Biology subjects

Guo, R.

Publications and source records attributed to Guo, R..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

ERK signaling drives evolutionary expansion of the mammalian cerebral cortex

The molecular basis for cortical expansion during evolution remains largely unknown. Here, we found that FGF-extracellular signal-regulated kinase (ERK) signaling promotes the self-renewal and expansion of cortical radial glial (RG) cells. Furthermore, FGF-ERK signaling induces Bmp7 expression in cortical RG cells, which increases the length of the neurogenic period. We demonstrate that ERK signaling and SHH signaling mutually inhibit each other in cortical RG cells. We also provide evidence that ERK signaling is elevated in cortical RG cells during development and evolution. We conclude that the evolutionary expansion of the mammalian cortex, notably in human, is driven by ERK-BMP7-GLI3R signaling pathway in cortical RG cells, which participates in a positive feedback loop through antagonizing SHH signaling. We also propose that the molecular basis for cortical evolutionary dwarfism, exemplified by the lissencephalic mouse which originated from a larger and gyrencephalic ancestor, is due to mouse cortical RG cells receiving higher SHH signaling that antagonizes ERK signaling.

neuroscience↗

bioRxiv2023

Analytical code sharing practices in biomedical research

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71x10-9). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10-07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

scientific communication and education↗

bioRxiv2023

CircRNAs and their regulatory networks associated with the antioxidant enzymes and immune responses of Asian honey bee larvae to fungal infection

Non-coding RNA (ncRNA) plays an important role in the regulation of immune responses, growth, and development in plants and animals. Here, the identification, characteristic investigation, and molecular verification of circRNAs in Apis cerana cerana larval guts were conducted, and the expression pattern of larval circRNAs during Ascosphaera apis infection was analyzed. This was followed by exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 3178 circRNAs in the larval guts of A. c. cerana were identified, with a length distribution ranging from 15 nt to 96007 nt. Additionally, 45, 33, and 48 up-regulated circRNAs, as well as 110, 62, and 38 down-regulated circRNAs were identified in the A.-apis-inoculated 4-, 5-, and 6-day-old larval guts in comparison with the corresponding uninoculated larval guts. These DEcircRNAs were predicted to target 29, 25, and 18 parental genes, which were relative to 12, 20, and 17 GO terms as well as 144, 114, and 61 KEGG pathways, including five cellular and four humoral immune pathways containing melanization, phagosomes, lysosomes, endocytosis, apoptosis, MAPK, Ras, and Jak-STAT signaling pathways. Furthermore, complex competing endogenous RNA (ceRNA) regulatory networks were detected as being formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The target DEmRNAs were engaged in 36, 47, and 47 GO terms as well as 331, 332, and 331 pathways, including six cellular and six humoral immune-related pathways. In total, nineteen DEcircRNAs, five DEmiRNAs, and three mRNAs were included in the sub-networks relative to three antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST). Finally, back-splicing sites within 15 circRNAs and the difference in the 15 DEcircRNAs expression between uninoculated and A.-apis-inoculated larval guts were confirmed utilizing molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions, but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. c. cerana larvae against A. apis invasion.

molecular biology↗

bioRxiv2023

Theranostic Bottle-Brush Polymers Tailored for Universal Solid-Tumour Targeting

Nanomedicines involving nanotechnologies and engineering of nanomaterials for medicines have shown great promise in diagnosis and treatment of diseases including cancers. A major hurdle that limits the successful clinical translation of nanomedicines, however, is how to overcome the cascaded biological barriers and improve the delivery efficacy towards the disease sites and minimize the toxicity against healthy tissues and cells. Here, we report a type of bottle-brush-like polymers systematically optimized in their chemical structures, sizes, and surface charges that lead to their outstanding pharmacokinetics and tumour-targeting performances in a variety of both subcutaneous and orthotopic tumour models. The potential mechanism has been studied by revealing the structure-activity relationship of these polymers in overcoming the biological barriers, including their avoidance by the immune system and deep tumour infiltration. Our study may offer insight for a rational design of highly efficient delivery platform of polymeric nanomedicines that could effectively overcome the cascaded biological barriers and thus lead to high tumour-targeting efficacy and low toxicity.

bioengineering↗

bioRxiv2023

Replication Protein A1 is essential for DNA damage repair during mammalian oogenesis

Persistence of unrepaired DNA damage in oocytes is detrimental and may cause genetic aberrations, miscarriage, and infertility. RPA, an ssDNA-binding complex, is essential for various DNA-related processes. Here we report that RPA plays a novel role in DNA damage repair during postnatal oocyte development after meiotic recombination. To investigate the role of RPA during oogenesis, we inactivated RPA1 (replication protein A1), the largest subunit of the heterotrimeric RPA complex, specifically in oocytes using two germline-specific Cre drivers (Ddx4-Cre and Zp3-Cre). We find that depletion of RPA1 leads to the disassembly of the RPA complex, as evidenced by the absence of RPA2 and RPA3 in RPA1-deficient oocytes. Strikingly, severe DNA damage occurs in RPA1-deficient GV-stage oocytes. Loss of RPA in oocytes triggered the canonical DNA damage response mechanisms and pathways, such as activation of ATM, ATR, DNA-PK, and p53. In addition, the RPA deficiency causes chromosome misalignment at metaphase I and metaphase II stages of oocytes, which is consistent with altered transcript levels of genes involved in cytoskeleton organization in RPA1-deficient oocytes. Absence of the RPA complex in oocytes severely impairs folliculogenesis and leads to a significant reduction in oocyte number and female infertility. Our results demonstrate that RPA plays an unexpected role in DNA damage repair during mammalian folliculogenesis.

developmental biology↗

bioRxiv2023

Engineering transposon-associated TnpB-1 ωRNA system for efficient gene editing and disease treatment in mouse

Transposon-associated ribonucleoprotein TnpB is known to be the ancestry endonuclease of diverse Cas12 effector proteins from type-V CRISPR system. Given its small size (409 aa), it is of interest to examine whether engineered TnpB could be used for efficient mammalian genome editing. Here, we showed that the gene editing activity of native TnpB in mouse embryos was already higher than previously identified small-sized Cas12f1. Further stepwise engineering of noncoding RNA ({omega}RNA or reRNA) component of TnpB significantly elevated the nuclease activity of TnpB. Notably, an optimized TnpB-{omega}RNA system could be efficiently delivered in vivo with single adeno-associated virus (AAV) and prevented the disease phenotype in a tyrosinaemia mouse model. Thus, the engineered miniature TnpB system represents a new addition to the current genome editing toolbox, with the unique feature of the smallest effector size that facilitate efficient AAV delivery for editing of cells and tissues.

molecular biology↗

bioRxiv2023

Lipid Bilayer Strengthens the Cooperative Network of a Membrane-Integral Enzyme

Although membrane proteins fold and function in a lipid bilayer constituting cell membranes, their structure and functionality can be recapitulated in diverse amphiphilic assemblies whose compositions deviate from native membranes. It remains unclear how various hydrophobic environments can stabilize membrane proteins and whether lipids play any role therein. Here, using the evolutionary unrelated -helical and {beta}-barrel membrane proteins of Escherichia coli, we find that the hydrophobic thickness and the strength of amphiphile- amphiphile packing are critical environmental determinants of membrane protein stability. Lipid solvation enhances stability by facilitating residue burial in the protein interior and strengthens the cooperative network by promoting the propagation of local structural perturbations. This study demonstrates that lipids not only modulate membrane proteins stability but also their response to external stimuli.

biophysics↗

bioRxiv2023

Characterization of Target Gene Regulation by the Two Epstein-Barr Virus Oncogene LMP1 Domains Essential for B-cell Transformation

The Epstein-Barr virus (EBV) oncogene latent membrane protein 1 (LMP1) mimics CD40 signaling and is expressed by multiple malignancies. Two LMP1 C-terminal cytoplasmic tail regions, termed transformation essential sites (TES) 1 and 2, are critical for EBV transformation of B lymphocytes into immortalized lymphoblastoid cell lines (LCL). However, TES1 versus TES2 B-cell target genes have remained incompletely characterized, and whether both are required for LCL survival has remained unknown. To define LCL LMP1 target genes, we profiled transcriptome-wide effects of acute LMP1 CRISPR knockout (KO) prior to cell death. To then characterize specific LCL TES1 and TES2 roles, we conditionally expressed wildtype, TES1 null, TES2 null or double TES1/TES2 null LMP1 alleles upon endogenous LMP1 KO. Unexpectedly, TES1 but not TES2 signaling was critical for LCL survival. The LCL dependency factor cFLIP, which plays obligatory roles in blockade of LCL apoptosis, was highly downmodulated by loss of TES1 signaling. To further characterize TES1 vs TES2 roles, we conditionally expressed wildtype, TES1 and/or TES2 null LMP1 alleles in two Burkitt models. Systematic RNAseq analyses revealed gene clusters that responded more strongly to TES1 versus TES2, that respond strongly to both or that are oppositely regulated. Robust TES1 effects on cFLIP induction were again noted. TES1 and 2 effects on expression of additional LCL dependency factors, including BATF and IRF4, and on EBV super-enhancers were identified. Collectively, these studies suggest a model by which LMP1 TES1 and TES2 jointly remodel the B-cell transcriptome and highlight TES1 as a key therapeutic target. ImportanceEpstein-Barr virus (EBV) causes multiple human cancers, including B-cell lymphomas. In cell culture, EBV converts healthy human B-cells into immortalized ones that grow continuously, which model post-transplant lymphomas. Constitutive signaling from two cytoplasmic tail domains of the EBV oncogene Latent Membrane Protein 1 (LMP1) is required for this transformation, yet there has not been systematic analysis of their host gene targets. We identified that only signaling from the membrane proximal domain is required for survival of these EBV-immortalized cells and that its loss triggers apoptosis. We identified key LMP1 target genes, whose abundance changed significantly with loss of LMP1 signals, or that were instead upregulated in response to switching on signaling by one or both LMP1 domains in an EBV-uninfected human B-cell model. These included major anti-apoptotic factors necessary for EBV-infected B-cell survival. Bioinformatics analyses identified clusters of B-cell genes that respond differently to signaling by either or both domains.

cancer biology↗

bioRxiv2022

Cataloguing and profiling of the gut virome in Chinese populations uncover extensive viral signatures across common diseases

The gut viral community has been linked to human physiology and health, but our knowledge of its genetic and functional contents and disease dependence is far from complete. Here, we collected 11,327 bulk or viral metagenomes from fecal samples from large-scale Chinese populations to establish a Chinese gut virus catalogue (cnGVC) comprising 67,096 nonredundant viral genomes. This catalogue included [~]70% of novel viruses that are not represented in existing gut viral databases, and allowed us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we 1) profiled the gut virome in large-scale populations and evaluated their sex- and age-related variations, 2) investigated the diversity and compositional patterns of the gut virome across common diseases by analyzing 6,314 bulk metagenomes spanning 28 disease or unhealthy statuses, and 3) identified a large number of universal viral signatures of diseases and validated their predictive ability for health status. Overall, our resources and results would contribute to the grand effort of expanding the knowledge of the human gut virome and addressing a full picture of the associations between viruses and common diseases.

microbiology↗

bioRxiv2022

Differential expression patterns and potential regulatory function of piRNAs in western honey bee larval response to Ascosphaera apis infestation

piRNAs are a class of small non-coding RNAs that play an essential part in genomic defense, as well as in modulation of gene expression and diverse biological processes such as host-pathogen interaction. However, little is known about the expression pattern of the regulatory function of piRNAs in interactions between honey bees and pathogens. In this work, on the basis of our previously obtained high-quality small RNA-seq datasets from western honey bee (Apis mellifera) larval guts, the differential expression profile of piRNAs in A. mellifera larval guts after Ascosphaera apis infestation was analyzed, followed by structural characterization, target prediction, and regulatory network investigation. The potential roles of differentially expressed piRNAs (DEpiRNAs) in regulating host response, especially immune response, were further discussed. In this study, 504, 657, and 587 piRNAs were respectively identified in the 4-, 5-, and 6-day-old larval guts infected by A. apis, with 411 (53.24%) piRNAs shared. The length distribution of these piRNAs ranged from 24 nt to 33 nt and their first base had a "C" bias, similar to piRNAs discovered in other mammals and insects. Additionally, 96, 103, and 143 DEpiRNAs were detected in the 4-, 5-, and 6-day-old comparison groups; among these, piR-ame-149736, piR-ame-1066173, and piR-ame-1125190 were the most up-regulated, while piR-ame-1202932 was the most down-regulated. There were 68 DEpiRNAs shared between these three comparison groups. The targets of the DEpiRNAs in the three comparison groups were engaged in a suite of crucial functions associated with biological processes, molecular function, and cellular components, including molecular transducer activity, biological regulation, and membrane part. These targets were also relevant to diverse vital pathways such as the phosphatidylinositol signaling system, inositol phosphate metabolism, and Wnt signaling pathway. Further investigation demonstrated that targets of DEpiRNAs were involved in three energy metabolism-related pathways, seven development-associated signaling pathways, and seven immune-relevant pathways, including lysosome and endocytosis, as well as the MAPK and Jak-STAT signaling pathways. The expression trends of five randomly selected DEpiRNAs were verified using a combination of RT-PCR and RT-qPCR. Moreover, the expression levels of six genes targeted by piR-ame-945760 were detected by RT-qPCR, with the results showing that their expression trends were the same as the expression trend of piR-ame-945760, indicative of the positive correlation between piR-ame-945760 and these targets. These results suggest that A.apis infestation increased the overall expression level of piRNAs and altered the expression pattern of piRNAs in A. mellifera larval guts. DEpiRNAs potentially participate in the A. apis response of the host by modulating the expression of target genes associated with energy metabolism and development, as well as cellular and humoral immune response. Our findings not only offer novel insights into A. mellifera larva-A. apis interaction, but also lay the groundwork for clarifying the mechanisms underlying DEpiRNA-regulated larval response.

molecular biology↗

bioRxiv2022

Effect of Ascosphaera apis infestation on the activities of four antioxidant enzymes in Asian honey bee larval guts

Ascosphaera apis exclusively infects bee larvae and causes chalkbrood, a lethal fungal disease that results in the sharp reduction in adult bees and colony productivity. However, little is known about the effect of A. apis infestation on the activities of antioxidant enzymes in bee larvae. Here, A. apis spores were purified and used to inoculate Asian honey bee (Apis cerana) larvae, followed by detection of the host survival rate and evaluation of the activities of four major antioxidant enzymes. At 6 days post inoculation (dpi) with A. apis spores, white mycelia penetrated the posterior end of the larva, extended to the anterior end, and eventually covered the entire larval body surface, presenting an obvious symptom of chalkbrood disease similar to that occurs in Apis mellifera larvae. Additionally, PCR identification showed that the expected fragment was amplified from the A. apis-inoculated larval guts and the A. apis spores, verifying the A. apis infection of A. cerana larvae. The survival rate of larvae inoculated with A. apis was high at 1-2 dpi, sharply decreased to 4.16% at 4 dpi, and reached 0% at 5 dpi; whereas that of un-inoculated larvae was always high at 1~8 dpi, with an average survival rate of 95.37%, indicating the negative impact of A. apis infection on larval survival. Furthermore, in comparison with those in the corresponding un-inoculated groups, the superoxide dismutase (SOD) and catalase (CAT) activities in the 4-day-old larval gut in the A. apis-inoculated groups were reduced (p > 0.05), while those in the 5- and 6-day-old larval guts were significantly decreased (p < 0.05); the glutathione S-transferase (GST) activity in the 4- and 5-day-old larval guts was significantly increased (p < 0.05), while that in the 6-day-old larval gut was reduced (p > 0.05); the polyphenol oxidase (PPO) activity in 4-day-old larval gut was increased (p > 0.05) and that in the 5-day-old larval gut was significantly increased (p < 0.05), whereas that in the 6-day-old larval gut was significantly reduced (p < 0.01). These results together suggested that the activities of SOD and CAT in the larval guts were suppressed during the process of A. apis infestation, while the GST activity was induced to activation, and the PPO activity was first enhanced and then inhibited. Our findings not only unravel the response of A. cerana larvae to A. apis infestation from a biochemical perspective, but also offer a valuable insight into the interaction between Asian honey bee larvae and A. apis.

molecular biology↗

bioRxiv2022

ame-miR-34 modulates the larval body weight and immune response of Apis mellifera workers to Ascosphara apis invasion

MiRNAs are critical regulators of numerous physiological and pathological processes. Ascosphaera apis exclusively infects bee larvae and causes chalkbrood disease. However, the function and mechanism of miRNAs in the bee larval response to A. apis infection is poorly understood. Here, ame-miR-34, a previously predicted miRNA involved in the response of Apis mellifera ligustica larvae to A. apis invasion, was subjected to molecular validation, and overexpression and knockdown were then conducted to explore the regulatory functions of ame-miR-34 in larval body weight and immune response. Stem-loop RT-PCR and Sanger sequencing confirmed the authenticity of ame-miR-34 in the larval gut of A. m. ligustica. RT-qPCR results demonstrated that compared with that in the uninfected larval guts, the expression level of ame-miR-34 was significantly downregulated (P < 0.001) in the guts of A. apis-infected 4-, 5-, and 6-day-old larvae, indicative of the remarkable suppression of host ame-miR-34 due to A. apis infection. In comparison with the corresponding negative control (NC) groups, the expression level of ame-miR-34 in the larval guts in the mimic-miR-34 group was significantly upregulated (P < 0.001), while that in the inhibi- tor-miR-34 group was significantly downregulated (P < 0.01). Similarly, effective overexpression and knockdown of ame-miR-34 were achieved. In addition, the body weights of 5- and 6-day-old larvae were significantly increased compared with those in the mimic-NC group; the weights of 5-day-old larvae in the inhibitor-miR-34 group were significantly decreased in comparison with those in the inhibitor-NC group, while the weights of 4- and 6-day-old larvae in the inhibi- tor-miR-34 group were significantly increased, indicating the involvement of ame-miR-34 in modulating larval body weight. Furthermore, the expression levels of both hsp and abct in the guts of A. apis-infected 4-, 5- and 6-day-old larvae were significantly upregulated after ame-miR-34 overexpression. In contrast, after ame-miR-34 knockdown, the expression levels of the aforementioned two key genes in the A. apis-infected 4-, 5- and 6-day-old larval guts were significantly downregu- lated. Together, the results demonstrated that effective overexpression and knockdown of ame-miR-34 in both noninfected and A. apis-infected A. m. ligustica larval guts could be achieved by the feeding method, and ame-miR-34 exerted a regulatory function in the host immune response to A. apis invasion through positive regulation of the expression of hsp and abct. Our findings not only provide a valuable reference for the functional investigation of bee larval miRNAs but also reveal the regulatory role of ame-miR-34 in A. mellifera larval weight and immune response. Additionally, the results of this study may provide a promising molecular target for the treatment of chalkbrood disease.

molecular biology↗

bioRxiv2022

Comprehensive investigation and regulatory function of lncRNAs engaged in western honey bee larval immune response to Ascosphaera apis invasion

Ascosphaera apis is a fungal pathogen that exclusively infects bee larvae, causing chalkbrood disease, which results in severe damage for beekeeping industry. Long non-coding RNAs (lncRNAs) are versatile regulators in various biological processes such as immune defense and host-pathogen interaction. However, expression pattern and regulatory role of lncRNAs involved in immune response of bee host to A. apis invasion is still very limited. Here, Apis mellifera ligustica 4-, 5-, and 6-day-old larvae inoculated by A. apis spores (AmT1, AmT2, and AmT3 groups) and corresponding un-inoculated larval guts (AmCK1, AmCK2, and AmCK3 groups) were prepared and subjected to deep sequencing, followed by identification of lncRNAs, analysis of differentially expressed lncRNAs (DElncRNAs), and investigation of DElncRNA-regulated host immune responses. In total, 3 746 A. m. ligustica lncRNAs were identified, including 78 sense lncRNAs, 891 antisense lncRNAs, 1 893 intergenic lncRNAs, 346 bidirectional lncRNAs, and 210 intronic lncRNAs. Compared with corresponding un-inoculated larval guts, 357, 236, and 505 DElncRNAs were discovered in the A. apis-inoculated 4-, 5-, and 6-day-old larval guts. Additionally, there were 32 shared DElncRNAs. In AmCK1 vs AmT1, AmCK2 vs AmT2, and AmCK3 vs AmT3 comparison groups, 217, 129, and 272 DElncRNAs were respectively predicted to regulate neighboring genes via cis-acting manner, and these targets were associated with a series of GO terms and KEGG pathways of great importance, such as response to stimulus and Jak-STAT signal pathway. Moreover, competing endogenous RNA (ceRNA) network analysis indicated that 197, 95, and 356 DElncRNAs in the aforementioned three comparison groups could target 10, eight, and 21 DEmiRNAs and further target 147, 79, and 315 DEmRNAs, forming complex regulatory networks. Further investigation suggested that these targets were relevant to several key cellular and humoral immune pathways, such as phagosome and MAPK signaling pathway. Ultimately, the expression trends of nine randomly selected DElncRNAs were verified by RT-qPCR, indicative of the authenticity and reliability of our transcriptome data. Findings in this current work not only provide candidate DElncRNAs for functional study, but also lay a foundation for unclosing the mechanism underlying DElncRNA-regulated larval immune responses to A. apis infection.

pathology↗

bioRxiv2022

First identification and investigation of piRNAs in the larval guts of Asian honey bee, Apis cerana

Piwi-interacting RNAs (piRNAs), a kind of small non-coding RNAs (ncRNAs), play pivotal parts in maintaining the genomic stability and modulating biological processes such as growth and development via regulation of gene expression. However, piRNAs in Asian honey bee (Apis cerana) is still largely unknown at present. In this current work, on basis of previously gained high-quality small RNA-seq datasets, piRNAs in the larval guts of Apis cerana cerana, the nominate species of A. cerana, was for the first time identified, followed by in-depth investigation of the regulatory roles of differentially expressed piRNAs (DEpiRNAs) in the developmental process of the A. c. cerana. Here, a total of 621 piRNAs were identified in the A. c. cerana larval guts, among which 499 piRNAs were shared by 4- (Ac4 group), 5- (Ac5 group), and 6-day-old (Ac6 group) larval guts, while the numbers of unique ones were 79, 37, and 11, respectively. piRNAs each group were ranged from 24 nt to 33 nt in length, and the first base of piRNAs had a cytosine (C) bias. Additionally, five up-regulated and five down-regulated piRNAs were identified in the Ac4 vs. Ac5 comparison group, 9 of which could target 9, 011 mRNAs; these targets were involved in 41 GO terms and 137 pathways. Comparatively, 22 up-regulated piRNAs were detected in the Ac5 vs. Ac6 comparison group, 21 of which could target 28, 969 mRNAs; these targets were engaged in 46 functional terms and 164 pathways. The results suggested the overall alteration of expression pattern of piRNAs during the developmental process of A. c. cerana larvae. Regulatory network analysis showed that piR-bmo-748815 and piR-bmo-512574 in the Ac4 vs. Ac5 comparison group as well as piR-bmo-716466 and piR-bmo-828146 in the Ac5 vs. Ac6 comparison group linked to the highest number of targets. Further investigation indicated that targets of DEpiRNAs in the above-mentioned two comparison groups could be annotated to several growth and development-associated pathways, such as Jak/STAT, TGF-{beta}, and Wnt signaling pathways, indicating the involvement of DEpiRNAs in modulating larval gut development via these crucial pathways. Moreover, the expression trends of six randomly selected DEpiRNAs were verified using a combination of stem-loop RT-PCR and RT-qPCR. These results not only provide a novel insight into the development of the A. c. cerana larval guts, but also lay a foundation for uncovering the epigenetic mechanism underlying the larval gut development.

molecular biology↗

bioRxiv2022

Transcriptome-wide characterization of piRNAs during the developmental process of European honey bee larval guts

piRNAs play pivotal roles in suppressing transposons, maintaining genome stability, regulating gene expression, and modulating development and immunity. However, there are few piRNA-associated studies on honey bee, and the regulatory role of piRNAs in the development of bee guts is largely unknown. In this current work, the differential expression pattern of piRNAs during the developmental process of the European honey bee (Apis mellifera) was analyzed, and target prediction of differentially expressed piRNAs (DEpiRNAs) was then conducted, followed by investigation of regulatory networks and the potential function of DEpiRNAs in regulating larval gut development. Here, a total of 843 piRNAs were identified in the larval guts of A. mellifera; among these, 764 piRNAs were shared by 4- (Am4 group), 5- (Am5 group), and 6-day-old (Am6 group) larval guts, while 11, 67, and 1, respectively, were unique. The first base of piRNAs in each group had a cytosine (C) bias. Additionally, 61 up-regulated and 17 down-regulated piR-NAs were identified in the Am4 vs. Am5 comparison group, further targeting 9, 983 genes, which were involved in 50 GO terms and 142 pathways, while two up-regulated and five down-regulated piRNAs were detected in the Am5 vs. Am6 comparison group, further targeting 1, 936 genes, which were engaged in 41 functional terms and 101 pathways. piR-ame-742536 and piR-ame-856650 in the Am4 vs. Am5 comparison group as well as piR-ame-592661 and piR-ame-31653 in the Am5 vs. Am6 comparison group were found to link to the highest number of targets. Further analysis indicated that targets of DEpiRNAs in these two comparison groups were seven development-associated signaling pathways such as Hippo and Notch signaling pathways, seven immune-associated pathways including endocytosis and the Jak/STAT signaling pathway, and three energy metabolism pathways, namely sulfur metabolism, nitrogen metabolism, and oxidative phosphorylation. Moreover, the expression trends of five randomly selected DEpiRNAs were verified based on stem-loop RT-PCR and RT-qPCR. These results were suggestive of the overall alteration of piRNAs during the larval developmental process and demonstrated that DEpiRNAs potentially modulate development-, immune-, and energy metabolism-associated pathways by regulating expression of corresponding genes via target binding, further affecting the development of A. mellifera larval guts. Our data offer novel insights into the development of bee guts and lay a basis for clarifying the developmental mechanism underlying the larval guts of European honey bee.

molecular biology↗

bioRxiv2022

A megaprotein-based molecular bridge critical for lipid trafficking and cold resilience

Cells adapt to cold by increasing levels of unsaturated phospholipids and membrane fluidity through homeostatic mechanisms conserved in nearly all forms of life. As most eukaryotic enzymes for lipid synthesis and desaturation localize on endoplasmic reticulum (ER) membranes, it remains unknown how ER-resident lipids rapidly distribute to plasma membranes (PM). Here we report an exceptionally large and evolutionarily conserved protein LPD-3 in C. elegans that plays critical roles in lipid trafficking and cold resilience. We identified lpd-3 mutants in a mutagenesis screen for genetic suppressors of the lipid desaturase FAT-7, and found that the 452 kDa megaprotein LPD-3 bridges ER and PM, consisting of a structurally predicted hydrophobic tunnel for lipid trafficking. Loss of LPD-3 caused abnormal cellular distribution of phospholipids, diminished FAT-7 abundance, and organismic vulnerability to cold. These phenotypic defects of lpd-3 mutants were rescued by Lecithin comprising unsaturated phospholipids. Importantly, we found that deficient lpd-3 homologues in Zebrafish and mammalian cells led to defects similar to those observed in C. elegans. As mutations in KIAA1109/BLTP1, the human orthologue of lpd-3, cause Alkuraya-Kucinskas syndrome, we propose that the LPD-3 family proteins may serve as evolutionarily conserved "highway bridges" critical for ER-associated non-vesicular trafficking of lipids and resilience to cold stress in eukaryotic cells.

cell biology↗

bioRxiv2022

Meta-analysis of fecal metagenomes reveals global viral signatures and its diagnostic potential for colorectal cancer and adenoma

IntroductionGut microbiome plays an important role in maintaining human health. Although mounting evidence has revealed the critical function of the gut bacteriome in the progression of CRC, the contribution of gut viral community to CRC is rarely studied. ObjectivesThe present study aimed to reveal the gut virome signatures of colorectal adenoma patients and CRC patients and decipher the potential viral markers to build clinical predictive models for diagnosis. Methods1,282 available fecal metagenomes data from 9 published CRC studies were collected. A new virus database was constructed based on a reference-independent virome approach for further analysis. Viral markers were filtered by statistical methods and used to build machine learning models such as Random Forest and Least Absolute Shrinkage and Selection Operator (LASSO) to distinguish patients from controls. New fecal samples were collected to validate the generalization of predictive model. ResultsThe gut viral composition of CRC patients was drastically altered compared with healthy, as evidenced by changes in several Siphoviridae viruses and a reduction of Microviridae, whereas the virome variation in adenoma patients was relatively low. The viral markers contained the phages of Porphyromonas, Fusobacterium, Hungatella, and Ruminococcaceae. In 9 cohorts and independent validation cohorts, a random forest (RF) classifier and LASSO model got the optimal AUC 0.830 and 0.906, respectively. While the gut virome analysis of adenoma patients identified 88 differential viruses and achieved an optimal AUC of 0.772 for discriminating patients from controls. ConclusionOur findings demonstrate the distinctly different composition of gut virome between healthy controls and CRC patients, and highlight the potential of viral markers for clinical diagnosis.

microbiology↗

bioRxiv2022

In-depth investigation of microRNA-mediated cross-kingdom regulation between Asian honey bee and microsporidian

Asian honey bee Apis cerana is the original host for Nosema ceranae, a unicellular fungal parasite that causes bee nosemosis throughout the world. Currently, interaction between A. cerana and N. ceranae is largely unknown. Here, based on our previously gained high-quality RNA-seq and small RNA-seq data from N. ceranae-infected A. c. cerana workers midguts and clean spores, differentially expressed mRNAs (DEmiRNAs) in N. ceranae targeted by DEmiRNAs in host midguts and A. c. cerana DEmRNAs targeted by microsporidian DEmiRNAs were predicted using bioinformatics, and then target DEmRNAs in microsporidian and host were annotated and investigated, with a focus on targets involved in N. ceranae glycolysis/glyconeogenesis and virulence factors as well as A. c. cerana energy mechanism and immune response. Its found that 97 down-regulated (60 up-regulated) mRNAs in NcCKM vs NcTM1 were potentially targeted by eight up-regulated (six down-regulated) miRNAs in AcCKMI1 vs AcTMI1, 44 down-regulated (15 up-regulated) mRNAs in NcCKM vs NcTM2 were putative targets of seven up-regulated (two down-regulated) miRNAs in AcCKMI2 vs AcTMI2. Additionally, miR-60-y and miR-676-y were found to up-regulate in AcCKMI1 vs AcTMI1 and target genes engaged in spore wall protein and glycolysis/gluconeogenesis, while miR-60-y in AcCKMI1 vs AcTMI1 was up-regulated and potentially targeted a glycolysis/gluconeogenesis-associated gene. Comparatively, 343 down-regulated (138 up-regulated) mRNAs in AcCKM1 vs AcTM1 were putative targets of 121 up-regulated (112 down-regulated) miRNAs in NcCKMI vs NcTMI1, 247 down-regulated (110 up-regulated) mRNAs were putatively targeted by 110 up-regulated (104 down-regulated) miRNAs in NcCKMI vs NcTMI2. Further analysis showed that 31 up-regulated miRNAs in NcCKMI vs NcTMI1 potentially targeted 12 down-regulated mRNAs in AcCKM1 vs AcTM1, which were involved in five immune-related pathways such as phagasome and Jak-STAT signaling pathway, whereas nine up-regulated miRNAs in NcCKMI vs NcTMI2 putatively targeted five down-regulated mRNAs in AcCKM2 vs AcTM2, which were engaged in three immune-related pathways including endocytosis, lysosomes, and regulation of autophagy. In addition, miR-21-x was observed to up-regulate in NcCKMI vs NcTMI1 and target a oxidative phosphorylation-related gene. Finally, potential targeting relationship between two host DEmiRNAs-microsporidian DEmRNAs pairs and two microsporidian DEmiRNAs-host DEmRNAs pairs were verified on basis of RT-qPCR. Our findings not only lay a foundation for exploring the molecular mechanism underlying cross-kingdom regulation between A. c. cerana workers and N. ceranae, but also offer valuable insights into Asian honey bee-microsporidian interaction.

pathology↗