Citations

Abstract Background Protein biomarkers are routinely measured for disease diagnosis and prognosis in clinical laboratories. Since most assays focus on protein quantity, information about proteoforms is often not acquired. Proteoforms of a protein represent the complex integration of genetic polymorphism, alternative splicing of RNA transcripts, and post-translational modifications (PTMs) on the amino-acid backbone. A detailed analysis of the post-translationally modified proteoforms (PTMPs), which are influenced by pathophysiological conditions, may lead to more precise diagnosis and prognosis. Content This article first discusses the methodologies used to accurately detect and characterize PTMPs, i.e., immunoassays, electrophoresis, chromatography, and intact and proteolysis-aided mass spectrometry techniques. Then it reviews specific examples of PTMP biomarkers that have been successfully translated from biomarker discovery to clinical use. The examples include β2–transferrin for cerebrospinal fluid leak diagnosis, phosphorylated tau proteoforms for Alzheimer disease diagnosis, and fucosylated alpha-fetoprotein for hepatocellular carcinoma prognosis. In addition, the article provides prospective views of novel analytical technologies and promising new PTMP biomarkers entering clinical practice. Summary In summary, PTMs are controlled by biochemical processes to modulate the functions of proteins by expanding their chemical diversity. PTM alterations in proteins can be indicators for pathophysiological conditions. Advances in analytical technologies are deepening our understanding of PTMPs and paving the way for their translation to clinical use. As research continues to discover the clinical meaning of PTMP biomarkers, they are poised to become valuable additions to the clinical testing menu for precision medicine.

PURPOSE Testing for germline BRCA1 and/or BRCA2 mutations (gBRCAm) is recommended for patients with human epidermal growth factor receptor 2–negative (HER2–) breast cancer (BC) to guide treatment selection with poly (ADP-ribose) polymerase inhibitors (PARPis). However, real-world data on germline BRCA1 and/or BRCA2 (gBRCA) testing and PARPi treatment patterns in metastatic BC (mBC) are limited. METHODS Deidentified patient data from adults diagnosed with HER2– mBC between 2014 and 2022 were captured from electronic health records in the US Flatiron Health database. gBRCA testing patterns and prevalence were examined by tumor subtype (hormone receptor–positive [HR+]/triple-negative) and disease stage at diagnosis. Demographic and clinical characteristics were described by receipt of gBRCA testing and PARPi. PARPi treatment patterns were assessed, and real-word overall survival (OS) was estimated in patients with gBRCAm diagnosed with mBC after January 1, 2018. RESULTS Of the 15,006 total patients, 4,654 (31.0%) received a gBRCA test. gBRCA testing rates mostly increased from 2014 to 2022 and were lower in patients with HR+ than triple-negative tumors. Of the patients who underwent gBRCA testing, 337 (7.2%) had gBRCAm. From 2018 to 2022, PARPi was initiated in 94 (45.6%) of 206 patients with gBRCAm. With a median follow-up of 22.8 months across patients with available first-line treatment start dates, real-world OS was numerically longer among 94 patients with gBRCAm who received PARPi (32.3 months [95% CI, 22.7 to 47.4]) than among 99 patients who did not (21.9 months [95% CI, 18.4 to not reached]). CONCLUSION Although gBRCA testing increased over time, testing and PARPi utilization rates remained suboptimal in potentially eligible patients with HER2– mBC. Exploratory analysis showed numerically longer OS in patients who received PARPi. Wider and timelier gBRCA testing is warranted to inform potentially optimal treatment decisions.

Abstract Nephrocalcinosis provides a nidus for stone formation and is strongly linked to renal injury and chronic kidney disease. Although the crucial role of macrophages in the formation and progression of calcium oxalate (CaOx) crystals has long been widely recognized, finding effective immunotherapies for nephrocalcinosis remains a challenge. In this study, we described an innovative macrophage‐based method that delivers interleukin‐10 (IL‐10) into the kidney, reduces the deposition of CaOx crystals, and alleviates renal injury in a mouse model of glyoxylate‐induced CaOx. Compared with recombinant IL‐10 direct injection, the macrophage‐based method has the advantages of biocompatibility and sustaining action. We found that the transplantation of engineered macrophages via the tail vein significantly reduced the volume of crystals in the kidney, thereby alleviating the kidney injury caused by crystal. In mechanistic studies, IL‐10‐secreting macrophages inhibited crystal formation and promoted crystal clearance by promoting macrophage M2 polarization, exerting a protective effect on renal tissue. Our data suggest that macrophage‐based delivery of IL‐10 to the kidney can be a potential treatment method for nephrocalcinosis.

e14555 Background: Natural killer (NK) cells are innate lymphocytes that engage in direct cytotoxic responses against malignant cells and promote pro-inflammatory tumor microenvironments. While studies have predominantly focused on conventional NK cell subsets, recent findings uncovered adaptive and tissue-resident (TR) subsets with unique functional properties. The influence of distinct NK cell subsets on tumor immunobiology and clinical outcomes remains unknown. Methods: Single-cell RNA-sequencing (scRNA-seq) of primary, therapy-naïve tumors from 276 patients across 14 cancer types, as well as 39 patients treated with immune checkpoint blockade (ICB), was accessed through publicly available datasets. We employed systematic computational analyses to phenotype and examine intra-tumoral NK cells. Gene signatures for NK cell subsets were applied to bulk RNA-sequencing from 212,105 tumor samples to delineate their associations with clinical outcomes using the Caris CODEai database. Results: Six main subsets of NK cells were identified in solid tumors, including conventional CD56 dim and CD56 bright NK cells, alongside adaptive, TR adaptive, TR CD56 bright , and TR CD56 bright /adaptive subsets. Across cancer, TR adaptive NK cells emerged as the most prognostic subset, with high infiltration conferring significantly longer overall survival (HR[95% CI] = 0.68[0.66-0.69], p < 0.001) than conventional CD56 dim and CD56 bright subsets. This was also observed in cohorts of head and neck, non-small cell lung, and esophageal cancers, particularly those treated with ICB. Notably, elevated TR adaptive NK cell infiltration was more prognostic than high tumor mutational burden in these settings. This was most apparent in ICB-treated head and neck cancers (HR = 0.48[0.41-0.57], p < 0.001 vs HR = 0.90[0.76-1.04], p = 0.16). Additionally, TR adaptive NK cells were strongly correlated to the infiltration of CD8 + T cells and B cells in tumors. Underlying these observations, our scRNA-seq analyses demonstrated that TR adaptive NK cells exhibit the highest immunomodulatory activity of all subsets, expressing high levels of pro-inflammatory cytokines ( CCL3 , CXCL13 , and IFNG ) and low levels of immunosuppressive cytokines ( TGFB1 ). Mechanistically, this activity was linked to the upregulation of transcription factors associated with NK cell activation, function, and persistence and downregulation of genes related to stress response and exhaustion. Interestingly, scRNA-seq from paired pre- and post-ICB-treated tumors revealed a unique expansion of cytotoxic GZMB + TR adaptive NK cells after treatment. Conclusions: TR adaptive NK cells represent a novel subset of NK cells that may drive anti-tumor immune responses, particularly in the context of ICB treatment. Features of this unique population may be harnessed to design more effective NK cell-based therapies against solid tumors.

5069 Background: Ra-223 improves the overall survival in patients with mCRPC to the bone. We assessed the safety of standard-of-care Ra-223 in combination with peposertib, a DNA-dependent protein kinase inhibitor, with or without avelumab, an anti-PD-L1 antibody. Methods: Patients with mCRPC and two or more skeletal metastases identified by bone scintigraphy with or without lymph node metastases up to 3 cm in size, but no visceral metastases, were eligible. Progression after progression after at least one androgen receptor pathway inhibitor or taxane was required. Phase 1 consisted of a two-step sequential safety lead-in using a 3+3 design. Step 1 combined 6 standard cycles of Ra-223 (55 kBq/kg), with increasing doses of peposertib: 50, 100, and 200 mg PO bid on days 3-26 of each cycle. Step 2 combined Ra-223 with the maximum tolerated dose of peposertib and added standard avelumab 800 mg IV every 14 days, starting at cycle 2 of Ra-223. Results: A total of 9 patients participated in Step 1, where the maximum tolerated peposertib dose of 200 mg PO bid with Ra-223 was deemed tolerable. A total of 6 patients participated in Step 2 and the combination of Ra-223, peposertib at 200 mg PO bid, and standard avelumab was deemed tolerable. Of the 15 patients in Phase 1, none experienced grade 4 or higher treatment-related toxicities, while 7 experienced grade 3 toxicities, including neutropenia (1), anemia (1), cardiac chest pain (1), fall (1), maculopapular rash (2), and lymphopenia (2). The median (Q1, Q3) PSA velocity from the beginning to the end of treatment was lower for Step 2 versus Step 1: 2.1 (-0.1, 4.6) versus 23.5 (18.6, 77.1) ng/mL/month (p = 0.0067). OS and PFS were calculated with the limitation that the Phase 1 was non-randomized. Median OS was not reached for Step 2, as only 1 of 6 patients had died, versus 15.2 months for Step 1, where 8 out of 9 patients had died (p = 0.0537). The patient who died in Step 2 discontinued therapy prematurely after 3 cycles due to progression and survived 15.2 months (the 5 alive completed all 6 cycles). The median radiographic PFS was 7 months for Step 2 versus 12.7 months for Step 1 (p = 0.8910). Conclusions: The combination of Ra-223 and peposertib, with or without avelumab was well tolerated. The triplet combination showed the most promising results at this early evaluation. We continue to accrue in the randomized Phase II portion of the trial. Clinical trial information: NCT04071236 .

Abstract Chronic overlapping pain conditions (COPCs) affect a wide population and incur a substantial disease burden including comorbid mental disorders. Although these comorbidities have been extensively documented, the longitudinal trajectories of their onset, particularly for those with three or more conditions, have been rarely studied. We conducted retrospective cohort studies to identify statistically significant COPCs and mental health trajectories in the All of Us Research Program (AoU v8, 338,170 persons) and the Mayo Data Warehouse (3,957,444 individuals). For each trajectory, cases were matched with controls by demographic factors. Logistic regression was then applied to assess the increased likelihood of the final condition given the prior conditions in that sequence. The significant trajectories were visualized as a “pain forest.” More than 88% of trajectories identified from AoU (Male: 78, Female: 361) were reproducible in the Mayo Data Warehouse data (Male: 361, Female: 1286), with female trajectories encompassing more than 96% of the male trajectories. The findings indicate that chronic low back pain generally occurs earlier than other conditions, while fibromyalgia tends to follow other COPCs. Endometriosis seems to be associated with an increased prevalence of COPCs in women. In addition, longer trajectories are associated with a greater risk of developing additional COPC or mental condition. The results offer new insights into the progression of COPCs and associated mental conditions, which may inform healthcare providers and patients in managing and preventing exacerbation of these conditions.

Objective Raynaud phenomenon (RP) is often the initial clinical manifestation of systemic sclerosis (SSc), but some patients develop other manifestations first. To help elucidate the diversity of SSc presentation in its early stages, we describe the initial clinical manifestations and antinuclear antibody (ANA) profiles of patients in two early SSc cohorts. Methods All patient data in the Genetics vs Environment in Scleroderma Outcomes Study (GENISOS) and Collaborative National Quality and Efficacy Registry (CONQUER) cohorts were reviewed. Both studies enrolled patients within five years of the first non‐RP symptom. Results In GENISOS and CONQUER, respectively, 194 (44.2%) of 439 and 292 (31.1%) of 938 patients had a non‐RP initial symptom, most commonly puffy fingers/hands. Black patients had a non‐RP symptom before RP more commonly than patients in other race and ethnicity categories. Non‐RP first patients were more likely than RP first patients to have diffuse cutaneous involvement and joint contractures at enrollment and had a higher prevalence of RNA polymerase III antibody positivity. Conclusion In two large US cohorts, >30% of patients began to manifest SSc with puffy fingers/hands or other symptoms, without the “warning sign” of RP as their initial symptom. These patients presented with more severe skin and musculoskeletal disease on average, highlighting the importance of early recognition. The most common autoantibody associated with this presentation was RNA polymerase III. These results should be considered in efforts to recognize SSc in its earliest stages. Puffy fingers/hands, even in the absence of RP, should prompt consideration of early SSc and testing for ANA and SSc‐associated autoantibodies, including RNA polymerase III.

ABSTRACTBackground/AimsMany patients with digestive symptoms describe underlying urinary or gynecologic symptoms, which may increase visceral sensitivity in the abdominopelvic region and amplify distress around digestive symptoms. The aim of this study was to describe the prevalence of urinary and gynecologic symptoms in patients with disorders of gut–brain interaction (DGBI).MethodsConsecutive adult patients with a female reproductive tract who were referred for GI behavioral medicine evaluation for DGBI at a tertiary care center between 2022 and 2023 were prospectively evaluated for symptoms associated with urinary and gynecologic dysfunction. Descriptive statistics were conducted to assess the prevalence of these symptoms within this population by anatomic region affected (esophagus, stomach, and bowel).ResultsA total of 432 patients were included in our cohort with a mean (SD) age of 40.0 years [Q1;Q3 29.0–52.0], with a predominantly White population (86.1%). Dysmenorrhea (61.0%) and menorrhagia (58.6%) were commonly reported among women with digestive symptoms. Urinary symptoms were less common, with 18.7% reporting pain with urination, 33.0% reporting difficulty voiding urine, and 26.1% reporting a history of frequent UTIs. 23% of women experienced ≥ 4 urinary/gynecologic symptoms. There were no significant differences in the type of urogynecologic symptoms reported based on the affected area of the GI tract.ConclusionUrogynecologic symptoms are common among patients with DGBIs affecting the entirety of the GI tract. We presume the presence of these comorbid symptoms is likely to impact symptom severity, quality of life, and could affect treatment response. Future studies are necessary to understand the mechanisms behind these shared conditions as well as develop effective treatments that address their overlap.

Objectives Generative artificial intelligence (GAI) tools can enhance the quality and efficiency of medical research, but their improper use may result in plagiarism, academic fraud and unreliable findings. Transparent reporting of GAI use is essential, yet existing guidelines from journals and institutions are inconsistent, with no standardised principles. Design and setting International online Delphi study. Participants International experts in medicine and artificial intelligence. Main outcome measures The primary outcome measure is the consensus level of the Delphi expert panel on the items of inclusion criteria for GAMER (Rreporting guideline for the use of Generative Artificial intelligence tools in MEdical Research). Results The development process included a scoping review, two Delphi rounds and virtual meetings. 51 experts from 26 countries participated in the process (44 in the Delphi survey). The final checklist comprises nine reporting items: general declaration, GAI tool specifications, prompting techniques, tool’s role in the study, declaration of new GAI model(s) developed, artificial intelligence-assisted sections in the manuscript, content verification, data privacy and impact on conclusions. Conclusion GAMER provides universal and standardised guideline for GAI use in medical research, ensuring transparency, integrity and quality.

Abstract Background and Aims Tyrosine kinase 2 is a downstream intracellular mediator of interleukin-23 signaling, which has a key role in the pathogenesis of inflammatory bowel disease. Deucravacitinib is a novel, oral, selective, allosteric tyrosine kinase 2 inhibitor currently approved for the treatment of adults with moderate to severe plaque psoriasis. Methods Here we describe 3 randomized, double-blind, placebo-controlled phase 2 studies of deucravacitinib in patients with moderately to severely active Crohn’s disease (LATTICE-CD [NCT03599622]) or ulcerative colitis (LATTICE-UC [NCT03934216] and IM011-127 [NCT04613518]). Patients were randomized to receive placebo or twice-daily deucravacitinib 3 or 6 mg (LATTICE-CD), 6 mg (LATTICE-UC), or 12 mg (IM011-127) for 12 weeks. Coprimary endpoints for LATTICE-CD were clinical remission and endoscopic response at week 12. The primary endpoint was clinical remission (per modified Mayo score) at week 12 for LATTICE-UC and clinical response (per modified Mayo score) at week 12 for IM011-127. Results A total of 239 (LATTICE-CD), 131 (LATTICE-UC), and 38 (IM011-127) patients were randomized. The primary endpoints were not met for all 3 studies, which resulted in early study termination for LATTICE-CD and IM011-127. High efficacy rates were observed in placebo groups throughout the studies. In all studies, the safety profile of deucravacitinib was consistent with the known safety profile observed in patients with psoriasis, and no new safety signals were observed. Conclusions Deucravacitinib at multiple doses did not demonstrate significant clinical benefit vs placebo in moderately to severely active Crohn’s disease or ulcerative colitis. Deucravacitinib was safe and well tolerated.