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Age-associated decline in RAB-10 efficacy impairs intestinal barrier integrity

Nature Aging volume 3, pages 1107–1127 (2023)Cite this article

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Abstract

The age-related decline in the ability of the intestinal barrier to maintain selective permeability can lead to various physiological disturbances. Adherens junctions play a vital role in regulating intestinal permeability, and their proper assembly is contingent upon endocytic recycling. However, how aging affects the recycling efficiency and, consequently, the integrity of adherens junctions remains unclear. Here we show that RAB-10/Rab10 functionality is reduced during senescence, leading to impaired adherens junctions in the Caenorhabditis elegans intestine. Mechanistic analysis reveals that SDPN-1/PACSINs is upregulated in aging animals, suppressing RAB-10 activation by competing with DENN-4/GEF. Consistently, SDPN-1 knockdown alleviates age-related abnormalities in adherens junction integrity and intestinal barrier permeability. Of note, the inhibitory effect of SDPN-1 on RAB-10 requires KGB-1/JUN kinase, which presumably enhances the potency of SDPN-1 by altering its oligomerization state. Together, by examining age-associated changes in endocytic recycling, our study sheds light on how aging can impact intestinal barrier permeability.

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Fig. 1: Aging leads to dysfunction of the adherens junctions, RAB-10 functionality decline and SDPN-1 expression increase.
Fig. 2: SDPN-1 is involved in regulating the endosomal localization of RAB-10 and the architecture of adherens junctions.
Fig. 3: SDPN-1 exhibits a preferential association with RAB-10(GDP).
Fig. 4: SDPN-1 interacts with DENN-4 and disturbs the distribution of DENN-4.
Fig. 5: SDPN-1 competes with the DENN domain for binding to RAB-10(GDP) and impedes the DENN-4-induced activation of RAB-10.
Fig. 6: Analysis of the interacting interfaces between RAB-10(GDP) and SDPN-1 or DENN-4, and SDPN-1 dimer is the primary form that competes with DENN-4.
Fig. 7: DENN domain overexpression alleviates the RAB-10 cytosolic dispersion and hTAC recycling abnormalities associated with SDPN-1 excess, whereas SDPN-1 deficiency relieves the age-related deterioration of adherens junctions and intestinal barrier permeability.
Fig. 8: Lack of KGB-1/JNK3 mitigates RAB-10 cytosolic dispersal and adherens junctional mislocalization in cells overexpressing SDPN-1.

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Data availability

All the data that support the findings of this study are present in the paper and its Supplementary Information files. In addition, source data are available with the paper.

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Acknowledgements

We thank J. Diao (University of Cincinnati College of Medicine) for assisting with imaging analysis and S. Xu (Zhejiang University) for the CRISPR–Cas9 single-copy transgene knock-in experiment setup. This work was supported by the National Key R&D Program of China (2021YFA1300302), the National Natural Science Foundation of China (32130027), the National Science Fund for Distinguished Young Scholars (31825017), the Major Research Plan of the Natural Science Foundation of China (92154001), all to A.S., and the China Postdoctoral Science Foundation (2020M672330), to J.Z. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China

    Jing Zhang, Zongyan Jiang, Changling Chen, Longfeng Yao, Ziwei Gao, Zihang Cheng, Yanling Yan, Hang Liu & Anbing Shi

  2. Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China

    Anbing Shi

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Contributions

J.Z., H.L. and A.S. designed the study. J.Z., Z.J., C.C. and Z.G. performed the experiments. J.Z., Z.J., C.C., L.Y., Z.G., Z.C. and Y.Y. contributed the reagents. J.Z., H.L. and A.S. analyzed the data. J.Z., H.L. and A.S. wrote the paper, with input and final approval from all authors.

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Correspondence to Hang Liu or Anbing Shi.

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Nature Aging thanks Peter Douglas, James Goldenring and the other, anonymous reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Aging does not impact apical endocytosis, cell polarity, or DLG-AJM domain distribution.

(A-Aꞌ) Confocal images showing apical uptake of rhodamine-dextran by intestinal cells in wild-type and rab-10(q373) animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. ns: no significance. (B-Bꞌ) Confocal images showing localization of ERM-1::GFP. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. ns: no significance. (C-Cꞌ) Confocal images showing localization of PAR-3::GFP. Line-scan profile on day 1 and day 9 of adulthood. (D-Dꞌ) Confocal images showing DLG-1::GFP in wild-type (n = 70 and 86 junctions on Day 1 and 9 of adulthood) and rab-10(q373) (n = 96) animals. The percentages of animals carrying proper DLG-1::GFP distribution were calculated per time point, each with 30-35 animals. (E-Eꞌ) Confocal images showing AJM-1::GFP in wild-type (n = 87 and 94 junctions on Day 1 and 9 of adulthood) and rab-10(q373) (n = 80) animals. The percentages of animals carrying proper AJM-1::GFP distribution were calculated per time point, each with 30-35 animals. (F-Fꞌ) Confocal images showing DAF-4::GFP distribution in wild-type and rab-10(q373) animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. *** p < 0.001 (p < 0.0001). (G-Gꞌ) Confocal images showing PPK-1::GFP distribution. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. ns: no significance. (H) mRNA level measurement indicating denn-4, let-413, and tbc-11 expressions. Data are the mean ± SEM of three repeats. (I-I’) The endogenous levels of DENN-4. The relative intensity of DENN-4 was calculated with reference to the Tubulin level. Data are the mean ± SEM of three repeats. P-value: two-sided Student’s t-test. *** p < 0.001 (p = 0.0005). (J-Jꞌ) Confocal images showing the localization of endogenous RAB-10 following RNAi-mediated SDPN-1 knockdown. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. *** p < 0.001 (p < 0.0001). Confocal images scale bars: 10 μm.

Source data

Extended Data Fig. 2 SDPN-1 is unlikely to engage in an interaction with RAB-8 or RAB-11.1.

(A-Bꞌ) Confocal images showing the distribution of GFP::RAB-8(SC KI) and GFP::RAB-11.1 in wild-type and sdpn-1(ok1667) animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. ns: no significance. Scale bars: 10 μm. (C-Dꞌ) Confocal images showing the co-localization (upper panels: Z-axis focal plane; lower panels: Y-axis focal plane) between SDPN-1::GFP(SC KI) and tagRFP- or mCherry-tagged RAB-8 and RAB-11.1. DAPI channel (blue color) indicates broad-spectrum intestinal autofluorescence. Mander’s coefficients were calculated using the Z-stack confocal slices, data are the mean with 95% CIs (n = 9 animals). Scale bars: 10 μm. (E-Eꞌ) Confocal images showing GFP::HMP-1 in wild-type (n = 91 junctions), rab-8(tm2526) (n = 90 junctions), and rab-11.1(RNAi) (n = 93 junctions) animals. Arrowheads indicate apical localization of GFP::HMP-1. The percentages of animals carrying irregular GFP::HMP-1 distribution were calculated, each with 30-35 animals. Scale bars: 10 μm. (F-Fꞌ) An examination of the adherens junctions was performed using TEM in wild-type, rab-8(tm2526), and rab-11.1(RNAi) animals. Red arrows indicate junction structures. Scale bars: 0.2 μm. Data are the average junction length ± SEM of 6 samples.

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Extended Data Fig. 3 RAB-10 is not required for the membrane recruitment of SDPN-1.

(A-Aꞌꞌ) Confocal images showing the localization of SDPN-1::GFP (SC KI) in wild-type and rab-10(q373) animals, as well as rab-10(q373) overexpressing RAB-10(Q68L) or RAB-10(T23N). Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. The p values were obtained by a one-way ANOVA followed by a post-hoc test (Tukey’s Multiple Comparison Test) for multiple comparisons. The exact p values are indicated on the plot. (B-Cꞌ) Confocal images showing the localization of SDPN-1::GFP(SC KI) in wild-type, rab-10(q373), rab-10(q373);cup-5(RNAi), rab-10(q373);mvb-12(RNAi), and rab-10(q373);rpt-3(RNAi) animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. The p values were obtained by a one-way ANOVA followed by a post-hoc test (Tukey’s Multiple Comparison Test) for multiple comparisons. The exact p values are indicated on the plot. (D-Eꞌ) Confocal images showing the co-localization between SDPN-1::GFP(SC KI) and FM4-64 or rhodamine-dextran. DAPI channel (blue color) indicates broad-spectrum intestinal autofluorescence. Mander’s coefficients were calculated using the Z-stack confocal slices, data are the mean with 95% CIs (n = 9 animals). P-value: two-sided Mann-Whitney test. ns: no significance. (F) The membrane-to-cytosol ratio (P/S) of SDPN-1::GFP(SC KI) in wild-type and rab-10(q373) animals. SDPN-1 in the supernatants and pellets was analyzed by western blotting using an anti-GFP antibody. The loading control was blotted by the anti-α-tubulin antibody. The membrane binding status of SDPN-1 was evaluated in three experimental replicates, and the average ratios are displayed below the blots. (G) The level of SDPN-1::GFP(SC KI) in wild-type and rab-10(q373) animals. Three experimental replicates were conducted. Average intensities were calculated with reference to the tubulin level and are displayed beneath the blots. Confocal images scale bars: 10 μm.

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Extended Data Fig. 4 The endosomal localization of SDPN-1 is mainly determined by PI(4,5)P2.

(A-Aꞌ) Confocal images showing the localization of SDPN-1::GFP(SC KI) in wild-type, rab-10(q373), rab-10(q373);ppk-1(RNAi), rab-10(q373);ppk-2(RNAi), rab-10(q373);ppk-3(RNAi), rab-10(q373);pifk-1(RNAi), rab-10(q373);age-1(RNAi), and rab-10(q373);vps-34(RNAi) animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. The p values were obtained by a one-way ANOVA followed by a post-hoc test (Tukey’s Multiple Comparison Test) for multiple comparisons. The exact p values are indicated on the plot. (B-Dꞌ) Confocal images showing the co-localization (Z-axis focal plane) between SDPN-1::GFP (SC KI) and mCherry-tagged PI(4,5)P2 biosensor Tubby-PH(R332H), PI(3)P biosensor 2xFYVE, and PI(4)P biosensor P4M in the intestinal cells. Arrowheads indicate structures labeled by both GFP and mCherry. DAPI channel (blue color) indicates broad-spectrum intestinal autofluorescence. Mander’s coefficients were calculated using the Z-stack confocal slices, data are the mean with 95% CIs (n = 9 animals). P-value: two-sided Mann-Whitney test. ns: no significance. Confocal images scale bars: 10 μm.

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Extended Data Fig. 5 Loss of SDPN-1 does not affect the subcellular distribution and membrane association of RAB-5.

(A-Aꞌ) Confocal images showing GFP::RAB-5 in wild-type and sdpn-1(ok1667) animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. *** p < 0.001 (p < 0.0001). (B) The membrane-to-cytosol ratio (P/S) of GFP::RAB-5 in wild-type and sdpn-1(ok1667) animals. RAB-5 in the supernatants and pellets was analyzed by western blotting using an anti-GFP antibody. The loading control was blotted by the anti-α-tubulin antibody. The ratios are displayed beneath the blots. (C-Cꞌꞌ) Confocal images showing the co-localization (upper panels: Z-axis focal plane; lower panels: Y-axis focal plane) between SDPN-1::GFP(SC KI) and tagRFP- or mCherry-tagged RAB-5, EHBP-1, RAB-7, MANS, and SP12. Arrowheads indicate structures labeled by both GFP and tagRFP or mCherry. DAPI channel (blue color) indicates broad-spectrum intestinal autofluorescence. Mander’s coefficients were calculated using the Z-stack confocal slices, data are the mean with 95% CIs (n = 9 animals). Confocal images scale bars: 10 μm.

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Extended Data Fig. 6 SDPN-1 interacts with DENN-4 and its activating factor LET-413.

(A) Western blot showing GST pulldown with in vitro translated HA-tagged GDI-1 and TBC-11. (B) Western blot showing GST pulldown with in vitro translated HA-SDPN-1. (C) Western blot showing GST pulldown with in vitro translated HA-tagged DENN-4 fragments (1-720 aa and 721-1544 aa). (D) Western blot showing GST pulldown with in vitro translated HA-tagged LET-413 fragments (LRR domain and PDZ domain). (E-Eꞌ) Confocal images showing the co-localization (upper panels: Z-axis focal plane; lower panels: Y-axis focal plane) between SDPN-1::GFP(SC KI) and mCherry-tagged LET-413. Arrowheads indicate structures labeled by both GFP and mCherry. DAPI channel (blue color) indicates broad-spectrum intestinal autofluorescence. Mander’s coefficients were calculated using the Z-stack confocal slices, data are the mean with 95% CIs (n = 9 animals). (F-Fꞌꞌ) Confocal images showing SDPN-1::GFP(SC KI) in wild-type and denn-4(RNAi) animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. *** p < 0.001 (p < 0.0001), ns: no significance (p = 0.874). (G-Gꞌ) Confocal images showing the localization of LET-413::GFP in wild-type, sdpn-1(ok1667), and SDPN-1 overexpressing animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. Asterisks indicate the significant differences in a one-way ANOVA followed by a post-hoc test (Dunn’s Multiple Comparison Test) for multiple comparisons. *** p < 0.001 (p < 0.0001). (H-Hꞌꞌ) Confocal images showing SDPN-1::GFP(SC KI) in wild-type and let-413(RNAi) animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. *** p < 0.001 (p < 0.0001), ns: no significance (p = 0.1664). Three experimental replicates were conducted to validate the results obtained from all pull-down assays. Confocal images scale bars: 10 μm.

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Extended Data Fig. 7 The presence of SDPN-1 does not interfere with the LET-413-DENN-4 or LET-413-RAB-10 interaction.

(A-Aꞌ) Western blot showing GST pulldown with in vitro translated HA-LET-413. In the presence of SDPN-1, the interaction between DENN-4(721-1544 aa) and LET-413 was not affected. Three independent experiments are represented in the histogram, and the p values were obtained by two-sided Mann-Whitney test. Data are the mean ± SEM, ns: no significance (p = 0.9853). (B-Bꞌ) Western blot showing GST pulldown with in vitro translated HA-RAB-10(T23N). In the presence of SDPN-1, the interaction between RAB-10(T23N) and LET-413 was not affected. Three independent experiments are represented in the histogram, and the p values were obtained by two-sided Mann-Whitney test. Data are the mean ± SEM, ns: no significance (p = 0.3765). (C-Dꞌ) Confocal images showing the co-localization (Z-axis focal plane) between GFP-tagged DENN-4 or RAB-10 and LET-413::mCherry. DAPI channel (blue color) indicates broad-spectrum intestinal autofluorescence. Mander’s coefficients were calculated using the Z-stack confocal slices, data are the mean with 95% CIs (n = 9 animals). P-value: two-sided Mann-Whitney test. ns: no significance. Confocal images scale bars: 10 μm.

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Extended Data Fig. 8 Analysis of the binding regions between RAB-10(GDP) and SDPN-1 or DENN-4.

(A-E) Western blot showing GST pulldown with in vitro translated HA-tagged RAB-10(T23N) mutants. (Eꞌ) Three independent experiments are represented in the histogram. The p values were obtained by a one-way ANOVA followed by a post-hoc test (Tukey’s Multiple Comparison Test) for multiple comparisons. The exact p values are indicated on the plot. Data are the mean ± SEM.

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Extended Data Fig. 9 KGB-1 acts as the primary upstream regulator of the RAB-10-SDPN-1 module to exert age-related effects on adherens junctions through its impact on endocytic recycling.

(A-Aꞌ) Confocal images showing the localization of ACT-5::GFP in wild-type, rab-10(q373), and SDPN-1 overexpressing animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. P-value: two-sided Mann-Whitney test. ns: no significance. (B-Bꞌ) Confocal images showing GFP::HMP-1 in wild-type (n = 73 and 72 junctions on Day 1 and 9 of adulthood) and DENN domain overexpressing (n = 73 junctions) animals. Arrowheads indicate apical and lateral localization of GFP::HMP-1. The percentages of animals carrying irregular GFP::HMP-1 distribution were calculated, each with 30-35 animals. (C-Cꞌ) Confocal images showing the localization of hTAC::GFP in wild-type, sdpn-1(RNAi), sdpn-1(RNAi);rab-10(q373), and DENN domain overexpressing animals. Box-and-whiskers (n = 24 regions): 10-90 percentile; dots, outliers; red midline, median of wild-type; boundaries, quartiles. The p values were obtained by a one-way ANOVA followed by a post-hoc test (Tukey’s Multiple Comparison Test) for multiple comparisons. The exact p values are indicated on the plot. (D-D’) Endogenous levels of SDPN-1 in both wild-type and kgb-1(RNAi) animals. The relative intensity of SDPN-1 was calculated with reference to the tubulin level. Data are the mean ± SEM of three repeats. P-value: two-sided Student’s t-test. ns: no significance. (E) mRNA level measurement indicating sdpn-1 expression in both wild-type and kgb-1(RNAi) animals. Data are the mean ± SEM of three repeats. (F) The absence of phosphorylation in the serine, threonine, and tyrosine residues of SDPN-1. Three experimental replicates were conducted to validate the results. (G-Gꞌ) Confocal images showing the co-localization between SDPN-1::GFP(SC KI) and KGB-1::mCherry(SC KI) in 1-day-old and 9-day-old adult animals. DAPI channel (blue color) indicates broad-spectrum intestinal autofluorescence. Mander’s coefficients were calculated using the Z-stack confocal slices, data are the mean with 95% CIs (n = 9 animals). P-value: two-sided Mann-Whitney test. *** p < 0.001 (p < 0.0001). (H-H’) Native-PAGE of purified Flag-SDPN-1 in the presence or absence of KGB-1. Three independent experiments are represented in the histogram. Data are the mean ± SEM. P-value: two-sided Student’s t-test. *** p < 0.001 (p = 0.0007). Confocal images scale bars: 10 μm.

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Supplementary information

Reporting Summary

Supplementary Table 1

Antibodies. The commercial antibodies used in this study are outlined in detail.

Supplementary Table 2

Bacterial strains. Bacterial strains were employed in this study for nematode feeding and protein expression.

Supplementary Table 3

Critical commercial assays. A detailed list of the molecular biology and biochemical reagents used in this research is included.

Supplementary Table 4

Chemicals, peptides and recombinant proteins. This table outlines the protein purification, protein function and other chemical reagents used in this study.

Supplementary Table 5

Organisms/strains. This table presents the nematode strains employed in this study, including both mutant and transgenic strains. Recombinant DNA. This table contains the vectors that have been prepared in this study for transgenic expression and in vitro protein expression. Oligonucleotides. This table primarily contains primers for CRISPR–Cas gene editing and vector sequencing.

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Zhang, J., Jiang, Z., Chen, C. et al. Age-associated decline in RAB-10 efficacy impairs intestinal barrier integrity. Nat Aging 3, 1107–1127 (2023). https://doi.org/10.1038/s43587-023-00475-1

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