Posts tagged ‘drug discovery’

In May 2017, the Leung lab visited several collaborating groups in Asia and shared with them our research vision on using zebrafish to find new drugs for retinal degeneration. In this blog post, we will share some pictures of our visit to the Department of Ophthalmology at the Osaka University School of Medicine. We met our long-term collaborator Dr. Motokazu Tsujikawa. He is a co-mentor of Logan Ganzen, a graduate student in our laboratory. Logan is a recipient of the predoctoral award from the Indiana Clinical and Translational Sciences Institute. During our Osaka trip, he presented a talk entitled “Visual Motor Response of a Transgenic Retinitis Pigmentosa Zebrafish Model” to Dr. Tsujikawa.

 

Logan in front of a new Center for Medical Innovation and Translational Research.

Fai and Dr. Motokazu in his zebrafish facility in the Center of Medical Innovation and Translational Research.

The Center is beautifully designed with lots of open space.

Logan presented his latest findings to Dr. Motokazu, who served as a co-mentor in Logan’s CTSI predoctoral fellowship.

We also visited the daily operation of the ophthalmology clinic and Osaka University Hospital, and participated in the grand rounds of the local ophthalmologists. We experienced firsthand the passion of translational research from our Japanese colleagues.

Entrance hall of the medical building

A panoramic view at the top floor of the hospital.

We joined the grand rounds of the local ophthalmologists. Dr. Kohji Nishida welcomed the group and gave an opening speech.  Even though we did not speak Japanese, we witnessed their passion to improve clinical service through research.

Needless to say, we were also well-fed by Dr. Tsujikawa with the finest Japanese food, and took some time to visit Kyoto, a magnificent ancient city.

Dr. Motokazu fed us with delicious Japanese food!

A torii path at the Fushimi Inari Taisha in Kyoto.

Kinkaku-ji in Kyoto

Genome editing

  1. Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science. 2015 Nov 13;350(6262):823-6. doi: 10.1126/science.aac6572. PubMed PMID: 26564855.
  2. Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJ, Ebrahimkhani MR, Collins JJ, Weiss R, Church G. Cas9 gRNA engineering for genome editing, activation and repression. Nat Methods. 2015 Nov;12(11):1051-4. doi: 10.1038/nmeth.3580. Epub 2015 Sep 7. PubMed PMID: 26344044.
  3. Reardon S. Leukaemia success heralds wave of gene-editing therapies. Nature. 2015 Nov 12;527(7577):146-7. doi: 10.1038/nature.2015.18737. PubMed PMID: 26560278.
  4. Mathews DJ, Lovell-Badge R, Chan S, Donovan PJ, Douglas T, Gyngell C, Harris J, Regenberg A. CRISPR: A path through the thicket. Nature. 2015 Nov 12;527(7577):159-61. doi: 10.1038/527159a. PubMed PMID: 26560284.
  5. Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Sep 16.
  6. Weber J, Öllinger R, Friedrich M, Ehmer U, Barenboim M, Steiger K, Heid I, Mueller S, Maresch R, Engleitner T, Gross N, Geumann U, Fu B, Segler A, Yuan D, Lange S, Strong A, de la Rosa J, Esposito I, Liu P, Cadiñanos J, Vassiliou GS, Schmid RM, Schneider G, Unger K, Yang F, Braren R, Heikenwälder M, Varela I, Saur D, Bradley A, Rad R. CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice. Proc Natl Acad Sci U S A. 2015 Oct 27. pii: 201512392. [Epub ahead of print] PubMed PMID: 26508638.
  7. Carroll D, Charo RA. The societal opportunities and challenges of genome editing. Genome Biol. 2015 Nov 5;16(1):242.
  8. Ma E, Harrington LB, O’Connell MR, Zhou K, Doudna JA. Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Mol Cell. 2015 Nov 5;60(3):398-407.
  9. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS,
    Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell. 2015 Sep 23. pii: S0092-8674(15)01200-3. doi: 10.1016/j.cell.2015.09.038. [Epub ahead of print] PubMed PMID: 26422227.
  10. Carrington B, Varshney GK, Burgess SM, Sood R. CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity. Nucleic Acids Res. 2015 Aug 7. pii: gkv802. [Epub ahead of print] PubMed PMID: 26253739.
  11. Varshney GK, Pei W, LaFave MC, Idol J, Xu L, Gallardo V, Carrington B, Bishop K, Jones M, Li M, Harper U, Huang SC, Prakash A, Chen W, Sood R, Ledin J, Burgess SM. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 2015 Jul;25(7):1030-42. doi: 10.1101/gr.186379.114. Epub 2015 Jun 5. PubMed PMID: 26048245; PubMed Central PMCID: PMC4484386.
  12. Bachu R, Bergareche I, Chasin LA. CRISPR-Cas targeted plasmid integration into mammalian cells via non-homologous end joining. Biotechnol Bioeng. 2015 May 5. doi: 10.1002/bit.25629. [Epub ahead of print] PubMed PMID: 25943095.

Genomics

  1. Grün D, van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015 Nov 5;163(4):799-810. doi: 10.1016/j.cell.2015.10.039. Review. PubMed PMID: 26544934.
  2. Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. Human promoters are intrinsically directional. Mol Cell. 2015 Feb 19;57(4):674-84.
  3. Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N; GAME-ON/ELLIPSE Consortium, Gayther SA, Joung JK, Freedman ML. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. Nat Med. 2015 Sep 23. doi: 10.1038/nm.3975. [Epub ahead of print] PubMed PMID: 26398868.
  4. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.PubMed PMID: 26432246; PubMed Central PMCID: PMC4617611.
  5. Cho MK. Preventive Genomic Sequencing in the General Population: Do PGS Fly? Am J Bioeth. 2015 Jul;15(7):1-2. doi: 10.1080/15265161.2015.1054160. PubMed PMID: 26147253.

Science Magazine Special Issue—Hunting Mutations, Targeting Disease

Statistics

  1. Lo A, Chernoff H, Zheng T, Lo SH. Why significant variables aren’t automatically good predictors. Proc Natl Acad Sci U S A. 2015 Oct 26. pii:201518285. [Epub ahead of print] PubMed PMID: 26504198.

Development

  1. Barsi JC, Tu Q, Calestani C, Davidson EH. Genome-wide assessment of differential effector gene use in embryogenesis. Development. 2015 Sep 28. pii: dev.127746. [Epub ahead of print] PubMed PMID: 26417044.
  2. Siklenka K, Erkek S, Godmann M, Lambrot R, McGraw S, Lafleur C, Cohen T, Xia J, Suderman M, Hallett M, Trasler J, Peters AH, Kimmins S. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science. 2015 Nov 6;350(6261):aab2006. doi: 10.1126/science.aab2006. Epub 2015 Oct 8. PubMed PMID: 26449473.

Stem cells

  1. Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol. 2015 Nov;33(11):1173-1181.
  2. Firth AL, Menon T, Parker GS, Qualls SJ, Lewis BM, Ke E, Dargitz CT, Wright R, Khanna A, Gage FH, Verma IM. Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs. Cell Rep. 2015 Aug 19. pii: S2211-1247(15)00852-9. doi: 10.1016/j.celrep.2015.07.062. [Epub ahead of print] PubMed PMID: 26299960.

Regeneration

  1. Ueki Y, Wilken MS, Cox KE, Chipman L, Jorstad N, Sternhagen K, Simic M, Ullom K, Nakafuku M, Reh TA. Transgenic expression of the proneural transcription factor Ascl1 in Müller glia stimulates retinal regeneration in young mice. Proc Natl Acad Sci U S A. 2015 Oct 19. pii: 201510595. [Epub ahead of print] PubMed PMID: 26483457.

Retina/Photoreceptor

  1. Taylor SM, Alvarez-Delfin K, Saade CJ, Thomas JL, Thummel R, Fadool JM, Hitchcock PF. The bHLH Transcription Factor NeuroD Governs  Photoreceptor Genesis and Regeneration Through Delta-Notch Signaling. Invest Ophthalmol Vis Sci. 2015 Nov 1;56(12):7496-7515.
  2. Hernández-Bejarano M, Gestri G, Spawls L, Nieto-López F, Picker A, Tada M, Brand M, Bovolenta P, Wilson SW, Cavodeassi F. Opposing Shh and Fgf signals initiate nasotemporal patterning of the retina. Development. 2015 Oct 1. pii: dev.125120. [Epub ahead of print] PubMed PMID: 26428010.
  3. Tsujimura T, Masuda R, Ashino R, Kawamura S. Spatially differentiated
    expression of quadruplicated green-sensitive RH2 opsin genes in zebrafish is determined by proximal regulatory regions and gene order to the locus control region. BMC Genet. 2015 Nov 4;16(1):130.
  4. Boije H, Rulands S, Dudczig S, Simons BD, Harris WA. The Independent
    Probabilistic Firing of Transcription Factors: A Paradigm for Clonal Variability in the Zebrafish Retina. Dev Cell. 2015 Sep 2. pii: S1534-5807(15)00525-0.
  5. Chow RW, Almeida AD, Randlett O, Norden C, Harris WA. Inhibitory neuron migration and IPL formation in the developing zebrafish retina. Development. 2015 Jun 26. pii: dev.122473. [Epub ahead of print] PubMed PMID: 26116662.
  6. Ogawa Y, Shiraki T, Kojima D, Fukada Y. Homeobox transcription factor Six7 governs expression of green opsin genes in zebrafish. Proc Biol Sci. 2015 Aug 7;282(1812). pii: 20150659. doi: 10.1098/rspb.2015.0659. PubMed PMID: 26180064.

Eye disease

  1. Zhao L, Chen XJ, Zhu J, Xi YB, Yang X, Hu LD, Ouyang H, Patel SH, Jin X, Lin D, Wu F, Flagg K, Cai H, Li G, Cao G, Lin Y, Chen D, Wen C, Chung C, Wang Y, Qiu A, Yeh E, Wang W, Hu X, Grob S, Abagyan R, Su Z, Tjondro HC, Zhao XJ, Luo H, Hou R, Perry JJ, Gao W, Kozak I, Granet D, Li Y, Sun X, Wang J, Zhang L, Liu Y, Yan YB, Zhang K. Lanosterol reverses protein aggregation in cataracts. Nature. 2015 Jul 30;523(7562):607-11. doi: 10.1038/nature14650. Epub 2015 Jul 22. Erratum in:  Nature. 2015 Oct 22;526(7574):595. PubMed PMID: 26200341.
  2. Makley LN, McMenimen KA, DeVree BT, Goldman JW, McGlasson BN, Rajagopal P, Dunyak BM, McQuade TJ, Thompson AD, Sunahara R, Klevit RE, Andley UP, Gestwicki JE. Pharmacological chaperone for α-crystallin partially restores transparency in cataract models. Science. 2015 Nov 6;350(6261):674-7. doi: 10.1126/science.aac9145. PubMed PMID: 26542570.
  3. Commentary: Quinlan RA. DRUG DISCOVERY. A new dawn for cataracts. Science. 2015 Nov 6;350(6261):636-7. doi: 10.1126/science.aad6303. PubMed PMID: 26542559.

Zebrafish

  1. Xu C, Volkery S, Siekmann AF. Intubation-based anesthesia for long-term time-lapse imaging of adult zebrafish. Nat Protoc. 2015 Dec;10(12):2064-2073.
  2. Pauli A, Montague TG, Lennox KA, Behlke MA, Schier AF. Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish. PLoS One. 2015 Oct 5;10(10):e0139504. doi: 10.1371/journal.pone.0139504. eCollection 2015. PubMed PMID: 26436892; PubMed Central PMCID: PMC4593562.

Research Career

  1. Jackson ST. Going where the science matters. Science. 2015 Oct
    30;350(6260):594. doi: 10.1126/science.350.6260.594. PubMed PMID: 26516284.

Medicine

  1. Henao-Restrepo AM, Longini IM, Egger M, Dean NE, Edmunds WJ, Camacho A, Carroll MW, Doumbia M, Draguez B, Duraffour S, Enwere G, Grais R, Gunther S, Hossmann S, Kondé MK, Kone S, Kuisma E, Levine MM, Mandal S, Norheim G, Riveros X, Soumah A, Trelle S, Vicari AS, Watson CH, Kéïta S, Kieny MP, Røttingen JA. Efficacy and effectiveness of an rVSV-vectored vaccine expressing Ebola surface glycoprotein: interim results from the Guinea ring vaccination cluster-randomised trial. Lancet. 2015 Aug 29;386(9996):857-66. doi: 10.1016/S0140-6736(15)61117-5. Epub 2015 Aug 3. PubMed PMID: 26248676.

In January, I visited the Center for Human Molecular Biology & Genetics at the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China [Chinese website of the Institute]. It is a large provincial hospital in Sichuan Province with a population of 80.8 million. The hospital served approximately 3.6 million outpatient and emergency cases, and carried out almost 75,000 surgeries in 2011. With this number of patients, the Center for Human Molecular Biology & Genetics collected extensive human samples and has been a leader in genetics study in China.

Prof. Zhengli Yang, the vice president of the hospital and the director of Center for Human Molecular Biology & Genetics, invited both me and a renowned eye geneticist Prof. Shomi Bhattacharya to discuss our current research on eye disease therapy. I discussed how my lab is setting up the foundation to use zebrafish to screen eye drugs at Purdue. Prof. Bhattacharya discussed his work on gene therapy and stem cell therapy. It was a great experience to interact with a world leader in genetics whom discovered many of the key genes in retinal degeneration, and a top notch research institution in China.

Yuk Fai Leung lectured at the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China

 

Prof. Shomi Bhattacharya lectured at the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China. Prof. Zhenglin Yang (right) hosted the symposium.

 

Audience from the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China.

Image courtesy: Lue Xiang @ Leung lab

We have been hoping to set up the zebrafish electroretinography in the lab to facilitate our drug discovery program for a while. When Prof. Kwoon Wong  from the Kellogg Eye Center at the University of Michigan visited our department in early December, we seized the opportunity to learn from him and asked for his help to put the components together.

Image courtesy: Lue Xiang @ Leung lab

Dr. Don Ready kindly let us used his fly ERG setup for our test. Dr. Wong spent an afternoon trying different parameters and finally we have obtained a very decent ERG trace.  Many more friends and colleagues contributed to this endeavour, including Dr. Woody Walls who gathered a number of components and laid down the foundation over a period of time, lab members Prahatha Venkatraman and Lue Xiang who collected ample healthy embryos for the test, and Lue Xiang as the assistant of Dr. Wong during the course of experimentation. We would like to optimize this system further and are seeking highly motivated students with physiology and/or engineering background. We are particularly interested in the talents who like electrophysiology and would like to contribute their effort to identify new drugs for patients.

Left: Dr. Wong explained various ERG concepts to the lab members. Top right: lab members shared their research with Dr. Wong over lunch. Middle right: Dr. Wong worked on the ERG setup. Bottom right: Dr. Wong and Fai learned from Dr. Ready on several critical components of the ERG setup. Image courtesy: Lue Xiang @ Leung lab

Dr. Woody Walls instructed us on using LabChart for data collection. Image courtesy: Lue Xiang @ Leung lab