Monocyte assay and targeted transcriptome sequencing as a functional tool for dysferlin detection and dysferlinopathy molecular diagnosis

Publications

Utilization of Targeted RNA-Seq for the Resolution of Variant Pathogenicity and Enhancement of Diagnostic Yield in Dysferlinopathy (2023)

Grant Duration
01/19 – 03/21

Dr. Samya Chakravorty has been doing a long standing project to use a monocyte assay for detection of dysferlin protein levels in the blood to help clarify the functional effects of DYSF variants and help support a diagnosis of dysferlinopathy. The project was expanded in 2017 to include targeted next-generation sequencing (NGS)-based transcriptome sequencing (RNA-Seq) using whole blood in order to clarify functional effects of identified DYSF variants, classify the pathogenicity of DYSF variants that are labelled as variants of uncertain significance (VUSs) and identify novel gene variants (e.g. deep intronic variants that affect splicing, deletions and duplication). Dr. Chakravorty is using a combinatorial approach of including data from clinical features, monocyte assay-derived protein expression, and RNA-Seq to enhance molecular diagnostics of dysferlinopathy and stratify patient samples based on genotype-phenotype correlation for better clinical trial readiness.

By Samya Chakravorty, PhD , Emory University|2025-05-06T20:48:35+00:00April 1st, 2021|Past Projects|Comments Off

About the Author: Samya Chakravorty, PhD , Emory University

Dr. Chakravorty is a principal investigator in the Department of Pediatrics and Human Genetics at Emory University (Atlanta, GA).

Bla/J mice (B6.A-Dysf^prmd/GeneJ)

Availability:
The Jackson Laboratory
Stock number: 012767
Strain information: http://jaxmice.jax.org/strain/012767.html
Phone: 800-422-MICE (800-422-6423)
610 Main Street, Bar Harbor, Maine 04609 USA

Please note that this strain has been cryopreserved by the Jackson Laboratories, but the Jain Foundation maintains a private colony of these mice for public use. To obtain these mice, please contact the Jain Foundation:

Jain Foundation Inc.
9706 Fourth Ave NE, Suite 101
Seattle, Washington 98115
Phone: 425-882-1492
Fax: 425-882-1050

Email: admin@jain-foundation.org

Development:
In these mice the progressive muscular dystrophy (prmd) allele from the A/J inbred strain is crossed onto the C57BL/6 genetic background. The cross was performed in the laboratory of Dr. Isabelle Richard at Genethon and the backcross generation reached N8. In collaboration with the Jain Foundation, Dr. Richard donated the strain to The Jackson Laboratory in 2010. Upon arrival, mice were bred to C57BL/6J for at least 2 generations to establish the colony.

Mutation:
An ETn retrotransposon (5-6kb) is inserted in intron 4 of the dysferlin gene.

Symptoms:
Disease onset is observed by 2 months and is characterized by the presence of centronucleated fibers and areas of inflammation. As seen with the original background A/J, mice homozygous for the prmd allele on the C57BL/6J background display an increasing number of centronucleated fibers and impairment in the majority of muscles by 4 months of age. In order of severity, the most affected muscles are psoas, quadriceps femoris, tibialis anterior, and gastrocnemius. Mice exhibit a decreased membrane repair capacity following laser wounding experiments. In an open space assay, mice cover less distance and are less active than wild-type. Mice that are homozygous for this allele are viable, fertile and normal in size.

Comparison with other disease strains:
Disease progression is similar to A/J: slightly slower than in SJL/J, Dysf-/- (Campbell), Dysf-/- (Brown), and C57BL/10.SJL mice. As in both SJL/J and Dysf-/- (Brown) mice, proximal muscles are more severely affected than distal muscles. As in Dysf-/- (Brown) mice, abdominal muscles are also affected.

Control strain(s):
C57BL/6 (for homozygotes); littermates (for heterozygotes).

References:
Lostal W; Bartoli M; Bourg N; Roudaut C; Bentaib A; Miyake K; Guerchet N; Fougerousse F; McNeil P; Richard I. 2010. Efficient recovery of dysferlin deficiency by dual adeno-associated vector-mediated gene transfer. Hum Mol Genet 19(10):1897-907.

PMID: 20154340

Below is a quick summary of the inclusion/exclusion criteria. Please review this information carefully prior to making any decision regarding participating.

Inclusion Criteria:

Must be Non-ambulant (cannot walk 10 meters in ≤ 30 sec) and age 18 years or older
Established mutations of the dysferlin gene on both alleles
Impaired muscle function but with sufficient muscle preservation to ensure muscle transfection based on magnetic resonance image of the EDB showing sufficient muscle preservation to permit transfection
Willingness of sexually active subjects with reproductive capacity to practice reliable method of contraception (If appropriate), during the first six months after gene transfer (females) or until two negative sperm samples are obtained post gene transfer (males).

Exclusion Criteria:

Active viral infection based on clinical observations or serological evidence of HIV, or Hepatitis A, B or C infection
The presence of dysferlin mutations without weakness or loss of function
Symptoms or signs of cardiomyopathy, including:
Dyspnea on exertion, pedal edema, shortness of breath upon lying flat, or rales at the base of the lungs
Echocardiogram with ejection fraction below 40%
Diagnosis of (or ongoing treatment for) an autoimmune disease
Persistent leukopenia or leukocytosis (WBC ≤ 3.5 K/µL or ≥ 20.0 K/µL) or an absolute neutrophil count < 1.5K/µL
Concomitant illness or requirement for chronic drug treatment that in the opinion of the PI creates unnecessary risks for gene transfer
Pregnancy
AAVrh74 or AAV8 binding antibody titers > 1:50 as determined by ELISA immunoassay
Abnormal laboratory values in the clinically significant range in the table below, based upon normal values in the Nationwide Children's Hospital Laboratory: GGT, Total Bilirubin, Cystatine, Hemoglobin, White Blood Cells
This first phase of the trial will be small and will only evaluate safety; patients enrolled are not expected to show improvement in their symptoms. If the initial trial is successful, a Phase 2 trial will be scheduled, which will look for efficacy (improvement in symptoms) as well as safety. Each phase would include more patients. So, it is a process and we are pacing ourselves as we support this major milestone in the field of therapeutic intervention for people suffering from dysferlinopathy.