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Article ; Online: Prevalence of NTRK Fusions in Canadian Solid Tumour Cancer Patients.

Silvertown, Joshua D / Lisle, Connie / Semenuk, Laura / Knapp, Colleen / Jaynes, Jillann / Berg, Doreen / Kaul, Nabodita / Lachapelle, Josianne / Richardson, Leslie / Speevak, Marsha / Sarras, Haya / Berman, David M / Carter, Ronald / Feilotter, Harriet / Feltis, Timothy

Molecular diagnosis & therapy

2022 Volume 27, Issue 1, Page(s) 87–103

Abstract: Introduction: Neurotrophic tyrosine receptor kinase (NTRK) gene fusions occur in ~ 0.3% of all solid tumours but are enriched in some rare tumour types. Tropomyosin receptor kinase (TRK) inhibitors larotrectinib and entrectinib are approved as tumour- ... ...

Abstract	Introduction: Neurotrophic tyrosine receptor kinase (NTRK) gene fusions occur in ~ 0.3% of all solid tumours but are enriched in some rare tumour types. Tropomyosin receptor kinase (TRK) inhibitors larotrectinib and entrectinib are approved as tumour-agnostic therapies for solid tumours harbouring NTRK fusions. Methods: This study investigated the prevalence of NTRK fusions in Canadian patients and also aimed to help guide NTRK testing paradigms through analysis of data reported from a national clinical diagnostic testing program between September 2019 and July 2021. Results: Of 1,687 patients included in the final analysis, NTRK fusions were detected in 0.71% (n = 12) of patients representing salivary gland carcinoma (n = 3), soft tissue sarcoma (n = 3), CNS (n = 3), and one in each of melanoma, lung, and colorectal cancer. All three salivary gland carcinomas contained ETV6-NTRK3 fusions. Thirteen (0.77%) clinically actionable incidental findings were also detected. Two of the 13 samples containing incidental findings were NTRK fusion-positive (GFOD1-NTRK2, FGFR3-TACC3 in a glioblastoma and AFAP1-NTRK2, BRAF c.1799T>A in a glioma). The testing algorithm screened most patient samples via pan-TRK immunohistochemistry (IHC), whereas samples from the central nervous system (CNS), pathognomonic cancers, and confirmed/ putative NTRK fusion-positive samples identified under research protocols were reflexed straight to next-generation sequencing (NGS). Conclusion: These findings highlight the benefit and practicality of a diagnostic testing program to identify patients suitable for tumour-agnostic TRK inhibitor therapies, as well as other targeted therapies, due to clinically actionable incidental findings identified. Collectively, these findings may inform future guidance on selecting the appropriate testing approach per tumour type and on optimal NTRK testing algorithms.
MeSH term(s)	Humans ; Canada/epidemiology ; Microtubule-Associated Proteins ; Neoplasms/genetics ; Neoplasms/metabolism ; Oncogene Proteins, Fusion/genetics ; Receptor, trkA/genetics ; Sarcoma/diagnosis ; Sarcoma/genetics
Chemical Substances	Microtubule-Associated Proteins ; Oncogene Proteins, Fusion ; Receptor, trkA (EC 2.7.10.1) ; TACC3 protein, human
Language	English
Publishing date	2022-10-04
Publishing country	New Zealand
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2232796-4
ISSN	1179-2000 ; 1177-1062
ISSN (online)	1179-2000
ISSN	1177-1062
DOI	10.1007/s40291-022-00617-y
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Article ; Online: Quantitative large scale gene expression profiling from human stem cell culture micro samples using multiplex pre-amplification.

Kibschull, Mark / Lye, Stephen J / Okino, Steven T / Sarras, Haya

Systems biology in reproductive medicine

2016 Volume 62, Issue 1, Page(s) 84–91

Abstract: Transcriptional profiling is a powerful tool to study biological mechanisms during stem cell differentiation and reprogramming. Genome-wide methods like microarrays or next generation sequencing are expensive, time consuming, and require special ... ...

Abstract	Transcriptional profiling is a powerful tool to study biological mechanisms during stem cell differentiation and reprogramming. Genome-wide methods like microarrays or next generation sequencing are expensive, time consuming, and require special equipment and bioinformatics expertise. Quantitative RT-PCR remains one of today's most widely accepted and used methods for analyzing gene expression in biological samples. However, limitations in the amount of starting materials often hinder the quantity and quality of information that could be obtained from a given sample. Here, we present a fast 4-step workflow allowing direct, column-free RNA isolation from limited human pluripotent stem cell (hPSC) cultures that is directly compatible with subsequent reverse transcription, target specific multiplex pre-amplification, and standard SYBR-Green quantitative PCR (qPCR) analysis. The workflow delivers excellent correlations in normalized gene-expression data obtained from different samples of hPSCs over a wide range of cell numbers (500-50,000 cells). We demonstrate accurate and unbiased target gene quantification in limiting stem cell cultures which allows for monitoring embryoid body differentiation and induced pluripotent stem cell (iPSC) reprogramming. This method highlights a rapid and cost effective screening process, allowing reduction of culture formats and increase of processing throughputs for various stem cell applications.
MeSH term(s)	Cell Differentiation ; Cell Line ; Cells, Cultured ; Cost-Benefit Analysis ; Embryoid Bodies ; Gene Amplification/genetics ; Gene Expression Profiling/economics ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Induced Pluripotent Stem Cells ; Microarray Analysis ; Polymerase Chain Reaction ; Stem Cells/metabolism ; Workflow
Language	English
Publishing date	2016
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2417234-0
ISSN	1939-6376 ; 1939-6368
ISSN (online)	1939-6376
ISSN	1939-6368
DOI	10.3109/19396368.2015.1062578
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Zs.A 1377: Show issues

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Article ; Online: Evaluation of bias associated with high-multiplex, target-specific pre-amplification

Steven T. Okino / Michelle Kong / Haya Sarras / Yan Wang

Biomolecular Detection and Quantification, Vol 6, Iss C, Pp 13-

2016 Volume 21

Abstract: We developed a novel PCR-based pre-amplification (PreAmp) technology that can increase the abundance of over 350 target genes one million-fold. To assess potential bias introduced by PreAmp we utilized ERCC RNA reference standards, a model system that ... ...

Abstract	We developed a novel PCR-based pre-amplification (PreAmp) technology that can increase the abundance of over 350 target genes one million-fold. To assess potential bias introduced by PreAmp we utilized ERCC RNA reference standards, a model system that quantifies measurement error in RNA analysis. We assessed three types of bias: amplification bias, dynamic range bias and fold-change bias. We show that our PreAmp workflow introduces only minimal amplification and fold-change bias under stringent conditions. We do detect dynamic range bias if a target gene is highly abundant and PreAmp occurred for 16 or more PCR cycles; however, this type of bias is easily correctable. To assess PreAmp bias in a gene expression profiling experiment, we analyzed a panel of genes that are regulated during differentiation using the NTera2 stem cell model system. We find that results generated using PreAmp are similar to results obtained using standard qPCR (without the pre-amplification step). Importantly, PreAmp maintains patterns of gene expression changes across samples; the same biological insights would be derived from a PreAmp experiment as with a standard gene expression profiling experiment. We conclude that our PreAmp technology can facilitate analysis of extremely limited samples in gene expression quantification experiments.
Keywords	Pre-amplification ; PreAmp ; Gene expression profiling ; Bias ; PCR ; ERCC ; Biology (General) ; QH301-705.5 ; Microbiology ; QR1-502
Subject code	612
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article: Evaluation of bias associated with high-multiplex, target-specific pre-amplification.

Okino, Steven T / Kong, Michelle / Sarras, Haya / Wang, Yan

Biomolecular detection and quantification

2015 Volume 6, Page(s) 13–21

Abstract	We developed a novel PCR-based pre-amplification (PreAmp) technology that can increase the abundance of over 350 target genes one million-fold. To assess potential bias introduced by PreAmp we utilized ERCC RNA reference standards, a model system that quantifies measurement error in RNA analysis. We assessed three types of bias: amplification bias, dynamic range bias and fold-change bias. We show that our PreAmp workflow introduces only minimal amplification and fold-change bias under stringent conditions. We do detect dynamic range bias if a target gene is highly abundant and PreAmp occurred for 16 or more PCR cycles; however, this type of bias is easily correctable. To assess PreAmp bias in a gene expression profiling experiment, we analyzed a panel of genes that are regulated during differentiation using the NTera2 stem cell model system. We find that results generated using PreAmp are similar to results obtained using standard qPCR (without the pre-amplification step). Importantly, PreAmp maintains patterns of gene expression changes across samples; the same biological insights would be derived from a PreAmp experiment as with a standard gene expression profiling experiment. We conclude that our PreAmp technology can facilitate analysis of extremely limited samples in gene expression quantification experiments.
Language	English
Publishing date	2015-12-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2821770-6
ISSN	2214-7535
ISSN	2214-7535
DOI	10.1016/j.bdq.2015.12.001
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Article ; Online: A novel amplification-based approach to enable gene expression profiling from small clinical tumor specimens.

Sarras, Haya / Wu, Megan / Celebre, Angela / Merico, Daniele / Karamchandani, Jason / Das, Sunit

Journal of neuro-oncology

2015 Volume 126, Issue 1, Page(s) 69–75

Abstract: Glioblastoma is the most common and deadly type of brain cancer. Over the past decade, several divergent genetic pathways have been implicated in the initiation, progression and clinical outcome of this disease. As our understanding of GBM expands and ... ...

Abstract	Glioblastoma is the most common and deadly type of brain cancer. Over the past decade, several divergent genetic pathways have been implicated in the initiation, progression and clinical outcome of this disease. As our understanding of GBM expands and identifies actionable targets specific to individual tumors, there will be a pressing need for the development of new tools that will maximize the use of limited clinical samples to enable the employment of personalized care paradigms. We used PrimePCR validated assays to generate a custom real-time PCR screening panel, containing 74 previously published mRNA targets showing gene expression changes in glioblastoma, and five house-keeping genes. A cohort of 19 frozen brain specimens were analyzed, including WHO Grade II oligodendroglioma (n = 3), WHO Grade II astrocytoma (n = 2), WHO Grade III astrocytoma (n = 1), and glioblastoma (n = 13). Four normal brain samples were also analyzed. We performed RNA extraction, followed by cDNA synthesis, multiplexed pre-amplification and SYBR-based qPCR, to generate expression profiles on all samples. We demonstrated that the workflow shows high tolerance to variation in RNA quality (RIN 8.5-4) and high sensitivity in detection. cDNA input that is equivalent to 3 ng of starting RNA was sufficient to conduct accurate semiquantitative analysis of the panel of 79 assays. Using principal component analysis, we were able to accurately separate glioblastoma from low-grade glioma. The two WHO Grade III tumors analyzed clustered with glioblastoma, but showed more similarity to Grade II gliomas. In this study, we have shown the feasibility of consolidating high-throughput data into a single functional panel capable of accurately classifying glioma specimens based solely on semiquantitative gene expression profiling.
MeSH term(s)	Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Brain Neoplasms/genetics ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/genetics ; Glioblastoma/genetics ; Humans ; Logistic Models ; Male ; Polymerase Chain Reaction ; Principal Component Analysis ; RNA, Messenger/metabolism
Chemical Substances	Biomarkers, Tumor ; RNA, Messenger
Language	English
Publishing date	2015-10-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604875-4
ISSN	1573-7373 ; 0167-594X
ISSN (online)	1573-7373
ISSN	0167-594X
DOI	10.1007/s11060-015-1953-4
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Zs.A 1825: Show issues

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Article ; Online: In search of a function for BCLAF1.

Sarras, Haya / Alizadeh Azami, Solmaz / McPherson, J Peter

TheScientificWorldJournal

2010 Volume 10, Page(s) 1450–1461

Abstract: BCLAF1 was originally identified as a protein that interacts with antiapoptotic members of the Bcl2 family. Initial studies indicated a role for this protein as an inducer of apoptosis and repressor of transcription. Subsequent studies have shown that ... ...

Abstract	BCLAF1 was originally identified as a protein that interacts with antiapoptotic members of the Bcl2 family. Initial studies indicated a role for this protein as an inducer of apoptosis and repressor of transcription. Subsequent studies have shown that BCLAF1 plays criticals roles in a wide range of processes that are not normally associated with actions of Bcl2 family members, including lung development, T-cell activation, and control of the lytic infection program of Kaposi's sarcoma-associated herpesvirus. Here, we provide an overview of findings from past studies that both support and challenge the role of BCLAF1 in cell death and transcriptional control. We also present recent findings from our laboratory and others indicating a role for BCLAF1 in post-transcriptional processes that impact mRNA metabolism, instead of a direct role for this protein in apoptosis or transcription.
MeSH term(s)	Animals ; Apoptosis/genetics ; Apoptosis/physiology ; Gene Expression Regulation ; Herpesvirus 8, Human/genetics ; Humans ; Lymphocyte Activation ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA Processing, Post-Transcriptional ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; Repressor Proteins/physiology ; Tumor Suppressor Proteins/genetics ; Tumor Suppressor Proteins/metabolism ; Tumor Suppressor Proteins/physiology
Chemical Substances	BCLAF1 protein, human ; MicroRNAs ; Repressor Proteins ; Tumor Suppressor Proteins
Language	English
Publishing date	2010-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2075968-X
ISSN	1537-744X ; 1537-744X
ISSN (online)	1537-744X
ISSN	1537-744X
DOI	10.1100/tsw.2010.132
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Article ; Online: In Search of a Function for BCLAF1

Haya Sarras / Solmaz Alizadeh Azami / J. Peter McPherson

The Scientific World Journal, Vol 10, Pp 1450-

2010 Volume 1461

Abstract	BCLAF1 was originally identified as a protein that interacts with antiapoptotic members of the Bcl2 family. Initial studies indicated a role for this protein as an inducer of apoptosis and repressor of transcription. Subsequent studies have shown that BCLAF1 plays criticals roles in a wide range of processes that are not normally associated with actions of Bcl2 family members, including lung development, T-cell activation, and control of the lytic infection program of Kaposi's sarcoma–associated herpesvirus. Here, we provide an overview of findings from past studies that both support and challenge the role of BCLAF1 in cell death and transcriptional control. We also present recent findings from our laboratory and others indicating a role for BCLAF1 in post-transcriptional processes that impact mRNA metabolism, instead of a direct role for this protein in apoptosis or transcription.
Keywords	Technology ; T ; Medicine ; R ; Science ; Q
Language	English
Publishing date	2010-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
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Article: A role for Mus81 in the repair of chromium-induced DNA damage.

Tamblyn, Laura / Li, Erica / Sarras, Haya / Srikanth, Prarthana / Hande, M Prakash / McPherson, J Peter

Mutation research

2009 Volume 660, Issue 1-2, Page(s) 57–65

Abstract: Hexavalent chromium (Cr[VI]) is a toxic environmental contaminant that is capable of producing a broad spectrum of DNA damage. The ability of Cr[VI] to induce mutagenesis and neoplastic transformation has been attributed to its genotoxic action, however ... ...

Abstract	Hexavalent chromium (Cr[VI]) is a toxic environmental contaminant that is capable of producing a broad spectrum of DNA damage. The ability of Cr[VI] to induce mutagenesis and neoplastic transformation has been attributed to its genotoxic action, however our understanding of molecular mechanisms involved in the repair of Cr[VI]-induced DNA damage remains incomplete. Here, we report that Mus81, an enzyme that participates with Eme1 in the resolution of replication fork damage caused by certain lesions, is involved in the repair of Cr[VI]-induced DNA damage. Mus81-deficient cells were found to be more susceptible to Cr[VI]-induced proliferation arrest and more sensitive to the long-term cytotoxic effects of Cr[VI] than isogenic wild-type cells. Following Cr[VI] exposure, Mus81-deficient cells displayed a lag in the disappearance of Rad51 foci, exhibited elevated replication-associated gamma-H2AX and showed an increased incidence of chromosomal instability compared to wild-type cells. Our findings support a role for Mus81 in the resolution of replication-associated DNA damage associated with this genotoxic agent, by converting Cr[VI]-DNA lesions into a form more amenable for homologous recombination.
MeSH term(s)	Animals ; Cells, Cultured ; Chromium/pharmacology ; DNA Damage/drug effects ; DNA Repair/physiology ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/physiology ; Endonucleases/genetics ; Endonucleases/physiology ; Flow Cytometry ; Karyotyping ; Mice
Chemical Substances	DNA-Binding Proteins ; Chromium (0R0008Q3JB) ; chromium hexavalent ion (18540-29-9) ; Endonucleases (EC 3.1.-) ; Mus81 protein, mouse (EC 3.1.-)
Language	English
Publishing date	2009-01-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	206607-5
ISSN	1873-135X ; 0027-5107 ; 1383-5718 ; 0165-1110 ; 0165-1161 ; 0165-7992 ; 0921-8777 ; 0165-1218 ; 1383-5726 ; 0167-8817 ; 0921-8734 ; 1383-5742
ISSN (online)	1873-135X
ISSN	0027-5107 ; 1383-5718 ; 0165-1110 ; 0165-1161 ; 0165-7992 ; 0921-8777 ; 0165-1218 ; 1383-5726 ; 0167-8817 ; 0921-8734 ; 1383-5742
DOI	10.1016/j.mrfmmm.2008.10.013
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Zs.A 1316: Show issues

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Article ; Online: Interplay between Np95 and Eme1 in the DNA damage response.

Mistry, Helena / Gibson, Lianne / Yun, Ji Weon / Sarras, Haya / Tamblyn, Laura / McPherson, John Peter

Biochemical and biophysical research communications

2008 Volume 375, Issue 3, Page(s) 321–325

Abstract: Mus81 (methyl methansulfonate UV sensitive clone 81) and Eme1 (essential meiotic endonuclease 1, also known as MMS4) form a heterodimeric endonuclease that is critical for genomic stability and the response to DNA crosslink damage and replication ... ...

Abstract	Mus81 (methyl methansulfonate UV sensitive clone 81) and Eme1 (essential meiotic endonuclease 1, also known as MMS4) form a heterodimeric endonuclease that is critical for genomic stability and the response to DNA crosslink damage and replication blockade. However, relatively little is known as to how this endonuclease is regulated following DNA damage. Here, we report mammalian Eme1 interacts with Np95, an E3 ubiquitin ligase that participates in chromatin modification, replication-linked epigenetic maintenance and the DNA damage response. Np95 and Eme1 co-localize on nuclear chromatin following exposure of cells to camptothecin, an agent that promotes the collapse of replication forks. The observed co localization following DNA damage was found to be dependent on an intact RING finger, the structural motif that encodes the E3 ubiquitin ligase activity of Np95. Taken together, these findings link Mus81-Eme1 with the replication-associated chromatin modifier functions of Np95 in the cellular response to DNA damage.
MeSH term(s)	Animals ; Chromatin/metabolism ; DNA Damage ; Endodeoxyribonucleases/genetics ; Endodeoxyribonucleases/metabolism ; HeLa Cells ; Humans ; Immunoprecipitation ; Mice ; NIH 3T3 Cells ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; RING Finger Domains/genetics ; Two-Hybrid System Techniques ; Ubiquitination
Chemical Substances	Chromatin ; Nuclear Proteins ; Uhrf1 protein, mouse ; Eme1 protein, mouse (EC 3.1.-) ; Endodeoxyribonucleases (EC 3.1.-)
Language	English
Publishing date	2008-10-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2008.07.146
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Zs.A 116: Show issues

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Article ; Online: Elevated PICK1 mRNA in schizophrenia increased SRR mRNA in suicide.

Sarras, Haya / Semeralul, Mawahib O / Fadel, Marc P / Feldcamp, Laura A / Labrie, Viviane / Wong, Albert H C

Schizophrenia research

2010 Volume 120, Issue 1-3, Page(s) 236–237

MeSH term(s)	Analysis of Variance ; Bipolar Disorder/genetics ; Bipolar Disorder/metabolism ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Gene Expression Regulation/physiology ; Humans ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; RNA, Messenger/metabolism ; Racemases and Epimerases/genetics ; Racemases and Epimerases/metabolism ; Schizophrenia/genetics ; Schizophrenia/metabolism ; Schizophrenic Psychology ; Suicide
Chemical Substances	Carrier Proteins ; Nuclear Proteins ; PICk1 protein, human ; RNA, Messenger ; Racemases and Epimerases (EC 5.1.-) ; serine racemase (EC 5.1.1.16)
Language	English
Publishing date	2010-07
Publishing country	Netherlands
Document type	Letter
ZDB-ID	639422-x
ISSN	1573-2509 ; 0920-9964
ISSN (online)	1573-2509
ISSN	0920-9964
DOI	10.1016/j.schres.2010.03.002
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