Life Sciences Research Articles

Pan-Cancer Interrogation of B7-H3 (CD276) as an Actionable Therapeutic Target across Human Malignancies.

B7-H3 (CD276) is a transmembrane glycoprotein of the B7 immune checkpoint superfamily that has emerged as a promising therapeutic target. To better understand the applicability of B7-H3-directed therapies, we analyzed 156,791 samples comprising 50 cancer types to interrogate the clinical, genomic, transcriptomic, and immunological correlates of B7-H3 mRNA expression. DNA (592-gene/whole-exome) and RNA (whole-transcriptome) sequencing was performed from samples submitted to Caris Life Sciences (Phoenix, AZ). B7-H3 high versus low expression was based on top and bottom quartiles for each cancer type. Patients' overall survival was determined from insurance claims data. Pathway analysis was performed using Gene Set Enrichment Analyses (GSEA). Immune cell fractions were inferred using quanTIseq. B7-H3 is expressed across several human malignancies including prostate, pancreatic, ovarian, and lung cancers. High B7-H3 expression is associated with differences in overall survival, possibly indicating a prognostic role of B7-H3 for some cancers. When examining molecular features across all cancer types, we did not identify recurrent associations between B7-H3 expression and genetic alterations in TP53, RB1, and KRAS. However, we find consistent enrichment of EMT, Wnt, TGF-beta, and Notch signaling pathways. Additionally, tumors with high B7-H3 expression are associated with greater proportions of M1 macrophages, but lower fractions of CD8+ T cells. We have begun to define the genomic, transcriptomic, clinical, and immunological features associated with B7-H3 expression in 50 cancer types. We report novel clinical and molecular features of B7-H3-high tumors which may inform how current B7-H3 therapeutics should be deployed and prioritized.

Open Resources for Biology Education (ORBE): a resource collection.

In undergraduate life sciences education, open educational resources (OERs) increase accessibility and retention for students, reduce costs, and save instructors time and effort. Despite increasing awareness and utilization of these resources, OERs are not centrally located, and many undergraduate instructors describe challenges in locating relevant materials for use in their classes. To address this challenge, we have designed a resource collection (referred to as Open Resources for Biology Education, ORBE) with 89 unique resources that are primarily relevant to undergraduate life sciences education. To identify the resources in ORBE, we asked undergraduate life sciences instructors to list what OERs they use in their teaching and curated their responses. Here, we summarize the contents of the ORBE and describe how educators can use this resource as a tool to identify suitable materials to use in their classroom context. By highlighting the breadth of unique resources openly available for undergraduate biology education, we intend for the ORBE to increase instructors' awareness and use of OERs.

Excitation signal optimization for minimizing fluctuations in knock out slow extraction

The synchrotron is a circular particle accelerator used for high energy physics experiments, material and life science, as well as hadron cancer therapy. After acceleration to the desired energies, particle beams are commonly extracted from the synchrotron using the method of resonant slow extraction. The goal is to deliver a steady particle flux—referred to as spill—to experiments and treatment facilities over the course of seconds while slowly emptying the storage ring. Any uncontrolled intensity fluctuations in the spill are detrimental to the efficiency of beam usage, as they lead to detector pileups or detector interlocks, hindering experiments and cancer treatment. Among the most widely used extraction scheme in medical facilities is the Radio Frequency Knock Out (RF-KO) driven resonant slow extraction, where the stored beam is transversely excited with a radio frequency (RF) field and the spill intensity is controlled by the excitation signal strength. This article presents particle dynamics simulations of the RF-KO system with the focus on finding effective mechanism for minimizing the intensity fluctuations while maintaining a good extraction efficiency and other advantages of KO extraction. An improved beam excitation signal which optimizes these main objectives is found, and is rigorously compared experimentally with other commonly applied techniques.

186 Evaluation of the effects of a Lactobacillus postbiotic product (LumensaM) in medicated and non-medicated nursery pig diets

Abstract Two studies in weanling pigs were conducted to evaluate the effects of a Lactobacillus postbiotic product (LFP; Lumensa, Verdesian Life Sciences, Salt Lake City, UT) in medicated and non-medicated nursery pig diets on performance, daily fecal scores and some fecal microbiome measures. A 2 X 3 factorial factorial design with main effects of in-feed medication (0 vs 55 ppm of Carbadox) and LFP inclusion rate (0, 0.075, or 0.15%) was used in each study. In study 1, LFP in liquid form was added to the treatment diets, and in study 2 LFP in dry form was used in the treatment diets. Each study used 36 pens containing 10 weanling pigs (PIC 800 x 1050; 21 d of age) per pen, and there were 6 pens for each treatment group. A pelleted three-phase commercial nursery feeding program was used. Dry LFP product increased final body weight (BW) linearly (P < 0.05) and tended to improve gain to feed ratio (G:F; P = 0.07) in study 2. Final BW was increased (P = 0.006) in nursery pigs fed medicated diets in study 2 but not in study 1. Feeding the dry LFP in study 2 improved growth performance (P < 0.05) in nursery pigs when they were fed non-medicated diets. In study 1, it was found that feeding LFP tended (P = 0.10) to decrease final BW variability (pen BW CV) on d 42. Daily fecal scores were recorded during both studies, and no treatment effects were observed. During study 2, fresh fecal samples were collected from each pen on d 21 and d 42 for microbial analysis. The Shannon Index was found to be moderately correlated (P < 0.05) to BW results on d 21 and 42 (Study 1, r = -0.31 and 0.19; Study 2, r= -0.49 and 0.27, d 21 and d 42, respectively). It was found that feeding LFP decreased the proportion of Gammaproteobacteria, which includes several Gram-negative pathogens, on d 21 (P < 0.05). In conclusion, feeding LFP to nursery pigs as dry product may increase average daily gain in pigs fed non-medicated diets and decrease BW variability (pen BW CV) when pigs are fed nursery diets containing carbadox. Also, feeding LFP may lead to changes in the fecal microbiome.

Understanding and Addressing AI Hallucinations in Healthcare and Life Sciences

Purpose: This paper investigates the phenomenon of "AI hallucinations" in healthcare and life sciences, where large language models (LLMs) produce outputs that, while coherent, are factually incorrect, irrelevant, or misleading. Understanding and mitigating such errors is critical given the high stakes of accurate and reliable information in healthcare and life sciences. We classify hallucinations into three types input-conflicting, context-conflicting, and fact-conflicting and examine their implications through real-world cases. Methodology: Our methodology combines the Fact Score, Med-HALT, and adversarial testing to evaluate the fidelity of AI outputs. We propose several mitigation strategies, including Retrieval-Augmented Generation (RAG), Chain-of-Verification (CoVe), and Human-in-the-Loop (HITL) systems, to enhance model reliability. Findings: As artificial intelligence continues to permeate various sectors of society, the issue of hallucinations in AI-generated text poses significant challenges, especially in contexts where precision and reliability are paramount. This paper has delineated the types of hallucinations commonly observed in AI systems input-conflicting, context-conflicting, and fact-conflicting and highlighted their potential to undermine trust and efficacy in critical domains such as healthcare and legal proceedings. Unique contribution to theory, policy and practice: This study's unique contribution lies in its comprehensive analysis of AI hallucinations' types and impacts and the development of robust controls that advance theoretical understanding, practical application, and policy formulation in AI deployment. These efforts aim to foster safer, more effective AI integration across healthcare and life sciences sectors

Future proofing core facilities with a seven-pillar model.

Centralised core facilities have evolved into vital components of life science research, transitioning from a primary focus on centralising equipment to ensuring access to technology experts across all facets of an experimental workflow. Herein, we put forward a seven-pillar model to define what a core facility needs to meet its overarching goal of facilitating research. The seven equally weighted pillars are Technology, Core Facility Team, Training, Career Tracks, Technical Support, Community and Transparency. These seven pillars stand on a solid foundation of cultural, operational and framework policies including the elements of transparent and stable funding strategies, modern human resources support, progressive facility leadership and management as well as clear institute strategies and policies. This foundation, among other things, ensures a tight alignment of the core facilities to the vision and mission of the institute. To future-proof core facilities, it is crucial to foster all seven of these pillars, particularly focusing on newly identified pillars such as career tracks, thus enabling core facilities to continue supporting research and catalysing scientific advancement. Lay abstract: In research, there is a growing trend to bring advanced, high-performance equipment together into a centralised location. This is done to streamline how the equipment purchase is financed, how the equipment is maintained, and to enable an easier approach for research scientists to access these tools in a location that is supported by a team of technology experts who can help scientists use the equipment. These centralised equipment centres are called Core Facilities. The core facility model is relatively new in science and it requires an adapted approach to how core facilities are built and managed. In this paper, we put forward a seven-pillar model of the important supporting elements of core facilities. These supporting elements are: Technology (the instruments themselves), Core Facility Team (the technology experts who operate the instruments), Training (of the staff and research community), Career Tracks (for the core facility staff), Technical Support (the process of providing help to apply the technology to a scientific question), Community (of research scientist, technology experts and developers) and Transparency (of how the core facility works and the costs associated with using the service). These pillars stand on the bigger foundation of clear policies, guidelines, and leadership approaches at the institutional level. With a focus on these elements, the authors feel core facilities will be well positioned to support scientific discovery in the future.

Towards controlled and simple design of non-enzymatic amperometric sensor for glycerol determination in yeast fermentation medium.

Glycerol is a widely used signaling bioanalyte in biotechnology. Glycerol can serve as a substrate or product of many metabolic processes in cells. Therefore, quantification of glycerol in fermentation samples with inexpensive, reliable, and rapid sensing systems is of great importance. In this work, an amperometric assay based on one-step designed electroplated functional Pd layers with controlled design was proposed for a rapid and selective measurement of glycerol in yeast fermentation medium. A novel assay utilizing electroplated Pd-sensing layers allows the quantification of glycerol in yeast fermentation medium in the presence of interfering species with RSD below 3% and recoveries ranged from 99 to 103%. The assay requires minimal sample preparation, viz. adjusting of sample pH to 12. The time taken to complete the electrochemical analysis was 3min. Remarkably, during investigations, it was revealed that sensitivity and selectivity of glycerol determination on Pd sensors were significantly affected by its adsorption and did not depend on the surface structure of sensing layers. This study is expected to contribute to both fundamental and practical research fields related to a preliminary choice of functional sensing layers for specific biotechnology and life science applications in the future.

Mid-infrared Photothermal Imaging: Instrument and Life Science Applications.

Mid-infrared Photothermal Imaging: Instrument and Life Science Applications.

Abstract PO4-24-01: Comprehensive Molecular and Immunological Characterization of Invasive Ductal Triple-Negative Breast Cancer

Abstract Background: Triple-negative breast cancer (TNBC) is a heterogeneous disease and characterized by poor outcomes with a lack of targeted therapies. A comprehensive analysis of the molecular and immune landscape of invasive ductal TNBC can help improve our understanding of TNBC biology and identify novel targets and/or pathways for better management of this disease. Here, we characterized the molecular and immune signature of invasive ductal (ID) TNBC. Methods: 13,036 BC samples (ID TNBC, n=392; ID non-TNBC, n=927) were analyzed by NGS (592, NextSeq; WES, NovaSeq), WTS (NovaSeq) (Caris Life Sciences, Phoenix, AZ). A total of 10 pro-apoptotic (BAX, BAK1, BID, BAD, BIK, BCL2L11, BMF, HRK, PMAIP1, BBC3) and 6 anti-apoptotic (BCL2, BCL2L1, BCL2L2, MCL1, BCL2A1, BCL2L10) BCL2 family genes were analyzed. Immune cell fractions were calculated by deconvolution of WTS: Quantiseq. Real world overall survival (OS) and treatment-associated survival was extracted from insurance claims and calculated from tissue collection or treatment start to last contact using Kaplan-Meier estimates. Statistical significance was determined using chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q < 0.05). Results: ID TNBC had a higher frequency of TP53, RB1, NF1, PIK3R1, NOTCH1, CREBBP, BRCA1, FANCI, and HRAS mutations (Table 1), NOTCH2 (4.3% vs 0.47%), EGFR (3.4% vs 0%), NFIB (4% vs 0.6%), MYB (3.5% vs 0.5%), CCNE1 (4.4% vs 1.1%) and AKT2 (2.4% vs 0.3%) copy number alterations, and NOTCH2 (1.6% VS 0.2%) fusion (all p < 0.05) compared to invasive ductal non-TNBC. Analysis of inferred immune cell infiltrates showed that ID TNBC had increased infiltration of Tregs (2% vs 1.7%), DC (3.2% vs 2.4%), CD8 T cells (0.5% vs 0.1%), and M1 macrophages (M) (3.4% vs 2.9%), but decreased infiltration of B cells (4.5% vs 6%) and M2M (2.9% vs 4.5%) (all p < 0.05). ID TNBC had increased T cell inflamed score (23 vs -9, p < 0.05), IFNy score (-0.24 vs -0.34, p < 0.05), MHC class I genes (HLA-A, HLA-B, TAP1, TAP2, FC: 1.1-1.5, all p < 0.05), immune checkpoint genes (CD274, PDCD1, CTLA4, PD-L2, FOXP3, IDO, FC: 1.1-2, all p < 0.05) and PD-L1 protein expression (SP142: 49.8% vs. 28.4%; 22c3: 41.7% vs. 16.8%, all p < 0.05). ID TNBC had differential expression of BCL2 family genes (upregulation: BAK1, BID, MCL1, BCL2A1, BCL2L10, FC: 1.1-2.0; downregulation: BAD, BIK, BBC3, BCL2, BCL2L1, BCL2L2, FC: 1.2-2.8, all p < 0.05) compared to invasive ductal non-TNBC. ID TNBC was associated with worse OS compared to ID non-TNBC (mOS: 24.5 vs 54.6 months; HR: 0.5, 95% CI 0.47-0.57; p < 0.00001) but trend towards better survival with pembrolizumab (mOS: 29.4 vs 8.8 month; HR: 0.67, 95% CI 0.28-1.5; p=0.3) treatment. No significant OS difference was noted for by high vs. low pro and anti-apoptotic BCL2 genes except for anti-apoptotic BCL2A1 (higher expression associated with better OS (mOS: 5.7 months, HR: 0.78, 95% CI 0.6-0.99; p=0.047). Conclusion: These data indicate that ID TNBC is associated with distinct mutational profile compared to non-TNBC, has increased T cell inflamed score, IFNy score, MHC class I and immune checkpoint gene expression, and differential immune cell infiltration. Interestingly, TNBC was associated with increased M1 and decreased M2M. There is evidence to suggest that transcriptomically defined M1 high tumors are clinically aggressive and have worse OS in TNBC. BCL2 family genes are not prognostic for TNBC outcomes except BCL2A1, which needs further prospective validation. Table 1: Mutation frequency in invasive ductal TNBC and invasive ductal non-TNBC Citation Format: Pooja Advani, Sachin Deshmukh, Sharon Wu, Jacob Andring, Joanne Xiu, Alex Farrell, Jose Leone, Priya Jayachandran, Stephanie Graff, Matthew Oberley, George Sledge Jr, Asher Chanan-Khan. Comprehensive Molecular and Immunological Characterization of Invasive Ductal Triple-Negative Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-24-01.

Abstract PS13-09: Molecular and immunological landscape of sex-based differences in breast cancer: a distinct disease in men

Abstract Background: Breast cancer (BC) in males represents a rare clinical entity, accounting about 1% of all breast malignancies diagnosed every year. Emerging evidence suggest that a gender medicine approach is critical in the research and treatment of cancer, based on the possibility that sex hormones, molecular differences, immune system, and other factors might play a crucial role in disease management. Here, we characterized molecular and immune differences between male BC (MaBC) and female BC (FeBC) across BC subtypes. Methods: 10,728 BC samples (male, n=137; female, n=10591) were analysed by next-generation sequencing (592, NextSeq; WES, NovaSeq), Whole Transcriptome Sequencing (WTS; NovaSeq) (Caris Life Sciences, Phoenix, AZ). Tumor mutational burden (TMB) totaled somatic mutations per tumor (high ≥10 mt/MB). Microsatellite-instability (MSI) was tested by IHC and NGS. Immune cell fractions were calculated by deconvolution of WTS: Quantiseq. Real world treatment-associated survival was extracted from insurance claims and calculated from sample collection to last contact using Kaplan-Meier estimates. Statistical significance was determined using chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q < 0.05). Results: MaBC represented higher HR+/HER2+ (6.61% vs 4.76%), HR+/HER2- (80.17% vs 60.66%) and lower HR-/HER2+ (1.65% vs 3.5%), TNBC (11.57% vs 31.08%) molecular subtypes compared to FeBC. Compared to HR+/HER2+ FeBC, MaBC had higher frequency of CHEK2, RAD51B, TSC1 mutation (Table 1) and RARα (100% vs 13.61%), DAXX (10% vs 0.16%) copy number alteration (all p < 0.05). HR+/HER2- MaBC had higher frequency of BRCA2, FOXA1, CREBBP, FLCN mutation (Table 1), and FGF3 (21.62% vs 14.31%), MRE11 (1.75% vs 0.23%), MEN1 (1.75% vs 0.13%) copy number alteration, but lower frequency of TP53, CHD1, ESR1 and AKT1 mutation (Table 1) (all p < 0.05). HR-/HER2+ MaBC had higher frequency of BRCA1 (p < 0.05) mutation (Table 1). Male TNBC had higher frequency of CDKN2A, KMT2D, STK11, ASXL1, MYC, NF2, PPM1D, WT1, EPHA2, AMER1, ARHGAP35 mutation (Table 1) and BCL6 (4.35% vs 0.05%) copy number alteration, but lower frequency of TP53 mutation (all p < 0.05) (Table 1). MaBC had higher AR protein expression (82.5% vs 60%) but lower frequency of fusion variant-AR (0.7% vs 3.9%) (all p < 0.05) compared to FeBC. There was no difference in TMB high (7.1% vs 8.4%, p = 0.5) and dMMR/MSI-H (1.8% vs 0.8%, p = 0.1). Analysis of inferred immune cell infiltrates showed that MaBC had increased immune cell infiltration of B cells (5.8% vs 5.3%) and M2 Mφ (4.9% vs 4.3%), but decreased infiltration of DC (2% vs 2.6%) (all p < 0.05). MaBC had increased expression of MHC class II gene HLA-DQB2 (FC: 1.3), but decreased expression of immune-related genes CD274 (FC: 1.2), IDO (FC: 1.4), IL1A (FC: 1.3) and IL12A (FC: 1.5) (all p < 0.05). Correlative analyses with survival will be presented at the meeting. Conclusions: These data indicate that MaBC has a differential mutational frequency, copy number alteration, immune gene expression and immune cell infiltration and overall survival compared to their FeBC counterparts. A better understanding of these sex-based differences with additional research may help inform disease outcomes, provide a rationale for tailored therapeutic approaches and design future treatments. Table 1. Mutation frequency in male and female breast cancer Citation Format: Dario Trapani, Sachin Deshmukh, Sharon Wu, Joanne Xiu, Phil Walker, Pooja Advani, Nancy Lin, Giuseppe Curigliano, Stephanie Graff, Chadi Nabhan, George Sledge Jr, Sara Tolaney, Jose Leone. Molecular and immunological landscape of sex-based differences in breast cancer: a distinct disease in men [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS13-09.

Abstract PO2-09-10: Addressing Breast Cancer Disparities: Co-Creating Digital Interventions with Patients, Navigators & the Community to Address Social Determinants of Health in the Memphis Statistical Area

Abstract Background: The Memphis Statistical Area, which covers counties in Arkansas, Mississippi, and Tennessee, leads in disparities in mortality rates between Black breast cancer patients compared to White counterparts1. Urban Health Education & Support Services (UHESS), in partnership with RabbleHealth, and West Cancer Center & Research Institute (WCCRI), initiated a solutions-oriented, community-based scalable initiative in January 2023 to measurably address social determinants of health (SDOH), which often drive cancer inequities that disproportionately impact individuals of marginalized communities. By leveraging a community-driven, co-creation sustainable approach, the team sought to measurably improve breast cancer equality utilizing digital enablement and the knowledge of local breast cancer survivors and leading healthcare professionals, including navigators. Methods: A four-phase approach was leveraged to 1. improve access to locally available breast cancer services in communities that are traditionally underserved and 2. measure the public health impact against root causes of breast inequities (i.e., care pathway metrics), and 3. create a repeatable, scalable model to expand to other underserved communities. In Phase 1, UHESS leveraged the Mid-South Regional Breast Cancer Coalition, which convenes ten local breast cancer patient advocacy organizations, to recruit focus groups for co-creation throughout all phases of the initiative. The working group consisted of eight representatives from a variety of Memphis-based cancer organizations, faith-based organizations, navigator programs, and WCCRI. This phase centered around establishing trust with the local patient advocacy community. In Phase 2, an initial patient survey was circulated to identify key resources that reduce health inequities and barriers to access. Human-centered design facilitators supported a series of Listen & Learn workshops with patients to convey root causes of gaps in access to relevant services and with navigators to understand professional needs of navigators and scale the ability improve patient access to resources. To co-create a solution, facilitated patient and navigator workshops were held in Phase 3 to gather patient-centric user experience and design enhancements for a digital patient engagement app. These requirements as well as navigator-defined metrics needs were digitized and organized by SDoH. Phase 4, the Deploy & Measure phase, will begin in September of 2023 and the community-based deployment model focuses on three drivers including: (a) embedding within navigator workflow, (b) activating faith-based organizations, and (c) leveraging societies. Health equity performance data will be analyzed weekly to rapidly target those ZIP codes with the greatest need. Results: Co-design efforts included over 50 members of the Greater Memphis community and final initiative results will be presented at the meeting. Planning for further research regarding community impact and model scalability is already underway. Conclusion: By leveraging a community-driven, co-creation sustainable approach, this model enables a better way to measurably improve breast cancer equality utilizing digital enablement and the knowledge of local breast cancer survivors and leading healthcare professionals, including navigators. Initiative Funding Acknowledgements: Gilead Life Sciences & Blue Cross Blue Shield of Tennessee Foundation 1. Vidal G, Bursac Z, Miranda-Carboni G, White-Means S, Starlard-Davenport A. Racial disparities in survival outcomes by breast tumor subtype among African American women in Memphis, Tennessee. Cancer Med. 2017 Jul;6(7):1776-1786. doi: 10.1002/cam4.1117. Epub 2017 Jun 14. PMID: 28612435; PMCID: PMC5504313. Citation Format: Gregory Vidal, Stacey Tinianov, Aubrey Kelly, Andrea Curry, Carla Baker. Addressing Breast Cancer Disparities: Co-Creating Digital Interventions with Patients, Navigators & the Community to Address Social Determinants of Health in the Memphis Statistical Area [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-09-10.

Abstract PO4-24-02: Comprehensive Characterization of BCL2 Family Genes in Metaplastic Triple Negative Breast Cancer

Abstract Background: Metaplastic Breast Cancer (MBC) is rare (0.2-5%), aggressive form of BC characterized by chemotherapy resistance and has worse outcomes in comparison to other BC subtypes. Resistance to chemotherapeutic agents is related to defects in intact intrinsic apoptosis pathway and the BCL2 family of proteins are the central regulators of this pathway. Majority of MBC have triple-negative receptor status and have no standard therapeutic approach and validated prognostic markers. Here, we examine the association of BCL2 family pro-apoptotic and anti-apoptotic genes expression with metaplastic TNBC (MTNBC) patient survival. Methods: 13,036 BC samples (MTNBC, n=102; metaplastic non-TNBC, n=20) were analyzed by next-generation sequencing (592, NextSeq; WES, NovaSeq), Whole Transcriptome Sequencing (WTS; NovaSeq) (Caris Life Sciences, Phoenix, AZ). A total of 10 pro-apoptotic (BAX, BAK1, BID, BAD, BIK, BCL2L11, BMF, HRK, PMAIP1, BBC3) and 6 anti-apoptotic (BCL2, BCL2L1, BCL2L2, MCL1, BCL2A1, BCL2L10) BCL2 family genes were analyzed. MTNBC with PMAIP1-high(H) and -low(L) expression was classified by top and bottom quartile, respectively. Pathway enrichment was determined by GSEA (Broad Inst). Real world overall survival (OS) was extracted from insurance claims and calculated from tissue collection to last contact using Kaplan-Meier estimates. Statistical significance was determined using chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q < 0.05). Results: MTNBC had enrichment of apoptosis (NES: 1.4, FDR: 0.05), glycolysis (NES: 1.48, FDR: 0.03), PI3K/AKT/mTOR signaling (NES: 1.43, FDR: 0.05), P53 (NES: 1.51, FDR: 0.06), NOTCH signaling (NES: 1.39, FDR: 0.05), TGFβ signaling (NES: 1.41, FDR: 0.05), WNTβ catenin signaling (NES: 1.41, FDR: 0.05) and IL2/STAT5 signaling (NES: 1.33, FDR: 0.09) pathways compared to metaplastic non-TNBC. MTNBC had higher expression of BCL2 pro-apoptotic genes BAX (Fold Change (FC): 1.6), BAK1 (FC: 1.3), BID (FC: 2), BAD (FC: 1.6), BCL2L11 (FC: 2.5) and BBC3 (FC: 1.5), and anti-apoptotic genes BCL2L1 (FC: 1.6) and BCL2L2 (FC: 1.3) (all p < 0.05) compared to metaplastic non-TNBC. Higher PMAIP1 gene expression was associated with worse MTNBC patient survival (mOS: 14.3 month; HR: 0.37; 95% CI 0.19-1.41; p=0.002) (Table 1), but not in metaplastic non-TNBC (mOS: Inf; HR: 1.96; 95% CI 0.64-6.02; p=0.23). PMAIP1-H MTNBC had higher expression of immune checkpoint genes CD274 (FC: 2.8), PDCD1 (FC: 2.2), TIM3 (FC: 1.8), LAG3 (FC: 2.1) and IDO1 (FC: 5.7) (all p < 0.05), compared to PMAIP1-L MTNBC. PMAIP1-H MTNBC had higher frequency of IHC-PD-L1 positivity (68.4% vs 14.3%, p < 0.05). PMAIP1-H MTNBC had higher expression of stem cell related genes CD44 (FC: 1.7), ALDH1A2 (FC: 2.2), ALDH1A3 (FC: 2.6), SOX2 (FC: 5.21) and NANOG (FC: 2.13) (all p < 0.05) compared to PMAIP1-L MTNBC. Conclusion: This is the first comprehensive analysis of expression and prognostic role of BCL2 family proteins in MBC. Our data suggest a strong association of higher expression of PMAIP1 with worse MTNBC patient survival, potentially attributed to higher immune checkpoint, stem cell-related genes expression, and higher frequency of PD-L1 positivity in PMAIP1-H tumors. These findings indicate PMAIP1 as a potential prognostic biomarker candidate in MTNBC but needs further validation in large prospective studies Table 1. Overall survival of metaplastic TNBC patient based on BCL2 family gene expression. Citation Format: Pooja Advani, Sachin Deshmukh, Sharon Wu, Jacob Andring, Joanne Xiu, Alex Farrell, Milan Radovich, George Sledge Jr, Dario Trapani, Evanthia Roussos Torres, Stephanie Graff, Asher Chanan-Khan. Comprehensive Characterization of BCL2 Family Genes in Metaplastic Triple Negative Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-24-02.

Abstract PO4-24-08: Genomic Landscape of Malignant Phyllodes Tumors Identifies Subsets for Targeted Therapy

Abstract Introduction: Phyllodes tumors (PT) are rare fibroepithelial tumors of the breast, comprising ~1% of all breast cancers, a subset of which have considerable malignant potential. Malignant phyllodes tumors (MPTs) have aggressive biological behavior and high local and distant recurrence rates. Distant metastases of MPTs have a poor prognosis given the limited treatment options available. Surgery remains the primary treatment modality for these patients; however, initial investigations suggest a potential for targeted therapies in managing this disease. The identification of targetable opportunities and a comprehensive understanding of the mutational profiles of MPTs could greatly enhance treatment options. Therefore, we aimed to assess the molecular landscape of these tumors. Methods: Phyllodes tumor samples underwent molecular profiling at Caris Life Sciences through DNA (592-gene panel or whole exome) and RNA sequencing (whole transcriptome). The MPTs were classified into primary and metastatic based on the specimen biopsy site. PD-L1+ expression was tested by IHC (SP142; ≥2+, ≥5%). Tumor mutational burden (TMB)-High was defined as ≥10 mutation/Mb. Immune cell fractions in the tumor microenvironment (TME) were estimated using quanTIseq (Finotello, 2019). Mann-Whitney U, Chi-square, and Fisher-Exact tests were applied where appropriate. Results: We identified 57 analyzed MPTs, all from female patients, with a median age of 53 years (range: 19-88). Approximately half of samples (53%, n=30) were labeled as from primary breast sites, and the remaining sites were metastatic (47%, n= 27). Of metastatic sites, lung was the most common location (74.1%, n=20/27), followed by bone, sacrum, pancreas and small bowel. Alterations in MPT include TERT promoter (56.8%, n=21/37), MED12 (51.6%, n=16/31), TP53 (40.0%, n=22/55), and NF1 (31.8%, n=14/44) mutations, with less frequent mutations of EGFR (10.5%, n=6/57), PIK3CA (7.0%, n=4/57), and BRAF (3.5%, n=2/57). As compared to primary MPT, metastatic MPT had roughly 2-fold higher prevalence of NF1 (45.5%: n=10/22 vs 18.2% n=4/22, p=0.05), KMT2D (25.9%: n=7/27 vs 10.7%: n=3/28, p=0.18), and RB1 (25.0%: n=6/24 vs 9.5%: n=2/21, p=0.25) though not significant. Multiple gene mutations were observed exclusively in lung metastases, as compared to non-lung sites including: TERT promoter (64.3%: n=9/14 vs 0.0%, p=0.08), MED12 (60.0%: n=6/10 vs 0.0%, p =0.044), and RB1 (35.3%: n=6/17 vs 0.0%, p=0.01). Conversely, NF1 (43.8%: n=7/16 vs 50.0%: n=3/6, p=1.0) and KMT2D (20.0%: n=4/20 vs 42.9%: n=3/7, p=0.32) mutation prevalence was higher in other metastatic sites. PD-L1+ expression was observed in 13.3% (n=7) of MPT overall, with similar prevalence among local and metastatic sites. No dMMR/MSI-H was observed, while low LOH (those with genomic LOH in < 16% of segment analyzed) was seen across MPT. Compared to a large cohort of breast adenocarcinoma samples (n=9,926) representing both HER2+ and HER2- tumors, MPT had low ERBB2 expression comparable to HER2- samples. B cells, M2 macrophages and neutrophils had the highest median cell fractions in the TME of MPT. Additionally, one MPT sample harbored a pathogenic NTRK1 fusion (TPM4:NTRK1), and treatment with larotrectinib for over 16 months suggests a clinical response to therapy. Conclusions: Our study demonstrates the importance of employing next generation sequencing (NGS) in MPTs to detect actionable genomic alterations. To effectively analyze fusions, an NGS panel that include RNA sequencing is recommended, considering the occurrence of NTRK1 fusion reported herein. Although HER2 transcriptional expression was low, further investigations examining HER2 IHC in PTs are still necessary. These finding therefore highlight the importance of NGS in phyllodes tumors research, as it may uncover potential targeted treatment options for patients. Citation Format: Rani Bansal, Tolulope Adeyelu, Andrew Elliott, Antoinette Tan, Jane Meisel, Matthew Oberley, Stephanie Graff, Jorge Reis-Filho, George Sledge Jr, Sarah Sammons, Laura Rosenberger. Genomic Landscape of Malignant Phyllodes Tumors Identifies Subsets for Targeted Therapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-24-08.

Extraction Optimization, Structure Analysis and Antioxidant Activity of Polysaccharide from Sanghuangporus baumii

Introduction: In this study, we optimized the extraction process, analyzed the structure and assessed the antioxidant activity of Sanghuangporus baumii polysaccharide (SBP). The present results provide important information for the Sanghuangporus baumii polysaccharides in potential natural antioxidant effects. Background: The extraction and structural analysis of polysaccharides from Sanghuangporus has gained significant attention in the fields of chemistry, medicine, and life sciences. There is great significance in maximizing the extraction of polysaccharides from Sanghuangporus and developing their potential products in a scientific and rational manner. Objective: The study was designed to establish an efficient and practical extraction process for SBP, and then investigated the structure and the antioxidant activity. Methods: The Response Surface Methodology (RSM) based on Box-Behnken design was used to explore the ultrasound-assisted extraction of SBP, and the structure of SBP was studied by ultraviolet spectroscopy, infrared spectroscopy and other instrumental analysis methods. The total antioxidant capacity of SBP was studied by the Ferric Reducing Ability of Plasma (FRAP) method, and the scavenging capacity of ABTS+·, DPPH· and OH· was carried out as the index to investigate its antioxidant activity in vitro. Results: The statistical analysis results showed that the optimal conditions for extracting SBP were an ultrasound time of 20.74 min, ultrasound power of 268.40 W and material-liquid ratio of 1:25.71. Under optimal conditions, the experimental yield of SBP was 3.36 ± 0.01%. The RSM optimization process was applied to the experiment of complex enzyme extraction of SBP, and the yield increased to 4.72 ± 0.03%. Structural analysis showed that SBP mainly consisted of glucose, a small amount of mannose and galactose, and the molecular weight distribution was uneven, mainly concentrating in the three parts of 24.5,6.4,2.5 kDa. Moreover, SBP exhibited dose-dependent and strong reducing power and radical scavenging activity. For DPPH·, ABTS+· and OH· radical scavenging assays, IC50 values were 1.505 ± 0.050 mg/ml, 0.065 ± 0.036 mg/ml and 0.442 ± 0.007 mg/ml, respectively. Conclusion: In the present study, a β-linked heteroglucan (SBP) was extracted using the optimized process combining enzymes from the fruiting bodies of Sanghuangporus baumii. SBP exhibited effective and dose-dependent antioxidant activities. Our findings were of great value in terms of developing polysaccharides with potential natural antioxidants.

Front Cover

Journal of Biophotonics focuses on the interdisciplinary field of biophotonics, publishing cutting‐edge research on interactions between light and biological material. The journal covers photonics research in areas such as life sciences, medicine and biomedicine, environmental science, nutrition, biology, physics, and chemistry, ranging from fundamental research to the latest clinical applications. image

Cover Picture: Engineering in Life Sciences 5'24

Cover Picture: Engineering in Life Sciences 5'24

Can Citizens Do Science? Science in Common and Social Responsibility

Citizen science is an effective tool that unites ordinary citizens and scientists for a common cause. In particular, this tool enables ordinary citizens to participate in research and increases the likelihood of generating new knowledge. It is seen as the democratization of science. It is mainly applied in developed countries, and citizens usually help obtain environmental data with emerging technologies. However, training citizens to obtain good-quality data is one of the most significant challenges. It is also important to involve citizens in other phases, such as data analysis, discussion, and knowledge generation. Citizen science can be a tool for integrating different groups in science to promote social inclusion, including environmental, agricultural, earth, and life sciences. Thus, citizen science can contribute to education, sustainability, and climate change mitigation.

Synthesis, characterization, DFT calculations, and anticancer properties of VI-period and f-block elements-substituted zinc oxide nanopowders

Nanotechnology provides promising ways in which a wide range of new materials can be manufactured which appear to have enormous potential in the field of biomedicine and life sciences. ZnO can be applied in many physical and optical processes and used as a good anti-cancer agent. ZnO NPs are recognized as SAFE or GRAS, non-toxic and biocompatible particles. In this study, wurtzite ZnO samples co-doped by rare earth elements (Tb, Er) were prepared via sol-gel auto-combustion route and their crystallographic structure as well as their morphologies were examined using XRD and TEM techniques. The analysis disclosed that all synthesized products crystallized in a hexagonal structure and the crystallites/particles size diminished with the increase of co-doping content. The electronic structure and optical properties of the different products were assessed using DFT calculations. Doping Tb and Er rare earth elements into ZnO has a significant effect on its optoelectronic properties. The computational study showed that the co-doping of Tb and Er on pure ZnO decreased the band gap and increased the refractive index. The extinction spectrum of pristine ZnO showed a peak in the ultraviolet region at 5 eV, while those of the co-doped ZnO samples displayed stronger peaks in the infrared region (near 0.4 eV). The anticancer properties of Tb/Er co-doped ZnO nanoparticles were examined on cervical cancer (HeLa cells) and colon cancer (HCT-116) by using an in vitro MTT assay. The cell viability assay findings indicated a reduction in HeLa and HCT-116 cells after 48 hours of treatment of the synthesized samples. The treatment with co-doped ZnO nanoparticles produced chromatin condensation and formation of apoptotic bodies in HCT-166 cells, which indicates that the prepared co-doped ZnO nanoparticles induced programmed cell death in HCT-116 cells. According to these results, it can be concluded that the prepared Tb/Er co-doped ZnO nanoparticles have promising applications in developing new optoelectronic devices and also in treating cervical and colon cancers.

RCPA: An Open-Source R Package for Data Processing, Differential Analysis, Consensus Pathway Analysis, and Visualization.

Identifying impacted pathways is important because it provides insights into the biology underlying conditions beyond the detection of differentially expressed genes. Because of the importance of such analysis, more than 100 pathway analysis methods have been developed thus far. Despite the availability of many methods, it is challenging for biomedical researchers to learn and properly perform pathway analysis. First, the sheer number of methods makes it challenging to learn and choose the correct method for a given experiment. Second, computational methods require users to be savvy with coding syntax, and comfortable with command-line environments, areas that are unfamiliar to most life scientists. Third, as learning tools and computational methods are typically implemented only for a few species (i.e., human and some model organisms), it is difficult to perform pathway analysis on other species that are not included in many of the current pathway analysis tools. Finally, existing pathway tools do not allow researchers to combine, compare, and contrast the results of different methods and experiments for both hypothesis testing and analysis purposes. To address these challenges, we developed an open-source R package for Consensus Pathway Analysis (RCPA) that allows researchers to conveniently: (1) download and process data from NCBI GEO; (2) perform differential analysis using established techniques developed for both microarray and sequencing data; (3) perform both gene set enrichment, as well as topology-based pathway analysis using different methods that seek to answer different research hypotheses; (4) combine methods and datasets to find consensus results; and (5) visualize analysis results and explore significantly impacted pathways across multiple analyses. This protocol provides many example code snippets with detailed explanations and supports the analysis of more than 1000 species, two pathway databases, three differential analysis techniques, eight pathway analysis tools, six meta-analysis methods, and two consensus analysis techniques. The package is freely available on the CRAN repository. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing Affymetrix microarrays Basic Protocol 2: Processing Agilent microarrays Support Protocol: Processing RNA sequencing (RNA-Seq) data Basic Protocol 3: Differential analysis of microarray data (Affymetrix and Agilent) Basic Protocol 4: Differential analysis of RNA-Seq data Basic Protocol 5: Gene set enrichment analysis Basic Protocol 6: Topology-based (TB) pathway analysis Basic Protocol 7: Data integration and visualization.

Assessment of the feed additive consisting of l-cystine for all animal species for the renewal of its authorisation (Bretagne Chimie Fine [BCF Life Sciences]).

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the assessment of the application for the renewal of the authorisation of l-cystine as nutritional feed additive. The additive is authorised for use in all animal species (3c391). The applicant has provided evidence that the additive currently in the market complies with the existing conditions of authorisation. The EFSA Panel on Additives and Products or Substances used in Animal Feed concluded that the use of the feed additive in animal nutrition remains safe for the target species, the consumers and the environment. As regards the safety for the user, l-cystine is not an irritant to skin or eyes and is not a skin sensitiser. Exposure by inhalation of persons handling the additive cannot be excluded. The present application for the renewal of the authorisation does not include any modification proposal that would have an impact on the efficacy of the additive and therefore there is no need for reassessing the efficacy.