FY2022 Annual Report

Membranology Unit
Assistant Professor Keiko Kono

Abstract

 

1. Staff

• Dr. Yohsuke Moriyama, Science and Technology Associate
• Dr. Shinju Sugiyama, Postdoc
• Dr. Nurhanani Binti Razali, Postdoc
• Dr. Jigyasa Arora, Technician
• Mr. Hunter Barbee, Ph.D. Student
• Ms. Yatzu Chiu, Ph.D. Student
• Mr. Kojiro Suda, Ph.D. Student
• Mr. Jan Grašič, Ph.D. Student
• Mr. Yuta Yamazaki, Ph.D. Student
• Ms. Kamila Krystyna Kozik, Ph.D. Student
• Ms. Hitomi Ohtaki, Research Unit Administrator

Co-supervision

• Ms. Aisulu Maipas, Ph.D. Student@ Yamamoto Unit
• Ms. Sara Abdelaal, Ph.D. Student@ Terenzio Unit
• Mr. Masato Hirota, Ph.D. Student@ Ishikawa Unit

2. Collaborations

2.1 Immune-cell-like functions of epithelial cells

• Type of collaboration: Joint research
• Researcher: Dr. Takeshi Maruyama, TWIns, Waseda University

2.2 Plasma membrane damage response in laboratory yeast and industrial yeast for brewing

• Type of collaboration: Joint research
• Researchers: Dr. Nozomu Kamada, SUNTORY; Dr. Atsushi Fujita, SUNTORY

2.3 Academic Industrial collaboration

• Type of collaboration: Joint research
• Researchers: The team at the Otsuka Pharmaceutical

2.4 The molecular nature of cytosolic zoning

• Type of collaboration: Joint research
• Researcher: Prof. Nobuo Noda, Hokkaido University

2.5 The molecular mechanisms underlying plasma membrane repair

• Type of collaboration: Joint research
• Researcher: Dr. Hitoshi Nakatogawa, Tokyo Institute of Technology

2.6 The plasma membrane damage response in fly

• Type of collaboration: Joint research
• Researcher: Dr. Naonobu Fujita, Tokyo Institute of Technology

3. Activities and Findings

3.1 Plasma membrane damage limits replicative lifespan in yeast and induces premature senescence in human fibroblasts

Plasma membrane damage (PMD) occurs in all cell types due to environmental perturbation and cell-autonomous activities. However, cellular outcomes of PMD remain largely unknown except for recovery or death. Here, using budding yeast and normal human fibroblasts, we show that cellular senescence, irreversible cell cycle arrest contributing to organismal aging, is the long-term outcome of PMD. To identify the genes essential for PMD response, we developed a simple PMD-damaging assay using a detergent and performed a systematic yeast genome-wide screen. The screen identified 48 genes. The top hits in the screen are the endosomal sorting complexes required for transport (ESCRT) genes, encoding the well-described plasma membrane repair proteins in eukaryotes. Unexpectedly, the replicative lifespan regulator genes are enriched in our 48 hits. This finding suggests a close genetic association between the PMD response and the replicative lifespan regulations. Indeed, we show that PMD limits the replicative lifespan in budding yeast; the ESCRT activator AAA-ATPase VPS4-overexpression extends it. These results suggest that PMD limits replicative lifespan in budding yeast. Moreover, in normal human fibroblasts, we find that PMD induces premature senescence via the Ca²⁺-p53 axis but not the major senescence pathway, ATM/ATR pathway. Consistent with the results in yeast, transient overexpression of ESCRT-III, CHMP4B, suppressed the PMD-dependent senescence in normal human fibroblasts. Our study proposes that PMD limits cellular lifespan in two different eukaryotic cell types and highlights an underappreciated but ubiquitous senescent cell subtype, namely PMD-dependent senescent cells.

3.2 Time-resolved transcriptomic profiling of senescence-associated secretory phenotype (SASP) in multiple senescent cell subtypes

Cellular senescence, irreversible cell cycle arrest, is induced by various triggers including telomere shortening, oncogene activation, and DNA damage. Senescent cells exhibit the senescence-associated secretory phenotype (SASP), a pathological feature that contributes to organismal aging. We previously showed that transient plasma membrane damage (PMD) induces a novel subtype of cellular senescence (PMDS) accompanied by SASP, but the overall expression profiles of SASP during PMDS induction was unknown. Here, using mRNA-seq, qPCR, and bioinformatics, we revealed the time-resolved SASP transcriptomic profile in PMDS in comparison with calcium influx-induced senescence, DNA damage response-induced senescence, and replicative senescence. Although the expression of SASP factors was postulated to increase steadily during senescence, we counterintuitively found that the variety of SASP peaks in early PMDS. The pathway comparison analyses and Ingenuity Pathway Analysis suggest that, in early PMDS, wound-healing SASP factors, namely Il-6, Mmp1, and Mmp3, inhibit the GPVI collagen signaling pathway, which in turn further upregulates the same SASP factors, forming a feedback loop. At late senescence, common SASP factors including Il-6 and Ccl2 are upregulated in all senescent cell subtypes. Thus, SASP is diverse at early senescence and becomes relatively uniform at late senescence. Diverse SASP may contribute to senescent cell subtype-specific paracrine/autocrine functions in vivo.

4. Publications

4.1 Journals

1. Kono K*. “Cellular wound-healing in yeast”. Journal of the Brewing Society of Japan (Nippon Jozokyokai Shi). Accepted. Review. By invitation. Japanese.

4.2 Books and other one-time publications

1. Yamazaki Y, Kono K*. “Exocyst live-cell imaging during plasma membrane repair in yeast”. The Exocyst complex. The Exocyst complex edition. Methods in Molecular Biology (Springer Nature). By invitation. Accepted.

4.3 Oral and Poster Presentations

International

1. 〇Kono K*. “How do our cells age?” (2023 Feb) Interdisciplinary Science Conference in Okinawa (ISCO 2023), Okinawa, Japan. Invited talk.
2. 〇Moriyama Y and Kono K*. (2022 Oct) “Plasma membrane damage, immune response, and cellular senescence” The 28th East Asia Joint Symposium on biomedical Research, Shanghai Tech University, China and Zoom. Invited talk.
3. 〇Kono K*. “Plasma membrane damage limits replicative lifespan in yeast and induces premature senescence in human fibroblasts” (2022 Sep) The 23^rd Northeastern Asian Symposium Cellular Senescence: From Pathophysiology to Treatment, Tokyo, Japan and Zoom. Invited talk.
4. 〇Arora J*. "Temporal variation of microbial community assembly is driven by drift and selection: A meta–analysis" (2022 Oct) Tohoku University – OIST 3rd Joint Workshop on Biodiversity: From Genes and Species to Ecosystem Services and Resilience, Sendai, Japan. Invited talk.
5. 〇Barbee H, Moriyama Y, and Kono K*. “Plasma membrane damage-induced senescent cells accelerate wound healing via extracellular vesicles and soluble molecules” (2022 Dec) Cell Bio 2022 (ASCB/EMBO meeting), Washington DC, USA. Poster.
6. 〇Yamazaki Y, and Kono K*. “Clathrin-mediated trafficking of phospholipid flippases is required for local plasma membrane/cell wall damage repair in budding yeast” (2022 Dec) Cell Bio 2022 (ASCB/EMBO meeting), Washington DC, USA. Poster.
7. 〇Suda K, Moriyama Y, Razali N, Chiu Y, and Kono K*. “Plasma membrane damage limits replicative lifespan in yeast and induces premature senescence in human fibroblasts” (2022 Oct) EMBO Workshop 2022 The DNA damage response, immunity and aging, Singapore. Poster.
8. 〇Razali N, Moriyama Y, Chiu Y, Suda K, Turkki T and Kono K*. “Time-resolved transcriptomic profiling of senescence-associated secretory phenotype (SASP) in multiple senescent cell subtypes” (2022 Oct) EMBO Workshop 2022 The DNA damage response, immunity and aging, Singapore. Poster.
9. 〇Grašič J, Suda K, Razali N, and Kono K*. “Time-resolved proteomic profiling of plasma membrane damage-induced senescent cells” (2022 Sep) The 7^th international Cell Senescence Association Conference, Groningen, the Netherland. Poster.

Domestic

1. 〇Kono K*. “Plasma membrane damage induces cellular senescence” (2022 Oct 21), The institute of medical science, The University of Tokyo, Tokyo, Japan. Invited Seminar.
2. 〇Suda K*. "Membrane damage-dependent induction of cellular senescence through endoplasmic reticulum-mitochondria coordination" (2022 Nov 30) The University of Tokyo, Tokyo, Japan. Invited Seminar.
3. 〇Yamazaki Y, Kono K*. “Transport of plasma membrane repair factors is mediated by endocytosis and recycling pathways in budding yeast” (Sep 7-9, 2022) 55^th Yeast Genetics Forum, Okinawa, Japan. Talk.

4. 〇Sugiyama S*. “A mechanism for resolving competition between large structures on the cell membrane”, (Aug 5, 2022) OIST internal seminar, Okinawa, Japan. Talk.

5. 〇Sugiyama S*. “Identification of components of giant structures on the plasma membrane”, 8th meeting of Japanese Society for Yeast Young Researchers, Online (Oct 14, 2022)

6. 〇El-Agamy SE, Guillaud L, Kono K, Wu Y, Terenzio M*. "Roadblock1 regulates FMRP function by promoting its degradation" (2022 June-July), Neuro2022, Okinawa, Poster.
7. Suda K, Razali N, Moriyama Y, Kono K*. "Ca²⁺ accumulation in mitochondria mediates plasma membrane damage-dependent cellular senescence" (2022 Nov-Dec), The 45th Annual Meeting of the Molecular Biology Society of Japan. Fukuoka. Pitch and Poster. MBSJ2022 Science Pitch Award,  EMBO Science Pitch Prize

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 The 55th Yeast Genetics Forum

• Date: Sep 7-9, 2022
• Venue: OIST Auditorium and conference center and on line, Hybrid
• Participants: 238
• Oral presentation: 80
• Poster presentation: 84

6.2 Active mRNA metabolism is a key for the plastic regulation of cell potency in plants

• Date: July 5th, 2022
• Venue: OIST Lab3 C700
• Speaker: Dr. Misato Ohtani, Associate Professor, U Tokyo

6.3 Mystery of a protein adaptation Lessons learned from a DNA polymerase from the deep sea brine pool in the Red Sea

• Date: Nov 30th, 2022
• Venue: OIST Lab3 C700
• Speaker: Dr. Masateru Takahashi, Research Scientist, KAUST

7. Other

Prizes

Keiko Kono has received Yeast Genetics Forum President’s Prize from Yeast Genetics Forum (Sep 7-9, 2022).

Kojiro Suda has received MBSJ2022 Science Pitch Award from The Molecular Biology Society of Japan for the excellent presentation in the 45th Annual Meeting of the Molecular Biology Society of Japan (Nov 30-Dec 2, 2022).

Kojiro Suda has received EMBO Science Pitch Prize from European Molecular Biology Organization for the excellent presentation in the 45th Annual Meeting of the Molecular Biology Society of Japan (Nov 30-Dec 2, 2022).

Keiko Kono has received the Students' Choice Teaching Award from OIST graduate university student council (Sep 1, 2022)