Shorter Relapse-free Survival Research Articles

Prognostic significance of CRLF2 in patients with acute lymphoblastic leukemia: a meta-analysis and systematic review.

The association between cytokine receptor-like factor 2 (CRLF2) and clinical outcomes in acute lymphoblastic leukemia (ALL) has been a topic of ongoing debate, with divergent findings. This article intended to investigate the influence of CRLF2 alterations on ALL prognosis. Following the PRISMA 2020 guidelines, this meta-analysis was conducted. Hazard ratio (HR) values and confidence intervals (CIs) were the primary statistical measures used. Data heterogeneity was judged using the chi-square test and I2 statistic. Publication bias was appraised with funnel plots, Begg's test, and Egger's test. 16 studies with 6771 patients were finally screened out. CRLF2 over-expression (CRLF2 OE) was associated with poorer event-free survival (EFS) (HR = 1.70, 95% CI = 1.18-2.44, P = 0.004) and relapse-free survival (RFS) (HR = 1.70, 95% CI = 1.28-2.24, P = 0.000) in pediatric ALL. Patients with CRLF2-deregulation (CRLF2-d), also known as CRLF2 rearrangement, exhibited shorter overall survival (OS) (HR = 2.22, 95% CI = 1.49-3.32, P = 0.000), EFS (HR = 1.93, 95% CI = 1.43-2.60, P = 0.000), and RFS (HR = 2.2, 95% CI = 1.53-3.18, P = 0.000) compared to those without CRLF2-d. Subgroup analysis of multivariate HRs and corresponding CIs indicated that childhood with CRLF2 OE had a shorter RFS (HR = 1.70, 95% CI = 1.28-2.24, P = 0.006), and CRLF2-d was identified as an independent prognostic biomarker for OS (HR = 2.22, 95% CI = 1.49-3.32, P = 0.000), EFS (HR = 1.95, 95% CI = 1.44-2.64, P = 0.000), and RFS (HR = 2.2, 95% CI = 1.53-3.18, P = 0.000) in pediatric ALL patients. Both CRLF2 OE and CRLF2-d are associated with poor prognosis in ALL patients.

Polθ: emerging synthetic lethal partner in homologous recombination-deficient tumors.

The most remarkable finding in synthetic lethality (SL) is the hypersensitivity to PARP inhibitors (PARPis) of the tumors harboring defects in genes involved in homologous repair (HR) such as BRCA1/2. Despite initial responsiveness to PARPi, the penetrance of the synthetic lethal interactions between BRCA1/2 genes and PARPi is incomplete. Thus, a significant proportion of HR-defective tumors experience intrinsic or acquired resistance, representing a key challenge of clinical research. An expanded concept of SL is opening new ways and includes novel forms of genetic interactions, investigating not only traditional SL of pairs genes but also SL between biological pathways that regulate the same essential survival cell function. In this context, recent research showed that HR and theta-mediated end-joining (TMEJ) pathways exhibit SL. DNA polymerase theta (Polθ) is encoded by the POLQ gene and is a key component of the TMEJ, an essential backup pathway, intrinsically mutagenic, to repair resected double-strand breaks (DSBs) when the non-homologous end joining (NHEJ) and HR are impaired. Polθ is broadly expressed in normal tissues, overexpressed in several cancers, and typically associated with poor outcomes and shorter relapse-free survival. Notably, HR-deficient tumor cells present the characteristic mutational signatures of the error-prone TMEJ pathway. According to this observation, the loss of HR proteins, such as BRCA1 or BRCA2, contributes to increasing the TMEJ-specific genomic profile, suggesting synthetic lethal interactions between loss of the POLQ and HR genes, and resulting in the emerging interest for Polθ as a potential therapeutic target in BRCA1/2-associated tumors.This review summarizes the converging roles of the POLQ and HR genes in DNA DSB repair, the early-stage clinical trials using Polθ inhibitor to treat HR-defective tumors and to overcome BRCA-reversion mutations responsible for therapeutic resistance, and the novel pleiotropic effects of Polθ, paving the way for the development of unexplored synthetic lethality strategies.

Three-dimensional imaging of upper tract urothelial carcinoma improves diagnostic yield and accuracy.

Upper tract urothelial carcinoma (UTUC) is a rare form of urothelial cancer with a high incidence of recurrence and a low survival rate. Almost two-thirds of UTUCs are invasive at the time of diagnosis; therefore, improving diagnostic methods is key to increasing survival rates. Histopathological analysis of UTUC is essential for diagnosis and typically requires endoscopy biopsy, tissue sectioning, and labeling. However, endoscopy biopsies are minute, and it is challenging to cut into thin sections for conventional histopathology; this complicates diagnosis. Here, we used volumetric 3-dimensional (3D) imaging to explore the inner landscape of clinical UTUC biopsies, without sectioning, revealing that 3D analysis of phosphorylated ribosomal protein S6 (pS6) could predict tumor grade and prognosis with improved accuracy. By visualizing the tumor vasculature, we discovered that pS6+ cells were localized near blood vessels at significantly higher levels in high-grade tumors than in low-grade tumors. Furthermore, the clustering of pS6+ cells was associated with shorter relapse-free survival. Our results demonstrate that 3D volume imaging of the structural niches of pS6 cells deep inside the UTUC samples improved diagnostic yield, grading, and prognosis prediction.

Second Allogeneic Hematopoietic Cell Transplantation for Relapsed Adult Acute Myeloid Leukemia: Outcomes and Prognostic Factors

Second allogeneic hematopoietic cell transplantation (HCT2) is potentially curative for adults with acute myeloid leukemia (AML) or myelodysplastic neoplasm (MDS)/AML experiencing relapse after a first allograft (HCT1), but prognostic factors for outcomes are poorly characterized. To provide a detailed analysis of HCT2 outcomes and associated prognostic factors in a large single-center cohort, with a focus on identifying predictors of relapse and nonrelapse mortality (NRM), we studied adults ≥18 years who underwent HCT2 at a single institution between April 2006 and June 2022 for relapsed AML (n = 73) or MDS/AML (n = 8). With a median follow-up among survivors of 74.0 (range: 10.4 to 187.3) months, there were 30 relapses and 57 deaths, of which 29 were NRM events, contributing to the estimates for relapse, overall survival (OS), relapse-free survival (RFS), and NRM. Three-year estimates for relapse, RFS, and OS were 37% (95% confidence interval: 27% to 48%), 32% (23% to 44%), and 35% (26% to 47%). The rate of NRM at 100 days and 18 months was 20% (12% to 29%) and 28% (19% to 39%). Outcomes differed markedly across patient subsets and were substantially worse for patients who underwent HCT2 with active disease (ie, morphologic evidence of bone marrow and/or extramedullary disease), for patients who relapsed ≤6 months after HCT1, and for patients with higher HCT-specific Comorbidity Index (HCT-CI) or treatment-related mortality (TRM) scores. After multivariable adjustment, active disease was associated with a higher risk of relapse (hazard ratio [HR] = 3.19, P = .006) and shorter RFS (HR = 2.41, P = .008) as well as OS (HR = 2.17, P = .027) compared to transplant in morphologic remission without multiparameter flow cytometric evidence of measurable residual disease. Similarly, a relapse-free interval ≤6 months after the first allograft was associated with higher risk of relapse (HR = 5.86, P < .001) and shorter RFS (HR = 2.86; P = .001) and OS (HR = 2.45, P = .003). Additionally, a high HCT-CI score was associated with increased NRM (HR = 4.30, P = .035), and shorter RFS (HR = 3.87, P = .003) and OS (HR = 3.74, P = .006). Likewise, higher TRM scores were associated with increased risk of relapse (HR = 2.27; P = .024) and NRM (HR = 2.01, P = .001), and inferior RFS (HR = 1.90 P = .001) and OS (HR = 1.88, P = .001). A significant subset of patients with AML or MDS/AML relapse after HCT1 are alive and leukemia-free 3 years after undergoing HCT2. Our study identifies active leukemia at the time of HCT2 and early relapse after HCT1 as major adverse prognostic factors, highlighting patient subsets in particular need of novel therapeutic approaches, and supports the use of the HCT-CI and TRM scores for outcome prognostication.

Mutation patterns and prognostic implications in acute myeloid leukemia with chromosomal 7 deletions.

6547 Background: Chromosomal 7 deletions (del7/7q) are the most common adverse cytogenetic event in acute myeloid leukemia and are associated with high rate of relapse. We analyzed gene mutation profiles in del7/7q AML patients who relapsed after initial remission to identify molecular patterns associated with clinical outcomes. Methods: Out of 351 newly diagnosed AML patients with del7/7q, 115 (32%) achieved complete remission after first-line treatment between 2012-2023. Of the 115 patients, 77 (67%) patients relapsed during the study follow-up. Kaplan-Meier and Cox regression were used to analyze survival outcomes. Next-generation sequencing was performed on a targeted panel of 81 genes for 59 patients who relapsed on bone marrow samples at diagnosis and relapse for paired analysis. Results: The median age of the 115 patients at diagnosis was 74 (41-93). Thirty-four patients (30%) received intensive treatment. With 30.8-month median follow-up, the median overall survival (OS) was 10.4 months, with improved survival in patients without TP53 mutation (13.04 vs. 8.6 months, p=0.005) or complex karyotype (12.4 vs. 8.6 months, p=0.03). The median duration of response for the 77 patients who relapsed was 5 months (2-7). Allo-HSCT significantly improved median OS (not reached vs. 8.5 months, P=6e-06), and was identified as the key variable impacting survival in multivariate analysis. TP53 was the most commonly mutated gene at diagnosis (67%) and relapse (71%). Mutations in CBLC and KDM6A were cleared after induction therapy, while BCOR and BCORL1 were commonly acquired at relapse (Table). At diagnosis, a lower co-mutation burden was observed in TP53 mutant patients as compared with wild type (average 1.84 vs. 3.65 respectively, p=0.0001). Patients with mutated TP53 and coexisting mutations in GATA2, NF1, BCORL1, or RUNX1 at diagnosis had shorter relapse free survival (RFS, 2 vs. 5 months, p=0.01) and OS (7.2 vs. 10.4 months, p=0.01) compared to patients with solely mutated TP53 (HR 2.2; 95% CI 1.2-4; P = 0.004). Allo-HSCT significantly improved the OS in patients with mutated TP53 (13 vs. 8 months, p=0.01). Conclusions: Mutated TP53 clones persist from diagnosis to relapse in patients with del7/7q AML. In patients with mutated TP53, co-occurring mutations in GATA2, NF1, BCORL1or RUNX1 at diagnosis were linked to a shorter RFS and indicate a particularly high-risk subgroup that require proceeding to allo-HSCT in CR1 without delay. [Table: see text]

Serial Postoperative Circulating Tumor DNA Assessment Has Strong Prognostic Value During Long-Term Follow-Up in Patients With Breast Cancer.

Here, we report the sensitivity of a personalized, tumor-informed circulating tumor DNA (ctDNA) assay (Signatera) for detection of molecular relapse during long-term follow-up of patients with breast cancer. A total of 156 patients with primary breast cancer were monitored clinically for up to 12 years after surgery and adjuvant chemotherapy. Semiannual blood samples were prospectively collected, and analyzed retrospectively to detect residual disease by ultradeep sequencing using ctDNA assays, developed from primary tumor whole-exome sequencing data. Personalized Signatera assays detected ctDNA ahead of clinical or radiologic relapse in 30 of the 34 patients who relapsed (patient-level sensitivity of 88.2%). Relapse was predicted with a lead interval of up to 38 months (median, 10.5 months; range, 0-38 months), and ctDNA positivity was associated with shorter relapse-free survival (P < .0001) and overall survival (P < .0001). All relapsing triple-negative patients (n = 7/23) had a ctDNA-positive test within a median of 8 months (range, 0-19 months), while the 16 nonrelapsed patients with triple-negative breast cancer remained ctDNA-negative during a median follow-up of 58 months (range, 8-99 months). The four patients who had negative tests before relapse all had hormone receptor-positive (HR+) disease and conversely, five of the 122 nonrelapsed patients (all HR+) had an occasional positive test. Serial postoperative ctDNA assessment has strong prognostic value, provides a potential window for earlier therapeutic intervention, and may enable more effective monitoring than current clinical tests such as cancer antigen 15-3. Our study provides evidence that those with serially negative ctDNA tests have superior clinical outcomes, providing reassurance to patients with breast cancer. For select cases with HR+ disease, decisions about treatment management might require serial monitoring despite the ctDNA-positive result.

Vitamin D-metabolizing enzyme CYP24A1 affects oncogenic behaviors of oral squamous cell carcinoma and its prognostic implication.

Vitamin D is an essential molecule for cellular homeostasis, playing a critical role in cell fate decisions including cell proliferation, differentiation, and viability. Accumulating evidence has revealed that expression of the vitamin D-metabolizing enzyme CYP24A1 is dysregulated in different types of human malignancy. CYP24A1 has been shown to be involved in the oncogenic property of a variety of carcinoma cells. However, the pathological relevance of CYP24A1 expression level in human oral malignancy remains to be clarified. In the present study, suppression of CYP24A1 expression in oral squamous cell carcinoma (OSCC) cells increased cell proliferation, invasive activity, colony formation efficacy, and tumor growth in vivo. In addition, knockout of CYP24A1 expression inhibited cell death induced by two different types of anticancer drugs, i.e., fluorouracil and cisplatin. Gene clustering by RNA-sequence analysis revealed that several signaling molecules associated with MYC are involved in CYP24A1-mediated oncogenic behaviors. Furthermore, decreased expression level of CYP24A1 was observed in 124/204 cases (61%) of OSCC and was shown to be associated with short relapse-free and overall survival periods. The results showed that a low expression level of CYP24A1 promotes the oncogenic activity of OSCC and is significantly associated with poor prognosis in patients with this malignancy.

Phosphoproteomics Reveals Selective Regulation of Signaling Pathways by Lysophosphatidic Acid Species in Macrophages.

Lysophosphatidic acid (LPA) species, prevalent in the tumor microenvironment (TME), adversely impact various cancers. In ovarian cancer, the 18:0 and 20:4 LPA species are selectively associated with shorter relapse-free survival, indicating distinct effects on cellular signaling networks. Macrophages represent a cell type of high relevance in the TME, but the impact of LPA on these cells remains obscure. Here, we uncovered distinct LPA-species-specific responses in human monocyte-derived macrophages through unbiased phosphoproteomics, with 87 and 161 phosphosites upregulated by 20:4 and 18:0 LPA, respectively, and only 24 shared sites. Specificity was even more pronounced for downregulated phosphosites (163 versus 5 sites). Considering the high levels 20:4 LPA in the TME and its selective association with poor survival, this finding may hold significant implications. Pathway analysis pinpointed RHO/RAC1 GTPase signaling as the predominantly impacted target, including AHRGEF and DOCK guanine exchange factors, ARHGAP GTPase activating proteins, and regulatory protein kinases. Consistent with these findings, exposure to 20:4 resulted in strong alterations to the actin filament network and a consequent enhancement of macrophage migration. Moreover, 20:4 LPA induced p38 phosphorylation, a response not mirrored by 18:0 LPA, whereas the pattern for AKT was reversed. Furthermore, RNA profiling identified genes involved in cholesterol/lipid metabolism as selective targets of 20:4 LPA. These findings imply that the two LPA species cooperatively regulate different pathways to support functions essential for pro-tumorigenic macrophages within the TME. These include cellular survival via AKT activation and migration through RHO/RAC1 and p38 signaling.

Abstract PO1-15-03: Spatially resolved analysis of tumor microenvironment in invasive lobular carcinoma

Abstract Background: Invasive lobular carcinoma (ILC) is the second most common histological breast cancer subtype; however, little is known about its tumor microenvironment (TME). Here, we aimed to study ILC TME using spatial transcriptomics (ST). Methods: We performed ST (Visium 10x Genomics) on frozen tumor samples from 43 primary hormone receptor positive (HR+), HER2-negative (HER2-) ILCs. Of note, 9 samples were coming from patients who experienced disease relapse. Relative hematoxylin/eosin (H&amp;E) slides were morphologically annotated (QuPath software). xCell was used to perform cell type enrichment analysis on sample pseudo-bulks. After cross-samples integration, ST spots were clustered using hierarchical clustering (STutility R package). intNMF algorithm was used to perform clustering at the patient-level by combining: RNA sequencing information (relative percentage of spot-level clusters in each sample), morphology and level of colocalization between cancer cells and the other cell types of the tumor microenvironment. METABRIC (HR+, HER2- ILC samples, n = 122) was used as external validation cohort. Survival analyses (univariable and multivariable adjusting for clinicopathological features) were performed using Cox proportional hazard models. Results: The patient-level classification revealed four groups showing different biological characteristics. Differences in terms of morphology (annotation) and pathway enrichment analysis based on marker genes (GSEA) were observed between groups. This information allowed us to annotate our groups as: proliferative (P, n = 12, enriched in tumor cells and proliferation-related pathways), normal-stroma enriched (NSE, n = 10, enriched in fibroblasts and carcinoma in situ), metabolic (M, n = 9, enriched in metabolic-related pathways) and metabolic-immune enriched (MIE, n = 10, enriched in adipose tissue, metabolic and immune-related pathways). Interestingly, a significantly higher presence of macrophages M2 was found in MIE group. Using group-specific gene signatures, we were able to reproduce the same 4 groups in the METABRIC. Of note, we observed significant differences in relapse-free survival (RFS) in METABRIC (p = 0.03), with NSE presenting better outcome, while P, M and MIE presented worse prognosis. Analysing the area of contact between adipocytes and cancer cells typical of MIE group, we noticed an enrichment in metabolic and M2 macrophages-related pathways. In doing so, we derived a 28 gene signature relative to the tumor-adipocytes contact area. Importantly, our signature was highly expressed in M and MIE groups, and it was not correlated with proliferation-related signatures. Interestingly, the adipocytes-related signature was significantly associated with shorter RFS in ILC patients in METABRIC (univariable: HR 1.4, p = 0.023; multivariable: HR 1.6, p = 0.005). Since both proliferation and metabolism showed to be key processes in defining prognosis in ILC, we built a prognostic index by integrating our adipocytes-related signature with genomic grade index (GGI, a proliferation-related signature). Our index outperformed other existing prognostic signatures (e.g., Oncotype DX, MammaPrint, EndoPredict, LobSig) in assessing prognosis (RFS) in ILC in METABRIC (univariable: HR 1.7, p &amp;lt; 0.001; multivariable: HR 1.7, p = 0.002). Conclusions: We identified 4 biologically driven HR+, HER2- ILC groups describing tumor microenvironment heterogeneity. Of note, two of the three groups associated to worse disease outcome were related to metabolism, highlighting the importance of such process in ILC biology and in the future development of new treatment strategies. Moreover, the prognostic power of our index has the potential to refine the assessment of the risk of relapse in ILC. Further validation is warranted. Citation Format: Matteo Serra, Mattia Rediti, Laetitia Collet, Frédéric Lifrange, David Venet, Nicola Occelli, Xiaoxiao Wang, Delphine Vincent, Ghizlane Rouas, Ligia Craciun, Denis Larsimont, Laurence Buisseret, Miikka Vikkula, François Duhoux, Françoise Rothé, Christos Sotiriou. Spatially resolved analysis of tumor microenvironment in invasive lobular carcinoma [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-15-03.

Abstract 6683: The abundance of Fusobacteria nucleatum in tumor tissue is a prognostic factor in patients of right-sided colorectal cancer

Abstract Background: A significant association between the gut microbiome and colorectal carcinogenesis, as well as cancer progression. It has been reported that Fusobacteria nucleatum (F. nucleatum) is one of the most famous bacteria associated with colorectal cancer (CRC). It has been reported that the abundance of F. nucleatum is associated with colorectal cancer-specific survival (CSS), however it remains unclear for association with F. nulceatum and relapse-free survival (RFS). If F. nucleatum has a significant involvement in tumor progression of colorectal cancer, the abundance of F. nucleatum should be associated with not only CSS but also RFS in colorectal cancer. In this study, we measured the bacterial mass of F. nucleatum in tumor tissue of CRC patients in Stage II-III to explore the differences in prognosis. Methods: We included patients with CRC in stage II-III who underwent surgical treatment at Nippon Medical School Hospital between January 2017 and December 2020 except patients who received preoperative chemoradiotherapy and had multiple cancers. We measured the absolute of F. nucleatum copy number of the DNA exacted tumor tissues using droplet digital PCR. Results: 253 patients with CRC were included. 128 patients had pathological stage II and 125 patients had pathological stage III. Among 253 patients, 104 patients had right-sided CRC, 89 patients had left-sided, and 60 patients had rectal cancer. F. nucleatum was detected in 166 patients (65.6%), and the median of F. nucleatum copy number was 1.08 (range; 0.00 -2791.3). F. nucleatum copy number was more abundant in right-sided CRC than in left-sided and rectal cancer (p= 0.02, p=0.01). There was no significant difference between stage II CRC and stage III. We categorized patients into two groups based on the median cut point of F. nucleatum copy number: the F. nucleatum-high group and the F. nucleatum-low group for comparison with clinicopathological features and prognosis. Patients with high abundance of F. nucleatum exhibited T4 of tumor depth (p=0.03), right-sided CRC (p=0.01), longer tumor circumference (p &amp;lt;0.001), longer tumor length (p &amp;lt;0.001), and no lymph node metastasis (p=0.024). There was no significant difference in relapse-free survival between the F. nucleatum-high group and F. nucleatum-low group among whole patients (p=0.53). Analyzing divided tumor location, in right-sided CRC high abundance of F. nucleatum was significantly associated with shorter relapse-free survival than low abundance (p=0.02), while in left-sided and rectal cancer there was no significant difference (p=0.61). Conclusion: F. nucleatum was more abundant in right-sided CRC and associated with relapse-free survival only in right-sided CRC. F. nucleatum may make a greater impact on right-sided CRC than on left-sided and rectal cancer. Citation Format: Toshimitsu Miyasaka, Takeshi Yamada, Sho Kuriyama, Akihisa Matsuda, Kay Uehara, Seiichi Shinji, Yasuyuki Yokoyama, Goro Takahashi, Takuma Iwai, Kohki Takeda, Shintaro Kanaka, Hiroshi Yoshida. The abundance of Fusobacteria nucleatum in tumor tissue is a prognostic factor in patients of right-sided colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6683.

Abstract 3510: A radiogenomic approach for triple-negative breast cancer risk stratification

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive disease that accounts for 15-20% of all breast cancers. Expressions of ER, PR and HER2 receptors are lacking in this disease, and thus targeted therapies are not effective. TNBC has a shorter relapse-free survival, higher metastasis rate and decreased overall survival compared with other breast cancers. However, when undergoing standard treatment, some patients respond well, while others have poor outcome, suggesting TNBC heterogeneity. Early stratification of patients with long versus short survival could identify the subgroup of patients who would not benefit from exposure to toxicity of chemotherapy treatment. Here, we developed a non-invasive radiogenomic approach for TNBC risk stratification. Methods: A transcriptomic-based prognostic gene signature was previously developed using the TCGA-BRCA cohort (n=860). Briefly, LASSO Cox regression model analysis with the ‘glmnet’ R package was used to identify the transcriptomic signature gene-set consisting of 50 genes. We tested this signature to prognosticate overall survival in a Stanford cohort (n=63) and a previously published SCANB cohort (n=604). The patients were stratified into high- and low-risk groups based on the median risk-score. Next, we developed a machine learning model that identified a radiomic feature set to predict the prognostic transcriptomic risk-groups. Radiomic features were extracted from pre-treatment breast MRI. Radiomics features were extracted using PyRadiomics. The model utilized Decision Tree Classifier and LeaveOneOut method was used for cross-validation. Results: The transcriptomic signature low-risk group was significantly associated with improved overall survival in the two TNBC cohorts, with hazard ratios of 0.11 [95% CI: 0.01-0.88] for the Stanford cohort and 0.71 [95% CI: 0.52-0.97] for the SCANB cohort (log-rank p-values p=0.012 and p=0.032, respectively). Including this transcriptomic signature in a multivariate analysis, which adjusted for clinical features (patient age, grade, stage and Ki67%), the transcriptomic prognostic signature remained a significant prognostic factor (p&amp;lt;0.05). The radiomic feature set (consisting of 20 features) predicted the high- and low-risk transcriptomic groups with a mean accuracy of 72.2% and a mean AUROC of 71%. The precision, F1 and recall scores were 67%, 74% and 82%, respectively. In an independent dataset consisting of 116 Stanford TNBC patients, we used this model to predict risk groups based on the MRI radiomics features, and evaluated the prognostic effects of predicted risk groups. The overall survival of the predicted high-risk group was significantly poorer than the predicted low-risk group (p=0.013). Conclusions: We present a prognostic model that can non-invasively stratify TNBC patients for low versus high mortality risk using radiomic features derived from pre-treatment patient MRI data. Citation Format: Humaira Noor, Yuanning Zheng, Adam Mantz, Ryle Zhou, Andrew Kozlov, Wendy B. DeMartini, Shu-tian Chen, Satoko Okamoto, Debra Ikeda, Sarah Mattonen, Sandy Napel, Melinda L. Telli, George Sledge, Allison Kurian, Mina Satoyoshi, Olivier Gevaert, Haruka Itakura. A radiogenomic approach for triple-negative breast cancer risk stratification [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3510.

Pks-positive Escherichia coli in tumor tissue and surrounding normal mucosal tissue of colorectal cancer patients.

A significant association exists between the gut microbiome and colorectal carcinogenesis, as well as cancer progression. It has been reported that Escherichia coli (E. coli) containing polyketide synthetase (pks) island contribute to colorectal carcinogenesis by producing colibactin, a polyketide-peptide genotoxin. However, the functions of pks+ E. coli in initiation, proliferation, and metastasis of colorectal cancer (CRC) remain unclear. We investigated the clinical significance of pks+ E. coli to clarify its functions in CRC. This study included 413 patients with CRC. Pks+ E. coli of tumor tissue and normal mucosal tissue were quantified using droplet digital PCR. Pks+ E. coli was more abundant in Stages 0-I tumor tissue than in normal mucosal tissue or in Stages II-IV tumor tissue. High abundance of pks+ E. coli in tumor tissue was significantly associated with shallower tumor depth (hazard ratio [HR] = 5.0, 95% confidence interval [CI] = 2.3-11.3, p < 0.001) and absence of lymph node metastasis (HR = 3.0, 95% CI = 1.8-5.1, p < 0.001) in multivariable logistic analyses. Pks+ E. coli-low and -negative groups were significantly associated with shorter CRC-specific survival (HR = 6.4, 95% CI = 1.7-25.6, p = 0.005) and shorter relapse-free survival (HR = 3.1, 95% CI = 1.3-7.3, p = 0.01) compared to the pks+ E. coli-high group. Pks+ E. coli was abundant in Stages 0-I CRC and associated with CRC prognosis. These results suggest that pks+ E. coli might contribute to carcinogenesis of CRC but might not be associated with tumor progression.

Prognostic significance of the FSTL1-DIP2A axis in early-stage tongue cancer.

In tongue cancer, many patients already have metastasis at the time of diagnosis, and such cases are usually unresponsive to treatment, resulting in a poor prognosis. Therefore, there is an urgent need to develop more effective diagnostic and therapeutic methods to cure tongue cancer at the earliest possible stage in clinical practice. Follistatin-like 1 (FSTL1) is known as a negative effector molecule that induces and enhances the refractoriness of cancer cells directly and indirectly via suppressing anti-tumor immunity in various types of cancer. However, the molecular expression, functions, and clinical significance of FSTL1 and its receptor DIP2A in tongue cancer remains to be elucidated. In this study, we revealed that FSTL1, which is highly expressed in tongue cancer cells, plays a key role in its malignancy and is a significant risk factor for recurrence of early-stage tongue cancer. Basic study shows that FSTL1 is abundantly produced from human tongue cancer cell lines, and blocking FSTL1 with specific siRNAs or mAb significantly suppresses cellular functions. Clinical study shows that both FSTL1 and its receptor DIP2A are highly and correlatively expressed in tumor tissues of tongue cancer patients, and high expression levels of both in stage I tumors are significantly associated with shorter relapse-free survival. These suggest that targeting the FSTL1-DIP2A axis may be useful as a biomarker for early prediction of prognosis in tongue cancer patients, and as a therapeutic target for developing new drugs to treat tongue cancer more effectively. This strategy will contribute to improving clinical outcomes in tongue cancer.

Genomic Characterization of Acute Myeloid Leukemia with Aberrations of Chromosome 7: A Multinational Cohort of 523 Patients

Introduction: Aberrations of chromosome 7 [abn(7)] are found in ≈ 10% of newly diagnosed acute myeloid leukemia (AML) and associate with a dismal prognosis. A large-scale comprehensive exploration of the underlying genetic heterogeneity in AML with abn(7) has yet to be performed and could add essential insights into the outcome of this poorly understood patient group. Methods: We collected diagnostic samples from 523 adult AML patients (median age 59 years) with abn(7). Whole-exome sequencing (WES) was performed to discover potentially underestimated genetic lesions in 61 paired diagnostic / remission samples. Subsequently, a gene panel including 66 genes and a SNP backbone for copy-number aberration (CNA) detection was designed and applied to the remaining 471 samples. The majority of patients (78%) were diagnosed with de novo (dn) AML, whereas 22% had secondary (s) or therapy-related (t) AML. Intensive induction treatment was administered to 80% of the patients, while 36 % underwent allogenic stem cell transplantation. Apart from 43% of patients with concomitant complex karyotype (abn(7)/CK+), 24% had -7 as a sole abnormality (-7 sole) and 13% del(7q) sole. Results: A mean of 15.3 single-nucleotide variants (SNVs) and 7.5 CNAs per patient were found by WES. Here, the most frequent recurrent SNVs were identified in TP53 (29.5%), followed by mutations (mut) in genes involved in epigenetic regulation ( DNMT3A, TET2, ASXL1, IDH2), transcription factors ( RUNX1), and genes affecting RAS-signaling ( NF1, KRAS), Figure 1. Targeted sequencing revealed 1829 SNVs with a VAF≥ 2% in 64 genes (mean: 3.8 SNVs / patient). 30% of patients harbored at least one mutation in genes located within the commonly deleted region of 7q, most frequently KMT2C, EZH2CUX1, SAMD9L, SAMD9, LUC7L2 and BRAF. The number of driver gene mutations was higher in CK- than in CK+ patients (4.5 vs. 3.3 SNVs). We found KRAS (OR 3.76, CI 1.17-16.87, P= .044) and RUNX1 (OR 3.61, CI 1.62-8.78, P= .003) mutations to be enriched in -7 sole patients, and FLT3 mutations to be associated with del(7q) sole status (OR 0.33, CI 0.13-0.82, P= .019). With respect to previously unknown lesions, a high amount of KMT2C mutations (16.6%) and recurrent alterations in FAT1 and TACC2 were discovered (6.4% each; Fig. 1). For KMT2C - located on chr7q36.1 - a total of 98 SNVs with mainly missense (73.5%) and truncating (20.4%) mutations at known cancer hotspots were noted. KMT2Cmut was associated with dnAML and AML with maturation morphology. In the entire cohort, the most common co-occurring chromosomal alterations discovered by high-resolution CNA analysis were deletions in chromosomes 5, 17, and 12. Our approach enabled the identification of small fragment deletions (≤10Mb) affecting the TP53, NF1, and ETV6 loci in 5-9% of all cases, which were missed by conventional G-banding. Cancer Cell Fraction and Bradley-Terry models were used to simulate the sequential order of genomic aberrations. While mutations in TP53 and epigenetic-related genes were early events, -7 and del(7q) were often subclonal and SNVs in NRAS, KMT2C very late events in leukemogenesis. Survival analyses in intensively-treated patients (n= 414) revealed that 61% reached complete remission, 67% relapsed, and median overall survival (OS) was 11.9 months. Abn TP53 and high WBC count were independently associated with shorter relapse-free survival (RFS). For OS, besides older age and high WBC count, we identified abn TP53, PTPN11mut, TET2mut,-5, and -18 as poor prognostic factors in multivariate analysis (Table 1). In contrast, IDH2mutconferred an independent favorable prognostic effect for RFS and OS. Notably, abn TP53 outcompeted the prognostic impact of CK+ (Table 1). Compared to TP53wt, patients with abn TP53/CK+ and abn TP53/CK- had a similar poor outcome with median RFS of 6 and 4 months (CK+/CK-, P&amp;lt;.001) and OS of 6.8 and 8.6 months (CK+/CK-, P&amp;lt;.001). In contrast to other genomic studies in myelodysplastic syndrome, we found abn TP53 to be associated with poor outcome irrespective of the single- or multihit mutation status following definitions of the latest ICC classification (Blood, 2022). Conclusion: Our results offer novel insights into the genomic landscape and clonal trajectory of AML with abn(7). This work unravels formerly underestimated genetic lesions ( KMT2Cmut) and alterations with high prognostic impact (abn TP53 and IDH2mut) for better future risk stratification.

Clonal Dynamics of Gene Mutations during Oral Azacitidine Maintenance Therapy in Patients with Acute Myeloid Leukemia (AML): Outcomes from the QUAZAR AML-001 Trial

Background: Acute myeloid leukemia (AML) is a genetically heterogeneous disease and despite some patients (pts) achieving remission with frontline intensive chemotherapy (IC), most eventually relapse. In the QUAZAR trial (NCT01757535), oral azacitidine (Oral-AZA) prolonged overall survival and relapse-free survival (RFS) vs placebo (PBO) in older pts with AML in remission post IC (Wei et al, N Engl J Med 2020). Here, we studied the molecular landscape and clonal dynamics of pts treated with Oral-AZA/PBO in the QUAZAR study. The mutational landscape for older patients with AML in remission after IC may be confounded by persistence of pre-leukemic (PL) or age-related clonal hematopoietic (CH) variants. The implications of these residual mutations on disease relapse and treatment (Tx) outcome are largely unknown. Aims: 1) characterize the mutational landscape from remission bone marrow at baseline (BL) prior to Oral-AZA maintenance (i.e., in remission post-IC); 2) determine the fate of variants over time and at relapse in the Oral-AZA vs PBO arms; 3) examine associations between mutational landscape and relapse risk between Tx arms. Methods: In QUAZAR, 472 pts (≥55 years) with AML with intermediate- or poor-risk cytogenetics in remission after IC (BL) were randomized 1:1 to Oral-AZA or PBO. Among pts who consented to biomarker analyses (n=310), targeted NGS (37 myeloid genes) was performed on bone marrow DNA at BL (Oral-AZA/PBO: n=165/145), cycle 6 (n=107/79) and relapse (n=83/77). Mean NGS coverage was 13K reads and median minimal detectable variant allele frequency (VAF) was 0.12% (range: 0.02-2.79). Clonal variants were categorized by the longitudinal association between VAF and blast percentage (slope of leukemic variants &amp;gt;0.1; PL/CHIP &amp;lt;0.1). RFS was computed from time of randomization to relapse (≥5% BM blasts) or death, estimated by Kaplan-Meier methods. Hazard ratios (HR) and 95% confidence intervals (CI) were obtained from Cox regression models. Nominal P values were derived from log-rank tests. Results: In the NGS cohort (n=310), median RFS (mRFS) for Oral-AZA vs PBO was 10.2 vs 4.7 months (mo), respectively. At BL, prior to maintenance Tx, 221 (71.3%) had detectable mutations, the most frequently occurring mutations (&amp;gt;5% of pts) were in DNMT3A (28.4%), TP53 (15.5%), IDH2 (12.3%), TET2 (11.9%), SRSF2 (11.0%), IDH1 (6.1%) and ASXL1 (5.5%). At BL, 110/310 (35.5%) pts had VAF &amp;gt;5%, potentially representing persistence of PL/CH variants in remission. Comparative analysis of all gene variants at BL and relapse revealed that some VAFs increased with blast frequency, while other variants remained largely static. Applying a variant classification algorithm, 97/258 pts had potential leukemic variants detected at BL. These involved DNMT3A (16.1%), SRSF2 (7.1%), TP53 (7.1%) and IDH2 (5.7%). PL/CH variants included DNMT3A (17.5%), TP53 (8%), IDH2 (5.7%) or TET2 (5.7%). TP53 was detected in 19.4% PL/CH variants (mean VAF 1.7%; range 0.2-13.4). Notably, when analyses were limited to potential leukemic variants at BL (&amp;lt;5% VAF), their presence was correlated with worse RFS (PBO: mRFS for 0, 1 or 2+ mutations was 6.1, 4.7 or 1.9 mo, respectively). The presence of ≥2 leukemic mutations was associated with shorter RFS only in PBO arm (mRFS vs &amp;lt;2 mutations: 1.9 vs 5.7 mo, P=0.02; Oral-AZA: 10.2 vs 10.2 mo). RFS favored Oral-AZA in pts with low mutational burden at BL (&amp;lt;2 mutations: mRFS 10.2 vs 5.7 mo [ P=0.003]; n=145 vs 122 [PBO]), and in a small subset of pts with higher mutational burden (≥2 mutations: mRFS 10.2 vs 1.9 mo [ P=0.008]; n=14 vs 13 [PBO]). Oral-AZA prolonged RFS vs PBO in pts across most mutational subtypes, when assessed for mutations that were deemed potentially leukemic (Figure). At relapse, the frequency of mutations, hotspots variants and co-mutations were comparable between Tx arms. Mutation-based pathway analysis indicated Ras pathway genes were enriched at relapse in PBO (28.6%) vs Oral-AZA arm (14.5%, P=0.03). Summary: In pts with AML in remission post IC, post-hoc analyses showed that Oral-AZA improved RFS vs PBO regardless of the mutational landscape at baseline. The spectrum of mutations at relapse was similar between Tx arms, suggesting that Oral-AZA maintenance prolongs remission without altering mutational heterogeneity.

Prognostic Role of Multiparameter Flow Cytometry-Based Measurable Residual Disease Assessment in Acute Myeloid Leukemia Patients with FMS3-like Tyrosine Kinase-3 Internal Tandem Duplication (FLT3-ITD)

Introduction Measurable residual disease (MRD) monitoring is predictive in acute myeloid leukemia (AML). Assessment of FMS3-like tyrosine kinase-3 in-frame internal tandem duplications (FLT3-ITD) is usually performed at diagnosis by polymerase chain reaction (PCR). Due to its relative lower sensitivity of 2%, FLT3-ITD PCR is not routinely used during response assessment. Next-generation sequencing is similarly limited by technical difficulties in capturing tandem duplications using the short base pair-based sequencing method. Long base pair-based sequencing has been reported, but its use is limited by financial restrictions. Multiparameter flow cytometry (MFC) can be a useful tool for MRD monitoring in this AML subtype until such time that molecular techniques for detecting FLT3-ITD MRD are optimized. Patients and methods The study evaluated the outcomes of FLT3-ITD mutated AML patients diagnosed and treated from 2018 to 2022 at Princess Margaret Cancer Centre. We compared outcomes according to MFC-MRD post-induction and FLT3-ITD allele frequency (AF) status at diagnosis. MRD cut-off was 0.1%. Data were locked as of June 30, 2023. Clinical outcomes evaluated include overall survival (OS) and relapse-free survival (RFS). The cumulative incidence of relapse (CIR) and non-relapse mortality (NRM) were calculated considering competing risk. The Kaplan-Meier method using a log-rank test and a multivariate Cox proportional hazard model was used for analyses, while the Gray test and Fine-Grey model were used for uni- and multivariate analysis for CIR and NRM. Results A total of 111 patients with a mean age of 63.5 years were included, of whom 90 received treatment. Secondary AML accounted for 12.7% of patients. Risk stratification according to European LeukemiaNet (ELN) 2022 was favorable in 2 (1.8%), intermediate in 67 (60.4%), and adverse in 42 patients (37.8%). Nucleophosmin 1 (NPM1) co-mutation was observed in 55 patients (49.5%). Seventy-nine patients (87.8%) could be assessed for overall response, including 69 (76.7%) who achieved complete remission (CR) or CR with incomplete count recovery (CRi). Of these, 54 achieved first CR/CRi (CR1) with 1 induction cycle. MFC-MRD data were available in 61 patients, of whom 44 (72.1%) were MRD negative, while 17 (27.9%) were MRD positive. With a median follow-up of 437 days, 50 patients (45%) were still alive. Median OS and RFS were 3.42 years and 1.05 years, respectively. Among patients who achieved CR1, post-induction MFC-MRD positivity correlated with an inferior OS (HR 2.35 [1.06-5.26], p=0.037) and a trend for a shorter RFS (HR 2.08 [0.99-4.35], p=0.052). We examined the impact of FLT3-ITD AF at diagnosis on long-term outcomes. By applying a binary recursive partitioning method, the cut-off of FLT3-ITD AF with the best risk stratification power for RFS, was defined at 54.6%. The group with a higher FLT3-ITD AF showed inferior OS (HR 1.86 [1.01-3.44], p=0.047) and RFS (HR 1.91 [1.09-3.33], p=0.023). Taking together FLT3-ITD AF at diagnosis and MFC-MRD status at CR1, patients with low FLT3-ITD AF and negative MRD had the highest OS rate of 86.2% at 12 months (p=0.023), and the highest RFS at 72.4% (p=0.096), while the corresponding values for low FLT3-ITD AF/positive MRD patients were 87.5% and 50%, respectively. In contrast, those with high FLT3-ITD AF/negative MRD had an OS of 72.7% and a RFS of 45.5%, while those with high FLT3-ITD AF/positive MRD showed the lowest OS (16.7%) and the shortest RFS (16.7%). There was no statistical difference in CIR and NRM among groups. Multivariate analysis with stepwise selection was performed, considering age at diagnosis, ELN 2022 risk, MFC-MRD at CR1, FLT3-ITD AF at diagnosis, cytogenetics, and NPM1 co-mutation. Predictive factors for OS were MFC-MRD post-induction (HR 2.49 [1.11-5.61], p=0.027) and FLT3-ITD AF (HR 2.29 [1.03-5.11], p=0.043). For RFS, age at diagnosis (HR 1.03 [1.00-1.06], p=0.038) and FLT3-ITD AF (HR 2.40 [1.15-5.01], p=0.019) were predictive, while MFC-MRD was not significant (HR 1.59 [0.72-3.53], p=0.25). Conclusion Our data demonstrate that MFC-based MRD assessment is feasible in AML with FLT3-ITD. Although better outcomes are expected in patients with a lower FLT3-ITD AF, patients who failed to achieve MRD negativity at CR1 showed inferior outcomes. The presence of both poor risk factors, a high AF of FLT3-ITD at diagnosis and MRD positivity at CR1, correlated with the worst treatment outcomes.

Development and validation of CT‑based radiomics model of PET-negative residual CT masses: apotential biomarker forpredicting relapse‑free survival innon-Hodgkin lymphoma patients showing complete metabolic response.

PET-negative residual CT masses (PnRCMs) are usually dismissed as nonviable post-treatment lesions in non-Hodgkin lymphoma (NHL) patients showing complete metabolic response (CMR). We aimed to develop and validate computed tomography (CT)-based radiomics model of PET-negative residual CT mass (PnRCM) for predicting relapse-free survival (RFS) in NHL patients showing CMR. A total of 224 patients who showed CMR after completing first-line chemotherapy for PET-avid NHL were recruited for model development. Patients with PnRCM were selected in accordance with the Lugano classification. Three-dimensional segmentation was done by two readers. Radiomic scores (RS) were constructed using features extracted using the Least-absolute shrinkage and selection operator analysis among radiomics features of PnRCMs showing more than substantial interobserver agreement (> 0.6). Cox regression analysis was performed with clinical and radiologic features. The performance of the model was evaluated using area under the curve (AUC). For validation, 153 patients from an outside hospital were recruited and analyzed in the same way. In the model development cohort, 68 (30.4%) patients had PnRCM. Kaplan-Meier analysis showed that patients with PnRCM had significantly (p = 0.005) shorter RFS than those without PnRCM. In Kaplan-Meier analysis, the high RS group showed significantly (p = 0.038) shorter RFS than the low-scoring group. Multivariate Cox regression analysis showed that high IPI score [hazard ratio (HR) 2.46; p = 0.02], treatment without rituximab (HR 3.821; p = 0.019) were factors associated with shorter RFS. In estimating RFS, combined model in both development and validation cohort showed AUC values of 0.81. The combined model that incorporated both clinical parameters and CT-based RS showed good performance in predicting relapse in NHL patients with PnRCM.

965P C14orf159 mutations are associated with shorter relapse-free survival and overall survival after liver transplantation in hepatocellular carcinoma patients meeting Hangzhou criteria

965P C14orf159 mutations are associated with shorter relapse-free survival and overall survival after liver transplantation in hepatocellular carcinoma patients meeting Hangzhou criteria

Prognostic role of minute ventilation/carbon dioxide production slope for perioperative morbidity and long-term survival in resectable patients with non-small-cell lung cancer: A prospective study using propensity score overlap weighting.

The role of minute ventilation/carbon dioxide production (/CO2) slope, a ventilation efficiency marker, in predicting short- and long-term health outcomes for patients with non-small-cell lung cancer (NSCLC) undergoing lung resection has not been well investigated. This prospective cohort study consecutively enrolled NSCLC patients who underwent a presurgical cardiopulmonary exercise test from November 2014 to December 2019. The association of /CO2 slope with relapse-free survival (RFS), overall survival (OS), and perioperative mortality was evaluated using the Cox proportional hazards and logistic models. Covariates were adjusted using propensity score overlap weighting. The optimal cut-off point of the E/CO2 slope was estimated using the Receiver Operating Characteristics curve. Internal validation was completed through bootstrap resampling. A cohort of 895 patients (median age [interquartile range], 59 [13] years; 62.5% male) was followed for a median of 40 (range, 1-85) months. Throughout the study there were 247 relapses or deaths and 156 perioperative complications. The incidence rates per 1000 person-years for relapses or deaths were 108.8 and 79.6 among patients with high and low E/CO2 slope, respectively (weighted incidence rate difference per 1000 person-years, 29.21 [95% CI, 7.30 to 51.12]). A E/CO2 slope of ≥31 was associated with shorter RFS (hazard ratio for relapse or death, 1.38 [95% CI, 1.02 to 1.88], P=0.04) and poorer OS (hazard ratio for death, 1.69 [1.15 to 2.48], P=0.02) compared to a lower /CO2 slope. A high E/CO2 slope increased the risk of perioperative morbidity compared with a low E/CO2 slope (odds ratio, 2.32 [1.54 to 3.49], P<0.001). In patients with operable NSCLC, a high E/CO2 slope was significantly associated with elevated risks of poorer RFS and OS, and perioperative morbidity.

Poor Prognosis in Patients With Stage III Colorectal Cancer Receiving Adjuvant FOLFOX/CAPOX Therapy Is Predicted by the Presence of Many Poorly Differentiated Clusters.

Poorly differentiated clusters (PDCs) have been reported to be a useful grading system for predicting prognosis in patients with colorectal cancer (CRC). We investigated the association between the number of PDCs and prognosis in patients with stage III CRC treated with oxaliplatin-based adjuvant chemotherapy. This is a retrospective study of 49 patients with stage III CRC who underwent curative surgery followed by oxaliplatin-based adjuvant chemotherapy. PDC was defined as a cluster of ≥5 cancer cells without glandular structure at the invasive front of the primary tumor. During the observation period, 12 patients experienced relapse. The patients were divided into two groups (<7 and ≥7 PDC groups), and receiver operating characteristic (ROC) curves were calculated [area under the curve (AUC)=0.743]. Patients with ≥7 PDCs had a much shorter relapse-free survival (RFS) than those with <7 PDCs (p<0.0001). The overall survival (OS) was also significantly worse in patients with ≥7 PDCs than in those with <7 PDCs (p<0.0001). Multivariate analysis revealed that PDC was the only significant prognostic factor measured that could predict RFS (p=0.002) and OS (p=0.0047) in patients with stage III CRC treated with oxaliplatin-based adjuvant chemotherapy. In patients with stage III CRC treated with post-resection oxaliplatin-based adjuvant chemotherapeutic regimens, the presence of ≥7 PDCs at the invasive front of the primary tumor predicted unfavorable prognosis.