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PNAS Papers on Single-Cell SNV Detection, Bone Healing-Related Immune Features, More

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

Investigators at Harvard, Dana-Farber Cancer Institute, and Peking University outline a single-cell whole-genome amplification approach aimed at improving single nucleotide variant (SNV) detection in individual cells profiled by single-cell DNA sequencing. The team's "multiplexed end-tagging amplification of complementary strands," or META-CS, approach relies on transposon sequence tagging and fragment barcoding to dial down false positive variant calls in individual cells by labeling and amplifying each strand of a DNA molecule separately. After validating the approach in individual sperm cells and in cells stemming from the same expanded human haploid cell line, the authors applied META-CS to other human tissue types, uncovering informative SNV patterns in individual neurons and in distinct cell types found in the blood. "With highly accurate SNVs identified by META-CS, we were able to distinguish cell types based on single-cell mutational spectra," they report, concluding that the approach "will expand our understanding of fundamental biology including development, aging, and generation of diseases such as cancer."

A Georgia Institute of Technology-led team takes a look at systemic immune features linked to bone regeneration in a rodent model of orthopedic traumatic injury, searching for biomarkers coinciding with delayed or enhanced healing. Using flow cytometry, multiplexed arrays, and related assays, the researchers profiled systemic immune features in blood samples collected over time for up to 20 weeks in rats with regenerating femur bones being tracked with in vivo micro-computed tomography. Their results suggested that higher-than-usual levels of myeloid-derived suppressor cells and an immunosuppressive cytokine called interleukin-10 in the blood coincided with slower bone healing, consistent with an early systemic immune influence on bone regeneration. "These results suggest that the early systemic immune response to trauma can help predict the long-term effectiveness of bone healing treatments," the authors explain, "and may inform the development of immunotherapies for orthopedic repair."

Children's Hospital of Philadelphia researchers report on a role for the transcription factor SOX9 in post-natal processes influencing cartilage growth plates and the health of a form of cartilage known as articular cartilage in mouse models of these processes. Based on laser capture microdissection, RNA sequencing, immunostaining assays, and other experiments in conditional knockout mice missing SOX9 or other genes, the team found that SOX9 appears to influence cartilage growth plate closure and protects articular cartilage from osteoarthritis-related deterioration by keeping chondrocyte dedifferentiation and osteoblast redifferentiation pathways in check. "These findings provide insights into cellular plasticity and its molecular control in development, physiological, and pathological processes within and beyond the skeletal system," the authors write.