Exploring metalloproteins found in the secretion of venomous species: Biological role and therapeutical applications.

Several species during evolution suffered random mutations in response to various environmental factors, which resulted in the formation of venom in phylogenetically distant species. The composition of the venom of most species is poorly known. Snake venom is well characterized while most species have poorly known composition. In contrast, snake venoms are well characterized which proteins and peptides are the main active and most abundant constituents. 42 protein families have been identified, including metalloproteins known as metalloproteinases. These macromolecules are enzymes with zinc in their active site derived from the disintegrin A and metalloproteinase (ADAM) cellular family and are categorized into three classes (PI, PII and PIII) according to their domain organization. The snake venom metalloproteinases (SVMP) are cytotoxic, neurotoxic, myotoxic and/or hematotoxic with a crucial role in the defense and restraint of prey. In this scenario envenoming represents a danger to human health and has been considered a neglected disease worldwide, particularly in tropical and subtropical countries. Nevertheless, recently advances in "omics" technologies have demonstrated interesting biological activities of SVMPs such as antimicrobial, anticancer, against cardiovascular diseases and nervous system disorders. Metalloproteins have the therapeutic potential to be converted into drugs as other components of the venom have undergone this process (e.g., captopril, tirefiban and eptifibatide). So, this chapter is focused on the metalloproteins found in the secretions of venomous species, highlight some aspects such as structure, biological activity, pharmacological therapeutic potential and on.

CCAR1 promotes DNA repair via alternative splicing.

DNA repair is directly performed by hundreds of core factors and indirectly regulated by thousands of others. We massively expanded a CRISPR inhibition and Cas9-editing screening system to discover factors indirectly modulating homology-directed repair (HDR) in the context of ∼18,000 individual gene knockdowns. We focused on CCAR1, a poorly understood gene that we found the depletion of reduced both HDR and interstrand crosslink repair, phenocopying the loss of the Fanconi anemia pathway. CCAR1 loss abrogated FANCA protein without substantial reduction in the level of its mRNA or that of other FA genes. We instead found that CCAR1 prevents inclusion of a poison exon in FANCA. Transcriptomic analysis revealed that the CCAR1 splicing modulatory activity is not limited to FANCA, and it instead regulates widespread changes in alternative splicing that would damage coding sequences in mouse and human cells. CCAR1 therefore has an unanticipated function as a splicing fidelity factor.

Significant increase in the number of occupational exposures reported to the Dutch Poisons Information Centre (2016-2022): the importance of poison centre data in health surveillance.

INTRODUCTION: Exposure to hazardous substances in the workplace can result in injuries and fatalities. This study aimed to investigate the characteristics and trend of occupational exposures reported to the Dutch Poisons Information Centre and to investigate whether the COVID-19 pandemic had an impact on the trend. METHODS: A retrospective analysis of all acute occupational exposures reported to the Dutch Poisons Information Centre between 1 January 2016 and 31 December 2022 was performed. Data on patient and exposure characteristics, symptoms and treatment recommendations were analyzed. RESULTS: Between 2016 and 2022, the Dutch Poisons Information Centre received 5,508 calls regarding acute occupational exposures. The annual number of calls on acute occupational exposures almost doubled over the years studied (from 475 in 2016 to 936 in 2022). During and after the COVID-19 pandemic (March 2020-December 2022), the number of calls stabilized, but the upward trend was not significantly affected. There were an estimated 0.20 calls per 1,000 human exposure calls per month (95 per cent confidence interval: -0.14; 0.53). Victims were often exposed through multiple routes, with inhalation being the most common route (44 per cent), followed by ocular (32 per cent) and dermal contact (30 per cent). Acids (1,138 exposures) and alkalis (912 exposures) were often involved. The Dutch Poisons Information Centre had information on 6,334 patients, although the total number of exposed patients was not known as some victims did not seek medical assistance, or were treated by healthcare professionals who did not consult our Centre. At the time of contact, 13 per cent (n = 795) of the patients reported no symptoms, 76 per cent (n = 4,805) reported mild to moderate symptoms and 3 per cent (n = 183) reported potentially severe symptoms. Information on symptoms was missing for 9 per cent (n = 551) of the patients. Hospital observation and treatment were recommended for 5 per cent (n = 325) of the patients. DISCUSSION: This study highlights the necessity for poisoning prevention strategies to reduce the number of work-related incidents involving hazardous substances. CONCLUSION: The continuing increase in the number of workplace incidents involving hazardous substances is of concern. A comprehensive and multidisciplinary approach should be taken to gain a full understanding of occupational exposure to hazardous substances and to identify risk factors.

Imaging Assays to Detect DNA Damage in Trypanosome Parasites Using γH2A.

Diseases caused by trypanosomatid parasites remain a significant unmet medical need for millions of people globally. Trypanosomatid parasites such as Trypanosoma cruzi and subspecies of Trypanosoma brucei cause Chagas disease and human African trypanosomiasis (HAT), respectively. Although efforts to find novel treatments have been successful for HAT, Chagas disease is still treated with decades-old therapies that suffer from long treatment durations and severe safety concerns. We recently described the identification and characterization of the cyanotriazole compound class that kills trypanosomes, in vitro and in vivo, by selective inhibition of the trypanosome nuclear topoisomerase II enzyme. To evaluate whether inhibition of the topoisomerase II enzyme led to parasite death due to lethal double-strand DNA breaks, we developed assays for detecting DNA damage in both intracellular amastigotes of T. cruzi and bloodstream-form T. brucei by using the canonical DNA damage marker γH2A. Herein, this article describes the protocols for detecting DNA damage using an immunofluorescence assessment of γH2A by microscopy in trypanosome parasites. Key features • Immunofluorescence-based assay to detect the γH2A response in T. brucei and T. cruzi parasites. • Robust DNA damage pathway-based cellular assays to evaluate topoisomerase II poisons' ability to cause DNA damage. • A 384-well plate-based T. cruzi protocol allows high-resolution and high-throughput evaluation of compounds that cause DNA damage by measuring γH2A in intracellular parasites. • This assay could be modifiable for evaluation of DNA damage responses in various intracellular and extracellular eukaryotic pathogens.

Rapid availability of ethylene glycol test results with enzymatic assay.

BACKGROUND: Ethylene glycol poisoning causes metabolic acidosis, organ injury, and death. Ethylene glycol testing is unavailable in many areas. Our laboratory uses an automated glycerol dehydrogenase enzymatic assay to screen for ethylene glycol. We sought to determine how often ethylene glycol results were available within 12 h of the first dose of fomepizole. METHODS: Records from a single poison center were reviewed from December 2016 to December 2019. Cases were identified by searching for cases that received fomepizole. Outcomes included whether results were available within 12 h, and the turnaround time from time of laboratory order to result. RESULTS: Of the 125 cases of suspected toxic alcohol poisoning identified, 73 had screening for ethylene glycol by enzymatic assay. Results were available within 12 h of the initial fomepizole dose in 58 (79%) cases with a median turnaround time of 391 min. DISCUSSION: We have demonstrated clinically acceptable turnaround times using an automated screening ethylene glycol assay. The major limitations include lack of approval for this test at this time, the use of voluntarily reported poison center data, and lack of assessment of patient outcomes. CONCLUSION: Enzymatic screening for ethylene glycol yielded results within 12 h in 79% of cases.

How does pharmacological and toxicological knowledge evolve? A case study on hydrogen cyanide in German pharmacology and toxicology textbooks from 1878 to 2020.

Little is known about how pharmacological and toxicological knowledge evolves. The aim of this study was to investigate the changes in the presentation of the poison hydrogen cyanide in sixteen German-language pharmacology and toxicology textbooks from 1878 to 2020. The categories of structure, molecular mechanism of action, occurrence, effects, resorption, areas of application, lethal dose, acute symptoms of intoxication, treatment of hydrogen cyanide poisoning, and recommended therapeutic preparations were evaluated. The knowledge on the structure, lethal dosage, and occurrence of hydrogen cyanide has remained constant. In contrast, knowledge on molecular mechanism of action and recommended preparations of the poison has changed dramatically. Until 1944, the binding of hydrogen cyanide to hemoglobin was considered the mechanism of action, whereas from 1951 onwards, the interaction of hydrogen cyanide with the Fe3+ of cytochrome oxidase was described. The number of preparations containing hydrogen cyanide decreased into obsolescence until 1951. The areas of application of hydrogen cyanide also show a change, as from 1919 onwards, mainly industrial areas of application of the poison are described instead of medical ones, and from 1951 onwards, criminalistic areas of application are also mentioned. Thus, pharmacological and toxicological knowledge develops non-linearly, molecular mechanism and uses being the most dynamic areas, whereas the knowledge about hydrogen cyanide's chemical structure, lethal dose, and occurrence remained constant. Older pharmacology and toxicology textbooks were better than newer ones at discussing changes in scientific concepts. Pharmacology and toxicology textbooks also mostly failed to discuss the misuse of hydrogen cyanide (Zyklon B) during the Nazi regime, missing an important opportunity to showcase the ethical responsibility of pharmacology and toxicology. Thus, future pharmacology and toxicology textbooks should improve on discussing the development of pharmacological and toxicological concepts and the ethical responsibility of the discipline.

Recurrent erythema multiforme-like reaction secondary to recurrent poison ivy exposure.

A 14-year-old boy developed an erythema multiforme-like reaction following Toxicodendron radicans (poison ivy) allergic contact dermatitis three separate times over the course of 3 years. The severity of each erythema multiforme-like reaction corresponded to the severity of the allergic contact dermatitis which preceded it.

A 19-year longitudinal assessment of gyromitrin-containing (Gyromitra spp.) mushroom poisonings in Michigan.

Mushroom poisonings are common in the United States. Gyromitrin (acetaldehyde N-methyl-N-formylhydrazone) is a clinically significant mycotoxin primarily associated with the lorchel (i.e. the false morel) Gyromitra esculenta. Resemblance between 'true and false morels' has resulted in misidentification of Gyromitra spp. as edible and sought after Morchella spp., resulting in toxicity. Despite literature evidence outlining toxic sequalae, Gyromitra spp. mushrooms are commonly consumed and prepared for culinary purposes. Classic clinical teachings emphasize significant neurotoxicity, including seizures, associated with ingestion of gyromitrin-containing mushrooms, stemming from gyromitrin's terminal metabolite monomethylhydrazine. We performed a longitudinal descriptive review of the clinical toxicity associated with ingestion of mushroom species known or suspected to contain gyromitrin in cases reported to the Michigan Poison & Drug Information Center between January 1, 2002, to December 31, 2020. Our 19-year descriptive case series of gyromitrin-containing mushroom ingestions reported to our Center demonstrated a preponderance of gastrointestinal signs and symptoms, including hepatotoxicity. Of 118 identified cases, 108 (91.5%) of the reported ingestions involved Gyromitra esculenta. The most frequent clinical findings associated with symptomatic ingestions (n= 83) were the aforementioned gastrointestinal symptoms (n=62; 74.7%). Neurological symptoms were less frequent (n=22, 26.5%) while hepatotoxicity occurred in fewer patients (n=14; 16.9%). Of symptomatic patients, most were treated with symptomatic and supportive care (n=58; 70%). Pyridoxine was used in a total of seven patients (n=7; 8.4%) with either hepatotoxicity or neurotoxicity. Medical outcomes ranged from minor to major, with no reported deaths. Patient presentations (i.e. GI vs. neurotoxic symptoms) following ingestion of gyromitrin-containing mushrooms may be highly variable and multifactorial, owing to differences in dose ingested, geographical distribution, genetic variability of both patient and mushroom species, and species-specific differences in toxin composition. Future research warrants species-level identification of ingested gyromitrin-containing mushrooms and investigating the contribution of genetic polymorphisms to differences in clinical toxidromes.

Fatal Viscerocutaneous Brown Recluse Envenomation With Orbital Compartment Syndrome.

Loxosceles is an arachnid genus comprising several species in the United States, popularly known as brown recluse spiders. The venom is cytotoxic, complex, and has a mixture of many proteins, some of which function as proteases. Envenomation can cause necrotic skin lesions that may become extensive and take many months to heal. Even more rarely, venom may cause systemic effects, leading to widespread hemolysis, coagulopathy, and death. These symptoms typically occur rapidly within 24-48 hours following the bite. We describe a rare case of a 44-year-old male with fatal systemic loxoscelism with orbital compartment syndrome requiring emergent lateral canthotomy and cantholysis.

Use of large language models to optimize poison center charting.

INTRODUCTION: Efficient and complete medical charting is essential for patient care and research purposes. In this study, we sought to determine if Chat Generative Pre-Trained Transformer could generate cogent, suitable charts from recorded, real-world poison center calls and abstract and tabulate data. METHODS: De-identified transcripts of real-world hospital-initiated poison center consults were summarized by Chat Generative Pre-Trained Transformer 4.0. Additionally, Chat Generative Pre-Trained Transformer organized tables for data points, including vital signs, test results, therapies, and recommendations. Seven trained reviewers, including certified specialists in poison information and board-certified medical toxicologists, graded summaries using a 1 to 5 scale to determine appropriateness for entry into the medical record. Intra-rater reliability was calculated. Tabulated data was quantitatively evaluated for accuracy. Finally, reviewers selected preferred documentation: original or Chat Generative Pre-Trained Transformer organized. RESULTS: Eighty percent of summaries had a median score high enough to be deemed appropriate for entry into the medical record. In three duplicate cases, reviewers did change scores, leading to moderate intra-rater reliability (kappa = 0.6). Among all cases, 91 percent of data points were correctly abstracted into table format. DISCUSSION: By utilizing a large language model with a unified prompt, charts can be generated directly from conversations in seconds without the need for additional training. Charts generated by Chat Generative Pre-Trained Transformer were preferred over extant charts, even when they were deemed unacceptable for entry into the medical record prior to the correction of errors. However, there were several limitations to our study, including poor intra-rater-reliability and a limited number of cases examined. CONCLUSIONS: In this study, we demonstrate that large language models can generate coherent summaries of real-world poison center calls that are often acceptable for entry to the medical record as is. When errors were present, these were often fixed with the addition or deletion of a word or phrase, presenting an enormous opportunity for efficiency gains. Our future work will focus on implementing this process in a prospective fashion.

The Tanta University risk model could help identify patients with acute poisoning who would require intensive care unit level of care.

OBJECTIVE: To independently validate the negative predictive value of the Tanta University risk model for intensive care requirements in poison center telephone consultations with other physicians. METHODS: This study included 400 consecutive patients with acute poisoning. Clinical and laboratory parameters were recorded during the initial consultation with the poison center. Patients who were already ventilated or on vasopressors at the time of consultation were excluded. The Tanta University risk model score was calculated from the data according to the following equation: Tanta University risk model score = 1.966*Glasgow Coma Scale + 0.329*oxygen saturation (percent) + 0.212*diastolic blood pressure (mmHg) - 0.27*respiratory rate (breaths/minute) + 0.33*standard bicarbonate (mmol/L). Twenty-four hours later, the patients' courses were followed up by telephone. The Tanta University risk model was then compared to a composite endpoint indicating the requirement for admission to an intensive care unit (vasopressors, need for intubation, or death). RESULTS: Four hundred patients with acute poisoning were included. Thirty-seven patients had a complicated clinical course as defined by the composite endpoint. Receiver operating characteristic analysis revealed the area under the curve to be 0.87 (95 percent confidence interval 0.83-0.90). An unfavorable Tanta University risk model score was defined as less than 73.46, using a cut-off derived from a previous study of an unrelated series of patients with acute poisoning admitted to our service. Thirty-one of 37 patients with complicated courses had an unfavorable Tanta University risk model score compared to six patients with complicated courses among 306 patients with a favorable Tanta University risk model score (P < 0.0002, Fisher's exact test). Sixty-three patients had an unfavorable Tanta University risk model score but an uneventful course. The negative predictive value of the Tanta University risk model was 0.98 (95 percent confidence interval 0.96-0.99), sensitivity was 0.84, and specificity 0.83. CONCLUSIONS: In the present study of poison center telephone consultations, the Tanta University risk model was significantly related to the outcomes in patients with acute poisoning. Patients with a favorable Tanta University risk model score (greater than or equal to 73.46) were unlikely to need intensive care unit level of care.

Severe morel mushroom poisonings in France - a nationwide French poison centres study 2010-2020.

INTRODUCTION: In 2023, two fatalities attributed to the ingestion of uncooked morels (Morchella spp.) were reported in the United States; both patients developed severe gastrointestinal symptoms. Morel-induced gastrointestinal toxicity is well recognized, but no deaths had been reported until 2023, suggesting a potential shift in the severity of morel poisoning. METHODS: Using the Poisoning Severity Score, we analyzed the severity of symptomatic cases of morel ingestion recorded in the French National Database of Poisonings from 2010 to 2020. RESULTS: We found 446 cases of exposure in which morels were the sole mushroom species involved. Of these, 83.6 per cent and 53.3 per cent developed gastrointestinal and neurological symptoms, respectively. Eight patients developed shock attributed to severe gastrointestinal symptoms, resulting in two deaths. DISCUSSION: Morel ingestion can lead to severe complications. As in the United States, the deaths reported in this study were attributed to imported cultivated morels. The shift, since 2006, towards a predominance of cultivated over wild morel sales may have played a role in the reporting of severe cases of morel poisoning. CONCLUSIONS: Reports of severe morel poisoning highlight the need for cautious consumption, particularly of raw or undercooked preparations. Emerging complications signal potential changes in toxicity. Surveillance and awareness are key to reducing the risks of consuming morels.

Lessons From the Household Humidifier Disinfectant Tragedy (HHDT) With Focus on the Chemical Poisoning Surveillance System: Review and Recommendation.

BACKGROUND: Lessons learned from the Household Humidifier Disinfectant Tragedy (HHDT) in Korea, which poisoned thousands of citizens over a period of years, necessitated an examination of national poison prevention and surveillance systems. The objectives of this study are to identify essential changes needed in chemical poisoning prevention regulations and surveillance systems for effective poison control by comparing recent trends in international poison control center (PCC) operations, and to delineate the critical elements for establishing a state-of-the-art poison control surveillance system in Korea based on recent advances in PCCs with toxicovigilance. METHODS: A comprehensive review of Korea's regulatory and surveillance systems for chemical health hazards, with a focus on household products under the HHDT, was conducted. A review of toxicovigilance systems in major countries shows that creating an effective national PCC requires key elements: a centralized database of toxic substances and poisoning cases, mandatory or voluntary reporting of poisoning cases, real-time alerts, collaboration among health organizations, and targeted follow-up of poisoned individuals. RESULTS: Significant deficiencies in Korea's legislation, toxicological data management, and poisoning surveillance systems, explained the inadequate response of the Korean government to the HHDT for nearly 17 years until the end of 2011. Based on a review of PCC toxicovigilance systems in major countries, a national framework with five core components is recommended for establishing a modern comprehensive Korea PCC system with toxicovigilance capacity. The core components include establishment of a centralized database of toxic substances information and clinical poisoning cases, implementation of mandatory or permissive reporting of poisoning cases, real-time alert mechanisms, collaborative systems among health-related organizations, and clinical follow-up of poisoned sub-groups. CONCLUSION: A rationale and framework for a state-of-the-art national Korean PCC with toxicovigilance is justified and offered. This proposed system could assist neighboring countries in establishing their own sophisticated, globally integrated PCC networks.

Plant Dermatitis.

Plant dermatitis is a common pathology that plagues those who work and recreate in the North American outdoors. The most common plant family to cause dermatitis is the Toxicodendron genus, which includes the plants known by the common names of poison ivy, poison oak, and poison sumac. While mortality is usually quite low for this pathology, the incidence and prevalence of the disease leads to substantial healthcare burden and financial implications across the population. The mainstays of treatment have focused on prevention, corticosteroids, and antihistamines.

Comparative analysis of immunological changes following realgar and arsenic trioxide treatments in a murine model of myelodysplastic syndrome.

BACKGROUND: Myelodysplastic syndrome (MDS) is a prevalent hematological neoplastic disorder in clinics and its immunopathogenesis has garnered growing interest. Oral and intravenous arsenic agents have long been used to treat hematological malignancies. The main component of oral arsenic is realgar (arsenic disulfide), while arsenic trioxide is the main component of intravenous arsenic. METHODS: This study aimed to assess the effects of ATO and Realgar on the enhancement of peripheral blood, drug safety, and T cell immune status in the NUP98-HOXD13 (NHD13) mice model of MDS, specifically in the peripheral blood, spleen, and liver. RESULTS: The study findings indicate that realgar and arsenic trioxide (ATO) can improve peripheral hemogram in mice, whereas realgar promotes higher peripheral blood cell production than ATO. Furthermore, the clinical administration method and dose did not cause significant toxicity or side effects and thus can be considered safe. Coexistence and interconversion of hyperimmune function and immunosuppression in mice were also observed in this study. In addition, there were interactions between immune cells in the peripheral blood, spleen, and liver to regulate the immune balance of the body and activate immunity via T-cell activation. CONCLUSION: In summary, oral and intravenous arsenic agents are beneficial in improving peripheral hemogram and immunity in mice.

Enhancing food safety: A low-cost biosensor for Bacillus licheniformis detection in food products.

To enhance food safety, the need for swift and precise detection of B. licheniformis, a bacterium prevalent in various environments, including soil and food products, is paramount. This study presents an innovative and cost-effective bioassay designed to specifically identify the foodborne pathogen, B. licheniformis, utilizing a colorimetric signal approach. The biosensor, featuring a 3D-printed architecture, incorporates a casein-based liquid-proof gelatine film, selectively liquefying in response to the caseinolytic/proteolytic activity of external enzymes from the pathogen. As the sample liquefies, it progresses through a color layer, causing the migration of dye to an absorbent layer, resulting in a distinct positive signal. This bioassay exhibits exceptional sensitivity, detecting concentrations as low as 1 CFU/mL within a 9.3-h assay duration. Notably, this cost-efficient bioassay outperforms conventional methods in terms of efficacy and cost-effectiveness, offering a straightforward solution for promptly detecting B. licheniformis in food samples.

Carbon Monoxide Poisoning: From Occupational Health to Emergency Medicine.

Carbon monoxide poisoning remains a leading cause of accidental poisoning worldwide (both at home and at work), and it is also a cause of suicidal poisoning. Such poisoning can arise following prolonged exposure to low levels of CO or following brief exposure to high concentrations of the gas. In fact, despite exposure limits, high safety standards, and the availability of CO alarms, nearly 50,000 people in the United States visit the emergency department each year due to poisoning. Additionally, CO poisoning in the United States causes up to 500 deaths each year. Despite the widespread nature of this form of poisoning, known about for centuries and whose damage mechanisms have been recognized (or rather hypothesized about) since the 1800s, early recognition, especially of late complications, and treatment remain a medical challenge. A well-designed therapeutic diagnostic process is necessary so that indication for hyperbaric or normobaric therapy is correctly made and so that patients are followed up even after acute exposure to diagnose late complications early. Furthermore, it is necessary to consider that in the setting of emergency medicine, CO poisoning can be part of a differential diagnosis along with other more frequent conditions, making its recognition difficult. The last thirty years have been marked by a significant increase in knowledge regarding the toxicity of CO, as well as its functioning and its importance at physiological concentrations in mammalian systems. This review, taking into account the significant progress made in recent years, aims to reconsider the pathogenicity of CO, which is not trivially just poisonous to tissues. A revision of the paradigm, especially as regards treatment and sequelae, appears necessary, and new studies should focus on this new point of view.

General pattern of paediatric poisoning in Jordan during 2018-2019.

Introduction: Acute accidental poisoning in children remains a significant public health issue and a predictable cause of morbidity around the world. To take preventive measures, it is necessary to identify the pattern of this problem. Objective: To determine the extent and characteristics of paediatric poisoning, an epidemiological investigation specific to each country is required. The goal of our research was to determine the current pattern of acute poisoning in children between (0-5) years old in Jordan. Methods: This retrospective study performs a descriptive analysis of the Jordan University Hospital's National Poison Information Center (NPIC) database and describes the epidemiology of acute poisoning in children between (0-5) years old during a period of two years (2018-2019). Results: Paediatric poisoning (0-5) years old accounts for approximately 88% of poisoning cases in Jordan between 2018 and 2019.Out of 3531 paediatric poisoning cases, 44.9% of cases were in children between (2-3) years old, 63.4% of subjects were male. 40.9% of calls were from governmental hospitals. Most cases occurred at home (98.7%) and were unintentional (98.6%). Medication poisoning was the commonest among cases (71.0%). Besides, 89.4% were asymptomatic at the time of call, and Central Nervous System (CNS) symptoms being the most common (3.6%) among the symptomatic cases. Conclusions: Most cases of paediatric poisoning handled by the NPIC was due to medications. To prevent or minimize these cases, it is necessary to educate parents and other caregivers about proper medication storage and use, and in case of poisoning, urgent referral to health facilities is required.

Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.

Long-read RNA sequencing has shed light on transcriptomic complexity, but questions remain about the functionality of downstream protein products. We introduce Biosurfer, a computational approach for comparing protein isoforms, while systematically tracking the transcriptional, splicing, and translational variations that underlie differences in the sequences of the protein products. Using Biosurfer, we analyzed the differences in 32,799 pairs of GENCODE annotated protein isoforms, finding a majority (70%) of variable N-termini are due to the alternative transcription start sites, while only 9% arise from 5' UTR alternative splicing. Biosurfer's detailed tracking of nucleotide-to-residue relationships helped reveal an uncommonly tracked source of single amino acid residue changes arising from the codon splits at junctions. For 17% of internal sequence changes, such split codon patterns lead to single residue differences, termed "ragged codons". Of variable C-termini, 72% involve splice- or intron retention-induced reading frameshifts. We found an unusual pattern of reading frame changes, in which the first frameshift is closely followed by a distinct second frameshift that restores the original frame, which we term a "snapback" frameshift. We analyzed long read RNA-seq-predicted proteome of a human cell line and found similar trends as compared to our GENCODE analysis, with the exception of a higher proportion of isoforms predicted to undergo nonsense-mediated decay. Biosurfer's comprehensive characterization of long-read RNA-seq datasets should accelerate insights of the functional role of protein isoforms, providing mechanistic explanation of the origins of the proteomic diversity driven by the alternative splicing. Biosurfer is available as a Python package at https://github.com/sheynkman-lab/biosurfer.