Clinical Outcomes and Evolution of Clonal Hematopoiesis in Patients with Newly Diagnosed Multiple Myeloma

Clonal hematopoiesis (CH) at time of autologous stem cell transplant (ASCT) has been shown to be associated with decreased overall survival (OS) and progression-free survival (PFS) in patients with multiple myeloma not receiving immunomodulatory drugs (IMiD). However, the significance of CH in newly diagnosed patients, including transplant ineligible patients, and its effect on clonal evolution during multiple myeloma therapy in the era of novel agents, has not been well studied. Using our new algorithm to differentiate tumor and germline mutations from CH, we detected CH in approximately 10% of 986 patients with multiple myeloma from the Clinical Outcomes in MM to Personal Assessment of Genetic Profile (CoMMpass) cohort (40/529 transplanted and 59/457 non-transplanted patients). CH was associated with increased age, risk of recurrent bacterial infections and cardiovascular disease. CH at time of multiple myeloma diagnosis was not associated with inferior OS or PFS regardless of undergoing ASCT, and all patients benefited from IMiD-based therapies, irrespective of the presence of CH. Serial sampling of 52 patients revealed the emergence of CH over a median of 3 years of treatment, increasing its prevalence to 25%, mostly with DNMT3A mutations.

SIGNIFICANCE

Using our algorithm to differentiate tumor and germline mutations from CH mutations, we detected CH in approximately 10% of patients with newly diagnosed myeloma, including both transplant eligible and ineligible patients. Receiving IMiDs improved outcomes irrespective of CH status, but the prevalence of CH significantly rose throughout myeloma-directed therapy.

Cross center single-cell RNA sequencing study of the immune microenvironment in rapid progressing multiple myeloma

Despite advancements in understanding the pathophysiology of Multiple Myeloma (MM), the cause of rapid progressing disease in a subset of patients is still unclear. MM's progression is facilitated by complex interactions with the surrounding bone marrow (BM) cells, forming a microenvironment that supports tumor growth and drug resistance. Understanding the immune microenvironment is key to identifying factors that promote rapid progression of MM. To accomplish this, we performed a multi-center single-cell RNA sequencing (scRNA-seq) study on 102,207 cells from 48 CD138- BM samples collected at the time of disease diagnosis from 18 patients with either rapid progressing (progression-free survival (PFS) < 18 months) or non-progressing (PFS > 4 years) disease. Comparative analysis of data from three centers demonstrated similar transcriptome profiles and cell type distributions, indicating subtle technical variation in scRNA-seq, opening avenues for an expanded multicenter trial. Rapid progressors depicted significantly higher enrichment of GZMK+ and TIGIT+ exhausted CD8+ T-cells (P = 0.022) along with decreased expression of cytolytic markers (PRF1, GZMB, GNLY). We also observed a significantly higher enrichment of M2 tolerogenic macrophages in rapid progressors and activation of pro-proliferative signaling pathways, such as BAFF, CCL, and IL16. On the other hand, non-progressive patients depicted higher enrichment for immature B Cells (i.e., Pre/Pro B cells), with elevated expression for markers of B cell development (IGLL1, SOX4, DNTT). This multi-center study identifies the enrichment of various pro-tumorigenic cell populations and pathways in those with rapid progressing disease and further validates the robustness of scRNA-seq data generated at different study centers.

Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of multiple myeloma bone marrow samples from 18 patients assessed by single-cell RNA sequencing (scRNA-seq), mass cytometry (CyTOF), and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to understand the concordance of measurements among single-cell techniques. Cell type abundances are relatively consistent across the three approaches, while variations are observed in T cells, macrophages, and monocytes. Concordance and correlation analysis of cell type marker gene expression across different modalities highlighted the importance of choosing cell type marker genes best suited to particular modalities. By integrating data from these three assays, we found International Staging System stage 3 patients exhibited decreased CD4+ T/CD8+ T cells ratio. Moreover, we observed upregulation of RAC2 and PSMB9, in natural killer cells of fast progressors compared with those of nonprogressors, as revealed by both scRNA-seq and CITE-seq RNA measurement. This detailed examination of the immune microenvironment in multiple myeloma using multiple single-cell technologies revealed markers associated with multiple myeloma rapid progression which will be further characterized by the full-scale immune atlas project.

Significance

scRNA-seq, CyTOF, and CITE-seq are increasingly used for evaluating cellular heterogeneity. Understanding their concordances is of great interest. To date, this study is the most comprehensive examination of the measurement of the immune microenvironment in multiple myeloma using the three techniques. Moreover, we identified markers predicted to be significantly associated with multiple myeloma rapid progression.

Abstract A38: A novel clinical-grade liquid biopsy platform for multiple myeloma

Direct-to-patient (DTP) multiple myeloma (MM) research studies have been launched recently, including PCROWD (NCT02269592), PROMISE (NCT03689595), and the MMRF CureCloud Research Initiative (NCT03657251), aimed at enrolling thousands of individuals from whom comprehensive molecular and immune analyses will be generated from blood specimens and the resulting data aggregated with the correlating clinical information. To support the molecular characterization of liquid biopsies for such DTP efforts, a myeloma-specific hybrid selection panel was developed that captures 70 commonly altered genes. The assay detects somatic point mutations and indels present in a patient’s circulating-free DNA (cfDNA). For this MM 70-Gene cfDNA Assay, samples are received as blood in a Streck’s tube and DNA is extracted from buffy coat using magnetic bead-based chemistry. Coverage sequencing (80,000x depth) is performed and duplex BAM files are generated with UMI alignment and de-duplication. As will be presented, MM blood specimens present a unique challenge as circulating MM cells are often present at significant levels in the buffy coat blood fraction used as the source of normal genomic DNA. The performance of the 70-Gene cfDNA Assay was thoroughly validated in order to establish the sensitivity, specificity, and reproducibility of the technical approach. First, the reference genomic DNA from unrelated healthy individuals was sequenced in replicate at deep coverage. Next, two cohorts were used, one from Dana-Farber and one from the MMRF CureCloud pilot. For both cohorts, tumor DNA samples from bone marrow aspirates (BMAs) with matched normal DNA from blood were sequenced on an orthogonal platform and compared to results from the MM 70-Gene Assay on cfDNA extracted from the same individuals. The yield of extracted cfDNA ranged from 6 ng to 80 ng, and about two third of cases yielded enough material to attempt sequencing, with failures coming mostly from individuals in remission. As will be presented, there was a very strong correlation between BMA and cfDNA and additional events could actually be detected in the blood that were not seen in the BMAs. Because this MM 70-Gene cfDNA Assay may potentially be used by treating physicians for management of care, a clinical-grade (CLIA) pipeline was established. For that CLIA pipeline, the variants reported are a subset of all the events detected by the MM 70-Gene Assay. The events detected in the assay are reviewed by a Genomic Tumor Board within the appropriate subset of territory predefined for reporting. The territory limitations are defined by the Genomic Tumor Board knowledgebase of actionable genomic territory available. In summary, we have developed a robust and very sensitive clinical-grade next-gen liquid biopsy sequencing platform allowing for less invasive monitoring of MM disease genomics that can be used to complement other more classical approaches and to help support direct-to-patient Initiatives.

Citation Format: Mark W. Bustoros, Carrie Cibulskis, Teni Dowdell, Svetlana Gavrilov, Cody Boehner, Jennifer Yesil, Steven E. Labkoff, Shaadi Mehr, Jihye Park, Romanos Sklavenitis Pistofidis, Salomon Manier, Annette S. Kim, Keith L. Ligon, Niall Lennon, Viktor Adalsteinsson, Jane Wilkinson, Irene M. Ghobrial, Daniel Auclair. A novel clinical-grade liquid biopsy platform for multiple myeloma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A38.

The unforeseen business and medical consequences of EHR data collection for a real-world data multiple myeloma registry

e19528

Background: Record retrieval on behalf of a consenting patient within the context of real-world data is not well understood. As the need for real-world data continues to expand, methods for the efficient transfer of information across consenting parties will be critical to enable research collaborations. This need was highlighted through a partnership between COTA and the Multiple Myeloma Research Foundation (MMRF). As one component of the pilot study, COTA managed the record retrieval of consenting patients before going on to abstract the data for use in a registry. Methods: The pilot study identified 23 patients that consented to the release of medical records at 54 institutions across 20 states. COTA partnered with a retrieval vendor and employed its own outreach efforts for acquisition. Outreach and retrieval techniques were similar across COTA and the vendor, including targeted calls, delivery of IRB-approved consent materials, and on-site requests. The 30-day release parameter for a covered entity under 45 CFR 164.524(b)(2) of HIPAA’s Privacy Rule was used to evaluate the observed return rates. Results: A total of 56 medical records were requested, and 48 records were retrieved. The mean (±SD) retrieval time across all sites was 33 (±58) days. We found that 54% of records were released in < = 30 days, and 32% of records > 30 days. 14% of requested records were never released, despite a median of 19 outreach attempts (range 10 to 43). Cited issues for delay or non-release consisted of 22 institutions questioning the validity of the certified electronic patient signature, 6 requiring a physical signature, and 5 requiring their own authorization forms. In no cases did the records contain structured metadata, such as LOINC, MedDRA, and RxNorm. Conclusions: This pilot showed an unpredictable variance associated with the release of records in the context of real-world data. This variance contributed to barriers and delays in broader research efforts. The lack of accompanying metadata with released records resulted in additional required data processing. Future studies should be conducted to establish best practices in the release and retrieval of medical records used to support real-world data research.

Good Citizenship Made Easy: A Step-by-Step Guide to Submitting RNA-Seq Data to NCBI

The analysis of transcriptome data from non-model organisms contributes to our understanding of diverse aspects of evolutionary biology, including developmental processes, speciation, adaptation, and extinction. Underlying this diversity is one shared feature, the generation of enormous amounts of sequence data. Data availability requirements in most journals oblige researchers to make their raw transcriptome data publicly available, and the databases housed at the National Center for Biotechnology Information (NCBI) are a popular choice for data deposition. Unfortunately, the successful submission of raw sequences to the Sequence Read Archive (SRA) and transcriptome assemblies to the Transcriptome Shotgun Assembly (TSA) can be challenging for novice users, significantly delaying data availability and publication. Here we present two comprehensive protocols for submitting RNA-Seq data to NCBI databases, accompanied by an easy-to-use website that facilitates the timely submission of data by researchers of any experience level. © 2018 by John Wiley & Sons, Inc.

Ondansetron in acute food protein-induced enterocolitis syndrome, a retrospective case-control study

BACKGROUND

Therapy for moderate to severe acute food protein-induced enterocolitis syndrome (FPIES) typically consists of intravenous fluids and corticosteroids (traditional therapy). Ondansetron has been suggested as an adjunctive treatment. We aimed to evaluate the efficacy of the parenteral (intravenous or intramuscular) ondansetron vs traditional therapy to resolve the symptoms of acute FPIES.

METHODS

Cases of FPIES who had a positive oral food challenge (OFC) were retrospectively examined at two major hospitals over a two-year period (Rome, Italy; and Sydney, Australia). The efficacy of therapy, based on the percentage of cases who stopped vomiting, was compared in cases who received parenteral ondansetron and in cases who received traditional therapy or no pharmacological therapy.

RESULTS

A total of 66 patients were included: 37 had parenteral ondansetron, 14 were treated with traditional therapy, and 15 did not receive any pharmacological therapy. Nineteen percentage of children treated with ondansetron continued vomiting after the administration of the therapy vs 93% of children who received traditional therapy (P < 0.05, relative risk = 0.2). Children who received ondansetron or no therapy were less likely to require an admission overnight compared with those who received traditional therapy (P < 0.05).

CONCLUSIONS

Parenteral ondansetron is significantly more effective than traditional therapy in resolving acute symptoms of FPIES. The relative risk = 0.2 greatly reduces the bias linked to the lack of randomization. These findings suggest an effective treatment for vomiting in positive FPIES OFCs and allow for more confidence in performing OFCs.

Comparative genomics explains the evolutionary success of reef-forming corals

Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years.

DOI:http://dx.doi.org/10.7554/eLife.13288.001

For millions of years, reef-building stony corals have created extensive habitats for numerous marine plants and animals in shallow tropical seas. Stony corals consist of many small, tentacled animals called polyps. These polyps secrete a mineral called aragonite to create the reef – an external ‘skeleton’ that supports and protects the corals.

Photosynthesizing algae live inside the cells of stony corals, and each species depends on the other to survive. The algae produce the coral’s main source of food, although they also produce some waste products that can harm the coral if they build up inside cells. If the oceans become warmer and more acidic, the coral are more likely to become stressed and expel the algae from their cells in a process known as coral bleaching. This makes the coral more likely to die or become diseased. Corals have survived previous periods of ocean warming, although it is not known how they evolved to do so.

The evolutionary history of an organism can be traced by studying its genome – its complete set of DNA – and the RNA molecules encoded by these genes. Bhattacharya et al. performed this analysis for twenty stony coral species, and compared the resulting genome and RNA sequences with the genomes of other related marine organisms, such as sea anemones and sponges. In particular, Bhattacharya et al. examined “ortholog” groups of genes, which are present in different species and evolved from a common ancestral gene. This analysis identified the genes in the corals that encode the proteins responsible for constructing the aragonite skeleton. The coral genome also encodes a network of environmental sensors that coordinate how the polyps respond to temperature, light and acidity.

Bhattacharya et al. also uncovered a variety of stress-related pathways, including those that detoxify the polyps of the damaging molecules generated by algae, and the pathways that enable the polyps to adapt to environmental stress. Many of these genes were recruited from other species in a process known as horizontal gene transfer.

The oceans are expected to become warmer and more acidic in the coming centuries. Provided that humans do not physically destroy the corals’ habitats, the evidence found by Bhattacharya et al. suggests that the genome of the corals contains the diversity that will allow them to adapt to these new conditions.

DOI:http://dx.doi.org/10.7554/eLife.13288.002

Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment

We report the identification and characterization of two new members of a family of bilirubin-inducible fluorescent proteins (FPs) from marine chlopsid eels and demonstrate a key region of the sequence that serves as an evolutionary switch from non-fluorescent to fluorescent fatty acid-binding proteins (FABPs). Using transcriptomic analysis of two species of brightly fluorescent Kaupichthys eels (Kaupichthys hyoproroides and Kaupichthys n. sp.), two new FPs were identified, cloned and characterized (Chlopsid FP I and Chlopsid FP II). We then performed phylogenetic analysis on 210 FABPs, spanning 16 vertebrate orders, and including 163 vertebrate taxa. We show that the fluorescent FPs diverged as a protein family and are the sister group to brain FABPs. Our results indicate that the evolution of this family involved at least three gene duplication events. We show that fluorescent FABPs possess a unique, conserved tripeptide Gly-Pro-Pro sequence motif, which is not found in non-fluorescent fatty acid binding proteins. This motif arose from a duplication event of the FABP brain isoforms and was under strong purifying selection, leading to the classification of this new FP family. Residues adjacent to the motif are under strong positive selection, suggesting a further refinement of the eel protein’s fluorescent properties. We present a phylogenetic reconstruction of this emerging FP family and describe additional fluorescent FABP members from groups of distantly related eels. The elucidation of this class of fish FPs with diverse properties provides new templates for the development of protein-based fluorescent tools. The evolutionary adaptation from fatty acid-binding proteins to fluorescent fatty acid-binding proteins raises intrigue as to the functional role of bright green fluorescence in this cryptic genus of reclusive eels that inhabit a blue, nearly monochromatic, marine environment.

Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)

Background

The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce.

Results

We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response.

Conclusions

We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1565-6) contains supplementary material, which is available to authorized users.

Baked egg food challenges - clinical utility of skin test to baked egg and ovomucoid in children with egg allergy

BACKGROUND

Many children with IgE-mediated egg allergy can tolerate products containing extensively heated (baked) egg. Aside from food challenge, there are no tests which reliably predict tolerance to baked egg in egg-allergic individuals.

OBJECTIVES

To determine if skin prick test (SPT) to baked egg (muffin) and ovomucoid can predict the outcome of baked egg challenges in egg allergic patients.

METHODS

In this prospective study, children with a recent history of immediate allergic reactions to egg [and corroborative positive SPT or serum-specific IgE (ssIgE) to egg] or those with SPT/ssIgE > 95% PPV for egg allergy were invited to undergo an open standardized baked egg (muffin) challenge. SPT to egg white, ovomucoid, and fresh muffin were performed immediately prior to challenge.

RESULTS

One hundred and forty-three egg allergic children underwent baked egg challenge and of these, 90 (63%) tolerated 1 g of egg protein in a baked muffin. Of the 53 positive challenges, eight (15%) had respiratory and/or cardiovascular symptoms. The median SPT diameters in positive challenges compared with negative challenges were baked muffin - 6.0 mm/4.0 mm and ovomucoid 7.5 mm/5.0 mm respectively. Receiver operating characteristic (ROC) curves were generated for SPT to baked egg and ovomucoid. The area under the curve was 0.68 for baked egg, and 0.67 for ovomucoid. A muffin SPT of < 2 mm had a negative predictive value of 88% and an ovomucoid SPT ≥ 11 mm had a positive predictive value of 100%.

CONCLUSIONS AND CLINICAL RELEVANCE

A SPT of < 2 mm to muffin had a high negative predictive value to baked egg challenge. Ovomucoid SPT ≥ 11 mm was very likely to predict a reaction to baked egg. In these children, deferring the challenge would be appropriate.

Bacterial colonization of toys in neonatal intensive care cots

OBJECTIVES

To investigate the bacteria and fungi contaminating toys in neonatal intensive care unit (NICU) cots, the colonization rates, and factors that influence them.

METHODS

A cross-sectional, longitudinal bacteriologic survey of all toys in the cots of infants in an NICU. All the toys in an infant's cot were cultured weekly for 4 weeks. Data were collected on the infant's postnatal age, the type of cot, whether humidity was added, characteristics of the toy, and any infant infections.

RESULTS

Over the 4-week period, there were 86 cultures from 34 toys of 19 infants. Bacteria were grown from 84/86 (98%): 84 of the cultures grew coagulase-negative Staphylococcus, 50 Micrococcus sp, 21 Bacillus sp, 13 methicillin-resistant Staphylococcus aureus, 12 diphtheroids, 4 group B streptococcus, 3 S aureus, 3 nonhemolytic streptococci, 3 group D streptococci, 4 alpha-hemolytic streptococci, and 2 coliforms. None grew fungi. The colonization rate did not differ with cot type, presence of humidity, size of the toy, toy fiber length, or the fluffiness score. Eight (42%) of the infants had positive blood culture results and 5/8 of the isolates (63%) were of the same type as that colonizing their corresponding toy.

IMPLICATIONS

With time, all the toys in NICU cots became colonized with bacteria. Many were potentially pathogenic. Toys may be reservoirs for potential infantile nosocomial sepsis. infant, newborn, toys, infection, neonatal intensive care.

The effect of draw-up volume on the accuracy of electrolyte measurements from neonatal arterial lines

OBJECTIVES

Contamination by infusate of blood samples withdrawn from arterial lines has been recognized but not well documented for neonates. The aim of this study was to investigate, using in vitro and in vivo studies, the effects of different draw-up volumes (withdrawn from the line prior to the sample being taken) on the concentration of sodium.

METHODS

In-vitro study: The tip of an umbilical artery catheter (dead space 0.6 mL), infused with half normal saline containing 1 unit/mL of heparin was placed in a beaker of normal saline. The line was flushed with 1 mL of this infusate just before each sample was taken. Volumes from 0.5 mL to 2.0 mL of infusate/normal saline were withdrawn in 0.1 mL increments from a three-way tap and discarded. A sample was then taken from the line into a blood gas syringe for analysis of the sodium concentration by the 860 Blood Gas Analyzer (Chiron Diagnostics, Bayer, Scoresby). Control samples were taken from the beaker. In-vivo study: A 22 gauge intravenous catheter was inserted into a vein of an adult male volunteer. The dead space was also 0.6 mL. The line was flushed with 5 mL of half-normal saline immediately before sampling. Draw-up volumes of 0.6, 0.9, 1.3, and 1.6 mL were withdrawn and discarded. 10 mL was used as a control. A 0.5-mL blood sample was then taken and the electrolyte concentrations analysed immediately.

RESULTS

In-vitro: A minimum draw-up volume of 1.3 mL was required before the sodium concentration was not significantly different from the control samples. In-vivo: A minimum draw-up volume of 1.6 mL was required before the sodium concentration was not significantly different from the control samples. There were similar trends in the effect of draw-up volume for glucose, calcium, potassium, chloride and lactate.

CONCLUSION

: A minimum volume of 1.6 mL should be withdrawn from neonatal arterial lines (dead space 0.6 mL) before taking blood for analysis.