Publications by authors named "Cody Ramirez"

Neural circuits in the spinal cord are composed of diverse sets of interneurons that play crucial roles in shaping motor output. Despite progress in revealing the cellular architecture of the spinal cord, the extent of cell type heterogeneity within interneuron populations remains unclear. Here, we present a single-nucleus transcriptomic atlas of spinal V1 interneurons across postnatal development.

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Synaptic plasticities, such as long-term potentiation (LTP) and depression (LTD), tune synaptic efficacy and are essential for learning and memory. Current studies of synaptic plasticity in humans are limited by a lack of adequate human models. Here, we modeled the thalamocortical system by fusing human induced pluripotent stem cell-derived thalamic and cortical organoids.

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Super-enhancers (SEs) are expansive regions of genomic DNA that regulate the expression of genes involved in cell identity and cell fate. We recently identified developmental stage- and cell type-specific modules within the murine Vsx2 SE. Here, we show that the human VSX2 SE modules have similar developmental stage- and cell type-specific activity in reporter gene assays.

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Article Synopsis
  • Personalized cancer vaccines targeting neoantigens show promise for treating follicular lymphoma (FL) by using advanced sequencing technologies to identify unique tumor mutations.
  • In a study involving 58 tumor samples from 57 FL patients, researchers predicted and filtered high-quality neoantigens, finding an average of 52 mutations per patient with multiple high-quality neoantigens identified.
  • A pilot clinical trial using these personalized neoantigen vaccines combined with PD-1 blockade has been initiated, showing early signs of feasibility, safety, and potential therapeutic benefits for patients with relapsed or refractory FL.
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Synaptic plasticities, such as long-term potentiation (LTP) and depression (LTD), tune synaptic efficacy and are essential for learning and memory. Current studies of synaptic plasticity in humans are limited by a lack of adequate human models. Here, we modeled the thalamocortical system by fusing human induced pluripotent stem cell-derived thalamic and cortical organoids.

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Article Synopsis
  • The study utilizes ultra-deep exome sequencing to analyze the scarce malignant Hodgkin and Reed Sternberg (HRS) cells in classical Hodgkin lymphoma (cHL), enabling better detection of somatic mutations compared to traditional methods.* -
  • Researchers identified novel mutations in several genes and recurrent patterns affecting pathways related to Hippo signaling, thereby expanding the understanding of genetic factors involved in cHL.* -
  • Additionally, single-nuclei RNA sequencing confirmed the presence of somatic mutations in specific cell clusters, providing insight into the malignant characteristics of HRS cells and establishing a methodology for future genomic studies in larger cHL patient cohorts.*
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Super-enhancers (SEs) are expansive regions of genomic DNA that regulate the expression of genes involved in cell identity and cell fate. Recently, we found that distinct modules within a murine SE regulate gene expression of master regulatory transcription factor in a developmental stage- and cell-type specific manner. is expressed in retinal progenitor cells as well as differentiated bipolar neurons and Müller glia.

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Previous studies have demonstrated the dynamic changes in chromatin structure during retinal development that correlate with changes in gene expression. However, a major limitation of those prior studies was the lack of cellular resolution. Here, we integrate single-cell (sc) RNA-seq and scATAC-seq with bulk retinal data sets to identify cell type-specific changes in the chromatin structure during development.

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Article Synopsis
  • Follicular lymphoma (FL) varies greatly among patients, with some needing immediate treatment due to aggressive disease while others can monitor their condition without intervention.
  • A study analyzed the genetic alterations in FL across 370 patients, discovering that higher mutation burdens were present in relapsed or transformed FL but not linked to better outcomes in newly diagnosed cases.
  • A set of 7 specific gene mutations (MAP signature) was identified that indicates a shorter progression-free survival in newly diagnosed FL, which could help better predict patient outcomes beyond existing prognostic tools.
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Neoantigens are tumor-specific peptide sequences resulting from sources such as somatic DNA mutations. Upon loading onto major histocompatibility complex (MHC) molecules, they can trigger recognition by T cells. Accurate neoantigen identification is thus critical for both designing cancer vaccines and predicting response to immunotherapies.

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Super-enhancers are expansive regions of genomic DNA comprised of multiple putative enhancers that contribute to the dynamic gene expression patterns during development. This is particularly important in neurogenesis because many essential transcription factors have complex developmental stage- and cell-type specific expression patterns across the central nervous system. In the developing retina, Vsx2 is expressed in retinal progenitor cells and is maintained in differentiated bipolar neurons and Müller glia.

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Introduction: Recent advances have led to the design of a new cephalomedullary nail, which aims to decrease the risk of failures in patients with intertrochanteric hip fractures by allowing for insertion of two interdigitating screws into the head segment. The goal of this study is to evaluate the safety and efficacy of this two-screw cephalomedullary nailing system.

Patients/participants: Patients 18 years of age and older who underwent intramedullary nailing of their intertrochanteric femoral fracture using the InterTAN nailing system (Smith and Nephew, Memphis, TN) from 2012 to 2016 were included in this retrospective study which was performed at two urban certified level-1 trauma centers and one urban certified level-3 trauma center.

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Purpose: Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability.

Methods: This manual review standard operating procedure (SOP) consists of methods to annotate variants with four different calls and 19 tags.

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Most patients with follicular lymphoma (FL) experience multiple relapses necessitating subsequent lines of therapy. Ibrutinib, a Bruton tyrosine kinase (BTK) inhibitor approved for the treatment of several B-cell malignancies, showed promising activity in FL in a phase 1 study. We report the results of a phase 2 trial evaluating ibrutinib in recurrent FL.

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CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and predisposing relevance of inherited and somatic variants of all types. CIViC is committed to open-source code, open-access content, public application programming interfaces (APIs) and provenance of supporting evidence to allow for the transparent creation of current and accurate variant interpretations for use in cancer precision medicine.

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