bluuebunny/crossref_metadata_2025 huggingface dataset:
Preclinical analysis and clinical validation to identify biomarkers of regorafenib efficacy in patients with metastatic colorectal cancer.
Authors: Suenaga Mitsukuni , Mashima Tetsuo , Kawata Naomi , Dan Shingo , Seimiya Hiroyuki , Yamaguchi Kensei
Published: January 2024

171

Background: In the identification of biomarkers for anticancer drugs, the lack of objectivity in the selection of candidate factors makes it difficult to interpret the mechanism. We performed preclinical analysis and translational validation study to identify the candidate cytokines for regorafenib efficacy in metastatic colorectal cancer (mCRC) patients. Methods: As a first preclinical process, we selected candidate cytokines according to our gene chip analysis using a panel of human cancer cell lines (JFCR39). We then validated predictive value of the cytokines in mCRC patients receiving regorafenib (discovery, N=54) and FTD/TPI (control, N=16). Blood samples were obtained at baseline (BL), before second cycle (2nd) and progressive disease (PD), and cytokine levels were measured using ELISA. Finally, we measured changes in cytokine levels and cell number in colorectal cancer cell lines treated with regorafenib. Progression-free survival (PFS) and overall survival (OS) were analyzed using Kaplan-Meier curves. Results: Our gene chip analysis showed association between high matrix metalloproteinase (MMP)-14 expression and high sensitivity to regorafenib, and the MMPs pathway was examined in blood samples. In the discovery cohort, high MMP14 levels at BL (mean 2.66 vs. 1.91 ng/ml, P=0.006) and PD (mean 2.34 vs. 1.71 ng/ml, P=0.02) were associated with tumor shrinkage, and high MMP14 levels at PD were associated with longer PFS (3.7 vs. 2.5 mos, HR0.45, 95%CI: 0.21-0.95, P=0.03). Patients with decreased MMP9 levels at 2nd had higher disease control rate (74% vs. 29%, P=0.002) and tumor shrinkage (52% vs. 13%, P=0.006), longer PFS (4.5 vs. 2.0 mos, HR0.34, 95%CI: 0.18-0.65, P<0.001) and OS (13.6 vs. 5.2 mos, HR0.35, 95%CI:0.18-0.68, P=0.001) than those with increased changes. These findings were not observed in the control cohort, but MMP9 levels decreased at 2nd in 93.8% of patients. In a regorafenib-sensitive cell line, HT29, MMP14 levels were increased whereas there was no change in regorafenib-resistant HCT15 cells. Conclusions: Our preclinical data-based translational validation study suggests that MMP14 and MMP9 may serve as a prognostic marker of regorafenib, and the results also provide insight for novel combination therapy with anti-MMP9 agent or FTD/TPI.
Outcomes with immunotherapy between Lynch syndrome vs non-Lynch syndrome microsatellite instability-high colorectal cancer.
Authors: Eslinger Cody , McGary Alyssa , Walden Daniel , Emiloju Oluwadunni Eunice , Ahn Daniel H. , Sonbol Bassam Bassam , Bekaii-Saab Tanios S. , Zhu Mojun , Hubbard Joleen M. , Wu Christina
Published: January 2024

175

Background: Alterations to mismatch repair (MMR) genes such as MLH1, MSH2, MSH6, and PMS2, can lead to microsatellite instability-high (MSI-H) tumors. MMR mutations can be inherited in Lynch syndrome (LS) but can also be a result of de novo alterations resulting in MSI-H malignancies. Treatment with immune checkpoint inhibitors (ICIs) have been shown to improve survival in such patients (pts) compared to systemic chemotherapy. However, there is a paucity of information in the literature with respect to outcomes of pts with germline vs somatic MMR mutations in MSI-H colorectal cancer (CRC). Furthermore, the presence of underlying BRAF mutation confers resistance to chemotherapy in pts with CRC, however data regarding outcomes with immunotherapy in such pts with MSI-H CRC is lacking. Methods: Pt records from the Mayo Clinic (AZ, MN, FL) between 2008-2023 denoted as MSI-H CRC, were included for retrospective review. Pt demographics, treatment courses, and genomic profiles were collected. Overall survival (OS) and progression-free survival (PFS) were estimated using the Kaplan-Meier method. Outcome differences between sub-groups were accessed with the log rank test and univariate analyses were assessed with Cox-regression. Results: A total of 81 pt records were identified (n = 18 LS, n = 63 non-LS). Stage IV disease was found in 28% of LS pts vs 59% of non-LS pts at diagnosis. Pembrolizumab was the most common ICI selected for metastatic CRC pts for both LS and non-LS pts (65% vs 94%) with median treatment duration for each group 11.7 vs 8.8 months. There were no differences in OS or PFS for any stage between LS vs non-LS. Median OS for all patients was 82 months. For all stage IV patients, median OS was 44 months, and median PFS was 19 months. Interestingly, for stage IV pts treated with immunotherapy, tumors that harbored BRAF V600E mutation (n = 21) vs BRAF wild type (n = 20) had a significantly lower median OS 19 vs 113 months (HR = 2.69, p = 0.043) as well as median PFS 12 vs 95 months (HR = 2.48, p = 0.041). Conclusions: In this study, we found that patient treated with ICIs have similar outcomes in the presence of germline vs. somatic MMR mutations in MSI-H CRC. The presence of an associated BRAF V600E mutation, which occurs in non-LS MSI-H CRC conferred worse outcomes.
Identification of dMMR in metastatic colorectal and non-colorectal cancers in a private Mexican institution.
Authors: Filio Georgina , Dorantes-Heredia Rita , Motola Daniel , Escamilla-López Mariam , Tellez-Bernal Eduardo , Conde-Flores Emilio , Escalera Daniel , Medina-Ceballos Emilio , Jimenez-Aguilar Paulina , Ruiz-Morales Jose Manuel , Dorokhova Elena , Flores Lucia
Published: January 2024

177

Background: DNA mismatch repair is a process in which normal cells maintain their original genomic information avoiding errors in mismatched nucleotides or base modifications from recombination processes. The failure of this process could drive carcinogenesis due to increased mutation rate as well as high microsatellite instability. It is estimated that the global average prevalence of dMMR/MSI-H across tumor types and stages is approximately 16%, with higher rates reported for early stages. However, the prevalence for colorectal (CRC) and non-colorectal cancers for this biomarker in Mexico has not been reported. Objective:To explore the prevalence of dMMR in metastatic CRC (mCRC) and non-CRC (gastric, esophageal, and endometrial cancer) from a private Mexican institution. Methods: In this retrospective study, the dMMR status of 215 samples were analyzed from a primary database of stored biopsies from patients diagnosed with metastatic CRC, gastric, esophageal, or endometrial cancers between January 2017 and December 2020. 65 records had information about MMR status. Samples were analyzed using a commercial kit to detect dMMR (BioSb). Prevalence of dMMR was stratified by age and gender and expressed as frequencies. Statistical analysis was conducted in SPSS. Results: dMMR was found in 18.5% (N=27) endometrial cancer cases, 12.7% (N=150) of CRC cases, and 8.3% (N=24) of gastric cancer cases. However, it was not detected in any cases of esophageal cancer (N=14). In CRC, we found a higher percentage of incidence in men than in women, 15.6% (n = 14/90) vs. 8.3% (n = 5/60) respectively. By age groups, the highest total percentage (20%) was observed among those 41-50 years old. The age group with the lowest dMMR rate was 31- 40 yo, with 7.7%. All cases of CRC patients over 91 yo (n=3), were pMMR. Conclusions: Even though this data is not representative for the entire Mexican population, it provides preliminary prevalence dMMR estimates for some key cancers. Additional research is needed to give the limited sample sizes available for non-CRC.
Survival by race and ethnicity among insured patients with early-onset colorectal cancer.
Authors: Lee Jeffrey , Jensen Christopher , Kang James , Badalov Jessica , Levin Theodore R. , Kane Kevin , Tan Amie , Reilly Norelle , Gurai Sheena , Udaltsova Natalia , Corley Douglas
Published: January 2024

18

Background: Colorectal cancer (CRC) incidence and mortality have decreased in the United States over the past 3 decades, but the incidence is increasing in those <50 years of age (i.e., early-onset CRC). Studies have examined racial and ethnic differences in CRC incidence in this age group, but little is known about differences in survival. Examining survival by race and ethnicity among patients with early-onset CRC may provide insights about differences in risk factors, access to care, and treatment. Methods: This retrospective cohort study included Kaiser Permanente Northern California health plan members 18-49 years of age and diagnosed with CRC between 2006-2019. Race and ethnicity were self-reported as Asian/Pacific Islander, Black, Hispanic, or White. 5-year survival probability was assessed using Kaplan-Meier analyses. Cox regression with adjustment was used to evaluate associations between race and ethnicity and 5-year survival. Results: Of 1620 patients, median age was 45.4 years, 47% were female, 20% were Asian/Pacific Islander, 8% Black, 22% Hispanic, and 50% non-Hispanic White persons. Adjusted for age, sex, and comorbidities, Hispanic persons had a higher risk of death at 5 years compared to White persons (hazard ratio [HR]: 1.41; 95% confidence interval [CI]: 1.09-1.83) (Table). Sequentially adding annual household income and neighborhood deprivation index had no impact on the association; adding tumor stage decreased the HR to 1.14 (0.87-1.49) and adding tumor and treatment factors decreased the HR to 1.08 (0.82-1.42). Risk of death among Asian/Pacific Islander and Black patients did not differ from White patients. Conclusions: Among insured patients with early-onset CRC, Hispanic patients had a higher risk of death at 5 years than patients of White race. The higher risk was associated with differences in tumor stage at diagnosis, tumor factors, and treatment factors. Targeted interventions to improve CRC symptom awareness and remove barriers to CRC diagnosis and treatment among vulnerable populations may be needed to eliminate disparities in early-onset CRC survival. [Table: see text]
The genomic landscape of patients with advanced colorectal adenocarcinoma with PIK3CA mutations using comprehensive cell free tumor DNA next generation sequencing.
Authors: Verma Nilesh , Kazmi Syed Mohammad Ali , Tsai Jill
Published: January 2024

181

Background: PIK3CA mutations ( PIK3CAm) are highly prevalent in advanced CRC but the prognostic value is unclear. PIK3CAm are associated with advanced stage disease, tumor aggressiveness, resistance to therapy, and a poorer prognosis. In some cases, PIK3CAm co-occur with other genetic alterations leading to complex signaling networks. Understanding these genetics are crucial to devise effective treatments. In this study, evaluated the genomic landscape of PIK3CAm in advanced CRC using cell free tumor DNA (ctDNA) next generation sequencing. Methods: This analysis assessed advanced CRC samples between 2020-2022 from the Guardant360 database using plasma-based ctDNA (~15000 patients, ~17000 samples). PIK3CAm were assessed by patient demographics, MSI-H status, TMB score, and frequency of co-occurring alterations via cbioportal. A sub analysis was collected between 2021-2022 (~8000 samples) to examine the frequency of PIK3CA exon 9 vs. 20 mutations between BRAF V600E and non- V600E BRAF mutations, and separately between KRAS G12C and G13D. Comparisons were analyzed by two-sided Fisher’s exact test. Results: PIK3CAm were detected in ~21% (~3500) of mCRC samples. Of these samples, the median age was 63 years old and the sex distribution was 56% males. MSI-H was reported in 3.3% of samples. PIK3CAm included 25% E545 (Exon 9), 13% E542 (Exon 9), 5% Q546 (Exon 9), and 10% H1047 (Exon 20). PIK3CAm had increased median alterations per sample to PIK3CA not detected (8 vs. 5) and a significant increase in co-occurrence with most genes in the panel. Relevant clinical co-occurrences were APC (73.7% vs. 57.4%), BRAF (19.9% vs. 13.0%), EGFR (34.7% vs. 24.9%), ERBB2 (9.2% vs. 6.0%), and KRAS (62.9% vs. 41.2%). Additionally, PIK3CAm samples had higher median TMB scores (13.4 vs. 9.8 mut/Mb), with >25% of PIK3CAm reporting a TMB score above the 80th percentile (20.19 mut/Mb). In a sub analysis, there were significantly greater frequencies of PIK3CAm in exon 20 in BRAF V600E samples vs. non-V600E BRAFm samples (p=0.0003) with no significant differences in exon 9 or 20 mutations in KRAS G12C vs. G13D. Conclusions: Our study shows the frequency of PIK3CAm and distribution of exons 9 and 20 are similar to those found previously in the literature by Tan (Xie) et al., 2022. Our results demonstrate PIK3CA having a low frequency of MSI-H co-occurrence, higher TMB scores, and increased co-occurring alterations with notable increased in APC, BRAF, EGFR, ERBB2 and KRAS, which may suggest higher genomic instability. Our findings underscore the clinical significance of PIK3CAm in the context of CRC, emphasizing their role as key drivers of oncogenesis, and supports the development of tailored therapeutic strategies such as combining PIK3CAi with immunotherapy or other targeted therapies.
Identification of MAPK and mTOR pathway alterations in HER2-amplified colorectal cancer.
Authors: Cheng Svea , Gonzalez Cyndi , Ferrell Morgan , Giza Richard , Syed Masood Pasha , Magge Tara , Bao Riyue , Singhi Aatur D. , Saeed Anwaar , Sahin Ibrahim Halil
Published: January 2024

185

Background: Human epidermal growth factor receptor 2 (HER2) amplification is now a highly actionable alteration for patients with colorectal cancer (CRC) with distinct combination therapies. Recent studies have shown that oncogenic KRAS, BRAF, and PIK3CA mutations, may serve as biomarkers of response to HER-directed treatments such as Trastuzumab and Tucatinib/Pertuzumab. In this study, we investigated the incidence of MAP kinase and mTOR pathway alternations in patients with HER2-amplified CRC. Methods: The cBioPortal for Cancer Genomics was utilized to obtain data and graphics on HER2 amplification in CRC. cBioPortal was queried to select 21 published studies that contain CRC specimens (assessed April 2023). Clinical, specimen, copy number alteration (CNA), and somatic mutation data of each study were downloaded and aggregated across all studies, followed by filtering, standardization, and harmonization to generate ~30 analysis-ready fields encompassing demographic variables, HER2 amplification, and KRAS/NRAS/PIK3CA/BRAF mutations. Results: Among a pool of 4822 CRC patients with known gender, 44.4% (2139) were female and 55.6% (2683) were male. The incidence of HER2 amplification in the overall cohort was 2.6% (123/4822) and was noted to be higher in males (3.1%, 82/2683) than in females (1.9%, 41/2139). The incidence of HER2 amplification was highest in Asian CRC patients (3.9%, 9/228), followed by Black CRC patients (3.0%, 9/298), and then Caucasian CRC patients (2.7%, 57/2118). Rates of HER2 amplification were similar in the colon and the rectum at 2.6% (61/2360 and 26/1015, respectively). After analyzing rates of concurrent MAPK and mTOR pathway mutations in patients with HER2-amplified CRC, KRAS mutations were noted to be the most common mutation in HER2-amplified colon cancer (27.9%, 17/61), but were less common in HER2-amplified rectal cancer (7.7%, 2/26). PIK3CA mutations were also common, with an incidence of 13.1% (8/61) in HER2-amplified colon cancer and 7.7% (2/26) in HER2-amplified rectal cancer. NRAS mutations occurred at comparable, low rates in HER2-amplified colon and rectal cancer, at 3.3% (2/61) and 3.8% (1/26) respectively. No BRAF mutations were reported in either disease group. Conclusions: In this study, we identified that MAPK and mTOR pathway alterations are relatively common among patients with HER2-amplified CRC. These somatic events appear to be more common in HER2-amplified colon cancer than rectal cancer. Next generation based molecular profiling is recommended to identify potential resistance mechanisms before initiation of HER2-directed therapy.
The landscape of the comprehensive genomic profile for patients with bowel cancer.
Authors: Yamaguchi Tatsuro , Ikegami Masachika , Aruga Tomoyuki , Kanemasa Yusuke , Horiguchi Shin-ichiro , Takao Akinari , Takao Misato , Kawai Kazushige
Published: January 2024

189

Background: The aim of study was to clarify the landscape of comprehensive genomic profile in bowel cancer. Methods: This study included 57,103 patients between June 1, 2019 and August 18, 2023 (version 20230821) with a nationwide retrospective design. Patients underwent one of three CGP tests, including OncoGuide, FoundationOne CDx (F1CDx), and FoundationOne Liquid (F1LCDx) CDx, at the physician's choice. We evaluated the pathogenicity of the detected variants based on the public database and gene function. Results: Of the 57,103 patients, 9,595 (16.8%) were bowel cancer, including 911 for OncoGuide, 7,711 for F1CDx and 810 for F1LCDx. In the tumor site, COADREAD was the most common bowel tumor, followed by SBC and APAD. TP53 was the most common gene with SNV/Indels, followed by APC, TP53, KRAS and PIK3CA. FLT3 was the most frequently amplified gene, followed by CDK8 and FLT1. For gene deletions, SMAD4 was the most frequently deleted gene, followed by PTEN and CDKN2A. For genomic rearrangements, EML4-ALK was the most common. A total of 46 (5.0%) germline pathogenic variants were identified in OncoGuide in mismatch repair genes in 12 patients, in BRCA1/2 genes in 11 patients, and in the APC gene in 7 patients. Conclusions: The detected variants should be re-annotated due to the inclusion of several benign variants in the CGP testing, and the landscape of the variants derived from these results in the CGP testing, including FoundationOne CDx, FoundationOne Liquid CDx, and OncoGuide, will help researchers and physicians interpret these results.
Incidence and genomic characteristics of gene fusions in a large Chinese colorectal cancer cohort.
Authors: Kou Furong , Shen Lin , Li Jian , Wang Zhenghang , Xu Ting , Qian Juanjuan , Zhang Enli , Cui Lisha , Zhang Lijun , Wang Xicheng
Published: January 2024

192

Background: Gene fusion is rare in colorectal cancer (CRC). With the advent of fusion-targeted therapeutics, such as entrectinib for NTRK fusion and selpercatinib for RET fusion, the identification of gene fusions holds clinical significance. Reports providing a comprehensive description of fusions in CRC are limited, and understanding the molecular characteristics of CRC with fusions will contribute to efficient fusion screening. Here, we investigate the incidence and genomic features of gene fusions in a large Chinese CRC population. Methods: We systematically analyzed next-generation sequencing results of tumor tissue from 5534 CRC patients between January 2020 and August 2023. The sequencing panel covers 769 cancer-related genes and can detect fusions, single nucleotide variants and indels, and microsatellite instability (MSI). Statistical significance was determined using chi-square test. Results: Overall, the median age of patients was 62 years (inter-quartile range [IQR]: 53-70), and 40% were female. Gene fusions were detected in 4.4% (242/5534) of all the patients. The incidence is 0.98% (54/5534) if only reported clinically actionable fusions are considered. The median age of the 242 fusion-positive patients was 64 years (IQR: 54-70), and 43% were female. The most highly detected potentially actionable gene fusions were NTRK (0.89%) and FGFR (0.81%), accounting for 39% of the fusion-positive patients. The other fusion genes were ERBB2 (0.52%), RET (0.38%), BRAF (0.31%), EGFR (0.27%), ALK (0.22%), MET (0.09%) and ROS1 (0.07%). Consistent with previous reports, patients with MSI-High were more likely to have fusions compared with those with microsatellite stability (MSS) or MSI-Low (9.9% vs 4.0%, p < 0.001). Besides, RAS or BRAF mutated patients accounted for 59% of the cohort, of whom 2.5% (83/3273) had fusions detected, while 7.0% (159/2261) of the RAS and BRAF wildtype patients had positive fusions ( p < 0.001). Moreover, 404 (7.3%) patients had RNF43 splice or truncating mutations, and gene fusions were detected in 12.9% of these patients. Combining these markers increased the detection rate of fusions, with 28% (33/118) of the RAS/ BRAF wildtype and MSI-H patients having fusions detected. Furthermore, in patients with wildtype RAS/BRAF and MSI-H and RNF43 splice or truncating mutations, the fusion detection rate was as high as 49% (32/65), including 24 patients with actionable fusions of definite clinical significance. Conclusions: Gene fusions were detected in 4.4% of the Chinese CRC population and tended to occur in patients with wildtype RAS/BRAF, MSI-H, or RNF43 mutations. Combining the mutational status of RAS, BRAF, and RNF43 along with MSI status can improve the fusion detection rate and help select candidates for fusion testing and targeted therapy.
RAS mutation specific survival in patients with metastatic colorectal cancer treated with trifluridine/tipiracil.
Authors: Grell Peter , Batko Stanislav , Pirsthuk Alina , Borilova Simona , Polachova Katerina , Mazuchova Blanka , Tomasek Jiri , Fabian Pavel , Berkovcova Jitka , Bardelcik Miroslav , Obermannova Radka , Buchler Tomas , Kiss Igor
Published: January 2024

197

Background: Trifluridine/tipiracil (T/T) is effective in patients with pretreated metastatic colorectal cancer (mCRC). RAS mutational status could predict magnitude of T/T effect (van de Haar et al, Nat Med. 2023), but the data are conflicting. Methods: We retrospectively reviewed the clinical data of 402 patients consecutively treated with T/T in two institutions in the Czech Republic and analysed the potential predictive value of different RAS mutations. Results: Baseline characteristics: median age 65 (range 28-84), female 32.8%, ECOG PS 0 in 32.8% and 1 in 64.9%, primary tumor location left colon in 76.3%. The median line in which T/T was administered was 3 (range 2-8). Median number of T/T cycles administered was 3 (range 2-27). Median follow-up was 32.4 months, 358 patients died (89.1%). Overall survival (OS) was 9.3 months (95% CI 8.7 to 10.3) and progression-free survival (PFS) 3.5 months (3.2 to 3.6). RAS mutation was detected in 54.2% patients. KRAS G12 mutation was found in 117 patients (29.1%), KRAS G13 in 19 (4.7%), other RAS mutation in 25 (6.2%), non-specified RAS mutation in 57 (14.2%), and BRAF mutation in 14 (4.8%). No difference in OS in RAS wildtype (wt) vs mutated group (P=.50) was observed. OS in the defined groups was found: wtRAS group (9.1 months), KRAS G12 (9.1 m), KRAS G13 (5.6 m), and other RAS mutations (10.6 m, P=.180). Patients with KRAS G13 had worse OS vs all other patients (P=.029; HR 1.97), vs wt (P=.02; HR 2.08), vs other mutated (P=0.067; HR 1.75), vs KRAS G12 mutated patients (P=.069; HR 1.75). Patients with KRAS G12 had no OS difference vs other groups of patients. In KRAS G12 group we found that specific gene variants have different OS (for G12C, 7 patients, OS was 6.0 months; for G12D, 41 patients, 9.0 m; for G12V, 45 patients, 10.5 m; for G12S, 7 patients, 16.1 m; for G12A, 11 patients, 7.6; other G12 variants, 5 patients, 10.0 months, P=.028). BRAF mutation was associated with worse OS (6.6 vs 9.1 months, P=.02, HR 2.46). Conclusions: We did not confirm the negative predictive value of KRAS G12 mutation in patients treated with T/T, however, OS depends on the specific G12 mutation. In contrast, patients with KRAS G13 mutation had worse survival.
Prognostic factors for anti-angiogenic treatment in patients with metastatic colorectal cancer: New insights for an old issue from a single institution experience.
Authors: Lai Eleonora , Ziranu Pina , Mariani Stefano , Loi Francesco , Palmas Enrico , D'Agata Alessandra Pia , Dell'Utri Veronica , Deias Giulia , Balconi Francesca , Rizzo Daiana , Papalexis Giulia , Codipietro Claudia , Sanna Giorgia , Moledda Giusy , Donisi Clelia , Spanu Dario , Pretta Andrea , Pusceddu Valeria , Puzzoni Marco , Scartozzi Mario
Published: January 2024

206

Background: Anti-angiogenic drugs represent a cornerstone of metastatic colorectal cancer (mCRC) patients (pts) treatment. Currently, no prognostic/predictive biomarkers were validated to identify who is more likely to benefit from these agents. We performed at our Centre a retrospective research to assess potential prognostic/predictive factors in this population. Methods: We retrospectively collected laboratory, radiological and clinical data of mCRC pts receiving anti-angiogenic agents at the Medical Oncology Unit of Cagliari University Hospital (2018- 09/2023) in order to assess their correlation with overall survival (OS) and progression free survival (PFS) from the treatment start. Statistical analysis was performed with MedCalc (survival distribution: Kaplan-Meier; survival comparison: log-rank test; cut-off: ROC curves). Results: Globally, 32 mCRC pts were included in our research (19 male, 13 female; 12 RAS wild-type, 21 left-sided primary). 10 received anti-angiogenic drugs in the 1st-line, 12 in the 2nd-line (bevacizumab and aflibercept) and 10 in 1st-2nd line. Median OS was 34.8 months (m) (95%CI:24.7-41.6). We observed a statistically significant improve in OS (34.8 months [m] versus [vs] 8.2 m) in pts with higher monocyte count (>0.3x103/μL; 95%CI 26.5-39.5 vs 95%CI 8.2-24.7, p=0.0103, HR 0.01), lower alcalin phosphatase (ALP; <136 U/l; p=0.0001, HR=0.0001; 95%CI 12-39.5 vs 95% CI 8.2-10.4), lactate dehydrogenasis (LDH; <365 U/l; p<0,0001, HR=0.0000006; 95%CI 24.7-39.5 vs 95% CI 8.2-10.4) and platelet to lymphocyte ratio (PLR; ≤253; p<0.0001, HR= 0.00000062; 95%CI 24.7-39.5 vs 95% CI 8.2-10.4). Median PFS was 14.9 m (95% CI 9.5-18.5). The same factors were significantly related to PFS, which was 18.3 m vs 2.7 m for higher monocyte count (95%CI 11.4-22.1 vs 95%CI 2.7-14, p=0.0386, HR=0.05), lower LDH (95%CI 11.4-22.1 vs 95%CI 2.7-8.9, p=0.0024, HR=0.004), lower PLR (95%CI 11.4-22.1 vs 95%CI 2.7-8.9, p=0.0024, HR=0.004) and 18.3 m vs 8.9 m for lower ALP (95%CI 11.4-23.3, p=0.0369, HR=0.04). Furthermore pts not developing bleeding during treatment showed a significant benefit in OS (39.5 m [95%CI 26.5-41.6] vs 8.2 m [95%CI 8.2-12], p< 0.0001, HR 0.000001761) and improved PFS (17.9 m [95%CI 9.9-18.4] vs 2.4 m [95%CI 2.4-2.7]; p<0.0001). Conclusions: Our findings showed a promising prognostic role of baseline monocytes, ALP, LDH and PLR and absence of bleeding occurrence in mCRC patients receiving anti-angiogenic drugs, even if in a limited population. Further larger prospective studies are encouraged for confirmation.
Serum angiopoietin-like protein 2 level in patients who received bevacizumab-containing chemotherapy for metastatic colorectal cancer.
Authors: Kim Jung Hoon , Kim Jae-Joon , Oh Sung Yong , Oh Sang-Bo , Jeon Youngkyung , Hong Kyung Wook , Kwag Seung-Jin
Published: January 2024

209

Background: Anti-angiogenic agents are important for treating patients with advanced colorectal adenocarcinoma, however, their efficacy is not long-lasting and survival benefits are modest. Reliable biomarkers and novel targets for angiogenesis are still required in this era. Angiopoietin-like protein 2 (AGLP-2) is an emerging biomarker for angiogenesis in cardiovascular disease, but its role in the oncology area is yet to be elucidated. Methods: Serum samples from patients with advanced colorectal carcinoma treated with bevacizumab-containing chemotherapy were retrospectively studied. Blood samples at baseline and at disease progression of the first line systemic therapy were selected. Serum angiopoietin-like protein 2 (AGLP-2) concentrations were measured using ELISA kit, serial changes, and the relationship with progression-free survival and overall survival on the systemic therapy were statistically analyzed. Results: 68 patients were enrolled. Their median age was 66 years old (range, 38-82), and 14 (20.6%) patients had metastatic lesions at 3 or 4 organs. The median serum AGLP-2 levels at baseline and at disease progression (PD) were 41,618 pg/ml (95% confidence interval (CI) 34,560-40,713), and 49,706 pg/ml (95% CI 39,853-49,017), respectively. There was a tendency of difference between AGLP-2 levels at baseline and at PD ( p=0.057). Patients whose baseline serum AGLP-2 levels with 40,000 pg/ml or above showed relatively shorter overall survival (median 31.4 months with 95% CI, 14.4-38.6) compared with patients with serum AGLP-2 level below 40,000 pg/ml at baseline (median 38.6 months with 95% CI, 23.6-127.3), but not statistically significant ( p=0.0946). There was no survival difference observed according to serum AGLP-2 levels at disease progression on the first line bevacizumab-containing chemotherapy. Conclusions: Serum angiopoietin-like protein-2 has potential as a new target for novel anti-angiogenic therapy in metastatic colorectal cancer.
Surveillance of resected metastatic colorectal cancer utilizing circulating DNA.
Authors: Naleid Nikolas , Zablonski Kevin , Kakish Hanna , Lumish Melissa Amy , Bajor David L , Selfridge J. Eva , Conces Madison , MOHAMED AMR , Chakrabarti Sakti , Mahipal Amit
Published: January 2024

214

Background: There is limited data to guide surveillance in patients with metastatic colorectal cancer (CRC) who have had curative resection using circulating tumor DNA (ctDNA) in addition to labs and imaging studies. Minimal residual disease (MRD) assays utilize circulating tumor DNA (ctDNA) for the purposes of monitoring for early recurrence and predicting therapeutic response. In this study, we aim to investigate the utility of ctDNA monitoring in the setting of resected metastatic CRC. Methods: Patients were identified through retrospective search at a tertiary care and several satellite settings to identify patients with metastatic CRC who had undergone curative resection and later had ctDNA monitoring (using Signatera assay). IRB approval was obtained for the study. We recorded demographic information (sex, race, age at diagnosis), disease characteristics (stage at diagnosis, site of primary cancer, site of metastasis), treatment regimens, clinical outcomes (recurrence, survival) and follow-up data. Our primary outcome was to evaluate the rate of recurrence in patients with metastatic CRC who had curative resection in two different population, ctDNA positive or ctDNA negative, post-surgery. Results: We identified 35 patients with a median age of 55 years (range 31 – 82) at the time of metastatic diagnosis. In this study cohort, 20 (57%) were female; 23 (66%) were white, and 10 (29%) were African American. 22 (63%) patients had left-sided primary tumors and the remaining (47%) had right-sided primary tumors. At the time of presentation, 23 (66%) patients had synchronous metastases and 12 (34%) developed metachronous metastases. ctDNA positivity was reported in 21 (60%) pts post-curative therapy. Median time from curative therapy to ctDNA positivity was 62 days. 22 (63%) pts experienced recurrence of disease post-curative resection. Median time to recurrence after ctDNA test was first positive was 6.6 months. Among 21 patients in ctDNA positive group, 19 (86%) developed recurrences and among 14 ctDNA negative patients, only 3 (21%) developed recurrences (p-value <0.01). Recurrence free survival was significantly shorter in patients who were ctDNA positive post surgery (Median RFS: 7.17 months, 95% CI: 4.4-18.0 months) compared to those who were ctDNA negative (Median RFS: 30.8 months; 95% CI: 12.6-NR) (p-value=0.005). Conclusions: In patients with metastatic CRC who underwent curative resection ctDNA may have utility in predicting disease recurrence at both academic and community sites. Larger studies are needed for validation of ctDNA as an adjunct test for surveillance in broader population.
Use of micronuclei DNA from erythrocytes in early-stage colorectal cancer detection.
Authors: Yao Xingyun , Sun Haobo , Pan Jie , Jiao Yurong , Kong Xiangxing , Liu Chengcheng , Zhu Fangchao , Meng Fei , Liang Honghao , Cao Yanfei , Li Jun , Gao Xiaofei
Published: January 2024

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Background: Current development in stool- and cell-free DNA (cfDNA)-based technologies have demonstrated promising potentials in colorectal cancer (CRC) diagnosis. However, early detection of CRC and advanced adenoma (AA) remains challenging. Micronuclei (MN) are extranuclear bodies containing chromatin segments resulting from errors in DNA repair. Elevated levels of MN+ erythrocytes have been studied in genotoxicity testing and cancer diagnosis. We have developed a method (WO2021/228246 A1) for purifying and sequencing micronuclei DNA (mnDNA) in erythrocytes from peripheral blood. Here, we compared mnDNA between healthy donors (HDs) and CRC patients and explored its application for early cancer diagnosis. Methods: Peripheral blood (1ml) was obtained from a training cohort of 987 individuals, a validation cohort of 246, and an independent test cohort of 193. mnDNA was isolated and sequenced from erythrocytes. Genome-wide analysis identified distinctive mnDNA features between HD and CRC. Predictive models using these features were developed to differentiate CRC and AA from HDs. A clinical trial comparing mnDNA with an approved multitarget stool DNA test (sDNA-FIT) was also conducted on 60 individuals (42 HDs, 6 AAs, and 12 CRCs). Results: Genome-wide analysis of mnDNA revealed substantial differences in distribution patterns between HDs and CRC patients. The predictive model built on mnDNA features achieved an AUC of 92.98% (95%CI: 87.85-98.12%), with an 88.64% sensitivity and 92.75% specificity in the independent test cohort. The model identified early-stage (stage I-II) CRC and AA with sensitivities of 83.33% or 69.56%, respectively. Comparing mnDNA to sDNA-FIT showed superior overall sensitivity (83.33% vs. 61.11%), AA sensitivity (83.33% vs. 16.66%), with comparable specificity (85.71% vs. 88.10%). Conclusions: Our results demonstrate that mnDNA from a small amount of peripheral blood enable accurate detection of AA and early-stage CRC. As a type of cytoplasmic DNA, mnDNA can provide a valuable tool for early cancer detection, offering different underlying mechanisms compared to current methods. A larger clinical study (NCT05875584) is ongoing and will further validate the application of mnDNA in early cancer detection.
Nivolumab (NIVO) plus (+) chemotherapy (chemo) or ipilimumab (IPI) vs chemo as 1L treatment for advanced esophageal squamous cell carcinoma (ESCC): First comprehensive biomarker analyses from CheckMate 648.
Authors: Lei Ming , Doki Yuichiro , Kitagawa Yuko , Kato Ken , Chau Ian , Yao Jin , Xu Jianming , Wyrwicz Lucjan S. , Motoyama Satoru , Ogata Takashi , Kawakami Hisato , Hsu Chih-Hung , Adenis Antoine , El Hajbi Farid , Di Bartolomeo Maria , Braghiroli Maria Ignez , Holtved Eva , Blum Murphy Mariela A. , Novosiadly Ruslan , Ajani Jaffer A.
Published: January 2024

252

Background: NIVO + chemo and NIVO + IPI demonstrated superior overall survival (OS) vs chemo in previously untreated patients with advanced ESCC in CheckMate 648 (NCT03143153), resulting in approvals in many countries. We present first comprehensive exploratory biomarker analysis results from this trial. Methods: Whole exome sequencing (WES) of baseline tumor tissue and matching blood was performed to assess tumor mutational burden (TMB) and select gene alterations. TMB-high tumors were defined as ≥ 199 mutations/exome. RNA sequencing of baseline tumor tissue was used to assess gene expression signatures (GES). GES subgroups were defined by signature score tertiles. Results: In total, 60% (191/321) of patients receiving NIVO + chemo were both WES- and GES-evaluable; 62% (200/325) and 58% (188/325) of patients receiving NIVO + IPI and 59% (190/324) and 59% (192/324) receiving chemo were WES- and GES-evaluable, respectively. In the NIVO + chemo arm, patients with TMB-high tumors had numerically longer median OS (mOS) compared with TMB-low tumors, whereas mOS was similar between TMB subgroups treated with NIVO + IPI, although the number of patients with TMB-high tumors was small (Table). Higher inflammation and lower β-catenin GES scores were associated with improved OS benefit of NIVO + chemo or IPI vs chemo (Table). Lower fibroblast GES scores were associated with improved OS benefit of NIVO + IPI vs chemo (Table). Additional biomarker analyses, including select gene alterations and GES in tumor cell PD-L1 subgroups, will be presented. Conclusions: These results further support the clinical efficacy of NIVO + chemo and NIVO + IPI in 1L ESCC and suggest enhanced OS benefit in multiple biomarker subgroups. The clinical utility of these biomarkers should be validated in future trials. Clinical trial information: NCT03143153 . [Table: see text]
Disparities in survival in Asian American, Native Hawaiian, and Pacific Islander patients with gastric adenocarcinoma: An NCDB analysis.
Authors: Mishra Anjali , Hu Robert , Silberstein Peter T.
Published: January 2024

253

Background: Asian American, Native Hawaiian, and Pacific Islander (AANHPI) individuals exhibit stark disparities in gastric cancer mortality rates, with AANHPI men facing a two-fold higher risk of death and AANHPI women encountering a 2.5-fold elevated risk compared to their Non-Hispanic White (NHW) counterparts. However, the AANHPI community is a diverse group, including over 21 ethnic groups. Here, we identify disparities among AANHPI subpopulations with gastric adenocarcinoma. Methods: Using the National Cancer Database, which gathers data from over 1,500 accredited hospitals and facilities across the United States, this retrospective cohort study identified 141,906 patients with gastric adenocarcinoma (ICD code “8140”). Races listed as “unknown/other” or “Other Asian” were excluded. Kaplan Meier and Cox Regression model were performed. Results: This study compared mean overall survival (OS) of NHW (n=111,137), East Asian (EA) (n=3,745), South Asian (SA) (n=760), Southeast Asian (SEA) (n=1,379), and Native Hawaiian or Pacific Islander (NHPI) (n=325) patients with gastric adenocarcinoma. When aggregated, AANHPI had statistically significant improved OS compared to NHW (21.6 months vs 14.1 months, p < 0.001). After disaggregating, the mean OS was 26.9 months for EA; 21.3 months for SA; 14.5 months for SEA; and 14.3 months for NHPI. Only SA and EA had significantly improved OS than NHW (p<0.001 for both). SEA and NHPI had significantly worse outcomes than EA (p<0.001 for both) and SA (p<0.001 for SEA, and p = 0.033 for NHPI). Multivariate analysis accounted for age at diagnosis, insurance status, median income quartile, Charlson-Deyo comorbidity score, facility type, stage at diagnosis, and time to treatment. SA (HR=0.82; 95% CI, 0.726 to 0.925; p<0.001)), EA (HR=0.644; 95% CI, 0.609 to 0.68; p<0.001), and SEA (HR=0.896; 95% CI, 0.821 to 0.978, p=0.014) had lower survival hazard ratios compared to NHW. NHPI (HR=0.931, 95% CI 0.775 to 1.119, p=0.448) did not have a statistically significant relationship compared to NHW. EA (HR = 0.637; 95% CI 0.548 to 0.741, p<0.001) and SA (HR = 0.793; 95% CI 0.667 to 0.943, p=0.007) had significantly lower survival hazard ratios compared to NHPI. Conclusions: Survival disparities exist among AANHPI subgroups with gastric adenocarcinoma. At first glance, OS appeared significantly greater for AANHPI patients compared to NHW. However, disaggregation of AANHPI subpopulations revealed that Southeast Asian and NHPI actually had comparable OS with NHW. After controlling for socioeconomic factors, NHPI had significantly worse hazard ratios compared to South Asian and East Asian. This highlights the need to disaggregate AANHPI data so that disparities among these diverse subpopulations can be identified, investigated and ultimately addressed.
Reliability of computed tomography to determine the eligibility of conversion surgery for gastric cancer with para-aortic lymph node metastasis.
Authors: Wada Takeyuki , Yoshikawa Takaki , Sakon Ryota , Hayashi Tsutomu , Yamagata Yukinori
Published: January 2024

259

Background: Although gastric cancer (GC) with para-aortic lymph node (PAN) metastasis is diagnosed as stage IV and basically treated with chemotherapy, it can be the candidate of conversion surgery when PAN metastasis was limited in localized area as oligometastatic status. Recently, we reported that pathological complete response at PAN (pCR at PAN) after chemotherapy was a good surrogate marker in conversion surgery for GC with PAN metastasis. However, it is difficult to predict pCR at PAN before surgery. Computed tomography (CT) is a standard procedure for clinical diagnosis of lymph node metastasis in GC.This study aimed to evaluate the reliability of CT to predict pCR at PAN after chemotherapy. Methods: The study examined patients who received radical gastrectomy with D2 and PAN dissection after chemotherapy for gastric cancer with PAN metastasis (#16a2/b1) from 2004 to 2020. PAN greater than 10mm in long axis was diagnosed as clinically positive. Patients were classified into 2 groups as pPAN-CR and pPAN-nonCR according to the pathological diagnosis of PAN. Accuracy, sensitivity, specificity, positive predictive value, and negative predictive values for PAN diagnosis were retrospectively investigated. Moreover, the relationship between shrinkage ratio at PAN and pathological diagnosis was also investigated. Results: A total of 46 patients were examined in the present study. The number of pPAN-CR and pPAN-nonCR patients were 31 and 15, respectively. 5-year overall survival rate was 76% in pPAN-CR and 0% in pPAN-nonCR patients. The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of PAN were 52.2%, 60.0%, 48.4%, 36.0%, and 28.6%, respectively. Median shrinkage ratio of PAN was 38% (-20%-88%) in pPAN-CR and 40% (-20%-75%) in pPAN-nonCR patients. There was no statistically significant relationship between shrinkage ratio and pathological diagnosis of PAN ( p=0.655). Conclusions: CT diagnosis for PAN after chemotherapy was not reliable. The indication of conversion surgery for GC with PAN metastasis should not be determined based on the size and shrinkage of PAN.
Unveiling proteomic diversity: A quantitative study of antibody drug conjugate and chemotherapy targets in gastroesophageal cancer.
Authors: Thyparambil Sheeno P. , Ghafourian Negin , Heaton Robert , Strasbaugh Amanda , Melkie Marya Abebe , Chou Chung-Jen James , Ling Xuefeng
Published: January 2024

261

Background: Gastroesophageal cancer (GEC), is a significant global health concern with a 5-year relative survival of 7% for metastatic GEC. Standard treatments often include surgery, chemotherapy, and radiation therapy, but their effectiveness can be limited. Chemotherapy is frequently utilized in the treatment of GEC, although no biomarkers for chemotherapy are used in the selection of the chemo agent. There are several well-known biomarkers of resistance and sensitivity for various chemo agents. We used targeted proteomics to quantify protein expression levels of several protein biomarkers associated with chemotherapy efficiency in 125 GEC patients. These include resistance markers for platinum agents (ERCC1), and tubulin inhibitors (TUBB3). It also includes sensitivity markers for irinotecan/topotecan (Topo1), and doxorubicin/etoposide (Topo2A). We also assessed the protein levels of several antibodies-drug conjugate markers (EGFR, Her2, Trop2, FR-alpha, Mesothelin, Axl, CLDN18.2, and Nectin-4). Methods: FFPE tumor tissues from 125 clinical GC patients were microdissected and solubilized for mass spectrometry-based targeted proteomic analysis in our CLIA-certified laboratory. 72 proteins were quantified from 2-3 sections of FFPE tissue. Results: 5-Fluorouracil (5-FU), taxanes, and platinum agents (such as carboplatin) are among the chemotherapy agents that are frequently used to treat GEC. TYMP, a sensitivity marker for 5-FU, was expressed in 32% of GEC cases. ERCC1, a resistance marker for platinum drugs, was expressed at 34%. Additionally, 48% of GEC exhibited TUBB3, a resistance marker for paclitaxel and docetaxel. Topoisomerase 1 (Topo1) is the target for irinotecan or topotecan, and is also the target for some ADCs (e.g. trastuzumab deruxtecan, sacituzumab govitecan etc.). Topo1 was expressed in 92% of GEC with a 10x range (415 - 4195 amol/μg). Another topoisomerase, Topo2A, targetable by etoposide, epirubicin, and doxorubicin, was expressed in 59% of GEC with 19x range (402-7804 amol/μg). ADC targets, such as EGFR (82% detected with 184x range of distribution), Her3 (18%, 4x), AXL (18%,7x), MET (27%, 19x), and Trop2 (50%, 57x) showed a wide range of protein expression. With a 56x range (318 - 17786 amol/μg), Her2 was found in 46% of GEC, of which 12% of GEC had overexpression of Her2 (>740 amol/μg), suggesting that the majority of GEC has low levels of Her2 (318-690 amol/μg), which is potentially targetable by newer anti-Her2 agents. Conclusions: Every cancer is different, and the ability to quantitate simultaneously 72 protein biomarkers from 2-3 FFPE sections provides a wealth of actionable information that, when combined with other multi-omics biomarker data, will help guide clinical treatment or patient stratification for clinical trials.
Development and application of an ultra-sensitive ctDNA mutation profiling assay in monitoring therapy response and drug resistance.
Authors: Zhang Tom , Singh Harshabad , Tan Lu , Wang Xiaohong , Zhao Zhixin , Zhou Kemin , Luo Shujun , Jia Shidong , Du Pan
Published: January 2024

264

Background: Next-generation sequencing (NGS) assays offer efficient high-throughput profiling methods for analyzing circulating tumor DNA (ctDNA) in blood or other liquid biopsy specimens. The ctDNA mutant allele fractions of patients after treatment is often very low and below the detection limit of regular cfDNA assays. Here we report the development and clinical application of a CLIA-certified ultra-sensitive NGS cfDNA assay in detecting the low-frequency ctDNA mutations and monitoring therapy response and drug resistance in patients with metastatic gastroesophageal adenocarcinoma under combined blockade treatments. Methods: PredicineCARE ULTRA cfDNA assay with 100,000X sequencing depth was validated under CLIA settings. Limit of blank (LoB) and limit of detection (LoD) were established by profiling 38 healthy donor plasma samples, 23 contrived human cfDNAs samples from patients with various cancers, and 30 replicates of well-established ctDNA reference standards. In silico down-sampling of FASTQ files was carried out to test the sensitivity of this assay with a lower coverage (50,000X). This assay was then adopted for longitudinal sequencing of 57 serial plasmas from 6 patients with HER2+ gastroesophageal adenocarcinomas (GEC) who underwent combined treatments (capecitabine, oxaliplatin, bevacizumab and trastuzumab) at different time points (baseline, response, and progression). Results: PredicineCARE ULTRA cfDNA assay exhibited exceptional sensitivity in calling single-nucleotide variants and indels, with a 98.0% detection rate at a LoD of 0.075% mutant allele frequency (MAF) for 60 ng cfDNA. This is significantly lower than the LoD (0.25% MAF) of a standard PredicineCARE cfDNA assay. The ultra-sensitive assay also displayed decent analytical specificity (>99.99%) and precision (intra-assay 100%; inter-assay 99.41%). In 6 GEC patients’ longitudinal samples, PredicineCARE ULTRA cfDNA assay detected 36 additional somatic mutations with the MAFs spanning in a range from 0.024% to 0.1% beyond 124 baseline mutations identified using standard PredicineCARE. In two representative cases presented here, all baseline mutations (genes TP53 and PIK3CA etc.) were consistently reported in the follow-up time points with a noticeable MAF reduction (lowest MAFs from 0.046% to 0.024%) during response. Subsequent elevations were observed in more genes, including low-frequency mutations (KRAS and ERBB2) not detected at baseline or only detected in PredicineCARE ULTRA. Conclusions: This study demonstrated the promise and clinical utility of the ultra-sensitive cfDNA molecular profiling at 100,000X sequencing depth in treatment selection, therapy monitoring, and drug resistance studies.