Biology subjects

Bajwa, A.

Publications and source records attributed to Bajwa, A..

9 recordsLinked to original sources

bioRxiv2026

Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles

Epigenetic state modulates gene regulation in a manner not always predictable from DNA sequence alone, yet current genomic deep learning models do not leverage epigenetic state as input. We present MethylSeqNet, a model that conditions pretrained sequence embeddings on CpG methylation, a stable epigenetic mark increasingly available from long-read sequencing data. Using a novel conditioning mechanism enabling scalability and interpretability, MethylSeqNet improves predictions in cases where differential epigenetic state drives regulatory variation. We show improvements over a sequence-only baseline for cell-type-specific chromatin accessibility and transcription. Epigenetic conditioning enables prediction of phenomena not encoded in allele sequence, including parent-of-origin imprinting, random monoallelic activity, and X-inactivation. We highlight a promising application of methylation conditioning by predicting the effects of a structural rearrangement in one rare disease patient case study. In silico motif insertion analysis confirms that MethylSeqNet learns methylation-dependent regulatory grammar, establishing a paradigm for integrating epigenetic information into genomic deep learning with immediate applications in rare disease interpretation.

genomics↗

bioRxiv2025

Androgens Drive SOX9 Upregulation in Injured Proximal Tubular Cells

IntroductionSex influences susceptibility, recovery, and long-term outcomes after acute kidney injury (AKI) in humans. Rodent models have been invaluable for elucidating AKI mechanisms; however, most studies have focused on males, assuming direct applicability to females, an assumption that remains largely untested. In males, the transcription factor SOX9 regulates injury-associated proximal tubule cell states, supporting survival during injury but also contributing to maladaptive repair. Given the well-described role of SOX9 in sex determination during development and its emerging importance in AKI, we investigated whether it mediates sex-specific tubular responses in the adult kidney. MethodsWe first optimized differential ischemic and cisplatin conditions in males and females to generate injury-matched models. We then used these models to ask whether proximal tubular cell responses, particularly Sox9 upregulation, are sex dependent. Tubule-specific knockout models of Sox9, Sox4, Sox11, Vgf, Zfp24, and the androgen receptor (Ar), along with gonadectomy and hormone replacement studies, combined with gene and protein analyses, were used to define regulatory networks. ResultsIn both ischemic and nephrotoxic AKI, SOX9 expression was markedly blunted in females, with levels more than fivefold lower than in males. While injury biomarkers such as NGAL and KIM1 were equally induced in both sexes, Sox9 and its downstream target Vgf showed markedly reduced induction in females, whereas the upstream regulator Zfp24 was functionally relevant only in males. Deletion of Sox9, Zfp24, or Vgf worsened injury in males but not in females. In contrast, Sox4 and Sox11 were equally upregulated and protective in both sexes. Castration or proximal tubule-specific deletion of Ar in males abolished Sox9 induction, establishing a testosterone-dependent regulatory axis. ConclusionsThese findings define a hormone-driven, male-specific tubular repair program and demonstrate that injury and recovery pathways differ fundamentally between sexes, underscoring the need for sex-inclusive therapeutic strategies for AKI. Translational StatementSex influences susceptibility and outcomes after AKI, but the molecular basis remains unclear. SOX9, a transcription factor recently identified as one of the most highly upregulated genes in proximal tubular cells during AKI in both mice and humans, has been presumed to mediate a universal protective program. Using injury-matched murine models of AKI, we now demonstrate that this response is restricted to males, driven by testosterone and androgen receptor signaling, while SOX9 induction is markedly blunted and functionally dispensable in females. These findings reveal that tubular protective pathways differ fundamentally between sexes despite equivalent injury severity. Because SOX9 activation confers epithelial protection in males, therapeutic targeting of this pathway may have clinical relevance primarily in male patients. These data underscore the importance of incorporating biological sex into mechanistic, translational, and clinical studies of kidney injury and recovery.

cell biology↗

bioRxiv2025

Genetic Modulation of Lifespan: Dynamic Effects, Sex Differences, and Body Weight Trade-offs

The dynamics of lifespan are shaped by DNA variants that exert effects at different ages. We have mapped genetic loci that modulate age-specific mortality using an actuarial approach. We started with an initial population of 6,438 pubescent siblings and ended with a survivorship of 559 mice that lived to at least 1100 days. Twenty-nine Vita loci dynamically modulate the mean lifespan of survivorships with strong age- and sex-specific effects. Fourteen have relatively steady effects on mortality while other loci act forcefully only early or late in life and with polarities of effects that invert. A distinct set of 19 Soma loci shape the negative correlation between weights of young adults with their life expectancies--much more strongly so in males than females. Another set of 11 Soma loci shape the positive correlation between weights at older ages with life expectancies. The Vita and Soma loci share 289 age-dependent epistatic interactions (LODs [≥]3.8) but fewer than 4% are common to both sexes. We provide two examples of how to move from maps toward potential mechanisms. Our findings provide an empirical bridge between evolutionary theories on aging and genetic and molecular causes. These loci and their interactions are key to begin to understand the impact of interventions that may extend healthy lifespan in mice and even in humans.

genetics↗

bioRxiv2023

Characterizing uncertainty in predictions of genomic sequence-to-activity models

Genomic sequence-to-activity models are increasingly utilized to understand gene regulatory syntax and probe the functional consequences of regulatory variation. Current models make accurate predictions of relative activity levels across the human reference genome, but their performance is more limited for predicting the effects of genetic variants, such as explaining gene expression variation across individuals. To better understand the causes of these shortcomings, we examine the uncertainty in predictions of genomic sequence-to-activity models using an ensemble of Basenji2 model replicates. We characterize prediction consistency on four types of sequences: reference genome sequences, reference genome sequences perturbed with TF motifs, eQTLs, and personal genome sequences. We observe that models tend to make high-confidence predictions on reference sequences, even when incorrect, and low-confidence predictions on sequences with variants. For eQTLs and personal genome sequences, we find that model replicates make inconsistent predictions in >50% of cases. Our findings suggest strategies to improve performance of these models.

genomics↗

bioRxiv2023

Exogenous mitochondrial transfer increases energy expenditure and attenuates adiposity gains in mice with diet-induced obesity

Obesity is associated with chronic multi-system bioenergetic stress that may be improved by increasing the number of healthy mitochondria available across organ systems. However, treatments capable of increasing mitochondrial content are generally limited to endurance exercise training paradigms, which are not always sustainable long-term, let alone feasible for many patients with obesity. Recent studies have shown that local transfer of exogenous mitochondria from healthy donor tissues can improve bioenergetic outcomes and alleviate the effects of tissue injury in recipients with organ specific disease. Thus, the aim of this project was to determine the feasibility of systemic mitochondrial transfer for improving energy balance regulation in the setting of diet-induced obesity. We found that transplantation of mitochondria from lean mice into mice with diet-induced obesity attenuated adiposity gains by increasing energy expenditure and promoting the mobilization and oxidation of lipids. Additionally, mice that received exogenous mitochondria demonstrated improved glucose uptake, greater insulin responsiveness, and complete reversal of hepatic steatosis. These changes were, in part, driven by adaptations occurring in white adipose tissue. Together, these findings are proof-of-principle that mitochondrial transplantation is an effective therapeutic strategy for limiting the deleterious metabolic effects of diet-induced obesity in mice.

physiology↗

bioRxiv2023

Unveiling APOL1 Haplotypes: A Novel Classification Through Probe-Independent Quantitative Real-Time PCR

IntroductionApolipoprotein-L1 (APOL1) is a primate-specific protein component of high- density lipoprotein (HDL). Two variants of APOL1 (G1 and G2), provide resistance to parasitic infections in African Americans but are also implicated in kidney-related diseases and transplant outcomes in recipients. This study aims to identify these risk variants using a novel probe- independent quantitative real-time PCR method in a high African American recipient cohort. Additionally, it aims to develop a new stratification approach based on haplotype-centric model. MethodsGenomic DNA was extracted from recipient PBMCs using SDS lysis buffer and proteinase K. Quantitative PCR assay with modified forward primers and a common reverse primer enabled us to identify single nucleotide polymorphisms (SNPs) and the 6-bp deletion quantitatively. Additionally, we used sanger sequencing to verify our QPCR findings. ResultsOur novel probe-independent qPCR effectively distinguished homozygous wild-type, heterozygous SNPs/deletion, and homozygous SNPs/deletion, with at least 4-fold differences. High prevalence of APOL1 variants was observed (18% two-risk alleles, 34% one-risk allele) in our recipient cohort. Intriguingly, up to 12-month follow-up revealed no significant impact of recipient APOL1 variants on transplant outcomes. Ongoing research will encompass more time points and a larger patient cohort, allowing a comprehensive evaluation of G1/G2 variant subgroups categorized by new haplotype scores, enriching our understanding. ConclusionsOur cost-effective and rapid qPCR technique facilitates APOL1 genotyping within hours. Prospective and retrospective studies will enable comparisons with long-term allograft rejection, potentially predicting early/late-stage transplant outcomes based on haplotype evaluation in this diverse group of kidney transplant recipients.

genetics↗

bioRxiv2021

Nephrotoxicity of the BRAF-kinase inhibitor Vemurafenib isdriven by off-target Ferrochelatase inhibition

A multitude of disease and therapy related factors drive the frequent development of renal disorders in cancer patients. Along with chemotherapy, the newer targeted therapeutics can also cause renal dysfunction through on and off-target mechanisms. Interestingly, among the small-molecule inhibitors approved for the treatment of cancers that harbor BRAF-kinase activating mutations, vemurafenib can trigger tubular damage and acute kidney injury (AKI). To investigate the underlying mechanisms, here, we have developed cell culture and mouse models of vemurafenib nephrotoxicity. Our studies show that at clinically relevant concentrations vemurafenib induces cell-death in transformed and primary murine and human renal tubular epithelial cells (RTEC). In mice, two weeks of daily vemurafenib treatment causes moderate AKI with histopathological characteristics of RTEC injury. Importantly, RTEC-specific BRAF gene deletion did not influence renal function under normal conditions or alter the severity of vemurafenib-associated renal impairment. Instead, we found that inhibition of ferrochelatase (FECH), an enzyme involved in heme biosynthesis contributes to vemurafenib nephrotoxicity. FECH overexpression protected RTECs and conversely FECH knockdown increased the sensitivity to vemurafenib nephrotoxicity. Collectively, these studies suggest that vemurafenib-associated RTEC dysfunction and nephrotoxicity is BRAF-independent and caused in part by off-target FECH inhibition. Translational StatementBRAF is the most frequently mutated protein kinase and a critical oncogenic driver in human cancers. In melanoma and other cancers with BRAF activating mutations, BRAF targeted small-molecule therapeutics such as vemurafenib, and dabrafenib have shown remarkable clinical benefits. However, recent clinical studies have shown that a significant number of patients that receive vemurafenib develop AKI through mechanisms that remain unknown. The present study describes the development of novel experimental models of vemurafenib nephrotoxicity and reveals the underlying off-target mechanisms that contribute to renal injury.

pharmacology and toxicology↗

bioRxiv2020

SOX9 promotes stress-responsive transcription of VGF nerve growth factor inducible gene in kidney epithelial cells

Acute kidney injury (AKI) is a common clinical condition associated with diverse etiologies and abrupt loss of renal function. In patients with sepsis, rhabdomyolysis, cancer, as well as cardiovascular disorders, the underlying disease or associated therapeutic interventions can cause hypoxic, cytotoxic, and inflammatory insults to renal tubular epithelial cells (RTECs) resulting in the onset of AKI. To uncover stress-responsive disease-modifying genes, here we have carried out renal transcriptome profiling in three distinct murine models of AKI. We find that Vgf nerve growth factor inducible gene upregulation is a common transcriptional stress response in RTECs to ischemia, cisplatin, and rhabdomyolysis-associated renal injury. The Vgf gene encodes a secretory peptide precursor protein that has critical neuro-endocrine functions; however, its role in the kidneys remains unknown. Our functional studies show that RTEC-specific Vgf gene ablation exacerbates ischemia, cisplatin, and rhabdomyolysis-associated AKI in vivo and cisplatin-induced RTEC cell death in vitro. Importantly, addback experiments showed that aggravation of cisplatin-induced renal injury caused by Vgf gene ablation is partly reversed by TLQP-21, a Vgf-derived peptide. Finally, in vitro and in vivo mechanistic studies showed that injury-induced Vgf upregulation in RTECs is driven by the transcriptional regulator Sox9. These findings reveal a crucial downstream target of the Sox9-directed transcriptional program and identify Vgf as a stress-responsive protective gene in kidney epithelial cells.AbbreviationsAKIAcute kidney injuryRTECrenal tubular epithelial cellsBUNblood urea nitrogenChIPchromatin immunoprecipitationSox9SRY-Box transcription factor 9.View Full Text

cell biology↗

bioRxiv2020

The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet

ObjectiveAs an active interface between the host and their diet, the gut bacteriome influences host metabolic adaptation. However, the contribution of gut fungi to host metabolic outcomes is not yet understood. Therefore, we aimed to determine if host metabolic response to an ultraprocessed diet reflects gut fungal community composition. DesignWe compared jejunal fungi and bacteria from 72 healthy mice with the same genetic background but different starting mycobiomes before and after 8 weeks on an ultra-processed or standardized diet using 16S and internal transcribed spacer region 2 ribosomal RNA sequencing. We measured host body composition using magnetic resonance imaging, examined changes in metabolically active host tissues and quantified serum metabolic biomarkers. ResultsGut fungal communities are highly variable between mice, differing by vendor, age and sex. After exposure to an ultra-processed diet for 8 weeks, persistent differences in fungal community composition strongly associate with differential deposition of body mass in male mice compared to mice on standardized diet. Fat deposition in the liver, genomic adaptation of metabolically active tissues and serum metabolic biomarkers are correlated with alterations in fungal diversity and community composition. Variation in fungi from the genera Thermomyces and Saccharomyces most strongly associate with increased weight gain. ConclusionsIn the gut of healthy mice, host-microbe metabolic interactions strongly reflect variability in fungal communities. Our results confirm the importance of luminal fungal communities to host metabolic adaptation to dietary exposure. Gut fungal communities may represent a therapeutic target for the prevention and treatment of metabolic disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/158287v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1d80579org.highwire.dtl.DTLVardef@14f5729org.highwire.dtl.DTLVardef@1e379bcorg.highwire.dtl.DTLVardef@14d2ab6_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefO_LIWhat is already known about this subject? Gut bacterial communities have evolved to influence the metabolic outcomes of the host in mammals. Evidence from across the lifespan suggests that differences in composition of these communities is associated with energy consumption. However, gut microbial communities, while often equated to bacteria, are diverse, multi-kingdom ecologies and limited information is available for the role of other kingdoms of life, such as fungi. C_LIO_LIWhat are the new findings? Gut fungal communities, collectively termed the mycobiome, are less diverse and abundant than bacterial communities in the gastrointestinal tract. This study identifies the considerable influence of the environment and dietary exposure on the composition of jejunal fungal communities in healthy mice with the same genetic background. After exposure to processed diet, differences in fungal community composition in male mice were strongly correlated with persistent differences body composition and markers of metabolic tone. C_LIO_LIHow might it impact on clinical practice in the foreseeable future? These results verify that the baseline metabolic tone of health mice strongly reflects the ecological complexity of the gastrointestinal mycobiome. Variation in the composition of gut fungal communities is likely an underappreciated source of experimental and clinical variability in metabolic studies. Gastrointestinal fungi are likely a target for prevention and treatment of metabolic disease. C_LI

microbiology↗