Biology subjects

Lindquist, K.

Publications and source records attributed to Lindquist, K..

5 recordsLinked to original sources

bioRxiv2026

Predicting Endometriosis Status and Menstrual Cycle Phase Using DNA Methylation

Endometriosis is a chronic inflammatory disease associated with pelvic pain, infertility, and delayed diagnosis. Growing evidence suggests that altered DNA methylation contributes to disease development and could serve as a biomarker for disease. We developed a leakage-safe machine learning pipeline to classify endometriosis case-control status and menstrual cycle phase using genome-wide DNA methylation data from eutopic endometrial tissue. The dataset consisted of 984 samples profiled using the Illumina Infinium MethylationEPIC array, with measurements across approximately 759,000 CpG sites. Technical variation was corrected using SmartSVA batch correction. Ridge logistic regression models were trained using stratified 80/20 train-test splits, with regularization strength selected via stratified cross-validation. Feature selection approaches included ridge coefficient ranking, per-CpG t-tests, and univariate logistic regression with FDR correction. Model validity was evaluated using label-shuffling analyses. Menstrual cycle phase classification showed strong performance (mean cross-validation AUROC: 0.971, held-out test AUROC: 0.989), reflecting genome-wide hormonally driven methylation. Ridge regression produced lower but meaningful performance for endometriosis classification (mean cross-validation AUROC: 0.854, held-out test AUROC: 0.875). Ridge coefficient-based feature selection identified compact predictive CpG sets, supporting the hypothesis that endometriosis-associated methylation signal is distributed across many loci rather than a few highly predictive CpGs. Pathway enrichment analyses identified substantial enrichment for menstrual cycle phase but limited enrichment for disease status following FDR correction, consistent with a diffuse endometriosis-associated signal. These findings demonstrate that ridge regression can detect methylation patterns associated with both endometriosis and menstrual cycle phase, highlighting the importance of accounting for cycle-related epigenetic variation in endometrial DNA methylation studies.

bioinformatics↗

bioRxiv2024

Investigating Mechanically Activated Currents from Trigeminal Neurons of Non-Human Primates

IntroductionPain sensation has predominantly mechanical modalities in many pain conditions. Mechanically activated (MA) ion channels on sensory neurons underly responsiveness to mechanical stimuli. The study aimed to address gaps in knowledge regarding MA current properties in higher order species such as non-human primates (NHP; common marmosets), and characterization of MA currents in trigeminal (TG) neuronal subtypes. MethodsWe employed patch clamp electrophysiology and immunohistochemistry (IHC) to associate MA current types to different marmoset TG neuronal groups. TG neurons were grouped according to presumed marker expression, action potential (AP) width, characteristic AP features, after-hyperpolarization parameters, presence/absence of AP trains and transient outward currents, and responses to mechanical stimuli. ResultsMarmoset TG were clustered into 5 C-fiber and 5 A-fiber neuronal groups. The C1 group likely represent non-peptidergic C-nociceptors, the C2-C4 groups resembles peptidergic C-nociceptors, while the C5 group could be either cold-nociceptors or C-low-threshold-mechanoreceptors (C-LTMR). Among C-fiber neurons only C4 were mechanically responsive. The A1 and A2 groups are likely A-nociceptors, while the A3-A5 groups probably denote different subtypes of A-low-threshold-mechanoreceptors (A-LTMRs). Among A-fiber neurons only A1 was mechanically unresponsive. IHC data was correlated with electrophysiology results and estimates that NHP TG has [~]25% peptidergic C-nociceptors, [~]20% non-peptidergic C-nociceptors, [~]30% A-nociceptors, [~]5% C-LTMR, and [~]20% A-LTMR. ConclusionOverall, marmoset TG neuronal subtypes and their associated MA currents have common and unique properties compared to previously reported data. Findings from this study could be the basis for investigation on MA current sensitizations and mechanical hypersensitivity during head and neck pain conditions.

neuroscience↗

bioRxiv2023

Sensory innervation of masseter, temporal and lateral pterygoid muscles in common marmosets

Myogenous temporomandibular disorders (TMDM) is associated with an increased responsiveness of nerves innervating the masseter (MM), temporal (TM), medial pterygoid (MPM) and lateral pterygoid muscles (LPM). This study aimed to examine sensory nerve types innervating MM, TM and LPM of adult non-human primate - common marmosets. Sensory nerves are localized in specific regions of these muscles. Pgp9.5, marker for all nerves, and NFH, a marker for A-fibers, showed that masticatory muscles were predominantly innervated with A-fibers. The proportion of C- to A-fibers was highest in LPM, and minimal (6-8%) in MM. All C-fibers (pgp9.5+/NFH-) observed in masticatory muscles were peptidergic (CGRP+) and lacked mrgprD, trpV1 and CHRNA3, a silent nociceptive marker. All fibers in masticatory muscles were labeled with GFAP+, a myelin sheath marker. There were substantially more peptidergic A-fibers (CGRP+/NFH+) in TM and LPM compared to MM. Almost all A-fibers in MM expressed trkC, with some of them having trkB and parvalbumin. In contrast, a lesser number of TM and LPM nerves expressed trkC, and lacked trkB. Tyrosine hydroxylase antibodies, which did not label TG, highlighted sympathetic fibers around blood vessels of the masticatory muscles. Overall, masticatory muscle types of marmosets have distinct and different innervation patterns.

neuroscience↗

bioRxiv2021

Nurturing Diversity and Inclusion in AI in Biomedicine through a Virtual Summer Program for High School Students

Artificial Intelligence (AI) has the power to improve our lives through a wide variety of applications, many of which fall into the healthcare space; however, a lack of diversity is contributing to flawed systems that perpetuate gender and racial biases, and limit how broadly AI can help people. The UCSF AI4ALL program was established in 2019 to address this issue by promoting diversity and inclusion in AI. The program targets high school students from underrepresented backgrounds in AI and gives them a chance to learn about AI with a focus on biomedicine. In 2020, the UCSF AI4ALL three-week program was held entirely online due to the COVID-19 pandemic. Thus students participated virtually to gain experience with AI, interact with diverse role models in AI, and learn about advancing health through AI. Specifically, they attended lectures in coding and AI, received an in-depth research experience through hands-on projects exploring COVID-19, and engaged in mentoring and personal development sessions with faculty, researchers, industry professionals, and undergraduate and graduate students, many of whom were women and from underrepresented racial and ethnic backgrounds. At the conclusion of the program, the students presented the results of their research projects at our final symposium. Comparison of pre- and post-program survey responses from students demonstrated that after the program, significantly more students were familiar with how to work with data and to evaluate and apply machine learning algorithms. There was also a nominally significant increase in the students knowing people in AI from historically underrepresented groups, feeling confident in discussing AI, and being aware of careers in AI. We found that we were able to engage young students in AI via our online training program and nurture greater inclusion in AI.

scientific communication and education↗

bioRxiv2020

Deletion of the mitochondrial matrix protein cyclophilin-D prevents parvalbumin interneuron dysfunction and cognitive deficits in a mouse model of NMDA hypofunction

Redox dysregulation and oxidative stress are final common pathways in the pathophysiology of a variety of psychiatric disorders, including schizophrenia. Oxidative stress causes dysfunction of GABAergic parvalbumin-positive interneurons (PVI), which are crucial for the coordination of neuronal synchrony during sensory- and cognitive-processing. Mitochondria are the main source of reactive oxygen species (ROS) in neurons and they control synaptic activity through their roles in energy production and intracellular calcium homeostasis. We have previously shown that in male mice transient blockade of NMDA receptors during development (subcutaneous injections of 30 mg/kg ketamine (KET) on postnatal days 7, 9, and 11) results in long-lasting alterations in synaptic transmission and reduced parvalbumin expression in the adult prefrontal cortex (PFC), contributing to a behavioral phenotype that mimics multiple symptoms associated with schizophrenia. These changes correlate with oxidative stress and impaired mitochondrial function in both PVI and pyramidal cells. Here, we show that genetic deletion (Ppif-/-) of the mitochondrial matrix protein cyclophilin D (CypD) prevents perinatal KET-induced increases in ROS and the resulting deficits in PVI function, and changes in excitatory and inhibitory synaptic transmission in the PFC. Deletion of CypD also prevented KET-induced behavioral deficits in cognitive flexibility, social interaction, and novel object recognition. Taken together, these data highlight how mitochondrial activity may play an integral role in modulating PVI-mediated cognitive processes. Significance StatementMitochondria are important modulators of oxidative stress and cell function, yet how mitochondrial dysfunction affects cell activity and synaptic transmission in psychiatric illnesses is not well understood. NMDA receptor blockade with ketamine during development causes oxidative stress, dysfunction of parvalbumin-positive interneurons (PVI), and long-lasting physiological and behavioral changes. Here we show that mice deficient for the mitochondrial matrix protein cyclophilin D show robust protection from PVI dysfunction following perinatal NMDAR-blockade. Mitochondria serve as an essential node for a number of stress-induced signaling pathways and our experiments suggest that failure of mitochondrial redox regulation can contribute to PVI dysfunction.

neuroscience↗