Molecular Stratification Research Articles

Reproducible imaging-based prediction of molecular subtype and risk stratification of gliomas across different experience levels using a structured reporting system.

To determine reproducible MRI parameters predictive of molecular subtype and risk stratification in glioma and develop a structured reporting system. All study patients were initially diagnosed with glioma, 141 from the Cancer Genome Atlas and 131 from our tertiary institution, as training and validation sets, respectively. Images were analyzed by three neuroradiologists with 1-7 years of experience. MRI features including contrast enhancement pattern, necrosis, margin, edema, T2/FLAIR mismatch, internal cyst, and cerebral blood volume higher than normal cortex were reported using a structured reporting system. The pathology was stratified into five risk types: (1) oligodendroglioma, isocitrate dehydrogenase [IDH]-mutant, 1p19q co-deleted; (2) diffuse astrocytoma, IDH-mutant, grade II-III; (3) glioblastoma, IDH-mutant, grade IV; (4) diffuse astrocytoma, IDH-wild, grade II-III; and (5) glioblastoma, IDH-wild, grade IV. Significant predictors were selected using multivariate logistic regression, and diagnostic performance was tested using a validation set. Reproducible imaging parameters exhibiting > 50% agreement across readers included the presence of necrosis, T2/FLAIR mismatch, internal cyst, and predominant contrast enhancement. In the validation set, prediction of risk type 5 exhibited the highest diagnostic performance with AUCs of 0.92 (reader 1) and 0.93 (reader 2) with predominant enhancement, followed by risk type 2 with AUCs of 0.95 and 0.95 with T2/FLAIR mismatch sign and no necrosis, and risk type 1 with AUCs of 0.84 and 0.83 with internal cyst or necrosis. Risk types 3 and 4 were difficult to visually predict. Imaging parameters with high reproducibility enabling prediction of IDH-wild-type glioblastoma, IDH-mutant/1p19q co-deletion oligodendroglioma, and IDH-mutant diffuse astrocytoma were identified. • Reproducible MRI parameters for determining molecular subtypes of glioma included the presence of necrosis, T2/FLAIR mismatch, internal cyst, and predominant contrast enhancement. • IDH-wild type glioblastoma, IDH-mutant/1p19q co-deletion oligodendroglioma, and IDH-mutant low-grade astrocytoma were identified using MRI parameters with high inter-reader reproducibility. • Identification of IDH-wild type low-grade glioma and IDH-mutant glioblastoma was difficult by visual analysis.

Mismatch repair proteins PMS2 and MLH1 can further refine molecular stratification of IDH-mutant lower grade astrocytomas

The diagnostic role of Isocitrate Dehydrogenase (IDH) mutation status in adult lower grade astrocytomas was first formally presented within the WHO Classification of Tumours of the Central Nervous System (2016). IDH-mutant astrocytomas are not as common as IDH-wildtype astrocytomas but are of better prognosis. Our previous study provided an evident that IDH-mutant lower grade astrocytomas is not a homogeneous group and could be further stratified by PDGFRA amplification, CDK4 amplification and CDKN2A deletion. In this study, we detected the expressions of DNA mismatch repair (MMR) proteins (PMS2, MLH1, MSH2, MSH6) and PD-L1 by immunohistochemistry in 147 IDH-mutant lower grade astrocytomas and explored their clinical relevance. The loss of was identified in 28.6%, 1.4%, 8.8% and 13.6%, respectively. PD-L1 expression was detected in 1.4% of this cohort. Survival analysis revealed that loss of PMS2 was correlated with shorter OS (p < 0.001) and PFS (p = 0.005). Loss of PMS2 or MLH1 was associated with shorter OS (p < 0.001) and PFS (p = 0.008). In IDH-mutant lower grade astrocytomas without CDKN2A deletion, loss of PMS2 was associated with poorer OS (p < 0.001) and PFS (p = 0.001). Furthermore, among IDH-mutant lower grade astrocytomas lacking the three biomarkers (PDGFRA, CDK4 and CDKN2A), loss of PMS2 was also associated with a poorer OS (p < 0.001) and PFS (p = 0.003). Our data illustrated the potential application of MMR genes in stratification of IDH-mutant lower grade astrocytomas without PDGFRA, CDK4 and CDKN2A copy number alterations.

Omitting lymphadenectomy in obese endometrial cancer patients undergoing sentinel lymph node mapping: when more is less

<h3>Objectives:</h3> Obese patients present unique surgical and technical challenges to their surgeons and anesthesiologists given their multiple comorbidities, difficult anatomy, and excessive weight. Thus, any surgical procedure that prolongs surgical time and potentially increases risk for complications in this population, needs to be carefully evaluated and minimized.The aim of this study is to evaluate the feasibility of sentinel lymph node (SLN) mapping in obese endometrial cancer patients, and to determine whether omitting lymph node dissection (LND) from surgical staging where SLN sampling is performed, impacts oncologic outcomes. <h3>Methods:</h3> Between December 2007 and August 2017, 722 patients with uterine cancer underwent surgical staging in our institution. We excluded patients with sarcomas (n=32), patients with stage 4 disease (n=9), patients who received neoadjuvant therapy (n=5) and patients whose body mass index (BMI) was below 35.0 kg/m² (n=453). The approach for LND at our center changed over the years: all surgeries from January 2008 to August 2014 included bilateral pelvic LND, with para-aortic LND at the surgeon's discretion (LND±SLN cohort). In addition to LND, all consecutive patients from December 2010 to August 2014 underwent SLN mapping with a cervical injection. With the establishment of SLN mapping algorithm feasibility, patients operated from August 2014 to August 2017 went through SLN mapping without LND (SLN cohort). <h3>Results:</h3> Out of 223 patients with a median BMI of 40.6 kg/m², 140 patients underwent LND (± SLN) and 83 patients underwent SLN. The median operative time for surgical staging in SLN only group was shorter in 47.5 minutes than for patients in the LND±SLN group (190.5 minutes (108-393) vs. 238 minutes (131-440), respectively, (p<0.001)), and they had reduced estimated blood loss (EBL) compared to the LND±SLN group (30 ml (0-300) vs. 40 ml (0-800ml), P=0.03). At a 24 months' follow-up cut-off, 98% of the patients were alive and 95.5% were free of disease, without significant differences in OS, DSS and PFS between the two groups (p=0.7, p=0.8 and p=0.4, respectively).Overall, 171 patients underwent SLN biopsy (±LND) and stratified by the tracer used for mapping (ICG versus blue dye). The ICG injected group had higher successful mapping and bilateral detection rates (92.8% vs 71.7%, p<0.001 and 80.2% vs 43.3%, p<0.001, respectfully). <h3>Conclusions:</h3> The obese population is at increased risk for intraoperative and postoperative complications associated with prolonged operative time from secondary to challenges in the surgical and anesthesia process. The advantage of minimizing the surgery towards SLN approach, as reflected in our results by shorter operative time and minimal bleeding is of particular importance in this set of patients. Omitting LND from surgical staging where SLN is performed was not associated with inferior survival outcomes. Given the higher successful detection and metastatic nodes rates with ICG and NIR fluorescence imaging compared to previously reported rates with blue dye based SLN, ICG should be the dye of choice in obese and morbid obese EC patients. Future studies should focus on molecular stratification of obese EC patients into risk groups for nodal disease, selecting patients for LND in cases of failed mapping.

A case report of response to crizotinib in chemotherapy-refractory metastatic gallbladder cancer with met amplification and acquired resistance resulting from the loss of MET amplification.

Gallbladder cancer (GBC) is a highly invasive disease and the most prevalent malignancy of the biliary system. Patients with GBC are commonly diagnosed at a late stage and have an unfavorable prognosis. Palliative chemotherapy has been the standard care for recurrent or metastatic disease in the past decades. Recently, several targeted therapies have been investigated in advanced biliary tract cancer (BTC) including inhibitors of genes or pathways such as FGFR2 fusions or rearrangements, IDH1 mutations, and NTRK gene fusions. Also, several clinical studies involving molecular stratification have been performed in defined patient groups, for example, BRAF V600E and HER2. Mesenchymal epithelial transition(MET)encodes a tyrosine kinase receptor and its ligand hepatocyte growth factor is a proto-oncogene. Targeting the MET signaling pathway is an effective strategy in numerous cancer types. However, the poor efficacy of MET inhibitors has been demonstrated in several phase II studies, but currently no reports have explained the potential mechanisms of resistance to MET inhibitors in BTC. In this article, we report a case of metastatic GBC with MET amplification that exhibited a rapid response to crizotinib after the failure of two lines of chemotherapy. After the patient had progressed and discontinued crizotinib, cabozantinib was introduced. Analysis of circulating tumor DNA (ctDNA) by next-generation sequencing (NGS) indicated a loss of MET amplification status. To our knowledge, this is the first case study demonstrating the use of NGS in ctDNA to monitor the development of acquired resistance during anti-MET treatment in GBC.

AGR2 and AGR3 play an important role in the clinical characterization and prognosis of basal like breast cancer

Introduction: Basal-like Breast Cancer (BLBC) represents an important molecular subtype of breast cancer characterized by an aggressive behavior, molecular pathology poorly understood and a limited treatment. Objective: We aim to search for molecular differences between non-BLBC and BLBC tumors in order to propose possible diagnostic and prognostic biomarkers using databases. Metodology: Microarray processed data were downloaded from GEO database considering non-BLBC and BLBC. Enrichment analysis was evaluated using GO consortium and Ingenuity, protein–protein interaction, gene Ontology and co-expression analysis using STRING. Gene expression data was extracted using TCGA, METABRIC and Breast Cancer Gene-Expression Miner v4.2 databases. The Survival was evaluated using The Kaplan–Meier plotter. Results: Were identified 58 upregulated and 58 downregulated genes enriched in signaling pathways like PDGF, Angiogenesis, Integrin and WNT. AGR2 and AGR3 expression were reduced in BLBC in relation to non-BLBC tumors, patients aged ≤51 years, and with negativity of ER, PR and HER-2 and nodal status. Low expression of AGR2 and AGR3 were associated with worse OS and RFS for all breast cancer cases. But according to the molecular stratification, low AGR2 conferred worst OS in luminal A, worst RFS in BLBC and good OS and RFS in luminal B. High AGR3 conferred worse OS and RFS in BLBC, but low AGR3 attributed worse OS in luminal A. Conclusion: AGR2 and AGR3 expression were able to differentiate non-BLBC from BLBC. Downregulation of AGR2 and AGR3 was associated with BLBC clinical phenotype. Furthermore, both genes behave different when considering prognosis and molecular stratification.

Efficacy of Carboplatin and Isotretinoin in Children With High-risk Medulloblastoma

Brain tumors are the leading cause of disease-related death in children. Medulloblastoma is the most common malignant embryonal brain tumor, and strategies to increase survival are needed. To evaluate therapy intensification with carboplatin as a radiosensitizer and isotretinoin as a proapoptotic agent in children with high-risk medulloblastoma in a randomized clinical trial and, with a correlative biology study, facilitate planned subgroup analysis according to World Health Organization consensus molecular subgroups of medulloblastoma. A randomized clinical phase 3 trial was conducted from March 2007 to September 2018. Analysis was completed in September 2020. Patients aged 3 to 21 years with newly diagnosed high-risk medulloblastoma from Children's Oncology Group institutions within the US, Canada, Australia, and New Zealand were included. High-risk features included metastasis, residual disease, or diffuse anaplasia. Patients were randomized to receive 36-Gy craniospinal radiation therapy and weekly vincristine with or without daily carboplatin followed by 6 cycles of maintenance chemotherapy with cisplatin, cyclophosphamide, and vincristine with or without 12 cycles of isotretinoin during and following maintenance. The primary clinical trial end point was event-free survival, using the log-rank test to compare arms. The primary biology study end point was molecular subgroup classification by DNA methylation array. Of 294 patients with medulloblastoma, 261 were evaluable after central radiologic and pathologic review; median age, 8.6 years (range, 3.3-21.2); 183 (70%) male; 189 (72%) with metastatic disease; 58 (22%) with diffuse anaplasia; and 14 (5%) with greater than 1.5-cm2 residual disease. For all participants, the 5-year event-free survival was 62.9% (95% CI, 55.6%-70.2%) and overall survival was 73.4% (95% CI, 66.7%-80.1%). Isotretinoin randomization was closed early owing to futility. Five-year event-free survival was 66.4% (95% CI, 56.4%-76.4%) with carboplatin vs 59.2% (95% CI, 48.8%-69.6%) without carboplatin (P = .11), with the effect exclusively observed in group 3 subgroup patients: 73.2% (95% CI, 56.9%-89.5%) with carboplatin vs 53.7% (95% CI, 35.3%-72.1%) without (P = .047). Five-year overall survival differed by molecular subgroup (P = .006): WNT pathway activated, 100% (95% CI, 100%-100%); SHH pathway activated, 53.6% (95% CI, 33.0%-74.2%); group 3, 73.7% (95% CI, 61.9%-85.5%); and group 4, 76.9% (95% CI, 67.3%-86.5%). In this randomized clinical trial, therapy intensification with carboplatin improved event-free survival by 19% at 5 years for children with high-risk group 3 medulloblastoma. These findings further support the value of an integrated clinical and molecular risk stratification for medulloblastoma. ClinicalTrials.gov Identifier: NCT00392327.

Differential impact of tumor suppressor gene (TP53, PTEN, RB1) alterations and treatment outcomes in metastatic, hormone-sensitive prostate cancer

BackgroundAltered tumor suppressor genes (TSG-alt) in prostate cancer are associated with worse outcomes. The prognostic value of TSG-alt in metastatic, hormone-sensitive prostate cancer (M1-HSPC) is unknown. We evaluated the effects of TSG-alt on outcomes in M1-HSPC and their prognostic impact by first-line treatment.MethodsWe retrospectively identified patients with M1-HSPC at our institution treated with first-line androgen deprivation therapy plus docetaxel (ADT + D) or abiraterone acetate (ADT + A). TSG-alt was defined as any alteration in one or more TSG. The main outcomes were Kaplan–Meier-estimated progression-free survival (PFS) and overall survival, analyzed with the log-rank test. Clinical characteristics were compared with the χ2 test and Kruskal–Wallis rank sum test. Cox regression was used for univariate and multivariable analyses.ResultsWe identified 97 patients with M1-HSPC: 48 (49%) with ADT + A and 49 (51%) with ADT + D. Of 96 patients with data available, 33 (34%) had 1 TSG-alt, 16 (17%) had 2 TSG-alt, and 2 (2%) had 3 TSG-alt. The most common alterations were in TP53 (36%) and PTEN (31%); 6% had RB1 alterations. Median PFS was 13.1 (95% CI, 10.3–26.0) months for patients with normal TSGs (TSG-normal) vs. 7.8 (95% CI, 5.8–10.5) months for TSG-alt (P = 0.005). Median PFS was lower for patients with TSG-alt vs TSG-normal for those with ADT + A (TSG-alt: 8.0 [95% CI, 5.8–13.8] months vs. TSG-normal: 23.2 [95% CI, 13.1–not estimated] months), but not with ADT + D (TSG-alt: 7.8 [95% CI, 5.7–12.9] months vs. TSG-normal: 9.5 [95% CI, 4.8–24.7] months). On multivariable analysis, only TSG-alt predicted worse PFS (hazard ratio, 2.37; 95% CI, 1.42–3.96; P < 0.001).ConclusionsThe presence of TSG-alt outperforms clinical criteria for predicting early progression during first-line treatment of M1-HSPC. ADT + A was less effective in patients with than without TSG-alt. Confirmation of these findings may establish the need for inclusion of molecular stratification in treatment algorithms.

Abstract 2836: Effect of autophagy inhibition on epithelial mesenchymal transition in breast cancer cell lines

Abstract The aim of our work is to evaluate potential undesirable effects of autophagy inhibition in breast cancer subtypes which are not sensitive to the inhibition of autophagy. Worldwide, BC is the most frequent cancer in women. Despite recent advances in diagnosis, molecular stratification and targeted therapy, BC is still the leading cause of cancer-related death in women. Thus, it is a public health issue that must be attended. In cancer, autophagy has a pro-tumorigenic role that helps tumor cells survive metabolic stress and growth factor deprivation, hypoxia, maintain tumor initiating cells, confer therapy resistance and modulate epithelial mesenchymal transition (EMT). Because tumor cells benefit from autophagy, it has been proposed that autophagy inhibition could be beneficial for cancer treatment. Nowadays, there are clinical trials where autophagy is being inhibited with promising results that encourage this approach. However, in these clinical trials, cancer types are not been stratified and autophagy is being inhibited in many solid tumor types. In this regard, there is also in vitro evidence in which autophagy inhibition in some cancer types induces EMT, which in the clinic could be detrimental for patients. This highlights the urgency for stratifying patients that will benefit the most from autophagy inhibition. In this work, autophagy inhibition in MCF7 ER+ cell line increased secretion, inflammation and EMT related pathways suggesting induction of malignancy. Autophagy inhibition induced changes in cell morphology in ER+ breast cancer cell lines (MCF7 and T47D) when evaluated by aspect ratio estimation changing from a cobblestone -like epithelial morphology to a fibroblast-like morphology. No changes in cell morphology were found in MCF10A and MDAMB231 cell lines. Changes in morphology were accompanied by a decrease in E-cadherin protein levels suggesting induction of EMT. Our results suggest that CQ treatment in ER+ BC cells could induce a malignant process related to EMT. Thus, ER+ BC patients may not benefit from autophagy inhibition. Nowadays, there are clinical trials where autophagy is being inhibited and no subtype stratification is being done, so we encourage to stratify patients to determine who will be benefited the most from autophagy inhibition and who will not. Citation Format: Guadalupe Rojas, Nidia Pazos, Paola Maycotte. Effect of autophagy inhibition on epithelial mesenchymal transition in breast cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2836.

Molecular subtype identification and prognosis stratification by a metabolism-related gene expression signature in colorectal cancer

BackgroundMetabolic reprograming have been associated with cancer occurrence and progression within the tumor immune microenvironment. However, the prognostic potential of metabolism-related genes in colorectal cancer (CRC) has not been comprehensively studied. Here, we investigated metabolic transcript-related CRC subtypes and relevant immune landscapes, and developed a metabolic risk score (MRS) for survival prediction.MethodsMetabolism-related genes were collected from the Molecular Signatures Database and metabolic subtypes were identified using an unsupervised clustering algorithm based on the expression profiles of survival-related metabolic genes in GSE39582. The ssGSEA and ESTIMATE methods were applied to estimate the immune infiltration among subtypes. The MRS model was developed using LASSO Cox regression in the GSE39582 dataset and independently validated in the TCGA CRC and GSE17537 datasets.ResultsWe identified two metabolism-related subtypes (cluster-A and cluster-B) of CRC based on the expression profiles of 539 survival-related metabolic genes with distinct immune profiles and notably different prognoses. The cluster-B subtype had a shorter OS and RFS than the cluster-A subtype. Eighteen metabolism-related genes that were mostly involved in lipid metabolism pathways were used to build the MRS in GSE39582. Patients with higher MRS had worse prognosis than those with lower MRS (HR 3.45, P < 0.001). The prognostic role of MRS was validated in the TCGA CRC (HR 2.12, P = 0.00017) and GSE17537 datasets (HR 2.67, P = 0.039). Time-dependent receiver operating characteristic curve and stratified analyses revealed the robust predictive ability of the MRS in each dataset. Multivariate Cox regression analysis indicted that the MRS could predict OS independent of TNM stage and age.ConclusionsOur study provides novel insight into metabolic heterogeneity and its relationship with immune landscape in CRC. The MRS was identified as a robust prognostic marker and may facilitate individualized therapy for CRC patients.

Aberrant Expression of Long Non Coding RNA HOTAIR and De-Regulation of the Paralogous 13 HOX Genes Are Strongly Associated with Aggressive Behavior of Gastro-Entero-Pancreatic Neuroendocrine Tumors

Gastro-entero-pancreatic neuroendocrine neoplasms (GEP-NENs) are rare diseases occurring in the gastrointestinal tract and pancreas. They are characterized by the loss of epithelial tubular gland elements, and by the increased expression of neuroendocrine markers. GEP-NENs are subdivided into two histo-pathological types, gastro-entero-pancreatic neuroendocrine tumors (GEP-NETs) and gastro-entero-pancreatic neuroendocrine carcinomas (GEP-NECs). According to WHO 2017 and 2019 classification criteria are graded and staged in four categories, NET-G1, NET-G2, NET-G3, and NEC-G3. The molecular characterization of these tumors can be fundamental for the identification of new diagnostic, prognostic and predictive biomarkers. The main purpose of this study was to analyze the expression of the paralogous 13 HOX genes, normally involved in embryogenic development and frequently deregulated in human cancers, and of the HOX regulating lncRNA HOTAIR in GEP-NENs. The expression of HOX genes is gradually lost in the transition from GEP NET G1 to NET/NEC G3 tumors, while HOTAIR expression, inversely correlated with HOX genes expression and weakly expressed in low-grade GEP NENs, becomes aberrant in NET G3 and NEC G3 categories. Our data highlights their potential role in the molecular stratification of GEP-NENs by suggesting new prognostic markers and potential therapeutic targets.

Abnormal Long Non-Coding RNAs Expression Patterns Have the Potential Ability for Predicting Survival and Treatment Response in Breast Cancer.

Abnormal long non-coding RNAs (lncRNAs) expression has been documented to have oncogene or tumor suppressor functions in the development and progression of cancer, emerging as promising independent biomarkers for molecular cancer stratification and patients’ prognosis. Examining the relationship between lncRNAs and the survival rates in malignancies creates new scenarios for precision medicine and targeted therapy. Breast cancer (BRCA) is a heterogeneous malignancy. Despite advances in its molecular classification, there are still gaps to explain in its multifaceted presentations and a substantial lack of biomarkers that can better predict patients’ prognosis in response to different therapeutic strategies. Here, we performed a re-analysis of gene expression data generated using cDNA microarrays in a previous study of our group, aiming to identify differentially expressed lncRNAs (DELncRNAs) with a potential predictive value for response to treatment with taxanes in breast cancer patients. Results revealed 157 DELncRNAs (90 up- and 67 down-regulated). We validated these new biomarkers as having prognostic and predictive value for breast cancer using in silico analysis in public databases. Data from TCGA showed that compared to normal tissue, MIAT was up-regulated, while KCNQ1OT1, LOC100270804, and FLJ10038 were down-regulated in breast tumor tissues. KCNQ1OT1, LOC100270804, and FLJ10038 median levels were found to be significantly higher in the luminal subtype. The ROC plotter platform results showed that reduced expression of these three DElncRNAs was associated with breast cancer patients who did not respond to taxane treatment. Kaplan–Meier survival analysis revealed that a lower expression of the selected lncRNAs was significantly associated with worse relapse-free survival (RFS) in breast cancer patients. Further validation of the expression of these DELncRNAs might be helpful to better tailor breast cancer prognosis and treatment.

Increased colonic expression of ACE2 associates with poor prognosis in Crohn\u2019s disease

The host receptor for SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2), is highly expressed in small intestine. Our aim was to study colonic ACE2 expression in Crohn's disease (CD) and non-inflammatory bowel disease (non-IBD) controls. We hypothesized that the colonic expression levels of ACE2 impacts CD course. We examined the expression of colonic ACE2 in 67 adult CD and 14 NIBD control patients using RNA-seq and quantitative (q) RT-PCR. We validated ACE2 protein expression and localization in formalin-fixed, paraffin-embedded matched colon and ileal tissues using immunohistochemistry. The impact of increased ACE2 expression in CD for the risk of surgery was evaluated by a multivariate regression analysis and a Kaplan–Meier estimator. To provide critical support for the generality of our findings, we analyzed previously published RNA-seq data from two large independent cohorts of CD patients. Colonic ACE2 expression was significantly higher in a subset of adult CD patients which was defined as the ACE2-high CD subset. IHC in a sampling of ACE2-high CD patients confirmed high ACE2 protein expression in the colon and ileum compared to ACE2-low CD and NIBD patients. Notably, we found that ACE2-high CD patients are significantly more likely to undergo surgery within 5 years of CD diagnosis, and a Cox regression analysis found that high ACE2 levels is an independent risk factor for surgery (OR 2.17; 95% CI, 1.10–4.26; p = 0.025). Increased intestinal expression of ACE2 is associated with deteriorated clinical outcomes in CD patients. These data point to the need for molecular stratification that can impact CD disease-related outcomes.

Molecular Subtypes of Plasma Cell Neoplasms with Circulating Neoplastic Plasma Cells

Background:Circulating neoplastic plasma cells (CNPCs) are frequently seen in plasma cell neoplasms (PCN). Prior studies have shown that CNPCs are usually associated with a higher tumor burden and disease progression. Additionally the percentage of CNPCs in newly diagnosed PCN as quantified by flow cytometric analysis is found to be an independent predictor of survival.The UAMS myeloma group has established a molecular classification of PCNs based on unsupervised hierarchical clustering of gene expression profiling (GEP) data, and has identified 7 subgroups: Hyperdiploidy (HY), Cyclin D-1 (CD-1), CD-2, Low Bone (LB), Proliferation (PR), MMSET/FGFR3 (MS) and MAF (MF). This molecular subtyping in conjunction with the UAMS GEP 70 gene signature profile has been found to be clinically useful in identifying low risk group with superior event-free and overall survival from high-risk group.The purpose of this study was to determine if a particular PCN molecular subtype was more likely to be associated with CNPCs. To the best of our knowledge, the association between the different molecular subtypes and CNPCs has not been studied before.Design:A retrospective review was performed to determine the number of PCN patients with CNPCs during 2015-2016. Peripheral blood immunophenotyping was performed using 8-color multi-parameter flow cytometry analysis. PCN molecular subtypes and GEP risk stratification was performed on CD138-enriched plasma cells from bone marrow aspirate based on our previously established protocol. Additional data including clinical classification, bone marrow plasma cell tumor burden and karyotype analysis were also collected.Results:A total of 305 patient had peripheral blood flow cytometric analysis performed during the study period; 147 patients showed presence of CNPCs (48.19%). Only 120 of the 147 cases with CNPCs had all the additional data and were included for further analysis.Based on UAMS GEP 70 signature risk score, 86 patients (71.7%) showed low risk gene classification compared to 34 patients (28.3%) with high risk gene classification. Distribution of molecular subgroups defined by GEP data, identified that the HY group was the largest subgroup (n=29, 24.2%), followed by CD-2 (n= 24, 20%), PR (n=19, 15.8%), MF (n=15, 12.5%), MS (n=12, 10%), CD-1 (n=12, 10%) and LB (n=9, 7.5%). However, further analysis of low risk group patients identified equal distribution of HY (n=24) and CD-2 (n=23) subgroups. Further analysis of molecular subgroups based on bone marrow tumor burden is listed in Table 1.Based on the international myeloma working group diagnostic criteria, most patients had multiple myeloma (MM) (n=112, 93.3%); smoldering myeloma (n=5, 4.2%) and MGUS (n=3, 2.5%) was less common. Of the MM group, two patients met the criteria for plasma cell leukemia and showed extensive bone marrow involvement. Bone marrow involvement in a cases ranged from <5% to 95% plasma cells; with most patients (72.5%) showing <60% cellularity replacement by plasma cells. Cytogenetic analysis revealed abnormal/complex karyotype in the majority of the patients (n=89, 73%) compared to normal karyotype (n=31, 26%).Conclusions:Our study indicates that CNPCs occurs more frequently in patients with low risk multiple myeloma based on UAMS GEP 70 signature classification especially CD-2 and Hyperdipoidy (HY) subtypes. This correlation is best observed in cases with <60% bone marrow tumor burden. These patients are also more likely to have abnormal/complex karyotype. Further long-term studies should be performed to determine the prognostic significance of these findings. [Display omitted] DisclosuresMorgan:Celgene: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria; Bristol Myers: Consultancy, Honoraria. Davies:Takeda: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Janssen: Consultancy, Honoraria.

Improving Outcomes for Patients with High-Risk Myeloma Via Prospective Trial Evidence: The Myeloma UK Nine Optimum Trial

Abstract INTRODUCTION Outcomes for patients with molecular high-risk (HR) multiple myeloma (MM) are poor with traditional approaches. Recent trials have demonstrated that novel combination therapies such as daratumumab/lenalidomide/dexamethasone improve outcome for HR disease at relapse, but access to these novel combination therapies remains limited in many public health care systems. Innovative clinical trials with robust and inclusive molecular testing strategies are needed to generate evidence for stratified therapy for HRMM in standard care. We reported that genetic double-hit, i.e. presence of two or more HR genetic lesions, predicts poor outcome in MM (Shah V, Leukemia 2017). Gene expression profiling (GEP) with the EMC92/SKY92 signature (SkylineDx) identifies patients with short survival (Kuiper R, Leukemia 2012). We present here updated data on an integrated genetic and GEP molecular risk stratification strategy, which will be used in the Myeloma UK (MUK) nine OPTIMUM trial to generate evidence for improved treatment of HRMM. METHODS AND RESULTS We present updated survival analyses (data cut-off July 2016) for 336 representative patients from the transplant-eligible cohort of the UK NCRI Myeloma XI trial (median follow-up 42 months). For all patients a complete dataset for adverse genetic lesions del(1p32), gain(1q21), del(17p), adverse translocations was generated using MLPA and qRT-PCR (Shah V, Leukemia 2017). All tumors were GEP risk profiled using the SKY92 MMprofiler on an Affymetrix DX2 platform. 32% of MM tumors carried at least one HR genetic lesion, and 22% carried a double-hit. Double-hit was associated with a hazard ratio of 2.1 for progression-free survival (PFS) (P The phase IIb MUKnine OPTIMUM trial investigates innovative combination therapy with Daratumumab, Cyclophosphamide, Velcade, Lenalidomide, Dexamethasone (DCVRd) induction followed by high dose melphalan + ASCT augmented by Velcade, intensified consolidation (DVR) and maintenance (DR) in patients with molecular high risk status as above. Its design follows recommendations for trials in rare cancers (Bogaerts J, Eur J Canc 2015), using a Bayesian strategy to compare outcomes with DCVRd against near-concurrent control data from the Myeloma XI trial, as reported above. The primary endpoint is PFS, with interim futility analyses of PFS and Minimal Residual Disease (MRD) negativity in OPTIMUM patients vs. Myeloma XI HR patients defined by the same molecular criteria. OPTIMUM is designed to detect an increase in PFS of 25% compared to Myeloma XI control data and, based on Bayesian modelling, up to 620 newly diagnosed patients will be molecularly screened for HR disease and up to 105 patients with HR status will be treated on the OPTIMUM trial. All other patients will be treated according to UK standard and data will be collected as for the HR group. Secondary endpoints include response, PFS2 and OS. Exploratory research accompanying the trial is planned to include longitudinal MRD dynamics and diffusion-weighted MRI imaging. CONCLUSION The UK Myeloma Research Alliance (MRA) MUKNine OPTIMUM study is one of the first trials in MM designed to provide comparative evidence for stratified treatment of patients with molecular high-risk MM. The trial has regulatory approval and is scheduled to start Q3 2017 in 22 hospitals of the Myeloma UK Clinical Trial Network. Disclosures Owen: Celgene: Consultancy, Honoraria, Research Funding; Takeda: Honoraria, Other: travel support; Janssen: Consultancy, Other: travel support. Drayson: Abingdon Health: Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Gregory: Celgene: Consultancy, Honoraria; Janssen: Honoraria. Jackson: Chugai: Honoraria; JJ Amgen: Honoraria; Takeda: Honoraria; Celgene: Honoraria. Cook: Glycomimetcs: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria; Takeda: Consultancy, Honoraria, Research Funding, Speakers Bureau; Amgen: Consultancy, Honoraria, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Research Funding, Speakers Bureau; Sanofi: Consultancy, Honoraria, Speakers Bureau. Jenner: Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel Support, Research Funding, Speakers Bureau; Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel Support , Research Funding, Speakers Bureau; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Chugai: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau. Kaiser: Janssen: Honoraria; Amgen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Takeda: Consultancy; BMS: Consultancy, Other: Travel expenses; Chugai: Consultancy.

The Impact of Sex on Clinical Outcome and Toxicity in Children and Adolescents with Acute Lymphoblastic Leukemia. a Report from the BFM Study Group

IntroductionMale sex has been described as an adverse prognostic factor in various hematologic and solid tumors in adult as well as in pediatric patients. Results from two large studies of the POG (n=3717, 1986 - 1994) and St. Jude Cancer Research Hospital (n=2055, 1962 - 1994) in acute lymphoblastic leukemia (ALL) have shown an inferior outcome for boys compared to girls. The reasons for these differences are not fully understood. The aim of this study was to analyze the impact of sex on outcome and toxicity in patients treated according to the ALL-BFM studies.MethodsEight-thousand two-hundred and fifty-six patients treated in three consecutive ALL trials (ALL-BFM 90 (n=2103), BFM-95 (n=2075) and 2000 (n=4000)/Interfant-99 (n=78)) between 1990 and 2008 were analyzed with respect to demographic, clinical and biological features for their prognostic relevance.ResultsThe male/female ratio was 1.18 in 7115 (86%) B-cell precursor (BCP)-ALL patients (median age: 4.5 vs 4.6 years) and 2.67 in 1141 (14%) T-ALL patients (median age: 9.1 vs 8.6 years). No sex-related differences among BCP-ALL were found for initial patient characteristics (age, initial leukocyte count, DNA index, specific leukemic translocations t(12;21), t(4;11), t(9;22)) as well as prednisone response and risk group allocation to clinical criteria apart from a tendency for a higher prevalence of boys in the high risk group compared to girls (98/1496 (6.6%) vs 63/1311 (4.8%)) according to molecular stratification in study ALL-BFM 2000 (P=0.08). The inferior event-free survival (EFS) at 6 years in study BFM 90 for boys with BCP-ALL compared to girls (76.7% vs 82.8%; P<0.001) markedly improved over time (BFM 95: 79.1 vs 81.7, P=0.123; BFM 2000: 82.0% vs 83.3%, P=0.392) while the EFS in females remained largely unchanged. The cumulative incidence of relapse at 5 years was higher for boys with BCP-ALL in all three studies (BFM 90 (n=331): 20.1% vs 12.4%, P≤0.001; BFM 95 (n=295): 17.6% vs 13.8%, P=0.032 and BFM 2000 (n=444): 14.3% vs 11.2%, P=0.006; respectively). Cumulative incidence of testicular relapses decreased from 1.5% to 0.8%.In T-ALL male predominance increased with age. The male/female ratio in patients between 1 and 6 years was 2.3 in contrast to 3.9 in those ≥15 years. Outcome in children with T-ALL among the three studies improved by 17.9% in boys from 61.1% to 79.0% and by 20.2% in girls from 62.4% to 82.8% without significant differences in EFS and relapse incidence between both sexes with the exception of older adolescents. EFS in this subgroup (n=91) was 68.6% for boys vs 94.7% for girls (P=0.023).Cumulative incidence of chemotherapy-related deaths was significantly higher for girls than boys with BCP-ALL in BFM 2000/Interfant-99 (3.7% vs 2.3%, P=0.015) compared to previous studies (BFM 90: 0.5% vs. 0.4%; P=0.271; BFM 95: 0.6% vs 0.4%, P=0.079). No significant differences between boys and girls were found in patients with T-ALL. Life-threatening infections documented in BFM 2000/Interfant-99 showed increased susceptibility for girls in total (7.2% vs 4.6%) and especially in induction therapy (4.4% vs 2.1%).ConclusionsRelapse rate decreased by 5.8% in boys with BCP-ALL compared to 1.2% in girls while significant improvement has been achieved in treatment of T-ALL for patients of both sexes. Together with an increase in TRM in girls, this led to similar EFS rates for girls and boys in the most recent trial ALL-BFM 2000/Interfant-99. Reasons for a higher relapse rate in boys might to a small extend be attributed to testicular relapses. Sex-specific polymorphisms for drug metabolism at least in BCP-ALL together with other yet not well defined factors may play a role in this setting. DisclosuresSchrappe:SigmaTau: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; JAZZ Pharma: Consultancy, Research Funding; Baxalta: Consultancy, Research Funding; Medac: Consultancy, Research Funding.

Comprehensive Genomic and Transcriptomic Analysis for Guiding Therapeutic Decisions in Patients with Rare Cancers.

The clinical relevance of comprehensive molecular analysis in rare cancers is not established. We analyzed the molecular profiles and clinical outcomes of 1,310 patients (rare cancers, 75.5%) enrolled in a prospective observational study by the German Cancer Consortium that applies whole-genome/exome and RNA sequencing to inform the care of adults with incurable cancers. On the basis of 472 single and six composite biomarkers, a cross-institutional molecular tumor board provided evidence-based management recommendations, including diagnostic reevaluation, genetic counseling, and experimental treatment, in 88% of cases. Recommended therapies were administered in 362 of 1,138 patients (31.8%) and resulted in significantly improved overall response and disease control rates (23.9% and 55.3%) compared with previous therapies, translating into a progression-free survival ratio >1.3 in 35.7% of patients. These data demonstrate the benefit of molecular stratification in rare cancers and represent a resource that may promote clinical trial access and drug approvals in this underserved patient population. SIGNIFICANCE: Rare cancers are difficult to treat; in particular, molecular pathogenesis-oriented medical therapies are often lacking. This study shows that whole-genome/exome and RNA sequencing enables molecularly informed treatments that lead to clinical benefit in a substantial proportion of patients with advanced rare cancers and paves the way for future clinical trials.See related commentary by Eggermont et al., p. 2677.This article is highlighted in the In This Issue feature, p. 2659.

Adjuvant Therapy for High-risk Endometrial Carcinoma

About one-fifth of endometrial cancers are ‘high risk’, which carries a poorer prognosis. Management strategies to optimise their survival have been under investigation for many years. Despite recent advances, their overall survival remains relatively poor. The definition of high risk in endometrial cancers has been based on clinicopathological factors until recently, when molecular profiling has shown greater discrimination. There is, however, poor correlation between traditional clinicopathological factors and their molecular profile. This is the subject of ongoing trials to better individualise adjuvant post-hysterectomy treatment. The management of high-risk tumours is traditionally based on surgery followed by radiotherapy, despite no proven overall survival benefit in early stages. The place of chemotherapy remains under investigation, with recent trials showing benefit in more advanced stages. The Post Operative Radiation Therapy in Endometrial Carcinoma (PORTEC) and Gynecologic Oncology Group trials support the use of chemoradiation and chemotherapy for stage III and adverse histological subgroups. In addition, there is now early evidence of correlation between benefit from adjuvant chemotherapy based on molecular alterations in the tumour cells. In this review, we look at the current evidence on management strategies in the evolving era of molecular diagnosis and stratification.

Comprehending the Proteomic Landscape of Ovarian Cancer: A Road to the Discovery of Disease Biomarkers.

Despite recent technological advancements allowing the characterization of cancers at a molecular level along with biomarkers for cancer diagnosis, the management of ovarian cancers (OC) remains challenging. Proteins assume functions encoded by the genome and the complete set of proteins, termed the proteome, reflects the health state. Comprehending the circulatory proteomic profiles for OC subtypes, therefore, has the potential to reveal biomarkers with clinical utility concerning early diagnosis or to predict response to specific therapies. Furthermore, characterization of the proteomic landscape of tumor-derived tissue, cell lines, and PDX models has led to the molecular stratification of patient groups, with implications for personalized therapy and management of drug resistance. Here, we review single and multiple marker panels that have been identified through proteomic investigations of patient sera, effusions, and other biospecimens. We discuss their clinical utility and implementation into clinical practice.

Characteristics of early-stage endometrial cancer and factors that influence disease recurrence.

e17567 Background: Early-stage endometrial cancer (EEC) with FIGO stage I-II generally has a favorable prognosis and overall survival (OS). However, up to 10% of EEC patients (pts) relapse and risk factors for recurrence remain unclear. We evaluated clinical and histopathologic characteristics of EEC and correlated them with OS and recurrence free survival (RFS) through a single-center retrospective analysis. Methods: We conducted a retrospective chart review on 511 pts with EEC identified by our cancer registry from 1/1/2009 to 12/31/2019. The two main histologic groups were endometrioid adenocarcinomas (E) and other subtypes (O) including carcinosarcoma, undifferentiated, and clear cell carcinomas. Papillary serous histology was excluded. Histopathologic and clinical findings recorded included age, FIGO stage and grade, tumor size, presence of recurrence, adjuvant therapies received, percent of myometrial invasion (MI), and lymphovascular invasion (LVI). OS and RFS were estimated, and each predictor was compared using the log-rank test. The association between OS and each continuous characteristic was examined using the Cox proportional hazards model. Factors significantly associated with OS and RFS in the univariable analysis (p &lt; 0.05) were included in a multivariable analysis to examine the joint effects of those factors on survival. Results: A total of 511 cases were reviewed. The analysis included 501 pts (E = 485, O = 16), of which 47 had recurrent disease (E = 45, O = 2) and 17 had died without recurring (E = 15, O = 2) as of their last follow-up. Overall median age was 63 years. Factors significantly associated with recurrence in the multivariable analysis were FIGO grade, (Hazard Ratios (HR): Grade 2 vs 1: 1.95, 95% CI: 1.06-3.58, p = 0.0320, Grade 3 vs 1: 2.88, 95% CI: 1.50-5.52, p = 0.0015), LVI (HR: 2.03, 95% CI: 1.10-3.75, p = 0.0244), and greater than 50% of MI (HR: 3.15, 95% CI: 1.35-7.36, p = 0.0080). The overall RFS was 92% and 86% at three and five years, respectively. On univariate analysis, among pts with a measurable tumor size (n = 446), larger tumors were not significantly associated with OS (p = 0.65) but was associated with increased recurrence (HR 1.22, 95% CI: 1.10-1.37, for a unit increase, p = 0.0003). On univariate analysis, pts who received adjuvant therapy were more likely to recur (p = 0.0002) with RFS of 86% and 76% at three and five years respectively, versus RFS of 94% and 90%, for those who did not. Conclusions: We confirmed the clinical and histopathologic characteristics that are currently considered to increase risk of recurrence in EEC. On multivariate analysis, risk of recurrence was associated with FIGO grades 2 and 3, presence of LVI, and &gt; 50% MI. A limitation of this study is the lack of molecular analysis. Further molecular stratification may help us identify the subset of pts who are at high risk of recurrence, enabling customized adjuvant therapy in EEC.

Identification of pancreatic adenocarcinoma molecular subtypes on histology slides using deep learning models.

4141 Background: Pancreatic adenocarcinoma (PAC) is predicted to be the second cause of death by cancer in 2030 and its prognosis has seen little improvement in the last decades. PAC is a very heterogeneous tumor with preeminent stroma and multiple histological aspects. Omic studies confirmed its molecular heterogeneity, possibly one of the main factors explaining the failure of most clinical trials. Two and three transcriptomic subtypes of tumor cells and stroma respectively, were described with major prognostic and predictive implications. The tumor subtypes, Basal-like and Classical, have been shown by several groups to be predictive of the response to first line chemotherapy. As of today, these subtypes can only be defined by RNA profiling which is limited by the quantity and quality of the samples (formalin fixation and low cellularity) as well as by the analytical delay that may restrict its application in routine care. In addition, tumors may harbor a mixture of several subtypes limiting their interpretation using bulk transcriptomic approaches and thereby their clinical use. Here, we propose a multistep approach using deep learning models to predict tumor components and their molecular subtypes on routine histological preparations. Methods: 728 whole-slide digitized histological slides corresponding to 350 consecutive resected PAC from four centers with clinical and transcriptomic data were assembled and used as a discovery set. PAC from TCGA (n = 134) was used as a validation set. Tumor regions from slides of the discovery set were annotated to train a multistep deep learning model that first recognizes tumor tissue and then predicts tumor and stroma cells molecular subtypes assessed by the published PurIST algorithm. Results: The tumor detection model was very efficient (AUC = 0.98 in the TCGA validation cohort). In the discovery set, the Basal-like/Classical classification performance of the model by cross validation was 0.79 (AUC) and reached 0.86 when restricted to samples with a high-confidence RNA-defined molecular subtype.Subtypes defined by the model were independently associated with overall survival in multivariate analysis (HR = 2.56 [1.87 - 3.49], pval &lt; 0.001), and association was higher relatively to PurIST RNA subtypes (HR = 1.60 [1.17 - 2.19] pval &lt; 0.001). In the validation cohort, the model had an overall AUC of 0.82, and 0.89 in the subset of “subtype-pure” tumors. In addition to demonstrating the value of histology-based deep learning models for tumor subtyping in PAC, these results also show the limit of molecular-based subtyping in highly heterogeneous samples. Conclusions: This study provides the first PAC subtyping tool usable worldwide in clinical practice, finally opening the possibility of patient molecular stratification in routine care and clinical trials.