MIB-1 immunoreactivity correlates with blood vessel density and survival in disseminated malignant melanoma

Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy

Immunotherapy has emerged as a crucial strategy to combat cancer by "reprogramming" a patient's own immune system. Although immunotherapy is typically reserved for patients with a high mutational burden, neoantigens produced from posttranscriptional regulation may provide an untapped reservoir of common immunogenic targets for new targeted therapies. To comprehensively define tumor-specific and likely immunogenic neoantigens from patient RNA-Seq, we developed Splicing Neo Antigen Finder (SNAF), an easy-to-use and open-source computational workflow to predict splicing-derived immunogenic MHC-bound peptides (T cell antigen) and unannotated transmembrane proteins with altered extracellular epitopes (B cell antigen). This workflow uses a highly accurate deep learning strategy for immunogenicity prediction (DeepImmuno) in conjunction with new algorithms to rank the tumor specificity of neoantigens (BayesTS) and to predict regulators of mis-splicing (RNA-SPRINT). T cell antigens from SNAF were frequently evidenced as HLA-presented peptides from mass spectrometry (MS) and predict response to immunotherapy in melanoma. Splicing neoantigen burden was attributed to coordinated splicing factor dysregulation. Shared splicing neoantigens were found in up to 90% of patients with melanoma, correlated to overall survival in multiple cancer cohorts, induced T cell reactivity, and were characterized by distinct cells of origin and amino acid preferences. In addition to T cell neoantigens, our B cell focused pipeline (SNAF-B) identified a new class of tumor-specific extracellular neoepitopes, which we termed ExNeoEpitopes. ExNeoEpitope full-length mRNA predictions were tumor specific and were validated using long-read isoform sequencing and in vitro transmembrane localization assays. Therefore, our systematic identification of splicing neoantigens revealed potential shared targets for therapy in heterogeneous cancers.

PRAME expression in cutaneous melanoma does not correlate with disease-specific survival

BACKGROUND

Immunohistochemistry-based protein biomarkers can provide useful prognostic information in cutaneous melanoma. The independent prognostic value of Ki-67 has been studied with variable results. PReferentially expressed Antigen in MElanoma (PRAME) immunohistochemistry is a useful new ancillary tool for distinguishing cutaneous nevi from melanoma; however, its prognostic value has not been well studied. We evaluated PRAME as a prognostic marker in cutaneous melanoma, compared to Ki-67.

METHODS

We analyzed the immunohistochemical expression of PRAME and Ki-67 in 165 melanocytic lesions, including 92 primary melanomas, 19 metastatic melanomas, and 54 melanocytic nevi using tissue microarrays. PRAME immunostaining was scored based on the percentage of positive nuclei: 0 <1%, 1+ 1%-25%, 2+ 26%-50%, 3+ 51%-75%, and 4+ >75%. The percentage of Ki-67-positive tumor nuclei was used to calculate the proliferation index.

RESULTS

PRAME and Ki-67 both showed significantly increased expression in melanomas compared to nevi (p < 0.0001 and p < 0.001, respectively). There was no significant difference in PRAME expression in primary versus metastatic melanomas. By contrast, the Ki-67 proliferation index was higher in metastatic melanoma than in primary melanoma (p = 0.013). Increased Ki-67 index correlated with ulceration (p < 0.001), increased Breslow depth (p = 0.001), and higher mitotic rate (p < 0.0001), whereas increased PRAME expression correlated with higher mitotic rate (p = 0.047) and Ki-67 index (p = 0.007). Increased Ki-67 index correlated with worse disease-specific survival in patients with primary melanoma (p < 0.001), but PRAME expression did not show prognostic significance in disease-specific survival (p = 0.63). In a multivariable analysis of patients with primary melanoma, tumor Breslow depth, ulceration, mitotic rate, and Ki-67 index were each independent predictors of disease-specific survival (p = 0.006, 0.02, 0.001, and 0.04, respectively); however, PRAME expression was not predictive of disease-specific survival (p = 0.64).

CONCLUSION

Ki-67 is an independent prognostic marker; although increased PRAME expression correlates with the Ki-67 proliferation index and mitotic rate, PRAME is not an independent prognostic marker for cutaneous melanoma. PRAME and Ki-67 are useful ancillary tools for distinguishing benign from malignant melanocytic lesions.

Microvessel Density in Patients with Cutaneous Melanoma: An Up-to-Date Systematic Review and Meta-Analysis

Background

We conducted a meta-analysis, in order to appraise the effect of microvessel density (MVD) on the survival of patients with cutaneous melanoma.

Methods

This study was conducted according to the PRISMA guidelines and the Cochrane Handbook for Systematic Reviews of Interventions. A systematic literature search in electronic databases (MEDLINE, Web of Science, and Cochrane Central Register of Controlled Clinical Trials) was performed. Fixed Effects or Random Effects model was used, based on the Cochran Q test.

Results

In total 9 studies (903 patients) were included. Pooled HR for overall survival (OS) and disease-free survival (DFS) were 2.62 (95% CI: 0.71–9.60, p = 0.15) and 2.64 (95% CI: 0.82–8.47, p = 0.10), respectively. Odds ratios of overall survival between high and low MVD groups, at 12 (1.45, 95% CI: 0.16–13.24), 36 (2.93, 95% CI: 0.63–13.59), and 60 (4.09, 95% CI: 0.85–19.77) months did not reach statistical significance. Significant superiority of low MVD group, in terms of DFS, at all time intervals (OR: 4.69, p < 0.0001; OR: 2.18, p = 0.004; OR: 7.46, p = 0.01, resp.) was documented.

Discussion

MVD does not affect the HR of OS and DFS. A strong correlation with DFS rates at 12, 36, and 60 months was recorded.

A high proliferative index of recurrent melanoma is associated with worse survival

OBJECTIVE

Previous melanoma studies evaluating prognostic factors of survival at recurrence have focused on primary tumor characteristics and clinical variables at first recurrence. We examined the prognostic relevance of recurrent tumor proliferation.

METHODS

114 melanoma patients with available recurrent tissues who were prospectively enrolled at New York University Medical Center were studied. Standard of care prognostic variables (e.g. stage at initial diagnosis and lactate dehydrogenase level) and recurrent tissue expression of proliferative marker Ki-67 were evaluated for their association with overall survival.

RESULTS

High Ki-67 expression was observed in 57 (50%) of the 114 recurrent melanomas. On univariate analysis, the median overall survival of patients whose recurrent tumors overexpressed Ki-67 was significantly shorter than that of patients whose recurrent tumors had low Ki-67 expression (3.6 vs. 9.5 years, p = 0.03). On multivariate analysis, a high proliferative index of the recurrent melanoma remained an independent predictor of worse overall survival, controlling for stage at initial diagnosis, disease-free survival, and stage at first recurrence [HR = 2.09 (95% CI 1.24-3.54), p = 0.006].

CONCLUSIONS

Our results demonstrate the prognostic relevance of tumor proliferation in recurrent melanoma patients. Data also support restratification of risk assessment upon recurrence that considers tumor biology in addition to clinical variables evaluated as part of the standard of care.

Tissue biomarkers for prognosis in cutaneous melanoma: a systematic review and meta-analysis

In the clinical management of early-stage cutaneous melanoma, it is critical to determine which patients are cured by surgery alone and which should be treated with adjuvant therapy. To assist in this decision, many groups have made an effort to use molecular information. However, although there are hundreds of studies that have sought to assess the potential prognostic value of molecular markers in predicting the course of cutaneous melanoma, at this time, no molecular method to improve risk stratification is part of recommended clinical practice. To help understand this disconnect, we conducted a systematic review and meta-analysis of the published literature that reported immunohistochemistry-based protein biomarkers of melanoma outcome. Three parallel search strategies were applied to the PubMed database through January 15, 2008, to identify cohort studies that reported associations between immunohistochemical expression and survival outcomes in melanoma that conformed to the REMARK criteria. Of the 102 cohort studies, we identified only 37 manuscripts, collectively describing 87 assays on 62 distinct proteins, which met all inclusion criteria. Promising markers that emerged included melanoma cell adhesion molecule (MCAM)/MUC18 (all-cause mortality [ACM] hazard ratio [HR] = 16.34; 95% confidence interval [CI] = 3.80 to 70.28), matrix metalloproteinase-2 (melanoma-specific mortality [MSM] HR = 2.6; 95% CI = 1.32 to 5.07), Ki-67 (combined ACM HR = 2.66; 95% CI = 1.41 to 5.01), proliferating cell nuclear antigen (ACM HR = 2.27; 95% CI = 1.56 to 3.31), and p16/INK4A (ACM HR = 0.29; 95% CI = 0.10 to 0.83, MSM HR = 0.4; 95% CI = 0.24 to 0.67). We further noted incomplete adherence to the REMARK guidelines: 14 of 27 cohort studies that failed to adequately report their methods and nine studies that failed to either perform multivariable analyses or report their risk estimates were published since 2005.

In vivo assessment of the antiproliferative properties of interferon-alpha during immunotherapy: Ki-67 (MIB-1) in patients with metastatic renal cell carcinoma

The aim of the present study was to investigate the in vivo antiproliferative effect of interferon alpha (IFN-α) in patients with metastatic renal cell carcinoma (mRCC). Core needle biopsies of metastatic and/or the primary kidney cancer were obtained before interleukin-2 (IL-2)- and IFN-α-based immunotherapy in 34 patients and repeated after 5 weeks in 25 patients. Tumour proliferation was assessed by use of the anti-Ki-67 antibody MIB-1 and evaluated in multiple, random systematic sampled fields of vision. Ki-67 labelling index (LI) at baseline was median 13.6% (range 1.2–85.0) and median 10.6% (range 1.3–48.6%) at week 5 with a median overall decline of 15.2% (range −95 to +258%) from baseline to week 5. There was no difference between responding and nonresponding patients. Ki-67 LI at week 5 was significantly correlated to survival. Thus, median survival of patients with Ki-67 LI ⩽10.6% at week 5 was 25.1 months compared to 11.5 months for patients with Ki-67 LI >10.6% (P=0.016). Baseline or change in Ki-67 LI did not correlate to survival. These data suggest that IFN-α in vivo has only modest effect on tumour proliferation in patients with mRCC. Tumour Ki-67 (MIB-1) reactivity after 1 month of immunotherapy appears to be a significant predictor of patient survival.

Proliferation rates in human malignant melanoma: relationship to clinicopathological features and outcome

This prospective study investigated the clinical significance of cell kinetics, measured using bromodeoxyuridine injection and flow cytometry, in primary and metastatic cutaneous malignant melanoma. The findings illustrate that melanoma is a relatively slowly proliferating tumour, with a median potential doubling time (T(pot)) of 8.6 days. There were no significant differences in cell kinetics between primary and secondary disease. Both the duration of the S phase (T(s)) and T(pot), but not the labelling index (LI), showed a correlation with some of the main clinicopathological features in primary disease, including Breslow thickness. On univariate analysis, a short T(pot) and a high LI were associated with shorter disease-free intervals and overall survival for metastatic but not primary lesions. On multivariate analysis, these parameters retained significance when analysed separately with the main clinicopathological variables. These findings suggest that assessment of proliferation in melanoma is able to refine the available prognostic information and identify patients with a poor clinical outcome.

Immunohistochemically detectable bcl-2 expression in metastatic melanoma: association with survival and treatment response

OBJECTIVE

The antiapoptotic protein Bcl-2 is supposed to influence the treatment responsiveness of different malignancies. In the present study the prognostic and predictive significance of Bcl-2 expression for survival and response to an administered therapy was explored in patients with metastatic melanoma. Also, the correlation between Bcl-2 expression and proliferation activity of tumor cells was defined to examine the regulatory role of Bcl-2 in proliferation.

MATERIALS AND METHODS

Sixty metastatic melanomas obtained from patients treated with chemoimmunotherapy were examined by immunohistochemistry with anti-Bcl-2 and anti-Ki-67 (MIB-1) antibodies. Proliferation activity was expressed in percentages as MIB-1 index.

RESULTS

The presence of Bcl-2 immunoreactivity was associated with a significantly lower MIB-1 index (p = 0.016), and a longer disease-free survival (p = 0.004). The lack of Bcl-2 expression was related to a higher response rate to therapy in comparison to a diffuse and focal pattern of Bcl-2 expression (p = 0.017). Although the presence of Bcl-2 immunoreactivity as such did not correlate with survival after the initiation of chemoimmunotherapy, the focal Bcl-2 expression pattern was strongly associated with a worse prognosis compared to a diffuse expression or a lack of Bcl-2 staining (p < 0.0001).

CONCLUSIONS

Our results support the role of Bcl-2 in the regulation of cell proliferation and suggest that an increase of metastatic potential and progression of malignant melanoma is associated with a loss of Bcl-2 expression. The lack of Bcl-2 expression could be a predictor of the response to chemoimmunotherapy, whereas the Bcl-2 expression pattern, possibly indicating the heterogeneity of the tumors, might be a potential prognostic factor for survival after the initiation of therapy.

Structural examination of tryptase-, and VIP-positive mast cells in the common bile duct of patients with lithiasis

The morphology of tryptase-, and vasoactive intestinal polypeptide (VIP)-positive mast cells was examined immunohistochemically in 38 common bile ducts collected from patients with secondary chronic cholangitis and varying degrees of inflammatory activity. Mast cells numbers in chronic exacerbated and chronic sclerotic cholangitis were significantly higher as compared with those in controls (72.4 cells/mm2 and 25.2 cells/mm2 vs. 5.9 cells/mm2; p < 0.0001, Student's t test). The increased number of tryptase-positive mast cells in chronic exacerbated cholangitis correlated with the severeness of inflammatory infiltration. In cases of chronic exacerbated cholangitis, the increased number of mast cells was detected in conjunction with active fibroplasia. In chronic sclerotic cholangitis mast cells were lower in number as compared with exacerbated cholangitis and were observed in relation with inactive fibrosis. Numerous VIP-positive mast cells were found in all patients with cholangitis. Ultrastructural immunocytochemistry showed tryptase positivity to be localized over either electron-dense or particulate granules with a mean diameter of 0.261+/-0.073 microm or 0.171+/-0.053 microm, respectively. VIP positivity was formed as a finely or coarsely granular pattern over larger electron-dense granules of 0.475+/-0.14 microm in diameter. Tryptase-positive mast cells were located mainly in and around surface and glandular epithelium. The involvement of tryptase- and VIP-positive mast cells in inflammation, fibrosis and epithelial reactions in the common bile duct is discussed.

Transcription factors and other dysregulated proteins in melanoma prognosis

Approximately one third of patients with cutaneous melanoma later develop a metastatic disease, having then an extremely poor rate of survival. Because of the highly unpredictable nature of melanomas, finding those patients who are likely to develop a metastatic disease and those patients who probably will survive is an ongoing challenge. The current "conventional" prognosticators, such as Breslow thickness, Clark level of invasion, and ulceration, cannot perfectly predict the clinical course of this disease at an individual level. Although the sentinel lymph node biopsy procedure and reverse transcription polymerase chain reaction techniques have significantly improved the staging of patients with melanoma, new molecular prognostic markers may help in selection of appropriate patients for strenuous adjuvant therapies and for randomized clinical trials. Furthermore, these markers also improve our basic understanding of the biology of cutaneous melanoma, potentially offering new targets for novel treatment strategies. This paper reviews the current literature on transcription factors and other dysregulated proteins involved in melanoma prognosis.

High collagenase-1 expression correlates with a favourable chemoimmunotherapy response in human metastatic melanoma

Matrix metalloproteinases (MMPs) are proteolytic enzymes that can degrade extracellular matrix and thus enhance metastasis. We have studied the expression of two collagenolytic MMPs in 37 samples obtained from 26 patients treated for metastatic melanoma. Interestingly, the samples showed a different expression pattern of collagenase-1 (MMP-1) and collagenase-3 (MMP-13). The samples with high expression levels of MMP-1 (n = 18) were more frequently MMP-13 negative (14 out of 18), whereas those with low expression levels of MMP-1 (n = 15) were predominantly positive for MMP-13 (nine out of 15) (P = 0.027). High expression levels of MMP-1 were associated with a favourable response to chemoimmunotherapy. Responders (n = 13) frequently had intensively MMP-1-expressing metastases (nine out of 13), especially those who achieved a complete response (five out of six). Response failures (n = 7) mainly had metastases with a low intensity of MMP-1 expression (six out of seven) (P = 0.019). There was a tendency towards longer survival among patients with intensively MMP-1-expressing tumours (median 14.3 versus 6.7 months, P = 0.068). The high expression levels of MMP-1 correlated with low MIB-1 (to nuclear antigen Ki-67) (P = 0.019) and positivity for MMP-13 was associated with high MIB-1 expression (P = 0.00048), suggesting that their different expression patterns may affect tumour growth and contribute to differences in patient survival.