Basic Information

Academic Degree

• 博士（農学）(岡山大学)
• 修士（農学）(岡山大学)

Academic Resume (Graduate Schools)

• 岡山大学, 大学院環境生命科学研究科博士前期課程生物生産科学専攻, 修了
• 岡山大学, 大学院環境生命科学研究科博士後期課程農生命科学専攻, 修了

Academic Resume (Undergraduate School/Majors)

• 岡山大学, 農学部総合農業科学科, 卒業

Research History

• From Aug. 2022, To Present

  京都大学 医生物学研究所, 助教
• From Aug. 2022, To Present

  京都大学 大学院生命科学研究科, 助教
• From Jun. 2021, To Jul. 2022

  京都大学 ウイルス・再生医科学研究所（2022年4月,医生物学研究所に改称）, 特定助教
• From Apr. 2019, To Jun. 2021

  Japan Society for the Promotion of Science, Overseas Research Fellow
• From Dec. 2016, To Jun. 2021

  Duke University School of Medicine, Department of Cell Biology, Tata Lab, Postdoctoral Associate
• From Oct. 2016, To Nov. 2016

  Japan Society for the Promotion of Science, Research Fellow (PD)
• From Apr. 2014, To Sep. 2016

  Japan Society for the Promotion of Science, Research Fellow (DC1)

Profile

• Profile

  岡山大にてウシ卵管機能調節機構の解明をテーマとして学位を取得いたしました。2016年12月よりDuke University・Purushothama Rao Tata Lab (North Carolina, USA) において、博士研究員として呼吸器（肺および気管）の幹細胞に関する研究を遂行し、Stem Cell Biology ならびに NGS 解析の知識と技術を得ました。大学院時ならびに博士研究員時のバックグラウンドを活かし、2021年6月より京都大学ウイルス・再生医科学研究所 (2022年4月、医生物学研究所に改称）・組織恒常性システム分野において、組織再生・リモデリングにおける細胞間・臓器間連携メカニズムや、疾患・組織修復時に認められる性差のメカニズムなどについて研究を遂行しております。共同研究のお誘い等お問い合わせはこちらのメールアドレスにどうぞ: kobayashi.yoshihiko.2p at kyoto-u.ac.jp

Language of Instruction

• Japanese
• English

ID,URL

• J-Global ID

  201801003278786819

researchmap URL

• https://researchmap.jp/yoshi_kobayashi

Research

Research Interests

• 肺
• Tissue regeneration
• Mint-ChIP
• Single-cell ATAC-seq
• Single-cell RNA-seq
• Oviduct
• Respiratory system
• Tissue stem cells

Research Areas

• Life sciences, Laboratory animal science
• Life sciences, Animals: biochemistry, physiology, behavioral science
• Life sciences, Applied molecular and cellular biology
• Life sciences, Molecular biology
• Life sciences, Dermatology
• Life sciences, Respiratory medicine

Papers

• Sex differences in resilience to ferroptosis underlie sexual dimorphism in kidney injury and repair

  Ide S*; Ide K*; Abe K*; Kobayashi Y; Kitai H; McKey J; Strausser SA; O’Brien LL; Tata A; Tata PR; Souma T. *Contributed equally.

  Cell Reports, Nov. 2022, Peer-reviewed

  
• Coupled myovascular expansion directs cardiac growth and regeneration

  DeBenedittis P; Karpurapu A; Henry A; Thomas MC; McCord TJ; Brezitski K; Prasad A; Baker CE; Kobayashi Y; Shah SH; Kontos CD; Tata PR; Lumbers RT; Karra R

  Development, 15 Sep. 2022, Peer-reviewed

  
• Multi-apical polarity of alveolar stem cells and their dynamics during lung development and regeneration

  Konkimalla A; Konishi S; Kobayashi Y; Murthy PKL; Macadlo L; Mukherjee A; Elmore Z; Kim S; Pendergast AM; Lee PJ; Asokan A; Knudsen L; Bravo-Cordero JJ; Tata A; Tata PR

  iScience, Sep. 2022, Peer-reviewed

  
• Lung Stem Cells in Development, Health and Disease - Epithelial stem cells at the intersection of tissue regeneration and pulmonary fibrosis

  Plate M; Kobayashi Y; Chambers RC; Tata PR

  European Respiratory Society Publications (ERS Monograph), Apr. 2021, Peer-reviewed, Invited

  
• Human distal lung maps and lineage hierarchies reveal a bipotent progenitor

  Murthy PKL*, Sontake V*, Tata A, Kobayashi Y, Macadlo L, Okuda K, Conchola AS, Nakano S, Gregory S, Miller LA, Spence JR, Engelhardt JF, Boucher RC, Rock JR, Randell SH, Tata PR, *Contributed equally.

  Nature, 07 Apr. 2022, Peer-reviewed

  
• Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

  Muus C*; Luecken MD*; Eraslan G*; Sikkema L*; Waghray A*; Heimberg G*; Kobayashi Y*; Vaishnav ED*; Subramanian A*; Smilie C*; Jagadeesh KA*; Duong ET*; Fiskin E*; Triglia ET*; Ansari M*; Cai P*; Lin B*; Buchanan J*; Chen S*; Shu J*; Haber AL*; Chung H*; Montoro DT*; Adams TS; Aliee H; Allon SJ; Andrusivova Z; Angelidis I; Ashenberg O; Bassler K; Becavin C; Benhar I; Bergenstrahle J; Bergenstrahle L; Bolt L; Braun E; Bui LT; Callori S; Chaffin M; Chichelnitskiy E; Chiou J; Conlon TM; Cuoco MS; Cuomo ASE; Deprez M; Duclos G; Finem D; Fischer DS; Ghazanfar S; Gillich A; Giotti B; Gould J; Guo M; Gutierrez AJ; Habermann AC; Harvey T, He P; Hou X; Hu L; Hu Y; Jaiswal A; Ji L; Jiang P; Kapellos TS; Kuo CS; Larsson L; Leney-Greene MA; Lim K; Litvinukova M; Ludwig LS; Lukassen S; Luo W; Maatz H; Madissoon E; Mamanova L; Manakongtreecheep K; Marquette CH; Mayr CH; Mbano IM; McAdams AM; Nabhan AN; Nyquist SK; Penland L; Poirion OB; Poli S; Qi C; Queen R; Reichart D; Rosas I; Schupp JC; Shea CV; Shi X; Sinha R; Sit RV; Slowikowski K; Slyper M; Smith NP; Sountoulidis A; Strunz M; Sullivan TB; Sun D; Talavera-Lopez C; Tan P; Tantivit J; Travaglini KJ; Tucker NR; Vernon K; Wadsworth MH; Waldman J; Wang X; Yan W; Zhao W; Ziegler CGK; The NHLBI LungMAP; Consortium; The Human Cell; Atlas Lung Biological Network. *Contributed equally.

  Nature Medicine, Mar. 2021, Peer-reviewed, Lead author

  
• Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair.

  Ide S*, Kobayashi Y*, Ide K, Strausser SA, Abe K, Herbek S, O’Brien LL, Crowley SD, Barisoni L, Tata A, Tata PR, Souma T. *Contributed equally.

  eLife, 19 Jul. 2021, Peer-reviewed, Lead author

  
• Human lung stem cell-based alveolospheres provide insights into SARS-CoV-2 mediated interferon responses and pneumocyte dysfunction

  Katsura H*; Sontake V*; Tata A*; Kobayashi Y*; Edwards CE*; Heaton BE; Konkimalla A; Asakura T; Mikami Y; Fritch EJ; Lee PJ; Heaton NS; Boucher RC; Randell SH; Baric RS; Tata PR. *Contributed equally.

  Cell Stem Cell, Oct. 2020, Peer-reviewed, Lead author

  
• Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis

  Kobayashi Y; Tata A; Konkimalla A; Katsura H; Lee RF; Ou J; Banovich NE; Kropski JA; Tata PR

  Nature Cell Biology, 13 Jul. 2020, Peer-reviewed, Lead author

  
• Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury.

  Tata A; Kobayashi Y; Chow RD; Tran J; Desai A; Massri AJ; McCord TJ; Gunn MD; Tata PR

  Cell Stem Cell, May 2018, Peer-reviewed

  
• Niche-mediated BMP/SMAD signaling regulates lung alveolar stem cell proliferation and differentiation

  Chung M; Bujnis M; Barkauskas CE; Kobayashi Y; Hogan BLM

  Development, 01 May 2018, Peer-reviewed

  
• Pulmonary Neuroendocrine Cells: Sensors and Sentinels of the Lung.

  Kobayashi Y; Tata PR

  Developmental Cell, May 2018, Peer-reviewed, Lead author

  
• Remodeling of bovine oviductal epithelium by mitosis of secretory cells

  Ito S; Kobayashi Y; Yamamoto Y; Kimura K; Okuda K

  Cell and Tissue Research, Nov. 2016, Peer-reviewed

  
• Regulation of bovine oviductal NO synthesis by follicular steroids and prostaglandins

  Kobayashi Y; Yamamoto Y; Kageyama S; Hirayama H; Kimura K; Okuda K

  Reproduction, Jun. 2016, Peer-reviewed, Lead author

  
• Roles of EDNs in regulating oviductal NO synthesis and smooth muscle motility in cows

  Kobayashi Y; Yoshimoto Y; Yamamoto Y; Kimura K; Okuda K

  Reproduction, Jun. 2016, Peer-reviewed, Lead author

  
• Summer heat stress affects prostaglandin synthesis in the bovine oviduct

  Kobayashi Y; Wakamiya K; Kohka M; Yamamoto Y; Okuda K

  Reproduction, Aug. 2013, Peer-reviewed, Lead author

  
• Identification of distinct non-myogenic skeletal-muscle-resident mesenchymal cell populations.

  Leinorth AP; Mirando AJ; Rouse D; Kobayashi Y; Tata PR; Rueckert HE; Liao Y; Long JT; Chakkalakal JV; Hilton MJ

  Cell Reports, 10 May 2022, Peer-reviewed

  
• Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity

  Murthy PKL; Xi R; Arguijo D; Everitt JI; Kocak DD; Kobayashi Y; Bozec A; Vicent A; Ding S; Crawford GE; Hsu D; Tata PR; Reddy T; Shen X

  Developmental Cell, Feb. 2022, Peer-reviewed

  
• Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis.

  Wang L; Wang E; Balcazar JP; Wu Z; Xiang K; Wang Y; Huang Q; Negrete M; Chen K; Li W; Fu Y; Dohlman A; Mines R; Zhang L; Kobayashi Y; Chen T; Shi G; Shen JP; Kopetz S; Tata PR; Moreno V; Gersbach C; Crawford G; Hsu D; Huang E; Bu P; Shen X

  Advanced Science, 10 Aug. 2021, Peer-reviewed

  
• Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia

  Okuda K; Dang H*; Kobayashi Y*; Carraro G*; Nakano S; Chen G; Kato T; Asakura T; Gilmore RC; Morton LC; Lee RE; Mascenik T; Yin W; Cardenas SMB; O’Neal YK; Minnick CE; Chua M; Quinney NL; Gentzsch M; Anderson CW; Ghio A; Matsui H; Nagase T; Ostrowski LE; Grubb BR; Olsen JC; Randell SH; Stripp BR; Tata PR; O'Neal WK; Boucher RC. *Contributed equally.

  American Journal of Respiratory and Critical Care Medicine, 15 Dec. 2020, Peer-reviewed

  
• A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics

  Sapoznik E; Chang B; Huh J; Ju RJ; Azarova EV; Pohlkamp T; Welf ES; Broadbent D; Carisey AF; Stehbens SJ; Lee K; Marín A; Hanker AB; Schmidt JC; Arteaga CL; Yang B; Kobayashi Y; Tata PR; Kruithoff R; Doubrovinski K; Shepherd DP; Millett-Sikking A; York AG; Dean KM; Fiolka RP

  eLife, 12 Nov. 2020, Peer-reviewed

  
• Yolk-sac-derived macrophages progressively expand in the mouse kidney with age

  Ide S; Yahara Y; Kobayashi Y; Strausser SA; Ide K; Watwe A; Xu-Vanpala S; Privratsky JR; Crowley SD; Shinohara ML; Alman BA; Souma T

  eLife, 17 Apr. 2020, Peer-reviewed

  
• Essential role for InSyn1 in dystroglycan complex integrity and cognitive behaviors in mice.

  Uezu A; Hisey E; Kobayashi Y; Gao Y; Bradshaw TW; Devlin P; Rodriguiz R; Tata PR; Soderling S

  eLife, Dec. 2019, Peer-reviewed

  
• IL-1 and TNFα Contribute to the Inflammatory Niche to Enhance Alveolar Regeneration.

  Katsura H; Kobayashi Y; Tata PR; Hogan BLM

  Stem Cell Reports, Apr. 2019, Peer-reviewed

  
• Acute stimulation of a smooth muscle constrictor by oestradiol-17β via GPER1 in bovine oviducts

  Nishie T; Kobayashi Y; Kimura K; Okuda K

  Reproduction in Domestic Animals, 2018, Peer-reviewed

  
• Adrenomedullin regulates the speed of oviductal fluid flow in cattle

  Yoshimoto Y; Nishie T; Ito S; Kobayashi Y; Yamamoto Y; Okuda K; Kimura K

  Molecular Reproduction and Development, Aug. 2017, Peer-reviewed

  
• Local effect of lysophosphatidic acid on prostaglandin production in the bovine oviduct

  Yoshimoto Y; Kobayashi Y; Woclawek-Potocka I; Sinderewicz E; Yamamoto Y; Kimura K; Okuda K

  Reproduction, Fertility and Development, Apr. 2017, Peer-reviewed

  
• Endothelin as a local regulating factor in the bovine oviduct

  Yamamoto Y; Kohka M; Kobayashi Y; Woclawek-Potocka I; Okuda K

  Reproduction, Fertility and Development, 2016, Peer-reviewed

  
• Purified Culture Systems for Bovine Oviductal Stromal Cells

  Yamamoto Y; Kobayashi Y; Okuda K

  Journal of Reproduction and Development, Feb. 2014, Peer-reviewed

  

Presentations

• 肺胞組織修復過程に一過性に出現する上皮細胞状態と、肺胞線維化との関係性

  小林 芳彦

  第22回日本再生医療学会総会, シンポジウム「呼吸器の幹細胞・オルガノイド研究の現状と再生医療の実現に向けて」, 23 Mar. 2023, Invited

  
• 肺胞組織修復過程に出現する一過性の上皮細胞状態

  日本肺サーファクタント・界面医学会第58回学術研究会, シンポジウム「肺構成細胞からみた肺環境の恒常性と再生修復」, 24 Sep. 2022, Invited

  
• Reservoir of tissue-resident stem cells for regeneration of airway epithelium

  Yoshihiko Kobayashi; Aleksandra Tata; Purushothama Rao Tata

  第19回幹細胞シンポジウム, 28 May 2022

  
• 組織修復時に一過性に認められる上皮細胞種と、慢性呼吸器疾患におけるその蓄積

  小林芳彦

  第62回日本呼吸器学会学術講演会, シンポジウム「肺の微小環境と疾患病態」, 23 Apr. 2022, Invited

  
• Accumulation of regeneration-specific transitional cell state in pulmonary fibrosis

  Kobayashi Y; Tata A; Tata PR

  Online Trial Meeting 2020, the Japansese Society of Developmental Biologists, 25 Sep. 2020

  
• Accumulation of regeneration-specific transitional cell state in pulmonary fibrosis

  Kobayashi Y; Tata A; Tata PR

  53rd Annual Meeting of the Japansese Society of Developmental Biologists, May 2020

  
• Dynamic uni- and multi-potent progenitors contribute to airway glandular tissue regeneration.

  Kobayashi Y; Tata, PR

  Cold Spring Harbor Laboratory Meeting – Stem Cell Biology, 18 Sep. 2019

  
• 基底膜下 stem-like cells による卵管上皮組織リモデリング

  小林 芳彦; 伊藤 さやか; 木村 康二; 奥田 潔

  第109回日本繁殖生物学会大会, Sep. 2016

  
• A system for remodeling the oviductal epithelium by stem-like cells

  Kobayashi Y; Yamamoto Y; Kimura K; Okuda K

  75th Annual Meeting of Society for Developmental Biology, 06 Aug. 2016

  
• Regulation of nitric oxide synthesis and spontaneous waves of contraction and relaxation

  Kobayashi Y; Yoshimoto Y; Yamamoto Y; Kimura K; Okuda K

  International Conference on Biology and Pathology of Reproduction in Domestic Animals, 28 Sep. 2015

  
• Interaction between nitric oxide and endothelin-1 in the bovine oviduct

  Kobayashi Y; Yamamoto Y; Okuda K

  9th International Ruminant Reproduction Symposium, 26 Aug. 2014

  
• Effects of ovarian steroid hormones and prostaglandins on nitric oxide synthesis in the bovine oviduct.

  Kobayashi Y; Yamamoto Y; Kageyama S; Hirayama H; Okuda K

  47th Annual Meeting of Society for the Study of Reproduction, 19 Jul. 2014

  
• 卵管におけるエンドセリンと一酸化窒素の相互調節

  小林 芳彦; 山本 ゆき; 奥田 潔

  第18回日本生殖内分泌学会学術集会, Dec. 2013

  
• ウシ卵管における性ステロイドによる一酸化窒素の合成制御

  小林 芳彦; 幸岡 美紗; 山本 ゆき; 奥田 潔

  第106回日本繁殖生物学会大会, Sep. 2013

  
• Prostaglandins regulate the production of nitric oxide by cultured bovine oviductal epithelial and stromal cells

  Kobayashi Y; Yamamoto Y; Okuda K

  46th Annual Meeting of Society for the Study of Reproduction, 25 Jul. 2013

  
• 卵管における一酸化窒素の合成制御メカニズム

  小林 芳彦; 山本 ゆき; 奥田 潔

  おかやまバイオアクティブ研究会第43回シンポジウム, Jun. 2013

  
• ウシ卵管における性ステロイドによる一酸化窒素の合成制御

  小林 芳彦; 幸岡 美紗; 山本 ゆき; 奥田 潔

  日本畜産学会第116回大会, Mar. 2013

  
• 卵管における一酸化窒素産生の局所的調節機構

  小林 芳彦; 奥田 潔

  第17回日本生殖内分泌学会学術集会, Dec. 2012

  
• ウシ卵管における一酸化窒素産生の局所的調節機構

  小林 芳彦; 奥田 潔

  第105回日本繁殖生物学会大会, Sep. 2012

  
• Effect of elevated temperatures on prostaglandin synthesis in bovine oviductal epithelial cells.

  Kobayashi Y; Wakamiya K; Sakumoto R; Okuda K

  15 Aug. 2012

  
• ウシ卵管における一酸化窒素産生に及ぼす prostaglandin E2 の影響

  小林 芳彦; 作本 亮介; 奥田 潔

  日本畜産学会第115回大会, Mar. 2012

  
• ウシ卵管上皮細胞における prostaglandin 合成に及ぼす培養温度の影響

  小林 芳彦; 若宮 香理; 作本 亮介; Acosta Tomas J; 高橋 昌志; 奥田 潔

  第104回日本繁殖生物学会大会, Sep. 2011

  

Books and Other Publications

• 実験医学 - Lab Report ラボ立ち上げ期の新米PIのもとで - 理系大学院修了後の選択の一例

  小林芳彦

  羊土社, Oct. 2021

  
• Lung Stem Cells in Development, Health and Disease - Epithelial stem cells at the intersection of tissue regeneration and pulmonary fibrosis

  Manuela PlateYoshihiko KobayashiRachel Clare ChambersPurushothama Rao Tata

  European Respiratory Society Publications, Apr. 2021

  
• 実験医学 - Current topics 肺胞再生において一過性に出現する上皮細胞と、肺線維症におけるその蓄積

  小林芳彦, Single work

  羊土社, Dec. 2020

  

Industrial Property Rights

• 特願2022-519551, Lung fibrosis model and methods of using the same.

  Tata PR; Tata A; Konkimalla A; Kobayashi Y

  

External funds: Kakenhi

• 卵巣ステロイドホルモンによる非生殖器官の組織リモデリングメカニズム

  Grant-in-Aid for Early-Career Scientists

  Basic Section 42030:Animal life science-related

  Kyoto University

  小林 芳彦

  From 01 Apr. 2022, To 31 Mar. 2024, Granted

  皮膚;妊娠;女性ホルモン;組織リモデリング

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K15023/