Circular RNAs in human pain · UNM School of Medicine
We study circular RNAs (circRNAs), a class of RNA that many standard sequencing methods miss, in human pain-sensing neurons. We mapped the circRNA landscape of human dorsal root ganglia and found that opioid exposure is associated with changes in them. Our goal is to add this hidden layer to the human pain atlas and turn it into new non-addictive treatments.
Our focus
Circular RNAs form when a gene's RNA is spliced back onto itself. They are extraordinarily enriched in the mammalian brain and highly enriched in synapses.
Rybak-Wolf et al., Mol Cell 2015Human pain atlases were built to read linear RNAs with poly(A) tails, the RNAs that define cell types. CircRNAs lack a poly(A) tail, and in RNA sequencing they are distinguished from linear RNA only by reads spanning the back-splice junction, so these methods largely miss them.
Szabo and Salzman, Nat Rev Genet 2016Using total RNA sequencing of donor DRG, we characterized the circRNA landscape of human pain-sensing tissue and showed that opioid exposure is associated with lower overall abundance, including reduced circNTRK2.
Koch et al., PAIN 2026Our goal is to add the circular RNA layer to the human pain atlas, cell type by cell type, and to test which circRNAs shape pain and the response to opioids. New to circRNAs? Start with our circRNA in pain resource.
Many pain treatments that work in rodents have not worked in people. We work with dorsal root ganglia donated through New Mexico Donor Services and with human stem cell-derived neurons, so our findings start where patients are.
Morphine strongly switches on P2RY11 in human pain-sensing neurons. Mice and rats lack this gene, so rodent studies cannot detect it.
Read the paperNeurons from different human donors responded differently to gabapentin, a common pain drug, and RNA sequencing of DRG from the more responsive donor pointed to the pathways involved.
Read the paper
June Bryan de la PeñaPrincipal Investigator
Bon CampomayorPostdoctoral Fellow
Jenna DemeterResearch Scientist
Maddy KochPhD Student
Quisha LeyritaMS Student
Madison HochreinMedical Student
Sean McNallyMedical Student
Gracie SwensenMedical Student
Jeanette MontoyaUndergraduateResearch philosophy
Research is the freedom of being able to ask questions, make hypotheses, test them, make mistakes, and solve problems along the way. It is not just about publishing papers or getting grants, which are also important, but having the ability to use creativity, follow clues, and work hard, hoping that one day what we have learned in the lab can positively impact the lives of those who are suffering from chronic conditions such as ongoing pain.
We are recruiting graduate students, postdoctoral fellows, and undergraduates interested in RNA biology, human sensory neuroscience, and pain.
How to apply
Assistant Professor of Research, Department of Anesthesiology & Critical Care Medicine
Secondary appointment, Department of Neurosciences
University of New Mexico School of Medicine
Full bioSupported by the National Institutes of Health (NIH HEAL Initiative through NCATS and NINDS, and NIGMS), UNM Health Sciences Center, the RNA Society, and Anthropic. See funding
Research
We study how RNA regulation in human sensory neurons shapes chronic pain and the response to opioids. Most of what is known about pain biology comes from rodents, and some human pain pathways have no rodent counterpart. Thus, we work directly with human dorsal root ganglia (DRG) from organ donors and human stem cell-derived nociceptors, and we use mouse models to test mechanisms.
Circular RNAs (circRNAs) are stable, covalently closed RNAs that can regulate gene expression. Using high-coverage total RNA sequencing, we mapped the circRNA landscape of human DRG and compared tissue from opioid-exposed donors with age- and sex-matched controls. Opioid exposure was associated with a global reduction in circRNA abundance and with changes in 43 differentially expressed circRNAs. Among these, circNTRK2, derived from the gene encoding the TrkB neurotrophin receptor, was reduced both in opioid-exposed tissue and after repeated morphine exposure in a nociceptor-like cell line (Koch et al., Pain 2026, Editor's Choice). We are now testing how opioid-responsive circRNAs regulate nociceptor function.
Single-cell and spatial atlases of human DRG were designed to capture the linear, polyadenylated RNAs that define cell types, and they now give the field a shared reference. CircRNAs lack a poly(A) tail, and in RNA sequencing they are distinguished from linear RNA only by reads spanning the back-splice junction (Szabo and Salzman, Nat Rev Genet 2016), so they are not yet part of that reference. Our long-term goal is to add this circular layer to the human pain atlas, using total RNA sequencing, long-read sequencing, and spatial methods that can be registered to existing cell-type maps.
Dorsal root ganglia donated by organ donors, with and without opioid exposure.
Keeps RNAs that lack a poly(A) tail, including circRNAs, which poly(A)-based methods largely miss.
CircRNAs are identified by sequencing reads that span the back-splice junction, where the loop is closed.
Associated with lower overall circRNA abundance and 43 differentially expressed circRNAs, including circNTRK2.
Using time-series RNA sequencing of human iPSC-derived nociceptors, we found that P2RY11, which encodes the purinergic receptor P2Y11, was the most robustly induced transcript after morphine exposure. P2Y11 is expressed in human DRG neurons, including peripherin- and TRPV1-positive nociceptors, and its immunoreactivity increased after morphine (Cells 2026). Because P2RY11 has no mouse or rat ortholog, this pathway cannot be studied in standard mouse or rat models.
We test analgesics directly on human DRG tissue. Our study of gabapentin revealed donor-specific electrophysiological and transcriptomic profiles, which suggests that individual variation in human nociceptors may shape drug response (Demeter et al., Mol Pain 2025).
Oxaliplatin, a common chemotherapy drug, frequently causes peripheral neuropathy, which can be painful and long-lasting, and no treatment is approved to prevent it. Supported by an NIH HEAL Initiative R03, we are testing whether the protein PRR14 shapes how human sensory neurons respond to oxaliplatin, using human DRG tissue and cultured human DRG neurons (NIH RePORTER).
Dr. de la Peña directs a satellite Human Tissue Repository operated with New Mexico Donor Services, which banks DRG and matched blood from consented organ donors. The lab also applies spatial transcriptomics (10x Genomics Xenium) to map RNA expression in human DRG at single-cell resolution.
During postdoctoral training, Dr. de la Peña led or contributed to work showing that RNA control mechanisms in DRG neurons shape pain plasticity. This work showed that inhibiting nonsense-mediated decay induces nociceptive sensitization through the integrated stress response (de la Peña et al., J Neurosci 2023), that the RNA-binding protein HuR is integral to nociceptor function in mice and humans (Kunder et al., J Neurosci 2022), and that a peptide encoded by an upstream open reading frame promotes pain sensitization (Barragan-Iglesias et al., Pain 2021). It also identified Arc as a regulator of neurogenic inflammation in the skin (de la Peña et al., J Neurosci 2021) and c-Fos as a downstream target of S6 kinase signaling in inflammatory pain (de la Peña et al., Br J Pharmacol 2021).
Before pain research, Dr. de la Peña's work in South Korea (1) defined the long-term effects of adolescent cigarette smoke exposure, (2) evaluated the abuse potential of anesthetics and novel psychoactive substances, (3) developed transcriptomic models of ADHD-like phenotypes, and (4) characterized natural products with sedative, anxiolytic, and antidepressant-like effects.
People
We are looking for motivated students and researchers who are passionate about neuroscience, molecular biology, and pain research.
Hello, I'm Bryan! My journey began in the humble town of Capoocan, Leyte in the Philippines. I'm a Registered Nurse, holding a Bachelor's degree in Nursing from Western Leyte College of Ormoc City. My fascination with the human body and its intricate workings led me to dedicate my career to helping others. It was during this time that I discovered my passion for research.
To further my education and delve into the world of research, I pursued advanced studies at Sahmyook University in Seoul, South Korea. There, I earned both my Master's and PhD degrees in Pharmacology, specializing in Neuropharmacology. Subsequently, I pursued postdoctoral training in molecular biology and functional genomics at the University of Texas at Dallas and later at the University of Wisconsin-Madison.
Today, I am an Assistant Professor of Research in the Department of Anesthesiology & Critical Care Medicine, with a secondary appointment in the Department of Neurosciences, at the University of New Mexico School of Medicine, where I founded my lab in September 2023 as part of the Translational Pain Research Group. I also co-founded the New Mexico RNA Club, an RNA Society-accredited RNA Salon, and serve as a DOST Balik Scientist, returning to the Philippines to help build neuroscience research capacity.
My research primarily focuses on unraveling the intricate molecular mechanisms underlying chronic pain and its associated disorders, including addiction, depression, and anxiety. My ultimate goal is to develop effective and non-addictive pain therapeutics. I'm deeply passionate about my research because I firmly believe it has the potential to make a significant impact on the lives of millions of individuals who suffer from chronic pain.
Bon investigates the neuromolecular mechanisms that drive chronic pain, with the long-term goal of contributing to non-addictive pain therapeutics.
Bon grew up in the coastal town of Carigara, Leyte in the Philippines, where an early fascination with marine life and the natural world set the foundation for his research journey. He earned his bachelor's degree in Marine Biology from Visayas State University (ViSCA), focusing on phytoplankton ecology, before pursuing graduate studies abroad. At Sahmyook University in Seoul, South Korea, he completed his MS in Convergence Science specializing in plant cytogenetics. His work included developing microsatellite probes for subgenome discrimination in economically valued crops.
He later transitioned into neuroscience and completed his PhD in Convergence Science with a focus on neuropharmacology. His doctoral work examined molecular pathways underlying Alzheimer's disease, Parkinson's disease, major depressive disorder, sleep and chronic stress-related dysfunction, aging-associated cognitive decline, and drug addiction using rodent models. His research spans molecular, cellular, and behavioral approaches.
In the de la Peña Lab within the Department of Anesthesiology & Critical Care Medicine at the University of New Mexico, Bon investigates the neuromolecular mechanisms that drive chronic pain. His long-term goal is to contribute to the development of non-addictive pain therapeutics that can meaningfully improve the lives of individuals living with persistent pain.
Jenna harnesses the rich information contained within human transcriptomic data and employs complementary wet lab approaches to identify cellular mechanisms and therapeutic targets of various chronic pain conditions. She is first author of the lab's P2RY11 study (Cells 2026) and gabapentin study (Molecular Pain 2025).
Jenna grew up in Springfield, Ohio, where she began to appreciate the intricacies of disease, including its cellular basis and multifactorial influences. Jenna further developed her fascination with the cellular and molecular underpinnings of physiology and pathophysiology at the University of Tennessee, Knoxville. She pursued a bachelor's in Biochemistry and Cellular and Molecular Biology and contextualized cellular phenomena in a broader social context through a Public Health minor. There Jenna also gained a deeper understanding of metabolic and nutritional influences on physiology and disease while pursuing a master's in Biomedical Nutrition Science. Her undergraduate and graduate research focused on the interplay of transcriptional and metabolic processes on cellular differentiation and metabolic states, specifically in adipose tissues.
Maddy characterizes circular RNAs in the dorsal root ganglia and how opioid exposure changes them. She is first author of the lab's 2026 PAIN Editor's Choice paper on the circRNA landscape of human DRG and of a 2025 Methods in Molecular Biology protocol chapter.
Maddy was born and raised in Bradenton, FL and earned a bachelor's in Biology from the University of South Florida. Here, Maddy investigated cryptic genetic diversity in coastal isopod species. Maddy then entered the Biomedical Sciences graduate program in 2021, first working with Dr. Nikolaos Mellios studying circular RNAs (circRNAs) in psychiatric disorders before moving into Dr. de la Peña's lab, where her research focuses on characterizing circRNAs in the dorsal root ganglia and the effects of opioid exposure.
Quisha is a Registered Chemist and a graduate student at Mindanao State University-Iligan Institute of Technology (MSU-IIT). Her work focuses on drug repurposing. She is co-mentored by Dr. Charlie Lavilla Jr. at MSU-IIT and supported by DOST-ASTHRDP.
Quisha is a Registered Chemist whose lifelong fascination with chemical interactions has evolved into a dedicated research career. Originally from Butuan City, Philippines, she earned her undergraduate degree in Chemistry from Mindanao State University-Iligan Institute of Technology (MSU-IIT).
Currently a graduate student at MSU-IIT and a visiting research scholar at the University of New Mexico Health Sciences Center, Quisha's work primarily focuses on drug repurposing, where she leverages her expertise in computational and bioinorganic chemistry to discover new therapeutic potentials for existing compounds.
Madison analyzes demographics and trends in chronic pain patients at UNM Hospital over a ten-year period, bridging research and clinical care. She is a co-author of the lab's circRNA study (Koch et al., PAIN 2026).
Madison is a native New Mexican, and was born and raised in Albuquerque, New Mexico. She has always had a deep passion for biology and chemistry and a strong desire to help others. She received her bachelor's degree in Biochemistry from the University of New Mexico with a minor in Spanish. During her time as an undergraduate Madison worked for four years in an engineering lab at Sandia National Laboratories where she focused on additive manufacturing and materials science. She also worked as part of the COVID-19 response team at Sandia National Laboratories during the pandemic to aid in COVID-19 testing for the employees and dependents of three National Laboratories.
In her time as an undergrad, she had a deepened interest in physiology and pharmacology which furthered her interest in medicine and lifelong dream of becoming a physician. She is a medical student at the University of New Mexico School of Medicine, and her research in Dr. de la Peña's lab focuses on data analysis of demographics and trends in chronic pain patients from UNMH over a ten-year period, with the goal of bridging both the research aspect of chronic pain with the clinical aspect to work towards a solution for chronic pain and addiction.
Sean studies the genetic and neuroimmune mechanisms driving chronic pain conditions. He is second author of the lab's P2RY11 study (Cells 2026).
Sean was born and raised in the rural four corners region of northwestern New Mexico. Growing up in one of the most medically underserved regions in the country, Sean was inspired to pursue medicine watching his father's work within rural and tribal communities. From a young age, he became acutely aware of the deep-rooted healthcare disparities faced by rural populations, fueling a lifelong commitment to studying and addressing health inequities.
Sean completed his undergraduate education through the Combined BA/MD Program at the University of New Mexico. Studying at the University of New Mexico and the University of Sheffield in the UK, Sean received a B.A. in Health, Medicine, and Human Values with a concentration in Health, Humanities & Society and a minor in Chemistry from the University of New Mexico in 2024. He is a medical student at the University of New Mexico School of Medicine.
Sean's research interests are shaped by personal and community experiences with chronic pain and neurological illness, particularly among workers in mining, farming, and oil fields who are chronically exposed to neurotoxic substances. In 2023, he joined the Department of Anesthesiology and Critical Care Medicine at UNM as an undergraduate researcher studying the neuroimmune mechanisms underlying chronic neuropathic pain. In 2025, he joined the de la Peña Lab to continue this work, with a focus on the genetic and neuroimmune mechanisms driving chronic pain conditions.
Gracie studies the molecular mechanisms underlying opioid use and withdrawal.
Gracie is a medical student at the University of New Mexico School of Medicine. She received her B.S. in Biomedical Sciences from Arizona State University before returning home to New Mexico to pursue her MD. Her research interests include anesthesiology, pain management, and the molecular mechanisms underlying opioid use and withdrawal. In the de la Peña Lab, she studies how opioid exposure and withdrawal relate to circular RNA (circRNA) expression. Through this research, she hopes to contribute to a better understanding of opioid-related conditions and to improvements in withdrawal treatment, pain management, and overall patient care.
Jeanette is an Albuquerque native and a Biochemistry major at UNM working toward medical school. She is a co-author of the lab's P2RY11 study (Cells 2026).
Jeanette is an Albuquerque native through and through, born here, raised here, and fully convinced that nowhere else will ever feel like home. She grew up surrounded by New Mexico sunsets, family, and a whole lot of farming, so staying here for the long run just makes sense to her. She first fell in love with science at Bosque Preparatory School, where hands-on labs and science-heavy coursework hooked her early. Research appeals to her because it's the perfect mix of curiosity, problem-solving, and getting to actually do things, not just read about them. When she's not in class, Jeanette's usually exploring her city, hanging out with the people (and dogs) she loves, or finding new ways to stay connected to the community she plans to be part of forever.
If you are interested in a position in this lab, email jdelapena@salud.unm.edu with your latest CV and a note explaining your background, what projects you might be interested in, and why you want to join the lab.
We currently welcome applications from graduate students, postdoctoral fellows, and undergraduates. UNM undergraduates can also join through BIOM 410 research credit.
Equal Opportunity Employer
Publications
Every entry below was checked against PubMed, or against Google Scholar for journals PubMed does not index. Last checked October 2026.
Bold marks Dr. de la Peña.
Koch MR, Campomayor NBA, de la Peña JBI. Expanding the Human Sensory Atlas to Circular and Long Non-Coding RNAs. Invited Topical Review, submitted to PAIN.
Funding
Our research is supported by the following sponsors. We are grateful to the organ donors and their families, and to New Mexico Donor Services, whose generosity makes our human tissue research possible.
| Sponsor | Award | Title | Role | Period |
|---|---|---|---|---|
| NIH HEAL Initiative, National Center for Advancing Translational Sciences (funded by NINDS) | 1R03TR005864-01 | Role of PRR14 in Human Sensory Neurons in Oxaliplatin-Induced Peripheral Neuropathy | Contact PI (with Sascha R. Alles) | Sept 2025 to Aug 2027 |
| NIH, National Institute of General Medical Sciences, AIM CoBRE (P20GM121176) | Research Project 5203 | Investigating the Role of CircRNAs in Pain and Nociceptive Sensitization | Project Leader | 2025 to 2027 |
| UNM Health Sciences Center | Pilot Funding Program | Pain, opioids, and circular RNAs | PI | 2026 |
| Anthropic | AI for Science award | Role of circRNA in pain and nociception | PI | 2026 |
| RNA Society, co-sponsored by Lexogen | RNA Salon award | New Mexico RNA Club | Organizer | 2025 to 2028 |
| UNM Department of Anesthesiology & Critical Care Medicine | Start-up funds | Lab establishment | PI | Since 2023 |
NIH awards as listed in NIH RePORTER, checked October 2026.
News
Milestones, papers, and events from the de la Peña Lab.
| Date | News |
|---|---|
| Nov 6, 2026 | Upcoming: hands-on RNA Workshop, "Advances in RNA Technologies for Functional Genomics Research," at UNM Health Sciences Center. Details and registration (deadline November 1). |
| Oct 2026 | The lab receives an AI for Science award from Anthropic for "Role of circRNA in pain and nociception." |
| Sept 24, 2026 | New Mexico RNA Club annual retreat and anniversary, with invited speaker Dr. Praveen Patidar (New Mexico Tech). |
| Sept 2026 | The RNA Society renews the New Mexico RNA Club's RNA Salon award for two years (2026 to 2028). |
| Sept 2026 | NIH NIGMS continues funding for the lab's AIM CoBRE research project on circular RNAs in pain for 2026 to 2027. |
| Aug 31, 2026 | Study of sex-specific neuroimmune signatures in a mouse model of chronic back pain published in The Journal of Pain, in collaboration with the Alles Lab. |
| Aug 15, 2026 | Jenna Demeter's first-author paper identifying P2RY11 as an opioid-induced receptor in human nociceptors published in Cells. |
| Jul 2026 | Dr. Nicole Bon A. Campomayor joins the lab as a postdoctoral fellow. |
| May 7, 2026 | Maddy Koch's first-author paper on the circular RNA landscape of human DRG published online in PAIN and selected as an Editor's Choice. |
| Mar 28, 2026 | Dr. de la Peña speaks at the SASE West Regional Conference 2026 Science Workshop at UNM: "Breaking the Pain Cycle: How Circular RNAs Are Redefining Pain Research." |
| Mar 19, 2026 | New Mexico RNA Club Trainee Mini-Symposium: five trainee lightning talks and three RNA Society membership awards. |
| Sept 1, 2025 | The lab's NIH R03 on PRR14 in human sensory neurons and oxaliplatin-induced neuropathy begins, with Dr. Sascha Alles as multiple PI. |
| Aug 26, 2025 | Collaborative study of a humanized anti-P2X4 antibody fragment in human DRG neurons published in Molecular Pain. |
| Jul 14, 2025 | Jenna Demeter's first-author study of gabapentin in human DRG published in Molecular Pain. |
| 2025 | The lab's AIM CoBRE research project, "Investigating the Role of CircRNAs in Pain and Nociceptive Sensitization," is funded by NIH NIGMS. |
| 2025 | The RNA Society accredits the UNM RNA Club as an RNA Salon, co-sponsored by Lexogen. |
| Jan 23, 2025 | Inaugural meeting of the RNA Club at UNM Health Sciences Center. |
| Sept 2023 | The de la Peña Lab opens at the University of New Mexico School of Medicine. |
| Date | Item |
|---|---|
| Mar 2026 | 2026 Outstanding Mentor of the Year, Biomedical Sciences Graduate Program, UNM Health Sciences Center |
| 2024 | Early-Career Stage Travel Award, NIH PURPOSE Pain Network Meeting |
| Sept 22, 2023 | Interview with CNN Philippines. Dr. de la Peña was a resource person on CNN Philippines and DOSTv's ExperTalk, discussing the cognitive benefits of brain puzzles and his path from Leyte to South Korea, the USA, and his own lab at UNM. Watch the interview |
| Jan 26, 2023 | Balik Scientist, EVSU researchers to catalyze research in neuropharmacology (Eastern Visayas State University) |
| Nov 26, 2022 | Balik Scientist ng Leyte (An Pukot, PSHS-Eastern Visayas Campus) |
| Nov 2022 | Balik Scientist Dr. June Bryan de la Peña: first leg of engagement in the region (Eastern Visayas Health Research and Development Consortium) |
| 2022 | Balik Scientist Dr. de la Peña amplifies EVHRDC member institutions' research productivity through capacity-enhancement activities (Eastern Visayas Health Research and Development Consortium) |
| 2021, 2022 | Balik Scientist Award, Department of Science and Technology, Philippines |
| Sept 7, 2018 | Cold Spring Harbor Laboratory Visitor of the Week: June Bryan de la Peña |
circRNA in pain
A starting point for anyone studying circular RNAs (circRNAs) in pain: the basics, a curated reading list, methods notes, human reference datasets, and data from our lab.
CircRNAs form by back-splicing, which links the two ends of an RNA into a closed loop. Because of these linked ends, they resist exonucleases that degrade linear RNA.
Xiao and Wilusz, Nucleic Acids Res 2019CircRNAs are extraordinarily enriched in the mammalian brain, well conserved in sequence, and highly enriched in synapses.
Rybak-Wolf et al., Mol Cell 2015In stimulated cells, circRNAs stayed stable while mRNAs and microRNAs changed within minutes. Most circRNAs detected were relatively long-lived.
Enuka et al., Nucleic Acids Res 2016Detection is typically based on short-read RNA sequencing processed with computational tools. In a benchmark of 16 tools, precision was similar, but the number of circRNAs called differed widely.
Vromman et al., Nat Methods 2023Reading list
Curated by the lab and checked against PubMed in October 2026. Each summary restates the paper's own abstract. Newest first within each group. Know a paper we missed? Send it to us.
Studies that measured circRNAs in human samples.
Koch MR, Demeter JB, Hochrein M, Alles SRA, Westlund KN, Ehsanian R, de la Peña JBI. Characterization of the circular RNA landscape of human dorsal root ganglia reveals a neurotrophin-related circRNA is modulated by opioid exposure. Pain. 2026;167(7):1615-1630. doi: 10.1097/j.pain.0000000000003987. PMID: 42152618.
Total RNA sequencing of human DRG from opioid-exposed donors and matched controls. Opioid exposure was associated with a global reduction in circRNA abundance and 43 differentially expressed circRNAs, including lower circNTRK2.
Irie T, Shum R, Deni I, Hunkele A, Le Rouzic V, Xu J, Wilson R, Fischer GW, Pasternak GW, Pan YX. Identification of Abundant and Evolutionarily Conserved Opioid Receptor Circular RNAs in the Nervous System Modulated by Morphine. Mol Pharmacol. 2019;96(2):247-258. doi: 10.1124/mol.118.113977. PMID: 31243060.
Opioid receptor circRNAs (circOprm1) were detected in rodent and human brain and spinal cord. Chronic morphine increased two of these circRNAs 1.5- to 1.6-fold relative to linear Oprm1 mRNA in mouse brain.
Wang L, Luo T, Bao Z, Li Y, Bu W. Intrathecal circHIPK3 shRNA alleviates neuropathic pain in diabetic rats. Biochem Biophys Res Commun. 2018;505(3):644-650. doi: 10.1016/j.bbrc.2018.09.158. PMID: 30286957.
circHIPK3 was highly abundant in serum from people with type 2 diabetes and neuropathic pain, and in DRG from diabetic rats. Silencing circHIPK3 alleviated neuropathic pain in the rats.
Rodent findings are hypotheses for human tissue, not conclusions about it.
Liu XD, Jin T, Tao Y, et al. DHX9/DNA-tandem repeat-dependent downregulation of ciRNA-Fmn1 in the dorsal horn is required for neuropathic pain. Acta Pharmacol Sin. 2023;44(9):1748-1767. doi: 10.1038/s41401-023-01082-x. PMID: 37095197.
ciRNA-Fmn1 fell in spinal dorsal horn neurons after nerve injury. Blocking that decrease attenuated pain hypersensitivity in mice.
Xiong W, Wei M, Zhang L, Wang J, Liu F, Wang Z. Chronic constriction injury-induced changes in circular RNA expression profiling of the dorsal root ganglion in a rat model of neuropathic pain. BMC Neurosci. 2022;23(1):64. doi: 10.1186/s12868-022-00745-5. PMID: 36376788.
Sequencing of rat DRG after chronic constriction injury identified 374 differentially expressed circRNAs (290 up, 84 down).
Cai W, Zhang Y, Su Z. ciRS-7 targeting miR-135a-5p promotes neuropathic pain in CCI rats via inflammation and autophagy. Gene. 2020;736:144386. doi: 10.1016/j.gene.2020.144386. PMID: 31978512.
ciRS-7 in the spinal dorsal horn tracked with neuropathic pain in rats and acted by sponging miR-135a-5p.
Zhang SB, Lin SY, Liu M, et al. CircAnks1a in the spinal cord regulates hypersensitivity in a rodent model of neuropathic pain. Nat Commun. 2019;10(1):4119. doi: 10.1038/s41467-019-12049-0. PMID: 31511520.
Nerve ligation increased circAnks1a in dorsal horn neurons. Knockdown attenuated pain-like behavior, and circAnks1a raised VEGFB through YBX1 and by sponging miR-324-3p.
Broader overviews of non-coding RNAs in pain.
Zhang C, Gao R, Zhou R, Chen H, Liu C, Zhu T, Chen C. The emerging power and promise of non-coding RNAs in chronic pain. Front Mol Neurosci. 2022;15:1037929. doi: 10.3389/fnmol.2022.1037929. PMID: 36407760.
Review of miRNAs, circRNAs, and lncRNAs across neuropathic, inflammatory, and cancer pain, including candidate biomarkers.
Jiang M, Wang Y, Wang J, Feng S, Wang X. The etiological roles of miRNAs, lncRNAs, and circRNAs in neuropathic pain: A narrative review. J Clin Lab Anal. 2022;36(8):e24592. doi: 10.1002/jcla.24592. PMID: 35808924.
Narrative review of non-coding RNA changes reported in neuropathic pain, including circHIPK3, ciRS-7, and circAnks1a.
Xu D, Ma X, Sun C, Han J, Zhou C, Chan MTV, Wu WKK. Emerging roles of circular RNAs in neuropathic pain. Cell Prolif. 2021;54(12):e13139. doi: 10.1111/cpr.13139. PMID: 34623006.
Summarizes circRNA profiling studies in neuropathic pain and the mechanisms of specific circRNAs.
Papers we rely on when detecting and quantifying circRNAs.
Vromman M, Anckaert J, Bortoluzzi S, et al. Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nat Methods. 2023;20(8):1159-1169. doi: 10.1038/s41592-023-01944-6. PMID: 37443337.
Sixteen detection tools were compared. Precision was high and similar across tools, but the number of circRNAs each tool predicted ranged from 1,372 to 58,032.
Zhang J, Chen S, Yang J, Zhao F. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun. 2020;11(1):90. doi: 10.1038/s41467-019-13840-9. PMID: 31900416.
CIRIquant quantifies circRNAs and corrects for RNase R treatment bias, with a built-in differential expression pipeline.
Xiao MS, Wilusz JE. An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3' ends. Nucleic Acids Res. 2019;47(16):8755-8769. doi: 10.1093/nar/gkz576. PMID: 31269210.
Standard RNase R protocols can fail to digest more than 20% of highly expressed linear RNAs. Adding a poly(A) tail first and replacing K+ with Li+ in the buffer largely solve this.
Hansen TB. Improved circRNA Identification by Combining Prediction Algorithms. Front Cell Dev Biol. 2018;6:20. doi: 10.3389/fcell.2018.00020. PMID: 29556495.
Compared 11 algorithms. Algorithm-specific false positives were resolved by keeping circRNAs called by two or more tools.
Szabo L, Salzman J. Detecting circular RNAs: bioinformatic and experimental challenges. Nat Rev Genet. 2016;17(11):679-692. doi: 10.1038/nrg.2016.114. PMID: 27739534.
Review of the experimental and bioinformatic biases that complicate circRNA discovery, and statistical ways to address them.
Public human DRG resources from other groups that circRNA data can be compared against.
Arendt-Tranholm A, Mwirigi JM, Price TJ. RNA isoform expression landscape of the human dorsal root ganglion generated from long-read sequencing. Pain. 2024;165(11):2468-2481. doi: 10.1097/j.pain.0000000000003255. PMID: 38809314.
Long-read sequencing of human DRG from 3 donors documented 19,547 validated isoforms of protein-coding genes.
Zeidler M, Tavares-Ferreira D, Brougher J, Price TJ, Kress M. NOCICEPTRA2.0 - A comprehensive ncRNA atlas of human native and iPSC-derived sensory neurons. iScience. 2023;26(12):108525. doi: 10.1016/j.isci.2023.108525. PMID: 38162030.
A searchable database of small non-coding RNAs in human DRG and stem cell-derived sensory neurons.
Tavares-Ferreira D, Shiers S, Ray PR, et al. Spatial transcriptomics of dorsal root ganglia identifies molecular signatures of human nociceptors. Sci Transl Med. 2022;14(632):eabj8186. doi: 10.1126/scitranslmed.abj8186. PMID: 35171654.
Spatial transcriptomics of DRG neurons from 8 organ donors defined 12 human sensory neuron clusters.
Ray P, Torck A, Quigley L, et al. Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research. Pain. 2018;159(7):1325-1345. doi: 10.1097/j.pain.0000000000001217. PMID: 29561359.
RNA-seq of human DRG from organ donors compared with mouse DRG, released as an online searchable repository.
Total RNA sequencing of human DRG from opioid-exposed and control donors (Koch et al., PMID 42152618). Data are available to qualified researchers on request under a data transfer agreement, and submission to the Sequence Read Archive (SRA) is in progress.
Request the dataSupplementary data for "Gabapentin's effect on human dorsal root ganglia: Donor-specific electrophysiological and transcriptomic profiles" (PMID 40657722).
Open the data folderStep-by-step protocol chapter from the lab, published in RNA Analysis.
View on PubMedA pipeline for quantifying mRNA, lncRNA, and circRNA from total RNA sequencing. We are still building it, and we will share the code here when it is ready.
Invited Topical Review by Koch, Campomayor, and de la Peña, submitted to PAIN. We will link it here once it is published.
New Mexico RNA Club
The New Mexico RNA Club is a statewide community of RNA researchers, trainees, and core staff. Founded at UNM Health Sciences Center in January 2025, the club is an RNA Society-accredited RNA Salon co-sponsored by Lexogen. We meet in person, with hybrid options when useful, to share new RNA science and to build collaborations across New Mexico.
(1) Stimulate RNA research in New Mexico, (2) give students and postdocs opportunities to present and lead, (3) connect wet-lab, computational, clinical, and core groups, (4) introduce emerging RNA technologies, and (5) link New Mexico researchers with the RNA Society.
Co-founders and organizers: June Bryan de la Peña and Arun Kumar Ganesan
Senior advisors: Viswanathan Palanisamy and Nora Perrone-Bizzozero
Partner: UNM HSC Analytical & Translational Genomics Shared Resource
Links: RNA Society Salon listing · RNA Society · Lexogen
A hands-on workshop on current RNA methods, including bulk RNA-seq, single-cell and single-nucleus RNA-seq, spatial transcriptomics, RNA targeting and editing, and imaging. Sessions include a tour of the Analytical and Translational Genomics (ATG) Shared Resource, hands-on polysome fractionation and RNA isolation, and RT-qPCR setup and data analysis. Speakers and instructors: Dr. de la Peña, Dr. Viswanathan Palanisamy, Dr. Kel Cook, Dr. Aniruddha Das, and Dr. Arun Kumar Ganesan.
Open to students, postdoctoral fellows, faculty, and research staff. No prior experience is required, and certificates of participation are provided. Space is limited.
Register by November 1, 2026More dates for the 2026 to 2027 season will be posted here. To join the RNA Club or present at a monthly meeting, email jdelapena@salud.unm.edu or AGanesan@salud.unm.edu.
| Date | Event |
|---|---|
| Sept 24, 2026 | Annual retreat and anniversary. Dr. Praveen Patidar (New Mexico Tech): "PARP1-XRN2-DDX23 Axis in Preventing R-loop-Associated Genomic Instability" |
| Mar 19, 2026 | Trainee Mini-Symposium (lightning talks). RNA Society membership awards: Jayden Montoya (undergraduate), Cynthia Taylor (graduate), Sumira Phatak (postdoc) |
| Dec 18, 2025 | Autumn T. LaPointe (Seoul virus RNA replication kinetics); William H. Wylie, MD ("Neural circ-uitry: Circular RNA and Mental Illness") |
| Nov 11, 2025 | UNM Research & Discovery Week session: "Advancing RNA Biology in the UNM Community" |
| Oct 23, 2025 | First meeting as an accredited RNA Salon. Vasudevan Sekar (HuR as a therapeutic target for oral mucositis) |
| May 22, 2025 | Aravinthkumar Jayabalan (G3BP1/G3BP2, stress granules to lysosomes); Nora Perrone-Bizzozero (HuD/KHSRP regulation of alternative splicing in neurons) |
| Apr 23, 2025 | Spatial technologies seminar with 10x Genomics and the UNM Comprehensive Cancer Center: Xenium In Situ and Visium HD |
| Mar 27, 2025 | ATG Shared Resource session on single-cell, spatial, long-read, small-RNA, tRNA-seq, and bioinformatics services |
| Feb 20, 2025 | Himadri Nath (ISG15 splice variant and influenza polymerase); Amy Gardiner ("RNA and sugar: what could be better?") |
| Jan 23, 2025 | Inaugural meeting. Maddy Koch (circRNA regulation of BDNF in pain); Arun Ganesan (heavy metal toxicity and epigenetic instability in colon cells) |