetic variants in the cGAS-STING pathway may predict first-line treatment outcome in mCRC pts treated with bevacizumab/cetuximab-based chemotherapy. Methods: Genomic DNA from blood samples of pts enrolled in two independent randomized trials, FIRE-3 (cetuximab arm, n = 129; bevacizumab arm, n = 107) and TRIBE (bevacizumab arm, n = 215), was genotyped through the OncoArray, a customized array manufactured by Illumina including approximately 530K SNP markers. The impact on outcome of 7 selected SNPs in 3 genes involved in the STING pathway (cGAS, STING, IFNB1) was analyzed. Results: In the Cetuximab cohort, pts with STING rs1131769 any T allele (N = 29) showed significantly shorter overall survival (36.3 vs 56.07 months) compared to carriers of C/C (N = 95) in both univariate (hazard ratio [HR] = 2.08; 95% confidence interval [CI]: 1.06-4.07; p = 0.003) and multivariate (HR = 2.98; 95%CI 1.35-6.6; p = 0.00848) analysis; Pts carrying IFNB1 rs1051922 any A allele (N = 68) showed significant shorter progression-free survival (10.23 vs 14.1 months) than carriers of G/G (n = 59) in both univariate (HR = 1.87; 95%CI 1.26-2.78; p = 0.00163) and multivariate (HR = 2.03; 95%CI 1.25-3.3; p = 0.004) analysis. No association were observed in the bevacizumab cohort of TRIBE and FIRE-3. Conclusions: Our study demonstrates for the first time that STING and IFNB1 polymorphisms could predict outcomes of Cetuximab-based treatment in mCRC patients; These finding may provide insight for the combination of STING agonist and anti-EGFR treatment in mCRC patients.