Publications
In the previous column we showed how hidden states driving observable changes in a cell can be modeled as a hidden Markov model (HMM). To confidently use the HMM for inference or prediction, we must first train it to accurately represent observed data.
Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide and represents a heterogeneous group of tumours, the majority of which are treated with a combination of surgery, radiation and chemotherapy. Fluoropyrimidine (5-FU) and its oral pro-drug, capecitabine, are commonly prescribed treatments for several solid tumour types including HNSCC. 5-FU-associated toxicity is observed in approximately 30% of treated patients and is largely caused by germline polymorphisms in DPYD which encodes dihydropyrimidine dehydrogenase (DPD), a key enzyme of 5-FU catabolism and deactivation. Although the association of germline DPYD alterations with toxicity is well-described, the potential contribution of somatic DPYD alterations to 5-FU sensitivity has not been explored. In a patient with metastatic HNSCC, in-depth genomic and transcriptomic integrative analysis on a biopsy from a metastatic neck lesion revealed alterations in genes that are associated with 5-FU uptake and metabolism. These included a novel somatic structural variant resulting in a partial deletion affecting DPYD, a variant of unknown significance affecting SLC29A1 and homozygous deletion of MTAP. There was no evidence of deleterious germline polymorphisms that have been associated with 5-FU toxicity, indicating a potential vulnerability of the tumour to 5-FU therapy. The discovery of the novel DPYD variant led to the initiation of 5-FU treatment that resulted in a rapid response lasting 17 weeks, with subsequent relapse due to unknown resistance mechanisms. This suggests that somatic alterations present in this tumour may serve as markers for tumour sensitivity to 5-FU, aiding in selection of personalized treatment strategies.
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Lung group 2 innate lymphoid cells (ILC2s) drive allergic inflammation and promote tissue repair. ILC2 development is dependent on the transcription factor retinoic acid receptor-related orphan receptor (RORα), which is also expressed in common ILC progenitors. To elucidate the developmental pathways of lung ILC2s, we generated RORα lineage tracer mice and performed single-cell RNA sequencing, flow cytometry, and functional analyses. In adult mouse lungs, we found an IL-18Rα+ST2- population different from conventional IL-18Rα-ST2+ ILC2s. The former was GATA-3intTcf7EGFP+Kit+, produced few cytokines, and differentiated into multiple ILC lineages in vivo and in vitro. In neonatal mouse lungs, three ILC populations were identified, namely an ILC progenitor population similar to that in adult lungs and two distinct effector ILC2 subsets that differentially produced type 2 cytokines and amphiregulin. Lung ILC progenitors might actively contribute to ILC-poiesis in neonatal and inflamed adult lungs. In addition, neonatal lung ILC2s include distinct proinflammatory and tissue-repairing subsets.
Haploid cell lines are a valuable research tool with broad applicability for genetic assays. As such the fully haploid human cell line, eHAP1, has been used in a wide array of studies. However, the absence of a corresponding reference genome sequence for this cell line has limited the potential for more widespread applications to experiments dependent on available sequence, like capture-clone methodologies. We generated ~15× coverage Nanopore long reads from ten GridION flowcells and utilized this data to assemble a de novo draft genome using minimap and miniasm and subsequently polished using Racon. This assembly was further polished using previously generated, low-coverage, Illumina short reads with Pilon and ntEdit. This resulted in a hybrid eHAP1 assembly with >90% complete BUSCO scores. We further assessed the eHAP1 long read data for structural variants using Sniffles and identify a variety of rearrangements, including a previously established Philadelphia translocation. Finally, we demonstrate how some of these variants overlap open chromatin regions, potentially impacting regulatory regions. By integrating both long and short reads, we generated a high-quality reference assembly for eHAP1 cells. The union of long and short reads demonstrates the utility in combining sequencing platforms to generate a high-quality reference genome de novo solely from low coverage data. We expect the resulting eHAP1 genome assembly to provide a useful resource to enable novel experimental applications in this important model cell line.
PURPOSE
In Canada, Indigenous peoples’ cancer rates have increased, but cancer screening rates tend to be lower. When coupled with poor cancer prognosis, treatment barriers, and inaccessible health care, Indigenous patients with cancer experience many unmet needs. Further complicating their journey is a multijurisdictional system that complicates cancer control services, treatments, patient supports, and cancer surveillance. To address these issues, the Canadian Indigenous Research Network Against Cancer (CIRNAC) was developed. This article describes the forerunners and consultative process that created the network and the consensus model developed to ground this network with, by, and for Indigenous peoples.
METHODS
A consultative workshop was held to (1) establish and increase network membership, (2) enhance partnerships with Indigenous communities and other researchers, and (3) develop an Indigenous-led research program, new funding, and related initiatives.
RESULTS
Participants viewed the CIRNAC as a reflective parallel network led by Indigenous peoples that would identify research priorities within Canada, assess how these priorities align with Indigenous patients’ cancer care and research needs, and cross-check to see if these priorities align with each other. The network would also advocate for Indigenous elders/knowledge holders and community grassroot processes to drive research and training, thus demonstrating the power of the community voice and lived experience in research. In addition, the network would foster research partnerships to investigate alternative Indigenous models for cancer prevention, care, treatment, and support.
CONCLUSION
The CIRNAC evolved as a viable vehicle to address cancer with, for, and by Indigenous peoples. The network is guided by a preamble, a set of aims, and an inclusion engagement circle model. It is evolving through major world initiatives, with the aim of formally becoming an internationally linked national network.
Biobanking, genomic research, and their potential for clinical applications are playing a primary role in the evolution of cancer care in Canada and around the world. Although this is having an impact on everything from screening and diagnosis to treatment and the foundational understanding of disease, its success has become a potential driver of persisting health inequities in Canada. Although Canada plays a prominent role in oncogenomic research, it should be noted that this is primarily localized to metropolitan centers that have the associated academic institutions, genomic laboratories, human resources, and research budgets to permit this. Northern, rural, and Indigenous populations are at best minimally represented and at worst actively excluded from this research and its beneficial effects downstream. It is anticipated that addressing this broadening gap—often termed the “genomic health divide”1—will be necessary to prevent an untenable growth in the inequities of cancer care and outcomes.
Background: There is a lack of molecularly-informed biomarkers for patients with metastatic renal cell carcinoma (RCC). Plasma cell-free DNA (cfDNA) sequencing is a minimally-invasive alternative to tissue for profiling the genome in other cancers but relevance in metastatic RCC remains unclear.
Materials and methods: Whole blood was collected from 55 patients with metastatic RCC. Plasma cfDNA and leukocyte DNA were subjected to targeted sequencing across 981 cancer genes. Matched tumor tissue from 14 patients was analyzed.
Results: Thirty-three percent of patients had evidence for RCC-derived circulating tumor DNA (ctDNA), significantly lower than patients with metastatic prostate or bladder cancer analyzed using the same approach. Among ctDNA-positive patients, ctDNA fraction averaged only 3.9% and showed no strong association with clinical variables. In these patients, the most commonly mutated genes were VHL, BAP1, and PBRM1, and matched tissue concordance was 77%. Evidence of somatic expansions unrelated to RCC, such as clonal hematopoiesis of indeterminate potential, were detected in 43% of patients. Pathogenic germline mutations in DNA repair genes were detected in 11% of patients. CtDNA-positive patients had shorter overall survival and progression-free survival on first-line therapy. Patients with evidence of clonal hematopoiesis of indeterminate potential had an intermediate prognosis compared with ctDNA-positive and -negative patients.
Conclusions: CfDNA sequencing enables straightforward characterization of the somatic RCC genome in a minority of patients with metastatic RCC. Owing to low ctDNA abundance, and the presence of non-RCC derived somatic clones in circulation, cfDNA sequencing may not be a simple pan-patient alternative to tissue biopsy in metastatic RCC.