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Longitudinal transcriptomic analysis of mouse sciatic nerve reveals pathways associated with age-related muscle pathology

Journal of cachexia, sarcopenia and muscle

2023 Mar 10

Comfort, N;Gade, M;Strait, M;Merwin, SJ;Antoniou, D;Parodi, C;Marcinczyk, L;Jean-Francois, L;Bloomquist, TR;Memou, A;Rideout, HJ;Corti, S;Kariya, S;Re, DB;
PMID: 36905126 | DOI: 10.1002/jcsm.13204

Sarcopenia, the age-associated decline in skeletal muscle mass and strength, has long been considered a disease of muscle only, but accumulating evidence suggests that sarcopenia could originate from the neural components controlling muscles. To identify early molecular changes in nerves that may drive sarcopenia initiation, we performed a longitudinal transcriptomic analysis of the sciatic nerve, which governs lower limb muscles, in aging mice.Sciatic nerve and gastrocnemius muscle were obtained from female C57BL/6JN mice aged 5, 18, 21 and 24 months old (n = 6 per age group). Sciatic nerve RNA was extracted and underwent RNA sequencing (RNA-seq). Differentially expressed genes (DEGs) were validated using quantitative reverse transcription PCR (qRT-PCR). Functional enrichment analysis of clusters of genes associated with patterns of gene expression across age groups (adjusted P-value < 0.05, likelihood ratio test [LRT]) was performed. Pathological skeletal muscle aging was confirmed between 21 and 24 months by a combination of molecular and pathological biomarkers. Myofiber denervation was confirmed with qRT-PCR of Chrnd, Chrng, Myog, Runx1 and Gadd45ɑ in gastrocnemius muscle. Changes in muscle mass, cross-sectional myofiber size and percentage of fibres with centralized nuclei were analysed in a separate cohort of mice from the same colony (n = 4-6 per age group).We detected 51 significant DEGs in sciatic nerve of 18-month-old mice compared with 5-month-old mice (absolute value of fold change > 2; false discovery rate [FDR] < 0.05). Up-regulated DEGs included Dbp (log2 fold change [LFC] = 2.63, FDR < 0.001) and Lmod2 (LFC = 7.52, FDR = 0.001). Down-regulated DEGs included Cdh6 (LFC = -21.38, FDR < 0.001) and Gbp1 (LFC = -21.78, FDR < 0.001). We validated RNA-seq findings with qRT-PCR of various up- and down-regulated genes including Dbp and Cdh6. Up-regulated genes (FDR < 0.1) were associated with the AMP-activated protein kinase signalling pathway (FDR = 0.02) and circadian rhythm (FDR = 0.02), whereas down-regulated DEGs were associated with biosynthesis and metabolic pathways (FDR < 0.05). We identified seven significant clusters of genes (FDR < 0.05, LRT) with similar expression patterns across groups. Functional enrichment analysis of these clusters revealed biological processes that may be implicated in age-related changes in skeletal muscles and/or sarcopenia initiation including extracellular matrix organization and an immune response (FDR < 0.05).Gene expression changes in mouse peripheral nerve were detected prior to disturbances in myofiber innervation and sarcopenia onset. These early molecular changes we report shed a new light on biological processes that may be implicated in sarcopenia initiation and pathogenesis. Future studies are warranted to confirm the disease modifying and/or biomarker potential of the key changes we report here.
Development and use of a high-throughput screen to identify novel modulators of the corticotropin releasing factor binding protein

SLAS discovery : advancing life sciences R & D

2022 Oct 07

Haass-Koffler, CL;Francis, TC;Gandhi, P;Patel, R;Naemuddin, M;Nielsen, CK;Bartlett, SE;Bonci, A;Vasile, S;Hood, BL;Suyama, E;Hedrick, MP;Smith, LH;Limpert, AS;Roberto, M;Cosford, NDP;Sheffler, DJ;
PMID: 36210051 | DOI: 10.1016/j.slasd.2022.09.005

Stress responses are believed to involve corticotropin releasing factor (CRF), its two cognate receptors (CRF1 and CRF2), and the CRF-binding protein (CRFBP). Whereas decades of research has focused on CRF1, the role of CRF2 in the central nervous system (CNS) has not been thoroughly investigated. We have previously reported that CRF2, interacting with a C terminal fragment of CRFBP, CRFBP(10kD), may have a role in the modulation of neuronal activity. However, the mechanism by which CRF interacts with CRFBP(10kD) and CRF2 has not been fully elucidated due to the lack of useful chemical tools to probe CRFBP.We miniaturized a cell-based assay, where CRFBP(10kD) is fused as a chimera with CRF2, and performed a high-throughput screen (HTS) of 350,000 small molecules to find negative allosteric modulators (NAMs) of the CRFBP(10kD)-CRF2 complex. Hits were confirmed by evaluating activity toward parental HEK293 cells, toward CRF2 in the absence of CRFBP(10kD), and toward CRF1 in vitro. Hits were further characterized in ex vivo electrophysiology assays that target: 1) the CRF1+ neurons in the central nucleus of the amygdala (CeA) of CRF1:GFP mice that express GFP under the CRF1 promoter, and 2) the CRF-induced potentiation of N-methyl-D-aspartic acid receptor (NMDAR)-mediated synaptic transmission in dopamine neurons in the ventral tegmental area (VTA).We found that CRFBP(10kD) potentiates CRF-intracellular Ca2+ release specifically via CRF2, indicating that CRFBP may possess excitatory roles in addition to the inhibitory role established by the N-terminal fragment of CRFBP, CRFBP(27kD). We identified novel small molecule CRFBP-CRF2 NAMs that do not alter the CRF1-mediated effects of exogenous CRF but blunt CRF-induced potentiation of NMDAR-mediated synaptic transmission in dopamine neurons in the VTA, an effect mediated by CRF2 and CRFBP.These results provide the first evidence of specific roles for CRF2 and CRFBP(10kD) in the modulation of neuronal activity and suggest that CRFBP(10kD)-CRF2 NAMs can be further developed for the treatment of stress-related disorders including alcohol and substance use disorders.
Editorial: Cognitive and Motor Control Based on Brain-Computer Interfaces for Improving the Health and Well-Being in Older Age

Frontiers in human neuroscience

2022 Apr 06

Belkacem, AN;Falk, TH;Yanagisawa, T;Guger, C;
PMID: 35463924 | DOI: 10.3389/fnhum.2022.881922

STANDARDIZED FECAL MICROBIOTA TRANSPLANTATION INCLUDING MICROBIAL BASED DONOR SELECTION IN ACTIVE ULCERATIVE COLITIS PATIENTS: A RANDOMIZED,

Acta Gastro 

2022 Jan 01

Caenepeel, C;Deleu, S;

Introduction: Four randomized controlled trials studying fecal microbiota transplantation (FMT) in active ulcerative colitis (UC) patients showed variable success rates. The efficacy of FMT appears to be influenced by various factors including donor- and procedure-specific characteristics. Aim: We hypothesized that the outcome of FMT in patients with active UC could be improved by donor preselection on microbiota level, by using a strict anaerobic approach, and by repeated FMT administration. Methods: The RESTORE-UC trial (NCT03110289) was a national, multi-centric double-blind, sham-controlled randomized trial. Active UC patients (Total Mayo score 4-10 with endoscopic sub-score > or = 2) were randomly allocated (1:1) to receive 4 anaerobic-prepared superdonor (S) FMT or autologous (A) FMT by permutated blocks (2- 4) and stratified for weight, concomitant steroid use, and therapy refractoriness. S-FMTs were selected after a rigorous screening excluding samples with Bacteroides 2 enterotype, high abundances of Fusobacterium, Escherichia coli and Veillonella and the lowest microbial loads (Q1). A futility analysis after 66% (n=72) of inclusions was planned per protocol including a modified intention-to-treat (mITT) analysis using non-responder imputation (NRI) for patients receiving at least one FMT. The primary endpoint was steroid-free clinical remission (Total Mayo ≤ 2, with no subscore >1) at week 8. Secondary outcomes included steroid-free PRO-2 remission (Combined Mayo subscores of ≤1 for rectal bleeding plus stool frequency) and response (≥3 points or/and ≥50% reduction from baseline in combined Mayo subscores for rectal bleeding plus stool frequency) and steroid-free endoscopic remission (Mayo endoscopic subscore ≤1) and response (Mayo endoscopy subscore ≤1 and ≥1 point reduction from baseline). Results: Between March 2017-2021, 72 patients signed the ICF and 66 were randomly allocated to S-FMT (n=30) or A-FMT (N=36) and received at least one FMT. Both study arms were matched for baseline characteristics, yet a trend (p= 0,07) towards higher concomitant biological use in the S-FMT arm was observed. A remarkably high proportion of patients were previously exposed to biologicals (58.3% and 60.0% for the A-FMT and S-FMT group respectively). In the S-FMT and the A-FMT respectively 4 and 5 patients terminated the trial early due to worsening of colitis (4 in both arms) or FMT enema intolerance (1 A-FMT). They were included in the mITT analysis using NRI, showing after 66% of intended inclusions, the primary endpoint was reached in 3/30 (mITT with NRI 10.0%) S-FMT and 5/31 (13.9%) patients randomized to A-FMT (p=0.72). As the predefined minimum difference of 5% between both treatment arms was not attained, the study was stopped due to futility. Steroid-free PRO-2 remission was achieved in 7/30 (23,3%) patients on S-FMT and 10/36 (27,8%) on A-FMT (p= 0,78). Steroid-free PRO-2 response was attained by respectively 9/30 (30,0%) patients in the S-FMT arm and 12/36 (33,3%) patients in the A-FMT arm (p= 0,80). Steroid-free endoscopic response and remission were noted in 5/30 (16,7%) assigned to the S-FMT arm compared with 7/36 (19,4%) allocated to the A-FMT arm (p= 1.0). Of note, no patients on concomitant biologicals reached the primary endpoint, and there were 2 serious adverse events in the A-FMT arm: dysuria requiring hospitalization and worsening of UC requiring colectomy. Conclusions: In this double-blind sham-controlled trial comparing repeated administrations of anaerobic-prepared S-FMT with A-FMT in patients with active UC, no significant difference in steroid-free remission rates at week 8 were observed. The FMT procedure was generally well tolerated, and no new safety signals were observed.
STANDARDIZED FECAL MICROBIOTA TRANSPLANTATION INCLUDING MICROBIAL BASED DONOR SELECTION IN ACTIVE ULCERATIVE COLITIS PATIENTS

Acta Gastro-Enterologica Belgica

2022 Jan 01

Caenepeel, C;Deleu, S;Arnauts, K;Castellanos, JV;Braekeleire, S;Machiels, K;Baert, F;Mana, F;Pouillon, L;Hindryckx, P;Lobaton, T;Louis, E;Franchimont, D;Ferrante, M;Sabino, J;Vieira-Silva, S;Falony, G;Raes, J;Vermeire, S;

Introduction: Four randomized controlled trials studying fecal microbiota transplantation (FMT) in active ulcerative colitis (UC) patients showed variable success rates. The efficacy of FMT appears to be influenced by various factors including donor- and procedure-specific characteristics. Aim: We hypothesized that the outcome of FMT in patients with active UC could be improved by donor preselection on microbiota level, by using a strict anaerobic approach, and by repeated FMT administration. Methods: The RESTORE-UC trial (NCT03110289) was a national, multi-centric double-blind, sham-controlled randomized trial. Active UC patients (Total Mayo score 4-10 with endoscopic sub-score > or = 2) were randomly allocated (1:1) to receive 4 anaerobic-prepared superdonor (S) FMT or autologous (A) FMT by permutated blocks (2- 4) and stratified for weight, concomitant steroid use, and therapy refractoriness. S-FMTs were selected after a rigorous screening excluding samples with Bacteroides 2 enterotype, high abundances of Fusobacterium, Escherichia coli and Veillonella and the lowest microbial loads (Q1). A futility analysis after 66% (n=72) of inclusions was planned per protocol including a modified intention-to-treat (mITT) analysis using non-responder imputation (NRI) for patients receiving at least one FMT. The primary endpoint was steroid-free clinical remission (Total Mayo ≤ 2, with no subscore >1) at week 8. Secondary outcomes included steroid-free PRO-2 remission (Combined Mayo subscores of ≤1 for rectal bleeding plus stool frequency) and response (≥3 points or/and ≥50% reduction from baseline in combined Mayo subscores for rectal bleeding plus stool frequency) and steroid-free endoscopic remission (Mayo endoscopic subscore ≤1) and response (Mayo endoscopy subscore ≤1 and ≥1 point reduction from baseline). Results: Between March 2017-2021, 72 patients signed the ICF and 66 were randomly allocated to S-FMT (n=30) or A-FMT (N=36) and received at least one FMT. Both study arms were matched for baseline characteristics, yet a trend (p= 0,07) towards higher concomitant biological use in the S-FMT arm was observed. A remarkably high proportion of patients were previously exposed to biologicals (58.3% and 60.0% for the A-FMT and S-FMT group respectively). In the S-FMT and the A-FMT respectively 4 and 5 patients terminated the trial early due to worsening of colitis (4 in both arms) or FMT enema intolerance (1 A-FMT). They were included in the mITT analysis using NRI, showing after 66% of intended inclusions, the primary endpoint was reached in 3/30 (mITT with NRI 10.0%) S-FMT and 5/31 (13.9%) patients randomized to A-FMT (p=0.72). As the predefined minimum difference of 5% between both treatment arms was not attained, the study was stopped due to futility. Steroid-free PRO-2 remission was achieved in 7/30 (23,3%) patients on S-FMT and 10/36 (27,8%) on A-FMT (p= 0,78). Steroid-free PRO-2 response was attained by respectively 9/30 (30,0%) patients in the S-FMT arm and 12/36 (33,3%) patients in the A-FMT arm (p= 0,80). Steroid-free endoscopic response and remission were noted in 5/30 (16,7%) assigned to the S-FMT arm compared with 7/36 (19,4%) allocated to the A-FMT arm (p= 1.0). Of note, no patients on concomitant biologicals reached the primary endpoint, and there were 2 serious adverse events in the A-FMT arm: dysuria requiring hospitalization and worsening of UC requiring colectomy. Conclusions: In this double-blind sham-controlled trial comparing repeated administrations of anaerobic-prepared S-FMT with A-FMT in patients with active UC, no significant difference in steroid-free remission rates at week 8 were observed. The FMT procedure was generally well tolerated, and no new safety signals were observed.
First person- Xuming Zhu

Disease Models & Mechanisms

2023 Mar 01

Zhu, X;
| DOI: 10.1242/dmm.050160

First Person is a series of interviews with the first authors of a selection of papers published in Disease Models & Mechanisms, helping researchers promote themselves alongside their papers. Xuming Zhu is first author on ‘ FZD2 regulates limb development by mediating β-catenin-dependent and -independent Wnt signaling pathways’, published in DMM. Xuming is an instructor in the lab of Sarah E. Millar at Icahn School of Medicine at Mount Sinai, New York, NY, USA, investigating the molecular mechanisms that underlie the development of appendages, epithelial homeostasis and diseases.
Gut Microbiota And Metabolites Drive Persistent Pain In Sickle Cell Disease

The Journal of Pain

2023 Apr 01

Sadler, K;Atkinson, S;Ehlers, V;Waltz, T;Hayward, M;Rodriguez-Garcia, D;Salzman, N;Stucky, C;Brandow, A;
| DOI: 10.1016/j.jpain.2023.02.104

Severe debilitating pain is the most common complication and reason for hospitalization for individuals with sickle cell disease (SCD), a genetic blood disorder that affects 100,000 people in the US and over 3 million worldwide. Despite this, the biological basis of chronic SCD pain is not fully understood. Using transgenic SCD mice and fecal material transplant paradigms, we determined that gastrointestinal tract contents drive persistent SCD pain. Mechanical allodynia was temporarily alleviated in SCD mice following fecal transplant from wildtype animals. In contrast, wildtype mice developed mechanical and cold allodynia following fecal transplant from SCD animals. To identify gut bacterial species and metabolites responsible for SCD pain, we completed 16s rRNA sequencing and metabolomic screening respectively on transplant recipient feces. Bilirubin, a product of heme breakdown, was significantly elevated in the feces of SCD mice and mice that received SCD fecal transplants, as well as in the plasma of individuals with SCD. Oral administration of bilirubin induced mechanical allodynia in wildtype mice that depended on vagus nerve signaling. Using whole cell patch clamp recordings, we demonstrated that bilirubin directly activates vagal afferents and increases afferent excitability. Ongoing experiments are investigating the specific receptors through which bilirubin alters neuronal activity as drugs targeting these proteins may prove effective analgesics for SCD pain. In summary, these experiments are the first to demonstrate that sickle cell gut contents drive chronic widespread pain in this disease, and furthermore, are the first to identify gut metabolites that should be targeted for chronic SCD pain management. National Institutes of Health: K99HL155791(KS), R01HL142657(AB), R01NS070711 CS).
Skin Resident Memory T Cell Dysfunction In The Tibia Fracture Model Of Complex Regional Pain Syndrome

The Journal of Pain

2023 Apr 01

Wickman, J;Shenoda, B;Van Duyne, R;Kline, Z;Ajit, S;
| DOI: 10.1016/j.jpain.2023.02.060

Complex regional pain syndrome (CRPS) is a debilitating chronic pain disorder that with no effective treatments. Several microRNA (miRNA) are commonly dysregulated in CRPS patient and tibia fracture model of CRPS (TFM) mice, including miR-25 which is associated with positive treatment outcomes in patients. Interestingly, these miRNAs are predicted to target several genes critical to resident memory T cell (Trm) function. We hypothesize that miRNA dysregulation contributes to the pathology of CRPS through regulation of skin Trm development and maintenance. Therapeutic strategies blocking Trm development or maintenance may be beneficial in treating this disease. Whole blood samples were obtained from CRPS patients or healthy controls. miRNA and gene expression changes in blood and T cells were assessed by qPCR. Animals were treated with therapeutic agents after development of TFM and monitored for behavioral outcomes and T cell populations of collected tissues were analyzed at different time points by flow cytometry. There was an inverse correlation of miR-25 and CD69 in blood samples from CRPS patients compared to controls. TFM hindlimb skin shows increased epidermal CD8+ and CD4+ Trm, dermal CD4+ Trm. Epidermal CD8+ Trm, dermal CD4+ Trm are marked by increases in CD103+CD49a+ populations, and along with splenic CD8+ Tem show increased CD122+ cells. Therapeutic studies are ongoing. miRNA signatures in CRPS patients and TFM mice show common alterations which are capable of regulating CD69, a core Trm marker. TFM hindlimb skin shows increased pathological Trm populations and treatments targeting Trm development and maintenance may be beneficial in treating CRPS. 1RF1NS130481-01.
Spatial Proteomics for Further Exploration of Missing Proteins: A Case Study of the Ovary

Journal of proteome research

2022 Sep 15

Méar, L;Sutantiwanichkul, T;Östman, J;Damdimopoulou, P;Lindskog, C;
PMID: 36108145 | DOI: 10.1021/acs.jproteome.2c00392

In the quest for "missing proteins" (MPs), the proteins encoded by the human genome still lacking evidence of existence at the protein level, novel approaches are needed to detect this challenging group of proteins. The current count stands at 1,343 MPs, and it is likely that many of these proteins are expressed at low levels, in rare cell or tissue types, or the cells in which they are expressed may only represent a small minority of the tissue. Here, we used an integrated omics approach to identify and explore MPs in human ovaries. By taking advantage of publicly available transcriptomics and antibody-based proteomics data in the Human Protein Atlas (HPA), we selected 18 candidates for further immunohistochemical analysis using an exclusive collection of ovarian tissues from women and patients of reproductive age. The results were compared with data from single-cell mRNA sequencing, and seven proteins (CTXN1, MRO, RERGL, TTLL3, TRIM61, TRIM73, and ZNF793) could be validated at the single-cell type level with both methods. We present for the first time the cell type-specific spatial localization of 18 MPs in human ovarian follicles, thereby showcasing the utility of the HPA database as an important resource for identification of MPs suitable for exploration in specialized tissue samples. The results constitute a starting point for further quantitative and qualitative analysis of the human ovaries, and the novel data for the seven proteins that were validated with both methods should be considered as evidence of existence of these proteins in human ovary.
Neural mechanisms of comforting: Prosocial touch and stress buffering

Hormones and behavior

2023 Jun 08

Lim, KY;Hong, W;
PMID: 37301130 | DOI: 10.1016/j.yhbeh.2023.105391

Comforting is a crucial form of prosocial behavior that is important for maintaining social unity and improving the physical and emotional well-being of social species. It is often expressed through affiliative social touch toward someone in distress, providing relief for their distressed state. In the face of increasing global distress, these actions are paramount to the continued improvement of individual welfare and the collective good. Understanding the neural mechanisms responsible for promoting actions focused on benefitting others is particularly important and timely. Here, we review prosocial comforting behavior, emphasizing synthesizing recent studies carried out using rodent models. We discuss its underlying behavioral expression and motivations, and then explore both the neurobiology of prosocial comforting in a helper animal and the neurobiology of stress relief following social touch in a recipient as part of a feedback loop interaction.
1213P DKN-01 and tislelizumab + chemotherapy as first-line (1L) investigational therapy in advanced gastroesophageal adenocarcinoma (GEA): DisTinGuish trial

Annals of Oncology

2022 Sep 01

Klempner, S;Chao, J;Uronis, H;Sirard, C;Kagey, M;Baum, J;Song, J;Wang, J;Sonbol, M;Wainberg, Z;Ajani, J;
| DOI: 10.1016/j.annonc.2022.07.1331

Background Despite recent approval of anti-PD-1 antibodies as 1L therapy in advanced GEA, benefit is largely limited to PD-L1 combined positive scores (CPS) ≥5 patients (pts); novel therapeutic approaches are needed. DKN-01 is a targeted anti-DKK1 mAb which has demonstrated activity in GEA pts with elevated tumoral DKK1 expression, a subset of pts with more aggressive disease and shorter overall survival. Methods Phase IIa single arm trial investigating DKN-01 300 mg (D) + tislelizumab (TS) + CAPOX as 1L therapy in advanced HER2(-) GEA regardless of DKK1 status. Tumoral DKK1 mRNA expression was assessed by a chromogenic in situ hybridization RNAscope assay and assigned an H-score (0-300). Primary endpoint was ORR in modified intent to treat (mITT) population (>1 dose D); secondary endpoints included PFS and OS in intent to treat (ITT) population overall and by DKK1 expression: high (H-score ≥35) vs low. Results 25 pts enrolled (01 Sept 2020 - 08 Apr 2021). Median age 61 years (22, 80); 17 pts gastroesophageal junction adenocarcinoma; 8 pts gastric cancer. 21 GEA pts had RNAscope DKK1 expression; 57% were DKK1-high. 22 of 25 pts had vCPS: 73% were vCPS
Recapitulating folliculogenesis and oogenesis outside the body: encapsulated in vitro follicle growth

Biology of reproduction

2022 Sep 22

Converse, A;Zaniker, EJ;Amargant, F;Duncan, FE;
PMID: 36136744 | DOI: 10.1093/biolre/ioac176

Folliculogenesis is a tightly coordinated process essential for generating a fertilization-competent gamete while also producing gonadal hormones that sustain endocrine function. In vitro follicle growth systems have been critical to our understanding of key events in folliculogenesis, such as gonadotropin-independent and -dependent growth, steroid hormone production, and oocyte growth and maturation (cytoplasmic and meiotic). Although there are several successful follicle culture strategies, the following protocol details an encapsulated in vitro follicle growth (eIVFG) system for use with mouse ovarian follicles. eIVFG is performed with alginate hydrogels, which are biologically inert, maintain cell-to-cell interactions between granulosa cells and the oocyte, and preserve follicle architecture as found in the ovary. The system supports follicle growth, development, and differentiation from the early primary follicle to the antral follicle stage. Moreover, post-folliculogenesis events including meiotic maturation, ovulation, and luteinization are also supported. Importantly, the culture of secondary follicles has successfully resulted in viable pups after blastocyst transfer. This alginate-based eIVFG system is versatile and has broad applications as a tool for interrogating the fundamental biology of the ovarian follicle in a controlled manner, a screening platform for toxicity and bioactivity, and a potential fertility preservation method for endangered species as well as humans.

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Description
sense
Example: Hs-LAG3-sense
Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron#
Example: Mm-Htt-intron2
Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan
Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)
A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp
Example: Hs-PDGFB-No-XMm
Does not cross detect with the species (Sp)
XSp
Example: Rn-Pde9a-XMm
designed to cross detect with the species (Sp)
O#
Example: Mm-Islr-O1
Alternative design targeting different regions of the same transcript or isoforms
CDS
Example: Hs-SLC31A-CDS
Probe targets the protein-coding sequence only
EnEmProbe targets exons n and m
En-EmProbe targets region from exon n to exon m
Retired Nomenclature
tvn
Example: Hs-LEPR-tv1
Designed to target transcript variant n
ORF
Example: Hs-ACVRL1-ORF
Probe targets open reading frame
UTR
Example: Hs-HTT-UTR-C3
Probe targets the untranslated region (non-protein-coding region) only
5UTR
Example: Hs-GNRHR-5UTR
Probe targets the 5' untranslated region only
3UTR
Example: Rn-Npy1r-3UTR
Probe targets the 3' untranslated region only
Pan
Example: Pool
A mixture of multiple probe sets targeting multiple genes or transcripts

Enabling research, drug development (CDx) and diagnostics

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