bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.