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Additional file 6. Fig. S1. Kaplan-Meier plots of poor prognostic biomarkers. Fig. S2. Characteristics of the HRD-high cluster. Fig. S3. Characteristics of HRD-high tumors co-occurring with TP53 mutation. Fig. S4. Kaplan-Meier plots of expression-based prognosis markers. Fig. S5. Proliferative cluster enriched in poor prognostic markers. Fig. S6. Integrative analysis identified distinct prognostic clusters. Fig. S7. Molecular characteristics of integrative clusters. Fig. S8. Subtype switching driven by changes in PAM50 score composition. Fig. S9. Increased tumor growth and proliferation at PD. Fig. S10. IHC analysis of cell cycle markers. Fig. S11. Landscape of PD-specific genomic alterations. Fig. S12. RB1 LOF associated with increased APOBEC signature at PD. Fig. S13. APOBEC signature enriched in PD-specific tumor subclones.

Mercedes L Dalurzo,1,* Alejandro Avilés-Salas,2,* Fernando Augusto Soares,3,* Yingyong Hou,4,* Yuan Li,5,* Anna Stroganova,6,* Büge Öz,7,* Arif Abdillah,8,* Hui Wan,8,* Yoon-La Choi9,* 1Department of Pathology, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina; 2Department of Pathology, Instituto Nacional de Cancerología, Mexico City, Mexico; 3Department of Pathology, A.C. Camargo Cancer Center, São Paulo, Brazil; 4Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China; 5Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, People’s Republic of China; 6N.N. Blokhin National Medical Research Centre of Oncology, Russian Academy of Medical Sciences, Moscow, Russia; 7Cerrahpaşa School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey; 8Takeda Pharmaceuticals International AG – Singapore Branch, Singapore, Singapore; 9Department of Pathology and Translational Genomics, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, South Korea*These authors contributed equally to this workCorrespondence: Yoon-La ChoiDepartment of Pathology and Translational Genomics, Samsung Medical Centre, Sungkyunkwan University School of Medicine, 81, Irwon-ro, Gangnam-gu, Seoul, 06351, South KoreaTel +82 2 3410 2797Fax +82 2 3410 6396Email ylachoi@skku.eduAbstract: The treatment of patients with advanced non-small-cell lung cancer (NSCLC) in recent years has been increasingly guided by biomarker testing. Testing has centered on driver genetic alterations involving the epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) rearrangements. The presence of these mutations is predictive of response to targeted therapies such as EGFR tyrosine kinase inhibitors (TKIs) and ALK TKIs. However, there are substantial challenges for the implementation of biomarker testing, particularly in emerging countries. Understanding the barriers to testing in NSCLC will be key to improving molecular testing rates worldwide and patient outcomes as a result. In this article, we review EGFR mutations and ALK rearrangements as predictive biomarkers for NSCLC, discuss a selection of appropriate tests and review the literature with respect to the global uptake of EGFR and ALK testing. To help improve testing rates and unify procedures, we review our experiences with biomarker testing in China, South Korea, Russia, Turkey, Brazil, Argentina and Mexico, and propose a set of recommendations that pathologists from emerging countries can apply to assist with the diagnosis of NSCLC.Keywords: non-small-cell lung cancer, EGFR testing, ALK testing, immunohistochemistry, FISH, next-generation sequencing

The treatment of patients with advanced non-small-cell lung cancer (NSCLC) in recent years has been increasingly guided by biomarker testing. Testing has centered on driver genetic alterations involving the epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) rearrangements. The presence of these mutations is predictive of response to targeted therapies such as EGFR tyrosine kinase inhibitors (TKIs) and ALK TKIs. However, there are substantial challenges for the implementation of biomarker testing, particularly in emerging countries. Understanding the barriers to testing in NSCLC will be key to improving molecular testing rates worldwide and patient outcomes as a result. In this article, we review EGFR mutations and ALK rearrangements as predictive biomarkers for NSCLC, discuss a selection of appropriate tests and review the literature with respect to the global uptake of EGFR and ALK testing. To help improve testing rates and unify procedures, we review our experiences with biomarker testing in China, South Korea, Russia, Turkey, Brazil, Argentina and Mexico, and propose a set of recommendations that pathologists from emerging countries can apply to assist with the diagnosis of NSCLC. Takeda Pharmaceuticals International AG -Singapore BranchTakeda Pharmaceutical Company Ltd Medical writing support and editorial assistance were pro-vided by Brad Dalton, MSc, on behalf of Synergy Vision Ltd, London, according to Good Publication Practice guidelines, and were funded by Takeda Pharmaceuticals International AG -Singapore Branch.

Additional file 3: Table S3. Clinical characteristics between XALD and successful PDX engraftment.

Additional file 1: Table S1. The clinical chracteristics of LUSC patients.

Additional file 6: Figure S1. Rate of successful engraftment along the LUSC PDX passages.

Additional file 4: Table S4. The freqency of somatic mutations in LUSC patients and PDX models.

Additional file 5: Table S5. Somatic mutations and Differently expression genes (DEGs) in LUSC patients and PDX models.

SAdditional file 2: Table S2. Primary antibodies used in the study.

Background: Although epidermal growth factor receptor (EGFR), v-Ki-ras2 Kirsten rat sarcoma viral oncogene (KRAS), and anaplastic lymphoma kinase (ALK) mutations in non-small cell lung cancer (NSCLC) were thought to be mutually exclusive, some tumors harbor concomitant mutations. Discovering a driver mutation on the basis of morphologic features and therapeutic responses with mutation analysis can be used to understand pathogenesis and predict resistance in targeted therapy. Methods: In 6,637 patients with NSCLC, 12 patients who had concomitant mutations were selected and clinicopathologic features were reviewed. Clinical characteristics included sex, age, smoking history, previous treatment, and targeted therapy with response and disease-free survival. Histologic features included dominant patterns, nuclear and cytoplasmic features. Results: All patients were diagnosed with adenocarcinoma and had an EGFR mutation. Six patients had concomitant KRAS mutations and the other six had KRAS mutations. Five of six EGFR-KRAS mutation patients showed papillary and acinar histologic patterns with hobnail cells. Three of six received EGFR tyrosine kinase inhibitor (TKI) and showed partial response for 7–29 months. All six EGFR-ALK mutation patients showed solid or cribriform patterns and three had signet ring cells. Five of six EGFR-ALK mutation patients received EGFR TKI and/or ALK inhibitor and four showed partial response or stable disease, except for one patient who had acquired an EGFR mutation. Conclusions: EGFR and ALK mutations play an important role as driver mutations in double mutated NSCLC, and morphologic analysis can be used to predict treatment response.

Anaplastic lymphoma kinase (ALK) fusion is a common mechanism underlying pathogenesis of non-small cell lung carcinoma (NSCLC) where these rearrangements represent important diagnostic and therapeutic targets. In this study, we found a new ALK fusion gene, SEC31A-ALK, in lung carcinoma from a 53-year-old Korean man. The conjoined region in the fusion transcript was generated by the fusion of SEC31A exon 21 and ALK exon 20 by genomic rearrangement, which contributed to generation of an intact, in-frame open reading frame. SEC31A-ALK encodes a predicted fusion protein of 1438 amino acids comprising the WD40 domain of SEC31A at the N-terminus and ALK kinase domain at the C-terminus. FISH studies suggested that SEC31A-ALK was generated by an unbalanced genomic rearrangement associated with loss of the 3'end of SEC31A. This is the first report of SEC31A-ALK fusion transcript in clinical NSCLC, which could be a novel diagnostic and therapeutic target for patients with NSCLC. ispartof: Cancer Research and Treatment vol:48 issue:1 pages:398-402 ispartof: location:Korea (South) status: published

This study sought to identify factors related to the prognosis of intra-abdominal liposarcoma and to determine the optimal minimum duration for remnant tumor screening. Intra-abdominal liposarcoma is associated with high rates of incomplete resection and recurrence requiring a sophisticated follow-up strategy. Patients who underwent surgery for intra-abdominal liposarcoma were included. Cox analyses were used to analyze factors related to recurrence and survival. To determine the optimal minimum duration for remnant tumor screening, patients with recurrence after surgery despite gross complete resection were grouped by a postoperative detection time of 1, 3, or 6 months. Their survivals were compared to the gross incomplete resection group. A total of 168 patients were included. Kaplan–Meier 5-year disease-free survival was 35.9% and overall survival was 66.5%. Multiplicity (HR=2.528, CI=1.585–4.033, P

The amplification of MDM2 and CDK4 is the main molecular feature of well-differentiated liposarcomas (WDLS) and dedifferentiated liposarcomas (DDLS). Although the diagnostic usefulness of this molecular characteristic in liposarcomas has been investigated, its prognostic utility of quantitative gene level has not been explored. The aim of this study was to assess the prognostic significance of level of CDK4 amplification in MDM2-amplified WDLS/DDLS. MDM2 amplification in liposarcomas was confirmed by fluorescence in situ hybridization. The copy number of MDM2 and CDK4 was further determined by quantitative PCR (qPCR) and multiplex ligation-dependent probe amplification. Among 56 MDM2-amplified liposarcomas, 30 cases were assigned as WDLS, and 26 as DDLS. When liposarcomas were classified by qPCR-determined CDK4 amplification levels, the high-CDK4 group showed significantly poorer progression free survival (P=0.001) and disease specific survival (P=0.033) than the low-CDK4 group. However, MDM2 amplification level did not show prognostic significance. In WDLS/DDLS, the level of CDK4 amplification was useful for prognosis prediction and precise stratification of patients for targeted therapy.

The aim of this study was to evaluate the prevalence and prognostic role of increased gene copy number and protein expression of MET and EGFR in non-small cell lung cancer (NSCLC) patients. Samples were collected from 380 patients with surgically resected NSCLC, and fluorescence in situ hybridisation (FISH) and immunohistochemistry (IHC) were performed. EGFR amplification and high polysomy (EGFR FISH-positive) were observed in 9.7% and 17.4% of the patients, respectively. EGFR was overexpressed (EGFR IHC-positive) in 19.2% of the patients. Neither EGFR FISH-positive nor EGFR IHC-positive status affected survival after resection. Increased MET copy number (MET FISH-positive by University of Colorado Cancer Center criteria) was observed in 11.1% of the patients (high polysomy, 8.7%; gene amplification, 2.4%). According to the Cappuzzo system, 7.1% of the patients were MET FISH-positive. MET FISH positivity was a negative prognostic factor, especially in patients with adenocarcinoma histology (p=0.040), female gender (p=0.010), old age (p=0.084), and EGFR FISH negativity (p=0.020) at the univariate level but not at the multivariate level. MET was overexpressed (MET IHC-positive) in 13.7% of the patients and associated with shorter overall and disease-free survival (p=0.010 and p=0.056, respectively). Multivariate analysis revealed that MET IHC-positive patients had a significantly increased risk of death (hazard ratio, 1.618; 95% confidence interval, 1.066-2.456; p=0.024). Increased MET copy number and MET overexpression are negative prognostic factors for surgically resected NSCLCs

The prognostic significance of IDH1 mutations has been demonstrated in gliomas. It is unclear whether IDH1 mutation is also a prognostic factor in gliomatosis cerebri (GC). Primary GCs can be grouped into type 1 GCs, which have the classical diffuse growth pattern without mass formation, and type 2 GCs, which form neoplastic masses in addition to classic diffuse lesions. In this study, the prognostic relevance of IDH1/2 mutations in 74 GCs (43 type 1 and 31 type 2) was evaluated. We detected 33 (44.6%) IDH1 mutations, including R132H and R132S, by bidirectional Sanger sequencing. No mutations were detected in IDH2. The percentage of 2-year overall survival for wild-type IDH1 patients was 46 vs. 72% for patients with IDH1-mutated tumors. Mutations of IDH1 were strongly correlated with both increased overall survival (OS) and progression-free survival (PFS) in patients with type 2 GCs, and IDH1 mutations were also an independent prognostic factor predicting increased OS and PFS in type 2 GC patients in multivariate analysis. However, IDH1 mutations did not correlate with survival outcomes in patients with type 1 GCs. Finally, the subgroup of GC, which has IDH1 wild-type and additional solid component showed the worst prognosis.

Recently, the clonal integration of a new human polyomavirus (Merkel cell polyomavirus or MCPyV) has been reported in Merkel cell carcinoma (MCC). In order to investigate the presence of MCPyV in small cell carcinomas (SCCs) and small round cell tumors (SRCTs), we collected formalin-fixed paraffin-embedded tissue specimens including 14 MCCs, 24 SCCs, 7 Ewing sarcoma/primitive neuroectodermal tumors (ES/PNETs) and 5 neuroblastomas. We also collected specimens of other cancers including 12 malignant melanomas, 10 breast, 10 ovarian and 20 gastric cancers. We used 3 primer sets for which the sequences were previously published (LT1, LT3, and VP1) and 3 newly designed primer sets (LT1-1, LT1-1a, and LT3a). Quantitative real-time PCR was also performed with the LTq primer set. Nested PCR using the LT3a primer set detected more cases of MCPyV infection in MCC. In total, 12 of 14 (85.7%) MCC cases were positive for MCPyV by PCR, which was consistent with published data. Some SCC specimens were also positive for MCPyV (37.5%) by PCR. PCR products from MCC and SCC cases showed premature truncation and frameshift mutation. Furthermore, one case of ES/PNET and one gastric carcinoma showed MCPyV DNA. However, MCPyV DNA and transcript were only detected in MCCs with quantitative real-time PCR analysis. In addition, 11 of 13 (84.6%) MCC cases and 6 of 23 (26.1%) SCC cases showed immunoreactivity with monoclonal antibodies against MCPyV large T-antigen. Considering both PCR and IHC results, MCPyV was detected in all MCCs tested. The presence of MCPyV in all MCC cases tested and in some SCC cases suggests that MCPyV may be involved in the malignant transformation.

CD24 is known to be an important diagnostic and prognostic marker of several major cancers affecting females. We aimed to determine CD24 expression in normal, hyperplastic, and carcinomatous endometrium and its correlation with estrogen and progesterone receptor expression. A total of 271 cases including 62 normal/atrophic endometrium cases (47/15), 127 endometrial hyperplasia cases (51/52/24, simple/complex/atypical hyperplasia), and 82 endometrial carcinoma cases were immunohistochemically analyzed by using anti-CD24, ER, and PR antibodies that were embedded on paraffin blocks. Next, we assessed the CD24 mRNA expression in these tissues by using RT-PCR. In the normal endometrium, cyclic expression of membranous CD24 was detected during the regular menstrual cycle, i.e., down-regulation in the proliferative phase and up-regulation in the secretory phase. CD24 expression was very infrequent and weak in the atrophic endometrium. In hyperplasias and carcinomas, the expression of both membranous and cytoplasmic CD24 was found to be sharply reduced in the hyperplastic lesions and significantly enhanced in the carcinomas. In the case of carcinomas, high CD24 expression showed significant correlation with high-grade (G2 and 3) (P