Publications

Melaseq development and validation studies have been published in leading peer-reviewed scientific journals, including British Journal of Cancer, PLOS ONE, Melanoma Research and Biomarkers in Medicine.

 

 


Biomarkers In Medicine (2021)

Translation of a circulating miRNA signature of melanoma into a solid tissue assay to improve diagnostic accuracy and precision

Aim: Successful treatment of cutaneous melanoma depends on early and accurate diagnosis of clinically suspicious melanocytic skin lesions. Multiple international studies have described the challenge of providing accurate and reproducible histopathological assessments of melanocytic lesions, highlighting the need for new diagnostic tools including disease-specific biomarkers. Previously, a 38-miRNA signature (MEL38) was identified in melanoma patient plasma and validated as a novel biomarker. In this study, MEL38 expression in solid tissue biopsies representing the benign nevi to metastatic melanoma spectrum is examined.

Patients & methods: Nanostring digital gene expression assessment of the MEL38 signature was performed on 308 formalin-fixed paraffin-embedded biopsies of nevi, melanoma in situ and invasive melanoma. Genomic data were interrogated using hierarchical clustering, univariate and multivariate statistical approaches. Classification scores computed from the MEL38 signature were analyzed for their association with demographic data and histopathology results, including MPATH-DX class, AJCC disease stage and tissue subtype.

Results: The MEL38 score can stratify higher-risk melanomas (MPATH-Dx class V or more advanced) from lower-risk skin lesions (class I–IV) with an area under the curve of 0.97 (p < 0.001). The genomic score ranges from 0 to 10 and is positively correlated with melanoma progression, with an intraclass correlation coefficient of 0.85 with stage 0–IV disease. Using an optimized classification threshold of ≥2.7 accurately identifies higher-risk melanomas with 89% sensitivity and 94% specificity. Multivariate analysis showed the score to be a significant predictor of malignancy, independent of technical and clinical covariates. Application of the MEL38 signature to Spitz nevi reveals an intrasubtype profile, with elements in common to both nevi and melanoma.

Conclusion: Melanoma-specific circulating miRNAs maintain their association with malignancy when measured in the hypothesized tissue of origin. The MEL38 signature is an accurate and reproducible metric of melanoma status, based on changes in miRNA expression that occur as the disease develops and spreads. Inclusion of the MEL38 score into routine practice would provide physicians with previously unavailable, personalized genomic information about their patient’s skin lesions. Combining molecular biomarker data with conventional histopathology data may improve diagnostic accuracy, healthcare resource utilization and patient outcomes.

Citation: https://www.futuremedicine.com/doi/10.2217/bmm-2021-0289


Pathology Update (2019)

MEL38, A Multi-tissue miRNA Signature of Cutaneous Melanoma

Histopathologic examination of melanocytic neoplasms can be challenging and subjective, with no specific circulating or tissue-based biomarkers currently available. Recently, a circulating 38- microRNA profile of melanoma (Mel38) was described.

Aim: In this study, the expression of Mel38 in solid tissue is examined in the context of disease state, patient outcome and messenger-RNA regulation.

Methods: Mel38 was applied to newly-created and archival, clinically-annotated, solid-tissue genomic datasets representing benign naevi, primary and metastatic melanoma. Univariate and multivariate statistical analyses of the signature in relation to disease status, patient outcome and molecular pathways was performed.

Results: Mel38 was able to stratify genomic data from solid tissue biopsies on the basis of disease state and identify patient subgroups with significant differences in melanoma-specific survival. The 278 experimentally-verified messenger-RNA targets of Mel38 also exhibit significant prognostic expression patterns. Pathway and functional analysis showed that Mel38 regulates a significant subset of the Melanoma KEGG pathway as well as key gene categories required for melanoma development and progression.

Discussion: The Mel38 microRNA profile may have diagnostic and prognostic utility in solid tissue, as well as being a robust circulating biomarker of melanoma.

Link: https://www.pathologyjournal.rcpa.edu.au/article/S0031-3025(18)31011-0/abstract


PLOS ONE (2019):

Characterisation and validation of Mel38; A multi-tissue microRNA signature of cutaneous melanoma

Background: Histopathologic examination of melanocytic neoplasms can be challenging and subjective, with no specific circulating or tissue-based biomarkers currently available. Recently, a circulating 38-microRNA profile of melanoma (Mel38) was described. In this study, Mel38 expression and its impact on downstream mRNA regulation in solid tissue is examined.

Methods: Mel38 was applied to archival, clinically-annotated, solid-tissue genomic datasets representing benign naevi, primary and metastatic melanoma. Statistical analysis of the signature in relation to disease status, patient outcome and molecular pathways was performed.

Results: Mel38 is able to stratify genomic data from solid tissue biopsies on the basis of disease status and differences in melanoma-specific survival. Experimentally-verified messenger-RNA targets of Mel38 also exhibit prognostic expression patterns and represent key molecular pathways and events in melanoma development and progression.

Conclusion: The Mel38 microRNA profile may have diagnostic and prognostic utility in solid tissue as well as being a robust circulating biomarker of melanoma.

Citation: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0211504


Biomolecules:

Circulating MicroRNA Biomarkers in Melanoma: Tools and Challenges in Personalised Medicine (2018)

Effective management of melanoma depends heavily on early diagnosis. When detected in early non-metastatic stages, melanoma is almost 100% curable by surgical resection, however when detected in late metastatic stages III and IV, 5-year survival rates drop to ~50% and 10–25%, respectively, due to limited efficacy of current treatment options. This presents a pressing need to identify biomarkers that can detect patients at high risk of recurrence and progression to metastatic disease, which will allow for early intervention and survival benefit. Accumulating evidence over the past few decades has highlighted the potential use of circulating molecular biomarkers for melanoma diagnosis and prognosis, including lactate dehydrogenase (LDH), S100 calcium-binding protein B (S100B) and circulating tumor DNA (ctDNA) fragments. Since 2010, circulating microRNAs (miRNAs) have been increasingly recognised as more robust non-invasive biomarkers for melanoma due to their structural stability under the harsh conditions of the blood and different conditions of sample processing and isolation. Several pre-analytical and analytical variables challenge the accurate quantification of relative miRNA levels between serum samples or plasma samples, leading to conflicting findings between studies on circulating miRNA biomarkers for melanoma. In this review, we provide a critical summary of the circulating miRNA biomarkers for melanoma published to date.

“This highlights the benefit of using a collection of miRNAs as a signature as if used individually, many of the miRNAs in MEL38 cannot be considered as independent biomarkers, however when used in combination appear to provide a sensitive and specific tool.”

 


Melanoma Research (2018)

A plasma microRNA biomarker of melanoma as a personalised assessment of treatment response

New tools for monitoring response to primary melanoma treatment are needed to reduce recurrence rates and patient anxiety. A previously developed plasma-based microRNA signature (MEL38) was measured in four melanoma patient samples obtained before and 12–14 days after treatment (i.e. surgical excision), as well as in two nonmelanoma controls. The value of the MEL38 score and selected individual genes were compared between the time points.

The MEL38 scores of the four patients with melanoma became more ‘normal like’ after tumour excision, with a statistically significant 15% mean reduction. MicroRNAs involved in tumour suppression were upregulated in the postexcision samples and those involved in facilitating treatment resistance and tumour invasion were downregulated.

Based on these limited preliminary data, the MEL38 signature may have clinical utility in assessing an individual patient’s response to the most common form of melanoma treatment. Additional studies are needed on larger, clinically diverse patient cohorts, sampled over longer periods of time.

Citation: https://journals.lww.com/melanomaresearch/


British Journal of Cancer (2018):

Development and validation of a plasma based melanoma biomarker suitable for clinical use

Background:
In Australia, more money is spent on skin cancer than any other malignancy. Despite this, the mortality rate of melanoma, the deadliest form, has steadily increased over the past 50 years. Diagnostic imprecision and a lack of complementary molecular biomarkers are partially responsible for this lack of progress.

Methods:
Whole-microRNAome profiling was performed on plasma samples from 32 patients with histologically confirmed melanoma and 16 normal controls. A classification algorithm was trained on these data and independently validated on multiple previously published microRNA data sets, representing (i) melanoma patient- and normal-blood, (ii) melanoma and nevi biopsy tissue, and (iii) cell lines and purified exosomes.

Results:
Thirty-eight circulating microRNAs had biologically and statistically significant differences between melanoma and normal plasma samples (MEL38). A support vector machine algorithm, trained on these markers, showed strong independent classification accuracy (AUC 0.79–0.94). A majority of MEL38 genes have been previously associated with melanoma and are known regulators of angiogenesis, metastasis, tumour suppression, and treatment resistance.

Conclusions:
MEL38 exhibits disease state specificity and robustness to platform and specimen-type variation. It has potential to become an objective diagnostic biomarker and improve the precision and accuracy of melanoma detection and monitoring.

Citation: https://www.nature.com/articles/bjc2017477 


Healthcare IT News

Link: Healthcare IT News


Melbourne Health Accelerator (MHx) Spring Cohort Presentation

Geneseq Biosciences presented the following poster and presentation at the final meeting of the Melbourne Health Accelerator program in December 2017.


World Melanoma Congress 2017

Geneseq Biosciences will be presenting the results of their Melaseq development activities at the World Melanoma Congress, being held in Brisbane, Australia in October 2017.