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Simplified definition and imaging-based stratification of at-risk MASH using magnetic resonance elastography
Li, Jiahui , Wu, Hao , Glaser, Kevin J. , Ou, Fang‐Shu , Manduca, Armando , Venkatesh, Sudhakar K. , Sirlin, Claude B. , Shah, Vijay H. , Ehman, Richard L. , Wu, Hao , Sirlin, Claude B. , Loomba, Rohit , Ehman, Richard , Allen, Alina M , Manduca, A , Ou, Fang-Shu , Venkatesh, Sudhakar K , Li, Jiahui , Loomba, Rohit , Allen, Alina M. , Yin, Meng

Mayo Clinic

Hepatology Communications | August 11, 2026 | Volume: 10 | Issue: 9 | Pages: No page available

10.1097/hc9.0000000000001024 | PMID 42579768 Get It

Background: Accurate identification of patients with metabolic dysfunction–associated steatohepatitis (MASH) at risk of disease progression (at-risk MASH) is critical for guiding resmetirom and semaglutide therapy. Inconsistent definitions of at-risk MASH complicate clinical risk classification and comparisons across studies. This study aimed to standardize the definition of at-risk MASH and propose optimized MRE-based liver stiffness (LS-MRE) cutoffs to improve noninvasive risk stratification and better guide pharmacotherapy. Methods: In this prospective study, 413 patients with suspected or diagnosed MASLD from two medical centers underwent liver biopsy and MRE. Results: A simplified definition of at-risk MASH (MASH with fibrosis stage≥2) identified a broader group of patients requiring clinical attention than a stricter definition requiring NAFLD Activity Score≥4 with ≥1 point in steatosis, inflammation, and ballooning (n=122 vs. 77). LS-MRE alone showed the highest diagnostic accuracy for identifying at-risk MASH using the simplified definition (AUC 0.91 [0.87, 0.95]) and cirrhosis (AUC 0.93 [0.88, 0.99]), compared with FIB-4 and individual laboratory parameters (AST, ALT, and platelet count) ( p <0.01 for all, paired DeLong tests). Optimized LS-MRE cutoffs (2.8–6.4 kPa) captured 25 additional biopsy-proven pharmacotherapy candidates (28% of all eligible patients) compared to AASLD guidelines–recommended cutoffs (3.1–4.4 kPa), improving sensitivity (80% vs. 50%) with acceptable specificity (73% vs. 88%). Conclusions: A simplified definition of at-risk MASH enables broader identification of treatment candidates. LS-MRE demonstrates excellent diagnostic performance and improves noninvasive risk stratification when paired with optimized cutoffs. These findings support the use of MRE to guide resmetirom and semaglutide eligibility and improve access to emerging therapies.
A phosphorylation switch governs KIF11’s mechanical output during mitosis
Šemić, Amila , Reddy, Babu J.N., Muretta, Joseph M. , Vandal, Sarah E. , Thompson, Alex F. , Fonseca, Cindy L., Rosenfeld, Steven S. , Gross, Steven P. , Stumpff, Jason

Mayo Clinic

Proceedings of the National Academy of Sciences | August 11, 2026 | Volume: 123 | Issue: 33 | Pages: No page available

10.1073/pnas.2602415123 | PMID 42579498 Get It

The kinesin-5 motor protein KIF11 is crucial for mitotic spindle assembly, driving the separation of spindle poles through microtubule sliding. Src-family kinases phosphorylate KIF11 at multiple tyrosine residues within its motor domain, but the mechanistic consequences of these modifications remain unclear. Here, we dissect the role of phosphorylation at Y211 using phospho-mimetic (Y211E) and nonphosphorylatable mutants (Y211F) in biochemical, biophysical, and cellular assays. Optical trapping and Förster resonance energy transfer analyses reveal that Y211 phosphorylation slows neck-linker docking, reducing motor velocity and force generation under load. In human cells, Y211E expression impairs bipolar spindle formation and decreases spindle pole separation velocity, while Y211F shortens steady-state spindle length. Fluorescence recovery after photobleaching analyses show that Y211E accelerates motor turnover on spindle microtubules, consistent with the mutant motor’s heightened load sensitivity. Together, these findings support a model in which Src-mediated phosphorylation at Y211 acts as a rheostat to tune KIF11 mechanochemistry and spindle assembly dynamics, linking cancer-relevant kinase signaling to mitotic force generation.
Combined FAK and MEK inhibition suppresses chromosome 8 gain malignant peripheral nerve sheath tumors
Wang, Guangfeng , Wang, Jiawan , Zhang, Xiaochun, Yang, Liuzhan , Oztosun, Gorkem, Sears, James J., Xiao, Ke , Garana, Belinda B., Zoberi, Mark I., Bektas, Aaron U., Coma, Silvia, Pachter, Jonathan A. , Gosline, Sara JC, Pratilas, Christine A. , Szymanski, Jeffrey J. , Borcherding, Dana C. , Zhang, Xiaochun, Oztosun, Gorkem , Sears, James J. , Garana, Belinda B. , Rathore, Richa , Coma, Silvia, Gosline, Sara J.C. , Hirbe, Angela C.

Mayo Clinic

Journal of Clinical Investigation | August 11, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.1172/jci201331 | PMID 42579369 Get It

Aneuploidy is a hallmark of cancer often associated with inferior prognosis. Copy number gains of chromosome 8 (chr8) are recurrent in multiple cancers, including breast, prostate, colorectal cancers, and sarcomas such as malignant peripheral nerve sheath tumors (MPNSTs). MPNSTs are aggressive, hard-to-treat sarcomas frequently linked to the Neurofibromatosis type 1 (NF1) cancer predisposition syndrome. To investigate the role of chr8 gain in MPNST pathogenesis, we performed a CRISPR knockout screen and identified 58 essential genes on chr8, including PTK2, which encodes focal adhesion kinase (FAK). We evaluated FAK as a therapeutic target and tested small-molecule FAK inhibitors (FAKi) alone or combined with RAF/MEK inhibitors (RAF/MEKi), a class of agents relevant to NF1-deficient tumors with ERK pathway hyperactivation. Both pharmacological and genetic inhibition of FAK reduced MPNST cell proliferation in vitro and tumor growth in vivo. Combined FAKi and RAF/MEKi treatment further suppressed phosphorylation of FAK, STAT3, and AKT while increasing cleaved caspase-3 and PARP-1, indicating enhanced apoptosis. In MPNST patient-derived xenograft (PDX) models, combination therapy significantly reduced tumor growth, showing superior efficacy, particularly in chr8 gain MPNST-PDX. These results support FAK/RAF/MEK co-targeting as a promising therapeutic strategy for chr8 gain MPNST and related tumors.
BRAFV600E ‐Mutant Non‐Langerhans Cell Histiocytosis Clonally Related to Remitted Acute Myeloid Leukemia
Shimshak, Serena , Jiang, Liuyan , Sokumbi, Olayemi , Shimshak, Serena J E , Sokumbi, Olayemi

Mayo Clinic

Journal of Cutaneous Pathology | August 11, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.1111/cup.70192 | PMID 42578793 Get It

ABSTRACT We report a case of a 71‐year‐old female with acute myeloid leukemia (AML), treated with chemotherapy and hematopoietic stem cell transplant (HSCT), who developed a clonally related non‐Langerhans cell histiocytosis (NLCH). She presented with pink papules on the mid‐upper cutaneous lip and thighs 3 months following HSCT. Skin biopsies revealed a dermal proliferation of cells with eosinophilic cytoplasm. Immunohistochemistry (IHC) studies demonstrated positivity for CD68, CD163, BRAF, cyclin D1, and Factor XIIIa and negativity for CD1a, S100, MPO, and CD20. Next‐generation sequencing (NGS) with a comprehensive myeloid panel revealed corresponding pathogenic mutations to her AML, including BCOR Q176fs*40, IDH1 R132C, and TP53 Y163N, and an additional BRAF V600E mutation. Additional mutations in DNMT3A and KMT2A associated with her AML were not identified. These findings supported the diagnosis of NLCH sharing a clonal origin with the patient's AML. Work up demonstrated isolated cutaneous involvement without AML relapse; therefore, the skin lesions were treated with shave excision, topical tacrolimus 0.1% ointment, and topical clobetasol 0.05% cream without further systemic treatment. The acquired BRAF V600E mutation illustrates the potential for divergent myeloid differentiation and likely explains the emergence of a clonal NLCH after successful AML treatment. Genetic analysis in NLCH can establish clonality with associated hematologic malignancies, uncover actionable mutations, and guide treatment.
Catheter Ablation for Atrial Fibrillation in Cardiac Amyloidosis: A Systematic Review and Meta‐Analysis
Sripusanapan, Adivitch , Deepan, Natee , Pongsukvechkul, Bheem , Kittiwongsopon, Suphatcha, Sorajja, Dan , Shen, Win‐Kuang , Chokesuwattanaskul, Ronpichai , Tan, Min Choon , Rattanawong, Pattara , Sorajja, Dan , Chokesuwattanaskul, Ronpichai , Rattanawong, Pattara , Prasitlumkum, Narut

Mayo Clinic

Journal of Arrhythmia | August 11, 2026 | Volume: 42 | Issue: 4 | Pages: No page available

10.1002/joa3.70441 | PMID 42583105 Get It

ABSTRACT Background Atrial fibrillation (AF) is prevalent in cardiac amyloidosis (CA) and is associated with adverse clinical outcomes. Catheter ablation is increasingly used for rhythm control in this population, yet its clinical outcomes remain uncertain. We performed a systematic review and meta‐analysis to evaluate arrhythmia recurrence and clinical outcomes following catheter ablation compared with medical therapy in patients with CA. Methods We systematically searched MEDLINE, Embase, and Scopus from inception through December 2025 for studies evaluating catheter ablation of atrial arrhythmias in CA. Cohort studies reporting arrhythmia recurrence and/or clinical outcomes were included. The primary outcome was freedom from atrial arrhythmia (AA) following ablation. Secondary outcomes included all‐cause mortality, heart failure hospitalization, and stroke. Random‐effects models were used to pool event rates and odds ratios (ORs). Results Thirteen observational studies comprising 797 patients with CA and AF were included. The pooled rate of freedom from AA following catheter ablation was approximately 50% (95% CI 37%–63%; I 2 = 71.7%). The all‐cause mortality analysis included 4 observational studies comprising 616 patients. Catheter ablation was associated with lower odds of all‐cause mortality (OR 0.26, 95% CI 0.11–0.60; I 2 = 18.4%); however, this association should be interpreted with caution given the retrospective design and risk of bias. No statistically significant differences were observed for heart failure hospitalization or stroke. Conclusions In patients with CA, catheter ablation was associated with modest arrhythmia‐free survival and lower odds of all‐cause mortality. However, all contributing studies were observational cohorts. Randomized studies are needed to confirm these findings.
Combination treatment with RAF/MEK inhibitor avutometinib and FAK inhibitor defactinib in preclinical models of meningioma
Ijad, Nazanin, Yamazawa, Erika , Burgenske, Danielle, Torrini, Consuelo , Carlson, Brett L. , Summers, Elizabeth J, Migliarese, Christian, Marion, Braxton, Zhang, Britney Shela, Sullivan, Emily, Ellington, Claudia, Sasisekharan, Varun, Decker, Paul A, Kosel, Matthew, Eckel‐Passow, Jeanette E. , Galanis, E., Brastianos, Priscilla K, Brastianos, Priscilla K. , Waller, Katie L. , Nayyar, Naema , Burgenske, Danielle M. , Summers, Elizabeth, Marion, Braxton, Decker, Paul A. , Kosel, Matthew , Sarkaria, Jann N. , Wakimoto, Hiroaki , Vaubel, Rachael A. , Brastianos, Priscilla K.

Mayo Clinic

Neuro-Oncology Advances | August 11, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.1093/noajnl/vdag210 Get It

Abstract Background Meningiomas lack effective therapies for recurrent or aggressive disease. NF2 inactivation, commonly in meningioma, may sensitize tumors to FAK inhibition and interact with MAPK signaling. This study investigated the therapeutic activity of defactinib (FAK inhibitor) and avutometinib (RAF/MEK inhibitor) alone and in combination in preclinical meningioma models. Methods MAPK-altered meningioma cell lines, IOMM-Lee (NF2 wild-type, BRAF p.V600E) and CH157-MN (NF2 mutant, NRAS p.Q61K), BenMen-1 (NF2 mutant, MAPK wild-type), and three patient-derived NF2 mutant cell lines were cultured in matrigel and treated with defactinib and avutometinib in 3D cell viability assays. In vivo, flank and intracranial xenograft models of IOMM-Lee and CH157-MN were treated with VS-4718 (FAK inhibitor, superior pharmokinetics in mice), avutometinib, or combination. Tumor growth, survival, and pharmacokinetic/pharmacodynamic properties were assessed. Results In vitro, combination therapy showed synergistic or additive effects in CH157-MN and IOMM-Lee cells, respectively. Defactinib alone demonstrated activity in NF2-mutant patient-derived and BenMen-1 cells, while avutometinib did not. In vivo, avutometinib monotherapy suppressed tumor growth and extended survival in both flank and intracranial xenograft models, with evidence of favorable pharmacokinetic properties and target pathway inhibition in intracranial tumors. Combination therapy provided enhanced and sustained control of flank CH157-MN meningioma compared to avutometinib alone but did not significantly improve survival over avutometinib alone in intracranial models. Conclusions Avutometinib demonstrated robust anti-tumor effects in flank and intracranial models of MAPK-altered meningioma. Combination benefits were context dependent. Defactinib activity in NF2-mutant patient-derived cells without targetable MAPK-kinase alterations highlights the importance of genomic biomarkers to guide personalized strategies.
Prescription Trends for Bipolar Disorder With and Without Comorbid Substance Use and Anxiety Disorders: A Global Bipolar Cohort Collaborative Study
Yocum, Anastasia K. , Aouizerate, Bruno, Aubin, V. , Bellivier, Frank , Belzeaux, Raoul , Berk, Michael , Biernacka, Joanna M. , Budde, Monika , Burdick, Katherine E. , Coombes, Brandon J., Diaz‐Byrd, Claudia , Dubertret, Caroline, Fico, Giovanna, Godin, Ophélia , Gordon‐Smith, Katherine, Januel, Dominique, Lefrère, Antoine , Llorca, Pierre‐Michel, Mwangi, Benson, Olie, Emilie, Overs, Bronwyn J. , Petite, Joanne, Polosan, Mircea , Rey, Romain, Roberts, Gloria, Schwan, Raymund, Serretti, Alessandro , Soares, Jair C., Stross, Tatjana , Walter, Michel, Williams, Lana J., Wu, Mon‐Ju, Young, Allan H. , Zunta‐Soares, Giovana B., Frye, Mark A. , McInnis, Melvin G., Roberts, Gloria , Alda, Martin , Bellivier, F , Belzeaux, Raoul , Berk, Michael , Biernacka, Joanna , Budde, Monika , Burdick, K E , Chang, Yun-Hsuan , Courtet, Philippe , Dalkner, Nina , Etain, B , Fullerton, Janice M , Godin, Ophelia , Haffen, Emmanuel , Keramatian, Kamyar , Leboyer, Marion , Majd, Marzieh , Mitchell, Philip B , Polosan, Mircea , Roux, Paul , Samalin, Ludovic , Serretti, Alessandro , Sperry, Sarah , Strawbridge, Rebecca , Stross, Tatjana , Vieta, E , Williams, Lana J , Yatham, Lakshmi N , Young, Allan H , Yrondi, Antoine , Frye, Mark , Singh, Balwinder , Alda, Martin , Aouizerate, Bruno , Coombes, Brandon J. , Dubertret, Caroline , Étain, Bruno , Fico, Giovanna , Fullerton, Janice M. , Gordon‐Smith, Katherine , Januel, Dominique , Keramatian, Kamyar , Leboyer, Marion , Llorca, Pierre‐Michel , Mwangi, Benson , Olié, Émilie , Rey, Romain , Samalin, Ludovic , Schwan, Raymund , Soares, Jair C. , Sperry, Sarah H. , Strawbridge, Rebecca , Vieta, Eduard , Walter, Michel , Wu, Mon‐Ju , Yatham, Lakshmi N. , Zunta‐Soares, Giovana B. , McInnis, Melvin G. , Singh, Balwinder

Mayo Clinic

Bipolar Disorders | August 11, 2026 | Volume: 28 | Issue: 6 | Pages: No page available

10.1111/bdi.70167 | PMID 42578538 Get It

ABSTRACT Objectives To investigate pharmacological treatment patterns in individuals with bipolar disorder (BD) with and without comorbid substance use disorder (SUD) and anxiety disorder (AX), we leveraged the Global Bipolar Cohort to analyze cross‐regional practices across North America, Europe, and the Pacific. Methods Fourteen cohorts contributed aggregate data on pharmacotherapy, demographics, diagnostic subtypes, and comorbidities. Proportional meta‐analyses using generalized linear mixed models were conducted to examine prescription trends and identify clinical differences. Results The sample ( N = 11,521) was 60% female and 84% Caucasian. Participants were categorized into four mutually exclusive groups based on comorbidity status: those with comorbid AX only, comorbid SUD only, both AX and SUD, or neither. The AX+SUD subgroup showed higher rates of attention‐deficit/hyperactivity disorder (ADHD), post‐traumatic stress disorder (PTSD), rapid cycling, obesity, and unemployment, reflecting a more severe clinical profile. Regional variations were notable: North American cohorts reported higher prevalence of AX and SUD than European and Pacific cohorts. Antidepressants use for AX were more common in Europe and the Pacific, while North American prescribing patterns were more variable. Benzodiazepine use was high among individuals with SUD across all regions. Lithium and first‐generation antipsychotic prescriptions varied, with higher rates observed in Europe. Conclusions Findings underscore the heterogeneity of BD and the influence of comorbid AX and SUD on illness burden and treatment. Regional prescribing variations underscore the need for context‐specific guidelines. Gaps in data on medication‐assisted treatment for SUD point to areas for future research. These insights can support more individualized and effective care for complex BD presentations.
Evidence based interventions for bipolar disorder across phases and age groups: living umbrella review, evaluation, analysis, and communication hub (U-REACH) project
Miola, Alessandro , Croatto, Giovanni , Carvalho, Andre F, Berk, Michael, Nikolitch, Katerina , Saraf, Gayatri , Yatham, Lakshmi N, Frye, Mark A, Singh, Balwinder, Krinitski, Damir , Højlund, Mikkel , Serretti, Alessandro , Gomes, Fabiano A, Hansen, Anne Sofie , Nielsen, Rene Ernst, Manchia, Mirko, Vazquez, Gustavo, Siafis, Spyridon, Leucht, Stefan, Yıldız, Ayşegül, Delorme, Richard, Schaffer, Ayal , Stubbs, Brendon , Rubaiyat, Ruby , Vieta, Eduard, Correll, Christoph U, Moher, David, Cortese, Samuele, Fiedorowicz, Jess G, Solmi, Marco , Berk, Michael , Solmi, Marco , Berk, Michael , Serretti, Alessandro , Prisco, Michele De , Oliva, Vincenzo , Fornaro, Michele , Dragioti, Elena , Yatham, Lakshmi N. , Keramatian, Kamyar , Shorr, Risa , Frye, Mark A. , Singh, Balwinder , Fanelli, Giuseppe , Gomes, Fabiano A., Nielsen, René Ernst , Fusar‐Poli, Paolo , Paribello, Pasquale , Manchia, Mirko , Bahji, Anees , Vázquez, Gustavo Héctor , Siafis, Spyridon , Leucht, Stefan , Delorme, Richard , Vieta, Eduard , Correll, Christoph Ulrich , Moher, David , Cortese, Samuele , Fiedorowicz, Jess G. , Raduà, Joaquim , Gosling, Corentin J.

Mayo Clinic

BMJ | August 11, 2026 | Volume: 394 | Issue: No issue available | Pages: e100216

10.1136/bmj-2026-100216 | PMID 42580772 Get It

Abstract Objectives To systematically evaluate the certainty of evidence for treatment strategies across age groups and mood phases in bipolar disorder, and develop an open access web platform to facilitate shared decision making. Design Living umbrella review, evaluation, analysis, and communication hub (U-REACH) project. Data sources PubMed, PsycInfo, and Cochrane library databases, from inception to 19 November 2024. Eligibility criteria for selecting studies Systematic reviews with network or pairwise meta-analyses of randomised controlled trials of pharmacological, nutraceutical, psychosocial, brain stimulation, or circadian rhythm based treatments, administered as monotherapy (without concurrent interventions), augmentation treatment (interventions added to an ongoing treatment regimen), or combination treatment (simultaneous initiation of two different interventions), examining any age group, bipolar disorder phase (ie, acute bipolar depression, mania or mixed episodes, or maintenance), treatment, control, or outcome. Results 77 studies met the inclusion criteria (21 network meta-analyses and 56 pairwise meta-analyses), including 116 unique pharmacological (n=74), brain stimulation (n=18), nutraceutical (n=13), psychosocial (n=8), and circadian rhythm based (n=3) treatments as monotherapy, augmentation, or combination therapy, along with five control interventions. These studies covered 133 unique outcomes (45 efficacy outcomes and 88 safety outcomes) resulting in 2510 meta-analyses with Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) ratings of the certainty of the evidence as high (n=236), moderate (n=827), low (n=986), and very low (n=461). A communication hub, the Evidence Based Interventions for Bipolar Disorder (EBI-BD) platform, was developed and the full results are freely available ( https://ebibd-database.org ), including the preference based tool (12 interventions and 17 safety outcomes). Interventions effective across outcomes varied by phases. For bipolar depression, effective interventions in adults were cariprazine, divalproex or valproate, fluoxetine, ketamine (augmentation), lamotrigine, lumateperone, lurasidone, olanzapine, olanzapine with fluoxetine, and quetiapine, whereas effective interventions in children and adolescents were lurasidone and olanzapine with fluoxetine. For mania episodes, effective interventions in adults were aripiprazole, asenapine, carbamazepine, cariprazine, divalproex or valproate, haloperidol, lithium, olanzapine, paliperidone, quetiapine (also augmentation), risperidone (also as augmentation), tamoxifen, and ziprasidone, whereas effective interventions in children and adolescents were aripiprazole, asenapine, olanzapine, quetiapine, and risperidone. For maintenance, interventions effective across outcomes in adults were aripiprazole (also the long acting injectable formulation), asenapine, divalproex or valproate, lithium, olanzapine, group psychoeducation (augmentation), quetiapine, and risperidone long acting injectable formulation. Interventions effective across phases were aripiprazole (also as augmentation and as a long acting injectable formulation), asenapine, cariprazine, cognitive behavioural therapy (augmentation), divalproex or valproate, lamotrigine, lithium, olanzapine (also as augmentation), paliperidone, quetiapine (also as augmentation), and risperidone (also as augmentation and the long acting injectable formulation) (adults). Treatment effects by neuroscience based nomenclature classes are also reported. Conclusions The EBI-BD tool can help clinicians make evidence based, personalised treatment decisions for bipolar disorder. This resource can inform clinical guidelines and provides a foundation for continuously improving bipolar disorder care as new evidence emerges. Trial registration Open Science Framework https://osf.io/pjmvn/ Readers’ note This is a living systematic review and may be updated in the next two years if additional evidence emerges.
Repurposing the PMFF Pedicle Before Final Division: Distal Necrosis Salvage With Long‐Term Success
Gates, Carson , Daher, Ghazal S. , Hamilton, Grant S., Hamilton, Grant S.

Mayo Clinic

The Laryngoscope | August 11, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.1002/lary.70765 | PMID 42578308 Get It

Integrated coding-noncoding genome annotation expands single-cell transcriptomic discovery and identifies clinically relevant noncoding RNAs in multiple myeloma
Bakhtiari, Mojtaba , Henderson, Edward, Ferguson, Katherine , Pilcher, William C., Gonzalez-Kozlova, Edgar, Karagkouni, Dimitra, Matulis, Shannon M. , Acharya, Chaitanya R., Avigan, David, Vij, Ravi, Parekh, Samir, Ding, Li, Kumar, Shaji, Nooka, Ajay, Mulligan, George, Lonial, Sagar, Bhasin, Manoj, Michaud, Marina E. , Ohlstrom, Denis , Satpathy, Sarthak , Pilcher, William , Gonzalez‐Kozlova, Edgar , Karagkouni, Dimitra , Acharya, Chaitanya R. , Avigan, David , Vij, Ravi , Parekh, Samir , Cho, Hearn Jay , Vlachos, Ioannis S. , Kumar, Shaji , Gnjatic, Sacha , Nooka, Ajay K. , Lonial, Sagar , Boise, Lawrence , Bhasin, Manoj K

Mayo Clinic

No container title available | August 11, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.64898/2026.08.09.743753 Get It

Abstract Although the human genome encodes a vast repertoire of noncoding RNAs that regulate gene expression, the noncoding genome remains underexplored due to technical challenges. Specifically, during transcriptomic sequencing data alignment, the overlap between noncoding and coding loci can create ambiguous read alignments that are subsequently discarded from downstream analysis. For this reason, most of the noncoding genome is excluded from standard genomic annotations used for sequencing alignment. To address this challenge and enable concurrent profiling of the coding and noncoding transcriptome, we systematically integrated standard coding (GENCODE) and noncoding (LncBook) genome annotations, preserving coding gene annotations and removing overlapping noncoding regions. The resulting integrated genome annotation expanded the number of annotated noncoding genes from 40,785 to 138,296 while preserving all coding genes and reducing ambiguous read assignment. To evaluate the utility of our integrated genome annotation for uncovering novel, biologically relevant noncoding RNAs (ncRNAs), we realigned CD138-positive bulk RNA-seq (N = 942) and CD138-negative single-cell RNA-seq (N = 478) data from the MMRF CoMMpass study, generating a comprehensive coding-noncoding atlas of the myeloma bone marrow microenvironment with noncoding genes representing 51% of highly variable genes and displaying significant cell type specificity. Tumor expression profiling based on this integrated profiling identified 15 clusters, including two enriched for amp(1q21) or t(4;14) and associated with shorter progression-free survival (PFS). Differential expression and systematic filtering yielded 19 candidate high-risk ncRNAs, including previously uncharacterized ENSG00000310209 , which was associated with poor PFS (HR = 1.141, P = 0.0025), increased IRF4 activity, Wnt pathway activation, CCL5 signaling, and the accumulation of anergic-like CD8+ T cells. These findings establish integrated coding-noncoding analysis as a strategic approach for discovering functional ncRNAs from transcriptomic sequencing data.