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"Nassiri, Farshad"
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Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes
by
Voisin, Mathew R.
,
Zadeh, Gelareh
,
De Carvalho, Daniel D.
in
631/1647/2210/2213
,
692/308/53/2421
,
Biomarkers, Tumor - blood
2020
Definitive diagnosis of intracranial tumors relies on tissue specimens obtained by invasive surgery. Noninvasive diagnostic approaches provide an opportunity to avoid surgery and mitigate unnecessary risk to patients. In the present study, we show that DNA-methylation profiles from plasma reveal highly specific signatures to detect and accurately discriminate common primary intracranial tumors that share cell-of-origin lineages and can be challenging to distinguish using standard-of-care imaging.
A cell-free DNA-methylation sequencing assay accurately identifies different brain tumor types using plasma samples.
Journal Article
Degenerative cervical myelopathy — update and future directions
by
Badhiwala, Jetan H
,
Nassiri Farshad
,
Witiw, Christopher D
in
Medical diagnosis
,
Pathophysiology
,
Spinal cord
2020
Degenerative cervical myelopathy (DCM) is the leading cause of spinal cord dysfunction in adults worldwide. DCM encompasses various acquired (age-related) and congenital pathologies related to degeneration of the cervical spinal column, including hypertrophy and/or calcification of the ligaments, intervertebral discs and osseous tissues. These pathologies narrow the spinal canal, leading to chronic spinal cord compression and disability. Owing to the ageing population, rates of DCM are increasing. Expeditious diagnosis and treatment of DCM are needed to avoid permanent disability. Over the past 10 years, advances in basic science and in translational and clinical research have improved our understanding of the pathophysiology of DCM and helped delineate evidence-based practices for diagnosis and treatment. Surgical decompression is recommended for moderate and severe DCM; the best strategy for mild myelopathy remains unclear. Next-generation quantitative microstructural MRI and neurophysiological recordings promise to enable quantification of spinal cord tissue damage and help predict clinical outcomes. Here, we provide a comprehensive, evidence-based review of DCM, including its definition, epidemiology, pathophysiology, clinical presentation, diagnosis and differential diagnosis, and non-operative and operative management. With this Review, we aim to equip physicians across broad disciplines with the knowledge necessary to make a timely diagnosis of DCM, recognize the clinical features that influence management and identify when urgent surgical intervention is warranted.Degenerative cervical myelopathy is the leading cause of spinal cord dysfunction in adults worldwide. In this Review, the authors provide a comprehensive pathophysiological and clinical overview of the condition to equip physicians across broad disciplines with the knowledge needed for its diagnosis and management.
Journal Article
Anticoagulation Therapy Timing in patients with Atrial Fibrillation after Acute and Chronic Subdural Haematoma (ATTAACH): a pilot randomised controlled trial
by
Scales, Damon
,
Nassiri, Farshad
,
Pirouzmand, Farhad
in
Administration, Oral
,
Anticoagulants
,
Anticoagulants - administration & dosage
2024
IntroductionSubdural haematomas (SDHs), acute or chronic, are common neurosurgical diagnoses. These problems can occur among patients requiring direct oral anticoagulation (DOAC) for atrial fibrillation. There are currently no guidelines regarding the optimal timing to resume anticoagulation for these patients after SDH. The objective of this study is to evaluate the feasibility of conducting a future large randomised controlled trial (RCT) evaluating the safety and efficacy of resuming DOACs early (ie, at 30 days) vs late (ie, at 3 months) for patients with atrial fibrillation following diagnosis of SDH.Methods and analysisThis is a pilot, open-label, multicentre RCT that will enrol adults with newly diagnosed acute or chronic SDH with or without other intracranial bleeding who were receiving therapeutic anticoagulation with a DOAC as stroke prophylaxis for atrial fibrillation. Patients will be randomly allocated to resume a DOAC at standard dosing starting either days 30+7 or days 90±14. The primary outcomes for the pilot RCT are recruitment rate, protocol adherence and patient compliance with the randomly allocated interventions. Secondary outcomes are patient functional outcomes and safety and effectiveness outcomes, which will comprise key endpoints for the future planned RCT. This pilot RCT will provide important data to inform the feasibility of conducting a future, large RCT of early versus late resumption of DOACs for atrial fibrillation stroke prophylaxis in patients newly diagnosed with SDH. The future RCT will help inform management of a commonly encountered clinical dilemma with high associated morbidity and mortality.Ethics and disseminationThis study has been approved by the research ethics board of record. It will be conducted in accordance with the Declaration of Helsinki, Good Clinical Practice guidelines and regulatory requirements. Informed consent will be obtained from eligible patients or substitute decision-makers. Data from this study will inform the design of future, larger RCTs.Trial registration numberNCT05472766.
Journal Article
Programmed death ligand-1 (PD-L1) expression in meningioma; prognostic significance and its association with hypoxia and NFKB2 expression
2020
Management of clinically aggressive meningiomas is a considerable challenge. PD-L1 induced immune suppression has increasingly gained attention in clinical management of cancer; however, to date, the clinical significance and regulatory mechanisms of PD-L1 in meningioma is not yet fully characterized. We sought to characterize PD-L1 expression in meningioma and elucidate its regulatory mechanisms. Immunohistochemical staining of PD-L1 expression in meningiomas showed 43% positivity in both tumor and immune cells and we observed intra and inter tumoral heterogeneity. Univariate and multivariate analyses confirmed that PD-L1 protein expression is an independent prognostic marker for worse recurrence free survival in meningioma. Furthermore, our transcriptomic analysis revealed a strong association between PD-L1 expression and that of NFKB2 and carbonic anhydrase 9 (CA9). We also demonstrated that both of these markers, when co-expressed with PD-L1, predict tumor progression. Our studies on several meningioma cell lines cultured in hypoxic conditions validated the association of CA9 and PD-L1 expression. Here we show the clinical significance of PD-L1 in meningioma as a marker that can predict tumor recurrence. We also show an association PD-L1 expression with NFKB2 expression and its induction under hypoxic conditions. These findings may open new avenues of molecular investigation in pathogenesis of meningioma.
Journal Article
Clinical significance of checkpoint regulator “Programmed death ligand-1 (PD-L1)” expression in meningioma: review of the current status
by
Nassiri Farshad
,
Karimi Shirin
,
Bunda Severa
in
Brain cancer
,
Brain tumors
,
Clinical significance
2021
IntroductionMeningioma is the most common primary brain tumor. Most meningiomas are benign; however, a subset of these tumors can be aggressive, presenting with early or multiple tumor recurrences that are refractory to neurosurgical resection and radiotherapy. There is no standard systemic therapy for these patients, and post-surgical management of these patients is usually complicated due to lack of accurate prediction for tumor progression.MethodsIn this review, we summarise the crucial immunosuppressive role of checkpoint regulators, including PD-1 and PD-L1 interacting in the tumor microenvironment, which has led to efforts aimed at targeting this axis.ResultsSince their discovery, checkpoint inhibitors have significantly improved the outcome in many types of cancers. Currently, targeted therapy for PD-1 and PD-L1 proteins are being tested in several ongoing clinical trials for brain tumors such as glioblastoma. More recently, there have been some reports implicating increased PD-L1 expression in high-grade (WHO grades II and III) meningiomas. Several clinical trials are underway to assess the efficacy of checkpoint inhibitors in the therapeutic management of patients with aggressive meningiomas. Here, we review the immune suppressive microenvironment in meningiomas, and then focus on clinical and pathological characterization and tumor heterogeneity with respect to PD-L1 expression as well as challenges associated with the assessment of PD-L1 expression in meningioma.ConclusionWe conclude with a brief review of ongoing clinical trials using checkpoint inhibitors for the treatment of high-grade and refractory meningiomas.
Journal Article
Efficacy and Safety of Surgery for Mild Degenerative Cervical Myelopathy: Results of the AOSpine North America and International Prospective Multicenter Studies
by
Badhiwala, Jetan H
,
Witiw, Christopher D
,
Fehlings, Michael G
in
Cervical Vertebrae - surgery
,
Decompression, Surgical - adverse effects
,
Decompression, Surgical - statistics & numerical data
2019
Abstract
BACKGROUND
There is controversy over the optimal treatment strategy for patients with mild degenerative cervical myelopathy (DCM).
OBJECTIVE
To evaluate the degree of impairment in baseline quality of life as compared to population norms, as well as functional, disability, and quality of life outcomes following surgery in a prospective cohort of mild DCM patients undergoing surgical decompression.
METHODS
We identified patients with mild DCM (modified Japanese Orthopaedic Association [mJOA] 15 to 17) enrolled in the prospective, multicenter AOSpine CSM-NA or CSM-I trials. Baseline quality of life Short Form-36 version 2 (SF-36v2) was compared to population norms by the standardized mean difference (SMD). Outcomes, including functional status (mJOA, Nurick grade), disability (NDI [Neck Disability Index]), and quality of life (SF-36v2), were evaluated at baseline and 6 mo, 1 yr, and 2 yr after surgery. Postoperative complications within 30 d of surgery were monitored.
RESULTS
One hundred ninety-three patients met eligibility criteria. Mean age was 52.4 yr. There were 67 females (34.7%). Patients had significant impairment in all domains of the SF-36v2 compared to population norms, greatest for Social Functioning (SMD –2.33), Physical Functioning (SMD –2.31), and Mental Health (SMD –2.30). A significant improvement in mean score from baseline to 2-yr follow-up was observed for all major outcome measures, including mJOA (0.87, P < .01), Nurick grade (–1.13, P < .01), NDI (–12.97, P < .01), and SF-36v2 Physical Component Summary (PCS) (5.75, P < .01) and Mental Component Summary (MCS) (6.93, P < .01). The rate of complication was low.
CONCLUSION
Mild DCM is associated with significant impairment in quality of life. Surgery results in significant gains in functional status, level of disability, and quality of life.
Journal Article
The multiomic landscape of meningiomas: a review and update
2023
Purpose
Meningiomas are the most common primary brain tumor in adults. Traditionally they have been understudied compared to other central nervous system (CNS) tumors. However over the last decade, there has been renewed interest in uncovering the molecular topography of these tumors, with landmark studies identifying key driver alterations contributing to meningioma development and progression. Recent work from several independent research groups have integrated different genomic and epigenomic platforms to develop a molecular-based classification scheme for meningiomas that could supersede histopathological grading in terms of diagnostic accuracy, biological relevance, and outcome prediction, keeping pace with contemporary grading schemes for other CNS tumors including gliomas and medulloblastomas.
Methods
Here we summarize the studies that have uncovered key alterations in meningiomas which builds towards the discovery of consensus molecular groups in meningiomas by integrating these findings. These groups supersede WHO grade and other clinical factors in being able to accurately predict tumor biology and clinical outcomes following surgery.
Results
Despite differences in the nomenclature of recently uncovered molecular groups across different studies, the biological similarities between these groups enables us to likely reconciliate these groups into four consensus molecular groups: two benign groups largely dichotomized by
NF2
-status, and two clinically aggressive groups defined by their hypermetabolic transcriptome, and by their preponderance of proliferative, cell-cycling pathways respectively.
Conclusion
Future work, including by our group and others are underway to validate these molecular groups and harmonize the nomenclature for routine clinical use.
Journal Article
Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities
2023
Malignant peripheral nerve sheath tumor (MPNST) is a highly aggressive sarcoma, and a lethal neurofibromatosis type 1-related malignancy, with little progress made on treatment strategies. Here, we apply a multiplatform integrated molecular analysis on 108 tumors spanning the spectrum of peripheral nerve sheath tumors to identify candidate drivers of MPNST that can serve as therapeutic targets. Unsupervised analyses of methylome and transcriptome profiles identify two distinct subgroups of MPNSTs with unique targetable oncogenic programs. We establish two subgroups of MPNSTs: SHH pathway activation in MPNST-G1 and WNT/ß-catenin/CCND1 pathway activation in MPNST-G2. Single nuclei RNA sequencing characterizes the complex cellular architecture and demonstrate that malignant cells from MPNST-G1 and MPNST-G2 have neural crest-like and Schwann cell precursor-like cell characteristics, respectively. Further, in pre-clinical models of MPNST we confirm that inhibiting SHH pathway in MPNST-G1 prevent growth and malignant progression, providing the rational for investigating these treatments in clinical trials.
Malignant peripheral nerve sheath tumours are an aggressive form of sarcoma, with limited treatment options. Here, the authors utilise DNA methylation and transcriptomic data to identify two subtypes of tumours with potential therapeutic vulnerabilities.
Journal Article
Epigenomic, genomic, and transcriptomic landscape of schwannomatosis
by
Nassiri Farshad
,
Pugh, Trevor J
,
Ostrow, Kimberly
in
Chromosome 22
,
DNA methylation
,
Epigenetics
2021
Schwannomatosis (SWNTS) is a genetic cancer predisposition syndrome that manifests as multiple and often painful neuronal tumors called schwannomas (SWNs). While germline mutations in SMARCB1 or LZTR1, plus somatic mutations in NF2 and loss of heterozygosity in chromosome 22q have been identified in a subset of patients, little is known about the epigenomic and genomic alterations that drive SWNTS-related SWNs (SWNTS-SWNs) in a majority of the cases. We performed multiplatform genomic analysis and established the molecular signature of SWNTS-SWNs. We show that SWNTS-SWNs harbor distinct genomic features relative to the histologically identical non-syndromic sporadic SWNs (NS-SWNS). We demonstrate the existence of four distinct DNA methylation subgroups of SWNTS-SWNs that are associated with specific transcriptional programs and tumor location. We show several novel recurrent non-22q deletions and structural rearrangements. We detected the SH3PXD2A-HTRA1 gene fusion in SWNTS-SWNs, with predominance in LZTR1-mutant tumors. In addition, we identified specific genetic, epigenetic, and actionable transcriptional programs associated with painful SWNTS-SWNs including PIGF, VEGF, MEK, and MTOR pathways, which may be harnessed for management of this syndrome.
Journal Article
The central nervous system tumor methylation classifier changes neuro-oncology practice for challenging brain tumor diagnoses and directly impacts patient care
by
Zadeh, Gelareh
,
Suppiah, Suganth
,
Diamandis, Phedias
in
Biomedical and Life Sciences
,
Biomedicine
,
Brain
2019
Background
Molecular signatures are being increasingly incorporated into cancer classification systems. DNA methylation-based central nervous system (CNS) tumor classification is being recognized as having the potential to aid in cases of difficult histopathological diagnoses. Here, we present our institutional clinical experience in integrating a DNA-methylation-based classifier into clinical practice and report its impact on CNS tumor patient diagnosis and treatment.
Methods
Prospective case review was undertaken at CNS tumor board discussions over a 3-year period and 55 tumors with a diagnosis that was not certain to two senior neuropathologists were recommended for methylation profiling based on diagnostic needs. Tumor classification, calibrated scores, and copy number variant (CNV) plots were obtained for all 55 cases. These results were integrated with histopathological findings to reach a final diagnosis. We retrospectively reviewed each patient's clinical course to determine final neuro-pathology diagnoses and the impact of methylation profiling on their clinical management, with a focus on changes that were made to treatment decisions.
Results
Following methylation profiling, 46 of the 55 (84%) challenging cases received a clinically relevant diagnostic alteration, with two-thirds having a change in the histopathological diagnosis and the other one-third obtaining clinically important molecular diagnostic or subtyping alterations. WHO grading changed by 27% with two-thirds receiving a higher grade. Patient care was directly changed in 15% of all cases with major changes in clinical decision-making being made for these patients to avoid unnecessary or insufficient treatment.
Conclusions
The integration of methylation-based CNS tumor classification into diagnostics has a substantial clinical benefit for patients with challenging CNS tumors while also avoiding unnecessary health care costs. The clinical impact shown here may prompt the expanded use of DNA methylation profiling for CNS tumor diagnostics within prominent neuro-oncology centers globally.
Journal Article