P.189 Using in situ hybridization to delineate collagen VI genes' expression patterns in skeletal muscles of wild-type and COL6-related dystrophies mice

Neuromuscular Disorders

2022 Oct 01

Guirguis, F;Zhou, H;Bolduc, V;Muntoni, F;Bönnemann, C;
| DOI: 10.1016/j.nmd.2022.07.332

Collagen VI (COLVI) is a critical myomatrix protein for skeletal muscle health and maintenance. There are 6 COL6 genes (COL6A1-COL6A6). Pathogenic variants in COL6A1, COL6A2, or COL6A3 cause COLVI-related dystrophies (COL6-RDs) with early-onset muscle weakness and loss of ambulation. Identifying novel therapeutic targets is critical for developing COL6-RDs therapies. Here, using in situ hybridization, we aim to identify, quantify, and locate all cell types that express the wild-type (WT) COL6 genes and a common, recurrent pseudoexon (PE)-inserting COL6A1 mutation in limb skeletal muscles and diaphragms of WT and COL6-RDs male mice at 10-day-old, and 6- and 20-month-old. We first analyzed published mouse skeletal muscle RNA-seq datasets to identify potential sensitive and specific mRNA cell markers (3/cell type). Then, we conducted a pilot marker validation experiment with RNAscope. We quantified and assessed the expression of the selected 33 markers’ transcripts in 3 non-overlapping fields of a quadriceps section from 2-month-old and 6-month-old mice (n=1). The specificity was reported as % of cells that had a marker for one cell type and lacked the markers of all other cell types. Our preliminary data indicated markers that were specific (Pdgfra: Fibro-adipogenic progenitors (FAPs) (98-100% specific), Myod1: satellite cells (SCs) (88-96%), and Pecam1: endothelial cells (endo) (92-100%)), non-specific (Esam: endo (57-77%), and Asb5: SCs (55-81%)), or specific in only one age group (Dpt: FAPs (2-month: 73%; 6-month: 89%), and Cdh5: endo (2-month: 80%; 6-month: 100%). We are currently validating each marker's specificity and sensitivity. We will identify and locate the cells that express the Col6 genes and the PE and quantify their transcripts expression levels in the various models and age groups. The findings of this project will provide additional insights into the roles of COLVI-producing cells in the pathogenesis of COL6-RDs and help direct therapeutic approaches.

ORAL SECONDARY SYPHILIS IN PEOPLE LIVING WITH HIV: A 16-YEAR EXPERIENCE IN MEXICO CITY

Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology

2021 Jul 01

Anaya-Saavedra, G;Castillejos-García, I;Maldonado-Mendoza, J;Ramírez-Amador, V;
| DOI: 10.1016/j.oooo.2021.03.041

Background The increase in syphilis rates worldwide, particularly in people living with HIV (PLWH), as well as the challenging diagnosis that secondary syphilis represents, make essential the accurate recognition of its manifestations, particularly in easy-access sites like the oral mucosa. Objective To describe the clinicopathologic spectrum of oral secondary syphilis (OSS) in PLWH. Methods A cross-sectional and descriptive study that included PLWH with OSS from 3 HIV referral centers in Mexico City (2004-2020). Demographic and clinical data were obtained. A comprehensive oral examination was done. OSS was diagnosed following established criteria. Histopathologic/cytological procedures were performed to rule out specific oral lesions. In all patients, Venereal Disease Research Laboratory tests were assessed and, if possible, a confirmatory fluorescent treponemal antibody test or biopsy was performed. Statistical analysis was performed using SPSS v25. Results Forty-seven PLWH with OSS (97.8% male, median age: 32 years, 63.8% with acquired immunodeficiency syndrome) were included. Thirty-five were receiving combination antiretroviral therapy (74.5%; median of 1146 [Q1-Q3: 337.5-1971] days) with a median CD4+ count of 385 (Q1-Q3: 223-664) cells/mm3 and a Log10 HIV viral load of 4.1 (Q1-Q3: 3.7-5.3) copies/mL. Forty had a complete clinical-serological diagnosis (85.1%; 17 had histopathologic confirmation) and 7 had a clinical-histopathologic diagnosis. Twenty-nine individuals presented 1 lesion (61.7%), and mucous patch was the most common type mainly on oropharyngeal mucosa, followed by ulcers and macular lesions. Ten patients presented maculopapular dermatosis (21.3%). Conclusions In PLWH, oral lesions, particularly mucous patch and/or ulcers on the oral and oropharyngeal mucosa, must alert specialists to consider a diagnosis of syphilis and perform a comprehensive panel of confirmatory tests.

Association of vaping with decreased vascular endothelial growth factor expression and decreased microvessel density in cutaneous wound healing tissue in rats

Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society

2021 Jun 15

Jaleel, Z;Blasberg, E;Troiano, C;Montanaro, P;Mazzilli, S;Gertje, HP;Crossland, NA;Platt, M;Spiegel, J;
PMID: 34129265 | DOI: 10.1111/wrr.12945

Vaping is suggested to be a risk factor for poor wound healing akin to smoking. However, the molecular and histologic mechanisms underlying this postulation remain unknown. Our study sought to compare molecular and histologic changes in cutaneous flap and non-flap tissue between vaping, smoking and control cohorts. Animal study of 15 male Sprague-Dawley rats was randomized to three cohorts: negative control (n = 5), e-cigarette (n = 5) and cigarette (n = 5) and exposed to their respective treatments with serum cotinine monitoring. After 30 days, random pattern flaps were raised and healed for 2 weeks after which skin punch biopsies of flap and non-flap tissues were collected for quantitative-reverse transcription-polymerase chain reaction of three selected wound healing genes (transforming growth factor β [TGF-β], vascular endothelial growth factor [VEGF], matrix metalloproteinase-1 [MMP-1]); then, immunohistochemistry for CD68 expression, α-smooth muscle actin looking at microvessel density (MVD) and in situ hybridization to localize VEGF production were undertaken. In flap tissue, vaping (mean[SEM]) (0.61[0.07]) and smoking (0.70[0.04]) were associated with decreased fold change of VEGF expression compared with controls (0.91[0.03]) (p < 0.05, p < 0.05, respectively). In non-flap tissue, only vaping was associated with decreased VEGF expression (mean[SEM]) (0.81[0.07]), compared with controls (1.17[0.10]) (p < 0.05) with expression primarily localized to basal keratinocytes and dermal capillaries. Immunohistochemistry showed decreased MVD in smoking (0.27[0.06]) and vaping (0.26[0.04]) flap tissue compared to matched controls (0.65[0.14]) (p < 0.05, p < 0.05, respectively) and decreased areas of fibrosis compared with controls on gross histology. Vaping and smoking were similarly associated with decreased VEGF expression, MVD and fibrotic changes in flap tissue. The results suggest attenuated angiogenesis via decreased VEGF expression as a mechanism for poor wound healing in vaping-exposed rats.

Comparison of In Situ Hybridization, Immunohistochemistry and Reverse Transcription-Droplet Digital Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus 2 (SARSCoV-2)-Testing in Tissue

Archives of pathology & laboratory medicine

2021 Mar 15

Roden, AC;Vrana, JA;Koepplin, JW;Hudson, AE;Norgan, AP;Jenkinson, G;Yamaoka, S;Ebihara, H;Monroe, R;Szabolcs, MJ;Majumdar, R;Moyer, AM;García, JJ;Kipp, BR;
PMID: 33720333 | DOI: 10.5858/arpa.2021-0008-SA

Small case series have evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-detection in formalin-fixed paraffin-embedded (FFPE) tissue using reverse transcription-polymerase chain reaction (RT-PCR), immunohistochemistry (IHC) and/or RNA-in situ hybridization (RNAish). To compare droplet digital PCR (ddPCR), IHC, and RNAish to detect SARS-CoV-2 in FFPE tissue in a large series of lung specimens from coronavirus disease 2019 (COVID-19) patients. ddPCR and RNAish used commercially available probes; IHC utilized clone 1A9. Twenty-six autopsies of COVID-19 patients with FFPE tissue blocks of 62 lung specimens, 22 heart specimens, 2 brain specimens, and 1 liver, and 1 umbilical cord were included. Control cases included 9 autopsy lungs from patients with other infections/inflammation and virus-infected tissue or cell lines. ddPCR had the highest sensitivity for SARS-CoV-2 (96%) when compared to IHC (31%) and RNAish (36%). All 3 tests had a specificity of 100%. Agreement between ddPCR and IHC or RNAish was fair (κ=0.23, κ=0.35, respectively). Agreement between IHC and ISH was substantial (κ=0.75). Interobserver reliability was almost perfect for IHC (κ=0.91) and fair to moderate for RNAish (κ=0.38-0.59). Lung tissues from patients who died earlier after onset of symptoms revealed higher copy numbers by ddPCR (P=.03, pearson corr = -0.65) and were more likely to be positive by RNAish (P=.02) than lungs from patients who died later. SARS-CoV-2 was identified in hyaline membranes, pneumocytes, and rarely in respiratory epithelium. ddPCR showed low copy numbers in 7 autopsy hearts from ProteoGenex Inc. All other extrapulmonary tissues were negative. ddPCR was the most sensitive and highly specific test to identify SARS-CoV-2 in lung specimens from COVID-19 patients.

Identification of Immunohistochemical Reagents for In Situ Protein Expression Analysis of Coronavirus-associated Changes in Human Tissues

Applied immunohistochemistry & molecular morphology : AIMM

2021 Jan 01

Szabolcs, M;Sauter, JL;Frosina, D;Geronimo, JA;Hernandez, E;Selbs, E;Rapkiewicz, AV;Rekhtman, N;Baine, MK;Jäger, E;Travis, WD;Jungbluth, AA;
PMID: 33086222 | DOI: 10.1097/PAI.0000000000000878

We studied the suitability of commercially available monoclonal antibodies (mAbs) for the immunohistochemical (IHC) detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) in standard archival specimens. Antibodies were screened on HEK293 cells transfected with viral nucleoprotein, S1 subunit and S2 subunit of spike protein and on untransfected cells, as well as a panel of normal tissue. Lung tissue with presence of SARS-CoV2 confirmed by in situ hybridization (ISH) was also used. A total of 7 mAbs were tested: (1) mAb 001 (Sino Biological, 40143-R001), (2) mAb 007 (Sino Biological, 40150-R007), (3) mAb 019 (Sino Biological, 40143-R019), (4) mAb 1A9 (GeneTex, GTX632604), (5) mAb ABM19C9 (Abeomics, 10-10007), (6) FIPV3-70 (Santa Cruz, SC-65653), and (7) mAb 6F10 (BioVision, A2060). Only 2 mAbs, clone 001 to the nucleoprotein and clone 1A9 to the S2 subunit spike protein displayed specific immunoreactivity. Both clones showed strong staining in the acute phase of COVID-19 pneumonia, mostly in areas of acute diffuse alveolar damage, but were not completely congruent. Viral protein was also found in kidney tubules, endothelia of multiple organs and a nasal swab of a patient with persistent SARS-CoV2 infection. The other tested reagents were either poorly reactive or demonstrated nonspecific staining in tissues and lesions not infected by SARS-CoV2. Our study demonstrates that rigid specificity testing is mandatory for the evaluation of mAbs to SARS-CoV2 and that clones 001 to nucleoprotein and 1A9 to S2 subunit spike protein are useful for the in situ detection of SARS-CoV2.

The myonuclear domain in adult skeletal muscle fibres: past, present and future

The Journal of physiology

2023 Jan 11

Bagley, JR;Denes, LT;McCarthy, JJ;Wang, ET;Murach, KA;
PMID: 36629254 | DOI: 10.1113/JP283658

Most cells in the body are mononuclear whereas skeletal muscle fibres are uniquely multinuclear. The nuclei of muscle fibres (myonuclei) are usually situated peripherally which complicates the equitable distribution of gene products. Myonuclear abundance can also change under conditions such as hypertrophy and atrophy. Specialised zones in muscle fibres have different functions and thus distinct synthetic demands from myonuclei. The complex structure and regulatory requirements of multinuclear muscle cells understandably led to the hypothesis that myonuclei govern defined 'domains' to maintain homeostasis and facilitate adaptation. The purpose of this review is to provide historical context for the myonuclear domain and evaluate its veracity with respect to mRNA and protein distribution resulting from myonuclear transcription. We synthesise insights from past and current in vitro and in vivo genetically modified models for studying the myonuclear domain under dynamic conditions. We also cover the most contemporary knowledge on mRNA and protein transport in muscle cells. Insights from emerging technologies such as single myonuclear RNA-sequencing further inform our discussion of the myonuclear domain. We broadly conclude: (1) the myonuclear domain can be flexible during muscle fibre growth and atrophy, (2) the mechanisms and role of myonuclear loss and motility deserve further consideration, (3) mRNA in muscle is actively transported via microtubules and locally restricted, but proteins may travel far from a myonucleus of origin and (4) myonuclear transcriptional specialisation extends beyond the classic neuromuscular and myotendinous populations. A deeper understanding of the myonuclear domain in muscle may promote effective therapies for ageing and disease.

98P Induction of aggressive phenotype in a heterogeneous prostate cancer model

Annals of Oncology

2022 Oct 01

Kachalova, A;Potashnikova, D;Kovaleva, A;Saidova, A;
| DOI: 10.1016/j.annonc.2022.09.099

Background Prostate cancer (PCa) is one of the main causes of death in men all over the world. To date, the emerging issue is the search for new diagnostic and prognostic biomarkers to distinguish patients with different risk types. Recent studies of PCa biomarkers have drawn attention to the remarkable heterogeneity of this tumor. Tumor heterogeneity (TH) is the main limitation of the ability to use biomarkers’ gene panels in clinics because of different cell subclones within one tumor. Methods Here we describe the relationship between tumor cells in a model of heterogeneous prostate cancer. Our model was based on direct and indirect co-cultivation of 2 prostate cell lines with aggressive (PC3-GFP) and indolent (22Rv1) phenotypes. To evaluate the tumor aggressiveness, we described the surface phenotype of adhesion molecules, measured the expression of genes related to metastasis in prostate cancer (Ai et al., 2017; Fan et al., 2018) and performed the motility tests. Results In experiments with direct co-cultivation of PC3 (aggressive) and 22Rv1 (indolent) cancer cells, we found a decrease of CD29 (integrin beta 1) on PC3 cells within 3 days, while the expression of other surface adhesion molecules (CD54, CD38, CD24 and CD44) was not altered, the surface phenotype of 22Rv1 did not change. Next, we assessed the expression of genes related to metastasis and showed that after 3 days of direct co-cultivation the expression of FLNC, AMACR, SNCG, HPN genes increases at least 2.5 times in 22Rv1, while HPN and FASN are upregulated in PC3 cells (for all measurements p

VP.60 Every breath counts! Inspiratory muscle training in children with neuromuscular diseases: a cross-over randomised controlled trial

Neuromuscular Disorders

2022 Oct 01

Human, A;Corten, L;Lozano-Ray, E;Morow, B;
| DOI: 10.1016/j.nmd.2022.07.254

Progressive respiratory muscle weakness and ineffective cough contributes to morbidity and mortality in children with neuromuscular diseases (NMD). Inspiratory muscle training (IMT) aims to preserve or improve respiratory muscle strength and reduce respiratory morbidity. This study aimed to determine the safety and efficacy of IMT in children with NMD. A randomised cross-over study compared three-month intervention (IMT) with control periods. During the intervention, children with NMD (5-18 years) from two provinces in South Africa performed 30 breaths (at 30% of inspiratory muscle strength (Pimax)) with an electronic threshold device, twice daily. During the control period participants did not perform any IMT. Twenty-three participants (median (IQR) age of 12.33 (10.03-14.17) years), mostly male (n=20) and non-ambulant (n=14) were included. No adverse events related to IMT were reported. There was no evidence of a difference in median patient hospitalisation and respiratory tract infection rates between control and intervention periods (p=0.60; p=0.21). During IMT, Pimax and peak cough flow improved with a mean (SD) of 14.57 (±15.67) cmH2O and 32.27 (±36.60) L/min, compared to a change of 3.04(±11.93)cmH2O (p=0.01) and -16.59 (±48.29) L/min (p=0.0005) during the control period. There was no evidence of change in spirometry, functional ability and total health-related quality of life scores following intervention. Patient satisfaction with IMT was high (median 8/10 (IQR 5-10)) and adherence was good. A three-month IMT programme in children with NMD is well tolerated, appears to be safe and is associated with a significant improvement in respiratory muscle strength and cough efficacy.

In vitro high-content tissue models to address precision medicine challenges

Molecular aspects of medicine

2022 Aug 17

Afewerki, S;Stocco, TD;Rosa da Silva, AD;Aguiar Furtado, AS;Fernandes de Sousa, G;Ruiz-Esparza, GU;Webster, TJ;Marciano, FR;Strømme, M;Zhang, YS;Lobo, AO;
PMID: 35987701 | DOI: 10.1016/j.mam.2022.101108

The field of precision medicine allows for tailor-made treatments specific to a patient and thereby improve the efficiency and accuracy of disease prevention, diagnosis, and treatment and at the same time would reduce the cost, redundant treatment, and side effects of current treatments. Here, the combination of organ-on-a-chip and bioprinting into engineering high-content in vitro tissue models is envisioned to address some precision medicine challenges. This strategy could be employed to tackle the current coronavirus disease 2019 (COVID-19), which has made a significant impact and paradigm shift in our society. Nevertheless, despite that vaccines against COVID-19 have been successfully developed and vaccination programs are already being deployed worldwide, it will likely require some time before it is available to everyone. Furthermore, there are still some uncertainties and lack of a full understanding of the virus as demonstrated in the high number new mutations arising worldwide and reinfections of already vaccinated individuals. To this end, efficient diagnostic tools and treatments are still urgently needed. In this context, the convergence of bioprinting and organ-on-a-chip technologies, either used alone or in combination, could possibly function as a prominent tool in addressing the current pandemic. This could enable facile advances of important tools, diagnostics, and better physiologically representative in vitro models specific to individuals allowing for faster and more accurate screening of therapeutics evaluating their efficacy and toxicity. This review will cover such technological advances and highlight what is needed for the field to mature for tackling the various needs for current and future pandemics as well as their relevancy towards precision medicine.

The contribution of brain banks to knowledge discovery in amyotrophic lateral sclerosis: A systematic review

Neuropathology and applied neurobiology

2022 Aug 03

Mazumder, S;Kiernan, MC;Halliday, GM;Timmins, HC;Mahoney, CJ;
PMID: 35921237 | DOI: 10.1111/nan.12845

Over the past decade, considerable efforts have been made to accelerate pathophysiological understanding of fatal neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) with brain banks at the forefront. In addition to exploratory disease mechanisms, brain banks have aided our understanding with regard to clinical diagnosis, genetics and cell biology. Across neurodegenerative disorders, the impact of brain tissue in ALS research has yet to be quantified. This review aims to outline (i) how postmortem tissues from brain banks have influenced our understanding of ALS over the last 15 years, (ii) correlate the location of dedicated brain banks with the geographical prevalence of ALS, (iii) identify the frequency of features reported from postmortem studies and (iv) propose common reporting standards for materials obtained from dedicated brain banks. A systematic review was conducted using PubMed and Web of Science databases using key words. From a total of 1439 articles, 73 articles were included in the final review, following PRISMA guidelines. Following a thematic analysis, articles were categorised into five themes; clinico-pathological (13), genetic (20), transactive response DNA binding protein 43 (TDP-43) pathology (12), non-TDP-43 neuronal pathology (nine) and extraneuronal pathology (19). Research primarily focused on the genetics of ALS, followed by protein pathology. About 63% of the brain banks were in the United States of America and United Kingdom. The location of brain banks overall aligned with the incidence of ALS worldwide with 88% of brain banks situated in Europe and North America. An overwhelming lack of consistency in reporting and replicability was observed, strengthening the need for a standardised reporting system. Overall, postmortem material from brain banks generated substantial new knowledge in areas of genetics and proteomics and supports their ongoing role as an important research tool.

Effects of Daily Discrimination on Pain, Mood, and Sleep in People Living with HIV

The Journal of Pain

2022 May 01

Hobson, J;Gilstrap, S;Ho, M;Fehrmann, N;Gathright, J;White, D;Thomas, J;Goodin, B;Cody, S;
| DOI: 10.1016/j.jpain.2022.03.140

Emerging literature suggests that experiences of discrimination negatively influence health and well-being. It is unfortunately common for people living with HIV (PLWH) to be stigmatized and discriminated against because of their HIV status and other marginalized identities (e.g., ethnicity/race, sexual identity and orientation). To date, little research has specifically examined discrimination in PWLH and its associations with pain and other pain-relevant factors such as mood and sleep. The purpose of this ongoing study was to preliminarily analyze associations among daily experiences of discrimination, pain severity and interference, depressive symptoms, and sleep in PLWH. Participants included 24 PLWH recruited from a local HIV treatment center. Participants completed The Everyday Discrimination Scale (TEDS) followed by the Brief Pain Inventory - Short Form (BPI-SF), the Insomnia Severity Index (ISI), and the Center for Epidemiologic Studies - Depression Scale (CES-D). Initial findings tentatively suggest that more frequent daily experiences of discrimination may be significantly associated with greater pain interference on the BPI-SF (p = .030) and greater severity of insomnia symptoms on the ISI (p = .059). However, it appears that daily experiences of discrimination may not be meaningfully associated with pain severity on the BPI-SF (p = .401) or depressive symptoms on the CES-D (p = .235). Our findings highlight the potentially deleterious effects of daily discrimination experiences on pain and sleep in in PLWH. As this ongoing study recruits a larger sample of PLWH, data will need to be reanalyzed to better determine the durability of these preliminary findings. However, there is potential that findings from this study may assist in elucidating causal pathways linking discrimination to pain and pain relevant health behaviors like sleep in PLWH. Grant support from The Impact of Insomnia on Pain, Physical Function, and Inflammation in HIV (3R01HL147603-03S1).

Evaluation of the Suitability of RNAscope as a Technique to Measure Gene Expression in Clinical Diagnostics: A Systematic Review

Molecular diagnosis & therapy

2022 Jan 01

Atout, S;Shurrab, S;Loveridge, C;
PMID: 34957535 | DOI: 10.1007/s40291-021-00570-2

To evaluate the application of RNAscope in the clinical diagnostic field compared to the current 'gold standard' methods employed for testing gene expression levels, including immunohistochemistry (IHC), quantitative real time PCR (qPCR), and quantitative reverse transcriptase PCR (qRT-PCR), and to detect genes, including DNA in situ hybridisation (DNA ISH).This systematic review searched CINAHL, Medline, Embase and Web of Science databases for studies that were conducted after 2012 and that compared RNAscope with one or more of the 'gold standard' techniques in human samples. QUADAS-2 test was used for the evaluation of the articles' risk of bias. The results were reviewed narratively and analysed qualitatively.A total of 27 articles (all retrospective studies) were obtained and reviewed. The 27 articles showed a range of low to middle risk of bias scores, as assessed by QUADAS-2 test. 26 articles studied RNAscope within cancer samples. RNAscope was compared to different techniques throughout the included studies (IHC, qPCR, qRT-PCR and DNA ISH). The results confirmed that RNAscope is a highly sensitive and specific method that has a high concordance rate (CR) with qPCR, qRT-PCR, and DNA ISH (81.8-100%). However, the CR with IHC was lower than expected (58.7-95.3%), which is mostly due to the different products that each technique measures (RNA vs. protein).This is the first systematic review to be conducted on the use of RNAscope in the clinical diagnostic field. RNAscope was found to be a reliable and robust method that could complement gold standard techniques currently used in clinical diagnostics to measure gene expression levels or for gene detection. However, there were not enough data to suggest that RNAscope could stand alone in the clinical diagnostic setting, indicating further prospective studies to validate diagnostic accuracy values, in keeping with relevant regulations, followed by cost evaluation are required.

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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
EnEm	Probe targets exons n and m
En-Em	Probe 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

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