colocr: an R package for conducting co-localization analysis on fluorescence microscopy images

Egg multivesicular bodies elicit an LC3-associated phagocytosis-like pathway to degrade paternal mitochondria after fertilization

Mitochondria are maternally inherited, but the mechanisms underlying paternal mitochondrial elimination after fertilization are far less clear. Using Drosophila, we show that special egg-derived multivesicular body vesicles promote paternal mitochondrial elimination by activating an LC3-associated phagocytosis-like pathway, a cellular defense pathway commonly employed against invading microbes. Upon fertilization, these egg-derived vesicles form extended vesicular sheaths around the sperm flagellum, promoting degradation of the sperm mitochondrial derivative and plasma membrane. LC3-associated phagocytosis cascade of events, including recruitment of a Rubicon-based class III PI(3)K complex to the flagellum vesicular sheaths, its activation, and consequent recruitment of Atg8/LC3, are all required for paternal mitochondrial elimination. Finally, lysosomes fuse with strings of large vesicles derived from the flagellum vesicular sheaths and contain degrading fragments of the paternal mitochondrial derivative. Given reports showing that in some mammals, the paternal mitochondria are also decorated with Atg8/LC3 and surrounded by multivesicular bodies upon fertilization, our findings suggest that a similar pathway also mediates paternal mitochondrial elimination in other flagellated sperm-producing organisms.

Capturing the hierarchically assorted modules of protein-protein interactions in the organized nucleome

Nuclear proteins are major constituents and key regulators of nucleome topological organization and manipulators of nuclear events. To decipher the global connectivity of nuclear proteins and the hierarchically organized modules of their interactions, we conducted two rounds of cross-linking mass spectrometry (XL-MS) analysis, one of which followed a quantitative double chemical cross-linking mass spectrometry (in vivoqXL-MS) workflow, and identified 24,140 unique crosslinks in total from the nuclei of soybean seedlings. This in vivo quantitative interactomics enabled the identification of 5340 crosslinks that can be converted into 1297 nuclear protein-protein interactions (PPIs), 1220 (94%) of which were non-confirmative (or novel) nuclear PPIs compared with those in repositories. There were 250 and 26 novel interactors of histones and the nucleolar box C/D small nucleolar ribonucleoprotein complex, respectively. Modulomic analysis of orthologous Arabidopsis PPIs produced 27 and 24 master nuclear PPI modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region-containing proteins, respectively. These NPIMs successfully captured previously reported nuclear protein complexes and nuclear bodies in the nucleus. Surprisingly, these NPIMs were hierarchically assorted into four higher-order communities in a nucleomic graph, including genome and nucleolus communities. This combinatorial pipeline of 4C quantitative interactomics and PPI network modularization revealed 17 ethylene-specific module variants that participate in a broad range of nuclear events. The pipeline was able to capture both nuclear protein complexes and nuclear bodies, construct the topological architectures of PPI modules and module variants in the nucleome, and probably map the protein compositions of biomolecular condensates.

Systematic analysis of the effects of genetic variants on chromatin accessibility to decipher functional variants in non-coding regions

Genome-wide association study (GWAS) has identified thousands of single nucleotide polymorphisms (SNPs) associated with complex diseases and traits. However, deciphering the functions of these SNPs still faces challenges. Recent studies have shown that SNPs could alter chromatin accessibility and result in differences in tumor susceptibility between individuals. Therefore, systematically analyzing the effects of SNPs on chromatin accessibility could help decipher the functions of SNPs, especially those in non-coding regions. Using data from The Cancer Genome Atlas (TCGA), chromatin accessibility quantitative trait locus (caQTL) analysis was conducted to estimate the associations between genetic variants and chromatin accessibility. We analyzed caQTLs in 23 human cancer types and identified 9,478 caQTLs in breast carcinoma (BRCA). In BRCA, these caQTLs tend to alter the binding affinity of transcription factors, and open chromatin regions regulated by these caQTLs are enriched in regulatory elements. By integrating with eQTL data, we identified 141 caQTLs showing a strong signal for colocalization with eQTLs. We also identified 173 caQTLs in genome-wide association studies (GWAS) loci and inferred several possible target genes of these caQTLs. By performing survival analysis, we found that ~10% caQTLs potentially influence the prognosis of patients. To facilitate access to relevant data, we developed a user-friendly data portal, BCaQTL (http://gong_lab.hzau.edu.cn/caqtl_database), for data searching and downloading. Our work may facilitate fine-map regulatory mechanisms underlying risk loci of cancer and discover the biomarkers or therapeutic targets for cancer prognosis. The BCaQTL database will be an important resource for genetic and epigenetic studies.

Comprehensive Characterization of CK1δ-Mediated Tau Phosphorylation in Alzheimer’s Disease

A main pathological event in Alzheimer’s disease is the generation of neurofibrillary tangles originating from hyperphosphorylated and subsequently aggregated tau proteins. Previous reports demonstrated the critical involvement of members of the protein kinase family CK1 in the pathogenesis of Alzheimer’s disease by hyperphosphorylation of tau. However, precise mechanisms and effects of CK1-mediated tau phosphorylation are still not fully understood. In this study, we analyzed recombinant tau441 phosphorylated by CK1δ in vitro via mass spectrometry and identified ten potential phosphorylation sites, five of them are associated to Alzheimer’s disease. To confirm these results, in vitro kinase assays and two-dimensional phosphopeptide analyses were performed with tau441 phosphomutants confirming Alzheimer’s disease-associated residues Ser68/Thr71 and Ser289 as CK1δ-specific phosphorylation sites. Treatment of differentiated human neural progenitor cells with PF-670462 and Western blot analysis identified Ser214 as CK1δ-targeted phosphorylation site. The use of an in vitro tau aggregation assay demonstrated a possible role of CK1δ in tau aggregation. Results obtained in this study highlight the potential of CK1δ to be a promising target in the treatment of Alzheimer’s disease.

Quantifying colocalization: The case for discarding the Manders overlap coefficient

Colocalization measurements aim to characterize the relative distribution of two molecules within a biologically relevant area. It is efficient to measure two distinct features, co-occurrence, the extent to which the molecules appear together, and correlation, how well variations in concentration of the two molecules match. The Manders overlap coefficient (MOC) appears in most colocalization software but the literature contains three interpretations of its measurements: (a) co-occurrence, (b) correlation, or (c) a combination of both. This is surprising given the simplicity of the underlying equation. Testing shows that the MOC responds both to changes in co-occurrence and to changes in correlation. Further testing reveals that different distributions of intensity (Gaussian, gamma, uniform, exponential) dramatically alter the balance between the contribution from co-occurrence and correlation. It follows that the MOC's ability to differentiate between different patterns of colocalization is very limited, since any value is compatible with widely differing combinations of co-occurrence, correlation, and intensity distribution. To characterize colocalization, we recommend reporting both co-occurrence and correlation, using coefficients specific for each attribute. Since the MOC has no clear role in the measurement of colocalization and causes considerable confusion, we conclude that it should be discarded.

Quantification of colorimetric isothermal amplification on the smartphone and its open-source app for point-of-care pathogen detection

The increasing risk of infectious pathogens, especially in the under-developed countries, is demanding the development of point-of-care (POC) nucleic acid testing in the low-resource setting conditions. Here, we describe a methodology for colorimetric quantitative analysis of nucleic acid using an easy-to-build smartphone-based platform, offering low-cost, portability, simplicity in operation, and user-friendliness. The whole system consists of a hand-held box equipped with a smartphone, a film heater, a white LED, a loop-mediated isothermal amplification (LAMP) chip, and a DC converter, and all the processes were powered by a portable battery of 5 V. Upon the amplification of the target gene by an Eriochrome Black T-mediated LAMP reaction, the color of the LAMP reaction was changed from violet to blue that was real-time recorded by a smartphone camera. To keep track of the progress of the color change, we developed a novel mobile app in which a hue value was accepted as an indicator for color transition and for determining the threshold time of the amplification reaction. A calibration curve could be generated by plotting the logarithm of the known concentration of the DNA templates versus the threshold time, and it can be used to predict the copy number of nucleic acids in the test samples. Thus, the proposed mobile platform can inform us of not only qualitative but also quantitative results of the pathogens. We believe that this advanced colorimetric approach and the mobile app can expand the potentials of the smartphone for the future POCT system in the bio-diagnostic fields.