TCGA Classification Research Articles

Is it possible to predict the postoperative stage in early-stage endometrial cancer patients based on TCGA classification of preoperative dilatation & curettage tissue? Efforts for personalized surgical approaches

Is it possible to predict the postoperative stage in early-stage endometrial cancer patients based on TCGA classification of preoperative dilatation & curettage tissue? Efforts for personalized surgical approaches

Molecular classification of endometrial cancer: preliminary experience from a single Portuguese academic center.

Since the seminal publication of the TCGA consortium in 2013, the molecular classification of endometrial cancer has been widely accepted as a new and powerful tool to better understand the natural history of this malignancy. Adoption of routine molecular classification around the world has been limited. We sought to demonstrate our initial experience in incorporating the four molecular subtypes for endometrioid carcinomas. This was a retrospective analysis at a single center in Portugal. Molecular classification was determined using immunohistochemical staining for MMR and p53 and Sanger Sequencing to determine POLE mutation status as per published PROMISE method. Descriptive statistics were reported. 20 patients with endometrioid histology were included. Median age of the cohort was 64years (range 45-76). Median Body Mass Index (kg/m2) was 29.81 (range 21.3-43.1). In terms of tumor grading, 16 (80%) of the endometrial carcinomas of the cohort were low-grade (either grade 1 or grade 2). 16 (80%) of the cases were FIGO stage I. Regarding the molecular classification the tumors were classified as: MMRd [n = 6 (30%)]; p53 abn [n = 2 (10%)]; NSMP (n = 10 (50%)), POLE ultramut [n = 2 (10%)]. Despite the small sample size, we were able to show that molecular classification is feasible. To our knowledge this is the first cohort of endometroid endometrial carcinomas fully characterized according to the TCGA classification in Portugal, from one single center.

Identifying clinical features and molecular characteristics of the endometrial clear cell carcinoma.

The aim of this study was to verify TCGA subtypes in endometrial clear cell carcinoma (ECCC) and determine their clinical and molecular characteristics. We summarized and compared the clinical features of 28 clear cell carcinoma and 112 endometrioid carcinoma patients. Of the 28 ECCCs, 19 underwent TCGA classification, and other markers (ER, PR, ARID1A, ARIB1B, TAF1, and HER-2) were also detected by IHC, and outcomes were assessed. Compared to endometrioid carcinoma, ECCC had an older age of onset (median age, 64.5 years, range 31-81 years), higher rate of myometrial invasion (42.8% vs. 21.5% in endometrioid carcinoma), LVSI (33% vs. 16%), and more advanced FIGO stage. Among the ECCCs, LVSI was a poor prognostic factor. TCGA classification was performed for 19 ECCCs: two POLEmut cases (10.5%), three MMRd (15.8%), 11 p53wt (57.9%), and three p53abn (15.8%). Of the 19 ECCCs, six (31.6%) showed HER-2 positive expression, and eight (42.1%) had TAF1 expression loss. ECCCs possessed HER-2 and TAF1 expression had worse outcomes. Our study summarized the clinical features of ECCC. The outcomes of patients with ECCC with TCGA subtypes differed from those of patients with endometrioid carcinoma. HER-2 and TAF1 may be new prognostic factors.

Abstract 223: Identifying gene amplifications in p53 abnormal endometrial carcinomas by shallow whole genome sequencing

Abstract Endometrial carcinoma (EC) is the most common gynecologic cancer in North America. A clinically molecular classifier called ProMisE (Proactive Molecular Risk Classifier for Endometrial Cancer) was developed based on the TCGA classification. p53abn EC is the most aggressive of the four ProMisE prognostic molecular subtypes, responsible for 50-70% of EC mortality. Therapeutic advances are urgently needed to improve outcomes for these patients. This research focuses on determining the significance of HER2 and CCNE1 amplifications in p53abn EC to identify therapeutic opportunities for this aggressive cancer. Tumor DNA extracted from cores of 203 formalin-fixed paraffin-embedded (FFPE) p53abn EC were Shallow Whole Genome (sWGS) sequenced. sWGS is a high-throughput technology designed to achieve genome-wide genetic variation accurately and cost-effectively. Raw data were aligned and treated to correct CG content and discard low-quality reads. Copy number alterations were called considering 5 to 9 copies as amplification and more than 9 as high-level amplification. Amplification data was later compared to HER2 and CCNE1 whole-section immunohistochemistry (IHC). Gene amplification is one of the major molecular pathways that can drive tumorigenesis, and many amplified genes have emerged as biological markers and therapeutic targets. HER2 amplification has an important prognostic and therapeutic implications in breast and gastric cancer. It is also seen in EC, arising as a possible targeted treatment opportunity for p53abn EC using anti-HER2 drugs. CCNE1 amplifications have been reported in platinum resistance aggressive ovarian and endometrial cancers and is known to be a biomarker to predict responsive to low-dose WEE1i-ATRi. Amplifications in CCNE1 were identified in 13% (26/203) of the cohort while the IHC overexpression (2/3+) was recorded in 64% of cases. HER2 amplifications were observed in 11% (22/203) of p53abn ECs compared to the IHC overexpression (2/3+) detected in 21%. Significant intratumor heterogeneity was identified. We found discrepancy between the techniques, with IHC detecting a significantly greater proportion of p53abn ECs overexpressing HER2 and CCNE1 than amplification found on sWGS. This phenomenon may be explained by the intratumor heterogeneity that was identified during the IHC scoring. The IHC was performed in whole sections while cores were used to extract DNA for the sWGS, which may have missed the gene amplification areas. Although there are some limitations, sWGS is a relatively inexpensive assay that can be performed on FFPE, and it is able to obtain whole genome sequence at a very low coverage (between 0.4x and 1x) with over 99% accuracy for copy number calls. In recent years sWGS have been used efficiently for copy number profiling tumors and for amplification detection thus having the potential to be implemented in clinical practice to guide targeted therapy. Citation Format: Juliana Sobral de Barros, Amy Jamieson, Dawn Cochrane, Maxwell Douglas, Janine Senz, Blake Gilks, Christine Chow, Shelby Thornton, Jessica N. McAlpine, David G. Huntsman. Identifying gene amplifications in p53 abnormal endometrial carcinomas by shallow whole genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 223.

Immunohistochemistry-based molecular classification of gastric cancer in India: How are we different?

462 Background: TCGA and ACRG have classified gastric cancer (GC) into molecular subgroups using genomics. We attempted to classify GC from our region using IHC (Immunohistochemistry) to understand its prognostic significance and compare with similar data from other parts of the world. Methods: This was a retrospective cohort of GC patients from years 2017-18. EBV (LMP), MSI (MLH1, MSH2, PMS2, MSH6),p53, E-cadherin and PIK3CA were assessed by IHC. Clinicopathological characteristics and survival were evaluated for association with molecular subtypes as defined by TCGA and ACRG classification system. Results: A total of 191patients were included with EBV positivity 35 (18.3 %), MSI 33(17.3 %), p-53 aberration 25(13.1%), E-cadherin negative (29.3%). On univariate analysis, p53 aberration was associated with higher age (>60 yrs), E- cadherin negative with diffuse histology & antro-pyloric region as predominant site. MSI with intestinal histology & antro-pyloric region as predominant site with MSI. The TCGA classification revealed EBV 35 (18%), MSI 28 (15 % ), GS 48 (25 %) and CIN 80 (42% ) subtypes respectively. CIN subtype was seen predominantly above 40 yrs of age (P=0.04), GS subtype was frequently associated with diffuse histology P<0.0001. The ACRG classification revealed MSI 33(17%), MSS/EMT 51 (26.7%), MSS/ p53 normal 91 (47.6%) and MSS/p53 aberrant 16 (8.4) subtypes. MSS/E-cad- subtype was associated with diffuse histology. PIK3CA positivity was higher in CIN (TCGA )& MSI (dmr) (ACRG) respectively. The median OS in MSI was 35 and 32 months higher compared to other subtypes (P<0.0001) in TCGA and ACRG classification respectively. Conclusions: The TCGA and ACRG classification identified molecular subtypes based on IHC from our region and significantly correlated with clinical factors and survival. PIK3CA as an additional marker may be further explored to be included in the classification system. Abbreviation: EBV - Epstein–Barr-virus, MSI – Microsatellite-Instability, GS- Genomic-instability, CIN- Chromosomal-instability, MSS- Microsatellite-stable, EMT-Epithelial-mesenchymal-transition.[Table: see text]

Genomically Stable Gastric Cancer Characterized by Hypomethylation in Wnt Signal Cascade

Introduction: Gastric cancer is divided into four subtypes by their molecular features linked with genetic alterations, e.g., Epstein-Barr virus (EBV), microsatellite instability-high (MSI-high), chromosomal instability (CIN), and genomically stable (GS), called as TCGA classification. In this study, we tried to clarify the epigenetic features of the four GC subtypes according to aberrant methylation status in 23 loci. Methods: A total of 98 gastric cancers and their normal gastric mucosa samples were included in this study. We divided gastric cancers into TCGA subtypes which were determined in line with MSI-high, EBV, CIN, to GS by their molecular features. The 13 loci of polymorphic microsatellite sequences were used to determine loss of heterogeneity for the detection of CIN. The MSI status was determined by three mononucleotide repeat markers. Infection of EBV was determined by recovering EBV BNRF1 sequence from genomic DNA collected from gastric cancers. Methylation status of 23 loci was investigated by the combined bisulfite restriction analysis. Status of other findings, e.g., KRAS mutations, HER2 expression status, and infection of helicobacter pylori were confirmed. Results: Gastric cancers were divided into MSI (13%), EBV (7%), CIN (53%), and GS (27%). By histological classification, poorly differentiated adenocarcinoma was more in tumors categorized in MSI-high, and GS and signet-ring cell carcinoma (sig) were more in GS. Among the 23 loci investigated their methylation status, 18 loci were significantly hypermethylated in caner tissues. An unsupervised clustering divided gastric cancers into two clusters and revealed that most GS tumors clustered together in a cluster that exhibited lower methylation levels, distinct from the other subtypes. The inter-variable clustering revealed that a cluster contained the three loci (SFRP2-region 1/2 and APC) belonging to the Wnt signal cascade (Wnt-associated loci). The mean methylation score of Wnt-associated loci was the lowest in GS tumors (MSI-high: 2.7 [95% confidence interval, 2.3–2.9]; EBV: 2.1 [1.2–3.1]; CIN: 2.4 [2.2–2.7]; GS: 1.3 [0.8–0.7]). In contrast, the mean methylation score of the other 15 loci was significantly higher in MSI-high, while that in GS was as same as that in EBV or CIN (MSI-high: 10.4 [8.3–12.4]; EBV: 5.7 [1.7–9.7]; CIN: 4.4 [3.6–5.1]; GS: 3.4 [2.2–4.6]). Additionally, the lower methylation score of Wnt-associated loci was observed only in sig tumors. Conclusions: GS subtype tumors have the potential to possess distinct signatures in DNA hypomethylation profiles in Wnt signaling pathway, especially in sig.

Development of a streamlined NGS-based TCGA classification scheme for gastric cancer and its implications for personalized therapy

Development of a streamlined NGS-based TCGA classification scheme for gastric cancer and its implications for personalized therapy

Integration of Molecular Data in the Prognostic Stratification and Management of Endometrial Carcinoma

In the last years, the TCGA-based molecular classifier have been progressively integrated in the management of endometrial carcinoma. While molecular assays are increasingly available across pathology laboratories, the additional costs will expectedly be compensated by a reduction in overtreatments and a prevention of recurrences. The additional time might be shortened by assessing molecular markers on biopsy specimens. Retrospective data suggest that the molecular classifier will have a major impact of on the risk stratification, with many patients having their risk class down- or upstaged based on POLE mutations or p53 abnormalities, respectively. However, there are still several issues to be resolved, such as the prognostic value of the TCGA classifier in each FIGO stage, or the type of adjuvant treatment most suitable for each molecular group. Other issues regard the prognostic stratification of the mismatch repair-deficient and "no specific molecular profile" groups, which currently follows the same criteria; however, the former seems to be prognostically consistent regardless of FIGO grade and histotype, whereas the latter appears highly heterogeneous. Numerous clinical, histological, immunohistochemical and molecular markers have been proposed to refine the TCGA classification, but their prognostic value is still undefined. Hopefully, prospective data collected in the next years will help resolving these issues.

Investigation on the regulatory T cells signature and relevant Foxp3/STAT3 axis in esophageal cancer.

Regulatory T cells (Tregs) have an important role in accelerating the immunosuppression of tumor. Tregs regulation is a hopeful strategy to improve the dismal prognosis of Esophageal cancer (EC), while its mechanisms have not yet been fully clarified. To characterize the role of Tregs in EC, we comprehensively explored its prognostic value, clinical pathology partnership, related biological functions and potential mechanisms at transcriptome level. Through the integrated analysis of GEO and TCGA datasets, we comprehensively evaluated the Tregs infiltration patterns in EC patients. The correlation between Tregs infiltration and genomic characteristics, as well as biological functions were analyzed by a variety of computational algorithms. We observed that Tregs were significantly upregulated in EC and involved in various immune processes. According to TCGA and GEO transcriptional classification schemes, Tregs specific genes were observed to be highly expressed in tumor samples, as well as were closely associated with poor prognosis and worse clinical outcomes. In addition, EC patients can be stratified into high-risk and low-risk immune subgroups according to Tregs/macrophages infiltration level, and the results showed significant differences in tumor development, biological processes and probe gene expression pattern. The multi-variate analysis revealed that the interaction between STAT3 and Foxp3 was a potential prognostic signature of Tregs in EC, especially the modulation effect of STAT3 on Foxp3 expression, which has not been well studied in EC. We also identified that STAT3 and Foxp3 expression presented a high accuracy in predicting Tregs infiltration level in EC patients (AUC: 0.817; 95% CI: 0.756-0.878). Our results revealed that Tregs have the potential to predict prognosis and tumor deterioration in EC patients. A comprehensive landscape of Tregs regulation mechanisms will help us interpret the immunosuppression of tumor microenvironment (TME) and novel strategies for EC immunotherapy.

TCGA Molecular Prognostic Groups of Endometrial Carcinoma: Current Knowledge and Future Perspectives.

The four TCGA-based molecular prognostic groups of endometrial carcinoma (EC), i.e., POLE-mutant, mismatch repair (MMR)-deficient, p53-abnormal, and “no specific molecular profile” (NSMP), have recently been integrated into ESGO-ESTRO-ESP guidelines. The POLE-mutant and MMR-deficient groups are associated with high mutational load, morphological heterogeneity, and inflammatory infiltration. These groups are frequent in high-grade endometrioid, undifferentiated/dedifferentiated, and mixed histotypes. POLE-mutant ECs show good prognosis and do not require adjuvant treatment, although the management of cases at stage >II is still undefined. MMR-deficient ECs show intermediate prognosis and are currently substratified based on clinicopathological variables, some of which might not have prognostic value. These groups may benefit from immunotherapy. P53-mutant ECs are typically high-grade and often morphologically ambiguous, accounting for virtually all serous ECs, most carcinosarcomas and mixed ECs, and half of clear-cell ECs. They show poor prognosis and are treated with chemoradiotherapy; a subset may benefit from HER2 inhibitors or PARP inhibitors. The NSMP group is the most frequent TCGA group; its prognosis is highly variable and affected by clinicopathological/molecular factors, most of which are still under evaluation. In conclusion, the TCGA classification has improved diagnosis, risk stratification, and management of EC. Further studies are needed to resolve the points of uncertainty that still exist.

Prognosis of isolated tumor cells and the utility of molecular classification in early stage endometrioid endometrial cancer (243)

<b>Objectives:</b> To assess the prognosis of isolated tumor cells (ITCs) within sentinel lymph nodes (SLN) compared with node-negative (NN) disease in early-stage endometrioid endometrial cancer and to perform additional evaluation by molecular classification. <b>Methods:</b> Patients (pts) who underwent primary surgical management of uterine cancer from 2007-2019 with a final diagnosis of Stage IA, IB, and II endometrioid endometrial cancer were identified. All SLN underwent ultrastaging per institutional protocol. Cytokeratin-positive cells, ITCs with micrometastasis, and ITCs with macrometastasis were excluded. Clinical-pathologic variables were reviewed. Tumors were classified as POLE, MSI-H, CN-high, or CN-low, based on the TCGA, by utilizing MSK-IMPACT next-generation sequencing (NGS) results and tumor IHC staining. Appropriate statistical analyses were performed. <b>Results:</b> We identified 1381 pts who met the inclusion criteria: 1256 NN (91%) and 125 ITCs (9%). Adjuvant treatment was given to 85% of pts with ITCs compared to 40% of NN pts (p<0.01). Compared to NN patients, the presence of ITCs had a greater association with myoinvasion ≥50% (41% vs 13%, p<0.01), lymphovascular space invasion (77% vs 23%, p<0.01), and chemotherapy +/- radiation (62% vs 7%, p<0.01). The Median follow-up time was 36.5 months (0.4-167 months). There was no significant difference in survival when comparing node status (3-yr PFS: 94% ITC vs 90% NN, p=0.09; 3-yr OS: 98% ITC vs 96% NN, p=0.6). Progression-free survival of ITC-positive pts was not significantly different among those receiving no treatment, chemotherapy +/- radiation, or radiation (p=0.3; Figure 1). TCGA classification was available for 34 ITC and 300 NN pts. Distribution by molecular classification for ITC pts was 3% POLE, 35% MSI-H, 9% CN-high and 53% CN-low; for NN pts, 16% POLE, 36% MSI-H, 4% CN-high, and 43% CN-low (p=0.2). Molecular-based survival outcomes were performed for pts who underwent MSK-IMPACT prior to documented recurrence. There was a significant difference in survival when stratifying the entire cohort by molecular classification, with CN-high having worse outcomes (3-yr PFS: 73% vs 90-95%, p=0.046; 3-yr OS: 78% vs 94-100%, p=0.02). Nine NN patients and two ITC patients were classified as CN-high. Statistics were not applied due to limited numbers. <b>Conclusions:</b> ITCs are associated with less favorable pathologic features than NN disease but are not statistically significantly associated with survival outcomes. Molecular classification type does not have a significant association with the presence of ITCs, but CN-high remains a poor prognostic indicator that may be of clinical value. The role of postoperative therapy in the presence of ITCs or CN-high requires further investigation.

The Roles of TP53 and FGFR2 in Progress Made Treating Endometrial Cancer.

The morbidity and mortality caused by endometrial cancer (EC) is still rising worldwide. In recent years, a new system of tumor stratification has been proposed based on POLE-mutational status, TP53, and microsatellite stability status. The aim of the study was to analyze a vast panel on the genes potentially involved in the genesis of endometrial cancer in the Polish population. One hundred and three white female patients with confirmed endometrial cancer were enrolled on the study. We performed sequencing using the Hot Spot Illumina panel and microsatellite stability with immunohistochemistry. We confirmed a key role of the TP53 mutation in progress to high-grade EC and parallelly some role of FGFR2 mutation. Moreover, our data present a vast landscape of mutations in EC and their polymorphism. We reported the meaning of FGFR2 mutation and TP53 (high copy number) in high-grade ECs. Our observation in MSI contribution is comparable with other studies. Finally, we see a strong need for the implementation of the TCGA classification.

Diverse \u2018just-right\u2019 levels of chromosomal instability and their clinical implications in neoadjuvant treated gastric cancer

BackgroundThe Cancer Genome Atlas (TCGA) consortium described EBV positivity(+), high microsatellite instability (MSI-H), genomic stability (GS) and chromosomal instability (CIN) as molecular subtypes in gastric carcinomas (GC). We investigated the predictive and prognostic value of these subtypes with emphasis on CIN in the context of neoadjuvant chemotherapy (CTx) in GC.MethodsTCGA subgroups were determined for 612 resected adenocarcinomas of the stomach and gastro-oesophageal junction (291 without, 321 with CTx) and 143 biopsies before CTx.EBV and MSI-H were analysed by standard assays. CIN was detected by multiplex PCRs analysing 22 microsatellite markers. Besides the TCGA classification, CIN was divided into four CIN-subgroups: low, moderate, substantial, high. Mutation profiling was performed for 52 tumours by next-generation sequencing.ResultsEBV(+) (HR, 0.48; 95% CI, 0.23–1.02), MSI-H (HR, 0.56; 95% CI, 0.35–0.89) and GS (HR, 0.72; 95% CI, 0.45–1.13) were associated with increased survival compared to CIN in the resected tumours. Considering the extended CIN-classification, CIN-substantial was a negative prognostic factor in uni- and multivariable analysis in resected tumours with CTx (each p < 0.05). In biopsies before CTx, CIN-high predicted tumour regression (p = 0.026), but was not prognostically relevant.ConclusionA refined CIN classification reveals tumours with different biological characteristics and potential clinical implications.

804P Molecular typing and TMB correlation analysis of endometrial cancer based on targeted NGS

The TCGA classification has a definite guiding and suggestive effect on the treatment and prognosis of endometrial carcinoma. However, TCGA typing is based on the results of multi-omics studies such as gene mutation, gene expression and gene methylation, which is expensive and not suitable for clinical widespread application.

A co-formulation of interferons type I and II enhances temozolomide response in glioblastoma with unmethylated MGMT promoter status.

Temozolomide (TMZ) is a chemotherapeutic used for the treatment of glioblastoma. The MGMT repair enzyme (O'-(6)-methyl guanine-DNA-methyltransferase) promoter methylation is a predictive biomarker to TMZ response; interferons (IFNs) type I can downregulate MGMT expression improving survival in patients with unmethylated MGMT promoter. HeberFERON is a co-formulation of IFNs type I and II with higher antiproliferative effect over glioblastoma cell lines than individual IFNs. We investigated the proliferative response of patient-derived glioblastoma cultures to HeberFERON and its combination with TMZ in relation to MGMT promoter methylation and the regulation of MGMT transcript after HeberFERON treatment. Eleven glioblastoma-derived cultures, molecularly classified according to TCGA and MGMT promoter methylation, were assayed for proliferation inhibition with HeberFERON at low doses (1-25 IU/mL) [alone or combined with TMZ] or at higher doses (50-200 IU/mL) using CellTiter-Glo Luminescent Cell Viability Assay (Promega). Eight cultures were further treated with 100 IU/mL of HeberFERON for 72 h, total RNA purified (Qiagen) and converted to cDNA (Superscript III kit, Invitrogen) as quantitative PCR templates. Changes of MGMT&P53 transcripts level were monitored. Response of cultures to HeberFERON is variable, dose-dependent and apparently independent from TCGA classification and MGMT methylation status, based on the eight Classical cultures data. When combining HeberFERON with TMZ there was an increase in cell death for cultures, 2/4 with methylated and 5/5 with unmethylated MGMT promoter. In two out five cultures with unmethylated MGMT status, we observed a decrease of MGMT gene levels and an increase in P53 encoding gene levels. HeberFERON and TMZ combination should be further assayed in glioblastoma, mainly for those with unmethylated MGMT promoter.

Clinical characteristics and prognostic significance of TCGA and ACRG classification in gastric cancer among the Chinese population.

Molecular classifications of gastric cancer (GC) by the Asian Cancer Research Group (ACRG) and The Cancer Genome Atlas Consortium (TCGA) are useful for diagnosis and treatment of GC. However, their clinical significance is unknown. The present study aims to explore the associations between subtypes of GC and prognosis of patients with GC. Immunohistochemistry (IHC) was used in the ACRG molecular classification of GC, while next-generation sequencing technology was used in TCGA molecular classification. The results indicated that, out of a total of 65 cases of GC, some were classified as Epstein-Barr virus positive type (9.2%, 6 of 65), some as microsatellite instability (MSI) type (23.1%, 15 of 65), some as gene stable type (21.5%, 14 of 65) and some as chromosome instability type (46.2%, 30 of 65) according to TCGA typing standard. Of the total 65 GC cases, some were classified as MSI (21.5%, 14 of 65), some as microsatellite stable/epithelial-mesenchymal transition (MSS/EMT; 20.0%, 13 of 65), some as MSS/tumor protein 53 active (TP53+; 15.4%, 10 of 65) and some as MSS/TP53 inactive (43.1%, 28 of 65) according to ACRG typing standard. ARCG molecular subtype (P=0.010) and Lauren classification (P=0.011) were independently correlated with the overall survival of patients with GC. In conclusion, TCGA classification based on a Chinese population is the same as TCGA typing based on a European population in terms of proportion and clinical characteristics, but there are differences in gene amplification and gene mutation. ACRG molecular classification could be performed by IHC analysis and may be a valuable independent prognostic marker for patients with GC.

Identification and validation of poor prognosis immunoevasive subtype of muscle-invasive bladder cancer with tumor-infiltrating podoplanin+ cell abundance

ABSTRACT The choice of chemo- or immuno-therapy for muscle-invasive bladder cancer (MIBC) patients remains contentious. Podoplanin is newly identified as an immune checkpoint which intrigues us to explore the clinical significance and immunoregulatory role of tumor-infiltrating podoplanin+ cells (PDPN+ cells) in MIBC. A retrospective analysis of 259 MIBC patients from Zhongshan Hospital (n = 141) and Shanghai Cancer Center (n = 118) was conducted. A total of 406 MIBC patients from TCGA database were enrolled to investigate the relationship between PDPN and molecular characterization. We found that tumor-infiltrating PDPN+ cell abundance indicated an inferior overall survival and recurrence-free survival. pT2 MIBC patients with PDPN+ cell low infiltration could benefit more from adjuvant chemotherapy (ACT). Increased PDPN+ cell infiltration was associated with diminished GZMB and TNF-α expression while correlated with expanded PD-1, PD-L1, LAG-3 and TIM-3 expression and tumor-promoting regulatory T cell and M2 macrophage infiltration. Tumors with high PDPN mRNA expression mainly presented luminal-infiltrated and basal-squamous subtypes (2017 TCGA classification) or stroma-rich and Ba/Sq subtypes (consensus classification). Elevated PDPN mRNA expression was associated with less FGFR3 activation signature and more T-cell-inflamed signature and EGFR activation signature. In conclusion, tumor-infiltrating PDPN+ cells could be applied as an independent prognosticator for clinical outcome and a predictive biomarker for suboptimal ACT responsiveness, which was also associated with immunosuppressive contexture infiltration. Intratumoral PDPN expression had a correlation with MIBC molecular classification and therapy-related signatures. The novel immune checkpoint PDPN should be considered as a possible immunotherapeutic target for MIBC.

TCGA Molecular Subgroups in Endometrial Undifferentiated/Dedifferentiated Carcinoma.

We aimed to classify undifferentiated/dedifferentiated carcinoma (UDC/DDC) according to the four TCGA molecular subgroups of endometrial cancer: microsatellite-instable/hypermutated (MSI), POLE-mutant/ultramutated (POLE), copy-number-low/p53-wild-type (p53wt), and copy-number-high/p53-abnormal (p53abn), through a systematic review and meta-analysis. Electronic databases were searched from January 2013 to July 2019 for studies assessing the TCGA classification in endometrial UDC/DDC series. Pooled prevalence of each TCGA subgroup on the total UDC/DDCs was calculated. Three studies with 73 patients were included. Pooled prevalence of the TCGA subgroups were: 12.4% for the POLE subgroup, 44% for the MSI subgroup, 18.6% for the p53abn subgroup, 25% for the p53wt group. All TCGA groups are represented in UDC/DDC, with a predominance of the MSI group, indicating a biological heterogeneity. Hypermutated/ultramutated cancers constitute the majority of UDC/DDC, suggesting a crucial difference with other high-risk histologies of endometrial carcinoma.

EGFR amplification and classical subtype are associated with a poor response to bevacizumab in recurrent glioblastoma.

The highly vascular malignant brain tumor glioblastoma (GBM) appears to be an ideal target for anti-angiogenic therapy; however, clinical trials to date suggest the VEGF antibody bevacizumab affects only progression-free survival. Here we analyze a group of patients with GBM who received bevacizumab treatment at recurrence and are stratified according to tumor molecular and genomic profile (TCGA classification), with the goal of identifying molecular predictors of the response to bevacizumab. We performed a retrospective review of patients with a diagnosis of glioblastoma who were treated with bevacizumab in the recurrent setting at our hospital, from 2006 to 2014. Treatment was discontinued by the treating neuro-oncologists, based on clinical and radiographic criteria. Pre- and post-treatment imaging and genomic subtype were available on 80 patients. We analyzed time on bevacizumab and time to progression. EGFR gene amplification was determined by FISH. Patients with classical tumors had a significantly shorter time on bevacizumab than mesenchymal, and proneural patients (2.7 vs. 5.1 vs. 6.4 and 6.0 months respectively, p = 0.011). Classical subtype and EGFR gene amplification were significantly associated with a shorter time to progression both in univariate (p < 0.001 and p = 0.007, respectively) and multivariate analysis (both p = 0.010). EGFR gene amplification and classical subtype by TCGA analysis are associated with significantly shorter time to progression for patients with recurrent GBM when treated with bevacizumab. These findings can have a significant impact on decision-making and should be further validated prospectively.

ADAMTSL4, a Secreted Glycoprotein, Is a Novel Immune-Related Biomarker for Primary Glioblastoma Multiforme.

Background Researches on immunotherapy of glioblastoma multiforme (GBM, WHO grade IV) have increased exponentially in recent years. As a targeted therapy, a series of biomarkers have been identified in local tumor tissue, while circulating marker which could be detected in the body fluids is still lacking. ADAMTSL4, a secreted glycoprotein, was earlier found to play a critical role in a prognostic signature for primary GBM (pGBM). We aimed to investigate the role of ADAMTSL4 at transcriptome level and its relationship with clinical practice in pGBM. Methods A cohort of 88 pGBM patients with RNA-seq data from the Chinese Glioma Genome Atlas (CGGA) was analyzed, and 168 pGBM patients from TCGA were included as validation. Several bioinformatic methods and predictive tools were applied to investigate the ADAMTSL4-associated immune microenvironment status. Results We found that ADAMTSL4 was enriched in GBM (WHO grade IV), especially for those with IDH1/2 wild-type and MGMT unmethylated groups. According to the TCGA classification scheme, ADAMTSL4 can act as a potential marker for subtypes with poorer prognosis. Bioinformatic analyses revealed that ADAMTSL4 was significantly correlated to the immune-related processes in GBM (WHO grade IV), especially representing the infiltration of immune cells and complicated tumor microenvironment. Clinically, high expression of ADAMTSL4 was an independent indicator for poor prognosis. Conclusion The expression of ADAMTSL4 is closely related to the clinicopathologic characteristics of pGBM. Meanwhile, it may play a critical role in immune-related processes. As a secreted glycoprotein, ADAMTSL4 is a promising circulating biomarker for pGBM, deserving further investigations.