2024

Dec 9-13: Dr. Pai attended the 2024 Cold Spring Harbor Laboratory meeting on “Development and 3D Modelling of the Human Brain”. The meeting covers the latest research on using human brain organoids to model the typical human brain and brain disorders for basic and translational research. Dr. Pai presented two posters covering the lab’s research on the prenatal developmental origins of Group 3 and 4 medulloblastoma.

Dec 2-7: Nishka Kishore (Scientific Associate, Pai Lab) attended the 2024 Applied Organoid workshop in Toronto. Hosted by the Stem Cell Network, the workshop included a 2-day symposium and 3-day hands on workshop on growing human stem-cell derived organoids.

Dec 13: Jaskirat Singh Sandhu (PhD candidate, Pai Lab) was awarded a prestigious MITACS Accelerate Fellowship! Singh Sandhu's project involves performing a high-throughput pharmacological screen in patient-derived cell lines from primary and treatment-resistant glioblastoma tumours. The goal of the project is to identify novel epigenetic vulnerabilities that kill tumour cells. Finding such targets may pave the way to novel therapies for this devastating disease, on which the clinical needle has not really moved for 20 years. This project is in collaboration with the OICR Drug Discovery group with teams under Drs. Richard Marcellus, David Uehling, and Rima Al-Awar, and with neuro-oncologist Dr. Sheila Singh at McMaster University. We are fortunate to have skilled and collegial collaborators helping our laboratory venture into the space of pharmacology for discovery.

Nov 21: Dr. Pai travelled to Michigan and presented the lab’s research on medulloblastoma and glioblastoma as an invited speaker at the Biochemistry and Molecular Biology seminar at Michigan State University, and at the Van Andel Research Institute.

Aug 16: Xinghan Sun (PhD candidate, Pai Lab) and Jaskirat Singh Sandhu (PhD candidate, Pai Lab) are both awarded the 2024-2025 Medical Biophysics Excellent UTF Scholarship! MBP Excellence awards are merit-based internal scholarships funded by the Department of Medical Biophysics and the University of Toronto Fund. Congratulations Jaskirat and Xinghan!

Aug 9: Leo Lau and Hana Hajari present their summer research projects as part of the University of Toronto Medical Biophysics Summer Student Poster Day. Leo Lau presents his computational analysis work integrating mouse and human single-cell transcriptomes to discover human-enriched hindbrain neurons and their potential relevance for oncogenesis of Group 4 medulloblastoma. Hana Hajari presents her project performing siRNA knockdown of candidate molecules promoting stalled differentiation in Group 3 and 4 medulloblastoma.

May 10: Dr. Pai presents an invited talk at the Western University Bioinformatics Research Seminar. The talk titled, “Machine learning and brain epigenomes for precision medicine”, covered the netDx algorithm for multi-modal data integration and interpretable patient classification, which is published. Pai also talked about the discovery of non-coding biomarkers in schizophrenia and bipolar disorder. Finally, Pai outlined current projects in the lab on human hindbrain development, Group 3 and 4 medulloblastoma, and glioblastoma.

May 7: Dr. Pai describes the “spark” that led to the lab’s work in brain cancer, as part of OICR’s “What’s your Spark” series. Watch it on Youtube!

May 1: PhD trainees Jaskirat Singh Sandhu and Xinghan Sun present their ongoing work at the University of Toronto Medical Biophysics Symposium. Singh Sandhu is working on a small molecule screen in recurrent glioblastoma to discover novel vulnerabilities in this devastating disease. Sun’s thesis involves identification and characterization of enhancers in the developing hindbrain and non-coding genomic aberrations in Group 3 and 4 medulloblastoma.

Apr 25: Congratulations to Leo Lau for being awarded an NSERC-USRA for Summer of 2024!

Mar 28: Congratulations to Hana Hajari for receiving a 2024 Undergraduate Research Opportunities Program (UROP) award from the University of Toronto Medical Biophysics Department.

Mar 25: The Pai Lab attends the OICR Translational Research Conference in King City, Ontario. Ian Cheong and Ellen Mak present research posters. Ellen (BSc candidate, McMaster university) presented her work optimizing CRISPRi target inhibition in Group 3 medulloblastoma cell lines. Ian (MSc candidate, University of Toronto) presented his work analyzing single-cell transcriptomes in the developing human and mouse cerebellum to identify evolutionarily-recent cell populations.

Mar 7: Congratulations to Leo Lau and Hana Hajari for being accepted into the MBP Summer Student Program.

Feb 12: Welcome to Leo Lau! Leo is an undergraduate co-op trainee from the University of Waterloo and will be joining the Pai Lab till the end of Summer 2024. Leo will perform bioinformatic analysis of human and mouse developmental single-cell transcriptomic data to identify evolutionarily-recent cells that may be causing Group 4 medulloblastoma.

Jan 3: Happy New Year - the Pai Lab is growing! Welcome to Nishka Kishore, Jaskirat Singh Sandhu, and Hana Hajari! Nishka joins our lab as Scientific Associate I and will head lab molecular biology and tissue culture operations.
Hana is an undergraduate trainee at McMaster University and will be part of the Pai Lab till the end of Summer 2024. Hana will perform CRISPRi perturbations of cancer targets in Group 3 and 4 medulloblastoma cell lines.
Jaskirat is a PhD candidate in University of Toronto’s Medical Biophysics program and will work on pharmacological screens in glioblastoma.

2023

Nov 18: Trainees Ian Cheong and Xinghan Sun attend the 2023 Canadian Epigenetics meeting in Banff, AB. Ian Cheong presents a poster on his Master’s thesis work titled, “Uncovering unique human gene regulatory networks in hindbrain development and Group 4 medulloblastoma”

Nov 17: Shraddha Pai presents a talk on “Developmental epigenomic origins of Group 3 and 4 medulloblastoma at the at the 2023 Canadian Cancer Research Conference in Halifax, N.S., November 12 - 14.

Sep 21: Our educational article, “Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy” is out in PLoS Computational Biology! The article draws on the experience of the COVID Schools Canada led by Shraddha Pai and provides tips on team building and logistics, infrastructure, media and industry outreach, and project archival and wrap-up.

1 Aug: The Pai Lab is awarded a 2023 Cancer Research Society Operating Grant. The award is $125K CDN over two years, and will fund research into the developmental origins of Group 3 and 4 medulloblastoma, the most common malignant childhood brain cancer. Using single-cell multi-omics, the Pai Lab is linking gene regulation in the developing human hindbrain to those in tumours, to identify what changes may drive developing brain cells to oncogenesis, and eventually discover how to reverse these in cancer. Federico Gaiti (UHN) is a co-investigator on the grant.

11 - 13 Jul: Pai Lab attends the 2023 Human Cell Atlas meeting held in Toronto. Ian Cheong presents a poster on his work finding evolutionarily recent gene regulatory networks in the developing human hindbrain, and link to Group 3 and 4 medulloblastoma.

27 - 28 June: Shraddha Pai leads the 2023 Canadian Bioinformatics Workshop on “Analysis Using R”, with co-instructor Delaram Pouyabahar, Chaitra Sarathy, and with Ian Cheong as Teaching Assistant.

29 May: Welcome to Xinghan Sun! Xinghan is a direct-entry PhD candidate in the Medical Biophysics department at the University of Toronto, and will be conducting his doctoral research in the Pai lab.

21 - 26 May: Shraddha attended the Gordon Research Conference on Cancer Genetics and Epigenetics in Italy, and presented a poster on ongoing single-cell and bulk tissue transcriptomic and DNA methylomic characterization of the fetal origins of Group 3 and 4 medulloblastoma.

8 May: Welcome to Ellen Mak!
Ellen is a 4th year Hon. Chemical Biology student at McMaster University. Ellen will spend May - December 2023 in the lab, developing a CRISPRi pilot. This work is tied to studying the developmental origins of Group 3 and 4 medulloblastoma and will be used to validate putative drivers of oncogenesis in cell culture models.

8 May: Welcome to Mingjie Zhao!
Mingjie is a senior BMath Data Science candidate at the University of Waterloo. He will spend summer 2023 in the lab working on optimizing a software pipeline for WDR family target prioritization. This project is a collaboration between the Adaptive Oncology and Drug Discovery teams at OICR to discover novel cancer therapeutics, funded by FACIT, OICR’s commercialization partner.

17 Apr: Our study on the genetics of peri-adolescent cognition is out in Cerebral Cortex! This work identifies SNPs within the FBLN1 locus as associated with performance in nonverbal reasoning in peri-adolescents, and integrates pharmacogenetic, GWAS, single-cell marker, and epigenomic maps to implicates genes relevant for performance in working memory performance.

14 Apr: Ian Cheong was selected to present a short talk to accompany his poster presentation at the Keystone Symposium on “Single Cell Biology: From Development to Cancer” this June. Ian will be presenting his single-cell genomics analysis to identify evolutionarily recent gene regulatory networks in the developing cerebellum, which may be involved in oncogenesis of pediatric medulloblastoma. Congratulations, Ian!

31 Mar: Shraddha Pai is a co-author on a study prototyping point-of-care detection technology for SARS-CoV-2 using quantum dot barcoding technology. The study titled, Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels, was published in Analytical Chemistry.

6 Mar: Welcome to Paul Wambo! Paul joins the lab as a Bioinformatics Research Associate working on epigenomic biomarker discovery and machine learning projects for precision medicine.

16 Feb: The Pai Lab is awarded $100,000CDN for a CIHR Project Grant Priority Announcement for Pediatric Cancer Research! This grant is a collaboration with the Gaiti Lab (Princess Margaret) and Stein Lab (OICR). The funds will support single-cell genomic studies of the developmental origins of pediatric medulloblastoma.

9 Jan: Welcome to Alex Chan and Soumya Menon! Alex and Soumya are University of Waterloo undergraduate co-op students in Biomedical Engineering and Mathematical Physics, and will spend four months in the Pai Lab. Alex’s project involves visualization of gene regulatory networks in the fetal hindbrain. Soumya will develop data processing pipelines for DNA methylome analysis of developing human hindbrain and glioblastoma.

2022

21 Oct: The study using COVID Schools Canada crowdsourced data in epidemiological analysis is out in eLife. COVID Schools Canada was a project led by Shraddha Pai and the epidemiological analysis was led by Dr. Paul Tupper of Simon Fraser University. Congratulations to the COVID Schools Canada team!

1 Jun: Ian Cheong is awarded an Ontario Graduate Scholarship at the Department of Medical Biophysics. Congratulations, Ian!

30 Apr: Ian Cheong is awarded an Canada Graduate Scholarship at the Master’s level, from the Department of Medical Biophysics. Congratulations, Ian!

11 Apr: Shraddha Pai is awarded an NSERC Discovery Grant award. Congratulations, Shraddha!

30 Mar: The Pai Lab is on a team awarded a PROSPECT Oncology award from FACIT, OICR’s commercialization partner. The award will support algorithm development for discovering novel cancer therapeutics and is a collaboration between OICR’s Adaptive Oncology team headed by Lincoln Stein and the Drug Discovery team headed by Rima Al-Awar. Read the press release here.

1 Jan: Welcome to Ian Cheong! Ian joins the lab as a Master’s candidate in the Department of Medical Biophysics at the University of Toronto.

2021

4 Jan: The Pai Lab starts at the Ontario Institute for Cancer Research in Toronto!