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Article: Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay efficiency.

Kolakada, Divya / Fu, Rui / Biziaev, Nikita / Shuvalov, Alexey / Lore, Mlana / Campbell, Amy E / Cortazar, Michael A / Sajek, Marcin P / Hesselberth, Jay R / Mukherjee, Neelanjan / Alkalaeva, Elena / Jagannathan, Sujatha

bioRxiv : the preprint server for biology

2024

Abstract: Nonsense variants underlie many genetic diseases. The phenotypic impact of nonsense variants is determined by Nonsense-mediated mRNA decay (NMD), which degrades transcripts with premature termination codons (PTCs). NMD activity varies across transcripts ... ...

Abstract	Nonsense variants underlie many genetic diseases. The phenotypic impact of nonsense variants is determined by Nonsense-mediated mRNA decay (NMD), which degrades transcripts with premature termination codons (PTCs). NMD activity varies across transcripts and cellular contexts via poorly understood mechanisms. Here, by leveraging human genetic datasets, we uncover that the amino acid preceding the PTC dramatically affects NMD activity in human cells. We find that glycine codons in particular support high levels of NMD and are enriched before PTCs but depleted before normal termination codons (NTCs). Gly-PTC enrichment is most pronounced in human genes that tolerate loss-of-function variants. This suggests a strong biological impact for Gly-PTC in ensuring robust elimination of potentially toxic truncated proteins from non-essential genes. Biochemical assays revealed that the peptide release rate during translation termination is highly dependent on the identity of the amino acid preceding the stop codon. This release rate is the most critical feature determining NMD activity across our massively parallel reporter assays. Together, we conclude that NMD activity is significantly modulated by the "window of opportunity" offered by translation termination kinetics. Integrating the window of opportunity model with the existing framework of NMD would enable more accurate nonsense variant interpretation in the clinic. .
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.10.575080
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Article ; Online: Role of calcium influx and modulation of local neurotransmitters as hallmarks of pediatric traumatic brain injury.

Jagannathan, Jay

publication RETRACTED

Biomarkers in medicine

2009 Volume 3, Issue 2, Page(s) 95–97

Language	English
Publishing date	2009-04
Publishing country	England
Document type	Editorial ; Retracted Publication
ZDB-ID	2481014-9
ISSN	1752-0371 ; 1752-0363
ISSN (online)	1752-0371
ISSN	1752-0363
DOI	10.2217/bmm.09.1
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Article ; Online: Molecular mechanisms of traumatic brain injury in children. A review.

Jagannathan, Pavan / Jagannathan, Jay

publication RETRACTED

Neurosurgical focus

2008 Volume 25, Issue 4, Page(s) E6

Abstract: Despite advances in molecular biology and genetics, the precise pathophysiology of traumatic brain injury (TBI) in children is unknown. In this paper the authors review what is currently known about intra- and extracellular responses to pediatric TBI and ...

Abstract	Despite advances in molecular biology and genetics, the precise pathophysiology of traumatic brain injury (TBI) in children is unknown. In this paper the authors review what is currently known about intra- and extracellular responses to pediatric TBI and relate these factors to future investigations. Although hyperemia and vascular congestion have long been thought to be the hallmarks of pediatric TBI, on a cellular level, calcium influx as well as modulation of local neurotransmitters appears to play a major role in its onset. Recent genetic and proteomic research has identified specific neurotrophic factors as well as apoptotic and antiapoptotic genes that appear to control the progression of inflammation and neuronal damage. The search for a therapeutic target will ultimately require a thorough understanding of these factors and their interplay on a proteomic, genomic, and neuromic level.
MeSH term(s)	Age Factors ; Animals ; Brain Injuries/genetics ; Brain Injuries/metabolism ; Brain Injuries/therapy ; Cell Death/physiology ; Child ; Gene Expression Regulation/physiology ; Humans ; Nerve Growth Factors/genetics ; Nerve Growth Factors/metabolism
Chemical Substances	Nerve Growth Factors
Language	English
Publishing date	2008-10
Publishing country	United States
Document type	Journal Article ; Retracted Publication ; Review
ZDB-ID	2026589-X
ISSN	1092-0684 ; 1092-0684
ISSN (online)	1092-0684
ISSN	1092-0684
DOI	10.3171/FOC.2008.25.10.E6
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Article ; Online: Review of spinal radiosurgery: a minimally invasive approach for the treatment of spinal and paraspinal metastases.

Sheehan, Jason P / Jagannathan, Jay

Neurosurgical focus

2008 Volume 25, Issue 2, Page(s) E18

Abstract: Intracranial radiosurgery has been proved effective for the treatment of brain metastasis. The treatment of paraspinal and spinal metastasis with spinal radiosurgery represents a natural extension of the principles of intracranial radiosurgery. However, ... ...

Abstract	Intracranial radiosurgery has been proved effective for the treatment of brain metastasis. The treatment of paraspinal and spinal metastasis with spinal radiosurgery represents a natural extension of the principles of intracranial radiosurgery. However, spinal radiosurgery is a far more complicated process than intracranial radiosurgery. Larger treatment volumes, numerous organs at risk, and the inability to utilize rigid, frame-based immobilization all contribute to the substantially more complex process of spinal radiosurgery. Beyond the convenience of a shorter duration of treatment for the patient, spinal radiosurgery affords a greater biological equivalent dose to a metastatic lesion than conventional radiotherapy fractionation schemes. This appears to translate into a high rate of tumor control and fast pain relief for patients. The minimally invasive nature of this approach is consistent with trends in open spinal surgery and helps to maintain or improve a patient's quality of life. Spinal radiosurgery has expanded the neurosurgical treatment armamentarium for patients with spinal and paraspinal metastasis.
MeSH term(s)	Humans ; Minimally Invasive Surgical Procedures/methods ; Radiosurgery/methods ; Spinal Neoplasms/pathology ; Spinal Neoplasms/secondary ; Spinal Neoplasms/surgery ; Spine/pathology ; Spine/surgery ; Treatment Outcome
Language	English
Publishing date	2008
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2026589-X
ISSN	1092-0684 ; 1092-0684
ISSN (online)	1092-0684
ISSN	1092-0684
DOI	10.3171/FOC/2008/25/8/E18
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Article ; Online: Iatrogenic spinal deformity.

Jagannathan, Jay / Sansur, Charles A / Shaffrey, Christopher I

publication RETRACTED

Neurosurgery

2008 Volume 63, Issue 3 Suppl, Page(s) 104–116

Abstract: Patients with postoperative spinal deformities are being identified with increasing frequency as the number of instrumented spinal operations increases. Thus, it is important for the neurosurgeon to understand ways to minimize postoperative deformity and ...

Abstract	Patients with postoperative spinal deformities are being identified with increasing frequency as the number of instrumented spinal operations increases. Thus, it is important for the neurosurgeon to understand ways to minimize postoperative deformity and to understand its operative and nonoperative management. A variety of intra- and postoperative risk factors have been associated with postoperative deformity, including patient age, operative positioning, preoperative medical condition, and the use of prior radiation therapy. The evaluation of all patients who have been suspected of iatrogenic deformity should include a detailed physical examination, plain x-rays, and computed tomographic or magnetic resonance imaging, depending on the condition. Conservative therapy includes physical therapy and pain control, which may be effective in some patients. However, patients with flat-back syndrome typically require reoperation. A wide variety of reoperative procedures may be performed, depending on the area of the pathological deformity, extent of disease, and patient condition.
MeSH term(s)	Humans ; Iatrogenic Disease ; Radiography ; Spinal Cord/abnormalities ; Spinal Cord/surgery ; Spinal Diseases/diagnostic imaging ; Spinal Diseases/surgery
Language	English
Publishing date	2008-09
Publishing country	United States
Document type	Journal Article ; Review ; Retracted Publication
ZDB-ID	135446-2
ISSN	1524-4040 ; 0148-396X
ISSN (online)	1524-4040
ISSN	0148-396X
DOI	10.1227/01.NEU.0000320386.08993.BE
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Article ; Online: Evaluation and management of Cushing syndrome in cases of negative sellar magnetic resonance imaging.

Jagannathan, Jay / Sheehan, Jason P / Jane, John A

Neurosurgical focus

2007 Volume 23, Issue 3, Page(s) E3

Abstract: The treatment of patients with Cushing disease and without magnetic resonance (MR) imaging evidence of Cushing disease (that is, negative MR imaging) is discussed in this paper. Magnetic resonance imaging is the diagnostic modality of choice in Cushing ... ...

Abstract	The treatment of patients with Cushing disease and without magnetic resonance (MR) imaging evidence of Cushing disease (that is, negative MR imaging) is discussed in this paper. Magnetic resonance imaging is the diagnostic modality of choice in Cushing disease, but in up to 40% of these patients negative imaging can be caused by tumor-related factors and limitations in imaging techniques. In cases in which the MR imaging is negative, it is critical to make sure that the diagnosis of Cushing disease is correct. This can be accomplished by performing a complete laboratory and imaging workup, including dexamethasone suppression tests, imaging of the adrenal glands, and inferior petrosal sinus sampling when appropriate. If these evaluations suggest a pituitary source of the hypercortisolemia, then transsphenoidal surgery remains the treatment of choice. The authors favor the endoscopic approach because it gives a wider and more magnified view of the sella and allows inspection of the medial cavernous sinus walls. Radiosurgery is an effective treatment option in patients with persistent Cushing disease. When a target cannot be found on MR imaging, one can target the entire sellar region with radiosurgery.
MeSH term(s)	Adrenocorticotropic Hormone/metabolism ; False Negative Reactions ; Humans ; Magnetic Resonance Imaging ; Neurosurgical Procedures ; Pituitary ACTH Hypersecretion/metabolism ; Pituitary ACTH Hypersecretion/pathology ; Pituitary ACTH Hypersecretion/therapy
Chemical Substances	Adrenocorticotropic Hormone (9002-60-2)
Language	English
Publishing date	2007
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2026589-X
ISSN	1092-0684 ; 1092-0684
ISSN (online)	1092-0684
ISSN	1092-0684
DOI	10.3171/foc.2007.23.3.4
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Article ; Online: Novel strategy to treat a case of recurrent lymphocytic hypophysitis using rituximab.

Schreckinger, Matthew / Francis, Todd / Rajah, Gary / Jagannathan, Jay / Guthikonda, Murali / Mittal, Sandeep

Journal of neurosurgery

2012 Volume 116, Issue 6, Page(s) 1318–1323

Abstract: Lymphocytic hypophysitis is an uncommon autoimmune condition that often results in significant morbidity. Although most cases resolve spontaneously or after a short course of steroids, rarely, refractory cases can cause persistent neurological deficits ... ...

Abstract	Lymphocytic hypophysitis is an uncommon autoimmune condition that often results in significant morbidity. Although most cases resolve spontaneously or after a short course of steroids, rarely, refractory cases can cause persistent neurological deficits despite aggressive medical and surgical management. A 41-year-old woman presented with progressive visual loss in the left eye and was found to have a sellar mass. She underwent transsphenoidal surgery because of lesion enlargement. Histopathology was consistent with adenohypophysitis with B-cell predominance. Despite steroid treatment, her neurological condition worsened and she experienced loss of vision in the right eye. Craniotomy with decompression of the right optic nerve was performed. Her condition improved initially, but she continued to have progressive visual compromise over the following months. She was therefore treated with rituximab, a monoclonal antibody against B cells. Her vision improved significantly within a few weeks. There was no clinical or radiographic exacerbation 2 years after starting immunotherapy. Rituximab, an anti-CD20 antibody that specifically depletes B lymphocytes, can be an effective treatment strategy for patients with steroid-refractory, B cell-predominant lymphocytic hypophysitis.
MeSH term(s)	Adult ; Antibodies, Monoclonal, Murine-Derived/therapeutic use ; Autoimmune Diseases/diagnosis ; Autoimmune Diseases/drug therapy ; Autoimmune Diseases/pathology ; B-Lymphocytes/drug effects ; B-Lymphocytes/pathology ; Biopsy ; Female ; Humans ; Immunologic Factors/therapeutic use ; Lymphocytosis/diagnosis ; Lymphocytosis/drug therapy ; Lymphocytosis/pathology ; Pituitary Diseases/diagnosis ; Pituitary Diseases/drug therapy ; Pituitary Diseases/pathology ; Recurrence ; Rituximab ; Visual Acuity/drug effects
Chemical Substances	Antibodies, Monoclonal, Murine-Derived ; Immunologic Factors ; Rituximab (4F4X42SYQ6)
Language	English
Publishing date	2012-06
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	3089-2
ISSN	1933-0693 ; 0022-3085
ISSN (online)	1933-0693
ISSN	0022-3085
DOI	10.3171/2012.2.JNS111456
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Article: Diagnosis and management of pediatric sellar lesions.

Jagannathan, Jay / Dumont, Aaron S / Jane, John A Jr

Frontiers of hormone research

2005 Volume 34, Page(s) 83–104

Abstract: Pituitary region tumors in pediatric patients are largely comprised of craniopharyngiomas and pituitary adenomas, each with their unique considerations. Craniopharyngiomas account for the majority of pediatric sellar masses. Pituitary adenomas are ... ...

Abstract	Pituitary region tumors in pediatric patients are largely comprised of craniopharyngiomas and pituitary adenomas, each with their unique considerations. Craniopharyngiomas account for the majority of pediatric sellar masses. Pituitary adenomas are relatively uncommon during childhood, although the incidence increases during adolescence. The diagnosis of sellar lesions involves a multidisciplinary effort, and detailed endocrinologic, ophthalmologic and neurologic testing are critical. The management of pituitary tumors varies depending on the entity. For most tumors, other than prolactinomas, transsphenoidal resection remains the mainstay of treatment. Less invasive modalities such as endoscopic transsphenoidal surgery, and stereotactic radiosurgery have shown promise as primary and adjuvant treatment modalities, respectively.
MeSH term(s)	Adolescent ; Adult ; Child ; Craniopharyngioma/diagnosis ; Craniopharyngioma/pathology ; Craniopharyngioma/surgery ; Female ; Humans ; Male ; Pituitary Neoplasms/diagnosis ; Pituitary Neoplasms/pathology ; Pituitary Neoplasms/surgery ; Prognosis ; Sella Turcica/pathology
Language	English
Publishing date	2005-07-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	0301-3073
ISSN	0301-3073
DOI	10.1159/000091574
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Article ; Online: Reverse and pseudoreverse cortical sign in thoracolumbar burst fracture: radiologic description and distinction--a propos of three cases.

Arlet, Vincent / Orndorff, Douglas G / Jagannathan, Jay / Dumont, Aaron

European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society

2008 Volume 18, Issue 2, Page(s) 282–287

Abstract: In thoracolumbar burst fracture the "reverse cortical sign" is a known entity that corresponds to a fragment of the posterior wall that has been flipped 180 degrees with the cancellous surface of the fragment facing posteriorly in the canal and the ... ...

Abstract	In thoracolumbar burst fracture the "reverse cortical sign" is a known entity that corresponds to a fragment of the posterior wall that has been flipped 180 degrees with the cancellous surface of the fragment facing posteriorly in the canal and the cortical surface (posterior wall) facing anteriorly. The identification of such reverse cortical fragment is crucial as ligamentotaxis is classically contraindicated as the posterior longitudinal ligament is ruptured. Recognition of such a flipped cortical fragment has relied so far on the axial CT. The advent of CT scans with sagittal reconstruction has allowed us to better describe such entities that have received little attention in the literature. The goal of this report was therefore to describe the appearance of the reverse cortical sign and its likes as they can appear on axial CT scans, sagittal reconstructions and MRI. During 1-year practice at our institution we had to treat three patients with thoracolumbar burst fracture associated with what looked like a reverse cortical sign on the axial CT scans. Further analysis of the sagittal reconstruction CT could differentiate the true reverse cortical sign from a new entity that we coined "the pseudoreverse cortical sign" as observed in two out of the three cases. In the pseudo reverse cortical sign what appears to be a flipped piece of posterior vertebral body is actually part of the superior or inferior endplate that is depressed into the comminuted vertebral body. In such cases the posterior longitudinal ligament appears to be in continuity and therefore such fracture can theoretically be treated with posterior ligamentotaxis as evidenced in one of our case. Careful analysis of the CT scan and specifically the sagittal reconstruction and MRI can differentiate two separate entities that may correspond to a different severity injury.
MeSH term(s)	Adult ; Female ; Humans ; Longitudinal Ligaments/diagnostic imaging ; Longitudinal Ligaments/pathology ; Longitudinal Ligaments/surgery ; Lumbar Vertebrae/diagnostic imaging ; Lumbar Vertebrae/pathology ; Lumbar Vertebrae/surgery ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Spinal Fractures/diagnostic imaging ; Spinal Fractures/pathology ; Spinal Fractures/surgery ; Thoracic Vertebrae/diagnostic imaging ; Thoracic Vertebrae/pathology ; Thoracic Vertebrae/surgery ; Tomography, X-Ray Computed
Language	English
Publishing date	2008-12-12
Publishing country	Germany
Document type	Case Reports ; Journal Article
ZDB-ID	1115375-1
ISSN	1432-0932 ; 0940-6719
ISSN (online)	1432-0932
ISSN	0940-6719
DOI	10.1007/s00586-008-0848-x
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Zs.A 3437: Show issues

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Article ; Online: Radiobiology of brain metastasis: applications in stereotactic radiosurgery.

Jagannathan, Jay / Sherman, Jonathan H / Mehta, Gautam U / Chin, Lawrence S

Neurosurgical focus

2007 Volume 22, Issue 3, Page(s) E4

Abstract: Stereotactic radiosurgery is a neurosurgical modality in which a target lesion can be irradiated while sparing normal brain tissue. In some respects, brain metastasis is well suited for radiosurgery, as metastatic lesions tend to be small and well ... ...

Abstract	Stereotactic radiosurgery is a neurosurgical modality in which a target lesion can be irradiated while sparing normal brain tissue. In some respects, brain metastasis is well suited for radiosurgery, as metastatic lesions tend to be small and well circumscribed and displace (but do not infiltrate) normal brain tissue, facilitating the delivery of radiation. Advances in stereotactic radiosurgical planning, such as blocking patterns and beam shaping, have allowed further targeting of discrete lesions while minimizing the effect of radiation toxicity on the central nervous system. In this paper the authors review the radiobiology of brain metastases and stereotactic radiosurgical approaches that can be used to treat these tumors safely.
MeSH term(s)	Brain/physiopathology ; Brain/radiation effects ; Brain Neoplasms/secondary ; Brain Neoplasms/surgery ; Cell Death/radiation effects ; Humans ; Neoplasm Metastasis/therapy ; Nerve Degeneration/etiology ; Nerve Degeneration/physiopathology ; Nerve Degeneration/prevention & control ; Postoperative Complications/etiology ; Postoperative Complications/physiopathology ; Postoperative Complications/prevention & control ; Preoperative Care/methods ; Preoperative Care/standards ; Radiation Dosage ; Radiation, Ionizing ; Radiosurgery/adverse effects ; Radiosurgery/methods ; Radiosurgery/standards
Language	English
Publishing date	2007-03-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2026589-X
ISSN	1092-0684 ; 1092-0684
ISSN (online)	1092-0684
ISSN	1092-0684
DOI	10.3171/foc.2007.22.3.5
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