Biology subjects

Makki, N.

Publications and source records attributed to Makki, N..

4 recordsLinked to original sources

bioRxiv2026

Massively parallel characterization of adolescent idiopathic scoliosis risk variants

Adolescent idiopathic scoliosis (AIS) is a common pediatric musculoskeletal disorder characterized by lateral spinal curvature, often leading to chronic pain and deformity. While a significant genetic component to AIS is recognized, the functional impact of most associated genetic variants, particularly those in non-coding regions, remains largely unknown. Using massively parallel reporter assays, we characterize 1,664 variant positions in linkage disequilibrium with 26 AIS lead variants identified by genome-wide association studies (GWAS) in chondrocytes, a major cell type implicated in AIS pathogenesis. Using a library of 7,173 candidate regulatory sequences we compare the 1,664 reference alleles against 4,708 alternate alleles in two human chondrocyte cell lines (TC28a2 and SW1353). Our analysis identifies 92 variants that exhibit significant differential regulatory activity between their reference and alternate alleles, 79 of which are predicted to disrupt transcription factor binding sites, often correlating with their observed regulatory effect. Notably, we validate rs9496392, a single-nucleotide variant near the ADGRG6 locus, which shows consistent differential regulatory activity in both cell lines. ADGRG6 is a key regulator of cartilage homeostasis, and its cartilage-specific knockout in mice results in a scoliosis-like phenotype. The AIS risk allele of rs9496392 (T) is predicted to strongly disrupt several TFBSs, including SP1. This study provides a foundational catalog of functional AIS-associated regulatory variants active in chondrocytes, offering crucial insights into the perturbed gene regulatory networks in AIS. These findings lay the groundwork for identifying biomarkers and potential therapeutic targets for this complex childhood disease.

genomics↗

bioRxiv2026

Integrated Transcriptomic and Functional Analysis Reveals Tissue-Specific Molecular Pathology in Adolescent Idiopathic Scoliosis

Adolescent idiopathic scoliosis (AIS), the spontaneous development of a lateral spine curvature during puberty, is the most common pediatric spine disorder, affecting [~]3% of children worldwide. As the underlying etiology remains unclear, AIS is treated purely symptomatically, initially by bracing and ultimately by highly invasive, costly surgeries. Genome-wide association studies (GWAS) have identified numerous risk loci in non-coding genomic regions, making it difficult to link them to a biological function. To address this, we performed a multi-tissue investigation to connect genetic risk to tissue-specific molecular pathology. We conducted RNA sequencing on the primary tissues implicated in AIS, paraspinal muscle and spinal cartilage, from patients and unaffected controls. In paraspinal muscle, we identified differentially expressed genes (DEGs) enriched for pathways related to muscle structure, myogenesis, and metabolism. Key upregulated genes include the transcription factor EGR1 and structural components such as MYH1. In spinal cartilage, we found enrichment of genes related to TGF{beta} and FoxO signaling, as well as metabolic pathways. Notably, genes crucial for chondrocyte differentiation (e.g. SOX5 and SOX6) were significantly downregulated. We then examined genes at known GWAS loci and found that several risk-associated genes were differentially expressed in one or both tissues. To investigate the function of non-coding variants at these loci, we identified and validated several enhancer elements harboring AIS risk SNPs at the BCL2, ADGRG6, BNC2, and FTO loci. We reveal distinct pathological signatures in muscle and cartilage and lay the foundation for connecting non-coding genetic risk to the dysregulation of key developmental and structural pathways.

genetics↗

bioRxiv2020

Genomic characterization of the adolescent idiopathic scoliosis associated transcriptome and regulome

Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is the most common pediatric musculoskeletal disorder, affecting [~]3% of the population worldwide. However, its genetic bases and tissues of origin remain largely unknown. Several genome-wide association studies (GWAS) have implicated nucleotide variants in noncoding sequences that control genes with important roles in cartilage, muscle, bone, connective tissue and intervertebral discs (IVDs) as drivers of AIS susceptibility. Here, we set out to define the expression of AIS-associated genes and active regulatory elements by performing RNA-seq and ChIP-seq against H3K27ac in these tissues in mouse and human. Our study highlights genetic pathways involving AIS-associated loci that regulate chondrogenesis, IVD development and connective tissue maintenance and homeostasis. In addition, we identify thousands of putative AIS-associated regulatory elements which may orchestrate tissue-specific expression in musculoskeletal tissues of the spine. Quantification of enhancer activity of several candidate regulatory elements from our study identifies three functional enhancers carrying AIS-associated GWAS SNPs at the ADGRG6 and BNC2 loci. Our findings provide a novel genome-wide catalog of AIS-relevant genes and regulatory elements and aid in the identification of novel targets for AIS causality and treatment.

genetics↗

bioRxiv2019

Homeostasis of the intervertebral disc requires regulation of STAT3 signaling by the adhesion G-protein coupled receptor ADGRG6

Degenerative changes of the intervertebral disc (IVD) are a leading cause of disability affecting humans worldwide. While this is primarily attributed to trauma and aging, genetic variation is associated with disc degeneration in humans. However, the precise mechanisms driving the initiation and progression of disease remain elusive due to a paucity of genetic animal models. Here, we discuss a novel genetic mouse model of endplate-oriented disc degeneration. We show that the adhesion G-protein coupled receptor G6 (ADGRG6) mediates several anabolic and catabolic factors, fibrotic collagen genes, pro-inflammatory pathways, and mechanical properties of the IVD, prior to the onset of overt histopathology of these tissues. Furthermore, we found increased IL-6/STAT3 activation in the IVD and demonstrate that treatment with a chemical inhibitor of STAT3 activation ameliorates disc degeneration in these mutant mice. These findings establish ADGRG6 as a critical regulator of homeostasis of adult disc homeostasis and implicate ADGRG6 and STAT3 as promising therapeutic targets for degenerative joint diseases.\n\nAuthor summaryDegenerative changes of the intervertebral disc (IVD) are a leading cause of disability affecting humans worldwide. While this is primarily attributed to trauma and aging, genetic variation is associated with disc degeneration in humans. However, the precise mechanisms driving the initiation and progression of disease remain elusive due to a paucity of genetic animal models. Here, we discuss a novel genetic mouse model of endplate-oriented disc degeneration. We show that the adhesion G-protein coupled receptor G6 (ADGRG6) mediates fibrotic collagen expression, causing increased mechanical stiffness of the IVD prior to the onset of histopathology in adult mice. Furthermore, we found increased IL-6/STAT3 activation in the IVD and demonstrate that treatment with a chemical inhibitor of STAT3 activation ameliorates disc degeneration in these mutant mice. Our results demonstrate that ADGRG6 regulation of STAT3 signaling is important for IVD homeostasis, indicating potential therapeutic targets for degenerative joint disorders.

developmental biology↗