Molecular Testing Research Articles

[Advances of pathological research and classification in malformations of cortical development associated with refractory epilepsy].

With rapid development of genetic testing techniques, neuroimaging and neuroelectrophysiological technologies, our understanding of malformations of cortical development continues to be deepened and updated. In particular, mutations in genes related to the mammalian target of rapamycin (mTOR) signaling pathway have been successively discovered in focal cortical dysplasia (FCD). At the same time, the classification consensus on FCD issued by the International League Against Epilepsy (ILAE) in 2011 has encountered problems and challenges in diagnostic practice. Therefore, in 2022, ILAE proposed an updated version of the FCD classification based on the progress in molecular genetics over the past decade. The main addition to the classification system is "white matter lesions, " and it is also suggested to integrate histopathological, neuroimaging, and molecular testing results for multi-level integrated diagnosis to achieve reliable, clinically relevant, and therapeutic targeted final diagnosis.

Laryngeal features in Lipoid proteinosis: a systematic review and meta-analysis of individual participant data.

Lipoid proteinosis (LP) or Urbach-Wiethe disease (OMIM 247100) is a rare syndrome characterised by early vocal folds infiltration and subsequent multi-organ involvement. LP is often unrecognised and its associated hoarseness is overlooked. The main objective of the study was to investigate hoarseness in LP and implement a diagnosis among otolaryngologists. PubMed/MEDLINE and OMIM databases were systematically searched. Authors concentrated the search on published articles starting from the discovery of the pathogenesis of LP by Hamada et al. in 2002. Only cases in which a diagnosis was reported both clinically and through biopsy and/or genetic molecular testing were included. Characteristics of the LP cases were extracted from each included study. Results were obtained through Generalized Estimating Equations. The search strategy yielded 217 articles, of which 74 (34.1%) met the selection criteria. A total of 154 cases were included. Hoarseness was described in all LP cases and clearly stated as the onset symptom in 68.8%. The onset was on average at 19months of age (CI: 3.00-20.00), while the mean age at diagnosis was 15years (CI: 10.00-30.00). Therefore, the diagnostic delay amounted to 13.42years (CI: 8.00-23.83). Hoarseness alone was responsible for an LP diagnosis in only 14.3% of cases. In 43.5% of cases, genetic analysis of the ECM1 gene was performed and exon 6 was the most frequently altered portion. Analysing the largest number of published cases, the study underlined that hoarseness is the key symptom for diagnosing LP since early childhood, though frequently overlooked.

Neurological features of Hansen disease: a retrospective, multicenter cohort study

To elucidate the neurological features of Hansen disease. The medical records of patients with confirmed Hansen disease transferred from the neurology department were reviewed, and all medical and neurological manifestations of Hansen disease were assessed. Eleven patients with confirmed Hansen disease, 10 with newly detected Hansen disease and 1 with relapsed Hansen disease, who visited neurology departments were enrolled. The newly detected patients with Hansen disease were classified as having lepromatous leprosy (LL, n = 1), borderline lepromatous leprosy (BL, n = 2), borderline leprosy (BB, n = 2), borderline tuberculoid leprosy (BT, n = 1), tuberculoid leprosy (TT, n = 2), or pure neural leprosy (PNL, n = 2). All of the patients with confirmed Hansen were diagnosed with peripheral neuropathy (100.00%, 11/11). The symptoms and signs presented were mainly limb numbness (100.00%, 11/11), sensory and motor dysfunction (100.00%, 11/11), decreased muscle strength (90.90%, 10/11), and skin lesions (81.81%, 9/11). Nerve morphological features in nerve ultrasonography (US) included peripheral nerve asymmetry and segmental thickening (100.00%, 9/9). For neuro-electrophysiology feature, the frequency of no response of sensory nerves was significantly higher than those of motor nerves [(51.21% 42/82) vs (24.70%, 21/85)(P = 0.0183*)] by electrodiagnostic (EDX) studies. Nerve histological features in nerve biopsy analysis included demyelination (100.00%, 5/5) and axonal damage (60.00%, 3/5). In addition to confirmed diagnoses by acid-fast bacteria (AFB) staining (54.54%, 6/11) and skin pathology analysis (100.00%, 8/8), serology and molecular technology were positive in 36.36% (4/11) and 100.00% (11/11) of confirmed patients of Hansen disease, respectively. It is not uncommon for patients of Hansen disease to visit neurology departments due to peripheral neuropathy. The main pathological features of affected nerves are demyelination and axonal damage. The combination of nerve US, EDX studies, nerve biopsy, and serological and molecular tests can improve the diagnosis of Hansen disease.

Burden and frequency of viral testing of kidney and non-kidney transplant recipients.

Transplant patients are at risk of infections due to long-term immunosuppression contributing to morbidity and mortality in this population. Post-transplant testing guidelines were established to monitor and guide therapeutic interventions in transplant recipients. We hypothesize that there are gaps in adherence to the recommended frequency of laboratory testing in post-transplant patients. We analyzed national reference laboratory data to compare viral post-transplant infection (PTI) testing frequency with their respective published guidelines to understand patient uptake and compliance. We evaluated the ordering patterns, positivity rates, and frequency of molecular infectious disease tests (MIDTs). We included 345 patients with International Classification of Diseases (ICD)-10 codes for transplant (Z940-Z942, Z944, Z9481, Z9483, Z9484) with at least two tests (within 7 days) in January 2019 and at least one test in December 2020 to find patients in the post-transplant period. We analyzed two cohorts: kidney transplant recipients (KTRs; 40%) and non-KTR (60%) then followed them longitudinally for the study period. In KTR cohort, high-to-low proportion of ordered MIDT was blood BK virus (bBKV) followed by cytomegalovirus (CMV); in non-KTR cohort, CMV was followed by Epstein-Barr virus (EBV). KTR cohort positivity was highest for urine BK virus (uBKV; 58%) followed by EBV (46%), bBKV (40%), and CMV (31%). Non-KTR cohort positivity was highest for uBKV (64%), EBV (51%), CMV (30%), bBKV (8%), and adenovirus (7%). All patients were tested at progressively longer intervals from the date of the first post-transplant ICD-10-coded test. More than 40% of the KTR cohort were tested less frequently for EBV and bBKV, and more than 20% of the non-KTR cohort were tested for EBV less frequently than published guidelines 4 months after transplant. Despite regular testing, the results of MIDT testing for KTR and non-KTR patients in the post-transplant period are not aligned with published guidelines.IMPORTANCEGuidance for post-transplant infectious disease testing is established, however, for certain infections it allows for clinician discretion. This leads to transplant center policies developing their own testing/surveillance strategies based on their specific transplant patient population (kidney, stem cell, etc.). The Organ Procurement and Transplant Network (OPTN) has developed a strategic plan to improve and standardize the transplant process in the US to improve outcomes of living donors and recipients. Publishing national reference lab data on the testing frequency and its alignment with the recommended guidelines for post-transplant infectious diseases can inform patient uptake and compliance for these strategic OPTN efforts.

Can incorporating molecular testing improve the accuracy of newborn screening for congenital adrenal hyperplasia?

Single-tier newborn screening (NBS) for CAH using 17-hydroxyprogesterone (17OHP) measured by fluoroimmunoassay (FIA) in samples collected at 24-48 hours produces a high false-positive rate (FPR). 2nd tier steroid testing can reduce the FPR and has been widely implemented. We investigated the accuracy of an alternative multi-tier CAH NBS protocol that incorporates molecular testing of the CYP21A2 gene and reduces the 1st tier 17OHP cutoff to minimize missed cases. Created a Minnesota-specific CYP21A2 pathogenic variants panel; develop a rapid, high-throughput multiplex, allele-specific-primer-extension assay; perform 1-year retrospective analysis of Minnesota NBS results comparing metrics between a conventional steroid-based two-tier protocol and a molecular-based multi-tier NBS protocol, applied post-hoc. CYP21A2 gene sequencing of 103 Minnesota families resulted in a Minnesota-specific panel of 21 pathogenic variants. Centers for Disease Control and Prevention (CDC) created a molecular assay with 100% accuracy and reproducibility. Two-tier steroid-based screening of 68,659 live births during 2015 resulted in 2 false negatives (FNs), 91 FPs, and 1 true positive (TP). A three-tier protocol with a lower 1st-tier steroid cutoff, 2nd-tier 21-variant CYP21A2 panel and 3rd-tier CYP21A2 sequencing would have resulted in 0 FNs, 52 FPs and 3 TPs. Incorporation of molecular testing could improve the accuracy of CAH NBS, although some distinct challenges of molecular testing may need to be considered before implementation by NBS programs.

Impact of molecular ciprofloxacin resistance testing in management of gonorrhoea in a large urban clinic

ObjectivesAntibiotic resistance in gonorrhoea is of significant public health concern with the emergence of resistance to last-line therapies such as ceftriaxone. Despite around half of Neisseria gonorrhoeae isolates tested in...

Detection of Oncogene Hotspot Mutations in Female NSCLC Tumor DNA and Cell-Free DNA

Non-small-cell lung cancer (NSCLC) is the most prevalent type of lung cancer, with extensively characterized mutational spectra. Several biomarkers (such as EGFR, BRAF, KRAS gene mutations, etc.) have emerged as predictive and prognostic markers for NSCLC. Unfortunately, the quality of the available tumor biopsy and/or cytology material is not always adequate to perform the necessary molecular testing, prompting the search for alternatives. Cell-free DNA (cfDNA) found in plasma is emerging as a highly promising avenue or a supplementary method for assessing the efficacy of cancer treatments. This is especially valuable in instances where conventional biopsy specimens, like formalin-fixed, paraffin-embedded (FFPE), or freshly frozen tumor tissues prove inadequate for conducting molecular pathology analyses subsequent to the initial diagnostic procedures. By leveraging cfDNA from plasma, clinicians gain an additional tool to gauge the effectiveness of cancer therapies, thereby enhancing their ability to optimize tailored treatment strategies. In this study, 51 Lithuanian females with NSCLC were analyzed, with adenocarcinoma being the predominant pathology diagnosis in 40 cases (78%). Target mutations were identified in 38 out of 51 patients (74.5%) in tumor tissue samples, while in plasma samples, they were identified in only 10 patients’ samples (19.6%). Even though we did not have enough voluminous plasma samples in our study, gene mutations were detected in plasma from ten women, three of whom were diagnosed with early stages of lung cancer (stages I and II). For these patients, the following mutations were detected: deletion in exon 19 of the EGFR gene and single nucleotide polymorphisms in the TP53 and MET genes. All other women were diagnosed with stages III or IV of lung cancer. This indicates that the later stages of cancer contribute more cfDNA in plasma, making extraction less complicated.

Pediatric neuropathology practice in a low- and middle-income country: capacity building through institutional twinning

BackgroundAccurate and precise diagnosis is central to treating central nervous system (CNS) tumors, yet tissue diagnosis is often a neglected focus in low- and middle-income countries (LMICs). Since 2016, the WHO classification of CNS tumors has increasingly incorporated molecular biomarkers into the diagnosis of CNS tumors. While this shift to precision diagnostics promises a high degree of diagnostic accuracy and prognostic precision, it has also resulted in increasing divergence in diagnostic and management practices between LMICs and high-income countries (HICs). Pathologists and laboratory professionals in LMICs lack the proper training and tools to join the molecular diagnostic revolution. We describe the impact of a 7-year long twinning program between Canada and Pakistan on pathology services.MethodsDuring the study period, 141 challenging cases of pediatric CNS tumors initially diagnosed at Aga Khan University Hospital (AKUH), Karachi, were sent to the Hospital for Sick Children in Toronto, Canada (SickKids), for a second opinion. Each case received histologic review and often immunohistochemical staining and relevant molecular testing. A monthly multidisciplinary online tumor board (MDTB) was conducted to discuss the results with pathologists from both institutions in attendance.ResultsDiagnostic discordance was seen in 30 cases. Expert review provided subclassification for 53 cases most notably for diffuse gliomas and medulloblastoma. Poorly differentiated tumors benefited the most from second review, mainly because of the resolving power of specialized immunohistochemical stains, NanoString, and targeted gene panel next-generation sequencing. Collaboration with expert neuropathologists led to validation of over half a dozen immunostains at AKUH facilitating diagnosis of CNS tumors.ConclusionsLMIC-HIC Institutional twinning provides much-needed training and mentorship to pathologists and can help in infrastructure development by adopting and validating new immunohistochemical stains. Persistent unresolved cases indicate that molecular techniques are indispensable in for diagnosis in a minority of cases. The development of affordable alternative molecular techniques may help with these histologically unresolved cases.

Abstract PO4-03-01: Enhancing Breast Cancer Subtyping: APIS Breast Cancer Subtyping Kit Proliferative Signature's Potential for Improved Proliferation Assessment and Recurrence Prediction

Abstract Background: Ki67, a widely recognized biomarker for measuring tumor cell proliferation in breast cancer (BC), plays a crucial role in classifying BC into luminal A and luminal B subtypes, subsequently aiding treatment decisions. However, the inconsistency in Ki67 assessment and the lack of standardization in methods and interpretation of immunohistochemistry (IHC) staining has hindered its recommendation for routine diagnostic use. The standardization of measurement techniques, especially for Ki67, holds immense potential for improving patient treatment outcomes. The APIS Breast Cancer Subtyping Kit (APIS BCS Kit) addresses these challenges by utilizing RT-qPCR to accurately determine the mRNA expression of BC markers, including Ki67, along with a novel four-gene proliferative signature, comprising four markers (MKI67, CCNA2, KIF23, and PCNA) associated with proliferation and expressed throughout all cell cycle stages, thereby providing a more accurate measure of tumor proliferation. In this study, we present the preliminary findings of our ongoing evaluation of the APIS BCS Kit proliferative signature's ability to distinguish between Luminal A and Luminal B subtypes and to determine the risk of recurrence in hormone receptor-positive (HR+) patients. Method: A total of N=153 retrospectively collected HR+/HER2 negative samples were provided by University of Basel. For each sample the following clinical annotations were included: relapse free survival, treatment regimen (Chemotherapy (ChT) or Hormone Therapy (HT)) as well as OncotypeDx (ODx) risk score (RS). N=40 samples underwent additional testing using PAM50 (Prosigna®) test. Only samples collected since 2018 were included, resulting in 10 observed relapse events (N=7 in HT cohort and N=3 in ChT cohort). RNA isolation from tissue sections and gene expression analysis were performed as per APIS BCS Kit instructions for use. The agreement of subtype calls between IHC, APIS BCS Kit, and PAM50 was assessed. The correlation between RS obtained from ODx, PAM50 and the APIS BCS Kit proliferation signature was also explored. Results: The agreement between IHC and the APIS BCS Kit subtype call, utilizing Ki67 alone as a measure of proliferation, was 67.3% (103/153). Replacing Ki67 with the APIS BCS Kit proliferation signature increased the concordance to 69.9% (107/153). The concordance between IHC and PAM50 subtype calls was comparable at 62.5% (25/40). The agreement between the APIS BCS Kit and PAM50 subtype call was notably higher (80%; 32/40). Significant association was observed between the APIS BCS Kit proliferation signature and ODx RS (P=.0001), and PAM50 RS (P=.002). In the HT cohort, both ODx and the APIS BCS Kit proliferation signature accurately predicted recurrence (by assigning high RS) in n=2 cases. In some cases both the APIS BCS Kit and ODx erroneously assigned low risk and subsequently missed n=4 recurrence events. Notably, APIS BCS Kit proliferation signature correctly identified one recurrence event (high RS), which was missed by ODx (low RS). Conclusion: The APIS Breast Cancer Subtyping Kit exhibits improved agreement with the PAM50 molecular subtype in contrast to the IHC-derived subtype, indicating that molecular testing may be a more suitable method for determining proliferation and distinguishing between luminal A and B subtypes. Furthermore, there is a significant correlation between the RS generated by APIS Breast Cancer Subtyping Kit proliferation signature and both PAM50 and Oncotype RS. These initial findings indicate that the APIS Breast Cancer Subtyping Kit proliferation signature has the potential to accurately identify patients at risk of recurrence, although additional studies including a larger proportion of events are needed to validate these results. Citation Format: Marcus Vetter, Anna Gasior, Elena-Diana Chiru, Joanna Gorniak, Leanne Gough, Mathew Harrison, Sara Rollinson, Simone Muenst, Christian Kurzeder. Enhancing Breast Cancer Subtyping: APIS Breast Cancer Subtyping Kit Proliferative Signature's Potential for Improved Proliferation Assessment and Recurrence Prediction [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 PO4-03-01.

Quantification of ovine gammaherpesvirus 2 in clinical cases of cattle with sheep-associated malignant catarrhal fever.

Ovine gammaherpesvirus 2 (OvGHV2) produces sheep-associated malignant catarrhal fever (SA-MCF), a frequently lethal, lymphoproliferative disease that is characterized by widespread vascular lesions. Most studies that evaluated the viral load in tissues of animals with SA-MCF were done in the Northern Hemisphere, with scant information from the Southern part of the globe. This study investigated the viral load of OvGHV2 in the tissues of cattle and an underdeveloped fetus with SA-MCF from three distinct biomes of Brazil. All animals had clinical and histopathological manifestations consistent with SA-MCF. Molecular testing identified the OvGHV2 tegument protein and glycoprotein B genes in the tissues of all animals and the fetus. Viral quantification based on the DNA polymerase gene detected elevated loads of OvGHV2 in tissues with histopathological evidence of SA-MCF and organs with unknown histological data, except for the tissues of the fetus, where the viral load was comparatively reduced. The viral loads detected in multiple organs of cattle from this study with SA-MCF are consistent with those identified in different animal species from the USA and Europe. The detection of a low viral load of OvGHV2 in fetal tissue confirmed transplacental dissemination since elevated viral loads were detected in multiple tissues of the cow with SA-MCF. Furthermore, the elevated viral loads detected in the pulmonary tissues of cattle with interstitial pneumonia indicate that OvGHV2 is an inductor of pulmonary disease in cattle.

Abstract PO3-20-12: A Case Report on the Management of a Patient with Local Breast Cancer, BIA-ALCL and Radiation Induced Metastatic Angiosarcoma: A Multidisciplinary Approach

Abstract A Case Report on the Management of a Patient with Local Breast Cancer, BIA-ALCL and Radiation-Induced Metastatic Angiosarcoma: A Multidisciplinary Approach  Abstract: Breast cancer recurrence presents a complex challenge in clinical practice. We present the case of a 60-year-old female with a history of stage 2A right breast cancer diagnosed on 12/1/2013. The patient underwent bilateral mastectomy and adjuvant chemotherapy, followed by breast reconstruction. The patient subsequently developed asymmetric right breast swelling, which was biopsied and was positive for T lymphocyte markers CD30, CD43, CD45, CD4 and she was diagnosed with anaplastic large cell lymphoma in 12/14/2018, which was thought to be associated with her breast implants. In May 2022, a right chest wall mass was detected, which demonstrated growth and increased vascularity on imaging. A biopsy on 5/5/22 confirmed poorly differentiated carcinoma initially thought to be a secondary intraductal carcinoma of the breast, invading the chest wall by metastasis or direct extension, negative for estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Further workup confirmed this mass to be angiosarcoma, most likely associated with the patient’s prior radiation therapy. The patient was started on neoadjuvant carboplatin/paclitaxel/pembrolizumab on 6/9/2022, and continued with Doxorubicin/Cyclophosphamide and pembrolizumab, which was completed on 11 November 2022. Imaging studies post-treatment showed a slightly smaller mass in the right mastectomy bed, indicating a partial response to treatment. However, a subsequent PET scan revealed a recurrence of breast cancer in the right chest wall. Considering the patient's history of prior radiation therapy and the inability to administer further radiation, the treatment plan was revised. She underwent reconstructive chest wall surgery on 1/4/2023, with complete resection and negative margins. She started on adjuvant pembrolizumab planned for one year, but the patient presented on 3/3/2023 with the growth of a chest wall mass and bleeding, consistent with progression. Liquid Tempus testing was obtained but negative for an actionable target. Options such as hyperthermia, enrollment to clinical trial, and re-irradiation were discussed, and the patient was restarted on weekly paclitaxel on 3/31/2023 due to a previous response. The patient had further local disease progression on 5/26/2023, and this regimen was stopped. The patient is planning to get Tempus testing on tumor tissue and start the next line palliative regimen with either doxorubicin or gentamicin and repeat re-irradiation if no response to these regimens. This case report highlights the challenges in managing breast cancer therapy-induced adverse conditions with two secondary tumors, both associated with the patient’s prior therapy. The importance of a multidisciplinary approach, including medical oncology, surgical oncology, radiation oncology, and sarcoma specialists, is emphasized. The use of molecular testing and consideration of clinical trials may provide additional treatment options. Further research and clinical trials are warranted to optimize the management of recurrent breast cancer with transformation to rare histological subtypes such as angiosarcoma. Citation Format: Liubou Varanitskaya, Serhan Unlu, Christina Clemow. A Case Report on the Management of a Patient with Local Breast Cancer, BIA-ALCL and Radiation Induced Metastatic Angiosarcoma: A Multidisciplinary Approach [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 PO3-20-12.

Abstract PO2-20-09: Hiding in plain sight: A heterogeneous response in a patient with metastatic HR+/HER2- breast cancer

Abstract INTRODUCTION: Metastatic breast cancer is an infamously heterogeneous disease—characterized by a range of clinical presentations and treatment responses. In light of this heterogeneity, ASCO guidelines recommend patients with new, accessible metastatic tumors undergo a biopsy to inform treatment decisions. Here, we present a patient with HR+/HER2- disease with a long history of unusually heterogeneous responses—and a repeat metastatic biopsy that provided an answer. CASE: A 55-year-old woman presented for consultation of treatment-refractory metastatic breast cancer. She was originally diagnosed with a right-sided Stage III HR+/HER2- invasive ductal carcinoma (IDC) at the age of 33. Upon staging, she was incidentally found to have a right lower-lobe lung carcinoid tumor that was removed by lobectomy. She underwent a partial mastectomy, axillary lymph node dissection, followed by adjuvant chemo- and radiation therapy. She tolerated one week of tamoxifen which was discontinued due to adverse effects. Fifteen years later, screening mammography revealed a suspicious lesion in the right breast—biopsy consistent with a new IDC. She underwent bilateral mastectomies which showed a pT1cNxM0 G2 IDC with associated DCIS (ER+/PR+/HER2 IHC 2+, FISH-negative, Oncotype RS 12). Genetic testing was negative. The patient trialed adjuvant tamoxifen, which was discontinued due to repeat adverse effects. Two years later, rising tumor markers prompted restaging scans that demonstrated an enlarging liver lesion. Liver biopsy was consistent with metastatic adenocarcinoma of the breast (ER+/PR+/HER2 IHC 0), GATA3 positive. Patient was started on letrozole with lupron and palbociclib with disease control for two years until progression in the bone, prompting a switch of letrozole to fulvestrant with continued palbociclib. Her disease was stable for two additional years until progression of multiple liver lesions. She was then started on single-agent paclitaxel. At this point, she was seen in our office for consultation and next-line therapy options. Repeat staging scans showed heterogeneous response in the liver with overall progression. ctDNA testing revealed a mutation in MEN1 (p.Q354*, 2.8% VAF) without other actionable alterations. Patient opted to enroll into a clinical trial of an experimental ER-antagonist but experienced progression of her liver lesions on first staging scans. A second liver biopsy was performed on a progressive lesion which showed ER-/PR-/HER2- disease. She opted to enroll into a Phase 1b/2 trial with sacituzumab govitecan-hziy in combination with a PARPi. Staging scans again showed a mixed response in the liver. Given a history of mixed responses and discordant receptor staining, the differential diagnosis included loss of hormone receptor expression in the breast carcinoma versus metastases from an occult neoplasm. Additional immunohistochemical studies were performed on a subsequent liver biopsy showing positivity for chromogranin, synaptophysin, and INSM1, and negative results for ER, PR, GATA3, and TRPS1. Next-generation sequencing of the progressive lesion revealed a MEN1 SNV (p.Q354*, VAF 82%) as well as loss of 11q (MEN1 locus) suggestive of biallelic loss of MEN1—providing molecular evidence of a metastatic carcinoid tumor. A history of mixed response in the liver was concluded to be two coexisting neoplasms—a metastatic HR+/HER2- breast cancer as well as a late recurrence of a right-lower lobe carcinoid tumor from 22 years prior. DISCUSSION: The unanticipated discovery of an occult, coexisting neoplasm in the setting of a metastatic HR+/HER2- breast cancer illustrates the value of meticulous pathological review, repeat molecular testing and the use of next-generation diagnostic tools such as tumor sequencing in the advanced setting—particularly when a clinical story defies conventional expectations—to personalize care and optimize oncologic management in the face of complex biology. Citation Format: Nolan Priedigkeit, Jane Brock, Olivia Cunningham, Molly Skeffington, Melissa Hughes, Nancy Lin, Susan Lester, Heather Parsons. Hiding in plain sight: A heterogeneous response in a patient with metastatic HR+/HER2- 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 PO2-20-09.

Abstract PO2-20-10: Exceptional long-term disease control on pembrolizumab monotherapy in a patient with TMB-high PMS2-mutated MMR-deficient triple negative breast cancer brain metastasis

Abstract Introduction The brain is among the most common sites of breast cancer (BC) spread. Prognosis of BC brain metastasis (BCBM) differs by receptor subtype, with poorest median overall survival (OS) for triple-negative (TN) BCBM at under 5 months. Though treatment guidelines have evolved in recent years, most strategies have focused on local therapies including surgery and stereotactic radiotherapy (SRT), rather than on systemic agents. The 2020 FDA approval of pembrolizumab (pembro) for patients (pts) with metastatic high-tumor mutational burden (TMB-h, ≥ 10 mutations/megabase) solid tumors, agnostic of primary site, combined with clinical trials in melanoma reporting efficacy of immune checkpoint inhibitors (ICI) against BM, suggest a potential use of ICI for pts with TMB-h BCBM. Results of the TAPUR study supported modest therapeutic benefit of pembro for 28 pts with metastatic BC selected for TMB-h, with median OS of 30.6 weeks, but did not include pts with active BCBM. TMB-h is uncommon in BC, and further genomic signatures remain to be elucidated to identify pts with BCBM responsive to ICI. We present a remarkable case of a pt with Lynch Syndrome (LS) due to a germline PMS2 mutation, who developed TMB-h, mismatch repair (MMR)-deficient TN BCBM, and has maintained stable disease for over 6 years on pembro monotherapy. Case description A 62-y.o. woman underwent screening mammography that identified a right breast mass. Pt has a family history of a mother with uterine and pancreatic cancer, and father with bladder cancer. Biopsy confirmed invasive ductal carcinoma (IDC), grade 1 (G1), ER/PR-positive, HER2 score 0. She underwent partial mastectomy, axillary dissection, radiation, and received adjuvant anastrozole. Three years later, while still on anastrozole, she presented with a 6 cm right breast mass. Mastectomy disclosed G3, ER/PR-negative, HER2-positive (3+, Her2:CEP17 ratio 5.6) IDC. She received adjuvant chemotherapy (AC-T) and 1 year of trastuzumab. Seven years later, pt presented with headaches and word finding difficulties. MRI identified a 3.6 cm frontal mass, which biopsy revealed as TN BCBM. Systemic imaging ruled out distant metastases. Pt proceeded with SRT and exemestane (despite receptor staining ER- in case of a possible false negative result). Despite radiotherapy, pt had BCBM progression within the same year with the largest mass diameter grown to 4.8 cm. Resection (followed by SRT) identified the dominant histology as G3 TNBC. Following transition of care to our institution, germline testing revealed a pathogenic mutation in PMS2 (c943C >T). Tumor sequencing of the resected brain metastasis showed TMB of 48 and MMR deficiency. Therefore, systemic therapy with pembro monotherapy was initiated and maintained with good tolerability. Two years later, concern for progression from rising tumor markers led to addition of concurrent carboplatin/gemcitabine for 5 cycles. Imaging and tumor markers stabilized, and pt returned to pembro monotherapy. Today, 3 years later, and over 6.5 years after initial TN BCBM diagnosis, pt continues to have stable disease on pembro with an excellent performance status (ECOG 0) and no evidence of intracranial or extracranial progression. Discussion We document an exceptional case of prolonged benefit to pembro in a pt with TMB-h PMS2-mutated MMR-deficient TN BCBM. This case highlights two major pragmatic points to clinical practice; (i) the significance of germline testing in all pts with metastatic BC, and (ii) the impact of molecular testing of tumor tissue to identify rare alterations which may have dramatic effects on pt outcomes. Altogether, this case is a remarkable addition to growing evidence that TMB could be a biomarker for predicting response to ICI therapy and provides an example of ICI efficacy in the setting of BCBM. Further research on additional genomic, clinical, and pathologic features associated with ICI responsiveness is warranted for greater precision in BCBM management. Citation Format: Jaeyoon Cha, Albert Grinshpun, Lauren Buckley, Brian Alexander, Sara Tolaney, Nancy Lin. Exceptional long-term disease control on pembrolizumab monotherapy in a patient with TMB-high PMS2-mutated MMR-deficient triple negative breast cancer brain metastasis [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 PO2-20-10.

Detection of <i>M. tuberculosis</i> Using Cartridge-Based Technology in Patients with Negative Sputum Microscopy Results in a Regional Laboratory

The objective: to evaluate results of M. tuberculosis detection and testing drug susceptibility to rifampicin using molecular genetic methods in tuberculosis patients with a negative sputum smear microscopy result.Subjects and Methods. Pulmonary tuberculosis patients registered in Arkhangelsk Region from 2016 to 2020 were enrolled in the study; those patients were notified as new cases and relapses with a negative sputum smear microscopy result before treatment and had results of molecular genetic testing (MGT) (Xpert MTB/RIF MTB/RIF) and BACTEC MGIT 960 available.Results. 479 people (40%) were registered as pulmonary tuberculosis cases with a negative sputum smear microscopy result. MGT was performed in 327 (68%) patients. A positive result of MGT was received in 120 (37%) patients, a positive result of BACTEC MGIT 960 was received in 165 (50%) people. Concordance of results was observed in 70% of cases. In 136 (41%) people, both tests did not detect Mycobacterium tuberculosis, in 95 (29%) both tests showed a positive result. Discrepancies between the results of two tests were observed in 30% of cases. In 71 (22%) cases, culture growth was observed in BACTEC MGIT 960 with negative results of MGT. In 8% of cases, DNA of Mycobacterium tuberculosis was detected, but there was no culture growth on the nutrient medium. 43/120 (36%) cases of resistance to rifampicin were detected. The median time from sputum collection to initiation of MDR-TB treatment based on sputum MGT results made 18 (IQR 10–29) days. Molecular genetic testing makes it possible to promptly detect the majority of TB patients with a negative sputum smear result, and reduce the time for drug susceptibility testing, which allows this testing to be used as the first test when examining for pulmonary TB.  

Diagnosing adult and pediatric extrapulmonary tuberculosis by MPT64 antigen detection with immunohistochemistry and immunocytochemistry using reproduced polyclonal antibodies.

Diagnosing extrapulmonary tuberculosis (EPTB) is challenging. Immunohistochemistry or immunocytochemistry has been used to diagnose tuberculosis (TB) by detection of MPT64 antigen from various extrapulmonary specimens and has shown good diagnostic performance in our previous studies. The test can distinguish between disease caused by Mycobacterium tuberculosis (Mtb) complex and nontuberculous mycobacteria and can be applied on formalin-fixed paraffin-embedded tissue. As the antibodies previously used were in limited supply, a new batch of polyclonal antibodies was developed for scale-up and evaluated for the first time in this study. Our aim was to assess the diagnostic accuracy of the MPT64 test with reproduced antibodies in the high burden settings of Pakistan and India. Patients were enrolled prospectively. Samples from suspected sites of infection were collected and subjected to histopathologic and/or cytologic evaluation, routine TB diagnostics, GeneXpert MTB/RIF (Xpert), and the MPT64 antigen detection test. Patients were followed until the end of treatment. Based on a composite reference standard (CRS), 556 patients were categorized as TB cases and 175 as non-TB cases. The MPT64 test performed well on biopsies with a sensitivity and specificity of 94% and 75%, respectively, against a CRS. For cytology samples, the sensitivity was low (36%), whereas the specificity was 81%. Overall, the MPT64 test showed higher sensitivity (73%) than Xpert (38%) and Mtb culture (33%). The test performed equally well in adults and children. We found an additive diagnostic value of the MPT64 test in conjunction with histology and molecular tests, increasing the yield for EPTB. In conclusion, immunochemical staining with MPT64 antibodies improves the diagnosis of EPTB in high burden settings and could be a valuable addition to routine diagnostics.

A decade of progress: advances in the third-line treatment of patients with metastatic colorectal cancer.

The treatment of metastatic colorectal cancer (mCRC) remains challenging. There has been substantial progress in understanding the molecular pathology of the disease that has led to meaningful advancements in treatment options with varying mechanisms of action, although treatment remains costly. Cytotoxic therapies, which are typically combined with targeted therapies, remain the mainstay of first- and second-line treatment for mCRC. While also relevant in earlier lines of therapy, molecular testing has become increasingly important to guide therapy across lines of therapy, for which treatment options are limited. A paucity of data exists in establishing clinical criteria for optimizing the sequencing of therapies in the third line and beyond. A customized approach should consider the efficacy of the therapy balanced with the patient's goals. Sequencing criteria should include a consideration for exposing patients to as many different modes of therapy as possible while preserving quality of life, avoiding serious toxicities, and accounting for the potential impact of cumulative toxicities from prior therapies.

Epidemiology and molecular characterization of adult genetic myopathies in a southeastern region of Spain.

Genetic myopathies constitute a collection of rare diseases that significantly impact patient functionality and quality of life. Early diagnosis of genetic myopathies can prevent future complications and provide families with genetic counselling. Despite the substantial impact of genetic myopathies on the adult population, the global epidemiology of these disorders is inadequately addressed in the literature. To enhance understanding of both the epidemiology and genetics of these disorders within the province of Alicante, situated in southeastern Spain. Between 2020 and 2022, a prospective observational study was conducted at the Alicante Health Area-General Hospital, enrolling patients aged 16 years or older with suspected genetic myopathies. Sociodemographic, clinical, and genetic data were collected. The reference date for prevalence calculation was established as December 31, 2022. Official demographic data of the health area were used to set the population at risk. In total, 83 patients were identified with confirmed genetically related myopathy, resulting in an overall prevalence of 29.59 cases per 100,000 inhabitants. The diagnostic yield for molecular genetic testing was found to be 69.16%. The most prevalent genetic myopathies identified included myotonic dystrophy (27.5%), dystrophinopathies (15.7%), and facioscapulohumeral dystrophy (15.7%). The prevalence of GMs can vary considerably depending on the geographical region and the studied population. The analysis of diagnostic yield suggests that genetic studies should be considered useful in the diagnosis of genetic myopathies.

Validation of a qualitative real-time PCR assay for the detection of Candida auris in hospital inpatient screening.

This study overviews the validation and implementation of a molecular screening tool for the detection of Candida auris in a College of American Pathologist-accredited clinical laboratory. This molecular laboratory-developed test is both highly sensitive and specific and has significant health-system cost-savings associated with significantly reduced turn-around-time compared to traditional standard-of-care culture-based work up. This method and workflow is of interest to support clinical microbiology diagnostics and to help aid in hospital inpatient, and infection prevention control screening.

Comparative analysis of stripe rust resistance in seedling stage and Yr gene incidence in spring and winter wheat from Xinjiang, China

BackgroundStripe rust, caused by the fungus Puccinia striiformis f.sp. tritici (Pst), poses a significant threat to global wheat production.ObjectivesThis study aims to analyze the distribution of stripe rust resistance genes, characterize resistance phenotypes at the seedling stage of 137 spring and 149 winter wheat varieties in Xinjiang, China, and discern differences in resistance between spring and winter wheat varieties.DesignWe used various Pst races (CYR23, CYR29, CYR31, CYR32, CYR33, CYR34) to characterize seedling resistance of spring and winter wheat varieties and to correlate resistance to the presence of wheat resistance genes (Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr41, Yr80, Yr81) using molecular markers.ResultsAmong spring wheat varieties, 62, 60, 42, 26, 51, and 24 varieties exhibited resistance to CYR23, CYR29, CYR31, CYR32, CYR33, and CYR34, respectively, with four varieties resistant to all varieties. Among winter wheat varieties, 66, 32, 69, 26, 83, 40 varieties demonstrated resistance to CYR23, CYR29, CYR31, CYR32, CYR33, and CYR34, respectively, with four varieties resistant to all varieties. Molecular testing revealed that, in spring wheat, 2, 17, 21, 61, 10, 0, 10, 79, and 32 varieties carried Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr41, Yr80, and Yr81 genes, respectively. In winter wheat, 40, 20, 7, 143, 15, 1, 6, 38, and 54 varieties carried Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr41, Yr80, and Yr81 genes, respectively. Notably, winter wheat exhibited a significantly higher resistance frequency than spring wheat, particularly in the incidence of Yr9, Yr10, Yr17, Yr18, and multi-gene combinations.ConclusionIn summary, this study provides information on seedling stage resistance to stripe rust 286 Xinjiang wheat varieties, elucidates the distribution of resistance genes in this population, and offers a mechanistic basis for breeding durable resistance in wheat. varieties from Xinjiang.

Oil blotting paper for formalin fixation increases endoscopic ultrasound-guided tissue acquisition-collected sample volumes on glass slides.

Endoscopic ultrasound-guided tissue acquisition (EUS-TA) is used for pathological diagnosis and obtaining samples for molecular testing, facilitating the initiation of targeted therapies in patients with pancreatic cancer. However, samples obtained via EUS-TA are often insufficient, requiring more efforts to improve sampling adequacy for molecular testing. Therefore, this study investigated the use of oil blotting paper for formalin fixation of samples obtained via EUS-TA. This prospective study enrolled 42 patients who underwent EUS-TA for pancreatic cancer between September 2020 and February 2022 at the Osaka International Cancer Institute. After a portion of each sample obtained via EUS-TA was separated for routine histological evaluation, the residual samples were divided into filter paper and oil blotting paper groups for analysis. Accordingly, filter paper and oil blotting paper were used for the formalin fixation process. The total tissue, nuclear, and cytoplasm areas of each sample were quantitatively evaluated using virtual slides, and the specimen volume and histological diagnosis of each sample were evaluated by an expert pathologist. All cases were cytologically diagnosed as adenocarcinoma. The area ratios of the total tissue, nuclear, and cytoplasmic portions were significantly larger in the oil blotting paper group than in the filter paper group. The frequency of cases with large amount of tumor cells was significantly higher in the oil blotting paper group (33.3%) than in the filter paper group (11.9%) (p = 0.035). Oil blotting paper can increase the sample volume obtained via EUS-TA on glass slides and improve sampling adequacy for molecular testing.