Abstract 782: Circulating tumour DNA-based molecular response predicts treatment outcome in multiple myeloma

Background: Multiple myeloma (MM) is an incurable and multi-focal plasma cell malignancy manifesting predominantly within the bone marrow (BM). BM-based minimal residual disease (MRD) assessment utilising next generation flow (NGF - EuroFlowTM) has become an important measure of treatment response and a validated predictor of patient outcome. However, MRD is a single-site BM-derived assay and is conceptually limited due to the spatially heterogenous nature of MM and response to treatment.

Objective: We investigated if the evaluation of circulating tumour DNA (ctDNA) can be utilised as an adjunct to MRD analysis in predicting patient outcome.

Methods: Peripheral blood plasma was obtained at baseline (B), cycle 3 day 1 (C3D1) and end of study (EOS)/relapse from a phase II, multicentre single arm study of carfilzomib-thalidomide-dexamethasone (KTd) in 50 transplant-eligible newly diagnosed MM patients who were refractory to or had demonstrated a suboptimal response to first-line therapy. Extracted ctDNA was assessed utilising high-sensitivity targeted amplicon sequencing (TAS) of 22 MM-relevant genes. The variant allele frequency (VAF) of mutations at B was utilised to calculate a fold change in VAF at C3D1 and/or EOS. A negative fold change was defined as a decrease in VAF (ctDNA-) and a positive fold change an increase in VAF (ctDNA+) with the average fold change across all mutations calculated for each patient. EuroflowTM was performed on BM obtained pre and post-autologous stem cell transplant (ASCT) and at EOS and the ‘best MRD response’ achieved (MRD+ or MRD-) was recorded. The ctDNA and MRD responses were combined and correlated with progression-free survival (PFS) calculated using Kaplan-Meier estimates.

Results: A total of 45 patients had one or more mutations identified at B that could be tracked at C3D1 and/or EOS and 40 patients had one or more mutations that emerged at C3D1, EOS and/or relapse. Of these, 33 patients were evaluable for both MRD and ctDNA response. Patients that were MRD- and ctDNA- as best response for B mutations had a significantly longer PFS compared to those who were MRD+/ctDNA- or MRD-/ctDNA+ (p<0.0001, Log-rank tests; 23.9 months vs not reached for MRD-ctDNA-, Log rank-tests). Patients that were MRD- and ctDNA- at C3D1 (as early response for B mutations) had a significantly longer PFS compared to those that were MRD+/ctDNA- or MRD-/ctDNA+ (p=0.0011, 26.4 months vs not reached in MRD-ctDNA-, Log-rank tests).

Conclusions: Our results demonstrate that treated MM patients manifesting a molecular response, as defined by a reduction in ctDNA mutational burden, and who are also MRD- have a superior outcome to those patients who are MRD- but without a molecular response. These results for the first time confirm the utility of ctDNA-based early molecular response as a predictor of patient outcome in MM.

Citation Format: Sridurga Mithraprabhu, Tiffany Khong, Flora Yuen, John Reynolds, Brian Durie, Andrew Spencer. Circulating tumour DNA-based molecular response predicts treatment outcome in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 782.

Abstract 3412: Liquid biopsy for t(11;14)/blc2 identification in multiple myeloma

Background: Multiple myeloma (MM) is a spatially heterogeneous plasma cell malignancy of the bone marrow (BM). Venetoclax is a potent inhibitor of the anti-apoptotic protein BCL2 with evidence in MM that t(11;14) and high BCL2 expression confers greater sensitivity to venetoclax. BM biopsy is required for fluorescent in-situ hybridisation (FISH) detection of t(11;14) and the evaluation of MM cell BCL2 expression, with success being entirely dependent on the quality of the BM sample procured. We hypothesised that a liquid biopsy strategy to enable interrogation of cell-free circulating tumour (ct)DNA and extra-cellular (ex)RNA would represent a more practical and less invasive alternative strategy to BM biopsy for the detection of t(11;14) and the determination of MM cell BCL2 expression, respectively.

Methods: Blood and BM were obtained from 24 FISH characterised MM patients - normal karyotype (n=9), t(11;14) (n=11) and t(4;14) (n=4). Plasma derived ctDNA and exRNA was extracted utilising the QIAamp circulating nucleic acid kit and matched PBMC DNA was obtained for germ line controls. BM CD138+ MM cells for DNA and RNA extraction were selected with Miltenyi Biotec CD138 microbeads. A low density custom panel of unique capture probes (SSEL XT HS2, SureSelect Custom Tier 2, Agilent Technology), spanning approximately 10% of the CCND1 and IGH loci involved in t(11;14), was used for sequencing with approximately 5 million reads per sample with adapter sequences trimmed from the reads and aligned to the hg38 using bwa mem algorithm. Structural variant caller, Lumpy was used for identifying translocations, with low confidence reads excluded with a defined Z-score threshold. Droplet digital PCR (ddPCR) for BCL2 was performed on exRNA.

Results: The low-density capture seq identified t(11;14) in 6 of 11 (55%) of the CD138+ BM samples, but not in paired germ-line samples nor in the non-t(11;14) cohort BM samples. Interrogation of ctDNA identified t(11;14) in 1 of 11 samples but also in ctDNA from a patient labelled as being t(4;14) positive raising questions about the validity of the FISH attribution. We are now utilising a modification of the assay using ultra-high density capture probes with coverage approaching 100% of the IGH region and higher ctDNA input to detect translocations involving the IGH region on chromosome 14 with any partner chromosome, including translocations undetectable by FISH. BCL2 exRNA transcripts were detected in all patients with a range of 2-120 copies/ml of plasma with 79% of patients classified as ‘high’ BCL2 expression (>40 copies/ml of plasma) compared to 59% of the matched CD138+ BM samples.

Conclusion: We provide proof-of-concept of the potential of ctDNA and exRNA for t(11;14) detection and ddPCR quantitation of BCL2 expression, respectively, providing a rationale for further exploration of ctDNA and exRNA liquid biopsy testing as a strategy for identifying patients with t(11;14) and/or high BCL2.

Citation Format: Andrew Spencer, Sridurga Mithraprabhu, Jaynish Shah, Kawa Choi, Ashley George, Carlos Hader, Tiffany Khong. Liquid biopsy for t(11;14)/blc2 identification in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3412.

Abstract 3373: Circulating tumour DNA mutations correlate with relapse in a phase II trial of bortezomib-primary refractory multiple myeloma patients receiving salvage therapy

Background: Multiple myeloma (MM), an incurable plasma cell malignancy, has a relative 5-year overall survival (OS) of 48.5% for newly diagnosed patients. Prospective real-world data reveals that 23% of transplant eligible MM patients relapse within 12 months of starting first-line bortezomib based therapy with a median OS of only 16.8 months (high-risk - HR). Genomic studies for these HR patients could inform rational secondary therapeutic options and prolong survival. Bone marrow (BM) genomic analysis in MM has methodological and conceptual shortcomings owing to the spatially and genomically heterogeneous nature of MM that can be largely overcome with circulating tumour DNA (ctDNA) analysis.

Objective: To determine whether ctDNA analysis can define the mutational spectrum of patients with HR MM.

Design: Phase II, multicentre single arm study of carfilzomib-thalidomide-dexamethasone (KTd) in 50 transplant-eligible newly diagnosed MM patients from September 2016 to April 2018 (Australasian Leukaemia and Lymphoma Group (ALLG) - MM17 trial) who were refractory (REF) to or demonstrated a suboptimal response (SOR) to bortezomib-based induction therapy. A total of 186 peripheral blood plasma and BM samples were obtained at baseline, at Cycle 3 day 1 (C3D1), end of the study (EOS) and/or at relapse. Somatic variants were identified with an ultra-sensitive targeted amplicon sequencing (TAS) assay incorporating 22-genes known to be mutated in MM. The mutational spectrum was correlated with progression-free survival (PFS) and OS.

Results: TAS of 31 BM samples and 48 ctDNA samples revealed that in BM, KRAS mutations were detected in 42% of patients followed by ATR in 29% while in ctDNA, ATR mutations were prominent (36%), followed by FGFR3 and ATM (27% and 26.8%). We compared the ctDNA mutational spectrum at baseline between non-relapse and relapse patients on KTd and identified a significant difference in the proportion of patients with specific mutations - RAS/RAF: 3% vs 25%; ATM/ATR/TP53: 17% vs 41%, respectively (p<0.0001). Patients with RAS/RAF and/or ATM/ATR/TP53 ctDNA mutations at baseline had significantly shorter PFS and OS (p=0.003 and p=0.02, respectively). Comparative ctDNA TAS for baseline, C3D1, EOS/relapse, demonstrated that in 87.5% of patients, one or more dominant mutations driving relapse in KTd were already present prior to starting salvage therapy. We also performed ctDNA analysis to compare patients who were REF or SOR to front-line therapy and identified 62% of REF patients had RAS/RAF or ATM/ATR/TP53 mutation compared to 35% of SOR patients (p=0.0002, Fisher’s exact test).

Conclusions: Our results demonstrate that RAS/RAF and ATM/ATR/TP53 mutations in ctDNA are prognostic biomarkers of outcome to secondary salvage therapy in HR patients thus enabling design of targeted therapeutic approaches to improve survival.

Citation Format: Sridurga Mithraprabhu, John Reynolds, Anna Kalff, Krystal Bergin, Rose Turner, Hang Quach, Noemia Horvath, Ian Kerridge, Flora Yuen, Kawa Choi, Malarmathy Ramachandran, Ashley George, Tiffany Khong, Brian Durie, Andrew Spencer. Circulating tumour DNA mutations correlate with relapse in a phase II trial of bortezomib-primary refractory multiple myeloma patients receiving salvage therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3373.

Abstract 3491: New targets and new approaches for multiple myeloma: Extracellular vesicles as functional liquid biomarkers

Background: We have previously demonstrated that stromal cells (HS5) pre-treated with small extracellular vesicles (sEV) enriched from blood plasma of myeloma (MM) patients promoted adhesion of human MM cell lines (HMCL), with preliminary proteomic profiling of MM-sEV (vs healthy donors-HD) revealing enrichment of factors implicated in cell migration and adhesion.

Aims: To demonstrate that plasma-derived MM-sEV induce a microenvironment favoring MM progression and identify the protein content of plasma-sEV that promotes this.

Methods: sEV were enriched from plasma (1mL) using a commercial kit. Proteomic profiling (nLC and high-resolution mass spectrometry, Orbitrap HF-X) of plasma-sEV derived from HD (x10) and patients with MM (x8) or pre-malignant conditions (monoclonal gammopathy of undetermined significance - MGUS x10; smouldering/asymptomatic MM - SMM x4), and functional studies (co-culture system HS5:HMCL) were performed.

Results: Stromal cells pre-treated with MM-sEV induced both HMCL proliferation (p < 0.05) and drug resistance (p < 0.0001) to anti-MM drugs (proteasome inhibitors) when compared to untreated stromal cells.The protein concentrations of MM-sEV positively correlated with tumor burden (r0.77; p=0.024).A total of 412 proteins were detected and quantified by proteomic profiling of plasma-sEV with 13 reported as highly enriched in EV marker databases (ExoCarta top 100) and 8/13 corresponding to universal cancer EV-markers proposed by Hoshino et al, Cell 2020. Gene ontology analysis of identified proteins (G:Profiler; p < 0.05) revealed enrichment for cellular component terms such as “extracellular vesicles/exosomes” and for several biological processes including “cell communication”, “endocytosis”, “cell migration”, “cellular response to stimulus”, “immune response”. Comparative analysis between our dataset and several publicly available datasets revealed sEV-markers with potential discriminatory specificity for MM, MGUS or SMM. Comparative analysis revealed 40, 40 and 41 proteins differentially regulated between HD-sEV and MM-sEV or MGUS-sEV or SMM-sEV (P < 0.05; log2 fold change ≥2). A specific protein signature identified in MM-sEV was found in ≥30% of MM-sEV but <30% HD-sEV. Specific protein signatures were also identified in MGUS-sEV (≥30% of MGUS-sEV but <30% HD-sEV or MM-sEV or SMM-sEV) and SMM-sEV (≥30% of SMM-sEV but <30% HD-sEV or MM-sEV or MGUS-sEV). These proteins were not found in human whole plasma (Lehallier et al, Nat medicine 2019) or solid tumors-derived sEV described by Hoshino et al (Cell 2020) and Vinik et al (Science Advances 2020).

Conclusions: MM-sEV may play an important role in disease progression by re-programming the tumor microenvironment. The characterization and proteomic profiling of disease-specific circulating sEV as a biomarker discovery strategy may provide translational applications in MM.

Citation Format: Antonia Reale, Tiffany Khong, Rong Xu, Irena Carmichael, Haoyun Fang, Nicholas Bingham, Sridurga Mithraprabhu, Maoshan Chen, Malarmathy Ramachandran, David W. Greening, Andrew Spencer. New targets and new approaches for multiple myeloma: Extracellular vesicles as functional liquid biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3491.

Circulating tumor DNA analysis and association with relapse in patients with primary refractory multiple myeloma receiving secondary salvage therapy

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Background: Multiple myeloma (MM) is an incurable plasma cell malignancy with a 5 year-median overall survival (OS) in newly diagnosed (ND) patients. Real-world data reveals that 23% of transplant eligible (TE) ND MM patients relapse within 12 months of starting first-line bortezomib (1LB) based therapy and of these ̃50% will fail secondary therapy and die within 18 months. It is currently impossible to identify these high-risk patients and genomic studies could potentially inform alternative secondary therapeutic options. We propose that circulating tumour DNA (ctDNA) analysis could provide a more holistic approach to determine genomics of high-risk patients than bone marrow (BM) tumour DNA analysis in this genetically heterogenous multi-site malignancy. Methods: Peripheral blood plasma and BM samples (n = 186) were obtained at baseline, cycle 3 day 1 (C3D1), end of the study (EOS) and/or relapse, whichever appeared earlier, from a Phase II multicentre single arm study of carfilzomib-thalidomide-dexamethasone (KTd) in 50 TE ND MM patients who were refractory or registered suboptimal response to 1LB (Australasian Leukaemia and Lymphoma Group - MM17 trial). Somatic variants were identified in BM or ctDNA with ultra-sensitive targeted amplicon sequencing of 22-genes known to be mutated in MM. Mutational spectrum was correlated to standard MM risk factors including International Staging System (ISS), response to 1LB and KTd, cytogenetics/FISH, lactate dehydrogenase (LDH) levels, progression-free survival (PFS) and OS. Results: Our initial analysis of ctDNA mutational proportions between patients who did not or did experience relapse on KTd revealed a significantly higher proportion of RAS/RAF (3% vs 25%), or ATM/ATR/TP53 (17% vs 41%; p < 0.0001), respectively, in relapse patients. Subsequently, we correlated ctDNA RAS/RAF and/or ATM/ATR/TP53 mutational presence to standard MM risk factors. We identified a shorter PFS and OS for ISS Stage 2 and 3 compared to Stage 1 patients (p = 0.002 and p = 0.02, respectively) and a significantly higher proportion of RAS/RAF or ATM/ATR/TP53 mutations in patients with refractory as compared to sub-optimal response to 1LB therapy (p = 0.0002). Patients with RAS/RAF or ATM/ATR/TP53 mutations in ctDNA at the time of starting salvage therapy also had a shorter PFS and OS on KTd (p = 0.003 and p = 0.02, respectively). Sequential ctDNA analysis discovered that in 87.5% of patients, one or more of the dominant mutations present at the time of relapse were already present at the start of salvage therapy. Conclusions: Our analysis reveals that RAS/RAF and ATM/ATR/TP53 mutations in ctDNA could be prognostic biomarkers of response to secondary salvage therapy in primary refractory patients thus providing the opportunity to design targeted salvage treatment paradigms in high-risk MM patients.

Translational Potential of RNA Derived From Extracellular Vesicles in Multiple Myeloma

The cross-talk between tumour cells and stromal cells is a hallmark of multiple myeloma (MM), a blood cancer that still remains incurable despite increased knowledge of its biology and advances in its treatment. Extracellular vesicles (EVs) derived from both tumour and stromal cells have been shown to play an important role in mediating this cross-talk ultimately favouring MM progression and drug resistance. Furthermore, EVs and their content including RNA (EV-RNA) have been successfully isolated from blood and are being explored as liquid biomarkers in MM with the potential to improve diagnosis and monitoring modalities with a minimally-invasive and repeatable analysis, i.e. liquid biopsy. In this review, we describe both the role of EV-RNA in defining the biological features of MM and their potential translational relevance as liquid biomarkers, therapeutic targets and delivery systems. We also discuss the limitations and technical challenges related to the isolation and characterization of EVs and provide a perspective on the future of MM-derived EV-RNA in translational research.

Phase II trial of single-agent panobinostat consolidation improves responses after sub-optimal transplant outcomes in multiple myeloma

Panobinostat is a pan-deacetylase inhibitor that modulates the expression of oncogenic and immune-mediating genes involved in tumour cell growth and survival. We evaluated panobinostat-induced post-transplant responses and identified correlative biomarkers in patients with multiple myeloma who had failed to achieve a complete response after autologous transplantation. Patients received panobinostat 45 mg administered three-times weekly (TIW) on alternate weeks of 28-day cycles commencing 8-12 weeks post-transplant. Twelve of 25 patients (48%) improved their depth of response after a median (range) of 4·3 (1·9-9·7) months of panobinostat. In responders, T-lymphocyte histone acetylation increased after both three cycles (P < 0·05) and six cycles (P < 0·01) of panobinostat when compared to baseline, with no differences in non-responders. The reduction in the proportion of CD127+ CD8+ T cells and CD4:CD8 ratio was significantly greater, after three and six cycles of panobinostat compared to pre-transplant, in non-responders when compared to responders. Whole marrow RNA-seq revealed widespread transcriptional changes only in responders with baseline differences in genes involved in ribosome biogenesis, oxidative phosphorylation and metabolic pathways. This study confirmed the efficacy of panobinostat as a single agent in multiple myeloma and established acetylation of lymphocyte histones, modulation of immune subsets and transcriptional changes as pharmacodynamic biomarkers of clinical benefit.

Human myeloma cell- and plasma-derived extracellular vesicles contribute to functional regulation of stromal cells

Circulating small extracellular vesicles (sEV) represent promising non-invasive biomarkers that may aid in the diagnosis and risk-stratification of multiple myeloma (MM), an incurable blood cancer. Here, we comprehensively isolated and characterized sEV from human MM cell lines (HMCL) and patient-derived plasma (psEV) by specific EV-marker enrichment and morphology. Importantly, we demonstrate that HMCL-sEV are readily internalised by stromal cells to functionally modulate proliferation. psEV were isolated using various commercial approaches and pre-analytical conditions (collection tube types, storage conditions) assessed for sEV yield and marker enrichment. Functionally, MM-psEV was shown to regulate stromal cell proliferation and migration. In turn, pre-educated stromal cells favour HMCL adhesion. psEV isolated from patients with both pre-malignant plasma cell disorders (monoclonal gammopathy of undetermined significance [MGUS]; smouldering MM [SMM]) and MM have a similar ability to promote cell migration and adhesion, suggesting a role for both malignant and pre-malignant sEV in disease progression. Proteomic profiling of MM-psEV (305 proteins) revealed enrichment of oncogenic factors implicated in cell migration and adhesion, in comparison to non-disease psEV. This study describes a protocol to generate morphologically-intact and biologically functional sEV capable of mediating the regulation of stromal cells, and a model for the characterization of tumour-stromal cross-talk by sEV in MM.

Male age is associated with sperm DNA/chromatin integrity

The diagnosis of sperm DNA integrity is increasingly recognized as being crucial to inform the clinical course in infertile couples. An internationally accepted sperm DNA fragmentation assay that determines the proportion of sperm and degree of broken sperm nuclear DNA with recognised clinical thresholds for identifying men at risk of infertility is the Sperm Chromatin Structure Assay (SCSA^®). In this study, SCSA^® test was utilised to evaluate the relevance of male age on sperm DNA quality in total of 6881 males of Indian origin. Analysis of proportions of DNA fragmentation index (%DFI) and high DNA stainability (%HDS) was performed based on four groups (<35, 35-40, 40-45, and >45 years of age). The impact of increasing male age on %DFI revealed that males >45 years of age had the highest %DFI and lowest %HDS compared to all other age groups (p<.001). This study is the largest population study and first of its kind in India that utilises SCSA^® to assess the relevance of %DFI and %HDS to increasing age with potentially important implications for the choice of clinical course based on age and sperm quality of infertile males in India.

Sperm chromatin structure assay versus sperm chromatin dispersion kits: Technical repeatability and choice of assisted reproductive technology procedure

Objective

The sperm DNA fragmentation index (DFI) guides the clinician’s choice of an appropriate assisted reproductive technology (ART) procedure. The DFI can be determined using commercially available methodologies, including sperm chromatin dispersion (SCD) kits and sperm chromatin structure assay (SCSA). Currently, when DFI is evaluated using SCD kits, the result is analyzed in reference to the SCSA-derived threshold for the choice of an ART procedure. In this study, we compared DFI values obtained using SCSA with those obtained using SCD and determined whether the difference affects the choice of ART procedure.

Methods

We compared SCSA to two SCD kits, CANfrag (n=36) and Halosperm (n=31), to assess the DFI values obtained, the correlations between tests, the technical repeatability, and the impact of DFI on the choice of ART.

Results

We obtained higher median DFI values using SCD kits than when using SCSA, and this difference was significant for the CANfrag kit (p<0.001). The SCD kits had significantly higher coefficients of variation than SCSA (p<0.001). In vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) would be chosen for a significantly higher proportion of patients if a decision were made based on DFI derived from SCD rather than DFI determined using SCSA (p=0.003).

Conclusion

Our results indicate that SCD kit-specific thresholds should be established in order to avoid the unnecessary use of IVF/ICSI based on sperm DNA damage for the management of infertility. Appropriate measures should be taken to mitigate the increased variability inherent to the methods used in these tests.

TOP2A expression predicts responsiveness to carfilzomib in myeloma and informs novel combinatorial strategies for enhanced proteasome inhibitor cell killing

Microarray was utilized to determine if a genetic signature associated with resistance to carfilzomib (CFZ) could be identified. Twelve human myeloma (MM) cell lines (HMCLs) were treated with CFZ and a cell-viability profile was assessed categorizing HMCLs as sensitive or resistant to CFZ. The gene expression profiles (GEP) of untreated resistant versus sensitive HMCLs revealed 29 differentially expressed genes. TOP2A, an enzyme involved in cell cycle and proliferation, was overexpressed in carfilzomib-resistant HMCLs. TOP2A protein expression levels, evaluated utilizing trephine biopsy specimens acquired prior to treatment with proteasome inhibitors, were higher in patients failing to achieve a response when compared to responding patients. Logistic-regression analysis confirmed that TOP2A protein expression was a highly significant predictor of response to PIs (AUC 0.738). Further, the combination of CFZ with TOP2A inhibitors, demonstrated synergistic cytotoxic effects in vitro, providing a rationale for combining topoisomerase inhibitors with CFZ to overcome resistance in MM.

Utility of Circulating Cell-Free RNA Analysis for the Characterization of Global Transcriptome Profiles of Multiple Myeloma Patients

In this study, we evaluated the utility of extracellular RNA (exRNA) derived from the plasma of multiple myeloma (MM) patients for whole transcriptome characterization. exRNA from 10 healthy controls (HC), five newly diagnosed (NDMM), and 12 relapsed and refractory (RRMM) MM patients were analyzed and compared. We showed that ~45% of the exRNA genes were protein-coding genes and ~85% of the identified genes were covered >70%. Compared to HC, we identified 632 differentially expressed genes (DEGs) in MM patients, of which 26 were common to NDMM and RRMM. We further identified 54 and 191 genes specific to NDMM and RRMM, respectively, and these included potential biomarkers such as LINC00863, MIR6754, CHRNE, ITPKA, and RGS18 in NDMM, and LINC00462, PPBP, RPL5, IER3, and MIR425 in RRMM, that were subsequently validated using droplet digital PCR. Moreover, single nucleotide polymorphisms and small indels were identified in the exRNA, including mucin family genes that demonstrated different rates of mutations between NDMM and RRMM. This is the first whole transcriptome study of exRNA in hematological malignancy and has provided the basis for the utilization of exRNA to enhance our understanding of the MM biology and to identify potential biomarkers relevant to the diagnosis and prognosis of MM patients.

Circulating Tumour DNA Analysis for Tumour Genome Characterisation and Monitoring Disease Burden in Extramedullary Multiple Myeloma

Mutational characterisation in extramedullary multiple myeloma (EM-MM) patients is challenging due to inaccessible EM plasmacytomas, unsafe nature of multiple biopsies and the spatial and temporal genomic heterogeneity apparent in MM (Graphical abstract). Conventional monitoring of disease burden is through serum markers and PET-CT, however these modalities are sometimes inadequate (serum markers), not performed in a timely manner (PET-CT) and uninformative for identifying mutations driving disease progression. DNA released into the blood by tumour cells (ctDNA) contains the predominant clones derived from the multiple disease foci. Blood-derived ctDNA can, therefore, provide a holistic illustration of the major drivers of disease progression. In this report, the utility of ctDNA, as an adjunct to currently available modalities in EM-MM, is presented for a patient with EM and oligosecretory (OS) disease. Whole exome sequencing of contemporaneously acquired tumour tissue and matched ctDNA samples revealed the presence of spatial and temporal genetic heterogeneity and the identification of pathways associated with drug resistance. Longitudinal monitoring of plasma samples revealed that ctDNA can be utilised to define the dynamic clonal evolution co-existent with disease progression and as an adjunct non-invasive marker of tumour burden.

Analysis of Circulating Tumor DNA

Circulating tumor DNA (ctDNA) analysis is currently gaining momentum as an innovative methodology for characterizing the tumor genome and monitoring therapeutic efficacy in the multifocal, genetically and spatially heterogeneous plasma cell malignancy, multiple myeloma (MM). Circulating cell-free DNA (cfDNA), which consists of a combination of DNA derived from both tumor and normal cells, is present in extracellular bodily fluids. The presence of ctDNA within this admixture has been demonstrated recently in MM. In this chapter, we describe the routinely utilized methodology for the extraction and longitudinal analysis of specific mutations present in ctDNA derived from peripheral blood plasma of MM patients.

Liquid biopsies for liquid tumors: emerging potential of circulating free nucleic acid evaluation for the management of hematologic malignancies

Circulating free nucleic acids; cell free DNA and circulating micro-RNA, are found in the plasma of patients with hematologic and solid malignancies at levels higher than that of healthy individuals. In patients with hematologic malignancy cell free DNA reflects the underlying tumor mutational profile, whilst micro-RNAs reflect genetic interference mechanisms within a tumor and potentially the surrounding microenvironment and immune effector cells. These circulating nucleic acids offer a potentially simple, non-invasive, repeatable analysis that can aid in diagnosis, prognosis and therapeutic decisions in cancer treatment.

Heavy menstrual bleeding and dysmenorrhea are improved by Magnetic Resonance Guided Focused Ultrasound Surgery (MRgFUS) of adenomyosis

Background

To assess reduction in heavy menstrual bleeding and dysmenorrhea following MRI guided Focused Ultrasound Surgery (MRgFUS) of focal and diffuse adenomyosis up to 12 months post-treatment a retrospective cohort study was done at a tertiary care academic medical center for obstetrics, gynecology and infertility.

Methods

MRgFUS for adenomyosis uterus was done for thirty-seven patients presenting with symptoms of heavy menstrual bleeding and dysmenorrhea with MRI-suspected adenomyosis. The main outcome measure, was reduction in heavy menstrual bleeding, dysmenorrhea and Symptom Severity Scoring (SSS) over a 3, 6 and 12 month period. Secondary outcome was evidence of fertility preservation post procedure. D’Agostino & Pearson omnibus normality test, one-way Ananova, Pearson’s correlation coefficient analysis was performed on the data. Statistical significances, p-value and r-value were determined.

Results

Out of 37 patients who were treated by MRgFUS, 26 had sufficient follow-up to be included in the analysis. SSS calculated at 3, 6 and 12 months was significantly over the baseline. Both heavy menstrual bleeding and dysmenorrhea, which were assessed separately, were found to significantly improve over time with a positive correlation between the two. No other intervention was required.

Conclusion

MRgFUS provides immediate and sustained relief for patients with focal and diffuse adenomyosis.

Electronic supplementary material

The online version of this article (doi:10.1186/s40738-016-0021-x) contains supplementary material, which is available to authorized users.

Dysregulated Class I histone deacetylases are indicators of poor prognosis in multiple myeloma

Histone deacetylases (HDAC) control gene expression through their ability to acetylate proteins, thereby influencing a diverse range of cellular functions. Class I HDAC (HDAC1-3 and 8) and HDAC6 are predominantly upregulated in malignancies and their altered expression in some cancers has a significant prognostic implication. The expression and prognostic consequence of dysregulated Class I HDAC and HDAC6, key players in multiple myeloma (MM), are unknown. This study hypothesized that HDAC are dysregulated in MM and patients with high expression have significantly poorer prognostic outcomes. Quantitative PCR for 11 HDAC (Class I, II, and IV) was performed in genetically heterogeneous human myeloma cell lines (HMCL) and primary MM and compared to normal plasma cells (PC). In HMCL, HDAC1-3 and 8 (Class I), and HDAC5 and HDAC10 (Class II) were significantly upregulated compared to normal PC. In primary MM, the median expression level of all of the HDAC, except HDAC1 and HDAC11, were elevated when compared to normal PC. Patients with higher levels of HDAC1-3, HDAC4, HDAC6, and HDAC11 transcripts demonstrated a significantly shorter progression-free survival (PFS). Immunohistochemical staining for HDAC1 and HDAC6 on bone marrow trephines from a uniformly treated cohort of transplant eligible MM patients revealed that HDAC1 protein was detectable in most patients and that higher levels of MM cell HDAC1 protein expression (≥90 % versus ≤20 % MM cell positivity) correlated with both shorter PFS (P = 0 .07) and shorter overall survival (P = 0 .003). Conversely, while the majority of patients expressed HDAC6, there was no correlation between HDAC6 levels and patient outcome. Together, these results indicate that overexpression of Class I HDAC, particularly HDAC1, is associated with poor prognosis in MM.

Abstract 1015: Targeting actin cytoskeleton pathway overcomes resistance to histone deacetylase inhibitors in multiple myeloma cells

Histone deacetylase inhibitors (HDACi) are novel therapeutics compounds being utilised in multiple myeloma (MM) clinical trials in combination with approved and investigational agents. While proteasome inhibitors are known to synergise effectively with HDACi, there is a lack of understanding concerning other potential partner drugs. In this report, utilising human myeloma cell lines (HMCL) as a paradigm, gene expression profile was performed to determine if a genetic signature associated with HDACi-resistance could be identified. Nine HMCLs were treated with HDACi (LBH589, SAHA or FK228) and cell death proportion determined after 48 hours through flow cytometric enumeration of propidium iodide staining. Of the nine cell lines, five were sensitive (70-90% cell death), two showed an intermediate response (70-40%) and two were resistant (40-10%) to HDACi. Following the determination of HDACi-response of HMCLs, RNA was extracted from untreated cell lines and gene expression profiling was performed utilising the Illumina HT-12 platform. Analysis revealed that 97 genes were differentially regulated between the sensitive and resistant cell lines. Gene ontology enrichment analysis identified six pathways that were significantly different and these included notch signalling pathway (p=0.01), protein processing in endoplasmic reticulum (p=0.02), glutathione metabolism (p=0.01), melanoma (p=0.02), regulation of actin cytoskeleton (p=0.03) and apoptosis (p=0.03). Furthermore, 4889 probes were tested for their correlation to grade of sensitivity using Spearmann rank algorithm and 35 genes were found to have &gt;80% correlation. Enrichment analyses indicated two pathways as being significantly different based on their correlation to HDACi-sensitivity and these included regulation of actin cytoskeleton (p=0.03) and protein processing in endoplasmic reticulum (p=0.02). The actin cytoskeleton represents a major network of proteins that impinge on motility, invasion, polarity, survival and growth of normal cells, and is often altered in tumour cells. Actin cytoskeleton modifications are known to be involved in MM cell metastasis and a number of agents that destabilize the action cytoskeleton have been utilised in MM pre-clinical studies. When HDACi-resistance cell lines were treated with a combination of HDACi and actin cytoskeleton pathway inhibitors (MEK inhibitor - GSK1120212, focal adhesion inhibitors - TAE-226 and PF-573228 and actin cytoskeleton destabilising agents - NVP-HSP990 and AUY922), synergistic cell death was observed, indicating that these agents can be used in combination with HDACi for MM therapy. This report provides a rationalistic approach for identification of HDACi partner drugs for anti-MM therapy and has provided the framework to identify promising new therapeutic combinations for the treatment of MM utilising HDACi.

Citation Format: Sridurga Mithraprabhu, Tiffany Khong, Andrew Spencer. Targeting actin cytoskeleton pathway overcomes resistance to histone deacetylase inhibitors in multiple myeloma cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1015. doi:10.1158/1538-7445.AM2013-1015

Abstract 1007: Histone acetylation mediated by inhibition of Class I histone deacetylases is critical for induction of cell death in multiple myeloma cells

Histone deacetylase inhibitors (HDACi) are being evaluated as novel chemotherapeutics in combination with approved and investigational drugs for multiple myeloma (MM) therapy. Despite the rapid advancement in the use of HDACi in MM therapy, it is still not clear which HDAC needs to be inhibited to attain maximal MM cell death. HDAC6, a mediator of the proteasome pathway through its ability to deacetylate tubulin, is considered to be a critical target to promote MM cell apoptosis. However the contribution of Class I HDACs is still unclear. To determine the HDAC that needs to be inhibited in MM, cell death induced by pan-HDACi (LBH589) was compared to Class I HDACi (FK228), selective Class I and HDAC6 inhibitors (ACY-1215, ACY-738) and a specific HDAC6 inhibitor (ACY-738) utilising human myeloma cell lines (HMCL). The specificity of these HDACi was determined by characterizing the acetylation induced in histones (H2A, H2B, H3 and H4) and tubulin through flow cytometry. The histone acetylation pattern of LBH589 and FK228 were similar, ACY-1215 and ACY-738 have comparatively lesser but discernible histone acetylation, while ACY-775 did not acetylate histones. ACY-1215, ACY-738 and ACY-775 acetylate tubulin at amounts significantly higher than LBH589, while FK228 did not acetylate tubulin. To determine if there was a correlation between the pattern of acetylation and MM cell death, eight HMCLs were treated with each HDACi and proportion of cell death measured through flow cytometric enumeration of propidium iodide staining. LBH589 (50 nM) or FK228 (50 nM) induced the same amount of cell death irrespective of the HMCL used whereas ACY-1215 and ACY-738 were able to induce cell death comparable to the LBH589 and FK228 only at the highest concentration used (10 μM). Conversely, ACY-775, which induces negligible histone acetylation, was not able to induce cell death comparable to the other inhibitors except against RPMI-8226 where ACY-775 (10 μM) alone was able to cause a significant amount of cell death. Assessment of apoptosis following exposure of primary MM cells (n=8) to HDACi recapitulated the findings with the HMCL wherein ACY-775 caused the least amount of cell death. ACY-1215 and ACY-738 at higher concentrations (10 μM) were comparable to LBH589 and FK228 in all samples tested and as in the case with the HMCLs, a minority of patients (2/8) showed some cell death with ACY-775 treatment alone. These data suggest that activity against Class I HDACs is more effective than HDAC6 alone in inducing MM cell death. Specific HDAC6 inhibition does induce comparable cell death of some MM cells suggesting that in a subset of patients, inhibiting HDAC6 alone may be as efficient as Class I HDAC inhibition and identifying these patients is important. However, it is clear that in several instances histone acetylation mediated by inhibition of Class I HDAC is sufficient to induce significant MM cell death.

Citation Format: Sridurga Mithraprabhu, Tiffany Khong, Simon S. Jones, Andrew Spencer. Histone acetylation mediated by inhibition of Class I histone deacetylases is critical for induction of cell death in multiple myeloma cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1007. doi:10.1158/1538-7445.AM2013-1007

Abstract 4710: Deactylases in multiple myeloma: Expression, inhibition and resistance to inhibition

Deacetylases (DACs) are a highly conserved group of enzymes that regulate a myriad of cellular functions through deacetylation of histones, transcription factors and molecular chaperones. Altered DAC expression is significantly associated with poor prognosis in solid and haematological malignancies, however the expression pattern and correlation of dysregulated expression to patient outcome has not been characterized in multiple myeloma (MM) cells. To address this, quantitative PCR was performed for DAC1-11 on MM (n=60) and normal plasma cells (n=11) purified from bone-marrow (BM) samples. Analyses revealed that median levels of all DACs, with the exception of DAC1 and DAC11, were significantly altered in MM. Interestingly, patients with increased DAC1, 2 and 6 levels had a significantly shorter progression-free survival from diagnosis compared to patients with lower levels. Inhibitors to DACs (DACi) are currently being used in clinical trials of multiple myeloma (MM), either alone or in combination with other novel and conventional anti-MM agents. Despite the rapid advancement in the use of DACi in MM therapy, it is still not clear which DAC needs to be inhibited to attain maximal MM cell death. To determine this, pan-inhibitors (LBH589 and SAHA) or isoform-specific inhibitors (FK228 and Tubacin) were tested for their cytotoxic potential on BM mononuclear cells from MM patients (n=10). Flow cytometric enumeration of CD38hi/CD45neg/APO2.7pos cell populations was performed to determine the proportion of apoptosis after 48 hours. Results indicated that inhibiting Class I DAC induced maximal MM cell death (75-90%) in 7/10 patient samples tested. Further experiments will include specifically targeting Class I DAC (DAC1, 2, 3 and 8) to determine which of these contribute to MM cell biology. Although DACi clinical trials show promising results, some patients are non-responsive to DACi therapy. Human myeloma cell lines (HMCLs) were used as a paradigm to identify genes associated with DACi resistance. Gene expression analysis was performed on nine HMCLs pre-determined to be DACi-sensitive or -resistant to identify genes differentially regulated between these categories. Of the 97 genes that were differentially regulated, 35-genes had &gt;80% correlation (positive or negative) to DACi-sensitivity. Future work will include validation of these genes to identify candidate biomarkers that can be used to predict the response of an MM patient to DACi-response. In conclusion, this study has established that DAC levels are altered in MM and this dysregulation correlates to poor outcome, and inhibiting class I DAC is critical to induce maximal MM cell death. In addition, preliminary data indicates the existence of a gene signature associated with DACi-sensitivity in MM cells providing the framework to identify candidate biomarkers to predict response of an MM patient to DACi therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4710. doi:1538-7445.AM2012-4710

Deactylase inhibition in myeloproliferative neoplasms

Myeloproliferative neoplasms (MPN) are clonal haemopoietic progenitor cell disorders characterized by the proliferation of one or more of the haemopoietic lineages (myeloid, erythroid and/or megakaryocytic). The MPNs include eight haematological disorders: chronic myelogenous leukemia (CML), polycythemia vera (PV), essential thrombocythemia (ET), primary myelofibrosis (PMF), systemic mastocytosis (SM), chronic eosinophilic leukemia, not otherwise specified (CEL, NOS), chronic neutrophilic leukemia (CNL), and unclassifiable MPN (MPN, U). Therapeutic interventions for MPNs include the use of tyrosine kinase inhibitors (TKIs) for BCR-ABL1(+) CML and JAK2 inhibitors for PV, ET and PMF. Histone deacetylase inhibitors (HDACi) are a novel class of drugs capable of altering the acetylation status of both histone and non-histone proteins, thereby affecting a repertoire of cellular functions in neoplastic cells including proliferation, differentiation, immune responses, angiogenesis and survival. Preliminary studies indicate that HDACi when used in combination with tyrosine kinase or JAK2 inhibitors may overcome resistance to the latter agents and enhance the pro-apoptotic effects on MPN cells. This review provides a review of pre-clinical and clinical studies that have explored the use of HDACi as potential therapeutics for MPNs.

Activin bioactivity affects germ cell differentiation in the postnatal mouse testis in vivo

The transforming growth factor beta superfamily ligand activin A controls juvenile testis growth by stimulating Sertoli cell proliferation. Testicular levels are highest in the first postnatal week, when Sertoli cells are proliferating and spermatogonial stem cells first form. Levels decrease sharply as Sertoli cell proliferation ceases and spermatogenic differentiation begins. We hypothesized that changing activin levels also affect germ cell maturation. We detected an acute and developmentally regulated impact of activin on Kit mRNA in cocultures of Sertoli cells and germ cells from Day 8, but not Day 4, mice. Both stereological and flow cytometry analyses identified an elevated spermatogonium:Sertoli cell ratio in Day 7 testes from Inhba(BK/BK) mice, which have decreased bioactive activin, and the germ cell markers Sycp3, Dazl, and Ccnd3 were significantly elevated in Inhba(BK/BK) mice. The flow cytometry measurements demonstrated that surface KIT protein is significantly higher in Day 7 Inhba(BK/BK) germ cells than in wild-type littermates. By Day 14, the germ cell:Sertoli cell ratio did not differ between genotypes, but the transition of type A spermatogonia into spermatocytes was altered in Inhba(BK/BK) testes. We conclude that regulated activin signaling not only controls Sertoli cell proliferation, as previously described, but also influences the in vivo progression of germ cell maturation in the juvenile testis at the onset of spermatogenesis.

Control of KIT signalling in male germ cells: what can we learn from other systems?

The KIT ligand (KITL)/KIT-signalling system is among several pathways known to be essential for fertility. In the postnatal testis, the KIT/KITL interaction is crucial for spermatogonial proliferation, differentiation, survival and subsequent entry into meiosis. Hence, identification of endogenous factors that regulate KIT synthesis is important for understanding the triggers driving germ cell maturation. Although limited information is available regarding local factors in the testicular microenvironment that modulate KIT synthesis at the onset of spermatogenesis, knowledge from other systems could be used as a basis for identifying how KIT function is regulated in germ cells. This review describes the known regulators of KIT, including transcription factors implicated in KIT promoter regulation. In addition, specific downstream outcomes in biological processes that KIT orchestrates are addressed. These are discussed in relationship to current knowledge of mammalian germ cell development.

170. TGFβ SIGNALING IN AN IN VITRO SEMINOMA MODEL

Testicular cancer, the second most common malignancy in young men, has a 95% cure rate but can result in infertility or subfertility. Its incidence has increased significantly in recent decades (1). This cancer is thought to arise during embryogenesis, based on the persistence of embryonic germ cell markers such as Blimp1 (2), Oct3/4 (3) and Nanog (3) in adult seminoma cells. TCam2 cells are a recently characterised in vitro seminoma model (4). We show by Q-PCR and immunofluorescence that they also express these early germ cell markers. TGFβ signaling plays a key role during germ cell development, and is implicated in the development of testicular cancers (5, 6). To investigate this further, we first determined whether the pathway is active in TCam2 cells. By Q-PCR we demonstrate expression of the TGFβ downstream transcription factors Smad 2, 3 and 4, and Activin type I and II receptors. Importantly, ActRIIA, which is undetectable in adult testicular germ cells, but readily detected in human foetal germ cells (7) and clinical seminoma samples (6), is readily detectable at both the mRNA and protein level in TCam2 cells. Furthermore, 24 hour treatment with Activin (5 and 50ng/ml) or BMP4 (5 and 50ng/ml) induces a 3-4 fold increase in ActRIIA mRNA levels, but not ActRIA, ActRIB or ActRIIB. Strikingly, in TCam2 cells BMP4 and to a lesser extent retinoic acid, but not activin, support survival and proliferation of TCam2 cells in the absence of serum. This is consistent with known roles of BMP4 and retinoic acid in enhancing murine foetal germ cell proliferation/self-renewal and survival (8, 9), and activin inhibition of foetal murine germ cell proliferation (10). This study is the first to demonstrate a functional response in seminoma cells consistent with their foetal germ cell-like identity and forms the basis for future mechanistic analyses of the role of TGFβ signaling in human testicular cancer.

249. Regulated expression of KIT protein in juvenile and adult germ cells of the rodent testis

KIT receptor is an established marker of differentiating spermatogonia and its activation is required to trigger spermatogonial maturation. KIT mRNA, however, can be detected in undifferentiated spermatogonia in the absence of protein expression, as previously established by us in the irradiated adult rat testes [1]. This differential regulation of mRNA and protein is presumably modulated by either local hormone action or by cues from the adult testicular microenvironment. Endogenous regulatory factors known to stimulate KIT synthesis in juvenile male germ cells in vitro are bone morphogenetic protein 4 (BMP4) and retinoic acid (RA), while factors known to suppress KIT at the onset of spermatogenesis have not yet been identified. Activin A, implicated in KIT downregulation in a murine erythroleukemia cell line [2], is produced within the juvenile mammalian testis and influences activities of spermatogonia and Sertoli cells. We hypothesised that activin acts to repress KIT expression in spermatogonia and therefore modulate spermatogonial behaviour. Evidence for this was first derived from Sertoli and germ cell co-cultures of day 8 wild type mouse testes in which exogenous activin addition caused a dose-dependent reduction of KIT mRNA. Whole testes mRNA analyses of two activin transgenic mouse models, the newborn Inhba−/− (lacking activin A) and postnatal InhbaBK/BK (decreased bioactive activin), revealed a significant elevation in KIT expression relative to wild type littermates. In the postnatal day 7 InhbaBK/BK testes, an elevated proportion of differentiated spermatogonia, increased cell surface KIT protein levels, enhanced mRNA levels of a known downstream target of KIT signalling pathway, cyclind3 and a meiotic marker, Sycp3, were observed. These data provide the first comprehensive evidence for activin modulation of KIT expression at spermatogenesis onset, in germ cells of the juvenile testis. This finding is of fundamental importance to other KIT-dependent processes. (1) Prabhu, S.M., et al. Expression of c-Kit receptor mRNA and protein in the developing, adult and irradiated rodent testis. Reproduction, 2006. 131(3): p. 489–99. (2) Hino, M., et al. Down-modulation of c-kit mRNA and protein expression by erythroid differentiation factor/activin A. FEBS Lett, 1995. 374(1): p. 69–71.