Eleftheria Tsolaki

Stem cell-based regenerative opportunities for the liver: State of the art and beyond

The existing mismatch between the great demand for liver transplants and the number of available donor organs highlights the urgent need for alternative therapeutic strategies in patients with acute or chronic liver failure. The rapidly growing knowledge on stem cell biology and the intrinsic repair processes of the liver has opened new avenues for using stem cells as a cell therapy platform in regenerative medicine for hepatic diseases. An impressive number of cell types have been investigated as sources of liver regeneration: adult and fetal liver hepatocytes, intrahepatic stem cell populations, annex stem cells, adult bone marrow-derived hematopoietic stem cells, endothelial progenitor cells, mesenchymal stromal cells, embryonic stem cells, and induced pluripotent stem cells. All these highly different cell types, used either as cell suspensions or, in combination with biomaterials as implantable liver tissue constructs, have generated great promise for liver regeneration. However, fundamental questions still need to be addressed and critical hurdles to be overcome before liver cell therapy emerges. In this review, we summarize the state-of-the-art in the field of stem cell-based therapies for the liver along with existing challenges and future perspectives towards a successful liver cell therapy that will ultimately deliver its demanding goals.

Evaluation of the prognostic role of centromere 17 gain and HER2/topoisomerase II alpha gene status and protein expression in patients with breast cancer treated with anthracycline-containing adjuvant chemotherapy: pooled analysis of two Hellenic Cooperative Oncology Group (HeCOG) phase III trials

BackgroundThe HER2 gene has been established as a valid biological marker for the treatment of breast cancer patients with trastuzumab and probably other agents, such as paclitaxel and anthracyclines. The TOP2A gene has been associated with response to anthracyclines. Limited information exists on the relationship of HER2/TOP2A gene status in the presence of centromere 17 (CEP17) gain with outcome of patients treated with anthracycline-containing adjuvant chemotherapy.MethodsFormalin-fixed paraffin-embedded tumor tissue samples from 1031 patients with high-risk operable breast cancer, enrolled in two consecutive phase III trials, were assessed in a central laboratory by fluorescence in situ hybridization for HER2/TOP2A gene amplification and CEP17 gain (CEP17 probe). Amplification of HER2 and TOP2A were defined as a gene/CEP17 ratio of >2.2 and ≥2.0, respectively, or gene copy number higher than 6. Additionally, HER2, TopoIIa, ER/PgR and Ki67 protein expression was assessed by immunohistochemistry (IHC) and patients were classified according to their IHC phenotype. Treatment consisted of epirubicin-based adjuvant chemotherapy followed by hormonal therapy and radiation, as indicated.ResultsHER2 amplification was found in 23.7% of the patients and TOP2A amplification in 10.1%. In total, 41.8% of HER2-amplified tumors demonstrated TOP2A co-amplification. The median (range) of HER2, TOP2A and CEP17 gain was 2.55 (0.70-45.15), 2.20 (0.70-26.15) and 2.00 (0.70-26.55), respectively. Forty percent of the tumors had CEP17 gain (51% of those with HER2 amplification). Adjusting for treatment groups in the Cox model, HER2 amplification, TOP2A amplification, CEP17 gain and HER2/TOP2A co-amplification were not associated with time to relapse or time to death.ConclusionHER2 amplification, TOP2A amplification, CEP17 gain and HER2/TOP2A co-amplification were not associated with outcome in high-risk breast cancer patients treated with anthracycline-based adjuvant chemotherapy.Trial registrationAustralian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12611000506998 and ACTRN12609001036202

Hematopoietic stem cells and liver regeneration: Differentially acting hematopoietic stem cell mobilization agents reverse induced chronic liver injury

Bone marrow (BM) could serve as a source of cells facilitating liver repopulation in case of hepatic damage. Currently available hematopoietic stem cell (HSC) mobilizing agents, were comparatively tested for healing potential in liver fibrosis. Carbon tetrachloride (CCl4)-injured mice previously reconstituted with Green Fluorescent Protein BM were mobilized with Granulocyte-Colony Stimulating Factor (G-CSF), Plerixafor or G-CSF+Plerixafor. Hepatic fibrosis, stellate cell activation and oval stem cell frequency were measured by Gomori and by immunohistochemistry for a-Smooth Muscle Actin and Cytokeratin-19, respectively. Angiogenesis was evaluated by ELISA and immunohistochemistry. Quantitative real-time PCR was used to determine the mRNA levels of liver Peroxisome Proliferator-Activated Receptor gamma (PPAR-γ), Interleukin-6 (IL-6) and Tumor Necrosis-alpha (TNFα). BM-derived cells were tracked by double immunofluorescence. The spontaneous migration of mobilized HSCs towards injured liver and its cytokine secretion profile was determined in transwell culture systems. Either single-agent mobilization or the combination of agents significantly ameliorated hepatic damage by decreasing fibrosis and restoring the abnormal vascular network in the liver of mobilized mice compared to CCl4-only mice. The degree of fibrosis reduction was similar among all mobilized mice despite that G-CSF+Plerixafor yielded significantly higher numbers of circulating HSCs over other agents. The liver homing potential of variously mobilized HSCs differed among the agents. An extended G-CSF treatment provided the highest anti-fibrotic effect over all tested modalities, induced by the proliferation of hepatic stem cells and decreased hepatic inflammation. Plerixafor-mobilized HSCs, despite their reduced liver homing potential, reversed fibrosis mainly by increasing hepatic PPAR-γ and VEGF expression. In all groups, BM-derived mature hepatocytes as well as liver-committed BM stem cells were detected only at low frequencies, further supporting the concept that alternative mechanisms rather than direct HSC effects regulate liver recovery. Overall, our data suggest that G-CSF, Plerixafor and G-CSF+Plerixafor act differentially during the wound healing process, ultimately providing a potent anti-fibrotic effect.

Prognostic Significance of ESR1 Gene Amplification, mRNA/Protein Expression and Functional Profiles in High-Risk Early Breast Cancer: A Translational Study of the Hellenic Cooperative Oncology Group (HeCOG)

Background Discrepant data have been published on the incidence and prognostic significance of ESR1 gene amplification in early breast cancer. Patients and Methods Formalin-fixed paraffin-embedded tumor blocks were collected from women with early breast cancer participating in two HeCOG adjuvant trials. Messenger RNA was studied by quantitative PCR, ER protein expression was centrally assessed using immunohistochemistry (IHC) and ESR1 gene copy number by dual fluorescent in situ hybridization probes. Results In a total of 1010 women with resected node-positive early breast adenocarcinoma, the tumoral ESR1/CEP6 gene ratio was suggestive of deletion in 159 (15.7%), gene gain in 551 (54.6%) and amplification in 42 cases (4.2%), with only 30 tumors (3%) harboring five or more ESR1 copies. Gene copy number ratio showed a significant, though weak correlation to mRNA and protein expression (Spearmans Rho <0.23, p = 0.01). ESR1 clusters were observed in 9.5% (57 gain, 38 amplification) of cases. In contrast to mRNA and protein expression, which were favorable prognosticators, gene copy number changes did not obtain prognostic significance. When ESR1/CEP6 gene ratio was combined with function (as defined by ER protein and mRNA expression) in a molecular classifier, the Gene Functional profile, it was functional status that impacted on prognosis. In univariate analysis, patients with functional tumors (positive ER protein expression and gene ratio normal or gain/amplification) fared better than those with non-functional tumors with ESR1 gain (HR for relapse or death 0.49–0.64, p = 0.003). Significant interactions were observed between gene gain/amplification and paclitaxel therapy (trend for DFS benefit from paclitaxel only in patients with ESR1 gain/amplification, p = 0.066) and Gene Functional profile with HER2 amplification (Gene Functional profile prognostic only in HER2-normal cases, p = 0.029). Conclusions ESR1 gene deletion and amplification do not constitute per se prognostic markers, instead they can be classified to distinct prognostic groups according to their protein-mediated functional status.

Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA.

Background—Aim Massively parallel sequencing (MPS) holds promise for expanding cancer translational research and diagnostics. As yet, it has been applied on paraffin DNA (FFPE) with commercially available highly multiplexed gene panels (100s of DNA targets), while custom panels of low multiplexing are used for re-sequencing. Here, we evaluated the performance of two highly multiplexed custom panels on FFPE DNA. Methods Two custom multiplex amplification panels (B, 373 amplicons; T, 286 amplicons) were coupled with semiconductor sequencing on DNA samples from FFPE breast tumors and matched peripheral blood samples (n samples: 316; n libraries: 332). The two panels shared 37% DNA targets (common or shifted amplicons). Panel performance was evaluated in paired sample groups and quartets of libraries, where possible. Results Amplicon read ratios yielded similar patterns per gene with the same panel in FFPE and blood samples; however, performance of common amplicons differed between panels (p<0.001). FFPE genotypes were compared for 1267 coding and non-coding variant replicates, 999 out of which (78.8%) were concordant in different paired sample combinations. Variant frequency was highly reproducible (Spearman’s rho 0.959). Repeatedly discordant variants were of high coverage / low frequency (p<0.001). Genotype concordance was (a) high, for intra-run duplicates with the same panel (mean±SD: 97.2±4.7, 95%CI: 94.8–99.7, p<0.001); (b) modest, when the same DNA was analyzed with different panels (mean±SD: 81.1±20.3, 95%CI: 66.1–95.1, p = 0.004); and (c) low, when different DNA samples from the same tumor were compared with the same panel (mean±SD: 59.9±24.0; 95%CI: 43.3–76.5; p = 0.282). Low coverage / low frequency variants were validated with Sanger sequencing even in samples with unfavourable DNA quality. Conclusions Custom MPS may yield novel information on genomic alterations, provided that data evaluation is adjusted to tumor tissue FFPE DNA. To this scope, eligibility of all amplicons along with variant coverage and frequency need to be assessed.

Prevalent somatic BRCA1 mutations shape clinically relevant genomic patterns of nasopharyngeal carcinoma in Southeast Europe

Genomic patterns of nasopharyngeal carcinomas (NPCs) have as yet been studied in Southeast Asian (SEA) patients. Here, we investigated genomic patterns of locally advanced NPC Southeast European (SEE) patients treated with chemoradiotherapy. We examined 126 tumors (89% EBV positive) from Greek and Romanian NPC patients with massively parallel sequencing. Paired tumor‐cell‐rich (TC) and infiltrating‐lymphocyte‐rich (TILs) samples were available in 19 and paired tumor‐germline samples in 68 cases. Top mutated genes were BRCA1 (54% of all tumors); BRCA2 (29%); TP53 (22%); KRAS (18%). Based on the presence and number of mutations and mutated genes, NPC were classified as stable (no mutations, n = 27); unstable (>7 genes with multiple mutations, all BRCA1 positive, n = 21); and of intermediate stability (1–7 singly mutated genes, n = 78). BRCA1 p.Q563* was present in 59 tumors (48%), more frequently from Romanian patients (p < 0.001). No pathogenic germline mutations were identified. NPC exhibited APOBEC3A/B and nucleotide‐excision‐repair‐related mutational signatures. As compared to TC, TILs demonstrated few shared and a higher number of low frequency private mutations (p < 0.001). In multivariate analysis models for progression‐free survival, EBV positivity was a favorable prognosticator in stable tumors; BRCA1 mutations were unfavorable only in tumors of intermediate stability. In conclusion, other than described for SEA NPC, somatic BRCA1 mutations were common in SEE NPC; these were shared between TC and TILs, and appeared to affect patient outcome according to tumor genomic stability status. Along with the identified mutational signatures, these novel data may be helpful for designing new treatments for locally advanced NPC.

Correlation of MYC Gene and Protein Status With Breast Cancer Subtypes and Outcome of Patients Treated With Anthracycline-Based Adjuvant Chemotherapy. Pooled Analysis of 2 Hellenic Cooperative Group Phase III Trials

Micro‐Abstract The prognostic/predictive value of aberrant MYC gene copies and protein expression is not clear. It was therefore evaluated in 1060 early breast cancer patients treated with anthracycline‐containing chemotherapy. MYC gene amplification in the absence of polysomy‐8 was associated with adverse disease‐free and overall survival, whereas nuclear Myc protein expression benefitted patients treated with paclitaxel. These data might aid in the interpretation of relevant findings from large clinical trials. Background: The prognostic/predictive value of aberrant MYC gene copies and protein expression is not clear in breast cancer. Patients and Methods: Early breast cancer patients were treated with anthracycline‐containing chemotherapy within 2 randomized adjuvant trials. MYC gene and centromere‐8 status, as well as Myc protein expression were investigated on 1060 paraffin tumors with fluorescence in situ hybridization and immunohistochemistry, respectively. Results: MYC amplification was present in 45% and polysomy‐8 in 23% of the tumors. Cytoplasmic staining was observed in 60% and nuclear staining in 26% of the tumors, strongly correlating with each other but not with MYC gene status. MYC gene amplification in the absence of polysomy‐8 was associated with adverse disease‐free survival (DFS) and overall survival (OS), and remained as an independent unfavorable prognostic factor in multivariate analysis (Wald P = .022 for DFS; P = .032 for OS), whereas patients with MYC amplification and polysomy‐8, with polysomy‐8 only, and with normal MYC without polysomy‐8 performed significantly better compared with those with MYC gene amplification only. Nuclear Myc protein expression benefitted patients treated with paclitaxel (interaction P = .052 for DFS; P = .049 for OS). This interaction remained independently significant in multivariate analysis for OS (overall P = .028). Conclusion: The effect of MYC gene status on breast cancer patient outcome seems to depend on the underlying chromosomal instability and appears unfavorable for tumors with MYC amplification without polysomy. Nuclear Myc protein expression seems predictive for benefit from adjuvant paclitaxel. These data might aid in the interpretation of relevant findings from large clinical trials.

Adjusting Breast Cancer Patient Prognosis with Non-HER2-Gene Patterns on Chromosome 17

Background HER2 and TOP2A gene status are assessed for diagnostic and research purposes in breast cancer with fluorescence in situ hybridization (FISH). However, FISH probes do not target only the annotated gene, while chromosome 17 (chr17) is among the most unstable chromosomes in breast cancer. Here we asked whether the status of specifically targeted genes on chr17 might help in refining prognosis of early high-risk breast cancer patients. Methods Copy numbers (CN) for 14 genes on chr17, 4 of which were within and 10 outside the core HER2 amplicon (HER2- and non-HER2-genes, respectively) were assessed with qPCR in 485 paraffin-embedded tumor tissue samples from breast cancer patients treated with adjuvant chemotherapy in the frame of two randomized phase III trials. Principal Findings HER2-genes CN strongly correlated to each other (Spearman’s rho >0.6) and were concordant with FISH HER2 status (Kappa 0.6697 for ERBB2 CN). TOP2A CN were not concordant with TOP2A FISH status (Kappa 0.1154). CN hierarchical clustering revealed distinct patterns of gains, losses and complex alterations in HER2- and non-HER2-genes associated with IHC4 breast cancer subtypes. Upon multivariate analysis, non-HER2-gene gains independently predicted for shorter disease-free survival (DFS) and overall survival (OS) in patients with triple-negative cancer, as compared to luminal and HER2-positive tumors (interaction p = 0.007 for DFS and p = 0.011 for OS). Similarly, non-HER2-gene gains were associated with worse prognosis in patients who had undergone breast-conserving surgery as compared to modified radical mastectomy (p = 0.004 for both DFS and OS). Non-HER2-gene losses were unfavorable prognosticators in patients with 1–3 metastatic nodes, as compared to those with 4 or more nodes (p = 0.017 for DFS and p = 0.001 for OS). Conclusions TOP2A FISH and qPCR may not identify the same pathology on chr17q. Non-HER2 chr17 CN patterns may further predict outcome in breast cancer patients with known favorable and unfavorable prognosis.

Abstract 3579: Routinely applicable, highly multiplexed triple-negative breast cancer (TNBC) genotyping

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA In order to address TNBC diversity, determining the individual clonal genotypes of each tumor is urged as prerequisite. However, the applicability of whole genome approaches on routinely processed paraffin tissue material (FFPE) is still limited. Herein, we used targeted massive parallel sequencing (MPS) for genotyping FFPE tumors from patients with operable TNBC treated with adjuvant chemotherapy. Methods: Centrally assessed FFPE TNBC (n=260) were evaluated for tumor cell content (TCC) and submitted for DNA extraction. A custom panel targeting genomic regions in 43 genes previously implicated in TNBC was submitted for primer design (286 amplicons covering 21216bp). Barcoded FFPE libraries were massively processed on Ion Proton™ Sequencer PI and on Ion PGM™ Sequencer 318 chips (30 samples with both platforms, at least 2 runs each). Variants were called and annotated at higher-than-default-stringency conditions (63% of all detected variants excluded). Amplicons were checked for sequence specificity, blood DNA and FFPE performance prior to accepting results (informative: 280/286). Annotated SNVs (coding and non-coding) were assessed for allelic imbalance (AI) based on allelic frequency and TCC (AI: >0.3 unstable SNVs/tumor). The rate of failed samples was significantly higher with PGM (29.5%) than with Proton (3%). Results: In total, 238 informative TNBC were analyzed. AI was noticed in 169 tumors (71%) for multiple genes, more often TP53 (124 tumors, 52.1%), TERT (39.9%), MDM2 (35.7%), MET (24.4%), BRCA1 (20.2%) and NOTCH1 (18.9%). Coding mutations were identified in 40/43 genes but their number varied extensively per tumor (0-87). SNV functional mutations were observed in 55 tumors (23.1%), more often in PIK3CA (12 tumors, 5%). Non-SNV mutations were observed in 153 tumors (64.2%), more often TP53 (128 tumors, 53.8%), CDH1 (17.2%), MAP3K1 (8%), PTEN (6.3%), and PIK3CA (4.6%). High frequency mutations (>50% tumor cells) were found in TP53, PTEN, PIK3CA. Individually, the presence of AI (unstable tumors) and mutations predicted for worse survival. Importantly though, in comparison to patients with unstable mutated tumors, patients with unstable nonmutated tumors had significantly better outcome (DFS, HR:0.41, 95%CI:0.20-0.84, Wald p=0.014; OS, HR:0.36, 95%CI:0.15-0.86, p=0.021), similar to that observed for the favorable stable tumors, where the presence of mutations did not add any effect on survival. The same survival pattern was observed when evaluating AI and high frequency mutations. Conclusions: Targeted MPS with custom panels is an attractive option for highly multiplexed FFPE tissue genotyping, although differences in the efficiency of available platforms should be considered. With respect to potential clinical implications, identifying tumors with allelic (in)stability and clonal mutations seems important for assessing TNBC patient outcome and merits further validation. Citation Format: Vassiliki Kotoula, Kyriaki Papadopoulou, Elpida Charalambous, Flora Zagouri, Sotiris Lakis, Angeliki Lymperopoulou, Eleftheria Tsolaki, George Pentheroudakis, Kostas Lilakos, Dimitrios Pectasides, George Fountzilas. Routinely applicable, highly multiplexed triple-negative breast cancer (TNBC) genotyping. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3579. doi:10.1158/1538-7445.AM2014-3579

Abstract P5-08-50: Associations of MYC protein expression and gene status with breast cancer subtypes and outcome in patients treated with anthracycline-based adjuvant chemotherapy

Background-Aim: Breast cancer is a heterogeneous disease and despite recent scientific progress there is still need for the identification of biomarkers associated with risk for relapse, as well as for markers identifying patients who will benefit from specific treatments. The aim of the present study was to investigate the role of MYC, as a clinically meaningful biomarker, in the outcome of breast cancer subtypes. Patients and Methods: We have pooled the patients and the respective breast carcinomas from two randomized anthracycline-based adjuvant phase III trials, consecutively conducted by the Hellenic Cooperative Oncology Group (HE10/97 and HE10/00). The HE10/97 trial included a non-paclitaxel arm. Tissue microarrays were constructed from 1,060 formalin-fixed paraffin-embedded tumor tissue samples that were collected retrospectively in the first and prospectively in the second trial. MYC was evaluated by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) in 986 cases. Results: In total 61.0% of the cases showed positive cytoplasmic MYC immunostaining, while 26.5% showed positive nuclear staining. 65-80% of the patients were characterized as non-amplified or loss/normal-low gain in all FISH cut-offs examined. A weak association was observed between FISH and nuclear protein expression of MYC. High histological grade was associated with MYC protein overexpression and gene amplification. In terms of disease-free survival (DFS), low (2.5-5 copies) and high (≥5 copies) gain of MYC was of adverse prognostic value compared to loss/normal ( Treatment with paclitaxel was found to differentiate the effect of MYC: CEP8 ratio ≥1.3 and polysomy 8 in terms of DFS and OS in our total cohort. Among patients with CEP8 ratio ≥1.3 and polysomy 8, those treated with paclitaxel performed significantly better than those not treated, while among patients not treated with paclitaxel, those with CEP8 ratio ≥1.3 and polysomy 8 performed much worse than those with CEP8 ratio Conclusions: Our data suggest that MYC has prognostic and predictive value in patients with breast cancer. MYC amplification and MYC protein overexpression are detected in breast cancer patients and are of adverse prognostic value for DFS and OS. Polysomy 8 is also associated with worse prognosis. Treatment with paclitaxel in the adjuvant setting benefits breast cancer patients with MYC:CEP8 ratio ≥1.3 and polysomy 8. Citation Format: Batistatou A, Razis E, Bobos M, Tsolaki E, Timotheadou E, Alexopoulou Z, Goussia A, Gogas H, Koutras A, Karina M, Pentheroudakis G, Efstratiou I, Petraki K, Sotiropoulou M, Pavlakis K, Koletsa T, Kotoula V, Fountzilas G. Associations of MYC protein expression and gene status with breast cancer subtypes and outcome in patients treated with anthracycline-based adjuvant chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-08-50.