{"doi":"10.18260/1-2--44938","title":"Elevated TMEM38B in the caudate nucleus with Alzheimer’s disease","abstract":"Background: Transmembrane proteins (TMEMs) such TMEM67 is known to cause hydrocephalus, when mutated, but the specificity and function of other TMEMs are elusive in Alzheimer's disease (AD). Question: Is mRNA expression of TMEM38B different in the caudate nucleus with AD? Hypothesis: We hypothesized that TMEM38B mRNA is elevated in AD but not in normal pressure hydrocephalus (NPH), given the limited preliminary assay on human postmortem specimens. Method: We assayed mRNA expressions of TMEM38B and other genes in the postmortem caudate nucleus using reverse transcription polymerase chain reaction (RT-PCR). We next conducted whole transcriptome RNA-sequencing Results: A large size dataset was produced: total 62,704 readings (# of genetic loci or genes) were identified at n=2-3/group. Of all data points (62,704 loci), 1 % (n=2-3, 608 genetic loci or genes out of 62,704) of the readings demonstrated a statistical significance at p<0.05. Thus, these datasets will be sorted per 1) p-value, and 2) effect size (fold change against the controls) to assess a variety of gene expressions in AD. Conclusion: The result of this study suggests that whole transcriptome RNA-seq. can provide a critical decision making in finding novel biomarkers and drug targets: one of them might pertain to haptoglobin (Hp) or Hp receptor gene. Human postmortem tissues. Postmortem tissues were requested from the National Institute of Health (NIH) NeuroBioBank (NBB), USA over a period of one year. Caudate nucleus specimens in frozen state were transported to our lab. Per the record provided by the NBB, the specimens were collected at postmortem intervals of 16 hours (mean+std; range 4 to 25 hours after death, n=7 in unaffected controls; n=2 in NPH; n=6 in AD). Total 15 cadavers (4 males, 11 females) were used whose sex was marked in Fig. 1c. Primer design. Human gene transcripts were searched using E!nsembl database (http://useast.ensembl.org/index.html). Using Primer3 online, we determined the sequences of a specific exon per gene transcript (https://bioinfo.ut.ee/primer3-0.4.0/). Then, lyophilized forms were manufactured and provided by the vendor (Thermofisher scientific, Waltham, MA). Seven human gene primers were designed (Table 1). Total RNA isolation and Whole Transcriptome RNA-seq. Total RNA was isolated from the caudate nucleus of the unaffected control, NPH, and AD specimens using QIA-ZOL based RNA isolation kit (RNeasy Lipid Tissue Mini Kit, QIAGEN). Concentration and quality of samples were analyzed with a NanoDrop spectrophotometer (Thermofisher). Total RNA (500 ng/reaction) was reverse-transcribed using the High-Capacity RNA-to-cDNA Kit (Thermofisher; Catalog number: 4368814) at ABI SimpliAmp Thermal Cycler System (Thermofisher). RT-PCR. RT-PCR was carried out in 25 l containing 250 ng cDNA following the manufacturer's instructions (GoTaqGreen Master Mix). Cycling conditions were composed of three steps: Denaturation at 95 C for 2 min, followed by 32 cycles of denaturation at 95 C for 30 sec, annealing at 60 C for 30 sec, and extension at 72 C for 30 sec (Promega, Madison, WI). The PCR products were then separated by electrophoresis on horizontal 1.25% agarose gels in 1x Tris/boric acid/EDTA (TBE) buffer and visualized by staining with Maestro dye (MaestroSafe, Maestrogen). The fluorescent signal was photographed with the built-in camera of an iPhone 12 (Apple). METH ODS Late-breaking Data Per the criteria of <50 Mbp proximity to telomeres and A+T content at >59%, TMEM67 gene is associated with mutations causing CH due primarily to high A+T content at 64% with a marginal proximity to telomeres. In contrast, ZCCHC8 gene is related with mutations causing CH due primarily to proximity to telomeres. Our result on the first factor suggests that causative genes located in chromosome 18 to 22 more likely meet proximity to telomeres (<50 Mbp) due to short chromosomal length. Factors-nucleotide size relationships suggest that the full-length size of a gene ","journal":"Papers on Engineering Education Repository (American Society for Engineering Education)","year":2024,"id":494099,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9671,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1260271,"name":"Emma Barrett","orcid":"0000-0003-0762-5196","position":1,"is_corresponding":false},{"id":773557,"name":"Joon W. Shim","orcid":"0000-0002-5490-684X","position":2,"is_corresponding":false},{"id":943746,"name":"Kaitlyn Legg","orcid":null,"position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:09:07.920649Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}