Imaging of type I procollagen biosynthesis in cells reveals biogenesis in highly organized bodies; Collagenosomes

Intracellular spatial transcriptomic analysis toolkit (InSTAnT)

Imaging-based spatial transcriptomics technologies such as Multiplexed error-robust fluorescence in situ hybridization (MERFISH) can capture cellular processes in unparalleled detail. However, rigorous and robust analytical tools are needed to unlock their full potential for discovering subcellular biological patterns. We present Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT), a computational toolkit for extracting molecular relationships from spatial transcriptomics data at single molecule resolution. InSTAnT employs specialized statistical tests and algorithms to detect gene pairs and modules exhibiting intriguing patterns of co-localization, both within individual cells and across the cellular landscape. We showcase the toolkit on five different datasets representing two different cell lines, two brain structures, two species, and three different technologies. We perform rigorous statistical assessment of discovered co-localization patterns, find supporting evidence from databases and RNA interactions, and identify associated subcellular domains. We uncover several cell type and region-specific gene co-localizations within the brain. Intra-cellular spatial patterns discovered by InSTAnT mirror diverse molecular relationships, including RNA interactions and shared sub-cellular localization or function, providing a rich compendium of testable hypotheses regarding molecular functions.

Deciphering the Binding of 5' Stem Loop RNA to the La Domain of Human LARP6

La-related protein 6 regulates the highly organized biosynthesis of type I procollagen polypeptides and affects proper assembly of procollagen peptides into heterotrimers of type I procollagen. LARP6-mediated regulation of collagen biosynthesis is mediated through interaction with the 5' stem loop motif found in type I and III collagen mRNA. Recent studies highlight the involvement of HsLARP6 in fibroproliferative diseases and its potential as a target for therapeutic intervention. The intrinsic instability of the La domain of HsLARP6 hampers studies probing the molecular basis of biologically- and disease-relevant structure-function relationship, particularly when high concentrations are required. This work provides detailed procedures to produce milligram amounts of RNase-free and functional La domain of HsLARP6. Furthermore, we investigated the effect of the construct length as well as RNA binding on protein stability. N- and C-terminal extensions greatly impact stability based on interactions with the core domain and modulation of the pI. When in complex with its cognate 5'SL RNA, the La domain shows unprecedented stability compared to the aggregation-prone unbound state. The protein-RNA complex remains stable for at least 50x longer than the unbound state, under identical conditions, likely due to a global change in conformational plasticity upon RNA binding. These results provide a foundation for further studies of the molecular recognition of 5'SL by HsLARP6 as well as a platform for refining potential antifibrotic therapeutics.

LARP6 Regulates Keloid Fibroblast Proliferation, Invasion, and Ability to Synthesize Collagen

Keloid is a skin fibroproliferative disease currently having no uniformly successful treatment. The lesion is composed of actively proliferating and collagen-overproducing fibroblasts. LARP6 is an RNA-binding protein able to regulate collagen synthesis in fibroblasts and to promote proliferation and invasion of tumor cells. To explore LARP6's likely functions in keloid pathogenesis, we performed immunohistochemistry staining on human keloid tissues and discovered markedly upregulated LARP6 expression in lesion fibroblasts compared with that of normal skin and hypertrophic scar tissues. In addition, the keloid tissue‒derived fibroblasts showed constitutive upregulation of LARP6 expression as well as significantly upregulated mRNA and protein expressions of type I collagen and enhanced cell proliferation and invasive behavior in cell culture system. Intriguingly, LARP6 knockdown by targeting with small interfering RNAs significantly inhibited type I collagen expression, proliferation, and invasion capability of keloid tissue‒derived fibroblasts relative to that of normal skin‒ and hypertrophic scar‒derived fibroblasts and control keloid tissue‒derived fibroblasts that were transfected with a scrambled small interfering RNA. In conclusion, the abnormally upregulated expression of LARP6 in fibroblasts may play an important role in the growth and invasive behavior of keloid lesions.