Biology subjects

Blaney, P.

Publications and source records attributed to Blaney, P..

7 recordsLinked to original sources

bioRxiv2025

Mining and e-waste recycling influence the spatial distribution of technology-critical elements, but not rare earth elements, in boreal lakes

Mining and more recent e-waste recycling have contributed trace elements (TEs) to the environment. However, the occurrence of emerging technology-critical elements (TCEs), including rare earth elements (REEs), remains poorly reported. Our study aims to i) investigate the spatial distribution of TEs, including TCEs, across different environmental matrices; ii) compare measured concentrations in water and sediment against environmental quality guidelines; and iii) assess potential risks to human health from fish consumption. In this study, we sampled water, sediment, and fish tissues (muscle and liver) across six boreal lakes near the historically mining region of Rouyn-Noranda, home to North Americas largest copper smelting and recycling facility (Horne Smelter). Concentrations of TEs (e.g., Cu, Se) were higher in lakes closest to the smelter. Similarly, some TCEs (i.e., Ti, Co, Tl) followed this same spatial distribution pattern, suggesting that their release may be linked to historical and current mining activities. Conversely, REEs displayed distinct spatial patterns, likely influenced by geological sources rather than pollution. Several TEs (e.g., Zn, Cd, Pb) exceeded Canadian water and sediment quality guidelines in lakes closer to the mining area. Muscle tissue from walleye or yellow perch showed Zn, Cd, or Pb concentrations above safety limits in at least one lake. This study highlights the importance of including emerging TCEs (e.g., Sr, Tl, Co) in biomonitoring programs. Our findings provide critical insights into the environmental distribution of TEs across multiple matrices of boreal lake ecosystems, contributing to global efforts in risk assessment and sustainable freshwater management in the context of growing electronic waste recycling. Highlights{blacksquare} First report of various TCEs and REEs in 3 matrices of boreal lakes {blacksquare}The spatial distribution of several newly reported TCEs is similar to that of historical TEs {blacksquare}REE concentrations are associated with geology rather than mining sources {blacksquare}Some TE concentrations in water and sediment are above guidelines in closest lakes {blacksquare}All lakes exceeded safety limits for at least one element (Zn, Cd, or Pb) in the muscle tissue of either walleye or yellow perch

ecology↗

bioRxiv2025

Live fast and die young: walleye populations adapt their life cycle to degraded lakes of the Canadian clay belt.

Despite its widespread distribution in North America, many populations of walleye (Sander vitreus) declined to the point where restoration measures, including restocking, are necessary. In this study, we compared population structure and dietary composition of walleye populations in two degraded lakes and two non-degraded lakes in the Abitibi-Temiscamingue region of Quebec, Canada. Food resources were assessed for walleye larvae, young-of-the-year, juveniles, and adults. Growth and relative abundance were also quantified for young-of-the-year, juvenile, and adult walleye. Young-of-the-year were more abundant and grew faster in degraded lakes compared to non-degraded controls, benefiting from high populations of spring zooplankton, which are a critical larval resource. The simplified food webs in degraded lakes lacked pollution-sensitive macroinvertebrates, which resulted in walleye diets being even more dominated by fish. Although juveniles and adults were equally or more abundant in degraded lakes compared to control lakes, premature adult mortality compromised population stability. We recommend focusing on improving adult fish habitat, manage for prey species, and review fishing regulations to enhance the survival of mature walleye and ensure sustainable populations.

ecology↗

bioRxiv2024

Temporal Genomic Dynamics Shape Clinical Trajectory in Multiple Myeloma

To comprehensively unravel the temporal relationship between initiating and driver events and its impact on clinical outcomes, we analyzed 421 whole-genome sequencing profiles from 382 patients. Using clock-like mutational signatures, we estimated a time lag of 2-4 decades between initiating events and diagnosis. In patients with hyperdiploidy, we demonstrate that trisomies of odd-numbered chromosomes can be acquired simultaneously with other chromosomal gains, such as 1q gain. We provide evidence that hyperdiploidy is acquired after canonical IGH translocation when both events are present. Finally, patients with early 1q gain had adverse outcomes similar to those with 1q amplification (>1 extra-copies), but faring worse than those with late 1q gain. This underscores that the prognostic impact of 1q gain/amp depends more on the timing of acquisition than on the number of extra copies gained. Overall, this study contributes to a better understanding of the life history of MM and may have prognostic implications.

cancer biology↗

bioRxiv2023

Impact of rare structural variant events in newly diagnosed multiple myeloma

Whole genome sequencing (WGS) of newly diagnosed multiple myeloma patients (NDMM) has shown recurrent structural variant (SV) involvement in distinct regions of the genome (i.e. hotspots) and causing recurrent copy number alterations. Together with canonical immunoglobulin translocations, these SVs are recognized as "recurrent SVs". More than half SVs were not involved in recurrent events. The significance of these "rare SVs" has not been previously examined. In this study, we utilize 752 WGS and 591 RNA-seq data from NDMM patients to determine the role of rare SVs in myeloma pathogenesis. 94% of patients harbored at least one rare SV event. Rare SVs showed an SV-class specific enrichment within genes and superenhancers associated with outlier gene expression. Furthermore, known myeloma driver genes recurrently impacted by point mutations were dysregulated by rare SVs. Overall, we demonstrate the association of rare SVs with aberrant gene expression supporting a driver role in myeloma pathogenesis. SIGNIFICANCECharacterization of multiple myeloma genome revealed that more than half structural variants are not involved in recurrent events. Here, we demonstrate that these rare SVs hold potential for myeloma pathogenesis through their gene expression impact. Rare SVs contribute to MM heterogeneity and have implications for development of individualized treatment.

cancer biology↗

bioRxiv2020

Copy number signatures predict chromothripsis and associate with poor clinical outcomes in patients with newly diagnosed multiple myeloma

Chromothripsis is detectable in 20-30% of newly diagnosed multiple myeloma (NDMM) patients and is emerging as a new independent adverse prognostic factor. In this study, we interrogate 752 NDMM patients using whole genome sequencing (WGS) to study the relationship of copy number (CN) signatures to chromothripsis and show they are highly associated. CN signatures are highly predictive of the presence of chromothripsis (AUC=0.90) and can be used to identify its adverse prognostic impact. The ability of CN signatures to predict the presence of chromothripsis was confirmed in a validation series of WGS comprised of 235 hematological cancers (AUC=0.97) and an independent series of 34 NDMM (AUC=0.87). We show that CN signatures can also be derived from whole exome data (WES) and using 677 cases from the same series of NDMM, we were able to predict both the presence of chromothripsis (AUC=0.82) and its adverse prognostic impact. CN signatures constitute a flexible tool to identify the presence of chromothripsis and is applicable to WES and WGS data.

genomics↗

bioRxiv2020

Accelerated single cell seeding in relapsed multiple myeloma

The malignant progression of multiple myeloma is characterized by the seeding of cancer cells in different anatomic sites followed by their clonal expansion. It has been demonstrated that this spatial evolution at varying anatomic sites is characterized by genomic heterogeneity. However, it is unclear whether each anatomic site at relapse reflects the expansion of pre-existing but previously undetected disease or secondary seeding from other sites. Furthermore, genomic evolution over time at spatially distinct sites of disease has not been investigated in a systematic manner. To address this, we interrogated 25 samples, by whole genome sequencing, collected at autopsy from 4 patients with relapsed multiple myeloma and demonstrated that each site had a unique evolutionary trajectory characterized by distinct single and complex structural variants and copy number changes. By analyzing the landscape of mutational signatures at these sites and for an additional set of 125 published whole exomes collected from 51 patients, we demonstrate the profound mutagenic effect of melphalan and platinum in relapsed multiple myeloma. Chemotherapy-related mutagenic processes are known to introduce hundreds of unique mutations in each surviving cancer cell. These mutations can be detectable by bulk sequencing only in cases of clonal expansion of a single cancer cell bearing the mutational signature linked to chemotherapy exposure thus representing a unique single-cell genomic barcode linked to a discrete time window in each patients life. We leveraged this concept to show that multiple myeloma systemic seeding is accelerated at clinical relapse and appears to be driven by the survival and subsequent expansion of a single myeloma cell following treatment with high dose melphalan therapy and autologous stem cell transplant.

cancer biology↗

bioRxiv2019

Revealing the impact of recurrent and rare structural variants in multiple myeloma

The landscape of structural variants (SVs) in multiple myeloma remains poorly understood. Here, we performed comprehensive classification and analysis of SVs in multiple myeloma, interrogating a large cohort of 762 patients with whole genome and RNA sequencing. We identified 100 SV hotspots involving 31 new candidate driver genes, including drug targets BCMA (TNFRSF17) and SLAMF7. Complex SVs, including chromothripsis and templated insertions, were present in 61 % of patients and frequently resulted in the simultaneous acquisition of multiple drivers. After accounting for all recurrent events, 63 % of SVs remained unexplained. Intriguingly, these rare SVs were associated with up to 7-fold enrichment for outlier gene expression, indicating that many rare driver SVs remain unrecognized and are likely important in the biology of individual tumors.

genomics↗