Search

Vemurafenib and dabrafenib are BRAF kinase inhibitors (BRAFi) used for the treatment of patients with melanoma carrying the V600E BRAF mutation. However, melanoma cells develop resistance to both drugs when used as monotherapy. Therefore, mechanisms of drug resistance are investigated, and new molecular targets are sought that could completely inhibit melanoma progression. Since receptor-interacting protein kinase (RIPK4) probably functions as an oncogene in melanoma and its structure is similar to the BRAF protein, we analyzed the impact of vemurafenib and dabrafenib on RIPK4 in melanomas. The in silico study confirmed the high similarity of BRAF kinase domains to the RIPK4 protein at both the sequence and structural levels and suggests that BRAFi could directly bind to RIPK4 even more strongly than to ATP. Furthermore, BRAFi inhibited ERK1/2 activity and lowered RIPK4 protein levels in BRAF-mutated melanoma cells (A375 and WM266.4), while in wild-type BRAF cells (BLM and LoVo), both inhibitors decreased the level of RIPK4 and enhanced ERK1/2 activity. The phosphorylation of phosphatidylethanolamine binding protein 1 (PEBP1)—a suppressor of the BRAF/MEK/ERK pathway—via RIPK4 observed in pancreatic cancer did not occur in melanoma. Neither downregulation nor upregulation of RIPK4 in BRAF- mutated cells affected PEBP1 levels or the BRAF/MEK/ERK pathway. The downregulation of RIPK4 inhibited cell proliferation and the FAK/AKT pathway, and increased BRAFi efficiency in WM266.4 cells. However, the silencing of RIPK4 did not induce apoptosis or necroptosis. Our study suggests that RIPK4 may be an off-target for BRAF inhibitors.

The progress in translational cancer research relies on access to well-characterized samples from a representative number of patients and controls. The rationale behind our biobanking are explorations of post-zygotic pathogenic gene variants, especially in non-tumoral tissue, which might predispose to cancers. The targeted diagnoses are carcinomas of the breast (via mastectomy or breast conserving surgery), colon and rectum, prostate, and urinary bladder (via cystectomy or transurethral resection), exocrine pancreatic carcinoma as well as metastases of colorectal cancer to the liver. The choice was based on the high incidence of these cancers and/or frequent fatal outcome. We also collect age-matched normal controls. Our still ongoing collection originates from five clinical centers and after nearly 2-year cooperation reached 1711 patients and controls, yielding a total of 23226 independent samples, with an average of 74 donors and 1010 samples collected per month. The predominant diagnosis is breast carcinoma, with 933 donors, followed by colorectal carcinoma (383 donors), prostate carcinoma (221 donors), bladder carcinoma (81 donors), exocrine pancreatic carcinoma (15 donors) and metachronous colorectal cancer metastases to liver (14 donors). Forty percent of the total sample count originates from macroscopically healthy cancer-neighboring tissue, while contribution from tumors is 12%, which adds to the uniqueness of our collection for cancer predisposition studies. Moreover, we developed two program packages, enabling registration of patients, clinical data and samples at the participating hospitals as well as the central system of sample/data management at coordinating center. The approach used by us may serve as a model for dispersed biobanking from multiple satellite hospitals. Our biobanking resource ought to stimulate research into genetic mechanisms underlying the development of common cancers. It will allow all available “-omics” approaches on DNA-, RNA-, protein- and tissue levels to be applied. The collected samples can be made available to other research groups.

Melanoma comprises BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ɛ, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified BARD1 splice variants in melanoma are warranted.

Agnieszka Adamczyk,1 Anna Kruczak,1 Agnieszka Harazin-Lechowska,1 Aleksandra Ambicka,1 Aleksandra Grela-Wojewoda,2 Małgorzata Domagała-Haduch,2 Anna Janecka-Widła,1 Kaja Majchrzyk,1 Anna Cichocka,1 Janusz Ryś,1 Joanna Niemiec1 1Department of Tumour Pathology, 2Department of Systemic and Generalized Malignancies, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Cracow Branch, Cracow, Poland Background: The aim of the study was to investigate if parameters associated with human epidermal growth factor receptor type 2 (HER2) status (HER2 gene copy number, HER2/CEP17 ratio or polysomy of chromosome 17) are related to various biological features potentially responsible for trastuzumab resistance (PTEN, IGF-1R, MUC4, EGFR, HER3, HER4, and mutation status of PIK3CA) as well as their influence on survival of HER2-positive breast cancer patients treated with adjuvant chemotherapy and trastuzumab. Patients and methods: The investigated group consisted of 117 patients with invasive ductal breast cancer (T≥1, N≥0, M0) with overexpression of HER2, who underwent radical surgery between 2007 and 2014. Status of ER, PR, and HER2 expression was retrieved from patients’ files. HER2 gene copy number was investigated by fluorescence in situ hybridization using PathVysion HER-2 DNA Probe Kit II. Expression of PTEN, IGF-1R, MUC4, EGFR, HER3, and HER4 was assessed immunohistochemically on formalin-fixed paraffin-embedded tissue sections. PIK3CA mutation status was determined by qPCR analysis. Results: Overexpression of HER2 protein (IHC 3+) and ER negativity corresponded to higher HER2 copy number and HER2/CEP17 ratio (p

Sarcomas and malignant mixed mesodermal tumours of the uterus (MMMT), also called carcinosarcomas, belong to rare uterine ne- oplasms usually characterised by very aggressive clinical behaviour. Due to their low incidence, unknown etiology as well as complex molecular characteristics, until now neither prognostic factors responsible for unfavourable prognosis nor optimal treatment methods have been definitely established. This study attempts to determine prognostic significance of selected morphological parameters. Based on the analysis of primary uterine neoplasms in 43 women (including 30 sarcomas and 13 MMMT) it was shown that prognosis is dependent on the histological type of the neoplasm. The worst prognosis was observed in patients with carcinosarcomas and high- grade endometrial stromal sarcomas. Additionally, it was demonstrated that both aforementioned neoplasms occur in significantly older age groups.

We report a case of 40-year-old Caucasian man presented with an asymptomatic nodule localized on his arm. The puzzle histiocytosis composed of juvenile xanthogranuloma and Langerhans cell histiocytosis was diagnosed. The results of immunohistochemical studies confirm the dual character of histological texture of the lesion.

Aim: Resistance to trastuzumab (which is a standard therapy for breast cancer patients with HER2 overexpression) is associated with higher risk of progression or cancer death, and might be related to activation of signalling cascades (PI3K/AKT/mTOR, Ras/Raf/MAPK) and decreased level of their inhibitors. Material and methods: Formalin-fixed paraffin-embedded tumour specimens from 118 HER2-overexpressing breast cancer patients treated with radical local therapy and trastuzumab in adjuvant setting were used for the assessment of: (1) PIK3CA gene mutations (p.H1047R and p.E545K) by qPCR, and (2) expression of Ki-67, EGFR, MUC4, HER3 and PTEN by immunohistochemistry. Results: Lower Ki-67LI was observed in EGFR-immunonegative and in PTEN-immunopositive tumours. MUC4-immunonegative tumours more frequently were PTEN- and HER3-immunonegative. Favourable metastasis-free survival was observed in patients with tumours characterized by Ki-67LI≤50% (p=0.027), HER3 immunonegativity or PTEN immunopositivity (vs. tumours with HER3 expression and lack of PTEN expression, p=0.043), additionally, the trend was observed for patients with pN0+pN1 pathological tumour stage (vs. pN2+pN3) (p=0.086). Cox model revealed that independent negative prognostic factors were: (i) Ki-67LI>50% (p=0.014, RR=4.6, 95% CI 1.4-15.4), (ii) HER3 immunopositivity together with PTEN immunonegativity (p=0.034, RR=3.7, 95% CI 1.1-12.5). Conclusion: The results of our study suggest that combined analysis of HER3 and PTEN expression might bring information on trastuzumab sensitivity in the group of HER2-positive breast cancer patients treated with trastuzumab in adjuvant setting.

Contrast-enhanced spectral mammography (CESM) is one of the new diagnostic modalities implemented in clinical practice. In the case of these techniques, there are two major issues to be addressed: (1) their diagnostic usefulness, and (2) the relation between parameters assessed using these techniques and well-known diagnostic/prognostic/predictive markers (histological, clinical, and molecular). Therefore, we studied the relationship between the tumour margin assessed on CESM and (1) tumour borders defined on the basis of macroscopic and microscopic examination, (2) pT, (3) pN, and (4) tumour grade in a group of 82 breast cancer patients. Based on CESM, the tumour border was defined as sharp, indistinct or spiculated, whereas in the case of lesions showing weak or medium enhancement on CESM the borders were classified as unspecified. We found a statistically significant relationship between tumour margin on CESM and (1) macroscopic border (a spiculated margin on CESM was found only in carcinomas with an invasive border on histological examination; p = 0.004), (2) pT (p = 0.016), and (3) pN (nodal involvement was observed most frequently in carcinomas with a spiculated or indistinct margin on CESM; p = 0.045). Moreover, in cases with an undefined margin on CESM (cases showing weak or medium enhancement on CESM), both invasive and pushing borders were found on histological examination. The results of our preliminary study suggest that it is possible to assess macroscopic borders of examined lesions on the basis of CESM imaging. This might be useful in planning the extent of surgical excision. On the other hand, the assessment of the tumour margin on CESM might not be precise in cases showing weak enhancement.

Background The aim of the study was to investigate if parameters associated with human epidermal growth factor receptor type 2 (HER2) status (HER2 gene copy number, HER2/CEP17 ratio or polysomy of chromosome 17) are related to various biological features potentially responsible for trastuzumab resistance (PTEN, IGF-1R, MUC4, EGFR, HER3, HER4, and mutation status of PIK3CA) as well as their influence on survival of HER2-positive breast cancer patients treated with adjuvant chemotherapy and trastuzumab. Patients and methods The investigated group consisted of 117 patients with invasive ductal breast cancer (T≥1, N≥0, M0) with overexpression of HER2, who underwent radical surgery between 2007 and 2014. Status of ER, PR, and HER2 expression was retrieved from patients’ files. HER2 gene copy number was investigated by fluorescence in situ hybridization using PathVysion HER-2 DNA Probe Kit II. Expression of PTEN, IGF-1R, MUC4, EGFR, HER3, and HER4 was assessed immunohistochemically on formalin-fixed paraffin-embedded tissue sections. PIK3C mutation status was determined by qPCR analysis. Results Overexpression of HER2 protein (IHC 3+) and ER negativity corresponded to higher HER22 copy number and HER2/CEP17 ratio (.

We compared the status of stromal podoplanin-positive cancer-associated fibroblasts (ppCAFs) between primary tumors and paired synchronous lymph node metastases (LNMs) and analyzed the prognostic significance of tumoral ppCAFs in 203 patients with human epidermal growth factor receptor 2-positive breast carcinoma. ppCAFs were found in 167/203 and in 35/87 tumors and LNM, respectively. ppCAFs were most frequently found in tumors and corresponding LNM (n=52, 59.8%; p=0.001). However, for all LNMs (n=12) without ppCAFs, their paired tumors also lacked ppCAFs. In both tumors and LNMs, ppCAFs were α-smooth muscle actin-positive and cluster of differentiation 21 protein-negative, suggesting them not to be resident lymph node cells. Moreover, in our series, the presence of ppCAFs in tumors was borderline related to poor disease-free survival (p=0.058). These results speak in favor of a hypothesis suggesting ppCAFs accompany metastatic cancer cells migrating from tumor to LNMs.

Department of Tumour Pathology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Krakow, Poland The review of literature indicates that several clinico-morphological factors such as location of the primary tumour as well as its size, histologic subtype, and grade or even selected molecular changes may significantly affect survival of liposarcoma (LPS) patients. Data concerning prognostic importance of DNA ploidy status in LPS cells are extremely limited and results of flow cytometry (FCM) studies have never been compiled with the current classification of malignant adipocytic tumours. Based on evaluation of material from 54 liposarcomas which was available for both histological and FCM analysis, we distinguished four prognostic groups of patients. The best prognosis was noticed for diploid and grade G1 well-differentiated or myxoid liposarcomas localised on extremities. None of the patients with lipoma-like WDLPS and myxoid liposarcoma grade 1 metastasised, while metastases were observed among patients with dedifferentiated LPS (70% of 5-year MFS) and cellular myxoid or round cell liposarcoma (20% of 5-year MFS, only). The metastasis-free survival curves for the above mentioned groups of patients differed significantly (p = 0.00001).

INI1 antigen is a product of the INI-1/SMARCB1 gene localized on chromosome 22q. It is well known that INI1 gene inactivation or loss of INI1 antigen expression is observed in epithelioid sarcomas; however, there are only few reports concerning specificity and sensitivity of immunohistochemical INI1 labeling as a marker of this neoplasm. That is why we decided to test 99 soft tissue sarcomas for the presence of the INI1 gene product. More specifically, the analyzed group consisted of 33 synovial sarcomas, 14 fibrosarcomas, 8 desmoid tumors, 8 DFSPs, 5 MPNSTs, 9 epithelioid sarcomas, 11 Ewing sarcomas/PNETs, 9 rhabdomyosarcomas and 2 clear cell sarcomas. Additionally, 7 malignant melanomas and 9 adenocarcinomas were included into the study. Positive staining with an antibody against the INI-1 gene product was observed in all studied cases of MPNST, Ewing sarcoma/PNET, rhabdomyosarcoma, malignant melanoma, clear cell sarcoma, and adenocarcinoma. On the contrary, none of 9 epithelioid sarcomas was labeled. The loss of INI1 expression was also detected in 7 (21.2%) synovial sarcomas, confirmed cytogenetically or by FISH. Considering the lack of reaction with INI-1 antibody as a diagnostic test for epithelioid sarcoma we estimated that its sensitivity reached 100% and specificity - 83.5% (p < 0.0001).

Resistance to trastuzumab in patients with HER2-overexpressing breast cancer is associated with higher risk of progression or cancer death, and might be related to activation of PI3K/AKT/mTOR and Ras/Raf/MAPK signaling cascades and a decreased level of their inhibitor (PTEN). HER2-overexpressing breast cancer patients (n=75) treated with radical local therapy and trastuzumab in adjuvant setting were included into the study. Deoxyribonucleic acid isolated from paraffin sections was used to assess mutational status of the PIK3CA gene (p.H1047R and p.E545K mutations) by the quantitative polymerase chain reaction technique. Expression of selected proteins (ER, PgR, AR, Ki-67, EGFR) was assessed using immunohistochemistry. In the studied group we found significantly higher Ki-67LI in EGFR-positive carcinomas (p=0.048). Moreover, EGFR immunonegativity was observed more frequently in low-grade (G1/G2) carcinomas as well as in estrogen/progesterone and androgen receptor immunopositive tumors (p=0.042, p=0.016, p=0.044, respectively). Favorable metastasis-free survival was observed in patients with pN0 and pN1 (vs. pN2+3) stage (p=0.040) and with tumors characterized by low Ki-67LI (≤50% vs. >50%) (p=0.014). Patients with tumor androgen receptor immunonegativity (weak or lack of expression) or strong PTEN expression survived 3 years without metastases (p=0.007). The results of our study suggest that androgen receptor and PTEN status might be considered as indicators of trastuzumab sensitivity.

It is assumed that lymphatic vessels are responsible for breast cancer dissemination.In 32 male breast carcinomas we evaluated the correlation between: (i) lymphatic vessel density (LVD), distribution of podoplanin-immunostained vessels (DPV), blood vessel density (BVD), infiltration of immune cells and (ii) known clinicopathological parameters.Lymphatic and blood vessels were found in 77.8% and 100% of breast carcinomas, respectively. Double-negative estrogen and progesterone receptor tumors (ER-/PR-) presented significantly higher LVD than ER/PR positive cases, while high-grade tumors exhibited significantly higher DPV than low-grade carcinomas. We detected significantly higher frequency of vascular invasion in high-grade and double-negative carcinomas than in low-grade and ER/PR-positive ones, respectively.The relationship between high number of lymphatic vessels and high tumor grade or steroid receptor negativity might confirm the hypothesis regarding the influence of lymphangiogenesis on the formation of a more aggressive phenotype in male breast cancer.

Male breast cancer is a rare form of carcinoma with an incidence rate of approximately 0.5-1% compared with cases of breast carcinoma as a whole. Male breast cancer reacts effectively to endocrine therapy because of a high frequency of hormone receptor expression.The aim of the present study was the assessment of correlations between stage, grade, expression of steroid receptors, basal/mesenchymal markers and proliferation index, as well as analysis of the impact of the above-mentioned parameters on overall (OS) and disease-free survival (DFS) in the group of 32 male breast cancer patients, treated at the Centre of Oncology in Cracow.We showed the significant positive correlation between MIB-1 LI and tumor stage, and hormone receptors (ER or PgR) immunonegativity, and expression of EGFR, vimentin (p

INI1 antigen is a product of the INI-1/SMARCB1 gene localized on chromosome 22q. It is well known that INI1 gene inactivation or loss of INI1 antigen expression is observed in epithelioid sarcomas; however, there are only few reports concerning specificity and sensitivity of immunohistochemical INI1 labeling as a marker of this neoplasm. That is why we decided to test 99 soft tissue sarcomas for the presence of the INI1 gene product. More specifically, the analyzed group consisted of 33 synovial sarcomas, 14 fibrosarcomas, 8 desmoid tumors, 8 DFSPs, 5 MPNSTs, 9 epithelioid sarcomas, 11 Ewing sarcomas/PNETs, 9 rhabdomyosarcomas and 2 clear cell sarcomas. Additionally, 7 malignant melanomas and 9 adenocarcinomas were included into the study. Positive staining with an antibody against the INI-1 gene product was observed in all studied cases of MPNST, Ewing sarcoma/PNET, rhabdomyosarcoma, malignant melanoma, clear cell sarcoma, and adenocarcinoma. On the contrary, none of 9 epithelioid sarcomas was labeled. The loss of INI1 expression was also detected in 7 (21.2%) synovial sarcomas, confirmed cytogenetically or by FISH. Considering the lack of reaction with INI-1 antibody as a diagnostic test for epithelioid sarcoma we estimated that its sensitivity reached 100% and specificity - 83.5% (p0.0001).

Paget disease (PD) of the nipple with coexisting intraductal (DCIS) and invasive carcinoma of the breast comprises 0.6-1.8% of all malignant epithelial neoplasms of this organ. Unlike invasive ductal carcinoma, there are many controversies concerning histological features of PD and the significance of the immunohistochemical characteristics of this neoplasm, which limits the optimal treatment protocols. Therefore, we decided to verify the immunohistochemical markers of PD basing on the retrospective analysis of postoperative material from 69 patients treated surgically. Microscopic examination revealed partial (7 cases) or total (62 cases) replacement of the squamous epithelium of the nipple with nests of atypical glandular cells spreading in an area ranging from 0.2 to 2.5 cm. DCIS coexisting with the PD lesions was present in all examined patients, and infiltrating carcinoma occurred in 31 (44.9%) patients. Both intraepidermal and DCIS components presented c-erbB2 overexpression. Positive estrogen and progesterone receptor staining was observed only in 7 (10.1%) and 2 (2.7%) tumours, respectively. Ki-67 proliferation index of PD cells ranged from 10% to 30%, whereas in DCIS it varied from 4% to 20%. The value of Ki-67 index exceeding 25% in the intraepidermal component of PD was associated with worse overall survival rate.

Giant cell tumour of soft part is a very rare neoplasm. The majority of these tumours are located superficially (in subcutaneous tissue) and occur in the proximal parts of the extremities. The deep-situated giant cell tumours of the neck are extremely rare. That is why we report a case of primary giant cell tumour of soft part localized in the trapezius muscle of a 19-year-old woman. We present both cytological and histological picture of the neoplasm. The cytological image of the smear is so representative that the proper diagnosis can be settled basing on the fine-needle aspiration cytology.

Objectives: The purpose of the study was to determine the influence of finger skin temperature on the vibrotactile per ception threshold at fingertips, determined according to the method described in ISO 13091-1 standard. Materials and Methods: The effect of the cooling and warming of hands on vibration perception was investigated in 21 healthy women. Vibration perception measurements were conducted using P8 pallesthesiometer (EMSON-MAT, Poland) designed according to ISO 13091-1 standard requirements. Vibrotactile perception threshold was measured in two series of experiments performed on the index finger of the right hand at frequencies of 4 Hz, 25 Hz and 125 Hz and skin temperature of 33°C, 28°C, 23°C, 18°C and 15°C. Results: The findings of the study showed that as the finger skin temperature decreased, the vibrotactile perception threshold increased, but only at the frequency of 125 Hz. The changes in finger skin temperature did not affect the vibration perception at 4 Hz and 25 Hz. No significant differences in VPT were found between the two experi mental series. Conclusions: A short-time cooling and warming of hands had a significant impact on increasing or decreasing vibrotactile perception threshold, only at the highest frequency mediated by Pacinian mechanoreceptors.

Objectives: The measurement of vibrotactile perception thresholds (VPTs) at fingertips in workers belongs in Poland among obligatory methods used to diagnose hand-arm vibration syndrome. The aim of the study was to compare vibrotactile perception threshold (VPT) values for healthy subjects using two different types of measuring equipment, i.e. a system designed according to the requirements of the ISO 13091-1 standard and a system that had so far been in use in Poland. Materials and Methods: 59 men and 22 women aged on average 40.4 years old participated in the study. The VPT measurements were carried out using a new pallesthesiometer P8 (EMSON-MAT, Poland), developed according to the ISO 13091-1 standard and a vibrotactile meter MCW 2K that had so far been used in Poland. Measurements were taken for the index, middle and ring fingers of both hands using the frequencies of 4, 25, 31.5, 63, 125, 250, 400 and 500 Hz for the ISO method and 63, 125, 250, 400 and 500 Hz for the Polish method. Results: The mean vibrotactile perception threshold values determined with the ISO 13091-1 method were significantly higher in comparison with the values obtained when the method used in Poland was employed. The differences between vibrotactile threshold levels were almost the same at the compared frequencies. Conclusions: The results of the VPT measurements obtained employing the standard method adopted in Poland may be used in further diagnostic examinations carried out with the ISO 13091-1 method only if an appropriate correction value is calculated in order to determine the difference in the VPT levels at a selected frequency.

The aim of the study was to determine differences between vibrotactile thresholds values in healthy women obtained with two psychophysical methods: the method drafted in ISO standard ISO 13091-1:2001 and the method hitherto used in Poland.Twenty two women (mean age, 37.9 +/- 9.7 years) participated in the study. Vibrotactile perception thresholds were measured in three fingers of both hands using the frequencies of: 4; 25; 31.5; 63; 125; 250; 400 and 500 Hz for the ISO method and respectively 63; 125; 250; 400 and 500 Hz for the Polish method.The mean vibrotactile perception threshold values determined with ISO 13091-1 method were significantly higher than those determined with the method used in Poland.The effect of individual finger skin temperature on vibrotactile perception values was obtained by ISO method.

Background Rarity and heterogeneity of liposarcomas (LPS) make their diagnosis difficult even for sarcoma-experts pathologists. The molecular mechanism underlying the development and progression of liposarcomas (LPS) remains only partially known. In order to identify and compare the genomic profiles, we analyzed array-based comparative genomic hybridization (array-CGH) profiles of 66 liposarcomas, including well-differentiated (WDLPS), dedifferentiated (DDLPS) and myxoid (MLPS) subtypes. Results Copy number aberrations (CNAs) were identified in 98% of WDLPS and DDLPS and in 95% of MLPS cases. The minimal common region of amplification at 12q14.1q21.1 was observed in 96% of WDLPS and DDLPS cases. Four regions of CNAs, including losses of chromosome 6, 11 and 13 and gains of chromosome 14 were classified as recurrent in DDLPS; at least one was identified in 74% of DDLPS tumors. The DDLPS-associated losses were much more common in tumors with increased genomic complexity. In MLPS, the most frequent CNAs were losses of chromosome 6 (40%) and gains of chromosome 1 (30%), with the minimal overlapping regions 6q14.1q22.31 and 1q25.1q32.2, respectively. Conclusions Our findings show that the application of array-CGH allows to delineate clearly the genomic profiles of WDLPS, DDLPS and MLPS that reflect biological differences between these tumors. Although CNAs varied widely, the subtypes of tumors have characteristic genomic profiles that could facilitate the differential diagnosis of LPS subtypes, especially between WDLPS and DDLPS. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0309-5) contains supplementary material, which is available to authorized users.